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.
No, there isn’t. In the ellipses Meyer simply offers the Cambrian explosion as an example [“in events such as the Cambrian explosion”]. Not as the only time new proteins and protein folds appeared.
What I am attempting to do is get people to follow the argument through to it’s conclusion. If you disagree with the conclusion fine, but first we have to get there.
So far I haven’t seen any lies, Nor have I seen any premises which are false. Not looking good for the critics, but it’s still early.
Yes there is Mung. The whole of Meyer’s book is about the Cambrian explosion. It is one of, if not THE largest diversification of animal life in the fossil record. Meyer absolutely relies on this fact when he also talks about “new animals” requiring “new cell types” which in turn require “new proteins”. The whole thing is about the Cambrian Explosion being too short a time for all those supposed new proteins to evolve. That’s the entire conclusion of the book. Too much in too little time. “Virtually overnight”.
No, clearly Meyer isn’t claiming that the Cambrian is the ONLY time when new protein folds appeared. But he IS claiming that the Cambrian would have required LOTS of new protein folds to appear BECAUSE it is a period of very rapid diversification of life.
That is, after all, why he claims:
It’s about the Cambrian being too short a time, for lots of new protein folds to appear. That’s the argument. A “not enough time in the Cambrian” argument.
No, you are actually trying to CHANGE the argument now. You’re now trying to bring Meyer’s argument AWAY from the Cambrian.
Mung, Meyer is relying on you not seeing anything. After all, you didn’t bother checking his references. I did.
I think Morton has lend you his demon.
Mung,
Elizabeth is pretty good about criticizing the content not the posters.
Good for her.
The question that many biology bloggers have asked is why Meyer made such rookie mistakes in Doubt. His underlying thesis is undeniable: the Cambrian produced too many new animal forms to be accounted for by undirected evolution.
The problem with the book is that his thesis is unsupported and wrong. It gets wronger and wronger with time, but it was clearly wrong when he wrote the book.
One obvious question is why would an honest person quote mine. Incompetence, or the need to support the unsupportable. And if it was an honest mistake, why no retraction after dozens of reviewers have pointed it out?
Mung,
Your Meyer quote is FALSE for the reasons outlined by Rumraket.
Well, she does know more about biology than either of those two. As do a number of other posters here. If you were willing to, you could learn some biology here.
To be honest, I’m a little shocked that a school as good as Illinois gave Cornelius a Ph.D.; maybe they just did it as a favor to Shankar to get CH out the door. It’s happened before. CH’s publication record is, err, underwhelming.
Meyer has a B.S. in Physics and Earth Science, not biology.
I agree with petrushka that Meyer’s failure to retract the more egregious errors (in both books) is highly suggestive.
DNA_Jock,
Why are you quoting what Meyer’s degree is in then, if you believe a degree in music is just as useful as a degree in Biology to consider yourself to be the expert.
Do you have the same problems with logic as our founder?
What’s your publication record like Jock, care to share with us?
Well, some people think Meyer has a degree in biology. He doesn’t. Lizzie, on the other hand, works as a biologist. But the qualifications (or his lack thereof) aren’t the basis for my judgement; it’s the stupid things he writes.
It is better than Cornelius and Stephen combined. I only mention the appeal to authority to illustrate the one-sided way in which IDists use it.
DNA_Jock,
So you are not using an appeal to authority, except when you are using an appeal to authority?
It’s not Meyer’s expertise that is principally being questioned here, it is his agenda and whether, as appears to me it does, it filters through into his ability to be objective. As others have said, the facts are against him. The diversification that occurs over the period when we know we have multicellular eukaryotes, certainly by 600 million years ago and likely 800 million years ago to the fossils of the Burgess shale of around 500 million years ago is largely a result of hard parts, shells, chitin exoskeletons etc. A process of diversification covering a period of 300 million years can hardly be described as an explosion.
He answered the question that you asked!
How on earth could you possibly know that? We haven’t even gotten past the first premise yet. If his argument turns out to have nothing to do with the Cambrian then it would be a non-sequitur. But we don’t know that yet.
And even if it’s a non-sequitur, it doesn’t make it false or a lie.
Are you so convinced that you are right that you are utterly unwilling to actually examine the argument? If that’s the case please say so because if you’re not willing to look at the argument you’re just wasting my time.
Just another evangelistic tent meeting at TSZ. Gathering the faithful. Who needs arguments anyways.
Which argument?
The reasons set forth in this post?
Mung,
As opposed to the IDists, whose critical and impartial evaluation of Meyer, Dembski, Hoyle, Shapiro and Behe is an example to all.
The one that begins with the text I quoted.
Which argument is Rumraket utterly unwilling to actually examine? Have you made an argument here about the Cambrian Period?
