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.
You need to put quotes around “peer-reviewed” and “published”. Axe’s work was pretty much a set of blog posts; they just happen to call their blog a journal.
Mung,
Nor do I.
No, it’s even worse.
It was refuted in an MS paint picture I did years ago.
Yes, and whether there is enough time in the cambrian to evolve lots and lots of new protein folds. And whether the cambrian even required lots and lots of new protein folds. As you yourself understood to begin with.
And there isn’t enough time in the cambrian, but the lots and lots of new protein folds aren’t required, as the one single reference Meyer gives argues, to the detriment of Meyer’s actual argument.
There isn’t enough time, period. Ever. That’s the argument of chapter 10. It follows from that, that there was not enough time in the Cambrian. It’s not a premise, it’s not the conclusion, it’s a corollary.
http://dictionary.reference.com/browse/corollary
Mung,
Axe’s work is the protein equivalent of saying that, because he tried to get by bus from New York to LA and got stuck in Chicago, it’s impossible that anyone ever made the trip.
One study I recall had him targetting residues on the protein surface. There is no evolutionary process that does this. Relax the mutational constraints and the landscape changes greatly.
Precisely because protein space is so large and the number of pathways so vast, you can’t prove its general inexplorability by historic life by simply failing to get anywhere in a small set of lab experiments.
There is much evidence from both the living world and the lab that the corner of protein space occupied by ‘real’ enzymes’ is rich in function and interconnectedness. There are many more mutational methods available than simple point mutation, and this exponentially increases the number of pathways, which is already pretty huge.
One can generate random proteins, within certain constraints, and pull out function at a rate easily obtained by the kinds of numbers living organisms throw at it. One can tune these random hits by selection. This is an actual application, with a bottom-line, that simply would not be possible if protein space were structured as Axe and fellow ID-ers appear to hope and feel he has ‘proven’.
Finally! Something we can agree on. 🙂
Is there some reason you are avoiding answering this question?
Did you just not see it?
If you follow the link that Patrick provided it begins as follows:
stcordova,
You need to show that the changes were substantial in a telescoped time frame. Otherwise they’re totally irrelevant to Meyer’s case. And for that you need a comparative study, bring in sister groups where available, all that. You need to embrace phylogeny! To repeat: it’s not just a question of comparing two proteins, when there are hundreds more available to help fill in the gaps.
That significant changes have occurred in Yeast and mammals since the common ancestor of their LOX’s is hardly going to be a matter of dispute here. What are we talking – 1.5 billion years’ worth of change, doubled for the 2 separate lineages?
Fundamentally, the authors of the Nature paper were happy to accept a phylogenetic history for LOX prior to the origin of metazoa. Not being as well-versed as them in all the ins and outs, I’m happy to accept it too. If you aren’t, you could take it up with them!
Mung,
Perhaps you could be more specific about which of Axe’s work you think refutes the claim that protein space is well-connected where it matters? The J. Mol Biol. paper is just talking about the entirety of space. Life doesn’t explore the entirety of space. It sticks to the corner with folds (where enzymes are concerned, at least).
I’m sure it exhibited the finest standards of scholarship.
stcordova,
I profoundly disagree.
Where was that claim published? Please don’t give me a link to a blog post. 😉
Mung,
Yes, I would disagree, though I’m not sure this is Meyer’s argument. You can’t really make any statement about protein space from that statistic.There are probably many more possible folds, but Life likely has the repertoire it needs.
Still, if there are only 1300 folds, but there are 10,000 different proteins per species and (say) 1,000,000 species, we could naively say that there are 10,000,000,000 different representations of those 1300 folds, or each fold has an average 7.7 million different ways of making it just in current life alone. (This will be an overestimate because of course many species have identical sequences.).
Not easy, no, But note that there are many, many ways of combining amino acids to make an alpha helix for instance, one of the basic structural units. It would be an easy enough matter to go from one alpha helix to a completely differently-sequenced one one letter at a time. Axe could try it. This is why, even with continuously functional proteins, common ancestry signals can, over time, be completely wiped out.
From the OP, quoting Ohno:
Actually, wouldn’t it be a pre-Cambrian pananimalia genome?
Me quoting Mung:
Mung,
It did the job. Heck, a carefully composed Twitter tweet could do the job.
(Peer review is just the first hurdle — any paper is then subject to scrutiny by experts in the field. Axe’s does not stand up to such scrutiny.)
