Category: science education

Human Phylogeography: The lessons learned, 1

June 4, 2019 • 9:10 am

by Greg Mayer

UPDATE. A couple of readers have drawn attention to the website, gcbias, of Graham Coop, a population geneticist at UC Davis. He has excellent discussions, with nice graphics, of issues in genetic genealogy, including calculation of the number of “genetic units” in particular generations. As an example, 7 generations back you have 256 ancestors, but only 286 genetic units produced by recombination, so although, on average, you will have a chunk from each of those 256, it is entirely plausible to have zero (since inheritance is stochastic). It’s well worth browsing, and this and this are good places to start. (Thanks to rich lawler and S. Joshua Swamidass for the pointers.)

In February, I posted the syllabus for a seminar class entitled “Human Phylogeography” that I was teaching with my colleague Dave Rogers. The seminar was based primarily on a close reading of David Reich’s (2018) Who We Are and How We Got Here (published by OUP in the UK). Well, the class has concluded now, and so I thought I’d report back on what happened.

First, I’d like to say that the class was a success. We had 16 students, double the most I’ve ever had in a number of similar seminar courses over the years, and the students were very successful in engaging with the subject in both written and oral contributions to the class. One of the students was a history major, and towards the end of the semester a colleague in computer science mentioned that, quite coincidentally, he was reading the book, so he joined the class for the last few meetings. In many ways, it was what college is supposed to be like (though too often isn’t). I hope the students learned a lot. I did, and here is the first of the three most striking things I learned.

1. Recombination is a lot rarer than you think.

If you think back to the last time you studied genetics, you’ll recall the phenomenon of recombination, one aspect of which is crossing over. Crossing over occurs during meiosis. Chromosomes come in homologous pairs (23 pairs in humans, for 46 total), and in meiosis the homologues can exchange pieces with one another. The chromosomes physically touch and cross one another, which is observable under the microscope, and are called, appropriately enough, chiasmata (chiasma, sing.)

Image result for crossing over meiosis
From BioNinja, https://ib.bioninja.com.au/standard-level/topic-3-genetics/33-meiosis/crossing-over.html

Recombination is important for a variety of reasons (for one, it increases genetic variability), but for our current purposes its importance is that it breaks up the nuclear genome from 23 genetic units into more, and smaller, units (as opposed to the mitochondrial genome, which has a number of genes, but all are inherited as a single genetic unit, since there is no recombination in mitochondria). In humans, it turns out, there are only 1-2 crossovers per chromosome per generation (1.2 per chromosome in fathers, 1.8 in mothers).

Now, I’d always thought that crossing over occurred frequently enough that we could think of the genome as essentially infinitely divisible. (There are 3 billion base pairs in the human genome, so, in the limit, there would be 3 billion genetic units, so not quite infinite!) But, it turns out that crossovers occur sufficiently infrequently that there is an appreciable chance that, if you go enough generations back, you share NO genes with your ancestor. This is because the number of ancestors goes up fast (2, 4, 8, 16, 32, 64, 128, 256, etc.), but the breaking up of the genome into smaller units by crossing over isn’t fast enough to ensure that the probability of sharing nothing is near zero.

Here’s a figure from Reich’s book showing how blocks of genes are broken up by recombination.

From Reich, 2018.

You start with an entirely Neanderthal chromosome (dark), which enters the anatomically modern human population by hybridization. A few generations later, the Neanderthal chromosome has been broken up, but it still occurs as largish blocks amongst the anatomically modern sections (gray). Still later, the blocks are smaller and fewer. (We’re assuming continued backcrossing into the anatomically modern population, so the % Neanderthal decreases; there could also be selection causing changes in the frequency of Neanderthal alleles). Finally, a present day individual has his Neanderthal DNA broken up into even smaller bits.

Here’s a figure from a talk by Svante Pääbo, showing in the top row for each chromosome (there are 22 listed, from 1-22) the entire genome of “Oase Boy” from 40K years ago in Romania. The green lines are Neanderthal sites in his genome. The five rows below Oase Boy are five modern human individuals; the colored lines are their “Neanderthal bits”. Note that for each chromosome, Oase boy has the biggest block of Neanderthal genes (green fluorescece):

From Pääbo , 2018. (Click to enlarge.)

