Shabby science reporting in the New York Times

January 10, 2021 • 11:00 am

I’ve noticed lately that the quality of science writing in newspapers has declined, even in The New York Times, which used to have some really good writing, especially by Carl Zimmer, who doesn’t seem to appear in its pages so often.

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CORRECTION:  Zimmer is still writing prolifically in the NYT, but covering a beat—vaccination—that I’d missed, (mis)leading me to believe that he was engaged in activities other than writing for the NYT. He’s asked me to correct this in a comment below, so I’ll just add his comment here:

If you had bothered to look at my author page at the Times, you’d see that I have been busier than ever there as I help cover the science of the pandemic. Over the past 10 months, I’ve written 93 stories about Covid-19, which comes to about two articles a week. Please correct your post. You are misleading your readers about my work. https://www.nytimes.com/by/carl-zimmer

I guess he was peeved. The misstatement was my fault, of course, and I’ve fixed it, but I have to say that this is a rather splenetic reply from someone whose work I’ve always praised.

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Rather, in place of long-form biology and physics, a variety of people now write for the Times‘s biological “Trilobite” column, and seem to take a more gee-whiz approach to science, producing short columns that are also short on information.

Part of the problem may be that many of these columns are written by freelancers who haven’t spent most of their writing career dealing with biology. My general impression is that the NYT is starting to reduce its coverage of science. That would be a damn shame since it was the only major paper to have a full science section (I don’t get the paper issues any longer, so I don’t know if they still have the Tuesday science section I’d read first).

The sloppy writing seems to be the case with this week’s column, a column reporting a new genome-sequencing study in Nature of monotremes: the platypus and the echidna (“spiny anteater”). I have only scanned the paper briefly, and will read it thoroughly, but on reading the NYT’s short summary I spotted two errors—not outright misstatements of fact, but statements that are incomplete descriptions of the truth, and where an extra word or two would have made the column not only more accurate, but more interesting.

Here’s the article (click on the screenshot):

 

Maybe I’m being petulant, but here are two quasi-misstatements in the piece. First, this one (emphases are mine):

When the British zoologist George Shaw first encountered a platypus specimen in 1799, he was so befuddled that he checked for stitches, thinking someone might be trying to trick him with a Frankencreature. It’s hard to blame him: What other animal has a rubbery bill, ankle spikes full of venom, luxurious fur that glows under black light and a tendency to lay eggs?

The facts: Only the males have ankle spurs, and of course only the males have venom. (This probably shows that the trait is used not for defense against predators, but for male-male competition during mating.) Females have no venom and have rudimentary spur nubs that drop off before maturing. Of course, females have the genes for producing ankle spurs and venom, as those genes don’t know which sex they’ll wind up in—just like human males have genes for vaginas and breasts and human females carry genes for penises. But the sex-development pathway prevents the expression of venom and spurs in females, just as it prevented me from developing a vagina.

The sex-limitation of the spurs isn’t mentioned in the Nature piece, but every biologist who knows their platypuses also knows that only the males have venom spurs. And, by the way, the echidna has some genes that used to produce venom, but they’re non-expressed “pseudogenes” that have become inactivated. That shows that the ancestral monotreme was almost certainly venomous (this isn’t mentioned in the NYT piece, either).

About those egg-yolk genes:

For instance, many birds and insects have multiple copies of a gene called vitellogenin, which is involved in the production of egg yolks.

Most mammals don’t have the vitellogenin gene, said Dr. Zhang. But the new genomes reveal that platypuses and echidnas have one copy of it, helping to explain their anomalous egg-laying — and suggesting that this gene (and perhaps the reproductive strategy itself) may have been something the rest of us lost, rather than an innovation of the monotremes. 

Well, yes, mammals do have the vitellogenin gene. In fact, our own species has three of them, but, as in other mammals they’re pseudogenes—genes that are there in the genome but are broken and not expressed. Humans and other placental mammals don’t require egg yolk because we’re nourished through the placenta, not yolks in shells. The platypus has two vitellogenin genes (described in the Nature paper as “genes”, so the statement that platypuses and echnidas have “one copy” is misleading)—they’re just not “functional” genes.

Now you may say this is quibbling, but it’s not. First of all, the statement that playtpuses have one copy of the egg yolk gene is wrong. They have two, but one doesn’t function. More important, the statement that there are nonfunctional yolk genes in all mammals says something powerful about evolution, something that I discuss in my book Why Evolution is True.  Those “vestigial” and nonfunctional genes are evolutionary remnants of our ancestors who did produce egg yolk. Why else would they be there in our genome, doing nothing? Chickens, who of course evolved from reptiles, as we did, have all three vitellogenin genes in working order.

Another error, then, is the statement “suggesting that this genes. . . may have been something the rest of us lost.” No, we didn’t lose it; it’s still there in our genomes. And there’s no “suggestion” about it: it’s sitting there in our DNA, has been sequenced, and has been shown to be nonfunctional. Finally, we KNOW that this gene is NOT an innovation of the monotremes, and have known that for a long time (e.g., see here). It was inherited from their reptilian ancestors.

This isn’t flat out erroneous science reporting, but it’s incomplete science reporting—the summary of a paper phoned in to the NYT. (I also find the Time’s summary curiously devoid of what’s really new in the paper; at least half of it reprises what we already knew.) More important, the reporter missed a good chance to give some powerful evidence for evolution, both in ourselves and in monotremes, whose genomes harbor some dead egg-yolk genes that are active in our avian and reptilian relatives. And yes, those echidnas have dead genes for venom.

h/t: Gregory

A vestigial trait of birds that may have been functional in ancestors: remote-sensing of vibrations in the bill (still active in the kiwi)

December 11, 2020 • 10:00 am

A new scientific paper from the Proceedings of the Royal Society Series B (first screenshot below) tells a rather complex story that I’ll deliberately simplify to save space. The paper is behind a paywall, but a pdf may be found via judicious inquiry, and the reference is at the bottom.

The article above is aptly summarized by Veronique Greenwood in the New York Times‘s “Trilobite” column

Three groups of birds have evolved a remarkable feature: the ability to remotely sense prey (i.e., detecting prey without touching them) by sticking their bills in the ground and sensing vibrations. These groups are the kiwis, the ibises, and some shorebirds. The detection can occur either through the direct sensing of vibrations of prey movement, or the reflection of sound waves off hard-shelled prey as the bird sticks its beak into the ground. This feature is called “remote touch.”

It turns out that the bill tips of “remote touch” birds are pitted with small depressions that contain cells called “Herbst corpuscles”, which are the motion-detecting organs. aThese birds also have an expanded area of the brain that is used to process the extremely important touch signals.

Other species have different ways of using their bills to detect prey by touch. Ducks and geese have a bony organ at the tip of their bills that also have pits with Herbst corpuscles, but they are organized differently, with mechanoreceptors beside them. These are what ducks use in “dabbling”—turning their butts up and sticking their beak into the dirt or sediments to forage. Finally, parrots have a different kind of bill-tip organ with receptors not located in the bone.

Below are photos from the paper showing the different types of bill tips. The authors also examined skulls of hundreds of living species and dissected beak tissue from many to see if there were Herbst cells associated with the bill pits.

First, a bird without remote sensing, as with most birds. It’s a kelp gull (Larus dominicus). There are a few pits at the tip of the bill, but soft tissue analysis showed no receptor cells. It does not forage by touch.

