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”!

_______________

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.

Revisiting an old paper, but a good one

October 13, 2020 • 9:30 am

I have to brag a bit in the title because if you say a paper is an “oldie,” you have to also say “it’s a goodie”. But I think this one is—it’s the first of two papers I wrote with my then-grad-student Allen Orr on the time course of speciation in Drosophila.  And it’s one of the few good ideas I’ve ever had. I don’t know how often it’s been cited—I don’t look up stuff like that—but it has been influential in inspiring others to do related work. I’m writing about this paper because I recently revisited it in an interview (see below).

Here’s a very brief summary of what we did. I realized one day, when I was at the University of Maryland, that there existed a tremendous amount of data about the sexual isolation and hybrid sterility/inviability of various Drosophila (fruit fly) species tested in the lab. There also existed, separately, a large amount of data on the “genetic distance” between these species as judged from gel electrophoresis. This genetic difference is a rough measure of the times since the species diverged. The more similar the electrophoretic profiles, the younger the species. (The actual real-time calibration of the distance is hard, as Drosophila has no fossil record, but we did our best.)

You could, I realized, take various pairs of species, see how much reproductive isolation they had between them—how much mating discrimination and whether the hybrids were viable and fertile—and correlate that with the genetic distance between members of each pair. If you plotted genetic distance against the degree of genetic isolation, you could get a “time course” of speciation, seeing which forms of isolation evolved earliest, what rate they evolved at, whether it would make a difference if the species lived in the same or different areas, and so on.

Of course there are lots of issues here, one being that measures of reproductive divergence between various pairs of species aren’t evolutionarily independent, so we had to do phylogenetic corrections. Further, sexual isolation and sterility/inviability are only two of the reproductive barriers that separate species, and we had to neglect types of genetic isolation that could operate in nature but couldn’t be measured in the lab (e.g., different preferences for food or microhabitats).

The results, though, were surprisingly clean and enlightening. For example, we found that sexual isolation—but not hybrid inviability—evolves ten times faster between species now found in the same area than those now found in different areas. This result, which has held up in repeats of our work, suggests that natural selection “reinforces”, or strengthens, mate discrimination between species when they live in the same place. That’s probably because there is a genetic penalty to be paid, in the form of hybrid problems, if you actually mate with the “wrong” species; and you only have that kind of selection operating in species that live in the same area, and have a chance to produce hybrids.

Here’s a graph from the second of our paper of papers showing two plots of the degree of sexual isolation between pairs of species (y axis) against their electrophoretic genetic distance (a measure of the divergence time between members of each pair). “Allopatric” taxa are pairs of species that are geographically isolated at present, while “sympatric” taxa are pairs of species that live in the same general area. (These data are phylogenetically corrected.) You can see that the degree of sexual isolation appears much earlier (at lower genetic distances) when the taxa live in the same area. This is a very striking result that is highly statistically significant. It suggests that natural selection operates on species living in the same place to “reinforce” their sexual isolation. You don’t see this difference for hybrid sterility or inviability, which are not expected to be reinforced by selection.

I digress, but it’s nice to think about this good old work.  Allen came on board the project at the beginning, and we spent several years collecting the data (which was scattered all over the literature), calculating statistics when only raw data were given, and analyzing the data. Thus the paper didn’t come out (in Evolution) until 1989, three years after we’d moved to Chicago.

Then electrophoretic data and reproductive-isolation data continued to accumulate, so in 1997 we published an update of the 1989 paper. The additional data confirmed the patterns we’d seen before. And now, since nobody does electrophoresis any more, and estimates of genetic divergence come from DNA sequences, we can’t do this analysis further. (DNA-sequence data does not exist for most of the species we used.)  Similar work has been done in fish and tomatoes, and at least two researchers have redone our analyses in flies using different techniques (the conclusions remain good).

The references to our two papers are given at the bottom, along with the links to them (free access).

This long introduction just wrote itself, when what I really want to do is call your attention to an interview I did about that first paper with Hari Sridhar at his site Reflections on Papers Past. Hari, a a post-doctoral researcher at the National Centre for Biological Sciences, Bengaluru (formerly Bangalore), India, has been interviewing scientists about well known papers in ecology and evolution since 2016.  He was kind enough to interview me about the first Coyne and Orr paper, and you can see the interview by clicking on the link below. I haven’t read the final version, which is a transcript of an audio conversation, so be aware that it’s spoken language. I did read a draft and corrected a few phrases that were unintelligible over the phone.