Mung,
Ah, not an argument about the Cambrian Period.
You left out Denton, Axe, Gauger, Richards, West, Marks, Ewert, Berlinski, Johnson, Moreland … I could go on.
Consider that nearly all the mammals larger than shrews, and all the birds species, have evolved in 60 million years.
Regulatory networks are pretty cool.
Allan, you’re just jealous because our tent is bigger than your tent. 😉
Mung,
Yes, and none of them escapes your gimlet eye. But it turns out, none of them has ever been wrong. Ever. They have passed the toughest test known to science: convincing an IDist of the correctness of an ID argument.
The lysyl oxidase in yeast has almost no sequence similarity to lysyl oxidase (LOX) in mammals, hence it is arguably a different protein that might do comparable function in some mammalian contexts, but not in others.
The yeast vs. mammal LOX also arguably has different folds and different specialized functions. Meyer wins this round, and all this slamming of what was written in popular press looks like straining at a gnat with the most uncharitable reading possible.
The relevant quote is behind the paywall here:
http://www.ncbi.nlm.nih.gov/pubmed/14690425
The OP treats Meyer’s popular book like a peer-reviewed paper. The issue of lysyl oxidase, in light of the above quotation seems to suggests Meyer is saying something that is no a surprise to people who are familiar with the family of LOX molecules and LOX folds. Meyer is right, and about the only complaint that can be mustered is there wasn’t adequate reference in a popular book even though I’ve just demonstrated, this is knowledge available in scientific literature for those willing to look rather than scoff.
What Meyer says is also believable for reasons stated in papers such as this (even though some of the data was for pre-cambrians, it still drives home a point):
http://www.ncbi.nlm.nih.gov/pubmed/19716618
It’s early too early to tell which side is right, but if TRGs are strongly diagnostic for identifying each phylum, even if they are not necessary to make a new bodyplan, they are non-the-less associated with explosion of new phylum- specific features that came with the Cambrian explosion.
There is dissent against the notion the Hox genes alone are the evo-devo cure-all for emergence of new body plans.
One can complain of Meyer’s writing style for a lay audience because it doesn’t read like a document for a specialist audience (which is the OPs complaint), but the evidence so far may eventually agree with his claim of new proteins and new folds needed for new features.
Merry Christmas.
PS
As a matter of transparency, I don’t even own Meyer’s book, I’m merely responding to the OP and comments.
I’m Ok with the OP talking about beating a dead horse because beating a dead horse is far more ethical than beating a live puppy.
But if they were right, one would be enough.
Because I can read the words you post, I understand the language, it is functionally entailed by the sentences you write.
The premise is functionally established in every single quote I have brought from Meyer. The book is even called Darwin’s Doubt: The Explosive Origin of Animal Life and the Case for Intelligent Design.
You’ll note it isn’t called Darwin’s Doubt: The slow fuse of de novo protein evolution over the entire history of life.
In Meyer’s short description of the book, it says:
It’s about the Cambrian Explosion, Mung. Didn’t you read the book?
So you didn’t read the book or the quotes I gave? That’s AMAZING. Then now is the opportunity for you to read the book. And remember to read the quotes I give. The title of his book. And the book description. And the blurbs from book reviewers on the books’ website. Notice all that stuff about the cambrian, the origin of novel proteins and novel genetic information, required for the “explosion” of animal life in the cambrian.
Mung, I’m not wrong, and instead of engaging in volitional denial, I suggest we move on now that the fact has been totally and unambigously established that Meyer is indeed arguing that the cambrian explosion does not have enough time to generate all those new protein folds supposedly required for the explosion of animal life.
No, that much we agree on. It is, however, false and a lie as I have shown now in multiple posts with references.
I am convinced that I, like all the positive reviewers of Meyer’s book writing the blurbs on his website, understood what the book was about. I understand the argument. I even said that it made some intuitive sense, just like you have been arguing. After all, as you yourself said:
So it seems we both understood the argument perfectly well. But now suddenly and curiously, you think it’s not about the cambrian after all. How did you manage to confuse yourself so much, and why are you now suddenly the only person who understands Meyer to making general comments about the entire history of life, instead of the Cambrian in particular?
That is truly remarkable Mung.
petrushka,
Absolutely! The basic biochemistry is where the heavy lifting gets done. Once you have eukaryotes and multicellularity, it’s just topology! 🙂
Try reading all my posts on the first page of posts. Read the papers. Read where I quote Meyer. Read what Meyer writes when he references Ohno, then read the Ohno reference. Generally, allow yourself to look at the information. Stop posting here, start reading.
Rhetorical question followed by ellipses, article behind a paywall.
What could go wrong?
Mung,
Not that much longer, actually. You’d run out of names long before those dismissive of intelligent design creationism run out of Steves.
