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Ard Louis and Vitalism

I once collected and cataloged the various arguments for evolution. It is fascinating to see smart people constructing elaborate schemes for the unlikely. One of the subtle, yet no less bizarre, arguments is the use of vitalism as a null hypothesis, a variation of which the brilliant physicist Ard Louis constructed recently. First, here’s what I wrote about this a year and half ago:  Read more

Early coffee: Traction, retraction, and self-plagiarism (when scientists retread what they should retire)

“This study reports evidence consistent with the ‘deliberate fraud’ hypothesis. The results suggest that papers retracted because of data fabrication or falsification represent a calculated effort to deceive.”:

Med Ethics doi:10.1136/jme.2010.038125Research ethics

Retractions in the scientific literature: do authors deliberately commit research fraud?

R Grant Steen
Correspondence to
R Grant Steen, Medical Communications Consultants LLC, 103 Van Doren Place, Chapel Hill, NC 27517, USA; g_steen_medicc@yahoo.com
Received 31 May 2010
Revised 29 July 2010
Accepted 13 August 2010
Published Online First 15 November 2010
Background Papers retracted for fraud (data fabrication or data falsification) may represent a deliberate effort to deceive, a motivation fundamentally different from papers retracted for error. It is hypothesised that fraudulent authors target journals with a high impact f actor (IF), have other fraudulent publications, diffuse responsibility across many co-authors, delay retracting fraudulent papers and publish from countries with a weak research infrastructure.

Methods All 788 English language research papers retracted from the PubMed database between 2000 and 2010 were evaluated. Data pertinent to each retracted paper were abstracted from the paper and the reasons for retraction were derived from the retraction notice and dichoto mised as fraud or error. Data for each retracted article were entered in an Excel spreadsheet for analysis.

Results Journal IF was higher for fraudulent papers (p<0.001). Roughly 53% of fraudulent papers were written by a first author who had written other retracted papers (‘repeat offender’), whereas only 18% of erroneous papers were written by a repeat offender (?=88.40 ; p<0.0001). Fraudulent papers had more authors (p<0.001) and were retracted more slowly than erroneous papers (p<0.005). Surprisingly, there was significantly more fraud than error among retracted papers from the USA (?2=8.71; p<0.05) compared with the rest of the world.

Conclusions This study reports evidence consistent with the ‘deliberate fraud’ hypothesis. The results suggest that papers retracted because of data fabrication or falsification represent a calculated effort to deceive. It is inferred that such behaviour is neither naï ve, feckless nor inadvertent.

For comments go here “The highest number of retracted papers were written by US first authors (260), accounting for a third of the total. One in three of these was attributed to fraud.”, or here (An excellent example of either crappy science reporting or crappy science …), for the view that it’s all a bum rap.

One site also offers a number of articles on the shortcomings of peer review. Also an article on self-plagiarism and one on self-plagiarism and bogus authorship. Read More ›

New Peer-Reviewed Pro-ID Paper in BIO-COMPLEXITY

A Vivisection of the ev Computer Organism: Identifying Sources of Active Information George Montañez, Winston Ewert, William Dembski, Robert Marks   Abstract ev is an evolutionary search algorithm proposed to simulate biological evolution. As such, researchers have claimed that it demonstrates that a blind, unguided search is able to generate new information. However, analysis shows that any non-trivial computer search needs to exploit one or more sources of knowledge to make the search successful. Search algorithms mine active information from these resources, with some search algorithms performing better than others. We illustrate these principles in the analysis of ev. The sources of knowledge in ev include a Hamming oracle and a perceptron structure that predisposes the search towards its target. Read More ›

Evolutionary psychology: Wisdom swings from the trees, it turns out

My Salvo 15 Deprogram column: LUCY SPEAKS Evolutionary Psychology Is Now Taking Your Questions When Britain’s Guardian newspaper first introduced its “evolutionary” agony aunt (advice columnist in America) in 2009—to honor 150 years of the culture birthed with Charles Darwin’s 1859 book, On the Origin of Species—I thought, “Aha! a send-up, to be sure.” I was wrong, but in fairness, when the evolutionary psychologist speaks, even an expert can’t always tell. No spoof. The Guardian burbled proudly about Carole Jahme, author of Beauty and the Beasts: Woman, Ape and Evolution and winner of the Wellcome Trust Award for Communication of Science to the Public. For the 2009 Darwin bicentennial celebrations, Jahme, who holds an M.A. in evolutionary psychology, put together Read More ›

Peer review: Have we run out of polish for the iron rice bowls?

