Archive for the ‘genetics’ category

For A Good Time On the ‘Tubes: David Dobbs, Sociable Genes edition

September 18, 2013

Dear all,

A little late — but it’s that time of the month again.  I’ll be doing my regular gig as one of the hosts of Virtually Speaking Science this evening at 6 EDT — just a little more than two hours from now.

My guest this time is David Dobbs, a wonderful science writer and (full disclosure) a good friend.  David has been focusing on neuroscience, genes and behavior for some time now.  Some of you may recall his big Atlantic feature on “the orchid hypothesis.”  There, David wrote about a fascinating line of scientific research that, among much else, showed how subtle and powerful the interactions of genes and environment can be.  Nature or nurture, that old debate, turns out (in this and in many other good works) to be a much richer, and much less dichotomized point of inquiry.

Jacopo_Bassano_-_Paradiso_terrestre_ca_1573

Flash forward to now.  David has been working on a book, The Orchid and the Dandelion, to be published by Crown in 2015, that extends the ideas and arguments of that magazine feature into a nuanced (and very tricky to write) account of how scientists are now trying to piece together the gene-to-behavior chain.  Some of that work led to the essay he just published at one of the delightful new web-based venues for serious, long-form public intellection, The Pacific Standard.  In that piece, “The Social Life Of Genes,” David writes about fascinating work on the way experience affects gene expression — which both takes the nature-nurture interaction to new, much more ephemeral time scales (itself a delightful shocker, at least to me) and points to the way the extraordinary advances in genetic and genomic research have reached a peculiar moment.  We know vastly more than we ever have before about the informational content of life.  We have tools that allow us to produce intimate moments in the daily life of genes and attendant molecules.  But that knowledge has gone just far enough to demonstrate how much more complex, intricate and so far ill-deciphered the genetic view of life remains.  We know more — and yet that knowledge leaves us much less certain about how a lot of biology works than we thought we understood a decade ago.

Which, of course, is just great.  (Physicists would kill for such wide open spaces!)  We live in interesting times — which, as I hope this conversation will demonstrate, is not always an accursed thing.

Tune in:  audio and later podcast here.

Also — do check out David’s website. Lots of good stuff there, but I’d draw the attention of any writers (or devoted readers) to David’s links to good work, and to his own  and others’ fine analyses of writing craft.

Image:  Jacopo Bassano, Earthly Paradisec. 1573

With Apologies to …

July 16, 2008

….Brad Delong (and to you readers, for whom this post was promised yesterday)…

UPDATE: Arrrgh. More apologies to all here. Brain bubbles affected my attribution of small pox vaccination to Jonas Salk, who, of course, invented the first effective polio vaccine. Edward Jenner performed the first smallpox vaccinations with a cowpox preparation in 1796. I conflated the two in my head as I have been thinking about the fact the difficulties faced in eradicating polio, compared with the success of the anti small pox campaign — which in fact formed the prompt for this post on the latest reported polio case in Pakistan. I regret the error.

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Why oh why can’t we have a David Brooks-free press corps, at least when it comes to bloviating about science?

In his most recent column, Brooks writes (under the pretentious and meaning-free headline, “The Luxurious Growth”) that the research community has grown “more modest about what we are close to knowing and achieving.”

That is, Brooks is once again channeling what “science” thinks — and he’s wrong, of course.

Headline writers may have made the kinds of claims he decries, that genetics would soon explain all of human behavior, but I can’t recall any scientist involved in, say, the genetics of alcoholism, claiming a single gene-behavior connection. Instead, fifteen seconds on Google turns up lots of statements like this.

Alcoholism is a complex, genetically influenced disorder. Multiple phenotypes – measurable and/or observable traits or behavior – contribute to the risk of developing alcoholism, particularly disinhibition, alcohol metabolizing patterns, and a low level of response (LR) to alcohol.

In other words: scientists have known as they do their research that individual studies of particular measurable and or observable phenomena will not produce a synoptic view of any complex behavior. Brooks knows this too. After all, with a magisterial air of explaining the hard truths to resistant materialists, he writes that

It’s now clear that one gene almost never leads to one trait. Instead, a specific trait may be the result of the interplay of hundreds of different genes interacting with an infinitude of environmental factors. must know this too — I can’t believe he’s that bloody ignorant, though perhaps I’m just too much of a polyanna here.

