Dr Michael Egnor challenges evolution!

So he can find design where there is none, but can't find papers on a subject when there is thousands.

Sounds like I would want to use a different doctor.

Have to say, I find the whole idea of a surgeon looking for a god in biological complexity kinda off-putting...

I think I prefer a more old-fashioned sort of surgeon. You know... the kind who think he is god.

Oh no. Dont tell Orac...

So, PZ, why don't you post this there? You are better equipped than I, a humble environmental geochemist (my BS is in zoology but very old) to counter what appears to be a full attack on Mr. Lemonick by the kooks. He could certainly use your expertise.

Oh no. Dont tell Orac...

I was just thinking that Orac won't like this.

So, PZ, why don't you post this there? You are better equipped than I, a humble environmental geochemist (my BS is in zoology but very old) to counter what appears to be a full attack on Mr. Lemonick by the kooks. He could certainly use your expertise.

PZ is probably affraid that he is going to hurt their feelings - they might call him the "pro-Darwin attack dog P.Z. Myers" again (and that is a direct quote BTW).

Nor, evidently, has he read the paper I cited in the reader comments on that blog:

Kimura, M. (1961) "Natural selection as the process of accumulation of genetic information in adaptive evolution." Genetical Research, 2:127-140.

It demonstrates that natural selection drives an increase the Shannon information content of the genome, and it's all of forty-six years old. Are these people inveterately incapable of reading the peer-reviewed lit?

I did post a comment with a link back here. They have to be approved by the author before they appear, though.

You don't need natural selection to create new information - mutation alone will do that just fine.

Nor do you need to study for years to perceive that this is true - it's obvious, and it's so very obvious that people would have to study for years to learn not to see it.

Newsweek had an article in November about antibiotic resistant infections, and how they "arise" and "develop". I wrote a short, succinct letter chastising them for not using the correct term "evolution", and how of course people can claim that they never see evidence for evolution when major news outlets don't use the proper terminology for it even when it's the entire basis for their story. It didn't get printed. I'm not surprised.

Weren't we just through this with Behe? Didn't Behe simply wave away all the material he says doesn't exist, on the grounds that it doesn't address his challenge, in his opinion? I'm confident that Egnor is staking out the same territory: Goddidit, papers claiming goddidit are disallowed by a biased establishment, papers looking for any other mechanism are completely missing the reality, and therefore irrelevant. Does anyone seriously expect Egnor to admit his faith is in error?

So he can find design where there is none, but can't find papers on a subject when there is thousands.

A combination which was of course pioneered by Michael Behe.

I just did a pubmed search for "natural selection Shannon information" and came up with not only an article demonstrating exactly what he asked for, but one available online for free to boot:

Evolution of biological information
Thomas D. Schneidera
Nucleic Acids Res. 2000 July 15; 28(14): 2794-2799.

http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedi…

"The results, which show the successful simulation of binding site evolution, can be used to address both scientific and pedagogical issues. Rsequence approaches and remains around Rfrequency (Fig. 2b), supporting the hypothesis that the information content at binding sites will evolve to be close to the information needed to locate those binding sites in the genome, as observed in natural systems (4,6). That is, one can measure information in genetic systems, the amount observed can be predicted, and the amount measured evolves to the amount predicted."

I gotta say that when I saw the title and first couple of lines of this essay, I thought it was going to be a hypothetical story, given the unusual name of Michael Egnor. So I tried reversing the letters of the last name and came out with "ronge". Pronounce it yourself.

OT and ad hominem, I know. Ironic nonetheless.

If you read through the comments, Egnor spouts a lot of other ridiculous clap-trap, showing that he knows nothing about evolution outside of what the IDists have told him.

Egnor claimed that the existence of irreducible complexity is a prediction of ID. In fact, as pointed out by Chris Ho-Stuart, it is a prediction of evolutionary theory actually made by Herman Muller, in 1918. As Elliott Sober points out in his recent article, "What is wrong with intelligent design?," it is easy enough to construct a version of ID that accommodates a set of observations already known. Sober shows in detail why that doesn't make it science.

Along these same lines are comments by Prof. Henry Schaefer of the University of Georgia, a highly-accomplished computational chemist. His inane arguments appeared in a column in the Atlanta Journal-Constitution:
Schaefer column

Here's a rebuttal.

Part of our problem is that there is seemingly a never-ending stream of this BS coming from the Creationist/ID/Magical Wahoo in the Sky'ers no matter how thoroughly or how often we refute their arguments. They just come back with something else that is utterly, or at least ultimately, void of logic, reason and evidence. I have, in actuality, argued extensively with certain of these people on various blogs to the point at which they eventually seem to shut up (although Egner seems incapable of shutting up no matter how insipid his arguments), but then they sneak back later.

The problem is that I simply don't have time to deal with them every time I see them bringing it up (which they often do in subtle ways to infect otherwise rational conversations), having a real job that addresses actual scientific issues of importance and all. I assume that most of us who read/blog on Pharyngula have the same situation (frankly I'm a little surprised that a brain surgeon has time and isn't busy continually honing skills in his actual area of knowledge).

Maybe we need to form some sort of tax-exempt organization that pays intelligent graduate students to counter this nonsense when it arises. If one of us spots something that is putatively aberrant with regard to science and promotes their presumptive "big guy in the sky" instead, then we notify the students to attack with logic and evidence. We certainly need something to counter the nonsense that is so prevalent in this very oddly-turned society of ours.

Quite frankly, the brain is far too complex to be understood. Certainly far too complex ever to hope to repair - especially via surgery. Anyone saying otherwise is a fraud and a liar and is under the spell of the radical fringe BrainSurgeonists - clearly a cult. There should be new rules that allow me to experiment with this demented idea - I'm sure that if I can demonstrate my inability to do brain surgery then I will completely prove once and for all it can't be done.

This is all an elitist plot against those of us that know, really deep down know in our guts, that leaches and blood letting are the only answers. If this wasn't so why would God have given us leaches and sharp objects.

So, creationists in the US dont seem to like evolution.
That's something disturbing to me, because it's really at the very core of everything that we are, all the Darwin stuff aside.
To explain what I mean, I need to clarify my view of what evolution is.

Evolution is a strive to better oneself, because you admit that you are not perfect.
If you have that strive within you, you will evolve as a human being and a as a person.
What evolution theory is saying is that all of reality has that urge to improve itself.

American christians creationists claim that our world and us humans where all created perfect to begin with, and the Lord wouldn't try to, or need to, improve on his creation.

That in itself kinda kills of the very idea of religion, now doesn't it?
According to christianity, man is a sinner and far from perfect, and the entire purpose of religion is for man to better himself.
I'm saying that maybe evolution is for nature what religion is for man in that sense.

Darwin claimed that the features that was most useful and enrichening for a spieces would flourish and that features that didn't made for a better survival - not only mere survival, because a number of the spiecies that died out could make it through the day already, only not good enough - would fade out and die.

He also claimed that this was a focused process that dumb luck could only interfere with on a very short-term basis, so it's a fair process.

Now, the entire of reality tries to improve an better itself, and the end result are some deeply humanistic values developed by a spieces that wont satisfy itself with mere survival, and which continuesly through history fights bitterly against forces like nazism, slavery, racism, rape, and mindless violence of any sort, forces that represents it's past and something it desperatly tries to shed.
Now, that's what happened sientifically speaking, because that's where we are right now, and therefor that's what evolution ended up producing, and sience will have to account for that fact whether they like it or not.
So, here we are then, after some 60-40 000 years of trying to better ourselves, and continuing a process that spanned all life that we know of since the dawn of time.
And this is an evil force, is it?
An evil force that encompasses the entire reality of this world, and every living thing on it?
No it's not, because regardless how this happened, sience and religion are facing the same facts and the same end results.
It's almost non-important who's right, considering this.

Some will jump in and say that religion played a big part in this effort to evolve humanistic values and democracy, and that's my point, regardless how I view that statment.
It's can be described that way, yes, from one point of view, and it's also evolution at the same time - because that's the very meaning of the word.
To evolve.

So, what am I missing here?

If it's in the very nature of our world, our reality, to improve itself, then what in Gods name is the conflict?

Well, the Bible kinda says that the world just ain't that old - not directly, but it kinda suggests that it isn't.
That's one hell of an argument..not.

Well, here's a thought, the good book says that it's to be read plainly, it actually instructs the reader to do so, for it not to be misread, or something.
So, it's probably not supposed be "decrypted" that way, so that one can assume stuff that isn't really there, like claims of the earths true age, because I've checked, and I can't find any such claim.