Here are two birds with remote sensing. First, the hadeda ibis (Bostrychia hagedash). Note the highly pitted bill tip organ (enlarged). It also has the Herbst cells as well as an enlarged bit of the brain for detecting touch. (This bird, like all other birds save the ratites and tinamous, falls into the large group of species called neognaths.)

Ditto for the kiwi, which falls into the other group of birds, the paleognaths, a small group that contains only the large flightless birds or ratites (emus, ostriches, etc.) plus the tinamous, which can fly, but not well. Its remote sensing organ with Herbst cells is located at the very tip of its long bill. Indeed, the ratio of bill length to skull size is one of several keys to diagnosing whether these birds have remote sensing.

Finally, the tinamou, a paleognath that= has a remote-sensing organ containing the pits but no Herbst corpuscles in them. But this species doesn’t feed by probing the ground. Other ratites, like the ostrich and emu, also have a pit-studded bill, but no vibration-detecting cells. The pits seem to be a leftover from an ancestor which had pits that were useful because they contained vibration-detecting cells. In other words, they’re a vestigial trait.

The other ratites also lack the expanded brain regions for processing information from the touch receptors. This makes sense, for while it may not cost much to retain some pits in the bill when you don’t need them, brain tissue is metabolically expensive, and if you’re not using it it would pay to divert those resources to other functions that would help you reproduce.

As I said, the presence of the pits in birds that don’t use them suggest that this trait is a vestigial trait carried over from an ancestor.  One can distinguish the remote-touch birds from other species by a combination of bill length/skull size ratio, number of pits, and spacing between the pits.

But which ancestor? It turns out that we have fossil skulls of ancient extinct birds, the lithornithids, which are very early paleognaths. Although soft tissue wasn’t available for these birds, some of the species show the mechano-sensing organ—as evidenced from the number and spacing of the pits, as well as the bill/skull ratios characterized by remote foragers. Here’s a photo of the two lithornithid skulls; captions under the photos are from the paper (click to enlarge photo).

Cranial fossils of two species of lithornithids, showing high degree of pitting on the surfaces of their beaks, similar to all extant palaeognathous birds, potentially indicative of a bony bill-tip organ. (e) Lithornis promiscuus: (i) skull and attached maxilla (USNM 391983) showing the shape of the beak relative to the skull; (ii) distal portions of maxilla and mandible (USNM 336535). ( f ) Paracathartes howardae: maxilla (USNM 404758) and distal portion of mandible (USNM 361437).

The conclusion is that putative ancestors of the paleognaths were remote-touch-sensing species. The fact that living paleognaths like emus and tinamous still retain the pits suggests that this nonfunctional “organ” is a useless remnant of a trait inherited by all paleognaths from a lithornithid ancestor.  Indeed, the authors think that the ancestor of all birds might have been a remote-sensing prober (my emphasis):

Our analyses corroborate that the basal palaeognaths, the small, volant lithornithids, had a tactile bony bill-tip organ enabling them to use remote touch to locate buried invertebrate prey items. This finding, combined with our understanding of the evolution of the lithornithids, suggests a Cretaceous origin of the remote-touch sensory system in modern birds before the palaeognathneognath split.

As for why among living paleognaths only the kiwi has a functional touch organ when it was present in an extinct ancestor, that could be explained by either of two scenarios. The first involves, the organ’s loss in a more recent ancestral species and then the re-acquisition of the organ in just the kiwi lineage. The second possibility is that the kiwi kept an ancestral remote-probing organ while all the other paleognaths lost it. The authors are unable to distinguish between these two scenarios.

What about the neognaths that have remote-sensing organs, like the ibis or shorebirds? Did they retain the ancestral touch organ while all other neognaths—the vast majority of living birds—lost it? Probably not; as the authors say, this is an independent case of evolution.

What is even more fascinating is the possibility that this ability to detect prey remotely may have been present in the reptilian ancestors of birds, which may scientists think are the theropod dinosaurs:

Interestingly, there is increasing evidence that some non-avian theropods had specialized sensory structures located on the distal portion of their rostra, based on a high degree of external foramina/pitting preserved on their mandibles. We speculate that perhaps such sensitive snouts in non-avian theropods may have been precursors to the evolution of remote touch in their avian relatives.

It’s interesting to note that alligators and crocodiles also have touch-sensitive “dome receptors” in their upper jaws, also associated with pitting in the bones.  The archosaurs are a group of early reptiles ancestral to both birds and crocodilians, and maybe the receptors we see in crocs and gators are related, in some way, to the pits in the beak of the kiwi.

This is all speculative, but what seems pretty solid is that the bill pitting and useless “touch organs” in non-kiwi ratites and tinamous are vestigial remnants of a functional organ in an ancient ancestor. And that’s evidence for evolution.

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Toit, C. J. d., A. Chinsamy, and S. J. Cunningham. 2020. Cretaceous origins of the vibrotactile bill-tip organ in birds. Proceedings of the Royal Society B: Biological Sciences 287:20202322.

Plant seeds evolve to mimic antelope droppings, and dupe dung beetles roll and bury the seeds

December 3, 2020 • 9:30 am

The first paper below is five years old, but I just read it yesterday because it’s a remarkable example of mimicry. In this case, seeds of a plant in South Africa have apparently evolved a size, shape, appearance AND smell that makes them resemble antelope droppings. Dung beetles, thinking that the seeds are fecal matter, roll them to a safe place and bury them, ensuring that the seeds are protected, dispersed a bit, and get planted. The paper, from Nature Plants, is below (click on screenshot), the pdf is here, and the reference is at the bottom. (If the article is paywalled, a judicious inquiry will yield it.)

This is one of the very few examples in which plant seeds have evolved to deceive animals, either physically or chemically, and in which the plant benefits but the animal loses. This is, in fact, the evolution of a plant that parasitizes an animal.

Here’s a later paper (2016) from the South African Journal of Science with a free pdf (click on screenshot):

The plant that’s evolved mimicry is Ceratocaryum argenteum, a shrubby plant that’s endemic to the Cape Province of South Africa:

Unlike seeds from other plants in the family Restionaceae—which are normally pretty flat, with a smooth, dark seed coat as well as elaiosomes (fleshy bits that are edible to ants, who carry the seeds to their nest, feed the elaiosomes to their larvae, and then discard the rest of the seed, which thereby gets dispersed)—C. argenteum has a “rough tuberculate and brown outer seed coat” which, to the authors’ noses, “has a pungent scent similar to herbivore faeces”.

Below: what the seed looks like (a-c) in contrast to other seeds in the area (h-j). (g) shows the dung of an antelope (a Bontebok). Note that the C. argenteum seeds are about the size and shape of the Bontebok dropping, and are round to facilitate rolling. Dung beetles roll balls of dung to a nearby location, bury them, and lay an egg with the dung so its larvae can feast on the feces. The beetle observed burying seeds was Epirinus flagellatus.

ac, Vertical (a) and side (b) views of a C. argenteum seed as well as one that has been cracked open (c) showing the endosperm and thick woody inner seed-coat layer and the outer tuberculate layer which together form the husk. d,e, Scanning electron microscopy (SEM) of the outer, tuberculate layer and inner seed-coat, with white silicon granules at the boundary between the two layers. fE. flagellatusg, Bontebok faeces. h,i, Vertical (h) and side (i) views of an L. sessile seed. jCannomois grandis seed with white elaiosome.

And the dung-maker, the small antelope most common in the area (80-100 cm or 31-39 inches at shoulder): the bontebok, Damaliscus pygargus pygargus. 

