That's all I can muster.
Francis S. Collins to be appointed to head National Institutes of Health
by behemot 21 Replies latest jw friends
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BurnTheShips
The more non-coding DNA gets studied, the more of it is found to have a function. "Junk DNA" may well turn out to be obsolete when all the data is in.
BTS
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BurnTheShips
The following items crossed my inbox today, for those that are interested.
http://www.genomeweb.com//node/920519?emc=el&m=444359&l=2&v=2b23e2533e
What They Don't Like About You
July 17, 2009
Josh Witten at the Rugbyologist goes through the list he calls "10 Things PZ Myers Hates About You, Francis Collins" to determine if it has merit. First, Witten says, yes, Collins was part of the "biggest of BIG SCIENCE" as that's what NHGRI required, that being a "gene jockey" isn't a bad thing as Collins has been looking for the cause of human disease, and that having a biomedical focus is actually necessary for the NIH. Then Witten adds some of the other complaints — that Collins thinks humans are not evolving or that he thinks that so-called "junk DNA" is functional — may stem from misinterpreted statements. "Collins is definitely not perfect, but we could do, and have done, a lot worse," he says.
On a related note, Nature News reports that Collins will step down from his position at BioLogos, the foundation that aims to reconcile faith and science, before taking the helm at NIH. "Discussion about the foundation and his involvement with it could readily become a distraction from the business of running the NIH," says Harold Varmus, a member of the President's Council of Advisors on Science and Technology and past NIH director.
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BurnTheShips
Here is the other one, Dr. Collins may not be wrong regarding "junk DNA"
http://www.edge.org/3rd_culture/selfish06/selfish06_index.html
Some species have enormous genomes and produce no more proteins than others. The idea was beginning to be abroad in the late '60s, early '70s, that this might just be junk — that an awful lot of the DNA in the genome might stand for nothing; it might have no purpose.
And in a lecture at MIT in 1972 Crick said, What is all this DNA for? Is it junk or is it an evolutionary reserve? Still thinking, though, in terms of what's it for in terms of the organism. And in 1978 Tom Cavalier-Smith suggested that perhaps it's there to support the rest of the DNA, to place the genes in the right parts of the nucleus, to spread the genes out, and things like that. And that's an idea that I'll come back to in a minute, because it has a second history. But it's in 1980 that the idea of selfish DNA is coined in two papers in Nature by Doolittle and Sapienza and Orgel and Crick, arguing that perhaps most of, or some of this DNA is simply selfish DNA, that it's there because it's good at getting itself there. It's good at replicating itself, it's good at copying itself. They were quite explicit, they said this idea is not new, it's sketched briefly but clearly by Dawkins in his book The Selfish Gene. There's no question that this originated as an idea with Richard. By the way, — in 1982 the first computer virus was created, the Elk Cloner virus — and that of course has an interesting parallel with the argument that I'm talking about.
Just to illustrate what we're talking about — genome size bears very little relation to the complexity of an organism; two creatures like a puffer fish and a zebra fish have very different size genomes, even though they look very similar.
From this end of the telescope, human beings look like they have quite a big genome, but if you turn the telescope around and look from another direction, the human genome looks rather a small one, compared with that of grasshoppers, which is at least three times as large, or deep-sea shrimps, which have ten times as much DNA as us.
Salamanders get even bigger, and the king of the genomes in the animal kingdom at least, is the marbled lung fish. Some people say amoebae have larger genomes at 500 gigabases, but they're almost certainly polyploid, as are lilies, which also have very big genomes. This is a perfectly ordinary diploid genome in the marbled lungfish, and it has as much digital information in it as about ten British Museum reading rooms.
So what's it all for? Well, it does appear that Richard was partly wrong. It does appear that the genome size is under selection, and that it's linked to the size of the cell. The bigger the nucleus the bigger the cell, it's a pretty good rule. And there's all sorts of evidence to suggest that animals are optimizing the size of their genomes, so parasites often minimize the amount of junk in their genomes in order to shrink themselves.
Malaria parasites have very little junk in their genomes, and very small cells. At the other extreme, ciliates have very large cells, and they achieve this with small genomes by making a huge macronucleus in which they put sort of working copies of all their genes in multiple numbers. They are an exception that proves the rules; they have a small genome but a large cell but only because they make a special sort of working nucleus that's a whole lot bigger.
