First off I must apologize for doing another post on a subject that’s been done to death around here, but I’ve been meaning to make a post about this for a while but other stuff kept coming up. Anyway, things have quietened down at work where I now only have to maintain some cell cultures, so I have a bit of time duing the christmas holiday.
My post, which is a repost of something I also brought up in a thread on Larry Moran’s sandwalk blog, is about a chapter in Stephen Meyer’s book Darwin’s Doubt and what I can, if I’m being generous, only attribute to extremely shoddy scholarship.
Having read the book, a recurring phenomenon is that Meyer time and again makes claims without providing any references for them. Take for instance the claim that the Cambrian explosion requires lots of new protein folds, from Chapter 10 The Origin of Genes and Proteins:
“Axe had a key insight that animated the development of his experimental program. He wanted to focus on the problem of the origin of new protein folds and the genetic information necessary to produce them as a critical test of the neo-Darwinian mechanism. Proteins comprise at least three distinct levels of structure:4 primary, secondary, and tertiary, the latter corresponding to a protein fold. The specific sequence of amino acids in a protein or polypeptide chain make up its primary structure. The recurring structural motifs such as alpha helices and beta strands that arise from specific sequences of amino acids constitute its secondary structure. The larger folds or “domains” that form from these secondary structures are called tertiary structures (see Fig. 10.2).
Axe knew that as new life-forms arose during the history of life—in events such as the Cambrian explosion—many new proteins must also have arisen. New animals typically have new organs and cell types, and new cell types often call for new proteins to service them. In some cases new proteins, while functionally new, would perform their different functions with essentially the same fold or tertiary structure as earlier proteins. But more often, proteins capable of performing new functions require new folds to perform these functions. That means that explosions of new life-forms must have involved bursts of new protein folds as well.”
In the whole section Meyer dedicates to the origin of novel folds, he makes zero references that actually substantiates that the cambrian diversification, or indeed any kind of speciation, or the that new cells types or organs, requires new protein folds. ZERO. Not one single reference that supports these claims. At first It reads like what I quote above, lots of claims, no references. Later on he eventually cites the work of Douglas Axe that attepts to address how hard it is to evolve new folds(and that work has it’s own set of problems, but never mind that). Axe makes the same claim in his ID-journal Bio-complexity papers (which eventually Meyers cites), but in Axe’s papers, that claim is not supported by any reference either. It’s simply asserted as fact. In other words, Meyer makes a claim, then cites Axe making the same claim. Neither of them give a reference.
Meyer mentions Ohno:
“The late geneticist and evolutionary biologist Susumu Ohno noted that Cambrian animals required complex new proteins such as, for example, lysyl oxidase in order to support their stout body structures. When these molecules originated in Cambrian animals, they also likely represented a completely novel folded structure unlike anything present in Precambrian forms of life such as sponges or one-celled organisms. Thus, Axe was convinced that explaining the kind of innovation that occurred during the Cambrian explosion and many other events in the history of life required a mechanism that could produce, at least, distinctly new protein folds.”
No reference is given here either. The claim is simply made initially, so it’s hard to check. Is Meyer and Axe willing to bet that a preceding evolutionary history of, for example, Lysyl oxidase cannot be found in structure and sequence of related molecules? That there ARE no related molecules? Is that his claim? That the Cambrian explosion required tonnes of bona fide Orphan proteins with no preceding history? Where are the references that support this? Did Meyer or Axe look for homologues of Lysyl Oxidase and found none?
It gets much worse, turns out Meyer is making assertions diametrically opposite to what his very very few references say. Remember what Meyer wrote above?
“The late geneticist and evolutionary biologist Susumu Ohno noted that Cambrian animals required complex new proteins such as, for example, lysyl oxidase in order to support their stout body structures.”
