john hawks weblog

paleoanthropology, genetics and evolution

Our future shrinking population

Fri, 2013-01-11 00:48 -- John Hawks

Jeff Wise in Slate has an essay about "World population may actually start declining, not exploding".

A somewhat more arcane milestone, meanwhile, generated no media coverage at all: It took humankind 13 years to add its 7 billionth. That’s longer than the 12 years it took to add the 6 billionth—the first time in human history that interval had grown. (The 2 billionth, 3 billionth, 4 billionth, and 5 billionth took 123, 33, 14, and 13 years, respectively.) In other words, the rate of global population growth has slowed. And it’s expected to keep slowing. Indeed, according to experts’ best estimates, the total population of Earth will stop growing within the lifespan of people alive today.

In other words, the global population has crossed the zero point of the Great Second Derivative of population growth. This is not news as UN and other projections have long predicted a "hump" in human population during the next century, but the article goes to an extreme: What if, once it stops growing and begins shrinking, the human population shrinks down to some very small number?

That might sound like an outrageous claim, but it comes down to simple math. According to a 2008 IIASA report, if the world stabilizes at a total fertility rate of 1.5—where Europe is today—then by 2200 the global population will fall to half of what it is today. By 2300, it’ll barely scratch 1 billion. (The authors of the report tell me that in the years since the initial publication, some details have changed—Europe’s population is falling faster than was previously anticipated, while Africa’s birthrate is declining more slowly—but the overall outlook is the same.) Extend the trend line, and within a few dozen generations you’re talking about a global population small enough to fit in a nursing home.

Notice how so many people who comment on the global population assume that human growth is a homogeneous process? That is, they understand that nations presently have different rates of growth, but conceive of them as being at different places in a process of Westernization. They treat the nations themselves as homogeneous entities.

That's not the right way to think about the future. We have heterogeneous national populations, with subgroups that have very high fertility rates. The largest contrast in terms of proportion of the population in most countries is rural/urban, where rural people have larger family sizes than city-dwellers. One of the biggest contributors to the decline in population growth has been urbanization, as city-dwellers tend to have kids later and have fewer of them. So as the populations of most countries make the transition to urban majorities, their growth rate slows.

There are many other factors, some cultural and others more broadly environmental. Religion is a key factor, and countries with diverse religious populations, like the U.S., have large variance in family sizes among different religious groups. The effect of religion on family size isn't absolute, as urbanization, education, and economic constraints lead to lower family sizes even among religious groups that encourage a "quiver-full" family size. However, I suspect that the variance among cultural groups within countries will persist, and that persistence in the face of a global reduction in growth will tend to increase the proportion of the population represented by fast-growing groups. As fast-growing groups increase in proportion, the overall growth rate of the population increases. So modeling a steady future decline in population assumes a uniform cultural effect on these heterogenous groups, which I doubt.

I also consider it an open question whether family size will be positively selected moving forward in time. All else being equal, bigger families will represent more and more of the population, and any genes that correlate with larger family size will increase in numbers. At present, we are seeing the large effect of environmental factors on reducing family size, just as environmental factors during the last 200 years have massively increased survival within populations with large family sizes. But as we equalize the environment in various ways, any effect of genes will become relatively more important in their contribution to variance in family size.

As Malcolm reminds us in Jurassic Park, "life finds a way"...

Twitter higher-ed pointer

Thu, 2013-01-10 12:00 -- John Hawks

Many professors and instructors are starting semesters in the next week or two, me among them. As I'm preparing materials for my spring course, I'll post a few things that I've found useful to shake things up in class.

Many readers will remember my post from last year, "Best practices and tips for Twitter in the higher-ed classroom". It has been consistently one of my top posts since I wrote it last year, and I've gotten some Twitter traffic for it this month. I thought it would be worth a link in case anyone is thinking of adding Twitter interaction to a course and may not have seen it.

Tags: 

Creative anatomy

Wed, 2013-01-09 22:13 -- John Hawks

Mike Taylor from Sauropod Vertebra Picture of the Week shows how anatomists get creative with their measurement instruments: "How to measure necks using Duplo":

I find the best way to get the neck exactly abutting the left (red) wall is to start with the neck in its natural position, with the anterior and posterior ends curving towards you, then sort of unroll it against the back wall, and finally push the posterior end into place with your little finger (see below). There is a satisfying moment of the back end popping into place — almost a click — and the neck slides along a little to right as necessary to accommodate the added length.

Starting my descent through The Descent of Man: Introduction

Wed, 2013-01-09 00:28 -- John Hawks

I have a number of goals for 2013. Several of them will play out here on the weblog, a few others will lead to publications. A handful have more speculative outcomes, and we'll see how they turn out.

One of my goals is to read and comment through the entirety of Darwin's The Descent of Man. That project I debut today.

I haven't done a similar close reading of the Origin, for several reasons. The Origin has something for every biologist but is read by startlingly few. Despite this deplorable lack of Darwin literacy, biologists read the Descent much, much less. So many historians of science and biologists have commented on the Origin that there remains little of value for me to add to its interpretation. By contrast Descent is uniquely interesting from an anthropological perspective.

