The British biologist J.B.S. Haldane is said to have remarked that the discovery of fossil rabbits in the Precambrian would falsify the theory of evolution. Over at Evolution News and Views, Dr. Cornelius Hunter has argued in a recent post that the sea anemone (whose genome turns out to be surprisingly similar to that of vertebrates) is “the genomic equivalent of Haldane’s Precambrian rabbit – a Precambrian genome had, err, all the complexity of species to come hundreds of millions of years later.” Apparently Dr. Hunter is under the impression that many of these ancestral genes would have been lying around unused for much of that time, for he goes on to triumphantly point out that “the idea of foresight is contradictory to evolutionary theory.” RIP, evolution? Not by a long shot.
An unfortunate misunderstanding
Dr. Hunter seems to have missed the whole point of the report that he linked to. A sentence toward the end of the report would have set him right, had he read it more carefully (emphases and square brackets are mine – VJT):
It’s surprising to find such a “high level of genomic complexity in a supposedly primitive animal such as the sea anemone,” [Dr. Eugene V.] Koonin [of the National Center for Biotechnology Information (NCBI) in Bethesda, Md.] told The Scientist. It implies that the ancestral animal “was already extremely highly complex, at least in terms of its genomic organization and regulatory and signal transduction circuits, if not necessarily morphologically.”
That’s right. Genomic complexity and morphological complexity are two completely different things. That was the take-home message of the report. It was also the message of the other report cited by Dr. Hunter:
It is commonly believed that complex organisms arose from simple ones. Yet analyses of genomes and of their transcribed genes in various organisms reveal that, as far as protein-coding genes are concerned, the repertoire of a sea anemone — a rather simple, evolutionarily basal animal — is almost as complex as that of a human. (Emphases mine – VJT.)
As if that were not clear enough, Figure 1, on the opening page of the report, spells it out:
Figure 1: Animal miRNAs and morphological complexity. Grimson et al.3 (data along red lines) reveal the evolutionary origin of animal miRNAs by examining organisms at the base of the animal tree. Combining their data with previous work, three different measures of complexity become apparent: the number of protein-coding genes, total number of neurons and number of miRNAs. There is relatively little correlation between morphological complexity and the number and diversity of protein-coding genes. However, miRNA number correlates well with the organism’s total number of neurons. Indeed, a large proportion of vertebrate miRNAs are expressed in the nervous system. These data also show the dynamic nature of the miRNA complement in each lineage, particularly visible in rapidly evolving species (Oikopleura and fruitfly).
Morphologically, the ancestral animal was a very simple creature – so simple that the only real debate going on at present is whether it was more like a comb jelly (a creature with muscles, a nerve net and sensory organs, but no brain or central nervous system, pictured above, image courtesy of Kevin Raskoff) or a sponge (which is sessile and which lacks a nervous system altogether). Certainly it was nothing like as complex as a fly or a worm.
Genetically, however, the ancestral animal seems to have been in some respects better endowed than a fly or a worm. As the report cited by Dr. Hunter puts it (emphases mine – VJT):
The genome of the sea anemone, one of the oldest living animal species on Earth, shares a surprising degree of similarity with the genome of vertebrates, researchers report in this week’s Science. The study also found that these similarities were absent from fruit fly and nematode genomes, contradicting the widely held belief that organisms become more complex through evolution. The findings suggest that the ancestral animal genome was quite complex, and fly and worm genomes lost some of that intricacy as they evolved… The researchers also discovered that exon-intron structure is very similar between modern vertebrates and sea anemones. Both have intron-rich genomes and about 80% of intron locations are conserved between humans and anemones. Fly and nematode genomes, on the other hand, have lost between 50 and 90% of the introns likely present in the animal ancestor.
Building the Precambrian genome – was foresight required?