And high-metabolism animals, like bats, and birds, have got rid of quite a lot of the junk in their genome, in order to be able, it appears, to have small blood cells with larger surface areas. A lesser horseshoe bat like this has a genome less than two gigabases, compared with three gigabases for us. Why the lungfish, the marble lungfish, has such a gigantic genome is not clear, but it does look like it may be something to do with having very big cells, in order to be able to store glycogen when it estivates during a drought, when it disappears into the mud and lives there for six months off its glycogen reserves. That's a possibility. But one of the strongest pieces of evidence that genome size is not — that it's not possible simply to expand your genome at length by letting parasites run riot is the ALU sequence, which is one of the commonest sequences in our genomes, which has appeared in the last 30 or 40 million years. Mice don't have it, but our genome is not bigger than mice. In other words it's come at the expense of another sequence, rather than added to it.
Just in passing, it does seem that big genomes go with small brains. This is particularly true in amphibia, where — in frogs and salamanders, the larger the genome the smaller the brain. A frog has about five gigabytes and a comparably large brain; a salamander has about 30 gigabytes and a smaller brain, and a mudpuppy has an 85- gigabase — sorry, I keep saying byte, I mean base — gigabase genome, and has an extremely small brain. Human beings luckily have larger brains than frogs. There are two reasons for this: the bigger your genome the slower you are at duplicating yourselves, so the harder it is to grow a big brain by multiplying cells. And also it's harder to fit the same number of neurons in your head if neuron bodies are bigger.
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leavingwt
Francis Collins and the God of the Gaps
Collins’s religious views may nevertheless be of some interest. The primary argument in his book The Language of God is what he calls the Moral Law (his capitalization). In Collins’s view, morality could not have evolved; therefore God exists. Specifically, Collins argues that morality can be found only among humans. The moral code transcends culture, he says, and therefore must be inborn. He notes that humans are often altruistic, by which he means truly altruistic in the sense of never expecting return on their altruistic investment. He briefly notes the arguments of sociobiologists to the effect that altruism can provide indirect benefit to the altruist and uses infanticide among monkeys to demonstrate that monkeys are not altruistic. He observes that worker ants are altruistic (maybe that should have been in quotation marks) because they have the same genes as the queen but dismisses the possibility that altruism among humans could have a genetic basis.
Now Collins may be right, but telling us that monkeys commit infanticide and neglecting to tell us that humans also commit infanticide is cherry-picking data in the worst way.
In short, the case that altruism or morality could have evolved is strong, and Collins makes no serious effort to refute it. He goes on to tell us that the “Moral Law shone its bright white light into the recesses of [his] childish atheism” and concludes, with no logical or convincing argument, that his God must be a theist god as opposed to a deist god. Collins drew his conclusions, according to his own testimony, after having read Mere Christianity, by C. S. Lewis, when he was 27.
In a subsequent chapter, Collins describes the joy he got from discovering something not previously known, from discovering a little bit of truth. He longs, however, for a greater Truth and conflates the presumed existence of that Truth with “something much grander than ourselves.” He presents no real evidence for the existence of such a Truth, but at least he doesn’t like Freud.
http://pandasthumb.org/archives/2009/07/francis-collins-3.html
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leavingwt
Sam Harris weighs in. . .
Science Is in the Details
There is an epidemic of scientific ignorance in the United States. This isn’t surprising, as very few scientific truths are self-evident, and many are counterintuitive. It is by no means obvious that empty space has structure or that we share a common ancestor with both the housefly and the banana. It can be difficult to think like a scientist. But few things make thinking like a scientist more difficult than religion.
Dr. Collins has written that science makes belief in God “intensely plausible” — the Big Bang, the fine-tuning of nature’s constants, the emergence of complex life, the effectiveness of mathematics, all suggest the existence of a “loving, logical and consistent” God.
But when challenged with alternative accounts of these phenomena — or with evidence that suggests that God might be unloving, illogical, inconsistent or, indeed, absent — Dr. Collins will say that God stands outside of Nature, and thus science cannot address the question of his existence at all.
Similarly, Dr. Collins insists that our moral intuitions attest to God’s existence, to his perfectly moral character and to his desire to have fellowship with every member of our species. But when our moral intuitions recoil at the casual destruction of innocents by, say, a tidal wave or earthquake, Dr. Collins assures us that our time-bound notions of good and evil can’t be trusted and that God’s will is a mystery.
Most scientists who study the human mind are convinced that minds are the products of brains, and brains are the products of evolution. Dr. Collins takes a different approach: he insists that at some moment in the development of our species God inserted crucial components — including an immortal soul, free will, the moral law, spiritual hunger, genuine altruism, etc.
As someone who believes that our understanding of human nature can be derived from neuroscience, psychology, cognitive science and behavioral economics, among others, I am troubled by Dr. Collins’s line of thinking. I also believe it would seriously undercut fields like neuroscience and our growing understanding of the human mind. If we must look to religion to explain our moral sense, what should we make of the deficits of moral reasoning associated with conditions like frontal lobe syndrome and psychopathy? Are these disorders best addressed by theology?