I am not a historian and cannot track down all the sources that Darwin would have known or used. What I can do is to give some perspectives on our current understanding of human evolution, making clear in which ways Darwin was prescient and in which other ways he was plain wrong.

The main reason why I've undertaken the close reading is that Darwin was the first to seriously propose mechanisms for human evolution. He cared not only what had happened, but how it happened. Darwin was an intensely thoughtful analyst, and searched for evidence in every source at his disposal. Even so, he has only weak evidence about human prehistory and comparative primate anatomy and behavior. The mechanisms of genetics were not known at all, beyond the mere observation of inheritance of some traits. At the time of the Origin, only the Feldhofer Neandertal was suspected to represent any kind of prehuman ancestor or collateral.

More than half of the full work, The Descent of Man, and Selection in Relation to Sex, is about the mechanism of sexual selection, including evidence for the process across the animal kingdom. I am neither qualified nor especially concerned with the success of the sexual selection hypothesis for insects and birds. I am interested in the process for just the same reason Darwin included it in the Descent: because sexual selection may explain some aspects of human biology and variation. I will probably limit my close reading and commentary to the portions of the text that reflect directly upon primate and human evolution, which will leave out nearly half the full work.

I will be referring to the Project Gutenberg version of the 1871 text, which is freely available to readers in many formats. The text of Descent is public domain, allowing me to reprint it in its entirety, along with my notes.

Introduction

The Introduction to the Descent is not the best place to start a close reading. It was finished too late in the process of writing, with Darwin having taken too great care and having used too solicitous a style in comparison to the rest of the work. Most important, the Introduction doesn't really present any arguments, just a summary of what will follow.

In other words, it's wimpy.

As I look at my notes on the Introduction, I see that my reactions are mostly about the connections to later material. My most salient reactions fall into two categories:

1. Darwin's description of his own work in light of reception of the Origin, first published twelve years earlier.

2. Darwin's allusions to the views of other scientists with whom, although agreeing on many general principles, he actually disagreed about many details and processes. Of particular interest are Charles Lyell, Alfred Russel Wallace, Thomas Huxley, and Ernst Haeckel.

In the Introduction to the work, Darwin emphasized the positive reviews of his earlier work, and de-emphasized his disagreement with earlier authors on human evolution.

The nature of the following work will be best understood by a brief account of how it came to be written. During many years I collected notes on the origin or descent of man, without any intention of publishing on the subject, but rather with the determination not to publish, as I thought that I should thus only add to the prejudices against my views. It seemed to me sufficient to indicate, in the first edition of my ‘Origin of Species,’ that by this work “light would be thrown on the origin of man and his history;” and this implies that man must be included with other organic beings in any general conclusion respecting his manner of appearance on this earth. Now the case wears a wholly different aspect. When a naturalist like Carl Vogt ventures to say in his address as President of the National Institution of Geneva (1869), “personne, en Europe au moins, n’ose plus soutenir la création indépendante et de toutes pièces, des espèces,” it is manifest that at least a large number of naturalists must admit that species are the modified descendants of other species; and this especially holds good with the younger and rising naturalists. The greater number accept the agency of natural selection; though some urge, whether with justice the future must decide, that I have greatly overrated its importance. Of the older and honoured chiefs in natural science, many unfortunately are still opposed to evolution in every form.

By waiting 12 years to write on human evolution, Darwin ceded ground to many other biologists, allowing them to write and promote theories about human origins before him. That decision had many drawbacks. But one central advantage is the authority that the intervening years and the acceptance of the Origin gave Darwin.

In consequence of the views now adopted by most naturalists, and which will ultimately, as in every other case, be followed by other men, I have been led to put together my notes, so as to see how far the general conclusions arrived at in my former works were applicable to man. This seemed all the more desirable as I had never deliberately applied these views to a species taken singly.

Is this really true? It certainly accords with the way anthropologists and biologists have divided up their subjects since Darwin. Evolutionary biologists study every kind of organism; anthropologists study the evolution of humans. Telling our story is special. But the following sentence is a great statement of why the human story must not be considered alone:

When we confine our attention to any one form, we are deprived of the weighty arguments derived from the nature of the affinities which connect together whole groups of organisms—their geographical distribution in past and present times, and their geological succession.

This is Darwin's defense of the comparative method. Restricting our field of view to a single lineage reduces our ability to understand the process of change. In this work, he will bring the geographical distribution in particular up to a level of substantiating relationships among organisms (humans and African apes, for example, to the exclusion of Asian apes) even where anatomical evidence was not compelling.

The homological structure, embryological development, and rudimentary organs of a species, whether it be man or any other animal, to which our attention may be directed, remain to be considered; but these great classes of facts afford, as it appears to me, ample and conclusive evidence in favour of the principle of gradual evolution. The strong support derived from the other arguments should, however, always be kept before the mind.

