Science smarts is no guarantee of ethics

What else can you say about a geneticist who says that, when taking people's DNA samples, "informed consent" does NOT include telling them what specific lines of study the research is intended to be about, or even, if such information is given, necessarily limiting oneself to such lines of study.

“I was doing good science,” Therese Markow, now a professor at the University of California, San Diego, said in a telephone interview.

Maybe you were doing going science, in a narrow definition, but you were doing terrible ethics.

Is it any wonder that indigenous people around the world, including the Havasupai Indians mentioned in the story, don't trust various life scientists treading into their homelands?

And, it gets worse.

“Everyone wants to be open and transparent,” said Dr. David Karp, an associate professor of internal medicine at the University of Texas Southwestern Medical Center in Dallas, who has studied informed consent for DNA research. “The question is, how far do you have to go? Do you have to create some massive database of people’s wishes for their DNA specimens?”

Yes, you do!

And, while the question is foremost for and about indigenous peoples, I know full well that I don't want scientists with the ethical stances of Karp or Markow asking me to participate in DNA research, either.

And, the historical obtuseness doesn't just stop there. The exploitation of Henrietta Lack's DNA, without informing her or her family, some 50 years ago, just became public earlier this year.

Nature VIA nurutre

If you haven't kept up with recent research on heredity, population genetics or anything similar, the new Time has a GREAT story on epigenetics. Look it up and read it. Then throw away any simplistic ideas you have about "genetic inheritance."

If you are familiar with the basic idea of epigenetics, some of the newest findings may still surprise you, such as the rate of influence, the depth of influence, and more. Giraffes' necks aside, maybe Lamarck wasn't so wrong. Certainly, Stan Prusiner looks ever more right on prions, in light of stuff like this.

Obviously, we are nowhere near the end of discovering what epigentic findings mean. But, I think we can put paid to a few of the more outlandishly positivistic ideas of late 20th-century genetics.

Individualized medicines? Not likely to happen, and certainly not any time soon. You'd have to check at least some epigenetic as well as genetic factors. The price for that and an even higher level of individualizing the medications, would seem to pretty much rule that out.

Insurance, insurance, privacy, snooping, pre-existing conditions? All in a new realm now.

Drug testing? Some lawyer will raise an epigenetic argument at some point, whether it's legit or a red herring.

New info on the whys of the Y chromosome

The way it divides during cell division is a major factor in a number of sex-related syndromes and conditions.

Pinker – Nature-nurture debate over, but on MY terms!

Cognitive psychologist Steven Pinker has a long interview in the New York Times Magazine. An extended comment of his on page 2 jumped out at me:

The most prominent finding of behavioral genetics has been summarized by the psychologist Eric Turkheimer: “The nature-nurture debate is over. . . . All human behavioral traits are heritable.” By this he meant that a substantial fraction of the variation among individuals within a culture can be linked to variation in their genes. Whether you measure intelligence or personality, religiosity or political orientation, television watching or cigarette smoking, the outcome is the same. Identical twins (who share all their genes) are more similar than fraternal twins (who share half their genes that vary among people). Biological siblings (who share half those genes too) are more similar than adopted siblings (who share no more genes than do strangers). And identical twins separated at birth and raised in different adoptive homes (who share their genes but not their environments) are uncannily similar.

I have several problems with this.

First, knowing a bit about addictive behavior, I know that predisposition to cigarette smoking or alcoholic drinking does NOT have “substantial fraction” due to heritability.

Second, on behaviors like that, people like Pinker have never even made an effort to sort out familiar social influence.

Third, the “uncannily similar” comes off as being nothing more than a door-slamming phrase, i.e., “How can you be scientific if you question it”?

Well, with twins, I question it on several grounds.

First, identical twins themselves differ on when after fertilization the twinning event occurred:
• Do they have separate amniotic sacs and placentas?
• Share a sac but with different placentas?
• Share even placentas?

All of the above are of course environmental and not genetic effects, but Pinker conveniently ignores that.

Second, are identical twins “uncannily similar”? Not necessarily. Again, Pinker refers us to no research; he just throws out a statement to us and demands we accept it as gospel truth.

’Tis true, Pinker does qualify both his own comments, and those of Turkheimer, with some more general versions of what I just noted, on the next webpage. But, to me, the carts was enough before the horse, and emphasized enough more, to tell me where Pinker falls.

And, on page 5, Pinker shows we still have far to go in our understanding of the how and of the specific genes of genetic heritability.

Height is widely acknowledged, due to the information from statistical correlation, as being the single most heritable human trait. But, as Pinker notes, in 2007 a genomewide scan of nearly 16,000 people turned up a dozen height-related genes. However, these genes collectively accounted for just 2 percent of the height variation; plus, a person who had most of the genes was barely an inch taller, on average, than the general population.

And, I haven’t even gotten to Pinker’s biggest flop, or deliberate oversight.

It’s becoming ever more clear that what has to this point been called “junk DNA” isn’t; rather, some of it may code for frequency of expression of a gene, or control what genes interact together and when, etc. And, though still looked askance by some geneticists precisely for what it hints at, Stanley Prusiner’s work on prions, along with other research, shows that the heritability pathway may not be a one-way street at the cellular level.

Pinker starts to wrap up his take on the science of personal genomics with this:

At the same time, there is nothing like perusing your genetic data to drive home its limitations as a source of insight into yourself.

Too bad, he doesn’t realize, or refuses to accept, the limitations of genetic data today go far beyond that.

Are your mom and dad fighting inside your brain?

No, I’m not talking Freudian psychology. Nor gestalt, nor modern humanistic or self-actualization theories.

I’m talking about the latest theory on the heritability of mental illness.

