Wednesday, July 13, 2011

Making the existing model obsolete

Numerous scientists in the past 150 years have repeatedly challenged the Darwinian macroevolution theory (few has problems with the microevo part though for which Darwin and 4 others deserve our great respect). And many in the future will continue to challenge it until it falls, with ever more devastating facts and reasons. Actually, if one wants to be really honest about it as future history book would tell it, the Darwinian speculation on macroevolution has already been knocked down cold nearly 50 years ago by the first observation in molecular evolution, the genetic equidistance result. That is the reason for the invention of the ad hoc epicycyle known as the molecular clock, which must negate natural selection at the level of molecules and hence made Darwinism irrelevant/false for molecular evolution. How can one then hold on to Darwinism if it is false for molecular evolution? Well, by disconnecting molecules from phenotypes as has been done by the ad hoc Neutral theory of macroevo (again the Neutral theory of microevo is fine) for the past 50 years. But that is truly an absurd ad hoc notion since all other areas of modern biology support a tight unity as the rule rather than the sideshow. Just imagine whether any Neutralist would happily expose himself to low dose radiation. Indeed, the molecular clock hypothesis and the Neutral theory have now been proven false for macroevolution (my paper is the latest for doing just that). As a result, the existing model is largely irrelevant/false for molecular macroevolution. It is the reason for numerous false conclusions on molecular phylogeny, which we are now trying to correct.

Therefore, it is already a forgone conclusion that there is zero chance that Darwin’s macroevo theory will ever be accepted as a law of nature the way Newton’s laws are. Furthermore, because of its counter-intuitive nature, there is no chance that it will ever be accepted by the majority of the lay public no matter what the majority of scientists may say about it. However, it would not go away simply because some scientists have openly attacked it with irrefutable reasons or how absurd it truly is at its core. It must be pushed away or replaced by a better theory. And that is the only possible way. As Buckminster Fuller famously put it: “You never change things by fighting the existing reality. To change something, build a new model that makes the existing model obsolete.” The Darwinian theory however must be the hardest to replace because no other theory in the past could match it in its immense non-scientific ramifications. Even though it is a doomed sitting duck, it would remain alive and well as long as it remains the best we have got and as long as the best we can do to it is to pick on its obvious problems.

So, is there a theory on the horizon that stands a realistic chance of making the Darwinian model obsolete? Numerous scientists as well as lay people have put forward many new evolution theories that purport to be better than the Darwinian orthodoxy. (One of the latest most outspoken critics who also happens to have published his own theory is the biology professor John A. Davison, who unfortunately is more focused on fighting rather than using his theory to solve real puzzles, which may not be by choice however since his theory really has little relevance to most details of evolution.) But none has so far gained any traction. The key reason as I see it is that these theories, regardless whether their main themes are right or wrong, all fail to make themselves relevant to the detailed facts of evolution that professionals are concerned with daily in their research. None of them is relevant to molecular evolution, the most active field of evolutionary research in the past 50 years and will continue to be so for any foreseeable future in light of the genome sequencing revolution that is going on at the momment. (From my perspective, this is to be expected since I am not aware of anyone who has properly understood molecular evolution.) They cannot offer alternative interpretations to most facts that are at least equally legitimate as the existing model. This weakness is rarely realized by others especially the theorists themselves but is obvious to me for the simple reason that my own theory is like no other theory in this regard. It explains more detailed facts and does so more coherently (with the least amount of ad hoc ‘epicycles’) than the existing model. Better still, it is relevant not only to historical problems but also to major problems of today, such as common diseases (manuscript in preparation). It is more than just about evolution. In comparison, the best Darwin’s theory has done to contemporary non-evolutionary problems is really trivial, such as bacteria drug resistance. The late NAS member professor Phil Skell is famous for his position that Darwinism does not serve as the cornerstone of biological thought that many claim it does.