The sole object of this work is to consider, firstly, whether man, like every other species, is descended from some pre-existing form; secondly, the manner of his development; and thirdly, the value of the differences between the so-called races of man. As I shall confine myself to these points, it will not be necessary to describe in detail the differences between the several races—an enormous subject which has been fully discussed in many valuable works.

This is an interesting passage. My impression has always been that Darwin had a distaste for the work of contemporaries who studied human races. It is also an area where his disagreement with Wallace was the greatest. The Descent itself includes a great deal about race, but does not consist of description. This passage may have insulated him from criticism that his work did not have the description of skulls that had recently been published by J. Barnard Davis ("J. Barnard Davis and the variation within races") or some earlier scholars.

The high antiquity of man has recently been demonstrated by the labours of a host of eminent men, beginning with M. Boucher de Perthes; and this is the indispensable basis for understanding his origin. I shall, therefore, take this conclusion for granted, and may refer my readers to the admirable treatises of Sir Charles Lyell, Sir John Lubbock, and others. Nor shall I have occasion to do more than to allude to the amount of difference between man and the anthropomorphous apes; for Prof. Huxley, in the opinion of most competent judges, has conclusively shewn that in every single visible character man differs less from the higher apes than these do from the lower members of the same order of Primates.

This work contains hardly any original facts in regard to man; but as the conclusions at which I arrived, after drawing up a rough draft, appeared to me interesting, I thought that they might interest others.

Characteristic understatement, in this case to the point of falsehood. Descent is chock-full of ideas that never appeared elsewhere. Where Darwin had famously left the subject of human evolution to the briefest statement in the Origin ("Light will be shed on man and his origins"), other authors in the intervening twelve years picked up the slack. Yet Darwin did have extensive notes on his ideas about human origins, and corresponded extensively with authors who published their ideas during the 1860s. The most interesting of those letters are to and from Wallace, as I'll note throughout.

It has often and confidently been asserted, that man’s origin can never be known: but ignorance more frequently begets confidence than does knowledge: it is those who know little, and not those who know much, who so positively assert that this or that problem will never be solved by science. The conclusion that man is the co-descendant with other species of some ancient, lower, and extinct form, is not in any degree new. Lamarck long ago came to this conclusion, which has lately been maintained by several eminent naturalists and philosophers; for instance by Wallace, Huxley, Lyell, Vogt, Lubbock, Büchner, Rolle, &c., and especially by Häckel. This last naturalist, besides his great work, 'Generelle Morphologie ‘(1866), has recently (1868, with a second edit. in 1870), published his ‘Natürliche Schöpfungsgeschichte, ‘in which he fully discusses the genealogy of man.

Haeckel's book was a highly popular, accessible German description of Darwinian theory and the history of life. It was later translated into English as The History of Creation, a translation that was edited by the prominent biologist E. Ray Lankester, but did not appear until 1874.

If this work had appeared before my essay had been written, I should probably never have completed it. Almost all the conclusions at which I have arrived I find confirmed by this naturalist, whose knowledge on many points is much fuller than mine. Wherever I have added any fact or view from Prof. Häckel’s writings, I give his authority in the text, other statements I leave as they originally stood in my manuscript, occasionally giving in the foot-notes references to his works, as a confirmation of the more doubtful or interesting points.

Haeckel's "full discussion of the genealogy of man" was organized into more than 22 stages, going all the way back to bacteria. It's really not very much like Darwin's Descent. Haeckel also devoted a chapter to describing theories about the migration and diversification of human races, and this shares more subject matter with Darwin's account, but is really quite brief compared to the corresponding portions of the Descent. All in all, it was generous of Darwin to point so prominently to Haeckel's book, which was already widely known in England, but as I'll describe further in later installments there was little chance of confusing Descent for Haeckel's work.

During many years it has seemed to me highly probable that sexual selection has played an important part in differentiating the races of man; but in my ‘Origin of Species’ (first edition, p. 199) I contented myself by merely alluding to this belief. When I came to apply this view to man, I found it indispensable to treat the whole subject in full detail. Consequently the second part of the present work, treating of sexual selection, has extended to an inordinate length, compared with the first part; but this could not be avoided.

Darwin lays out the theory of sexual selection with many varied and detailed examples, as was his special talent. Any editor today would have taken most of this material out of the book and put it in a separate book. I do not plan to treat these chapters in detail during my reading, except for those bearing specifically upon primates and humans. Darwin's motivation behind this part of the work was telegraphed in a letter to Wallace in 1864:

Secondly I suspect that a sort of sexual selection has been the most powerful means of changing the races of man. I can shew that the difft races have a widely difft standard of beauty. Among savages the most powerful men will have the pick of the women & they will generally leave the most descendants.

Wallace disagreed with Darwin on this point, and generally maintained that sexual selection was not powerful enough in humans to have affected human variation. The Wallace-Darwin disagreement on the power of selection was far-reaching. The two men clearly understood that their respective opinions had consequences across biology. But more on that point later.

