# Another Round on Probability and Evolution

I had not intended to do another post on this topic so soon after the last one. But I have just read
an astonishingly bad post over at Uncommon Descent that discusses this issue, and I cannot resist responding.

The post is called, “Where Do We Get the Probabilities?” It was written by Winston Ewert, and it opens like this:

What is the probability of a structure like the bacterial flagellum evolving under Darwinian processes? This is the question on which the entire debate over Darwinian evolution turns. If the bacterial flagellum’s evolution is absurdly improbable, than Darwinism is false. On the other hand, if the flagellum is reasonably probable than Darwinism looks like a perfectly plausible explanation for life.

This is poorly phrased, for reasons I explained in my earlier post. An absurdly low probability by itself would tell us nothing one way or the other about the plausibility of Darwinian evolution. As has often been noted, improbable things happen all the time. It could well be that any particular outcome of billions of years of evolution occurs with low probability. To go from a low probability of flagellar evolution to the conclusion that it is effectively impossible requires an additional argument, to show that this is not the sort of improbability that can be dismissed. The ID folks have been entirely unsuccessful in this regard. Ewert, of course, claims otherwise:

Dembski’s development of specified complexity depends on having established that the probability of structures like the bacterial flagellum is absurdly low under Darwinian mechanisms. Specified complexity provides the justification for rejecting Darwinian evolution on the basis of the absurdly low probability. It does nothing to help establish the low probability. Anyone arguing the Darwinian evolution has a low probability of success because of CSI has put the cart before the horse. You have to show that the probability of the bacterial flagellum is low before applying CSI to show that Darwinism is a bad explanation.

Sadly, there are two big problems with this. The first is that you cannot hope to do a relevant probability calculation without first clearly specifying the event in question. It is not that you first carry out the calculation, and then move on to the next step of showing that the structure is “specified.” The specification and the calculation have to go hand in hand, as otherwise you have no idea what you're calculating the probability of. Picking out the relevant event, though, is no small problem, as I pointed out in my earlier post.

The even bigger problem, though, is that there is no way to give any meaning to Dembski's notion of “specification” that is useful for drawing conclusions about the plausibility of evolution. That is why, in his writing, he nearly always only applies it to tinker toy examples and then argues by vague analogy to draw biological conclusions. The one place where he actually tried to do a calculation for the flagellum (in his book No Free Lunch), the whole effort was so riddled with errors it could hardly be taken seriously.

To see the problem, let's use a standard example. The specific sequence of H's and T's that arise in five hundred flips of a coin is exceedingly unlikely, but that is not necessarily suspicious since something had to happen. But five hundred heads would be suspicious, roughly because it conforms to an easily describable pattern. ID folks try to extrapolate this sort of reasoning to structures like the flagellum. It's not only improbable, they say, but it's “specified” by virtue of its functionality.

But this argument doesn't work at all, and for a simple reason. When we reason about what is, and is not, likely to occur when flipping a coin, we have a good grasp on the relevant probability space. We generally take it for granted that we are talking about a fair coin tossed in a fair way, meaning we are justified in equipping the space with a uniform probability distribution. That is precisely what we can not do when we are discussing genetic evolution. In this case we have no way of determining the correct distribution to apply to the space.

The prolonged action of natural selection ensures that most gene sequences have a probability close to zero of ever occurring (or persisting for long if they do occur) while the small percentage of functional sequences have a relatively high probability. That is why simplistic analogies with coin tossing (or any of the other stock examples ID folks use) do not work. We know enough about the relevant space so that five hundred heads immediately jumps out at us as requiring a special explanation. We have no such justification for arguing comparably with respect to the flagellum.

Ewert continues:

So what is the probability of a bacterial flagellum under Darwinian mechanisms? Obviously, we can’t expect to know the exact probability, but can we at least determine whether or not its absurdly improbable? That’s the question on which the whole debate rests. It seems that any arguments over Darwinism should be focused on arguments about this probability. It is the key to the whole discussion.

This is just nonsense. The inability to define the relevant probability space in assessing the outcomes of prolonged evolution scuppers the whole attempt to apply probability in the way ID folks prefer. We have no good way even of estimating the probability, and we would have no helpful way of interpreting the probability even if we could somehow estimate it.

These points are obvious to anyone who understands probability theory, which is why actual biologists do not try to carry out these sorts of calculations. To make probability the question on which the entire debate revolves betrays a complete incomprehension of the subject. Probability theory is very useful for understanding many aspects of evolution, but it is not useful for drawing grand conclusions about what is possible (or plausible) and what is not.

Ewert continues:

Intelligent design proponents have long offered a number of arguments attempting to show that Darwinian evolution accords a low probability to structures such as the bacterial flagellum. Darwin’s Black Box argues that irreducible complexity is highly improbable to evolve. The Edge of Evolution argues that non-trivial constructive mutations are too improbable for Darwinian evolution. Doug Axe’s protein work argues that protein evolution is too improbable. The fact is, almost every work by intelligent design proponents has been directed towards arguing that Darwinian evolution is too improbable to work. There is no mystery about why we intelligent design proponents think that evolution is improbable.

Intelligent design critics are going to dispute all of these arguments I mention. That’s fine. But dispute those arguments. Don’t act as though we’ve never given explanations for why we think that Darwinism is an improbable account of the complexity of life. Don’t attack specified complexity for not showing that Darwinism is improbable. That was never the intent of specified complexity. It is the intent of a host of other arguments put forward by intelligent design proponents.

This is a joke, surely. Who is Ewert talking about when he says ID's critics need to “dispute those arguments”? Who is acting like ID folks have never given explanations for what they believe? We have replied at length to all of the points Ewert raises. We do sometimes express incredulity that the ID folks could possibly believe what they are saying, but that is a different matter.