If you’re interested in papers in ecology and evolution, you might have a wander round Hari’s site; there are lots of interesting papers and interviews, many with people I know.

Click below to see the interview.

I want to add that although Allen was my grad student during much of the time we wrote these papers, it was a total collaboration. As with all my students, I don’t micromanage their work or ever tell them what research to do. Allen was interested in the project from the beginning, and contributed tons of work and many ideas to the two papers. And our collaboration continued in what I consider my most important scientific accomplishment, the book Speciation (Coyne and Orr, 2004; note that the book is now expensive but was about $50 when it first came out).

Here are Allen and I at the Evolution meetings in Portland in 2010. Allen was president of the Society for the Study of Evolution, and I was an incoming President, so he briefed me about the job. We had a great time in Portland, as that was before the city went nuts.

And as a measure of the fame of our work, you can’t get bigger than this. My collaboration with Allen was featured in the 2001 movie “Evolution” (a dreadful film!), as a scrawled reference on the blackboard behind two of the stars, David Duchovny and Orlando Jones. See below. It says “Read Coyne and Orr.  ‘Drosophila’ pp. xx8-450”. Note that the page numbers don’t correspond to either paper that we wrote, though it may refer to the book. But even in the book those pages don’t correspond to anything that would be a reading assignment.

Another ex-student of mine, Mohamed Noor, called me up and said he’d seen the movie and noticed a reference to our paper on the blackboard. I didn’t believe him, so I had to go see the movie myself. Sure enough, we were in there! Someone later sent me a screenshot (below).

I would call that real fame! Pity they got the page numbers wrong. I’ve always wondered who wrote that on the board and how they knew about our work.

_______________

Coyne, J. A. and H.A. Orr.  1989.  Patterns of speciation in Drosophila.  Evolution 43: 362-381.

Coyne, J. A., and H. A. Orr. 1997. “Patterns of speciation in Drosophila” revisited. Evolution 51:295-303.

Pre-Darwin “Darwinians”: a post by Andrew Berry

October 9, 2020 • 12:30 pm

JAC:  When I wrote my post two days ago about supposed Arab precursors to Darwin, I had some email and phone exchanges with my friend Andrew Berry, an instructor and advisor at Harvard who knows a ton about the history of evolutionary biology.  After a recent exchange in which he sent me an informative email, I asked him to flesh it out a bit, as I thought it would make a nice standalone post. Right now there seems to be a resurgence of the claim that many people before Darwin anticipated his ideas in surprising detail. My view is no, they did not: they anticipated the notion of evolution, but nowhere near in as much detail as did Darwin in The Origin; nor did they provide supporting detail to make their theory credible. Finally, nobody (save the Scot Patrick Matthew and, of course, A. R. Wallace) even came close to the mechanism of adaptive evolution—natural selection. I believe, in the essay below, Andrew agrees with that.

But I digress. Here are Andrew’s thoughts on the issue of The Harbingers of Darwinism. He begins by mentioning two errors in my earlier post, which have now been corrected.

*********************

Pre-Darwin “Darwinians”

by Andrew Berry

Jerry’s piece in response to a VICE article on several early Arab thinkers whose ideas presaged the theory of evolution raised a number of interesting points.

First off, a couple of utterly trivial things: 1. Patrick Matthew was Scottish, not English.  (Maybe an apparently minor distinction when viewed from the US side of the Atlantic, but not when viewed from the UK side, especially in this era of Brexit and Johnsonian perfidy).  2. Erasmus Darwin did not write a book about evolution.  He merely mentioned it in a number of places in his writings, often in verse (his preferred format).  In fact, he is responsible for what is surely the best statement ever made of the Descent with Modification component of his grandson’s theory (from Temple of Nature 1803):

Organic life beneath the shoreless waves
Was born and nurs’d in ocean’s pearly caves;
First forms minute, unseen by spheric glass,
Move on the mud, or pierce the watery mass;
These, as successive generations bloom,
New powers acquire and larger limbs assume;
Whence countless groups of vegetation spring,
And breathing realms of fin and feet and wing.

Put that on a T-shirt!