Returning to the Introduction:

I had intended adding to the present volumes an essay on the expression of the various emotions by man and the lower animals. My attention was called to this subject many years ago by Sir Charles Bell’s admirable work. This illustrious anatomist maintains that man is endowed with certain muscles solely for the sake of expressing his emotions. As this view is obviously opposed to the belief that man is descended from some other and lower form, it was necessary for me to consider it. I likewise wished to ascertain how far the emotions are expressed in the same manner by the different races of man. But owing to the length of the present work, I have thought it better to reserve my essay, which is partially completed, for separate publication.

The Expression of Emotions is itself a remarkable piece of work. It establishes an evolutionary theory of behavior, providing connections between behavior and anatomy in a way that would echo through the work of later ethologists.

OK, that's the Introduction. I've added quite enough here, and have probably gone on too long on some points without adding references. I want to get this up and get started on the meaty part of the text, which are not so much about Darwin's intentions and are devoted instead to statements of fact and theory.

Next, we get right into Darwin's argument for the body structure of humans as evidence for evolution.

Finding sequencing methods in the library

Tue, 2013-01-08 23:38 -- John Hawks

Jay Shendure and Erez Lieberman Aiden have a recent review in Nature Biotechnology that provides some recent data on the falling cost and increased use of genome sequencing [1]. They accentuate the massive reduction in cost of sequencing technology over the last seven years -- from $1000 per megabase to only 10 cents per megabase.

What is more interesting about the article is that the authors concentrate on the possible strengths of different sequencing platforms for different biological projects. They point out that the cheapest technology may not be the best for many purposes, and each application has different unique requirements.

They illustrate this with a "subway map" view, which illustrates the routes that different molecular techniques have followed, from one application to another, until they have come to be used for sequencing (the function at the "terminal").

Subway map view of sequencing technology and applications, from Shendure and Aiden 2012

From their later text:

The subway map analogy suggests that the development of new applications is likely to be best supported by a broad knowledge of existing and emerging sequencing protocols as well as a willingness to delve into the past 50 years of methods development in biochemistry and molecular biology. These sources effectively provide a toolbox that can be drawn on when evaluating potential routes to support new applications.

Of course, the next advances in sequencing methodology are probably already being developed by labs looking through these methods.


References

  1. Shendure J, Aiden EL. The expanding scope of DNA sequencing. Nature Biotechnology. 2012;30(11):1084 - 1094.

Do citation indices count in tenure review?

Tue, 2013-01-08 17:07 -- John Hawks

Amy Brand comments on journal citation metrics and tenure and promotion, from the viewpoint of a university administrator [1]. The piece is a reaction to those who believe that publishing in open access journals is harmful for the careers of junior scholars:

In 2010, Nature carried out a survey in which it asked readers about the use of metrics in decisions about new hires and tenure (Abbott et al., 2010). Three-quarters of the 150 readers who replied thought that metrics were being used in hiring decisions. However, provosts and other administrators contacted by Nature painted a different picture: ‘Metrics are not used a great deal,’ said Alex Halliday, head of the mathematical, physical and life sciences division at Oxford University. ‘The most important things are the letters, the interview and the CV, and our opinions of the papers published.’ Claude Canizares, vice president for research and associate provost at the Massachusetts Institute of Technology, had a similar message: ‘We pay very little attention, almost zero, to citation indices and counting numbers of publications’.

This is a little misleading. By the time a tenure application goes to the provost, it has already been through many layers of review. Letter writers, grant reviewers and departmental colleagues do pay attention to high-profile publications. It is true that calculating the citation index of a journal does not add much information to this process, but a scholar who publishes only in very obscure venues will be dinged for it at these levels of evaluation.

Fortunately, open access journals are no longer obscure. Additionally, access is becoming part of what it takes a publication to be perceived as high-profile. Particularly in anthropology, there is a strong argument that providing access to research results is an ethical obligation to our research participants.


References

Crowdsourcing paleoecology

Mon, 2013-01-07 23:55 -- John Hawks

Jacqueline Gill reports on a conference with a provocative organization: "Crowd-sourcing the 50 most pressing questions in paleoecology".

Conference attendees (of which I believe were around 60) were emailed the questions in advance, and asked to narrow them down to each of our own individual top fifty, as well as rank which subgroups we were most interested in– I ended up in Biodiversity Through Time. Every subgroup had a scribe (to record information about which questions were particularly contentious, or when concerns or points were raised), a chair, and a co-chair (for organizational and time-keeping purposes). Each subgroup was given dozens of questions, organized into loose themes, that we had to narrow down to twenty in the first day. This process was much more complex that it initially sounds– after an initial round of voting, there was a considerable amount of discussion, word-smithing, and merging of questions.

What a neat idea -- a conference with a real agenda and public product at the end of it. Like paleoanthropology, paleoecology is a field where data are hard to obtain and require very specialized analytical methods. Getting the public involved in the science means finding ways to get people engaged in the questions and hypothesis formation. A ranking of important questions is a great idea, and may help to shape granting priorities.

Scott on science literacy

Mon, 2013-01-07 23:34 -- John Hawks

Eugenie Scott, of the National Center for Science Education, has an editorial in the current Frontiers in Genetics. The title effectively conveys the piece's message about science literacy: "This I believe: we need to understand evolution, adaptation, and phenotype" [1].