Because of the age of the Oase sample, some of the black lines are missing data, and so Pääbo infers that there are seven large continuous blocks of Neanderthal genes (yellow bars above the Oase Boy line). Note that the modern individuals have less Neanderthal DNA, and it is not in large blocks.

Because the size of the blocks breaks up in a statistically predictable fashion, you can get a “recombination clock“, so that based on the size of the blocks you can estimate how many generations ago the hybridization occurred. For Oase Boy, Pääbo estimated that his Neanderthal ancestor occurred 4-6 generations back (his great great, or great great great, or great great great great grandfather).

From Pääbo , 2018, showing Oase’s Neanderthal ancestor (red) in the 5th generation (it could also be in the 4th or 6th).

Because the placement and frequency of crossing over is stochastic (random), the situation must be statistically modeled to derive sound estimates, and there will be a range of plausible estimates. And, since some of the fossils are well dated by other means, we can also estimate the long term human generation time, as was done by Priya Moorjani and her colleagues: it’s 26-30 years.

So, the low rate of recombination allows us to construct a “recombination clock”, and to estimate generation times. This is great stuff!

It also solved for me what was a puzzle. You may recall that last year Elizabeth Warren released the results of DNA tests showing that she had American Indian ancestry several generations back. This essentially confirmed what her family’s oral history said. The amount of her Indian ancestry was small (less than 1%), and a range of generations (6-10) was provided by the analysis (as was done by Pääbo for Oase Boy).

Now, there are a number of ways which these ancestry tests can be criticized, one of the most difficult for them being that there are very few North American Indian genotypes in the database used, and thus “American Indian” relationship is indicated by relationship to Central and South American Indians. Some critics of Warren, however, made erroneous criticisms. She did not contend, as some accused her of, of saying the results showed she was Cherokee—with few if any Cherokee in the database, the ancestry tests could not determine this. (And tribal membership is a legal matter, anyway, not directly dependent on genetic similarity.)

But some critics said that the data were consistent with her having no Indian ancestry at all. I wondered how they could say that– there are 3 billion bp, and 1 % of that is still a very large number. But now I realize my error. There are very many fewer genetic units– more than 23, but a lot less than 3 billion!– due to low rates of recombination. And, because of this, if you go back several generations, there is an appreciable probability of sharing no DNA with an indubitable ancestor. I now believe the critics must have looked at the latter fact, and realized Warren may not have DNA from all of her ancestors, and thus suggested she may have no Indian ancestry. But their error is that in saying she may lack DNA from an ancestor, say, 8 generations back, they are invoking an a priori probability. But in Warren’s case, her DNA was examined, and showed that she did have Indian ancestry.

Gravel, S. 2012. Population genetic models of local ancestry. Genetics 191:607-619. pdf

Ho, S. Y., Chen, A. X., Lins, L. S., Duchêne, D. A., & Lo, N. 2016. The genome as an evolutionary timepiece. Genome Biology and Evolution 8: 3006–3010. pdf

Huff, C.D. et mult. 2011. Maximum-likelihood estimation of recent shared ancestry (ERSA). Genome Research 21:768-774. pdf

Moorjani P, Sankararaman S, Fu Q, Przeworski M, Patterson N, Reich D. 2016. A genetic method for dating ancient genomes provides a direct estimate of human generation interval in the last 45,000 years. Proceedings of the National Academy of Sciences USA 113:5652-7. pdf

Pääbo, Svante. 3 October 2018. A Neanderthal Perspective on Human Origins. (video: embedded below)

Reich, D. 2018. Who We Are and How We Got Here: Ancient DNA and the New Science of the Human Past. Pantheon, New York.

National Review: Conservatives should accept evolution

May 15, 2019 • 1:00 pm

Both the Left and Right have their issues with evolution. On the Right, many are evangelical Christians and reject evolution on religious grounds. Even Orthodox Jews like Ben Shapiro have found themselves flirting with Intelligent Design, and when I saw Shapiro implicitly attacking modern evolutionary biology I gave up all hope for him. The voting base for the Right may be fine with those who attack or deny evolution, but in the long run you’re going to look pretty stupid if you reject it. (It’s curious that I know nothing about Trump’s views on the issue.)