Well, much later in the same chapter, Meyer finally references Ohno:
“Third, building new animal forms requires generating far more than just one protein of modest length. New Cambrian animals would have required proteins much longer than 150 amino acids to perform necessary, specialized functions.21”
What is reference 21? It’s “21. Ohno, “The Notion of the Cambrian Pananimalia Genome.”
What does that reference say? Let’s look:
“Reasons for Invoking the Presence of the Cambrian Pananimalia Genome.
Assuming the spontaneous mutation rate to be generous 10^-9 per base pair per year and also assuming no negative interference by natural selection, it still takes 10 million years to undergo 1% change in DNA base sequences. It follows that 6-10 million years in the evolutionary time scale is but a blink of an eye. The Cambrian explosion denoting the almost simultaneous emergence of nearly all the extant phyla of the kingdom Animalia within the time span of 6-10 million years can’t possibly be explained by mutational divergence of individual gene functions. Rather, it is more likely that all the animals involved in the Cambrian explosion were endowed with nearly the identical genome, with enormous morphological diversities displayed by multitudes of animal phyla being due to differential usages of the identical set of genes. This is the very reason for my proposal of the Cambrian pananimalia genome. This genome must have necessarily been related to those of Ediacarian predecessors, representing the phyla Porifera and Coelenterata, and possibly Annelida. Being related to the genome – possessed by the first set of multicellular organisms to emerge on this earth, it had to be rather modest in size. It should be recalled that the genome of modern day tunicates, representing subphylum Urochordata, is made of 1.8 x 10^8 DNA base pairs, which amounts to only 6% of the
mammalian genome (9). The following are the more pertinent of the genes that were certain to have been included in the Cambrian pananimalia genome.”
The bold is my emphasis. I trust you can see the problem here. So, Meyer makes a single goddamn reference to support the claim that the Cambrian explosion required a lot of innovation of new proteins, folds, cell-types and so on. What do we find in that references? That Ohno is suggesting the direct opposite, that he is in fact supporting the standard evo-devo view that few regulatory changes were what happened, that the genes and proteins were already present and had long preceding evolutionary histories.
Later Meyer gets a ID-complexitygasm when he asserts, again without any support, that:
“The Cambrian animals exhibit structures that would have required many new types of cells, each requiring many novel proteins to perform their specialized functions. But new cell types require not just one or two new proteins, but coordinated systems of proteins to perform their distinctive cellular functions.”
Where does he get this? His ass, that’s where.
I could go back to discussing the OP.
Here is what you say the OP is about:
Those are your words.
What does the next sentence after the highlighted one say? It’s about scholarship. What do I go on to specify the scholarship is shoddy on? The claim that the cambrian explosion requires lots of new protein folds to emerge
Someone else earlier in this thread (also prior to Torley’s flailing OP on UD) brought up “new organs” and “new cell types”, and my response was “these things are not in dispute”. Because, already to begin with, and now, and not having changed at any point in time, it’s about protein folds and the cambrian explosion.
At what point is it going to sink in? Are you capable of getting it?
Let me link you a post I made in response to you, on the first page of this thread (now 4 days ago):
How many times do I need to make it clear to you?
Like I said, if you want to re-write your OP no one is stopping you. Good luck making it about new protein folds without making it about new proteins or new genes. Or, for that ,matter. about new cell types. You have my blessing to try.
I have a possibly stupid question. How do we know that any new protein folds, or cell types, were required in the Cambrian explosion? Couldn’t those have already been present in the organisms preceding the “explosion”?
From your OP:
I am not obligated to believe that Meyer here is talking about new protein folds when he says new cell types and novel proteins. That’s the spin you need to put on it, but that’s not what Meyer says.
Perhaps you could re-post your OP crossing out what Meyer actually says and inserting [protein fold] after what he actually says so that people can clearly see what you’re up to.
You’re even stretching it when it comes to the Ohno quotes:
Again, those are your own quotes. You even left out the explicit reference to Meyer saying ‘they also likely represented a completely novel folded structure,” because that had nothing to do with your argument at that point.
