Abominable mysteries

One of the most annoying things I run across regularly is when someone takes a perfectly good piece of scientific research and twists it to support their own highly unscientific pre-existing beliefs.

The latest in this long parade of frustration I found out about because of my good friend, the amazing writer Gil Miller, who is a frequent contributor of topics for Skeptophilia.  Gil sent me a link to a fascinating paper that came out a month and a half ago in Nature about one of the most perplexing puzzles in evolutionary biology -- the sudden diversification of flowering plants during the Cretaceous Period, something on the order of 150 million years ago.  They went on to outcompete every other plant group, now comprising ninety percent of the known plant species, totaling about 13,600 different genera.  If you look around you, chances are any plant you happen to see that isn't a moss, fern, or conifer is a flowering plant.

What caused their explosive rise and diversification, however, is still unknown.  Their success might well be due to coevolution with pollinators, especially insects, which had a sudden spike in diversity around the same time, but that's speculation.  The current study vastly expands the genetic data we have on current genera of flowering plants, rearranging a few groups and solidifying what we know about the branch points of different clades within the group.  However, it still doesn't solve the reason behind what Darwin called "the abominable mystery" of why it all happened -- something the authors are completely up front about.

[Angiosperm phylogenetic chart from Zuntini et al., Nature, April 2024]

Well, any time an evolutionary biologist says "we don't yet understand this" -- especially if it's something Darwin himself noted as odd or mysterious -- it's enough to get all the anti-evolution types leaping about making excited little squeaking noises, and it didn't take long for this paper to appear in an article over at Evolution News (don't let the name fool you; the site is sponsored by the staunchly creationist Discovery Institute).  The article (so I can save you the trouble of clicking the link and adding to their hit rate) glosses over all of the stuff Zuntini et al. did explain, and highlights instead the fact that they never accounted for the reason behind flowering plant diversification (which wasn't even the purpose of the study).  The article ends with, "Nature clearly did make jumps in the history of life and this cannot be explained with an unguided gradual accumulation of small changes over long periods of time, but requires a rapid burst of biological novelty that is best explained by intelligent design."

Basically, what we have here is yet another iteration of the God-of-the-gaps argument; "we don't yet understand it, so musta been that God did it."  The problem is, you can't base a conclusion on a lack of data.  For the intelligent design argument to work, you'd have to show that it explains the data better than other models do.  Simply saying "we don't know, therefore God" isn't actually an explanation of anything, something that atheist philosopher Jeffrey Jay Lowder brought into sharp focus:

The objection I have in mind is this: the design hypothesis is not an explanation because, well, it doesn’t explain. ...  [I]t seems to me that a design explanation must also include a description of the mechanism used by the designer to design and build the thing.  In other words, in order for design to explain something, we have to know how the designer designed it.  If we don’t know or even have a clue about how the designer did it, then we don’t have a design explanation.

Which is it exactly.  Science works because it not only self-corrects, it holds explaining things in abeyance until there's enough data there to warrant a robust explanation.  A mystery is just a mystery; maybe we'll figure it out at some point and maybe we won't, but until then, it doesn't prove anything.  Science doesn't simply look at a lack of information and then throw its hands in the air and say, "Well, must be X, then."

To quote eminent astrophysicist Neil deGrasse Tyson, "If you don't know what it is, that's where the conversation stops.  You don't go on and say it 'must be' anything."

Honestly, it's astonishing that the creationist types are still using the God-of-the-gaps approach, because the truth is, it's more damaging to their position than it is helpful.  The reason was noted by German theologian Dietrich Bonhoeffer: "[I]t is [wrong] to use God as a stopgap for the incompleteness of our knowledge.  If in fact the frontiers of knowledge are being pushed further and further back (and that is bound to be the case), then God is being pushed back with them, and is therefore continually in retreat."

But that line of reasoning -- from a respected theologian, no less -- doesn't seem to be slowing them down any.

So I'll apologize to Zuntini et al. on behalf of the entire human race for these unscientific yayhoos taking a really lovely piece of research and claiming it supports their beliefs.  The tl;dr summary of this post is: it doesn't.  At all.  At worst, the study indicates that there's still stuff we don't understand, which is a damn good thing because otherwise the scientists would be out of a job.

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Stolen glance

Charles Darwin eloquently expressed his own struggle with imagining how the vertebrate eye could have evolved.  If you spend any time reading the writings of creationists or proponents of intelligent design (not recommended unless you have an extraordinary tolerance for pretzel logic), you'll find a quote from The Origin of Species:

To suppose that the eye with all its inimitable contrivances for adjusting the focus to different distances, for admitting different amounts of light, and for the correction of spherical and chromatic aberration, could have been formed by natural selection, seems, I freely confess, absurd in the highest degree.

