The evolution of whales, porpoises, and dolphins—the “cetaceans”—is well understood thanks to a plethora of fossils, mostly found in recent years (for a good general summary of the data, go here). Starting from a small, deerlike artiodactyl living around 48 million years ago (Indohyus may be related to the common ancestor of whales), this evolution proceeded rapidly, with the two groups of modern whales—Odontocetes (toothed whales, including dolphins) and Mysticetes (baleen whales), diverging only about 12 million years later. In other words, in a mere 12 million years—only about twice the time since we diverged from the lineage that led to modern chimps—evolution went from a terrestrial artiodactyl to a fully marine whale. That’s surely macroevolution, however you define it, and gives the lie to the creationist claim that major transitions aren’t seen to have occurred over time. (I discuss much of the fossil evidence in Why Evolution Is True).

Here’s a diagram of the evolutionary sequence of some of the forms, and the times they appear in the fossil record, taken from the UC Berkeley site Understanding Evolution. 

During this brief period, cetacean ancestors lost their hind legs and developed a fluke, the body became streamlined for swimming, body hair was lost (not needed in a fully marine whale), the nostrils evolved backward into a single blowhole, a lot of adaptations for diving evolved, as well as the ability of the species to collapse their lungs when diving, a layer of blubber evolved, and there were many other physiological and anatomical changes. These are described in a new paper in Science Advances (click on screenshot below, pdf here, reference at bottom of the post).

But the authors are not so concerned with the well-documented morphological changes, for they wanted to see what genes had changed, in particular, which genes in the ancestors of whales had been inactivated during whale evolution—inactivated because they were of no use to fully marine mammals.

To find these genes, the authors looked at whole genomes of cetaceans (bottlenose dolphins, killer whales, minke whales, and sperm whales) and compared them to the genomes of 62 placental mammals. They found 2472 genes in cetaceans that were broken: genes having deletions, stop codons, splice-site mutations, “frame-shift” mutations, and other changes that kept these genes from being expressed. They then carved out a subset of these genes that were not inactivated in 95% of the terrestrial mammals they used for comparison, so the broken genes were largely unique to all cetaceans. That took the sample of broken cetacean genes down to 350.

They then excluded genes already known to be broken in the cetacean lineage, including olfactory receptor genes (I discuss the loss of “smelling genes” in whales in WEIT) and keratin-associated genes, most involved in hair formation.

Finally, they excluded genes known to be broken in the closest living relative of whales—the hippopotamus, whose “broken genes” are not associated with a marine way of life. This left the authors with a final sample of 85 genes that were inactivated in all sampled whales (mysticetes and odontocetes) but not in their living relatives; these were presumably genes that got broken in the common ancestor of the two groups of whales, and whose broken state was passed on to all living cetaceans.

Why would a gene become inactivated in a group? Well, presumably because it’s not needed. But there are then two ways that a non-useful gene could become broken via the accumulation of inactivating mutations. First, an inactivation could be “neutral”: a gene that’s not needed and becomes nonfunctional may not have a selective advantage or disadvantage over the active form, and could eventually become “fixed” (present in all individuals in a population) via random genetic drift.

Alternatively, a broken gene could increase in frequency because it has a selective advantage over its functional competitors. That is, the non-production of a gene product could save energy that could be diverted to other functions, or it could reduce an unneeded organ or feature that could be damaged (both of these arguments have been used to explain why eyes largely disappear in cave animals who don’t “need” them). The authors posit that most of the broken genes in cetaceans accumulated by neutral processes, but it’s very hard to distinguish that scenario from an increase-by-selection argument, as this involves comparing DNA sequences and looking for a “signature of selection”: nearly impossible in such data.

But this is a side question. What’s important are two things. The first one I emphasized in WEIT:

1). The presence of nonfunctional genes in whale genomes—genes that are functional in their living relatives—is strong evidence for common ancestry of whales from terrestrial organisms and against any creationist scenario. It’s also evidence for macroevolution. You’d be hard pressed indeed to give reasons why an intelligent designer or a god would install useless genes in a genome that remain useful in the “outgroup” relatives. But this is exactly what is expected if whales evolved from terrestrial species in whose descendants those genes remain useful. But we’ve known about broken genes for a long time (e.g., olfactory genes), and IDers and creationists still can’t explain them.