How many times do I need to make it clear to you?
The prior existence of new cell types is probably a much harder sell than the prior existence of proteins which is a harder sell than the prior existence of protein folds.
I’m not sure anyone here is disputing the origin of new cell types in the Cambrian. I guess we’ll see. I am a bit baffled by people who say that my producing evidence of the need for new cell types does not support Meyers’ claims.
Multi-cellularity preceded the animals but I haven’t had time to check out what that means as far as new cell types is concerned.
What I don’t understand is why anyone would have an opinion on this either way. Is it not quite conceivable that there was a rich diversity of forms prior to the Cambrian explosion that for whatever reason, was not preserved? Might not the “explosion” be an illusion? An artifact of global environmental conditions? I’d like to see the explanation of why our understanding of the Cambrian explosion demands that new proteins and cell types must have (relatively) suddenly arose.
I don’t know of anyone who would be willing to accept that hypothesis. It would wreak havoc on multiple fields.
Right, that’s not quite the point I was attempting to make (and doing a bad job at). Not that it’s an illusion, just that we are only privileged to evidence that may not fully represent what was happening. Suppose the life forms that look to us like they “suddenly” appeared in the Cambrian explosion were actually evolving slowly over time, perhaps in a relatively small geographic location. Conditions changed, populations that were once marginal flourished, and in the fossil record it appears as an explosion of new forms. Why necessarily the need for new proteins or cell types?
okay, I think I understand what you’re saying. You envision a population explosion. Actually the explosion of multiple populations. These populations preceded the Cambrian, but in limited numbers, few if any of which were fossilized.
Have I got it?
This still doesn’t rid us of the need for new cell types and proteins, it just shifts the date of their origin and leaves us without a cause for the Cambrian explosion itself. All of these otherwise disparate populations of animals suddenly experience huge increases in number within a relatively short period of time. Do we have a theory of why?
Change in environment?
That’s sufficiently vague.
Let’s again refer to the OP:
So now the scope isn’t just chapter 10, but rather the entire book. But not really, it’s really just about protein folds.
The OP provides an example [a for instance] in support of the more general claim. To now claim that the OP is about this singular example is disingenuous at best. There is, thankfully, no rule of this site that states that I must play along.
You can believe whatever you want. It is telling that I have not anywhere objected to Meyer saying new cell types are required for “new life-forms”.
I concede I had not anticipated this level of volitional obtuseness. It’s strange, though, that everyone on “my side” of this debate seems to have got it.
I’m not stretching anything, Meyer explicitly talks about Ohno when he says:
It’s clear that he’s saying he gets this idea from Ohno, and that apparently Axe had the same thoughts about distinctly new protein folds had to originate in the cambrian explosion.
When he finally references his paper, it does not support the claim that:
No I didn’t. It’s right there immediately after. What OP are you reading? What “at that point” are you talking about?
I’m curious now, are you willing to say and do anything to avoid conceding that Meyer has made claims he can’t support and which are, actually, in conflict with reality? Because that’s what it looks like.
There is nothing disengenuous about any of this. It’s been about protein folds from the beginning. Lots of people understood this, the only people who want to make it about generalized “new organs” and “new cell types” are you guys, apparently because it’s the only claim you think you can support.
If Meyer had merely talked about new cell types and organs, and never mentioned new protein folds having to originate in the cambrian, I would not have had any reason to think he can’t support the claim. It was the very fact that Meyer wrote about protein folds in the context of the cambrian that motivated me to start hunting down his sources, because my own understanding of the subject was that it was wrong.
