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.
People hunt antelopes in jet airplanes?
I think he did
I see what you’re doing here, but — assuming your being serious and not facetious — I think it’s a terrible error.
The difference between philosophy and science is not that the former invokes posits and the latter doesn’t, but that the posits in science must be entangled in causal relationships that can be used to make predictions that can be confirmed or disconfirmed by measurements. The posits of metaphysical speculation aren’t constrained by that requirement.
I would never say that common descent is a “fact”; it’s rather the most reasonable inference to make from the available data, especially in light of consilience or convergence across multiple lines of evidence.
Say whaaaaat?
Just to be clear, Mung wrote
and then, immediately following this, he quotes the response in question, thus:
That’s a whole new level of flailing, mate.
Cue the “are quotations part of his response” flailing.
Was that supposed to make sense?
I agree.
“By making our explanation into the definition of the condition to be explained, we express not scientific hypothesis but belief. We are so convinced that our explanation is true that we no longer see any need to distinguish it from the situation we are trying to explain. Dogmatic endeavors of this kind must eventually leave the realm of science.”
Ronald Brady. On the Independence of Systematics
here
I’m hoping we’ll see more responses to your post than just mine. 🙂
I think you and I must be old school. Because I agree that what we have are certain “facts” which we gather into patterns and then attempt to explain via some theory or group of hypotheses.
“While dynamic sufficiency is an absolute and basic requirement for the building of an evolutionary theory, empirical sufficiency adds yet another stricture that may render a formally perfect theory useless. If one simply cannot measure the state variables or the parameters with which the theory is constructed, or if their measurement is so laden with error that no discrimination between alternative hypotheses is possible, the theory becomes a vacuous exercise in formal logic that has no points of contact with the contingent world. The theory explains nothing because it explains everything.”
Richard C. Lewontin. The Genetic Basis of Evolutionary Change.
For the benefit of fifth, colewd, and anyone else who is confused by this:
Mung’s mistake is a dumb and obvious logical error, and you don’t need to understand evolutionary theory in order to see that.
“B is an entailment of A” just means that if A is true, then so is B. In other words, A implies B. In standard logic notation:
If you want to show that “A → B” is mistaken, showing that that B could be true at the same time that A is false does not accomplish that. Why? Because “A → B” does not mean that “not-A → not-B”.
Simple example: Let A be “It was just raining” and B be “the lawn is wet”. Can I disprove “A → B” by showing that the lawn is wet and that it wasn’t just raining? Of course not. The lawn could be wet because I was running the sprinklers.
The right way to disprove “A → B” is to find a case where B is false and A is true. Stating that A could be false when B is true — as Mung did — doesn’t work.
Elementary logic.
It depends on how you are defining “common descent” and “evolution”. For example universal common descent is not an entailment of changes in allele frequency over time, ie evolution. Universal common descent is not an entailment of descent with modification, ie evolution. That said limited common descent, ie humans given rise to slightly different humans, is an entailment of descent with modification.
If you call hundreds to thousands of just-so genetic changes which we don’t even know will do the trick, parsimonious, then yes.
Keith’s mistake is a dumb and obvious logical error, and you don’t need to understand evolutionary theory in order to see that. My argument had nothing to do with whether or not common descent is an entailment of evolution.
I’ve explained that numerous times but better for him to ignore it so he can make more hay for his straw man.
What else is a “fact” in science but the most reasonable inference, etc., in cases where the inference is exceedingly strong?
Mung is having a(nother) bad thread.
You make things up. I point out that you made it up. Neil was the first to point out my alleged “mistake” and I promptly denied that I had meant what he thought I meant.
The facts don’t change just because you and Jock come along and repeat the same charge. You’re still not a mind reader and I still know why I didn’t say dazz’s comment was false and why you won’t be able to quote me arguing what you claim I argued.
And I granted that Neil had a valid point. And then he dropped it.
But you [keiths] can’t do that, because it would mean you are wrong. And we just can’t have that. Your problem.
From where I sit it’s not about proving that “A → B” is false. It all depends on what B is if is not a distinguishing entailment of A then the fact that “A → B” is trivial.
We have show that garden variety common decent is compatible with almost any thing including YEC.
IMO It cheapens the idea of entailment if you waste them on these sorts of trivialities
peace
fifth,
It was for Mung:
dazz:
Mung:
He actually thought he was contradicting dazz.
Another Mung logic fail.
