1. PZ says it's a "radial" tree, not a "radical" tree.
[Tree Source: David M. Hillis, Derrick Zwickl, and Robin Gutell, University of Texas]
Let's hope that Ecklund's unusually comprehensive assessment will help overturn the myth that scientists reject spirituality, or that science and religion are inherently incompatible.There may be a myth that all scientists reject spirituality. I really can't comment on that except to note that I have never, ever, heard anyone make this claim.
That myth persists among scientists and religious believers alike. In 2009 study by the Pew Research Center, 61% of Americans said that science poses no conflict with their own faith. Nonetheless, 55% of those same respondents said they view religion and science generally as "often in conflict." Evolution, for instance, has divided Americans since 1859, when Charles Darwin published "On the Origin of Species."
There is a better way, which will be demonstrated June 16 when leading scientists and a respected Christian minister engage in a free, public dialogue at the American Association for the Advancement of Science (AAAS).
1. I haven't mentioned the other illogical part of the argument; namely, that criticism of religion is "uncivil."
2. Please, let's not have any silly debate over whether Leshner is expressing a personal opinion or speaking for AAAS. Read his article and note how he identifies himself as author.
In spite of the advances, there have been some surprises and deepened mysteries. One of the greatest shocks was the finding that we have far fewer genes than scientists had assumed before they read out our genetic instructions. It takes no more genes to make a person than it does to make a simple microscopic worm. What makes a man different from a worm lies more in what researchers now calling the Dark Matter of the genome - 300 million letters of genetic code which work in currently mysterious ways.Note to Richard,
Richard Dawkins is an evolutionary biologist at Oxford University and the author of numerous books on evolution and genetics such as 'The Selfish Gene'. In interviews with scientists who led the initial effort to decode the genome and those who are now at the forefront of genetic research, Richard brings his evolutionary insights and fascination with the universal genetic code of life to illuminate how far we've come, and where we are heading in the Age of the Genome.
Mihaela Pertea and Steven L Salzberg have just published a paper in Genome Biology with an interesting title: Between a chicken and a grape: estimating the number of human genes. Part of their paper covers the history of gene number estimates and it includes the figure shown here.Figure 2. The trend of human gene number counts together with human genome-related milestones. Individual estimates of the human gene count are shown as blue diamonds. The range of estimates at different times is shown by the two vertical blue dotted lines. Note how this range has narrowed in recent years.This is really annoying because it perpetuates a myth that needs to be debunked. I've addressed it in an earlier posting [Facts and Myths Concerning the Historical Estimates of the Number of Genes in the Human Genome].
Given some uncertainties about estimating the numbers of genes present in multiple copies, we might say that the mammalian genome looks to be of the order of 30,000 - 40,000 gene functions.He published the same estimate in Genes IV in 1990.
[HatTip: Carl Zimmer]
King,J.L. and Jukes,T.H. (1969) Non-Darwinian evolution. Science 164; 788-798.
Ohno, S. (1972) So much "junk" in our genome. Brookhaven Symp. Biol. 23:366-310.
His fellow science writers often think that Nicholas Wade is among the best of their ilk. Wade writes for the New York Times and his latest article is: A Decade Later, Genetic Map Yields Few New Cures. A couple of paragraphs from that article deserve some kind of award.
But while 10 years of the genome may have produced little for medicine, the story for basic science has been quite different. Research on the genome has transformed biology, producing a steady string of surprises. First was the discovery that the number of human genes is astonishingly small compared with those of lower animals like the laboratory roundworm and fruit fly. The barely visible roundworm needs 20,000 genes that make proteins, the working parts of cells, whereas humans, apparently so much higher on the evolutionary scale, seem to have only 21,000 protein-coding genes.
The slowly emerging explanation is that humans and other animals have much the same set of protein-coding genes, but the human set is regulated in a much more complicated way, through elaborate use of DNA’s companion molecule, RNA.
Thanks to Jonathan Eisen at The Tree of Life, Nicholas Wade can now add the "Twisted Tree of Life Award" to his many others [Twisted tree of life award #5: Nicholas Wade & use of higher, lower, ladders, etc].
You see, Wade makes one of the most fundamental errors of evolutionary thinking when he writes about "higher" and "lower" on the "evolutionary scale."
There are two other flaws in his quoted excerpt. First, it did not come as a big surprise to all scientists that humans had about the same number of genes as other animals. That's a myth based on overemphasizing the opinions of some people and underemphasizing the opinions of the experts [Facts and Myths Concerning the Historical Estimates of the Number of Genes in the Human Genome]. This is part of what I call The Deflated Ego Problem and it's not endemic. It can be cured by reason.
