The marines learn the lessons of Abu Ghraib

In the face of war crimes that cannot be denied, the marines are now making the right moves:

Top Marine Visits Iraq as Probe of Deaths Widens

The commandant of the Marine Corps flew to Iraq to address his troops yesterday, and members of the Senate Armed Services Committee were briefed on allegations that Marines had purposely killed as many as two dozen Iraqi civilians in November...

Would the marines have pursued this if not for the TIME magazine article? I don't know, but they seem to be learning the lessons of Abu Ghraib. Instead of denial, they are preparing their response.

Modern HIV is 75 years old

Chimps seem to do fine carrying SIV, so presumably they've been infected for millenia - or longer. It now appears human infection is about 75 years old:

BBC NEWS | Health | HIV origin 'found in wild chimps'

The origin of HIV has been found in wild chimpanzees living in southern Cameroon, researchers report.

A virus called SIVcpz (Simian Immunodeficiency Virus from chimps) was thought to be the source, but had only been found in a few captive animals.

Now, an international team of scientists has identified a natural reservoir of SIVcpz in animals living in the wild.

It is thought that people hunting chimpanzees first contracted the virus - and that cases were first seen in Kinshasa, in the Democratic Republic of Congo - the nearest urban area - in 1930.

Humans may have contracted SIV before, but it never made the transition into an epidemic -- the victims would have died without passing on the disease. In 1930 it began the long ascent to its current pandemic status.

I was in medical school when HTLV-III was identified, I grew up in the pre-AIDS era. Things were different then.

The return of estrogen?

Some neuroscientists believe the female brain does badly off estrogen, and moves from better-than-male to worse-off following menopause.

Controversial? A bit.

So the idea persists is that estrogen-like drugs may have a role in Alzheimer's prophylaxis in women.

I thought this idea bit the dust two years ago, but apparently it's still around. Undoubtedly pharmas want to split off the alleged neurprotective effects of estrogen from its effects on breast tissue.

How to dismantle a democracy

Intelligence Czar Can Waive SEC Rules

The Bushies are writing the 21st century book on how to dismantle a democracy.

Why are we so different from one another?

It is the casual question at the end of this story that caught my attention (emphases mine). The story itself is quite remarkable. Once upon a time I was taught "one gene, one protein". That turned out to be untrue, though a useful initial simplification. The relation between genes and proteins (the builders) is many to many, not many to one or one to one. Later I was taught that nuclear DNA was the fundamental basis of heredity. Then we learned that mitochondria had their own DNA and that prions could carry encoded protein altering directions without DNA. Until today most of us thought that animal heredity worked through DNA and histone imprinting alone. Now that may not be quite true either...

BBC NEWS | Science/Nature | Spotty mice flout genetics laws [jf, aka: RNA directed paramutation in mice]

... Researchers found that mice can pass on traits to their offspring even if the gene behind those traits is absent.

The scientists suggest RNA, a chemical cousin of DNA, passes on the characteristic - in this experiment, a spotty tail - to later generations...

... They found the mutant Kit gene produces large amounts of messenger RNA molecules (a type of RNA which acts as a template for the creation of proteins) which accumulate in the sperm of these mice.

The scientists believe the RNA molecules pass from the sperm into the egg, and they "silence" the Kit gene activity in the offspring - even those who do not inherit a copy of the mutant gene. Silencing the activity in this gene leads to a spotted tail...

...The phenomenon whereby the characteristic of a gene is "remembered" and seen in later generations, even if that particular version of the gene is no longer present, is called paramutation.

It has previously been identified in plants, but this is the first time it has been shown in animals together with a proposed mechanism - if the explanation is confirmed in future experiments...

Could transfer of RNA in sperm explain other so-called epigenetic phenomena as well?

... "A particularly intriguing possibility," he writes, "is that such RNAs regulate other non-genetic modes of inheritance, such as metabolism or behavioural imprinting."...

... "This brings valuable information about modification of our genome," said Minoo Rassoulzadegan, "and perhaps this research may eventually help us to understand why we are all so different from each other."

