Blog carnival!

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The blog posts for this month’s carnival address fundamental problems in evoluitionary biology in novel and controversial contexts.

  • Hunan evolution
  • Mechanisms of evolution
  • Conduct of science and its representation in the media

Human evolution

Evolution and human races. A recent book by Nicholas Wade focuses controversy on the issue of whether human beings can be organized into races: Wade argues that they can be, and that people in the same race share behavior and other capacities because they share a common racial inheritance. Bradly Alicea challenges Wade by discussing the nature and interpretation of genetic variation and population differentiation in our species. Jennifer Raff, a postdoc at UT Austin with graduate level training both anthropology and genetics, challenges readers to identify a consistent account of race in Wade’s book and points out that Wade’s argument depends in a critical manner on his own intuitions about how many races there are.

Suzanne Sedadin answers the question, “What is the evolutionary benefit of having (menstrual) periods?” In brief, the answer is that menstruation results from conflicting needs of the developing fetus and the mother.

Dienekes’ Anthropology Blog summarizes arguments in a recent paper in the literature about human origins, in which it is claimed that there is support for the theory that our species originated in Africa in recent times.

Cleopatra’s royal incest. Phylonetworks.blogspot.com describes Cleopatra’s family tree, rife with inbreeding, including sister-brother matings between her and her siblings. It appears that keeping the royal family small and insular outweighs concerns about inbreeding depression.

Anne Buchanan, visiting the Italian countryside, was stimulated to reflect on Mussolini’s enthusiasm for racism by a barn a with a fascist saying emblazoned it, remaining from the WWII period. Though not connected with Wade’s book directly, Buchanan echos concerns voiced by Sedadin and Alicea, taking Mussolini’s persecution of the Jews as a cautionary tale against being too hasty to let emotions and prejudices guide our science.

Evolution of ethical norms. In one of seven blog postings, John Wilkins explores expectations about human morality, social structure, and behavior, given that we share an inheritance with the other apes. He concludes, “I do not know what I shall next write about. This series is taking a turn I did not anticipate,” after considering a thesis by Kim Sterelny and Ben Fraser about the evolution of morality.

Controlling our temper. Tom Denson reports intriguing results from a recent brain imaging study. He and his colleagues found that a variant of a gene for MAOA predisposes men to more violent behavior than others having other variants. The difference seems to be due to the genes’ effects on a man’s response to provocation, intriguing, because it might seem more intuitive to some that violent individuals are more easily provoked. Unlike in many cases in which a gene is identified with a certain human behavior, Denson explains some of the social and developmental aspects required for a person with the gene to become  more likely to be violent.

Mechanisms of evolution

Charles J. Goodnight, on the biology faculty at UVM, writes a series of posts arguing that the theory of multilevel selection (MLS) is a superior alternative to theories of kin selection for explaining evolution in social groups. Two other posts discuss Sewall Wright’s shifting balance theory of evolution and the explanatory device Wright often used to explain his theory, the adaptive landscape.

R. A. Fisher’s geometric model of mutation. Who can resist a blog posting entitled “Fitness landscape of beer?” Jeremy Fox’s “silly post with two serious points” explains new insights from R. A. Fisher’s model of the frequency of favorable mutations, using a spatial metaphor, illustrating an important case in which theoretical, mathematical models can be especially useful when used together with empirical results.

Convergent evolution. Janet Fang calls attention to research showing that, despite having a common ancestor no more recent than 500 million years ago, humans and squid evolved eyes different in construction, but in response to similar selection pressures, and as a result of differences in the Pax-6 control genes.

Patterns of selection in space and time. Kiyoko Gotanda describes a general method for determining the relative importance of variations in the strength of selection across space and time, explaining how the method is used to show that variation in space outweighs variation in time in a guppy population.

Coevolution and geographic expansion. GrrlScientist offers a comprehensive account of the adaptive radiation of hummingbirds. Over the 20 MYA+ history of the lineage, hummingbirds continue to diversify, owing to their coevolution with the plants they pollinate, and expansion into high-altitude niches in the Andes.

Pleiotropy. Jeremy Yoder reports results of a recent experiment purporting to show that pleiotropic genes, those responsible for multiple phenotypes, are subject to strong stabilizing selection, which is in line with what might be expected intuitively. If a gene combination is responsible for several important phenotypes, it seems right to say that selection against any one phenotype would be detrimental in the extreme, because the function of the other phenotypes at the same locus would also be disrupted.

Adaptation to drought conditions. Casey Terhorst’s post begins, “Global climate change will increase the frequency and duration of drought in many places,” reporting the surprising result that understanding the response of soil microbes to a drought requires an understanding of the reaction of plants with which they share the soil. Perhaps most striking is the claim that important evolutionary changes can occur in as few as three generations of the plants, an elapsed time of 6 months.

Conduct of science and its representation the media

Hype vs. evidence. Brian Switek directs the reader’s attention to fossils of “Predator X,” identified by journalists at the time of its discovery as one of the largest and most powerful predators ever to live on Earth. As evidence mounted, the basis for this claim became weaker; although it’s probably true that it was a fearsome carnivore, the superlatives do not appear to be warranted in light of deeper scientific investigation.

Carina Baskett discusses the thesis, first articulated by Darwin’s colleague Alfred Russell Wallace, that there is greater taxonomic diversity in the tropics than at other latitudes, and that biotic relationships are responsible. Her illuminating explanation of the hypothesis illustrates her claim that declaring a hypothesis “dead” can be harmful, because it’s rare that scientific results are so clear.