To solve major new problems, in addition to old ones such as the genetic equidistance result, for which the existing model has no clues about or has provided incorrect solutions, should be the most effective way of replacing the existing model. That is the way we have taken and should be the way for any challenger to take. We are unique or the first in this regard in the past 150 years since the “Origin”. It should be fun for me as well as those who have understood the new MGD hypothesis to watch in the coming years how the existing model will be made obsolete by our new one. It is only a matter of how and when rather than if, at least to me when not in my modest mood. It would be expectedly a long and hard struggle but nonetheless interesting to watch. It has been almost 4 years now and so far so good. We are still at the first stage of three stages that a new idea would typically go through on its way to accepted truth. This is the stage of being ignored. It is extremely positive at this stage however that we have not seen a knock out punch from any of the critics who are reviewers of our papers, friends, colleagues, and Internet forum commentators. Also positive is the fact that we are having easier and easier time getting published in mainstream journals and we have met a few good reviewers who have understood and liked our ideas. We are presently submitting manuscripts that would hopefully mark the end of the first stage. We are using our ideas to solve real world problems of everyday life, which would make it hard for people to ignore. We will force our ideas on to the working benches of medical genetists who could care less about evolution theories.

I view scientific discovery at the highest level, i.e., the level of laws, as creations, in the same sense as a great piece of art. I had an ambition and serious training to be an artist in my youth even though I also enjoyed mathematics. I speak in part from personal experience that science at this level is revolutionary art/artist in every important aspect, including aesthetics, simpliticity, seemingly impossible unity of polar opposites, fine tuned perfection, destruction, joy to the creator, solitude, struggle, and bipolar temparament. To anyone with an ambition of doing science at this level, the following words should be inspirational.

Every act of creation begins with an act of destruction.

Pablo Picasso

A successful work of art is not one which resolves contradictions in a spurious harmony, but one which expresses the idea of harmony negatively by embodying the contradictions, pure and uncompromised, in its innermost structure.

Theodore Adorno

(Yes, the MGD hypothesis coherently unites micro- and macro-evolution not by ignoring their differences/contradictions like the existing model does but by highlighting it and making a point of their opposite natures.)

The man with a new idea is a crank - until the idea succeeds.

Mark Twain

We think in generalities, but we live in detail.

Alfred Whitehead

(The MGD hypothesis has universal intutions and takes care of a vast number of details. The Darwinian model of macroevolution or any other evo theory in the past fails on both accounts: it has no presentable or sensible generalities and cannot account for key details such as the genetic equidistance result.)

A creation of importance can only be produced when its author isolates himself, it is a child of solitude.

Johann Wolfgang von Goethe

The reasonable man adapts himself to the world; the unreasonable one persists in trying to adapt the world to himself. Therefore all progress depends on the unreasonable man.

George Bernard Shaw

The mere formulation of a problem is far more often essential than its solution, which may be merely a matter of mathematical or experimental skill. To raise new questions, new possibilities, to regard old problems from a new angle requires creative imagination and marks real advances in science.

Albert Einstein

(The solution to the nearly half a century old puzzle of genetic equidistance and the realization of a new feature of it--the overlap feature—as we have achieved in recent papers should be a watershed event in the history of evolutionary science. I have come to realize that doing science at the highest level means asking new questions in places of detail where few thought there is a problem. The most important problems are not those grand ones out in the open, which are either logical next step questions or un-solvable ones with today’s knowledge. No science can be greater than revolutionary science. Revolution necessarily means to see unsolved problems in little details that the existing model does not see or has fooled everybody to think solved. More difficult for revolutionary science today, as compared to Copernicus’s days, is to not merely deem the existing model wrong but must also make its proven virtues shine even brighter as a part of the new model. This is difficult in practise because it means that you must know enough about the existing model but in doing so you risk being fooled by it or becoming an insider. And few revolutions were started by insiders. One way to get around this is to have your revolutionary idea first and then get yourself acquainted with the existing model. If the idea is of the axiom kind, one could in principle come up with it without any expertise in any particular branch of science. There is no reason that the First Axiom of Construction that I proposed should be beyond the capabilities of ancient people 5000 years ago.)