If you feel the OP is badly written, tough shit buddy. There is no excuse for now not getting that it’s about new protein folds in the cambrian. So rather than keep blathering about things I consider to be irrelevant and have considered to be irrelevant from day 1, start interacting with the subject matter. If you wish to keep discussing how badly written you think my OP is, write a new thread about it and go masturbate in there. Whatever it takes for you to avoid dealing with Meyer’s failure of scholarship, apparently. Or do you actually still believe Meyer can support the claim that lots of new protein folds had to originate in the cambrian explosion? Or do you refuse to even discuss that subject because you’re somehow mad that’s not the understanding you got from the OP to begin with? Get over it.
Chitin?
That’s because it’s not the claim of Meyer’s that’s in dispute. That, together with new organs, is one of the claims that both makes perfect sense and is actually known to be correct.
It is also strange that I gave three references on page 1 of this thread, that talks about protein folds, not organs or cell types. If I believed Meyer was wrong about cells and organs, I would given references to show this.
Technically they probably aren’t necessarily originating in the cambrian explosion, at least the molecular clocks implied the evolved before, and that the CE is really just an artifact of fossilization.
But this does not rid us of the question how they evolved, it merely pushes it back. So maybe the actual “explosion” was somewhere in the Ediacaran, and possibly more dragged out (a slower controlled burning, rather than the implied all-at-once of the CE). But regardless, it would still be true to say that when the novel organisms we see in the CE appeared, their emergence would be accompanied by new tissues with novel functions. The dispute is not about whether there was a lot of innovation in the functioning of cells, so as to produce specialized tissues (bones, shells, skin, tendons, ligaments, filtering organs like kidneys, livers and so on), there definitely was. The dispute is about how this was primarily achieved, what mechanism was mostly responsible for producing these new functions (and how long all of this actually took).
Meyer spends some significant amount of time developing the claim that it would have required proteins that fold into novel 3-dimensional structures not seen before, and that these would have had to originate in the cambrian explosion.
But the consensus view of biologists is that it was mostly due to changes in gene-expression (as in re-using already existing genes, coding for already existing proteins with already existing folds) in different ways.
Meyer also spends some time dismissing evidence that the CE is largely a fossilization artifact, by trying to downplay anything found in the Ediacaran can be considered ancestral stages of life, and particularly the phylogenetics and molecular clocks that imply the Cambrian fauna actually extends back significantly before the cambrian. He knows his audience well enough that, if he can make it appear like it all happened together at virtually the same time, that will make them think there was a supernatural designer actively at work to make it happen.
That’s why Meyer makes the argument the way he does.
1. No reason to believe in any ancestors.
2. The novelties require new protein folds.
3. Relatively speaking, a very short interval of time.
Rather than what the evidence collected by phylogeneticists and paleontologists actually show:
1. Ancestral species stretch back (according to molecular clocks and Ediacaran fossils) in some cases up to 100 million years.
2. Mostly regulatory element evolution rather than de novo protein folds.
Chitin is the material of exoskeletons, claws, arthropod jaws, an important element of arthropod eyes. Mineralized* chitin fossilises extremely well. The evidence for
olderearlier* animals prior to the arrival of chitin cuticle is much more enigmatic; tracks, casts and burrows.ETA older -> earlier
ETA 2 add “mineralized”.
Dr (Ph D in philosophy) Torley in a comment at UD addressed to Dr (Ph D in Biology) Matzke:
Classic burden-shift, Vincent! If Dr (Ph D in history and philosophy of science) Meyer is claiming that “it’s more common, however, for proteins capable of performing new functions to require new folds to perform these functions” then he should be producing his evidence to support his (or your paraphrase) assertion.
Alan Fox,
Lizzie (PhD in music?) says that she knows more about evolutionary theory than Cornelius Hunter (PhD in Biophysics and Computational Biology).
Were you trying to make a point about academics?
Today, Lizzie knows more biology than Cornelius, same as she did five days ago when you last tried to make this same point. My reply stands.
DNA_Jock (Ph.D. in molecular biology, but no longer an academic.)