I just wanted to add a general observation: that the VICE piece, and the academic articles it is based on, are part of a long tradition of finding hints of evolutionary thinking in a whole range of pre-Darwin writers.  As Jerry mentioned, Rebecca Stott’s Darwin’s Ghosts (2012) is an excellent recent exploration of this area.  As scholarship shifts away from a Western focus, my prediction is that Stott will have to produce another edition, with added thinkers from traditions that have not typically been regarded as relevant to what we might call pre-Darwinan studies.

As Stott recounts, many of these thinkers, western or non-western, took significant risks in challenging the reigning orthodoxy (usually religious ideas on origins).  My favourite is a Frenchman, de Maillet, who took out a threefold insurance policy against suffering the consequences of heresy for his evolutionary thinking.  First, he published his ideas posthumously (the book appeared in 1748, ten years after he died); second, he arranged for the manuscript to be edited by a Catholic priest to make sure his ideas were not too directly antithetical to church doctrine (the problem being that the resulting publication was deprived of de Maillet’s assertiveness), and, most creatively, third, he claimed that his ideas were not his own but were imparted to missionaries by an Indian sage called Telliamed. But de Maillet wasn’t willing to write himself entirely out of the story: Telliamed is ‘de Maillet’ backwards.

Darwin himself provided, in the later editions of the Origin, what he called ‘An Historical Sketch of the Recent Progress of Opinion on the Origin of Species’, as a preface to the Origin.  This was an account of previous evolutionary ideas.  This was not included in the first edition of the Origin and is typically supposed to have been included in later editions as a response by Darwin to criticism post-First Edition that he had ignored the giants whose shoulders he was standing upon.  The Origin, remember, was rushed out in response to Alfred Russel Wallace’s 1858 letter.  Darwin had been quietly working away on what he called his “big species book” when Wallace intruded, sending a manuscript which laid out, in outline, the very idea that Darwin had been gestating over the previous 20 years.  Darwin’s response?  To rush out the Origin.

As the students who are required to read it in my courses will tell you, the Origin, at around 500 pages, is a hefty tome.  However, for Darwin, it was merely a preliminary statement—a quick and dirty synopsis of his argument.  He wanted the word “Abstract” in the title to indicate that this wasn’t his theory in its entirety, but, rather, just a summary.  It was his publisher John Murray who persuaded him that 500 pages and “abstract” don’t really go well together.  As a result of the rush to print, the Origin has a breathlessness about it: there are no references or citations.

It was not only the references that got cut from the project.  We know from Darwin’s correspondence that, as a part of the big book project, he had been working on that Historical Sketch—a review of previous ideas on evolution.  However, he chose not to include this in the first edition.  As he explained in a letter shortly after the Origin came out in November 1859, “My health was so poor, whilst I wrote the Book, that I was unwilling to add in the least to my labour; therefore I attempted no history of the subject; nor do I think that I was bound to do so.”  I think, in fact, he is being a little disingenuous here.  The rush to publish the Origin, after all, was all about establishing precedence, declaring that the theory was his (not, implicitly, Wallace’s).  I suspect that Darwin’s neglect of prior authorities was, at least in part, deliberate.  Wallace is mentioned just four times in the first edition of Origin. And, in his autobiography, Darwin downplayed the influence of his grandfather even though surely his wonderful lilting evolutionary speculations were both historically significant and a prominent part of his family’s lore.  Darwin, I suggest, wasn’t above a little modest self-promotion.

Critics, however, were quick to take Darwin to task for trying, by oversight, to suggest that all the ideas in the Origin were entirely his own.  And it was presumably in part as a response to these critics that Darwin took to adding the Historical Sketch preface in later editions.  The critic most often cited in this regard is Baden Powell (father of Robert Baden-Powell, founder of Scouting; curiously, Baden Powell’s widow, upon his death in 1860, renamed their children to have his full name, Baden Powell, be their surnames, with a hyphen).