Rumraket, one of our rules here is that you must assume (not believe, you are free not to believe it, of course) that fellow posters are posting in good faith. So suggesting a fellow commenter is lying is not permitted.
stcordova,
Do you have any hard data to support this? I freely admit I didn’t provide any.
Patrick,
I was alluding to “100 authors against Einstein”. Though raising 100 ID authors might be a bit of a struggle!
Alan Fox,
I got that reference!
Putting them back in their graves even more so.
(Hmm, maybe it’s time to lay off the zombie novels.)
Right. But is beating a dead horse more or less ethical than beating a dead cow?
🙂
No Mung. These posts:
Rumraket,
Rumraket,
Rumraket,
A word of warning Mung: when you write things like that, you appear very, very dumb. Site rules…
Allan,
Thank you for asking. First of all, my understanding is that a paywall paper can be shared if you are helping me review and understand it’s contents. Would you at all be interested in the paper in question? It goes into agonizing detail of which Beta domains etc. are missing compared to other LOX implementations, etc. Lot’s picture from the X-ray crystallography to boot. You should salivate over this paper with your background in chem…..
There is a Nature paper on the LOX evolution, but it was painfully focused on phylogeny rather than comparative structural differences in the proteins. The Nature paper didn’t even bother pointing to what I just highlighted above.
If you PM me with an e-mail I can transmit the paper to, I can send you a PDF unless there are technical glitches. Use an e-mail address that you can throw away or something just to protect you.
Finally, Larry Moran might want to take up the issue of comparing the LOX in mammals vs. PPLO. It doesn’t have to be and ID vs. evolution question, but simple structural biology type question. If for nothing else it might clear up what Ohno meant!
Even though we disagree, at least maybe both of us can take away some meaningful knowledge for both of us in this discussion. The chem and physics stuff should be more my focus anyway. I’ve strayed too much into the philosophical lately.
Merry Christmas.
I don’t know if anyone posted this defence of DD.
http://www.evolutionnews.org/2013/10/does_darwins_do078001.html
Meyer states over and over that his argument is not god of the gaps, but then proceeds with his premises:
Which is just the gospel of god-of-the-gaps restated in the idiom of ID.
Rumraket, I am working within the confines of your OP using material you quoted. I ought to be able to assume that your OP is actually addressing that material, and in fact you clearly say it is. If you want to move the goalposts I cannot stop you. If you don’t want to actually address the argument which you yourself quoted, I cannot force you. Yes, the book is about the Cambrian explosion. So what. I’m looking at the argument that you quoted in the OP. You’re free to join me, or not.
Allan seemed to get it. Perhaps that’s why he all of a sudden went off on a tangent.
For good reason: the phylogeny is the point.
Here’s a link to the open access Nature paper (“Origin and evolution of lysyl oxidases”):
http://www.nature.com/articles/srep10568
Did someone forget to mention the “Phylogenetic trees of LOX enzymes in eukaryotes and prokaryotes”?
Arguably does not equal data.
One might expect it to have “almost no sequence similarity”. No matter, as it has structural homology with pfam01179, which you’ll find in pufferfish, zebrafish and, oh-err, MAN. i.e. Human diamine oxidase.
Not if you look for the right homolog. Meyer’s argument falls flat on its face, if you avoid making assumptions based on nomenclature.
Couldn’t find the homolog in the gnat, sadly.
Pedant,
Oh, Jeez. Meyer was even more wrong than I thought.
Does the man do zero research?
Pedant,
Thanks for the link Pedant. From the paper, I see:
Our phylogenetic analyses show a significant expansion of LOX types during metazoan evolution, giving rise to three LOX families in Porifera (sponges)* and two superfamilies in Eumetazoa (bilaterians and cnidarians).
*my emphasis. And there is evidence Porifera were around 800 million years ago!
I don’t know what argument Rumraket is talking about, I do know the one I am talking about. It’s the one I’ve consistently been quoting from in this thread. Here’ s the statement in full, from the OP:
Now, I ought not have to point this out, but here is the conclusion;
That means that explosions of new life-forms must have involved bursts of new protein folds as well.
Now, obviously, that would include the Cambrian explosion. But it does not depend on the Cambrian explosion. The Cambrian explosion is not a premise in the argument.
That’s such a shitty tactic of phoodoo’s.
I’m astonished that phoodoo is not ashamed of himself when he sees his own words in black and white.
It has low sequence similarity because it’s separated by almost a billion years of evolution. What is remarkable is that there is even any similarity left. That is what implies they evolved by common descent.
What would be remarkable was if there was NO lysyl oxidase (copper amine oxidases) homologues, and many other unique protein folds, in anything but animalia. If animal forms originating in the cambrian had large amounts of novel protein folds with zero homologous sequences or structures in anything that predated the cambrian.
