Why care about species extinctions?

The New Republic has a piece titled The Greatest Dying by Jerry Coyne & Hopi E. Hoekstra (see below the fold for how to read it for free if you don’t have a TNR subscription). The piece covers the a) general parameters of the mass extinction and b) the reasons why we should care. Coyne and Hoekstra immediately start out making the humanistic utilitarian case, i.e., “How does this help humanity be healthy, wealthy and secure?” But, they proceed to add near the end:

Our arguments so far have tacitly assumed that species are worth saving only in proportion to their economic value and their effects on our quality of life, an attitude that is strongly ingrained, especially in Americans. That is why conservationists always base their case on an economic calculus. But we biologists know in our hearts that there are deeper and equally compelling reasons to worry about the loss of biodiversity: namely, simple morality and intellectual values that transcend pecuniary interests. What, for example, gives us the right to destroy other creatures? And what could be more thrilling than looking around us, seeing that we are surrounded by our evolutionary cousins, and realizing that we all got here by the same simple process of natural selection? To biologists, and potentially everyone else, apprehending the genetic kinship and common origin of all species is a spiritual experience– not necessarily religious, but spiritual nonetheless, for it stirs the soul.

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Resources, resources

A comment below asked about a notation in a particular passage in a book I referenced. As it turns out the book is fully searchable on Amazon. Myself, I do searches on google books, and if there isn’t a “view” of the book I’m looking for (or that page isn’t viewable), I will check for the book on Amazon. This covers a large proportion of the “fact checking” one might need to do. Also, google scholar is pretty well integrated with books, so you might just want to start out there. Here are the libraries who have signed on to google books, so you can imagine that the coverage is pretty good.

One RNA to bind them all?

The Boston Globe has a long piece titled DNA unraveled. With the subtitle like “A ‘scientific revolution’ is taking place, as researchers explore the genomic jungle” you know what to except, lots of adjectives and a healthy dollop of hyperbole. I guess I lean toward the side of the conservatives in the article, but ultimately it doesn’t matter, nature always has the last laugh.
Update: Eye on DNA has a more thorough comment on this article and many others in the latest round up. Always worth checking out!

Heavenly metaphors….

I am now reading the translations of the basic writings of the Confucian Sage Xun Zi in my spare time. Like much of body of Chinese work on moral and political philosophy from this era the prose is allusive and often meanders from obscure analogy to opaque metaphor. But the passages from the chapter titled ‘A Discussion of Heaven’ are clear as day. An illustrative example:

You pray for rain and it rains. Why? For no particular reason, I say. It is just as though you had not prayed for rain and it rained anyway. The sun and moon undergo an eclipse and you try to save them; a drought occurs and you pray for rain; you consult the arts of divination before a decision on some important matter. But it is not as though you could hope to accomplish anything by such ceremonies. They are done merely for ornaments. Hence the gentleman regards them as ornaments, but the common people regard them as supernatural. He who considers them ornaments is fortunate; he who considers them supernatural is unfortunate.

Those familiar with Xun Zi would not be surprised by these sorts of comments. Of the early Confucians he was arguably the most rationally oriented as well as being thoroughly grounded in the empirical reality of the world. That should not be surprising since his life overlapped with the tumultuous period before the unification of China by the First Emperor. The nostalgia for the past and preoccupation with ancient exemplars which is a hallmark of Confucius’ thought is understandable insofar as the halcyon Golden Age of the Zhou had only just passed. In contrast by Xun Zi’s day such memories were very distant indeed, emulation of the past had to give some ground to compromise with the needs of the present so that one could live in the future where one could strive toward proper conduct.

That being said, I do think that Xun Zi’s comments should help us put into perspective the conceit that we moderns have that all ideas which gush from our minds are new to the world. In The Blind Watchmaker Richard Dawkins’ famously asserted that only with the emergence of Charles Darwin’s theory of evolutionary change via natural selection could one be an intellectually fulfilled atheist. In an act of historical psychoanalysis Dawkins offers that he believes that David Hume, who rejected God not because there was another explanation but simply because he did not find it be be any explanation at all, would have agreed with his assessment at the end of the day. Xun Zi expresses very Humean attitudes 2,000 years before Hume, and like the great Scottish philosopher he is content to observe that Heaven simply is. Instead of plumbing the ontological depths of the universe Xun Zi was rather more interested in the maintenance of a robust and stable social order which he noted was on the edge of collapse all around him. Faced with stress and uncertainty Xun Zi did not turn to the gods for salvation (and quite clearly he was skeptical of their very existence as personal entities), nor did he collapse in godless nihilism and give himself up to a life of Epicurean pleasure.