The essay expresses several reasons why each of these key concepts is essentials science knowledge. She writes against both genetic determinism and its opposite, environmental determinism:

But environmental or cultural determinism is also false and should also be avoided: even highly environmentally-influenced human traits, such as personality, sexual orientation, intelligence, aggression, and the like, still are phenotypes, with genetic as well as environmental components influencing their expression. Yes, the Tarahumara of the canyons of northwest Mexico value running to such a degree that they are famous for their 48-h jogs covering hundreds of miles. But recognizing the cultural forces at work here should not preclude asking the physiological question of whether the Tarahumara are genetically equipped to process energy more efficiently than the rest of us. If we are cultural determinists, we will never think to ask that question.


References

"No more complicated than setting up an Orange Julius franchise"

Mon, 2013-01-07 22:44 -- John Hawks

That quote is from Misha Angrist, about the coming genetic interpretation industry. It's part of an essay by Virginia Hughes, in Slate: "It’s Time To Stop Obsessing About the Dangers of Genetic Information". The essay will be worth discussion in courses that focus on human genetics. It ties together several claims: (1) widespread whole-genome testing is inevitable and nearly at hand, (2) social science research shows that people don't have increased anxiety or other negative reactions when they learn about health risks from genetics, and (3) medical professionals are not prepared for this near-future.

I don't endorse all the conclusions but Hughes expresses many aspects of the story clearly. For example, this passage on "informed consent" as applied to whole genomes:

The first problem boils down to the concept of “informed consent,” which usually means page after page of consent forms outlining the rights of a patient or research volunteer. (Whenever I talk to researchers about informed consent, they invariably compare it to the iTunes user agreement, where everybody checks the little box without reading the text.) Genome sequencing is so new that informed consent doesn’t always happen, resulting in doctors ordering tests without asking people ahead of time about what to do with the results.

Asking people what they want to know is tricky because you don’t know what will be relevant before you look at the data, notes Amy McGuire, director of the Center for Medical Ethics and Health Policy at Baylor College of Medicine. “It’s impossible at the front end to go through every possible piece of information they’d get back and ask them how they’d feel about that.”

Again, I've discussed these issues with many geneticists and I am continually surprised at how far behind most of them are in understanding what people are already learning about their own genetics.

Geno2 users showing unexpected Denisovan ancestry

Sun, 2013-01-06 23:08 -- John Hawks

I have been excited to hear in the last few days from several readers who have gotten results from the new Genographic Geno2 genotyping chip. One aspect of the result reporting is a person's estimated proportion of Neandertal ancestry, which is a simple percentage. This is like the report from 23andMe, and should be a pretty straightforward estimate given a model of Neandertal-human genetic similarity from complete genomes.

Another aspect of the Genographic results is an estimated proportion of Denisovan ancestry. This might seem a bit surprising, as for most participants in the project who lack Polynesian or Melanesian ancestry this proportion should be extremely low. I've written about Denisovan DNA similarity with living peoples a few times ("Denisovan DNA in the islands, and an Australian genome", "How widespread is Denisovan ancestry today?"). Based on the science published to date, I would have expected the Geno2 calculations just to confirm the very low ancestry estimation found in last year's research based on genotyping Asian and Australasian populations.

So I have been extraordinarily surprised to see that people are getting Geno2 results with up to 6% Denisovan ancestry!

What gives? None of my correspondents so far has anything other than European self-reported ancestry, making it seem very unlikely that have substantial Denisovan ancestry.

The first time I heard from a reader with this result, my immediate reaction was that there must be some problem with the algorithm. This one in particular wouldn't be to hard to get wrong considering the rarity of whole genome evidence from populations known to have substantial Denisovan ancestry. Or possibly, some problem with an individual's genotype chip data might trigger the algorithm to look more Denisovan. For many loci that vary among humans, Denisovans are very unlikely to have the derived human variant; so an individual with an unusual proportion of ancestral homozygote loci might look Denisovan in a human-Denisovan comparison.

However, this is all speculation without knowing the details of the Genographic analysis. And as I hear from more people with varied results, I am having trouble thinking of how data errors could be patterned. It's a tough one to think about because of the unique aspects of the Geno2 chip, and until I've gotten a feel for results from that platform compared to other datasets I probably won't have a solid idea.

I should point out that if there is a problem with the algorithm underlying ancestry prediction from Denisova, it almost certainly affects the Neandertal ancestry estimate also. The estimation from both these ancient genomes involves the same procedure, although with Denisovan DNA it requires subtracting out the DNA similarity with Neandertals first.

So I would be interested in hearing from anyone who is surprised to find that they have Denisovan ancestry. My preliminary assumption it that the result is spurious but I'll try to figure out if there is a possibility of some Denisovan fraction beyond what has been shown in published work.

Blog of the seven veils

Sun, 2013-01-06 16:37 -- John Hawks

Why should academics consider blogging, and when should they band together to work on a group blog? An interview from early 2012 helps to answer those questions: "Five minutes with Patrick Dunleavy and Chris Gilson: 'Blogging is quite simply, one of the most important things that an academic should be doing right now'".