Dr. Collins has written that “science offers no answers to the most pressing questions of human existence” and that “the claims of atheistic materialism must be steadfastly resisted.”
One can only hope that these convictions will not affect his judgment at the institutes of health. After all, understanding human well-being at the level of the brain might very well offer some “answers to the most pressing questions of human existence” — questions like, Why do we suffer? Or, indeed, is it possible to love one’s neighbor as oneself? And wouldn’t any effort to explain human nature without reference to a soul, and to explain morality without reference to God, necessarily constitute “atheistic materialism”?
Francis Collins is an accomplished scientist and a man who is sincere in his beliefs. And that is precisely what makes me so uncomfortable about his nomination. Must we really entrust the future of biomedical research in the United States to a man who sincerely believes that a scientific understanding of human nature is impossible?
http://www.nytimes.com/2009/07/27/opinion/27harris.html?_r=1&pagewanted=all
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leavingwt
Today, from Sam Harris. . .
The Strange Case of Francis Collins
[Author’s Note: My recent op-ed in the New York Times, in which I questioned the appointment of Francis Collins as head of the NIH, inspired a fair amount of discussion in the media and on the Internet. As many of Collins’ defenders do not seem to be fully acquainted with his beliefs, or take it for granted that others won’t be, I have written a longer essay on the subject. While most of this material is new, a few passages were previously published.]
. . .
There are, of course, ethical implications to believing that human beings are the only species made in God’s image and vouchsafed with “immortal souls.” History shows us that concern about souls is a very poor guide to ethical behavior—that is, to actually mitigating the suffering of conscious creatures like ourselves. Concern about souls leads to concerns about undifferentiated cells in Petri dishes and to ethical qualms over embryonic stem cell research. Rather often, it leads to indifference to the suffering of animals believed not to possess souls but which can clearly suffer in ways that three-day old human embryos cannot. The use of apes in medical research, the exposure of whales and dolphins to military sonar —these are real ethical dilemmas, with real suffering at issue. Concern over human embryos smaller than the period at the end of this sentence—when, for years they have been the most promising door to medical breakthrough—is one of the many delusional products of religion, which has led to one of its many predictable failures of compassion. While Collins appears to support embryonic stem cell research, he does so after much (literal) soul-searching and under considerable theological duress. Everything he has said and written about the subject needlessly complicates an ethical question that is—if one is actually concerned about human and animal wellbeing—genuinely straightforward.
The Obama administration still has not removed the most important impediments to embryonic stem cell research—allowing funding only for work on stem cells derived from surplus embryos at fertility clinics. Such delicacy is a clear concession to the religious convictions of the American electorate. While Collins seems willing to go further and support research on embryos created through somatic cell nuclear transfer (SCNT), he is very far from being a voice of ethical clarity in this debate. For instance, he considers embryos created through SCNT to be distinct from those formed through the union of sperm and egg because the former are “not part of God’s plan to create a human individual” while “the latter is very much part of God’s plan, carried out through the millennia by our own species and many others” (Collins, 2006, p. 256) There is little to be gained in a serious discussion of bioethics by talking about “God’s plan.” (If such embryos were brought to term and became sentient and suffering human beings, would it be ethical to kill them and harvest their organs because they had been conceived apart from “God’s plan”?) While his stewardship of the NIH seems unlikely to impede our mincing progress on embryonic stem cell research, his appointment seems like another one of President Obama’s efforts to split difference between real science and real ethics on the one hand and religious superstition and taboo on the other.
Collins has written that “science offers no answers to the most pressing questions of human existence” and that “the claims of atheistic materialism must be steadfastly resisted.” One can only hope that these convictions will not affect his judgment at the NIH. Understanding human wellbeing at the level of the brain might very well offer some “answers to the most pressing questions of human existence”—questions like, Why do we suffer? How can we achieve the deepest forms of happiness? Or, indeed, is it possible to love one’s neighbor as oneself? And wouldn’t any effort to explain human nature without reference to a soul, and to explain morality without reference to God, constitute “atheistic materialism”? Must we really entrust the future of biomedical research in the United States to a man who believes that understanding ourselves through science is impossible, while our resurrection from death is inevitable?
http://www.reasonproject.org/archive/item/the_strange_case_of_francis_collins2/
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SixofNine
Now Collins may be right, but telling us that monkeys commit infanticide and neglecting to tell us that humans also commit infanticide is cherry-picking data in the worst way.
The irony being that it always seems to be a religous nut who commits infanticide; or at least when it's the mother doing the killing.