Again — this is a revelation only to those who haven’t been paying attention for years. And I do think that Brooks knows that as well. But if he does, that means he has an ulterior motive for claiming that once arrogant science has learned humility — and he does, the usual one that data-averse ideologues acquire: nasty scientists who seek material explanations are evil:

Starting in the late 19th century, eugenicists used primitive ideas about genetics to try to re-engineer the human race. In the 20th century, communists used primitive ideas about “scientific materialism” to try to re-engineer a New Soviet Man.

And Jonas Salk, that commie, used his “primitive ideas” to invent a smallpox polio vaccine, the key step in what has become the first ever may yet, I hope, become the second eradication of a human viral pathogen….and so on; this is an old and stupid back and forth.

Brooks wants to say that there are other sources of insight into the human condition — that “novels and history can still produce insights into human behavior that science can’t match.”

I’m not sure what he means by “match,” in this case. I suppose we don’t need science to say that happy families are all alike (you sure about that, Leo?) or that England’s Catholic King James II fell not due simply to his religion but because of his political ineptitude. But such insights, no matter how valuable are of a different quality, a different explanatory timber, than that which has investigated, for example, something as material and as essential to the human condition as the evolution of tool use.

But again — I fear it gives Brooks too much credit to engage the debate at this level. His goal is not to examine honestly the power and limits of scientific inquiry into human nature. The goal is to devalue the enterprise to the point that inconvenient facts can be ignored. Brooks gives the game away about half way through the piece. He writes that

There is the fuzziness of the words we use to describe ourselves. We talk about depression, anxiety and happiness, but it’s not clear how the words that we use to describe what we feel correspond to biological processes. It could be that we use one word, depression, to describe many different things, or perhaps depression is merely a symptom of deeper processes that we’re not aware of. In the current issue of Nature, there is an essay about the arguments between geneticists and neuroscientists as they try to figure out exactly what it is that they are talking about.

Brooks takes as evidence of ignorance the fact that different disciplines argue about terms. By that token, as of 1900, the state of play on the nature of matter would have led us to conclude the issue was intractable. Chemists had used the concept of atoms as real material objects to enormous theoretical and practical advantage since the days of Dalton and Berzelius — that is for a century or so.

Histories written from a physicists point of view, by contrast, commonly date the confirmation of the reality of atoms from Einstein’s 1905 papers on molecular dimensions and on Brownian motion. So — I guess for a century all those chemists had no idea what they are talking about.

In fact, of course, there are valuable, vital working definitions of depression, and they are involved in the still imperfect, but real body of knowledge that identifies clinical depression as a material illness of the brain. That understanding is what permits interventions — chemical and surgical — that dramatically reduce human suffering in many cases. Cherry picking disciplinary debates may give the appearance of deep disagreement – but doing so, as Brooks does, is really just garden-variety intellectual dishonesty. Put it another way: acknowledging limits to knowledge is not the same thing as denying the power of the same body of knowledge up to that limit.

But, of course, that’s what Brooks needs to do if he is to make his real point:

This age of tremendous scientific achievement has underlined an ancient philosophic truth — that there are severe limits to what we know and can know; that the best political actions are incremental, respectful toward accumulated practice and more attuned to particular circumstances than universal laws.

Nice sleight of hand, eh? Brooks is back to his most comfortable role, masquerading as the honest broker, while anyone in hearing better hang on to his/her wallet. The con takes place in incremental steps. Limits to knowledge become “severe” — that is, forseeably unsurmountable. Sez who? Sez Mr. Brooks, of course. Trust him — he speaks so nicely and has a marvelous tan.

And then…we are supposed to pass over the lack of logical connection…that due to such scientific lacunae, it is a philisophical truth (no limits to knowledge for those emerging from the cave, eh?) that political incrementalism is best.