Bernard Crespi and Christopher Badcock claim this:

An evolutionary tug of war between genes from the father’s sperm and the mother’s egg can, in effect, tip brain development in one of two ways. A strong bias toward the father pushes a developing brain along the autistic spectrum, toward a fascination with objects, patterns, mechanical systems, at the expense of social development. A bias toward the mother moves the growing brain along what the researchers call the psychotic spectrum, toward hypersensitivity to mood, their own and others’. This, according to the theory, increases a child’s risk of developing schizophrenia later on, as well as mood problems like bipolar disorder and depression.

My first thought? It may not be Freudianism, but it carries as much sexual stereotyping baggage as Freud did.

That said, the story notes that their work leans heavily on David Haig. A decade ago, he argued that pregnancy was in part a biological struggle for resources between the mother and unborn child, with natural selection favoring mothers who could limit the nutritional “vampirism” of fetusus and fathers whose offspring were greedy as they could be in the womb.

So, Crespi and Babcock aren’t totally barking up the wrong tree.

But, beyond their sexist-sounding take on mental illness, they seem to have a black-and-white view of genetic and epigenetic effects, too, which leads them into their one-axis view of all mental health conditions.

So, right now, if mom and dad are fighting inside you, they are more likely to be fighting inside your mind rather than in genetic or epigenetic coding in your brain.

Genes — the 1 percent ‘solution’

Individualized genetic medicine? Not so fast there

Yes, that’s right.

The “binary” bits alleged to be the centerpiece of human heredity, beloved of evolutionary biologists, population geneticists, and above all, capital-letter Evolutionary Psychologists, in reality are only the 1 percent solution of heritability. Elementary!

As to WHY the gene is only the “1 percent solution,” here’s the details of the latest research.

First, one strand of DNA may code for several different proteins. (In a process known as alternative splicing, a cell can select different combinations of exons to make different transcripts, the story notes.)

Second, said “gene” can combine with several other different genes, in different situations, to produce yet more different proteins.

Third, genes often encode for RNA, not proteins.

So, throw out the 1 gene = 1 protein idea.

Beyond that, “genes” may make up as little as 1 percent of DNA. “Junk DNA,” which more and more is proving itself to be anything but junk, makes up much of the remainder.

And, non-coding introns can lie in the middle of a stretch of DNA that makes up a single coding exon.

Also, some DNA, such as methyl caps, and histones, controls whether or not an exon can even be expressed, or how. They’re part of “epigenetic marks,” an area of DNA far more poorly understood than genes, as traditionally described. And, it gets fun with them:

When an embryo begins to develop, the epigenetic marks that have accumulated on both parents’ DNA are stripped away. The cells add a fresh set of epigenetic marks in the same pattern that its parents had when they were embryos.

This process turns out to be very delicate. If an embryo experiences certain kinds of stress, it may fail to lay down the right epigenetic marks.

But, that’s not always the case. Sometimes, epigenetic marks can be inherited.

And, in a bit of quasi-Lamarckianism (though not quite as much so as prions), it takes RNA to guide these markers to the right spot on DNA.

And, if that’s not enough, studies of micro-RNA and half a dozen other “non-basic RNAs” show even more the role RNA plays, no subservience to DNA involved, in cellular development

So, this all his tie-ins for our commercial, chemical modern world.

Very preliminary research indicates that chemicals that appear to cause “genetic” damage may well be causing epigenetic damage instead.

That, in turn, throw the whole biotech tout sheet of “the promise of genetic medicine” into a big kink.

And, we haven’t even talked about the amount of viral DNA stuck inside yours and mine.

Native Americans arrival dated earlier

“Clovis-only” theory of Indians gets death blow

A new review in Science strongly confirms that the first “Native Americans” got to the New World at least 16,000 years ago. It would seem that nobody but old-school crabbed anthropologists could still defend the Clovis theory

A new review published in the research journal Science contends that that the first Americans had their roots in southern Siberia, ventured across the Bering land bridge probably around 22,000 years ago, and migrated down into the Americas as early as 16,000 years ago.

In the paper, Ted Goebel of Texas A&M University and colleagues argue that the latter date is when an ice-free corridor in Canada opened and enabled the migration.

The new account is bolstered by genetic evidence and the discovery of new archaeological sites and more accurate dates for old sites, according to the researchers.

Genetic evidence, they wrote, points to a founding population of less than 5,000 people at the beginning of the second migration in Canada.

Moreover, they added, archaeological evidence suggests the Clovis culture may have been relative latecomers to the Americas or descendants of earlier Paleo-Indian populations represented at archaeological sites such as Monte Verde in Chile. That site is thought to have been occupied 14,600 years ago.

This squares with my belief that a multiple-migrations theory of population of the Americas is more likely than a one-movement theory, with the likely exception of Inuit/Aleut, and perhaps Na-Dene. Along with that, this would seem to favor “splitters” rather than “lumpers” among linguists.

Anybody who has looked carefully at the phenotypic variety among Native Americans, trying to focus on those with little admixture from Caucasian or African backgrounds, and the phenotypic variety among east Asians, probably has an instinctual leaning toward multiple migrations, too, IMO.

‘Ol’ Blue Eyes,’ you’ve got a short ancestry

Sinatra’s oldest granddaddy is only 10,000 years old at most, scientists say. That’s when some University of Copenhagen researchers say a mutation produced the first blue eyes.

“Originally, we all had brown eyes,” said one of the researchers, Hans Eiberg. But a mutation affecting a gene called OCA2 “resulted in the creation of a ‘switch’ which literally turned off the ability to produce brown eyes.”

Interesting, the switch is actually in an adjoining gene, but it influences OCA2.

This also shows, that aside from their clear biases, the Charles Murrays of the word who continue to be hard core “naturists” don’t know jack about what we’re learning about how genetics really works.