Good Math, Bad Math

I’ve gotten my hands on a review copy of Michael Behe’s new book, “The Edge of Evolution”. The shortest version of a review is: Bad science, bad math, and bad theology, all wrapped up in a pretty little package.

As people who’ve followed his writings, lectures, and court appearances know, Behe is pretty much a perfect example of the ignoramus who makes a bad argument, and then puts his fingers in his ears and shouts “La la la, I can’t hear you” whenever anyone refutes it. He *still* harps on his “irreducible complexity” nonsense, despite the fact that pretty much *every aspect* of it has been thoroughly refuted. (The entire concept of IC is a pile of rubbish; the entire argument about IC is based on the idea that evolution is a strictly additive process, which is not true; there are numerous examples of observed evolution of IC systems, both in biology and in evolutionary algorithms. But none of these facts makes a bit of difference: like the energizer bunny of ignorance, he just keeps going, and going…)

Anyway, the new book is based on what comes down to a mathematical argument – a mathematical argument that I’ve specifically refuted on this blog numerous times. I’m not mentioning that because I expect Behe to read GM/BM and consider it as a serious source for his research; even if I were an expert in the subject (which I’m *not*), a blog is *not* a citable source for real research. But I mention it because the error is so simple, so fundamental, and so bleeding *obvious* that even a non-expert can explain what’s wrong with it in a spare five minutes – but Behe, who apparently spent several *years* writing this book still can’t see the problem. (In fact, one of the papers that he cites as *support* for this ridiculous theory contains the refutation!)


Behe’s argument is that what’s commonly referred to as the theory of evolution is actually made up of three parts:

1. Common Descent: all living creatures are derived from common ancestors by modification. I’m not quoting Behe’s explanation of this here, because it’s
astonishingly muddled for such a simple idea: he’s so eager to start throwing in
his digs at the idea of evolution that he muddles the explanation of common descent
with irrelevant gibberish. In fact, his explanation of this reads almost like an
endorsement of John Davidson’s “prescribed evolution”.
2. Natural Selection: Michael Egnor’s favorite. As Behe states it (on page 2 of TEoE), “the idea of natural selection says just that the more fit organisms of a species will replace the progeny of the less fit”.
3. Random Mutation: again, quoting Behe: “the only way a plant or animal becomes fitter
than its relatives is by sustaining a serendipitous mutation.” In the expansion of
this, he handwaves his way around, basically asserting not just that mutation is
random, but that the only kinds of mutation are single-point changes: no duplication, no frameshifting, etc.

This is already poor stuff – the muddled version of his explanation of common descent; his presentation of a shallow tautological form of natural selection; and his ignorance of any source of genetic diversity other that mutation.

As soon as he gets through that muddled explanation, he starts to launch his attack in earnest. And it’s a sad attempt:

>In the past hundred years science has advanced enormously;
>what do the results of modern science show? In brief, the evidence
>for common descent seems compelling. The results of modern DNA
>sequencing experiments, undreamed of by nineteenth-century
>scientists like Charles Darwin, show that some distantly related
>organisms share apparently arbitrary features of their genes that
>seem to have no explanation other than that they were inherited
>from a distant common ancestor. Second,
>that random mutation paired with natural selection can modify life
>in important ways. Third, however, there is strong evidence that
>random mutation is extremely limited. Now that we know the
>sequences of many genomes, now that we know how mutations
>occur, and how often, we can explore the possibilities and limits of
>random mutation with some degree of precision–for the first time
>since Darwin proposed his theory.

This is a careful verbatim quote from his book. What I found astonishing here is that he
asserts his conclusions in this paragraph as settled fact, *without even attempting to cite any evidence*. It’s typical, but pathetic. It’s not like he doesn’t use citations and footnotes through the book – he sometimes insert supportive citations of completely
trivial things. But this incredible statement: that “there is strong evidence that random mutation is extremely limited”, he doesn’t even *attempt* to support.

The rest of the book focuses an this alleged problem: that random mutation is somehow constrained, and can’t produce the necessary changes to explain the diversity of life.

The part of the book that is most annoying to me, and thus the part that I’ll focus the rest of this review on, is chapter three, “The Mathematical Limits of Darwinism”. This is, basically, the real heart of the book, and for obvious reasons, it seriously ticks me off. Behe’s math is atrociously bad, pig-ignorant garbage – but he presents it seriously, as if it’s a real argument, and as if he has the slightest clue what he’s talking about.

The basic argument in this chapter is the good old “fitness landscape” argument. And Behe makes the *classic* mistakes. His entire argument really comes down to the following points:

1. Evolution can be modeled in terms of a *static, unchanging* fitness landscape.
2. The fitness landscape is a smooth, surface made up of hills and valleys, where
a local minimum or maximum in *any* dimension is a local minimum or maximum in *all*
dimensions.
3. The fitness function mapping from a genome to a point of the fitness landscape is
monotonically increasing.
4. The fitness function is smoothly continuous, with infinitessimally small changes
(single-point base chanages) mapping to infinitessimally small changes in position
on the fitness landscape.

Of course, Behe doesn’t phrase it like that; in fact, I doubt that he even understands
that he’s making those assumptions: His grasp of math is extremely shallow, and his mathematical reasoning is glib at best.

First, I’ll repeat [what I've said in the past about what's wrong with each of these assumptions][landscape]. Then I’ll put out a couple of examples in the text of how Behe attemps to refute these criticisms, and show what’s wrong with them.

[landscape]: http://scienceblogs.com/goodmath/2007/05/using_bad_math_to_create_bad_m_1.php

Behe uses these assumptions about the fitness landscape, and the search process which is his model of evolution, to build his argument. He frequently talks about how things can get *trapped* at a local maximum. By Behe’s reasoning, once a species reaches a local maximum of a fitness landscape, that’s the *end* of any process of change in that species. When he talks about a *limit* of what can be done by mutation+selection, that’s what he’s talking about: the idea that local maxima are traps.

This is one of the oldest canards of the IDists: the mis-modeling of evolution as a search process over a static landscape. The problems with this are quite simple:

**First**, It assumes that the fitness landscape is fundamentally low-dimensional. If the fitness landscape truly has many independent dimensions, then there are very few (if any) true local maxima. To assume that local maxima are common requires assuming that when moving through one dimension brings you to a local maximum, moving through any other dimension will also bring you to a local maximum *at the same point* – which is really another way of saying that the dimensions are *not* independent – they all reach maxima and minima at the same places.

The idea of local maxima and minima being common comes from thinking of things in terms of low-dimensional surfaces. A fitness landscape with two variables forms a three dimensional graph – and in three dimensions, we do frequently see things like hills and valleys. But that’s because a local minima is the result of an interaction between *only two* variables. In a landscape with 100 dimensions, you *don’t* expect to see such uniformity. You may reach a local maxima in one dimension – but by switching direction, you can find another uphill slope to climb; and when that reaches a maximum, you can find an uphill slope in some *other* direction. High dimensionality means that there are *numerous* directions that you can move within the landscape; and a maximum means that there’s no level or uphill slope in *any* direction.

(As an interesting aside, IDists, when they’re quoting Dembski, like to talk about the No Free Lunch theorems. The NFL theorems are based on the idea that landscapes really aren’t smooth – that they don’t have uniform properties that permit a search strategy to work. Behe’s argument totally contradicts that – the kinds of landscapes that must be considered to make NFL work totally devastate Behe’s idea. )

**Second**, Behe assumes that the landscape can’t change. If it’s a local maximum today, it’s a local maximum tomorrow. The reason that he needs this is obvious: if todays local maximum can stop being a maximum, then it’s not any kind of a barrier. The argument *requires* that the landscape never change.

This is the biggest problem with the whole idea of modeling evolution as search over a fitness landscape: landscape search generally assumes a static landscape. But this doesn’t match reality at all. Just consider a simple example. Suppose you’ve got a local maximum in the landscape, and that that maximum represents a fitness point for a plant-eater: that point represents an adaptation to a diet that’s based on some kind of vegetation, and a behavior that protects it from predation. Because it’s a maximum, things that get anywhere near it end up climbing the slope to that maximum. The local maximum becomes a clustering point for plant-eating species. The fact of that clustering means that the population at that point is going to grow.

The growing population means that you’ll be creating another fitness point on the landscape: a point for a predator. That point didn’t exist before: when there wasn’t a population of plant-eaters for a predator to consume, there would be no advantage to evolving to fit the niche of eating the creatures that eat the vegetation; once there is a population of plant-eaters there, then you’ve got a new fitness point.

The growing population also means that the fitness of that point may start to decline: too much competition for the resources. Too many creatures trying to eat the same limited food source.

This is the reality of the “fitness landscape”: the landscape is shaped from the species that inhabit it; as the species change, the landscape changes. Those *traps* that Behe keeps talking about only exist if the landscape *doesn’t* change. But the only way that the landscape doesn’t change is if the species in it don’t change. The moment any species starts climbing a hill in the fitness landscape, the landscape must change to describe the new circumstances.

**Third**, Behe, as in his IC gibberish, insists on a monotonically increasing fitness function, *and* he insists on mutation behaving as a continuous function. According to Behe, the *only* changes are changes that produce an *immediate*
increase in fitness. So if you’re at a local maximum, there’s no way to escape it, because you can’t go *downhill*. There are two problems here: one is that it’s possible for a species to become *less* fit; the other is the continuity assumption.

With respect to that first issue, it’s possible in many circumstances, for a population to become *less* fit. When a species is not under strong selective pressure, it’s possible for numerous neutral or even slightly negative mutations to accumulate in the population. There’s nothing in reality preventing that: mildly negative mutations *do* occur in reality. In Behe’s model, that means that in reality, evolution isn’t a strict hill-climber; crossing a valley to get to a higher fitness summit is *not* impossible.

The second part if this is a *huge* problem for Behe’s argument. Behe wants to be able to argue that local maxima are traps. A local maxima is only a trap for a search process if the search has certain strict limitations: the search needs to behave as an *almost* continuous function. This is a bit messy, because we’re straddling the line between continuous math and discrete math here. But the idea is that Behe’s model is that there’s a function from a species genome to a point in the fitness landscape; and that mutation makes an small change to the genome, and that that small change to the genome *must* correspond to a proportionately small change in the mapped location on the landscape. So mutations can only produce small changes; and small changes can only result in small motions on the landscape. That means that the evolutionary search process can’t *jump* valleys in the landscape.

The problem is, that doesn’t correspond to reality. There are times when a small change can have a huge impact. The classic textbook example of this is the Panda’s thumb: a very small genetic change caused a change in the developmental process in the wrist of the panda, which produced what is effectively an extra thumb. The genetic change that produced this is *tiny*; the effect is huge. This is not an unusual thing: small changes can have huge effects. But small changes with large impacts totally blow Behe’s argument out of the water: they mean that Behe’s barriers *aren’t* barriers at all.

So Behe’s argument fails miserably, because it’s built on a pile of *obviously*
invalid, long-discredited assumptions. And yet he builds his entire book around them – and just acts as if the assumptions were obviously correct, and no one has ever refuted them. Even when the sources that he cites contradict him, he acts as if there’s nothing wrong: he cites several papers about modeling evolution with a fitness landscape that specifically discuss the dimensionality issues, and then *in the same paragraph as the citation*, talks
about the fitness landscape as a surface in three dimensions. The only explanation I can find for his is that he really doesn’t understand most of the math that he’s talking about. (I don’t think that Behe is above deliberately lying; but I think he’s smart enough that he wouldn’t cite things that contradict him so blatantly if he understood what they really said.)

Behe isn’t *entirely* ignorant of the criticisms of the landscape arguments – he does devote some space to arguing around them. Anyone care to guess what kind of argument he uses? Anyone?

What’s the favorite bullshit mathematical argument of creationist assholes worldwide? Why big numbers, of course! He starts to slap together some sloppy probabilities to argue how unlikely it is for a mutation to jump valleys in a fitness landscape. He goes through a
really sloppy argument about how unlikely it is for malaria to evolve chloroquine resistance, arguing that the odds of evolved resistance are one it 1020. Now, when you realize that each person infected with Malaria has *billions* of malaria cells in their bodies, and that number starts to *not* look so scary anymore: *billions* of cells reproducing daily in *millions* of individuals, which has been going on for decades of chloroquine use, and you start to realize that that’s not such a big number after all. But even so – it’s a *deliberately* inflated number, relying on things like the monotonicity assumption, and the assumption that resistance is all-or-nothing. But even with those sleazy assumptions, that number just isn’t compelling when it comes to malaria. So, he tries to take the inflated malaria number, and wave his hands around by applying it to human beings, because we reproduce so slowly compared to malaria:

>If all of these huge numbers make your head spin, think of it this
>way. The likelihood that Homo sapiens achieved any single mutation
>of the kind required for malaria to become resistant to chloro-
>quine–not the easiest mutation, to be sure, but still only a shift of
>two amino acids–the likelihood that such a mutation could arise just
>once in the entire course of the human lineage in the past ten million
>years, is minuscule–of the same order as, say, the likelihood of
>you personally winning the Powerball lottery by buying a single ticket.

What’s particularly astonishing about this is that even this rotten argument – taking an artifically inflated probability number based on the peculiarities of the biochemistry of one specific organism, and applying it to a completely different organism (waving hands
furiously to try to distract from the fact that it’s just nonsensical to cross that way), contains its own refutation. Yes, perhaps the odds of this happening are similar to the odds of winning at powerball. But the fact is *someone wins* the powerball lottery. He wants to pretend that it’s unlikely by pointing at *you specifically*, and saying that it’s like *you* winning the lottery. But in fact, the power of evolution is that it doesn’t just try *one thing*. It’s not a process of *one mutation*, wait and see if it works out and fixes in the population; it’s not a process with a predetermined destination. It’s a process of countless mutations happening at the some time – some propagate, some don’t – and if *any* of them work, then they take over. The real chance of evolution producing *something* are like the chances of *someone* winning the lottery. The chances of them producing humanity taken a priori are like the chances of *you* winning the lottery; but since humanity was *not* a predestined result, the chances of the evolutionary sweepstakes producing *something* is like the chances of *someone* winning the lottery – i.e., virtually inevitable.

Finally, I said that not just is Behe’s book bad science and bad math, but it’s bad theology. Behe claims to believe in an all-knowing, all-powerful God. But at the same time, his entire book is based on the argument that God created life on earth, and got it all going using an evolutionary process. But then, according to Behe, over and over again, his creation was woefully inadequate of facing the actual challenges that it would face, and so his all-powerful creator needs to *constantly* intervene, and tweak things in order to make them work. His God is a buffoon – a bumbling fool who isn’t capable of creating worlds in a way that *works*. Reading his book, I’m actually shocked that he’s a religious person: he’s clearly never bothered to think through his beliefs, and what his theories say about them. Again and again, reading the book, I kept finding myself saying two things: “How can this guy call himself a scientist, when he argues so sloppily?”, and “How can this guy be religious when he apparently believes that his creator isn’t capable of getting *anything* right?” Following Behe’s argument, it seems like it should be impossible for Behe’s god to have done the things Behe claims that he did, because they’re too hard for such a bumbler.

I’m sure that that aspect of Behe’s book isn’t deliberate. But it’s typical: he seems to be incapable of actually really thinking about an argument in any way deeper than asking “Does this agree with my conclusion?”; and even then, he doesn’t seem capable of recognizing when an argument *doesn’t* support his conclusion. It’s really appalling. Frankly, I’m really
shocked that this guy ever managed to get tenure anywhere – judging by his writing, he’s not particularly bright; he’s a remarkably disorganized and muddled thinker; and he’s incapable of comprehending or responding to arguments made by other researchers.

*(Note: several typos: a missing “not”, a missing “resistance”, and “got” for “god”, “lest” for “less” were corrected in the above. That’s what I get for trying to write in short bursts while waiting for builds.)*

Comments

  1. #1 Blake Stacey
    May 31, 2007

    Edit:

    how unlikely it is for malaria to evolve chloroquine, arguing

    The word “resistance” should follow chloroquine.

    The chances of them producing humanity taken a priori are like the chances of you winning the lottery; but since humanity was a predestined result, the chances of the evolutionary sweepstakes producing something is like the chances of someone winning the lottery – i.e., virtually inevitable.

    Imputing teleology to evolution?

  2. #2 J-Dog
    May 31, 2007

    Thanks for taking the time to do the review – I hope you were in proper anti-odor gear when reading his “book”. It seems to me that Behe is clearly saying “I am in it for the money” and his creo / DI overlords are willing to give it to him to shore up their diminishing post-Dover world.

  3. #3 trrll
    May 31, 2007

    The chances of them producing humanity taken a priori are like the chances of you winning the lottery; but since humanity was a predestined result, the chances of the evolutionary sweepstakes producing something is like the chances of someone winning the lottery – i.e., virtually inevitable.

    Do you really intend the word “predestined” here? I think that you are saying something other than what it sounds like–I think you are saying that it may well be that the chance of evolution producing something like humanity are small a priori (which may or may not be true), but we can’t apply that in reverse to argue that the existence of humanity is inconsistent with evolution, in the same sense that the probability of any particular individual winning the lottery is very small, but we cannot argue from the fact that a particular individual did win the lottery that the drawing was rigged. But I still wouldn’t say that that individual was “predestined” to win.

  4. #4 Blake Stacey
    May 31, 2007

    Typo:

    impossible for Behe’s got

  5. #5 Mark C. Chu-Carroll
    May 31, 2007

    trrll:

    Stupid typo – left out a “not”!

  6. #6 IanR
    May 31, 2007

    Even when the sources that he cites contradict him, he acts as if there’s nothing wrong…The only explanation I can find for his is that he really doesn’t understand most of the math that he’s talking about.

    Actually there’s another explanation – that he didn’t read the papers he cites, or never got past the abstracts. Of course that would be dishonest, but not exactly unheard of.

  7. #7 RoaldFalcon
    May 31, 2007

    I live within the Christian community, and I can assure you that the content of this book is completely irrelevant–all that matters is the book’s existence. Christians will thumb through the book and see big words and diagrams, and they will imagine all those wicked evolutionists shaking there fists and yelling “That Behe is ruining everything!” Students at Christian schools will quote this book–without understanding it–in their assignments, trusting that, whatever it says, it somehow refutes evolution. At no point will the “science” be examined.

    I know this because I was once one of those students.

  8. #8 pough
    May 31, 2007

    Great review! (and another typo: lest fit?)

  9. #9 SteveF
    May 31, 2007

    “He goes through a really sloppy argument about how unlikely it is for malaria to evolve chloroquine resistance, arguing that the odds of evolved resistance are one it 10^20.”

    This is weird. How did it evolve? Has God intervened in the last few decades? Is he basically moving on to reject even microevolution?

  10. #10 Mark C. Chu-Carroll
    May 31, 2007

    SteveF:

    I’m really not sure.. He’s amazingly cagey about things. For example, the way that he defines common descent isn’t what most people would mean by common descent – he really ultimately defines it as the fact that there’s a nested hierarchy of common features, *not* that things are descended from a common ancestor.

    But WRT the chloroquine resistance, it seems like his argument isn’t against microevolution. It’s that even a small change like that requires a huge number of generations to make it possible, and that while that’s possible for something with quadrillions of individuals reproducing every day, if you try to apply the same probabilities to primates, which have 6 or 7 orders of magnitude fewer individuals, and whose generations are decades not hours/days, that even small changes become too improbable to consider. So he’s pretty much arguing a classic christion position, that while something like evolution might work for those lowly animals, we humans are *special*, and what works to explain variations in animals can’t work to explain us.

    In other words, it’s a shabby “gosh aren’t we humans amazing, God must have made us” argument from incredulity. So when his argument about reproductive barriers gets knocked to pieces, he basically tries to duct tape them back together with big numbers and human chauvinism.

  11. #11 MarkH
    May 31, 2007

    Sounds like he read my HOWTO.

  12. #12 Rev.Enki
    May 31, 2007

    I have a feeling Behe isn’t being fully honest. His god makes even less sense than the god of the fundamentalists. His is not a particularly intelligent designer, but rather an inept tinkerer. He created life through an evolutionary process, but the process doesn’t work to do anything much, so he ended up having to do most of it manually anyway. While that may not be logically inconsistent, it surely doesn’t sound particularly compelling.

    Occam’s razor would lead me to speculate that it’s much more likely that he doesn’t believe in a god like that at all. Rather, that is the only god he can, with much handwaving and willful ignorance, conjure to fit the data. It seems probable that Behe doesn’t believe his own bullshit, and that he’s nothing more or less than another in a long line of pious liars.

  13. #13 Donald
    May 31, 2007

    Brilliant review. Keep it up.

  14. #14 Reed A. Cartwright
    May 31, 2007

    You missed an important criticism of his landscape argument.

    Individuals are the main level of selection, not populations. So instead of mapping a population genome to a point on the landscape, you map each individual’s genome to a point. Populations at local maxima are not a point at the maxima, but a cloud “centered” on it. As Wright pointed out when he developed the landscape analogy in the 1930′s, even on static landscapes, it is possible for outliers of a population at a local maxima to find another peak and their descendants can climb up it.

  15. #15 Bob O'H
    May 31, 2007

    Hmm, I hope for your blood pressure you didn’t have too many bugs.

    One question -

    The fitness function mapping from a genome to a point of the fitness landscape is monotonically increasing.

    Monotonically increasing in what? This seems to contradict point 2 (that there are local maxima). Do you mean that the mean fitness of the population is monotonically increasing in time (i.e. from Fisher’s Fundamental Theorem)?

    Oh, and just because I’m a pedant – a few maxima should be singular maximum(s).

    Other than that, it was a fun read: I guess I won’t have to read the original, then.

    Bob

  16. #16 Tyrannosaurus
    May 31, 2007

    The part of the book that is most annoying to me, and thus the part that I’ll focus the rest of this review on, is chapter three, “The Mathematical Limits of Darwinism”. This is, basically, the real heart of the book, and for obvious reasons, it seriously ticks me off. Behe’s math is atrociously bad, pig-ignorant garbage – but he presents it seriously, as if it’s a real argument, and as if he has the slightest clue what he’s talking about.
    In that respect Behe is following the footsteps of his “favorite mathematician” and friend William Dumbski. Put some numbers and equations together, make it look “sciency” and the gullible will bite it. Pathetic.

  17. #17 SteveF
    May 31, 2007

    It strikes me as a strange argument; if he is arguing that the evolution of malarial resistance is extremely unlikely given the probabilities supposedly involved, yet it happened anyway, what the hell is the point in talking about probabilities in the first place.

    The odds of me being born are pretty small, but I’m sitting here right now.

  18. #18 Olaf
    May 31, 2007

    SteveF: well, he’s saying the probability of malarial resistance evolving without god’s help are tiny. So the ‘it happened anyway’ doesn’t apply because, in his mind, god did interfere.

  19. #19 Tyrannosaurus
    May 31, 2007

    Reed is pointing in the right direction (it send me back to undergrad times). The maxima could be compared to an “average-of-some-sort” (but not exactly) centered in the values exhibited by the individuals in the population. So you can have “outliers” reaching towards other peaks.

  20. #20 Gerald Squelart
    May 31, 2007

    [Off topic]

    “while waiting for builds.”

    What? You mean Google doesn’t have some kind of distributed build system in place?

  21. #21 Bill
    May 31, 2007

    I suspect Behe’s not as dumb as his arguments would lead one to believe. The point is to give the ignorant/gullible something that sounds smart to lend credibility to the argument. For his audience, making any argument is as good as making a solid argument. I’m sure he really believes in creationism, but he might very well know his arguments are BS. He’s not out to convince smart people, just a slight majority of all people. I also suspect he feels his goals are noble, so the means are justified. Plus, he makes some money along the way.

  22. #22 Torbjörn Larsson
    May 31, 2007

    A good read whether it captures mere parts of Behe’s book or not.

    Part of the reason creationists like Behe get stuck on a constant fitness landscape ;-) is that they can’t envision or acknowledge other species evolving. I doubt Behe has internalized what his earlier admission of microevolution means in these terms, much less his prophetized ‘goddidits’ of new species.

    He’s amazingly cagey about things. For example, the way that he defines common descent isn’t what most people would mean by common descent – he really ultimately defines it as the fact that there’s a nested hierarchy of common features, *not* that things are descended from a common ancestor.

    More of the same thing. The basic observation of nested hierarchies of features (in characteristics of fossils or sequencing of genomes) is the fact that he must admit, while the consequent universal mechanism of descent by inheritance is what he can’t affirm.

    Behe is a splendid case of denialism, making his lone balance act on the edge of evolution.

  23. #23 _Arthur
    May 31, 2007

    The average human carries a mix of “good” genes, and a goodly number of so-so ones.
    Hopefully, most of our weak genes will be recessive, so not much of an hindrance.
    Alao there is vast redundancy in our whole organism, many people manage to live a normal live even missing important proteins, on a back-up system, or the back-up of the back-up.
    And, thru the mutation lottery, any of our weak genes can be promoted to a superior gene (in our offspring). Or even, assume a totally new functionality.

  24. #24 Token
    May 31, 2007

    4) The fitness function is smoothly continuous, with infinitessimally small changes (single-point base chanages) mapping to infinitessimally small changes in position on the fitness landscape.

    Do you really mean to have the word infinitessimally in there?

  25. #25 Mark C. Chu-Carroll
    May 31, 2007

    Token:

    Yes, I did mean infinitessimally. From his discription, Behe’s landscapes are low-dimensional continous integratable curves, and his notion of motion across them is of essential continous smooth motion: each step is nearly infinitely small – in fact, he’s quite explicit that his notion of mutation (the cause of motion in the landscape) does not permit anything but the smallest possible changes. So my image of it is very calculus-like: a continuous, differentiable curve, with motion over the curve described in terms of infinitessimals.

  26. #26 Anonymous
    May 31, 2007

    You’re right about various things, like the fact that the fitness landscape is far from static. However, your argument about local maxima being rare in high dimensions is incorrect. Generic high-dimensional functions do indeed have vast numbers of local optima, and I don’t see any conceptual reason why fitness landscapes shouldn’t. (For example, convexity could be a good reason, but that’s not true.) Is there something I’m missing?

    Your argument seems to me to work just as well in two dimensions as in 100. If you pick a one-dimensional slice and look for a critical point along that slice, then there’s no reason why it should be critical in the perpendicular direction. (This is the core of your argument about reaching a local maximum in one direction but then getting to switch direction.) However, that doesn’t mean there aren’t lots of critical points for the unrestricted function. If f is the objective function, then the points where df/dx vanishes generically form curves, as do those where df/dy vanishes. If the function is complicated enough, then these curves will wiggle around a lot and one expects them to cross in many locations. At these crossing points, df/dx=df/dy=0 so these are critical points. (I’ll address whether they are maxima in a moment.)

    The same thing happens in high dimensions. The sets on which each of df/dx_1,…,df/dx_n vanish are hypersurfaces, and one expects these hypersurfaces to intersect in a large set of points. In very loose terms, if each hypersurface wiggles back and forth k times across the fitness landscape, then one expects about k^n intersections. Aside from polynomials I don’t know how to make this rigorous, but the intuition is good. Of course we wouldn’t expect these critical points all to be local maxima: if we assume the eigenvalues of the Hessian are independent and each 50% likely to be positive (a bogus assumption but a decent first guess), then we expect about a 1/2^n fraction of the critical points to be local maxima. If we have k^n critical points with k>2, as we would expect for sufficiently complicated functions, then we expect an exponential number of local maxima.

    In practice, most continuous optimization problems in high dimensions do have vast numbers of local optima, unless some phenomenon like convexity intervenes. (Note that the heuristics above break down for convex functions: k=1, so we expect only one critical point, and the eigenvalues of the Hessian are far from independent.)