Now he’s denying the obvious instead of acknowledging his mistake like a grown-up.
keiths, I acknowledged my mistake to Neil, but it’s not the mistake you need, so you have to ignore my response to Neil.
Now I know you’ve got just this one thing, so you have to ride it and ride it hard. It’s just the sort of thing we expect from your prodigious mental storehouse.
There’s a huge difference between something being entailed and something merely being compatible. Almost any idea in science is compatible with any number of logical possibilities (miracles, aliens, prankster gods), while entailments that are borne out by the evidence are comparatively rare. Generally, if only one reasonable (compatible with known causes, etc.) idea entails what is seen, then it is considered to be the correct idea.
Of course today’s evolutionary theory doesn’t entail just any old common descent, it entails the patterns of similarities and dissimilarities that we happen to see in life. What are the odds that bats and birds share “deep” (very ancient) similarities, yet share no similarities in adaptations for flight–except for the constraints produced by the ancient homologies?
That is powerful evidence in science, and anywhere else, such as in judicial matters. It never amounts to proof, partly because any number of logical possibilities remain even when cause and effect closely match up in a crime or in science, but the odds that the cause is responsible for the effect become very great when the specific effects are what are entailed by the causes.
That’s why it doesn’t matter much if the similarities and dissimilarities seen in life “could have been” created by a designer or some such thing. What would be the point? One would expect a designer to use similarities according to the function, not according to heredity. By contrast, you’d expect evolution to use similarities according to heredity, not according to function. What do we see? The latter.
It’s a matter of being reasonable. And because people defending their religious beliefs very often are not, they end up arguing unreasonably, assuming that just because the Designer could mindlessly parrot evolution during design, that it’s just as good an explanation as evolution, if not better for not being limited. But it is the limitations that demand more limited causes, such as those in evolution, and pretending that the Designer would mimic mindless evolution should be insulting to those who believe it is God.
The absurdity is that such an insulting view of God very often is held onto for dear life by theists.
Glen Davidson
It’s not just this one thing, Mung.
This is a huge compilation of failures on your part that you’ve been avoiding from the get go
So there are unspoken assumptions when you all talk about common decent.
To that I would agree.
The problem is that you seem to be claiming evolution entails “the patterns of similarities and dissimilarities that we happen to see in life”. but only defending run of the mill common decent as an entailment.
If you truly mean to say that by “common decent” you mean “the patterns of similarities and dissimilarities that we happen to see in life” then evolution is falsified every time our understanding of those similarities and dissimilarities changes.
clarity is important, Exactly what do you mean by common decent.
peace
I don’t see an objection to respond to. By definition, fitness is measured by those who survive. Or, more accurately, those who produce the most viable offspring.
No, when it comes to evaluating a theory it’s a matter of distinguishing entailment. That is what the scientific method is all about.
String theory and the Multiverse are not waiting for us to think reasonably before they are accepted as science. They are waiting for distinguishing entailments
What exactly are the distinguishing entailments of Darwinian evolution?
please be specific
peace
So evolution supposedly entails that the fittest will survive. and we measure fitness by those who survive.
And you folks claim that I use circular reasoning 😉
Do you realize that defined in that way survival of the fittest is an entailment of any theory whatsoever.
I’ll ask you the same thing I asked Glen
What exactly are the Distinguishing entailments of “evolution”?
be specific
peace
Why’d you make that up? No one brought up unspoken assumptions except you.
WTF? What even is “run of the mill common descent?
You don’t get to just make up things as you go along, so that you can disagree with them.
You don’t even spell “descent” correctly, let alone understand what’s being discussed.
Well that’s another very stupid thing to write. First, the understanding doesn’t change much, and generally we’re honing the theory when it does. If you have to play the ludicrous Corny game of pretending that any changes mean that evolutionary theory is “falsified,” it hardly matters, since a better theory then replaces that one.
Why don’t you try understanding, rather than misunderstanding? You’re clearly good at the latter, and needn’t demonstrate that fact any further.
Clarity is important, and you lack it in spades. Learn the science and you’ll know what I mean by that term (well, when written intelligently instead of your way). I’m not here to deal with every mindless bit of shit you want to throw at what you don’t understand, when there’s so little that you do understand.
Glen Davidson
No, it doesn’t.
I told you, you unintelligent jerk.
Learn how to spell, think, and learn something about evolution, for once.
If evolution does not entail universal common descent, well, then it not that kind of common descent. It’s the other kind. It’s the kind of common descent entailed by evolution. See how that works?