That is why Meyer’s argument actually makes sense, because it would be true that the cambrian would be too short a time to produce vast swathes of novel protein folds in direct proportion to the animal diversification.
But that is simply not what we find, as Meyer’s own single reference also argues against. And as the many other references brought also show.
Nobody’s saying it is the same exact, carbon-copy identical enzyme that now exists in animals (not just mammals) doing the exact same thing. That would be amazing if it is not part of some super-critical basic cellular function no cell can live without. The point is there was an ancestor from which the lysyl oxidase we see in animals, evolved from, long prior to the cambrian explosion. It was there in fungi hundreds of millions of years prior to the cambrian, and the ones we see in animals and yeast today, are both derivations of that ancestral version.
What do you mean it “arguably” has different folds? Does it or does it not? If it has a different fold then it isn’t a lysyl oxidase. It is classified as such because it has THE LYSYL OXIDASE FOLD.
Is that one “arguably” too or do you actually have a reference for that?
I have a reference here about yeast lysyl oxidase (I’m at home so can’t access it before I get back to work tomorrow, but the abstract is interesting):
Edit: I notice that further down you yourself reference this paper, but I’m leaving this in because I’m lazy and can’t be bothered rewriting my post now 😛
The crystal structure of Pichia pastoris lysyl oxidase.
Note the thing in bold there. Funny stuff. Despite having the same overall fold, it is still different yet can do the same thing the mammalian version can .
That is straight up delusional.
That’s amazing. You’re bringing the same reference that argues against your position. Cordova, that reference is a point in favor of evolution and the established view of the cambrian explosion. It basically argues that you can almost entirely change the amino acid sequence of copper amine oxidases and yet they retain lysyl oxidase function in extremely distantly related organisms.
You people live in opposite-land. Where up is down and where evidence for evolution is evidence against evolution. What the actual fuck.
No, the op simply exposes the book for it’s dishonesty and failure to bring evidence that supports it’s claims. Meyer is citing a single reference that argues the opposite of what he claims. Pop-sci books don’t get a pass on such dishonesty either.
What the f… are you talking about? Meyer is literally claiming lysyl oxidase had to arise de novo at the base of the cambrian. He brings it up as an example for that very purpose. Literally everything we have both read, quoted and referenced so far, including Meyer’s own fucking citation, argues the diametrically opposite.
What Meyer is saying IS a surprise to anyone who’s actually bothered to come into contact with the literature.
No, Meyer isn’t at all right. Meyer is clearly and unambigously wrong.
What the FUCK is going on inside your head right now? Dude, you YOURSELF brought a reference that shows yeast lysyl oxidase can do the job of the mammalian version. It has basically the same structure. Both are derivations of an ancestral version. The sequence changes over time, but the overall structure and function is more conserved over time.
The stem metazoans identified in that study are removed by 540 million years of evolution. The fact that they each contain ORFan genes argues AGAINST them having to emerge in the short period of the cambrian explosion. Rather they are the result OF those susequent 540 million years of evolution. And besides, only very very few of them have been shown to have any function as you yourself acknowledge.
No, them being ORFans means they WEREN’T present at the cambrian. Rather it impies they have emerged gradually over those subsequent 540 million years of evolution after the stem groups diverged. Instead of all popping up de novo in less then 10 million years at the base of the cambrian.
Another question is, what do they look like? How many of them have resolved crystal structures? After all, yeast lysyl oxidase is almost entirely different in sequence from mammalian lysyl oxidase, yet is still clearly related in structure and function.
But since the vast majority of these putative ORFan genes are both of unknown structure and function, just because they have no sequence similarity to any known protein it doesn’t mean they don’t actually evolved from something else pre-existing for a significant amount of time. Given the fact that these are unresolved questions, it is highly disingeneous to try to save Meyer by appealing to unknowns about ORFan genes.
That makes sense, because it would be stupid to claim that Hox genes alone are the evo-devo cure-all for emergence of new body plans. As such, it just looks like an absurd and absolutist strawman of what is usually claimed. If we could, perhaps, refrain from making such blanket all-or-nothing statements, it would improve the discussion a bit?
No, the OP’s complaint is that Meyer’s claims are without support for most of the text, and where there’s an actual reference, it argues the opposite of what he claims. I have many pop-sci level books about a pretty diverse set of topics. I have yet to run into a case where an author argues the direct opposite of what his references say.
I know. I was talking about Meyer. The claim is Meyer is lying. Mung suggested he wasn’t, then I responded that I think he (Meyer) did. I don’t think Mung is lying.
Urk. Not that goddamn dishonest creationist slur about Darwin again.
Words cannot express how much I hate any person who tries to sneak that slur into discussion.