Archive for the ‘Gene follies’ category

History Matters (and so does the environoment) — Steven Pinker/Personal Genomics dept.

January 18, 2009

Steven Pinker has made something of a splash with his account of confronting his personal genome, published in the NY Times magazine last week.  The article is interesting, though Pinker’s hint of nervousness about just how much he wants to know of himself genetically gives it a slightly odd list to port.

There was also a problem, IMHO (humble, and without professional expertise, too) with the presentation of the article.  Though Pinker was careful to undermine from time to time what he recognized as one of the fascinations of personal genomics — that “the human mind is prone to essentialism — the intuition that living things house some hidden substance that gives them their form and determines their powers” — the piece still teetered on a kind of 1980s “We’ve discovered the gene for X!” hoopla.

Much of that impression was conveyed by the photos that accompanied the print version of the article, with headshots of Pinker captioned with the trait identified within his genome.  Partly, though, it derived from Pinker’s own ambivalence, as he acknowledged the pitfalls of essentialism in a genome in which so much of the information is not devoted to protein coding, and yet wrote sentences like this:

For some conditions, like Huntington’s disease, genetic determinism is simply correct: everyone with the defective gene who lives long enough will develop the condition.

This is true, of course, and yet…the genetic signature of Huntington’s disease involves the number of repeats of a short section of the genetic code, just three bases or genetic “letters,” associated with the Huntingtin gene.  There is a number of repeats below which someone is not at risk for the disease — less than 27 copies — and a number above which disease essentially always occurs — 39 repeats and up.  In the middle, the issue is more ambiguous, and a repeat total in that range may result in late onset of the disease, or even a progression to overt symptoms that is so slow that the affected individual dies of some unrelated cause before the production of the damaging form of the Huntingtin protein actually does enough harm to notice.

What governs the number of repeats is unclear; it is not, seemingly a matter of pure  inheritance.  Masha Gessen in her excellent Blood Matters tells the story of two brothers at risk for the Huntington gene.  One develops symptoms early, gets tested, and receives confirmation that he possesses the gene with sufficient repeats to account for his relatively early onset of the disease.  The other brother, who presumably inherited the same gene from the same parent, possesses an intermediate number, and may or may not end up with symptomatic Huntington’s at some later point in his life.

What does this all mean?  That even in cases where the overwhelming effect of heritable genes is obvious, where possession of a given form of genetic information directly correlates with a particular observable trait, there are processes involved in the replication and inheritance of that information that produce variation.

I am no biologist, so I’ll defer here to John Maynard Smith, with whom I had the good fortune to have a conversation the one time we met, a few years before he died.  He emphasized what I don’t think has seeped deeply enough into the popular understanding of modern genomics.  In his phrase, (from memory), the environment for a gene begins at the chromosome.

That is, the genes that actually code for a protein do not do their work or move from generation to generation in a vacuum.  Rather they exist in a physical environment that begins with its most immediate context — the DNA that exists surrounding coding regions — and the extends outward through the structure of DNA and other organic material that makes up the chromosome; the nucleus of a cell; the cell as a whole and so on and on and on. Things happen at each level of organization and between them that can affect what happens when the rubber hits the road and a protein gets made.

All of which to say is that even though Pinker certainly did not claim that genes are destiny in any crude way, his article still falls into a tradition that I do not think has fully caught up with the richness and the complexity of modern genetics and cell and organismic biology.

That said, the other matter that made my antennae twitch in Pinker’s article came in this paragraph:

Though the 20th century saw horrific genocides inspired by Nazi pseudoscience about genetics and race, it also saw horrific genocides inspired by Marxist pseudoscience about the malleability of human nature. The real threat to humanity comes from totalizing ideologies and the denial of human rights, rather than a curiosity about nature and nurture.

I agree with the last sentence (though I’d hardly say that it covered the sum of threats to humankind), but the claim that the genocides perpetrated by Marxist regimes are an example of blank-slate ideology gone very wrong is problematical on two levels.

