Archive for the ‘Evolutionary’ Category

A selected gene is like garlic mustard

October 25, 2008

That is from this post of John Hawks, which has several other interesting things to say too, as the following quote shows:

A selected gene is like garlic mustard. We may say that only a few members of the Roman elite intermarried with Britons. But if a single Roman married a Briton, carrying an advantageous gene, that gene has the chance to grow exponentially. That chance is not a guarantee, any more than a single garlic mustard seed is a guarantee. A single copy of an advantageous gene still has a very high probability of being lost by chance. But selected genes have a much higher chance of spreading than neutral ones. A very slight amount of long-distance gene flow can cause a selected gene to spread vastly faster than diffusion across a population.

Besides that, in this case, the history is incomplete. Roman legions occupied Britain for more than 400 years. Those legions were not only Italian, but included soldiers from across the empire, including in one famous instance thousands of Sarmatians. Sarmatians carried with them genes from the steppes of Central Asia, much farther than Rome. Soldiers were stationed for years, and many left the service and became local merchants, landowners, or minor nobles. They were not celibate. For that matter, neither were the early Latin clergy…

A must-read post. Have fun!

Afarensis reviews Shubin’s Your inner fish

August 18, 2008

I liked the only piece of Shubin that I have read so far: an essay in the book Intelligent thought. Now, I see from this review of Afarensis of Shubin’s Your inner fish, and the comments therein, it might be another piece of Shubin that might be worth reading:

Shubin starts with an anatomical puzzle, compares the anatomy to that seen in other organisms, discusses the developmental aspects, and then brings in the paleontological record to support his points. This is a powerful approach to doing science, and a powerful approach to explaining science. Overall, the book is an enjoyable read and I would recommend it to anyone interested in science.

Take a look!

Intelligent thought: a review

June 22, 2008

Slightly more than two years ago, one of my friends gifted me Intelligent thought — Science versus the intelligent design movement, an anthology edited by John Brockman. At first, I wasn’t too keen on the book — I knew that ID, as such, did not have any content whatsoever; so, why read a book that is going to tell me the same thing? However, my friend insisted that the book is not just about ID, but also about the science, and I might enjoy the science aspects of the book. So, I promised to read the book and blog about it too.

I am glad I did read the book; it is true that there are pieces in the book which did not excite me very much — the ones that deal with what Dembski or Behe have to say and how they are wrong, insincere, or, both; however, there are a few which I enjoyed thoroughly.

The first piece that I enjoyed a lot is Tim D White’s Human evolution; the evidence. In the essay, White writes about his paleontological studies and excavations in Ethiopia, and what they have to say about human origins and evolution.

The essay that follows White’s called The “Great” transition by Niel H Shubin was another that I liked very much; in this piece, Shubin recounts the story of the discovery of fossils of “fishapods”.

In my opinion, the finest piece in the book is the one by Frank J Sulloway titled Why Darwin rejected intelligent design. The essay begins with this vaguely Jane Austen-ish sentence:

There is considerable irony in the fact that Charles Darwin was at one time enthralled by the theory that all species are intelligently designed–a theory he later sought to banish from science in his Origin of species (1859).

And, it goes on to establish that

While in Galapagos, creationist theory primed Darwin in key ways for what he observed and understood there. Just as important, this theory also dictated what he failed to observe and understand.

Having just read Kuhn’s Structure of scientific revolutions, and not knowing that Darwin did fail to notice certain things which became a key part of his book and his legend, I could make some new connections between what my perceptions about Darwin and his work are and what he actually seems to have done, and put all of that in the paradigm perspective.

Even though the last four paragraphs of Sulloways essay are quotable in full, here are a few thought provoking sentences:

Ultimately, what Darwin’s transformation from creationist to evolutionist reveals about him–and about science generally–is that the best science is conducted in the service of really good theory. Darwin’s own scientific methodology was remarkably modern for a period when Baconian induction–supposedly letting the facts speak for themselves, independently of any theory–was the predominant scientific philosophy. … throughout his long career he employed what is known as the hypothetico-deductive method, by which hypotheses are used to generate predictions and to guide the collection of relevant evidence–information that is then used to confirm or reject the hypotheses.