2.) The broken genes give evidence about what the genes were used for in the ancestors, and why they weren’t needed in cetaceans. Thus, the authors looked at what the genes do when they’re functional, which helps tell us why they might not be needed in cetaceans. The broken genes fall into several classes; I’ll highlight just three:

a. Genes involved in blood coagulation.  When cetaceans dive, peripheral blood flow is reduced, making it more likely that damaging blood clots could form, especially when nitrogen microbubbles form in the blood (this is what causes “the bends” in divers). The authors found two genes involved in blood coagulation that were broken in whales. Like all of the broken genes, this scenario for why genes are inactivated is speculative, but can still prompt further research.

b. Genes involved in DNA repair. When tissues become short of oxygen, as when cetaceans are diving, but then get a surge of oxygen later, forms of “reactive” oxygen accumulate that can damage DNA. Cetaceans have lost an enzyme, POLM, that repairs DNA, but does so by inducing many errors in the repaired DNA. Since there are other less error-prone ways of repairing DNA, the authors speculate that the loss of POLM is a way to avoid a “mutagenic risk factor” in cetaceans, which are especially prone to damaged DNA.  The idea is that it’s better, if you’re susceptible to damaged DNA from diving, to get rid of a system that repairs quickly but makes errors, and rely instead on another system that repairs more slowly but with fewer errors.

c. Genes involved in melatonin biosynthesis. Whales, like ducks, sleep with only half of their brain at a time, with the other half active and awake to watch for danger and, in whales, to keep the animal swimming, surfacing, and breathing, maintaining body heat. The sides alternate over time so that the entire brain eventually gets a rest. (This shows how important sleep is, though we don’t yet know why.) Melatonin is a hormone synthesized by the pineal gland that helps keep animals entrained to daily (circadian) rhythms. The authors found that four genes involved in melatonin synthesis (AANAT, MTNR1A, MTNR1B, and ASMT) were inactive in cetaceans but not in their relatives.

The authors speculate that the loss of melatonin synthesis “helps decouple sleep-wake patterns from daytime,” as whales sleep with half their brains during both day and night. Further, since melatonin synthesis inhibits body-temperature regulation, its absence may help whales maintain their high body temperature in a chilly environment.

There were other pathways in which cetaceans showed broken genes, including those involved in transporting amino acids to the kidneys and genes expressed in the lungs, which may facilitate non-damaging lung collapse  that occurs in diving cetaceans. You can read about these in the paper; again, the reasons for their loss are plausible but speculative.

Finally, the authors looked at two other groups of aquatic mammals whose ancestors independently invaded the sea: manatees (sirenians, related to elephants and hyraxes) and pinnipeds like seals and sea lions (descended from terrestrial carnivores). Their goal was to see if there was independent “convergent” loss of similar genes between these groups and cetaceans. They found two genes, including AANAT, that were inactivated in manatees or pinnipeds, but not in their terrestrial relatives.

What does it all mean? As I said above, this paper gives further evidence for evolution in the form of dead genes, genes not needed in some groups of animals but needed (and “alive”) in their terrestrial relatives and presumably ancestors. This gives further evidence for evolution and especially common ancestry, though the evidence (even in the form of dead genes) is at this point somewhat superfluous.

More important, the work tells us what genes may have been useless—and therefore inactivated—in the ancestors of all cetaceans: genes that would be a hindrance to adapting to a fully marine way of life. Now we don’t know that the genes mentioned above were definitely inactivated because of new way of life, but the authors at least provide a suggestive but useful list for further investigation. Are these genes inactivated in all cetaceans? Do they do what they’re said to do when they’re active, and is their inactivation useful in cetaceans? This is all grist for further research.

Finally, what mechanism led to the gene inactivation? The authors posit mutation followed by the generation of “neutral” gene forms, with the inactive forms fixed in cetaceans by genetic drift:

Many of these gene losses were likely neutral, and their loss happened because of relaxed selection to maintain their function.

Well, that might be true, but such fixations of broken genes take a long time, and if they’re neutral they’re likely to keep both active and inactive forms of a gene around for a long time, especially in large populations. And why would the broken gene always be “fixed” in cetaceans rather than coexisting with the active form?

Given that the authors speculate that the loss of gene function might be adaptive in cetaceans, it seems more likely that natural selection swept the broken genes to fixation because they were adaptively superior to active genes (see above for reasons why). It’s a challenge for future work to try to determine, through DNA-sequence analysis, whether broken genes come to be fixed by positive selection or by random genetic drift due to “relaxed selection” (i.e., no selection either way on broken versus non-broken genes). That kind of analysis, as I said, is hard, but it helps us understand how genes get broken when they’re not useful.

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Huelsmann, M., N. Hecker, M. S. Springer, J. Gatesy, V. Sharma, and M. Hiller. 2019. Genes lost during the transition from land to water in cetaceans highlight genomic changes associated with aquatic adaptations. Science Advances 5:eaaw6671.

On pages 82-84 of Why Evolution is True I discuss the recurrent laryngeal nerve of humans (and other tetrapods) as an example of evolution. It’s evidence via “retrodiction”, which is what I call the situation when a previously unexplained and puzzling phenomenon can be understood only in light of a theory, thus supporting that theory—in this case, evolution.