Why does the Cambrian explosion necessarily have anything to do with protein evolution? Protein evolution could have merrily proceeded along for billions of years before the Cambrian explosion and continued afterwards. The fact of the Cambrian explosion does not have to be explained by the evolution of new proteins, just the utilization of existing ones. “New proteins” is an answer to a question that nobody is asking.
Axe chose to study a single protein, penicillinase. It’s a bad idea to make sweeping generalizations from a single example.
It’s also a bad idea to base an argument (aka religious apologetics) on limited science, which is what Meyer did twice, in his 2009 Signature in the Cell and again in Darwin’s Doubt (2013).
It’s as if nothing has happened in the study of structure-function relationships in proteins since 2004, the date of the Axe revelation.
It doesn’t necessarily. In fact, the case that I have been making in this thread is that the argument in chapter 10 of Meyer’s book only brings in the Cambrian as a corollary, not as a premise or even as the main conclusion. IOW, you have to read the entire chapter, not just two pages of it.
True. Meyer doesn’t dispute this. In fact, his argument relies upon it.
…in the classical model of gene evolution, random mutations must thrash about aimlessly in immense combinatorial space, a space that could not be explored by this means in the entire history of life on earth, let alone in the few million years of the Cambrian explosion. (p. 204)
And I think that’s an extra-ordinary claim that requires evidence. The claim that all the proteins needed by all the new Cambrian animals were already there, just waiting [the pananimalia genome], needs to be supported.
Axe is a liar and a con man isn’t going to cut it though. So can we rule out that it will be composed by Elizabeth?
But the evidence indicates he is a liar and a con man. Axe is way too scientifically savvy to not know his “declare ID is correct then cherry pick the evidence to support the claim while ignoring all the contradictory data” is dishonest non-science.
Chapter 10 of Darwin’s Doubt is titled The Origin of Genes and Proteins. It is subdivided into 11 sections and is 24 pages.in length (pp 185-208). It is primarily and fundamentally about the work of Douglas Axe involving functional protein folds and not about the Cambrian explosion per se at all.
Here’s a page by page breakdown of the mention of Cambrian explosion or Cambrian animal(s) / forms.
p. 185 0
p. 186 0
p. 187 0
p. 188 0
p. 189 1x
p. 190 0
p. 191 4x
p. 192 0
p. 193 0
p. 194 0
p. 195 0
p. 196 0
p. 197 0
p. 198 0
p. 199 0
p. 200 0
p. 201 0
p. 202 0
p. 203 0
p. 204 1x
p. 205 7x
p. 206 4x
p. 207 0
p. 208 1x
Pages 205 – 206 are where Meyer makes the connection (in a veritable explosion) between the Cambrian and what has come before in all the prior pages in the chapter. The references on p. 191 are in the section that Rumraket quotes from in the OP (The Importance Of Folds), but that’s not the section where Meyer makes his argument concerning the Cambrian (To Build An Animal).
Anyone with the book can verify this. This supports my claim about how the chapter ought to be read and understood.
Next I’ll support my claim that the main argument of the chapter encompasses the entire history of life, and not just the Cambrian.
Yes and I’m sure you make Elizabeth proud. After all, you’re doing no more and no less than she did. You both surely know how to attract more people with more diverse views to the site!
There are plenty of blogs and forums where people with like priors can hang out and scoff at those who do not share them.
Why don’t you trot off now and see if you can’t find one more to your liking Adapa.
Merry Christmas!
So you don’t deny there’s lots of evidence Axe is indeed a liar and a con man. That’s a good start on honest behavior Mung. I didn’t think you had it in you.
Well, it’s not really even a claim. When we’re trying to explain the diversity of forms that came out of the Cambrian explosion, protein evolution isn’t one of the explanations we look to. It’s not really on the radar. First of all we don’t have a record of what was going on with respect to protein evolution, we only have fossils (and inferences from comparative genomics). So, I think we have to assume a sort of “steady state” of protein evolution before and after the event.
Indeed, the facts of the Cambrian explosion, and our attempts to explain what was going on, do not in any way involve claims about protein evolution.
That sounds pretty reasonable, as long as you meant to include during the event as well and not just before and after. Much more reasonable than saying there were no new proteins or protein folds needed. It’s not like protein evolution would just halt during that particular time frame. 🙂
Well, with the holiday coming up I hope to find time to do some more reading/research. Meyer covers the various explanations for the Cambrian explosion on offer, I’ll check to see whether any of them include anything about protein evolution.
I have the Erwin and Valentine book which I’ll check.
