Of Whales and Timescales

Updated: May 11, 2019

By Andrew Jones

Joshua Swamidass, assistant professor in the Department of Pathology and Immunology at Washington University, has responded to an Evolution News article about whale evolution. The original article concluded:

We don’t find the “pattern” that evolution predicts “should be found in the fossil record at certain times.” Rather, we find that truly aquatic whales appear abruptly. And even if we accept some of the fossils as “intermediates” between whale and land mammals, there is not enough time for the complex adaptations needed for whales’ fully aquatic lifestyle to evolve. Whatever the correct explanation is for the origin of whales, unguided evolutionary mechanisms are not the answer.

Swamidass writes:

Looking at this progression [of skulls] we uncover an amazing fact. Surprisingly, whales have the same body plan as a terrestrial mammal! It’s the same body plan, with several intermediate forms. Looking at several features (e.g. ears, bone density, teeth), we can see this transition beautifully. Look how we can see the nostrils slowly move back to the top of the head…

Yes, it is beautiful. One adapted for land, another for water, and one is intermediate. But take care; nothing is actually moving in those pictures. Any transition is in the interpretive imagination of the beholder.

Getting back to the claim that millions of years is “not enough time.” There is no genetic or mathematical analysis to back up this conjecture. What types of genetic changes are required for whale evolution? How unlikely or likely are they?

Consider a paper published in PLOS Computational Biology, “The Time Scale of Evolutionary Innovation.” The authors explore how long it should take for evolution to make a complex coordinated change to a sequence. They find that mutation alone would be little different from creating a completely fresh sequence each time using random letters, but that if natural selection is acting to “regenerate” the original sequence, and if the original sequence happens to be near the target, then evolution is much more likely to make the transition. This should be common sense, I think. Note the core result: a sequence of length L requiring only k specific coordinated changes will require Lk+1 trials. They describe this as “polynomial” because it is polynomial in L but it is exponential in k.

What this means is, if it takes 100 generations for a specific mutation to occur, it will take (at least) 10 thousand generations for a specific set of 2 mutations to occur, and 100 million generations for a specific set of 4 mutations to occur. At human generation lengths that would be 2 billion years. Two billion years, for a 4-letter “innovation.” That puts a hard limit on what kind of magic we can expect from evolution. This basic problem is then greatly exacerbated by population genetic effects; each mutation must not only occur, it must become fixed or at least well established in the population, and there is no selection to help until you get the last mutation in the set.

Now consider the mutations that actually have occurred in humans in recent human history. Some have been interesting, including significant tweaks to melanism, and milk digestion, but none of them are spectacular (no X-Men) and certainly none have constructed new biochemical systems or new healthy morphology. The waiting times problem informs us that all the mutations in the history of the human species must have been similarly banal. Think about that for a moment. Are you surprised? You should be if you believe we evolved from something like an ape. Evolution has to work one step at a time. It cannot do the kind of complex coordinated magic that a human designer or engineer can. If you believe humans evolved, you have to believe it can happen without any complex coordinated changes at all (in this context complex means just 4 or more specific letters at the same time — not 4 new proteins). In fact, the exponential character of the waiting times problem tells us that all of evolution must have been similarly limited, right back to the Cambrian explosion. In turn, that raises the question of how the radical innovations of the Cambrian explosion could have occurred.

From a Batmobile to a Yellow Submarine

The Evolution News article argued that for a land mammal to become a whale, or a Batmobile to become a Yellow Submarine, it would require multiple coordinated changes. To many people this would be a trivial and common sense assumption, even without the detail given in the article. However, citing another paper, “Molecular evolution tracks macroevolutionary transitions in Cetacea,” Swamidass pushes back:

It is remarkable how many of the changes required for whale evolution are caused by loss of function mutations (which end causing “pseudogenes”), or small tweaks to proteins. This is one of the big surprises of mammalian evolution. Large changes can take place with tweaks to the genetic code. Eyes adapt to underwater vision by losing a rhodopsin gene. Hind Limbs are lost with the loss of a homeobox gene. Taste buds are lost when two genes are lost. Smell receptors are almost entirely lost in most species too. In all these cases, we see remnants of the broken genes, and in many cases the details of how these losses increase function are well understood.

This is all true. It is true that overall efficiency can be increased by losing unused functional components. On a design view, it makes sense to deactivate things that are not being used. Often this needs no more than a flip of a switch, and this no great challenge for evolution either. On the other hand, why would the random loss of information make a functional body plan? Researchers have created legless mice by knocking out a Hox gene, in an effort to understand snakes, but the resulting mice were simply paralyzed and could not mate. Also, note that at some point evolution has to explain the origin of all the proteins, Hox genes, as well as the rhodopsins and receptors that have been lost, and that is rather more difficult. An evolutionary process that creates nothing new is soon going to run out of other organisms’ proteins to borrow.

Remarkably, it does not appear any new enzymes or de novo genes are required in whale evolution. It appears that small tweaks to existing proteins, or loss or alteration of the function of existing genes, account for the changes we see at this point.

True, that is not where the challenge to whale evolution lies. But why is it remarkable to see no new genes? It turns out that a large number of genes are taxonomically restricted or ORFan genes. That means they seem to appear without evolutionary history in the twigs and leaves of the tree of life. Moreover, some even turn out to be essential, which would be very odd if they have been added last by evolution. The existence of these genes is a common problem elsewhere in the evolutionary story, even though it appears not to be relevant to whales.

This was just the first half of the original article to read the rest click on the link below.

Original Article: https://evolutionnews.org/2018/03/of-whales-and-timescales/

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