This quote causeth much crowing and fist-bumping amongst the holy, lo unto this very day, usually followed by something like "Even Darwin admitted that evolution by natural selection doesn't work."

It's wryly amusing, given the degree to which anti-evolutionists cherry-pick the scientific evidence they accept and the (much larger amount of) evidence they ignore completely, that this quote is itself cherry-picked, as you'd find out if you went on to read the next two sentences of the book:

When it was first said that the sun stood still and the world turned round, the common sense of mankind declared the doctrine false; but the old saying of Vox populi, vox Dei, as every philosopher knows, cannot be trusted in science.  Reason tells me, that if numerous gradations from a simple and imperfect eye to one complex and perfect can be shown to exist, each grade being useful to its possessor, as is certainly the case; if further, the eye ever varies and the variations be inherited, as is likewise certainly the case; and if such variations should be useful to any animal under changing conditions of life, then the difficulty of believing that a perfect and complex eye could be formed by natural selection, though insuperable by our imagination, should not be considered as subversive of the theory.

So the argument -- if I can dignify it by that name -- of the anti-evolutionists boils down to our old friend Argument from Incredulity: "I can't imagine how it could have happened, therefore it must be God."

The truth is, we understand the evolution of the eye pretty well.  Lots of animals (for example, flatworms) have light-sensitive spots; and as Richard Dawkins brilliantly explains in his tour-de-force defense of evolution The Blind Watchmaker, once you have any kind of light-sensing ability at all, incremental improvements can result in some amazingly complex structures.  The eye isn't "irreducibly complex" -- the intelligent design cadre's favorite phrase -- at all; simple photosensitive spots led to "cup eyes" which led to eyes like a pinhole camera, and so on.  In fact, the whole process has been repeated more than once.  Complex eyes have evolved independently at least three times, possibly more.

[Image licensed under the Creative Commons Kamil Saitov, Human eye iris 5, CC BY 4.0]

The vertebrate eye is a particularly interesting case.  The transparent proteins in the lens, appropriately named crystallins, were found in 1988 by molecular biologist Joram Piatigorsky to come from the same genes that produce heat-shock proteins, enzymes that protect other proteins against damage from fluctuating temperature.  Take heat-shock proteins and assemble them in layers, you get a lens.  This is an example of exaptation (also called preaptation or preadaptation), where a gene, protein, or structure that evolved in one context develops a function giving it an entirely different use, and that use kind of moves in and takes over.

It's another example of exaptation in the eye that is why the whole topic comes up; in fact, it's not only exaptation, it's exaptation of a gene that was borrowed from another organism entirely.  A paper this week in Proceedings of the National Academy of Sciences looked at a protein in all vertebrate eyes called IRBP (interphotoreceptor retinoid-binding protein), without which our sense of sight wouldn't work.  When light strikes your eye, protein-bound complexes containing retinol (a derivative of vitamin A) absorb the energy, causing them to kink.  This triggers a neuron to fire, sending a signal to your brain.  However, something needs to unkink the complex, thus resetting the switch so it can respond to the next photon to come along.

That's what IRBP does.  Without it, your retinal cells would be able to respond exactly once, then they'd shut down permanently.

This week's paper found something astonishing.  The gene that codes for IRBP doesn't exist in our nearest invertebrate relatives, nor in any other group studied, with one exception -- certain species of bacteria.  What apparently happened is that the common ancestor of all vertebrates swiped a gene from bacteria that coded for a pepsidase -- an enzyme that breaks down and recycles proteins.  This kind of gene-stealing isn't uncommon.  (I did a post a few years ago about a pair of viral genes that seem to be critical for our forming memories, if you want another good example of this phenomenon.)  But like the heat-shock proteins becoming crystallins, the pepsidase made by the gene our ancestors grabbed was useful for something else -- unkinking the protein complexes in our rapidly-evolving eyes.

So our eyes work not only because of proteins gaining additional functions, but because we stole a gene from bacteria.

"Horizontal gene transfer can help to endow organisms with new functions," said Julie Dunning Hotopp, of the University of Maryland School of Medicine’s Institute for Genome Sciences.  "Once these genes take root in a new species, evolution can tinker with them to produce totally new abilities or enhance existing ones.  It is the biological equivalent of upcycling that happens in my Buy Nothing Group."

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