Us Darwin lobbyists try to solve the mystery of Uncommon Descent

| 460 Comments

Over at UD, the ever-amazing Denyse O’Leary (writing as “News”) has gone after me.

I am apparently a “Darwin lobbyist” whose salary is “paid for under protest by people who don’t believe it”. (Of course UD News posts never insult people, do they?)

First she quotes the paleontologist T. Berra as saying that cars, like fossils, show “descent with modification”. Then she puts words in Berra’s mouth, implying that Berra has said that cars have genes and offspring, and that Berra has called automotive engineers liars.

Then she quotes some paragraphs by me about the mysterious “digital information” that ID types like Stephen Meyer are always announcing has been found in the genome. I made the point that it is nothing very new – actually it’s just the presence of protein-coding genes, RNA genes, and regulatory sequences, which we already knew were there. (I have heard Meyer speak on this issue and he did not explain what the mysterious “digital information” was – leaving his audience to infer that it was some mysterious new pattern previously unknown to science, but which could only have arisen by Intelligent Design).

She introduces the quote from me by misdescribing it as being

O’Leary:

on why genetic information requires no intelligence.

It of course wasn’t about that. It was reacting to Meyer’s mesmerizing phrase “digital information” and his statement that

Stephen Meyer:

the discovery of digital information in DNA provides strong grounds for inferring that intelligence played a causal role in its origin.

I was pointing out that Meyer wasn’t describing some new pattern that, by itself, proved intelligent design.

O’Leary has misunderstood my 2007 paper and which parts argue what. It is later in the paper that I take on William Dembski’s arguments for his Law of Conservation of Complex Specified Information and his No Free Lunch argument, and show (by arguments invented by others and some invented by me) that they don’t work. And of course those arguments in my paper are against Dembski’s alleged proof of Intelligent Design. They don’t prove that ID is impossible, just that Dembski has no proof that it is necessary.

I recommend that article to O’Leary.

460 Comments

Why use cars, or whirl winds in junkyards producing 747’s? Why not do some research?

I used to enjoy UD when the whole gang was there flailing, and blustering away. Now Dembski is at some religious dump bowing and scraping before his nut job OEC bosses, desperately denying his earlier vague admissions that the earth is actually older than a Bristle Cone Pine. The others have just kind of quietly abandoned Mrs O’Leary, making occasional half hearted attempts at keeping the flame burning. Now that it’s Denise by her IQ challenged self, skulking behind the moniker ‘News’ it’s lost any humourous appeal it once had. A sad Canadian hurling insults at a dead genious (‘that British toff’) and generally harming the image of a country I greatly admire; their health care system is sublime.

“Darwin lobbyists” apparently are in cahoots with Einstein lobbyists, Galileo lobbyists, and Lavoisier lobbyists.

All grand conspirators in the evil plan to demand actual cause and effect relationships in science (yes, in classical science, don’t quibble), rather than resorting to demonic possession and unseen spirits as the forces behind observable phenomena.

Glen Davidson

Not to mention the James Clerk Maxwell lobbyists, the Shannon-Kolgorov lobbyists, the Godel lobbyists, and so on. As a response to the Isaac Newton lobbyists, it reminds me of Intelligent Falling.

This is just getting weird.

Chris Lawson said:

Shannon-Kolgorov lobbyists,

Please, Kolmogorov!

Chris Lawson said:

As a response to the Isaac Newton lobbyists, it reminds me of Intelligent Falling.

Hey, don’t underestimate the gravity of the situation!

So I guess that all someone has to do to disprove the evolution of cars is to find a Precambrian Volkswagen Rabbit.

Well, I see that over at UD commenter David W. Gibson is asking sensible questions while we are in the meantime treated to the usual “bornagain77” brain dump and the usual loud invective from Gil Dodgen (all the while showing that he has not comprehended the issues).

While we’re waiting for sensible answers to Gibson’s comment no. 2, I wondered if people noticed the wording of the quote from Stephen Meyer (which I gave in my 2007 paper and O’Leary reproduced).