This from: The Preface to Darwin’s Origin of Species: The Curious History of the “Historical Sketch” Author(s): Curtis N. Johnson Source: Journal of the History of Biology , Sep., 2007, Vol. 40 pp. 529-556 [JAC: free download at the link]:

“Shortly after the Origin originally appeared in November, 1859, Darwin received a letter from Baden Powell, Savilian Professor of Geometry at Oxford (1827-60), apparently suggesting (from what may be inferred from Darwin’s response – the Powell letter unfortunately has not been found) – that Darwin’s “theory” had been at minimum anticipated well prior to Darwin’s publication, and perhaps, more strongly, that Darwin had been scooped altogether, by Powell and perhaps by others. In the first letter of response to Powell Darwin asserts that not even the “most ignorant [educated person]” could possibly suppose that Darwin “meant to arrogate to myself the origination of the doctrine that species had not been independently created,” and that “if I have taken anything from you, I assure you it has been unconsciously” – words that sound very much as though directed to someone who had suggested some unacknowledged borrowing.”

From 1861, Darwin made sure that his ‘An Historical Sketch of the Recent Progress of Opinion on the Origin of Species’ prefaced every edition of the Origin.

Darwin, naturally, sees his list of precursors as evidence of longstanding interest in the topic but not as evidence of a lack of originality on his part.  Stott’s book falls in the same tradition: she is pointing out that there was a great deal of interesting pre-Darwinian thought on evolution, but she does not see this as diminishing the significance of Darwin’s contributions.

There is, however, another strand of analysis of pre-Darwinian thought that insists that, by rights, these thinkers should displace Darwin: Darwin, by implication, was either a plagiarist or, at best, willfully ignorant of other thinkers’ work.  Or, even more damning, Darwin is wrong, having misinterpreted key components of this prior thinking.  Perhaps the fullest expression of this perspective appeared shortly before Darwin died: Samuel Butler’s Evolution Old & New (1879).  In it, Butler argues that Darwin’s ideas can all be found in a careful reading of Georges-Louis Leclerc, Comte de Buffon, of Erasmus Darwin, of Patrick Matthew, of Jean-Baptiste Lamarck, and, regardless, some of these ideas are in fact superior to Darwin’s.

Appropriately enough, Alfred Russel Wallace was the one who took up the book review cudgel against Butler in the pages of the then relatively youthful science magazine, Nature: “the main object of the book is to show that all these [pre-Darwinian] authors have been right, while Mr. Charles Darwin is altogether wrong; and that the works of the former contain a more philosophical, more accurate, and altogether superior view of the nature and causes of evolution in the organic world than those of the latter.”

Reading over both Darwin’s Historical Sketch and the new Arab additions to the list of pre-Darwinian evolutionists, I am reminded of a comment by historian Peter Bowler in his Evolution, History of an Idea (2009).  In recounting the proto-evolutionary conjectures of the Greeks, he notes that, with the benefit of hindsight, we tend, anachronistically, to see ancient thought as presaging modern ideas when perhaps the connection is not really there.  Bowler writes that, “Ancient thought is cut and stretched to fit a Procrustean bed defined by our modern categories of analysis.”  In our search for pre-Darwinian hints of evolution, I think we keep Procrustes busy.

But as Jerry points out, the single lesson we learn from analyses of pre-Darwinian thought, is that, though interesting and tantalizing, these shards are just parts of something that only became fully realized in the hands of Darwin and Wallace.  After all, the very reason Darwin (perhaps reluctantly) added his Historical Sketch preface was to point out that curious evolution-related speculations do not a theory of evolution make.

Covid 19 may hijack pain receptors, reducing pain and increasing the spread of the virus: a possible result of natural selection

October 8, 2020 • 9:00 am

The paper below, which has just been published (click on screenshot to go to page, then click the “download” button to the left to get the pdf), has a unique twist that may say something about evolution in pathogens, but the evolutionary angle hasn’t been mentioned. It’s a complex and technical paper, using rat models (i.e., tissue and analyses), to study whether the Covid-19 virus has the ability to reduce pain.

There’s also a publicity piece from the University of Arizona that explains the results in simpler language, and a two-minute video below that dumb things down a bit, but gives the gist.

From the publicity piece:

SARS-CoV-2, the virus that causes COVID-19, can relieve pain, according to a new study by University of Arizona Health Sciences researchers.

The finding may explain why nearly half of all people who get COVID-19 experience few or no symptoms, even though they are able to spread the disease, according to the study’s corresponding author Rajesh Khanna, PhD, a professor in the UArizona College of Medicine – Tucson’s Department of Pharmacology.