    This profusion of local maxima doesn’t matter: we know from physics that nature is just as happy to sit in a local optima as in the global optima. And of course you’re right that there are much deeper problems with Behe’s arguments (such as assuming a static fitness landscape, which is ridiculous).

  27. #27 snaxalotl
    May 31, 2007

    I wish behe and dembski would just make the one authoratative book so ID wasn’t impossible to criticize just because it’s a moving target … oh … wait …

    (and “a local minima” should read “… minimum”

  28. #28 John Vreeland
    May 31, 2007

    My experience with multi-dimensional solution spaces from the field of evolutionary computation suggests that local maxima are ubiquitous, and are a great problem in the real fields of “intelligent design”: electrical, aerospace, chemical and all the other forms of engineering. The idea of a constant fitness landscape is of course laughable, but instead of claiming that “it’s possible in many circumstances, for a population to become less fit,” wouldn’t it be better to point out that any given gene pool is chock full of less-than-optimal alleles?

    We can offer many examples of local maxima: the poor configuration of our own bodies is one, but it doesn’t mean that Behe can extrapolate this idea to stupidity.

  29. #29 ERV
    May 31, 2007

    Technorati hasnt picked up on it yet– but I drew some beautiful diagrams for the fitness landscape of HIV :) If Ive misspoken on fitness landscapes, I would greatly appreciate the criticism!

  30. #30 DavidSR
    May 31, 2007

    I would like to support anonymous and John Vreeland. Local optima in higher dimensional space do occure frequently, and search algorithms will not use the “search one dimension, then the next” approach, they would more likely use the set of partial derivatives at a point to derive a vector direction for maximum increase (or decrease for minima) and base a search algorithm on that.

    I have a larger issue both with Behe and yourself in that both of you seem to regard the “fitness landscape” as a real (as in actual) function. As I understand it, the concept was only ever intended as an illustration to help in the understanding of evolution. We know few of the actual function’s properties. It’s far from obvious that knowing them would provide anything of much predictive power, since for large bodied organisms at least we’re talking immense periods of time simply to validate them. It’s possible that investigating the function’s properties locally for single celled organisms might turn up something useful, but somehow I doubt that it would be more than is already being done in biology and medical research facilities already.

    In short, both Behe and yourself are arguing about a chimera, which to me is somewhat silly.

  31. #31 trrll
    May 31, 2007

    So is Behe actually arguing that the Generator Of Design intervened personally to miraculously confer chloroquine resistance on the malaria parasite? Hardly seems benevolent. Isn’t that taking the “not a sparrow falls” business a bit to an extreme?

  32. #32 trrll
    June 1, 2007

    Stuart Kaufman has done some very interesting simulations of theoretical fitness functions. Some of his results suggest that there are limits to the complexity of organisms (technically the number of interactions between different genes) that are capable of evolving, above which the fitness function becomes too uncorrelated for heuristic searches like natural selection to be efficient. This brings up an additional point–there is selection for evolvability. Organisms that are incapable of evolving efficiently by natural selection will be unable to track their fitness optimum when the landscape shifts (e.g. a new disease or predator emerges) and are at increased risk of extinction.

    One thing mutation studies have demonstrated is just how robust organisms are to mutation. Very often, biologists knock out a gene that is believed to have a crucial function and the organism turns out to be virtually normal due to compensation occurring in development. And in a recent study, the brains of transgenic mice engineered to express an additional photopigment in the eye exhibited improved color vision, demonstrating that the developing mouse brain was able to adapt to take advantage of the “mutation.” This is just the sort of thing that is expected if there is selection at the species level for ‘evolvability.’

  33. #33 RBH
    June 1, 2007

    Well Hell, Mark, you wrote (a good part of) the review I was making notes for. So I guess I’ll have to salvage the parts you didn’t cover — Behe’s dismissal of computer simulations of evolutionary processes — and make do with that. :)

    With respect to the discussion of the prevalence of local maxima in high-dimensioned spaces, I found it interesting that Behe used a figure from Gavrilets’ book, but apparently didn’t actually read the book, since Gavrilets argues (contra one or two people above) that higher dimensioned fitness landscapes are rich with neutral ridges connecting most parts of the landscape to most other parts (apologies for the reification).

  34. #34 Matthew Bardoe
    June 1, 2007

    I have to say that I too believe that in general higher degree functions will have very few extrema… While each partial derivative does define a hypersurface, we will look for places for ALL the hypersurfaces to equal zero, simultaneously. Each partial derivative is its own hypersurface and we must add one more equation that they all have value zero. This is an over-defined system, one where the number of equations to satisfy is greater than the degrees of freedom of the inputs. This means that there will in general be very few solutions, and after that we must take 1/2^(dimension of inputs), for consideration of convexity. Seems small to me.

  35. #35 Ichnemon
    June 1, 2007

    Excellent review, thanks for writing it. It certainly seems as if Behe hasn’t learned a thing from all the fallacies and sloppy mistakes he made in his first book.

    Or maybe he *has* learned something — he has learned that an anti-evolution book doesn’t have to make sense or hold up to the slightest scrutiny in order to sell like hotcakes, make a lot of money, and get the author fat lecture fees in front of gullible audiences who will pay to be told what they want to hear.

    One minor nitpick about your review — in the passage “focuses an this alleged”, the “an” should obviously be “on”.

  36. #36 Anonymous
    June 1, 2007

    Regarding Bardoe’s comment from 1:17am, the system isn’t over-determined: there is one constraint (saying that a partial derivative must vanish) for each variable, so there are exactly the same number of equations as variables. The mistake in the comment is “and we must add one more equation…” (each hypersurface already corresponds to where a partial derivative vanishes, so we don’t need any additional constraint to force the value to be zero).

  37. #37 Dustin
    June 1, 2007

    As an interesting aside, IDists, when they’re quoting Dembski, like to talk about the No Free Lunch theorems. The NFL theorems are based on the idea that landscapes really aren’t smooth – that they don’t have uniform properties that permit a search strategy to work. Behe’s argument totally contradicts that – the kinds of landscapes that must be considered to make NFL work totally devastate Behe’s idea.

    Yeah, Behe has somehow managed to be more wrong than Dembski. We should give him some kind of an award for that. If that kind of wrong was in World of Warcraft, its name would be purple.

  38. #38 Mel
    June 1, 2007

    The fitness landscape concept is (or was about 10 years ago when I was completing a PhD in behavioural ecology, a field I have since left) certainly used to model evolution of particular characteristics. But usually we’d just be looking at two or at most three dimensions, and one very specific behaviour. So the dimensions in, for example, studying rejection of possible brood parasites might be the probability of another bird laying its egg in your nest versus your own ability to distinguish your chicks from alien chicks and perhaps the cost to you of rearing an alien chick (ie huge if it’s a cuckoo, lower if it’s a cowbird). It’s actually quite a useful way of formalising and quantifying what behaviour you expect under different conditions, leading to testable predictions about what different species should do, instead of just waving your hands and saying behaviour a looks better than behaviour b.

    I think part of the problem that Behe is having is that he imagines that for a single organism there is a single maximum, whereas you have to think about all the different charactistics and behaviours that are in some senses being independently acted upon by natural selection. It’s not the individual that’s sitting on top of a local maximum, it’s the sum of each of its characteristics and behaviours, sitting on top of their separate ones.

    Even with just that very simple, single behaviour (reject a suspect chick or not), you can get quite complicated functions. But of course each individual has a huge repertoire of behaviour on which natural selection might act, not to mention physical characteristics. And all of them interact with each other. I don’t have the mathmatical expertise of the other commenters on this site, but it seems intuitively clear to me that optimising for one single physical characteristic or behaviour on a local maximum definitely doesn’t prevent change in another characteristic or behaviour, which could lead to the maximum for the original behaviours being different.

    Thinking about it, probably this is just a different way of saying what lots of you have already said about being able to move between maxima in various different ways, but from a non-mathematical biologist’s perspective.

    Mel

  39. #39 mel
    June 1, 2007

    I should have said in my comment above that obviously using the limited dimension landscape is an incredibly simplified way of representing the selection pressure on even just one behaviour, and that assessing even those simple sounding variables is very difficult. I just used it as a tool to help me think clearly about the question I was asking and make some predictions that were more than assertions about one thing being better than another.

  40. #40 demallien
    June 1, 2007

    Reed,

    Your point about population maxima, rather than individual maxima is just another way of stating Mark’s point about minor non-beneficial mutations (or non-beneficial recombinations of genes from any mechanism for that matter!).

    Actually, there’s a paper floating around that descibes how sexual reproduction increases the surface of the fitness landscape covered by a population, helping populations escape local maxima. This gives an obvious adaptability advantage to the species involved, hence the preference for sexual reproduction amongst complex species with low reproduction rates…

  41. #41 a
    June 1, 2007

    This is funny…
    People who have not ever seen Behe’s new book are saying like “Great review!”. I can not know, how many strawmen arguments Mark Chu-Carroll have made in his review. But one of his “arguments” was silliest I have heard today. He wrote:

    “Behe claims to believe in an all-knowing, all-powerful God. But at the same time, his entire book is based on the argument that God created life on earth, and got it all going using an evolutionary process. But then, according to Behe, over and over again, his creation was woefully inadequate of facing the actual challenges that it would face, and so his all-powerful creator needs to constantly intervene, and tweak things in order to make them work. His God is a buffoon – a bumbling fool who isn’t capable of creating worlds in a way that works.”

    I dont’t know, what Behe has now written. But your logic sounds terrible:
    If God is all-powerful, then he can do anything he wants to do. And then he could also use only some of his power in our universe if he wanted to. (And all-powerful agent could also make for example the world, where is not any life… or whatever.) So, even if God doesn’t want to do something (and that’s why “isn’t capable” to do something), he can be, and is all-powerful.

    You didn’t made bad theology. Your “theology” was so bad, that it was not even theology. You made only an logical error.

  42. #42 Sanford Small
    June 1, 2007

    “What’s the favorite bullshit mathematical argument of creationist assholes worldwide?”

    You lose reasonable civil people like me when you talk like this. Grow up for heavens sake.

    I have NEVER seen Behe or any other well known IDer blog that someone is an “asshole” or that their arguments are “bullshit.” You lose the majority of people when your argument is filled with such hateful attacks and the other side is actually, I don’t know, CIVIL.

  43. #43 Mark C. Chu-Carroll
    June 1, 2007

    a:

    You’re basically re-iterating my criticism of Behe as if Behe’s reasoning were my invention…

    *Behe* is the one who says that there is an all-powerful, all-knowing god who created the universe, created life, set it going down its evolutionary pathway, and then constantly had to tweak it, because it couldn’t work properly on its own.

    My point is that Behe’s description of how life developed, and what God supposedly did to prod it along is incompatible with his description of God.

    If there’s an omniscient god, and he created the universe with the intention of creating life, then creating it in such a way that he needed to constantly intervene to make a tweak here, a change there, a nudge somewhere else – is the sign of an utterly incompetent creator.

    As I’ve mentioned before, I’m a religious Jew, and I do believe in God. But I *don’t* believe in the sloppy interventionist god that Behe describes. The concept of an all-knowing, all-powerful being that created the universe and the bumbling idiot of Behe’s argument simply are not compatible.

  44. #44 ERV
    June 1, 2007

    Sandford– I have NEVER seen Behe or any other well known IDer blog that someone is an “asshole” or that their arguments are “bullshit.”

    Ignoring the fact that Professional Creationists actions are gravely dangerous compared to ‘name calling’ (Youre so holy Sanford! Youre a better person than all of us!), you havent been on the intrawebz much, have you?

    Why dont you Google ‘Dembskis Christmas Present’ from 2006. That was fun.

    ‘Asshole’ is the nicest possible descriptor I can think of for Professional Creationists. If you dont understand why, then maybe you need to spend some time on Google and see if you can figure out why people some people might be a little angry with Creationists behaviors.

  45. #45 windy
    June 1, 2007

    The likelihood that Homo sapiens achieved any single mutation of the kind required for malaria to become resistant to chloroquine…

    Would that be anything like the likelihood that Homo sapiens achieved a mutation that confers resistance to malaria, Dr. Behe? Or several such mutations in at least five different genes?

    Malaria is an incredibly stupid example to use if you want to demonstrate the impossibility of resistance mutations in humans. Does Behe discuss the sickle cell trait anywhere in the book? I bet he thinks it doesn’t count since it “does not add information to the genome” or something.

  46. #46 Mark C. Chu-Carroll
    June 1, 2007

    Sanford:

    http://rockstarramblings.blogspot.com/2006/11/doggerel-44-youre-just-rude.html

    So, one sentence of my review was rude. I think it was appropriately rude. Behe and friends constantly trot out the same old nonsense, over and over, ignoring all criticism of it, and constantly presenting it as the unrefutable truth.

    I’m particularly annoyed at the big-numbers argument, which I’ve written about lots of times before. It’s the argument where you pull a bunch of numbers out of the air, multiply them together, and say “Look how big that number is!”, as if proves anything.

    That’s exactly what Behe does. He comes up with completely unsupportable nonsense numbers, multiplies them together, asserts that they’re a meaningful probability, and then says that probability is so large that it means it’s impossible.

    It’s a crap argument, and the thing is, Behe *knows* it’s a crap argument. He just doesn’t *care* that he’s reciting crap.

    Calling him on it, and saying that it’s bullshit, and that *he knows* it bullshit is perfectly valid. You might not like the words, but this isn’t a debate about who writes prettier words, or who’s more polite, or who’s the nicer person. Behe would likely win *all* of those. But what we’re talking about is math, science, and facts – and Behe loses on all of those. And writing style and politeness have zip-all to do with that. He’s wrong, and he *knows* he’s wrong.

  47. #47 a
    June 1, 2007

    Mark C. Chu-Carroll:

    “You’re basically re-iterating my criticism of Behe as if Behe’s reasoning were my invention…”

    No.

    “My point is that Behe’s description of how life developed, and what God supposedly did to prod it along is incompatible with his description of God.”

    If there is an omnipotent God, He could do anything. And He could also decide, how He uses His power. If He were omnipotent, he could for example decide to use only some of his power (and thus reject some of his power) in our universe, if He wanted.

    That’s why I can’t understand, how Behe’s position couldn’t be compatible with the idea about omnipotent God. And that’s why I see your claim as a logical error:
    because all-powerful agent (by definition) could do anything – even to reject his power or to work like an “idiot”, (if He wanted)…

  48. #48 Sanford
    June 1, 2007

    Mark- I will assume that Behe doesn’t make arguments he KNOWS are wrong (“crap” as you called it). That’s just silly.

    Is it possible he’s right and you’re wrong? Of course it is.

    I read the link you posted. You’re a ‘skeptic’, then? I assume that is the case, as you linked to the post defending the behavior of skeptics.

    Civil behavior IS important. Civil people won’t ever take your side arguing like this.

  49. #49 windy
    June 1, 2007

    I have NEVER seen Behe or any other well known IDer blog that someone is an “asshole” or that their arguments are “bullshit.”

    Behe: “This continues the venerable Darwinian tradition of making grandiose claims based on piddling results.”

    Dembski: “…it’s not ID’s task to match your pathetic level of detail in telling mechanistic stories.”

    Such gentlemen. But at least they didn’t use any naughty words!

  50. #50 Sanford
    June 1, 2007

    ERV- to argue there’s danger in a creationist argument is absurd.

    The great majority of Americans don’t buy your side of the argument. I see no damage done. The world has yet to crumble. The earth hasn’t stopped rotating.

    Scare tactics don’t impress me much.

    You think there’s some danger in their arguments, so that makes it okay to use vulgar terms and call names? Really mature.

  51. #51 Sanford
    June 1, 2007

    Windy- you’re comparing apples and wrenches.
    Behe described results not a person. Dembski called something pathetic. How you compare that to the sentence Mark used, I have no clue.

    The point is- you will never win in the public arena as long as your rhetoric is so hateful. Adults make arguments without calling their opponents “assholes.”

  52. #52 gg
    June 1, 2007

    Sanford wrote: “Windy- you’re comparing apples and wrenches.
    Behe described results not a person. Dembski called something pathetic. How you compare that to the sentence Mark used, I have no clue.”

    Actually, Sanford, he was referring to your statement that “I have NEVER seen Behe or any other well known IDer blog … that their arguments are “bullshit.” You’re ignoring your own previous statements to try and make a specious point.

    What’s with all this concern about the word ‘asshole’ anyway? I haven’t run into anyone in the past decade who hasn’t used the word in public, including my ultra-conservative mother, father, sister, and 85-year-old grandmother. I’m guessing this is a red herring on your part, to try and draw the argument away from Behe’s indefensible ‘bullshit’ arguments and into a discussion of civility. I’ve noticed that you have no defense of Behe’s work.

    This sort of double standard has been a constant force in the conservative and right-religious world for years. Dick Cheney can tell a congressman to ‘go fuck himself’ on the Senate floor and be applauded for it, while Harry Reid can’t refer to Bush as a ‘loser’ without conservatives everywhere swooning and fainting in horror. Religious nutjobs can refer to scientists as ‘deluded fools’ without any justification or empirical argument whatsoever, but call a person an ‘asshole’ for such a statement and the nutjobs get all wide-eyed.

    Sorry, shock at the use of naughty words went out of style when the PG-13 rating came in. People who ignore the bulk of an argument because of the use of one or two profanities are either being utterly dishonest or irrational.

  53. #53 SteveF
    June 1, 2007

    Sanford,

    I agree, creationists never use cheap and possibly offensive rhetorical phrases. Next thing you know, somebody will be alleging that creationists have been tying in evolutionists with nazism.

  54. #54 Norman Levitt
    June 1, 2007

    It strikes me that Behe’s confusion is even more intense than let on here. Here can use a smooth fitness landscape if he wishes, but this matters little since, even with point mutations, he has to be talking about discrete changes in the fitness functon, not “infinitesimal” ones. Of course, one can, for convenientce, model the process as one of continuus change, i.e., as the evolution of a differential equatiion of some sort, and this may be pictorially helpful, but only at the expenxe of scarcificin key realism, which is vital as it happens for the points at issue. One needs as sell a basic grounding in multivariable critical point theory–Morse theory, if you will, in order to “classify” the fiefferent types of equilibria, stable and metastable alike. One must be able to switch to local coordinates without getting hopelessly confused as to the global picture.

    Finally, there are vital matters of scale here, which Behe seems utterly at sea about. Every mutation is, to a degree saltational; what is key is whether that saltation improves fitness, or decreases it. and whether the change puts the fitness point in the basin of attractiion of an entirely different local extreme. This is clearly a matter of geometry and scale and classification of possible directions.and can’t be decreed by fiat a priori–its an empiriical matter. A genome whose fitness is poiosed on a knifeedge can improve itself slightly by a small step in a particular direction; a small step in another direction will carry it precipitously downhill and thus, presumably, to extinction. The key is not the size of the step but the roughness of the landsape.

    Speaking of which, there’s nothing in this kind of analysis that requires a smooth landscape with smooth fitness functin. A continuous landscape with continuus, or even piecewise-continuous fintess functon works just as well, with, perhaps, a bit more realism.

  55. #55 Mark C. Chu-Carroll
    June 1, 2007

    Norman:

    You’re exactly right. The problem with Behe is that he’s invoking a particular model of evolution as a search over the fitness landscape; and that he’s relying in specific properties of the landscape and the search process – things like the shape of the landscape, the ratio of the size of possible changes relative to the sizes of the peaks of maxima, among others – but *without* ever making the case for *why* those properties have any relation to reality.

    This goes back to something I’ve written about before. Mathematical modeling is a great thing: it’s an incredibly useful technique, and personally, I find mathematical models of real phenomena to be absolutely fascinating. But to move from experiments/observations/analyses of mathematical models to predictions or statements about the real world, you need to *validate* that model, and show that it’s an accurate reflection of reality. Behe never even *pretends* to take that step. He merely asserts that the landscape is a valid model, never explicitly states his assumptions about that model, never even runs and experiments in the model, never tests how well his model matches real observations, and then argues that the conclusions that he draws on the basis of his model are valid conclusions about reality.

    The biggest condemnation of Behe’s argument is the *observations* of evolution: the numerous cases where we can witness that things that Behe’s model says are impossible can occur in reality.

  56. #56 Jud
    June 1, 2007

    a said: “If there is an omnipotent God, He could do anything. And He could also decide, how He uses His power. If He were omnipotent, he could for example decide to use only some of his power (and thus reject some of his power) in our universe, if He wanted.

    “That’s why I can’t understand, how Behe’s position couldn’t be compatible with the idea about omnipotent God.”

    The problem with your argument, a, is that it fits with absolutely any result. Behe’s position is compatible with an omnipotent God who chooses to use only part of his power in order make a Creation that needs constant tinkering. Mark’s position is compatible with an omnipotent God who chooses to allow his Creation to evolve in accordance with the principles of mutation (a/k/a “variation”) and selection first systematically discussed by Darwin.

    Since belief in an omnipotent God who can choose to do or not do absolutely anything doesn’t make either evolution or the arguments against it any more or less likely, perhaps you’ll agree we should turn to the scientific research being carried on every day by good, smart, sincere people in order to find out just what God *did* choose to do? Good, then the answer is that He chose to let Creation evolve.

  57. #57 did
    June 1, 2007

    Sanford –

    You haven’t looked very hard.

    did

  58. #58 hoary puccoon
    June 1, 2007

    Sanford has a point, which he’s proven quite effectively by posting over and over again about your shocking (tsk tsk!) language, and completely ignoring the substance of your review. Why give the creationists ammunition by using language they can endlessly drag around as a red herring? The last paragraph of your review was far more effective criticism. Professors get called asshole routinely, at least behind their backs– but wondering how the guy got tenure? Not one naughty word, but unless Behe’s completely out of touch with reality, that had to have stung.

  59. #59 SLC
    June 1, 2007

    Behe got tenure because he waited until he got tenure before turning into a whackjob. Contrast that with Prof. Gonazlez who turned into a whackjob before getting tenure.

  60. #60 ERV
    June 1, 2007

    Well, Sandford, if your oh-so-delicate sensibilities cannot tolerate being near a naughty word (like Ming vases, Creationists), youre more than welcome to look at my post, or any of the ones Blake Stacey collected to learn about Behes difficulties in the subjects he professes to have mastered.

    Can you do that, Sanford, or would you rather troll here as an attention whore?

    Or do you have nothing to contribute to this conversation besides being a cry baby?

  61. #61 trrll
    June 1, 2007

    If there is an omnipotent God, He could do anything. And He could also decide, how He uses His power. If He were omnipotent, he could for example decide to use only some of his power (and thus reject some of his power) in our universe, if He wanted.

    That’s why I can’t understand, how Behe’s position couldn’t be compatible with the idea about omnipotent God.

    Of course it could be. Indeed, there is absolutely nothing that is incompatible with the idea of an omnipotent, sufficiently capricious God, including the idea that the universe was created 5 minutes ago, fossils, memories, and all. That’s one reason why scientists reject the notion of ID as science, because it refuses to hypothesize as to the nature of the supposed Designer, which renders the theory completely untestable.

    On the other hand, from a theological point of view, I can easily see why many people find the notion of a capricious, arbitrary God unsatisfying. If God is intelligent enough to create a universe that fulfills His will simply by virtue of its fundamental nature, why would he keep tweaking it? Are we to conceptualize Him as some sort of cosmic hobbiest, rerouting the model trains for His own Personal amusement? If he can make a real thumb, why not give the panda one, too? Is this His idea of a joke? One tends to expect a higher standard of behavior for God.

  62. #62 trrll
    June 1, 2007

    Sanford has a point, which he’s proven quite effectively by posting over and over again about your shocking (tsk tsk!) language, and completely ignoring the substance of your review. Why give the creationists ammunition by using language they can endlessly drag around as a red herring?

    In my experience, the sort of people who nitpick about rude language will always find something trivial to complain about as an excuse for ignoring substance. If it’s not language, it will be spelling or grammar.

  63. #63 Jonathan Vos Post
    June 1, 2007

    Jesus comes back, and judges the sinners. “You, my dishonest son Michael Behe, are hereby sentenced to a thousand years in the Mesozoic era!” Gavel bangs, time portal opens…

    The higher-dimensional fiteness landscape leads to interesting Math, which no ID person I know of has read. For instance:

    arXiv:0705.4481
    Title: Singularities of generic projection hypersurfaces
    Authors: Davis C. Doherty
    Comments: 9 pages

    Linearly projecting smooth projective varieties provides a method of obtaining hypersurfaces birational to the original varieties. We show that in low dimension, the resulting hypersurfaces only have Du Bois singularities. Moreover, we conclude that these Du Bois singularities are in fact semi log canonical. However, we demonstrate the existence of counterexamples in high dimension — the generic linear projection of certain varieties of dimension 30 or higher is neither semi log canonical nor Du Bois.

  64. #64 GDC
    June 1, 2007

    So if my understanding is correct, it seems that Behe’s God created a system that was fundamentally flawed from the get-go, and incapable of performing its intended task on its own. As a result, the designer must frequently intervene by adding stuff as flaws are discovered.

    So essentially, Behe’s god is Microsoft.

  65. #65 Blake Stacey, OM
    June 1, 2007

    trrll:

    In my experience, the sort of people who nitpick about rude language will always find something trivial to complain about as an excuse for ignoring substance. If it’s not language, it will be spelling or grammar.

    Or the perceived moral character of the nitpickee, etc.

    I plan to play “amateur Coturnix” and collect links to posts on this topic. My list so far is here, down at the bottom.

  66. #66 Davis
    June 1, 2007

    Hey, thanks for the shout-out Jonathan. :)

  67. #67 Jonathan Vos Post
    June 1, 2007

    Well, it shows how I spend my reading time when I’m not reading Science Fiction, Mystery, or the like. Christoph Adami is way ahead of me in cool papers on evolution of abstract biomorphic networks. But I doubt that Behe et al are willing to use an evolutionary algorithm that they didn’t intentionally cripple:

    http://arxiv.org/ftp/arxiv/papers/0705/0705.4674.pdf

    arXiv:0705.4674
    Title: Evolution of complex modular biological networks
    Authors: Arend Hintze, Christoph Adami (KGI)
    Comments: 26 pages, 10 figures, 6 supplemental figures, and one supplementary table, in one pdf file

    Biological networks have evolved to be highly functional within uncertain environments while remaining extremely adaptable. One of the main contributors to the robustness and evolvability of biological networks is believed to be their modularity of function, with modules defined as sets of genes that are strongly interconnected but whose function is separable from those of other modules. Here, we investigate the in-silico evolution of modularity and robustness in complex artificial metabolic networks that encode an increasing amount of information about their environment while acquiring ubiquitous features of biological, social, and engineering networks, such as scale-free edge distribution, small-world property, and fault-tolerance. These networks evolve in environments that differ in their predictability, and allow us to study modularity from topological, functional, and gene-epistatic points of view. We find that functional and topological modules do not always correspond to each other, and are recapitulated differently by genetic interactions. Synthetic lethal pairs consist mostly of redundant genes that lie close to each other and therefore within modules, while dosage rescue pairs are farther apart and often straddle modules, suggesting that suppression rescue is mediated by alternative pathways or modules. We confirm that nodes with high betweenness centrality often connect modules, but find that such nodes also play essential roles within modules.

  68. #68 a
    June 1, 2007

    Jud wrote´:
    “The problem with your argument, a, is that it fits with absolutely any result.
    Behe’s position is compatible with …
    Mark’s position is compatible with an omnipotent God who…

    Yes, I think, that omnipotent agent could be compatible with any result. Perhaps it is not nice and plausible idea, but I think that it still logically follows by definition of omnipotence. And I think, that it is better to follow evidence and logical conclusions, than what someone thinks is nice.

    Since belief in an omnipotent God who can choose to do or not do absolutely anything doesn’t make either evolution or the arguments against it any more or less likely, perhaps you’ll agree we should turn to the scientific research being carried on every day by good, smart, sincere people in order to find out just what God *did* choose to do?”