Behe's book Darwin's Black Box was one of the most thoroughly reviewed scientific books in recent history, and it was not difficult for scientists to explain what was wrong with his argument. They pointed out that “irreducible complexity” as Behe defined it was a silly notion that was entirely unhelpful in assessing the plausibility of evolution. At a theoretical level it is trivial to devise scenarios through which such systems could evolve gradually, and actual research scientists have been very successful at showing how these scenarios have played out in specific cases.

Likewise for Behe's and Axe's bloviations about the nature of sequence space. In addition to the conceptual errors especially in Behe's book The Edge of Evolution, their whole approach plainly cannot justify the bold conclusions they are trying to draw. You're never going to be able to draw grand conclusions about the plausibility of protein evolution from a few small experiments undertaken on modern organisms. Moreover, actual research in protein evolution does not at all suggest that the relevant space is structured in the way they need to make their case. We know, for example, that most mutations are neutral, which already suggests that individual proteins are surrounded by groups of other functional proteins.

Actual researchers see not just that ID is putting forward bad arguments, but that its whole approach to the subject is just a conceptual dead end. So the issue is not that ID's critics have simply ignored the arguments ID folks have put forward. It is that they have replied at length, but people like Ewert don't like what they have said. So they heckle from the sidelines, demand a standard of proof under which anything less than a videotape of natural history is casually dismissed, and then just repeat ad nauseum the same points they have always made. Helpful when preaching to the choir, but not so helpful for saying anything interesting about natural history.

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### More like this

##### Another Round On Specified Complexity
There's a famous short story by Woody Allen called “The Gossage-Vardebedian Papers” that I like to reread from time to time. (It's very short, so follow the link if you've never read it before.) The story is told through the correspondence of Gossage and Vardebedian, as they argue about a game of…
##### Ewert Explains “Specified Complexity,” (Part Two)
Let us continue with our discussion of Winston Ewert's defense of the concept of “specified complexity.” In Part One we saw that Ewert's defense was actually rather tepid. He mostly gave away the game by writing: It is true that specified complexity does not in any way help establish that the…
##### Ewert Explains “Specified Complexity,” Part One
Over at the Discovery Institute's blog, Winston Ewert has a post up explaining, one more time, what specified complexity is. Since I am given a mention near the end, perhaps it's worth a look. For those not steeped in ID rhetoric, “specified complexity” is a term coined by William Dembski. It is…
##### Probability and Evolution
Returning now to my radio debate with Sean Pitman, another issue that arose involved the use of probability theory in understanding evolution. Sean argued, indeed, it was really his only argument, that natural selection was incapable in principle of crafting complex adaptations. He chided me for…

Note that once again Ewert doesn't provide any positive evidence for ID. He produces nothing but "evolution can't have happened, hence an Intelligent Designer blessed be Him/Her/It." That's not how science works.
It's pathetic.

Umm actual researchers cannot demonstrate that natural selection is a designer mimic. And evolutionists may not like irreducible complexity but they cannot demonstrate that natuiral selection can put together an IC system.

Lenski's E. coli- 50,000+ generations and not even a new protein, let alone a new multi-protein complex.

The problem with probabilities is your position cannot give any numbers because it has no methodology to do so.

So what do you have besides bad-mouthing ID and IDists?

When we reason about what is, and is not, likely to occur when flipping a coin, we have a good grasp on the relevant probability space. We generally take it for granted that we are talking about a fair coin tossed in a fair way, meaning we are justified in equipping the space with a uniform probability distribution. That is precisely what we can not do when we are discussing genetic evolution. In this case we have no way of determining the correct distribution to apply to the space.

A good example may be found in figure 4A here. (HT to Blaine...now on two different threads!). Researchers looked at flagella evolution and after some number of generations found two separate strains that evolved a similar developmental property (in this case, multiple flagella allowing "hyperswarming"). In each of those strains there were individual critters with multiple, different, point mutations. This opens up the question of how many other genetic mutations that didn't evolve may have had the same effect. Clearly any probability calculation that assumed one of these observed mutations was absolutely necessary ("specified?") for hyperswarming would have been wrong. But assuming the observed mutants are the only ones that lead to this development may be equally wrong. As Jason says, we simply do not know the probability space here. We have a few specific examples of which mutations worked. Though not published in the article, the researchers probably also have a bunch of examples of genetic codes that didn't lead to this effect. But we don't know the ratio of "mutations that don't lead to this outcome" to "mutations that do lead to this outcome." We do not know whether this developmental trait requires a very easy to achieve pattern ("in any string of coin flips, there must be 5 heads in a row") or a very hard to achieve pattern ("flips 1-80 and 84-100 must all be heads, flips 81-83 may be anything"). But we do know that the assumptions IDers often make - that there is only one way to achieve an evolutionary outcome ("flips 1-100 must all be heads") - is absolutely wrong in this case.

Joe G

So what do you have besides bad-mouthing ID and IDists?

Observed instances of mutation and natural selection. Would you like to show us your observed instances of God?

Joe G,
What makes you think that Lenski's critters are NOT producing any new protein ?
Lenski's experiment doesn't directly test the protein content of the bacteria. So you have no basis for your statement.
It is extremely likely, to the point of certainty, that each of the 12 separate strands of the Lenski critters have each developed unique proteins that were not present in the original bacteria.
We know that because at least one has developped a pathway to digest citrate, which is extremely likely to involve new metabolites, new proteins.

Lenski should try to get funding for an experiment to count and estimate the number of "new" (different from the original strain) proteins in each of the current lineages, to assuage your doubts.
So far, most of the tests done show changes in the DNA, which can affect either a protein structure, or control the expression of an existing protein.