Rajesh Khanna, PhD. (Photo: Kris Hanning/University of Arizona Health Sciences)“It made a lot of sense to me that perhaps the reason for the unrelenting spread of COVID-19 is that in the early stages, you’re walking around all fine as if nothing is wrong because your pain has been suppressed,” said Dr. Khanna. “You have the virus, but you don’t feel bad because your pain is gone. If we can prove that this pain relief is what is causing COVID-19 to spread further, that’s of enormous value.”

The paper, “SARS-CoV-2 Spike protein co-opts VEGF-A/Neuropilin-1 receptor signaling to induce analgesia,” was published today in PAIN, the journal of the International Association for the Study of Pain.

. . .The U.S. Centers for Disease Control and Prevention released updated data Sept. 10 estimating that 50% of COVID-19 transmission occurs prior to the onset of symptoms and 40% of COVID-19 infections are asymptomatic.

“This research raises the possibility that pain, as an early symptom of COVID-19, may be reduced by the SARS-CoV-2 spike protein as it silences the body’s pain signaling pathways,” said UArizona Health Sciences Senior Vice President Michael D. Dake, MD. “University of Arizona Health Sciences researchers at the Comprehensive Pain and Addiction Center are leveraging this unique finding to explore a novel class of therapeutics for pain as we continue to seek new ways to address the opioid epidemic.”

In other words, the virus’s famous spike protein nullifies the effect of another protein, VEGF—one of the several proteins that normally causes pain. And that’s all ye need to know unless you work on this system.

But here’s where the evolution comes in. Remember, pain is an adaptation whose evolution was doubtlessly prompted by its ability to tell us that there’s something wrong, like “Hey, your hand is in the fire.” People who don’t feel pain, like those with Hansen’s disease (leprosy) and some rare neurological conditions, often incur severe damage to their bodies because they’re unaware of injuries. The reason Hansen’s sufferers lose their fingers and other bits is not because the bacteria eat away at those bits; rather, it’s because the bacteria numb feelings of pain, and so you start damaging your body without being aware of it. So pain is a good thing to have, even though it feels bad.

But if a virus that normally causes pain because it injures your innards can somehow block that pain, it might spread faster. This would be true for viruses like COVID-19, which is spread by human-to-human contact, and depends on its transmission for people going about and infecting others. If you take to bed because you’re in pain, the virus won’t spread as well.

And what that means is that mutant variants of the virus that reduce pain will spread faster than forms that cause pain. This differential would create natural selection for the mutants that reduce pain, and the virus “species” would evolve painlessness as one “symptom”.

As far as I can see, nobody in either the paper or the puff pieces have mentioned this possibility. Now we don’t know if this speculation is true, or if it’s just fortuitous that the spike protein blocks pain receptors. Further, while this might be an evolved property of the virus, it could also be an inherent property of the spike protein, evolved for other reasons, that simply allowed the virus to spread quickly.

I’m merely suggesting this as one possibility in a field called “Darwinian medicine,” which analyzes symptoms of diseases from an evolutionary viewpoint. Other suggestions from this area involve things like malaria. When you have a malaria outbreak, the malaise and fever put you flat on your back. And that facilitates the spread of the malaria pathogen (a protozoan), because that protozoan is transmitted by mosquitoes. When you’re prostrate in bed and sick, you’re not as liable to slap a biting mosquito as when you’re walking around, and so those protozoans that knock you flat will more readily find a mosquito vector. (This is all speculation, of course.)

Another suggestion involves the virus for the common cold. It doesn’t debilitate you, but rather makes you a bit grotty but still able to walk around—and transmit the virus to other people. If a common cold were to knock you out like malaria, the virus wouldn’t spread so well.

And so many of the symptoms that are caused by pathogens may well have evolved in those pathogens to facilitate their own transmission. This must certainly be true in some cases, but of course proving it is very hard to do. You couldn’t do experiments in humans, though I suppose you could in model animals like rats, but I wouldn’t be keen on hurting animals to test evolutionary hypotheses. (I even anesthetized all my fruit flies before killing them.) It is curious, though, that I haven’t seen this new and striking result mentioned as a possible example of natural selection in the virus.

Here’s the video, though you might not learn much if you’ve read what’s above.

h/t: Charles

Click to access 2020.07.17.209288.full.pdf

Did Arabs come up with Darwinism before Darwin?