But in addition, social scientists have an obligation to society to contribute their observations to the wider world – and at the moment that’s often being done in ramshackle and impoverished ways, in pointlessly obscure or charged-for forums, in language where you need to look up every second word in Wikipedia, with acres of ‘dead-on-arrival’ data in unreadable tables, and all delivered over bizarrely long-winded timescales. So the public pay for all our research, and then we shunt back to them a few press releases and a lot of out-of-date academic junk.

This is exceptionally good advice, which made me want to link the piece even though it's from nearly a year ago:

Make sure your titles tell a story, and your findings are communicated early on. Academics normally like to build up their arguments slowly, and then only tell you their findings with a final flourish at the end. Don’t do this ‘Dance of the Seven Veils’ in which layers of irrelevance are progressively stripped aside for the final kernel of value-added knowledge to be revealed. Instead, make sure that all the information readers need to understand what you’re saying is up front – you’ll make a much stronger impression that way.

(via Christopher Lynn)

Darwin's primate phylogeny

Sat, 2013-01-05 23:24 -- John Hawks

I'm doing some reading and ran across a 2009 post by Brian Switek ("Darwin, Ardi and the African apes"), who touched on a little-appreciated aspect of Darwin's conception of human relationships:

Yet there is something else that has long gone overlooked about Darwin’s oft-quoted “African apes” passage. Today we take it to mean that out of all living apes our species shared a recent common ancestry with chimpanzees and gorillas, thus suggesting that humans evolved in Africa. Darwin did not have the details but the consensus is that he turned out to be right in a general sense. In truth, however, Darwin’s conception of human evolution may not have been as modern as we have presumed.

Darwin manuscript page with primate phylogeny illustrated

Darwin's 1868 drawing of primate phylogeny. He places "Man" as an outgroup to a 3-way trichotomy of chimpanzee-gorilla, orangutan and Hylobates clades. From the Darwin Online Manuscript Catalogue, digital image copyright Cambridge University.

As Switek describes, anthropologists often credit Darwin with a very modern conception of primate phylogeny. This credit comes because of a passage in the Descent of Man in which Darwin argues that chimpanzees and gorillas, the African apes, are the closest to people. In the course of my reading of the Descent this year, I will come to that passage and consider it in some detail. The important reason for anthropologists to note that passage is that it directly contradicted Haeckel, whose work on human evolution began earlier than Darwin, and who had claimed that humans are closer to the orangutans than the African apes.

The drawing above, which Darwin produced in 1868, does not follow the scheme described in the Descent. "Man", at the extreme left in the phylogeny, is a sister group to a three-way trichotomy of chimpanzee-gorilla, orangutan, and Hylobates branches. What I find even more interesting is that Darwin clearly changed the arrangement by reversing the branches with Hylobates and chimpanzee-gorilla written on them. If we take his tree strictly as a phylogeny, in which the topology is determined by the arrangement of the branches, then the left-right positions of these two branches do not matter since the branches form a trichotomy. But it is not obvious that Darwin had in the back of his mind what most undergraduates today think about these trees -- that putting species near each other on the page is a sign that they are more closely related.

This was a manuscript page in Darwin's notes, and from its context it is clear that Darwin himself was not ready to commit on the subject. The drawing was accompanied by a short description on the reverse side, which reads in part: "Arrangement as far as I can make out by comparing the view of various naturalists ... For myself I have no claim whatever to form an opinion."

Who were the naturalists on whom Darwin depended? One of them was Haeckel, whose 1868 Natürliche Schöpfungsgeschichte included a phylogeny that connected humans with Hylobates and orangutans as Asian "man-like apes" in opposition to African chimpanzees and gorillas.

But probably Darwin depended on Thomas Huxley for most of his knowledge of these apes, who had published an extensive description of what was known about orangutans, gibbons, chimpanzees and gorillas up to that time in his 1863 Evidence as to Man's Place in Nature. Huxley did not provide any phylogeny or textual assessment of which of the "man-like apes" may be the closest to humans. Huxley observed that many of the descriptions of these primates were unreliable, and he took the attitude that comparing descriptions across different apes was a way to test their veracity. Reading his text with this in mind, it is easy to take away the feeling that these apes mostly share characteristics with each other that make them different from humans. The exception in Huxley's text is his evocative description of upright posture and gait in gibbons. If one were to take Huxley's description and plot a phylogeny from it, I think it would look like the first version of Darwin's drawing above, with Hylobates placed closer to humans, but not necessarily more closely related to humans.

This scenario is also consistent with Wallace's 1864 argument about human evolution; that we are a long, independent lineage from other primates that originated as early as the Eocene period.

As I get to this section of the Descent I'll be looking very carefully at why Darwin shifted his view from this 1868 note.