The Left, too, while accepting Darwinian evolution in general, has problems with evolutionary psychology—not that the discipline is perfect. But wholesale rejection of it, by those like P. Z. Myers, is intellectually dishonest and ideologically driven. Many also imply that evolution tells us that there is a spectrum of not just gender, but of sex itself, so that sex is not “binary”.  In fact, three organismal biology societies, including the Society for the Study of Evolution (of which I was once President), issued a statement saying that “sex is a continuum” which is infuriatingly wrong. In our species, and many others, evolution has in fact favored a binary: male and female.

Denial or rejection of evolution, then, is based on ideology: largely religious on the Right and Blank Slate-ism on the Left.

It’s refreshing, then, to see an article in National Review, a conservative journal, arguing that a.) evolution is true and b.) conservatives shouldn’t be afraid of it. The article is below (click on screenshot); it’s by Razib Khan, a geneticist and science writer. He’s been criticized for writing for questionable publications that purvey racism and bigotry, and on that grounds the New York Times let him go as a temporary columnist. He surely must be a conservative; in fact, he identifies himself as one in the first sentence.

But whatever his past, the piece in the National Review isn’t half bad (click on screenshot):

He does point out the forms of evolution denialism I highlighted above, but of course his article is motivated by conservatives’ rejection of evolution, and to that end he takes out after Michael Behe, whose Intelligent Design views are much admired by conservatives like Shapiro. In general, though, Khan highlights how evolution has made testable predictions, and how much we know about these days. In short, he tells conservatives that it’s true, and to stop fighting it.

But I have mixed feelings about stuff like this:

But evolutionary biology is nothing for conservatives to fear, because it is one of the crowning achievements of modern Western civilization. It should be viewed not as an acid gnawing at the bones of civilization, but as a jewel. The science built upon the rock of Charles Darwin’s ideas is a reflection of Western modernity’s commitment to truth as a fundamental value. And many Christians well-versed in evolutionary science find it entirely compatible with their religious beliefs.

Further, while evolutionary biology does not tell us what is good, the truth of the world around us can inform our efforts to seek the good — and in this sense, the political implications of evolutionary biology do not favor the Left. Today many on the Left reject the very idea of human nature, to the point of effectively being evolution deniers themselves. They assert that society and values can be restructured at will. That male and female are categories of the mind, rather than of nature. In rejecting evolution, a conservative gives up the most powerful rejoinder to these claims.

Those who reject human nature on the Left are not mainstream Leftists, but extremist Leftists, and the data show that many more people on the Left accept evolution in general, including human evolution, than those on the Right. But it’s wrong to imply that the Left consists of wholesale deniers of evolution. True, Blank Slaters do reject mainstream science (and not just evolution—also evidence that male and females have different brains and show different innate preferences), and that’s to their discredit.

Here are data from a 2013 Pew poll showing that the problem is greater on the Right than on the Left:

Khan also errs, I think, when trying to show that evolution is compatible with religion. He uses the old trope that “some scientists were religious, ergo harmony”:

But what about the metaphysical implications? Richard Dawkins would have you believe that evolutionary biology is fundamentally atheistic. But he is one voice. There are in fact evolutionary biologists who are religious, including Evangelical Protestants. The most influential evolutionary biologist of the first half the 20th century, R. A. Fisher, was an Anglican and a political conservative. The existence of people who are Christians and evolutionary biologists shows that there is a wide range of opinions on how evolutionary biology relates to religious faith.

True, but newer data also show that religious people are far less accepting of evolution than nonreligious people, and of course the large majority of scientists in elite universities are out-and-out atheists. Here are more data from that Pew poll:

Note that the biggest acceptors of evolution are “unaffiliated” people and white mainline Protestants, while the more conservative religious show less acceptance—especially white evangelical Protestants.

And for good reason: evolution in fact does fly in the face of many religious beliefs—not just in its flat denial of Biblical claims like the Creation and of Adam and Eve as the progenitors of all of us (I’m looking at you, Vatican), but in other ways too. Here are two slides I use in my talks about the incompatibility of science and faith (many of these points are taken from Steve Stewart-Williams’s excellent book, Darwin, God and The Meaning of Life: How Evolutionary Theory Undermines Everything You Thought You Knew):

The points in red are the ones I consider most important in promoting rejection of evolution by religious people. Ergo, conservatives are still going to have trouble accepting evolution insofar as they need to comport it with their faith. Nevertheless, Khan is absolutely right when he says this:

But looking forward, the energies of the Right are not most fruitfully spent on debating descent with modification and the common origin of life.