Much Madness is divinest Sense —

To a discerning Eye —

Much Sense — the starkest Madness —

’Tis the Majority

In this, as All, prevail —

Assent — and you are sane —

Demur — you’re straightway dangerous —

And handled with a Chain —

Emily Dickinson

Making the simple complicated is commonplace; making the complicated simple, awesomely simple, that's creativity.

Charles Mingus

(To connect a simple intuition/axiom with a vast number of details of science is not obvious before it is done. It is no different and could be as hard as to go from axioms to a proof of a hard mathematical hypothesis. Biologists face the task of distilling the common pattern/axiom by observing a vast number of natural and seemingly isolated facts. The more facts and hence more complexity one needs to account for the harder it is to find the common simple pattern/axiom. Hence creativity at this level is hard and the outcome is the most beautiful. The ultimate beauty is the unity of the ultimate complexity with the ultimate simplicity. Professor Stephen Wolfram expressed similar views in his “New Kind of Science” that simple rules/patterns underlie the unfolding of complexity in nature.)

When I am working on a problem I never think about beauty. I only think about how to solve the problem. But when I have finished, if the solution is not beautiful, I know it is wrong.

Buckminster Fuller

Below is short piece inspired by the above quotations, titled “Science at its best is art”

In science, no ad hoc epicycles is a sure sign of simplicity and hence beauty. No ad hoc epicycles of course means no contradictions. To be a great scientist, it helps if not necessary to have training in classical art and to develop a good taste in aesthetics.

First, good taste concerns motivation and choice of fields. It would lead one to be bored with mere filling details kind of routine science. Nonetheless, science needs both kinds of scientists, the majority happy with routines while an extreme minority unhappy with it. Finding/creating laws of great importance is so much more aesthetically appealing than mere fact/stamp collection. Of course it is practically much harder to achieve success and carries a high risk of failure, but an appreciation for aesthetics is usually tied to idealism rather pragmatism. People whose first priority is to feed oneself and one’s family are less likely to be concerned with aesthetics or even truth. Not every one can afford to be idealistic and those few who can should consider themselves lucky. One thing positive out of China’s Cultural Revolution under Chairman Mao’s leadership is the upbringing of a generation of young idealistic dreamers who did not waste their youth devoted to passing exams and therefore were fortunate to have had a more complete development of all human faculties. If I would turn out to be successful, the Darwinists should in part blame it on a member of their own cohort, Mao.

Second, art training concerns standard of beauty and ability to spot ugliness. It would lead one to have a keen eye/sense for imperfections and imbalances, and to pay attention to the whole or the unity of details within the whole. The little imperfections/imbalances that most see as trivial would appear glaringly disturbing to the aesthetically gifted/trained. While doing painting in my youth, I learned to routinely look at my work from a distance in order to keep balance of the whole. "Go some distance away because the work appears smaller and more of it can be taken in at a glance, and a lack of harmony of proportion is rapidly seen." -- Leonardo da Vinci. So, training in art would almost surely lead one to become obsessed with harmony, an essential quality of a great scientist.

Good taste in aesthetics prevents the publication/release of premature productions. I am constantly amazed by the fine tuned perfection of a great piece of music or painting. Any little twist would make it worse and every little detail is a logical necessity. A great art is always born (meaning published or released to the public) perfect, with the creator alone deserving the sole credit for it. There are no peer reviewers or high impact journals necessary to make great art happen. The artist has a universal standard for perfection that he can apply to his work himself, which is beauty and harmony, which makes peer review unnecessary. The great scientist has that standard too and would not publish a work that lacks beauty. Beauty and a creater of good taste serve as the best safeguard against faulty productions. Beauty alone in his work is sufficient for a lone creator to challenge the world, not to mention betting his life on it.