And what were these genes doing in the original ancestor, anyway? Is there any evidence to suggest that they were placed there in an act of foresight, to be used only by the ancestor’s distant descendants? I’m afraid there isn’t. Dr. Hunter has made an inferential leap here. He isn’t the only one: Dr. Stephen Meyer makes a similar criticism in a 2001 paper which he co-authored with P. A. Nelson and Paul Chien, The Cambrian Explosion: Biology’s Big Bang. Referring to Dr. Susumu Ohno’s now-famous paper, The notion of the Cambrian pananimalia genome (Proceedings of the National Academy of Sciences, Vol. 93, pp. 8475-8478, August 1996), in which Ohno proposed that “all those diverse animals of the early Cambrian period, some 550 million years ago, were endowed with nearly identical genomes, with differential usage of the same set of genes accounting for the extreme diversities of body forms,” Dr. Meyer objects that Dr. Ohno “envisions the pananimalian genome arising well before its expression in individual animals. Specific genes would have arisen well before they were used, needed or functionally advantageous” (pp. 31-32). However, in his paper, Dr. Ohno makes it clear that the ancestral genome he is envisaging was “rather modest in size,” and he points out that all of the five genes which he argues were “certain to have been included in the Cambrian pananimalia genome” were in fact useful to organisms back in the Cambrian period: indeed, it was possession of these genes that “made the Cambrian explosion possible.” Finally, I would like to pass on a rather blunt but factually accurate observation made by Dr. Nick Matzke, in a comment on an Uncommon Descent post I authored back in 2015:
…[B]ecause he’s not a paleontologist, one thing Ohno misses, IIRC, is that there is clear evidence of bilaterians in the Precambrian — trackways and burrows indicating bilateral symmetry, a coelom, etc., and these continually increase in complexity through the small shelly fossils, only reaching the “classic” Cambrian Explosion tens of millions of years later. This is all true regardless of one’s interpretation of the Edicarans etc. Thus, it’s idiotic to say, as Meyer does, that Ohno’s hypothesis means “the pananimalian genome ar[ose] well before its expression in individual animals.” Fossil traces of bilaterians are there before the Explosion, they had worm-level complexity, all of those common genes between all the phyla basically are what is required to specify a bilaterian body plan, which is what worms have.
In a follow-up comment, Dr. Matzke added:
There was, in fact, not a huge amount of origination of genes and proteins required to produce the Cambrian phyla, and we know this because they all have the same basic complement of genes and proteins. The differences that they have are basically due to differential duplication of genes and subsequent modification of genes, and sometimes rearrangement/recombination of pre-existing gene chunks.
A mea culpa
At the time, I was prepared to concede that Dr. Meyer was “probably wrong” on the the question of when these genes and proteins originated, and that they may have arisen long before the Cambrian period. I was even prepared to allow that the genes in the ancestral pan-animalian genome, back in the Precambrian, may have originally had functions of their own, that were later co-opted or ex-apted by their Cambrian descendants, giving rise to new functions. But it seemed to me that Dr. Meyer’s larger point – that the likelihood of even one functional protein fold originating on the primordial Earth was vanishingly low – was still valid. In the end, I thought that Dr. Douglas Axe’s 2010 paper, The Case Against a Darwinian Origin of Protein Folds, clinched the matter, since at least some new protein folds would have had to have come into existence during the Cambrian explosion, even if (as Dr. Matzke pointed out) there were only a few folds that were actually unique to bilaterian animals (the group of animals in which the Cambrian Explosion occurred), with just 17 new domains at the root of bilateria, (sponges and cnidarians having originated earlier).
How wrong I was. Last year, Rumraket wrote an excellent post debunking Dr. Axe’s claim that only about one in 1077 sequences of 150 amino acids was capable of folding and thereby performing some function — any function. There are, at the present time, no good grounds for accepting such a claim, and there are several grounds for treating it with skepticism. In my review (written last year) of Dr. Axe’s book, Undeniable, I describe how my own confidence in the much-vaunted one in 1077 figure was shattered, when I emailed some scientists in the field who kindly set me straight. I would therefore like to offer my belated apologies to Rumraket and to Dr. Matzke. They were right and I was wrong.
If you’re going to argue for design in the genome, this is not the way to do it. Here’s a better way, which doesn’t even use the word “design.” The facts speak for themselves.
Two questions for Dr. Hunter
Finally, I’d like to pose two simple questions to Dr. Hunter, regarding the papers he cited:
(1) Do you agree with the claim that humans are scarcely more complex (genetically speaking) than sea anemones?