Amen!

Teaching Evolution: Sewall Wright: Evolution in space

March 9, 2019 • 10:30 am

by Greg Mayer

Our next installment of Teaching Evolution for this spring concerns Sewall Wright. His contributions were wide-ranging, but he is most noted for his integration of population structure (population size, migration) and selection into what he called the “shifting balance” theory. In this theory, genetic drift, migration, and selection interact to produce what he saw as the most favorable conditions for evolutionary advance. The reading is a brief precis of his much longer 1931 paper in Genetics, but in many ways was more influential, as it exposed a wider audience to his ideas. Modern appreciations of the shifting balance theory are given by Nick Barton (2016) and Norm Johnson (2008).

Sewall Wright, with guinea pig.

Sewall Wright (1889-1988) was, along with R.A. Fisher and J.B.S. Haldane, one of the founders of theoretical population genetics, which synthesized Mendelian inheritance with Darwinian natural selection, thus laying the foundations of modern evolutionary biology. His classic paper “Evolution in Mendelian Populations” (Genetics, 1931) laid out his synthesis, and led to his election to the National Academy of Sciences while still a young man. Like Darwin, Wright studied carefully the work of animal breeders, and this strongly influenced his ideas on evolution, which he called the “shifting balance” theory. Although sometimes caricatured as a theory emphasizing random genetic drift, Wright stressed the importance of the interaction of drift, selection, and migration in adaptive evolution. Wright strongly influenced Dobzhansky, and he coauthored five papers in the latter’s “Genetics of Natural Populations” series. Beginning with his graduate studies at Harvard, Wright’s organism of choice for genetic studies throughout his career, which ended with a very productive 33 year retirement at the University of Wisconsin, was the guinea pig (note what is in his left hand in the photo). He is author of the monumental four volume Evolution and the Genetics of Populations (1968-1978). William Provine has edited a collection of Wright’s most important papers, Evolution: Selected Papers (1986), and written an insightful and analytic biography, Sewall Wright and Evolutionary Biology (1986).

Reading:

Wright, S. 1932. The role of mutation, inbreeding, crossbreeding, and selection in evolution. Proceedings of the Sixth International Congress of Genetics 1:356-366.

Study Questions:

1. In this paper, Wright introduces the idea of a fitness surface or adaptive ‘landscape’ (see esp. Fig. 2). What do the x and y axes (the two dimensions of the ‘map’ on the paper) represent? What does the ‘altitude’ of a point on the landscape represent? What does a peak in the landscape represent? What does a valley in the landscape represent?

2. In one sentence in the first half of the paper, Wright succinctly states the Hardy-Weinberg equilibrium for allele frequencies, and its cause. Find and quote the sentence. Show that Wright understands the H-W principle.

3. Why is it difficult for a species to evolve across a valley from one peak to another if selection is the only evolutionary force? How does this lead Wright to argue for the importance of drift (inbreeding) and migration (crossbreeding), as well as selection, in allowing species to reach the highest adaptive peaks?

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

Jerry addendum:  While Wright’s theory was influential, and was incorporated by Theodosius Dobzhansky into his view of the Modern Evolutionary Synthesis (see his book Genetics and the Origin of Species), I find the theory deeply flawed. With two colleagues, Nick Barton and Michael Turelli, I wrote a long critique of that theory in 1997. Our paper was in turn criticized in two papers, one by Mike Wade and Charles Goodnight, and the other by Steven Peck et al.  We then rebutted these papers in another Evolution paper in 2000. All four references and links are below.

In my biased estimation, our critique did stem the tide of enthusiasm for Wright’s theory; in fact, Wright’s colleague James Crow at Madison said that our paper prompted him to stop accepting that theory. I’m not sure whether Greg mentions the critiques and attempted rebuttals in his lecture, but I’m putting them here for readers.