Quote: Huxley on traveler's tales and primate discovery

Sat, 2013-01-05 22:42 -- John Hawks

Thomas Huxley devoted his 1863 book, Evidence as to Man's Place in Nature, to describing what was then known about the anatomy and biology of the living apes, including gibbons, orangutans, chimpanzees and gorillas. Earlier descriptions of these primates had spawned endless confusion. Huxley showed (brilliantly) how the confusion resulted from incorrect accounts of the primates from travelers and the study by European anatomists of mostly juvenile skeletons carried away shipboard from the tropical homes of these primates. After this long discussion, he wrote, with great charity:

Once in a generation, a Wallace may be found physically, mentally, and morally qualified to wander unscathed through the tropical wilds of America and of Asia; to form magnificent collections as he wanders; and withal to think out sagaciously the conclusions suggested by his collections: but, to the ordinary explorer or collector, the dense forests of equatorial Asia and Africa, which constitute the favourite habitation of the Orang, the Chimpanzee, and the Gorilla, present difficulties of no ordinary magnitude: and the man who risks his life by even a short visit to the malarious shores of those regions may well be excused if he shrinks from facing the dangers of the interior; if he contents himself with stimulating the industry of the better seasoned natives, and collecting and collating the more or less mythical reports and traditions with which they are too ready to supply him. In such a manner most of the earlier accounts of the habits of the man-like Apes originated; and even now a good deal of what passes current must be admitted to have no very safe foundation.

I just love the way that passage starts!

Quote: Haeckel on our ape "heirlooms"

Sat, 2013-01-05 22:14 -- John Hawks

Ernst Haeckel, in the History of Creation, English translation in the Project Gutenberg version:

Thus, from a careful examination of the comparative anatomy of the Anthropoides, we obtain a similar result to that obtained by Weisbach, from a statistical classification and a thoughtful comparison of the very numerous and careful measurements which Scherzer and Schwarz made of the different races of Men during their voyage in the Austrian frigate Novara round the earth. Weisbach comprises the final result of his investigations in the following words: “The ape-like characteristics of Man are by no means concentrated in one or another race, but are distributed in particular parts of the body, among the different races, in such a manner that each is endowed with some heirloom of this relationship—one race more so, another less, and even we Europeans cannot claim to be entirely free from evidences of this relationship.”

Getting students into communicating anthropology

Sat, 2013-01-05 21:01 -- John Hawks

From Kristina Killgrove, a syllabus for a graduate course in Presenting Anthropology:

A lot of the "reading" for the course, though, is going to be mandatory web-surfing, listening to podcasts, watching videos, and playing interactive games. Those links are currently within a private course wiki, but I'll think of a way to make that public by the end of the semester. And hopefully I'll convince most of the students to share their work, either here or on their own public space, throughout the spring.

In this context, I also want to link to the excellent work by Christopher Lynn and his students at the University of Alabama. By instituting a departmental blog network where graduate students and others in anthropology courses are encouraged to post, Alabama has radically reduced the entry costs the prevent graduate students from sharing their work. Plus, they called me a superhero!

I am so happy to see graduate education starting to shift toward interaction and broader communication.

Against onanistic essays

Fri, 2013-01-04 22:23 -- John Hawks

Claire Potter at the Chronicle's "Tenured Radical" blog, has an interesting essay pondering why we assign students essays that nobody wants to read: "Grading in the age of mechanical reproduction".

If we don’t want to read the papers we assign, why would our students have any interest in writing them?

Then I came to yet another question:

Do the students not sense this lack of interest in their writing by many of their teachers, and might this not have something to do with the indifference they themselves sometimes display to the quality of their own work?

Emphasis in original. I put this philosophy into practice this some time ago. I would take Potter's argument even further: Assignments that students complete only for their instructor's consumption don't work. Students who do well on an assignment only for their instructor's benefit would be motivated to do well anyway. And students who perform poorly on such assignments duck responsibility for their performance, attributing poor grades to what they imagine as their instructor's ill will.

I found the article via Steven Krause, who has his own reactions ("Assigned interest").

Case in point: I decided to not to assign a long (15-20 page) researched seminar paper in 516. It might be the standard deliverable for English department graduate courses everywhere, but students too often come up short in these papers (and I don’t blame them for this), they are probably not fun to write, and they are frequently not much fun to read. So instead, I’m assigning a number of shorter essays, blog posts, and a shorter seminar paper, something of a length that might (hypothetically) be good for a journal like Present Tense.

I generally follow similar strategies. Additionally, I rely on peer feedback, explicitly assigning points to performance on feedback. In some courses I require video production, also with peer feedback in addition to the grading rubric. If the goal of assignments is to develop communication skills, writing is very important but no longer sufficient. Video is a great way to get students to edit, edit, edit.

Somewhat different from Krause, I do retain long researched papers in some courses. But I build up to them by requiring many shorter writing assignments and explicitly allowing students to compile these shorter exercises into their longer paper. I think this is important to developing their ability to carry out a scholarly writing project.

Recantation of a former genetic know-nothing

Fri, 2013-01-04 16:03 -- John Hawks

The text of this lecture by Mark Lynas is remarkable ("Lecture to Oxford Farming Conference, 3 January 2013"). Lynas gained prominence as a critic of genetically modified crops, and describes in the lecture how his activism developed and how he has come in the last few years to renounce his prior views. This happened as he learned to read the scientific literature in order to write books about climate change.