ID brings to mind Pauli's felicitous phrase, 'it is not even wrong.'
Where is the ID research project? Where are the ID experiments? Where is the ID hypothesis to be tested?

ID commits the fallacy of the false dichotomy in a massive way. Even assuming, for the sake of argument, that something is irreducibly complex, what could that possibly even mean? Why a designer and not designers? Maybe we're avatars in a simulation and a whole team of programmers are responsible for the design. As Pennock testified at the Kitzmiller v. Dover Area School District trial, maybe god created us 5 seconds ago with all our false memories.
One argues to the best explaination given the web of theories and knowledge the human community currently has...and the best explanation so far is that evolution explains things the best. ID offers absolutely nothing. As Pennock said, "ID is an interesting theological argument, but that it is not science."

ID == Cargo Cult science.

Still waiting for John Frum

Behe also claimed in Darwin's Black Box, while questioning common descent, that there were no intermediates between a supposed hoofed wolf-like animal that existed millions of years ago and present day whales and dolphins. Subsequently at least a dozen such intermediate fossils (Ambulocetus anyone) have been found, which forced him to testify at the Dover Trial that he now accepted common descent.

By colnago80 (not verified) on 04 Feb 2014 #permalink

What is the probability of a structure like the bacterial flagellum evolving under Darwinian processes?
...
Intelligent design proponents have long offered a number of arguments attempting to show that Darwinian evolution accords a low probability to structures such as the bacterial flagellum.

Note the switcheroo. First he asks about the probability of the flagellum evolving. Before the end, he is talking about the "probability of the structure." Not the same thing. A Darwinian explanation implies lots of small steps, with many of them conferring some small advantage. If we have no idea about the steps involved, how can we calculate the probability.

I will repeat my analogy from the last thread:

Consider fair coins, fairly tossed. A coin tossing event takes a given amount of time, say one second. What is the probability of ending up with 500 heads? Calculate under these two different scenarios:

1) A collection of 500 coins are tossed at once. If they do not all come up heads, repeat until success.

2) Toss a single coin. If it not heads, toss it again. Once it comes up heads, heave it and move on to the next coin.

It should be clear to the mathematically inclined that the first scenario involves a low probability, and a long mean time until success. The second scenario is much higher probability, and much shorter mean time to success.

The second scenario is something like a Darwinian explanation would be expected to provide: Many small steps, with advantage being gradual and cumulative. The first scenario is more like what an ID proponent would be likely to suggest.

By Reginald Selkirk (not verified) on 04 Feb 2014 #permalink

Joe G #2: The problem with probabilities is your position cannot give any numbers because it has no methodology to do so.

That would seem to be problematic for the ID side, since they claim that the probabilities are unreasonably low. And yet you have just admitted there is no way to get those numbers.

By Reginald Selkirk (not verified) on 04 Feb 2014 #permalink

Joe G,

It is actually very easy to present an evolutionary pathway that results in an IC system. The thing that you have to realize to do this is that evolution does not only add components, but it can remove them as well.

Consider a system consisting of two components, call them A and B and call the system AB, which is irreducibly complex. That is, neither A alone nor B alone is capable of performing the system's function. Let's say, however that there is some component C out there that is capable of performing this function. It is possible that an ancestral organism used C to perform this function. Via evolutionary process, component B was added to C to form system BC, which performed the function better than C alone. A further developement may have resulted in addition of component A to form system ABC. Now, we know (via our original assumption) that system AB can perform this function. Therefore, C is redundant, and loss of this component may well be advantageous; eg. an organism would not need to expend energy to maintain this component. Therefore, it is quite plausible that this component would be lost to form system AB, which is irreducibly complex.

IC systems, therefore, can in theory develop from an evolutionary process. Please stop trying to claim otherwise.

Arthur-

E, coli had the ability to digest citrate in an oxygen-free environment. All that happened was two potentiating mutations followed by a tandem duplicate of that gene- the gene that gets turned on in the anaerobic env.- and put it under control of a promoter that was on when oxygen was present.

Reginald Selkirk-

You misunderstand. We can't get the numbers because there aren't any numbers to get. Yours is a position almost entirely dependent on luck- it's all culled luck. Culled luck plus father time is not science.

eric-

There aren't any instances of observed mutation and natural selecytion (FYI-natural selection includes heritable random mutations) producing new multi-protein systems. There isn't any evidence that natural selection is a designer mimic.

Sean T.

Behe's mousetrap has 5 parts. No one has ever obseved naturalselecion putting toether a 5 part system, in which each part is differet and dependent upon the others for the system to function.

Whatwould th testable ypothesis look like wrt accumations of genetic accdent?

@JoeG: so what? As I'm not an expert on this matter let me temporarily assume you're right. So we (are supposed to) have a problem with Evolution Theory. How does that prove an Intelligent Designer? That jump, so popular amongst creacrappers like you, is based on the false dichotomy mentioned by Blaine in @6. His questions

"Where is the ID research project? Where are the ID experiments? Where is the ID hypothesis to be tested?"

are competely valid. He represents what I wrote in @1. Answer them and then come back; else you have nothing to show.
Until you do that you could apply illogic with equal (= zero) validity to superconductivity at relatively high temperatures. We don't have a theory for that. You should conclude that your god sustains them, if you were consistent. Remarkably no single creacrapper ever has argued that. So you're guilty of the ad hoc fallacy as well.

You misunderstand.

Not at all. You spin.
I repeat: how can you claim the probabliities of an event are unreachable if you cannot calculate them? Stop spinning and answer.

