In my second response to Arthur Hunt on the origin of the T-urf13 gene (which specifies a mitochondrial ligand-gating pore-forming receptor for T-toxin in maise), I briefly mentioned towards the end of my post Arthur Hunt’s comments on the Panda’s Thumb blog regarding the Axe (2004) result concerned with the rarity of catalytic domains within sequence space.

As I noted in my previous post, Axe’s 2004 JMB paper is not an isolated result. I cited a number of papers which attained similar results with respect to the rarity of functional domains within sequence space. In one study, published in Naturein 2001 by Keefe & Szostak, it was documented that more than a million million random sequences were required in order to stumble upon a functioning ATP-binding protein, a protein substantially smaller than the transmembrane protein specified by the gene, T-urf13, discussed by Hunt. In addition, I noted, a similar result was obtained by Taylor et al. in their 2001 PNAS paper. This paper examined the AroQ-type chorismate mutase, and arrived at a similarly low prevalence (giving a value of 1 in 10^24 for the 93 amino acid enzyme, but, when adjusted to reflect a residue of the same length as the 150-amino-acid section analysed from Beta-lactamase, yields a result of 1 in 10^53). Yet another paper by Sauer and Reidhaar-Olson (1990) reported on “the high level of degeneracy in the information that specifies a particular protein fold,” which it gives as 1 in 10^63. In my previous post, I also strongly encouraged Arthur Hunt and others to read Douglas Axe’s excellent review article in Bio-complexity which covers this topic in more detail, as well as to read the recently-published The Nature of Nature — Examining The Role of Naturalism in Science, which is highly accessible for non-specialists.

Yesterday, I posted a short itallicised update to my previous article, having now looked somewhat closer at the article to which Hunt referred me. For those that missed it, allow me to highlight just a few of the points at which Hunt errs.

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Or maybe not. From Britain’s Independent (Olly Bootle, 28 February 2011), we learn, “Our species is still evolving, but future humans might be more like Danny DeVito than Stuart Broad”: The realisation that differing fertility levels might be driving change in our species has led evolutionary biologist Stephen Stearns, from Yale University, to look at evolution in a radical way. By analysing data gathered in an otherwise unremarkable town, Framingham in Massachusetts, he can tell how the people of the town will evolve in the coming generations. His calculations have convinced him that people are still evolving, and in a surprising direction. “What we have found with height and weight basically is that natural selection appears to be operating to Read More ›

A friend put me onto this human genetic research program (no, no, it all sounds reasonable, keep your shirt on; no one is looking for the  missing link andyou are him and the genetic police are waiting outside … wake UP, will you?): Ethnically diverse people are donating DNA to science, and the wealth of genomic data emerging from the project already is shedding light on human evolution.A decade ago it was a big deal to spell out the entire DNA sequence of a single human being. That event marked the success of the initial Human Genome Project. Now hundreds of human genomes have been decoded. Scientists who study human evolution are using the new data to make discoveries about how Read More ›

On 3 Mar 2011, we learned from Britain’s Daily Telegraph that “Millions of NHS patients have been treated with controversial drugs on the basis of “fraudulent research” by one of the world’s leading anaesthetists,”:

He published dozens of papers “proving” their benefits and contradicting studies which suggested they could increase the risk of death in surgery and cause kidney failure, severe blood loss and heart failure.German medical authorities are scrutinising 92 of his key publications and a criminal investigation is under way into allegations that he forged documents, tested drugs on patients without their consent and fraudulently claimed payments for operations he had never performed.

[ … ]

Sources close to the investigation said that the editors would announce the formal retraction of 89 papers next month.Rhineland state prosecutors are investigating Mr Boldt over allegations that he forged the signatures of his alleged “co-authors” on his studies, conducted drugs trials without official approval and claimed money for operations that he never performed.

[ … ]

Dr Rupert Pearse, a senior lecturer in intensive care medicine at Barts and the London School of Medicine, and co-author of the British guidelines on fluid drugs, said last night: “…For me, it shakes the world I work in and makes me feel less confident in it, and if I were a member of the public I would feel the same.”

