Molecular Genetics of Whale Evolution

Why could plants get the job done but not animals?

If you accept an ancient earth (including ancient humans) and natural selection, what is it that you object to in the theory of evolution and why?

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15 posts were split to a new topic: Common Descent: Humans and Chimps / Mice and Rats

I found an article from one of my science newsfeeds this morning: Whole-genome sequencing of the blue whale and other rorquals finds signatures for introgressive gene flow

I haven’t read it yet, but it might be relevant to the conversation.


It says, among other things, that a branch of baleen whales called the “rorquals” took 3 million years to diverge. When it happened, three lines split off quickly, but it took 3 million years of building with some gene flow before the breaking point. I just keep looking at that first chart with Pakicetus and the Ambulocetus where they are shown about 200K apart even though the differences between say, a blue whale and a finback whale are very small compared to that. Indeed those two may still be cross-fertile.

@T.j_Runyon (@swamidass)

I wonder if your views are so widely embraced by the Young Earth Creationists you seem to be defending.

Why are you convinced that God used common descent, if you think it is perfectly logical for God to have
used different methods just as easily?

Why would God select just a few primates to have a broken Vitamin C gene? The point of your objection doesn’t answer the question: Why would God go through so much effort to make it look like he used Evolution, if Evolution wasn’t a fundamental tool for God’s creation?


Nice article ! Here is the abstract for it:

Reconstructing the evolution of baleen whales (Mysticeti) has been problematic because morphological and genetic analyses have produced different scenarios. This might be caused by genomic admixture that may have taken place among some rorquals. We present the genomes of six whales, including the blue whale (Balaenoptera musculus), to reconstruct a species tree of baleen whales and to identify phylogenetic conflicts.

Evolutionary multilocus analyses of 34,192 genome fragments reveal a fast radiation of rorquals at 10.5 to 7.5 million years ago coinciding with oceanic circulation shifts. The evolutionarily enigmatic gray whale (Eschrichtius robustus) is placed among rorquals, and the blue whale genome shows a high degree of heterozygosity. The nearly equal frequency of conflicting gene trees suggests that speciation of rorqual evolution occurred under gene flow, which is best depicted by evolutionary networks. Especially in marine environments, sympatric speciation might be common; our results raise questions about how genetic divergence can be established."

The sentence I put a bold emphasis on, regarding fast radiation, once again demonstrates that the pace of Evolution has a lot to do with an life form’s population being able to respond to a propitious wave of environmental changes … - - “catching the wave” of changes that are most likely to lead to changes in form and structure.

If there hadn’t have been suitable areas where strong-finned walking fish could move up onto land easily, as well as having something to eat up on the land, evolution from fish to tetrapod could have been delayed for millions of years more.

If the planet-killing asteroid had not wiped out the giant marine reptiles, there might not have been as much of a reason for a land mammal to start foraging for food in the ocean margins - - fish populations appear to have become quite large in the absence of constant reptile predation. But, further, if carnivorous terrestrial dinosaurs were still roaming the continents, no land mammal could have become big enough to survive hunting for fish in coastal waters . . . there are no “tiny otters” in the world’s inventory of marine mammals.

I believe God used evolutionary processes. I believe there are good reasons a priori and a posteriori to think he would do so. I’m not sure in what universe I’m defending YEC. I’m arguing against their interpretation of the data…

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A post was split to a new topic: Does Evolution Rule Out God?

Evolutionary theory explains this mathematically and quantitatively. Show me the math by which you arrive at 10x more different.

actually the time were mouse and rat split off is estimate to be between 10-30 my. so its not realy a prediction (300% different).

In science when quoting a date there is always an error bar quoted as well to give an indication of how precise the measurement was. In this case split occurred 20 mya +_ 10 my

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an error bar of 300%?

Sure why not. Error bars tend to come down as more measurements are done, measurement technology improves. Cosmology had huge error bars in the time of Hubble and Einstein. Now with very sensitive measurement the error bars are less than 1%

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The “predictions” usually mentioned are not in presented in the way you are presenting. For example, because of the sudden nature of a multi-branched part of the whale “tree” that had baleen instead of teeth.
In a world of special creation, obviously God specifically made these whales without teeth, right?

Evolutionists predicted that we would find traces of “teeth” in the genetic signature of these baleen whales.
But that would be silly, right? Why would God put useless teeth genes in whales beautifully designed to use baleen?

And yet … the prediction that teeth were genetically incipient was predicted and confirmed!:

Evolution: A Theory with Bite
“If indeed modern whales are descended from ancestral, four-limbed, terrestrial ancestors, then those ancestors, like mammals in general, had teeth. Modern toothed whales (order Odontoceti) have retained those teeth to the present day, but baleen whales have adopted a new way of life as filter-feeders.”