By Reginald Selkirk (not verified) on 04 Feb 2014 #permalink

Behe’s mousetrap has 5 parts.

Behe's choice of mousetrap is a designed object. So he built the answer into the question.

The simplest mousetrap need only have one part: a physical trap such as either a hole the mouse falls into or an adhesive surface. Consider the latter: natural versions exist. Exhibit A: the La Brea Tra Pits.

By Reginald Selkirk (not verified) on 04 Feb 2014 #permalink

Reginald Selkirk- Dr Johnson answers you in "Nature's Probability and Probability's Nature". Your position cannot demonstrate any probabilities. Don't blame us/.

MNb- I have never mag=de the jump that you say. However the design inference mandates eliminating necessity and chance- that's science.

ID research project? Easy, find out what else there is to living organisms besides matter and energy

That said there aren't any blind watchmaker research projects. No blind watchmaker experiments- why don't you lead by example?

Please describe an experiment to " find out what else there is to living organisms besides matter and energy", Joe.

By IDGuy Jim (not verified) on 04 Feb 2014 #permalink

so Joe, have you seen the designer and seen it design a protein from scratch? Perhaps you have a you tube video to show us staright from the designer's lab?

By Michael Fugate (not verified) on 04 Feb 2014 #permalink

In case you're interested, a standard reply to Behe on the issue of probability is from the philosopher Kitcher's article on this. He concludes that "once these points are recognized, it's clear that, for all its rhetorical force, Behe's appeal to numbers smacks more of numerology than of science."

http://www.stephenjaygould.org/ctrl/kitcher_behe.html

Joe G,

Numerous changes happened in the 12 separate E. Coli strains in the decades-long experiment.
If you have any scientific evidence that no protein was modified at any time during the experiment, please give the link.
Or, do you mean that modified proteins do not count as NEW proteins in your view ?

Joe,

I don't care if the IC system has 2, 3, 5, 25, or 25000 parts. The whole claim of the IC argument is that there is no way IN THEORY that an evolutionary process can produce an IC system. My post above demonstrates conclusively that this argument is fallacious.

Note, that to demonstrate that the IC argument is fallacious, one need not demonstrate the exact evolutionary process of an actual IC biological system. A theoretical, abstract demonstration, such as the one I gave, is sufficient to invaldiate the argument. Obviously, this does not, in and of itself, invalidate the entirety of ID (the complete lack of positive evidence for ID does that job well enough), but it does invalidate the argument from irreducible complexity.

Joe,

Since you ID'ers are always saying that such and such an event is too improbable to have ever occurred, please tell me, what is the cutoff probability? That is, what value for a probability of an event makes it possible to say that the event could not possibly have occurred? If you're going to argue that the evolution of certain biological systems is too improbable to have occurred, shouldn't you have some idea of how improbable something must be to have not occurred?

Joe G,

Final question: how do you propose that a strain of bacteria developed an entirely new metabolic pathway without also having developed new enzymes to catalyze the reactions that form that pathway? You do know, right, that ALL chemical reactions occurring in living organisms are catalyzed by enzymes. Additionally, all enzymes are proteins. Further, an entire metabolic pathway, such as the one allowing for the utilization of citrate for energy, would require mulitple reactions, and thus multiple enzymes, thus entailing a multi-protein system. You claim that such a multiple-protein system has never been observed to arise via evolutionary processes. Since that is the case, and since I have only a basic knowledge of biochemistry, I am eagerly awaiting your explanation of how a bacterial strain developed an entire metabolic pathway without also having developed enzymes to catalyze that pathway? The Nobel committee also is likely interested in your explanation, since it must certainly involve a complete and total overhaul of the very fundamentals of the field of biochemistry, and such a feat would certainly be Nobel-prize worthy.

We also need to know what it is that makes two proteins different proteins rather than just variants of the same protein. How many amino acids need be different? How much 2-D or 3-D structural difference? How much catalytic difference, if an enzyme? How much DNA sequence difference? What about sharing some but not all exons? We do need to know what we are looking for before we start observing.

By Michael Fugate (not verified) on 04 Feb 2014 #permalink

Joe G #20: Reginald Selkirk- Dr Johnson answers you in “Nature’s Probability and Probability’s Nature”. Your position cannot demonstrate any probabilities. Don’t blame us/.

Since you acknowledge the probabilities cannot be calculated, I take this as admission that claiming the probabilities are unlikely is unsupported.
Your attempt to reverse the burden of proof is noted, and stupid.

By Reginald Selkirk (not verified) on 04 Feb 2014 #permalink

Sean T #30: Additionally, all enzymes are proteins.

Wrong. The Nobel committee will already be aware of this, since they awarded a Nobel prize to Thomas Cech and Sidney Altman in 1989.

By Reginald Selkirk (not verified) on 04 Feb 2014 #permalink

Intelligent Design theory is not based on faith or beliefs. It is rather an observation of the reality or what's going on (to be more exact), which involves such methods as inference and induction. It's not religion. It's science that extends its reaches into what people suspect to be supernatural, like voices in mental illness, for instance.

The uniformity with which matter organizes itself, precise coincidences that pertain to a certain phenomenon that form a distinct pattern when these coincidences are looked at from a different angle create, at least, the impression that a mere chance is too good to be true.

There is no reason for the proponents of intelligent design to exclude evolution as an observable phenomenon, as it could be a method with which the creator, whoever or whatever it might be and is not specified, as it is irrelevant, manipulates matter into distinct perfectly defined shapes and forms.

As for the irreducible complexity of microbiological units, evolution could've easily played a role in their formation, as these units are not primeval but were rather REDUCED to ultimate efficiency from a possibly highly complex but full of redundancy FINAL biological unit.