The authors hypothesized that the size and smell of the C. argenteum seeds would facilitate them being buried, and so they put out seeds along with some camera traps.  They observed four-striped grass mice (Rhabdomys pumilio) eating husked seeds but never burying them.  In contrast, of 195 seeds put out after a rain (when dung beetles are active), at least 55 were buried (they used fluorescent threads to mark the seed paths).

In no case did the buried seeds have a dung beetle egg on them, so the beetles were first fooled, and then realized that something was wrong—but only after they had rolled away the seeds and buried them.

As I noted above, resembling dung to fool beetles is a good way to perpetuate your genes, as you get dispersed, protected by the soil from mice, and buried (planted). Further, C. argenteum plants can’t re-sprout after a fire, and thus the persistence of plant genes depends on a way to escape fire—by getting its seeds buried! For many reasons, then, selection might favor the seeds resembling dung, and because beetles detect dung by its odor, you’d want to smell like dung, too. The dung beetles are simply dupes, doing a lot of work and not getting anything out of it.

The authors also did gas chromatography and mass spectrometry to measure the amount of volatile compounds on seeds and dung, and found that the seeds had a significantly larger amount of volatiles than other seeds in the area, even when old and when corrected for surface area, and resembled the amount of volatiles in dung. Further, compounds in the seed volatiles were also identical to compounds in the volatiles of bontebok and eland dung (another antelope), with “various acids, the benzenoid compounds acetophenone, phenol, p-cresol and 4-ethyl-phenol, as well as the sulphur compound dimethyl sulphone.”

Here’s a two-dimensional plot showing the resemblance of the C. argenteum seed volatiles to dung volatiles; note that other seeds (green triangles) don’t have dung-like profile of volatiles:

(from the paper): Similarity in the composition of volatile blends of seeds and animal droppings is based on non-metric multidimensional scaling. Symbols for other Restionaceae (Methods, Supplementary Table 3) that overlap are slightly offset for clarity. The composition of scent sampled from Ceratocaryum seeds is very similar (R = 0.75, P = 0.33) to that of dung of local herbivores (eland and bontebok), but differs markedly (R = 1.0, P = 0.028) from that of seeds of other Restionaceae (nested ANOSIM permutation test).

In the second paper, the authors observed another dung beetle, Scarabaeus spretus, burying the seeds, flying rather than crawling to the piles of seeds put out. (It’s clear that odor rather than appearance is a major attractant, and one S. spretus flew directly into a paper bag of seeds!) This species moved seeds only about a quarter of a meter, while E. flagellatus could move them up to 2 meters away from the pile. (As you see, the dispersal is quite limited!) Here’s a figure showing beetles of both species rolling away the seeds and burying them:

(a) Epirinus flagellatus rolling a Ceratocaryum argenteum seed; (b) Scarabaeus spretus rolling a seed (the arrow indicates a Sphaerocerid Lesser Dung Fly); (c) the large hole made by Scarabaeus spretus for burying several seeds (the arrow indicates the location of the Dung Beetle); and (d) a female Sarcophagid Fly on a seed. Midgley & White (2016).

Further, the bontebok eats different kids of grasses from the eland (Taurotragus oryx), a larger species shown below, and the different species of grass have different ratios of nitrogen and carbon isotopes. By looking at the isotope ratios in the beetles (whose juvenile stages eat the dung), and in the antelope dung itself, the authors found that the ratios of the dung beetles (green diamonds and purple triangles) resemble the dung of the eland (light blue triangles) more closely than the dung of bontebok (red circles), as shown in the diagram below.

Conclusion: the dung used by both species of beetles is likely to be from eland rather than from bontebok. But as the authors showed above, the volatiles of both antelope dung are pretty similar, and still resemble the volatiles of the seeds.

The one puzzle is that the size of C. argenteum seeds are more similar to that of bontebok droppings than to eland droppings. Being much bigger, elands have larger scat—about twice as big. But since dung beetles can form smaller balls out of larger droppings, and because it may be too onerous for the plant to produce a seed twice as large as it does, this may not be a problem.

An eland:

So we have mimicry here that deceives the beetle, who comes to its senses only after it rolls away and buries a seed. In this case it doesn’t adhere to the Who’s dictum, “Won’t get fooled again.” It would be interesting, though, to do lab experiments with dung and seeds to determine if beetles eventually learn to avoid rolling and burying these mimetic seeds. It’s a lot of effort for nothing, and the beetle “knows” it since it doesn’t lay an egg on the seed.

h/t: Jean

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J. J. Midgley, J. D. M. White, S. D. Johnson and G. N. Bronner. 2015. Faecal mimicry by seeds ensures dispersal by dung beetlesNature Plants 1, 15141, https://doi.org/10.1038/nplants.2015.141

 

The “skunk rat” that chews toxic vegetation and spits the toxins onto its fur

November 27, 2020 • 9:30 am

In various parts of East Africa lives a black-and-white striped rodent, the African crested rat,  Lophiomys imhausi. (It’s also called the “maned rat”.) I call it the “skunk rat” because of its similar black-and-white striped pattern, because, like skunks, it moves slowly (especially for a rodent), and because, also like skunks, encounters with it are unpleasant.

The skunk is protected from predators by its noxious (but non-lethal) squirts from its butt, and it’s evolved a distinctive “aposematic” warning pattern that serves to warn predators to “stay away from me” (predator avoidance can be either learned or genetic). Like the skunk, the crested rat doesn’t need to move quickly, for it has little to fear from predators.

Why does this rat look and act like a skunk? It is in fact a poisonous mammal, and the world’s only poisonous rodent. Some shews, which aren’t rodents, are venomous, but that venom is made by the shrew itself.

The crested rat isn’t inherently poisonous: it becomes so by applying toxic plant compounds to its fur: compounds it gets from chewing the bark of the “poison arrow tree” Acokanthera schimperi (locals use it to make poison arrows, as the poison is stable for decades), and then “anointing itself”, spitting the toxic juice onto certain parts of its coat that it displays when predators are around. Those poisons, which are powerful cardenolides, have killed many a dog, and those dogs who survive subsequently don’t go near the rat, showing that the pattern is easily learned by predators. (Other potential predators of the rat include honey badgers, jackals, servals, hyenas, and leopards.)  Apparently the crested rat is immune to the poison, as it regularly chews on the bark.

It’s a large, long-lived rat, weighing up to a kilogram. Here’s what it looks like:

Here’s the tree, which has poisonous leaves and fruits as well (the rodents appear to use the bark):

Here’s the special line of brown hairs that are displayed and erected when predators are around or the rat is disturbed:

Another view from the paper below (see also the “Trilobite” article from the New York Times, which provided the picture at the top). Note that the hairs in the top photo are erected, like those of a fighting cat, and aren’t visible in the “normal” undisturbed rat shown in the photo at the top of this post. The caption of the pictures below (from the paper) are “An immature Lophiomys imhausi displaying specialized hairs and warning coloration (A) and the same individual (center) with an adult male (top right), and female (top left), from the same trap location. The juvenile is being groomed by the male (B).