Wordle: peer review Wordle: peer review

At Slate, Daniel Engber offers another slam at peer review:

When journal editors are asked about these ideas, they often quote Winston Churchill’s line, “Democracy is the worst form of government except all those other forms that have been tried from time to time.” Or rather, they quote other journal editors quoting that line. But it’s a poor analogy, since few alternatives to peer review have been tried in modern times. And democracy isn’t really a good description of peer review, either. Sure, peer review allows scientists to participate in a system of self-governance. But wouldn’t BMJ’s policy of open review or Ginsparg’s proposal for Web-published preprints be far more democratic?

So far, though, the Churchill quoters are winning.

You know, “The worst system , except for all the others.” The trouble is, any system can exhaust the benefits for which it was brought in- in this case, to cope with the flood of post-World War II science efforts. In my own view, it has become the same sort of drag on fresh thinking as reliance on Aristotle was in the early modern period of science.

If the object is to do good science while pleasing all possible reviewers, and the gist of the paper is an idea that disconfirms their theories, one may have to downplay findings, quit the field, or go nuts. Michael Behe is a rare example of someone who stood up to all the garbage, just to make a simple point or two about the shortcomings of Darwin’s Rice Bowl.

Other peer review alerts:

Read More ›

Ants Optimize Their Search

New research shows that when presented with a barrier, ants don’t just turn around and follow the scent back the way they came. Instead, they perform an advanced search:  Read more

The Weasel lives on, now at PNAS

ID critics often complain that ID advocates go ON AND ON (and ON) worrying about Weasel-type models of evolution, as illustrations of how undirected variation and selection can rapidly converge to apparently designed outcomes. No one takes such models seriously as biology, the critics say. Weasels are toys with a strictly limited teaching purpose. Over to the latest issue of the Proceedings of the National Academy of Sciences (PNAS). Looks like a weasel in the tall grass: Suppose that we are trying to find a specific unknown word of L letters, each of the letters having been chosen from an alphabet of K letters. We want to find the word by means of a sequence of rounds of guessing letters. Read More ›

Martin Gaskell, The Latest Victim

Astronomer Martin Gaskell, the latest victim of the gluttonous, one-minded, two-headed dragon known as “Evolution Promotion” and “Religious Persecution,” depending on which head one is referring to on the modern beast, has apparently been Expelled due to his critical remarks on evolution and for being “potentially evangelical.” Indeed, Mr. Gaskell was provoking both heads of this modern monster. How? By talking. You see, the beast hates words in plain language with real meaning that describe the eternal enemy called truth. The short, abrupt words with all the sense of sunlight sting its sensitive ears, which need the dark and gray smooth sounds of ambiguities and soft soap of appeasements.  This monstrosity has been spotted at several universities.  The latest sighting was in Kentucky:

No one denies that astronomer Martin Gaskell was the leading candidate for the founding director of a new observatory at the University of Kentucky in 2007 — until his writings on evolution came to light.

Gaskell had given lectures to campus religious groups around the country in which he said that while he has no problem reconciling the Bible with the theory of evolution, he believes the theory has major flaws. And he recommended students read theory critics in the intelligent-design movement.

That stance alarmed UK science professors and, the university acknowledges, played a role in the job going to another candidate.

Now a federal judge says Gaskell has a right to a jury trial over his allegation that he lost the job because he is a Christian and “potentially evangelical.”

Read More ›

How Proteins Evolved

Fifty years ago molecular biologists began to uncover the inner workings of the cell and one of their profound discoveries was that genetic information, stored in the double helix DNA molecule, was translated according to a code to produce a string of amino acids which, after being hitched to each other like train cars, folded up to produce a protein that did something useful in the cell. Interestingly, a given protein’s amino acid sequence was found to have some degree of flexibility. Hemoglobin proteins, for instance, across different species revealed quite a few changes to the sequence while still functioning as a hemoglobin.  Read more

The End of “Seeing Through”

jurassicmac has more to say in response to my “Gravity Does Not Account for Itself.”  He writes: I never said that gravity accounted for itself. Gravity explains the motion of the planets. In that same way, the laws of the universe that make evolution possible don’t account for themselves; but they do explain the current state of life. By your reasoning, it seems as if we could never ‘explain’ anything if we could always push the question back a step and say ‘Well, you can’t explain your explanation!’ Just so.  In his great “Abolition of Man” C.S. Lewis wrote: But you cannot go on ‘explaining away’ forever: you will find that you have explained explanation itself away. You cannot go Read More ›

But, Jerry, what about all those dogs?

Apparently, Jerry Coyne is now attacking me, re Behe’s recent paper. To judge from his blog post’s title, he has me confused with Discovery Institute.* (Behe’s paper is available for free download here.) . Dr. Coyne claims that Behe’s findings apply only to artificial selection in the lab. But, at the feet of the great Richard Dawkins, I learned that artificial selection like human breeding of dogs, has proved Behe both wrong and ridiculous, in Edge of Evolution. That is precisely because dog breeding is equivalent to the process that applies throughout nature: Don’t evade the point by protesting that dog breeding is a form of intelligent design. It is (kind of), but Behe, having lost the argument over irreducible Read More ›

Mid-morning mug: Are Darwinists running out of insults and profanity?