Ruese,
If I understand you correctly, you are basically claiming that ID is like the Far Side cartoon which says:
A + B --> then a miracle occurs --> c + d = X
If 'god' uses evolution to make the 'miracle' occur, what is the point of even bringing god into the explanation, if everything can be explained without reference to god. It's like the famous quote from an exchange between Laplace and Napoleon when he askes why Laplace's book didn't require god to explain things: 'Sir, I have no need for that hypothesis.'

Even if we accept that a 'miracle' occurs as a step in some evoutionary process, this brings us no closer to an explanation because no one can agree on what that could possible mean and we have no means of determining what it means.
So far, natural selection and similar concepts have been able to adequately explain things. So why bring in fruitless concepts when they are not required...Occham's razor comes to mind here.

The proponents of the Theory of Intelligent design do not make up concepts, and projects them on to the reality, as opposed to religion. I doubt that they even hypothesize. It's more like trying to understand what they see in what's going on. The proponents of Intelligent design observe the noticed phenomena.These is where the catch lies. What they observe, infer and deduce simply leads to a logical conclusion that natural selection alone would not be able to produce such uniformity, suspicious connections and patterns in series of perfect coincidences. It must have all been designed by some intelligent entity. And it can become really scary when you actually start paying attention.

Here's something that just occurred to me. Many ID proponents like to stress that ID is consistent with evolution, even including common descent as we know it, and possibly gradualism. If that's the case, how could an experiment possibly rule out ID?

Suppose that Lenski's bacteria finally reach one of the moving goalposts, and every change along the way is documented to ID's satisfaction. We would have a demonstration that a purely evolutionary process could produce every flavor of the month (irreducible complexity, functional specificity, comprehensible transfinite opacity, etc), just like the IDists have been requesting. This would set them back quite a bit, right?

Of course not. And I don't just mean that by way of cynicism. I mean that it would be intellectually dishonest for them to admit defeat, because they're already on the record as supporting the possibility of a purely gradual evolutionary process, just one that "happens to be" designed. Their entire argument is probabilistic alone. (At least, in some contexts it is.) Which means that this hypothetical experimental result could only be an instance of the designer "loading the dice".

From their perspective, such an outcome would be equivalent to witnessing a truly and repeatedly shuffled deck result in one straight flush after another, with no tampering observed. In their view, rather than conclude that "Poker-Darwin was right -- decks just plain can do that!", an honest scientist ought to conclude the best explanation was interference by a non-material agent. (Myself, I would still keep an eye out for basic trickery, which has been known to fool scientists before.)

And per their logic, this would be true even if the flushes were the result of some quasi-evolutionary process involving mutation and selection. It doesn't matter how detailed and plausible each individual step may seem, the fact of the final result necessarily proves design of some kind. They've run the numbers, you see.

So where does that leave us? It's tempting to simply conclude the total unfalsifiability of their position. But that doesn't seem fair, somehow, because intuitively it feels like they do have a point buried underneath the nonsense: it feels like some probabilistic threshold should be too far for evolution.

One of my answers is that in the absence of understanding alternatives (such as "design"), you can't assign probabilities to them, even fuzzy ones. Cheating at cards is a known and mechanically-detailed phenomenon, while gods are not. Hence, given a single "miracle" scenario, it would make complete sense to live in the null hypothesis of "We just don't know" rather than decide you've reached a point of so much ignorance that it's time to embrace the divine.

A related issue is that, again, we really don't know the proper reference frame. Is it eyes in particular, vision in general, or anything of :complexity" equivalent to an eye?

The final point I would raise is that evolution isn't a black box, where proto-DNA goes into one end and primates jump out the other. We know the steps. We not only have the fossils, but a very good grasp of genetics, and even epigenetics is becoming more robust every day. As such, it doesn't make much sense to talk about probabilities of grand events like the development of a flagellum, when there are lots of detailed steps to be considered.

To return to the card deck analogy, on observing an apparent phenomenon whereby a shuffled deck keeps producing flushes, we have to ask, What exactly is going on with the cards?

Magic loves to be unanalyzed by humans, and humans are often content to leave the magic unbothered. Jesus turned water into wine, but he didn't do anything with carbon atoms, he just turned water (that clear stuff we drink) into wine (that red stuff that gets us drunk), okay?

But science can't work that way. At a fundamental level, saying "This deck was well-shuffled" contradicts the not-so-shuffled result. How are the well-shuffled cards moving into place? Can they physically pass through one another?

Likewise with genetic steps. Whether or not design is the case, we have to ask the detailed chemical questions. And ID will always hem and haw on those.

What they observe, infer and deduce simply leads to a logical conclusion that natural selection alone would not be able to produce such uniformity,

"Logical conclusion" implies that they have a set of premises that leads deductively to a necessary conclusion. So, what are the premises that lead deductively to the conclusion that NS alone is not sufficient?

Secondly, mainstream science already recognizes that NS alone is not responsible for the diversity we see today. Sexual selection and horizontal gene transfer also occur. Which illustrates two things. First, your keystone premise is faulty. Secondly, it illustrates that you're using the same contrived dualism creationists have been using for decades, whereby you take "NS couldn't do it" to imply "designer must have done it." But the existence of non-NS, non-designer mechanisms demonstrates quite clearly just how bad that contrived dualism is.
Of course creationists should have know right from the start that the contrived dualism was fake. We have a 200+ year old case of it's utter failure: Newton's mechanics fails to account for the orbit of Mercury, and states it must therefore be angels. Einstein comes along and proves that "not these mechanics" /= "design."

"What they observe, infer and deduce simply leads to a logical conclusion that natural selection alone would not be able to produce such uniformity."