First, it is simply wrong.  For example Stalin’s war on the Kulaks — well-off peasants/farmers — treated Kulak resistance to collectivization as a symptom of an inherant, non-malleable quality, the class identity of the offending farmers. Similarly, Mao’s campaign against landlords (and others) immediately after the 1949 victory of the Chinese Communists, identified class and or occupation as a kind of original sin from which there could be no return.  The same basic notion underlines the horrors inflicted on class or educational level by other regimes.

Of course, in China and the Soviet Union, exterminations justified by the identification of a human stain that needed to be eradicated to open the possibility of forging a new Communist humanity had roots that have nothing to do with a real commitment to either essentialism or a blank slate view of humanity — though at different stages of the process, both ideas were invoked.  Rather they were all about power and resistance.

But at the same time, any finer grained look at what happened in the state-massacres of the 20th century does not support the simple-minded notion that as much or more harm was done to human beings through a commitment to a false perfectability of humankind as as was done through a commitment to a false notion of ineradicable genetic defects in particular groups.  Essentialism was an integral part of both Nazi and Communist murders.

And that leads to my second objection to what I see as Pinker’s false equivalence of two evils.  It isn’t just that he admits no complexity to the history; it is that the moral argument he seems to be making is itself highly suspect.

The real question Pinker avoids here isn’t whether evil comes to the world down multiple avenues.  It is whether or not evil flows from a given cause, and if so, what can be done about it.

That dictators have used many justifications to treat other human beings as things rather than moral ends in themselves does not let you — or Pinker — off the hook on the specific issue of the misapplication of genetic ideas to divide humanity into those worth keeping and those it is permissable to destroy.

It is therefore also true that the pursuit of genetic knowledge, of that part of the human condition that is genuinely in ourselves, and not in our circumstances, needs to be concerned about the moral and ethical hazards raised by the research.

Of course, the field(s) are in fact acutely aware of this, as is Pinker himself, no doubt.  But that he dredged up the old shibboleth that the Commies did it as his first response to the anticipated objection against the spectre of genetic determinsm betrays to me a kind of weariness with the argument.

I can understand that too — plenty of heat and not much light has been poured on this argument often enough.  But it is still a bit of rhetorical sleight of hand, and it’s been popping up a bit in defenses of the new genomics.  And that can’t be a good thing.

Update:  I omitted thanks due to Abel Pharmboy and Janet Stemwedel, each of whom looked over sections of the post above to help preserve me from my own ignorance.  Any errors that remain are, of course, all mine.

Image:  Giotto, “The Massacre of the Innocents,” 1304-306

Yes, Virginia, People Said Stuff Before Teh Google: Barack Obama has always been smart edition

September 11, 2008

From Gene Expression via Sullivan, Barack Obama takes on genetic determinism and Charles Murray.

NPR
October 28, 1994
SHOW: All Things Considered (NPR 4:30 pm ET)

Charles Murray’s Political Expediency Denounced
BYLINE: BARACK OBAMA
SECTION: News; Domestic
LENGTH: 635 words

HIGHLIGHT: Commentator Barack Obama finds that Charles Murray, author of the controversial “The Bell Curve,” demonstrates not scientific expertise but spurious political motivation in his conclusions about race and IQ.

BARACK OBAMA, Commentator: Charles Murray is inviting American down a dangerous path.

NOAH ADAMS, Host: Civil rights lawyer, Barack Obama.

Mr. OBAMA: The idea that inferior genes account for the problems of the poor in general, and blacks in particular, isn’t new, of course. Racial supremacists have been using IQ tests to support their theories since the turn of the century. The arguments against such dubious science aren’t new either. Scientists have repeatedly told us that genes don’t vary much from one race to another, and psychologists have pointed out the role that language and other cultural barriers can play in depressing minority test scores, and no one disputes that children whose mothers smoke crack when they’re pregnant are going to have developmental problems.