Rather than describe it again, here are two videos showing it and explaining how the configuration of that nerve supports evolution.

Creationists have an explanation for it, too (there’s nothing they can’t explain via God’s will, except perhaps the peculiar species composition of oceanic islands), but the goddy story is unconvincing and less parsimonious. Whereas the evolutionary explanation tells us why only one of the twinned cranial nerves does its crazy loop, and why it’s completely comprehensible via the known evolution of tetrapods, the creationist explanation is based solely on how the nerve works: a post facto “functional” explanation of why the creator would create the nerve’s tortuous path. But it doesn’t explain why the creator made that big loop to enervate the larynx when he could have sent a branch directly to the larynx without the loop.

Here Dr. Rohin Francis, a cardiologist and researcher in London, uses his expertise to show how the nerve supports the “tinkering” aspect of evolution:

Below Richard Dawkins attends the dissection of a giraffe, which has an extraordinarily long (5 meter) recurrent laryngeal nerve. Rohin, however, notes above that some long-necked sauropod dinosaurs certainly had a recurrent laryngeal nerve about 28 meters (92 feet) long! I believe I’ve posted this video before, but it goes well with the video above:

In my only visit ever to a human anatomy lab (I get freaked out by corpses), I myself watched the dissection of this nerve by an anatomy professor. And it’s just like the one above, only shorter.

h/t: Scott

One of the main mistakes creationists make is arguing that if a vestigial trait is actually used for something, then it is neither vestigial nor gives us evidence for evolution. (Such features testify to common ancestry.)  Both creationist claims are wrong. They rest on the false argument that if the appendix, for instance, actually has some useful function, then it can no longer be claimed as evidence for evolution—as a now-useless remnant of a much larger part of the intestine that was useful in our ancestors.

Why is that argument false? Because if a feature is an evolutionary modification of an obviously ancestral feature, like the flippers of penguins (which clearly evolved from wings), then it can be both useful and vestigial, and therefore testimony of evolution. It’s important that readers remember this, because creationists conveniently forget it.

One feature that can be both vestigial and useful is the human appendix. Once thought to be not only useless, but positively detrimental (our ancestors died from its inflammation), we’re now finding that it has some use, as it contains immune-system cells that may serve as a refuge for useful bacteria, bacteria that can repopulate our gut if it’s wiped clean by diseases like cholera. A February article on the science site Cosmos—unfortunately called “The Appendix—Darwin’s Mistake“—points out increasing evidence that the appendix has a function.

Author and physician Norman Swan writes this in Cosmos:

. . . over the last few years the thinking has changed. The appendix turns out not to be an evolutionary curiosity but a handy little organ with the potential to resuscitate the bowel. Back in 2007, researchers at Duke University in North Carolina proposed that the appendix was actually a “safe house” for normal gut bacteria that could be put to use when the bowel had been devastated by, say, an infection such as cholera and needed to be repopulated by healthy bacteria.

The Duke group had found colonies of protective microbes known as biofilms were disproportionately produced by the appendix. Ironically, the immune cells found in the gooey mucous lining of the appendix and bowel actually help these biofilms to form.

If this theory were true then people without an appendix might be more vulnerable to dangerous gut infections. A study a few years later found evidence for this. People who’d had their appendix removed were significantly more likely to suffer recurrently from the serious and potentially life-threatening recurrent Clostridium difficile infection.

. . . the lining of the appendix contains a newly discovered class of immune cells known as innate lymphoid cells. Other lymphoid cells must be specifically tuned to attack the latest strains of bacteria or viruses, but these cells come ready wired to respond to the wide range of biological insults that flow down the intestines from our daily diet.

Experimenting in mice, the researchers found that these innate lymphoid cells were critical to maintaining the tissue around the caecum. If the cells were removed, the caecum shrank, suggesting they played a vital role for the integrity of the tissue. They also found that mice without these innate lymphoid cells were more vulnerable to a pathological
gut infection. This supports the study I mentioned earlier where patients without their appendix were more likely to suffer from recurrent C. difficile infections.

Darwin mentioned in The Descent of Man that the appendix is “useless” and “a rudiment”, as well as being variable, so that humans have really different sizes of their appendixes, and some have none at all.

Was he wrong about the appendix being evidence for evolution? No. Yes, he was wrong about its being “useless”, but not about its variability or its status as a rudiment of the larger appendixes in our herbivorous relatives.

Granted, the data above might be true, but that doesn’t detract from the appendix’s use as evidence for evolution. Yet creationists love finding that rudimentary organs may still be useful for something, as they think (not very clearly, as usual) that if something has a use, it can’t possibly be vestigial.