Did you know that biologists are quite puzzled about why we humans, who seem so similar at the DNA level, are so different in practice? I'd thought that research in the control of gene expression suggested that tiny changes in DNA control could produce large changes in protein expression. It appears the question is not so settled.

Biology reminds me quite a bit of physics. When I was a child we had protons, neutrons, photons and electrons (at least in popular science books for children). Shortly thereafter there were bazillions of particles. A simple story became rather complex. So goes biology ...

US nursing gets it between the eyes

When rural areas had trouble recruiting physicians, economists would predict that benefits and salaries would rise. Instead visa rules were waived and foreign physicians filled the gaps for the existing wages. This is one of several reasons that American medical school graduates avoid primary care.

That was a love tap, however, compared to the shot aimed at US nurses. The Senate immigration legislation removes the limit on the number of foreign nurses who can immigrate to the US. Completely removes it.

The gates opened a while back, with about 50,000 nursing visas being used from 2005 to 2007. That's a lot of nurses. With the new rules the number is expected to increase by about 10% a year, reaching up to 100,000 nurses/year by 2014.

It would take very good data to persuade me that this kind of influx is not going to stabilize or reduce nursing compensation in the US. In the absence of this resource US payors would have had to increase benefits and compensation, and improve work conditions and career development, to fill empty slots. That costs money, so healthcare costs would rise. With this foreign resource, the US gets a supply of nurses with no training costs willing to work for lower wages.

A net gain for healthcare and for the US economy - sure. Great news for the immigrants and probably for their families. Good news for the hospitals that paid off the Senators through campaign contributions and PAC contributions. Bad news for their host countries and awful news for any US grad considering a career in nursing.

Tell me again how immigration does not impact workers in the US? Let the debate continue.

An exceptional survivor: Cousin May

My mother's cousin May died this weekend in Manchester England, she was a bit over 90. I'd never met her. Around 25 my mother went adventuring and landed in Montreal, where she ended up staying. England was another planet for us.

When I asked my mother what May was like as a young person, I learned a bit of history.

May was born about 1916, one of five children in a "working class" neighborhood (slum I suspect) in industrial Manchester. Her mother was my maternal grandfather's eldest sister. May's father died young, and her mother raised the children in a Manchester pub she came to own. It sounds like a rough life, but the children were known for their genteel diction. A bit of a puzzle.

As happened fairly often in the 1930s slums of Manchester, May developed tuberculosis. She spent the years from 17 to 21 in a Sanatorium (aka Sanitorium) -- I don't know which one. Sanitoria were common then, Davos in Switzerland started that way. Tuberculosis struck rich and poor alike, though certainly more of the latter. Somewhere along the way one of her diseased lungs was removed.

She died - 70 years later. I am sure that none of her caretakers ever imagined, in their wildest dreams, that their patient would outlive them, outlive the sanitoria, outlive perhaps everyone who entered there. I don't know how the rest of May's life went, I'm sure it was tough enough. All the same, she had her own victory.

The part that puzzles me though -- who paid for her stay? I've read that Sanitoria were not generally available to the poor of Manchester. Did her siblings have money? Did her mother sell the pub? That's a bit of a mystery ...

A wonderful lesson in evolution and survival: The Dicynodonts

Some of the best blogs are written by professionals that are between jobs, often graduate students in transition. Tetrapod Zoology is one of those blogs. This is an excerpt from a fascinating story ... a world about which I know little ...

Darren Naish: Tetrapod Zoology: Dicynodonts that didn’t die: late-surviving non-mammalian synapsids I

... Sad to say, during the Late Triassic, dicynodonts dwindled in diversity until by the Norian (the penultimate stage of the Late Triassic) they were down to just three genera, and all of these were close relatives within the clade Kannemeyeriiformes (King 1990, Maisch 2001). I always liked Richard Cowen’s suggestion that these last forms were ecologically peripheralised, endangered species that hung on to existence in remote ecosystems where life was harsh ... dwindling in numbers, and living in a world where big archosaurs were now controlling all the terrestrial ecosystems, those poor last dicynodonts gradually faded into oblivion, until they were but dust in the wind, dude. That was a Bill and Ted reference.