    Yes!

  69. #69 a
    June 1, 2007

    Trrll wrote:

    “If God is intelligent enough to create a universe that fulfills His will simply by virtue of its fundamental nature, why would he keep tweaking it? Are we to conceptualize Him as some sort of cosmic hobbiest, rerouting the model trains for His own Personal amusement? If he can make a real thumb, why not give the panda one, too? Is this His idea of a joke? One tends to expect a higher standard of behavior for God.”

    Bible answers:

    “who are you�”mere man that you are�”to talk back to God? Can an object that was molded say to the one who molded it, “Why did you make me like this?” A potter has the right to do what he wants to with his clay, doesn’t he? He can make something for a special occasion or something for ordinary use from the same lump. Now if God wants to demonstrate his wrath and reveal his power, can’t he be extremely patient with the objects of his wrath that are made for destruction?” (Rome 9:20-22)

  70. #70 brahim ben ketib
    June 1, 2007

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  71. #71 brahim ben ketib
    June 1, 2007

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  72. #72 Ørjan Johansen
    June 1, 2007

    I seem to detect a dichotomy in this discussion: That God would either have to have made a creation that works perfectly like clockwork without his further intervention, or he would have to be capricious or incompetent, someone we could never hope to understand and who might smite us if we tried.

    Why couldn’t God simply have decided from the outset on a balance: a universe that mostly works by itself, but where there is still room for him to stay in touch with creation?

  73. #73 KarmaPolice
    June 1, 2007

    Why couldn’t God simply have decided from the outset on a balance: a universe that mostly works by itself, but where there is still room for him to stay in touch with creation?

    Well, just my two cents, the theological problem is more in the way Behe characterizes this intervention:

    One of the common, and necessary, traits, attributed to the Christian God is that it possess an unchanging nature. That’s the incentive for believing his promises, accepting his word as true, etc.- because those things don’t change. If God possesses this fixedness of nature, than we should expect his creation to conform to this fixedness of nature as well- in other words, operate by laws and processes that are also fixed. That’s perhaps compatible with God who intervenes for a preplanned set piece or two- a flood or two, or sending the kid on vacation, at most. But it completely breaks down if you presume a god that is constantly intervening in large ways- for example, a god who created the universe last week but makes it appear to be millions of years old. That god would be unworthy of worship, outside of abject terror, because we could never really trust that what that God said he would or would not do to be equivalent to what would actually occur. This is true regardless of the reasons for his changeable nature- incompetence or capriciousness being two possibilities.

    So, I guess it boils down to where along this continuum one would place a god that was constantly and directly introducing, removing, and adjusting various species in completely novel and- to us- unpredictable ways, through the mechanism of divine will alone, as Behe large numbers argument suggests. (As opposed to the grand watchmaker version.) If one presumes that this god is particularly inclined towards human beings, and one considers that many of those species will interact in very negative ways with those human beings in ways they are unprepared to combat or foresee- then it would be reasonable to assume that that God lacked fixedness.

    Take the Malaria example. We could presume a purely natural intersection of processes: some of which led to malaria, another set that leads to the discovery of chloroquine, than a continuation of the prior processes that leads to resistance. If all the processes that lead up to this sequence were set in stone at creation, and occur in a hands off manner, this in no way impugns God’s fixedness. Compare this to a god who: 1) creates a debilitating and often fatal disease, 2) allows humans, through the application of the laws of the created universe, to discover a drug which shows promise of preventing the disease, then 3) solely through the intervention of his will changes the malaria to be resistant to the drug, against the imaginary odds of 1 in 100000000000000000000 of such a thing occurring by happenstance alone.

    Now multiply this by all the diseases he causes to develop resistances, to jump species barriers, or to suddenly mutate to become more virulent, etc. Such a God can not be trusted, because his creation lacks any cohesive order in fundamentally important ways, by his own hand- regardless of whether an ineffable plan, incompetence, capriciousness, or out-right malevolence is the fundamental cause. And that’s just in the microscopic world.

    Uh, just my two cents. Probably rambling a bit there. :)

  74. #74 Aaron C
    June 1, 2007

    Good job MarkCC,

    Two points. First, very quickly, in the text starting with, “The second part *if* this is a huge problem …” I’m pretty sure you meant *of*. Secondly, and much more importantly, let me add a point about natural selection, stated so that laymen can understand it. I myself am a math and computer science grad student, but I realize the need to bring things down to the kindergarten level favored by most creationists. Note that I am consciously trying to avoid any jargon from biology or mathematics.

    “Look, we all know that most people/animals, with the exception of identical twins, tend to be a little bit different. We also all know that the environment, seasons, and the weather are in a constant state of change, both short-term and long-term. Putting these two facts together, mutations in the *environment*, rather than the individual, can cause one person/animal and his offspring to be favored over another. Because the environment in one place or another is often changing, there isn’t really a ‘best’ way for any one type of animal to be for any length of time. Sometimes things settle down in places for a while and then an animal’s offspring can start to getting better at living in that particular spot. Behe suggests that maybe evolution might not be able to make the changes quick enough, but as the saying goes, ‘if ifs and buts were beer and nuts” then creationists would be a lot more fun to hang out with.

  75. #75 Science Avenger
    June 1, 2007

    a said: who are you mere man that you are to talk back to God?

    We aren’t talking back to God. We are talking back to you. We are saying the evidence suggests what you say about God is wrong.

  76. #76 Mark
    June 2, 2007

    Mark. Please post your review on Amazon where it will do more good. Also, the Shoreline Cinema ads before the movies might be another place … maybe not.

  77. #77 jotetamu
    June 2, 2007

    Mark,

    I have a linguistic quibble, but since none of the other pedants has picked it up, perhaps the language has changed since I formed my prejudices. To me, “… his creation was woefully inadequate of facing the actual challenges …” isn’t English. You could say “incapable of facing” or “inadequate to face”, but not “inadequate of facing”.

    I too would like to see your review more widely disseminated.

    Jim Roberts

  78. #78 dhogaza
    June 2, 2007

    Dembski chimes in at UD:

    Mark Chu-Carroll goes after Behe’s new book here. Judge for yourself whether this deserves to be called a review (Chu-Carroll thinks it does). Nick Matzke endorses Chu-Carroll’s blog post against Behe here. Are there any anti-ID writings, no matter how ill-conceived or mean-spirited, that PT won’t endorse?

    Of course, he makes no attempt to show *why* he thinks Mark’s review is “ill-conceived” …

  79. #79 Borne
    June 2, 2007

    How did Carroll ever get a Phd. in anything ? They seem to be selling them to the lowest bidder these days – at least in the US. All you have to do is yell, “Darwin is god!” and you’ll be handed a Phd in any field you choose.

    Lets just say that your review, if it may be called such, is itself BAD LOGIC, BAD MATH and the usual presumptions and ad homs of the typical Darwinist tripe panderers – Chu-Carroll a prime example.

    The reviewer clearly doesn’t understand a single thing Behe (or any other ID scientist) says.

    Darwinian anti-reasoning cripples the mind and causes mental illness. Specifically, illusionary blindness that impairs the mind from grasping basic elements of the rules of logic.

    Strange that a computer guy misses the boat completely in the logic department.

  80. #80 Unsympathetic reader
    June 2, 2007

    Ok, the previous post was really over the top.

    Honestly folks, we don’t need people like ‘Borne’ sneaking in here and impersonating creationists to make them look bad.

  81. #81 Blake Stacey, OM
    June 2, 2007

    Unfortunately, “Borne” hasn’t commented here before (at least under that ‘nym), so I can’t make the obvious joke:

    “Borne, again?”

    Thank you, thank you, I’ll be here all week!

    dhogaza:

    Of course, he makes no attempt to show *why* he thinks Mark’s review is “ill-conceived”

    Well, in Dembski’s book, the only good conception is an Immaculate conception by the Holy Spirit, right? :-)

  82. #82 Bob O'H
    June 2, 2007

    Of course, he makes no attempt to show *why* he thinks Mark’s review is “ill-conceived”

    Of course not. He doesn’t need to match our pathetic level of detail.

    Bob

  83. #84 trrll
    June 2, 2007

    “who are you�”mere man that you are�”to talk back to God? Can an object that was molded say to the one who molded it, “Why did you make me like this?” A potter has the right to do what he wants to with his clay, doesn’t he? He can make something for a special occasion or something for ordinary use from the same lump. Now if God wants to demonstrate his wrath and reveal his power, can’t he be extremely patient with the objects of his wrath that are made for destruction?” (Rome 9:20-22)

    Ah, but it is only “talking back to God” if I actually believe that God exists in the form supposed by ID/Creationists–capricious, irrational, unable or unwilling to create a universe that functioned properly without continued supernatural meddling. Why would anybody choose to believe in such a lame God, when one could just as well believe in a rational God with the foresight and elegance to design the fundamental laws of nature so that they fulfill His will without the need for continual tweaking? And no, I do not believe that the act of creation relieves one of moral responsibility toward one’s creation. I do not believe that parents are entitled to abuse their children, for example. I certainly could not respect, much less worship, a God with such an immoral attitude.

  84. #85 Julia
    June 2, 2007

    Aaron C –

    Monozygotic twins are not even 100% identical. Just ask the mother of any pair of them. GENETICALLY identical, sure, but even in the womb they experience slightly different environments that shape them to be at least slightly different.

  85. #86 Chris' Wills
    June 3, 2007

    Thank you Mark (and the others who have posted) for the understandable explanantion of why the arguements Behe uses in his forthcoming book are incorrect.

  86. #87 plunge
    June 3, 2007

    The posts over at UD are just plain… sad. Dembski offers no substantive criticism other than to suppose that computer scientists don’t know much about math. DaveScot spends a paragraph arguing with himself over whether this can be called a “review” or not, and then discusses Carrol’s inadequacies at length as compared to his own accomplishments… again never getting around to even mentioning the substantive issues at question.

    The few posters who do in passing actually address the subject matter recycle the same nonsense diatribe about Dawkin’s weasel discussion from Watchmaker, in which they criticize the example for having a goal… ignoring the fact that Dawkins puts EXACTLY that disclaimer in the example. Or failing to recognize that the example was meant to illustrate competitiveness in only a SINGLE dimension, again for the purposes of illustration, before going on to talk about more complicated matters.

    Then of course there is this knee-slapper: “Unfortunetaly for Darwinists, it has been shown that to achieve even a simple modification of a protein, let’s say two amino acid residues, evolution must cross a sequence space of mutations that provide no selective advantage.”

    Oh, it’s been shown, has it? Wait, which journal was that again? Which article? And did that groundbreaking refutation of “Darwinism” also explain how the almost numbingly routine papers on actual mutation by mutation adaptive changes are all in error, since even simple modifications are too improbable to make all of the findings of these papers possible?

    I’d post this over there, but there’s really no point in posting in a forum that routinely deletes criticism.

  87. #88 Dustin
    June 3, 2007

    Me, I wouldn’t even concede that the Weasel program is faulty because of its predetermined goals. Dawkins had another program that did spider web evolution, and it was almost identical but for the fact that the optimal web was determined by economics, not by Shakespeare. How the selective landscape was originally determined doesn’t make much difference. It’s there, and things will be forced along it by selection, not intelligence.

  88. #89 Jerome
    June 3, 2007

    RE:

    ————
    How the selective landscape was originally determined doesn’t make much difference. It’s there, and things will be forced along it by selection, not intelligence.
    ————-

    That eerily sounds like a statement of faith right there.

  89. #90 plunge
    June 3, 2007

    “Me, I wouldn’t even concede that the Weasel program is faulty because of its predetermined goals.”

    It’s not a question of whether it’s faulty or not: Dawkins says right at the outset that the example is to demonstrate how powerful selection can be working on randomly evolving strings and that it is not a good model for evolution because it has final goal. In the chapter, he’s working to explain the idea of selection and why its so powerful, and he does so like one would teaching physics in a textbook, teaching different elements bit by bit and then putting them all together as well as adding more of the real world complications. Presenting it as misleading because it doesn’t model evolution directly is ridiculous.

    What’s particularly laughable about the objections ID folk make to it is that having one single goal is actually a constraint: real life evolution has many many different dimensions of genetic change all of which just have to come up with some development in ANY direction that happens to improve overall fitness in a given environment. For some reason, ID critics manage to both complain that there is no single and known goal in real life but then ALSO act as if there is only one goal out there to find so that they can be incredulous about the odds of reaching that one goal.

  90. #91 plunge
    June 3, 2007

    “How the selective landscape was originally determined doesn’t make much difference. It’s there, and things will be forced along it by selection, not intelligence.
    That eerily sounds like a statement of faith right there.”

    Sigh, no. Observing a given and then working what happens from that given is not a statement of faith. Believing that the selective landscape we know exists came from God is a statement of faith. Observing that it exists (and not knowing how it came to be) and then seeing what follows from it is using reason.

  91. #92 Torbjörn Larsson, OM
    June 3, 2007

    ID scientist

    Good one, Borne of the Divine Wind.

    In 20 years of ‘research’ not a single ID creationist has published anything predictive or even descriptive. They just don’t want to work on that “level of pathetic detail”.

  92. #93 Blake Stacey, OM
    June 3, 2007

    plunge quotes Dembski as follows:

    Unfortunetaly for Darwinists, it has been shown that to achieve even a simple modification of a protein, let’s say two amino acid residues, evolution must cross a sequence space of mutations that provide no selective advantage.

    Whiskey Tango Foxtrot!? Has the man never heard of neutral mutations? (Look, here’s 3,620 papers he needs to brush up on.) This is basic biology. Either Dembski is completely ignorant, or he is supremely confident he is speaking only to the uninformed.

    Furthermore, Dembski’s complaint about MarkCC’s not being a math expert exhibits the same pattern. It is also the diatribe of the ignorant speaking to the unread. What kind of math are we talking about here? Is it supersymmetry theory derived from particle physics, the latest research efforts on the Riemann Hypothesis, or the abstruse corners of Andrew Wiles’s proof of Fermat’s Last Theorem? No, we’re talking about search algorithms. Doesn’t this sound like a topic with which a computer scientist should be familiar, even if other areas of mathematics are beyond their horizon?

  93. #94 plunge
    June 3, 2007

    That wasn’t Dembski, it was a commenter on the UD site. Just to be clear.

  94. #95 Ed Darrell
    June 4, 2007

    I have NEVER seen Behe or any other well known IDer blog that someone is an “asshole” or that their arguments are “bullshit.” You lose the majority of people when your argument is filled with such hateful attacks and the other side is actually, I don’t know, CIVIL.

    And when you were a kid, you didn’t learn that the kid who was always so nice and polite to your parents, didn’t use bad language around adults, etc., etc., etc., often was the one who’d stab you in the back at the first opportunity?

    The question you should be asking, Sanford, is whether Dr. Behe can distinguish manure from shoe polish. Polite language isn’t a demonstration that it can be done. Failure to use the proper label is an indication of lack of discrimination. As Hemingway noted, to get through life one needs a ‘solid gold bullshit detector.’ Do you have one? When it goes off loudly and the needle on the dial is blowing breezes your way, do you take a tea break to ponder “bovine excrement,” or do you yell “BULLSHIT!” at the top of your lungs?

    Have you never confronted a creationist in an official hearing situation? Then I suppose you can afford not to call bullshit, bullshit. The rest of us appreciate the timely warning.

  95. #96 Ed Darrell
    June 4, 2007

    The critic might be right on one small point: Blunt language is unlikely to persuade the readers of this “Christian” blog that Dr. Behe is not on the fast track to sainthood: http://theconstructivecurmudgeon.blogspot.com/2007/06/behe-strikes-again.html

    So, Sanford, how should we persuade the Christian philosopher who refuses to deal with reason, who doesn’t have the science background, but who has a platform at a seminary, that he shouldn’t support stuff like Behe’s book? Or, do we just say that Christianity has slipped back into the dark ages and write them all off?

    Just a warning, I think allowing Christianity to slip beyond the veil of reason is dangerous and stupid — as a Christian, I think that. Just my opinion.

    So you tell us, what works with those guys, if not blunt language? Can blunt language possibly be counterproductive with people like the “Constructive Curmudgeon?”

  96. #97 windy
    June 4, 2007

    Behe says:

    One heartening conclusion of intelligent design is that Darwinian evolution is not the relentless, Borg-like process we had thought. Random evolution is clumsy and limited. That means that, even when fighting pathogens such as malaria that occur in enormous numbers, if science can find the right monkey wrench to throw in its molecular machinery, random mutation and natural selection will be helpless to circumvent it.

    How the funk does Behe know that the designer won’t intervene again to produce more effective disease organisms? Did malaria, Ebola and HIV evolve or get designed? Both options translate to a really sucky predictive capacity for ID.

  97. #98 Chance
    June 4, 2007

    Ed Darrell-

    Just a warning, I think allowing Christianity to slip beyond the veil of reason is dangerous and stupid — as a Christian, I think that. Just my opinion

    I’ve seen you write similiar stuff in many places. What exactly do you find reasonable about religion at all? What makes you think any religion has ever stepped in front of the ‘veil of reason’?

  98. #99 Stephen
    June 4, 2007

    Dembski offers no substantive criticism other than to suppose that computer scientists don’t know much about math.

    Well, for heavens sake, I don’t claim to know much about maths. But as soon as Mark reported Behe’s claim of things getting trapped at a local maximum, I could immediately think of two objections (which Mark duly covered). And if I can do it, why on earth can’t Behe and Dembski? Presumably because they desperately don’t want to.

    So, ‘a’, when you said:

    This is funny… People who have not ever seen Behe’s new book are saying like “Great review!”

    … are you claiming that Mark lied about Behe’s statements about things getting trapped at a local maximum? Because given that, and what we already know about ID, we can see that Mark’s review follows. And given that it was well written, the comment “Great review!” is entirely appropriate.

    (Though I would like to know what the situation is w.r.t. high-dimensional fitness landscapes. I can’t work out whether Mark is right on that or not.)

  99. #100 Peter Wadeck
    June 4, 2007

    There are times when a small change can have a huge impact. The classic textbook example of this is the Panda’s thumb: a very small genetic change caused a change in the developmental process in the wrist of the panda, which produced what is effectively an extra thumb. The genetic change that produced this is tiny; the effect is huge.

    To extrapolate from the formation of a useless appendage to all of life is a tremendous leap of faith. What appears to be true, though, is that the use of profanity is inversely related to the strength of an argument. I’m still looking for compelling proof, not circumstantial evidence, that evolution can explain all life.

  100. #101 Anonymous
    June 4, 2007

    There is absolutely no aspect of science that would be weakened if no-one had ever thought up the idea of evolution. It’s propagated by people that have been mesmerized and it’s very sad. A 10th grader can fully understand every concept of the mythology of evolution. It’s a farce of the very worse kind.

    If evolutionists want to end the arguments all they have to do is, get their brilliant heads together and assemble a ‘simple’ living cell. This should be possible, since they certainly have a very great amount of knowledge about what is inside the ‘simple’ cell.

    After all, shouldn’t all the combined Intelligence of all the worlds scientist be able the do what chance encounters with random chemicals, without a set of instructions, accomplished about 4 billion years ago,according to the evolutionists, having no intelligence at all available to help them along in their quest to become a living entity. Surely then the evolutionists scientists today should be able to make us a ‘simple’ cell.

    If it weren’t so pitiful it would be humorous, that intelligent people have swallowed the evolution mythology.

    Beyond doubt, the main reason people believe in evolution is that sources they admire, say it is so. It would pay for these people to do a thorough examination of all the evidence CONTRARY to evolution that is readily available: Try answersingenesis.org. The evolutionists should honestly examine the SUPPOSED evidence ‘FOR’ evolution for THEMSELVES.

    Build us a cell, from scratch, with the required raw material, that is with NO cell material, just the ‘raw’ stuff, and the argument is over. But if the scientists are unsuccessful, perhaps they should try Mother Earth’s recipe, you know, the one they claim worked the first time about 4 billion years ago, so they say. All they need to do is to gather all the chemicals that we know are essential for life, pour them into a large clay pot and stir vigorously for a few billion years, and Walla, LIFE!

    Oh, you don’t believe the ‘original’ Mother Earth recipe will work? You are NOT alone, Neither do I, and MILLIONS of others!

  101. #102 Mark C. Chu-Carroll
    June 4, 2007

    Peter:

    The panda’s “thumb” is *not* a useless appendage. In fact, it’s pretty much crucial for the modern panda.

    As for “compelling proof”, what’s wrong with the evidence that’s out there? There’s so much, it’s overwhelming. Personally, given my background, I find the hierarchical relationships between species – independently developed from genetic sequencing and from anatomical similarity, combined with the direct observations of the processes of evolution in action around us to be particularly compelling. That hierarchy is really astonishing – and the way that it was independently produced using two very different kinds of data is a very powerful result. Combine that with the fact that we can watch steps that show how the branches in that tree could develop, and what more do you need?

  102. #103 TheBlackCat
    June 4, 2007

    Anonymous, scientists are currently working on doing that very thing. It was only within the last maybe 20 years at most that we even had the basic techniques that are needed to study a cell in enough detail to begin considering that. It was probably only in the last 10 years that our mastery of those techniques that we could begin learning what specific issues needed to be resolved in order to accomplish such a task. Now we are rapidly approaching the point where a fully synthetic cell can be built, and there are several groups actively working towards that specific goal.

    Of course, when that happens the argument will definitely not be over, because the anti-evolution community will simply find some excuse to ignore the results. Perhaps they will say that it is not as complicated as existing organisms. Perhaps they will say it was built by humans and not be natural processes. Of course the challenge they made does not call for either of these things, but they will conveniently forget that and fall back to a new, more difficult demand. They always do. Perhaps they will deny they ever made the challenge, a common technique. Perhaps they will criticize scientists for “playing God”, despite the fact that they requested it. Perhaps they will say it is all a hoax. Luckily they will not be able to fall back on their most common technique: ignore the event entirely. When, not if, this happens it will be such huge news that they will not be able to ignore it.

  103. #104 Tyler DiPietro
    June 4, 2007

    “To extrapolate from the formation of a useless appendage to all of life is a tremendous leap of faith. What appears to be true, though, is that the use of profanity is inversely related to the strength of an argument. I’m still looking for compelling proof, not circumstantial evidence, that evolution can explain all life.”

    You know, I’ve noticed that whenever a critique of ID gets a lot of attention on the net, ID-flaks tend to don the comment threads with criticisms ranging from “you suck because you used a swear word!” and “nyah nyah nyah nyah nyah!” in intellectual content. Apparently they can’t think of anything better.

  104. #105 Torbjörn Larsson, OMa
    June 4, 2007

    After all, shouldn’t all the combined Intelligence of all the worlds scientist be able the do what chance encounters with random chemicals, without a set of instructions, accomplished about 4 billion years ago,according to the evolutionists

    Is it really so hard to understand that this isn’t part of todays evolutionary biology? Evolutionary biology describes well the structures of existing life as we currently observe it. Its purpose is not to describe how life once got started.

    It is akin to a theory of gravitation, Newton’s say, which describes well the structures of existing planetary system as we currently observe it. But the description of how they once got started is somewhat lacking and different.

    It is sad that people 150 years after the start of a *science* among others thinks it is different for one reason or another. It is not sad that what MILLIONS of people believe does not affect the extent of our collected knowledge. The Medieval Period is long gone.

  105. #106 Torbjörn Larsson, OM
    June 4, 2007

    There is absolutely no aspect of science that would be weakened if no-one had ever thought up the idea of evolution.

    This is what we nowadays calls an Egnorant. No one who knows something about biology or epidemiology would start to think so. A quick googling on Egnor and for example The Panda’s Thumb will lead to posts by scientists who picks apart such outright stupidity.

    But to demonstrate the status of evolutionary biology as the most well tested science by far, the 100 of 1000′s of papers testing it and its utility for other sciences in the last 150 years is not the most impressive measure. I much prefer the basic demonstration of its hallmark, explaining nested hierarchies of characteristics. (Be they genomes, proteomes, tissues, organs, or other phenomes.)

    The number of possible trees describing the nesting (the common descent) grows very quickly. Yet biologists can narrow it down to a few handful possibilities. While the probability of finding two similar trees by chance via two independent methods is extremely small.

    Tests and measurements for general relativity may give results in the percent range. But

    And consequently,

    the standard phylogenetic tree is known to 38 decimal places, which is a much greater precision than that of even the most well-determined physical constants.

    ( http://www.talkorigins.org/faqs/comdesc/section1.html#independent_convergence )

  106. #107 John
    June 4, 2007

    Peter wrote:
    “What appears to be true, though, is that the use of profanity is inversely related to the strength of an argument.”

    Then I would hope that if you live in the US, you refused to vote for the presidential candidate who called a reporter an “asshole” and the vice presidential candidate who told a senator, “Go fuck yourself.”

    “I’m still looking for compelling proof, not circumstantial evidence, that evolution can explain all life.”

    Science doesn’t deal in proof, doofus. The most compelling evidence that evolution can explain all the varieties of life now in existence is the nested hierarchies from sequencing.

    Further evidence that this evidence is extremely compelling is the predictable, incredibly dishonest misrepresentation of nested hierarchies as mere “similarity” by those who doubt evolutionary theory.

    Have you looked at any of this evidence for yourself, Peter, or are you afraid to? It’s all freely available, along with the software for analyzing it.

  107. #108 Torbjörn Larsson, OM
    June 4, 2007

    Sorry, I messed up the blockquotes. You will find the discussed figure at the link.

  108. #109 Leni
    June 4, 2007

    MarkCC wrote:

    This goes back to something I’ve written about before. Mathematical modeling is a great thing: it’s an incredibly useful technique, and personally, I find mathematical models of real phenomena to be absolutely fascinating. But to move from experiments/observations/analyses of mathematical models to predictions or statements about the real world, you need to *validate* that model, and show that it’s an accurate reflection of reality. Behe never even *pretends* to take that step. He merely asserts that the landscape is a valid model, never explicitly states his assumptions about that model, never even runs and experiments in the model, never tests how well his model matches real observations, and then argues that the conclusions that he draws on the basis of his model are valid conclusions about reality.

    As I was reading your post I was thinking that maybe you hadn’t given Behe the benefit of the doubt.

    Models of very complex things are always simplistic by comparison. Plus they are often representations of only a few aspects of the subject, simply because it isn’t always practical, feasible or even necessary to consider every possible variable. Idealistic models can also be useful to point us in the right direction. Also, there’s a certain amount of learning curve- typically our efforts improve over time, especially if we take the criticisms of our peers to heart.

    Anyway, I thought that even if Behe was being overly restrictive and unrealistic, this might not mean that he was entirely wrong or that his model is worthless.

    That is, until you said this:

    What’s the favorite bullshit mathematical argument of creationist assholes worldwide? Why big numbers, of course! He starts to slap together some sloppy probabilities to argue how unlikely it is for a mutation to jump valleys in a fitness landscape.

    That is just unforgiveable. If his model is overly idealistic and not a perfect reflection of reality he could just admit that. Many models are and there is always room for improvement, he could point out under which circumstances (assuming there are any) the model does work for. Instead, Behe seems to think it would be easier to get reality to conform to his model.

    Further, I fully support your use of the word bullshit. That’s what it is, and frankly it’s a better description of reality than Behe’s model so you are still ahead of the game on that count.

  109. #110 Bunc
    June 5, 2007

    Hi, I have been having a bit of a civillised debate with a christian fundamentalist software engineer about this whole issue of design space and evolution/natural selection. I asked him to review this article from his persepctive on the design space issue and you might be interested in his response. Would anyone care to comment on the points that he makes? Please no personal abuse though as we have been having a civilised discussion.
    His post is at http://looneyfundamentalist.blogspot.com

  110. #111 Lebrone
    June 5, 2007

    In critiquing The Edge of Evolution, Chu doesn’t offer any alternatives, and seems to be saying a Fitness Landscape is impossible to model, reducing Natural Selection to a tautology. Whatever survives must be the most fit. And if a strain of bacteria was never observed before, then it MUST be a recent mutation, not a simple change in population ratios. So even if Chu’s critique of Behe is correct – Darwinism remains squarely under faith based naturalistic philosophy – not fact-observation science.

