Friday, November 26, 2010

Very good points by Nigel Goldenfeld and Carl Woese

I just finished reading a very good recent paper by Nigel Goldenfeld and Carl Woese, Life is physics: evolution as a collective phenomenon far from equilibrium.

Carl Woese of course is famous for defining the Archaea bacteria in 1977.

Below I comment on some of their writings which I found remarkable.

Goldenfeld and Woese: "In short, a unified view prevents the unnecessary multiplication of hypotheses that is the sure sign of a lack of fundamental understanding (think epicycles!)."

Yes. The field of evolution is full of ad hoc hypotheses that is good for only one or a few phenomena. The molecular clock hypothesis is one.

Goldenfeld and Woese: "Thus, in this picture, evolution is es- sentially synonymous with population genetics. Genes are assumed to be the only dynamical variables that are tracked, and are associated with a fitness benefit that is difficult to define or measure precisely, but is quanti- fied by a fitness landscape that describes how the pop- ulation fitness depends on the genotype[56–59]. Traits are simply associated with genes, and gene interactions are often ignored, or at best handled through the fitness landscape[59, 60]."

Indeed, evolution is widely treated as the same as population genetics. Michael Lynch has this at his website "Nothing in evolution makes sense except in the light of population genetics". But this is not true at all. The overlap feature of the genetic equidistance result is the best evidence for a clear distinction between population genetics and macroevolution.

Goldenfeld and Woese: "Not only is the Modern Synthesis afflicted by strong interactions, but its very foundation is questionable. The evident tautology embodied by “survival of the fittest” serves to highlight the backwards-looking character of the fitness landscape: not only is it unmeasurable a priori, but it carries with it no means of expressing the growth of open-ended complexity[90] and the generation of genetic novelty. Thus, the Modern Synthesis is, at best, a partial representation of population genetics, but this on its own is a limited subset of the evolutionary process itself, and arguably the least interesting one."

Indeed, the modern evolution theory is only a theory of population genetics, which is the least important and interesting aspect of evolution. The more important one is the growth of open-ended complexity, which has now been described by my MGD hypothesis.

Goldenfeld and Woese: "Thus, although complexity is hard to define precisely and usefully, we regard the defining characteristic of complex- ity as the breakdown of causality[138]. Simply put, com- plex systems are ones for which observed effects do not have uniquely definable causes, due to the huge nature of the phase space and the multiplicity of paths."

I could not agree more. No unique genes define complexity. All genes contribute to complexity by reducing their level of random mutations, as described by the MGD hypothesis. It is futile to try to find a few genes responsible for disorders of the complex brain, as has been demonstrated by the failure of the GWAS effort. We are currently studying the genetic causes of common disorders of the brain as a way of further proving the MGD hypothesis.

Wednesday, November 24, 2010

Kimura said that the strongest evidence for the neutral theory is the molecular clock

A recent comment from a reviewer of my primate phylogeny manuscript again said the same thing as Scott Page has said over at Nature Precedings where my manuscript is posted that “the concept of the moleculr clock has little bearing on molecular phylogenetic studies that do not enforce a molecular clock criterion in their analyses.” Thus, there is a strong consensus in the field that even if the molecular clock is implausible which nearly everyone admits, one can still use other methods to infer molecular phylogeny within the overall paradigm originally started by the molecular clock concept. It is a self-deceiving illusion in my opinion, and I have just inserted the following into my revised manuscript (under review) to dispel it in the clearest way possible.

All traditional molecular phylogeny methods are based on the neutral theory. Early methods made explicit use of the molecular clock idea. But since the molecular clock has been widely known as implausible today, other methods have also been developed that are supposed to not to depend on the molecular clock. However, these methods are still based on the neutral theory and the neutral theory is in turn based on the molecular clock, as admitted by Kimura and Ohta: “Probably the strongest evidence for the theory is the remarkable uniformity for each protein molecule in the rate of mutant substitutions in the course of evolution.” (1). Therefore, we can conclude that all traditional molecular phylogeny methods are either explicitly or implicitly based on the molecular clock. The non-existence of the molecular clock in macroevolution as demonstrated by the overlap feature of the genetic equidistance result is sufficient to deem all traditional molecular phylogeny methods invalid for macroevolution.