(2) Can you cite a single proponent of either Intelligent Design or creationism who predicted this discovery, prior to 2005?
Complexity – good and bad metrics
Regarding (2), I can attest that leading ID proponents fought against the claim, tooth and nail, appealing to the “fact” that human beings have 210 cell types, while Cambrian animals had about 50 and sponges, only 5 (see this paper, for instance), and arguing that new genes and proteins would have been required to generate these additional cell types. However, the oft-repeated assertion that humans have 210 cell types turns out to be a myth, which has been roundly debunked by Professor P.Z. Myers. What’s wrong with this assertion?
The short answer: this number and imaginary trend in cell type complexity are derived entirely from an otherwise obscure and rarely cited 60 year old review paper that contained no original data on the problem; the values are all guesswork, estimates from the number of cell types listed in histology textbooks. That’s it.
And here are the original references cited to back up those figures about the number of “cell types” (a term which has never been explicitly defined) in various kinds of animals (emphases mine – VJT):
5. Andrew, W. 1959. Textbook of Comparative histology. Oxford Univ. Press, London
13. Borradaile, L.A., L.E.S. Eastham, F.A. Potts, & J. T. Saunders. 1941. The Invertebrata: A manual for the use of students. 2nd ed. Cambridge Univ. Press, Cambridge.
85. Maximow, A.A. & W. Bloom. 1940. A textbook of histology. W. B. Saunders Co., Philadelphia.
126. Strasburger, E., L. Jost, H. Schenck, & G. Karsten. 1912. A textbook of botany. 4th English ed. Maximillian & Co. Ltd. London.
Further comment is superfluous.
I’d also like to draw readers’ attention to a 2007 post by Professor Larry Moran, titled, The Deflated Ego Problem, in which he gently pokes fun at scientists who clung to the belief that the complexity of the human genome was far greater than that of “primitive” animals like flies and worms, and listed seven proposals (all invalid, in his view) for redeeming the complexity of the human genome.
Dr. Hunter’s statement that “we repeatedly find early complexity” when investigating the history of animals suggests that he would answer question (1) in the affirmative: our genes are about as complex as a sea anemone’s. As for morphological complexity, I can only state that as far as I can tell, there isn’t any straightforward way of measuring it, although I have no doubt that I’m structurally far more complex than a worm or a sea anemone. (Insects I’m not so sure about – see below.)
I understand that a recent paper in Nature (which unfortunately I cannot access) has finally addressed the origin and evolution of cell types in a rigorous fashion, and that Steven McCarroll’s Lab at Harvard Medical School and the Broad Institute is attempting to map the different kind of cells in the body, using micro-RNA.
I’d like to conclude with a quote from P.Z. Myers’ 2007 post, Step away from that ladder, on the subject of complexity, which is well worth reading (emphases mine – VJT):
I’m fairly familiar with the insect neurodevelopment literature, so when I saw papers saying arthropods only have 50-60 cell types, alarm bells started ringing...
I’m also familiar with some embryonic vertebrate nervous systems, and I can say that they tend to have many more cells in them — but they don’t seem to be as precisely identified at the single cell level as the invertebrate CNS. We have large populations of cells with similar patterns of molecular specification, rather than this kind of precise, cell-by-cell programmatic identity.
Now, from a genetic perspective, which pattern is more complex? I don’t know. They’re both complex but in very different ways — it’s basically impossible at this point to even identify a quantifiable metric that would tell us how complex either of these kinds of systems are. How many cell types are present in this whole animal? I don’t know that either… I bet it’s many more than 60, though.
I’ll go out on a limb and make a prediction: any difference in the degree of complexity, assuming an objective method of measurement, in the triploblastic metazoa [basically, all animals except sponges, placozoans, cnidaria and possibly comb jellies – VJT] will much be less than an order of magnitude, and that the vertebrates will all be roughly equivalent… and that if any group within the vertebrates shows a significant increase in genetic complexity above the others, it will be the teleosts. I’ll also predict that any ‘extra’ complexity in members of these groups will not be a significant factor in their fitness, although it might contribute to evolvability.
What do readers think? Over to you.
If you consider “shit happens” to be a prediction.