Now, it shouldn’t take a genius to figure out that with early intervention such problems can be prevented. But Mr. Murray isn’t interested in prevention. He’s interested in pushing a very particular policy agenda, specifically, the elimination of affirmative action and welfare programs aimed at the poor. With one finger out to the political wind, Mr. Murray has apparently decided that white America is ready for a return to good old-fashioned racism so long as it’s artfully packaged and can admit for exceptions like Colin Powell. It’s easy to see the basis for Mr. Murray’s calculations. After watching their income stagnate or decline over the past decade, the majority of Americans are in an ugly mood and deeply resent any advantages, real or perceived, that minorities may enjoy.

I happen to think Mr. Murray’s wrong, not just in his estimation of black people, but in his estimation of the broader American public. But I do think Mr. Murray’s right about the growing distance between the races. The violence and despair of the inner city are real. So’s the problem of street crime. The longer we allow these problems to fester, the easier it becomes for white America to see all blacks as menacing and for black America to see all whites as racist. To close that gap, we’re going to have to do more than denounce Mr. Murray’s book. We’re going to have to take concrete and deliberate action. For blacks, that means taking greater responsibility for the state of our own communities. Too many of us use white racism as an excuse for self-defeating behavior. Too many of our young people think education is a white thing and that the values of hard work and discipline andself-respect are somehow outdated.

That being said, it’s time for all of us, and now I’m talking about the larger American community, to acknowledge that we’ve never even come close to providing equal opportunity to the majority of black children. Real opportunity would mean quality prenatal care for all women and well-funded and innovative public schools for all children. Real opportunity would mean a job at a living wage for everyone who was willing to work, jobs that can return some structure and dignity to people’s lives and give inner-city children something more than a basketball rim to shoot for. In the short run, such ladders of opportunity are going to cost more, not less, than either welfare or affirmative action. But, in the long run, our investment should payoff handsomely. That we fail to make this investment is just plain stupid. It’s not the result of an intellectual deficit. It’s theresult of a moral deficit.

ADAMS: Barack Obama is a civil rights lawyer and writer. He lives in Chicago.

Don’t Know Nothing ‘Bout Causality (or science): Washington Post Edition…

March 5, 2008

…Or why you can’t infer from one truly awful writer that all writers are dumb as a box of rocks.

By now, pretty much everyone in the blog reading world (or at least those I imagine are the readers of this blog) has heard of, and maybe even read Charlotte Allen’s unwitting (witless?) self parody (immolation?) in last Sunday’s Washington Post.

 

You can find all the responses you want with a quick google search — here are a couple that catch the zeitgeist pretty well. (For a post with links to a lot more see this one.)

So, with all that out there, what more to add? Two things, actually, or maybe two and a half.

First, this blog has gone on, perhaps to the point of exhaustion, about the importance of even very simple quantitative reasoning as both the starting point for thinking within the scientific world view — and just for making sense of the everyday world of experience.

Allen’s inability to do this reaffirms how important it is — not least for keeping yourself from looking like a true idiot in front of a national audience. Here’s the problem: one of the early “arguments” (sic) that Allen uses to suggest that “several of the supposed myths about female inferiority are true,” is that “Women really are worse drivers than men” according to a ten year old study out of Johns Hopkins.

Jake Young whaled on this one here, proving once again (take a memo certain Post editors!) that it really, really helps to read and understand a paper before you glom onto its abstract. But that critique, useful as it is, misses the simplest stupidity that Young (and her editors) commit.

Young writes that the study

revealed that women clocked 5.7 auto accidents per million miles driven, in contrast to men’s 5.1, even though men drive about 74 percent more miles a year than women.

Stop and think about that for a moment.

Now change the activity in question, and maybe turn the groups being distinguished into ones that have a little less political affect:

Say you have some working stiffs who play golf once a week on the weekends, and some biometrically equivalent trust fund golfers who get to hit the links three times a week. Next, breathlessly report that the weekend duffers “clock 5.7 bogies per 18 holes, in contrast to the trust funded group, who cut their bogie rate to 5.1, even though they play 300 percent more holes than poor folk.

D’oh.

