Biology

Some of you might have heard that Jonathan Schaeffer and his team at the U. of Alberta recently solved the game of checkers. It made big news in the computer science world.

I first met Jon at the First Computer Olympiad in London (organized by the famous David Levy of chess and computer-chess fame) at which Jon’s program won the gold medal and mine won the silver.

Jon and his team eventually computed the eight-piece endgame database for checkers, and later my colleague Ed Trice and I computed it as well. Jon and I compared results, and it turned out that his database had errors that had evaded his error-detection scheme. This scheme produced internally consistent results, despite the errors. Later, Jon detected errors in my database, which were traced back to a scratch on a CD that evaded my error-detection scheme.

All the errors were eventually traced to data transfer anomalies and not the generative computational algorithms, so CRC (cyclic redundancy check) methods were used to solve the problem.
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BOOK REVIEWED–In Pursuit of the Gene: From Darwin to DNA by James Schwartz Harvard University Press: 2008. 384 pp. Fruitful collaborations were formed in Thomas Hunt Morgan’s fly genetics lab. When I was a student, ‘doing genetics’ meant crossing two different strains or species. Now it means sequencing DNA, preferably human. Between these two poles lies the history of genetics, a pathway fraught with sharp turns, steep gradients and dead ends — and engagingly recounted in James Schwartz’s new book. Despite its subtitle, In Pursuit of the Gene is not a comprehensive history of genetics, but focuses solely on classical genetics. Schwartz, a science writer, begins with Charles Darwin’s ill-fated ‘pangenesis’ theory of the inheritance of acquired characteristics, and runs Read More ›

I watch very little television, but I enjoy The History Channel (THC). I’ve learned a lot from it. When it comes to hard science and engineering they do a very good job. I’ve particularly enjoyed their programs about the history of aviation, since I’m a software engineer in the aerospace R&D industry with hundreds of hours of airtime in hang gliders and have a special interest in aerodynamics and aviation history.

When it comes to aviation, THC gets it right, virtually all of the time.

It was thus with trepidation that I watched “How Life Began” last evening. The title of the show was a dead giveaway about what I would see, hear, and experience. The title of the show should have been “How Did Life Begin?” and the answer should have been, “No one has the faintest idea.”

But no, we are presented with endless speculation that doesn’t withstand even the most trivial scrutiny, and are given the impression that “science” has the solution well in hand, with only minor details to be filled in.

We are also greeted with the usual obligatory assurances that “religion” and “evolution” are perfectly compatible, if one has a proper intellectually and materialistically enlightened interpretation of religion*. White-collared Fr. Coyne is prominently displayed as an apologist for this thesis, and assures viewers that “intelligent design” is superbly unnecessary as an explanation for the origin of life. Eugenie Scott would be proud of him.

The big problem with “How Life Began” is that no hard questions are ever asked, much less addressed. We take a journey into the Life, Inc. factory, where all the mysteries of the origin of life are explained.

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Core ID and ID-compatible hypotheses have various predictions. For example, there’s the confirmed predictions related to junk DNA and genetic nature of the platypus, the predictions about designer drugs, long-term preservation mechanisms for conserving information that is not currently implemented, and retroviruses being capable of being used to implement designed changes. At this time the scientific research we have so far does not provide conclusive positive evidence for some of these predictions, although there are tantalizing glimpses that such predictions may become known to be true. There’s also some types of observed changes that happen so rapidly and repeatedly that they would seem to defy being within the domain of strictly Darwinian processes. But such research is just beginning. (And Ken Miller claims that ID cannot make predictions and research cannot occur…)

But then there’s the predictions specific to ID-compatible hypotheses such as front-loading.
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Leaves have been found to regulate temperature to “around 21.4° Celsius plus or minus 2.2 degrees,” during photosynthesis. That appears to me to be a design to increase or optimize photosynthesis.