Finally, the brown stripe is made of special porous hairs that absorb the toxins, which is why they’re displayed, for this is the part of the rat’s coat that will kill or sicken attacking predators (picture from the NYT):

Here’s a video showing the rat chewing on A. schimperi bark and spreading it on its fur:

Another video showing how absorbent the specialized fur is:

The paper below (click on screenshot to access) is from the Journal of Mammalogy, and the facts above have been known for some time. What this paper does is elucidate some new things about the social behavior of the rats, and provide observations of its grooming behavior, as well as determining whether chewing the plant and applying the toxin to its fur affects the animal’s behavior (it doesn’t). The pdf is here, and the full reference is at the bottom of this post:

Besides providing a good summary of the fragmentary literature on L. imhausi, the paper finds out this stuff:

a). The rat appears social and is probably monogamous. Monogamy is rare for a rodent, and although this is only inferred for this species by repeatedly seeing pairs of crested rats at camera traps or seeing interactions between males and females in captivity, other features of the species, like its large body size, long life, low reproductive rate, and females who are more aggressive than males, are often characteristic of monogamy in mammals.

b.) The species is dense. The authors estimate 4-15 individuals per square kilometer, which is pretty dense. It lives in riparian forest (along rivers), and although the species is labeled “of least concern” by conservationists, its habitat is disappearing and is also patchy, so it may one day be threatened.

c.) Application of the toxins to the fur is sporadic (at least in captivity). Only half of the 22 rats captured and observed, all given fruits, leaves, and bark of the poison arrow tree, applied toxins to their fur. This is no puzzle to me, though it concerns the authors. I suspect it’s because, as the authors suggest, the poisons are stable and long-lived (for decades!), and rats don’t need to keep applying bark juice to their fur constantly.

All of the captive rats got the toxins from chewing bark while ignoring the other bits of the tree.  Here’s a photo of a rat chewing bark (A) and anointing its fur after chewing (B):

So we know a bit more about this species, and although much of what is described in the paper (and in the NYT article) was known before, it wasn’t studied systematically. I for one was unaware of this bizarre rodent. Its existence raises several questions.

Is the chewing and anointing behavior learned or evolved? The authors didn’t test this—or even raise the question—but given that the rats are born with the specialized fur that absorb the poison, I suspect that the chewing-and-anointing behavior is hard-wired. That could be tested by hand-raising newborn crested rats and seeing if they perform the behavior in captivity. If they do, it’s instinctive.

How did the evolution of this behavior evolve? Was the rat immune to the poison from the outset? Since they don’t ingest the bark, how did this whole thing get started? Did a rat chew on some bark, find it unpalatable, and then wipe its mouth on its fur? Such behavior could of course be subject to natural selection, as rats who did this would be less likely from the outset to be eaten by predators.

Once the rat had evolved toxicity, the evolution of aposematic coloration would follow. (The coloration could not evolve before the toxicity-inducing behaviors, as it would make the rat more visible and more likely to be eaten, as it would have no protection.) This is a fairly straightforward evolutionary process, as toxic rats that were a bit more conspiculous would be more easily recognized by predators that had encountered them before, and thus less likely to be attacked more than once by the same predator. Other predators, however, would have to learn one by one—unless (and this is sometimes the case) the predators themselves evolved an innate avoidance to the aposematic black-and-white pattern. This too could be tested by exposing naive predators—ones that had never encountered a crested rat—to one of those rats, and seeing if they instinctively shy away. That is research for the future, and is certainly feasible. While the mechanistic questions are largely answered, the evolutionary questions still dangle tantalizingly before us.

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S. B. Weinstein, K. N. Malanga, B. Agwanda, J. E Maldonado, and M. D. Dearing. 2020. The secret social lives of African crested rats, Lophiomys imhausi, Journal of Mammalogy online  https://doi.org/10.1093/jmammal/gyaa127

 

Thread: On the “On the Origin of Species”

November 24, 2020 • 9:30 am

As I noted in my Hili post, today is Evolution Day: the anniversary of the day on which Darwin published The Origin in 1859.  It’s one the book I’ve read more than any other: I used to go through it once a year or so, but it’s been about three years now. My copy of the first edition is old and battered, and the inside cover (below) shows that I bought it shortly after I started my doctoral work at Harvard. (I hadn’t read it before then). Note, too, the title, which we should all know in full (Richard Dawkins, to his embarrassment, was once asked the full title by a creationist but couldn’t recall it, and that was used against Richard by those looking for reasons to demonize him.)

On the Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life

That’s the title of the first five editions; in the Sixth (the last), the initial word was dropped.

There will be a quiz.

My Pelican Classics edition is now held together with tape, and I have about four other copies, including the Sixth Edition. But I recommend reading the First Edition to get the full feeling of how Darwin’s ideas hit the world in the solar plexus. Like the fatal punch that did in Houdini, the book put paid to creationism, Biblical or otherwise, in one blow.

As I’m occupied with University business this morning, I’ll throw this one out to the readers. In general, I’ll ask you to give your take on the book and, if you’ve read it, to tell us what impressed (or didn’t impress) you. If you haven’t read it, shame on you, for I’ve always say that any person who wants to be considered “educated” needs to have read The Origin.  

It’s not an easy read: my introductory-evolution students always bridled at the Victorian prose, and even the abridged Dover edition turned them off. Further, some of the chapters, like that on “Hybridism” are particularly dense and even opaque. But as “one long argument,” as Darwin called it, it is an incomparable journey into the mind of a captious naturalist, one who always searched for flaws in his own ideas.  If you haven’t read it, please start now (you can explain your dilatory behavior below). If you have, please enlighten us with your thoughts about it.

My own take is that it’s the greatest science book of all time, but of course I’m biased.

Thoughts on The Origin

by Greg Mayer

Jerry asked me to weigh in here with some thoughts on The Origin, and I’m happy to do so. Before seeing what Jerry wrote, I reached up and took down my first copy of The Origin off the bookshelf, just like Jerry did! And, just like Jerry, I have four other copies, including a facsimile of the sixth edition!

This is the Harvard University Press facsimile of the first edition, with an introduction by Ernst Mayr (third printing, 1975). I also have a later printing of this version, since this copy got pretty beat up from frequent use.

A specimen of my early handwriting.

In October 1976, I was a sophomore at SUNY Stony Brook, and bought this in the bookstore there. It wasn’t for a course that I was taking, but I often bought books for other courses that I thought interesting. In fact, I already knew who Mayr was, because in high school I had purchased a copy of his Populations, Species, and Evolution at the Stony Brook bookstore. My recollection is that I first read The Origin start to finish while doing field work on Grand Cayman while in graduate school. My copy is well-annotated. The annotations were written at various times, but I can’t usually tell when they were made. I’ve always been interested in island life, so here are a couple of pages on oceanic islands with my notes.

Like Jerry, I have often assigned parts (sometimes large parts) of The Origin as reading for my evolution classes. (I think Jerry may have influenced me in this regard.) But unlike Jerry (or at least Jerry’s students), I find The Origin eminently readable– I think the prose is terrific! It is an excellent model and exemplification of scientific argument.

Jerry made note in this morning’s Hili Dialogue about John van Wyhe’s posting of some newly uncovered Darwin manuscripts, and you can read them all here at John’s wonderful website, Darwin Online. If you’re interested in The Origin as a document, his website is also the place to go, with authoritative discussion of the publication history, many scanned versions available to read online, and a complete listing of editions. John and his collaborators have continued the work of R.B. Freeman, who compiled an authoritative (as of 1977) catalog of all of Darwin’s works; Freeman’s catalog is available at Darwin Online. The Harvard University Press edition is “Freeman 602“, which is a facsimile of “Freeman 373“. As we’ve had occasion to note many times before here at WEIT, John van Wyhe and his collaborators have done an inestimable service to students, scientists, and historians in gathering together and making available these materials.

 

JAC Response: I didn’t claim that the book was unreadable, but that it was “not an easy read” and that parts were opaque or tough. It isn’t an easy read, for it requires you to stop and think frequently, which is a good thing. “Easy reads” are those books you can just breeze through. I find the book eminently readable—except for the “Hybridism” chapter!