1. Kimura M, Ohta T (1971) Protein polymorphism as a phase of molecular evolution. Nature 229: 467-479.

Saturday, November 20, 2010

Laws of Biology

As is well known, there are no laws in biology as in physics, which is the reason I called an idea of mine the First Axiom of Biology. Recently, however, I noted that there are in the recent literature four laws of biology. One paper is titled The three laws of biology by Trevors and Saier.

One book is titled Biology’s First Law by McShea and Brandon, which got a book review in this week’s Science magazine.

Here are the three laws of biology according to Trevors and Saier:
The First Law of Biology: All living organisms obey the laws of physics and chemistry.
The Second Law of Biology: All living organisms consist of membrane encased cells.
The Third Law of Biology: All living organisms arose in an evolutionary process.

Here is Biology’s First Law, also called “Zero-Force Evolutionary Law” (ZFEL) according to McShea and Brandon:
ZFEL (special formulation): In any evolutionary system in which there is variation and heredity, in the absence of natural selection, other forces, and constraints acting on diversity or complexity, diversity and complexity will increase on average.

Here is what ZFEL supposed to mean:
Imagine a yard containing a number of trees, and imagine that the wind blows from each point of the compass with equal probability. Come autumn, the result will be an increase in the dispersal of the leaves over time. This, they suggest, is a zero-force state because there are no directional forces acting on the leaves. Yet there is a change over time (unlike the phenomenon described by the law of inertia in physics)—the leaves that were originally clustered about the trees become more dispersed. And if an evolutionary system is similarly in a zero-force state, it too will experience an increase in divergence over time.

If there are weaknesses to these laws, it would be formost in my opinion that they are all empirically based and not axioms or self evident. No one could have come up with these laws from priori reason without knowing a lot of biology details. But it seems that most fundamental laws should be simple and self evident. Newton's laws of mechanics are all self evident and Newton called them Axioms.

Second, a major flaw of ZEEL is that it equals random diversity with complexity. It fails to recognize my First Axiom of Construction or First Axiom of Biology that that random diversity must be suppressed in order for complexity/order to advance. Complexity means order which is intuitively obvious. The human brain is the most complex. It is also the most ordered as it is capable of tasks such as mathematics. Fallen leaves become more diverse with time but do not become more ordered or reach a higher level of complexity with higher degree of order. A junk yard become more diverse with time but do not become more ordered and complex. Evolution towards higher complexity is a process from disorder to order or a process of decreasing entropy. I have found that the entropy loss is reflected by the loss of randomness/mutations in the genetic building blocks.

Third, none of the Three Laws of Biology proposed by Trevors and Saier is necessarily true. It could be easily argued that it is realistically possible for exceptions to be found in the future. There may be already exceptions if we just take a look at the existing data from a different perspective and the popular perspective is based on assumptions rather than proven truth. We have not solved the mystery of evolution and the origin of life. What we know about life may look impressive in terms of amount of data but we really know very little about what they really mean.

Finally, these four laws fail as a scientific theory by the only standard that counts which is to explain facts and predict new experiments. For example, they all have nothing to say about molecular evolution phenomenon and cannot compet/replace the neutral theory. And yet the neutral theory is inadequate for macroevolution and fails to explain most key molecular macroevolution phenomenon. Without understanding evolution, one cannot understand biology. Without understanding molecular evolution, one cannot understand evolution. For a law of biology to have little to say about molecular evolution, it can only be a trivial law.

Thus, it is safe for me to conclude that the first real fundamental law in biology is the First Axiom of Biology.