As far as your lack of education in the science of simplicity to complexity have you never read Dawkins? Climbing Mount Improbable and A Devil’s Chaplain both come to mind.
I agree, and that’s what my post did. If I had simply responded that he was mistaken then perhaps the “gotcha” that you and keiths both flew to could be defended. But I explained myself. Rather clearly.
I am the most reliable source I know. 🙂
Yes, you were responding to PaV and yes I responded to you.
If a simplification makes an organism more fit, the simplification will persist. evolution simply predicts that changes that improve fitness will tend to persist. More complex, less complex, larger, smaller, drunk parrot, sober parrot, makes no difference to evolution.
Simplification logically entails complexity. If you allow that things can start out complex then you may as well embrace Sir Fred Hoyle and beg his forgiveness.
I agree. We can usually rely on you to be wrong. But, in this, you are a rank amateur compared to FrankenJoe the drunk parrot.
🙂
It is good to hear that others also find me reliable.
Agreed. But once there is any level of “complexity” evolution does not predict that the only path forward is ever increasing complexity.
Nor does it predict that ever increasing complexity will stop. It doesn’t predict squat.
shit happens
Don’t forget it’s all descended from a common pile of S**T
peace
Mung,
You made a very dumb, very basic logic mistake. Don’t bother trying to bluff your way out of it.
Exactly how do we know what will improve fitness ahead of time so we can verify that prediction?
peace
Yes, I had to get a nights sleep though, since I was already staying up late.
Evolution doesn’t predict an increase in complexity.
It doesn’t follow that if evolution doesn’t predict an increase in complexity, then life had to start complex.
It doesn’t follow that if evolution does not predict an increase in complexity, then it doesn’t predict anything and is unfalsifiable.
You’re the one denying that a precambrian rabbit would falsify evolution and common descent. If you could believe in both a precambrian rabbit and common descent at the same time, what would it be descended from?
So you believe in a caricature of common descent that is not tied to evolution (descent with -gradual- modification) where anything goes: precambrian stuff giving birth to rabbits, invertebrates giving birth to vertebrates, etc…
It’s YOUR caricature of common descent that is unfalsifiable.
It’s YOUR caricature of common descent that “poofs” complexity into existence.
Poofing stuff is your thing, you mock it, you mock yourself. You can keep misrepresenting our position all you want to try and make it look as ridiculous as yours but that won’t change the fact that you’re tacitly conceding defeat right there
Hi Mung,
Back again. Just a few quick points about Dr. Hunter:
1./ As you correctly point out, he writes about genomic complexity in his article. My chief complaint is that he doesn’t differentiate between genomic and morphological complexity, when such a distinction is clearly called for.
2./ What Dr. Hunter doesn’t appear to realize is that the theory of evolution doesn’t predict an increase in genomic complexity over time, for any particular lineage or even for most lineages. The most one can say is that the “outer envelope” of evolution tends towards greater complexity.
3./ Also, there’s nothing in the theory of evolution that dictates that a creature whose morphology is more complex than its distant ancestor should also have a more complex genome than that ancestor.
4./ Even with regard to genomic complexity, Dr. Hunter is a little careless with his facts. We can’t really say that the genome of the original Ur-bilaterian was more complex than that of modern insects. We can say that much (say, around 50%) of the Ur-bilaterian’s original complexity has been lost in the insect lineage. But at the same time, insects have acquired new genes, over the last 400 million years, so comparing the complexity of their genome to that of the Ur-bilaterian is a bit like comparing apples and oranges. Cheers.
I think Dr. Hunter understands that is an not a prediction .That understanding is just not helpful to the point he is making.
You’re amusing keiths. Sometimes. But that’s not the same as being right. Wouldn’t the world be a better place if you didn’t start out assuming from the start that people can’t recognize even a very basic logic mistake and avoid making it?
I don’t need to bluff because I am “holding the nuts.” 🙂
Don’t blame me if you’re uncomfortable when I start to squeeze.
Again, you need to tell that to Richard Dawkins.
Hi VJT, thank you for your response. By your numbers.
1./ I hope we can just agree to disagree on this. I just don’t see the distinction as relevant to his argument.