I’d also like to look into the claims about the requirements for new types of proteins for new cell types and tissues/organs.
A lot on the plate just on this one issue, lol.
Mung,
Merry Christmas to you.
Regarding supposed similarity of lysyl oxidase in yeast vs humans, there is not very much in the amino acid level, and most certainly not at the level of nucleotides when the entire gene (with introns) is considered. The genes are so different, one can at most argue only for functional convergence, maybe 9% amino acid pairwise similarity (which is only maybe barely above random), but only 0% above random (random is around 25% similarity) at the nucleotide level.
Can we say ORFan or TRG?
The amazing thing is all that exon splicing translated to a protein that had only 9% similarity between yeast and human, and given that maybe 5% is random, that ain’t much above random!
I ran BLAST of the nucleotide sequences, and the result are even worse. Do evolutionists ignore the introns as if they don’t count for anything? Is the idea introns=junk needed to maintain an evolutionary story line?
Here is the result:
Read that, NO SIGNIFICANT SIMILARITY FOUND! Pretty much 0% above random.
The reader can run his own BLAST comparison:
The human LOX gene with introns:
http://useast.ensembl.org/Homo_sapiens/Gene/Sequence?g=ENSG00000113083;r=5:122063195-122078285;redirect=no
The Pichia Pastoris lysyl oxidase gene
http://www.ebi.ac.uk/ena/data/view/AF358434
One can understandably criticize Meyer for the way he phrased things, but clearly the human LOX gene is novel relative to the functional counter part in yeast.
This is akin to comparing a carburetor in a carbureted engine to a fuel injector in a fuel injected engine — they may work toward the same final result in mixing gas with air, but their mechanism and structure are different. At the very least, there is NO DATA that indicate lysyl oxidase in yeast has any structural similarity worth mentioning to lysyl oxidase in humans, certainly almost no amino acid similarity, and no nucleotide similarity above random for the genes that code the proteins.
One is still free to assert organismal phylogeny, but one can’t assert it for the lysyl oxidase genes in particular.
One thing that can be appreciated is how similar functions can be converged upon by such different genes much like engineers creating the same function in engine systems via different means.
If phylum specific TRGs are in the range of 5% to 20% of the genes, that could be a problem for explaining the Cambrian explosion if they require high specificity.
It is an interesting question if lysyl oxidases implementations are phylum specific. The Nature paper on the origin of lysyl oxidase seemed to not want to touch some of the problems I just highlighted, I would suspect unwitting confirmation bias was in play.
Thank you! And I wish you a Merry Christmas as well.
I was thinking I’d give everyone here a gift and stay away, but maybe I’ll be on and just behave myself. 🙂
Happy New Year!
(Does this post break any “guidelines?)
For those following the lysyl oxidase discussion, Meyer brings it up again on p. 206.
…as previously noted, many of these Cambrian animals needed the complex protein lysyl oxidase to support their stout body structures.
Again citing Ohno.
No doubt. 🙂
We really shouldn’t take all Ohta’s ideas about the Cambrian explosion all that seriously; consider his bizarre misunderstanding of Hallucigenia, for example. Likewise his ideas about the time from the ur-bilaterian to the end of the Cambrian explosion are naive.
A few points:
1. Pairwise comparison is a terrible way to assess evolutionary relationships. A huge taxon sample is more likely to enable reconstruction of intermediates. I don’t know if human and yeast lysyl oxidases are homologous, but you haven’t tested that question at all.
2. Introns are junk, which is why they evolve comparatively quickly. They aren’t useless at all in phylogenetic analysis, but they don’t work on anything as ancient as the divergence between humans and yeast (and this is made worse by pairwise comparison). They work find for divergences within birds, though.
…the generation of the incredible diversity of animal forms is largely a consequence of the formation of new networks of gene interactions and new ways of regulating these interactions. Most gene families basic to the metazoan developmental toolkit evolved very early in the history of animals (and some within their ancestors) and have been highly conserved during their subsequent evolution.
– Erwin and Valentine p. 264
Here’s what I take from this:
1. gene families basic to the metazoan developmental toolkit code for functional proteins/enzymes.
2. they evolved very early in the history of animals
3. Some evolved in the ancestors of the animals
Fair reading?
In the section, Expansion of Cell Type Numbers and Functions, on page 279 of Erwin and Valentine:
…many cell lineages have certainly evolved functions that were not within the range of their ancestral cells…
Frustratingly, they failed to cite their source.
ETA: This is all in the context of the Cambrian explosion.