In The Geography of Thought the author argues that one major chasm which separates the Eastern and Western cognitive styles is that the former is less systematic, more open toward contradiction in the service of a pragmatic short term solution to a problem. In contrast, Westerners, exemplified by the Greeks, reveled in their exploration of the nooks and crannies of cognitive paradoxes as the sine qua non of the highest levels of reflective philosophy. Xun Zi’s shallow naturalism, his punting of the mysteries of the origin of life and its ravishing diversity, may not be intellectual satisfying if the essence of thought is to assemble nature together at all its joints in a vast seamless arc, but it is a very conventional and common attitude among a wide range of people. In India the Carvaka movement promoted a materialistic philosophy which resembled Epicureanism. In the Greek world Epicureanism, Skepticism and Cynicism were all schools which exhibited naturalistic streaks. Their attempts, if made, to provide a grounding for the existence and dynamism of the world around us are rather laughable, though perhaps less so in an intellectual climate where some might have taken Hesiod’s cosmogony seriously (see clarification). The purported systematic and idealistic bent of the Greeks when it came to the rationalization of atheism seems to be so much window dressing. At the end of the day it seems that they simply didn’t believe, the gods were ludicrous, and if that was good enough for Hume and Xun Zi, it was good enough for them.

It may be that there are two sets of atheists in the world. One set of atheists is historically contingent and one set is not. The former may find Darwinian evolution, which draws in part from Paley’s Argument for Design, a satisfying narrative for their thirst for why. Prior to Darwin these atheists might have had to quench their thirst for the why with some form of theism, not for them the dispassionate ignorance of Hume, they require some gnosis. The second set of atheists are ahistorical, not only do they not thirst overwhelmingly for the ultimate why, but their intuition as to the naturalistic nature of the universe mitigates any unease that their agnosticism might foster.1 This is where Xun Zi exhibits a lack of systematic thinking, he plainly asserts that there must be a cause for every effect, a point which to a typical teleological human would imply a world filled with bubbling godlings. But no, for Xun Zi there is only impersonal and unfathomable Heaven to which notables may make fictional sacrifices to maintain public order and satisfy the need for rites. In The Blind Watchmaker Richard Dawkins comes close to giving his fellow countryman Charles Darwin credit for inventing the idea which slew God, as if atheism hinged upon the British imagination. These perceptions are confirmed in works such as God’s Funeral: The Decline of Faith in Western Civilization, which narrates the shift toward agnosticism on the part of British intellectuals in the 19th century concomitant with the rise of Darwinian theory, prefigured by the ideas of Hume and Edward Gibbon. But Xun Zi shows the Humean strain in Chinese thinking which existed long before the birth of Christ, an intellectual tradition which persisted across the centuries down to the early modern era and sparked Sinophilia on the part of free thinkers such as Voltaire. In A Farewell to Alms the economic historian Gregory Clark describes the massive gains in income to the masses over the last 200 years and the radical equalization of the social order. The middle class American consumer has nothing in common in their daily life with the marginally alive Chinese peasant of Xun Zi’s day. On the other hand, the ruminations of the typical literary intellectual, the pundit caste given space on our op-ed pages, might be no better than the reflections of the ancient Chinese political philosophers, who played being both humanists and social scientists. While the great lift off in natural sciences has occurred only in the past few hundred years, perhaps the vast majority of the genuine original value from the humanities and philosophy was generated within the first few hundred years of the Iron Age?

1 – To be clear, these two sets of humans are atypical and narrow slices to begin with. Most people, I believe, do not need genuine explicit gnosis, rather they simply believe in an unreflective manner. In many ways the second set of atheists, who naturally have little intuitive belief in a supernatural order or a need for an ontological buoy in the universe, may have more in common with the typical human in their unreflectiveness. Where they differ is that their basal intuition is atypical; most humans intuitively grasp the likelihood of a supernatural order while some atheists do not.In contrast, a small minority of humans have deep and passionate fixations on the why questions. I would argue these are the most attracted toward philosophies which purport to explain it all via theology, scientism or mysticism. Their souls demand and account for why they exist to demand an account in the first place.

