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paleoanthropology, genetics and evolution

history of genetics

  • James F. Crow, 1916-2012

    Wed, 2012-01-04 23:23 -- John Hawks

    I received today the sad news that my friend and colleague James F. Crow has died, at the age of 95. Jim was a legend in the field of population genetics, who remained active until his final year.

    James F. Crow

    Jim was always extraordinarily gracious and generous with his time, and was kind to me throughout the ten years I have known him. At our last meeting, before I went to Siberia last summer, Jim told me the story of his meeting Dmitry Belyaev, early in the days of his famous fox experiment. I was eager to see the foxes and I conveyed Jim's greetings and reminiscences to the researchers in Novosibirisk. Again and again during the years, I found Jim to be a rich source of information about topics in population genetics. Even as my work brought me to consider fundamentals often outside the current mainstream, Jim invariably had encountered similar problems and given them deep thought long before I arrived on the scene.

    During the last 25 years, Jim took on a role as unofficial historian for the field of genetics. He coedited the Perspectives feature in the journal Genetics, and for many of those years wrote the lion's share of them. He was proud to note that his birth coincided with the first issue of the journal (January,1916), but although he arrived on schedule, the first issue of the journal was mailed two months late! Reviewing the major figures in the history of genetics, Jim gave a narrative history of the science often from his own memories.

    During the next few months, the journal Genetics will be running a series of perspectives in Jim's honor, reviewing aspects of his extraordinary career. I recommend the introduction to the series, printed in the December 2011 issue [1], and the first entry written by Daniel Hartl about Jim as a teacher and advisor [2]. From the editorial introduction by Michael Turelli and Charles Langley:

    Jim Crow is a living link between our generations and the founders of population genetics. Jim was Sewall Wright's colleague at the University of Wisconsin, Madison, for decades (1955–1988); Jim initiated a friendship with Ronald Fisher over an impromptu champagne tête-à-tête in the 1940s; and he hosted J. B. S. Haldane for a memorable lecture visit to Madison in the early 1960s (after learning from the New York Times that North Carolina had just canceled a public lecture by this famous Communist). There are few population geneticists who do not owe Jim a significant intellectual debt; none are unaware of his mastery of our field and of human interactions. For many of us, Crow and Kimura (1970) was an inspiring and elegant introduction to the mathematical models that form the foundation of population genetics theory. Crow instantiates the ideal of a cherished era when manners and dress were a sign of gentility. And no one who meets Jim is surprised to learn that he is an accomplished violist.

    And from Hartl's contribution:

    Professor Crow ran his laboratory on the principles of bringing smart people together to pursue their passions and encouraging interaction, mutual respect and support, constructive criticism, and the free sharing of ideas and resources. There were no formal group meetings or reports, as there was so much daily interaction that group meetings would have been superfluous. He would advise, suggest, and encourage, but never direct or cajole. The standard of mutual respect was set by Professor Crow himself and extended not only to members of the lab but also to everyone in the field. I never heard him utter an unkind word about anyone. He also treated everyone in the lab as a colleague. One day he came to me and said, “Dan, there’s a matter on which I’d like your advice.” He must have seen how flattered I was at being asked because he quickly added, “That doesn’t mean I’ll take it. It only means I want to hear it.”

    Hartl gives some of the flavor of Crow's laboratory in the 1960's, when he was already one of the most prominent geneticists in the world, and was a frequent host to the field's legends and advisor to some of the brightest students. I can only wish that someday I will be so lucky.

    Several years ago, colleagues from several departments here at the University of Wisconsin-Madison succeeded in a long-time ambition of Jim's to found an Institute for the Study of Evolution. He had envisioned that the institute should be named for Sewall Wright, who had been important to Jim himself and forms a major part of the legacy of genetics and evolution. But the future institute's members insisted instead to name the new entity in honor of Jim. It is a fitting legacy for a great evolutionary geneticist.


    References

    Synopsis: 
    In memory of a friend and colleague, one of the most prominent figures in the history of genetics
  • Eighth day of creation

    Sun, 2011-07-17 16:13 -- John Hawks

    Larry Moran muses on the recent death of Horace Judson, author of The Eighth Day of Creation: Makers of the Revolution in Biology. This excellent history is rarely picked up by students anymore (and I will note, it's not available on Kindle), and Moran ties it to a broader theme: new molecular work in eukaryotes that ignores the long literature of work in bacteria:

    How does this happen? I think it's because modern researchers are completely unaware of the history of their field. That's partly because the work on bacteria and bacteriophage—where the basic concepts were often discovered—is no longer taught in biochemistry and molecular biology courses. This leads to the false idea, as expressed in the press release, that all new discoveries in eukaryotes are truly new concepts that nobody ever thought of before.