DNA_Jock,
Your reply (but Lizzie works in Biology!) stands. Its was as dumb then as now.
phoodoo,
You must have missed my next sentence, which was
I (and I was not the first) was alluding to the fact that Vince Torley refers to “Dr Meyer” and yet to “Nick Matzke” in his OP at UD. Do you think he was trying to make a point about academics?
PS Dr Liddle also has a Ph D in psychology, phoodoo.
Remarkable amount of word-gaming going on. Anything but admit that Meyer has anything to demonstrate in support of his thesis.
Depends on what you mean by “explosion”. Meyer’s explosion is not (for example) Erwin & Valentine’s explosion. The latter, which is mainstream paleontology, is a gradual expansion of eumetazoan diversity and disparity from around 560ma to 520ma, a less gradual increase in skeletonization starting around 550ma, and a window of Burgess-type preservation starting around 520ma. Meyer’s explosion is apparently nearly instantaneous, starting around 520ma with no precursors to speak of.
I’d be interested to know what either you, Meyer, or both of you think actually happened in the Cambrian, rather than a claim about what didn’t happen (evolution), in as much detail as you can muster. Then we could argue about the evidence for competing hypotheses rather than just trying to poke holes in or defend the standard theories. ID is a positive research program, right?
John Harshman,
Vincent Torley is using a classic fascist technique in propaganda.
Omitting the earned-and-deserved term of respect from one side while according it to the other is particularly effective in communication where the listeners will absorb the unbalanced message without consciously noticing.
The last thing Vincent Torley wants to do is make a point about academics. He’s not that dumb; he knows “his side” loses if that’s the point. All he wants to do is get his audience to react based on the unspoken lie: Matzke / nobody — Meyer / respectable Doctor.
Mung, are you denying that Meyer mentioned protein folds at all? If you accept that, then regardless of the other topics he may or may not touch upon in that chapter, you accept that he did cite a source that directly contradicted his claim on protein folds, without ever letting the reader know. That is dishonest.
Yes, that’s the idea. And it’s not so much shifting the date of the origins of new proteins and cell types, but extending the period over which these things evolved. The Cambrian explosion refers to the sudden (relatively) appearance of animal phyla in the fossil record, not necessarily the sudden appearance of animal phyla.
The origin of sponges has just been pushed back 60 million years, so it is likely that as micro fossil techniques improve, the record will improve.
After giving away the farm:
Ex-academic and English teacher, Vincent Torley goes on to demand:
Crashing to the ground? It never made it as far as a working hypothesis. The criticisms of evolutionary theory, which is all that ID proponents have managed so far, generally miss the target by misunderstanding evolutionary theory. There’s nothing to refute, Vincent. There is no theory of “Intelligent Design”.
I see a star rising. You need to hope Nick takes up surfing as a distraction!
Axe 2010 refuted.
This is my MS paint picture. All you need to know to see what is wrong with Axe’s work is in there.
The great irony here is that Axe and Gauger inadvertently test one of the popular (and very ad-hoc) design-postulates (similarity = common design), but deliberately ignore the evolutionary postulate.
They don’t do ancestral sequence reconstruction and try to infer the most probable ancestral sequence using phylogenetics (as evolutionary biologists would have them do). Instead, they do what many design-proponents postulate their designer did, they take one sequence (Kbl2) and try to directly convert it into another distantly related structural homologue (BioF2), by handpicking certain surface residues they speculate can capture the function of BioF2.
They discover that doing this BREAKS THE ENZYME. It stops working. Seemingly affirming the many claims of the creationists and ID proponents, that mutations invariably destroy function, that there are too large distances of nonfunctionality between isolated “islands” of function in the conceptual phenotypical space of protein functions.
But this is not what evolution postulates took place, this is NOT what is done with ancestral sequence reconstruction. Here both sequences (actually more, you need 3 sequences or more to do ancestral sequence reconstruction) evolved from a different common ancestor to both of them, they did not change directly one into the other. There was a long history of divergence from a common ancestor, that took a totally different evolutionary route than the direct conversion Axe and Gauger is attempting, and the result of which they deceptively use to insinuate falsifies evolution.