Heavy human harvesting of a valuable medicinal plant leads to evolution of new leaf and flower colors

November 22, 2020 • 10:30 am

If humans harvest an animal or plant, especially if they harvest it heavily, the species often evolves to make itself less “harvestable”.  For example, commerical fisheries that take the larger fish in the sea have led to the evolution of individuals that mature earlier at a smaller size, for it is the small reproducing fish who don’t get caught. Elephants harvested for their ivory have, in some populations, evolved smaller tusks or even tusklessness, for it’s the tuskless elephants who leave more offspring. (The condition for all such evolution, of course, is that the evolved conditions have at least a partial genetic basis.)

Finally, there’s a similar phenomenon called “Vavilovian mimicry”—named after the great Russian geneticist and botanist Nikolai Vavilov, who was imprisoned by the Soviets and died in the gulag because he dared to embrace Western genetics and science against the teachings of the charlatan Lysenko.

In Vavilovian mimicry, weeds are selected among agricultural crops with which they grow to get themselves in the next generation of the crop. Farmers have mechanical ways to sort out the weed seeds during harvesting, and this imposes selection on the weeds to produce seeds of the same size and shape as the crop; it’s those mutant weed seeds that get replanted the next year.

A cool and famous example is how the common vetch (Vicia sativa), a weed, has evolved in crop areas so that its seeds come to closely resemble that of the edible lentil (Lens culinaris), a crop that the weed infests.  Because lentil seeds, which are what’s eaten, are tasty but vetch seeds are bitter, farmers have used mechanical and visual sorting to discard the wild vetch seeds. Over time, the vetch seeds have undergone what’s called “unnatural selection” (for Vavlovian mimicry) to have the same size, color, and shape (flattened) as the lentil seeds. Here’s a diagram showing the cultivated lentils (A) along with the wild vetch seeds growing on their own (B), and the seeds of the same vetch, but which have grown in lentil fields. Look at the big evolutionary change in the vetch seeds!:

Today we have another example of plants mimicking other things—in this case the environment—to hide themselves from being harvested.  Fritillaria delavay, is a perennial alpine Asian plant that grows from a bulb, living about five years. The bulbs, particularly the small ones, are very prized in Chinese medicine, especially for treating tuberculosis, fetching up to nearly $500 per kilogram. (Since they’re small, it takes about 3,500 bulbs to make a kilogram.) They are picked visually, with harvesters looking for the bright green leaves and flowers of the plant that stand out against their rocky background.

Since harvesting is heavy, you can guess how the plant evolved. That evolution is documented in this new paper in Current Biology (click on screenshot below, or go here to get the pdf, both of which are free).  If you want a journalistic summary, there’s one in the Times and another in the Guardian.

In short, the plant has undergone evolution of both leaf and flower color to make it more inconspicuous and thus harder to find and harvest (harvesting, since it takes the bulb, kills the plant). You’re more likely to reproduce if you’re not seen, and in harvested areas those plants with mutations making them match the background better are those that survive. Herbivores apparently aren’t involved in this system, as nothing has been observed to eat the plant, which is full of alkaloids and toxic.

Here are pictures F. dlavayi in an unharvested area (left) and one in an area heavily harvested (right). You can guess which is which. Note the difference in the color of both leaves and flowers. In fact, the green color can evolve to either reddish, brownish, or grayish colors depending on the color of the background.

 

In the paper, the authors collected plants from eight populations in southwest China, and found significant divergence of color among the populations using a special “vision model” to measure the colors and luminescence seen by humans. Here’s a plot of the variation among the eight populations (each dot has a color that is related to the plant color, with each color representing a single population):

(From paper): Plant Color Variation of Fritillaria delavayi among Populations. (A) Color divergence from eight populations in human CIE L∗a∗b∗ color space

Are the plants camouflaged in their local area, and is the degree of the camouflage correlated with how heavily the plants are harvested? The authors derived a measure of how camouflaged a plant was by comparing leaf and flower color with the color of the soil or rock background (also measured using the human-vision algorithm). Collection intensity was assessed by questioning the locals and deriving an estimate of intensity = [amount of bulbs collected]/[relative abundance of the plant in the area]. The higher this fraction, the heavier the collection effort (i.e., the proportion of the population that gets taken by collectors).

As you see from the plot below, the higher the collection intensity in a population (position to the right), the better the mimicry (lower values on the Y axis). The relationship is highly statistically significant (p < 0.001). Clearly, the prediction that the color evolved in response to human harvesting is supported.

Finally, the authors looked at an ancillary relationship: that between the difficulty of digging up bulbs (some are hidden under dirt and rock piles) and the degree of camouflage of the population. The relationship they found is shown below. One predicts that the easier it is to dig up a bulb, the more camouflaged the population would be, for easier digging makes for heavier harvesting and thus stronger “unnatural selection”. The relationship below affirms the prediction, though they left out one population where collection is easy but the plant is green—yet collection isn’t heavy in this population. (This sounds like post-facto discarding of data, but could be kosher.)

Whether each dot is statistically independent of the others, which seems to be the assumption when doing the nonparametric correlations, is dubious, since plants in a given area are related to one another, and each plant didn’t evolve its color independently—the population as a whole evolved its color as a gene pool.

Leaving that possible quibble aside, the authors finally did a computer experiment on target slides showing plants matching their background to various degrees. They found, as expected, that the locals took longer to detect a plant when it matched the background, confirming that your chance of escaping “predation” is likely higher when you’re better camouflaged.

Here’s one more photo from the paper showing the cryptic nature of the plant in brown and gray backgrounds (C and D), and how readily the bright green plants stands out against a scree background (A and B; this is clearly a low-harvest area).

Plant Color Variation of Fritillaria delavayi among Populations

There are no new principles demonstrated in this paper, but the results are still fascinating, and show a mixture of artificial and natural selection that’s called “unnatural selection.” That is, the color isn’t a deliberate product of the breeder, like the grotesquely long bodies and minuscule limbs of wiener dogs, but is an inadvertent result of “artificial” selection. (I’m not even sure I’d call this artificial selection, for humans are part of nature and are gathering something they need.) And, like natural selection, all this process requires is differential reproduction of individuals that have different genetic variants.

If you want to read more about “unnatural selection” and how it’s affected many species, click on the screenshot below.

h/t: Ben, Matthew, Florian

_________________

Niu, Y., M. Stevens, and H. Sun. 2020. Commercial Harvesting Has Driven the Evolution of Camouflage in an Alpine Plant. Current Biology. Online. https://doi.org/10.1016/j.cub.2020.10.078

How does altruism evolve?

November 20, 2020 • 1:30 pm

The short answer: through kin selection.

According to the new paper from the Proceedings of the National Academy of Sciences (PNAS) shown below, and in general in evolutionary biology, altruism is defined as “a behavior decreasing the expected survival and/or reproduction (fitness) of the actor while increasing the fitness of the recipient.”

The simplest example of such altruism involves parental care. A human mother taking care of her child is using resources (milk, time, effort) that in fact reduces her chance of survival or of having future kids. But the kid itself, the recipient, benefits. Parental care evolves because the cost to the mom is less than the benefit to the kid she tends.

Likewise with any sacrifice people make for their relatives. The reason this has evolved is that genes promoting parental behavior do entail a cost to their carriers, but they more than repay that cost by helping the perpetuation of the same genes (“genes identical by descent”) in the offspring, which has a 50% of getting a parental-care gene from the parent. Thus the gene gets a net boost from the behavior it produces.