So-called “junk” DNA. Carl Zimmer assesses a recent controversy in which none other than EE&O’s Editor-in-Chief, T. Ryan Gregory, features prominently. Only a small fraction of our DNA codes for proteins; when this was initially discovered, the non-coding DNA was termed “junk.” Reporting on results suggesting that the overwhelming majority of DNA in our genome has a function, Science announced, “ENCODE Project writes eulogy for junk DNA.” This is too hasty, Zimmer explains, judging by Gregory and his colleagues’ arguments that much non-coding DNA lacks any function.

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  • John Harshman

    Only a small fraction of our DNA codes for proteins; when this was initially discovered, the non-coding DNA was termed “junk.”

    You didn’t really just say that, did you?

    • John Harshman

      Hey, is anyone reading this?

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  • John Harshman

    OK, I’ll try again. The problem with this –

    Only a small fraction of our DNA codes for proteins; when this was initially discovered, the non-coding DNA was termed “junk.”

    – is that it equates non-coding DNA with junk, and this has never, ever been true. Structural RNAs and regulatory elements were known before the term “junk DNA” was first used. Zimmer himself makes that point in the post you refer to. The equation of “non-coding” with “junk” is a common strawman used by those who want to use the discovery of this or that regulatory sequence to announce that junk DNA is dead. About 2% of your genome is protein-coding. About 90% is junk. The remaining 8% or so is functional, non-coding DNA, and that’s what your statement provides no room for.

    And that’s my complaint.

    • Adam Michael Goldstein

      To be clear, I didn’t intend to claim that “junk DNA” is helpful or accurate, or indeed, to take any position whatever on what portion of the genome codes for proteins, serves a regulatory function, or anything else besides. My intention was to report what Zimmer said in his post, and to reflect what seems to be at stake in the controversy. My statement “Only a small fraction of our DNA codes for proteins; when this was initially discovered, the non-coding DNA was termed `junk’” is so brief that it is hard to see what I might have wanted to get across by it. I might have been clearer.

      Here are the passages I had in mind when I was reporting on Zimmer’s blog posting:

      begin{quote}
      Meanwhile, scientists were also finding pieces of DNA in the genome that appeared to be neither protein-coding genes nor regulatory elements. In the 1960s, for example, Roy Britten and David Kohne found hundreds of thousands of repeating segments of DNA, each of which turned out to be just a few hundred bases long. Many of these repeating sequences were the product of virus-like stretches of DNA. These pieces of “selfish DNA” made copies of themselves that were inserted back in the genome. Mutations then reduced them into inert fragments.
      .
      .
      .
      Scientists also started referring to “junk DNA.” Different scientists used the term to refer to different things. The Japanese geneticist Susumu Ohno used the term when developing a theory for how DNA mutates. Ohno envisioned protein-coding genes being accidentally duplicated. Later, mutations would hit the new copies of those genes. In a few cases, the mutations would give the new gene copies a new function. In most, however, they just killed the gene. He referred to the extra useless copies of genes as junk DNA. Other people used the term to refer broadly to any piece of DNA that didn’t have a function.
      end{quote}

      These statements and others by Zimmer are at least not incompatible with my interpretation of his view that he wanted to say that “only a small fraction of our DNA codes for proteins; when this was initially discovered, the non-coding DNA was termed `junk’.”

      • John Harshman

        First, thanks for the eventual reply. But your idea that Zimmer’s statements are compatible with yours is incorrect. Note the wording “neither protein-coding genes nor regulatory elements“. Zimmer explicitly acknowledges that regulatory elements are neither protein-coding nor junk, and that regulatory elements were known before the label “junk” was used. Nor did anyone’s definition of junk ever include all non-protein-coding DNA, which Zimmer also points out.

        Let me stress that the reason I’m so exercised about this is that it’s a common misconception among science journalists (though not Zimmer) and even among some scientists, all of whom should know better. And this misconception has been used to hype a number of what would otherwise have been unremarkable discoveries, among them the ENCODE project.

  • Guest

    Josh

    I had written a response earlier—I don’t see it appearing here though. Sorry. . . . I’ll see if I can figure out what went wrong.

    • John Harshman

      Josh?

      • Adam Michael Goldstein

        Hi John,

        Sorry about making the mistake about your name! I have deleted the initial reference to it. Again I hope can can accept my apologies.

        Yours

        Adam

        • John Harshman

          I can, but getting my name wrong is less objectionable than getting the facts wrong.

  • adamgoldstein

    John,

    I’m reading this!…Here are some thoughts in response to your comment…

    What’s the source of puzzlement here? That I said it (the quoted it about DNA), that Zimmer said it, that Gregory and others accept it, or that it might be true? Or that “junk” is used to describe it? The view Zimmer first mentions is that it was thought that apparently functionless DNA does have a function that isn’t known yet. The reasoning is based on the idea that natural selection acts on almost all parts of the genome, including its size, so that it can reasonably be concluded that DNA of unknown function has one. Gregory’s argument (as explained by Zimmer) is that, if natural selection were acting strongly enough to explain the adaptedness of all of the supposedly functionless DNA, the level of mortality of the species would be so high that it would have become extinct. This is not a novel kind of argument; it has the same logic that others using arguments about what’s termed “the cost of selection.”

    For my part, it sounds eminently plausible. I am an old drifter, to borrow a phrase from Dobzhansky, because I think that the amount of non-adaptive change (due to drift and other non-adaptive processes) is probably underestimated, and its role not well understood.