Larry Moran caught quote mining

There are few things that irritate me more than the deliberate distortion of an argument. It’s especially irritating when I end up believing said distortion. An example:

Larry Moran has been railing (as he is wont to do) against what he calls “adaptationists”[1] in a couple recent posts. The “adaptationist” is a scientist who believes that every phenotypic trait is an adaptation to some selective pressure. It is clear that this view is wrong– it’s certainly plausible that phenotypes evolve neutrally, and the examples in Moran’s posts are possible candidates, though there’s no evidence for neutrality (other than Moran’s intuition, of course). The high frequency of the O blood group in Native Americans is a better candidate–the population bottleneck as humans expanded into the Americas likely involved large stochastic changes in allele frequency.

In fact, the view Moran attributes to the “adaptationist” is so obviously wrong I wondered whether perhaps we should append the word “mythical” to this creature’s name. Moran responded, quoting this passage from Richard Dawkins’s The Extended Phenotype:

The biochemical controversy over neutralism is concerned with the interesting and important question of whether all gene substitutions have phenotypic effects. The adaptationism controversy is quite different. It is concerned with whether, given that we are dealing with a phenotypic effect big enough to see and ask questions about, we should assume that it is the product of natural selection. The biochemist’s ‘neutral mutations’ are more than neutral. As far as those of us who look at gross morphology, physiology and behaviour are concerned, they are not mutations at all. It was in this spirit that Maynard Smith (1976b) wrote: “I interpret ‘rate of evolution’ as a rate of adaptive change. In this sense, the substitution of a neutral allele would not constitute evolution …” If a whole-organism biologist sees a genetically determined difference among phenotypes, he already knows he cannot be dealing with neutrality in the sense of the modern controversy among biochemical geneticists.

This certainly seems to place Dawkins as an “adaptationist”, one who thinks that all differences in phenotypes are adaptations. I was a little surprised by this, but the quote seemed clear, and I wasn’t going to take the time to find my original.

Luckily, another commenter pointed out that The Extended Phenotype is searchable at Google Books. And funny, the very next line after Moran stops quoting is possibly relevant:

If a whole-organism biologist sees a genetically determined difference among phenotypes, he already knows he cannot be dealing with neutrality in the sense of the modern controversy among biochemical geneticists. He might, nevertheless, be dealing with a neutral character in the sense of an earlier controversy (Fisher & Ford 1950; Wright 1951). A genetic difference could show itself at the phenotypic level, yet still be selectively neutral.

Dawkins goes on to express some skepticism about some arguments for evolution by drift, but he’s certainly not an “adaptationist” in the Moran sense.

I suppose I’m somewhat naive: distorting someone’s argument through selective quotation is a classic creationist tactic, and Moran has written a bit about the propaganda techniques used by that crowd. Little did I know his familiarity is not of an entirely academic sort.

[1] As opposed to “pluralists”, as he likes to call himself. For someone who (rightfully, in my opinion) is disdainful of “framing” (the view that scientists need to spin their results in order to resonate better with the public), he certainly knows how to frame.

Pro-Choicer Advocates Limits On Reproductive Freedom

Dissent has published an article on how pro-choice advocates should start thinking about the prospects of designer babies and the author broaches the subject of regulating, and perhaps prohibiting, access to such procedures. What’s striking about the article is the heavy reliance on the “barn door effect” wherein pro-choice advocates, once through the barn door, slam it shut in order to prevent others from using the same rationales to get through the door. For example:

Now, we who support abortion rights may fear that regulating reproductive technologies could endanger our cause. There is no doubt that maintaining the legality of abortion-and fighting to reverse harmful restrictions of it-is paramount. But it is also important for us to sustain a larger moral vision.