These cases are so common now, it might be worth taking a look at reasons that aren’t anyone’s direct fault: Read More ›

In a review of several recent science books, Dartmouth professor Alan Hirshfeld offers us a view of the Royal Society (former employer of sinner in the hands of an angry god, Michael Reiss), and similar societies, as engines of perpetual revolution (The Wall Street Journal) , opining “The Royal Society’s history of open-minded debate epitomizes science as a self-correcting process”: The group is more effective than the individual at sussing out weak hypotheses, flawed experiments or biased observations, and one of the vital contributions of Europe’s “natural philosophers” during the Enlightenment was the creation of societies to disseminate and evaluate their ideas. Such conclaves served as intellectual hubs before the rise of modern research universities and institutes, and remain important Read More ›

The last decade has witnessed three contenders for the title: earliest identifiable human ancestor. These are Ardipithecus, Orrorin and Sahelanthropus. All of them generated great excitement at the time of their discovery and, for many, they were evidence that the lineage of the human genus was being clarified. However, those willing to read research papers (rather than media reports) were more aware that the research community was not of one mind about the significance of these fossil remains. Recently, Wood and Harrison have contributed a major review paper that revisits these arguments and finds that the various claims for human ancestry are not rigorous. They offer alternative explanations for these three fossil hominines. “In their paper, Wood and Harrison caution Read More ›

At ScienceDaily (Mar. 5, 2011), we are invited to contemplate, “Has Earth’s Sixth Mass Extinction Already Arrived?”, With the steep decline in populations of many animal species, from frogs and fish to tigers, some scientists have warned that Earth is on the brink of a mass extinction like those that occurred only five times before during the past 540 million years.Each of these ‘Big Five’ saw three-quarters or more of all animal species go extinct. Is a three-quarters disappeance – as hinted by the University of California, Berkeley, paleobiologists who published a study in Nature, March3, – at all likely to happen, short of a worldwide nuclear holocaust or giant asteroid hit? Tigers are featured in the article but – Read More ›

Scratch that. Partial answer just in. One already has. Here (Retreating Into Silence, March 6, 2011), Mark Steyn tells a prescient story: A prominent British imam has been forced to retract his claims that Islam is compatible with Darwin’s theory of evolution after receiving death threats from fundamentalists.This is not in Lahore or Cairo but in London, at what is described as “a prominent mosque which also runs one of the country’s largest sharia courts” – in other words, a religious institution that already enjoys the imprimatur of state approval, albeit not (yet) to the same degree as in Pakistan. The imam, Dr Hasan, has issued a groveling apology – “I seek Allah’s forgiveness for my mistakes” – but they Read More ›

The Zed and I agree about David Brooks’ revolting Social Animal theories, to judge from his Salon review: I made it almost a third of the way through the arid wasteland of David Brooks’ didactic novel, “The Social Animal: The Hidden Sources of Love, Character, and Achievement,” before I succumbed. I had begun reading it determined to be dispassionate and analytic and fair, but I couldn’t bear it for long: I learned to loathe Harold and Erica, the two upscale avatars of upper-middle-class values that Brooks marches through life in the story. And then I began to resent the omniscient narrator who narrates this exercise in unthinking consumption and privilege that is, supposedly, the ideal of happiness; it’s like watching Read More ›

In response to someone who wondered whether American scientists might be letting their imaginations run away with them about this spectacular new alien life find, Rob Sheldon offers “absolutely not”. Au contraire, the French were onto it and NASA dropped the ball. On why that happened, he says, NASA’s attitude is an example of

… “pathological science” and was extensively discussed by Irving Langmuir in 1953 and subsequent publications

I can assure you, nothing in Hoover’s [the discovering scientist’s] work comes within a mile or so of being pathological. Hoover has several gigabytes of pictures taken in every single CI meteorite he can get his hands on. The pictures have made him a sensation in the French Academy, the Belgian Academy and the Russian Academy. Experts in microbiology have examined the pictures and not only verified their biological identity, but asked how he obtained such clarity that exceeds what they can accomplish in the laboratory. (Freeze dry for a thousand years…) The only people that continue to shun him are the US and NASA. Ultimately it is ideology that prevent people from taking the pictures seriously, a prior commitment to “life only exists on Earth”. Some of those people are conservative Christians, some are dedicated Darwinists. I really don’t think it is a well-reasoned position, but still, there’ a lot of ideological opposition.

By the way, Fox News is offering updates, comments from relevant scientists, though as of ten minutes ago, I couldn’t yet find them. Keep checking back.

I suppose some Evolution Sunday clergy will now be preaching sermons about how to adjust to the fact that we now “know” how life got started purely by chance (abiogenesis). Our ID community’s rebbe, Moshe Averick, told me,

I don’t think it has any implications at all for abiogenesis. No one really has much of a clue how abiogenesis could have occured on earth, the best that could be said is that not only is life on earth inexplicable, but life elsewhere in the universe is also inexplicable.