Coyne, J. A., N. H. Barton, and M. Turelli.  1997.  A critique of Sewall Wright’s shifting balance theory of evolution.  Evolution 51:643-671.

Wade, M. and C. J. Goodnight. 1998. The theories of Fisher and Wright in the context of metapopulations: when nature does many small experiments. Evolution 52:1537–1553.

Peck, S. L., S. P. Ellner, and F. Gould. 1998. A spatially explicit stochastic model demonstrates the feasibility of Wright’s shifting balance theory. Evolution 52:1834–1839.

Coyne, J. A., M. Turelli, and N. H. Barton.  2000.  Is Wright’s shifting balance process important in evolution? Evolution 54: 306-317.

 

Five Books: Adam Hart-Davis’s choice of the best books on popular science

February 28, 2019 • 1:00 pm

Adam Hart-Davis is an English writer, photographer, and broadcaster, known for being the presenter of several popular BBC series. In a Five Books piece (click on screenshot below), Hart-Davis lists and discusses what he sees as the five best popular-science books. According to the site,

“Adam Hart-Davis says clear simple writing is the key to an accessible science book. Selects the five books he believes offer the best introduction to Popular Science. Includes works from Darwin, Watson and Hawking.”

I’ll show his choices and give a few of his words about the book (indented) and my own take (flush left):

Micrographia, by Robert Hooke.

In 1665 he produced this extraordinary book. I have a facsimile edition here, not an original. It is big, about a foot high and nine inches wide. It is beautifully printed – there is all this old-fashioned type with the long S and so on and it contains lovely pictures. He was, luckily for us, a very good draftsman. And some of the drawings are just the same as the pages and some of them pull out to make a picture about two foot square. The most famous of all is this picture of a flea. He was almost the first person to use a microscope as a scientific instrument and he looked at things like fleas and drew wonderful pictures of them – and showed people a new world.

JAC: Haven’t read it, though I’m sure Matthew Cobb did for his book The Egg and The Sperm Race. Readers who have read it should weigh in below. It does seem an odd choice, though

Stonehenge Decoded by Gerald S. Hawkins

Well, this book was really interesting for me because it was the first popular science book I had come across. It was published in 1965 originally. I was doing my PhD at the time and this book came to me because I had just joined one of those new-fangled books clubs! I was surprised that there were science books that were readable. I had heard about treatises on the electron or whatever it is but I had never come across a book like this.

. .  it was certainly quite important to me to see that science could be made popular in this way and I think it influenced me quite a lot. I think it showed a lot of people science could be written for the layman.

JAC: I’ve never heard of this book, and it’s quite dated now. Further, it was apparently chosen for sentimental reasons rather than its intrinsic merit. I’ll give this one a pass.

A Brief History of Time by Stephen Hawking. 

Well, I actually did read it. I got stuck in Chapter Six and I then read it again recently and it is a lovely book. It is very hard because he is trying to describe very complicated things, but he has actually done a very good job. I have started on his latest book, The Grand Design, which I think is rather easier. But this book is important not just because he is stuck in a wheelchair and is a brilliant cosmologist but also because it is a really difficult subject aimed at the general reader. This sort of cosmology, looking at whether or not black holes emit radiation, is a very esoteric sort of question. It is not like Stonehenge where people ask things that we can all understand, like, if you look through this gap can you see Capella.

JAC: I really did try to read it, and, like Adam, got stuck. I never finished it, joining the ranks of those who give it the reputation of “The Least-Read Popular Science Book of All Time.” When I read a technical science book, I prepare for a long slog and make sure my brain is well oiled, but for popular science books I expect them to be easier reads, which may be a flaw in my reading style. But I found Hawking’s book tedious and not well written. I still claim that one can make cosmology intelligible without its being a slog.

The Double Helix by James D. Watson.

This is a really interesting story. The discovery of the double helix was fascinating because various people were working on it – Linus Pauling in California and Rosalind Franklin in King’s College London and she was very close. James Watson acquired her results without asking her, which I think was really bad news. And they went off and made this wild guess and they guessed right. And full marks – they were bright young men both of them – but they made a brilliant guess and the result was that they and Maurice Wilkins shared a Nobel Prize and Rosalind Franklin didn’t, which was very unfair.