The larger moral vision which the author seeks to protect imposes a cost of loss of reproductive freedom on couples who wish to use reproductive technologies. During the Abortion Wars the pro-choice advocates rejected the very notion of a larger moral vision being protected at the cost of individual reproductive freedom yet now, through the use of selective definition, wherein abortion is synonymous with reproductive freedom and the use of reproductive technologies falls outside the definition, some seem fine with the very idea of limiting individual choice in order to advance their vision of a societal interest.

One of the lines of argument she develops begins with the premise that “individual choices can have larger social consequences.” I wonder what the author’s response would have been to this same premise being used in the early abortion battles, for abortions themselves also create larger social consequences. As women exercise their individual right to abortion they create effects that ripple through society. The same process is at work with regard to access to birth control.

The author makes much of the arbitrary line in the sand she’s drawn wherein she places high value on individual liberty for women to control their own bodies and timing of reproduction yet she devalues the individual choice of embryonic trait selection which leads me to question whether she stands for principle or outcome. If the principle of individual liberty is paramount, as we see with free speech cases where disagreeble speech is frequently defended, then we should expect support for individual exercise of reproductive freedom even when one may personally disagree with the choice made. If the outcome is of the highest importance, then we should see the jettisoning of principle when it is no longer convenient. I believe the author is arguing the latter position and this may come to be exploited by those who oppose her viewpoints on abortion, for if one jettisons principle when it is inconvenient to one’s immediate concerns then it becomes harder to argue on the basis of principle when one’s position is threatened.

I find it interesting to watch these early stumblings on the question of reproductive technologies and the shifting alliances that may result. Earlier I took a rudimentary stab at outline the shifting alliance in the post The Turning of the Tides. One of the most glaring examples of the conundrum reproductive technologies pose for dogmatic feminists was laid bare within this post, Feminist != Support for Reproductive Rights.

While the ideological contortions are interesting to watch what I find most amazing is the penchant for social engineering by fiat. The belief that legislation which restricts a couple’s reproductive choice will adequately address what the author see as a problem and that people shall willingly constrain their reproductive choices. Bush and Kennedy championed a law (NCLB) which mandated that all students shall meet proficiency standards in their educations. How’s that working out? Is the War on Drugs eliminating all drugs from society? Before abortion was widely legalized, did laws against abortion prevent abortions from taking place? Do Bio-Luddites really believe that prohibitions on advanced reproductive technologies will eliminate choice for parents? The most likely effect will be to drive such parents to underground providers or to exercise their choice overseas, in countries like China, where attitudes on this topic are quite different:

A survey of Chinese scientists working in the field of genetics suggests they overwhelmingly support eugenics to improve public health.

The theory of eugenics – which is considered highly controversial in the West – suggests that the human race can be improved by selective breeding. The survey, which was conducted in 1993 among 255 geneticists throughout China, was reported in the British magazine New Scientist. Almost unanimously – by 91% – the scientists said that couples who carried the same disease-causing genetic mutation should not be allowed to have children. More than three-quarters believed that governments should require pre-marital tests to detect carriers of hereditary disease. They also supported the routine genetic testing of job applicants by employers. There was also strong backing for the genetic testing of children to see if they are susceptible to problems such as alcoholism.

If the authors worried about a class divide developing between the “GenRich” and the rest of the population then the surest way to bring this about is to create a regulatory framework where only those with means can access the service by traveling overseas in order to have their embryos transfered. Does the author imagine that US Customs will maintain a pregnancy screening service for Americans arriving back in the country, or that abortions will be forced on people who have been found to have used reproductive technologies, or that the children, once born, will be born with a Scarlett Letter emblazoned on their foreheads announcing to the world that they are “GenRich.”

Is the public as stupid as you think?

The other day, I mentioned a silly article in Nature Review Genetics complaining about the state of science journalism. The author seems to think that journalists are promoting “genetic determinism”, so let’s consider her evidence. The study she cites asked focus groups, “What does ‘a gene for heart disease’ mean?”, and coded their answers as “No risk”, “Absolutely determined”, or “Heightened risk”.

Now, before I tell you the results, here’s Condit’s interpretation of them: “Most people interpret statements of genetic causation in a highly deterministic fashion…Avoiding deterministic implications is consequently challenging.” So most people must have fallen into the “absolutely determined” category, right?

