## Monday, December 26, 2005

### Evolution and the genome

The editors of the Science magazine have chosen the evolution - more precisely, the direct observations of evolution through the genome - to be the scientific breakthrough of 2005.

I think it is a fair choice. The analyses of the genome are likely to become a massive part of "normal science" with a lot of people working on it and a lot of successes and potential applications for the years to come. I expect many discoveries in this direction to shed light on the past lifeforms; on the explicit relationships between the currently existing species and their common ancestry; the evolutionary strategies of diseases and our strategies to fight them; and finally on the new possible improvements of the organisms that are important for our lives, and - perhaps - the human race itself.

Stem cell fraud

Incidentally, the breakthrough of the year 2005 for the U.S. particle physics is called "Particle physicists in the U.S. would like to forget about 2005" which may be fair, too. However, the situation is still better than in stem cell research where some of the seemingly most impressive results in the past years - those by Hwang Woo Suk from Korea - have been identified as an undisputable fraud. Steve McIntyre points out that Hwang was one of Scientific American's 50 visionaries together with Michael Mann who, after a comparable incident (one involving the "hockey stick graph"), was not fired but instead promoted. Steve McIntyre has also written the world's most complete chronology of the scandal. Google tells you more about the sad story of scientific consensus behind the former Korean national hero. It's amazing how this fraud that no one could apparently reproduce immediately gained 117 citations. Should we believe the Koreans - without testing them - because they are so skillful in manipulating the chopsticks? Or perhaps because it is nice to see that the U.S. science is falling behind - "certainly" because of George W. Bush? Have the people in that field lost their mind? Or is it really the case that the whole cloning field - or perhaps even all Bush critics in the world - are participating in a deliberate international fraud?

Back to the positive story: the genetic evidence for evolution.

New tools make questions solvable

New scientific methods and technologies often have the capacity to transform an academic dispute whose character used to be almost religious into an obvious set of facts. Let me give you two examples.

The death of hidden variables

The first example are Bell's inequalities. Before they were found, it was thought that no one could ever determine whether the quantum mechanical "randomness" was just an emergent process based on some classical "hidden variables"; this debate was thought to be a philosophical one forever. After the inequalities were found and the experimental tests confirmed quantum mechanics, it became clear that the quantum mechanical "randomness" is inherent. It cannot be emergent - unless we would be ready to accept that the underlying hidden variables obey non-local (and probably non-relativistic) classical laws of physics which seems extremely unlikely.

Sun's chemistry and spectroscopy

My second example goes back to the 19th century. Recall that the philosopher Auguste Comte, the founder of positivism, remarked in his "Course de philosophie positive" that the chemical composition of the Sun would forever remain a mystery.

It only took seven years or so, until 1857, to show that Comte was completely wrong. Spectroscopy was discovered and it allowed us to learn the concentration of various elements in the Sun quite accurately. Unfortunately, this discovery came two years after Comte's death and therefore he could not see it. Incidentally, two more years later, in 1859, Darwin published his theory.

The last we-will-never-know people

Many people have been saying similar things about physics in general: physics could never determine or explain UV or XY - and all of these people have already been proved wrong except for those who argue that the parameters of the Standard Model can't be calculated with a better accuracy than what we can measure; the latter group will hopefully be proved wrong in our lifetime.

Speed of evolution

What do the new discoveries tell us about the evolution? First of all, evolution is not fuzzy. It is "quantized", if you allow me to use physics jargon, and the evolutionary changes are directly encoded in the genes that can be equally easily decoded.

A related and equally important observation is that the evolutionary changes are quite abrupt. We have never observed skeletons of bats with one wing and similar creatures - as the creationists (including those in a cheap tuxedo, using the words of pandas from level 2) have been quite correctly pointing out for decades. Indeed, it often takes a single mutation only to establish a new species.

Many mutations are harmful and they become immediately a subject of natural selection. Some mutations allow the organisms to survive. All these changes were making the tree of life ramify all diversify - and they are still doing so although this process is nowadays slower than some other types of developments.

Let me finally choose an article from Dembski's blog in which he reposts

It is entertaining to see a text whose political part is more or less true but the scientific one is so clearly and completely wrong. Let's clarify some errors of Buchanan's:

• In his “Politically Correct Guide to Science,” Tom Bethell ...

Surprisingly, the book is called "Politically Incorrect...", not "Politically correct...". Tom Bethell is rather unlikely to be politically correct.

• For generations, scientists have searched for the “missing link” between ape and man. But not only is that link still missing, no links between species have been found.

Because there are no highly refined intermediate links of the type Buchanan suggests; one mutation often makes these changes occur and the evolution is far from being a smooth, gradual, and continuous process. However, chimps' genome has been decoded. We can not only see that chimpanzees are our closest relatives but also deduce the existence of a common ancestor. Our relationship with the chimps is no longer a matter of superficial similarity; a long sequence of bits - a microscopic genetic information - reveals a much more detailed picture.

• As Bethell writes, bats are the only mammals to have mastered powered flight. But even the earliest bats found in the fossil record have complex wings and built-in sonar. Where are the “half-bats” with no sonar or unworkable wings?

Half-bats with unworkable wings are predicted by Darwin to die quite rapidly, so there should not be too many fossils around. Observations seem to confirm this prediction of Darwin's theory, too. Indeed, such changes must proceed quickly and today we know that a single change of the genome is capable to induce these macroscopic changes.

• Their absence does not prove — but does suggest — that they do not exist. Is it not time, after 150 years, that the Darwinists started to deliver and ceased to be taken on faith?

Don't tell me that you don't think that this comment of Pat Buchanan sounds just like Peter Woit. ;-) Let me remark, in both cases, that 150 years and maybe even 30 years is probably a long enough time to start to think about the possibility that the "alternatives" to evolution or string theory can't ever work.