In June 1915 several fragmentary fossil bones were discovered near Hughenden in Queensland (Australia)... a 2003 reappraisal of the specimens by Tony Thulborn and Susan Turner showed that the bones could not belong to anything other than a dicynodont....

But here’s the big deal: the fossils are from the late Early Cretaceous, and thus something like 100 million years younger than the previously known youngest members of the group... So dicynodonts didn’t disappear in the Late Triassic as we’d always thought. They had in fact been sneakily surviving somewhere, and as Thulborn & Turner (2003) wrote, their persistence in Australia and absence from everywhere else suggests that ‘Australia’s tetrapod fauna may have been as distinctive and anachronistic in the Mesozoic as it is at the present day’ (p. 991)...

We mammals are but the shards of rich group of species that mostly died in the Triassic ...

This is why blogs are great, even though they are transient. Soon Darren will be too busy to put this kind of mini-article together.

Zolpidem and the nature of consciousness

The BBC has a fascinating report on non-responsive persons who become transiently partly responsive while taking the drug Zolpidem.

It's not completely surprising. Over the past few years it's become apparent even to laypersons that consciousness (whatever that is), and lack of consciousness, are not simple or binary states. A human can have a lot of intact nervous system and yet not be "conscious", conversely humans can be "conscious" and responsive with a lot of damaged tissue. (One of the reasons Ms. Schiavo's physicians were confident of her prognosis was that she was both non-conscious and had severe tissue damage.)

The theory is that this medication can allow non-damaged parts of the brain to 'go online' and allow responsiveness, even in the absence of the normal mechanism of consciousness.

The story suggests that there are many grades and states of "consciousness" arising from interacting "islands" of neuronal subsystems, and that this and similar medications allows "islands" that are normally unable to interact, perhaps due to a physiologic suppression mechanism, to interact with each other and with the sensory and motor systems. Whether those interacting subsystems could ever produce a "person", and whether that would be the same "person" as the "original", is a matter for some thought. I would suspect that they may lack access to memory ...

[55 yo veterans of past "altered states of consciousness" can comment below ...]

The evolution of Christianity: a feature of the Da Vinci code

I've not read the famous novel and might never get to it, but something good has come of it. Theologians have been compelled by the book's back story to explain how Christian thought developed before 500 AD.

It's a fascinating tale. I'd like to read some of the wannabe gospels that didn't make it into the Book. Gnostic shmostic, what about Philip, Thomas, Mary, Didache and Hermas? I suspect the book's success will give those writings a platform.

I am left, however, as the author no doubt intended, with the impression that Dan Brown was perhaps trying to push an odd agenda as well as tell a fun story. Given the number of people who bought into the Left Behind narrative I'm sure there are millions that will believe just about anything ...

Minnesota - point!

Another point for Minnesota:

Crooked Timber� Incarceration Rates

... Maine and Minnesota had the lowest rates of incarceration (with 0.3 percent or less of their state residents incarcerate)d.

This really is a pretty decent state -- despite the Republican governor. We have a much larger urban population than Maine, so I'd say we come in first.

Ok. I need to say something positive once in a while! The rest of the article points out that the US puts more people in jail than Belarus or Russia. About four times as many people, per capita, as does Canada. Minnesota is inline with the civilized world. What the heck must life be like in those states that bring our average up to its current insane level?

The price of criticism: Science and the Bushies

Just another small example of the Bush culture of loyalty:

Uncertain Principles: Loose Lips Sink Research Grants:

... this year's talk by a program director from the Department of Energy raised the average blood pressure at our table by a good bit.

... she took pains to state several times that both Democrats and Republicans in Congress support science, in a tone that basically came across as chiding us for thinking otherwise. That was annoying by itself, but at the very end of the talk, she specifically warned against taking partisan positions, citing the letter supporting John Kerry that was signed by a couple dozen Nobel laureates as something that made it harder to keep science funding. She said that after that, when she met with administration officials about budget matters, she could see them thinking 'Damn scientists...'