That may be what ID proponents generally believe. I’m sure it is. There are no references that support this. Axe’s work doesn’t support this. Axe argues it, to be sure, but that is another matter for the purpose of this discussion. I recommend you start a new thread if you want to discuss whether that is actually true.
What I’m focusing on here is whether the cambrian diversification really did require lots and lots of new protein folds to originate in the cambrian explosion, because they supposedly didn’t exist in any precambrian organisms.
In chapter 10 Meyer talks about Axe first, to argue that lots and lots of new specialized protein folds would have to accompany the diversification of the cambrian explosion (but strangely enough doesn’t give a reference where Axe supports or even argues this).
Then later in chapter 10, Meyer finally mentions Ohno:
Where he says this, there is no refernce to Ohno, that comes even later.
Eventually he finally produces a reference, where he says:
So, lots and lots of new distinct protein folds would have had to not just originate(be generated) in the cambrian, they also have to be large. As he says to begin with: “When these molecules originated in Cambrian animals, they also likely represented a completely novel folded structure unlike anything present in Precambrian forms of life“
They’re in his mind new, have no ancestral homologues, and were divinely created in the cambrian. You yourself agreed with this claim, it made sense to you.
The reference is (Ohno 1996) http://www.ncbi.nlm.nih.gov/pmc/articles/PMC38696/.
Which argues the opposite of what Meyer is imagining. That there was almost no new protein evolution in the cambrian, that the vast majority of them pre-existed in the pre-cambrian animals and single-celled organisms. That they had evolved long before the cambrian.
In other words, the complete opposite of: “When these molecules originated in Cambrian animals, they also likely represented a completely novel folded structure unlike anything present in Precambrian forms of life“
I fully admit my MS paint picture is not a scholarly piece of work. But I’ve been told that’s okay when you write for a lay audience. At least I’m not referencing material that argues the diametrically opposite of what I myself is arguing.
1. Genes can move around by duplication and shuffling. It happened in the LTEE. The citrate transporter was put under control of a different promoter active under aerobic conditions.
2. Introns are known to move around too. And mutate a lot faster than much more conserved protein coding regions, because they’re mostly just junk.
3. The yeast and mammalian LOX’s are separated by over a billion years of history.
4. Phylogeny is not constructed with two sequences. You’re missing the big picture Sal.
You’re just pulling random and irrelevant facts that do nothing to alter the facts of the phylogeny of Lysyl oxidases, out of thin air in some desperate attempt to try and insist there is no basis for thinking they’re related.
Edit: I see Allan has explained this to you several times also. We can see a gradual progression of dissimilarity in the LOX’s the more distantly related the organisms are.
If we really only had two LOX’s, one in yeast and then one, virtually identical version in all mammals, then you might have had a point. But that’s not the situation we are in.
.. who argues the diametrically opposite of Axe. That the molecule (and many others) existed in pre-cambrian life and had evolved long before.
So it does not support Meyer’s claim that “When these molecules originated in Cambrian animals, they also likely represented a completely novel folded structure unlike anything present in Precambrian forms of life“
Fair but not entirely correct.
The gene families are not so much enzymes (though I’m sure there are some) as they are regulatory elements. Many of them are proteins to be sure, but they’re often proteins that just bind to specific sequences of DNA, or each other, either to initiate or prevent transcription. DNA binding domains (or folds, if you will) go back the entire history of life. These are the kinds of molecules that evolve by duplication and point mutations, they don’t have to originate de novo and then by some extreme luck happen to produce a DNA or protein-protein binding domain from somewhere isolated in protein sequence space.
Yes but there’s a big difference between a new cellular function and a new protein fold. A new cellular function could be to “produce a shit-ton of extra-cellular collagen” (of which the effect could be to form a tough tissue, like a sinew/tendon) or “significantly stiffen the cytoskeleton”. Both of which can be accompanied by changes in regulation of already existing protein-coding genes, instead of having to produce entirely new protein folds never before seen in life.
Mung,
I don’t think the claim is being made that the Cambrian explosion is ‘explained by the utilisation of existing proteins’. That’s not really a causal explanation at all.
But to the extent that change in protein was involved (which, to some extent, it must, since that is essential to divergence) it is easy enough to check whether a given protein is present in a sister group to the animal clade, and hence was present in a common ancestor – ie, ‘pre-existed’.