There are hundreds of excellent publications by actual competent evolutionary biologists and biochemists, utilizing ancestral sequence reconstruction to test ancient versions of extant proteins, and they all CURIOUSLY find functional intermediates, contrary to Axe and Gauger’s deceptive pretensions.
By the way, poor Vincent Torley can rest easy knowing my qualifiations are next to none. I’m a lowly lab-tech. Meyer’s much more qualified than me, which makes it all the worse that I have such an easy time picking his work apart.
Of course not.
The Ohno paper has nothing to do with protein folds. Meyer cites lysyl oxidase as an example of a new protein, not as an example of a new protein fold.
“The late geneticist and evolutionary biologist Susumu Ohno noted that Cambrian animals required complex new proteins such as, for example, lysyl oxidase in order to support their stout body structures. “
The proteins in the Ohno paper do have something in common, and it’s not anything to do with folding.
So, no, I don’t accept that.
Talking about lack of certainty about the functionality of unknown proteins, Vincent Torley lambasts the scientific profession;
Oh the irony!!!
Any suggestions from ID proponents how to proceed? Dr Axe? Anyone?
*guffaws*
Yeah, who’s the lazy bum here? Hunt clarifies that in that very review:
The uncertainties in estimating the densities of functional sequences are very high. Obviously, we all would like to home in on a narrower range. This is complicated by the technical and theoretical shortcomings of the various approaches. The “reverse” approach is tied to a single family of sequences and functions and makes assumptions that may not be warranted (Section 2 here is an example). The “forward” approach may find too many things, some (many?) of which may have no biological relevance. Sorting these things out is a tough nut to crack experimentally
So what is the evidence that the diversity observed in the Cambrian can be produced by natural selection, drift and neutral changes? How can we test the claim that changes to the regulatory networks can account for the diversity?
By doing phylogenetics.
That doesn’t support natural selection nor drift. It doesn’t even support common descent.
Sadly lacking from the OP. Surely you could have shown Meyer to be wrong.
But of course, just looking at Hox genes alone we know that there was diversification.
Oh okay, I can totally see how I was wrong all along under that powerful rebuttal.
Phylogenetics is lacking from the OP? What do you mean?
LoL! You have to make a case. All you did was say “phylogenetics” as if that is all there is to it. Unfortunately phylogenetics do not support the proposed mechanisms.
You do not understand the basics of phylogenetic inferences it seems.
No, I’m not going to explain it to you.
It’s the phylogeny, stupid.
That’s quite a new book. Have you actually read it? I haven’t, but I disagree with the sentiment. It isn’t a phylogenetic problem as we understand the term today. The phylogenetic problem is solved when we determine the phylogeny, i.e. that choanoflagellates are the sister group of metazoans and the basal relationships within Metazoa. It’s a problem of character evolution, which phylogeny can inform but which isn’t a phylogenetic problem.
I’ve read only sections. Haven’t completed any full chapter yet. Think I might skip ahead to Chapter 10.
Torley via Alan Fox,
Axe appears to basically be determining that new protein folds must return to the well of random protein sequence in order to discover a new fold completely from scratch. There’s no evidence this is what happened. In fact, if Axe is right, it would be impossible to do domain phylogeny.
Not that I think a more thorough refutation of Axe would cause the ‘scientific case’ for ID to go anywhere; that’s just rhetorical puffing. He’s saying what seems perfectly reasonable to people with a vague grasp of proteins (such as Hoyle). ‘Scientific’ refutation – including, indeed, the very techniques of phylogenetic reconstruction – elicit little more than blinking.
That’s the ‘anti-ID’ challenge, really, to present a complex case to people drawn almost instinctively to the simplistic one. ‘Stands-to-reason’ science.
Mung,
How dare he not make the OP about something other than what he made it about!
Yes, and?