  111. #112 LRM
    June 5, 2007

    Lebrone wrote:

    In critiquing The Edge of Evolution, Chu doesn’t offer any alternatives, and seems to be saying a Fitness Landscape is impossible to model, reducing Natural Selection to a tautology.

    Are you familiar with the phrase “non-sequitur”, Lebrone? Biological fitness landscapes *are* impossible to model in a realistic manner. Doesn’t mean that selection isn’t real, or impossible to measure. Or are you under the impression that just because something cannot be accurately modeled mathematically, it doesn’t exist?

    And if a strain of bacteria was never observed before, then it MUST be a recent mutation, not a simple change in population ratios.

    Here, educate yourself. This article links to a study of in vivo evolution of multi-drug resistance in a strain of initially non-resistant bacteria, tracing over thirty invididual mutations that conferred improved resistance. But I suppose it’s all just one big happy tautology to you.

  112. #113 Stephen Wells
    June 5, 2007

    To refute Sanford- I’m a polite and civil person, but I’m completely with Mark on this one. Sometimes you have to call a spade a spade, no? And claiming that creationists have never been uncivil about scientists is ludicrous.

    On the “Who are you to talk back to God?” question- I can talk back to God because I exist. God doesn’t, so far as I can tell, have this advantage. But if there is a God, and he can’t tolerate a little criticism from a passing ape, then it’s a moral duty for all of us to defy that petty, fascistic little dictator.

  113. #114 AJS
    June 5, 2007

    “What’s the favorite bullshit mathematical argument of creationist assholes worldwide?”

    You lose reasonable civil people like me when you talk like this. Grow up for heavens sake.

    Is just calling someone out on an ad hominem like this, without contributing anything to the argument except to criticise the arguer’s technique, an ad hominem in its own right?

  114. #115 Peter Wadeck
    June 5, 2007

    Mark:

    The panda’s “thumb” is *not* a useless appendage. In fact, it’s pretty much crucial for the modern panda.

    You said: “produced what is effectively an extra thumb.” This means a second thumb, making it redundant.

    “What more do you need?

    I must confess my ignorance of the hierarchical relationships between species. I am more familiar with cell biology and the fossil record. Given the complexity of the simplest unicellular creatures and the Cambrian explosion , I find the random fluctuation mechanism deficient. The examination of the mechanism of life tends to infinite complexity, not blind random chance. The concept of random fluctuation has lead to many incorrect conclusions. The tree of human evolution is one example were simplistic comparisons were made only to be proven wrong time and time again. Nor does evolution explain the rapid speciation after mass extinction events. One could say that punctuated equilibrium describes natural history, but I can’t see how punctuated equilibrium is evolution (many evolutionists share this sentiment also I believe).

  115. #116 Mark C. Chu-Carroll
    June 5, 2007

    Peter:

    In other words, you are not familiar with the evidence, but you nevertheless insist that it isn’t adequate, and that we must provide you with more.

    If you haven’t even bothered to look at the reams of evidence that already exist, then why on earth should we believe that showing you more evidence would accomplish anything?

  116. #117 Jud
    June 5, 2007

    “Nor does evolution explain the rapid speciation after mass extinction events.”

    Let’s see – Normal mutation rate, less competition, so more ecological niches for which these mutations may fit the organisms in which they occur. In other words, approximately the same number of variations, and a greater variety of situations in which those variations are favorably selected.

    There, that wasn’t hard, was it?

    “The examination of the mechanism of life tends to infinite complexity, not blind random chance.”

    This is just flat wrong. Re complexity, there are amoebae with more genes than we have. Re “blind random chance,” probability theory has been used to work out the math of evolution since relatively early in the last century, and its predictions fit exceedingly well with reality. (If you’re interested in learning as opposed to mere uninformed argument, have a look at Sean B. Carroll’s “The Making of the Fittest,” where this math is presented in readily digestible form.)

  117. #118 Bob LaRue
    June 5, 2007

    There are still many disconcerting typos… “if” for “is”, “his” for “this” and others. Minor stuff, but still, Ouch!

  118. #119 SteveF
    June 5, 2007

    Mark,

    With regards to this part of your argument:

    “when you realize that each person infected with Malaria has billions of malaria cells in their bodies, and that number starts to not look so scary anymore: billions of cells reproducing daily in millions of individuals, which has been going on for decades of chloroquine use, and you start to realize that that’s not such a big number after all.”

    I imagine Behe would respond by saying (from a quote on PZs blog):

    “resistance to chloroquine has appeared fewer than ten times in the whole world in the past half century.”

    In other words, despite such a vast amount of mutation, resistance didn’t arise very often. At least, thats what I think he would say (which is essentially part of the same argument, but nevermind that).

  119. #120 David Ratnasabapathy
    June 5, 2007

    Peter Wadeck:

    Mark:

    The panda’s “thumb” is *not* a useless appendage. In fact, it’s pretty much crucial for the modern panda.

    You said: “produced what is effectively an extra thumb.” This means a second thumb, making it redundant.

    Perhaps you are unaware of the anatomy of a panda’s paw? Here’s a picture.

    A panda’s “real” thumb doesn’t function well as a thumb. Hence the necessity for a sixth “finger”, made by enlarging a wristbone. Mark is correct. The second thumb is crucial to the modern panda.

  120. #121 truth machine
    June 6, 2007

    Mark- I will assume that Behe doesn’t make arguments he KNOWS are wrong (“crap” as you called it). That’s just silly.

    Indeed your assumption is silly, since there are numerous examples of people doing just that. Sometimes people manage to forget, while they are giving a crap argument, that they know it’s a crap argument, but that doesn’t change the fact that they know it’s crap (that’s a funny thing about the tense of mental predicates). Sometimes this is evident in their readily recognizing that the reasoning is crappy when someone else used it, or agreeing in the past that their argument is crappy, possibly denying that they employ such an argument.

    Is it possible he’s right and you’re wrong? Of course it is.

    Suppose that someone followed you around, and every time you made a statement or an argument, especially when it was lengthy and carefully laid out, they said “Is it possible that you’re wrong? Of course it is.” without paying any attention to the content of your argument, its validity, the quality of the logic and facts? Is it possible that you would think that person was, well, an asshole?

    I read the link you posted. You’re a ‘skeptic’, then? I assume that is the case, as you linked to the post defending the behavior of skeptics.

    You should really stop making assumptions; you’re not very good at it. Since the only thing that all skeptics have in common is that they are skeptical, there is no such thing as “the behavior of skeptics”. If you read it, then perhaps you could indicate enough of a grasp of what was written to challenge or agree with its specific points.

    Civil behavior IS important. Civil people won’t ever take your side arguing like this.

    The latter would only follow if *only* civil behavior matters. But anyone who values fact and reason over ad hominem — and addressing the civility or rudeness of someone making an argument is just that — will take MarkCC’s side because they can see that his side is correct. And a lot of those people are civil, so your claim is simply false. And some of those people don’t put much stock in civility — like me, you stupid effing rude trolling asshole. The fact that you trolled this blog with your irrelevant and emotionally immature drivel about poopoo words shows that you have no place in civil society.

  121. #122 truth machine
    June 6, 2007

    You said: “produced what is effectively an extra thumb.” This means a second thumb, making it redundant.

    Even if it were redundant, that wouldn’t make it useless.

    Ever notice how nearly all evolution deniers are both ignorant and stupid?

  122. #123 truth machine
    June 6, 2007

    “There are times when a small change can have a huge impact. The classic textbook example of this is the Panda’s thumb:”

    To extrapolate from the formation of a useless appendage to all of life is a tremendous leap of faith.

    To misrepresent a “classic textbook example” as a grand extrapolation is tremendously stupid and/or tremendously dishonest.

  123. #124 truth machine
    June 6, 2007

    Is just calling someone out on an ad hominem like this

    Calling someone an asshole creationist while pointing out that he uses a form of dishonest argumentation common to asshole creationists is not ad hominem. “ad hominem” is not a synonym for “insult”; “an ad hominem” refers to an instance of a particular fallacy, not to an insult word, and MarkCC did not commit that fallacy. The fallacy would be to claim that Behe’s argument is wrong because he’s an asshole. On the contrary, he’s an asshole because he makes the argument.

    without contributing anything to the argument except to criticise the arguer’s technique, an ad hominem in its own right?

    Indeed Sanford Small’s contributions have been entirely ad hominem — more explicit than most ad hominems, stating outright that “civil” people always take the “side” that is expressed more “civilly”.

  124. #125 truth machine
    June 6, 2007

    Bible answers:
    “who are you�”mere man that you are�”to talk back to God?

    If I were foolish enough to believe in a God capable of hearing and speech, I would at least hope for an intellectually honest one who was willing to entertain my questions and provide rational responses.

    Can an object that was molded say to the one who molded it, “Why did you make me like this?” A potter has the right to do what he wants to with his clay, doesn’t he?

    Um, so the justification for God’s behavior is to be found in his property rights?

    It’s bad enough to believe in this garbage oneself, but to actually offer it up to others in support of an argument … yeesh.

  125. #126 AJS
    June 6, 2007

    truth machine:

    “an ad hominem” refers to an instance of a particular fallacy, not to an insult word, and MarkCC did not commit that fallacy. The fallacy would be to claim that Behe’s argument is wrong because he’s an asshole. On the contrary, he’s an asshole because he makes the argument.

    Now that’s just brilliant!

    And yes, I agree that Sanford’s calling-out was a poor arguing tactic. Even if it’s not quite an ad hominem, it’s a non sequitur because plain speaking does not affect the truth or falsity of a statement.

  126. #127 Robert Maynard
    June 6, 2007

    “Behe’s math is atrociously bad, pig-ignorant garbage”
    - Mark Chu-Carroll, scienceblogs.com/goodmath

    Seriously, someone needs to print that on stickers, and stick it on copies of TEoE at their local bookstore.

    Or not.. I wouldn’t want to get someone in trouble as a result of my advice.

    Great review.

  127. #128 Peter Wadeck
    June 6, 2007

    David Ratnasabapathy #120

    Thanks for the link. That describes the Panda’s ‘thumb much better than the other commentators. I now understand their argument better. The thumb is more like a stump anatomically, but functions like a thumb. If this was produced by a genetic modification as claimed, then I agree that this improved functionality could have evolved. This however is extremely far from proving all of life came from a single celled creature. This proves simple adaptations in nature occur. This however is already well known. The evolution of simply anatomical structures like the Panda’s ‘thumb’ does not prove complex structures evolved.

  128. #129 Peter Wadeck
    June 6, 2007

    Mark #116

    If you could supply a couple of links, that would be helpful. I tried WIKI and google but I can not find a good page describing the hierarchical relationships between species. :)

  129. #130 Looney
    June 6, 2007

    With all of the smoke and dust, it is difficult to see what is going on. I would have to rank Behe as the clear winner because:

    a) After almost a century and a half, evolutionists still haven’t been able to settle on a definition of evolution that won’t stop morphing every few minutes. (What would the abstract mathematicians have to say about that?!!!)

    b) The issue of design spaces and multiple maxima are well known in engineering and can’t be overcome with a simple Chu-Carroll handwave. We should probably assume some fractal like characteristics to the shape of the fitness space, rather than exactly one maximum (Dawkins) or a number of maxima that is in the single digits.

    c) Changing from a continuous variable paradigm to a discrete variable paradigm merely sinks Dr. Chu-Carroll’s arguments even further: Performing discrete genetics on binary executables will have an obvious, catastrophic result. We all know where that leads.

    Final Score: Behe 1, Chu-Carroll 0.

  130. #131 Mark C. Chu-Carroll
    June 6, 2007

    Looney:

    (1) Evolution is a theory that continues to develop – that means that as people study it, they learn more, and they’re able to further elucidate on the exact mechanisms of it. The basic, fundamental theory hasn’t changed: common descent, variation, selection. As we’ve learned to understand the mechanisms, we’ve been able to explain more about how variation and selection occur, which has led to more precise descriptions and predictions; but the basic theory remains.

    (2) You don’t get to just *assert* that a fitness landscape has some happy nice property that makes it work for your argument. (Your man Dembski showed that!) If you want to assert that there is a fixed fitness landscape with some particular set of properties, you need to show *why* the fitness landscape has the properties that your argument requires. That’s what Behe doesn’t do: he *assumes* a static landscape; he *assumes* a landscape with low-dimensional characteristics and frequent isolated maxima. He doesn’t even *attempt* to argue for *why* those are valid assumptions. And they *aren’t*: see for example http://endogenousretrovirus.blogspot.com/2007/06/look-ma-no-math.html.
    And I notice that you don’t even *attempt* to actual defend Behe’s thoroughly invalid model.

    (3) Evolution *can’t* be modeled in a continuous paradigm; genes are discrete. And further, we do know what happens when you do discrete modifications: you get discrete changes. Far from catastrophic: we observe discrete genetic changes *all the time*; sometimes they’re bad, sometimes they’re neutral, and sometimes they’re good (as described in a specific example in the link above). Even in the realm of genetic algorithms (which is where your non-sequitur about “executables” comes from, I assume), we can easily show that discrete mutations in actual executable code are *far* from “catastrophic”, but are rather the *entire* basis for the success of genetic algorithms. Try looking at the Breve software to see an example of that in action: breve uses a psuedo-genetic code to describe programs, and then visualizes those programs in action. You can even run it as a screensaver, and see how frequent good, neutral, bad, and fatal changes are relative to each other.

  131. #132 Looney
    June 6, 2007

    (1) Evolution and change are synonyms. If something changed, it evolved. If it evolved, then it changed. There is no theory of evolution. There are tens of thousands of theories of evolution and they come and go according to the whim of the evolutionist. That is the reason the definition is always changing.

    (2) I did read Darwin’s Black Box and n-dimensional fitness spaces for design are my profession. I still insist that you are evading the issue of multiple maxima.

    (3) I well aware that ID implementations of GA methods can do some amazing things. (Been there done that with both discrete and continuous.) They are hopelessly inferior to pure ID methods. The convergence rates and tendencies to head for the nearest maximum preclude any rational hope for macro evolution.

  132. #133 Looney
    June 6, 2007

    Regarding static vs. dynamic fitness space, the relationship is quite simple: In engineering, we face this all the time. Usually we optimize one part at a time holding other parts fixed due to the intractability of solving the overall problem. Thus, we encounter the static/dynamic problem routinely, but overcome it through ID.

    In biology, we have a dynamic fitness space if we look at one organism at a time in competition with others. If, on the other hand, we change our reference to the entire problem (say, an entire vehicle for the engineer, or “a balanced eco-system” for the biologist), then we are back to a relatively static fitness space. The number of design variables is the sum of all of the variables in all of the species that make up an ecosystem and the objective function now becomes unimaginably complex. Since all the ecosystems of Earth are linked … I presume you have heard of concepts such as convergence rates and problem order.

    Anyway, fitness spaces are something that evolutionists are better off keeping swept under the rug.

  133. #134 Mark C. Chu-Carroll
    June 6, 2007

    Looney:

    First:

    You don’t seem to understand the problem with Behe’s argument – or with your defense of it.

    Behe’s argument *only* works if the fitness landscape can be correctly modeled as a low-dimensional space with frequent maxima, and where the maximum change distance is *smaller* that the minimum distance between maxima.

    If Behe (or you) want to argue that evolution is impossible based on the “inescapable maxima” argument, you need to show that your model is valid: that the evolutionary landscape *has those properties*.

    The space of possible fitness landscapes is huge. Your argument relies on the *necessity* of that landscape having properties that belong only to a *small minority* of those landscapes. But you just weasel your way around by shouting “not a problem, not a problem”, without ever showing *why it’s a valid step to constrain the set of possibly landscapes to the the set of landscapes with the property that you want.

    Second: your handwave about the difference between static and dynamic landscapes doesn’t work. Life is an *inevitably* moving target. Even if you pick a different reference frame like “a balanced eco-system” (which, incidentally, *doesn’t work* for Behe’s argument against evolution – his argument is specifically talking about landscapes for individual species), you *still* don’t get a static fitness landscape: the variations of things like weather will *still* cause the “fitness maxima”, if they exist, to move. Static landscapes simply are *not* a valid mathematical model.

  134. #135 Blake Stacey, OM
    June 6, 2007

    Looking more closely at his “test case,” the evolution of chloroquine resistance in malaria-causing parasites, Behe doesn’t seem to understand even sequential mutations of increasing fitness. I have some notes on this here.

  135. #136 Xanthir, FCD
    June 6, 2007

    1) I’m sure it’s fun to define things yourself and then insist that the definitions don’t make sense, but that doesn’t say anything except that you enjoy arguing with yourself. Evolution is, essentially, two things: change, and then selection. It’s not very difficult.

    The myriad types of evolution you reference? They’re all just different types of selection. You can have the classic ‘survival of the fittest’, you can have sexual selection, kin selection, even neutral drift where simple chance determines what is selected for and what isn’t. Nobody argues about whether or not evolution is correct, but they may disagree about the relative importance of the different kinds of selection.

    2) And you, as most creationists do, evade the issue of a changing fitness landscape. Areas on the landscape that are maximums at one time may cease to be later. For a trivial, obvious example, if a number of species coalesce on a particular point, that indicates overcrowding. If that point is, say, the ability to digest a particularly nutritious food, then when lots of animals develop that ability the food supply drops due to overuse. It then becomes more advantageous to take advantage of a different food supply that is in greater abundance.

    3) “ID implementations of GA methods”? What the hell does that means? That humans designed a GA? Yes, that’s right – we have yet to discover a software program in the wild, so we are stuck with the programs that we design ourselves.

    I’ve talked with you before, and even if I grant that you are telling the truth about your profession, you are hopelessly wrong about the efficacy of genetic algorithms. You just repeat blatantly false tropes that are debunked through simple experimentation.

    GAs are best suited for multivariable problems, where the interactions between variables are too complex for humans to get a good grasp on. When we *can* model a process properly, of course our optimized program will do better than a GA – GAs are inefficient by their very nature. However, the same properties that make them inefficient also make them *very* good at exploring extremely complex problems. So, when we can’t model the space well, GAs can do a better job than anything else.

    Read the talk.origins page for a number of very interesting examples of GAs put to good use.
    http://www.talkorigins.org/faqs/genalg/genalg.html

    Of particular import to me is the development of Anaconda, a checkers-playing program developed with a GA. It can perform at an extremely high level against opponents. It’s been pitted against the very best engineered algorithms, and though it ended up losing, it wasn’t by much. The main reason it lost was because the opposing algorithm had a complete end-game book going back about a dozen moves – at that point, it is literally impossible for the program to make a mistake. Anaconda couldn’t think quite that far ahead at the time, and so would occasionally make a mistake in the endgame. Note, though, that this work was done in 2001. Doing the same thing with today’s computers would see Anaconda developed in much less time, and with much greater abilities.

    In response to your next post, first, I doubt that looking at the ecosystem as a whole would make the space suddenly become static, or close to it. Second, who cares if it does? Ecosystems don’t evolve – species do. While you probably could, potentially, develop a fitness function to evaluate an ecosystem, that doesn’t say a damned thing about the evolution of life.

    Fitness spaces are something that creationists should actually study, rather than blindly asserting their opinions on them.

  136. #137 Looney
    June 6, 2007

    I always love this. When ever someone provides a theoretical objection to evolution, the evolutionist always argues that the theory is too complicated to be understood. Then he demands to present to the children that evolution was theoretically proven a century ago. No, the fitness landscape methodology is correct and valid for biological systems.

    We both work in Silicon Valley, so we see ID every day, although I hear Google is a pretty sleepy place. On the other hand, ID has been scientifically proven to be impossible!

    I will leave you with your bipolar disordered view of science.

  137. #138 David Ratnasabapathy
    June 6, 2007

    Peter Wadeck #128

    …If this [the Panda's enlarged wristbone] was produced by a genetic modification as claimed…

    Are you suggesting that maybe the enlarged wristbone of the Panda is not genetic in origin? e.g. maybe that it’s a product of the Panda’s lifestyle, like big muscles emerge from exercise?

    …This however is extremely far from proving all of life came from a single celled creature… The evolution of simply anatomical structures like the Panda’s ‘thumb’ does not prove complex structures evolved.

    Um, you’re missing the point. Mark Chu-Carrol wrote:

    There are times when a small change can have a huge impact. The classic textbook example of this is the Panda’s thumb: a very small genetic change caused a change in the developmental process in the wrist of the panda, which produced what is effectively an extra thumb. [emphasis mine].

    Mark’s point was that small genetic changes can have big effects on an organism’s body. He cited the Panda’s thumb to support that point. Not to support claims about the origin of life or the origin of complex structures.

  138. #139 Mark C. Chu-Carroll
    June 6, 2007

    Looney:

    Where did I say that the theory is too complicated to be understood? What I keep saying is: the model of evolution using a static low-dimensional fitness landscape is invalid.

    Mathematical modeling of real phenomena always involves two steps: developing a model that seems to describe the phenomena, and then validating that model against the reality.

    The static low-dimensional model used by Behe fails *miserably* in the validation. It does not accurately model the real world.

    Could there perhaps be a *reason* why you keep skittering around and ignoring that point? Like, perhaps, you can’t show that the fitness landscape fits Behe’s constraints?

  139. #140 Xanthir, FCD
    June 6, 2007

    We both work in Silicon Valley, so we see ID every day, although I hear Google is a pretty sleepy place. On the other hand, ID has been scientifically proven to be impossible!

    Again, it must be really fun to make up arguments and then disprove them, since you seem to do it constantly.

    1) ID is not seen every day in Silicon Valley. The word you want is probably ‘engineering’. You’re attempting to conflate the notion that a superbeing was necessary to create life (and yet didn’t require a supersuperbeing to create the superbeing) with the fact that, as intelligent creatures, we can make stuff that doesn’t show up in nature. You’re doing it very clumsily as well.

    2) ID has not been ‘scientifically proven to be impossible’. It is conceivable that life on earth was created by an intelligent entity, though that entity would have had to try really, really hard to make it look like he had no place in the design. What ID *has* been shown to be, though, is intellectually vacuous. It says *nothing*. If ID was a real scientific theory, then it would have, I dunno, theories or something. You know, predictions of exactly what design would look like and how to reliably detect it. However, what the ID movement in real life amounts to is a bunch of failed theocrats lying about evolution and blindly asserting things that are untrue, such as “Genetic algorithms can never outperform a human” or “, while simultaneously avoiding *any* assertions about ID itself that can be rigorously tested.

  140. #141 AJS
    June 6, 2007

    This is how it looks from the sidelines:

    IDist: All roses are red.
    Scientist: No they aren’t. [Produces white rose] Here you go — a white rose.
    IDist: That is not a rose. It cannot be a rose because it is not red. All roses are red.
    Scientist: Of course it’s a rose! This is a white rose. [Performs some kind of test showing beyond reasonable doubt that the white flower is indeed a rose]
    IDist: Well, OK then, I accept that it may be a rose, but you still haven’t disproved my theory. Even you must surely have to admit that it is sort of a bit red-ish. No, it’s not a white rose — it’s just a very pale red rose. You still haven’t disproved my theory. All roses are red!
    Scientist: Now you’re just talking bollocks.
    IDist: Waaaah! You used a naughty word! Well, that just proves it, doesn’t it? All roses are red. I win. Come on, mummy, buy me an ice cream!

  141. #142 Xanthir, FCD
    June 6, 2007

    Peter Wadeck:

    If you could supply a couple of links, that would be helpful. I tried WIKI and google but I can not find a good page describing the hierarchical relationships between species.

    There are plenty of information resources out there, but for a start check out talkorigins.org.

    Now, what is meant by ‘multiple hierarchical relationships’ is this:

    If life were designed, we would expect to see hierarchies in the design. For example, we might start with a general group of ‘animal’ characteristics, then split it into two groups, ‘carnivore’ and ‘herbivore’. Taking each schematic, we can further split it and specialize the details. This sort of scheme minimizes the amount of work that must be done (because we define as much as possible in the early steps), and leaves clear traces in the final designs. We can group the designs according to the hierarchy.

    Different details, though, would likely follow different hierarchies. When I’m defining the digestive system, I’d want to create a hierarchy based on what the animal eats, so that all the carnivores everywhere use the same stuff. However, when I’m designing the skeleton I want to take into account where the animal lives, so that river creatures get skeletons well suited to swimming in rapid water, mountain creatures get skeletons well suited for climbing, and plains creature get skeletons well suited for running.

    In the end, I’ll have tons of these different hierarchies intersecting in various ways. Carnivores all digest in the same way, whether they’re on the plains or in the river. Plains creatures all run in the same way, whether they eat plants or animals.

    In fact, though, we don’t see multiple hierarchies intersecting in various ways – they all mirror each other. Everything follows the exact same hierarchy. This defeats the purpose of using hierarchies at all if you’re consciously designing things – for example, you’d have to create the digestive systems for river and plains creatures separately, using different chemicals and processes entirely. That doesn’t save you any work. However, this *does* look exactly how we’d expect if common ancestry were true, where problems *were* solved multiple times, in different ways, and then passed on down the line.

    In life, all the hierarchies correspond – you can draw a tree based on skeletal structures, particular genetic markers, developmental processes, or protein sequences, and you get the same tree every time (more or less). This is *not* what you’d expect from design at all, but it’s *precisely* what you’d expect to see from evolution.

  142. #143 Bunc
    June 6, 2007

    Hi Looney,

    I read your contribution here on Mark Chu-Carroll’s post. As you know I make no pretence of taking either of you on in terms of actual detailed maths – but I dont think this is necessary anyway as there are more fundamental issues at play.

    As I made the point to you before the mathematical modelling of evolution via design space and fitness seems to me a reasonable approach in trying to improve understanding of the interplay of randomness and selection (I simplify outrageously)

    However I must say that I find Chu-Carroll’s argument that the fitness space must be dynamic very compelling.

    The point was made in the comments on his site that even looking at things like the weather (or better climate change) one can see that what may be maximally fit at one time may not be so at another.

    As was pointed out the interactions within and across species and with the broader changing environment and the variable availability of niches mean that evolution and natural selection take place as an incredibly complex parallel process.

    Whether or not any particular mathematical model entirely satisfactorily describes this is besides the point. We observe it happening. We see evidence in the fossil record. We can produce it over short timescales in the lab.

    An analogy here could be observing the rotation of heavenly bodies. At one time this could be observed and the first mathematical models aproximated the motion. We did not seek to refute that there was rotation of the bodies simply because the maths didn’t exactly work to the nth degree. ( or because we were using the wrong model)

    We start with the observations and seek to refine our models until they describe the observations as accurately as possible. At the same time we look for the mechanisms behind the process. In astronomy this resulted in Newtonian mechanics and later Einstein’s more detailed mathematical modelling of space time.

    In biology we have vast sets of data entirely consistent with a theory based on reproduction with variation and selection (of various types).
    What do we do if our models dont quite fit the observed evidence? Refine the models! We dont simply try to ignore the evidence!

  143. #144 Looney
    June 6, 2007

    OK Dr. CC., I will bite:

    “Could there perhaps be a *reason* why you keep skittering around and ignoring that point? Like, perhaps, you can’t show that the fitness landscape fits Behe’s constraints?”

    I will suggest you read Dawkins. There is always an uphill direction and only one maximum in his design universe. Behe almost certainly got his fitness space from Dawkins or some peer reviewed biological instruction materials. My continuing gripe about evolutionists is that they make arguments without any regard for whether an earlier argument that was considered compelling had used mutually exclusive assumptions.