And in any way, the catholics probably know more about this than I do, and the good Pope agrees with me.
The true message is how man should relate to God and nature, and it's not about engaging in some obscure statistical mathematical excercises.
If God wanted us all to be mathematicans, he would have made us much better scientists, and that can't be right, can it?

Right!

Typical crap from people who have egos so big they think they must have been designed by god.

I am asking a simple question: show me the evidence (journal, date, page) that new information, measured in bits or any appropriate units, can emerge from random variation and natural selection, without intelligent agency.

Actually, if you know how to translate this request correctly, you won't bother messing around looking for citations from PubMed. What we need is someone competent in math and statistics who has the time to fiddle around for a while playing with equidistant letter sequences in the Book of Genesis.

Mikael Bergkvist wrote:

What evolution theory is saying is that all of reality has that urge to improve itself.

Uh oh. Will I be the first to point out: "No. No, that is not what evolution theory is saying at all. That is a distortion of the theory as filtered through a spiritual mindset, and promoting this as the way to 'reconcile' science with religion will not only be unscientific, but will end up causing more misunderstanding, confusion, and problems, rather than less?"

Depends on how fast I can type, and who else is online, I think.

Oh no. Dont tell Orac...

Too late. I've been aware of Dr. Egnor for a few days now, because he's been even more of an idiot of himself than usual. It's so depressing that I don't know if I'll even bother to blog about it. There seem to be so many damned idiot surgeons falling for this crap that I have a hard time working up a healthy head of Respectful (or not-so-respectful) Insolence about it right now.

"That is a distortion of the theory as filtered through a spiritual mindset"

No it's not.
It depends on how you define "improve", but if there's no curve of increased density of information, then evolution becomes a flat line, and the word itself pointless.

No doubt Dr. Egnor will show up in the comments here if PZ's link is approved.

Should I go and get the paper bag for my head again, after our orthopedic surgeon "friend" Dr. David Cook embarrassed me for the ignorance about basic biology that so many of my profession seem to like to trumpet to the world?

Oh, and, of course, they will accuse me (and PZ) of being "uncivil," as well.

I plead that, after refuting the same canards over and over and over again, I have come to lack the patience to be nice to antievolutionists, particularly when I've been on call for the past six days and am presently sitting around waiting for a patient to hit the ER.

"causing more misunderstanding, confusion, and problems, rather than less?"

You ended that with a question mark, and that says it all, I think. :-)

Sometimes we need to IGNORe the EGNORs of the world. Sometimes we need to expose them to their peers and this is probably Orac's job.

Mikael, I don't have the time or spirit to refute your every point but I have to say you have a basic misunderstanding of what we are discussing in terms of evolution. (Others, please forgive my oversimplifications herein). Biological evolution doesn't have some vague notion of "betterment" in mind, it is merely a response in terms of the reproductive success of individuals within a group to pressures and habitat stresses upon potentially varying organism phenotypes. Certain types of stressors might result in certain phenotypic variants being more reproductively successful within that environment. Should the stressing variable persist, physical isolation occur, etc., then the changes might become dominant and persistent within that subgroup of the population. Sigh. Etc.

Ah, but how many of these papers give units for this elusive quantity, "information"? You'll note that is what he was asking for - not that mutation can produce new functions, structures or alter/improve old ones, so he gets to keep his point of view. Of course, he really ought to tell us what he means by "information" and why it is required.

"Biological evolution doesn't have some vague notion of "betterment" in mind, it is merely a response in terms of the reproductive success"

I know that, I went to school like everyone else here.

Regardless, it's the result that we see, and I'm not saying it's any thought behind it mind you, but it's how it ends up that interests me.

My point is that christians are taking a stand against evolution on a unsound theological ground - and their point of view is theological, is it not?
Their basis of critique flies in the face of the very purpose of religion, which is betterment, or evolution, and the word has an actual meaning you know, regardless of how that happens, whether it's a result of actual thought or of how nature is set up.
Therefor, it's not logical for christians to react this way.
They should expect evolution in some form or another, but instead they react as if they think they are already perfect and dont need to better themselves.
- It's just not what the good book says they should do, and I wanted to point this out.
Sofar, science is the only one expected to explain itself, and maybe it's time to turn the tables.

.. and why in goods name did you feel that you had to explain evolution to me?
It's not like it's not common knowledge.
Insulting people is not very productive, and that's a free advice from me.

They should expect evolution in some form or another, but instead they react as if they think they are already perfect and dont need to better themselves.
- It's just not what the good book says they should do, and I wanted to point this out.

So you are a christian endeared with evolution?
Not sure this is the right place to come gunning for god, even when endorsing evolution. ;-)

I explained it because the underlying premise of your lengthy post incorrectly posited betterment with the processes of biological evolution in your statement, particularly the last sentence below:

"Evolution is a strive to better oneself, because you admit that you are not perfect.
If you have that strive within you, you will evolve as a human being and a as a person.
What evolution theory is saying is that all of reality has that urge to improve itself."

I find the argument about "complexity" perhaps the stupidest argument ever. I'm not an engineer, but I work with many of them. One hallmark of a well-designed process is simplicity, not complexity. Something with a lot of parts that all must work is a recipe for a process that breaks down a lot.

After reading the DI story (and that truly is what it is, is it not?), it's just their usual "we look for any 2-second-long excuse to prove evolution wrong" vitriol.

All the elements are there for the preaching and self-victimization to take place:

- dissenting "scientists"
- touted up figures on the numbers of "dissenters"
- statements from said dissenters ringing the same ol' creationist bells about Darwin's theoretical inadequacy
- assertions that Darwin's theory "crumbles" by the minute
- assertions of questions tens of thousands (indeed likely more) of scientists have somehow completely overlooked for 150+ years
- hollow calls and encouragement for "real scientific inquiry" and consideration
- et al ad nauseum

Every single creationist/ID article asserting evolution's fallacy follows this same pattern. I certainly hope Mr. Egnor comes over and asks his questions, because he doubtless will be given the research for the very answers he seeks.

To clarify..

"So, creationists in the US dont seem to like evolution.
That's something disturbing to me, because it's really at the very core of everything that we are, all the Darwin stuff aside"

So, aside of the evolution theory, we have the generic evolution concept in itself, and it puzzles me that christians react so violently to this at all, since science as a whole seem to be ok by them.
They dont seem to mind microwaved food or cars, or tv for that matter, all products of sience.
It's the notion that creation needs to 'better itself' that somehow insults their belief that God is perfect, that maybe he didn't 'get it right from the start', but this is where they loose me, because the Bible clearly states that man and the animals are anything but perfect.
- Christianity exists solely to correct man, infact.
So, being in their mindset, I dont really get how they arrived at this point of view.
I'd like someone christian to explain that to me.

Why is evolution such a problem?

--

Aside of that, I'm not going to endure further lessons of common knowledge.
Thanks.

"So you are a christian endeared with evolution?"

*Sigh*, no.

I'm just curious about this very wierd mindset of theirs, because I can't identify the source of it.
How the hell did they arrive at it?

Went looking for some information/background on Dr. Egnor and found this perhaps pretinent statement--by none other than Jesus himself.

It seems that Dr. Egnor and his friends at Discovery Institute, Focus on the Family, and other organizations and persons that feel that their worldview is threatened by "just a theory" (read: heresy) as natural selection would agree with this revelation which heads a reposting of the great mandate of the 700 at the blog "Our Lady Of The Roses" by "Baysides":

http://curezone.com/blogs/m.asp?f=159&i=358

Quote:

Ranks of renowned scientists doubting Darwin's theory on the rise - 700 now on public list...

Only One Creator...

Ranks of renowned scientists doubting Darwin's theory on the rise - 700 now on public list...

"Man shall not create a new world as he seeks. For there cannot be a lasting world without His God. And I speak not of the false idols and gods that man creates in his human nature! There is only one Creator....
"Little by little you go forward--I say, little by little, but I should stress that many is running fast and faster to the edge of the abyss. In his seeking for power and knowledge, man seeks to dethrone his God and create his own god. But who shall set himself above his Creator, even attempting to control birth and death? I say unto you, you shall never learn the secrets, the sacred secrets of death and life, for these are controlled by the Eternal Father."

- Jesus, February 10, 1978

(snip)
Unquote.

Jesus said it, they believe it, that settles it.

Posting also includes a definitive image of YHWH doing his creation thing. (His beard strangly seems evocative of Darwin's in several depictions.)