Second, the explanations for similar numbers of genes in animals come from genetics and developmental biology over the past fifty years. It may have been "slowly emerging" back when I first started teaching but it's now fully emerged and has been for twenty years. Long before the human genome was sequenced we knew that major morphological changes could be caused by small mutations in regulatory sequences. During the 1980s and 1990s it became apparent that animals such as Drosohila and humans shared many important development genes1 and even more of the genes involved in basic metabolism. This was not a surprise.
It may be true that RNA places a much more important role in regulating gene expression than we thought. The jury is still out on that one. However, even if RNA is part of the regulation picture that fact does not change the basic principle that molecular biologist developed over the past thirty years; namely, that the same basic gene set is just regulated differently in different animals. This is the contribution of Evo-Devo.
There's one other logical flaw made by those with deflated egos. What they're looking for is some specific mechanism that explains the marvelous complexity of humans relative to the "lowly" fruit fly or nematode. What they need in order to satisfy this longing is a mechanism that we have and they don't. As far as I know, there isn't (hardly) anyone who claims that regulatory RNAs have only evolved in humans. The genome sequences of all animals is pointing in the same direction. If there are abundant regulatory RNAs then there are lots in nematodes and fruit flies as well. It's not going to solve the pseudoproblem that Nicholas Wade imagines.
1. Perhaps you've heard of homeotic genes and HOX genes?
Nature Publishing Group has responded to the potential boycott of its products by the Universities of California [Nature vs. The University of California]. Here's what they have to say for themselves ... [Public statement from Nature Publishing Group regarding subscription renewals at California Digital Library (CDL)].The implication that NPG is increasing its list prices by massive amounts is entirely untrue. We have been publishing our academic site licence pricing for several years on our librarian gateway. Dollar list price increases have been reasonable (averaging roughly 7 % over 4 years), and publicly available throughout. A 7% cap on annual list price increases is currently in place.Translation: It's completely untrue that NPG is increasing its prices. It's only massively increasing prices for the Universities of California. Price increases for other schools are "only" 7%.
The complication with CDL is that they have been on a very large, unsustainable discount for many years, to the point where other subscribers, both in the US and around the world, are subsidising them. The origins of this discount can be found in the lack of clear definitions around consortia and 'single institute, multisite' subscribers, as well as previous accommodations of CDL's budget limitations.
If we regard CDL as a consortium of multiple libraries (not least suggested by CDL's membership of International Coalition of Library Consortia (ICOLC), and the libraries' ARL listings), the CDL discount on list price is 88%. By their own figures, CDL receives average discounts of 55% from publishers. After several attempts, we are now trying to bring them close to a 50% discount (although this leaves CDL on better terms than many other consortia). We do recognise the situation can be viewed from different perspectives, and we remained committed to ongoing discussions.
Our own projections show CDL will be paying roughly $0.56 per download under the new prices. This represents incredible value for money across any publisher's range of titles. We now call on CDL to reveal how much it spends with all the major publishers, and how this translates into cost per use, and/or other indicators of value. If NPG represents poor value for money, we will work with CDL to readjust their pricing. If, as we expect, NPG represents good value for money compared with other publishers, even at the new proposed pricing, we want to work with CDL to have this reflected in our agreement. We sincerely hope that no boycotts will occur, not least because it is detrimental to the advance of science, but we will not be bullied into continuing CDL's subsidy by our other customers.Translation: We're embarrassed and we probably will be bullied into making a much lower offer to CDL. Furthermore, we equate the advance of science with the business of publishing. It's it reduces our profits then it must be bad for science.
This is a topic that's dear to my heart? Why? Because it's one of the few things where Denyse O'Leary and I completely agree—the silliness of evolutionary psychology.The cringeworthy "dad dancing" witnessed at wedding receptions every weekend may be an unconscious way in which ageing males repel the attention of young women, leaving the field clear for men at their sexual peak.No comment is necessary except to say that psychology better do something to clean up its image or the entire discipline is going to become a joke.
"The message their dancing sends out is 'stay away, I'm not fertile'," said Dr Peter Lovatt, a psychologist at the University of Hertfordshire who has compared the dancing styles and confidence levels of nearly 14,000 people.
His research has backed up scientific studies showing a connection between dancing, hormones and sexual selection.
Men between the ages of 35 and 60 typically attempt complex moves with limited co-ordination – an observation that will be obvious to anyone who saw George W Bush shake his stuff with a troupe of West African performers in 2007.
Dr Lovatt pointed to research showing that women could gauge the testosterone levels of their dance partners by the style and energy of their moves, and suggested that "dad dancing" may be a way of warning women of child-bearing age that they might be better off looking elsewhere.
"It would seem completely unsurprising to me that since middle-aged men have passed their natural reproductive age, and probably have a family already, evolution would act to ensure they are no longer attractive to 18-year-old girls," Dr Lovatt said.
[Photo Credit: That's my daughter Jane at her wedding in June 2007. And that's me, demonstraing my infertility in the same way my cavemen ancestors might have done.]