And, that sentence about “science conducted in the service of a really good theory” reminded me of the pushing your cookie versus theoretical prostitution discussion of Teppo at Orgtheory.

To summarise, if only for Sulloway’s piece, Intelligent thought is worth your time and money. Along the way, you might also find a few more interesting pieces. Have fun!

Evolution for non-biologists

June 21, 2008

John Hawks is starting a series; and, as you can see from its description, it sounds very, very interesting:

I’m going to start a series of articles about the common sense aspect of evolutionary theory. What about evolution is actually practical knowledge? How can it help people understand things relevant to their own work or lives? This goes beyond the gee-whiz, “Where do we come from,” National Geographic-kind of interesting question. That’s nothing more than a framework for idle curiosity: it presents evolution as a kind of adjunct or substitute for religious inquiry.

I want to convey something more important. It matters that we evolved. The process of evolution allows scientific predictions that we can use to make things happen, to make them work. Evolutionary biology illustrates and informs us about decisions that society will have to make in the next 20 years; decisions that I want my students to be informed about.

When I teach evolution, I emphasize a common sense perspective. Understanding a science means knowing the boundaries of the possible. Biologists sometimes say that anything might be possible in biology — it is, after all, highly dependent on historical events that might have turned out very differently. But while it’s true that a wide range of things might have happened, it is not true that anything at all might have happened. Knowing evolutionary theory — including its mathematical basis — lets us understand the limits of the possible, the likely, and the fundamental trade-offs that balance them.

I can’t promise that every example I describe will outline a practical problem, but they will all apply to the problems that face us today. Gene testing, behavioral modification, conservation, biotechnology, global warming — all those are problems that demand not only economic logic but also biological logic

1. Should we be worried about the polar bears?

2. Up to sixteen percent of American elementary students are categorized as ADD/ADHD. This diagnosis often comes with additional investment and help with learning, but also with social stigmatization and pressure to take pharmaceuticals such as Ritalin and Adderall. If this behavior pattern is so bad, why does it exist?

3. The U. S. government routinely recommends high consumption of dairy foods on the part of its citizens, for a healthy life. Yet vast majority of the world’s adult population, including millions of Americans, exhibit ill effects from drinking whole milk, and certain milk products, in the recommended amounts. Why?

4. Honeybees are dying. So are frogs. Is it a crisis? Why is it happening?

5. Geneticists are finding alleles that contribute to the risk of chronic diseases like cardiovascular disease, lung cancer, and diabetes. Many of these alleles occur in a few populations but not others — for instance, Europeans versus Africans. Why?

6. We are told that polar bears are endangered because of global warming. Yet some people claim that polar bears are simply brown bears underneath the fur. Are they right? Does it matter?

7. The ratio of boy births to girl births varies among human populations. Some of this variation is natural, some is influenced by human practices such as selective abortion. How can we tell which is which?

8. Corn (maize) is increasingly important to the world’s economy. It is the single largest mode of converting solar energy into starch, making it useful for food, feedstock, and ethanol conversion. Maize is a new species, which has existed for less than 10,000 years. How did this happen? What more is possible?

9. The number of known primate species has vastly increased during the past 30 years. Yet almost none of these represent populations new to science. What gives?

10. Some futurists are predicting a coming “singularity,” in which humans merge with unimaginably intelligent machines to create a future beyond the scope of any current predictions. What does our past evolution say about this prospect?

My series will be covering many of these topics and many others. I’ll be drawing from human genetics, ecology, agricultural sciences, geology, paleontology, and history. Remember that my audience is broad, so if you’ve seen part of one of my stories before, I apologize — most people probably don’t know the story, and most of my readers haven’t been following the blog since it started.

Where possible, I’ll draw things back toward humans. No, I don’t think humans are always the most important topic in evolutionary biology. But let’s face it: I’m an anthropologist!

I plan to publish an essay here every Friday for the foreseeable future.

Needless to say, I am looking forward to it, and those of you who are not subscribed to his blog, might want to add John Hawks to your feed readers!