My second climate book, Six Degrees, was so sciency that it even won the Royal Society science books prize, and climate scientists I had become friendly with would joke that I knew more about the subject than them. And yet, incredibly, at this time in 2008 I was still penning screeds in the Guardian attacking the science of GM – even though I had done no academic research on the topic, and had a pretty limited personal understanding. I don’t think I’d ever read a peer-reviewed paper on biotechnology or plant science even at this late stage.

I find that completely jaw-dropping. Here is someone who had never read a scientific study on the subject, purporting to be an advocate in the popular press, and having his ignorant statements printed widely by multimillion-dollar media organizations. I understand that he is an exception only in his newfound candor about his ignorance. But this is the totally unacceptable problem in science communication: Big media uncritically spreads the word of ignoramuses to fit a political agenda.

Should we laud Lynas for his current change of heart? I'm glad to see that he started reading instead of mindlessly parroting ignorant anti-science propaganda. But his current stance even if honest seems transparently opportunistic, as he has found books more profitable than his former advocacy. I would rather see him name names about his former anti-science associates who likewise worked on the basis of complete ignorance.

Building a virtual skeletal collection

Fri, 2013-01-04 15:15 -- John Hawks

From The Independent (UK), a teaser about a 3-d virtual skeletal collection: "Forensic scientists need skeletons to train – but they’re down to bare bones".

[M]any universities are struggling to provide the next generation of crime scene investigators with actual bones on which to practice.

Now a British company, Anthronomics, hopes to solve the problem by working with computer game developers to create new software which scans existing skeletal collections and makes 3D digital images of them available on tablet devices such as the iPad.

There are some free options already out there, including eSkeletons from the University of Texas-Austin, and some paid options including a few anatomy-centric iPad apps. What they lack is an ability to compare samples to understand variation. Here at the University of Wisconsin-Madison, we have a very good teaching collection for most skeletal elements, but could definitely use a broader representation of variation to give students the ability to learn about geographic differences among populations, more about sexual dimorphism in humans and other primates, and pathology. Virtual models cannot replace contact with the skeletal material, but I see an important role for such models as a supplement to what we can do in the laboratory.

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Space radiation

Fri, 2013-01-04 14:44 -- John Hawks

Maggie Koerth-Baker, on "How space radiation hurts astronauts". I did not know about this part:

Cucinotta calls this pre-flight calibration. Scientists take a blood sample from an astronaut before the launch. While the astronaut is in space, the scientists divide that blood sample up and expose it to various levels of gamma rays — the kind of damaging radiation we're used to dealing with on Earth. Then, when the astronaut comes back, they compare those gamma ray-affected samples to what has actually happened to the astronaut while in space. "You see about a two-to-three fold difference across the population of astronauts," Cucinotta told me.

The sample size of astronauts is small enough that I was surprised to see significant effects for one condition: cataracts. The article notes that the Mercury and Gemini astronauts had less spaceflight time than Mir and Skylab cosmonauts and astronauts, which is obvious, but I wonder how they control for the extensive flight time of astronauts who were former test pilots and the consequent history of radiation exposure before going to space.

The stress-free professoriate

Fri, 2013-01-04 11:33 -- John Hawks

I have to drive some more traffic to this post on Forbes' website ("The least stressful jobs of 2013"), because it has me laughing out loud. Number one on the list is "University Professor". The comments section already has the author of the post backtracking away from what she wrote, which is ludicrous:

University professors have a lot less stress than most of us. Unless they teach summer school, they are off between May and September and they enjoy long breaks during the school year, including a month over Christmas and New Year’s and another chunk of time in the spring. Even when school is in session they don’t spend too many hours in the classroom. For tenure-track professors, there is some pressure to publish books and articles, but deadlines are few. Working conditions tend to be cozy and civilized and there are minimal travel demands, except perhaps a non-mandatory conference or two. As for compensation, according to the Bureau of Labor Statistics, the median salary for professors is $62,000, not a huge amount of money but enough to live on, especially in a university town.

Another boon for professors: Universities are expected to add 305,700 adjunct and tenure-track professors by 2020, according to the BLS. All of those attributes land university professor in the number one slot on Careercast.com’s list of the least stressful jobs of 2013.

I'm so glad I don't deal with all the stress of being paid over the summer, and I'm now looking forward to the stress-free prospect of having my colleagues replaced by adjuncts over the next few years. Those non-mandatory conferences are so awesome I'm glad to pay my own way. Thanks, Forbes!

More seriously, it is possible to be a university professor without a lot of stress. I feel great about my work for exactly the reasons the Forbes post suggests -- for me it is important to operate independently, being in control of my own work. But many other professors don't respond to that opportunity by reducing their internal stress level, and pre-tenure is highly stressful for everyone.

And beyond research, all the other demands of the job are increasing greatly as administration grows and teaching staff shrinks. Definitely not a job that is decreasing in stress over the next year.

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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.