To add onto what @38 (Eric) mentioned:
Your statement about going from observation, to deduction is an inductive argument which I hope you realize is not logically sound. No amount of observations can ever prove a hypothesis. There will always be unobserved events that have either occured or will occur in the future. This is why science is now done in a falsificationist framework.
How would you test for your 'conclusion that natural selection alone would not be able to produce such uniformity.' If I conclude the opposite, how do we adjudicate the issue without resorting to ad hominem arguments?

Joe G,
However improbable the flagella, it clearly exists.
How much more improbable is an eternal omnipotent omniscient invisible father figure?

What is the probability that before the universe, there was an intelligent, omnipotent being? Give me odds.

By Howard Brazee (not verified) on 05 Feb 2014 #permalink

@Reginald Selkirk:

Thanks for the education. My biochemistry knowledge is certainly rudimentary. However, please edit my "all" to a "most" and my point would stand. I'm pretty confident that evolution of an entirely novel metabolic pathway would involve evolution of some new proteins.

Sean,
Follow my link in @3 and you'll find a paper discussing the formation of new developmental structures (additional flagellar whips) that allow for new behavior (hyperswarming). In that paper, the researchers present the changes in the genetic code observed (fig. 4A). But here's the point: those changes are reported in terms of amino acid residues, which is a techincal way of saying that the researchers are showing you the new proteins produced by the mutations.

So yes, evolution of new biological pathways or structures can involve the development of new proteins. But this has been observed. Just go look at the paper. Read 4A. You'll notice the letters used are not just C,G,T, and A. Why not? Because the authors are using the one-letter codes for the amino acids and showing you the differences in the amino acid chains (i.e., proteins) produced by mutant and parent strains.

Sean T #42: I’m pretty confident that evolution of an entirely novel metabolic pathway would involve evolution of some new proteins.

Yes, but it depends on your definition of "new." Enzymes may catalyze more than one reaction. Dpulication of the gene for that enzyme could then lead to a split, where one version gets further selected for one reaction & pathway, while another gets selected for the other. Would that be a "new" enzyme, or just a modified old one?

How about a modification that radically changes an enzyme? The usual example here is an enzyme which digests nylon. The mutation involved was as "frame shift" mutation, in which a small change at the gene level resulted in a big change at the protein level. Would that be a "new" protein or not?

By Reginald Selkirk (not verified) on 05 Feb 2014 #permalink

@ Blaine
Hypothesizing is redundant and useless when you rely purely on observing what's going on. Even labelling can lead to the distortion of what you observe. There is no need to apply the "test" method to coincidences because they are obvious to any observer, and there is internal logic in a series of coincidences that pertain to a certain phenomenon. Logic alone, however, is insufficient in establishing whether something is real or not because the observable can fail the rationality and plausibility tests.

Hypothesizing is redundant and useless when you rely purely on observing what’s going on.

No, it's absolutely necessary because without a hypothesis, you don't know what it's worth your time to go out and observe. There's a near-infinite number of possible things you could try and observe; hypotheses and theories guide your decisions on which observations are likely to be worth your time, and which aren't.

Let's say your refrigerator is buzzing. You want to make observations that will help you figure out why. Do you observe: (1) the moon all night, (2) your neighbor's dog's walking trail, or (3) parts of your refrigerator? Your decision reflects your hypotheses.

No to mention, we need to put new observations into an existing theoretical framework. Does it fit with what we currently know or doesn't it? If it doesn't we need to change something to make it fit.

By Michael Fugate (not verified) on 05 Feb 2014 #permalink

I'd like to hear Joe G or any ID supporter explain why, if there really is a mathematical/probabilistic problem with evolution, why aren't the world's mathematicians and statisticians up in arms about it? I don't mean hand-picked hacks - you can find isolated supporters for anything. I mean entire mathematical organizations. Your argument that mainstream biologists may have an emotional or professional bias towards evolution, but that won't work with the mathematicians. All they care about is the math, and if there WERE a mathematical problem with evolution, no power on earth could shut them up about it. Why then such silence, if not outright antagonism, to what you claim?

Occam and I agree on the answer: because you're full of it. Tell me why I, and all of htem, are wrong.

By Science Avenger (not verified) on 05 Feb 2014 #permalink

"Intelligent Design theory is not based on faith or beliefs. It is rather an observation of the reality or what’s going on (to be more exact), which involves such methods as inference and induction."

No it isn't. It's a political, watered-down version of creationism designed to get past the courts. Sorry to pull the curtain away from the man pulling the levers, but this "let's pretend" game gets tiresome after a while. The whole thing is a ruse, and its important to not forget that,

By Science Avenger (not verified) on 05 Feb 2014 #permalink

I’ve been quite busy these last few days, so I’m just catching up on this thread.

Regarding Joe G’s Positive evidence for ID: http://intelligentreasoning.blogspot.com/2014/02/the-explanatory-filter…

This is bogus. There is no evidence on this site that I can see, only argumentation. Its primary claim is to an Explanatory Filter (EF); but this “explanatory filter” is defective. The last “test” in it is to ask if the subject phenomena was “specified” which means “was it designed”. This asks one to assume that which is to be proved.

Contrary to its claim, this EF does not track “Newton’s four rules”, not even approximately. Newton’s first rule (according to the site) is admit no more causes of natural things than are both true and sufficient to explain their appearances yet any ID is a “cause” beyond that sufficient to explain. After all, any ID is itself likely to be deemed “designed”—unavoidably introducing circular reasoning.

Given the incomplete nature of human knowledge, the possibility of an as-yet-unknown cause of some phenomena is not extraordinary. To claim we already possess all significant knowledge is the extraordinary claim.

sean s.