How science is done: the nuts-and-bolts edition

April 6, 2008

Karen James writes a BPR3 post on her own research:

It’s been over a month–that’s about seven thousand blog years–since my PLoS ONE paper came out and I’m only just now getting around to giving it a proper blog treatment. In defense of my tardiness, the paper is pretty small-fry in terms of its newsworthiness. It didn’t even get a press release (though maybe that’s a good thing). In other words, it’s still fresh to the blogosphere. Well, that’s my excuse at least.

At first I wondered: is this normal? Blogging on one’s own peer-reviewed research, that is? But Bora Zivkovic (PLoS ONE Online Community Manager/crazy uncle of the science blogging community) and Liz Allen (PLoS Director of Marketing and Business Development) have made it clear that giving my own paper the BPR3 treatment is not only normal, it is expected.

There are several ways I might approach writing this post. The most obvious is to simply summarise the paper In Plain English. Problem is, I’ve already done that by writing a news blurb for the Natural History Museum website, and I don’t really feel like repeating myself (though of course I will, but only to the extent to which it is necessary to tell my story).

A second approach is to critically analyse the paper. But you can see the problem with that right away: since I wrote it, I’ve already critically analysed it. Critical analysis necessarily belongs to someone who isn’t an author on the paper.

A third approach, and the one I am going to go with, is to tell the whole story of this project: the blood, sweat and occasional tears, not just the part that appears in the paper itself. This will be by far more interesting than a simple recap of the key findings of the paper itself (which, as I said, you can get elsewhere). Moreover, the whole story illuminates the reality of the scientific process in a way that’s intelligible to the non-scientist; well, that’s my aim anyways.

A must-read post; link via Bora who recommends the methodology strongly.

Darwin in Indian biology textbooks (the absence of)

March 31, 2008

Prof. Balaram, in his latest editorial at Current Science, brings some disturbing news to our attention (pdf):

 … I wondered how much are our children are taught about Darwin. I took a clandestine look at a X standard biology textbook and found a picture of Gregor Mendel, but no mention of Darwin. There were sections on cell structures, genetics, respiration, nervous and reproductive systems, population and health, but surprisingly not even a passing mention of the origins of biological diversity. On enquiry, the owner of the textbook was dismissive: “Only you and the BBC are interested in Darwin”.

Considering the accepted importance of evolutionary  concepts in biology, the cavalier treatment meted out to Darwin in the high school textbook puzzled me. But, I quickly discovered that “evolution” is a word that is avoided elsewhere too.

Till I read the editorial, I was under the impression that in India at least, we did not have any problems with teaching evolution. May be my impression was incorrect; may be the biology textbooks that we perused also did not have any reference to Darwin, and all of what I know about Darwin and his work stem from my non-textbook reading. In any case, I only hope that Prof. Balaram’s editorial will be a starting point for the revision of the textbooks!

Do (self-proclaimed) Darwinists hate anthropologists?

March 21, 2008

Jon Marks at Savage Minds seems to think so, and puts forth his ideas using rather strong language:

The movements – Social Darwinism, eugenics, Darwinian segregationism, sociobiology, and evolutionary psychology – share very little in terms of their particular content. But they do share two notable attributes: (1) the claim to speak on behalf of Darwinism, and (2) a rhetoric explicitly repudiating the field of anthropology.

In Consilience (1998), E. O. Wilson actually wrote, “Ignorance of the natural sciences by design was a strategy fashioned by the founders [of social science], most notably Emile Durkheim, Karl Marx, Franz Boas, and Sigmund Freud, and their immediate followers.” Now, a decade later, he’s come around to realizing that group selection actually does happen in humans, so I guess all that reductionist posturing from the early days was mainly blather (Quarterly Review of Biology, 82:327, 2007).

Anyway, I’m sitting around on February 12 – “Darwin Day” – reading “The God Delusion” by Richard Dawkins. Richard Dawkins and his acolytes in Darwinian atheism also don’t care too much for anthropology. Since they believe that religion is only for children and morons, and anthropologists tend to think that religion is for everybody – that is to say, anthropologists believe in cultural relativism – Dawkins has us in an enemy camp. He used to ask, “When you actually fly to your international conference of cultural anthropologists, do you go on a magic carpet or do you go on a Boeing 747?”