This is more than a logical idiocy. It is historical nonsense as well. Incrementalism is good sometimes — perhaps most of the time. But consider: It would have been respectful, of course, not to dismiss the loving succour of King George III, but John Adams, no incrementalist at the moment of truth, persuaded his compatriots otherwise. Humans have owned slaves since earliest human memory; surely, respect for accumulated practice makes the 14th amendment a travesty. Peculiar circumstances can be invoked to justify polygamy and child marriage — and yet it seems possible to object on a range of more abstract and universal grounds, and so on….

That is — Brooks wants to be able to pick and choose, based on criteria known only to him, what change meets some ill-defined criteria of respect and particularity. This is nothing more than a cartoon version of what some conservatives say conservatism is about (though the last few years might give an honest man pause about the incompatibilty of this flavor of conservatism and power). Brooks would rather not have to defend it in detail (see revolution, American in the paragraph above), so instead he comes up with a parody of scientism and hopes that it sounds grand enough to deflect scrutiny.

As Delong says so often, why, oh why, can’t we do better than this codswallop.

That is all.

Image: Vincent van Gogh, “Sorrow,” 1882. Location: Wallsall Museum and Art Gallery, the Garman Ryan Collection. Source: Wikimedia Commons.

Breast cancer news, a lesson on genes and environment.

January 10, 2008

A day late, but I wanted to link to this post in Tara Parker-Pope’s Well Blog on nytimes.com. First — the study Tara highlights is important, adding nuance (and difficulty) for women who discover they have certain mutations tied to very high probabilities of getting breast (and ovarian) cancer who try to interpret that knowledge.

As Tara writes, mutations in genes BRCA1 and BRCA2 had been viewed as almost certain indicators of cancers to come. Now, a report by a team at the Memorial Sloan Kettering found that the risks seem both to be somewhat lower than previously thought, and — this is the crucial bit — to vary significantly depending on other factors in different subgroups of patients.

The low end of the scale they observed was around a 36% chance of getting cancer by age 70 — still bad, from where I sit — but clearly a significantly different risk profile than the almost pure genetic determinism of the bad gene = cancer view.

(By the way, this is exactly the stuff that Masha Gessen deals with eloquently and in depth in her forthcoming book, Blood Matters, which I highly recommend when it goes on sale in April.)

Beyond the news itself, there is an important idea lurking in the background:  in their report, the authors suggest that other, still-unknown genetic differences, underlie the differences in outcomes for the women they observed in their study.

That is: the genomic environment of surrounding the known cancer-implicated genes is what they believe shapes whether and when BRCA1 and 2 mutations lead to disease in a given patient

John Maynard Smith, one of the less publicly celebrated great biologists of the 20th century, emphasized the importance of this kind of finding  when I had the good fortune to interview him a few years ago.  He demanded that I understand that the environment for a gene begins with the chromosome on which it finds itself, and then broadens out to include the rest of the genome in which it lies, and then on out from there. What happens in the molecular environment of the gene is crucial, both in regulating the normal interaction between different genes and non-coding bits of DNA, or when some variation or derangement of normal function affects the action of any given gene.

That subtlety gets lost, often, when genetics hits the public square.  See, for example, Lucky Jim Watson genes-and-IQ skirmishes of late last year.  It’s easy for both researcher and reporter to fall into a kind of naive genetic determinism. One looks for the gene for some trait or disease; one reports that the gene for a given problem has been found — and then later, sometimes years later, it becomes clear that whatever is going cannot be that simple.

John Maynard Smith was very elderly when I met him, and had seen a lot, the entire modern history of genetics, from the double helix on. He knew better. It’s an important lesson to remember.

Image: Charles Alston, “Modern Medicine.” Location: Harlem Hospital. The work was commissioned by the US Government and is hence public domain. Source: Wikipedia Commons.

Missing details on a good book to come

December 20, 2007

I realize that in a post below, I forgot the crucial info.

Masha Gessen’s new book, Blood Matters, is coming in April from Harcourt. You can see the minimal catalogue copy here. I’ve just read it galleys, and it’s simply wonderful — a book that begins as memoir and then rides that story through to the complexity, human struggles with and implications of contemporary genetic medicine. This is what science writing can do when it is done right.

I’ll blog in more detail on the book nearer its pub date. Full disclosure: I have never met Gessen, nor have I read any of her other work, but she and I share both a publisher and an editor.