ID Hypothesis: Trees, and other biotic systems regulate leaf temperature to increase or optimize photosynthesis. There will be temperature and/or humidity sensors and transpiration regulation systems to achieve this temperature control.
Corollary: Net primary productivity would be substantially lower without such temperature regulation.
Global Warming Impact: This finding may invalidate tree ring temperature proxies in extrapolating to past temperatures to evaluate climate change.
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Goldilocks tree leaves
by Susan Milius, June 11th, 2008,

Sweating in the heat or huddling in the cold keeps temperatures favorable
JUST RIGHTTree leaves can do plenty to keep their temperatures just right for photosynthesis. Read More ›

Muller received the Nobel Prize for “for the discovery that mutations can be induced by x-rays”. He studied the effects of mutation on populations, and indirectly spawned ideas which were elaborated in the book Genetic Entropy by Cornell geneticist John Sanford.

The theory of genetic entropy has the potential to overturn Darwinism on empirical grounds alone. Darwinism argues for inevitable progress, genetic entropy argues the opposite.

The thesis of genetic entropy can be explored by considering the amount of mutation in the human genome at present. Muller offers his thoughts:

it would in the end be far easier and more sensible to manufacture a complete man de novo, out of appropriately chosen raw materials, than to try to fashion into human form those pitiful relics which remained…

it is evident that the natural rate of mutation of man is so high, and his natural rate of reproduction so low, that not a great deal of margin is left for selection…

it becomes perfectly evident that the present number of children per couple cannot be great enough to allow selection to keep pace with a mutation rate of 0.1..if, to make matters worse, u should be anything like as high as 0.5…, our present reproductive practices would be utterly out of line with human requirements.

Hermann Muller quoted by John Sanford
Appendix 1, Genetic Entropy

“u” is the mutation rate. As John Sanford observes, Darwinian selection cannot keep pace with reality. Deterioration of the genome seems to be in evidence, and the efficacy of Darwinian mechanisms has been essentially falsified with respect to the human genome. Here is an excerpt of Sanford commenting on Muller’s work:

Muller calculated that the human fertility rate of that time (1950) could not deal with a mutation rate of 0.1. Since that time, we have learned that the mutation rate is a least 1,000-fold higher than he thought. Furthermore, fertility rates have declined sharply since then.

John Sanford

Walter ReMine was kind enough to point me to a more modern day version of Muller’s concerns: Why have we not died 100 times over? by Kondrashov (also from Cornell).
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Multiple mutations needed for E. coli

An interesting paper has just appeared in the Proceedings of the National Academy of Sciences, “Historical contingency and the evolution of a key innovation in an experimental population of Escherichia coli”. (1) It is the “inaugural article” of Richard Lenski, who was recently elected to the National Academy. Lenski, of course, is well known for conducting the longest, most detailed “lab evolution” experiment in history, growing the bacterium E. coli continuously for about twenty years in his Michigan State lab. For the fast-growing bug, that’s over 40,000 generations!
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Here’s an interesting article in the NYTimes regarding science education in Texas. Laura Beil, the author, outlines the long-standing (pre-Dover) attempt by critics of evolutionary theory to teach the theory’s “strengths and weaknesses.” Although mandating that the weaknesses of evolutionary theory be taught falls well short of attempts to mandate the teaching of intelligent design, this too is unacceptable with hardcore evolutionists such as the National Center for Selling Evolution (NCSE). Their strategy to counter it? Treat any attempt to teach weaknesses of evolutionary theory as stealth creationism, therefore as religion, and therefore as unconstitutional. This approach, however, may backfire. The NCSE cannot simply deny that there are any known weaknesses to evolutionary theory, because laundry lists outlining failures of Read More ›

Awesome. The alternative biofuel part of the talk starts at 13 minutes. I highly recommend watching it all.