    Besides this, I am also skittering around because I haven’t read Behe’s new book.

    The other issue is that I was quite amazed that my 30-dimensional quadratic optimization test cases worked using when I did bit-based discrete mutations on my continuous variables. Impressive! It only slowed the convergence rate by a factor of 10 million.

    And as I mentioned earlier: Any competent engineer knows how to convert a dynamic fitness space resulting from one component in an unknown design environment to a static fitness space by considering the entire problem. Ditto for evolution. The only advantage of using the single species dynamic paradigm is that it is intractable and thus permits the imagination to run wild.

  144. #145 Torbjörn Larsson, OM
    June 6, 2007

    Peter:

    The evolution of simply anatomical structures like the Panda’s ‘thumb’ does not prove complex structures evolved.

    Look again on the panda’s thumb, there is nothing simple about it. It is a bone that has arisen as a consequence of changes in development, and evo-devo is quite complicated.

    Your assertion out of the blue that there is a magical barrier that at some arbitrary point blocks evolution of character does not prove that complex structures can’t evolve. And the phenome record shows again and again that this has happened by phylogeny. Fossils even shows this illustratively.

    Looney:

    Evolution and change are synonyms.

    But biological evolution isn’t just change, by definition. It is common descent (nested hierarchies of characteristics). You are confusing the observed facts which lead to the theory with the mechanisms in the theory.

    The smallest workable set of a model including selection is “variation and selection with hereditary”. (Note “variation”, since “change” happens with both variation and selection. Sorry, Xanthir!)

    But it is still a small part of the observed mechanisms, you must add genetic drift, finite population descriptions, et cetera.

  145. #146 Jud
    June 6, 2007

    Looney, just one simple question:

    What’s the scientific explanation of how a being complex enough to design all life on Earth arose in a Universe that is unable to produce so much as a flagellum by natural means?

  146. #147 Looney
    June 6, 2007

    “But biological evolution isn’t just change, by definition. It is common descent (nested hierarchies of characteristics). You are confusing the observed facts which lead to the theory with the mechanisms in the theory.”

    If you read Dawkins chapter on the Tree of Life in the Blind Watchmaker, I think you will find that the notion of biological evolution as heirarchies doesn’t hold up. Thus, “scientists” have postulated virus moving genes at random between various branches. Consistency guys!

    “What’s the scientific explanation of how a being complex enough to design all life on Earth arose in a Universe that is unable to produce so much as a flagellum by natural means?”

    The California AP Biology test has the Miller-Urey experiment on it. How much biological machinery does a minimum lifeform capable of doing genetics take? Sure, Dr. CC and I can both emulate GA on our computers, but computers are products of ID. In the end, your choice is still God or spontaneous generation. There are no alternatives.

  147. #148 Torbjörn Larsson, OM
    June 6, 2007

    Looney:

    My continuing gripe about evolutionists is that they make arguments without any regard for whether an earlier argument that was considered compelling had used mutually exclusive assumptions.

    This is a bit more sympathetic argument. It is certainly difficult to get to grips with a science, especially one so dynamic, since new results comes in and theories changes.

    But that is exactly why an outsider should be satisfied with what is established. You see the same problem everywhere. In cosmology dark energy is recently confirmed, but is it the cosmic constant or another beast? In physics string theory is isomorphic to some field theories, but is it applicable to describe new physics as well? And so on ad infinitum.

    The problem is that you say “evolutionist” as if it describes something else than evolutionary biologists. For example, AFAIK Dawkins is an adaptionist par excellence. Maybe most biologists would include more of genetic drift in a general illustration of how biology works than Dawkins may have done.

    But AFAIK (you don’t specify books or papers) these are mere illustrations for popular disseminations, and I am certain that biologists have reviewed and criticized Dawkins plenty for his mistakes and perhaps onesided descriptions.

    While Behe is attacking and perverting the science itself in a popularized format, and should get at least as much criticism.

  148. #149 Torbjörn Larsson, OM
    June 6, 2007

    Looney:

    I think you will find that the notion of biological evolution as heirarchies doesn’t hold up.

    You are confusing hierarchies from species with hierarchies of properties. Lateral genetic transfer complicates the hierarchies so instead of species trees you have bushes with several roots.

    Lateral transfer can fuzzify the species concept, which for asexual creatures is different from the usual biological one anyway, and largely useless. (Biological species are defined by interbreeding barriers.) But it is still the same principles.

    Consistency guys!

    Sorry, biology is science. Anything can change without giving previous notice. :-)

    How much biological machinery does a minimum lifeform capable of doing genetics take?

    Non sequitur. Prebiotic chemistry had no genetic machinery, yet you can have breeding by external production.

    Btw, you shouldn’t marry yourself with a particular genetic machinery, there are plenty of reasons to suspect that DNA was introduced to replace less stabler RNA genetics. In fact, some thinks it happened three times! By way of DNA viruses, one time each for the three domains Archaea, Bacteria, and Eucarya.

  149. #150 Looney
    June 6, 2007

    “Lateral transfer can fuzzify the species concept, which for asexual creatures is different from the usual biological one anyway, and largely useless. (Biological species are defined by interbreeding barriers.) But it is still the same principles.”

    OK. So at a macro level, the heirarchies are too fuzzy to be useful for anything, but it is vital that we accept heirarchies for the understanding of evolution! Again, Dawkins outlined a number of other areas where heirarchical analysis was problematic. It sounds to me like y’all are expecting people to have faith in the unknowable …

  150. #151 Anonymous
    June 6, 2007

    Dr. CC wrote:

    “Where did I say that the theory is too complicated to be understood? What I keep saying is: the model of evolution using a static low-dimensional fitness landscape is invalid.”

    This reminds me of Dawkins using a fitness plane in n-dimensions to show how any point could be arrived at in n-dimensions. Apparently this is a commonly accepted paradigm for genetic analysis, in spite of its direct conflict with the notion of survival of the fittest. No, you didn’t say that all theoretical models were invalid. On the other hand, the facts of Operations Research are not considered valid for informing biology as to what is or is not possible. The facts of intelligent design that drive product innovation are likewise dismissed as invalid. My impression is that what is accepted or not as valid mathematical analysis of macro-evolution is completely ad hoc, with the only criteria that it must achieve predetermined results.

  151. #152 Looney
    June 6, 2007

    Sorry for not getting my name and link on. And I must say that I am impressed with Dr. CC’s openness on this blog.

  152. #153 Xanthir, FCD
    June 7, 2007

    I will suggest you read Dawkins. There is always an uphill direction and only one maximum in his design universe. Behe almost certainly got his fitness space from Dawkins or some peer reviewed biological instruction materials. My continuing gripe about evolutionists is that they make arguments without any regard for whether an earlier argument that was considered compelling had used mutually exclusive assumptions.

    Um, what? Are you referring to the Weasel program? The Weasel program was simply an example of how cumulative mutation-with-selection can converge on something much faster than random chance will. It was not in any way an example of actual evolution.

    Nobody with a functioning brain would *ever* suggest that life itself and the humongous genome driving it is described by a low-dimension space. What this suggests about Behe is left to the reader.

    The other issue is that I was quite amazed that my 30-dimensional quadratic optimization test cases worked using when I did bit-based discrete mutations on my continuous variables. Impressive! It only slowed the convergence rate by a factor of 10 million.

    Once again, I’m astounded at how fun you must find disproving your own statements, because nobody said anything about quadratic optimization. I’m not familiar enough with it to say anything about it, or what the effects of changing from a continuous value to a course-grained discrete value would be (of course, assuming you’re using a computer, every value you work with is bit-based and discrete by definition).

    What I do know is that it’s not the same as genetic algorithms, which are explicitly bit-based and discrete, and yet converge to excellent solutions in reasonable time periods. Again, I present the following link:
    http://www.talkorigins.org/faqs/genalg/genalg.html
    I have no doubt that you’ll ignore it, Looney, as you have shown that you have no idea what genetic algorithms are, what they do, or what they have been used for, nor do you show any inclination to educate yourself, but for the viewers at home, roughly the middle third of the article is nothing but successful applications of GAs in both science and business. For example, Qwest uses GAs to plot where it should lay new fiber optic cable, saving themselves “$1 million to $10 million each”, in their own words.

    And as I mentioned earlier: Any competent engineer knows how to convert a dynamic fitness space resulting from one component in an unknown design environment to a static fitness space by considering the entire problem. Ditto for evolution. The only advantage of using the single species dynamic paradigm is that it is intractable and thus permits the imagination to run wild.

    Ah, now I see what you’re saying. Yes, if you model the entire system, it becomes static. The issue there, you see, is that you have to model THE ENTIRE EARTH. Animals are affected by other animals, which are affected by their environments, which are affected by the weather, which is affected by the environment, which is affected by animals. It’s a great, big, intractably large circle. Congratulations on accomplishing diddly-squat.

    Now, on the other hand, Behe *does* use the single-species model – he just pretends that it’s static. So he’s not even theoretically right.

    If you read Dawkins chapter on the Tree of Life in the Blind Watchmaker, I think you will find that the notion of biological evolution as heirarchies doesn’t hold up. Thus, “scientists” have postulated virus moving genes at random between various branches. Consistency guys!

    It’s not a perfect hierarchy, but the consistency is very high. As well, viral-driven movement of genetic material has been observed as a real phenomena. What’s the problem here?

    “What’s the scientific explanation of how a being complex enough to design all life on Earth arose in a Universe that is unable to produce so much as a flagellum by natural means?”

    The California AP Biology test has the Miller-Urey experiment on it. How much biological machinery does a minimum lifeform capable of doing genetics take? Sure, Dr. CC and I can both emulate GA on our computers, but computers are products of ID. In the end, your choice is still God or spontaneous generation. There are no alternatives.

    So, my choices are incoherent or wrong? I daresay there are additional choices.

    As well, engineering is not ID. Your use of the term is dishonest. ID refers to the idea (not theory, as there’s no, well, theory behind it) that life is so complex that it could only have been created by a superbeing (who is, himself, *not* created by a greater superbeing, despite being more complex than life itself). I will continue to reiterate this as long as you continue to conflate idiocy with engineering, a respectable field of science that makes actual predictions and has real results.

    “Lateral transfer can fuzzify the species concept, which for asexual creatures is different from the usual biological one anyway, and largely useless. (Biological species are defined by interbreeding barriers.) But it is still the same principles.”

    OK. So at a macro level, the heirarchies are too fuzzy to be useful for anything, but it is vital that we accept heirarchies for the understanding of evolution! Again, Dawkins outlined a number of other areas where heirarchical analysis was problematic. It sounds to me like y’all are expecting people to have faith in the unknowable …

    You quoted the sentence, and still got it 100% wrong. The concept of species is fuzzy, because frankly it doesn’t exist. It’s a convenient fiction that we use to divide the world into sections. An excellent counterexample is the idea of Ring Species, as illustrated by this Wikipedia article:
    http://en.wikipedia.org/wiki/Ring_species

    The first example, that of the Larus gull, is easy to explain. It starts in Britain as the Herring Gull. It can fly to North America, where it can interbreed with the American Herring Gull. These birds can, in turn, go to Russia, where the same thing happens. A couple more jumps across Siberia, and you end up back in Britain with a further new species. This final link in the chain, the Lesser Black-Backed Gull, cannot interbreed with the Herring Gull, even though there is a chain of species which *can* all interbreed and thus would be the same species under a strict breeding-based definition of species.

    So we’re starting with a fuzzy concept, and viral genetic transfer just makes it worse.

    “Where did I say that the theory is too complicated to be understood? What I keep saying is: the model of evolution using a static low-dimensional fitness landscape is invalid.”

    This reminds me of Dawkins using a fitness plane in n-dimensions to show how any point could be arrived at in n-dimensions. Apparently this is a commonly accepted paradigm for genetic analysis, in spite of its direct conflict with the notion of survival of the fittest. No, you didn’t say that all theoretical models were invalid. On the other hand, the facts of Operations Research are not considered valid for informing biology as to what is or is not possible. The facts of intelligent design that drive product innovation are likewise dismissed as invalid. My impression is that what is accepted or not as valid mathematical analysis of macro-evolution is completely ad hoc, with the only criteria that it must achieve predetermined results.

    Not sure where your example of Dawkins comes from (though, judging from your treatment of Dawkins’ writing elsewhere, you’re likely misunderstanding him).

    The point is, despite your irrelevant impressions, evolution has been proven to work again and again in software. It’s been shown in the laboratory and in the hospital. I’m sorry to bring this up, but evolution killed Mark’s father, and will kill many, many other people if doctor’s don’t get it in their head that the evolution of antibiotic resistance is something important that we need to protect against.

    As well, engineering is not ID. Your use of the term is dishonest. ID refers to the idea (not theory, as there’s no, well, theory behind it) that life is so complex that it could only have been created by a superbeing (who is, himself, *not* created by a greater superbeing, despite being more complex than life itself). I will continue to reiterate this as long as you continue to conflate idiocy with engineering, a respectable field of science that makes actual predictions and has real results.

  153. #154 Looney
    June 7, 2007

    “I have no doubt that you’ll ignore it, Looney, as you have shown that you have no idea what genetic algorithms are, what they do, or what they have been used for, nor do you show any inclination to educate yourself, but for the viewers at home …”

    You might as well have told Dr. CC that he doesn’t know what a computer is. Pick up a book on Operations Research. GA is just a form of Operations Research, but most OR books don’t mention GA because GA is inferior to the existing methods in terms of both convergence and reliability. QWest may have “saved money” relative to not doing any optimization at all, but they almost certainly lost money relative to doing the optimization properly. I am sure Darwin will be pleased with the sacrifice. (That isn’t completely fair, because most GA systems are ID/GA hybrids that emulate classical OR methods. The traveling salesman problem being an especially clever GA/ID hybrid. This achieves the benefits of ID, avoids the pitfalls of genetics, while the glory goes to Darwin. ref. “Evolutionary computation for Modeling and Optimization” by Ashlock)

    Another giggle is hearing the complaint that I didn’t do GA right. Yes, of course. Someone with better ID skills could have made it converge faster! I could have made it converge faster by tweaking mutation rates and survival methodology. What will that prove other than the fundamentalists are right?

    The FAQ on GA success is just a red herring. Yes, GA/ID hybrids can solve problems. No, they can’t solve them better than ID alone and no, they can’t solve anything at all without ID intervention. Now, back to the real world …

    “As well, engineering is not ID.”

    The definition of engineering is Science + ID. (Got that from the dean of engineering at UCLA.) You cannot disprove ID without also disproving that Thomas Edison invented the light bulb. It is impossible to have a consistent scientific world view and believe in macro evolution.

    “It’s been shown in the laboratory and in the hospital. I’m sorry to bring this up, but evolution killed Mark’s father, and will kill many, many other people if doctor’s don’t get it in their head that the evolution of antibiotic resistance is something important that we need to protect against.”

    Darwinists don’t own micro evolution. This is just plain irresponsible scaremongering and FUD. In fact, if y’all would separate micro-evolution from macro-evolution and prehistoric speculation, there would be a hell of a lot less resistance to teaching micro-evolution, not to mention a lot more time.

    My son reported on his California AP Biology test: “Any answer is correct, as long as it mentions evolution”. That kind of teaching isn’t going to save anyone either.

  154. #155 Mark C. Chu-Carroll
    June 7, 2007

    Looney:

    All your doing is arguing that because GAs aren’t an effective solution *for operations research problems*, they must not be an effective solution for *any* problem.

    I spent the last 7 or so years working in a field called software configuration management. One of the main algorithms that I was constantly pounding away at to optimize its performance and memory use is the longest common subsequence (LCS) problem. LCS happens to be a problem which is particularly well-suited towards an approach called dynamic programming. In fact, I’ve *never* seen anyone solve it with anything but a dynamic programming algorithm; while there *are* other ways to solve it, the dynamic programming one is the optimal solution strategy.

    By your reasoning, I can conclude that recursive solutions to solving problems simply aren’t applicable in the real world. They just don’t work! Because when I’m doing subsequence identification work, recursive solutions produce a solution that is *at least* one order slower than dynamic programming – and on realistic size problems, that order makes the problem non-tractable on current hardware. (O(N^2) worst case is *bad* when N=10^6; O(N^3) is undoable.)

    Biology isn’t operations research. Evolution isn’t operations research. The fact that an evolutionary algorithms approach to operations research problems doesn’t work says nothing about whether evolutionary algorithms approaches to *other* kinds of problems work. And demonstrably, they *do* work in other areas.

    I also find the whole “but EA is ID” to be a non-sequitur. I’ve spent some time playing with Breve creatures, which is a very nice EA system for the Mac. One of the most interesting things to watch in it is the evolution of moving creatures. It’s true that the basic framework of it was built by a person. But once that framework is in place, there is *no* human intervention at all: it’s pure randomness to produce mutations, and then a form of sexual recombination, and selection based on how far the resultant “organism” moves.

    The results are fascinating. In different runs, I’ve seen it produce things that walk on legs, that slither like snakes, that crawl like inchworms, and that slither sideways like a sidewinder. All with no human intervention – just random mutation and selection.

    The important thing about this is that the fact that the framework is, in a deep sense, irrelevant. The argument against evolution by folks like you and Behe is that *random mutation + selection cannot produce the kinds and degrees of variation that we see in nature. And yet, in Breve, without human intervention, the “genome” of the walker is changing through nothing but random mutation and selection, and is producing an astonishing variety of sophisticated results. That’s exactly what you’re saying it *can’t* do.

    If random mutation + selection can produce astonishingly complex behaviors and effective algorithms in a few hundred to a few thousand generations in a GA system that uses a population of a couple of dozen individuals per generation, then why should we believe that it can’t do the same thing in nature in 1,000 generations with a population of millions or billions of individuals?

    And finally, with respect to my fathers illness… The infection that killed him was a very peculiar pnuemonia. It had a *very* different cell-wall structure than most pneumonia bacteria (which allowed it to be completely resistant to *all* penicillin-family antibiotics), as well as several other novel biochemical features. If we found it in nature, and were evaluating it without any knowledge of where it came from, we would certainly call it a different species. The differences between it and its ancestors is so substantial, it’s considerably greater than what we normally consider a species distinction in bacteria. We wouldn’t recognize it as a descendant if it weren’t for the fact that we *witnessed* its evolution over the last fourty years or so. Calling it “micro-evolution” is just hand-waving your way past something that might interfere with your pre-decided conclusions; we’re talking about a huge, dramatic change in the biochemistry, the physical structure, and the metabolism of an organism. That kind of change really doesn’t seem to qualify to *me* as microevolution. In fact, it’s a kind of change which is considerably more substantial than the chloroquine resistance that Behe rambles on and on about. Behe’s argument basically says that the bacteria that killed my father *could not* have evolved by random mutation+selection; that it’s too large a change, and that it must be the result of intelligent design. Do you agree with him? If not, how do you explain that it did what Behe says is impossible?

  155. #156 Thony C.
    June 7, 2007

    Looney wrote:

    You cannot disprove ID without also disproving that Thomas Edison invented the light bulb.

    Just for the record Looney, Thomas Edison did not invent the light bulb. He improved the light bulb and made it commercially viable as did his main competitor Swan but neither of them invented it.

  156. #157 Looney
    June 7, 2007

    Dr. CC, I will have to leave the penicillin and chloroquine items until I have the proper amount of time to review them.

    Regarding the random mutations and GA, I will challenge that you almost certainly aren’t using truly random mutations. Typically the GA algorithms do things like interchanges of objects within a graph with some random decision making. (Hence one of the complaint about Behe’s definition of evolution.) The traveling salesman problem is implemented with exchange type mutations and a special ad hoc modification to make sure that no city occurs twice after the breeding. This eliminates an astronomical part of the design space. Even if this works, a high-level object oriented GA algorithm on always-viable building blocks should never be presented as an analogy for how real world evolution might do things. This is just as deceptive as what you accuse Behe of doing.

    Of course, if anything at all is known about the general problem class, the distribution of the random decision making can usually be adjusted and the convergence improved. This is why ID is always needed and should be emphasized in teaching over evolution.

    The LCS problem is also near and dear to my heart, although I am usually preoccupied with the physics of my simulations. Probably I should check into what you have been doing.

  157. #158 Looney
    June 7, 2007

    “Just for the record Looney, Thomas Edison did not invent the light bulb. He improved the light bulb and made it commercially viable as did his main competitor Swan but neither of them invented it.”

    Thanks for the correction.

  158. #159 Science Avenger
    June 7, 2007

    Looney said: Regarding the random mutations and GA, I will challenge that you almost certainly aren’t using truly random mutations.

    Neither does nature. The relevant issue is that the mutations are random with regard to the final outcome, ie, not front-loaded.

  159. #160 Mark C. Chu-Carroll
    June 7, 2007

    Looney:

    First: how do you know that Breve doesn’t do random mutation? It seems to me that your argument is entirely circular: an evolutionary algorithm can’t work without intelligent direction, therefore any example of an evolutionary framework can’t possibly produce anything unless it’s got intelligent guidance, therefore an evolutionary framework that produces something must not have been random, because it couldn’t have produced anything without intelligent guidance.

    Second: “random mutation” doesn’t mean exclusively single point mutation: duplication, reordering, and recombination, and insertion can all be random events. And all of them are things which have been observed to occur in nature.

  160. #161 plunge
    June 7, 2007

    “I will suggest you read Dawkins. There is always an uphill direction and only one maximum in his design universe.”

    Uh, WHAT? Cite please? What are you talking about? As another poster guessed, you might be talking about Dawkin’s weasel example. If that is the case, did you miss the copious in text disclaimer Dawkins included with that example about how it was simply an illustration of a single element at work and does not well reflect evolution?

    “My continuing gripe about evolutionists is that they make arguments without any regard for whether an earlier argument that was considered compelling had used mutually exclusive assumptions.”

    Anyone can claim they have a gripe. So far, you haven’t given us a reason to think that your gripe is anything more than a baseless accusation.

  161. #162 Looney
    June 7, 2007

    Dr. CC wrote: “First: how do you know that Breve doesn’t do random mutation? ”

    It looks like Breve is fairly flexible, so I presume lots of things could be implemented. The source code didn’t turn up quickly when I googled(heh!) it. I have looked over enough articles on GA to know that it is typically not done at a bit level on binary representations. So I am using an induction mode of reasoning which could potentially be falsified.

    “Second: “random mutation” doesn’t mean exclusively single point mutation: duplication, reordering, and recombination, and insertion can all be random events. And all of them are things which have been observed to occur in nature.”

    Bravo! The traveling salesman problem via GA uses reordering, but not duplication and many other forms of mutation for obvious reasons. The ID designer makes subtle changes to the GA methodology. The more experienced we are, the less self-awareness we have of our ID processes. I have a high suspicion that the LCS implementations selectively use mutation types together with heuristics.

    Or to put it another way, if LCS is best implemented with a GA algorithm (absent ID), then why did you need to work seven years on the problem? Presumably all you needed was a black box GA package off the shelf and that would have been the end of it.

    Why do evolutionist insist on using the analogy of geneticish algorithms dominated by ID to promote a theory of macro evolution absent an ID entity? It looks a bit like an induction argument, but a faulty one rather than a merely falsifiable one.

  162. #163 Science Avenger
    June 7, 2007

    Looney said: …I presume lots of things could be implemented… I have a high suspicion that the LCS implementations selectively use mutation types together with heuristics.

    Yep, Mark nailed it. Circular logic: assume any counterevidence has a fatal flaw in it.

    Why do evolutionist insist on using the analogy of geneticish algorithms dominated by ID to promote a theory of macro evolution absent an ID entity?

    Why, for the same reasons you guys are so desperate to discredit them, of course – They devastate your position. They allow us to see, in some cases right in front of our fucking faces, things happening via nondeterministic variation and a selection mechanism that you guys keep claiming are impossible without some sort of front-loading of the solution.

    Nobody who understands how computers work is buying your bullshit, and the situation is only going to get worse as the computers and their programs get better. You’re like my poor grandmother in 1969 watching Neil Armstrong stepping on the moon and claiming it had to be fake. It’s real, so deal.

  163. #164 Anonymous
    June 7, 2007

    To all,

    I’ve published a theory of a intelligent design compatable with modern physics, in my view, which can be found on various places on the internet under “holographic principle theory of mind.” The following is a brief summation:

    The Holographic Principle holds the information in any region of space and time exists on the surface of that region. Layers of the holographic, universal “now” go from the inception of the universe to the present. Universal Consciousness is the timeless source of actuality and mentality. Information is experience, and the expansion of the “now” leads to higher and higher orders of experience in the Universe, with various levels of consciousness emerging from experience. The brain consists of a nested hierarchy of surfaces which range from the most elementary field through the neuron, neural group, and the whole brain. Evidence from the evolution and structure of the brain shows that optimal surface areas in a variety of structures are conserved with respect to underlying surfaces. Microgenesis, the becoming of the mental state through a process of recapitulation of development and evolution, is in full accord with the Holographic Principle. Evidence from a wide variety of contexts indicates the capacity of the mind for total recall of past life events and for access to universal information, indicating connection with the holographic surfaces of prior “nows” and with the Universal holographic boundary. In summation, the Holographic Principle can help us explain the unity and mechanisms of perception, experience, memory, and consciousness.

    I see in the press now that “God” is being touted as an evolutionary device, or “neuron module” that helps us to survive, i.e. that “God” is a product of natural selection for the “God delusion.” I think scientists need to keep an open mind.

    Mark Germine

  164. #165 Jonathan Vos Post
    June 7, 2007

    An RNA-making reactor for the origin of life

    Eugene V. Koonin

    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894

    PNAS | May 29, 2007 | vol. 104 | no. 22 | 9105-9106

    Given the overwhelming complexity and difficulty of the origin of life problem, the most astonishing thing about it is that life actually has evolved on at least one planet in our universe (1). Indeed, it is entirely conceivable that the origin of life involved a series of highly unlikely events, and a substantial part of the explanation for why there is life on earth comes from the anthropic principle (2), i.e., our planet just happens to be one of the extremely rare parts of the universe where such a series of events was realized (3). The anthropic world view, however, by no means frees the students of early evolution from the obligation to explore all possible ways to decrease the improbability of life by demonstrating plausible paths to one or another of the milestones that need to be reached before life actually takes off. The paper by Baaske et al. (4) in this issue of PNAS seems to do just that by describing a simple abiotic system ensuring striking concentration of mono- and polynucleotides in inorganic compartments that might be suitable hatcheries for life….

    #1 Davies, P. (2000) The Fifth Miracle: The Search for the Origin and Meaning of Life (Simon & Schuster, New York,).
    #2 Livio, M & Rees, MJ. (2005) Science 309, 1022-1023.
    #3 Koonin, EV. (2007) arXiv: q-bio.PE/0701023.
    #4 Baaske, P, Weinert, FM, Duhr, S, Lemke, KH, Russell, MJ & Braun, D. (2007) Proc Natl Acad Sci USA 104, 9346-9351.

  165. #166 Anonymous
    June 7, 2007

    You might as well have told Dr. CC that he doesn’t know what a computer is. Pick up a book on Operations Research. GA is just a form of Operations Research, but most OR books don’t mention GA because GA is inferior to the existing methods in terms of both convergence and reliability. QWest may have “saved money” relative to not doing any optimization at all, but they almost certainly lost money relative to doing the optimization properly. I am sure Darwin will be pleased with the sacrifice. (That isn’t completely fair, because most GA systems are ID/GA hybrids that emulate classical OR methods. The traveling salesman problem being an especially clever GA/ID hybrid. This achieves the benefits of ID, avoids the pitfalls of genetics, while the glory goes to Darwin. ref. “Evolutionary computation for Modeling and Optimization” by Ashlock)

    Uh, they didn’t just pick up a GA off the shelf, shrug, and put it to work. Previously, they had experts employed precisely for the purpose of figuring out optimal network layouts. It took a single expert two months to put a design together (by their own admission in the article).