Stephen Meyer:

So the discovery of digital information in DNA provides strong grounds for inferring that intelligence played a causal role in its origin.

That’s like saying we have these things called “books”, but only recently have we made a great new discovery … that they have alphabetically-encoded information in them!.

I think Meyer is saying that DNA was not only known, and known to be the genetic material, but now … it has been discovered that there are these four bases that code for things. Wow!

The time I heard Meyer use this one on an audience, they clearly took it to mean that someone had, presumably recently, discovered that not only was DNA there, it had some pattern called “digital information” in it, which proved intelligent design was correct. He did nothing to disabuse them of this misconception.

The other thing I notice Meyer do with this phrase is to go back and forth between “digital information” that is the contents of the DNA (the actual sequences), and “digital information” that is the coding system (the code table and translation machinery). These are not the same thing, but he’s completely ambiguous about that.

Mike Elzinga said:

So I guess that all someone has to do to disprove the evolution of cars is to find a Precambrian Volkswagen Rabbit.

If I was drinking coffee it would be all over the monitor right now … High marks for that one!

robert van bakel said:

The others have just kind of quietly abandoned Mrs O’Leary, making occasional half hearted attempts at keeping the flame burning.

It’s Denyse O’Leary having her usual cow.

And speaking of flames and cows; wasn’t it Mrs. O’Leary’s cow that was responsible for burning down half of Chicago back in 1871?

Maybe this time (fingers crossed) it will be the Discovery Institute.

Stephen Meyer:

the discovery of digital information in DNA provides strong grounds for inferring that intelligence played a causal role in its origin.

So are we to assume that, if a quasi-crystal like DNA can be a template for the subsequent development of an organism, we infer that intelligence played a causal role in its origin?

Then can we also assume that other types of crystals and quasi-crystals that form the templates for subsequent developments are indications of intelligence playing a causal role in their origins?

So the seeds for snowflakes have intelligent origins? So all crystalline solids and polycrystalline solids have their origins in intelligence? How about benzene? How about any polymer chain or sheet?

I’m going to hazard a guess here; but, for ID/creationists, it appears that the only thing that qualifies a template as having an intelligent origin is that it produces a living organism.

If templates on top of templates on top of templates leads to anything complicated, it is the product of intelligent origin only if it produces life.

Superconductivity and super-fluidity don’t count, even though there are precision dances of organization and self-sustaining processes within. It has to be alive.

O’Leary has misunderstood my 2007 paper

Don Henley must have had O’Leary in mind when he wrote this:

She looked at me uncomprehendingly

Like cows at a passing train

Mike Elzinga said:

So I guess that all someone has to do to disprove the evolution of cars is to find a Precambrian Volkswagen Rabbit.

Well, there was one in Ben Hur.

“First she quotes the paleontologist T. Berra as saying that cars, like fossils, show “descent with modification”. Then she puts words in Berra’s mouth, implying that Berra has said that cars have genes and offspring, and that Berra has called automotive engineers liars.”

Well, according to Gould, Mickey Mouse displays “descent with modification” as well. Somehow, I don’t think he was using this analogy to disprove evolution though.

Here is a great paper in Nature on the subject of the digital code in DNA:

http://www.nature.com/nature/journa[…]re01410.html

DNA has two types of digital information — the genes that encode proteins, which are the molecular machines of life, and the gene regulatory networks that specify the behaviour of the genes.

There is no naturalistic explanation for the existence of both digital codes and information. Felsenstein is right that the genetic code itself is an issue for abiogenesis / origin of life researchers whereas the information contained in protein sequences is a problem for the molecular evolutionist. The belief is that natural selection and random drift (a blind and open search) can somehow conspire to build novel motifs from scratch even though there is absolutely no evidence that they can.

Atheistoclast said:

Here is a great paper in Nature on the subject of the digital code in DNA:

http://www.nature.com/nature/journa[…]re01410.html

DNA has two types of digital information — the genes that encode proteins, which are the molecular machines of life, and the gene regulatory networks that specify the behaviour of the genes.