• No one denies “micro-evolution” — i.e., species adapting to their environment. It is macro-evolution that is in trouble.

First of all, it is not a trouble - it was chosen to be the most spectacularly confirmed scientific paradigm by discoveries done in 2005. Second of all, the difference between "micro-evolution" and "macro-evolution" is just a quantitative one. Most of the errors that Buchanan and other creationists do can be blamed on this particular error in their thinking: they incorrectly believe that objects in the world can be dogmatically and sharply divided to alive and not alive; intelligent and not intelligent; micro-evolution and macro-evolution. (And of course, someone would also like to divide the whole human population to believers and non-believers.)

Neither of these categories can be quite sharply defined. Even though the species are defined by "discrete", "quantized" bits of information encoded in the genome, it does not mean that each species can be classified according to some old, human-invented adjectives. Science does not break down but the adjectives used in the unscientific debate - or the Bible - certainly do break down when we want to understand life (or the whole Universe, for that matter) at a deeper level.

The world is full of objects whose "aliveness" is disputable - such as the viruses. The same world also offers evolutionary steps that can be safely classified neither as micro-evolution nor as macro-evolution. Finally, there are many organisms in the world that are only marginally intelligent, and I am afraid that this group would include not only chimps but maybe also some syndicated columnists. ;-)

• The Darwinian thesis of “survival of the fittest” turns out to be nothing but a tautology. How do we know existing species were the fittest? Because they survived. Why did they survive? Because they were the fittest.

I completely agree that the operational definition of the "fittest" is circular. It is the whole point of Darwin's notion of natural selection that "being the fittest" and "have a higher chance to survive" are equivalent. However, there is also a theoretical way to derive whether an animal is "the fittest" which can be used to predict its chances to survive. Such a derivation must, however, use the laws of nature in a very general sense - because it is the laws of nature that determine the chances to survive. Sometimes it is easy to go through the reasoning. A bird without legs in between the tigers does not have a bright future. Sometimes the conclusion is much harder to make. But the main message is that these questions can be studied scientifically and the answers have definitely influenced the composition of the species on our planet.

• While clever, this tells us zip about why we have tigers.

"Why we have tigers?" is not a scientifically meaningful question unless a usable definition of a tiger is added to it as an appendix. The Bible can answer such verbal, non-scientific question, by including the word "tiger" in one of the verses (and by prohibiting everyone to ask where the word and the properties of the animal came from). Science can only answer meaningful questions. For example, we may try to answer the question why the hairy mammals - beasts of prey - whose maximum speed exceeds 50 mph have evolved.

• It is less a scientific theory than a notion masquerading as a fact.

It is somewhat entertaining that the word "notion" is apparently supposed to have a negative meaning. Notions, concepts, and ideas are an essential part of our theories - and the word "theory" is not negative either because the best and most reliable things we know about the real world are theories based on notions and ideas.

• For those seeking the source of Darwin’s “discovery,” there is an interesting coincidence.

Those who judge the validity of a scientific theory according to the coincidences that accompanied its original discovery are intellectual equivalents of chimpanzees, and therefore they are another piece of evidence for evolutionary biology.

• As Bertrand Russell observed, Darwin’s theory is “essentially an extension to the animal and vegetable world of laissez-faire economics.”

I completely agree with that. This is why both Darwin's theory as well as capitalism are the leading paradigms among their competitors. Many general ideas are shared by these two frameworks; other ideas are quite independent.

• If it is science, why can’t scientists replicate it in microcosm in a laboratory?

Of course that they can replicate many particular examples in their labs. They can't replicate them exactly with the same speed as they occured in Nature because such labs would have to cover 510 million squared kilometers and they would have to work for 5 billion years. Nevertheless, the process can be sped up in many ways, at least in some particular situations.

• If scientists know life came from matter and matter from non-matter, why don’t they show us how this was done, instead of asserting it was done, and calling us names for not taking their claims on faith?

Let me assume that the first sentence talks about the reheating, to be specific. The reason why I probably can't show Pat Buchanan how different forms of matter or non-matter are transforming into each other according to the laws of quantum field theory or string theory - and why we know that it is the case without any religious beliefs - is that Pat Buchanan apparently does not have a sufficient intelligence to understand my explanations. It's that simple.

• Clearly, a continued belief in the absolute truth of Darwinist evolution is but an act of faith that fulfills a psychological need of folks who have rejected God.

That may well be the case but such an ad hominem observation is completely irrelevant if there are clear proofs that the picture is correct.

• Hence, if religion cannot prove its claim and Darwinists can’t prove their claims, we must fall back upon reason, which some of us believe is God’s gift to mankind.

Unfortunately for Mr. Buchanan, this is not our situation because the Darwinists can prove their claims quite convincingly. By the way, the discovery of evolutionary biology is certainly one of God's big gifts to mankind, too. ;-)

• And when you consider the clocklike precision of the planets in their orbits about the sun and ...

The motion of the planets is exactly predictable by our theories. It is clocklike but not atomic-clock-like. Indeed, we can easily measure the irregularities in their motion - which means, among other things, that we will have to insert a leap second between 2005 and 2006 once again to counterbalance Nature's (or God's?) imperfection, so to say.

• ...the extraordinary complexity of the human eye, does that seem to you like the result of random selection or the product of intelligent design?

It is the result of very sophisticated laws of Nature - physics, biology, and so on - whose important "emergent" feature responsible for much of the progress is the natural selection. Natural selection is not quite random even though it can sometimes look so at short enough time scales.

• Prediction: Like the Marxists, the Darwinists are going to wind up as a cult in which few believe this side of Berkeley and Harvard Square.

It would be a bit nicer if only a few around Harvard Square believed marxism. ;-)