    On the other hand, once they replaced them with a genetic algorithm, they cut down layout design to two days, and achieved sufficiently better results than the expert ever did.

    In other words, no, you didn’t read the article or anything surrounding it, and instead just automatically dismissed my summary of that one section.

    Another giggle is hearing the complaint that I didn’t do GA right. Yes, of course. Someone with better ID skills could have made it converge faster! I could have made it converge faster by tweaking mutation rates and survival methodology. What will that prove other than the fundamentalists are right?

    The FAQ on GA success is just a red herring. Yes, GA/ID hybrids can solve problems. No, they can’t solve them better than ID alone and no, they can’t solve anything at all without ID intervention. Now, back to the real world …

    Wanna talk about red herrings? How about your insistence that GA can’t perform better than an expert, when the article on GAs that I linked to clearly talks about several instances when GAs were brought in and compared to human experts and well-proven algorithms, and the GAs did equal or better.

    Again, it’s clear that you refuse to read the article or, well, anything at all about GAs that might contradict your preset opinion about them.

    The definition of engineering is Science + ID. (Got that from the dean of engineering at UCLA.) You cannot disprove ID without also disproving that Thomas Edison invented the light bulb. It is impossible to have a consistent scientific world view and believe in macro evolution.

    That’s… absolutely retarded. Every single sentence of that paragraph was wrong. None of it corresponds with reality in the slightest.

    Darwinists don’t own micro evolution. This is just plain irresponsible scaremongering and FUD. In fact, if y’all would separate micro-evolution from macro-evolution and prehistoric speculation, there would be a hell of a lot less resistance to teaching micro-evolution, not to mention a lot more time.

    As Mark implied, the distinction between micro- and macro-evolution is artificial and false. It amounts to drawing a line in the sand and saying, “Evolution can change things this much, but no further.” It says this without any reason why evolution wouldn’t be able to go past that point, and what’s more flies directly in the face of reams of actual data. It’s basically akin to splitting math into micro- and macro-arithmetic, and saying that numbers greater than a billion are part of macro-arithmetic and don’t occur through natural counting processes, and thus things that involve numbers past that line must have been created whole rather than building up from smaller quantities. The problem with that, of course, is that you can always add 1. Same thing here – you can always add one more mutation.

    Regarding the random mutations and GA, I will challenge that you almost certainly aren’t using truly random mutations. Typically the GA algorithms do things like interchanges of objects within a graph with some random decision making. (Hence one of the complaint about Behe’s definition of evolution.) The traveling salesman problem is implemented with exchange type mutations and a special ad hoc modification to make sure that no city occurs twice after the breeding. This eliminates an astronomical part of the design space. Even if this works, a high-level object oriented GA algorithm on always-viable building blocks should never be presented as an analogy for how real world evolution might do things. This is just as deceptive as what you accuse Behe of doing.

    Wrong, wrong, wrong. A genetic algorithm requires a ‘genome’ to mutate – usually this is done as a binary string (or equivalently, a list of numbers). Your assertion about typical GAs is blatantly false as even a cursory survey of actual GA literature will show.

    Genetic programming does often represent its genome in the form of a graph, but that’s because it’s much more suited for the problem domain. GP is a very specific subset of GA in general, though.

    The Traveling Salesman problem is specially constructed because it must obey certain rules. By specifying that only certain types of mutations occur, they prevent large amounts of needless computer cycles being spend on generating invalid solutions. It’s eliminating most of the design space, true, because most of the design space is composed of a priori invalid solutions. All this does is speed up convergence – it doesn’t change the problem itself at all. With enough processing power (or patience) this wouldn’t be necessary and they could allow all mutations.

    The thing is, you’re damning actual evolution here too. Cells don’t just string together random proteins and see if they can be used as nuclear material – instead, they use only a handful of molecules chosen from the imcomprehensibly large possible design space and employ a fairly basic set of mutations. Does this mean that evolution makes itself impossible?

    Finally, your entire point is a non-sequitur. I assume by ‘truly random’ you mean something like “anything can happen!” That’s not at all necessary – you can achieve perfectly good results even when you restrict yourself to quite simple mutations. The fact that most GAs are weaker than biological evolution, and yes still achieve excellent results, shows how strong evolution is all by itself.

    Or to put it another way, if LCS is best implemented with a GA algorithm (absent ID), then why did you need to work seven years on the problem? Presumably all you needed was a black box GA package off the shelf and that would have been the end of it.

    WTF? See, now we *really* know you’re simply skimming anything presented to you, looking for soundbites that you can rebut. When Mark was talking about LCS, he didn’t mention using GAs at all. He was using an analogy to show that a particular paradigm performing badly on one problem says nothing about the paradigm’s performance on all problems. He only mentioned dynamic programming and recursive functions. No GA at all.

    As well, we already know that GAs are best passed by if we have a good analytical grasp of the problem. GAs are inherently inefficient, as I mentioned before, but the properties that make them inefficient are precisely their strengths as well – they can cover huge areas of a problem space in their search for an optimal solution, they don’t need any prior knowledge of the problem at all, just a well-designed fitness function to judge them, and they’re great at optimizing multiple variables at once. However, if the problem is of a type that we already know how to solve, it’s almost always better to use a different type of solution. One wouldn’t use GAs to solve LCS problems, but one *would* use them to help design a new aircraft wing that simultaneously optimizes multiple complex, conflicting variables. (And, of course, they’ve been put to exactly this task, as outlined on the talkorigins.net page I’ve linked to twice already. They equaled or exceeded the designs of expert aerospace designers.) You would use them to design battle plans taking into account hundreds of variables about troops, vehicles, terrain, weather, and enemy tactics (which, of course, they’ve also been applied to, outperforming expert military tacticians as well. When they gave the GA solutions to the experts to go over and revise, the original GA solutions *still* won out, showing that the experts weren’t even skilled enough to recognize when they were making a strategy worse!)

  166. #167 Xanthir, FCD
    June 7, 2007

    That last comment was me. >_<

  167. #168 Blake Stacey, OM
    June 7, 2007

    Xanthir, FCD said:

    As Mark implied, the distinction between micro- and macro-evolution is artificial and false. It amounts to drawing a line in the sand and saying, “Evolution can change things this much, but no further.” It says this without any reason why evolution wouldn’t be able to go past that point, and what’s more flies directly in the face of reams of actual data. It’s basically akin to splitting math into micro- and macro-arithmetic, and saying that numbers greater than a billion are part of macro-arithmetic and don’t occur through natural counting processes, and thus things that involve numbers past that line must have been created whole rather than building up from smaller quantities. The problem with that, of course, is that you can always add 1. Same thing here – you can always add one more mutation.

    This I like. :-)

  168. #169 Looney
    June 8, 2007

    Well, the latest text books on operations research that I just picked up from Stanford don’t mention GA at all. Wonder Why? My last copy of Numerical Recipes doesn’t mention GA. Wonder Why? I have two recent texts on Genetic Algorithms and neither will run a benchmark against a traditional method, although the traditional methods are all about performance benchmarks.

    Since I have been doing optimization and engineering/scientific programming for almost 30 years and interacted with the world’s experts, I will give you two points of advice:

    1) GA doesn’t have any supernatural powers. Sorry guys.
    2) You can’t believe everything you read – especially when it is about GA.

  169. #170 Xanthir, FCD
    June 8, 2007

    Well, the latest text books on operations research that I just picked up from Stanford don’t mention GA at all. Wonder Why? My last copy of Numerical Recipes doesn’t mention GA. Wonder Why?

    I finally looked up OR since you keep going on about it, and several of the things listed as being under the scope of OR have had GAs successfully applied to them, with the result of the GAs producing a better result in less time than a human can. The examples are right there on talkorigins – real companies risking real money, and finding that GAs pay off.

    Specifically, the things I noticed which were mentioned on talkorigins are:
    # designing the layout of a computer chip to reduce manufacturing time (therefore reducing cost)
    # managing the flow of raw materials and products in a supply chain based on uncertain demand for the finished products
    # efficient messaging and customer response tactics
    # roboticizing or automating human-driven operations processes
    scheduling:
    * personnel staffing
    * manufacturing steps

    As for why your specific textbooks don’t talk about it, there could be many reasons. For one, GAs still aren’t widely used. They aren’t traditional. Since I have no experience with the field, I have no idea of what the textbooks are like.

    I have two recent texts on Genetic Algorithms and neither will run a benchmark against a traditional method, although the traditional methods are all about performance benchmarks.

    GAs aren’t meant to be used in situations that *have* a traditional method. If there is an efficient algorithm for solving a problem, it will outperform the GA. On the other hand, for problems that are excessively complex and that do not admit a simple solution, GAs are ideal. We’ve been over this.

    Since I have been doing optimization and engineering/scientific programming for almost 30 years and interacted with the world’s experts, I will give you two points of advice:

    Appeals to authority are irrelevant.

    1) GA doesn’t have any supernatural powers. Sorry guys.

    And how many times have I said that GAs are inefficient and shouldn’t be used when you have an analytical solution? They don’t need to have supernatural powers to be useful, and they are, within their domain. You’re the one that keeps insisting that GAs are proclaimed to be the Holy Grail of algorithms. That’s not true. We recognize the limit of genetic algorithms – you keep attributing them magic powers and then saying that your model is unrealistic.

    2) You can’t believe everything you read – especially when it is about GA.

    Non sequitur. I can believe actual results, which are well-demonstrated.

  170. #171 Torbjörn Larsson, OM
    June 8, 2007

    Looney:

    So at a macro level, the heirarchies are too fuzzy to be useful for anything, but it is vital that we accept heirarchies for the understanding of evolution! Again, Dawkins outlined a number of other areas where heirarchical analysis was problematic.

    Since I haven’t done any cladistics obviously, I am a non-biologist, I can’t answer about the specific problems. But there are different phenomes, and the biological species concept (one out of many) isn’t applicable for quasispecies (or fossils, obviously, they need other definitions). While as you can see from the figures I gave that one can track genomes, proteomes and organelles.

    So the specific descriptions in hierarchies have specific limits. At some point the basic observation of hierarchies breaks down. For example in abiogenesis where we don’t have faithful or even internal reproduction at the start. (But as I noted, abiogenesis is outside evolutionary theory proper, since that describes hereditary.)

  171. #172 Torbjörn Larsson, OM
    June 8, 2007

    Looney:

    It sounds to me like y’all are expecting people to have faith in the unknowable …

    No, I think science expects laymen to either accept the results up front, or to study them and ask for clarifications. Oh, and to refrain from claiming, from ignorance or political reasons, it isn’t science but faith…

    My son reported on his California AP Biology test: “Any answer is correct, as long as it mentions evolution”.

    I’m quite sure that in reality any answer was correct as long as it described evolution. Which is not surprising since “nothing makes sense in biology without evolution”. Evolution is the basic theory in biology science. Compare with thermodynamics for physics – even QM computers can be understood in terms of it.

    Regarding the random mutations and GA, I will challenge that you almost certainly aren’t using truly random mutations.

    Oh, please! It is creationists that insists that evolution only uses random mutations. Without ever defining “random”, which is a multifaceted subject which always must be defined. (Probably naive equi-probability, though.)

    As I described before (comment #145) the minimal model including selection is “variation and selection with hereditary”. There is no constraint on variation here. AFAIK it can be very far from “random”, in any sloppy sense of the word (equi-probable, unpredictable, uncorrelated, …).

    And no, that doesn’t mean that the variability was designed. Ever heard of mutations? ;-) Point mutations doesn’t need to be (probably isn’t, in fact) equi-probable or uncorrelated.

  172. #173 Xanthir, FCD
    June 8, 2007

    Blake Stacey: You are welcome to it! ^_^

    Looney: I’ve been thinking on why GAs may be excluded from your OR texts (assuming that you’re telling the truth, as always). Aside from the extremely obvious and likely reason of inertia, which I’ve already been over, there’s also the simple fact that using a GA doesn’t require a lot of training.

    Designing a really good GA requires knowledge of the subject matter, yes. But the actual implementation of the GA is nearly trivial. All you need to do is decide on an encoding of the genome, then decide on a fitness function. Beyond that, GAs are all pretty similar.

    This is as opposed to, well, virtually every other algorithm in the world, which generally require a lot of skill and knowledge to use correctly.

  173. #174 Torbjörn Larsson, OM
    June 8, 2007

    Xanthir:

    Are you referring to the Weasel program?

    Oh, frak! I should have understood that it was a strawman. Unfortunately I don’t speak “intelligent-designese”. :-)

    engineering, a respectable field of science that makes actual predictions and has real results

    Well, not all of it as such, much is craft, trial-and-error, or optimization (but not ‘ID’) methodology outside the knowledge building (from own efforts or from science).

    But I like Axiomatic Design theory when it comes to demonstrating some science parts of the engineering process itself. However AD limitations in the actual process, one can study the interdependency of different design solutions numerically and predict the best optimization.

    Jonathan:

    Thank you, I have been looking for the publication of the original (Baaske et al) paper!

    The RNA world suddenly seems so much more realizable. And since I recently started to appreciate the recurring motif of large FeS surfaces in simple organic catalysts ( http://en.wikipedia.org/wiki/Ferredoxin ; http://en.wikipedia.org/wiki/Rieske_protein ) participating in basic metabolic reactions, it is even more exciting. Simple beginnings near such surfaces may have been the ticket.

    Now we really need clarification of viable production mechanisms for nucleotides…

  174. #175 MartinM
    June 8, 2007

    Or to put it another way, if LCS is best implemented with a GA algorithm (absent ID), then why did you need to work seven years on the problem? Presumably all you needed was a black box GA package off the shelf and that would have been the end of it.

    Off-the-shelf GAs will evolve solutions. They probably won’t evolve the solutions the user requires. The programmer’s input is not to make the GA work, but to make it work for you.

  175. #176 Looney
    June 8, 2007

    Now that we have totally muddled the discussion over whether or not GAs that are 99% ID are an appropriate analogy for evolution of life without any ID, I need to get y’all to take a step back and start to see the scope of the entire problem.

    GA is just a form of Optimization Research, but OR is just a microstep in the entire ID process. First, we conceive of a widget and recursively break it down into things we think might be tractable. We make abstract representations of component properties based on familiar patterns. A key part of this is coming up with a minimal set of objects that uniquely define the widget. Finally, we do a sophisticated ID mapping that allows us to take the abstract representations to a specific OR form(s) that we can deal with. At this point, we can use a traditional method or a GA method. Frequently, we don’t much care because many methods will work. Anyway, whether or not the OR method converges and how fast is critically dependent on how well we did the problem setup. OR experience tells us when a simple change of variables will have a drastic effect on whether OR will work or not.

    The next observation is that the OR algorithm is just a plug-in after the real ID work is done, although the OR results usually feed into more ID work. My conclusion is that there is exactly zero evidence that the role of ID can be diminished by genetics. That isn’t to say that some trivial, contrived predator-prey experiments might not do something interesting. All our technological experience, however, suggest that the credit belongs to the Ph.D. students who are the ID entities behind the cute predator-prey experiments. Fortunately for these students, the professors usually agree and award them a Ph.D. in recognition of their ID abilities.

  176. #177 Science Avenger
    June 8, 2007

    I suspect part of Looney’s problem is his perspective is out of date. He keeps talking about his 30 years of experience. Now maybe some of the computer scientists will correct me, but given the phenominal progress in computers over the last 30 years, I’d say most of that experience is about as relevant as someone’s experience shooting a flint lock is when using a machine gun.

  177. #178 Science Avenger
    June 8, 2007

    Looney dissembled thusly: Now that we have totally muddled the discussion over whether or not GAs that are 99% ID are an appropriate analogy for evolution of life without any ID, I need to get y’all to take a step back and start to see the scope of the entire problem.

    OK, I need a new ironymeter, as Myopiaman declares everyone else lacking in scope.

    We also see the ever-expanding definition of ID being used here. By this definition, nature is ID as well.

    More IDer word games? Whoda thunk it?

  178. #179 SteveF
    June 8, 2007

    I might be a bit late on this but with regards to malaria Behe is arguing that the billions of malaria just about make it possible for resistance to evolve. However, there aren’t billions and billions of humans, for example, therefore evolution can’t have a significant impact. It seemed to me that Mark missed the point here; Behe accepts evolution of Chloroquine resistance, his point is what this tells us about wider evolutionary processes.

  179. #180 Jud
    June 8, 2007

    SteveF said: “It seemed to me that Mark missed the point here; Behe accepts evolution of Chloroquine resistance, his point is what this tells us about wider evolutionary processes.”

    Did you happen to read Mark’s post? Mark never accuses Behe of failing to accept the evolution of chloroquine resistance in Plasmodia. (Behe could hardly fail to accept it, not being named Egnor.) What Mark does say is that the conclusions Behe draws from the chloroquine resistance example are incorrect to start with, and are then further munged by plugging them into a faulty mathematical model of those “wider evolutionary processes” you mentioned.

  180. #181 SteveF
    June 8, 2007

    Yes I read it. I also never said that Mark was accusing Behe of not accepting evolution of chloroquine resistance.

    Basically, as I see it, Behe is saying that evolution of resistance is an unlikely event. Mark, quite reasonably points out that because there are billions of bacteria, it is perfectly possible for it to happen. However, in response to this Behe would say (and this is what I think Mark is missing) that this yes this type of evolutionary innovation is possible because of the sheer number of individuals involved. There isn’t such a possibility in humans, for example, so this represents the “edge of evolution”.

    Mark goes on to point out why applying this number (which others have shown elsewhere to be faulty) elsewhere is invalid so in general I havent got a problem. Its just my feeling that the review was stressing (at this point) the eminent evolbability of resistance, which isn’t a direct refutal of Behe’s point. I’m nitpicking, but I’ve seen enough ID responses in which someone like Behe will pick up on certain points and ignore others (even when they directly follow as in this case).

  181. #182 Looney
    June 8, 2007

    “and are then further munged by plugging them into a faulty mathematical model of those “wider evolutionary processes” you mentioned.”

    Actually, Behe’s line of reasoning is identical to the reasoning that justifies drug cocktails for use against HIV. In fact, his “faulty mathematical model” is already accepted in medicine, but this probably shouldn’t be mentioned!

  182. #183 Jonathan Vos Post
    June 8, 2007

    I agree with Torbjörn Larsson that biogenesis has little to do with Evolution, although ID-ists keep confusing the two. And biogenesis is beginning to have good models, in a robust way, in vitro and in silico. I failed several times to submit a lengthy comment on this, and emailed MarkCC the text.

    Mathematical models are apparently too complex for Behe et al to understand, but some interesting models are in the recent literature.

    See, for instance:
    arXiv:q-bio/0703033 (replaced)
    http://arxiv.org/PS_cache/q-bio/pdf/0703/0703033v2.pdf
    Title: Complex population dynamics as a competition between multiple time-scale phenomena
    Authors: Ioana Bena, Michel Droz, Janusz Szwabinski, Andrzej Pekalski
    Comments: 15 pages, 12 figures. Accepted for publication in Phys. Rev. E
    [7 June 2007]

    If Looney wants to catch up with the literature, he can do so. The door is wide open. Nobody is stopping him.

  183. #184 Xanthir, FCD
    June 8, 2007

    “and are then further munged by plugging them into a faulty mathematical model of those “wider evolutionary processes” you mentioned.”

    Actually, Behe’s line of reasoning is identical to the reasoning that justifies drug cocktails for use against HIV. In fact, his “faulty mathematical model” is already accepted in medicine, but this probably shouldn’t be mentioned!

    Wanna detail just what exactly his mathematical model is, why it justifies drug cocktails, and where it is said to be accepted in medicine?

    ‘Cause I’m just seeing him multiplying some numbers together and declaring them too big for evolution to produce. It’s macromathematics! Numbers larger than a billion can’t be produced by adding together smaller numbers!

  184. #185 Anonymous
    June 8, 2007

    To all,

    I think of evolution as like a train. Natural selection is like a ticket to get on the train, it does not drive the train or direct it along the tracks. The Holographic Principle gives us a universal theory of evolution as I have discussed in a recent paper, to be found at:

    http:www//cejournal.org/GRD/Holo.pdf

    I’m sorry if this doesn’t come out as a link, but would appreciate any comment.

    Mark Germine

  185. #186 Keith Thompson
    June 8, 2007

    In comment #34, Matthew Bardoe writes:

    I have to say that I too believe that in general higher degree functions will have very few extrema… While each partial derivative does define a hypersurface, we will look for places for ALL the hypersurfaces to equal zero, simultaneously. Each partial derivative is its own hypersurface and we must add one more equation that they all have value zero. This is an over-defined system, one where the number of equations to satisfy is greater than the degrees of freedom of the inputs. This means that there will in general be very few solutions, and after that we must take 1/2^(dimension of inputs), for consideration of convexity. Seems small to me.

    Some of the math is beyond me, but I’m going to go out on a limb and disagree with this, with a whole lot of handwaving. Intuitively, a 100-dimensional landscape should still have plenth local maxima (and local minima).

    A local maximum in the landscape has to be a local maximum in every one of the 100 dimensions, which is going to be relatively rare; there are going to be a lot more “saddles” than maxima. But I think there will still be plenty of maxima, and they aren’t hard to find. Start at a random point, and move in the direction of the steepest uphill slope. (For a one-dimensional surface in 2-space, you can move left or right. For a 2-D surface in 3-space, you can choose any direction from 0 to 360 degrees. For a 3-D surface in 4-space, you have something like 10000+ square degrees to choose from, if my calculation is correct. And so on.) Keep doing this iteratively, and you should eventually reach a local maximum.

    It occurs to me that this might get you stuck at a saddle point, but (thinking about a 2-D surface in 3-space), you can escape by moving up the ridge in either direction; you have consider more than just the first derivative, or something like that.

    Loosely speaking, having 100 dimensions might tend to make local maxima rarer, but there’s a whole heck of a lot of room up there.

    As far as Behe’s arguments are concerned, I think this just means that if his ridiculous assumptions (a static landscape, infinitesimal changes always increasing fitness, etc.) are valid, then a species (or is it an organism?) could get “stuck” at a local maximim. And hey, maybe some of them do; there are species that haven’t changed much in tens of millions of years. But that doesn’t refute the theory of evolution.

  186. #187 Keith Thompson
    June 8, 2007

    In comment #185, Mark Germine anonymously writes:

    http:www//cejournal.org/GRD/Holo.pdf

    I’m sorry if this doesn’t come out as a link, but would appreciate any comment.

    You misplaced the “//”. The correct URL is:

    http://www.cejournal.org/GRD/Holo.pdf

  187. #188 Looney
    June 9, 2007

    Jonathan wrote: “Mathematical models are apparently too complex for Behe et al to understand, but some interesting models are in the recent literature.

    See, for instance:
    arXiv:q-bio/0703033 (replaced)
    http://arxiv.org/PS_cache/q-bio/pdf/0703/0703033v2.pdf
    Title: Complex population dynamics as a competition between multiple time-scale phenomena
    Authors: Ioana Bena, Michel Droz, Janusz Szwabinski, Andrzej Pekalski
    Comments: 15 pages, 12 figures. Accepted for publication in Phys. Rev. E
    [7 June 2007]

    If Looney wants to catch up with the literature, he can do so. The door is wide open. Nobody is stopping him.”

    Well, I looked at this paper. The fitness function is the following:

    Fi = 1-|Zi-PHI| (equation 2)

    The features are: 1 maximum, a constant gradient leading to the maximum. PHI is taken to be a function of time. The index i is used for both “traits” and “individuals” which leaves things a bit ambiguous on equation 2. The writeup indicates that this is a common analysis procedure. Although there is a time varying effect.

    It is a set of assumptions which is preposterous, but does have the nice effect of showing evolution in the best possible light. Behe’s stuff isn’t any worse than this.

    Thanks Jonathan for letting me feel smug.

    Regarding the number of maxima in n-dimensions, y’all need to start imagining n-dimensional fractals.

  188. #189 Jonathan Vos Post
    June 9, 2007

    Looney: Thank you for reading the paper I cited. This shows open-mindedness and good faith on your part.

    My point was not that the assumptions were other than “preposterous” as you put it (though even good models have to simplify to the point that they seem preposterous to some people). My point was to show complex emergent evolutionary behavior with even very simple fitness functions, in changing environments, where what was once optimum is no longer optimum, and vice versa.

    The great Terry Tao says:

    (Career Advice, on his blog)

    “The point of rigour is not to destroy all intuition; instead, it should be used to destroy bad intuition while clarifying and elevating good intuition. It is only with a combination of both rigorous formalism and good intuition that one can tackle complex mathematical problems; one needs the former to correctly deal with the fine details, and the latter to correctly deal with the big picture. Without one or the other, you will spend a lot of time blundering around in the dark (which can be instructive, but is highly inefficient). So once you are fully comfortable with rigorous mathematical thinking, you should revisit your intuitions on the subject and use your new thinking skills to test and refine these intuitions rather than discard them. One way to do this is to ask yourself dumb questions; another is to relearn your field.”

    http://terrytao.wordpress.com/career-advice/there%E2%80%99s-more-to-mathematics-than-rigour-and-proofs/

  189. #190 Smokey
    June 9, 2007

    Looney,

    If God designed us and God is intelligent, why did He design our immune systems to recognize foreign antigens by random (wrt fitness) variation filtered by selection?

    Are you claiming to be smarter than the designing God you believe in?

  190. #191 Looney
    June 9, 2007

    Jonathan, I agree with you that simplistic assumptions frequently give us extremely useful results, because I have seen this too many times in many different fields. The population dynamics model can probably be used to deduce some useful behavior.

    Still, the fitness function has an assumption of unlimited, easy macro evolution built in. We can’t then turn around and use dynamic models which are based on this assumption to make a claim that dynamic models are able to mathematically demonstrate unlimited macro evolution.

    Of course, there might be some dynamic models out there that haven’t presupposed unlimited, easy macro evolution, but do imply improved macro evolution capabilities …

    I would love to know because it would potentially be quite helpful to my optimization work.

  191. #192 Looney
    June 9, 2007

    Smokey wrote: “If God designed us and God is intelligent, why did He design our immune systems to recognize foreign antigens by random (wrt fitness) variation filtered by selection?”

    Well, I wrote a little computer program for fun that uses random variations filtered by selection to solve a specific class of problems. If someone took a look at that program and then declared, “Aha, it employs random variation filtered by selection, therefore Looney couldn’t have written it!”, how should I respond?

  192. #193 Jud
    June 9, 2007

    Looney said: “Behe’s line of reasoning is identical to the reasoning that justifies drug cocktails for use against HIV.”

    Hmm – Behe says evolution of resistance to a single drug in the malaria parasite is painstakingly slow, while the reason for drug cocktails in the HIV fight is that a virus, with far fewer genes (thus fewer potential mutations) than the malaria parasite, evolves resistance to single drugs so rapidly that the only alternative is to hit it with enough drugs that it can’t evolve resistance to all of them simultaneously. Apparently the virus hasn’t been paying attention to Behe.

    Looney then said: “In fact, his ‘faulty mathematical model’ is already accepted in medicine….”

    Ah, so “medicine” accepts an incorrect model of evolution? Where can one find good, clear evidence of how medical science has gone off the rails in this regard?

    Also, do you have an answer to the question I asked back at #146?

  193. #194 Looney
    June 9, 2007

    Jud, the answer to #146 is exactly the same as the answer for how the first DNA replicating machine came into being: They are theoretically impossible and no one has a clue.

    The simplified RNA replication explanation is in the same class as the claim that the first microprocessor washed up on the beach at Santa Cruz due to wave action on silicon crystals.

    Drug cocktails work because they set up a simple, macro-evolutionary barrier to the HIV virus. Of course, if macro-evolution is so easy, then drug cocktails would never work. The theory of macro-evolution is thus falsified by the effectiveness of drug cocktails.