JAC: Whatever you think of Watson, who has ruined his own reputation through bigoted remarks, this book belongs on the list. I think it’s the best account of a scientific discovery I’ve ever read.  It’s engaging, takes you right back to Cambridge when the discovery was made, and doesn’t spare the controversy and personal animosity involved in a race for a great discovery. As for Rosalind Franklin’s work, I share the view of Matthew Cobb, who wrote a piece about the Crick/Watson/Franklin/Wilkins controversy in the Guardian four years ago:

It is clear that, had Franklin lived, the Nobel prize committee ought to have awarded her a Nobel prize, too – her conceptual understanding of the structure of the DNA molecule and its significance was on a par with that of Watson and Crick, while her crystallographic data were as good as, if not better, than those of Wilkins. The simple expedient would have been to award Watson and Crick the prize for Physiology or Medicine, while Franklin and Wilkins received the prize for Chemistry.

Sadly, Franklin had died of ovarian cancer before the prize was awarded, so she never got her medal.

Watson has written several books since this one, including books on genetics and more personal volumes along the lines of The Double Helix, but none of the latter are nearly as good as The Double Helix. 

The Formation of Vegetable Mould through the Action of Worms, with Observations on their Habits by Charles Darwin.

It’s a wonderful Victorian title. Of course his most famous book is On The Origin of Species and that is actually rather hard work because he was desperately trying to persuade people of his thesis and he collected an absolute mountain of data and you had to wade through this stuff. But he was actually rather a good writer if he was able to let his hair down. His account of the Voyage of the Beagle is lovely. It is a sort of travel book full of derring-do and wonderful adventures. But I love this book about earthworms, which wasn’t published until 1896, because it just shows what a lovely naturalist he was.

JAC: Yes, this is an engaging and underappreciated book, larded with probably unintended humor and “citizen scientist” observations. It’s also short and, as Adam says, not as “hard work” as The Origin. But the place of The Origin in science, and indeed in human history, is overwhelming and secure, while Earthworms at best can be seen as instantiating Darwin’s evolutionary view that slow and tiny processes can create big changes over a long span of time. I would still say that The Origin is the one to read for the science. Remember, it was intended for the public, and was a bestseller in Darwin’s time. It’s not an easy read, to be sure, but there are parts that are wonderfully written and the “one long argument” is compelling and thrilling. If you want to read other Darwiniana, don’t forget The Voyage of the Beagle.

What else would be on my list? Well, I’ve already done a Five Books article on evolution books, which include not just The Origin but also The Blind Watchmaker, which I see as Dawkins’s best fusion of scientific exposition and lyrical writing. Those two would be on my “top five” list.

For other science books, I can’t leave out The Peregrine by J. A. Baker, which is a natural-history book—the best book on a single species ever written. The prose is ineffably moving. I quite like The Microbe Hunters by Paul de Kruif, which had a huge influence on my becoming a scientist. But I haven’t read it in years and it may be dated or I might have outgrown it. I prefer to leave it unread in my dotage.

Carl Sagan’s The Dragons of Eden must be considered, as well as The Demon-Haunted World: Science as a Candle in the Dark and The Varieties of Scientific Experience: A Personal View of the Search for God. Stephen Jay Gould’s books are in the second rank, though I think his books of essays, especially the early ones, should be considered.

I haven’t been overly impressed by more recent science books, and can’t think of one written in the last 15 years that excited me enough to even consider it for the “top five.”

Readers, of course, are welcome and invited to suggest their favorite popular science books.

Teaching Evolution: Theodosius Dobzhansky: Genetics of natural populations

February 27, 2019 • 10:30 am

by Greg Mayer

Readers may recall that last spring I began what Jerry called a “mini-MOOC” on evolutionary biology. Because I began making posts fairly late in the semester, I got to only seven installments before the semester ended. I’m teaching the same course, BIOS 314 Evolutionary Biology, this spring, and so I’d like to start up again.