There is no naturalistic explanation for the existence of both digital codes and information. Felsenstein is right that the genetic code itself is an issue for abiogenesis / origin of life researchers whereas the information contained in protein sequences is a problem for the molecular evolutionist. The belief is that natural selection and random drift (a blind and open search) can somehow conspire to build novel motifs from scratch even though there is absolutely no evidence that they can.

Once again we have an example of people using the same word (or phrase) to mean different things. What do you suppose the authors of that paper would have to say about Meyer’s use of “digital information” and the conclusion he rationalizes using it? I only glanced at the paper, but good luck finding anything ID-friendly in that paper, Joseph.

Atheistoclast, please show us exactly where the paper states that its findings demonstrate irrefutable proof of an Intelligent Designer, aka God of the Bible, while simultaneously magically disproving evolution as never having existed and or is evil.

You know, like you constantly falsely state.

There is no naturalistic explanation for the existence of both digital codes and information.

It’s exactly the opposite.

DNA is a naturally occurring organic chemical. Whether it “did” first occur naturally - a question for the field of abiogenesis - it unequivocally CAN.

Therefore by your own standards, DNA provides an example of a “naturalistic” occurrence of what you refer to as a “digital code”.

So is a natural, living, breathing, non-supernatural human using natural resources to generate a computer program for that matter.

No magic required.

P.S. It’s not nice to misrepresent the meaning of original authors - pretending that they meant an analogy or metaphor literally is an extreme example of this.

Matt G said: Once again we have an example of people using the same word (or phrase) to mean different things. What do you suppose the authors of that paper would have to say about Meyer’s use of “digital information” and the conclusion he rationalizes using it? I only glanced at the paper, but good luck finding anything ID-friendly in that paper, Joseph.

The mean exactly what Steve means. There is a digital code in DNA and it is used to represent digital(discrete) information. The reason why you don’t see this as supporting ID is because you spectacularly fail to realize that codes and information theory always relate to the work of intelligent designers and not to natural processes. Not only is the genetic code a work of immaculate design but it is also designed to be as fault-tolerant and effective as possible. Of the zillions of possible ways of representing all 20 proteinogenic amino acids and a stop site using 64 nucleotide triplets, only one code is in use (although slightly different for prokaryotes who use more than one start site). Incidentally, if you know anything about asynchronous serial communication, you will know that “frames” are bounded by start and stop bits just as “reading frames” are in DNA. Fascinating!

Let me ask you something: Why are you so resistive to the inferential evidence for ID? Why are you so scared at the prospect that there may be an Intelligent Agency at work in the universe and life? Why is this so upsetting for you? I find it absolutely intriguing that there exists a Being who is so much more intelligent than any human. It opens up my mind to the true nature of reality.

harold said: DNA is a naturally occurring organic chemical. Whether it “did” first occur naturally - a question for the field of abiogenesis - it unequivocally CAN.

Therefore by your own standards, DNA provides an example of a “naturalistic” occurrence of what you refer to as a “digital code”.

Harold, the code and DNA are not the same thing. The code does not exist in DNA as some people seem to believe. It is just the format or procedure used by the translational machinery (enzymes and ribosomes) for constructing proteins, amino acid by amino acid, based on what is transcribed from DNA. You could use the genetic code outside of the context of molecular biology to represent just about everything.

And, in any case, there is no naturalistic explanation for the origination of DNA. Sure, it is natural in the sense that gasoline is natural and not supernatural. But you need to refine gasoline from crude oil - DNA needs to be synthesized from other chemicals. It does not spontaneously arise in Nature like carbon dioxide.

Sorry to be OT, but could someone please point me to instructions for breaking up a post so I can respond sentence by sentence? Athiestoclast has blood in the water and I can’t resist. Thanks.

Matt G said:

Sorry to be OT, but could someone please point me to instructions for breaking up a post so I can respond sentence by sentence? Athiestoclast has blood in the water and I can’t resist. Thanks.

That’s Atheistoclast. I hate making typos.… Sorry again.

Matt G said:

Sorry to be OT, but could someone please point me to instructions for breaking up a post so I can respond sentence by sentence? Athiestoclast has blood in the water and I can’t resist. Thanks.