So there’s a calculus involved for genes that reduce your fitness but help that of the recipient. This calculus is expressed in “Hamilton’s rule,” introduced by the great evolutionary biologist W. D. Hamilton. In general, a gene producing altruistic behavior—reducing the fitness of its carrier but helping others who carry copies of the same gene—will evolve by natural selection (i.e., increase in frequency) if it satisfies this equation:

r  x b > c

where c is the fitness cost to the donor of performing the act, b is the benefit to the recipient, and r is the “degree of relationship”, i.e., the chance that the recipient actually carries a copy of the altruism-producing gene because it’s related to the donor (“identity by descent”).

So, for example, r for parents vs. offspring is 0.5: the chance that an offspring will inherit an altruism gene (gene form, actually: an “allele”) from a parent is 50% due to segregation and assortment during reproduction. One can conclude that a gene that makes you expend effort to help your kid will be favored by natural selection if the fitness benefit to your kid is at least twice the cost to you. r for siblings is also 50% (brothers and sisters share half their genes), so a gene could be favored that causes you to help your siblings if the cost to you is also less than half the benefit to your siblings. r for uncles compared to nieces and nephews is 25% (therefore, for Uncle Joe, his altruism will evolve if the cost to him is less than a quarter of the benefit to niece Sarah, and so on.

The interaction between relatives, close or distant gentically, is the way that most evolutionists think that altruism has evolved. For a gene that incurs fitness costs in its bearer, but doesn’t give a benefit to those carrying other copies of the same gene, will go extinct. This is why when we observe self-sacrifice in nature, it’s nearly always to help relatives. (Think of the “broken wing” display in which a mother bird, feigning injury but risking her life, lures a predator away from her chicks.)

And when animals have a way to recognize and avoid taking care of unrelated organisms, they can. Here’s a note evolutionist Bruce Lyon sent me about the work of him and his colleagues on coots:

American coot females lay eggs in each others’ nests and they recognize and the host parents deal with the brood parasitic eggs/offspring at two stages: they recognized about a third of parasitic eggs and reject them by burying them down in the nest and they can also learn to recognize some parasitic chicks, and if they recognize the chicks they kill them.

. . . Lots of other birds have been shown to be able to recognize their own chicks, as in colonial seabirds, but they don’t use this to kill other chicks but instead insure that they feed their own kids.

This makes no sense unless parental care involves relatedness.  (If you have questions about this, I’ll ask Bruce to answer them in the comments.)

It doesn’t have to be direct relatedness, either. If a population is viscous, with individuals not moving around much, people will become related simply because they mate more often with nearby individuals. That’s why there’s a high degree of relatedness in small religious communities like the Dunkers and Amish, who don’t marry their siblings or cousins but marry those in the community. Over time, this causes an increase in relatedness in such communities.

Hamilton proposed his “rule” in 1964, but others hit on it as well, including J. B. S. Haldane, who was reported to say that he’d lay down his life for two brothers or eight cousins (you’d have to save all the relatives’ lives for this to work), and the idea was also worked out mathematically by the eccentric biologist George Price.

But in the last two decades, several biologists have claimed that altruism could evolve without this kind of kin selection—without individuals behaving in a way to favor their relatives. Most prominent among these contrarian biologists is Martin Nowak at Harvard, who has said that altruism doesn’t need relatedness to evolve, simply requiring a particular population structure. Other biologists have said that kin selection could work, but so could population structure alone.

It turns out that in all these cases, the population structure proposed in fact causes individuals to be related and favors altruism because of that relatedness. While many biologists recognize the mathematical equivalence of “population structure” and “kin selection models”, Nowak has denied this, stating that geographic population structure alone (his model of “spatial selection”), even if it doesn’t create a web of relatedness, could favor the evolution of altruism.

Nowak is wrong. This is demonstrated in the new paper in PNAS by Kay, Keller, and Lehmann (click on link to get it, pdf here, and reference at bottom). The upshot: you can’t get the evolution of altruism with population-structure alone, unless that population structure creates kin relationships that satisfy Hamilton’s rule. Kin selection remains the sine qua non for the evolution of altruism.

 

What the authors did is simple: they looked up all the scientific papers that showed the evolution of altruism, including those that ignored kin selection as well as those that denied kin selection was operating, and then analyzed whether the models indeed created a structure in which relatedness was important to determine whether kin selection—even if ignored or denied—was crucial for evolving altruism. They found 89 papers of theoretical models in which altruism evolved. The authors parsed them this way (my emphasis):

Among the 89 altruism models, 46 adopted Hamilton’s conceptual framework, attributing the evolution of altruism to positive relatedness. The remaining 43 all claimed alternative mechanisms. To evaluate the veracity of their claims, we first subdivided these 43 papers into those where the role of relatedness was denied (17 cases; SI Appendix, Table S3), and those which made little or no mention of relatedness (26 cases; SI Appendix, Table S4).

Among the 17 papers where the presence/role of relatedness was denied (SI Appendix, Table S3), our analysis of the life cycles of the models showed that the proposed scenario led to positive relatedness between interacting agents in every case. Moreover, in most of these models, agents reproduced clonally (e.g., “parents pass on their type to their offspring”) with interactions occurring among nearest neighbors, as in the stepping-stone model of Fig. 1, with only one individual per node/group. This represents the tritest instance of kin selection.

As for the remaining 26 models which proposed non-kin mechanisms for the evolution of altruism but didn’t mention relatedness, this is what Kay et al.’s analysis showed:

The 26 papers which make little or no mention of relatedness attribute the evolution of altruism to diverse alternative mechanisms including “social diversity,” “social viscosity,” “topological heterogeneity,” “network heterogeneity,” “network reciprocity,” “spatial reciprocity,” “spatial structure,” and “multiplex structure” (SI Appendix, Table S4). Analysis of these models revealed that in every case interacting individuals are related, relatives benefit from each other’s altruism, and kin selection therefore operates.

So none—zero, zip, bukes—of the “alternative” models could evolve altruism without kin selection and relatedness. This isn’t so mendacious when the authors just ignore kin selection, proposing models that nevertheless produce the interactions that allow kin selection. But it IS bad behavior when authors like Nowak claim that the evolution of altruism has nothing to do with kin selection and relatedness. That is a form of careerism—proposing some new mechanism when you haven’t done the scientific legwork (like Kay et al. did) to show that the new boss is the same as the old boss.

The upshot: the evolution of biological altruism, in which individuals sacrifice their own fitness to help others, cannot proceed without kin selection. There would be no selection on parents to help adopted children, since they aren’t related. (The fact that they do, in both humans and animals, is certainly a case of misplaced parental instinct. Warblers feeding cuckoo chicks, who aren’t even in the same species, is a prime example of hijacking of parental impulses.)

Why do so many authors ignore kin selection or say it isn’t operating in the evolution of altruism? (Nowak isn’t the only one of the latter.) Kay et al. give three suggestions. The first is careerism, as I’ve mentioned above: you don’t get famous by just showing what’s already been demonstrated. But they also note that some models are made by people who aren’t evolutionists and thus may be unaware of Hamilton and Price’s work (these people are economists, physicists, and so on). Finally, some authors know and understand Hamilton’s rule but are so steeped in it that they simply don’t bother to bring it up explicitly in their models.

So don’t believe claims that altruism can evolve without kin selection.