And I’m thinking to myself, “If this schmuck speaks for Darwinism, isn’t that an argument against evolution?”

But you know what’s worse? There are even bigger schmucks out there claiming to speak for Darwin. After all, that’s who James Watson was invoking last autumn, when he wrote that “there is no firm reason to anticipate that the intellectual capacities of peoples geographically separated in their evolution should prove to have evolved identically. Our wanting to reserve equal powers of reason as some universal heritage of humanity will not be enough to make it so.”

So here is my proposition. Scientific racism is worse than un-scientific creationism. After all, nobody was ever killed or maimed or sterilized in the name of creationism.

So as we look towards the upcoming Darwin anniversary (bicentennial of birth, 150 years since the Origin) maybe we need to think less about the creationists – the external enemies – and think more about the erosion from within. The creationists can’t embarrass science; only scientists can do that. Darwin always has ventriloquists behind him, putting thoughts and words in his mouth, and somehow the job always falls to anthropologists to keep his name unsullied.

That last sentence is a bit intriguing though: are anthropologists the only self-proclaimed Darwinists who do not put their thoughts and words in his mouth? So, I guess, I need to modify my title, by asking, do (self-proclaimed — non-anthropologist) Darwinists hate anthropologists?!

Anyway, an interesting thought — take a look!

Did thought precede language?

February 25, 2008

Bolles at Babel’s Dawn, after reading a recent piece by Chomsky on the evolution of language wonders if his own thinking and ideas on the problem need overhauling:

The founder of modern linguistics, Noam Chomsky, was famous for decades for his dismissal of interest in the evolution of language. In recent years he has moderated his position and in a lecture recently made available on line (here, registration required) he outlines his scenario for how language evolved. It is about as different from the account being developed on this blog as a theory can be, making it of keen interest because it forces me to ask whether I have gone hopelessly astray and should change course quite sharply.

Bolles goes on to summarise the arguments of Chomsky in a lucid manner:

Suppose I say

John is too angry to eat.

I can take that to mean John won’t eat anything because he is angry, but it could also be understood to mean I won’t eat John because he is too angry. This last reading may seem ridiculous, but it is exactly how we would be likely to interpret the sentence John is too angry to invite. I won’t invite John because he is so angry. As Chomsky says in one of his charmingly gotcha sentences, “The surface form in themselves tell us little about the interpretation.” [p. 16]

The syntactical explanation for the different interpretations is that the verb to eat requires an object, e.g., eat an apple. If no object is presented, we assume a general one (won’t eat anything). The verb to invite requires an indirect object, e.g., invite to a party. If that is missing, we assume a general one (won’t invite to anything). The meaning of the sentence came from “the generative procedures that yield the expressions, but cannot be detected in the physical signal.” He goes on:

For that reason it seemed then [fifty years ago]—and still seems—that the language acquired must have the basic properties of an internalized explanatory theory. [p. 17]

That’s why language must be primarily an internal process and that any external features must be secondary: the surface structure of a sentence does not include enough information to make its meaning clear. To be understood we must have access to the generative mechanisms producing the sentence. A speaker generates and knows what it means because of the generative process. The listener reverse engineers the sentences, understanding them by discovering the rules that generated them.

In the late 1950s Chomsky argument carried the day because his opponent gave no place to any internal processes, either perceptual or conceptual. Behaviorism described only reflexive responses to unambiguous stimuli. The replacement school, cognitive psychology, gives us an internal symbol processor, but still has no room for sensation-based knowledge (perception). If you take as your axioms that animals are computers and language becomes meaningful by organizing symbols, it is hard to escape Chomsky’s logic. The only reason I can resist is that I believe animals think perceptually rather than conceptually, and that meaning comes from piloting attention rather than following syntactical rules.

Take a look!

PS: May be it is because I am not a native speaker of English; but, if somebody says John is too angry to invite, I would have assumed that John will not invite me because he is too angry; if it indeed is the meaning that Bolles attributes to the sentence that I have in my mind, I would have said John is too angry to be invited, or John is too angry for me to invite him. But given a context, I can see why I would infer the same meaning as Bolles advances to that sentence.