You just use the “blockquote” tags as you would for bold or italic in html.

Harold, the code and DNA are not the same thing. The code does not exist in DNA as some people seem to believe. It is just the format or procedure used by the translational machinery (enzymes and ribosomes) for constructing proteins, amino acid by amino acid, based on what is transcribed from DNA. You could use the genetic code outside of the context of molecular biology to represent just about everything.

That’s a semantic argument. It’s equally true of a computer program. It’s not a set of instructions except in the proper context.

And, in any case, there is no naturalistic explanation for the origination of DNA. Sure, it is natural in the sense that gasoline is natural and not supernatural. But you need to refine gasoline from crude oil - DNA needs to be synthesized from other chemicals. It does not spontaneously arise in Nature like carbon dioxide

At the end of the day, the very final ID argument that people fall back on always seems to be declaring human technological work to be magic. That’s a fascinating and ancient impulse. In fact, technology has indeed always seemed like magic to those who did not understand it fully. Over and over again, the “a human did it so it must too be magic” argument appears.

There used to be scientific idea called “vitalism”. It was the idea that life could not be understood in terms of underlying physical principles. It was abandoned when urea was synthesized. Not because anyone claimed that the chemical synthesis of urea was identical to the biochemical synthesis - it wasn’t - but because it proved that a biochemical wasn’t magical - it COULD be synthesized.

Both DNA and gasoline can be synthesized without magic.

Now, if you want to argue that DNA was, nevertheless, synthesized once by magic, at the dawn of cellular life, be my guest - that gap will be there to jam your god into for a while, until a really good model of the origin of DNA genomes is developed. After all, the Flying Spaghetti Monster can magically synthesize anything humans can naturally synthesize.

But the salient point is that DNA does not NEED to be synthesized by magic.

Moderators - this is my final reply to Atheistoclast. As I have noted, his first few posts, while he is declaring his own ideas unchallenged, are, although always wrong, usually wrong in rather interesting and often classical ways. As we all know, he doesn’t respond well to civil critique, and things tend to degenerate after about three or four comments.

Matt G said:

Sorry to be OT, but could someone please point me to instructions for breaking up a post so I can respond sentence by sentence? Athiestoclast has blood in the water and I can’t resist. Thanks.

Use the greater than and less than signs where I use “[“.

The html code is “[blockquote]text[/blockquote]

There is a digital code in DNA and it is used to represent digital(discrete) information. The reason why you don’t see this as supporting ID is because you spectacularly fail to realize that codes and information theory always relate to the work of intelligent designers and not to natural processes.

Intelligent processes aren’t natural processes?

Of course this gets to the core of ID ignorance, the idea that linguistic categories like “intelligence” determine very real differences. In some uses, “human intelligence” in fact is not “natural,” although in more common usage it very much is. It is in fact in our “nature” to develop intelligence.

True, just because all known intelligence is in fact natural, and our machines that mimic intelligence (I don’t want to quibble over whether or not computers are intelligent, just treating as not for convenience) owe their existence to natural forces such as humans, does not mean that humans made DNA. That’s because Atheistoclast isn’t interested in asking any question, merely in stating an extremely biased presupposition, “that codes and information theory always relate to the work of intelligent designers and not to natural processes.” Said without any evidence, and, in fact, quite contrary to the evidence that DNA’s codes and information evolved.

I mentioned some of the evidence for evolution of the DNA code in my Signature in the Cell review at Amazon. But Meyer might have done better with respect to ID propaganda had he stuck with saying that the DNA code was designed, since we don’t have great evidence for how it evolved. Of course we have abundant evidence that proteins evolved, something that he also denies, since he really doesn’t differentiate between abiogenesis and evolution even as he claims to be discussing just the former.

Atheistoclast and Meyer deny the evolution that is all that can explain the rampant homologies between proteins of divergent life, and phenomena such as protein families. We set up strong falsification criteria, that if life hasn’t evolved, homologies won’t exist across various proteins within an organism, a species, or across the species. We test that falsification criterion, and evolution passes.