In the class I have the students read a series of what I regard to be classic papers or extracts–—one each week—and these are what I want to share with WEIT readers. Each reading is accompanied by a brief biography and illustration of the author, and a small number of study questions, designed to guide the student in understanding the reading. I sometimes assign these questions as homework essays, or include them on exams. When possible, I will provide links to the readings. The installments so far have been Charles Darwin, A.W.F. Edwards, George Gaylord Simpson, Charles Lyell, Alfred Sherwood Romer, Alfred Russel Wallace, and Richard C. Lewontin. We pick up with Theodosius Dobzhansky. Dobzhansky was a key figure in the “Modern Synthesis” of evolutionary biology in the 20th century (as described below). Jerry had intended to do his doctoral work with “Doby” (as he was known later in his career; students from earlier knew him as “Dodik”), but wound up studying with Dick Lewontin, who had been a student of Doby’s, and thus Jerry is Doby’s academic grandchild.

Theodosius Dobzhansky (1900-1975) was a Russian-American geneticist who was arguably the most important evolutionary biologist of the 20th century. Completing (although never formally receiving) an undergraduate degree at the University of Kiev, he began his career conducting field studies of coccinellid beetles and laboratory experiments on Drosophila. In 1927 he received a fellowship to come to America and work with T. H. Morgan at his famed “fly room” at Columbia University. As a geneticist working at the epicenter of American genetics, Dobzhansky was well aware of the important empirical and theoretical advances being made in genetics; as a field worker and experimentalist, he was able to tie these developments more closely into the phenomena of natural populations. He synthesized the theoretical, experimental, and field approaches in his classic book Genetics and the Origin of Species (1937). It was through this book, much more so than through the previous synthetic, but more theoretical, works of Fisher, Haldane and Wright, that the biological community as a whole became aware of the developments in evolutionary biology, and the book inspired an outpouring of work carried on in the same synthetic spirit. Dobzhansky is well known for his two aphorisms, “Nothing in biology makes sense except in the light of evolution”, and “Heaven is where, when the experiment is over, you don’t need statistics to figure out what happened.” His major works include Genetics and the Origin of Species (3rd ed., 1951), Mankind Evolving (1962) and Genetics of the Evolutionary Process (1970). His monumental 43-paper series on the “Genetics of Natural Populations” (1938-1975) has been reprinted, with extensive historical and biographical commentary, as Dobzhansky’s Genetics of Natural Populations I-XLIII (1981), edited by Lewontin, Wallace, Moore, and Provine.

Reading:
Dobzhansky, Th.1951. Genetics and the Origin of Species. 3rd ed. Columbia University Press, New York. Excerpts from Chap. III. “Mutation in Populations” (pp. 50-55, 70-75) and Chap. V. “Adaptive Polymorphism” (pp. 108-123, 129-134).

Study Questions:

1. What is blending, as opposed to particulate, inheritance? What are the consequences of the two sorts of inheritance for the evolutionary process? What analogy does Dobzhansky use to illustrate the effect of blending inheritance?

2. How does Dobzhansky see the “stored” genetically variability of natural populations and the generally deleterious nature of mutations nonetheless leading to populations being adapted to their conditions of existence?

3. Can a phylogeny be estimated for infraspecific variants? [We usually think of phylogeny being estimated for species, so that we can say, for example, lions and tigers share a more recent common ancestor than either does with the house cat. But could we construct a phylogeny for, say breeds of house cat? Or subspecies of tiger? Or mitochondrial haplotypes of the lion? See Dobzhansky’s Fig. 4 (p. 113 in the reading) for his answer.]

4. What is balanced polymorphism? How does balanced polymorphism relate genetic variability and natural selection?

 

Human Phylogeography

February 23, 2019 • 11:33 am

by Greg Mayer

For the spring semester, my colleague Dave Rogers and I are teaching a seminar class entitled “Human Phylogeography.” Phylogeography is the study of the history of the genetic variation, and of genetic lineages, within a species (or closely related group of species), and in the seminar we are looking at the phylogeography of human populations. DNA sequencing now allows a fine scale mapping of the distribution of genetic variation within and among populations, and, remarkably, the ability to sequence ancient DNA from fossil remains (including Neanderthals). The seminar is based primarily on a close reading of David Reich’s (2018) Who We Are and How We Got Here (published by OUP in the UK).

A Krapina, Croatia, Neanderthal woman, photo by Jerry.

