Saturday, March 23, 2013

The Chaotic Paths of Evolution

Evolutionary Paths. In a paper published in the November 2012 issue of BioScience (1) researchers led by Shozo Yokoyama at Emory University have labeled “highly questionable” assumptions relied upon to study the evolution of protein molecules. One of these assumptions is that changing a particular gene in a known location would affect the properties of ancestral and modern protein forms in the same way. That assumption allows computers to infer likely evolutionary paths leading to the forms of proteins found in modern organisms.

Doubts on Molecular Adaption. In experiments designed to test these assumptions, Yokoyama created hypothesized ancestral visual pigments and variants of them that might have been produced by mutation. What he found was that properties of related version of proteins often changed in different ways when the same mutation was introduced in each. This caused standard computational and statistical methods to rarely be able to identify the experimentally supported evolutionary pathway. Yokoyama concludes that his studies cast “serious doubt” on the “fundamental principles of molecular adaptation” used in thousands of papers.

No Going Back. In a related article (2), a University of Oregon team found that evolution can never go backwards. The team reconstructed the gene for a glucocorticoid receptor in the version that existed more than 400 million years ago. They found that over a rapid period of time, random mutations in other proteins caused changes in the protein’s structure which made it incompatible with the receptor’s primordial form. In other words, there is evolutionary bridge burning, which implies that the direction evolution took may be neither ideal nor inevitable.

Thursday, March 14, 2013

Mind and Cosmos

In his new book, Mind and Cosmos, Thomas Nagel, an atheist and professor of philosophy at New York University, joins a growing number of other philosophers and scientists in challenging evolution, albeit without offering an alternative.

Nagel’s argument is with reductive materialism, the idea that atoms and molecules and physical laws can explain everything in biology, including evolution. As pointed out in several reviews (e.g. NY Times) his knowledge of biology and evolution is superficial and, at times, outdated. As he readily admits, his discussion “is just the opinion of a layman.” But in his layman's opinion evolution is counterintuitive, it “flies in the face of common sense.” It doesn’t seem to occur to him that if that were the basis of scientific research, quantum theory, the most counterintuitive area of physics, would never have been accepted, despite the overwhelming evidence that it accurately describes reality as we know it.

Consciousness? Despite the false starts, Nagel’s argument eventually turns to more solid footing, that of consciousness. As he argued in his influential paper in the 1970s "What Is It Like To Be a Bat?" the experience a bat feels in its own mind is not knowable by simply knowing the chemistry of its brain. Nagel doubts that mind and consciousness could ever be explained by a materialistic description. Since Neo-Darwinian evolution is based on materialism, it can never explain mind and consciousness. Despite efforts to describe consciousness by invoking brain function, biologists have had a very difficult time in even defining consciousness.

Wednesday, March 6, 2013

The Universe We Created

John Wheeler (1911-2008) was an eminent physicist, dreamer, colleague of Albert Einstein and Niels Bohr, mentor to many of today’s most eminent physicists, and the coiner of such terms as black hole, quantum foam, and wormhole. And he is also the creator of an intriguing thought experiment in quantum physics which may mean that we are the creators of our own universe.

One of the main tenets of quantum mechanics is that our observation of the universe directly affects its properties and behavior. In the traditional double slit experiment, the way one observes a photon, for example, determines whether the photon travels like a wave or a particle.

Delayed Choice Experiment
Wheeler’s thought experiment, called the delayed choice experiment, took it one step further. What if one makes the decision of whether or not to observe the photon at the last moment, after the photon has already passed a certain point and “has already made its decision” of whether it will be a particle or a wave? Wheeler proposed this thought experiment on a grand scale by proposing that we observe light from a quasar, light which has been traveling for billions of years long before there were any humans to observe it. The measurements made now, according to Wheeler, would determine the photon’s past.

Monday, March 4, 2013


It has been an accepted fact that basic research is something that only government can invest in and promote on a large scale since private industry needs commercial payoff relatively quickly. Our leadership in the world has depended on government investment in basic research. Today, however, the NIH budget stands at a woefully low level.

Lowest Investment
In constant dollars adjusted for inflation, the NIH budget in fiscal year 2012 is $4 billion less than it was in 2003 and is at the lowest level since 2001. The number of research grants funded by NIH has declined since 2004. In 2012 NIH funded 3,100 fewer grants than in 2004.