ID makes no predictions, save obvious, known, and unentailed “predictions” like life will be complex, “irreducibly complex” by some definitions. These unentailed “predictions” are found, but are meaningless to ID. ID doesn’t actually predict the sorts of changes that we find in cars (at one point, radios unrelated to the rest of the electrical system were jammed into cars, later computers were. In neither case was there any kind of evolutionary development from earlier components), and it by no means explains anything about homologies (Behe’s “evolution” doesn’t either, except by stealing from actual science).

In their conceptions, they won’t allow testing of real design predictions. In real design, evolutions occur (not like biological evolution, however), but revolutions do too. Submarines now run on nuclear power, power systems which have virtually no similarities to earlier diesel engines. That’s what you look for in design, but they don’t look for that, of course, because they know that they won’t find it. Also, they don’t care that evolution’s predictions regarding the evolution of proteins and of the information in DNA actually exist, they just repeat their ignorant presuppositional prejudices about information.

What can you do after meaningful ID predictions have been falsified by the evidence, though?

Glen Davidson

Btw, Joe Felsenstein wrote a response to Bill Dembksi a while ago about the issue of “information” and “digital codes”:

http://ncse.com/rncse/27/3-4/has-na[…]liam-dembski

Here are some excerpts of his remarks and my responses to them:

The mysterious digital information turns out to be nothing more than the usual genetic information that codes for the features of life, information that makes the organism well-adapted.

OK, but it is digital information and one has to ask how this molecular communication arose. We know that the digital information we use has an intelligent source so it logically follows that this is so for that encoded in our chromosomes.

If we have a population of DNA sequences, we can imagine a case with four alleles of equal frequency. At a particular position in the DNA, one allele has A, one has C, one has G, and one has T. There is complete uncertainty about the sequence at this position. Now suppose that C has 10% higher fitness than A, G, or T (which have equal finesses). The usual equations of population genetics will predict the rise of the frequency of the C allele. After 84 generations, 99.9001% of the copies of the gene will have the C allele.

No. Because fitness has nothing to do with information. The C allele can still be advantageous (reproductively) but actually serve to degrade functionality and add noise to information. There are countless examples of such loss-of-function mutations having adaptive effects.

This is an increase of information: the fourfold uncertainty about the allele has been replaced by near-certainty. It is also specified information — the population has more and more individuals of high fitness, so that the distribution of alleles in the population moves further and further into the upper tail of the original distribution of fitnesses.

Wrong. Selection did not reduce uncertainty. It reduced variation. The information content has nothing to do with the fitness function. What matter is what effect the C allele has on the protein. It could have been simply to compensate for a change elsewhere to restore structural stability. This results in conservation and not innovation.

So the only law we have is one that does predict the creation of specified information by natural selection.

Natural selection has no creative powers. It cannot create specified information like this because it can only select what is useful and functional (the homeobox motif):

RRRKRTAYTRYQLLELEKEFLFNRYLTRRRRIELAHSLNLTERHIKIWFQNRRMKWKKEN

At most it can fine-tune, optimize or conserve it.

harold said:

There used to be scientific idea called “vitalism”. It was the idea that life could not be understood in terms of underlying physical principles. It was abandoned when urea was synthesized. Not because anyone claimed that the chemical synthesis of urea was identical to the biochemical synthesis - it wasn’t - but because it proved that a biochemical wasn’t magical - it COULD be synthesized.

In the end, “Vitalism” was pissed away.

Ah, the irony, I love it.

Atheistoclast said:

The reason why you don’t see this as supporting ID is because you spectacularly fail to realize that codes and information theory always relate to the work of intelligent designers and not to natural processes.

You keep making this unsupported assertion.

Not only is the genetic code a work of immaculate design but it is also designed to be as fault-tolerant and effective as possible.

Another unsupported assertion. And why do you use the word immaculate? Is that a scientific term I’m just not familiar with?

Let me ask you something: Why are you so resistive to the inferential evidence for ID?