Some mathematical links!

February 23, 2008

The March issue of American Mathematical Monthly is full of wonderful reading material:

Take a look!

CoM and lumbar lordosis during pregnancy

December 16, 2007

CoM stands for center of mass. Lumbar Lordosis, I understand, is an inward curvature of the lower back. Pharyngula explains the connection between the two:

… pregnant women are carrying this low-slung 7kg (15lb) weight, and the closest we males can come to the experience would be pressing a bowling ball to our bellybutton and hauling it around with us everywhere we go. This is the kind of load that can put someone seriously out of balance, and one way we compensate for a forward-projecting load is to increase the curvature of our spines (especially the lumbar spine, or lower back), and throw our shoulders back to move our center of mass (COM) back.

Here’s the interesting part: women have changed the shape of individual vertebrae to better enable maintenance of this increased curvature, called lordosis, and fossil australopithecines show a similar variation.

Pharygula’s post is about a recent paper published in Nature titled Fetal load and the evolution of lumbar lordosis in bipedal hominins by Whitcome, Shapiro and Lieberman:

As predicted by Darwin, bipedal posture and locomotion are key distinguishing features of the earliest known hominins. Hominin axial skeletons show many derived adaptations for bipedalism, including an elongated lumbar region, both in the number of vertebrae and their lengths, as well as a marked posterior concavity of wedged lumbar vertebrae, known as a lordosis. The lordosis stabilizes the upper body over the lower limbs in bipeds by positioning the trunk’s centre of mass (COM) above the hips. However, bipedalism poses a unique challenge to pregnant females because the changing body shape and the extra mass associated with pregnancy shift the trunk’s COM anterior to the hips. Here we show that human females have evolved a derived curvature and reinforcement of the lumbar vertebrae to compensate for this bipedal obstetric load. Similarly dimorphic morphologies in fossil vertebrae of Australopithecus suggest that this adaptation to fetal load preceded the evolution of Homo.

Pharyngula goes on to supply some alternative hypotheses and a few criticisms of the results reported in the paper:

I have some significant disagreements with the evolutionary interpretations of the paper. They claim to have identified evidence of an evolutionary novelty, but they haven’t tested the alternative hypothesis, that this is not an evolutionary adaptation, but a physiological one, and they haven’t adequately distinguished cause and effect.

My first thought on reading the results was that this is an example of developmental plasticity. Bones are flexible; they respond to stress with changes in shape and size that accommodate them to the pattern of activity they experience. This is an indirect evolutionary adaptation, of course — that bones have this response is a product of their genetic and developmental potential. However, the shape of an individual vertebra may not be so precisely specified, but may emerge as a product of the strains put upon it.

I’d make an alternative hypothesis. The female L3 vertebra is not wedge-shaped because women need to bear a fetal load, but instead, because women bear a fetal load, the L3 vertebra is wedge-shaped. In particular because their own data shows a significant amount of variability in vertebral shape, I’d be hesitant to assign a direct genetic cause on the pattern.

Unfortunately, the data in this paper do not touch on this possibility. All of it is from either pregnant women, or from skeletal remains of adults of child-bearing age. What I’d like to see is some developmental information, especially measurements of lumbar vertebrae in pre-pubertal children. If the difference precedes the child-bearing experience, then I’d agree that they’ve found a sexual dimorphism that could have an evolutionary cause.

Other data I’d like to see: is there a difference in vertebral morphology between women who have had children and those who have not? Another sex difference that could generate variation in vertebral morphology besides pregnancy is breast size; like carrying a fetus, women have another forward projecting weight that can shift the center of mass. Do large-breasted women have a consistent change in vertebral morphology that isn’t found in small-breasted women or men? How does obesity affect vertebral shape?

The authors have identified an interesting sexual dimorphism, but I think the paper was far too quick in assigning an evolutionary selective cause for the difference, and that it did not adequately examine the more likely (to my mind, at least) explanation of physiological adaptation.

Take a look; and, while you are at it, do not miss the comments section too!