By sean samis (not verified) on 05 Feb 2014 #permalink

I know I'm a little late to this party and others here are doing a fine job picking apart the IDists' main attempted points, but I thought this statement by Ruese above deserved some pouncing upon, not to mention repeated jumping up and down:

"...the creator, whoever or whatever it might be and is not specified, as it is irrelevant..."

The mind boggles. This is a key ID notion that I've encountered before in various forms, but I don't think I've ever seen it stated with such nonchalant baldness. It's hard to think of a less scientific attitude than that of someone who encounters supposed evidence of a mysterious creative intelligence of vast and heretofore unrecognized powers and is completely uninterested in investigating, or even speculating upon, its nature or history.

Can you imagine an archaeologist who discovers apparent artifacts of a previously unknown civilization and dismisses any possible details about its inhabitants as "irrelevant"? Or imagine an ornithologist discovering a birds' nest of previously unknown type, but who is content to simply examine and catalog the nest, uninterested in finding out about the bird that built it.

Which brings me to my next related point... what would someone who operates in this way even study? What would ID biology look like? What is there for it to do? Is every observation explained by saying, "An unknown designer designed this feature in the past by unknown means and for unknown purpose, forever to remain unknown"? And then what?

If we take the IDists at their word that all they're trying to do is follow the science where it takes them, then a position such as Ruese articulates is inexplicable. However, it makes perfect sense if they're trying to imply the designer is/was God without actually saying it (yet) - which is, of course, the central project of the ID movement.

By Michael Wells (not verified) on 05 Feb 2014 #permalink

Ruese wrote,

Intelligent Design theory is not based on faith or beliefs. It is rather an observation of the reality or what’s going on (to be more exact), which involves such methods as inference and induction. It’s not religion. It’s science that extends its reaches into what people suspect to be supernatural, like voices in mental illness, for instance.

This is wrong on many levels.

Biology (the study of life) is a science, as is Chemistry (the study of chemicals). What is ID the “study of”? Intelligent design is not an area of study, it’s a conclusion; it’s not a science.

Further, intelligent design is not reasonably regarded as science because, even in the best case it would be nigh-on to worthless. The most a legitimately scientific ID theory could do is suggest the MERE POSSIBILITY that some phenomena MIGHT BE designed. But that is always a mere possibility. It is never a presumption because further research which might reveal that the phenomena could well be “natural”. If the origin of some phenomena is in doubt, regarding it as “probably natural” is preferable; except for human-made objects, nothing has ever been found that provably not natural and we simply don’t know the actual limits of what nature can produce. The rational course is to presume that a cause will be revealed with further study. If it never is, that is a different kettle of fish.

Saying that something “appears” designed is nearly useless. When humans look at an artifact (whether a phonograph record or a flagellum) they base their opinion about its “design” on criteria like whether humans make similar items, whether we can clearly see a way to create something like the object for ourselves, or whether we never find such objects “in nature”. The latter criteria is very weak because even for the purest natural phenomena, there must be “the first time” it was seen.

Trying to deduce that a complex microscopic artifact is “designed” is even riskier. Microscopic objects frequently exhibit remarkable regularity (ex: crystals) and most of the microscopic world was invisible to us until the last few centuries—much was unobservable until the last few decades. We simply don’t have a depth of experience with it like we do with the macroscopic world.

Trying to deduce the “design” status of microscopic objects based on “uniformity with which matter organizes itself, precise coincidences that pertain to a certain phenomenon that form a distinct pattern when these coincidences are looked at from a different angle create, at least, the impression that a mere chance is too good to be true” is unreliable.

Here in lies the problem: our impression that something’s attributes are “too good” to be natural makes an uninformed assumption about what “natural” objects must be like. Flagellum are regarded (by IDers) as designed because they don’t “look natural”. Scientists see flagellum and wonder how, creationists see flagellum and think they already know. IDers don’t seek the facts, they impose a biased conclusion. Intelligent design IS based on beliefs (opinions, biases).

Michael Wells correctly noticed that whoever or whatever the ID might be is VERY relevant; especially if it is claimed that some phenomena is definitely designed. If the contrary was claimed, that something was definitely natural, no one would accept the claim that the natural process was “irrelevant”; likewise the supernatural creator is, if true, very relevant. Whatever arguments apply against the natural origin of things like flagellum; those same arguments apply with vastly greater force against the existence of an ID of life.

And as Michael noticed, if a Creator could have used evolution to create something, then why would we think the Creator exists? Or is necessary? ID could only identify objects as “designed” if evolution IS excluded.

As for the irreducible complexity of microbiological units this is all unsubstantiated conjecture. No living system has ever been proven “irreducibly complex”.

sean s.

By sean samis (not verified) on 06 Feb 2014 #permalink

I was surprised that Joe G could blithely assert that "no new protein" was produced at any time during Lenski's experiment.
What was the basis for this statement ? Did he read it in any of the several reseach papers based on the experiment ?
Or can the "Desing Inference" allows him to state confidently that no new protein will be generated by a bacteria, EVER ?

If so, then Intelligent Design Creationism is _not_ based on observation at all. Experiments are useless since ID knows the answers in advance.

The wrong answers, as it turns out. Many new enzymes, that weren't present in the original culture, have been observed in the 12 separate strains, each strain coming up with different proteins for their cell walls.
The article I linked to, http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2632098/
studied PBPs, penicillin-binding proteins, generated by Lenski's critters. And yes, they do generate new (as in modified) proteins.

So, the predictive powers of ID, if such a theory actually exists, rate as a FAIL.