Because it is not an inference, it is a rationalization. In science, if the evidence were different, the conclusions would be different. In ID, the conclusion is always the same: the Intelligent Designer did it this way (and we mere humans can’t understand how, why, etc.).

Why are you so scared at the prospect that there may be an Intelligent Agency at work in the universe and life? Why is this so upsetting for you?

I am not scared, though I suspect you are projecting your own fear which you remedy by believing in this Intelligent Agency. I am not upset, except by those who misrepresent science (of which I am rather fond) to pursue ideological agendas. Doesn’t it scare you that this agency might be tampering with your brain and that your thoughts and feelings might not be your own…?

I find it absolutely intriguing that there exists a Being who is so much more intelligent than any human. It opens up my mind to the true nature of reality.

You sound more passionate than dispassionate here, Joseph. Your religious beliefs seem to have blinded you to the nature of science as well as the nature of reality. Your invoking of supernatural agency adds nothing to our understanding of the natural world, and in fact takes from it by opening the door to empty “inferences.”

rossum said:

Atheistoclast said:

In any case, I am referring to highly specific domains like the homeobox - the scope for variation in it is greatly limited.

How limited? What are the number of possible variations? What is the impact of that number on the calculations in your papers? Without knowing the number of allowed variations we cannot tell how accurate are the numbers you have shown us up to now. How can anyone be sure that you are not in error by 93 orders of magnitude?

rossum

It depends on the particular motif sequence. Sure, some flexibility with variation is usually allowed, but I doubt you can have a functioning homeobox without at least half of the residues in the consensus sequence present. Moreover, any variation tends to be limited to chemically similar amino acids…like lysine for arginine rather than proline. The numbers I referred to were for completely specific sequences. If we allow for some variation, it reduces the improbability of chancing upon them somewhat, but certainly not to the point where they become extremely improbable but still remotely possible.

rossum said:

Atheistoclast said:

In any case, I am referring to highly specific domains like the homeobox - the scope for variation in it is greatly limited.

How limited? What are the number of possible variations? What is the impact of that number on the calculations in your papers? Without knowing the number of allowed variations we cannot tell how accurate are the numbers you have shown us up to now. How can anyone be sure that you are not in error by 93 orders of magnitude?

rossum

OK, let us say for the sake of argument that 50% of the 60 residues in the homeobox motif can be replaced with any other amino acid. This is not true, but let us countenance the idea all the same. That leaves 30 residues which cannot be changed.

As such, the probability of reaching the target is reduced from the inverse of 20^60 (1.15*10^78) to the inverse of 20^30 (1.073*10^39). That is a difference of 39 orders of magnitude. But does it really help? We still have a greatly improbable feat which, for all intents and purposes, is impossible.

Let us also do one more calculation.

Suppose that in the 60 residue homeobox motif, each amino acid can be replaced by just one other. That means that the probability of chancing upon it is the inverse of (20/2)^60 or 1*10^60.

Let us suppose that each residue can be replaced by as many as 4 other amino acids. This means that the probability now becomes the inverse of (20/4)^60 or 8.67*10^41.

So we now manage to reduce some of the improbability, but not to the extent where it helps the Darwinist. Sorry. Just accept that the math is against you.

Atheistoclast said: OK, let us say for the sake of argument that 50% of the 60 residues in the homeobox motif can be replaced with any other amino acid. This is not true, but let us countenance the idea all the same. That leaves 30 residues which cannot be changed.

As such, the probability of reaching the target is reduced from the inverse of 20^60 (1.15*10^78) to the inverse of 20^30 (1.073*10^39). That is a difference of 39 orders of magnitude. But does it really help? We still have a greatly improbable feat which, for all intents and purposes, is impossible.

Let us also do one more calculation.

Suppose that in the 60 residue homeobox motif, each amino acid can be replaced by just one other. That means that the probability of chancing upon it is the inverse of (20/2)^60 or 1*10^60.

Let us suppose that each residue can be replaced by as many as 4 other amino acids. This means that the probability now becomes the inverse of (20/4)^60 or 8.67*10^41.