2./ Perhaps one day I will do an OP on this, because if you read the writings of evolutionists, evolution certain must proceed from simple to complex. Granted, perhaps not predictable in any specific lineage, but without a progression from simple to complex you may as well believe in miracles.
3./ If genome complexity is unrelated to morphological complexity then it stands to reason that organisms are carrying around genomes that are unnecessarily complex. Under what evolutionary principle would they do so?
4./ I don’t think counting the number of genes is an indicator of genome complexity, but what do I know? 🙂
Best wishes VJT!
Earth to dazz!
what
No, Mung,
You made a dumb logic mistake.
You quoted dazz thus:
and responded (in your second repsonse)
That’s a failure to understand what ‘entailment’ means, your subsequent flailing notwithstanding.
Revealingly, you made the same failure to comprehend logic in your first response to the same dazz post:
Dazz:
You clearly failed to catch the import of the phrase that I highlight here, since you responded:
No. The alternative is that the statement is not universally true. Which was dazz’s point. Which you missed.
I hope that this isn’t a serious question.
How did you get Barry’s purse?
So you can confirm that you’re capable of making the same mistake as keiths. So what.
It’s semi serious.
The standard straw-man criticism of Darwinism is that we determine what is more fit by what survives.
I want to know how you would respond to that objection.
peace
Let me show you how it’s done Jock.
Well, Mung. I don’t believe you. I think you’re lying. I don’t think you gave a second thought to what you actually wrote and are now just trying to squirm out of it because you’re a dishonest turd.
Avoiding it doesn’t help you save face. You’ve dropped the ball multiple times on this one. Your admission that you intentionally avoid the relevant topics (not like it wasn’t plenty obvious anyway) only makes you look even worse
Nobody does self-righteous butthurt like the Mungster. 🙂
No. Mung,
I did not say that you were a dishonest turd; that was all you. I do think that you are flailing, though. You appear to be squirming, too.
In your effort to “show me how it’s done”, you omitted your final sentence to Neil, to wit:
No, you did not. You explained why the statement “common descent is an entailment of evolution.” was “simply mistaken”. Not any conflation you might claim dazz was making, the statement.
And your explanation consisted of demonstrating that CD could be true, but ToE false. Which is, if you know what ‘entailment’ means, not on point.
Dammit, Mung, if only you had thought just a teensy bit more about your choice of words, you might have come up with “You are mistaken.” , which might have provided an escape hatch. But you wrote “This is simply mistaken.”
“How it’s done”, indeed.
ROFL
By “common decent” do you mean universal common decent or just that two particular divergent organisms share a common ancestor?
Because it’s pretty obvious that the idea of universal common decent is an entailment of evolution is “simply mistaken”
peace
Isn’t common descent an entailment of evolution (descent with modification)?
Practically, it can often be difficult. However, the easiest are probably the “Red Queen” evolutionary scenarios, where you have predator and prey rather committed to dealing with each other, and all that can happen evolutionarily is that the prey get better at escaping, while predators get better at catching them.
Cheetahs preyed on pronghorn “antelopes” in America 10,000 years ago or so. If you’d been around when their ancestors first encountered each other, what would be a reasonable prediction for cheetahs and for pronghorns? They’ll both become faster animals. What else? There might be other factors, like dodging or what-not, but as long as there’s room for improvement on speed it’s almost certainly going to be selected for in both species. Speed will always be important for both cheetah and pronghorn.
In many cases the trade-offs will make robust predictions difficult to impossible, at least at the present time. Presumably, stronger, larger teeth will be of value to most toothed animals, but there’s always a host other factors involved that will prevent teeth from becoming ever larger, such as the need for bigger jaws with bigger teeth (with heavier heads, then probably with heavier bodies, so becoming less speedy and maneuverable without compensatory changes).
But relatively straightforward requirements, such as the need for speed in both predator and prey where outrunning the prey is important, are fairly predictable. So of course the cheetah is fast, and the pronghorn is still one of the fastest animals in the Americas.
Glen Davidson
Very good, fifth, you are paying attention. Darwin would agree with us.
Likewise, it’s pretty obvious that the idea that common descent [sans modifier] is an entailment of evolution is NOT “simply mistaken”.