Third, art trains the intuitive sense, essential for creativity in science as in anything else.

Finally, art trains the mind to be able to better spot the main features/patterns among noises. The trained or gifted in art can paint a portrait of a live person that looks like the real person but the others cannot. Learning to paint nature the way it is may help the mind to more easily grasp nature for what it is in scientific terms. Both the artistic and scientific renditions of nature require a common faculty of the mind, a keen sense for the major features of nature. A common error for most evolutionary biologists is to mistake the noise and trivial as the main feature. Their portraits of nature are like the paintings of the untrained.

Saturday, July 9, 2011

Second Axiom of Construction and Second Axiom of Biology

The Second Axiom of Construction and the Second Axiom of Biology posit that any system can allow a certain degree of random noises or errors in its building blocks, and such limited degree of random errors may confer zero, negative, or positive values to the functioning/survival of the system under certain random environmental circumstances.

This axiom underlies the whole of the modern evolution theory composed of Neo-Darwinism and Kimura’s Neutral theory and is the foundation for microevolution and population genetics where there is no change in system complexity over time. (In contrast, the First Axiom of Biology is the foundation for macroevolution where there is change in system complexity over time.)

For the neutral errors that confer zero values to the functioning/survival of the system under a certain random environmental circumstance, the accumulation of such errors is determined by random drift and linearly related to time, as described by Kimura’s neutral theory. For the non-neutral errors that confer either negative or positive survival values, the survival values are dependent on the environmental circumstances, which are and can only be random in nature. Thus, the accumulation of non-neutral errors is determined by random natural selection by random environmental circumstances. Since natural selection is overall a completely random process (see my post on April 9, 2009 and other posts on the random nature of natural selection), the fixation of non-neutral mutations by natural selection is effectively no different from that of neutral mutations and is therefore also linearly related to time given long enough time that allows for multiple rounds of selection and de-selection. Thus, the genetic distance between any two species is linearly related to time like a clock, regardless whether the errors that contribute to such distance are fixed due to random drift or random natural selection. Evidence for beneficial mutations to behave in a clock like manner has been shown recently (Barrick et al., 2009). Our recent molecular dating study has also shown a remarkable concordance between molecular dating and fossil dating. Thus empirical evidence supports the notion that there is a strong linear correlation between genetic distance and time of divergence even if such distance is largely contributed by non-neutral mutations. In theory, as long as we correctly view natural selection to be what it really is (it really is random), we can easily make sense of the clock like behavior of the non-neutral mutations within the neutral theory framework. The fixation of the non-neutral mutations has one fundamental property in common with that of the neutral mutations. They are both random. Over long periods of time and numerous random environmental changes, the number of positive selections will roughly equal the number of negative selections. Thus, the canceling out of each other the positive and negative selections makes non-neutral mutations to effectively behave as no different from neutral mutations.

So, the modern evolution theory (Neo-Darwinism plus the Neutral theory) is not completely counter-intuitive or non-sensible. As a theory of microevolution and population genetics, it is completely sensible or intuitive and flows readily from the self-evident Second Axiom of Biology. But as a macroevolution theory, it is completely non-sensible or counter-intuitive as it must negate the First Axiom of Biology. The more complete MGD hypothesis takes into account both of the Axioms of Biology and fully grants the modern evolution theory to be what it really is or has been proven to be (a theory of population genetics and microevolution or the microevolutionary phase of macroevolution).

I may formally introduce The Second Axiom of Construction and Second Axiom of Biology in a future paper.

Barrick, J.E., Yu, D.S., Yoon, S.H., Jeong, H., Oh, T.K., Schneider, D., Lenski, R.E., and Kim, J.F. (2009). Genome evolution and adaptation in a long-term experiment with Escherichia coli. Nature 7268, 1243-1247.