So we now manage to reduce some of the improbability, but not to the extent where it helps the Darwinist. Sorry. Just accept that the math is against you.

Your comments keep getting dumber, Atheistofraud.

You only show why most mutations of the homeobox genes are harmful, which would be one explanation of why miscarriages happen so often. You don’t rule out completely changes in the homeobox sequences, you idiot.

dalehusband said:

Atheistoclast said: OK, let us say for the sake of argument that 50% of the 60 residues in the homeobox motif can be replaced with any other amino acid. This is not true, but let us countenance the idea all the same. That leaves 30 residues which cannot be changed.

As such, the probability of reaching the target is reduced from the inverse of 20^60 (1.15*10^78) to the inverse of 20^30 (1.073*10^39). That is a difference of 39 orders of magnitude. But does it really help? We still have a greatly improbable feat which, for all intents and purposes, is impossible.

Let us also do one more calculation.

Suppose that in the 60 residue homeobox motif, each amino acid can be replaced by just one other. That means that the probability of chancing upon it is the inverse of (20/2)^60 or 1*10^60.

Let us suppose that each residue can be replaced by as many as 4 other amino acids. This means that the probability now becomes the inverse of (20/4)^60 or 8.67*10^41.

So we now manage to reduce some of the improbability, but not to the extent where it helps the Darwinist. Sorry. Just accept that the math is against you.

Your comments keep getting dumber, Atheistofraud.

You only show why most mutations of the homeobox genes are harmful, which would be one explanation of why miscarriages happen so often. You don’t rule out completely changes in the homeobox sequences, you idiot.

Well, the issue is how much variation is allowed in the homeobox sequence for it to remain functional. My last calculation allowed for quite a bit, but still produced an infinitesimally small number of possible combinations.

Let’s actually look at some homeobox sequences [cd00068 at NCBI] - of the 60 amino acids that comprise the motif, there are only 14 positions where the consensus amino acid is present in the MAJORITY of proteins. There are only SIX positions where the consensus amino acid is present in three-quarters of the proteins - heck, you could almost define a homeobox as being [F19, V44 or I44, W47, F48, N50, R52] but that would leave out my favorite homeoprotein, which LACKS amino acids 46 and 47 !!).

Getting 14 positions exactly right (not that we need to) is a one in 10^18 chance.

But the HomeoBox is a subgroup of a more diverse H-T-H family of DNA binding proteins.

Let’s look at H-T-H sequences [cd00093], there are only 9 positions where the consensus amino acid is present in the majority of proteins, and getting nine amino acids exactly right is one in 10^11 (which number is, appropriately, the number of bacteria in one gram of excrement). Your calculations appear to be off by up to 10^20.

Finally, we actually know what is involved in moving from one H-T-H protein to another with a completely different function (provides resistance to superinfection by a different bacteriophage…) one in 10^5.

See pmid 4033758 and 3413061.

The H-T-H family, and its homeobox subset, are a fairly good example of of how accessible variations on a theme can create diverse functionality. I am surprised that you would pick them as your example of inaccessible sequence space. But then again, you did claim that the degeneracy in the genetic code mirrors the prevalence of the amino acids, which is wonderfully, wonderfully wrong (compare M with C, and K with S)

DNAJock

Sorry, cd00068 should read cd00086.

https://me.yahoo.com/a/VCNNdkJ8n848[…]6fbjhynPM5Uw–#7e243 said:

Let’s actually look at some homeobox sequences [cd00068 at NCBI] - of the 60 amino acids that comprise the motif, there are only 14 positions where the consensus amino acid is present in the MAJORITY of proteins. There are only SIX positions where the consensus amino acid is present in three-quarters of the proteins - heck, you could almost define a homeobox as being [F19, V44 or I44, W47, F48, N50, R52] but that would leave out my favorite homeoprotein, which LACKS amino acids 46 and 47 !!).

Getting 14 positions exactly right (not that we need to) is a one in 10^18 chance.

But the HomeoBox is a subgroup of a more diverse H-T-H family of DNA binding proteins.