Although rarely under that rubric, human phylogeography has been a frequent topic of discussion here at WEIT, by Jerry, Matthew, and myself, including our several discussions of Neanderthals (or Neandertals) and Denisovans. So it may be of interest for WEIT readers to follow along. Below the fold I’ve placed the course syllabus, which includes the readings, and links to many newspaper articles of interest, and online postings, including many here at WEIT, and also from John Hawks Weblog, a site we’ve recommended on a number of occasions when discussing human evolution. (The newspaper links appear as images; just click to go to the story.) We just finished our third meeting, and I’ve been quite impressed by the students’ discussion and writing. We’re fortunate to have some students from anthropology or with some anthro background.

Please read along with us, or browse what seems interesting below. If you have questions or comments, post them here, and I’ll be looking in.

Continue reading “Human Phylogeography” →

Americans’ acceptance of evolution: does it depend on how you ask them?

February 15, 2019 • 1:19 pm

One thing you learn from looking at surveys of American acceptance of evolution: the statistics vary dramatically depending on which organization asks the question. And it also depends on how the question is asked. About a week ago, a Pew Survey tested this by assessing acceptance of human evolution in two ways. Read their summary—and the whole survey, if you wish—at the website below (click on the screenshot):

Pew used to ask the evolution question in a two-step process. First, they asked if people thought humans had evolved over time or had existed in their present form since the beginning of time. Then, if they answered that humans had evolved, they asked those people whether they thought humans had evolved through natural, unguided, un-divine processes, or through processes guided or allowed by God.

They now test a new way, in which all three alternatives are given to people at once.  The results, shown below, differ pretty strikingly:

As you see, if you give people three alternatives at once, pure creationism falls from 31% to 18%, theistic (guided) evolution rises from 27% to 48%, and, surprisingly, unguided, natural evolution falls from 40% to 33%. Somehow Pew sees this as good news, though I don’t: if you lump those who see God directing evolution (a watered down form of creationism, like Behe’s) with de novo creationists, the total of non-“naturalists” under the new protocol is 66%, while it was 58% before. And there are 7% fewer people who accept naturalistic evolution under the new protocol.

But Pew, like many accommodationists, likes to see theistic evolutionists, for although they see God’s working in the process, at least they accept evolution. I’m not so charitable! Naturalism is naturalism, and what we see now are fewer naturalists than we thought. That’s not good news.

That said, giving all three alternatives at once does seem a better course, and Pew explains why this might affect the data:

The results of the new experiment indicate that there are some people who do believe that humans have evolved over time, but who, for whatever reason, did not say so in our traditional method of asking about the topic. Perhaps without the opportunity to immediately connect evolution to God, some religious respondents may be concerned that expressing belief in evolution places them uncomfortably on the secular side of a cultural divide.

That purports to explain the reduced proportion of pure de novo creationists, but does that really explain the increase in number of theistic evolutionists—those who think that evolution occurred but God had a hand in it? After all, are those people not still expressing faith in God?

In truth, I have no explanation for these results, and they should be repeated, but I’ll grant that how you ask questions, or who or how you do a survey, does affect the answer. Here, for example, are the Gallup poll data for the same issue: human evolution, divided into pure naturalists, creationists, and theistic evolutionists. Here they asked the three-part question that Pew favors, and have asked the question since 1982:

Yet the data from the most recent year (2017) differ strikingly from the Pew data, even with the identical three choices:

Pure de novo creationism:  Pew 18%, Gallup 38%
Theistic evolution: Pew 48%, Gallup 38%
Naturalistic evolution: Pew 33%, Gallup 19%

I have no explanation for these discrepancies, since the questions are virtually identical.

There is other interesting stuff, too, but I have work to do and will probably post on it in the next few days. But I wanted to put up one more figure from the Pew survey, which shows that religion poisons everything and that atheists are, as expected, the most avid acceptors of pure, naturalistic evolution. We don’t even like Theistic evolution!

Also, women, as expected, are more keen on creationism, as women are more religious than men. And, as always, older people are less accepting of naturalistic evolution, as are the less educated. The age effect may be due largely to younger people being less religious.

If the data below show anything, it’s that religion impedes acceptance of evolution. But we’ve known that for a long time, though organizations like the National Center for Science Education don’t like to admit it. After all, it shows that religion poisons the mind.

Read and be enlightened: