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  • Life history invariants: broken beyond repair?

    Fri, 2005-08-19 00:50 -- John Hawks

    Here's a study that won't be reported in the science press, but is much more important to evolutionary theory than anything else I've read this month.

    Sean Nee and colleagues write in the August 19 Science that attempts to construct an overarching theory of animal life history evolution may be written off because of a fundamental methodological error.

    The problem comes down to a simple error in interpreting log-log plots.

    Here's the abstract:

    Life-history theory attempts to provide evolutionary explanations for variations in the ways in which animal species live their lives. Recent analyses have suggested that the dimensionless ratios of several key life-history parameters are the same for different species, even across distant taxa. However, we show here that previous analyses may have given a false picture and created an illusion of invariants, which do not necessarily exist; essentially, this is because life-history variables have been regressed against themselves. The following question arises from our analysis: How do we identify an invariant?

    The development of the idea of "invariants" in life history is due to Eric Charnov (reviewed in Charnov 1993). The idea is that if you examine the ratio of two dimensions of life history -- for example, the ratio of maturation age to average adult life span -- that the ratio is constant across species. If this were true, then a major aim of life history theory would be to explain why these invariant ratios have the values they do. Presumably, the ratios found across animal species would reflect ecological trade-offs -- for example, bigger animals require more time to develop, and therefore must extend their adult life span proportionately longer to allow for the risks of juvenile mortality, costs of investing more in offspring, or some other constraint.

    The idea of invariants is not derived from theory -- it is an argument based on empirical observations. When you plot an life history traits from different species against another trait, in many cases you find that the logarithm of one is linearly related to the logarithm of the other, with a slope very near 1.0. This would be precisely the relationship you would expect if the ratio between the two traits were constant.

    What Nee and colleagues demonstrate is that the converse is not true. Although an invariant ratio does lead to a log-log slope near 1.0, a log-log slope near 1.0 may result from many relationships other than an invariant ratio. In particular, a random set of ratios will still generate a log-log slope near 1.0.

    A commentary by Gerdien de Jong (subscription required) explains the paper.

    But Nee et al. (2) describe the general rationale of how slopes of 1 at high R2 arise in log-log plots, independent of the distributions of the traits. The culprit is a variable on the y axis that is a fraction of the x-variable: The plot is of y = cx, with c . In a log-log plot of cx versus x, a slope of 1 follows automatically. A wide range on the x axis--from rabbit to whale--guarantees a high R2. The evidence for life history invariants vanishes as the method of finding them evaporates (de Jong 2005:1194).

    Why does this happen? Simply put, a short-lived species must have a shorter maturation age than its average life span, but not too much shorter. The slope of 1.0 comes from this fact alone: one variable is constrained to be close to the other, owing to the fact that it is some substantial proportion of that other variable.

    Why should the correlation be high? The answer to this should be familiar to any paleontologist: it's a mouse to elephant curve. The independent variable ranges across so many orders of magnitude that the variance about the regression essentially disappears.

    The essential emptiness of the theory arises here:

    The most notable invariants are typically taken to be those that hold over several orders of magnitude of variation in the value of the biological characters; we now see that it is this wide variability of the characters that inevitably makes the invariants notable (Nee et al. 2005: 1238).

    When I read through Charnov's book (Life History Invariants: Some Explorations of Symmetry in Evolutionary Ecology), it was with an eye toward the relationship of average life span to maturation age. Personally, I found the log-log plots less than convincing, because there was too much variation hidden in them. A 0.95 correlation on a log-log plot across primates still allows individual values to vary by a lot, just because a log-log plot appears to smash the variation down so much.

    This study attacks the basis of the theory much more directly:

    From the time of the introduction of invariants, many other studies and discussions have accepted their existence on the basis of these sorts of demonstrations and attempted to explain them theoretically or infer their consequences. For example, in his review of the canonical monograph on life-history invariants (1), Maynard Smith refers to the M/b data we have just discussed and says "M/b is approximately constant (0.2) for species as different as the tree sparrow and wandering albatross"(31). This is in spite of the fact that the data to which he is referring show the ratio varying between 0.1 and 0.5. Maynard Smith was not the only reviewer to accept that this ratio is constant (32), and the status of these life-history invariants is such that they have now found their way into the popular physics literature (33). In fact, in a population of constant size, the ratio M/b is, essentially, the probability of surviving from egg to breeding age and therefore is constrained to be between 0 and 1 (Nee et al. 2005: 1238).

    This was certainly my perception for the primates. There was a strong claim that the values of interest were invariants, despite the fact that the data themselves show fairly wide variation in the actual ratios.

    What is the solution to this problem for life history theory? Nee et al. suggest comparisons with other dimensionless values; de Jong suggests a direct examination of fitness relations in different species. The latter approach seems the most likely for hominoids, although this essentially amounts to a species-specific examination in each case.

    What I wonder is whether other kinds of relations -- ones we may be more familiar with -- may prove to be manifestations of the same error. I'm going to be looking through some papers in the next few days with that in mind.

    References:

    Charnov E. 1993. Life History Invariants: Some Explorations of Symmetry in Evolutionary Ecology. Oxford University Press, Oxford.

    de Jong G. 2005. Is invariance across animal species just an illusion? Science 309:1193-1195. Full text (subscription required)

    Nee S, Colegrave N, West SA, Grafen A. 2005. The illusion of invariant quantities in life histories. Science 309:1236-1239. Full text (subscription required)

  • Bringing Kurzweil's dream to earth

    Wed, 2005-08-17 23:22 -- John Hawks

    I've seen a lot of attention to the new Ray Kurzweil book, Fanstastic Voyage: Live Long Enough to Live Forever, but only now have I seen a review by someone knowledgeable about the evolutionary biology of aging. Tom Kirkwood is just such a person, and Nature has his review of the book, along with another book on the same topic (by Philip Lee Miller and the Life Extension Foundation, with Monica Reinagel --- does that sound like a 70's funk band, or what?).

    The review is basically supportive of the actual content of the books, but at the same time critical of the hype. Here's a sample:

    Peel away the gloss, however, and these two books turn out to be rather humdrum contributions to the growing genre of 'how to' manuals that aspire to tell us "how to benefit from cutting edge science and add years to your life" and "how to extend the prime of your life and rejuvenate your body, mind and spirit". Both books do a fair job of summarizing the current state of knowledge about factors that can affect the ageing process and about what can sensibly be done to increase your chances of living into old age in good health.

    And there is this interesting passage:

    We know, for example, that, in model organisms, boosting some of the mechanisms for cellular maintenance and repair can indeed extend life-span. This does not mean that the same techniques will necessarily work in humans, because we know from comparative studies that humans are already endowed, for good evolutionary reasons, with much better maintenance systems than shorter-lived species. By analogy, a design modification that boosts the performance of my own modest car will not necessarily make a Maserati go faster, as the Maserati is engineered for peak performance already. But we can try.

    One might say the best thing about immortality is getting to see the full effects of compound interest. But don't bet on it yet.

    References:

    Kirkwood T. 2005. Live long and prosper (combined review). Nature 436:915-916. Full text (subscription required).

  • Weismann's mosaicism

    Wed, 2005-08-10 22:41 -- John Hawks

    I've been reading Ron Amundson's new history of biology book, The Changing Role of the Embryo in Evolutionary Thought.

    I'll be posting a lot on this book over the next couple of weeks, as I have taken a lot of notes. In short, I find it to be a very interesting and thought-provoking revision of the history of evolutionary theory. I often find when I'm reading a history that things didn't happen the way I learned in school. Amundson gives example after example of the way that the history of biology was constructed to defend a specific set of beliefs -- those that constituted the Evolutionary Synthesis. The result is that in many particulars, the history of pre-Darwinian and post-Darwinian biology that you thought you knew just isn't the way things really happened. Amundson's particular interest is development, and especially the ways that developmental biology was jettisoned along the road to neodarwinism.

    On page 144, August Weismann enters the story. If you know the history of biology, then you probably remember one key fact about Weismann: he innovated the distinction between germline and somatic cells. You probably remember this because the sequestration of the germline explains why Lamarckian inheritance is impossible --- changes to the somatic cells cannot affect the germline cells that ultimately produce gametes. That's an essential insight to population genetics: it underlies particulate inheritance. It also is usually taken to mean that the transmission of genes to offspring is independent of the processes of development; in other words, it underlies the distinction between transmission genetics and developmental genetics.

    You may know a lot more than this about Weismann, but I certainly didn't, so I was intrigued by the real motivation for his theory.

    Weismann enters Amundson's narrative as an example of pre-synthesis models of heredity. As it turns out, under Weismann's theory, the germline sequestration was necessary not to refute Lamarckian inheritance, but to allow embryonic development itself:

    The central problem of the study of embryological development is explaining the increase in heterogeneity in the developing embryo. Seen in terms of the cell theory, increased heterogeneity could be conceived as cellular differentiation. How does the single cell of the zygote give rise through division to the specialized cells of the various parts of the body? The answer given by Weismann and [Wilhelm] Roux was the mosaic theory of development. Roux stated his version of the mosaic theory in 1885, the same year that Weismann proposed the germ-soma distinction. Mosaic or autonomous theories of development assert that the nature of body parts is determined in advance of their acutal development, and determined independently of the body parts around them. In contrast, regulative theories of development claim that body parts take their nature from their position within the embryo (Amundson 2005:145, emphasis in original).

    How did this "mosaic theory" work? The cytoplasm was theorized to contain particles (ultimately called determinates) that comprised all the hereditary information. As the embryo differentiated, different cells received different subsets of the original determinates. Cells that received bone-determinates became bone cells, those that received heart-determinates became cardiac cells, and so on. Therefore the original heritable material was parcelled out to different somatic cells, meaning that no somatic cell contained all the determinates necessary to construct an entire body. In this theory, heredity and ontogeny were inextricably linked: indeed, the hereditary particles were directly responsible for the development of the organism.

    It is easy to see that under this theory, the sequestration of the germline is essential, otherwise reproduction would be impossible. Only by setting aside a group of cells that would retain all the hereditary determinates could the ability to produce another individual be transmitted to the next generation. Weismann's mechanism of development dictated the germ-soma distinction.

    As Amundson describes, the mosaic theory fell out of favor for two reasons. Embryologists didn't like it because it didn't really explain the formation of different tissues. Although the theory was intended to explain why the differentiation occurred (through the progressive assortment of determinates into different tissues), it didn't explain how those determinates actually got into their ultimate positions or how they determined the actual properties of different tissues.

    And it was found to be inconsistent with the burgeoning field of genetics, under the influence of Thomas Hart Morgan. Cells were found to divide equally in all cases, and genetic material was found to assort equally into both daughter cells. This removed any empirical support for the "determinates", and left the mosaic theory without a credible mechanism.

    Amundson's point in describing the theory is to point out that before Morgan, heredity was universally assumed to involve development: individuals inherited not an information-bearing particle, like DNA, but instead the ontogenetic program. This concept of heredity could not lead to population genetics, because it did not admit a mathematical analysis of inheritance along Mendelian lines. Instead, population genetics developed upon Morgan's assertion that the tranmission of traits from parents to offspring could be studied even in the absence of knowledge of how the traits develop.

    Weismann's germ-soma distinction was thus resurrected as a key to Mendelian inheritance: it explained the transmission of genetic material to offspring as independent of the process of development. Amundson cites John Maynard Smith to this effect, and adds:

    In 1927, Weismann was the emblem of the integration of development and heredity; in 1982, he was the hero who had divorced the two fields. Why the change? ... Embryology itself was almost forgotten, and Weismann's mosaic embryological theory was totally forgotten. This enabled a replacement of the historical Weismann ... with the modern pseudo-Weismann (whose germ line-soma distinction seemed to anticipate the genotype-phenotype distinction. References to Weismann were absent from formative Synthesis literature. Later in the century, Weismann was recalled to mind -- he was the person who had refuted Lamarckism with his germ line-soma distinction (ibid., 219).

    Weismann has gained special importance in evolutionary theory for his argument against use-inheritance for a good reason: Darwin himself embarrassingly (at least to the modern sensibility) assumed that use-inheritance was an important source of heredity. Thus, Weismann's germ-soma distinction is placed as a corrective to Darwin, and thereby a major advance toward modern evolutionary theory.

    In view of Weismann's actual ideas, this posturing is highly ironic.

    UPDATE: I have intended to give Gould's Structure of Evolutionary Theory another look after finishing Amundson to compare their treatment of the embryology. But upon writing this, I felt like checking what Gould had to say about Weismann. Apparently he didn't get Amundson's point at all --- perhaps the genotype-phenotype distinction was drilled into Gould once too often, also. Instead, Gould focuses on Weismann's later theory of germinal selection as a precursor to his own multilevel selection ideas. Thus he gives Weismann a good 20 pages, but doesn't outline the importance of his mechanism of heredity to the germ-soma distinction.

  • "Ape to Man" to debut Sunday evening

    Tue, 2005-08-02 23:04 -- John Hawks

    The History Channel is showing its new human evolution program, "Ape to Man" this Sunday, August 7, at 9:00 EDT / 8:00 CDT. The show has a website, which gives the list of interviewees (Leslie Aiello, Joe Cain (history of science), Chris Stringer, and Colin Menter (fossil sites of South Africa). There is also a quick synopsis:

    Highlights of APE TO MAN include:

    Reenactments of the work of Eugene DuBois, an Amsterdam physician who left his practice in 1890 in search of the Missing Link and found what would be called Homo erectus, a 500,000-year old ape-like skeleton, in Sumatra. DuBois' assertion that he has found the Missing Link results in his rejection by the scientific community. Only later did people realize the impact of the discovery.

    Examination of the key elements that marked the evolution from ape to man, including the ability to walk upright, the use of tools, the harnessing of fire, the ability to form communities, and the ability to reason and plan.

    The story of Piltdown Man, a skeleton discovered in England in 1912 which was, for a time, considered by many to be the definitive Missing Link, but later discovered to be one of the greatest hoaxes in the history of science.

    Raymond Dart's 1924 discovery of Taung Child, a fossilized brain in Africa, nearly two million years old. It was the oldest finding to date, but was completely ignored by the scientific community because people still believed in the erroneous story of Piltdown Man.

    The two key shifts in thinking that led to our understanding today: the shift to Africa as the birthplace of the human species and the shift from the thinking that brain size was the driving force of evolution, to the understanding that the use of tools was really the key step.

    The online preview shows a Dalmatian running in front of a Land Rover, so I assume they'll have reenactments of the Leakeys also.

    I found the online game to be strangely entertaining, since you have to navigate a little Indiana Jones-looking archaeologist around his campsite to find fossils, while avoiding spiders, bees, and quicksand, and returning to the water bucket every couple of minutes for a drink. Of course, when you do it the third time around, and "Zhoukoudian" looks exactly like "Olduvai Gorge" except with more spiders and bees, well, you get the picture. The "quiz" I found less entertaining since several of the questions give out slightly wrong information, and one is really wrong (Dubois' Trinil discovery is around a million years old, not 50,000, in case you're wondering).

    But at the end of the game, there is a cool newspaper, with the headline, "MISSING LINK FOUND!", a photo of the Bone Clones version of Toumaï, and the story:

    One of the greatest riddles in human history has been solved after leading anthropologist Dr. John Hawks found The Missing Link in human evolution. The discovery came after a grueling quest that spanned three continents, and tested the very limits of human endurance.

    Almost enough to get me to watch!

  • Genetics of the superfertile

    Tue, 2005-06-21 16:50 -- John Hawks

    Reuters reports on a research study by Dr. Neri Laufer (Hadassah University Hospital, Jerusalem) into the genetic variation underlying fertility in older women. The newsworthy finding is the identification of a "select group of genes" that influence late fertility:

    Using gene chip technology, [Laufer] and his team compared the genetic profiles of eight women chosen from 250 who had had children past the age of 45 with profiles of six others who had finished their families by the age of 30.

    "These women appear to differ from the normal population due to a unique genetic predisposition that protects them from the DNA damage and cellular aging that helps age the ovary," he said.

    Conceiving naturally past the age of 45 is rare because a womanÕs supply of eggs diminishes as she ages and approaches the menopause, which normally occurs around the age of 50.

    The report implies that the alleles may be more common in some groups than others. Although it does not say, the geographic extent of the samples was almost certainly limited, so the following cannot be considered conclusive, but it is interesting:

    All the super-fertile women in the study were Ashkenazi Jews, descended from the Jewish communities of central and eastern Europe. Most had had six or more children, did not use contraception and had a low miscarriage rate.

    "They challenged their reproductive system until the menopause," said Laufer, who added that the distinct genetic fingerprint was not unique to them.

    He found a similar profile in Bedouin women who also had children late in life.

    It might be highly localized, it might be global. Whichever is the case, this is certainly interesting from the standpoint of the evolution of life history traits in humans. The persistence of fertility into later adulthood would seem to be highly adaptive, unless the allele has some cost for earlier survival or reproduction. The distribution of the allele and that of linked loci could tell us if it has been recently spreading, or if it is an ancient polymorphism. To my knowledge, this is the first examination of the determinants of fertility late in life, as opposed to genetic determinants of mortality. The shape of human life histories is affected by selection on both, so this is an important step.

  • Aristotelian dental logic

    Fri, 2005-06-17 23:45 -- John Hawks

    Every introductory class in biological anthropology talks about wisdom teeth, the common name for human third molars. Around ninety percent of my students in any given semester have had these pulled, or never got them at all. Problems with the eruption or alignment of the third molars are very common, causing pain or infection. Even in cases where the teeth might ultimately not pose a long-term problem, many dentists pull them as a prophylactic. Natural cases of non-eruption are fairly common also. Sometimes these are nevertheless present, and may be removed surgically. Other times, the third molars never formed at all. As a result of both natural variation and orthodontic practice, it is increasingly rare for adults to have wisdom teeth.

    Since this natural variation is so well-known to anthropologists, I was intrigued to find in a comment to a post at Gene Expression that Aristotle believed men had more teeth than women. I went in search of the essential citation, and found it in "The History of Animals," book 2, part 1 (translated by D'Arcy Wentworth Thompson):

    Males have more teeth than females in the case of men, sheep, goats, and swine; in the case of other animals observations have not yet been made: but the more teeth they have the more long-lived are they, as a rule, while those are short-lived in proportion that have teeth fewer in number and thinly set.

    Part 4

    The last teeth to come in man are molars called 'wisdom-teeth', which come at the age of twenty years, in the case of both sexes. Cases have been known in women upwards. of eighty years old where at the very close of life the wisdom-teeth have come up, causing great pain in their coming; and cases have been known of the like phenomenon in men too. This happens, when it does happen, in the case of people where the wisdom-teeth have not come up in early years.

    There may be no accounting for Aristotle's claim that men have more teeth than women, since on average they are the same. On the other hand, with the variation in third molar eruption it is quite possible that the women available for Aristotle to examine might have -- by chance -- had fewer teeth. The idea that there is a systematic difference between men and women would appear to be belied by the following section, where Aristotle clearly discusses the presence of the wisdom teeth in both sexes. This part is a vivid illustration of the problems of the posterior dentition in general -- ancient Greeks and modern Americans alike.

    I was similarly fascinated to see that "wisdom teeth" was a translation from the ancient Greek. Here's the entry from the Online Etymology Dictionary:

    Wisdom teeth so called from 1848 (earlier teeth of wisdom, 1668), a loan-translation of L. dentes sapientiae, itself a loan-transl. of Gk. sophronisteres (used by Hippocrates, from sophron "prudent, self-controlled"), so called because they usually appear ages 17-25, when a person reaches adulthood.

    Here I thought it was just one of those old sayings nobody could account for. And did you know that "catty-corner" comes all the way from Middle English?

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  • Overweight is best?

    Wed, 2005-04-20 21:59 -- John Hawks

    The New York Times reports a new study in JAMA on the mortality risk associated with different BMI classes. The study found that obesity and underweight classes faced a higher mortality risk, but that overweight people were just as well off as normal weight.

    In our analysis, we did not find overweight (BMI 25 to

    The authors speculate that there may have been a recent reduction in mortality associated with obesity and overweight because of increasingly successful treatment of chronic high blood pressure and high cholesterol. Likewise people with extra weight may have an advantage in maintaining bone density and muscle strength into old age compared to normal or underweight people.

    References:

    Flegal KM, Graubard BI, Williamson DF, Gail MH. 2005. Excess deaths associated with underweight, overweight, and obesity. JAMA 293:1861-1867. JAMA Online

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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.