It is incumbent on a proponent of the ‘gene novelty’ theory of Cambrian diversification to provide the evidence, not on doubters to do the spade work as if they are the ones making the ‘extraordinary claim’. Exaptation and functional continuity through serial amendment are very ordinary claims, for anyone with a working knowledge of gene families, protein chemistry and phylogeny.
stcordova,
That’s just obtuse. You’ve done a BLAST (a tool written in 1989, based on one particular way of analysis) and come up with a figure of 9% end-to-end acid similarity by interpreting two figures. Then you bring in silent substitutions (which are expected to erase all signal after 1.5 billion years!) and come up with 0%.
Then you decide that that 9% can only be due to homoplasy. Why? I mean, you don’t even believe in homoplasy! You have given no reason to exclude erasure of the remainder of the signal of common descent from a common ancestor. You have made zero reference to any intermediates that would resolve this question.
‘Maybe barely above random’. Care to put some statistical flesh on those bones? There are many circumstances where ‘9% above random’ (even if that were a valid approach) is definitely not random. It’s not just a question of matching single positions protein-wide and ignoring clustering. Proteins are not under uniform constraint along their entire length, still less the bitwise nucleotide sequence. Your approach is invalid.
stcordova,
No, introns simply aren’t under the same evolutionary constraint as a position that leads to an amino acid. They change faster, so erase signal quicker. You can see that in phylogenetic analysis!
stcordova,
Sal, don’t just compare the two deeply-separated sequences if you have more! It’s just silly.
Mung,
This has been extensively discussed. Ohno does not say they needed a new lysyl oxidase. This is how Meyer (and you?) are interpreting this. They need extracellular crosslinks, which might be a novel application, but the lysyl oxidase function was already present, utilised intracelullarly. You can tell from the distribution of homologues.
Many of the structural proteins of multicellular animals have homologues in primitive eukaryotes or even bacteria – actin, myosin, for example, aren’t just used for animal locomotion.
All the focus on yeast vs humans can be traced back to a lame, chemically inaccurate, joke of mine. But it is funny how these have become the sole residents of the data set.
Let the readers see an example where there is substantial amino acid sequence similarity, the classic example that generated the cytochrome C dayhoff diagram:
http://chemistry.umeche.maine.edu/CHY431/Cyto-Seq.jpg
Contrast that to the supposed phylogeny of the lysyl oxidase and one will see that even under the assumption of organismal UCA the lysyl oxidase looks like functionally convergent TRGs, not UCA products. Hence Meyer’s mention of lysyl oxidases being novel for animals stands.
As suggested by two papers above (one on TRGs the other on enzymatic convergence), the idea of evolutionary convergence and TRGs is a mainstream idea. I don’t know why my opponents in this discussion want to insist on “UCA explains all patterns” even when there are no patterns to speak of.
The complaint of BLAST being 1989 is like complaining about calculus being old math. BLAST is a heuristic of the Smith-Waterman optimal alignment concept. Like minima and maxima of calculus, there is a certain quality about the concept of optimal alignment that doesn’t become obsolete.
The failure isn’t the BLAST comparison, the failure is this “UCA explains all” mentality even when clearly UCA is a lousy explanation for the divergent lysyl oxidases.
The lack of similarity is especially obvious when the presence of similarity is easily seen for classic phylogenetic examples such the cytochrome-C protein and the 16s Ribosomal RNA(DNA):
http://biotech.bio5.org/sites/default/files/pdf/16s%20rDNA%20SeqAnal.pdf
Let the reader scroll down to see the following comparison of the 16S ribosomal RNA(DNA):
vs. Yeast
That’s what real nucleotide similarity looks like! Not the imagined patterns that Rumraket and Allan Miller insist exist, but which I’ve demonstrated (with the actual sequences and BLAST tools no less) does not. They are arguing for imaginary entities which can plainly be seen not to exist. I’ve just provided two examples where similarity is discerned (one example at the amino acid level and one at the nucleotide level). Hence the OP is based on a mythological entity that careful examination of the actual amino acid sequences, post translational modifications, and underlying nucleotide sequences has demolished.
Despite the fact Meyer might have phrased things to be more clear, Meyer’s point about mammalian lysyl oxidase (contrasted with lysyl oxidase of a unicellular eukaryote) — Meyer’s point — stands.
PS
Even the cytochrome C and other molecules under the assumption of phylogeny create enormous paradoxes like molecular clocks running at different rates for different proteins, and what is especially bad is INTRA (within group) lack of divergence. But at least cytochrome C gives more phylogenetically believable sequences than lysyl oxidases between yeast and humans.