Why do you guys keep up this fantasy?
The atheists who entered the fields of Origins in physics and cosmology--who went there to prove the universes parameters to a complex structure were WIDE--have conceded that the Math indicates even more Design than the universes own appearance. This universe is impossible. Thats why they introduced the laughable multiverse.
DNA, abiogenesis and the like have probabilities that are infinitely worse than the odds of the fine tuning--yet you persist? You are essentially believing in Magic at this point.

You're just digging a hole deeper and deeper into stupidity--all with smug arrogance. When the only people who buy this nonsense are the atheists who went into these fields to confirm their bias to begin with all we are left with is just a bunch of pathetic whiners who are preaching to the choir. No one buys this pipe dream.

A donkey can see chance cannot build the dna code and its operating system so why are you still wasting your time? Oh yeah..because the answer dooms you. Who concedes their own doom? We all just sit here and are astonished at the willful self deception and wonder how many irrational thoughts have to piled on top of one another to accept something virtually no rational human being agrees with.

The Universe and life were designed. You are defeated at every turn. There is simply no other viable explanation for the world as we see it. About 126 people on earth think there is an infinite magical everything maker machine that just happens to create universes out of nothing and everyone else that ever lived clearly see God. If you think one more article is gonna make everyone so crazy to believe the UV popped out of nothingness and built conscious observers, you may need to rethink things.

So if someone believes the universe is too unlikely to exist without a creator, one should postulate something even less likely to to exist, a creator that has the ability to create the universe?

By Howard Brazee (not verified) on 10 Feb 2014 #permalink

In reply to by James (not verified)

James, do you acknowlege that horses and donkeys had a common ancestor, which was a species that was neither horse nor donkry ?

James, you think that rant will convince us we are wrong? Which god is it that you clearly see? What does it look like?

By Michael Fugate (not verified) on 10 Feb 2014 #permalink

who went there to prove the universes parameters to a complex structure were WIDE–have conceded that the Math indicates even more Design than the universes own appearance

Can you point us to these published revelations by your unnamed scientists?

"DNA, abiogenesis and the like have probabilities that are infinitely worse than the odds of the fine tuning"

Baloney. No one has done these calculations correctly, because no one knows the background probabilities of the components of the formula, which is what Jason's coin flipping example illustrated. the point apparently sailed right over your head.

The process used by IDers to claim various things too improbable to occur could be used to declare every lotto winner invalid. They either don't know what they are doing, or they are lying.

By Science Avenger (not verified) on 11 Feb 2014 #permalink

In my college biology class, we are discussing Darwin's theory of evolution, and from what I understand it to be, Behe seems to not consider the probability as something that must be known in order to provide factual information on flagellum evolution. But is that really something you need to know to recognize Evolution as a plausible theory? I think it is perfectly acceptable to look at creation from both standpoints, intelligent design and evolution. But, one must be able to look at both reasonably from a scientific point of view. And as of this point in time, the theory of evolution most definitely has the most scientific evidence. Especially since we use things like protein sequencing and phylogenetic trees to compare different species and see exactly how related each is to the other. The data gathered through these things can only point to one thing.

By Ajcarpenter (not verified) on 12 Feb 2014 #permalink

@Science Avenger,

It's actually even more than that. The part that ID'ers leave out is that it's not the probability of the occurrance of evolution that matters. What is relevant is the probability of occurrance of evolution RELATIVE to the probability of some alternative explanation. It doesn't really do any good to say that the evolution of some system has, for instance, a one in a trillion chance of occurring naturally if your alternative explanation only has a probability of one in 10^18. Evolution would be a million times more likely, so we should stick to evolution in that case.

If you are postulating design, you must, at the very least, come up with a probability that the designer arose. If it's improable for complex systems to arise by natural processes, then how probable is it that a designer that is intelligent enough to create all life on earth would arise? By ID'ers own logic, this must be highly improbable. An intelligent designer must surely be a more complex system than, say, a bacterium, right? A bacterium (especially its flagellum) is much too complex to have arisen by natural processes, so an intelligent designer must likewise be too complex to result from natural processes.

If ID really wants to be scientific and not religious, the probability argument fails on this alone; evolution is much more probable than ID. Of course, ID does not really want to be non-religious, does it?

I think we are missing the point. The probability stuff is ID’s chosen field of battle. As Jason learned, if you fight on their field – you loose. Nye fought on science’s field and won. Science is based on prediction and usefulness to mankind.
What does winning mean? The goal of creationism (ID) is to have ID be a recognized science and taught in schools as a science. I think it has been shown that if 10% of population is true believers, they can sway the remainder into accepting their ideas even if those ideas destroy the society. The people they want to convince are the lay Bible Christian public. A scientist debating ID puts the win in the ID court unless the scientists can win. Talking of probabilities doesn’t do this. Science is never going to convince the true believer. But we can remind the Bible Christians of the benefit of science.

We cannot stick our heads in the sand. True believers have won in the past much to the detriment of society and mankind. If we let ID win, our children and our society will suffer. We can already see the collapse of the US coming. The replacement of the US by a faith based group that dictates beliefs will delay human progress another 1000 years like it did before.

I think we should stop referring to ID as a “theory”. That implies science. It is an unsupported speculation at best.

I totally agree with @63 John, which is why this discussion, given the course it has taken, doesn't interest me very much.

"Science is based on prediction and usefulness to mankind."
As soon as ID is capable of making testable predictions we can talk about probability. Granted, IDers have tried to make some testable predictions. They all have failed.

"The probability stuff is ID’s chosen field of battle."

Not really. Scientific method requires testing, and probability is a relatively easy test method. Removing your candidate from the arena when serious scrutiny begins is a chosen retreat.