Let’s look at H-T-H sequences [cd00093], there are only 9 positions where the consensus amino acid is present in the majority of proteins, and getting nine amino acids exactly right is one in 10^11 (which number is, appropriately, the number of bacteria in one gram of excrement). Your calculations appear to be off by up to 10^20.

Finally, we actually know what is involved in moving from one H-T-H protein to another with a completely different function (provides resistance to superinfection by a different bacteriophage…) one in 10^5.

See pmid 4033758 and 3413061.

The H-T-H family, and its homeobox subset, are a fairly good example of of how accessible variations on a theme can create diverse functionality. I am surprised that you would pick them as your example of inaccessible sequence space. But then again, you did claim that the degeneracy in the genetic code mirrors the prevalence of the amino acids, which is wonderfully, wonderfully wrong (compare M with C, and K with S)

DNAJock

So we now have four reasons why Joe is wrong:

1) Proteins don;t evolve, genes evolve. He isn’t even talking about the right molecule, let alone considering the genetic code.

2) Genes don’t evolve from nothing. In this case, we know the ancestral sequences from which the hox genes evolved, they were not random, so his starting point is meaningless.

3) His target is meaningless. We know that a wide variety of sequences work just fine, joe hasn’t done anything but hand waving, even though he knows that this dramatically affects the probability. Besides, with gene duplication which occurs frequently in hox gene evolution, nonfunctional intermediates or new functions can also arise.

4) THe calculations assume that al amino acids are equally frequent. This is not the case, but Joe hasn’t even considered this possibility.

WHen you put this all together it shows two things:

1) Joe is completely ignorant and is doing nothing more that attempting to fool people with fake calculations. Meanwhile, he can’t even begin to calculate the “information” in any real sequence. And all of this while he crows about what an expert he is!

2) The probability of a new protein arising through repeated rounds of random mutation and natural selection is undoubtedly many orders of magnitude greater than anything that Joe will ever admit to. That makes it a virtual certainly in billions of living organisms reproducing over billions of years.

3) Joe is still ignoring all of the examples and all of the real mechanisms by which new genes and new functions are known to arise. He is completely ignorant of the literature in this field. Who would take his word for anything?

DS said: 1) Proteins don;t evolve, genes evolve. He isn’t even talking about the right molecule, let alone considering the genetic code.

Er…yes protein do evolve…they do so through changes in genes, stoooopid.

2) Genes don’t evolve from nothing. In this case, we know the ancestral sequences from which the hox genes evolved, they were not random, so his starting point is meaningless.

We are talking about distinct protein motifs, stoooopid.

3) His target is meaningless. We know that a wide variety of sequences work just fine, joe hasn’t done anything but hand waving, even though he knows that this dramatically affects the probability. Besides, with gene duplication which occurs frequently in hox gene evolution, nonfunctional intermediates or new functions can also arise.

The sequences work fine because they are arranged in a highly specific syntactic arrangement, stoooopid.

4) THe calculations assume that all amino acids are equally frequent. This is not the case, but Joe hasn’t even considered this possibility.

Those amino acids in the sequence with relatively few codons make the calculation a conservative estimate, stoooopid.

1) Joe is completely ignorant and is doing nothing more that attempting to fool people with fake calculations. Meanwhile, he can’t even begin to calculate the “information” in any real sequence. And all of this while he crows about what an expert he is!

And what it your definition of “information”, genius?

2) The probability of a new protein arising through repeated rounds of random mutation and natural selection is undoubtedly many orders of magnitude greater than anything that Joe will ever admit to. That makes it a virtual certainly in billions of living organisms reproducing over billions of years.

And how did you calculate that one, genius?

3) Joe is still ignoring all of the examples and all of the real mechanisms by which new genes and new functions are known to arise. He is completely ignorant of the literature in this field. Who would take his word for anything?

And what exactly have I ignored, genius?

OK, enough. Everyone has had their say and everyone can claim victory, and now everyone is calling each other names. Further discussion can take place on the Wall. I am closing comments for this discussion.

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This page contains a single entry by Joe Felsenstein published on September 9, 2011 5:43 PM.

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