I love evolutionists.
No, what Glen means is that as we know more about how evolution happened, future discoveries won’t fit in an evolutionary narrative unless they’re consistent with previously existing data.
For example, evolution doesn’t predict that we should have a fused chromosome two, but if the evolutionary history has to be consistent with all that we know about our recent split with chimps and gorillas, and considering all of those have an extra pair of chromosomes, then the only way that the whole thing adds up from an evolutionary perspective is that two of our chromosomes fused in the human lineage.
Gravity on it’s own doesn’t predict the orbit of Mercury, but if you put all the other available data on the table (observed planets in the solar system…) gravity doesn’t work unless Mercury orbits the Sun in a very precise way
dazz, Glen said that “today’s evolutionary theory doesn’t entail just any old common descent, it entails the patterns of similarities and dissimilarities that we happen to see in life.”
And that’s just bullshit.
UCD is a more restrictive form of CD. UCD is an observation, for all I know: it adds explanatory detail to common descent.
It’s not “the other kind” of common descent, it’s a subset of it, perfectly consistent with the entailment of evolution and therefore perfectly consistent with the theory.
No it’s not! Current evolutionary theory is informed by new discoveries! That’s why “it doesn’t entail just any old common descent”
That’s why a precambrian rabbit would falsify evolution despite of your stupid objections!
Yes, we should all practice common decency.
</spelling-nazi>
It’s entailed by the rules of the site.
We measure resistance by calculating V/I. Yet Ohm’s law is not a tautology, and circuit theory is not circular reasoning.
http://www.talkorigins.org/indexcc/CA/CA500.html
Do you need a nap??
quote:
I was terrible in English. I couldn’t stand the subject. It seemed to me ridiculous to worry about whether you spelled something wrong or not, because English spelling is just a human convention – it has nothing to do with anything real, anything from nature.
end quote:
Richard P. Feynman
peace
Exactly what theory entails Ohm’s law?
peace
So the claim is that evolution entails that future discoveries will be consistent with previously existing data?
Doesn’t absolutely any theory that assumes continuity in nature entail this?
once again…..
What if any are the distinguishing entailments of “evolution”?
peace
I always assumed that this claim was a straw man. Apparently Acartia disagrees.
quote:
I don’t see an objection to respond to. By definition, fitness is measured by those who survive. Or, more accurately, those who produce the most viable offspring.
end quote:
I’m just trying to understand what the actual distinguishing entailment is.
can you help the skeptics out?
peace
fifth, quoting Feynman:
The difference is that Feynman’s sloppiness with language didn’t spill over into his scientific thinking, which demonstrated brilliance and rigor. Your scientific (and mathematical and philosophical and theological and computational) thinking, on the other hand, is just as sloppy, lazy and nonrigorous as your language usage.
You’re no Feynman, fifthman.
It’s a core part of electric circuit theory, though ‘resistance’ is usually generalized to ‘impedance’.
If you start with maxwell’s equations and hold the magnetic field constant you can derive Ohm’s Law.
Duh, of course. That’s why I used an analogy with gravity.
If any? LOL
If a “theory” has no entailments, it’s impossible to find data that’s consistent with it! That’s what explanatory power is all about!
Off the top of my head, a couple of entailments of evolution would be nested hierarchies and gradual change in populations. I’m sure the local experts can come up with a few more.
My point was that as more and more data becomes available, data itself narrows the spectrum of future data that would be consistent with the theory. The more we know, the “easiest” it is to falsify a theory. Again, the orbit of Mercury and Newtonian gravity would be a great example
This is basic stuff FFM. I mean REALLY basic.
When you creos ask for entailments, or what “we think” would count as supporting evidence for a theory, or what “we believe” would falsify this or that, you’re essentially admitting that you don’t know what the theory says because anyone should be able to derive those entailments from the theory itself. Science is not religion! it doesn’t rely on testimony, it’s not a matter of opinion!
Of course it’s not always so straightforward, it’s OK to ask the pros when we don’t understand a theory or what follows from it, but you get the idea. don’t you?
Survival of the fittest is a straw man. Evolutionism allows for the survival of the fit enough. And fitness is an after-the-fact assessment.
As for entailments, unless one defines what is meant by the words used then figuring out the entailments is a fool’s errand
Resistance is the proper word when using DC and impedance when using AC or some wave
Be careful, you might get punched by the tolerant left.
That is how to slap down PRATTs!