“Researchers were curious to see if traces of a “toothed past” could be found in the genomes of modern baleen whales, so they went hunting for remnants of genes devoted to making teeth. Such defective gene remnants would be examples of pseudogenes, and we have discussed pseudogenes previously in this series.”

“[While pseudogenes in and of themselves are powerful evidence for evolution, pseudogenes that are “out of place” are especially so. One such example we have seen before is the human vitellogenin pseudogene, the remains of a gene used for yolk production in egg-laying organisms found in the exact location in the genome that evolution would predict for it. As mammals that receive embryonic nourishment through a placenta, we have no need of egg-yolk genes.]”

“Similarly, baleen whales have no need for genes responsible for making teeth, and finding the remnants of such genes would make a strong case for an evolutionary origin of baleen whales as the modified descendents of toothed whale ancestors.”

“Some of the genes known to be used in all mammals for tooth formation were the obvious candidate genes to start with: the products of the ameloblastin, amelogenin, and enamelin genes are all used in the formation of tooth enamel, the hardest structure in the vertebrate skeleton. Researchers went looking for these genes in several Mysticete (i.e. toothless whale) species. The results showed that all the species studied did indeed have these three genes present as pseudogenes…”

“Finding these genes as pseudogenes in toothless whales was exactly what evolution predicted, but there was a catch: none of the mutations that removed the functions of these three genes were shared between different species, suggesting that these genes lost their function independently in the species studied.”

“This finding was at odds with data from the fossil record, which suggested that teeth were lost only once, and early in the lineage leading to all modern toothless whales. So, the researchers seemed to have two lines of evidence that at face value contradicted each other. The fossil record suggested that tooth loss occurred once in the common ancestor of all toothless whales, but these three genes seemed to have been inactivated independently, several times over, suggesting that loss of teeth should be happening later in Mysticete evolution, and more than once.”

“One proposed explanation for the apparent discrepancy (among several put forward) was to predict that a fourth gene required for enamel formation was lost early in Mysticete evolution. The loss of any one gene necessary for forming enamel would be enough to prevent the process altogether. In this case, the loss of this fourth gene would prevent tooth enamel from forming, even though the genetic sequences of the other three enamel genes would still be intact. Once enamel function was lost, random mutations in the remaining enamel genes could then accumulate later in Mysticete evolution after speciation in this group was already underway.”

“To test this hypothesis, the research group went hunting for other enamel genes in toothless whales. The smoking gun for tooth loss in Mysticetes turned out to be exactly what was predicted: a fourth gene, necessary for enamel production, and mutated with the same inactivating mutation in all modern toothless whales. The gene in question, named enamelysin, was destroyed when a mobile genetic element called a SINE transposon inserted into it, breaking it into two halves and removing its function: [see image below]”

[ ^ Be sure to click on image to enlarge the text for easier reading! ]


By the way, a 300% error bar means “3 times”… not “300 times”.


This is evidently true, but then wouldn’t it also be an argument against Francis Collins assertion that “after the first cell, no special supernatural intervention was required”?

The case for secular versions of evolution (see Patrick!) is that random changes can be shown to be all that is needed for evolution to do what it has done (that “random” being left undefined and probably incoherent, but including mainly unknown but law-based changes).

The atheist accepts the same, demonstrable laws of nature as the theistic evolutionist, so if (as per Deb Haarsma and others) evolution is believed to be driven entirely, or nearly entirely, by divinely designed laws, that too is theoretically demonstrable, and evolution would then prove to be guided by the laws, the only difference between the atheist and the Christian being whether the laws are a brute undesigned fact or a divine provision - randomness would not enter the question at all.

If (as most biologists following Monod seem to believe) evolution is not entirely lawlike, but contingent, then there would arise a true competetion between the powers attributed to chance and the powers of real-time divine choices. In that case, given the rarity of beneficial mutations, there would seem to be some demonstrable loading of the mutational device in delivering so much help in so short a time to Mr Whale.

Of course, if evolution only works as it does because it is guided, then guidance is entering the empirical realm against Epicurean chance.


Thanks for stating this so eloquently, and even elegantly, @jongarvey . This is, in fact, the point I thought would be obvious when I raised this question in the first place. Cheers! Evolution, while demonstrably present, is simply not enough.

incorrect. since their split happened a long time ago evolution doesnt predict anything about that. if we were find no such pseudogene evolution will be just fine. and its also true for the rest “predictions”.


Please don’t ask me to reply to your posts. You do not understand general principles of science well enough to even discuss these points with you.