This site seems to pass along various visions and revelations received by one particular sect of the faithful, with a strict adherence to their own true catechism.

By their words ye shall know them.

Couple things I've noticed today..

1st, Disco has discovered the Time blog too:
http://www.evolutionnews.org/2007/02/times_magazines_darwinist_thou.html
I actually only clicked on the Google news link to get the actual link for the DI blog.

2nd, following the links on the Creationist sites I got to this article (http://www.tldm.org/News8/evolutionAntiScience.htm) that appears outright upset that we have advanced out of the medieval times:

The medieval man understood the concept of a Creator, a concept which, despite the continual discoveries of our universe's complexity, is paradoxically losing ground today.

Yes, we are much less superstitious today. We haven't burned a witch in years. What a shame...

Coincidentally, today, a surgeon who knows a lot about appendices debunks creationist "facts" about the human appendix.

Maybe I can't understand their mindset simply because there's no mind to be set..

Maybe we need to form some sort of tax-exempt organization that pays intelligent graduate students to counter this nonsense when it arises.

As an underpaid graduate student, I would be very pleased to be involved in such a program. I occassionally consider myself "intelligent" (at least as intelligent as their moronic designer, anyways), and I spend far too much time on-line reading and responding to IDiot claptrap already.

If I register myself as a charity, can the Pharynguloids please send me a cheque the next time I tackle one of these asstards?

Does anyone have an estimate of how many scientists there are in the world? I'm thinking of the "classic" sciences here--like biology, chemistry, physics, etc--not the social sciences.

For what it's worth.. the people defending ID refer to the complexity of information as their argument, and this is perhaps the oldest trick in the book.
It's essentially the Chewbacka defense from the now famous eisode of South park.. "It makes no sense, so please ignore all the other parts of this case that does make sense.."

Bang, heads explode..

Evolution is not a theory of how life has come into existence, it's about how it evolved *once it did*, and the amassed evidence of evolution taken place, from dated archeological findings to correlating features inbetween spieces, is basically irefutable, unless you are a complete nitwit.

Nature has driven evolution forward, and we can see features evolve layer by layer, there's no point in denying it by lazy observations of DNA, which we dont even fully understand yet, and therefor cannot draw any conclusions from, supporting either viewpoint.

We can't test DNA according to predictions unless we know the mechanisms well enough to evaluate the results properly, we dont even know for sure if 'junk DNA' really is 'junk'.

Any claims by ID'ers relating to the complexity of DNA is therefor void.
It's the Chewbacka defense.
We dont get this part, so we'll skip the rest too.

Complexity that we do not fully understand yet, set against facts and findings from dated rock that we understand completely, and can test in a multitude of ways in accordence with both physics, anatomy, and chemistry, all established fields of science.
The choice is pretty obvious.
It's not that evolution does not have unanswered questions, but that it has a wealth of answered questions, and in that, it's similar to all scientific fields.
- In comparison with astrophysics, wrestling with dark matter and dark energy, it's downrigth easy to understand.

This simple fact tends to get lost all the time for some reason though, especially when discussing the matter with those of faith.
They also tend to lock down on the 'fact' that evolution cannot explain how life came to be - ignoring the fact that this theory doesn't have to explain that.

From the point in time when life appeared, regardless of how it happened, evolution has left very visible footprints behind, embedded in solid rock.

I have a copy of the NSF's Science and Engineering Indicators for 1998 (I've also got some more recent editions, but they started distributing them on CD; the paper copy is so much easier to work with). In the US, there were 3.3 million scientists and engineers working in 1998. About 40% are engineers, 10% biologists, 9% physicists and chemists, 10% social scientists, 30% math and computer scientists.

This is a US-centric document, so it doesn't say much about other countries. It does mention that about 20% of the science degrees in the world are issued by the US.

I don't know how many scientists there are in the world. However, 93% of all scientists in the US Academy of Sciences do not believe in any God.

[Cheap shot warning]

I think we now have a new term for surgeons and other medical practitioners who flaunt their medical credentials while saying stupid things about science:

"EGNORamuses"

[We now return you to reasoned debate]

everyone here is quick, to point out fallacious arguments, and provide counter-claims. these rebuttals only serve a purpose if the proponents of ID are truly ignorant. i think there's a case to be made for deliberate deception on their part. spamming the net with pro-ID pages advances their agenda. I'm no expert on him, but i've heard leo strauss, an influential political science professor at harvard openly advocated lying to constituents, if it could be considered in thier best interests, ie. "saving souls"

Most humorous is Egnor's confidence that because he hasn't received answers to his satisfaction in the comment section of a weekly, general interest, pop'lar news magazine's blog, "Darwinists" have no answers.
Although I'm disappointed in Lemonick, in that he could have pointed readers in the right directions in his responses (which he appends at the end of others' posts). Instead he's feeding chum to the self-caged.

PZ, I think you should post your comment left at the "Time Mag" site here so that we can see it now, and craft seperate responses.

PS: I hope it is not just a link back here. That would be weak.

Part of the problem comes from writers and readers who think that the "biomedical" community is a single homogeneous pool of experts and expertise.

Not all doctors are scientists. Not all scientists are doctors.

Different paradigm. Different methodology. Different education. Different literature.

The medical profession USES some results from Biology, the same way that Engineers and Technologists use some results from pure Science.

But doctors are trying to prevent disease, ameliorate suffering, and not trying to do research on humans.

Does it matter if the airline pilot on your next flight has a PhD in Aerodynamics? Do you care if the guy spraying insecticide to kill termites is an Aerosol Sciences researcher? Do you care if your auto mechanic does Combustion Science research? Do you care if the guy who mows your lawn is a Botanist?

Once I had to have some stitches taken out of a wounded hand. A friend at the time said: "Why go to a doctor? You're a Scientist, right?"

Do you care if the President and Vice President of the United States are Political Scientists or Cliometric Researchers? Oh, never mind about that one. Too late.

For more ignorant ranting about evolution:

http://tinyurl.com/2wsmyj
(http://www.townhall.com)

In medical school we had a joke, "Q: Why don't surgeons have hemorrhoids?

A:God made them perfect Ass Holes."

Very popular at psychiatry faculty parties.

The come back is, "Q: What is a surgeon?

A: A physician able to finish training."

For more ignorant ranting about evolution:

http://tinyurl.com/2wsmyj
(http://www.townhall.com)

"Once I had to have some stitches taken out of a wounded hand. A friend at the time said: "Why go to a doctor? You're a Scientist, right?"

Good question. 33 years ago, I had some 30 odd stitches to remove from my scalp. I taught my wife to do it. If I can reach them, I do it myself. Putting them in is a different matter.

What was your friend's point?

Gary Hurd: What was your friend's point?

I thought at the time that he didn't know a scientist from a doctor. But you cast reasonable doubt on that hypothesis. I suppose that I could have removed the stitches myself, but I had a scientist's doubt that there might be something necessary that I didn't know, such as what symptoms of complications to look for, given that 2 specialists had examined the freshly bleeding wound at the Royal Hospital in Edinburgh, Scotland, to make sure that there was no damage to my future ability to type (and thus continue to earn a living).

Doctor, will I be able to play the violin when I recover from this injury?

PZ, your reply to Egnor makes no sense.

Egnor's question was in the context of the genetic code: from whence comes the symbolic representation of amino acids by nucleotide triplets?

Your reply was to google "gene evolution duplication". I fail to understand your line of reasoning. Please explain.

Let's look at Egnor's question.

Egnor: "Can random heritable variation and natural selection generate a code, a language, with letters (nucleotide bases), words (codons), punctation (stop codons), and syntax?"

Egnor: "In 150 years, Darwinists have failed to provide even rudimentary evidence that significant new information, such as a code or language, can emerge without intelligent agency."

Egnor: "I am asking a simple question: show me the evidence (journal, date, page) that new information, measured in bits or any appropriate units, can emerge from random variation and natural selection, without intelligent agency."

My response to Egnor: Your question is misguided. Of course random heritable variation and natural selection are inadequate to generate the genetic code that is itself the source of heritable variation. Realize that the theory of evolution by natural selection does not seek to explain the origin of the genetic code. There is not yet a consensus theory for the origin of the genetic code. The inadequacy of the theory of evolution by natural selection to explain the origin of the genetic code is not a problem because the theory need not explain every biological phenomenon to be useful. Scientists who loosely speak of evolution as if it were a catchall umbrella (e.g. "Nothing in biology makes sense except in the light of evolution.") are not correct. The light of evolution illuminates only a limited domain of biological phenomena and the origin of the genetic code lies outside that domain.

