2010

In the 2005 Kitzmiller v. Dover Area School District court case, federal judge John Jones was heavily influenced by the first expert witness, evolutionist Ken Miller. As Jones later recalled, he “was taken to school.” Unfortunately what Miller “taught” Jones was a series of scientific misrepresentations. Miller focused on two examples from molecular biology: a pseudogene and a fused chromosome. In both cases Miller gave Jones many facts but the lessons were carefully tailored to misrepresent both the science and evolutionary theory.  Read more

SCIENCE: “Now THAT’s a genome. A rare Japanese flower named Paris japonica sports an astonishing 149 billion base pairs, making it 50 times the size of a human genome—and the largest genome ever found. Until now, the biggest genome belonged to the marbled lungfish, whose 130 billion base pairs weighed in at an impressive 132.83 picograms. (A picogram is one-trillionth of a gram). The genome of the new record-holder, revealed in a paper in the Botanical Journal of the Linnean Society, would be taller than Big Ben if stretched out end to end. (The smallest genome known among organisms with nuclei is that of a mammalian parasite known as Encephalitozoon intestinalis, with a relatively paltry 2.25 million base pairs). The Read More ›

Philosophers and scientists who know their business recognize that any attempt to seek knowledge presupposes the existence of a rational universe ripe for investigating. The fact that we even bother to make the effort says something about our nature. As Aristotle says, “all men by nature want to know.” That is why the discovery of a new fact or truth can be a joy for its own sake. To be sure, knowledge also provides practical benefits, empowering us to pursue a self-directed life style, but it also edifies us, leading us on the road to self-actualization. To be intellectually healthy is to be curious.

On the other hand, we can, by virtue of our free will, act against our natural desire to know. For better or worse, there are some truths that many of us would prefer not to know about. The compelling nature of an objective fact can pull us in one direction while the force of our personal desires can pull us in the opposite direction. When this happens, a choice must be made. “Either the thinker conforms desire to truth or he conforms truth to desire.”–E. Michael Jones

Because we experience this ambivalence about the truth, we must be on guard against two errors: (a) talking ourselves out of things that we should believe [hyperskepticism] or (b) talking ourselves into things that we should not believe [gullibility]. Hyperskeptics attempt to justify the first error by calling attention to the second error, as if there was no reasonable alternative to either extreme. On the contrary, the ideal solution is to seek a rational midpoint –to balance a healthy skepticism about unconfirmed truth claims with a healthy confidence in truths already known. The one thing a thinker should not do is be skeptical or open-minded about the first principles of right reason, without which there is no standard for investigating or discoursing about anything “Merely having an open mind is nothing. The object of opening the mind, as of opening the mouth, is to shut it again on something solid.”– G. K. Chesterton

In the spirit of public service, then, I present this little test for analyzing our readers’ proclivity for hyperskepticism. Hopefully, those who indulge will not find any predictable patterns, since I strove to keep them at a minimum. Read More ›

Review Of Programming of Life By Donald Johnson, ISBN-10: 0982355467

There are some science writers that quite simply have a knack for combining the detail of their subject of expertise with a talent for exposition that a wide audience can easily understand. Donald Johnson is one of them. After carefully defining the various types of information- functional, prescriptive and Shannon- that information theorists have set out in their realm of study, Johnson takes the reader on a tour of cellular gene expression by focusing on the digital code of DNA. Shannon information, which provides a mathematical measure of improbability without regard to functionality does not help us in the description of life since the digital code of DNA is rich in what Johnson terms “functional prescriptive information”. Read More ›

In reflecting on the 2005 Kitzmiller v. Dover Area School District court case over which he presided, federal judge John Jones recalls that he “was taken to school.” Ever since his liberal arts days at Dickinson College, Jones has never doubted evolution. But his knowledge of the biological details, what little there was to begin with, was by 2005 quite stale. All that changed in the Kitzmiller case where Jones learned from various expert witnesses. It was, Jones recalled, “the equivalent of a degree in this area.” And Jones is confident his new knowledge served him well. “Folks who disagree with my opinion will tell you I never got it right,” he explains, “but I’m confident that I did.” Did Read More ›