Research often shows no apparent effect (phenotype) of deleting most genes. Hillenmeyer et al now find that 97% of yeast genes have an important biological function. Optimal growth requires nearly all genes in absence of “rich” medium in the lab. Sounds like robust design. Read More ›

John Wakeley1 Abstract Arising from: N. Patterson, D. J. Richter, S. Gnerre, E. Lander & D. Reich Nature 441, 1103–1108 (2006); Patterson et al. Genetic data from two or more species provide information about the process of speciation. In their analysis of DNA from humans, chimpanzees, gorillas, orangutans and macaques (HCGOM), Patterson et al.1 suggest that the apparently short divergence time between humans and chimpanzees on the X chromosome is explained by a massive interspecific hybridization event in the ancestry of these two species. However, Patterson et al.1 do not statistically test their own null model of simple speciation before concluding that speciation was complex, and—even if the null model could be rejected—they do not consider other explanations of a Read More ›

For many years I was an avid hang glider pilot, and one of my specialties in aerospace R&D is Guidance, Navigation and Control software development for precision-guided airdrop systems.

During many of my hang glider flights I had the opportunity to observe, from an unusual perspective, hawks in their native environment — the air. Flying wingtip to wingtip at the same airspeed, one gets a profound appreciation for these amazing creatures and their GN&C.

On a number of my hang glider flights, hawks came up close. They always seemed to be curious about me, flying my lumbering 32-foot-wingspan Dacron and aluminum aircraft. Up this close, I could observe the subtle adjustments they made in their primary feathers to compensate for the turbulence in the air, and they would glance furtively at me.
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I recently assisted my daughter with a most interesting project for her 8th grade science class. The assignment was to learn about a Biome, write a report on it, then design an animal to live in it.
The students were to provide a description of the characteristics of their animal which suited it to life in the Biome they selected, and make a model of the animal for display. My daughter selected arctic tundra for the Biome. We read up on it, she did the report, then the fun began.

She has a housecat, (felis-catus) named Chester of whom she is very fond. He seemed a good starting point. We designed several adaptations to Chester to enable him to thrive in the arctic tundra. First, and most obviously, we made him all white to blend into the snow. Then we regressed his legs to vestigial stumps and flattened him out dramatically so he could hug the ground and better avoid being picked off by predators, as well as stay low out of the wind. His species is therefore felis-flatus. (That’s “flatus” as in flat to the ground, rhymes with “catus” not the other meaning which my son already had fun with.)
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Experimenters have recently found that genes–whereby they mean particular sequences of DNA–can “find” one another without the intervention of proteins or other factors. It appears to be strictly an effect caused by electrical charges along the DNA strand; the longer the ‘gene’ (that is, sequence length), the greater theapparent ease in ‘finding’ one another. The experimenters feel that this finding is a help for figuring out what happens during homologous recombination.

Here’s part of what they say: The researchers observed the behaviour of fluorescently tagged DNA molecules in a pure solution. They found that DNA molecules with identical patterns of chemical bases were approximately twice as likely to gather together than DNA molecules with different sequences.

Professor Alexei Kornyshev from Imperial College London, one of the study’s authors, explains the significance of the team’s results: ‘Seeing these identical DNA molecules seeking each other out in a crowd, without any external help, is very exciting indeed. This could provide a driving force for similar genes to begin the complex process of recombination without the help of proteins or other biological factors. . . .’

The article from ScienceDaily is here.

I have an OOL question: This study strongly suggests that similar DNA sequences have a preferential attraction for one another. And the longer the similar sequence, the greater the attraction. If that is the case, then, if a particular ‘gene’ began to ‘replicate’, wouldn’t the replicated ‘genes’ congeal together?

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Because of a prediction, a very strong prediction, I made on another thread, I’ve had reason to look into just what has been happening to Darwin’s finches way off on the Galapagos Islands.

Here is a paper published last year in Science Magazine by the Grants, experts in Darwin’s finches. I looked at their paper, looked at their data, and have come to the conclusion that what I predicted as the ultimate explanation to changed beak sizes is the more reasonable interpretation of the data they present.

But before we even get to the data, here’s a remark from a National Geographic website review of the article that supports my basic position:

“ Researchers from New Jersey’s Princeton University have observed a species of finch in Ecuador’s Galápagos Islands that evolved to have a smaller beak within a mere two decades.
Surprisingly, most of the shift happened within just one generation, the scientists say.”

The shift happened in ONE year? What kind of population genetics are at play here?

Well, to the data:
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