    I suppose we could rephrase Santayana: Those who ignore history feel privileged to reinvent it.

  • Galton remembered

    Thu, 2011-06-23 17:17 -- John Hawks

    Steve Jones writes in the BBC News on the occasion of the hundredth anniversary of Francis Galton's death: "Francis Galton: The man who drew up the 'ugly map' of Britain". He cites many interesting tidbits, this was my favorite:

    In a letter to Nature in 1879 entitled The Average Flush of Excitement, Galton recounts a visit to the Derby. He noted that while he was there he was able to assess what he called "the average tint of the complexion of the British upper classes" by observing the distant crowd through his opera glass.

    He observed that after the race started, the crowd became "suffused with a strong pink tint, just as though a sun-set glow had fallen upon it". Galton found that he could work out the mood of a mass of people even without being able to distinguish one person from the next.

  • Timmer on HGP

    Tue, 2011-02-22 00:16 -- John Hawks

    John Timmer tells us "Ten years on: why a complete human genome mattered," from the perspective first of a bench scientist, then later as a science writer:

    The results of the human genome project first made my life easier; now they make it more interesting.

    An aside -- you'll often hear people say that the Human Genome Project didn't really deliver on its promises, it didn't crack the secrets of human diseases, or it could have been done more cheaply later. I get very tired of this. Without the draft genome, most of the computational tricks that make today's sequencing methods cheap simply would not work.

  • Quote: Dobzhansky on the tropics

    Thu, 2010-10-07 08:30 -- John Hawks

    Theodosius Dobzhansky, concluding a paper titled, "Evolution in the Tropics", which considered the role of physical environment versus other factors as evolutionary pressures:

    The effectiveness of natural selection is by no means proportional to the severity of the struggle for existence, as has so often been implied, especially by some early Darwinists. On the contrary, selection is most effective when, instead of more or less random destruction of masses of organisms, the survival and elimination acquire a differential character. Individuals that survive and reproduce are mostly those that possess combinations of traits which make them attuned to the manifold reciprocal dependences in the organic community. Natural selection becomes a creative process which may lead to emergence of new modes of life and of more advanced types of organization.

  • Gene number in humans the old-fashioned way

    Sun, 2010-06-20 16:37 -- John Hawks

    While doing some other research, I ran across a remarkable short paper by James Spuhler, "On the number of genes in man," printed in Science in 1948.

    We've been hearing for the last ten years how the low gene count in humans -- only 20,000 or so genes -- is "surprising" to scientists who had previously imagined that humans would have many more genes than this.

    So here's the next to the last line of Spuhler's article:

    On the basis of these speculations there are then some 19,890-30,420 gene loci in man.

    He actually estimated the total gene number in two ways. The first, based on estimates of chromosome length in Drosophila and humans, coupled with Bridges' estimate of fruit fly gene number (5000), led to an estimate of 42,000 genes in humans. This means of estimation was probably closer to those that later suggested a high gene number in humans.

    Spuhler's second means of estimating gene number was a lot more interesting. He observed that among human pregnancies, more males than females are lost to miscarriages. Spuhler assumed that a high proportion of these fetal losses were caused by X-linked lethal mutations, and used that as a means of working out the total lethal mutation rate on the X chromosome.

    Haldane had given an estimate of the mutation rate to X-linked hemophilia, based on its novel occurrence in pedigrees in the population. Taking this estimate for one locus, Spuhler could estimate the number of loci on the X. And then, the length of the X as measured cytologically could be used to estimate the total number of genes in the human genome.

    His estimate on this basis, roughly between 20,000 and 30,000, is much like what we think today.

    On the other hand, Spuhler's numbers were imprecise. Later, Frota-Pessoa revisited Spuhler's estimate. Frota-Pessoa found the means of estimation very attractive because they did not rely on extrapolation from other animals. However, there are other causes of fetal loss than lethal mutations, and we must recognize that the conception ratio is not 50/50, so that the proportion of male to female fetal losses can't estimate the X-linked lethal rate without some correction. Frota-Pessoa arrived at an estimate of human gene number less than a third that of Spuhler's range: only 5900 to 11,700 genes.

    That estimate also gives the lie to the idea that geneticists always expected a very high gene count in humans. What's remarkable to me is that the entire means of estimation required no knowledge of gene sequences or DNA; the estimates required only epidemiology coupled with cytological estimates of chromosome lengths.

    References:

    Frota-Pessoa O. 1961. On the number of gene loci and the total mutation rate in man. Am Naturalist 95:217-222.

    Spuhler JN. 1948. On the number of genes in man. Science 108:279-280.