Lawyer Hal G.P. Colebatch observes, re atheist science fiction: A magazine I frequently write for (not this one) recently published a review of a book of essays advocating atheism. The reviewer pointed out with some enthusiasm that a large number of the contributors were science-fiction writers. This left me somewhat nonplussed. I publish a good deal of science fiction myself, I have also read quite a lot of it, and I am quite unable to see why writing it should be held to particularly qualify anyone to answer the question of whether or not there is a God. I don’t know if it is an actual requirement for the job, but certainly a number of astronauts are believers and Buzz Read More ›

Hal Lewis* reminisces for Society president, Curtis G. Callan, Jr. of Princeton University, charging:

When I first joined the American Physical Society sixty-seven years ago it was much smaller, much gentler, and as yet uncorrupted by the money flood (a threat against which Dwight Eisenhower warned a half-century ago). Indeed, the choice of physics as a profession was then a guarantor of a life of poverty and abstinence—it was World War II that changed all that. The prospect of worldly gain drove few physicists. As recently as thirty-five years ago, when I chaired the first APS study of a contentious social/scientific issue, The Reactor Safety Study, though there were zealots aplenty on the outside there was no hint of inordinate pressure on us as physicists. We were therefore able to produce what I believe was and is an honest appraisal of the situation at that time. We were further enabled by the presence of an oversight committee consisting of Pief Panofsky, Vicki Weisskopf, and Hans Bethe, all towering physicists beyond reproach. I was proud of what we did in a charged atmosphere. In the end the oversight committee, in its report to the APS President, noted the complete independence in which we did the job, and predicted that the report would be attacked from both sides. What greater tribute could there be?

How different it is now. The giants no longer walk the earth, and the money flood has become the raison d’être of much physics research, the vital sustenance of much more, and it provides the support for untold numbers of professional jobs. For reasons that will soon become clear my former pride at being an APS Fellow all these years has been turned into shame, and I am forced, with no pleasure at all, to offer you my resignation from the Society.

Lewis is motivated by the Climategate attempt at censorship of dissenting views on manmade global warming:

It was a fraud on a scale I have never seen, and I lack the words to describe its enormity. Effect on the APS position: none. None at all. This is not science; other forces are at work.

(The really big scandal, in my view, is that Climategate wasn’t treated as a scandal, just business as usual.)

But now, what say you physicists among us: Were the good old days really better? Has love of money been the root of all evil? Read More ›

In, “Document Sheds Light on Investigation at Harvard (Chronicle Review, August 19, 2010),” Tom Bartlett reports that Harvard has told evolutionary psychologist Marc D. Hauser to explain issues around a few of his journal articles:

The experiment tested the ability of rhesus monkeys to recognize sound patterns. Researchers played a series of three tones (in a pattern like A-B-A) over a sound system. After establishing the pattern, they would vary it (for instance, A-B-B) and see whether the monkeys were aware of the change. If a monkey looked at the speaker, this was taken as an indication that a difference was noticed.

The method has been used in experiments on primates and human infants. Mr. Hauser has long worked on studies that seemed to show that primates, like rhesus monkeys or cotton-top tamarins, can recognize patterns as well as human infants do. Such pattern recognition is thought to be a component of language acquisition.

Researchers watched videotapes of the experiments and “coded” the results, meaning that they wrote down how the monkeys reacted. As was common practice, two researchers independently coded the results so that their findings could later be compared to eliminate errors or bias.

According to the document that was provided to The Chronicle, the experiment in question was coded by Mr. Hauser and a research assistant in his laboratory. A second research assistant was asked by Mr. Hauser to analyze the results. When the second research assistant analyzed the first research assistant’s codes, he found that the monkeys didn’t seem to notice the change in pattern. In fact, they looked at the speaker more often when the pattern was the same. In other words, the experiment was a bust.

But Mr. Hauser’s coding showed something else entirely: He found that the monkeys did notice the change in pattern—and, according to his numbers, the results were statistically significant. If his coding was right, the experiment was a big success.

Well, the long and short of it is that no one in Hauser’s own lab could replicate his results.