BUT, what about those cases in which, say, humans help others, risking their lives for people who aren’t related to them? I often use as examples volunteer firemen, who risk their lives for people they don’t even know. Or, in war, soldiers have died by throwing themselves on a grenade to save their platoon. This is certainly altruism, but it doesn’t involve kin. This kind of sacrifice is almost completely unknown in other species, where individuals aren’t seen to risk their lives for non-relatives. That alone gives you a clue that there is some cultural aspect to this kind of altruism in humans. But you are as good as I am in speculating about this, and I’ll leave it as a thought exercise.

Coda: I never met Hamilton even though we overlapped in time (he lived from 1936-2000, dying at only 63 from what may have been a combination of an ulcer and malaria). But I know many people who knew Hamilton well, and without exception they paint him as an unassuming and genial man—an all-around nice guy as well as a scientific genius (he was also a keen naturalist and spent a lot of time in the tropics). He had some bizarre ideas, but also some ideas that became foundational in the evolution of behavior. Here he is (I just noticed that he looks a bit like me, but with longer hair).

________________

Kay, T., L. Keller, and L. Lehmann. 2020. The evolution of altruism and the serial rediscovery of the role of relatedness. Proceedings of the National Academy of Sciences 117:28894-28898.

A philosopher infected with confirmation bias explains why evolution proves God

November 15, 2020 • 9:15 am

Religious affirmations like those in this video make me angry, wanting to call philosopher Holmes Rolston III a chowderhead who’s taking money under false pretenses. But I will refrain from such name-calling. Nevertheless, what you hear coming out of Rolston’s mouth in this short Closer to Truth interview is pure garbage: not even passable philosophy. It should dismay all rational people that such a man is not only expressing laughable confirmation biases, but is getting paid for it.

And yet here are Rolston’s bona fides from Wikipedia:

Holmes Rolston III (born November 19, 1932) is a philosopher who is University Distinguished Professor of Philosophy at Colorado State University. He is best known for his contributions to environmental ethics and the relationship between science and religion. Among other honors, Rolston won the 2003 Templeton Prize, awarded by Prince Philip in Buckingham Palace. He gave the Gifford Lectures, University of Edinburgh, 1997–1998.
And remember that the Templeton Prize, was worth over a million bucks, even back in 2003. What did he get it for? This is from Templeton’s press release when they gave him the Prize:

The world’s best known religion prize, [The Templeton Prize] is given each year to a living person to encourage and honor those who advance spiritual matters.  When he created the prize, Templeton stipulated that its value always exceed the Nobel Prizes to underscore his belief that advances in spiritual discoveries can be quantifiably more significant than those honored by the Nobels.

. . . .Rolston has lectured on seven continents including throughout Europe, Australia, South America, China, India, and Japan.

Seven continents? They left out Antarctica, and I doubt that Rolston has lectured there.  His prize-winning thoughts:

. . . science and religion have usually joined to keep humans in central focus, an anthropocentric perspective when valuing the creation of the universe and evolution on Earth.  Rolston, by contrast, has argued an almost opposite approach, one that looks beyond humans to include the fundamental value and goodness of plants, animals, species, and ecosystems as core issues of theological and scientific concern.  His 1986 book, Science and Religion — A Critical Study and his 1987 Environmental Ethics have been widely hailed for re-opening the question of a theology of nature by rejecting anthropocentrism in ethical and philosophical analysis valuing natural history.

Do I denigrate him unfairly? Shouldn’t I read his many books to give him a fairer assessment? Not on your life: I’m through with the Courtier’s Reply gambit.  Just let me add that Rolston is a believer, with a degree from Union Presbyterian Seminary, the same year he was ordained to the ministry of the Presbyterian Church (USA).  

Have a listen, and don’t be drinking liquids when you do. The good part is that this is only a bit less than seven minutes long.

Rolston gets a sense of “divine creativity” from the gradual and incremental changes wrought by neo-Darwinian evolution. But in this video he dwells more on serendipity, the “surprises” that punctuate the history of evolution. These include these “adventures that turned out right”:

a.) Swim bladders evolving into lungs (most people think it’s the other way around, but Rolston is right). This is a simple case of an “exaptation“, as Gould called it: the adaptation of an evolved feature into something with a new function.

b.) The capture of a photosynthetic bacterium by another cell to form photosynthetic eukaryotes: plants. (The same happened with mitochondria.) Yes, this is unpredictable, as is all of evolution, and was a major innovation, but it’s not evidence for God.

c.) The evolution of hearing began with a pressure-sensitive cell in a fish. This is another exaptation, though the function didn’t change, but altered a bit. Hearing still depends on pressure change, but we use it for apprehending and interpreting language and other sounds in air. Animals use it for intraspecies communication and detection of predators (which fish also use it for).

I could give a gazillion examples of such “surprises” in evolution, like the evolution of the ovipositor of insects into the stinging apparatus of bees and wasps, the doubling of an entire ancestral genome—twice—during the evolution of the vertebrates, and so on. Nobody can predict where evolution will go, for, as Jacques Monod famously noted in 1977, evolution is a tinkerer. And what about the “adventures that turned out wrong“, like the evolution of large dinosaurian reptiles? God killed ’em off by sending a big asteroid plummeting towards Earth.

The fact is that nothing we see in evolution contradicts the claim that it’s a purely naturalistic process, proceeding via unpredictable events—mutations and environmental change. This is the most parsimonious hypothesis given that we have not an iota of convincing evidence for God.

Then, in response to a softball question by the host, Rolston avers that he sees a theological underpinning of surprise, co-option, and serendipity. But since he also sees the hand of god in gradual Darwinian evolution, he sees the hand of God in all of evolution. In other words, there is nothing Rolston could observe about evolution that wouldn’t, for him, constitute evidence for God. As he says:

“It leaves open a place for surprising creativity . . . that I think exceeds any Darwinian capacity for explanation. Now I said when I began that I can find the presence of God in incremental evolutionary genesis. But maybe if the world is surprising as well as predictable that might further invite places where you might think if I should say, ‘God might sneak into the evolutionary process.’. . . .God may like serendipity as well as law-like prediction and determinism.”

So, If evolution is gradual and smooth, it’s evidence for God. But if there are “surprises”, as there have been, well, that’s also evidence for God. In other words, EVERYTHING is evidence for God. It is an academic crime that someone not only gets paid—and wins a huge prize—for spouting this kind of pabulum, but also is respected for it, for, after all, Rolston is a minister and a believer.

My contempt for this kind of reasoning knows no bounds. It could be filed in the Philosophical Dictionary under “confirmation bias; religion”. (Is that heading a redundancy?) Everything that happens is evidence for God because it’s “what God likes.” But of course if you argue that “whatever happens must be what God likes,” then you have yourself a million-dollar airtight, circular argument.  Some philosophy!

I guess the host, Robert Lawrence Kuhn, sees his brief as drawing out the guest rather than challenging him, and that’s okay. But I would have been pleased had Kuhn asked him this: “Is there anything about evolution that doesn’t give you evidence for God?”  I would think, for instance, that the evolution of predators and parasites that inflict horrible suffering on animals might make one question the existence of God, as it did for Darwin, but I’m sure Rolston has his explanation. Maybe it’s “God likes a little drama in his creation.”

 

h/t: Mark

A genomic and evolutionary analysis of an extinct saber-toothed cat

October 18, 2020 • 1:00 pm

A recent article in Current Biology, which you should be able get for free by clicking on the screenshot below, describes sequencing the entire genome of an extinct saber-toothed cat, thereby gaining some insight into its evolutionary history. (You can get the pdf here, and the full reference is at the bottom. If you can’t see the piece, make a judicious inquiry.)