From that you could conclude, I guess, that the evolutionary history that produces poor people also contains genes for lousy golf, and the reverse for the rich folk. Or you could propose that maybe hitting a few more balls might improve your game.

I don’t truly know if practice makes you a better driver. It seems a reasonable hypothesis — but you’d have to do some real research to say so with any confidence, of course.

I don’t even care if this fact has something to do with whatever the Johns Hopkins people observed.

Here’s the point: A couple of times over the last few years I’ve given a talk in which I’ve come out “against science literacy.” Allen’s article is an illustration of what I mean. She’s marginally literate in science-yness at least. She uses words like “genes” and botches that old chestnut about brain sizes and so on. But it doesn’t matter how many Tuesday Science Times section she reads. If she can’t think, it doesn’t matter how many words she knows. And thinking in this context means, at a minimum being able to understand the basics of the statistics she chooses to bandy.

So that’s one point. The other derives from the second half of my job title: I’m a science writer, and I have to say that there is one other quality of Allen’s piece that has not, I think, received all the ridicule it deserves. Boy, is that one badly written stretch of fish-wrap!

And here, I’m not talking about the global issues of logic, accuracy and argument, but the butt-ugly sentences and phrases she unleashed on who knows how many Sunday hangovers.

This post is long enough, so one example will do:

This female taste for first-person romantic nuttiness, spiced with a soupçon of soft-core porn, has made for centuries of bestsellers — including Samuel Richardson’s 1740 novel “Pamela,” in which a handsome young lord tries to seduce a virtuous serving maid for hundreds of pages and then proposes, as well as Erica Jong’s 1973 “Fear of Flying.”

That’s damn near unreadable. Look at that construction:”This female taste for first-person…blah, blah, blah…as well as Erica Jong’s 1973 Fear of Flying.”

Did Allen miss that fourth grade lesson on run-on sentences, in which vital topics of syntax, usage and style were covered, as well as her college expos class? (Sorry. Couldn’t help myself.)

I teach writing at the college and graduate level. My least articulate MIT freshman, fluent in Python, not in English, doesn’t commit crap like this.

Which leads to my last half point. The real damage here is to whatever is left of the Post’s editors’ reputation. Leave aside all the things that can (and have) been said about the vapidity or worse of every paragraph in the piece. How did anyone licensed to wield a red at the paper let uglification like this get through?

Just askin…

Images: James Gilray, engraver, “Physical air,-or-Britannia recover’d from a trance,” 1803. Source: Wikimedia Commons.

Gunnar A. Sjögren, “Saab Formula Junior,” illustration on page 23 of The SAAB Way – the first 35 years of SAAB cars, 1949-1984, 1984. Released for uses clearly not contradictory to Saab’s interests.” Source: Wikimedia Commons.

Horace Hutchinson, British Golf Links, 1897 J. S. Virtue & Co, London, page 9. Source: Wikimedia Commons.

John Leech, ” published in The Comic History of Rome, p. 88 c. 1850. Source: Wikimedia Commons.

NY Times on Watson’s African DNA

December 10, 2007

A bit meta perhaps, but there is a choice moment right at the top of today’s NYT Lede blogpiece on the “Lucky” Jim Watson’s DNA. It seems that 16 % of the former chancellor of Cold Spring Harbor’s genetic make-up comes from Africa. (UPDATE: Whatever that means — which is most likely not much. See this NYTimes article for examples of the shaky business of DNA roots research.)

That opens up the way for a pleasant little snark — but check out how the Lede folks tagged the piece:

“racism, science”

That’s spot on: the right thought in the right order.

Remember folks: when someone claims that they have the final, biological scientific proof that one group or another is inherently inferior, the default response is that the alleged science is bullshit. You might be wrong someday, but not so far, after a century and a half of attempts to spread this manure.

This is not to say that one couldn’t imagine such a claim turning out to be true. It’s just that the burden of proof rests with the claimant, and the standard of proof is really, really high. So far, no one has come close, as recently summarized here and, gleefully, here.