Deepak Chopra's lecture at the University of Toronto—the one sponsored by the Royal Ontario Museum—has been canceled [Shame on the Royal Ontario Museum]. I'd like to say that the cancellation was due to the outrage expressed by skeptics all over the world but, alas, that wasn't the reason. The lecture was canceled because of the G20 summit being held in Toronto at the end of June. The University is shutting done from June 21st to June 27th and that's why his lecture was canceled.
Keith Yamamoto is organizing the boycott. Keith Yamamoto is a professor of molecular biology and executive vice dean of the School of Medicine at UC-San Francisco. He stands ready to help organize a boycott, if necessary, a tactic he and other researchers used successfully in 2003 when another big commercial publisher, Elsevier, bought Cell Press and tried to raise its journal prices.Way to go, Keith!
After the letter went out on Tuesday, Mr. Yamamoto received an "overwhelmingly positive" response from other university researchers. He said he's confident that there will be broad support for a boycott among the faculty if the Nature Group doesn't negotiate, even if it means some hardships for individual researchers.
"There's a strong feeling that this is an irresponsible action on the part of NPG," he told The Chronicle. That feeling is fueled by what he called "a broad awareness in the scientific community that the world is changing rather rapidly with respect to scholarly publication."
Although researchers still have "a very strong tie to traditional journals" like Nature, he said, scientific publishing has evolved in the seven years since the Elsevier boycott. "In many ways it doesn't matter where the work's published, because scientists will be able to find it," Mr. Yamamoto said.
[HatTip: Janet Stemwedel]
Boudry, M., Blancke, S., and Braeckman, J. (2010) How Not to Attack Intelligent Design Creationism: Philosophical Misconceptions About Methodological Naturalism. Foundations of Science doi:10.1007/s10699-010-9178-7.
Abstract
In recent controversies about Intelligent Design Creationism (IDC), the principle of methodological naturalism (MN) has played an important role. In this paper, an often neglected distinction is made between two different conceptions of MN, each with its respective rationale and with a different view on the proper role of MN in science. According to one popular conception, MN is a self-imposed or intrinsic limitation of science, which means that science is simply not equipped to deal with claims of the supernatural (Intrinsic MN or IMN). Alternatively, we will defend MN as a provisory and empirically grounded attitude of scientists, which is justified in virtue of the consistent success of naturalistic explanations and the lack of success of supernatural explanations in the history of science (Provisory MN or PMN). Science does have a bearing on supernatural hypotheses, and its verdict is uniformly negative. We will discuss five arguments that have been proposed in support of IMN: the argument from the definition of science, the argument from lawful regularity, the science stopper argument, the argument from procedural necessity, and the testability argument. We conclude that IMN, because of its philosophical flaws, proves to be an ill-advised strategy to counter the claims of IDC. Evolutionary scientists are on firmer ground if they discard supernatural explanations on purely evidential grounds, instead of ruling them out by philosophical fiat.
So why are Matheson and Moran so sure that huge portions of introns don’t have functions? According to Matheson, it’s because “Larry Moran and I clearly know a whole lot more about molecular genetics” than Sternberg.Here's what undergraduates learn when they read what I wrote in my textbook. Maybe I should send copies to Wells and Sternberg?
A more naked appeal to authority would be hard to find. It sounds like an undergraduate trying to score points in a late-night bull session (“I know all about that; I took a course in it…”), not a college professor engaged in a scientific debate.
But Matheson didn’t stop there. He demeaned Sternberg by calling him “poor Richard.” He also claimed that Sternberg is “disastrously clueless” because he doesn’t understand “the important and very basic distinction between a transcript and an intron.” Since every undergraduate biology student learns that an intron is a segment of DNA, while a transcript is a segment of RNA encoded by DNA, this last jibe is on a par with Moran’s insult that Sternberg can’t do elementary arithmetic. And it is equally unjustified.
Internal sequences that are removed from the primary RNA transcript are called introns. Sequences that are present in the primary transcript and in the mature RNA molecule are called exons. The words intron and exon also refer to the regions of the gene (DNA) that encode corresponding RNA introns and exons. Since DNA introns are transcribed, they are considered part of the gene.
1. I'm ignoring the fact that Sternberg's calculation assumed that every intron in a gene must be alternatively spliced. That assumption is/was not based on anything in the scientific literature but it's unlikely that Sternberg will admit his error.
PZ Myers want to see Agora [I want to see this movie]. So do I. Here's the website [Agora] and here's the synopsis.A historical drama set in Roman Egypt, concerning a slave who turns to the rising tide of Christianity in the hopes of pursuing freedom while also falling in love with his master, the famous female philosophy professor and atheist Hypatia of Alexandria.I hear that the producers are having trouble getting widespread distribution in America. I wonder why? It's a movie about an atheist woman standing up to a Christian mob hell bent on destroying Alexandria and the library.