October 7, 2020 • 1:15 pm

Several people sent me the link to a VICE article (below) arguing that Arab scholars—it’s not clear that all of them were Muslims—essentially hit on the essentials of Darwin’s theory centuries before Darwin, and that their contributions have been neglected.

I have neither the time nor will to give this piece a proper critique, but let me say that yes, people don’t often know about the precursors to Darwin, and there were many who broached some of his ideas.

Evolution in particular was one of them; it would be odd if nobody before Darwin thought that organisms had transformed by one process or another over time. (The key reference here is Rebecca Stott’s book, Darwin’s Ghosts.) One such precursor was Erasmus Darwin, Charles’s grandfather, who wrote several times about the possibility of evoltuion. But, like the Arab scholars below, Erasmus lacked the key novel feature of Darwin’s theory: a mechanism for evolutionary change. And that was natural selection.

As I always say, the essence of Darwin’s theory was fivefold: evolution;  evolution being gradual rather than instantaneous, involving the change of proportion of heritable forms in a population due to differential reproduction; a branching process whereby one original species could produce the millions today, speciation; the concomitant realization that any pair of species had a common ancestor; and, what Darwin saw as his most original contribution, the process of natural selection, which resulted in the appearance of adaptation. (This fivefold contribution was first limned by Ernst Mayr.)

The reason Darwin is given almost full credit for the theory of evolution (which of course has changed a bit since 1859), is that he not only suggested these five ideas in one great work, On the Origin of Species, but also provided evidence for them. Darwin’s “theory” was more than just speculation, for he provided enough evidence to convince most educated Westerners within a decade that evolution was true. (It took another 70 or so years until natural selection was generally accepted.)

Others had thought of evolution before, and a few, most notably the Scot Patrick Matthew, had even come close to the idea of natural selection (as, of course, had Alfred Russel Wallace). But nobody put together all the pieces in as comprehensive and convincing a way as did Darwin. That’s why his theory is more or less sui generis, and owes little to those who mused about evolution before him. (It did owe a lot to geologists and natural historians.)

Yet this VICE article suggests that many people anticipated Darwin, including Arab scholars writing in the eighth century. And the article is misleading in several ways. First, yes, some Arab scholars did broach ideas that organisms transformed themselves over time. But none suggested anything close to natural selection as the mechanism for adaptive change, and a lot of the “transformation” was Lamarckian—not due to changes in the frequency of heritable variants, but to the effects of the environment. Second, none of the scholars, despite the claims of their advocates, had any influence on Darwin’s own ideas. Third, the article below appears to be more than just a corrective in the history of science, but also as a way to empower people of color by showing them that Arabs (apparently considered people of color), had come up with something pretty close to Darwin’s theories a millennium before him. And if the latter is wrong, which it is, then how much empowerment can result? Further, as I argue below, getting people resistant to evolution to come around to it doesn’t depend on scientific “identity politics”, but on overcoming religious objections, for most people oppose evolution on religious grounds.

Click below to read the VICE piece.

Shayla Love’s piece cites a number of Arabs who supposedly anticipated Darwin, but her article is woefully short on quotations that show how accurate that anticipation was. Let’s take one of the scholars she cites:  Al-Jahiz, who, suggests Love, came up with the idea of natural selection before Darwin.  I found one 1983 paper on Al-Jahiz by another scholar, who gives direct quotes, and it shows that Al-Jahiz never even came close to Darwin (the paper is from Bayrakdar, Mehmet Islamic Quarterly; Jan 1, 1983; 27, 3; Periodicals Archive Online pg. 149). One must be careful in taking the words of scholars who characterize the work of early Arabs; it’s always best to check the original quotes. The paper below is free online, so you can read Al-Jahiz’s quotes for yourself.

And here are some quotes that Mehmet Bayrakdar (the author), say show Al-Jahiz’s own theory of Darwinian natural selection. (The quotes are in quotation marks.)