The cat is Homotherium latidens, also known as the European saber-toothed cat (it’s also called a “scimitar-toothed cat” because its teeth were smaller than true sabertooths like Smilodon), and it probably lived from a few million years ago until fairly recently (the late Pleistocene, about 12,000 years ago). It may thus have encountered modern humans. It was about the size of a male African lion, and a reconstruction from Prehistoric Fauna looks like this (note the saber teeth and very short bobtail).

The species was also widespread: as the article below notes, “it once spanned from southern Africa, across Eurasia and North America, to South America, arguably the largest geographical range of all the saber-toothed cats.” Although it was clearly a hunter, like all sabertooths, we know nothing about its social life, or whether it was social—nor about whether it hunted by day, night, or twilight (“crepuscular”). Some of these issues were addressed by the authors using the DNA sequence.

Click to read:

The data come from a single specimen found in the Yukon and in the possession of the Yukon Government paleontology program. A section of humerus was used for dating (the fossil was about 47,000 years old), and then was crushed up to extract DNA. The authors were able to get a substantial amount of sequence from the bone, and they compared that sequence to DNA taken from living lions, sand cats, fishing cats, leopard cats, and caracals.

The conclusions about where this cat fits on the evolutionary tree of felids are pretty sound, based as they are on lots of DNA sequence. However, the conclusions about what genes may have propelled its evolution are a lot more speculative. Here are the main conclusions.

1.) The species was long diverged from the lineage that led to modern cats.  The lineage that led to this species diverged from that of all living cats a long time ago: about 22.5 million years. We knew of this substantial age from mitochondrial DNA sequencing in previous work, but it’s dicey to make conclusions about family trees from mitochondrial DNA alone. The date above is one that we can rely on, though, as it’s based on DNA divergence in the whole genome that’s been calibrated from the fossil record.

Here’s the deduced phylogeny, showing where H. latidens (in red) fits in with 17 cats and two hyenas. You can see that it diverged from living cats over 20 million years ago.

2.) There doesn’t seem to have been much hybridization between this species and the ancestors of living cats, which began diverging from each other about 14 million years ago (see phylogeny above). The authors could have detected such hybridization by finding sections of the genome that were discordant in divergence from living cats—perhaps sections of DNA that got into the saber-toothed tiger from species after the divergence of modern cats about 14 million years ago. That is, most genes would show similar amounts of divergence from the same genes in the modern-cat lineage, but a few would be much less diverged, suggesting that those genes got into the H. latidens genome after hybridization with cats that diverged much later.

They didn’t find any such discordance, suggesting that H. latidens simply didn’t hybridize with cats that evolved in the last 14 million years. For some reason this absence caused a lot of consternation for the authors.  I guess they expected to find some evidence of hybridization and “introgression” (transfer of genes between species after speciation had occurred), and they go on at great length to speculate about this absence. They mention things like low population density (so members of different species don’t meet), ecological or behavioral isolation, and so on. But the most obvious possibility, which they don’t mention, is simply that speciation between the scimitar cat and its relatives had been completed by the time they encountered each other, so that no gene flow was possible. Yes, sometimes reproductive barriers are complete, as they are now between our own species and every other species on the planet.  And this is true for lots of species. Just because hybridization is more common than we thought doesn’t mean that nearly every species occasionally exchanges genes with others.

3.) The authors found genes in the H. latidens genome that apparently underwent natural selection. The way geneticists judge this is to look for which regions of a gene have changed relative to the genes of its relatives. This is expressed in what’s called the dN/dS ratio. That ratio gives the frequency of evolutionary changes in “non-silent” parts of proteins (dN: those parts where a mutation changes the protein sequence of the gene) to the changes in “silent” parts of genes (dS: those parts where a mutation is in a noncoding part of the gene or in a third position of a “codon”, where a mutation doesn’t usually change the protein sequence).

If genes just change randomly, without selection, this ratio should be about one. If the ratio is higher than one, protein sequences are changing faster than they would under a “neutral” process in which no changes in the gene alter its effect on reproduction (“fitness”). The authors used a cutoff ratio of dN/dS of between 2 and 5 as a criterion for selection, and they found 31 genes in this range out of the 2,191 analyzed. Eighteen of these genes, potential targets for selection in this cat, are shown in the diagram below (They don’t mention what the other 13 genes do.)

You can see they fall into four general classes, and into subclasses as well, like genes affecting vision fitting into the the “diurnal” class. The authors note that while dN/dS ratios are only suggestions of what genes in the lineage of this species may have been subject to positive natural selection, they do speculate at length about the form of selection. The cats, for example, could have been selected to adapt to daylight hunting (as opposed to most cats), with consequently improved vision. Selection on “endurance” genes may have facilitated “cursorial” hunting (i.e., running down prey). And there may have been positive selection on genes known to involve social behavior—in mice. From that they speculate that this cat may have become more social and thus able to hunt down big prey in groups.

I call this kind of speculation “genomic sociobiology”, because it involves making up “just so” stories about how genetic change impacted an extinct creature. It’s fine to single out genes like this for further examination, but one has to realize that if you see selection acting on a gene affecting social behavior, for instance, it could be reducing social behavior instead of increasing it. How do we know that the ancestors of this cat weren’t social, but then there was selection on those genes to reduce sociality in favor of a more solitary lifestyle? Ditto for all the other genes. That is, showing selection itself, even if these ratios do show selection, doesn’t mean you know the direction of selection. In fact, some media outlets, like this one, have bought uncritically the notion that this study has revealed that the cat evolved to become more social.

4.) This individual, and thus its species, was very genetically diverse. That is, if you looked at the two copies of a gene in the H. latidens genome—remember, we all carry two copies of nearly all our genes except for those on mitochondria and sex chromosomes in the heterogametic sex—there was a high probability that they would be different. This “heterozygosity” would not be the case if the species were in small populations that would lose genetic variation, or in an inbred species. We can conclude that the species was genetically diverse—no surprise given how wide ranging it was.

As to why H. latidens went extinct, well, we just don’t know. Given its genetic diversity, it probably wasn’t inbreeding, and could have been stuff like competition with cats that were better hunters, a disease or parasite, climate change, or any number of things.

Overall, this is a decent paper, and a good one insofar as doing whole-genome sequencing and phylogenetic analysis of a long-extinct species. The conclusions about natural selection are speculative, and the authors realize that. If there’s a flaw in the paper, I think it’s that the authors do go on too long with the natural selection business, especially given that it’s purely guesswork based on ratios of substitutions in DNA, and because we’re totally ignorant about what these genetic changes really meant for the evolution of these cats.

Oh, and I’m disappointed that they didn’t see positive selection in “tooth genes”!

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Barnett, R., M. V. Westbury, M. Sandoval-Velasco, F. G. Vieira, S. Jeon, G. Zazula, M. D. Martin, S. Y. W. Ho, N. Mather, S. Gopalakrishnan, J. Ramos-Madrigal, M. de Manuel, M. L. Zepeda-Mendoza, A. Antunes, A. C. Baez, B. De Cahsan, G. Larson, S. J. O’Brien, E. Eizirik, W. E. Johnson, K.-P. Koepfli, A. Wilting, J. Fickel, L. Dalén, E. D. Lorenzen, T. Marques-Bonet, A. J. Hansen, G. Zhang, J. Bhak, N. Yamaguchi, and M. T. P. Gilbert. 2020. Genomic Adaptations and Evolutionary History of the Extinct Scimitar-Toothed Cat, Homotherium latidens. Current Biology.