Recently, biochemist Michael Behe published an article in Quarterly Review of Biology, titled “Experimental Evolution, Loss-of-Function Mutations and ‘The First Rule of Adaptive Evolution’,” arguing that “the most common adaptive changes seen … are due to the loss or modification of a pre-existing molecular function.” So, not only must the long, slow process of Darwinian evolution create every exotic form of life in the blink of a geological eye, but it must do so by losing or modifying what a life form already has. This, apparently, got evolutionary biologist Jerry Coyne’s recent attention: Anyway, Behe reviews the last four decades of work on experimental evolution in bacteria and viruses (phage), and finds that nearly all the adaptive mutations in these Read More ›

Back to School Part IX

We continue to examine the work of authors George Johnson and Jonathan Losos in their biology textbook, The Living World ((Fifth Edition, McGraw Hill, 2008). In their chapter on evolution and natural selection, these accomplished evolutionists begin by (1) misrepresenting the relationship between microevolution and macroevolution and biological variation here, (2) making a non scientific, metaphysical, truth claim that just happens to mandate the truth of evolution here, (3) making the grossly false statement that the fossils themselves are a factual observation that macroevolution has occurred here and here, (4) making a series of misrepresentations by carefully selecting the evidence to provide to the student and protecting it with circular reasoning here, (5) misrepresenting the molecular evidence here, (6) presenting Read More ›

Sunday afternoon coffee: Did your old science teacher know the Tarot?

From The Scientist (8th October2010): Science tarot A whimsical deck of cards shuffles the worlds of logic and mythology On a Thursday night in San Francisco, three elaborately costumed women sit in a lively hall giving tarot readings. One wears ornamental snakes in her hair, and another sports a headdress with oversized purple eyeballs. This isn’t your everyday divinatory gathering — they’re at the California Academy of Sciences, surrounded by glass cases of stuffed antelopes and lions. And instead of knights and kings, their cards display images of mitochondria, neurotransmitters, and Darwin. This unusual scene is the launch party of Science Tarot, a collaboration between science communicators, artists, and other creative thinkers who have produced a science-inspired deck of tarot Read More ›

Another nugget from the quote mine: In evolutionary biology, “almost no findings are replicated”

Jerry Coyne is always fun. He has the distinction of being a Darwinist who is perfectly honest about the war between Darwinism and any belief in the uniqueness of humans – many examples here, and such relief from any contact with Christian Darwinists.

Recently, he commented on an article in The New Yorker by Jonah Lehrer, “The truth wears off: is there something wrong with the scientific method?”.

Basically, Lehrer says, an initial demonstration in science tends to weaken or disappear when attempts are made to replicate it:

On September 18, 2007, a few dozen neuroscientists, psychiatrists, and drug-company executives gathered in a hotel conference room in Brussels to hear some startling news. It had to do with a class of drugs known as atypical or second-generation antipsychotics, which came on the market in the early nineties. The therapeutic power of the drugs appeared to be steadily falling. A recent study showed an effect that was less than half of that documented in the first trials, in the early nineties. Before the effectiveness of a drug can be confirmed, it must be tested again and again. The test of replicability, as it’s known, is the foundation of modern research. It’s a safeguard for the creep of subjectivity. But now all sorts of well-established, multiply confirmed findings have started to look increasingly uncertain. It’s as if our facts are losing their truth.Read more here [some more there, but you must pay for the rest].

Coyne writes in “The ‘decline effect’: can we demonstrate anything in science?”

I tend to agree with Lehrer about studies in my own field of evolutionary biology. Almost no findings are replicated, there’s a premium on publishing positive results, and, unlike some other areas, findings in evolutionary biology don’t necessarily build on each other: workers usually don’t have to repeat other people’s work as a basis for their own. (I’m speaking here mostly of experimental work, not things like studies of transitional fossils.) Ditto for ecology. Yet that doesn’t mean that everything is arbitrary. I’m pretty sure, for instance, that the reason why male interspecific hybrids in Drosophila are sterile while females aren’t (“Haldane’s rule”) reflects genes whose effects on hybrid sterility are recessive. That’s been demonstrated by several workers. And I’m even more sure that humans are more closely related to chimps than to orangutans. Nevertheless, when a single new finding appears, I often find myself wondering if it would stand up if somebody repeated the study, or did it in another species.

Good thing to wonder about. Time more people wondered about that. Breath of fresh air. Read More ›