Our George Hunter will doubtless comment shortly on his regular blog, but I overheard him say, Read More ›

While searching Discover, I ran up against this from Perimeter Institute cosmologist Neil Turok, “Will We Discover That the Universe Had No Beginning and Has No End?” (October 2010): In the conventional picture of the origin of the universe, the Big Bang is the beginning of time. This is one of the greatest mysteries in science, and I’ve spent the last few years trying to work out how to make sense of the moment when, in that picture, the universe emerged from a point of infinite density and temperature—what’s known as the initial singularity. I’m exploring the idea that the singularity was not the beginning of time. In this new view, time didn’t have a beginning, and the Big Bang Read More ›

No, not a joke. From “Exclusive: NASA Scientist Claims Evidence of Alien Life on Meteorite” by Garrett Tenney (March 05, 2011) here: Dr. Richard B. Hoover, an astrobiologist with NASA’s Marshall Space Flight Center, has traveled to remote areas in Antarctica, Siberia, and Alaska, amongst others, for over ten years now, collecting and studying meteorites. He gave FoxNews.com early access to the out-of-this-world research, published late Friday evening in the March edition of the Journal of Cosmology. In it, Hoover describes the latest findings in his study of an extremely rare class of meteorites, called CI1 carbonaceous chondrites — only nine such meteorites are known to exist on Earth. Though it may be hard to swallow, Hoover is convinced that Read More ›

While rummaging through Discover Magazines Top 2010 stories relevant to our blog’s interests, I sailed into #46: Do Physical Laws Vary From Place to Place? by Tim Folger (January-February special/December 16, 2010) by These tentative findings raise the possibility that the physical laws that allow life to exist may hold true only in our particular part of the universe. “There could be regions with different values for the constants of physics,” Webb says. “We inevitably find ourselves in one that allows us to be here.” If so, we must seek a replacement for the word “constant”. Such large speculations on such tentative findings, and it’s in the top 50 stories. I am glad no one allows cosmologists near stock brokerages Read More ›

… and served with cold mashed potatoes, lumpy gravy, and wan, limp lettuce.

Here, University of Alabama science historian Michael Flannery, laments that Darwin’s co-theorist Wallace has been “Darwinized”, referencing the many efforts by Darwinists to downplay his involvement in evolutinary theory, principally because he was not a materialist atheist. For example,

Quammen writes, “he was a man of crotchety independence and lurching enthusiasms, a restless soul never quite satisfied with the place in which he lived, a believer in spiritualism and séances, a devotee of phrenology, a dabbler in mesmerism, a later apostate from Darwinian theory when it came to the development of the human brain, an opponent of smallpox vaccination, and an advocate of nationalizing large private landholdings, who by these and other eccentricities gave his detractors some grounds for dismissing him as a crank. Which they did. The question that no scholar or biographer has adequately answered is: How to reconcile such brilliant achievements, radical convictions, and incautious zealotries within one human character–the character of a consummate empiricist and field naturalist?”

Alfred Russel Wallace: A Rediscovered Life does precisely that. These disparate features CAN be reconciled if you quit casting Wallace’s spiritualism, socialism, belief in mesmerism, and his opposition to vaccination dismissively as “eccentricities.” Recast properly, Wallace becomes a prescient figure who called for much-needed land reform, women’s rights, a broadened view of science expanded beyond the strictures of a dogmatically held methodological naturalism, a man who refused to yield on issues of individual freedoms and public health when serious questions remained, a precursor to intelligent design, and a vocal opponent of the ethical and moral dangers of the rising tide of eugenics. Viewed in this way Wallace’s convictions seem less “radical,” his “zealotries” less “incautious,” his “lurching enthusiasms” more understandable — the very epitome of a “consummate empiricist and field naturalist” truly willing to go where the evidence would lead him.

For more, go here.

One thing I learned from reading Flannery’s biography of Wallace is that he developed his passion for land reform as a result of his experiences as a land surveyor, surveying in areas where traditional common lands had been enclosed and country folk were left without resources. Opinions differ as to whether the move was necessary, but the suffering wasn’t.

Here I learned that Darwin’s inner circle was very much pro-enclosure: Read More ›

Jane Harris-Szovan’s book, Eugenics and the Firewall (when social Darwinism hit the Canadian province of Alberta), has been getting lots of attention, here for example, and here. She notes,

If you’re wondering why only the left is interviewing me, then you need to learn a bit about who runs my province. [Not the left. – d., 😉 ] Still, l it makes me sad, that the Christian and right wing media are running away from this issue like ‘fraidy cats. I expected it, but I am sad that I was right.)

The embarrassment here is that eugenics in Alberta was spearheaded by evangelical Christians, including a premier whose soubriquet was “Bible Bill.” The left has a stake in exposing this scandal, not the Christian groups. But it’s time someone did, just to clear the air.

It’s interesting to reflect on how seductive the idea must have been back then. I doubt you’d get any prominent Christian leaders on board for compulsory sterilization today. Read More ›