I suspect this would be quite familiar to any Soviet-era scientist. Criticism has a price. Just another brick in the wall ...

It's noteworthy because the Bush culture of loyalty has settled far down into our government. It's a spreading poison ...

Newton's editor? Emilie du Châtelet.

A biographer has made an extraordinary claim about a woman previously known (by a few) as Voltaire's lover...

Love and the Enlightenment | The woman behind the man | Economist.com:

EVERYONE, just about, has heard something about Voltaire, and most of it is flattering. Freethinker, dramatist, poet, scientist, economist, spy, politician and successful speculator to boot, he embodies the intellectual breakthrough of the Enlightenment...

... Almost nobody has heard of the woman with whom he shared most of his life, Emilie du Châtelet. But you can make a good case that she was a more rigorous thinker, a better writer, a more systematic scientist, a formidable mathematician, a wizard gambler, a more faithful lover and a much kinder and deeper person. And she did all this despite being born a woman in a society where female education was both scant and flimsy. Her mother feared that anything more academic than etiquette lessons would make her daughter unmarriageable.

David Bodanis's new biography of Emilie, Marquise du Châtelet, is a belated treatment of a startlingly neglected story...

... Born in 1706, Emilie had three pieces of great good fortune in her life. The first was to be born with a remarkable brain. Her greatest work was to translate the “Principia”, the path-breaking work on physics by the secretive Cambridge brainbox, Isaac Newton, who died when Emilie was 20. She did not just translate his writing from Latin to French; she also expressed Newton's obscure geometric proofs using the more accessible language of calculus. And she teased out of his convoluted web of theorems the crucial implications for the study of gravity and energy. That laid the foundation for the next century's discoveries in theoretical physics. The use of the square of the speed of light, c², in Einstein's most famous equation, E=mc² is directly traceable to her work.

Ok. That's not exactly a modest claim. If it's true there's one hell of a story that's been missed for far too long. We need to get this story into In Our Times, and start rewriting those history of science texts ...

How many individual dinosaurs were there?

My son Ben and I visited the Minnesota science museum last night. An interactive display featured children's questions, including one I've almost wondered about -- how many individual dinosaurs were there?

The guest paleontologist took a rather wild statistical swag at it. Sad to say, I can't recall whether he said "40 quadrillion" or 40,000 quadrillion. I think it was the former. In any case he was far braver than the Google responses, which decline to answer the far duller question of how many have been identified based on the fossil record. Cowardly wimps.

That's 40 million billion, or roughly the national debt in dollars of the United States in 2000. About 5 million dinosaurs for each human alive today. That's fecundity. It gives one a sense of how successful triceratops must have been, and how many wonders remain forever lost (barring a time machine).

Actually, the question I've wondered is how many individual Homo erectus (erecti?) there were to have generated as many fossils as we find ...

I'm surprised science and history books don't give us more numbers. You get a very different sense of American history when you realize how very few people lived in Boston. Just about everyone in town must have known Ben Franklin ...

Real ID: our National ID card

Time claims that our coming National ID card (Real ID) is no big thing:

TIME.com: The National ID Card That Isn't, Yet -- Page 1

...Most of the privacy rights — if there really are such things — vulnerable to a nationalized ID card have already been trampled under the wheels of increased security, more efficient law enforcement and better business long ago.

Actually, I think TIME is correct that our privacy is history with or without Real ID (it's a national ID card, let's not pretend otherwise). I do think a reliable and robust indentifier will move things along faster than they would otherwise, but probably only by a four to five years.

We should assume that anyone with money or power (but I repeat myself) will be able to know anything about us that they care to know. If you don't like that, don't vote Republican. If that's ok with you -- well, we'll see.

PS. I fully expect our government will have sold us out so comprehensively that the Real ID program will end up facilitating identity theft rather than alleviating it. What can I say? Don't vote Republican.