The research that was the catalyst for the inquiry ended up being tabled, but only after additional problems were found with the data. In a statement to Harvard officials in 2007, the research assistant who instigated what became a revolt among junior members of the lab, outlined his larger concerns: “The most disconcerting part of the whole experience to me was the feeling that Marc was using his position of authority to force us to accept sloppy (at best) science.”

Hauser was found to be solely responsible for the discrepancies, and as of the date of the Chronicle Review article, was on leave.

The whole story is testimony to the sheer need some have to prove that apes and monkeys are just fuzzy people or we are just naked apes. Life, whatever it is, is not that simple.

According to Hauser’s Edge bio, Read More ›

In Isaac Asimov’s 1958 futuristic short story “The Feeling of Power,” Myron Aub is a technician who rediscovers arithmetic. Aub’s future world is one dominated by computers which do all the number crunching and people who not only are mathematically-challenged but, more importantly, don’t see the point. What good is math anyway? Today evolution has had a similar effect on our thinking. Just as computers can dull our mathematical skills, evolution dulls our critical thinking skills.  Read more

“Keep walking back with your kite.  There you go.  Now stop where you are.  The distance between you and me right now is equivalent to about half the height of California redwoods—the tallest trees on earth.  Can you imagine that?” This was my stab at an illustration of how tall trees can really get.  But my eight year old son was having none of it.  “Wind all that string around the reel Dad, and let’s go home!”  Disappointed as I was with his response to my efforts, it was plainly obvious that he had to see something a lot more well-grounded than an unwound length of string tied onto a diamond-shaped piece of flyable canvas. Read More ›

Since I am a cell biologist and immunologist by training, it is with great interest that I read Kathryn Applegate’s May BioLogos posts drawing parallels between adaptive immunity and evolution. In the first essay she claims that antibody “production requires randomness at multiple levels” and that God may use random processes to create “life over long periods of time.” In the second post Dr. Applegate goes on to suggest that evolution uses “the same kinds of mechanisms, except the mutations occur in germ cells…”

These are interesting hypotheses, but I am not convinced that the elegant processes whereby B cells differentiate and germ cells are formed actually give rise to the conclusions drawn. Good science is dependent on accurately distinguishing between data, interpretation of data, extrapolation from data, and even speculation; in these posts this has not been adequately accomplished. In fact, even the science is faulty in places. To explain, the data shows that B cells manufacture over 1015 different antibodies using less than a couple of hundred gene segments. They accomplish this feat by rearrangements and excision of DNA sequences—these occur in a highly regulated fashion that has been extensively described in the literature. These facts have been established by interpretation of vast amounts of data.

However, I would like to suggest that the claims that B cell differentiation is 1) random, 2) a model for the way that God created life, and 3) that evolution “works” by B-cell-like mutations in the germ cell line, or 4) that germ cell formation is in any way analogous to antibody formation are based on a one-sided explanation of the science and much speculation. Dr. Applegate states that God could have done it this way; I do not dispute this. After all, if He is God, it is logical that He can do whatever He wants. Read More ›

I’m debating Michael Shermer at Washburn University in Topeka Kansas tonight at 7:00pm CST. The topic of the debate is on ID and its scientific status. The debate is being streamed here (scroll down): http://www.challengewashburn.com

Conventional, and fairly obvious, wisdom would suggest that the bear avoids being noticed by its prey by blending in with the landscape and moving through the snow on silent feet. Evolving that way should be easy enough – the colour gene drops out, and … We readily assume that the prey is on land, casting a wary eye around. Not necessarily. Some remarkable BBC footage suggests it may not be so simple: You can see it, no problem, but you must click the BBC link. – d. Here, you will hear the bear stomping and see it clearly visible above clear ice – as it would be to a seal approaching a blowhole. Presumably, the seal – apprised of an Read More ›

Shortly after World War II Mochitsura Hashimoto was summoned to the United States to give testimony in the trial of Charles McVay. Hashimoto’s and McVay’s fates intersected just after midnight, July 30, 1945, when the Japanese submarine I-58, commanded by Hashimoto, sunk the cruiser, the USS Indianapolis, commanded by McVay.  Read more