  • Chimp trivia

    Fri, 2010-04-02 19:14 -- John Hawks

    Courtesy of Jon Cohen in Science ("The Chimpanzee Genome Project's Seedy Origins"), a detail that I hadn't heard before:

    To begin, [Pieter] de Jong asked Yerkes for a sample of chimp sperm, and researchers there chose Clint—not because he was a hardy male representative of Pan troglodytes or had some other meaningful attribute. Clint, it turns out, became the genome chimp because he was particularly fond of providing sperm samples.

    Apparently it all started with Evan Eichler, who needed to make a bacterial artificial chromosome with chimpanzee X chromosome sequence.

  • Quote: R. A. Fisher on chance and natural selection

    Thu, 2010-03-04 09:40 -- John Hawks

    From p. 37 of the Genetical Theory of Natural Selection (1930):

    The statement of the principle of Natural Selection in the form of a theorem determining the rate of progress of a species in fitness to survive (this term being used for a well-defined statistical attribute of the population), together with the relation between this rate of progress and its standard error [Fisher describes here his Fundamental Theorem], puts us in a position to judge of the validity of the objection which has been made, that the principle of Natural Selection depends on a succession of favourable chances. The objection is more in the nature of an innuendo than of a criticism, for it depends for its force upon the ambiguity of the word chance, in its popular uses. The income derived from a Casino by its proprietor may, in one sense, be said to depend upon a succession of favourable chances, although the phrase contains a suggestion of improbability more appropriate to the hopes of the patrons of his establishment. It is easy without any very profound logical analysis to perceive the difference between a succession of favourable deviations from the laws of chance, and on the other hand, the continuous and cumulative action of these laws. It is on the latter that the principle of Natural Selection relies.

  • We control the horizontal

    Wed, 2010-01-27 10:03 -- John Hawks

    New Scientist has an article by Mark Buchanan discussing horizontal transfer as a mechanism for the evolution of early life: "Horizontal and vertical: The evolution of evolution"

    There's a lot of "evolution doesn't work the way we thought" stuff in the article, which focuses on Carl Woese:

    How could modern biology have gone so badly off track? According to Woese, it is a simple tale of scientific complacency. Evolutionary biology took its modern form in the early 20th century with the establishment of the genetic basis of inheritance: Mendel's genetics combined with Darwin's theory of evolution by natural selection. Biologists refer to this as the "modern synthesis", and it has been the basis for all subsequent developments in molecular biology and genetics. Woese believes that along the way biologists were seduced by their own success into thinking they had found the final truth about all evolution. "Biology built up a facade of mathematics around the juxtaposition of Mendelian genetics with Darwinism," he says. "And as a result it neglected to study the most important problem in science - the nature of the evolutionary process."

    In particular, he argues, nothing in the modern synthesis explains the most fundamental steps in early life: how evolution could have produced the genetic code and the basic genetic machinery used by all organisms, especially the enzymes and structures involved in translating genetic information into proteins. Most biologists, following Francis Crick, simply supposed that these were uninformative "accidents of history". That was a big mistake, says Woese, who has made his academic reputation proving the point.

    I don't see any inconsistency between the modern synthesis and the idea of horizontal gene transfer. This is a failure of history -- of people reading only Ernst Mayr as a representative of the synthetic view. Other voices -- especially Stebbins -- emphasized gene transfer. The dynamics of genes themselves, as opposed to genes as mere parts of organisms, surely underlie the next generations of evolutionary theoriests, including Dawkins' gene-centric perspective, and Williams' idea of "levels of selection".

    Woese is working to discover modes of evolution of gene (and even sub-gene) replicators, before the "hardening" of genomes into organisms. Before the organismal level of selection existed, there can only have been the gene level (taking "gene" to mean replicating element). That's not anti-synthesis, it's what we would expect of replicators at the sub-organismal level.

    It's also no surprise as applied to horizontal transfer in more recent lineages. Humans have gotten DNA from viruses during the past few million years, some of which has been fixed in the genomes of the present population. That's no challenge to the way we understand evolution, it's saying that one kind of mutational process is acquisition of viral DNA. Likewise, the introgression of genes between species is no challenge to evolution. It is good evidence that speciation is a evolutionary process -- otherwise boundaries between sister species would be impermeable.

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Neandertals

For years, I've worked on their bones. Now I'm working on their genes. Read more about the science studying these ancient people.

Denisova

From a finger bone of an ancient human came the record of a completely unexpected population. My lab is working on the science of the Denisova genome.

Acceleration

The advent of agriculture caused natural selection to speed up greatly in humans. We're uncovering some of the ways that populations have rapidly changed during the last 10,000 years.

Malapa

Just outside Johannesburg, the Malapa site is producing some of the most exciting finds in human evolution. This site is the headquarters of the Malapa Soft Tissue Project.