I wonder if there's some sort of pattern to the stooges and shop-dummies the ID Creationists find to parade around. Eg enough of one such that some (evolutionary?) computer software could make reasonable predictions over whom they'll target next (and perhaps allow that putative posse of impoverished students a chance to head them off at the pass instead, with a spot of remedial education).

PZ, your reply to Egnor makes no sense.

Egnor's question was in the context of the genetic code: from whence comes the symbolic representation of amino acids by nucleotide triplets?

Actually, PZ's answer perfectly addresses the question that appears in the quote. The fact that Egnor throws out a bunch of other, mostly unrelated claims doesn't mean that PZ is on the hook to provide an answer for all of them. People like Egnor use that tactic precisely because it's very difficult to address multiple, randomly strung together claims all at once.

It's clear though that Egnor thought he had a knock-down argument by saying that new "information" could not evolve. Most ID flunkies would know better than to use that one. It's the kind of claim that can be easily addressed with empirical evidence.

Q: Doctor, will I be able to play the violin when I recover from this injury?

A: I don't see why not.

Q: That funny, I never could before!

Marx brothers, IIRC.

"i think there's a case to be made for deliberate deception on their part. spamming the net with pro-ID pages advances their agenda. I'm no expert on him, but i've heard leo strauss, an influential political science professor at harvard openly advocated lying to constituents, if it could be considered in thier best interests, ie. "saving souls"" -Jaydee

Jaydee: Ronald Bailey had a nice article on this, coincidently in the context of neo-cons advocating intelligent design:

http://www.reason.com/news/show/30329.html

I have a degree in electrical engineering, so most of the time, I'm simply trying to absorb all the biology on this blog.

But the challenge from Dr Egnor is purely a mathematical one, so step aside, biologists - he asks how new information, measured in bits, can emerge from random variation. He also asks for a specific journal cite. Since a mathematician hasn't answered this yet here, an EE will have to do as a substitute.

The amount of information in a message is determined by its complexity, and the very essence of complexity is randomness. A string of one million bits (ones and zeros) that simply alternate 0-1-0-1-0-1-0-1... has very little complexity, thus very few bits of information. But generate that series of one million bits randomly and guess how many bits of information you have? Answer: very close to one million.

Random changes to genes almost always increase the mathematical complexity, and thus the bits of information, in the gene. Of couse, it's then up to natural selection to filter out which of those mutations are viable.

Instead of a journal article for Dr Egnor, he just needs to read a little in an undergraduate textbook on information theory.

Random changes to genes almost always increase the mathematical complexity, and thus the bits of information, in the gene. Of couse, it's then up to natural selection to filter out which of those mutations are viable.

This is all good and true, but the underlying, insidious nature of the argument has nothing to do with actual information theory (Dembski and Scordova claimed to have revolutionized the field with their own quantifications but have thus far failed to even semi-rigoriously define anything recognizable to any professionals in the field). All it is is a recycled version of the "2LOT disproves evolution" permuted with irrelevant jargon.

FYI: The current edition of the NSF Science and Engineering Indicators (2006) can be found online at http://www.nsf.gov/statistics/seind06/

A very handy reference tool.

There are 2807 papers indexed by PubMed on this subject. Michael Egnor has been unable to find any of them...

Even more strange, Michael Egnor won't be able to find these publications, even if you print 'em out and whack him on the head with them! I think this phenomenon itself demonstrates evolution, don't you think?

Part of the complaint of the "Damn it Jim, I'm a Doctor, not a Scientist" and one of the commenters -- I mention no names -- is that it's hard for an uneducated person to understand how the mechanism of evolution itself can evolve, and so, in some half-assed recursive intuition, if evolution can't evolve the mechanism of evolution in a way that a fool can guess, then evolution must be wrong.

Here's the head-end of a neat paper on how real scientists considers the issue.

===============

Robustness Can Evolve Gradually in Complex Regulatory Gene Networks with Varying Topology

Stefano Ciliberti1,2, Olivier C. Martin1,2,3,4,5, Andreas Wagner6*

1 Laboratoire de Physique Théoique et Modèles Statistiques, Universite Paris-Sud, Orsay, France, 2 Centre National de la Recherche Scientifique, Universite Paris-Sud, Orsay, France, 3 Laboratoire de Genetique Vegetale du Moulon, Universite Paris-Sud, Gif-sur-Yvette, France, 4 L'Institut National de la Recherche Agronomique, Universite Paris-Sud, Gif-sur-Yvette, 5 Centre National de la Recherche Scientifique, Universite Paris-Sud, Gif-sur-Yvette, France, 6 Department of Biochemistry, University of Zurich, Switzerland

The topology of cellular circuits (the who-interacts-with-whom) is key to understand their robustness to both mutations and noise. The reason is that many biochemical parameters driving circuit behavior vary extensively and are thus not fine-tuned. Existing work in this area asks to what extent the function of any one given circuit is robust. But is high robustness truly remarkable, or would it be expected for many circuits of similar topology? And how can high robustness come about through gradual Darwinian evolution that changes circuit topology gradually, one interaction at a time? We here ask these questions for a model of transcriptional regulation networks, in which we explore millions of different network topologies. Robustness to mutations and noise are correlated in these networks. They show a skewed distribution, with a very small number of networks being vastly more robust than the rest. All networks that attain a given gene expression state can be organized into a graph whose nodes are networks that differ in their topology. Remarkably, this graph is connected and can be easily traversed by gradual changes of network topologies. Thus, robustness is an evolvable property. This connectedness and evolvability of robust networks may be a general organizational principle of biological networks. In addition, it exists also for RNA and protein structures, and may thus be a general organizational principle of all biological systems.

Funding. This work was supported by US National Institutes of Health grant GM063882 to AW, by the European Economic Community's (EEC) FP6 Programme under contract IST-001935 (EVERGROW), and by the EEC's Health Protection and Promotion under contracts HPRN-CT-2002-00307 (DYGLAGEMEM) and HPRN-CT-2002-00319 (STIPCO).

Competing interests. The authors have declared that no competing interests exist.

Editor: Roy Kishony, Harvard University, United States of America

Citation: Ciliberti S, Martin OC, Wagner A (2007) Robustness Can Evolve Gradually in Complex Regulatory Gene Networks with Varying Topology. PLoS Comput Biol 3(2): e15 doi:10.1371/journal.pcbi.0030015

Author Summary

Living things are astonishingly complex, yet unlike houses of cards they are also highly robust. That is, they have persisted for billions of years, despite being exposed to an endless stream of environmental stressors and random mutations. Is this robustness an evolvable property? Do different biological systems vary in their robustness? Has natural selection shaped this robustness? These questions are very difficult to answer experimentally for most systems, be they proteins or large gene networks. Here we address these questions with a model of the transcription regulation networks that regulate both cellular functions and embryonic development in many organisms. We examine millions of such networks that differ in the topology or architecture of their regulatory interactions, that is, in the "who interacts with whom" of a network. We find that radically different network architectures can show the same gene expression pattern. The networks' robustness to both mutations and gene expression noise shows a broad distribution: some network architectures are highly robust, whereas others are quite fragile. Importantly, the entire space of network architectures can be traversed through small changes of individual regulatory interactions, without changing a network's gene expression pattern. This means that high robustness in gene expression can evolve through gradual and neutral evolution in the space of network architectures. Our results show that the robustness of transcriptional regulation networks is an evolvable trait that natural selection can change like any other trait.

===============

As a computational biologist in my so-called spare time, I think that is so very cool!

I think this phenomenon itself ...

I thought that "deserves (empirical) investigation" was going to follow that feeder line.

"A string of one million bits (ones and zeros) that simply alternate 0-1-0-1-0-1-0-1... has very little complexity, thus very few bits of information. But generate that series of one million bits randomly and guess how many bits of information you have? Answer: very close to one million."

Curt, I'm not sure what definition of information you are using. In my area (neuroscience) we tend to use Shannon information from my experience, where a purely random sequence is defined as having exactly zero information. A repeating sequence like you listed would have low information, but more than zero. I am not an expert, but I can't imagine a definition of information that can have a purely random sequence containing large amounts of information. Such a definition would have no correlate to actual useful information.

To me one can think of information in a sequence as your knowledge of what is generating that sequence based on the content of the sequence. That is intuitively what information means to me and when translated into mathematics is basically what Shannon information describes. If that is the case then a sequence you know is purely random will tell you nothing about what is generating it. You can come up with whatever definition of information you wish, but I think the key to any definition of information that is meant to agree with our use of the word is that it gives some relationship between inputs and outputs, which a purely random sequence as an output does not.

The article by Ronald Bailey, referenced by Middle Professor, although fairly old, suggests something I have long suspected - that at least part of the reason that some creationists of all stripes propogate their lies not necessarily because they believe them themselves, but because they think that society will fall apart without letting the masses have their beliefs. I find this rather ironic considering the common "elitest" claim made about liberals, given that it seems that at least some conservatives believe that the people will not be able to control themselves without believing (what they themselves believe is) a lie.

Is it possible that otherwise intelligent people like Dr. Egnor (for starters) actually think that they are preventing the breakdown of our social fabric by coming up with their demonstrably false satements? I guess that's a laudable goal, but too close to "ends justifying the means" philosophy. Additionally, I would say that religious societies historically have broken down just fine without the aid of evolution. Having a society that is religious is no guarrantee of stability.

Note: in suggesting this, I am leaving out shills making money on this BS such as Dembski from the "laudable" efforts.

Curt, I'm not sure what definition of information you are using. In my area (neuroscience) we tend to use Shannon information from my experience, where a purely random sequence is defined as having exactly zero information.

The definition of information used by Curt is a standard one - Shannon entropy will be maximized for a completely random sequence. There is clear relationship between compressibility (e.g., by zipping software) and information content. A repetitive message (e.g., 0-1-0-1-0-1...) is highly compressible while a random message cannot be compressed without losing information.

That is why the ID crowd propose "complex specified information" or CSI - which might an interesting concept if it could be defined in an objective manner (of course, the assertions of ID proponents that mutation+selection cannot produce CSI are BS). Shannon entropy or Kolmogorov complexity doesn't tell you whether any biological information you are looking at is functionally important.

But this gets at the bigger issue of why Egnor's question is problematic. The mapping between genotypic information and phenotype is incompletely understood, so asking somebody to demonstrate the mutational events that led from organism X to organism Y is absurd. So we are left (for now) with the question of whether the amount of new information generated by various mutational processes (point mutation, insertions, duplications, rearrangements) is sufficient to explain the differences among organisms in complexity.

The amount of information generated by mutational processes - combined with the sieve of natural selection - appears to be sufficient. But that is hardly convincing to somebody who is refusing to believe for deep-seated psychological reasons. After all - the evidence for quarks is pretty solid. But do you think that somebody would buy asymptotic confinement if it contradicted their holy book? Wait... didn't Jack Chick have an issue with quarks or gluons?

Yes, TheBlackCat, you are very confused. Chuck your intuitions immediately because they have lead you very badly astray.

From Shannon's 1948 paper:
cm.bell-labs.com/cm/ms/what/shannonday/shannon1948.pdf

"The fundamental problem of communication is that of reproducing at one point either exactly or approximately a message selected at another point. Frequently the messages have meaning; that is they refer to or are correlated according to some system with certain physical or conceptual entities. These semantic aspects of communication are irrelevant to the engineering problem. The significant aspect is that the actual message is one selected from a set of possible messages."

from Shannon, Claude E. and Warren Weaver, _The Mathematical Theory of Communication_, The University of Illinois Press, 1949, page 10

"A physical system, or a mathematical model of a system which produces such a sequence of symbols governed by a set of probabilities, is known as a stochastic process [i.e. "random" -Foggg]. We may consider a discrete source, therefore, to be represented by a stochastic process. Conversely, any stochastic process which produces a discrete sequence of symbols chosen from a finite set may be considered a discrete source."

Shannon defines information as the probability that a message will be received from a pool of possible messages. It's just a measure of the probabilities that sequences of symbols will be reproduced at the receiver. Shannon information is created every time the probabilities vary. The most unpredictable messages (equivalent to the most "random" messages) have the maximal Shannon "surprisal" and thus the maximal Shannon information. (Selection changes the probability distributions, and so creates information all the fricking time. This information=meaning is a naive terminological scam being played either by Egnor or on Egnor.)
There's no information measure (Shannon or Kolmogorov-Chaitin or Fischer etc.) that relates to the meaning of a pattern in any way. The most efficient encodings have statistics that are hard to distinguish from random noise. In the Shannon-Weaver sense, gene duplication results in more "information" as the compressibility of the message is decreased (in the K-C algorithmic information sense, the length of the descriptor increases).

I am not an expert, but I can't imagine a definition of information that can have a purely random sequence containing large amounts of information. Such a definition would have no correlate to actual useful information.

This is incorrect. Information in it's algorithmic (K-C-S) formulation is exactly that. Randomness, in terms of incompressibility, is the exact measure of information. Therefore, a long and yet incompressible string has a high algorithmic information content.

Also being in neuroscience, let me clarify the information theory perspective we have. When TheBlackCat said that a purely random sequence has zero information, what he might have meant is that a channel with so much noise that any message sent through it comes out completely uncorrelated will have zero information. This is because the rate of information transmitted in a message communicated over a channel is:
Rate = H(x) - Hy(x), where H(x) is the entropy of the message, Hy(x) is the entropy of the noise (aka ambiguity of the signal), and all are measured in bits.

Thus, for a channel with no noise, the rate of transmission will be equal to the entropy of the message (Hx). Any kind of noise on the line (Hy)will decrease the rate of information transmission.

I think the confusion comes from whether or not you assume the channel has zero noise on it. In many cases it is an unspoken assumption.

Mind you, to solve for these one must know the conditional probabilities of the signal put into the channel (stimuli into nervous system) with the output of the system (firing of a neuron). When done over many trials, one can estimate the rate of information transmitted.

Another important point with Shannon information is what your symbol set is. In the case of a signal such as 0101010101..., if your symbol set is 0 and 1, then there is an equal probability of either symbol occurring and your Shannon entropy will be:
prob0*log2(prob0) + prob1*log2(prob1)
-(0.5*log2(0.5) + 0.5*log2(0.5))
-(0.5*-1 + 0.5*-1) = 1 bit
However, if you instead define your symbol set as 00, 10, 01, 11 then it works out to:
-(prob00*log2(prob00)+ prob10*log2(prob10)+ prob01*log2(prob01)+ prob11*log2(prob11))
-(0+0+1*log2(1)+0) = 0 bits
These differences lead to optimal coding theories and such.

If ever there was a site that demonstrated The Church of Evolution to be as dogmatic and self-righteous as any of its "competitors," this is... by God (*wink*)... it. Though it's likely wasted bandwidth and time for it to be posted here, it is evident that you're not so different from the Reverend Phelps mentality as you may like to think, my friends. *sigh*

The whole Egnor kerfluffle does have its amusing aspect. Telic Thoughts claimed, in a post, that the fact that Egnor doubts evolution means that Dobzhansky's quote "Nothing in biology makes sense except in light of evolution" is wrong. Apparently being a brain surgeon is the precise same as being a biologist. Which means that being a surfer or plumber is the same as being a specialist in fluid mechanics, being a car mechanic is to be a specialist in Newtonian physics, being an electrician makes you an expert in the physics of electricity and magnetism....

If ever there was a site that demonstrated The Church of Evolution to be as dogmatic and self-righteous as any of its "competitors," this is... by God (*wink*)... it.

Evidently you meant to type, "I'm far too dim to make any attempt to understand any of the large amount of actual scientific content posted on the site, so I'll just parade my fashionably inane 'open-mindedness' instead." Hope this helps.

When I finished reading it, I haven't already satisfied, because the writing is not a full version of experiment result. So, I still have some question about it.

I think that gene duplication is another name for genetic mutation, because the result of "gene duplication" mentioned in that writing is this: 'The duplications described consist of two alleles of ace-1, one susceptible and one resistant to insecticide, located on the same chromosome'. This is not duplication. This is mutation. Then why the researchers didn't use genetic mutation term for their title's writing? Here are the reasons:

1. Israeli biophysicist Lee Spetner said: Evolution cannot be built by accumulating mutations that only degrade specificity, (Dr. Lee Spetner, "Lee Spetner/Edward Max Dialogue: Continuing an exchange with Dr. Edward E. Max," 2001, http://www.trueorigin.org/spetner2.asp )

2. The genetic change that could illustrate the evolution theory must not only add information to the Mosquito Culex pipien's genome, it must add new information to the biocosm. The horizontal transfer of genes only spreads around genes that are already in some species.

3. The evolutionist biologist Francisco Ayala said: 'The genetic variants required for resistance to the most diverse kinds of pesticides were apparently present in every one of the populations exposed to these man-made compounds', (Francisco J. Ayala, "The Mechanisms of Evolution," Scientific American, Vol. 239, September 1978, p. 64)

4. That research said that the "duplications"reduced advantageous heterozygosis. As far as I know, advantageous heterozygosis is one of the 10 factors of equilibrium population. So, what happened to the 9 factors of equilibrium population of Mosquito Culex pipien?

Steve, why the presumption of ignorance? Why the presumption that I'm not totally in agreement with practically everything said here?

I guess you meant to write, "I'm far too self-congratualatory to stoop down to considering what my vast accumulation of knowledge has done to my attitude toward real people with real lives and real needs, so I'll provide the obligatory verbal slap across your proverbial face, have my laugh at your stupidity, and be done with you."

So be it. You sure put me in my place.

"actual scientific content posted on the site"

Nice of you to write 'content' instead of 'proof'.
It's like candy - lot's of 'content' there..

Steve, why the presumption of ignorance?

Well, if you actually understand the pernicious idiocy of the stuff Adams has been purveying, that only gives you even less of an excuse for defending him.

Steve:

I defended no one, you or Adams or otherwise. An admitted rookie trolling the blog, I merely made an observation about the metacommunication going on in this thread, and that it brings to mind some of the same tone of those to whom few if any of us want to have any association, vis-a-vis the aforementioned Reverend Phelps. Just an attempt to interject some consistency to how we think about and demonize/disrespect people on the basis of their most closely-held beliefs/behaviors... and hoping that the mental exercise can make us better than that.

(Nothing more, nothing less.)

P.Z.,

Thanks for your comments on my correspondence with Mike Lemonick, and I appreciate the comments by the folks on this blog (most of them, at least!).

I'm not an enemy of evolutionary biology. I believe in evolution as much as you do, in the sense that living things have changed over time. I just don't think that the evidence supports the view that all biological complexity arose by the process of random variation (and natural selection). I think that some aspects of living things, particularly the specified information in biological molecules, are more reasonably explained as the consequence of design.

Obviously, this raises profound philosophical and theological questions. If some aspects of living things show evidence of design, where does the design come from? This philosophical conundrum isn't anything new in science. We don't know where the laws of physics come from either, but that doesn't preclude the scientific inference that there are laws of physics. Newton's demonstration of a 'clockwork' physical world that adhered to mathematical laws played an important role in the rise of Deism in the 18th century. The religious implications of Newton's work didn't place Newtonian mechanics outside science.

I am not an evolutionary biologist, and my research (on cerebrospinal fluid dynamics and cerebral blood flow) is certainly not closely related to evolutionary biology. There isn't any area of medicine that makes much routine use of evolutionary biology, except perhaps microbiology, and most of microbiology is molecular and cellular biology. Doctors don't deal much with evolutionary biology, since eugenics went out of fashion. So I'm not an expert. My questions shouldn't present much of a challenge to you.

How much new specified information can random variation and natural selection generate? Please note that my question starts with 'how much'- it's quantitative, and it's quantitative about information, not literature citations. I didn't ask 'how many papers can I generate when I go to PubMed and type 'gene duplication evolution'. I asked for a measurement of new specified information, empirically determined, the reference(s)in which this measurement was reported, and a thoughtful analysis as to whether this 'rate of acquisition' of new specified information by random heritable variation and natural selection can account for the net information measured in individuals of the species in which the measurement was made. Mike Lemonick was wrong that this isn't an important question in evolutionary biology. This is the central question.

Your example of Labbe's paper on gene duplication is, presumably, not to be taken too seriously. If you count copies as new information, you must have a hard time with plagiarism in your classes. All that the miscreant students would have to say is 'It's just like gene duplication. Plagiarism is new information- you said so on your blog!'.

Duplication of information isn't the generation of new information. No one doubts that living things can copy parts of themselves. You have presented no evidence that the process of (slightly imperfect) copying is the source of all that can be copied and the source of what actually does the copying. I was hoping (but not really expecting) that experts like you could do more than Mike Lemonick did. Lemonick just threw out cant, and you just gave me citation chaff. No measurements of actual new information.

There is obviously a threshold of the information-generating power of RM + NS. If I were to leave a culture of S. Aureus, mixed with a few drops of penicillin, in an incubator, and came back a few weeks later to find penicillin-resistant organisms growing in the culture, I would have no problem with theory that that RM+NS accounted for it.

Yet, if I found cockroaches crawling in the bacterial culture after two weeks, I wouldn't accept RM+NS as an explanation for the cockroaches in the culture. They came from somewhere else. They didn't evolve from the bacteria, in two weeks.

So what's the threshold, quantitatively? It seems to be a threshold of information generating capability. But the information in living things is specified; it does things, specific things. In that sense, it differs completely from Shannon information, which is a measure of randomness and the extent to which a message can be compressed. Shannon information is not relevant to biological information.

Regarding your PubMed literature search, I must not have used the words 'Information', 'Measurement, and 'Random' often enough in my discussion with Mike Lemonick, and you thought I said 'gene' 'duplication' and 'evolution'. I understand; we all make mistakes. If you actually want to answer my question, type 'information', and (not 'or'!) 'measurement', and 'random', and the name of the species in which you wish to look for experimental measurement of information generation by random processes.

I did a PubMed search just now. I searched for 'measurement', and 'information' and 'random' and 'e coli'. There were only three articles, none of which have any bearing on my question. The first article, by Bettelheim et al, was entitled 'The diversity of Escherichia coli serotypes and biotypes in cattle faeces'.

I searched for an actual measurement of the amount new information that a Darwinian process can generate, and I got an article on 'cattle faeces'. I love little ironies.

Mike Egnor

Mike: You ask "How much new specified information can random variation and natural selection generate?"

What exactly do you mean by 'specified information'? How would you determine its value? Does a dish of bacteria or a cockroach have more specified information, and how do you know? It seems to me that this is a term used but not defined or measured by Dembski but no-one else. As others have commented, you need to define what you mean by information before anyone can attempt to reply to your questions.

Why do you think there is a threshold for the 'information generating capacity'? There is no evidence that, given enough time, there is any limit. In your example with penicillin-resistant bacteria, you refer to coming back to them after a few weeks, so you clearly recognize that time is involved in the process. Isn't it reasonable to expect that, with more time, bigger changes would be possible?

Dr. Egnor: I asked for a measurement of new specified information, empirically determined, the reference(s)in which this measurement was reported...

Can you give us a reference in which the "specified information" of any system is measured? Or could you tell us how it's done? Maybe you can give us an example for a simple system like, say, a liter of water.

Mike Egnor wrote:
Shannon information is not relevant to biological information.

Can you explain why not? Your original search was for how random variation can result in an increase in information content, and even suggested bits as an appropriate measurement. Shannon explains how an increase of randomness is itself an increase in information, measured in bits. That seems like exactly what you were asking for.

Doctors don't deal much with evolutionary biology, since eugenics went out of fashion.

A jab? Not one that makes contact.

Michael Egnor, despite being cited fawningly yet again on the DI blog, has yet to respond to my simple answer to his silly question about the origin of new genetic information.

Here's my answer again:

The Discovery Institute blog just linked to this thread, so I am just now coming to it.

Regarding Egnor's question about the ability of random mutation and natural selection to produce new genetic information --

Michael Egnor is just ignorantly repeating some of the dumbest lines from the ID propaganda manual. This paper explains the origin of new genetic information, reviewing 20+ examples where the origin of new genes with new functions has been reconstructed in detail:

Long M, Betran E, Thornton K, Wang W. (2003). The origin of new genes: glimpses from the young and old. Nature Reviews Genetics. 4(11):865-75.

The paper is free online in various places -- as is Manyuan Long's vita, which contains dozens of papers specifically on this topic.

http://www.google.com/search?sourceid=mozclient&ie=utf-8&oe=utf-8&q=ori…

Egnor has probably never read this paper or any similar work, which is why he has such a beknighted view of the relevant science. Dr. Egnor: admit you were wrong on your very first argument, and that the headquarters of the ID movement, the Discovery Institute, was also wrong in praising your argument here, and let's start this discussion over.

(PS: Regarding gene duplication -- sure, an exact duplicate isn't "new" information. But after duplication -- sit down for this shocker -- mutation and selection can change a copy. Now you have two genes with divergent sequences and different functions. This is new information in anyone's book.

As for a "limit" -- why should anyone think there is any particular limit to the amount of information this process can generate? If evolution can generate three new genes (known as of 2003) in the Drosophila melanogaster genome in 3 million years (see Long et al. 2003, Table 2), it can obviously do much more with millions of species and billions of years. Any arbitrary line can be crossed by saying "add one more new gene". Game over, man.)

(PPS: Dr. Egnor, did you ever work on animal models in any of your training or research as a neurosurgeon? Just why do you think humans share so many anatomical details with other animals, anyway?)

Nick writes:
"PS: Regarding gene duplication -- sure, an exact duplicate isn't "new" information. But after duplication --sit down for this shocker -- mutation and selection can change a copy. Now you have two genes with divergent sequences and different functions. This is new information in anyone's book."

Nick, before the gene duplicated, where did the information in that original gene come from?

Nick, before the gene duplicated, where did the information in that original gene come from?

Not knowing anything about the gene in question, much of it was probably copied from other genes. As for the rest, some of that would have come from the environment, via the process of natural selection. And some of it would be just arbitrary; just dumb luck as to exactly which sequence evolves. But this is all beside the point; Nick's point about new information being created would be true even if God sat down one afternoon to write the original gene.

Dr. Egnor said,

"There isn't any area of medicine that makes much routine use of evolutionary biology, except perhaps microbiology, and most of microbiology is molecular and cellular biology. Doctors don't deal much with evolutionary biology, since eugenics went out of fashion. So I'm not an expert."

But we'll try and help enlighten you about some of those exceptions "only microbiologist" deal with.

Here's are several evolutionary-bio links you may find interesting.
http://news.yahoo.com/s/nm/20070219/sc_nm/environment_species_dc;_ylt=A…

and this:
http://news.yahoo.com/s/nm/20070218/sc_nm/autism_dc;_ylt=AoSja0lp80iACE…

and this:
http://webreprints.djreprints.com/1646641311092.html

as you can see, we all may want to consider updating our professional skills and knowledge.

"There isn't any area of medicine that makes much routine use of evolutionary biology, except perhaps microbiology, and most of microbiology is molecular and cellular biology. Doctors don't deal much with evolutionary biology, since eugenics went out of fashion. So I'm not an expert."

So, in about the eigth week of a sinus infection and the Nth round of antibiotics, I sat down with my physician and told him I was troubled a bit by the "Christian music" in the waiting room, and asked whether his distaste for evolution had anything to do with his failure to figure out how to get rid of my bug. He asked how that could possibly relate, and I asked him if he knew whether my infection was a new variety, a mutated variety, or even if he knew the species at all.

He made a new round of tests, discovered I didn't have the normal stuff, but instead a rather odd little staph. A quick change of antibiotics produced immediate relief and a cure.

Evolution has little place in medicine? My view may be skewed, since in my legislative staffing days I spent a lot of time looking at cancer research, viral diseases and organ transplants -- but can anyone name any part of medicine that is not much better informed today as a result of practical, applied evolution theory? As Mr. Matzke reminds us above, even surgery, today, is largely a result of testing on analog animals, analogs as a result of evolution.

Dr. Egnor, please go here: http://darwinianmedicine.org/

Dr. Randolph Nesse has complained for years about the dangers of ignorance of evolution among medical practitioners. Dr. Egnor might be considered a good candidate for poster boy for Nesse's campaign.

http://www.theproblemsite.com/codes/binary.asp

In a computer, it contain 2 binary numbers: 0 and 1 (on and off).It can be arrange, duplicate, or lost. But can the binary number 2 (not off or on switch, but maybe a dimmer switch) be added without the inventor?

I see the lite [superimposed superficiality]: the DNA code duplication becomes a permutation and a new species!

I'm going to put my Mad magazine in my copier, let 'er rip and in time I'll probably get a modern Illiad [or one of them fancy-dancy Ph.D. thesis approved by a group-think, tenured $tatus driven, codependent committee replicating the past ignorance]! Which begs the question: if the best and brightest are at our universities, were are the answers to the precarious human plight?

Perhaps it's because a secularized higher education isn't high enough! There is no man made religion dimension to reality but there are the idols of material-only scientism and liberalism-as-license, not cross-referenced liberty!

Clintonesque: it's the super UNnatural, stupid and the war for manKIND. Spiritual viruses, like computer viruses, that program human actors and one dimensional scientists [material consciousness only], not human beings! Go see the Matrix again.

Wow. The kooks are coming out of the woodwork.
They sure love themselves some delusion.

"I searched for an actual measurement of the amount new information that a Darwinian process can generate, and I got an article on 'cattle faeces'. I love little ironies."

A pro-ID's 'research' only uncovers 'cattle faeces' and then infers that it only applies to evolution. I too love ironies. Its sweeter when the person who thinks he understands the joke, doesn't realize that everyone is laughing at him.

As to his comments about plagiarism, the analogy doesn't hold up. He is asking for a process that increases the total 'information.' Gene duplication does this. It doesn't matter how this new 'information' relates to the previous information. On the other hand, a student is asked to do something different, and that is to take in information, processes it and understand it. The student does not generate much if any new information. Even when they are doing a research project, only a little new information is generated. This is because most of the paper should deal with how the new information relates to previous work. Plagiarism shows that the student did not actually process or understand the information, and that is why the student should fail. The only propose of this analogy is to associate an explanation of why he is wrong, with something that people know is immoral. By using this analogy, Engor is comparing apples to oranges and then declaring that all peaches are evil.

PS. I would refer to ID more a frass than feces. Frass usually refers to the undigested plant material within feces. All of the nutritional value of the material contained within the frass is unused. And that is what most ID is. Information enters an IDist, but does not get processed within the IDist. The IDist does not think about it, nor do they extract and knowledge from it. Instead it is spewed out in much the same way it entered.

I did a PubMed search just now. ... There were only three articles, none of which have any bearing on my question.

Extraordinary. Michael Egnor is actually boasting about his own incompetence at using PubMed without realising that's what he's doing. He isn't even competent enough to recognise his own incompetence - ie that if a search fails, there's a good chance it's because the searcher hasn't the remotest clue what they're talking about (especially if they are already infamous for not having a clue about that topic) rather than that the topic isn't there at all.

It's akin to a child guessing and looking half-heartedly under all the wrong letters in a dictionary, when trying to find out how to spell a word, and then summarily declaring it not to be there. (I actually witnessed a child do just that. The word was oesophagus - admittedly a tough one at rather a young age. However, the amusing part was that every vowel other than o was guessed and tried!)

The pdf article cited by Nick is quite unimpressive after a quick glance in my humble opinion... but I will leave others to decide for themselves. It simply describes (in nauseating detail) how genes change over time and uses all kinds of "models" to support how these might acquire new functions. It appears to be assuming what it is trying to prove. It does not show that the genes of a drosophila, for example, slowly acquire new information resulting in 'evolution' into something with new body parts or new bodily functions. This appears to be another example of claiming that a research paper proves much more than it really does.

(I actually witnessed a child do just that. The word was oesophagus - admittedly a tough one at rather a young age.

That's why it's spelled with an 'e'.

Yet, if I found cockroaches crawling in the bacterial culture after two weeks, I wouldn't accept RM+NS as an explanation for the cockroaches in the culture.

without even reading the surely dozens of shocked responses at such an idiotic comment, I would only say:

Holy crap!

er, duh, neither would anybody else.

does such a ridiculous statement even qualify as a strawman?

is there something even more illustrative of how false and ridiculous this statement is than "strawman"?

to hear these words coming out from a persona that perhaps under other circumstances might be considered intelligent, just goes to show how cognitive dissonance can rot one's brain to the point of mush.

skeptical:

It simply describes (in nauseating detail) how genes change over time and uses all kinds of "models" to support how these might acquire new functions.

"he blinded me with science!"

LOL. you did a great job of saying you don't like to read, and can't understand what you are reading if it's above gradeschool level.

damn those "models"!!!

all this science i don't understand just MUST be EEEEVVVIILLL!

you should become a contributor to Overwhelming Evidence.

That's why it's spelled with an 'e'.

Not in English it isn't. Of course, if you're an American speaking outside your field of competence then that would put you in much the same position as Michael Egnor.

Not in British English it isn't.

Corrected that for you. I suppose you think there's a 'u' in 'color', and that a performance place is a 'theatre'.

Oh, you Brits, always with your crazy spellings. Why couldn't we have inherited Spanish, or German, with their regularized orthographic systems? No, we had to be the colony of the nation that loves silent letters and that randomly picked between the eight different post-Medieval spellings of any arbitrary word when they finally decided to settle their language down.

Explain to me how the pronunciation of the word 'through' gives rise to its spelling, eh? Then we'll talk.

You appear to be missing the (branching) evolution metaphor too. Quite a wide range of incompetences you have there. Any more you'd like to display to us? Michael Egnor could probably do with the competition.

DI proclaim loudly: 'Just because science blogs has answered Egnor's question any number of times, don't think we won't present a particular uninterested response as a weakness. Oh, and since he is a "professor of neurosurgey [sic]" we will claim you are responseless.' I think they have to rethink that strategy now, silently.

Salvador Cordova has taught Egnor well. Always try to project an affable atmosphere while stabbing opposite discussion participants in the back.

"I believe in evolution as much as you do, in the sense that living things have changed over time. ... I think that some aspects of living things, particularly the specified information in biological molecules, are more reasonably explained as the consequence of design."

The obvious contradiction doesn't bother Egnor. Nor does the problem of distinguishing aspect from aspect. Instead he is perfectly willing to conflate science with pseudoscience. Perhaps for him cancer is tissue as much as brain tissue - and a neurosurgeon can as well leave it in there.

"There isn't any area of medicine that makes much routine use of evolutionary biology"

Except that cancer and their treatments rely heavily on evolutionary effects. Perhaps Egnor need some help with PubMed searches here too. I'm sure we can oblige in that case.

Oh, and neurosurgeons doesn't bother much with the background behind tissue matching either. After all, our heart surgery colleges are perfectly willing to transplant any animal heart. It was probably just bad luck that the patient that got a baboon instead of a chimp heart immediately died from rejection in spite of a "class A" match. ( http://query.nytimes.com/gst/fullpage.html?sec=health&res=9A0DE6DE1F39F… )

"Doctors don't deal much with evolutionary biology, since eugenics went out of fashion."

That is another Cordova specialty, take an issue that has been appropriated by political or other means (here medical) and pretend that it was the fault of science.

You appear to be missing the (branching) evolution metaphor too.

The development of humans did not result in the extinction of the other branches of apes, as you've amply demonstrated. The fact that chimps exist alongside humans does not imply that the first is the equal of the second.

as you've amply demonstrated

subtle.

;)

Rather than "why are there still monkeys?", I see it more as the Neanderthal equivalents gone West while the ancestors of modern man continued developing what turned out to be the more advanced culture.

Though the actual answer to your "Why couldn't we have inherited ..." would be "survival of the fittest". Though it does also illustrate your own inability to choose in the manner you apparently now regard as "better" on that side of the pond! Plus another language (even from a different root) could still "win" anyway. Spanish is taking over from French and German in some schools here in the UK. Chinese hasn't exactly gone extinct.

There is no 'Chinese' language. There are multiple languages, each with many dialects, spoken across the nation of China.

Skeptical writes:

The pdf article cited by Nick ...does not show that the genes of a drosophila, for example, slowly acquire new information resulting in 'evolution' into something with new body parts or new bodily functions.

Has Internet access and still believes no new functions etc. have ever been seen in Drosophila mutants. Seymour Benzer is spinning somewhere.

does such a ridiculous statement even qualify as a strawman?

No, that's unkind to Friends of Dorthy.

I searched for an actual measurement of the amount new information that a Darwinian process can generate, and I got an article on 'cattle faeces'. I love little ironies.

Why is this even relevant? If information does not mean total genetic content and is not related to functions, what does it matter?

I asked for a measurement of new specified information, empirically determined, the reference(s)in which this measurement was reported, and a thoughtful analysis as to whether this 'rate of acquisition' of new specified information by random heritable variation and natural selection can account for the net information measured in individuals of the species in which the measurement was made.

This reminds me of new-agey types who like to discuss 'energy' and 'force' and 'flow' as if they're something relevant or quantifiable. They're meaningless, but they're great for adding a bit of loftiness to an argument.

Egnor is taking a real word and using it in a Lewis Carroll sense. We might as well say: "I asked for a measurement of new specified gweeblethorp ... ".

'Information' is a contextual construct. It is not an objective, external measure. It sounds lofty, but unless it is defined, it is as meaningless and useless as chakras, pyramids and crystals.

Oh, and by the way, Dr. Egnor: The rate of acquisition of new specified gweeblethorps by random variation is 3.7 yipsils, more than enough to result in the progression we have seen in this scant 3.5 million trapsulleurs.

Rather than "why are there still monkeys?", I see it more as the Neanderthal equivalents gone West while the ancestors of modern man continued developing what turned out to be the more advanced culture.

Which, I'm sure, is why Britain has the strongest economy in the world and despite recent atrophy still leads the world in scientific and technological development, and has the highest average standard of living in the world, and despite the growing challenge from China remains, in a very real sense, the world's sole superpower.

Though the actual answer to your "Why couldn't we have inherited ..." would be "survival of the fittest". Though it does also illustrate your own inability to choose in the manner you apparently now regard as "better" on that side of the pond! Plus another language (even from a different root) could still "win" anyway. Spanish is taking over from French and German in some schools here in the UK. Chinese hasn't exactly gone extinct.

I don't think it's unreasonable to conclude that silent letters and words whose relationship of spelling to pronunciation radically contradicts the general patterns of English phonetics are maladaptive. They make the language more difficult to pronounce and learn, they make it more difficult to type and spell properly, and they waste time. The only comprehensible reason for your inordinate esteem of such stems from a combination of misguided aesthetics (the same sort that results in people breeding "longfin" fish and finding models with unreasonable proportions and weight attractive) and what might be characterized as a sort of cranky-old-man nationalism ("Damn Yanks! Get off my lawn!"). You've lost your empire; you've lost your position as a world power; you probably know deep down how fortunate you are that I'm not bringing up the fact that we saved you from a stupid endless war in the second decade of the 20th century and from eventual annihilation in the fourth, to say nothing of the Revolutionary War (oops); and your customs and idiosyncrasies, though they're a running joke in much of the world, are all you've got left.

Hey, you're right, being sneeringly and gratuitously ethnocentric IS kind of fun.

You apparently don't understand the meaning of "culture", in particular the "advanced" aspects of it, since you are mis-equating it with being a world superpower and having economic dominance (as well as misrepresenting history in regard to wars) instead of noticing the relative numbers of rabid gun-toting religious fundamentalists in the two places. It's not by accident of random distribution that the US is overrun with such culturally backwards types. They self-selected themselves to be there. Unfortunately they keep trying to re-infect the UK as well.

Meanwhile, Caledonian is apparently too stupid or ignorant to notice that the relatively single genotype (written form) but very variable, environmentally-sensitive phenotype aspects of Chinese (spoken forms) vs the multiple alleles of English (written and accents), actually add to the analogy rather than detract from it.

But at least the US does have *some* intelligent and culturally-advanced people, eg PZ. The question is whether the large neanderthal contingent will "win" and wipe out much of the rest of the interesting stuff on the planet in the process.

DI proclaim loudly: 'Just because science blogs has answered Egnor's question any number of times, don't think we won't present a particular uninterested response as a weakness. Oh, and since he is a "professor of neurosurgey [sic]" we will claim you are responseless.' I think they have to rethink that strategy now, silently.

Salvador Cordova has taught Egnor well. Always try to project an affable atmosphere while stabbing opposite discussion participants in the back.

"I believe in evolution as much as you do, in the sense that living things have changed over time. ... I think that some aspects of living things, particularly the specified information in biological molecules, are more reasonably explained as the consequence of design."

The obvious contradiction doesn't bother Egnor. Nor does the problem of distinguishing aspect from aspect. Instead he is perfectly willing to conflate science with pseudoscience. Perhaps for him cancer is tissue as much as brain tissue - and a neurosurgeon can as well leave it in there.

"There isn't any area of medicine that makes much routine use of evolutionary biology"

Except that cancer and their treatments rely heavily on evolutionary effects. Perhaps Egnor need some help with PubMed searches here too. I'm sure we can oblige in that case.

Oh, and neurosurgeons doesn't bother much with the background behind tissue matching either. After all, our heart surgery colleges are perfectly willing to transplant any animal heart. It was probably just bad luck that the patient that got a baboon instead of a chimp heart immediately died from rejection in spite of a "class A" match. ( http://query.nytimes.com/gst/fullpage.html?sec=health&res=9A0DE6DE1F39F… )

"Doctors don't deal much with evolutionary biology, since eugenics went out of fashion."

That is another Cordova specialty, take an issue that has been appropriated by political or other means (here medical) and pretend that it was the fault of science.