  194. #195 Torbjörn Larsson, OM
    June 10, 2007

    Looney:

    Still, the fitness function has an assumption of unlimited, easy macro evolution built in. We can’t then turn around and use dynamic models which are based on this assumption to make a claim that dynamic models are able to mathematically demonstrate unlimited macro evolution.

    See, this doesn’t make sense for a scientist. Let me rephrase for a less controversial (?) theory:

    ‘Still, the gravitation potential has an assumption of unlimited, easy gravitation built in. We can’t then turn around and use dynamic models which are based on this assumption to make a claim that dynamic models are able to mathematically demonstrate unlimited gravitation.’

    If a model makes contact with earlier domain knowledge, it is a useful hypothesis. If it predicts observed behavior, it is a feasible model. And if it successfully predicts behavior that wasn’t known earlier, it is a valid model.

    If someone took a look at that program and then declared, “Aha, it employs random variation filtered by selection, therefore Looney couldn’t have written it!”

    The proper analogy would be “See, Looney thinks genetic algorithms are useful too”.

    And Smokey is pointing out that the speculated creationist designer obviously thinks the same.

  195. #196 Anonymous
    June 10, 2007

    Looney:

    They are theoretically impossible and no one has a clue.

    What theory of biology can dismiss DNA replication mechanisms, and how do they do that? According to evolution theory they are eminently evolvable since there are a priori not any constraints besides physical.

    And the suggested reason for observed adoption is that DNA is stabler than RNA. Thus while viruses may choose to use RNA as they use a stable cell environment to reproduce, the faithful cells that use DNA is superior to RNA replicators. I linked to a paper that makes a fair case that this selection happened three (!) times.

    The simplified RNA replication explanation is in the same class as the claim that the first microprocessor washed up on the beach

    Now you are leaving evolution and Jud’s question on religion to discuss biogenesis.

    But anyway, Jonathan referenced a paper that shows how easy it is for nucleotides to assemble to replicators in a natural environment. (And the next step for sloppy replicators are quasispecies, which happens to describe viruses in todays biology.)

    The proper question now is probably “how were nucleotides produced naturally?” Which question I believe the answer is currently “we don’t know for all of them”. To get back to Behe’s book, this is perhaps the current “Edge of biogenesis”.

  196. #197 Smokey
    June 10, 2007

    I wrote: “If God designed us and God is intelligent, why did He design our immune systems to recognize foreign antigens by random (wrt fitness) variation filtered by selection?”

    Looney evaded: “Well, I wrote a little computer program for fun that uses random variations filtered by selection to solve a specific class of problems. If someone took a look at that program and then declared, “Aha, it employs random variation filtered by selection, therefore Looney couldn’t have written it!”, how should I respond?”

    I don’t see any parallel to my question. You claim that random variation and selection constitute an inferior solution. I’m simply pointing out that random variation and selection is the mechanism by which your immune system works in real time. If God designed it, why did He use an inferior mechanism? Are you smarter than God, Looney?

  197. #198 Gordon J. Glover
    June 10, 2007

    The Edge of Meteorology: The Search for the Limits of Forecasting.

    It’s too long to repost here, but if you want to read a humorous review of Behe’s book that shows how the ID argument can be applied to other challenging fields of science, go to http://www.blog.beyondthefirmament.com/2007/06/10/the-edge-of-evolution/ and scroll down to “How to write an ID best-seller”.

    -GJG

  198. #199 Unsympathetic reader
    June 10, 2007

    Looney: “Drug cocktails work because they set up a simple, macro-evolutionary barrier to the HIV virus. Of course, if macro-evolution is so easy, then drug cocktails would never work. The theory of macro-evolution is thus falsified by the effectiveness of drug cocktails.

    Hmm.. A virus with only *nine* genes has problems getting around simultaneous exposure to 3-4 drugs. That’s your assumption of the selective pressures experienced by all species at all times? Why not say the ‘theory of macroevolution’ fails because turtles dropped out of airplanes never learn to fly?

    Hey, a question for you: Do the anti-HIV cocktails fail? And if so, how?

    *******************************
    From further up:
    Looney: “In biology, we have a dynamic fitness space if we look at one organism at a time in competition with others. If, on the other hand, we change our reference to the entire problem (say, an entire vehicle for the engineer, or “a balanced eco-system” for the biologist), then we are back to a relatively static fitness space.

    No, you are not “back to a relatively static fitness space”, even if you move up to the level of species. A “balanced eco-system” is not a static one. Even “steady-state” is seldom the same as “stasis” in biology. Describe for us, if you would, a reference point where the entire problem of biological fitness modeling resolves into a static solution, perhaps something with a scope smaller than the heat death of the universe would be useful.

  199. #200 Keith Eaton
    June 10, 2007

    As a first class intellect and a proponent of IC and ID and a Christian, (religion is not my bag, but relationship is), I find the review, inaccurate, inceomprehensible, full of ad hominem attacks, red herrings, strawmen, arguments from popularity and essentially every point of sophistry I have come to expect from the “I’m tenured on time in place, not on competence and besides that my grant income is up this year, crowd of egomaniacal cultists, psuedointellectuals who constitute the hardline evolutionary I hate God and I’m smarter than anyone else in the universe crowd.

    1) Biology BS degrees include math all the way up to college algebra and it shows constantly in your posts. I’ve reviewed about a dozen from prominent universities.

    2) The Biotic Message by Walter ReMine is more refined and if understood by the general population in full would immediately relegate evolution to the ash heap of history… where such nonsense belongs.

    3) The ignornace of the author is displayed by crediting Behe with the concept of local maxima standing while it is actually (Hartl,1980,p 335-336), an evolutionist of considerable reputation.

    4) Evolutionist understanding of higher math is trivial in general although Robert Shapiro understood sufficiently probability theory to completely discourage his faith or sufficiently do so to cause him to accept “life force” and alien seeding metaphysics. He is a rarity, however.

    5) The Remine book refers to a multidimensional fittness terrain, with canyons and crevices, thus discontinuous in nature and moderately dynamic. Extreme dynamics deliver no hope for natural selection to operate as the terrain would become a totally random ,short term unstable, operating space…hopeless.

    6) Walter Remine is a respected communications engineer who studied (12 years intensely) evolution in all its myriad of alternative formulations, postulates, sub-postulates, excuse mechanisms, endless alternative speculations…etc. and with the support of Dr. Kurt Wise and others systematically destroyed this blight on science from floor to ceiling, for any trained, thinking, reasoning, mind not blinded by the pervasive grant creed, tenure tactics, and mindless, selfwilled, sychophantic, true believer cult mentality.

    7) Behe is copletely familiar with ReMine’s work and has not departed from it in any substantitive respect.

    Thus we are left with a psychotic drift into crude, arrogant, childlike, personal attacks without merit, without gravitas, without content, form or any resemblance to true argument …just the typical sophistry and ranting from the evo camp.

    Alas another empty evo suit, bellowing in incomprehensible blasts of pure sophistry.

    Is there an intellect in the camp …please introduce me to same..it would be a first.

  200. #201 Zarquon
    June 10, 2007

    ReMine’s a monomaniacal crank, and his work is worthless as shown by the fact that no-one has adopted it as useful to biology in any way.
    BTW you’re misrepresenting ReMine.

  201. #202 Torbjörn Larsson, OM
    June 10, 2007

    Comment #195 was mine.

  202. #203 Torbjörn Larsson, OM
    June 10, 2007

    And while I’m at it, I can add to #195 what I forgot to mention, that there are indications that early life was RNA based.

    First, we know that some organelles in cells contain their own genetic material. The usual examples are mitochondries and plants chloroplasts, which contains DNA. It is generally considered that these organelles are incorporated endosymbionts. ( http://en.wikipedia.org/wiki/Endosymbiotic_theory ) And it seems all three domains (prokaryotes, eucaryotes, archaea) have them (http://en.wikipedia.org/wiki/Organelle ).

    Now, mtDNA does not contain all the sufficient genes for the mitochondrion by far, in humans about 40 of 3000 genes. It is suspected that some of the original genes have been incorporated in the nucleus instead, while others are probably developed de novo and some nonessential where lost. ( http://en.wikipedia.org/wiki/Transfer_of_mitochondrial_and_chloroplast_DNA_to_the_nucleus )

    [Split to avoid spam trapping from having many links.]

  203. #204 Torbjörn Larsson, OM
    June 10, 2007

    And while I’m at it, I can add to #195 what I forgot to mention, that there are indications that early life was RNA based.

    First, we know that some organelles in cells contain their own genetic material. The usual examples are mitochondries and plants chloroplasts, which contains DNA. It is generally considered that these organelles are incorporated endosymbionts. ( http://en.wikipedia.org/wiki/Endosymbiotic_theory ) And it seems all three domains (prokaryotes, eucaryotes, archaea) have them (http://en.wikipedia.org/wiki/Organelle ).
    [Split to avoid spam trapping from having many links.]

  204. #205 Torbjörn Larsson, OM
    June 10, 2007

    [The earlier comment part will likely be duplicated. Sorry about that.]

    Now, mtDNA does not contain all the sufficient genes for the mitochondrion by far, in humans about 40 of 3000 genes. It is suspected that some of the original genes have been incorporated in the nucleus instead, while others are probably developed de novo and some nonessential where lost. ( http://en.wikipedia.org/wiki/Transfer_of_mitochondrial_and_chloroplast_DNA_to_the_nucleus )

    But what is interesting with this here is that there are plenty of organelles which incorporate nucleotides, but that not all of them need to be DNA. It may be that centrosomes, which are essential for cell division and are able to copy themselves, carry their own genetic machinery in RNA ( http://www.bioinfo-online.net/modules/wordpress/2006/06/07/mbl-scientists-find-evidence-of-rna-in-organelle-essential-to-cell-division/ ).

    Second, another basic cell component are the ribosomes which are essential for protein synthesis. They contain RNA at the core function in all three domains. This makes it likely that the first organisms able to synthesize proteins were RNA based.

    I find it awesome that we can see traces of the early life lingering in todays cells. Evolution is a great jury-rigger.

  205. #206 Jud
    June 10, 2007

    Keith Eaton said: “As a first class intellect….”

    Ahahahaha! Great one, Keith!

    Reminds me of an old Dick Cavett Show I saw where Dick’s guest was Norman Mailer. Mailer described himself as having a “huge intellect.” Cavett changed seats, leaving an empty chair between himself and Mailer. Mailer (somewhat slow on the uptake) asked Cavett what he was doing. Cavett answered, “Making room for your huge intellect.” Mailer frowned as the audience roared.

    Keith, we are that audience, and you ought to be frowning right about now.

  206. #207 Jud
    June 10, 2007

    Looney said: “Jud, the answer to #146 [What is the scientific explanation for the origin of a Designer if something as relatively simple as a flagellum cannot arise naturally?] is exactly the same as the answer for how the first DNA replicating machine came into being: They are theoretically impossible and no one has a clue.

    “The simplified RNA replication explanation is in the same class as the claim that the first microprocessor washed up on the beach at Santa Cruz due to wave action on silicon crystals.”

    Unh-uh, no handwaving past the implications, which are as follows:

    (1) If a Designer did arise by natural means, then of course it is relatively much easier for far less complex life (microorganisms, humans) to arise by the same natural means, and thus there is no need for a Designer in the first place.

    (2) Conversely, if there is no way that primitive life could arise by natural means, then there is no way that an infinitely more complex Designer could arise naturally.

    Thus ID is not a viable alternative scientific explanation for complexity, because any objection re complexity raised against evolutionary theory applies even more strongly against ID.

  207. #208 Looney
    June 11, 2007

    “Thus ID is not a viable alternative scientific explanation for complexity, because any objection re complexity raised against evolutionary theory applies even more strongly against ID.”

    In “What is this thing called science” by Chalmers, the primary characteristics of bad science (e.g. Marxism and astrology) are that they are “vague and multifarious”. Evolution is the most vague and multifarious theory in the universe. Like Marxism, it is completely unsurprising that evolution can explain anything. Like Marxism, the explanations aren’t worth a whole lot. Now you can object that ID doesn’t explain things. I agree. ID explains why you can’t explain some things. It is actually quite healthy to have a theory which denies some explanatory powers next to a theory which claims to be able to trivially explain everything.

  208. #209 AJS
    June 11, 2007

    Now you can object that ID doesn’t explain things. I agree. ID explains why you can’t explain some things. It is actually quite healthy to have a theory which denies some explanatory powers next to a theory which claims to be able to trivially explain everything.

    Forgive my directness, but that is bollocks and you are talking out of your arsehole.

    The entire point of science is that it has to explain things — or explain why they cannot be explained.

  209. #210 Jud
    June 11, 2007

    Looney said: “ID explains why you can’t explain some things.”

    As AJS says a bit more, ehm, informally, that’s not correct. ID is trivially self-contradictory: “Nothing as complex as a flagellum can arise unaided, so we posit that first a Designer arose, a being much *more* compl – oh, oops.”

    A hypothesis that is trivially self-contradictory is simply wrong, and thus explains nothing.

  210. #211 Torbjörn Larsson, OM
    June 11, 2007

    Looney:

    Evolution is the most vague and multifarious theory in the universe.

    Again, I can have some sympathy for the argument in this context, since some of what you are now discussing (by no fault of Jud, I might add) is bordering on philosophical arguments instead of what the theory and facts describes. But there is still meat to the arguments.

    The argument from parsimony, Jud 207:1a, is correct and would be used as one criteria to choose between equally powerful theories. (Parsimony is used to choose parametrization of cosmological models and, I think, as deciding likelihood for cladistic models.)

    It wouldn’t be a very strong criteria by its own though, models need to be tested. Of course, the reason evolution is used is exactly because it has passed numerous tests while design can’t even be tested. That is some difference in power. ;-)

    The argument from probability, Jud 207:1b, is correct and would be used as one criteria to choose between equally parsimonious theories. It would be a fairly strong criteria in a theoretical discussion between alternative natural models IMHO.

    But as applied in this case no one would buy an undetectable and improbable mechanism. The implicit suggestion Jud caught you with is so much handwaving that you have left solid ground. It looks like a miracle. :-)

    The argument from complexity, Jud 207:2, is mostly philosophical, but none the less valid as well.

    It can be subsumed in the general fine-tuning argument. What Jud is claiming, correctly, can be interpreted as that finetuning gives a probability for a natural universe at least as (in Jud’s version definitely more) strong than the probability for a non-natural explanation. See the Ikeda & Jeffery’s analysis of finetuning ( http://en.wikipedia.org/wiki/Fine-tuned_universe ).

  211. #212 Looney
    June 11, 2007

    “The argument from parsimony, Jud 207:1a, is correct and would be used as one criteria to choose between equally powerful theories. (Parsimony is used to choose parametrization of cosmological models and, I think, as deciding likelihood for cladistic models.)”

    I dealt with it at the high level, but the problem should also be reflected at the low level. In physics we begin with F=MA or V=IR and start deriving. Things would look quite different if I were to start with F=M+A. If you pick up a typical molecular biology text, there is probably an exclamatory introduction (“holy evolution Batman”) and perhaps some ID analogies. Derivations begin, however, with some equation from chemistry, physics or math if there is any derivation at all. There is no equation of evolution, so you have no choice but to start with something else. At the end of the derivations, the conclusions are either left hanging or projected back onto evolution – which wasn’t part of the derivation. The paper that was recommended in post #188 was typical of this pattern.

    To choose between competing theories which have plausible scientific standing is a valuable excercise. I have yet to see any evidence that a scientific theory of evolution even exists.

  212. #213 Jud
    June 11, 2007

    Looney said: “There is no equation of evolution….”

    That’s incorrect. There are quite detailed population genetics equations in evolutionary theory that are borne out extremely well by observations in nature.

    Additionally, there are biochemical characteristics of genes predicted by evolutionary theory that are, once again, borne out by observations.

    For example, there are “synonymous” (non-product-altering) and “non-synonymous” (product-altering) gene base substitutions. For genes not under selection, where the products don’t matter to the organism’s survival, there is a predicted proportion of synonymous to non-synonymous changes. For genes under selection, where the products do matter to the organism’s survival, in accordance with evolutionary theory the proportion of synonymous changes should be elevated relative to that where genes aren’t under selection. And that is exactly what is observed in nature.

    If there is a Designer, on the other hand, there is no reason for synonymous changes at all, since there’s no design reason for them. But that’s not what the data show.

    Evolutionary theory also predicts that variation/mutation can only work with what it’s given, so the same effect should be achieved by different means, depending on the ancestral genome. And again, that is precisely what is observed in nature – for example, the derivation of the gene that makes “antifreeze” for northern hemisphere icefish is completely different than that of the gene responsible for the protein that keeps Antarctic icefish from freezing.

    If there is a Designer, there is no such limitation, and one would expect substantial predominance of iterated genetic means to reach a given end. But this is not at all what is observed in nature.

    So yes, there are in fact quite simple and fundamental mathematical and biochemical predictions made by evolutionary theory that have consistently been verified by the data. The fact that you don’t know about them, and confidently declare on the basis of ignorance that they don’t exist, is roughly equivalent to a child clapping her hands over her eyes and shouting, “I’m invisible.” As one would gently try to teach the child – the fact that *you* don’t see it doesn’t mean it isn’t apparent to those who bother to look.

    On the other hand, the fact that nothing in the observed data can be predicted or explained by reference to a Designer isn’t at all surprising when one remembers that ID is self-contradictory and hence explains nothing (see #210).

  213. #214 Smokey
    June 11, 2007

    “I dealt with it at the high level,…”

    You have dealt with nothing, Looney.

    “…If you pick up a typical molecular biology text, there is probably an exclamatory introduction (“holy evolution Batman”) and perhaps some ID analogies.”

    You’ve never read a molecular biology text, much less a typical one. Your incoherent riffing on “random” (failing to realize that mutations are only random wrt fitness) and belief that you are attacking Darwinism by doing so shows that you haven’t read Darwin, either.

    “Derivations begin, however, with some equation from chemistry, physics or math if there is any derivation at all.”

    Derivations begin with DATA, you fool.

    “There is no equation of evolution,…”

    There are many equations that are used in evolutionary theory. Your ignorance is showing.

    “… so you have no choice but to start with something else. At the end of the derivations, the conclusions are either left hanging or projected back onto evolution – which wasn’t part of the derivation.”

    You’re simply lying. Isn’t that a violation of one of the Commandments you claim to follow?

    “The paper that was recommended in post #188 was typical of this pattern.”

    Cite other papers that have this pattern, then.

    “To choose between competing theories which have plausible scientific standing is a valuable excercise.”

    Yes, it is, and real scientists do so by examining the predictions of those theories (only the ones that differ between them) are borne out by new data. Behe does nothing of the sort, and neither do you. Your approach is intellectually fraudulent.

    For example, the premise that an intelligent designer designed our immune system is not consistent with your arrogant claim that variation + selection is inadequate to explain the spectrum of life that we see, because our immune system generates new proteins that tightly bind to virtually any epitope not found within the self within two weeks.

    Your response to this challenge was completely dishonest, and you know it. Your hypotheses (that we were designed by God, and that genetic algorithms “are hopelessly inferior to pure ID methods,” have to explain all the extant data. The fact that you dishonestly evade addressing why your God would design something so important with a method you have judged to be hopelessly inferior speaks volumes.

    “I have yet to see any evidence that a scientific theory of evolution even exists.”

    That’s because you are afraid of the evidence. You can’t even come close to representing any of the mechanistic theories of evolution.

    Here’s a test: discuss the fulfillment of a mathematical prediction Darwin made by sequence data. Start by stating the prediction accurately and honestly, and continue by examining actual evidence that is freely available to the public. BTW, the mathematical tools used to test Darwin’s prediction are freely available too.

    If you don’t know what I’m talking about, you haven’t come close to an honest attempt to grapple with Darwin or more modern evolutionary theory.

  214. #215 Jonathan Vos Post
    June 11, 2007

    There is such a field as Mathematical Biology, and has been for quite some time. There is such a field as Computational Biology, and has been for quite some time. It seems that some people arguing about evolution are unaware that such fields exist, what journals cover those fields, what conferences breing the experts together, who the experts are, and what the consensus basic results are.

    Looney said something earlier, which made no sense to me, about drug cocktails. I’d suggest as a paper to actually read for understanding:

    Lamei Chen and Christopher Lee, Distinguishing HIV-1 drug resistance, accessory, and viral fitness mutations using conditional selection pressure analysis of treated versus untreated patient samples, Biology Direct 1 (2006), 14.

    http://www.biology-direct.com/content/1/1/14

    Abstract

    HIV can evolve drug resistance rapidly in response to new drug treatments, often through a combination of multiple mutations [1-3]. It would be useful to develop automated analyses of HIV sequence polymorphism that are able to predict drug resistance mutations, and to distinguish different types of functional roles among such mutations, for example, those that directly cause drug resistance, versus those that play an accessory role. Detecting functional interactions between mutations is essential for this classification. We have adapted a well-known measure of evolutionary selection pressure (Ka/Ks) and developed a conditional Ka/Ks approach to detect important interactions.

    Results

    We have applied this analysis to four independent HIV protease sequencing datasets: 50,000 clinical samples sequenced by Specialty Laboratories, Inc.; 1800 samples from patients treated with protease inhibitors; 2600 samples from untreated patients; 400 samples from untreated African patients. We have identified 428 mutation interactions in Specialty dataset with statistical significance and we were able to distinguish primary vs. accessory mutations for many well-studied examples. Amino acid interactions identified by conditional Ka/Ks matched 80 of 92 pair wise interactions found by a completely independent study of HIV protease (p-value for this match is significant: 10-70). Furthermore, Ka/Ks selection pressure results were highly reproducible among these independent datasets, both qualitatively and quantitatively, suggesting that they are detecting real drug-resistance and viral fitness mutations in the wild HIV-1 population.

    Conclusion

    Conditional Ka/Ks analysis can detect mutation interactions and distinguish primary vs. accessory mutations in HIV-1. Ka/Ks analysis of treated vs. untreated patient data can distinguish drug-resistance vs. viral fitness mutations. Verification of these results would require longitudinal studies. The result provides a valuable resource for AIDS research and will be available for open access upon publication at http://www.bioinformatics.ucla.edu/HIV

    Reviewers

    This article was reviewed by Wen-Hsiung Li (nominated by Eugene V. Koonin), Robert Shafer (nominated by Eugene V. Koonin), and Shamil Sunyaev.

  215. #216 Looney
    June 11, 2007

    Jud wrote:

    “If there is a Designer, on the other hand, there is no reason for synonymous changes at all, since there’s no design reason for them. But that’s not what the data show.”

    According to my medical researcher friend, pigs are preferred for research rather than monkeys because pigs are more like humans in much of their biology. Dawkins cited some similar examples in The Blind Watchmaker. This does not at all fall out of evolution.

    As an engineer, I have used synonymous changes many times as I make different programs. Per this reasoning, I could not have done this. It remains a simple fact that evolution is so vague and multifarious that it has no trouble fitting anything.

    As for the existence of equations that are attributed to evolution, this too is meaningless. Evolution and change are synonyms. I can attribute any equation to the theory of change, because the theory of change automatically encompasses all equations and theories whether true or false, real or imaginary. This gets to the core of the “multifarious” objection to evolution. Even if one equation is correct, all of the others could still be wrong. If I pick a dozen researchers at random and ask “what is the equation of evolution?”, I will probably get more than dozen answers. Evolution is only a philosophical fog.

  216. #217 Jonathan Vos Post
    June 11, 2007

    Looney, #215: “As for the existence of equations that are attributed to evolution, this too is meaningless…”

    Okay, so now we know that Looney has not yet caught up to the state of Mathematrical Biology in 1930. Quite a lot has been learned in these past 77 years. At least by those of us who are willing to learn. I recommend John Holland’s “Adaptation in Natural and Artificial Systems” from over 30 years ago, as that book proved the key theorems on the Genetic Algorith, My bias being that I beta tested the book (read it in manuscript and communicated with prof. Holland), and was the first person in the world to use the GA to evolve equations that solved a previously unsolved problem in the scientific literature, and the first to evolve working programs (APL) to fit empirical data from a scientific experiment. Koza patented what I had already lectured at in 3 or 4 universities.

    In population genetics, R. A. Fisher’s fundamental theorem of natural selection was originally stated as:

    “The rate of increase in fitness of any organism at any time is equal to its genetic variance in fitness at that time.”

    Or, in more modern terminology:

    “The rate of increase in the mean fitness of any organism at any time ascribable to natural selection acting through changes in gene frequencies is exactly equal to its genic variance in fitness at that time”. (A.W.F. Edwards 1994)

    The theorem was first formulated by R. A. Fisher in his 1930 book The Genetical Theory of Natural Selection. Fisher held that “It is not a little instructive that so similar a law should hold the supreme position among the biological sciences”. However, for forty years it was misunderstood, it being read as saying that the average fitness of a population would always increase, and models showed this not to be the case. The misunderstanding can be seen largely as a result of Fisher’s feud with the American geneticist Sewall Wright primarily about adaptive landscapes.

    The American George R. Price showed in 1972 that Fisher’s theorem was correct as stated, and that the proof was also correct, given a typo or two. Price showed the result was true, but did not find it to be of great significance. The sophistication that Price pointed out, and that had made understanding difficult, is that the theorem gives a formula for part of the change in gene frequency, and not for all of it. This is a part that can be said to be due to natural selection.

    More recent work (reviewed in Grafen 2003) builds on Price’s understanding in two ways. One aims to improve the theorem by completing it, i.e. by finding a formula for the whole of the change in gene frequency. The other argues that the partial change is indeed of great conceptual significance, and aims to extend similar partial change results into more and more general population genetic models.

  217. #218 Smokey
    June 11, 2007

    “According to my medical researcher friend, pigs are preferred for research rather than monkeys because pigs are more like humans in much of their biology.”

    They may be preferred in your friend’s research, but there is no single answer. The choice is a combination of availability, track record, affordability, and biology, with the biological aspects heavily influenced by modern evolutionary theory. For example, no one is using pigs to study basic questions in mammalian genetics.

    “Dawkins cited some similar examples in The Blind Watchmaker. This does not at all fall out of evolution.”

    I suggest that you broaden your survey. Why are mice the preferred model in mammalian genetics, Looney?

    “As an engineer, I have used synonymous changes many times as I make different programs.”

    Ah, but you don’t insert synonymous changes that have no functional relevance, as biology does. The only way you can address nested hierarchies is with lies, particularly lies of omission, Looney. The biggest lies used by your mentors wrt nested hierarchies is that they are mere similarities, ignoring the mathematics underlying them, just as you did above.

    Your writing this while avoiding my Darwinist challenge above is amusing.

    “Per this reasoning, I could not have done this. It remains a simple fact that evolution is so vague and multifarious that it has no trouble fitting anything.”

    The simple fact is that you are being utterly, deliberately dishonest in your misrepresentations of evolution and the theories about its mechanisms.

    “As for the existence of equations that are attributed to evolution, this too is meaningless.”

    There’s your deliberate dishonesty again. I wrote, “There are many equations that are used in evolutionary theory.” See the word THEORY in there, Looney? The theories are about the MECHANISMS of evolutionary change. You can’t even be bothered to familiarize yourself with them before spouting sweeping judgments.

    “Evolution and change are synonyms.”

    Yes. Evolution is a fact. Evolutionary theory is about the MECHANISMS of change.

    Here’s a test: discuss the fulfillment of a mathematical prediction Darwin made by sequence data. Start by stating Darwin’s prediction accurately and honestly, and continue by examining actual evidence that is freely available to the public. BTW, the mathematical tools used in these modern tests of Darwin’s prediction are freely available too.

    If you don’t know what I’m talking about, you haven’t come close to an honest attempt to grapple with Darwin or more modern evolutionary theory.