But the thing that has us all rolling in the aisles is Mung’s attempt to demonstrate that “common descent is an entailment of evolution” is “simply mistaken” by showing that CD could be true, but ToE false.
Do you agree that THAT is irrelevant, fmm?
If CD is an entailment of evolution, falsifying CD would falsify evolution
If CD is an not entailment of evolution, falsifying CD would not falsify evolution
It seems to me that falsifying CD would falsify evolution. What am I missing?
DNA_Jock,
This would be much easier if there was a clear description of the ToE.
The Princeton Guide to Evolution
The Princeton Guide to Evolution is a comprehensive, concise, and authoritative reference to the major subjects and key concepts in evolutionary biology, from genes to mass extinctions. Edited by a distinguished team of evolutionary biologists, with contributions from leading researchers, the guide contains some 100 clear, accurate, and up-to-date articles on the most important topics in seven major areas: phylogenetics and the history of life; selection and adaptation; evolutionary processes; genes, genomes, and phenotypes; speciation and macroevolution; evolution of behavior, society, and humans; and evolution and modern society. Complete with more than 100 illustrations (including eight pages in color), glossaries of key terms, suggestions for further reading on each topic, and an index, this is an essential volume for undergraduate and graduate students, scientists in related fields, and anyone else with a serious interest in evolution.
Actually, organisms precede shit.
And I deny this. I nowhere made that argument. My argument had nothing to do with whether common descent is an entailment of evolution. And I say I am in a better position than you to know what I was thinking.
I wonder why the atheists here get so incensed when someone tells them what they believe. keiths bangs his head against this wall all the time and I see no reason for you to join him because it’s a fools errand. I know what I was thinking and you’re not about to change my mind about what I know I was thinking.
Why not take a page from Neil’s book instead. [ETA: Ah, I see you did. Sort of.]
It depends on what you mean by common descent.
Let’s say that life had three independent origins corresponding to three domains of life. Would that falsify common descent?
If evolution is descent with modification, what does it even mean to say that common descent is an entailment of evolution?
Evolution is descent with modification, therefore common descent is an entailment of evolution.
Have at it Jock.
Thanks for the honesty
In such a situation wouldn’t be “fitter” to evolve a way out of the particular predator/prey relationship? If not why not?
Again thanks for the honesty. Does the lack of robust predictions make Darwinism “evolution” difficult to falsify at the present time?
peace
I searched in vain for where my response to dazz said ToE or “theory of evolution.”
Well, no. So what?
If organisms evolve by slight modifications generation after generation, it follows that in the long tun you’ll get a tree of life: common descent
I did not understand that to be his claim.
It seems that to say that run of the mill common decent is an entailment of evolution is like saying that the existence of life is an entailment of evolution it’s sort of true but entirely trivial.
I thought common decent was being promoted as an entailment that distinguished Darwinian evolution from it’s alternatives and clearly it’s not that
peace
So by “common descent” you don’t mean “universal common descent.” So the theory of evolution does not entail universal common descent. Agreed?
Your position now becomes compatible with creationism. Congratulations.
If organisms evolve for any reason whatsoever or no reason at all by slight or large significant modification. It follows that in the long turn you’ll get a tree of life: common descent
peace
I’d thought that common descent is the most parsimonious explanation (i.e. “inference to the best explanation”) for the observed patterns of biogeography, embryology, paleontology, etc. — and that natural selection acting on inheritable phenotypic variability (which we do observe) is then posited as one of the mechanisms by which common descent is implemented.
Is that a misunderstanding on my part?
Man hunt antelope on foot. Antelope get faster. Man hunt antelope on horse. Antelope get faster. Man hunt antelope in car. Antelope get faster. Man hunt antelope in helicopter. Antelope get faster. Man hunt antelope in jet airplane.
…
I think it depends on whether one is trying to make logical deductions or whether one is trying to take an empirical (scientific) approach.
If common descent is a fact, or if evolution is a fact, then things like parsimony and mechanisms can be dispensed with. We can do philosophy rather than science. 🙂
And only science deniers question the factual status of common descent and the mechanisms of evolution.