Here are the results:

No risk: 15%
Absolutely determined: 28%
Heightened risk: 56%

So the majority of the individuals got it right! In a world where 1 in 5 Americans believes the sun revolves around the Earth, that is absolutely astonishing, and perhaps a sign that the public is getting the message about genetics on its own. Of course, if that were the case, there would be no need for scientific communications experts like Dr. Condit…

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Cornell Editorial on Affirmative Action

Tim Krueger writing in the Cornell Daily Sun focuses on the higher admissions hurdles that Asian applicants to Cornell face and advocates that something be done about this injustice. By his back of the envelope calculations:

In the interest of space I’ll put the calculations on The Sun website instead of here. The figure I arrive at suggests that Cornell would have around 258 more domestic Asian/Pacific Islander undergrads in the absence of racial considerations in our admissions process.

He began his editorial with some promise by making note of the distorting effect of racial preferences, but he just couldn’t commit to the consequences of a merit system and falls back on tinkering with racial gerrymandering but unlike most of the advocates of Affirmative Action, with their stale, run of the mill, pronouncements, Mr. Krueger offers us a grand vision:

Noting that Cornell is a truly global institution, can the geographic limits of its responsibility to educate defensibly be established within the U.S.? I would argue not. And if Cornell has a global responsibility, any affirmative action policy rooted in this second “instrumental” argument would be expected to aim for a student body that’s a microcosm of global, not simply U.S., demographics.

Seeing as a) Asian Americans have indeed been subject to extreme experiences, even within the past century (deportation, concentration camps, reproductive manipulation, ghettoization), and b) even aggregating the domestic and international Asian populations at Cornell only gives us less than half of 42 percent – the percentage of the world projected to be Asian by 2011 – I find it hard to justify Cornell’s policies towards prospective Asian students.

So let’s cut to the chase, what does he propose be done about the plight of Asians not being admitted on merit? Implement a merit-based admissions system? Nope:

Does this mean Cornell should end racial considerations in admissions? Of course not – the rest of Berkeley’s demographic story boasts a black population of only 3.8 percent. . . . . Either of the above constructions of affirmative action justifies its application towards blacks, Latinos and Native Americans. The loosening of admissions standards for Asians should instead come at the expense of white applicants. This would strengthen the academic caliber of our student body while furthering our commitment to diversity; the combination should not be taken lightly.

I eagerly await news of Mr. Krueger’s withdrawal from Cornell in order to make room for the meritorious Asian or the Diversity-embodying Black, Hispanic or Native American. Come on Mr. Krueger, do your part.

Behavioral genetics getting molecular

This week’s Science has a news article detailing the strides being made in dog genetics since the publication of the dog genome. Dogs should be one of the best model organisms for studying the genetics of behavior– artificial selection on behavioral traits over the centuries should allow the relevant genes to be isolated with much more ease than normal. It will be an interesting few years:

The rapid progress in dog genetics is prompting some researchers to get back to studies that motivated a canine genome project in the first place: tracking down genes associated with behavioral traits. Neff has teamed up with Illumina Inc. in San Diego, California, to use a microarray to look for SNPs associated with “pointing.” About 40 breeds point–freezing and lifting a paw in the direction of a rabbit or other quarry. “I finally feel we have a chance to understand the behavior,” says Neff, who worked with Rine in the 1990s.

At the Norwegian School of Veterinary Science in Oslo, Frode Lingaas is taking a similar tack in looking into “cocker rage.” In this syndrome, generally amiable pets turn on their owners, exhibiting frighteningly aggressive behavior. He and his European colleagues assess the dogs’ personalities through interviews with the owners and questionnaires. Several hundred samples will come from English cocker spaniels, but a few will come from English springer spaniels, which are also prone to this mental disorder. These dogs should get the researchers close to the gene, and a comparison with golden retrievers, which can also be four-legged Jeckylls and Hydes, should get them within striking distance.

Liberals and low IQ believe in astrology more

The Inducivist is always digging into the GSS and coming back with interesting stuff. For example, he reports:
Percent who believe astrology is very or sort of scientific
43.3% Extremely liberal
32.2% Liberal
31.4% Slightly liberal
25.9% Moderate
25.9% Slightly conservative
26.1% Conservative
25.0% Extremely conservative

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