In fact one  creationist website takes this quote from Why Evolution is True to show that the evidence for evolution is weak:

We humans have many vestigial features proving that we evolved. The most popular is the appendix… our appendix is simply the remnant of an organ that was critically important to our leaf-eating ancestors, but is of no real value to us.

But the whole section, appearing on pages 60 and 61, notes that the appendix may have a function:

We humans have many vestigial features showing that we evolved. The most famous is the appendix.  Let’s look at it closely. Known medically as the vermiform (“worm shaped”) appendix, it’s a thin, pencil-sized cylinder of tissue that forms the end of the pouch, or caecum, that sits at the junction of our large and small intestines.  Like many vestigial features, its size and degree of development are highly variable: in humans, its length varies from about an inch to over a foot. A few people are even born without one.

In herbivorous animals like koalas, rabbits, and kangaroos, the caecum and its appendix tip are much larger than ours. This is also true of leaf-eating primates like lemurs, lorises, and spider monkeys. The enlarged pouch serves as a fermenting vessel (like the “extra stomachs” of cows), containing bacteria that help the animal break down cellulose into usable sugars. In primates whose diet includes fewer leaves, like orangutans and macaques, the caecum and appendix are reduced.  In humans, who don’t eat leaves and can’t digest cellulose, the appendix is nearly gone. Obviously the less herbivorous the animal, the smaller the caecum and appendix.  In other words, our appendix is simply the remnant of an organ that was critically important to our leaf-eating ancestors, but of no real value to us.

Does an appendix do us any good at all?  If so, it’s certainly not obvious.  Removing it doesn’t produce any bad side effects or increase mortality (in fact, removal seems to reduce the incidence of colitis).  Discussing the appendix in his famous textbook  The Vertebrate Body,  the paleontologist Alfred Romer remarked dryly, “Its major importance would appear to be financial support of the surgical profession.”  But to be fair, it may be of some small use.  The appendix contains patches of tissue that may function as part of the immune system.  It has also been suggested that it provides a refuge for useful gut bacteria when an infection removes them from the rest of our digestive system.

But these minor benefits are surely outweighed by the severe problems that come with the human appendix.  Its narrowness makes it easily clogged, which can lead to its infection and inflammation, otherwise known as appendicitis.  If not treated, a ruptured appendix can kill you. You have about one chance in 15 of getting appendicitis in your lifetime. Fortunately, thanks to the evolutionarily recent practice of surgery, the chance of dying when you get appendicitis is only 1%.  But before doctors began to remove inflamed appendixes in the late 18^th century, mortality probably exceeded 20%. In other words, before the days of surgical removal, more than one person in a hundred died of appendicitis. That’s pretty strong natural selection.

So yes, the appendix may have a function, but it’s still a vestigial organ, and evidence for evolution. The only remaining question is this: is it a detrimental  feature? Well, because of doctors it isn’t now, but it may well have been over the bulk of human evolution, as I note above. And that may be the reason it’s not only small but variable among people. Features that are crucial for our survival and reproduction don’t vary nearly that much. Perhaps its marginal use as a refuge for bacteria wasn’t useful enough to overcome the disadvantage of its being prone to infection.

Saying that there is a “function” to the appendix isn’t enough. To show that its presence is (or was) adaptive compared to its non-presence, you have to show that the benefits of having a bacterial refuge (in terms of future reproduction) outweighed the problems of having an infection-prone organ.  And nobody has showed that. So, it’s still possible that the appendix, while vestigial and rudimentary (and highly variable: the sign of a feature, like wisdom teeth, that’s disappearing over time), may have been detrimental in our ancestors and is detrimental now.

Nevertheless, creationists continue to harp on a functionality of the appendix as disproving evolution. If there is a lesson from this post, just remember: THAT IS NOT TRUE.

But let us for the moment grant the creationists their argument: that the appendix is not a remnant of a useful feature, but a feature that evolved, or is maintained, by a net reproductive benefit to its carrier. Does that disprove evolution? Hardly, given the massive evidence for evolution from a gazillion other areas.

And there are features that don’t seem, even under scrutiny, to have any positive effect on your reproduction. If you want a feature that is almost certainly does not enhance fitness, try our vestigial ear muscles (also variable among people), or, better yet, the hundreds of “dead genes” that we harbor in our genome: genes that had a function in our ancestors but have been silenced. (Olfactory-receptor genes and yolk-protein genes in humans are two examples.) Let the creationists explain why the creator put nonfunctional “dead” genes in our DNA, and just those genes that are active and adaptive in our ancestors.

And seriously, Dr. Swan: “Darwin’s mistake?” What are you implying by that? As I said, it may well be true that, over the bulk of human evolution, having an appendix was, on net, detrimental. “Detrimental” is “worse than useless,” so Darwin might not have been so wrong after all.

h/t: Barry