Struggle for Existence: al-Jahiz placed the greatest weight on evolution by. the struggle for existence, or, in a larger sense, by natural selection. It operates in conjunction with the innate desire for conservation and permanence of the ego. According to al-Jahiz, between every individual existence, there is a natural war for life. The existence are in struggle with each other. Al-Jahiz’s theory of struggle for existence may accordingly be defined as a differential death rate between two variant class of existence, the lesser death rate characterizing the better, adapted and stronger class. And for al-Jahiz, the struggle for existence is a divine law; God makes food for some bodies out of some other bodies’ death. He says, “The rat goes out for collecting his food, and it searches and seizes them. it eats some other inferior animals, like small animals and small birds. . .  it hides its babies in disguised underground tunnels for protecting them and himself against the attack of the snakes and of the birds. Snakes like eating rats very much. As for the snakes, they defend themselves from the danger of the beavers and hyenas; which are more powerful than themselves. The hyena can frighten the fox, and the latter frightens all the animals which are inferior to it. . . This is the law that some existences are the food for others. . . All small animals eat smaller ones; and all big animals cannot eat bigger ones. Men with each other are like animals. .. God makes cause of some bodies life from some bodies’ death and vice versa. . . ”

And according to al-Jahiz, the struggle does not exist only between the members of different species, but also between the members of the same species.

From what al-Jahiz has said, we can make an assertion that God has created Nature in a prodigal reproductive character and He has also established a law, which is the biological struggle for existence in order to keep it within a limited ratio. Otherwise, the disorder could appear in Nature and it could lose some of its riches and species. We can see the germs of Darwin’s and Neo-Darwinian’s theory of Natural Selection in this remarkable passage which we have mentioned above.

The whole of natural selection is contained in the second paragraph, a single sentence that fails to quote al-Jahiz. Instead, author Bayrakdar refers back to the “remarkable passage” above which shows interspecies interactions and says nothing about natural selection operating among individuals of a species, with differential reproduction causing that species to transform over time. If al-Jahiz was close to Darwin in discerning natural selection from “a struggle between members of the same species”, why didn’t Bayrakdar quote him?

Further, Bayrakdar asserts that “Indeed, Darwin and his precursors took up the theory of al-Jahiz as the base for the essentiality of their evolutionary theories, and they formulated it in a more scientific way in the context of eighteenth and nineteenth centuries development of science.”  Everything in that assessment is wrong. Darwin was not influenced in the slightest by al-Jahiz.

In the VICE piece, Love quotes several other Arab scholars who had ideas about evolutionary change, but none of them come anywhere close to Darwin. (By the way, Love calls Darwin’s book “On the Origins of Species,” getting the title wrong.)

In the end, some of the motivations of Love’s piece becomes clear with her finale:

Including more diverse sources of evolution scholarship could make the study of evolution more accessible in places where it is currently a taboo subject, which can include Muslim countries. It might help for students to see these are ideas that people from their own cultures have been thinking about for thousands of years too.

. . .But for those who think evolution is synonymous with the “West” or atheism, then there might be a level of hesitance that is unnecessary. “If you think that these ideas are only coming from a Victorian era of noblemen, actually that is not the case,” Hameed said. [Salman Hameed is “the director of the Centre for the Study of Science in Muslim Societies at Hampshire College in Amherst, Massachusetts”].

It can have a lot of impact as well for young people of color to see themselves represented in the dialogue of scientific ideas throughout history, said Qidwai.

And even for those not of Arab descent, the inclusion fosters a view of science that is iterative and collaborative, rather than individual. “Multiple people are involved,” Qidwai said. “Different players are contributing in certain ways. It really shows that it’s much more interconnected than, you know, a brilliant person had this idea.”

Now I don’t want to be too hard on this aspiration. It may indeed help Muslims embrace evolution to see that some of their ancestors were toying with the idea centuries ago. And it is interesting to see how the idea of evolution popped up now and again through human history—and not just among Arabs.  Further, we do owe Arabs a tremendous debt of intellectual gratitude—for their work on astronomy and mathematics, for their preservation of Greek thought, which would have been lost had it not been appreciated by Arabs, and for other advances that I don’t have the expertise to describe.

But I don’t really think that recounting this history will move Muslims or people of color towards an acceptance of evolution, for the rejection of evolution is based largely on religion, not on whether science was advanced by people sharing your racial background.

And we shouldn’t imply, as the VICE article does, that although Arabs occasionally broached the idea of evolution, they are important founders of a modern scientific theory.  Darwin’s theory is, like Einstein’s, amazing because of its sui generis character—because it didn’t involve much standing on the shoulders of giants who came before. And that is why we celebrate Darwin (and, to a lesser extent, Wallace), and don’t hail Arabic scholars as unrecognized harbingers of evolutionary theory.

 

h/t: Andrew Berry