    Are you afraid of the math, Looney?

  218. #219 Looney
    June 11, 2007

    “The rate of increase in fitness of any organism at any time is equal to its genetic variance in fitness at that time.”

    Hmmm, an equality between two unmeasurable quantities … Genius at work!

    “It is not a little instructive that so similar a law should hold the supreme position among the biological sciences”

    Indeed!

  219. #220 Jonathan Vos Post
    June 11, 2007

    JVP: “… fitness… genetic variance in fitness.”

    Looney: “Hmmm, an equality between two unmeasurable quantities…”

    Unmeasurable? Both have been emasured hundreds of thousands of time, in many different populations of many different organisms. I hesitate to invoke a paper which mentions “entropy” as that word has proven problematic to the ID community, as previously deconstructed on this very blog. But…

    Are you denying the data, or the elementary definitions? Or the applicability to human beings?

    “The Measurement of Darwinian Fitness in Human Populations”,
    L. Demetrius, M. Ziehe
    Proceedings of the Royal Society of London. Series B, Biological Sciences, Vol. 222, No. 1226 (Jul. 23, 1984), pp. 33-50
    This article consists of 18 page(s).

    Abstract

    Darwinian fitness of a biological trait refers to the contribution to successive generations made by individuals possessing the trait. This contribution depends on the age-specific fecundity and mortality of the individuals in the population. This paper gives, for human populations, an empirical study of two measures of Darwinian fitness: the Malthusian parameter, which describes the rate of increase of the actual population size, and entropy which describes the rate of increase of the effective population size. This empirical study indicates that Darwinian fitness is measured by entropy. This finding is in accord with the predictions of recent theoretical studies.

    On the other hand, in fairness to Looney et al, there is quite a bit of confusion as to the proper definition(s) of “fitness.”

    To excerpt from a pper that you may find on the web site of Tetsuji Iseda:

    Changes in the concept of “fitness” in evolutionary biology

    1. Introduction

    Philosophers of science have been speculating on the way scientific theories change, but it is quite recently that they start to found their speculations on concrete historical researches on actual changes in science. Hull’s (1988a and 1988b) and Darden’s (1991) theories on conceptual changes are two of such recent attempts (Hull uses taxonomy in biology, and Darden uses Mendelism). In this paper I would like to examine their arguments by applying them to another case in biology. The example I use is the concept of “fitness.” This concept has been a central concept in evolutionary biology, but at the same time it has been confusing one, and we can find many different usages (Dawkins 1982 distinguished five major usages and added more. 179-194). The history may partly support Hull’s account of conceptual change (Hull 1988a and 1988b), but this cannot be the whole story. We will recognize that some theoretical requirements drove the changes, and need to admit something like Darden’s view on conceptual change (Darden 1991). In the course of the tracing of the history, we will also see how philosophical conceptual analyses help the understanding of the history.

    In section 2, I summarize Hull’s and Darden’s views on conceptual change. In section 3 through section 6, I go through case studies from the history of the concept. Section 3 deals with Spencer’s original introduction of “fitness” and Darwin’s adoption of it. Section 4 deals with Social Darwinism and its use of “fitness” as a normative word. In section 5, I discuss biologists’ attempt to measure “fitness” and the problem this attempt caused, namely the tautology problem. Section 6 deals with Hamilton’s “inclusive fitness” and its influence. Finally in the last section, I shall summarize the history and factors that have acted on the history. The tables at the end of the paper review and compare different notions of “fitness” dealt with in the paper.

  220. #221 Looney
    June 11, 2007

    Thanks Jonathan. That paper looks more reasonable and something I should take a look at. From the mathematical side, we must make some rash assumption regarding the shape of the fitness surface before an analysis can even start.

    The other side of the equation is genetic variation, but keep in mind that the reference was from 1930. How is someone in 1930 going to measure genetic variation? DNA will be discovered and understood much later. Maybe we can do this today with some sequencing techniques, but is it cost prohibitive? I have read that genetic variation varies from gene to gene along with mutation rates so that the computation resources needed to properly evaluate such relationships are quite high in addition to the data acquisition costs.

    Even if I accept all of that, all you now have is some data set correlated to a theory for a micro-evolution condition. No one (um, no one I know) is arguing with micro-evolution. I wasn’t bothered at all with the variation-fitness theory from my ID perspective. It just struck me as an arbitrary pronouncement.

  221. #222 Jud
    June 11, 2007

    Looney said: “As an engineer, I have used synonymous changes many times as I make different programs.”

    Programming in the same language to do exactly the same operation, you deliberately took more time and effort to achieve the same result you could simply have copied-and-pasted from an equally good previous program? How often do you make a practice of this, and do you proudly proclaim it during salary/promotion reviews?

    Or are you just being rather sloppy about what you define as “synonymous changes”?

  222. #223 Jud
    June 11, 2007

    “According to my medical researcher friend, pigs are preferred for research rather than monkeys because pigs are more like humans in much of their biology.”

    Yes, I’m sure this is especially true of research into finger surgery techniques, tool-making, and symbolic communication.

    “This does not at all fall out of evolution.”

    Really? Why should a pig share any deep biological characteristics with humans if not for shared ancestry?

  223. #224 windy
    June 11, 2007

    The other side of the equation is genetic variation, but keep in mind that the reference was from 1930. How is someone in 1930 going to measure genetic variation?

    Not genetic variation, genetic variance. It’s statistics. Genetic variance is traditionally measured by studying the inheritance of traits in organisms, comparing relatives and so on. Nowadays people can look at both the genotype and the phenotype, of course.

    Maybe we can do this today with some sequencing techniques, but is it cost prohibitive?

    No. Look up “quantitative trait loci”. They have been around for ages.

    I have read that genetic variation varies from gene to gene along with mutation rates so that the computation resources needed to properly evaluate such relationships are quite high in addition to the data acquisition costs.

    You might be thinking about phylogenetics. If genetic variation is studied in closely related individuals, as you would do for heritability studies, mutation rates can be measured directly. Cool, no?

    And about those computational resources… ever notice how computers are getting cheaper and more powerful every year?

  224. #225 Science Avenger
    June 11, 2007

    Looney said: Evolution is the most vague and multifarious theory in the universe.

    To me there is no greater example of creationist projection than this masterpiece. Evolution, a scientific theory that makes, and has made, tons of falsifiable predictions of various specificity, isn’t vague at all. It is ID/creationism, which has “God could have done it that way”, that is the vague nonfalsifiable dog in this hunt.

    Aside from cases of sheer intellectual dishonesty, some creationists seem to make this argument because they think evolution’s scientific status means it has to make a prediction about everything. Thus, the fact that the process pushes some species larger, and some smaller, appears that evolution “explains everything”. Well, in that case, yes, but so what? That’s true of any scientific theory.

    What seperates evolution from ID/creationism (apologies to the 95% of you that don’t need this basic reminder), is that evolution COULDN’T explain a pre-Cambrian rabbit, or a human genome competely lacking the corresponding one in the other apes, or a pegasus, or the nearly endless other examples one could site. There is no such thing on the other side of the aisle.

  225. #226 Tyler DiPietro
    June 11, 2007

    “Evolution and change are synonyms.”

    Wrong. Only in the literal sense are the two roughly synonymous. In a scientific sense evolution involves not only change but retention and selection of changes.

    “I can attribute any equation to the theory of change, because the theory of change automatically encompasses all equations and theories whether true or false, real or imaginary.”

    Exactly what “theory” of “change” are you talking about here, exactly? There are lots of scientific ways to measure and describe various changes. Be more specific, otherwise this criticism holds no water pertaining the argument you object to.

  226. #227 Torbjörn Larsson, OM
    June 12, 2007

    Looney:

    I dealt with it at the high level, but the problem should also be reflected at the low level.

    Sigh! The whole bit with this being philosophical problems which you draw into a discussion about science was wasted on you, wasn’t it?

    Scientific theories are tested, and so has evolutionary biology or we would not accept it as a science. And I described how parsimony in some special cases are valuable in practice, but the resulting models are still tested.

    There is no equation of evolution, so you have no choice but to start with something else.

    There are plenty of math in evolutionary biology, in population genetics (bottom up, model based gene aware) and quantitative genetics (top down, model free, gene blind) for example ( http://scienceblogs.com/gnxp/2007/03/population_vs_quantitative_gen.php ).

    And you can use one to check the other ( http://scienceblogs.com/gnxp/2007/05/breeding_the_breeders_equation.php ).

    There is also math in statistics for genomes and other data bases, et cetera.

    Note that the quoted scientist ends his exposition (in the first link) with the prediction that the math will become more complex:

    In the Post-Genomic Era single locus diallelic models really aren’t going to cut it, we’re going to have to grapple with enormous genomic scale data sets. A quantitative sense of large numbers and ranges needs to come back into play.

    But it is nothing remarkable if you pick up a few biology papers and they happen to assume the accepted evolution context without leading up to a test. Real tests of new data are sparse in any science with a well established theory, since most of them have been done earlier.

  227. #228 Looney
    June 12, 2007

    Y’all will be happy to know that I am tiring!

    From http://www.talkorigins.org/faqs/comdesc/ we have:

    “Evolution, the overarching concept that unifies the biological sciences, in fact embraces a plurality of theories and hypotheses.”

    What is the definition of “multifarious”? Based on my readings ranging from prof. Moran at Sandwalk to Dawkins to other biology texts, it seems that any argument that employs any physical or mathematical concept is automatically part of evolution, hence any physical or mathematical concept is implicitly included in the theory of evolution. Evolution = change = everything.

    “Common descent … specifically postulates that all of the earth’s known biota are genealogically related”

    I certainly can’t argue with a postulate, but the article proceeds to list a bunch of examples which verify the postulate. Unfortunately, the only way to verify the postulate using these examples is to interpret the examples according to the postulate! Circular reasoning 101. If you want to postulate, then postulate. Just don’t try to use the postulate to prove itself. Anyway, we have plenty of common descent examples in engineering (Chrysler and Dodge). No one has yet proposed any of them as evidence for the non-existence of engineers. (OK, in the case of Chrysler, maybe it is proof …)

    Finally, the “Caveats with determining phylogenetic trees” section gets to the core of the “vague” accusation, although I would be very surprised if this evolution advocacy site hadn’t toned down the topic a bit.

    Thus, I will stick to my accusation that a scientific theory of macro-evolution doesn’t exist.

  228. #229 Torbjörn Larsson, OM
    June 12, 2007

    Looney:

    As an engineer, I have used synonymous changes many times as I make different programs. Per this reasoning, I could not have done this.

    You are constrained by your materials, methods and personality. The point is that non-modeled designer/designers isn’t, so we can’t test such an idea. It isn’t a useful, feasible or valid hypothesis (see comment # 195).

    As for the existence of equations that are attributed to evolution, this too is meaningless. Evolution and change are synonyms. I can attribute any equation to the theory of change,

    Can you explain how the model neutral and evolution free quantitative genetics can agree with the evolution based math of population genetics above?

    One is attributed to evolution, one is not.

    If I pick a dozen researchers at random and ask “what is the equation of evolution?”, I will probably get more than dozen answers. Evolution is only a philosophical fog.

    I see. So the fact that Newton gravitation and general relativity can agree to a high degree in most cases is just a philosophical fog, not different models of science.

    Well, the scientists beg to think differently.

    Even if I accept all of that, all you now have is some data set correlated to a theory for a micro-evolution condition.

    The equations describes populations and/or genes, there is no magical barrier that tells us when evolution of characters stops.

    In fact, there is a common misconception that transitional characters in fossils are about species, wrongly called ‘missing links’ in papers and creo talk. But speciation is another thing. (And is harder to track in fossils than characters since you observe minimum dates instead of average dates.)

    What you are saying is akin to claiming (out of the black, as it where :-) that general relativity only describes gravitation for planetary and stellar systems, but not gravitation in cosmology.

    Thus, the fact that the process pushes some species larger, and some smaller, appears that evolution “explains everything”. Well, in that case, yes, but so what? That’s true of any scientific theory.

    And to continue my analogy on Science Avenger’s observation of some creationist mind sets, their thinking is akin to claiming that we only know that the specific planetary and stellar systems that we have measured and modeled must be said to be explained by general relativity. D’oh!

  229. #230 Torbjörn Larsson, OM
    June 12, 2007

    Looney:

    it seems that any argument that employs any physical or mathematical concept is automatically part of evolution,

    Of course evolutionary biology may use all available sciences in its models. For example, astronomy use physics and math, but also chemistry, geology, atmospheric and climate models, et cetera.

    You are have some funny preconceptions of how science works. Did you know that computer science use (gasp!) math?

    Unfortunately, the only way to verify the postulate using these examples is to interpret the examples according to the postulate! Circular reasoning 101. If you want to postulate, then postulate.

    But you miss the point entirely!

    You should continue to read the excellent article, it lists 29+ tests of evolution, things that it predicted that had no been described or modeled before. For example, the phylogenetic tree modeling that I described in comment #106 which you now seems to check up on.

    In a falsifying test, you assume a hypothesis or theory, predicts what it would say on the data given and if it does so with say 95 % certainty (for biology) it is successful and can be accepted. Even better if it predicts effects that are later verified (to reject confirmation bias).

    Um, and circular reasoning or so called tautology is the result of knowing the correct theory – what it predicts is true. But not trivially so, in case of new data/new effects!

    Finally, the “Caveats with determining phylogenetic trees” section gets to the core of the “vague” accusation, although I would be very surprised if this evolution advocacy site hadn’t toned down the topic a bit.

    That is a baseless accusation, it is important to list known caveats in such a section.

    But let’s see what it says:
    - Lateral inheritance is a problem for “organismic phylogeny”. I noted that in comment #149, the species “tree” will become a “bush”. But if you can track inherited phylogenetic material like organelles, it is doable.
    - Then follows a list with 11 technical caveats.

    Honestly, I don’t see the difference between such caveats or caveats for applying say classical mechanics: – few bodies (or computer or virial approximation) – non-relative speeds – non-quantum systems – few and known constraints – no friction – no EM effects, et cetera, et cetera. Would you call classical mechanics a “vague” science?

    Considering that evolutionary biology and phylogenetic trees are much more complex (and so much more powerful), I think 11 caveats is a short and fair list.

  230. #231 Torbjörn Larsson, OM
    June 12, 2007

    Looney:

    [TL:] no EM effects

    Um, unless one subsumes it in the model as a constraint of course, or conversely incorporate mechanics into a mixed model with EM. More caveats. :-)

    JVP: “… fitness… genetic variance in fitness.”

    Looney: “Hmmm, an equality between two unmeasurable quantities…”

    Unmeasurable? Both have been emasured hundreds of thousands of time, in many different populations of many different organisms.

    There are many quantities that can be used to measure fitness, btw.

    “A simple definition of fitness is ‘the number of viable offspring produced per unit time.’ This is absolute, a property of individuals, and applies to all organisms. [...]

    Fundamentally, fitness is all about the reproductive success of individuals. From there, we can address the average fitnesses for different groups of individuals, and the relative fitnesses of such groups. We could then move on to fitness over multiple generations, inclusive fitness, components of fitness through life histories, and other issues.

    There is an excellent discussion of these issues in Douglas Futuyma’s Evolutionary Biology, Third Edition (1993), p. 349.”

    ( http://scienceblogs.com/evolvingthoughts/2007/01/fitness.php#comment-322053 )

  231. #232 paul
    June 12, 2007

    Reply to The Black Cat June 4

    As to what the creationists will say about your synthetically designed cell,should it ever be created. They will say,”Thank-you for proving our point. It took very much intelligent design for you to succeed in your creation.”

  232. #233 Jud
    June 12, 2007

    Hello, Looney. :-)

    I’ll use this comment to bid adieu to you and this thread. Thank you for staying around and engaging in a lengthy but civil discourse. To learn more about some interesting details of evolution, so it won’t seem quite so vague or foggy (more details to disagree with! ;-) I’d recommend Sean B. Carroll’s books.

    Take care.

  233. #234 Looney
    June 12, 2007

    I appreciate all of your inputs too and apologize for some of my condescending attitudes. You have left me with a lot of information to digest and links to pursue.

  234. #235 truth machine
    June 14, 2007

    “As a first class intellect and a proponent of IC and ID and a Christian”

    The second clause disproves the first clause.

    As for Looney/realpc, is such a dense and intellectually dishonest troll really worthy of so much attention?

  235. #236 truth machine
    June 14, 2007

    “Thus, I will stick to my accusation that a scientific theory of macro-evolution doesn’t exist.”

    Morons sticking with their silly “accusations” won’t change the fact that we have an effective scientific theory. Ignoramuses like Looney who view evolution as a topic of parlor room debate, facilitated by the web, have no clue of the concrete role that the ToE plays in the work of thousands of scientists. It’s like accusing mathematicians of perpetrating a fraud with imaginary numbers, which obviously don’t exist because, hey, they’re imaginary.

  236. #237 Xanthir, FCD
    June 14, 2007

    truth machine:
    I doubt that anything we said had any effect on Looney, though who knows what goes on in the minds of men. My arguments were, instead, meant to convince other people who happened to read the exchange. Allowing false ideas to spread unchallenged is asking for them to be taken up by unaware minds. We must always counteract them with reason and evidence, so as to convince those on the fence, strengthen those on our side, and pull toward us those on the opposite.

  237. #238 Norm Breyfogle
    June 14, 2007

    The above types of discussions could be avoided if religious believers would stop confusing their faith/beliefs/speculations/opinions/metaphors with science (and to a lesser degree, if some scientists would more clearly recognize this same distinction without ridiculing the latter). The empirically provable takes us only so far at any one time in history, and beyond that we’re free to speculate or wax poetic, but the distinction between objective fact and either speculation or art shouldn’t be so easily blurred by so many. The fact that it is so easily blurred by so many adults suggests a need to be teaching psychology and philosophy in our public schools from kindergarten on up (tailored to the appropriate level of understanding of each age group, of course). The ability to be objective about one’s own cognitive processes is the cause of a lot of wasting of time and energy in pointless noise throughout human cultures.

    Of course, I understand that attempting to implement the above suggestion would immediately run up against the same pointless noise from the very beginning of the legislative process on. Sheesh. So the cycle continues.

    “If man had created man he’d be ashamed of his performance.” – Mark Twain

  238. #239 Norm Breyfogle
    June 14, 2007

    Oops; correction:

    This:

    “The ability to be objective about one’s own cognitive processes is the cause of a lot of wasting of time and energy in pointless noise throughout human cultures.”

    should instead read:

    “The INability to be objective about one’s own cognitive processes is the cause of a lot of wasting of time and energy in pointless noise throughout human cultures.”

  239. #240 AJS
    June 14, 2007

    The problem is that Science and Religion are fundamentally incompatible.

    Science has just three “articles of faith” (i.e., things which are accepted as true, though by their very nature they can never be proved nor disproved). (1) Everything can be explained in terms of a series of laws. (2) These laws are universal — that is, the same laws apply to everything in the universe. (3) These laws are immutable — that is, they have never changed and are never going to change.

    Religion starts out assuming that some things, such as the Immaculate Conception, the Resurrection, the Assumption of the Blessed Virgin Mary and Transubstantiation, cannot be explained — they must simply be accepted as Mysteries.

    This obviously runs contrary to the Scientist’s first assumption. There is no way to reconcile science (which assumes all things are explainable) with religion (which explicitly defines some things as unexplainable).

  240. #241 Bronze Dog
    June 14, 2007

    At least science has the fewest assumptions, and the ones most easily falsifiable. Find one instance of a time or place where a law doesn’t apply, and we’ll change the law as appropriate, for example.

    Besides, I prefer science’s optimism: It’s done some great things that started out from idle curiosity. The sky is not the limit, and there’s always another surprise around the next corner.

    The fundies and woos, however, would love to wall off everything, saying that we can’t expand our knowledge, that we’ve learned everything we can learn, and we should just shut up and stop asking questions. I could never be that pessimistic and depressing.

  241. #242 Norm Breyfogle
    June 14, 2007

    Science and religion typically are incompatible but aren’t *necessarily*; such depends on exactly how one defines “religion” (or “spirituality” or whatever term one prefers) for oneself. Trancendental, translogical, or metaphorical outlooks are of a totally different class of thinking than are literalistic religious ones OR scientific ones, and as long as one’s thinking doesn’t contradict any rational rules of thought there should be no conflicts.

    And to assume that only strictly scientific thought has any “meaning” or “truth” to it is to entirely forget about or miss the point of art, literature, poetry, and yes, even some mystical/spiritual expressions.

    Art and science aren’t fundamentally incompatible. The error I’m pointing out is that of viewing religious expressions as literalistic and scientifically falsifiable ones. This distinction is missed by all religious fundamentalists and even by some scientifically-minded people.

    What I’m asserting is that religion is art, not science, and too many people mix them up (mostly the religious folks, but also some science-minded folks).

  242. #243 Torbjörn Larsson, OM
    June 15, 2007

    Science has just three “articles of faith” (i.e., things which are accepted as true, though by their very nature they can never be proved nor disproved).

    Well, I don’t agree. Some of these assumptions can certainly be in need to be extended into domains that aren’t probed, but as a rule we don’t rely on them much.

    There is also nothing ‘faithful’ or dogmatic about assumptions – if science wouldn’t work, they would be abandoned.

    (1) Everything can be explained in terms of a series of laws.

    That is metaphysical naturalism, a philosophical stance.

    Science however operates under methodological naturalism – observational facts may be amenable to natural explanations (i.e. theories in terms of objects whose interactions can lead to have observable consequences).

    (2) These laws are universal — that is, the same laws apply to everything in the universe. (3) These laws are immutable — that is, they have never changed and are never going to change.

    Well, no – if we are nitpicky, laws and theories may have limited application and be contingent on application. Classical mechanics are certainly not universal in the sense that it applies to everything, that is why we have QM.

    But some laws and theories are thought to be universal. The usual description is about symmetries (and technically gauges) that these theories obey.

    One can also state a few universal principles that guide theories, such as the principle of mediocrity (roughly, humans aren’t privileged observers), or an assumption of a null hypotheses.

    But above all, these principles are tested within the observable Hubble volume. Gravitation and EM forces seems to be the same everywhere and everywhen.

  243. #244 Christiaan
    June 15, 2007

    Then why haven’t we observed any structural advancement in Malaria . . . we’ve observed something like 10^20 genterations of the stuff. Something novel should have come around by now.

  244. #245 Mark C. Chu-Carroll
    June 15, 2007

    Christiaan:

    We *have* seen significant changes in Malaria. We used to have multiple treatments that were pretty much universally effective at getting rid of malaria. Now, we have malaria strains that are immune to all of the standard treatments. Resistance to anti-malaria drugs isn’t a trivial change – it’s generally a pretty significant change to the biochemistry of the organism.

    We also see amazing differences between malaria strains in different places. For example, the peak time for mosquitos is different in africa versus indonesia – and we find that malaria emerges from the human cells that it infects *just before* that peak time.

  245. #246 Torbjörn Larsson, OM
    June 15, 2007

    we’ve observed something like 10^20 genterations of the stuff. Something novel should have come around by now.

    Moreover, different versions of sickle cell anemia has developed 4 (!) times in humans since it confers resistance ( see http://en.wikipedia.org/wiki/Sickle_cell_anemia and especially the maps).

    Malaria is thought to have been the greatest selective pressure on the human genome in recent history.

    ( http://en.wikipedia.org/wiki/Malaria )

    Other established new traits securely or tentatively associated with malaria resistance are the set of thalassemias, non-expression of Duffy antigens, and changes in G6PD, HLA, and IL4 molecules.

  246. #247 Torbjörn Larsson, OM
    June 15, 2007

    different versions of sickle cell anemia has developed 4 (!) times in humans since it confers resistance

    That should read: different versions of sickle cell anemia has developed 4 (!) times in humans and become established since it confers resistance. (Most side-effects are severe, it would probably not become established otherwise.)

    Oh, and we aren’t talking 10^20 individual selection events in humans, evolution of the different sickle cell anemias happened 3000 to 6000 generations ago in a fairly low population average.

  247. #248 Anders
    June 28, 2007

    There is a review of this book in today’s Nature:
    http://www.nature.com/nature/journal/v447/n7148/full/4471055a.html

  248. #249 SpasticWilliams
    July 13, 2007

    Nice work! Your critique was easy to read and easy to understand.

  249. #250 Jonathan Vos Post
    July 24, 2007

    The idea of the “Landscape” is applied in the below-linked paper to the publication of science papers.

    http://arxiv.org/ftp/arxiv/papers/0707/0707.3261.pdf
    Title: Scaling rules in the science system: influence of field-specific citation characteristics on the impact of research groups
    Authors: Anthony F. J. van Raan
    Comments: 17 pages, 1 table, 11 figures
    Subjects: Physics and Society (physics.soc-ph); Data Analysis, Statistics and Probability (physics.data-an)

    We propose a representation of science as a citation-density landscape and investigate scaling rules with the field-specific citation density as a main topological property. We focus on the size-dependence of several main bibliometric indicators for a large set of research groups while distinguishing between top-performance and lower performance groups. We demonstrate that this representation of the science system is particularly effective to understand the role and the interdependencies of the different bibliometric indicators and related topological properties of the landscape.

  250. #251 sonic
    December 29, 2008

    250 comments. Not one mention of the actual argument from the book.
    Interesting.

  251. #252 Jonathan Vos Post
    December 29, 2008

    Re #251: “Not one mention of the actual argument from the book”

    When someone has thrown a handful of pseudoarguments against a wall, hoping that some of them stick, what does a reviewer do?

    One approach is to unpack them one by one, refute each, and thus reveal that the handful might as well have been filled with excrement.

    This, however, gives more credit to the book than it is due, and makes a too-long review of limited audience appeal.

    Another approach is to pick the most egregiously wrong argument, and refute it.

    This suffers the problems of allowing the True Believers to think that everything else in the book is true, and that the reviewer is merely nitpicking.

    How, one might wonder, does one refute something wich is not wrong, but is “not even wrong”?

    To cite from today’s version of wikipedia:

    An apparently scientific argument is said to be not even wrong if it is based on assumptions that are known to be incorrect, or alternately theories which cannot possibly be falsified or used to predict anything. The phrase was coined by the early quantum physicist Wolfgang Pauli, who was known for his colorful objections to incorrect or sloppy thinking.[1] Peierls (1960) writes of Pauli, “… a friend showed him the paper of a young physicist which he suspected was not of great value but on which he wanted Pauli’s views. Pauli remarked sadly, ‘That’s not right. It’s not even wrong’ “.[2] In science and philosophy, it is known as the principle of falsifiability.

    Statements which are “not even wrong” may be well-formed, but lack reference to anything physical (as in “Souls are immortal”, because the noun “soul” is not well-defined in terms of experimental results), or may simply be gobbledygook which appears meaningless (as in some of the Time Cube writings).

    The phrase “not even wrong” is often used to describe pseudoscience or bad science, and is considered derogatory.[3]

    1. Shermer M (2006). “Wronger Than Wrong”. Scientific American. http://www.sciam.com/article.cfm?id=wronger-than-wrong.
    2. Peierls R (1960). “Wolfgang Ernst Pauli, 1900-1958″. Biographical memoirs of fellows of the Royal Society (Royal Society (Great Britain)) 5: 174-92. doi:10.1098/rsbm.1960.0014.
    3. Oliver Burkeman (September 19, 2005). “Not even wrong”, The Guardian.

    If you prop up the “not even wrong” argument to make it meaningful, but wrong, then you stand accused of attacking a straw man.

    For reasons including these, I stand in full support of Dr. Mark Chu-Carroll. Behe is “not even wrong” — but his blather has moral, ethical, and intellectual consequences which ARE wrong. Biomedical practices predate Science as a profession, because of the life or death results. Behe, whatever he may believe, is de facto on the side of Death.