Monday, 20 October 2014

Darwin's Doubt

In this essay I discuss Stephen C. Meyer's book Darwin's Doubt (2013) in which he makes a case for Intelligent Design. How convincing is his case? Should we consider Intelligent Design as a viable alternative to the neo-Darwinist theory of evolution? What are the options on the table?

I received Darwin's Doubt as a birthday present from my two daughters. I love good books - and I enjoyed reading the book. Meyer's style is very relaxed but at the same time includes in-dept discussions of issues that other authors merely touch on. Although he is not a biologist, as a philosopher of biology at the Discovery Institute and the Biologic Institute in the US he is clearly a master of his topic. The book gives a good overview of the historical development of Darwin's theory of evolution as well as the central issues in contemporary debate. He argues that neo-Darwinism has come at a cross-roads since more and more senior biologists acknowledge that it cannot explain macro-evolution. In this regard he sets aside whole chapters to discuss technical issues in a manner that is easy to understand. He also discusses some of the growing number of post-Darwinian viewpoints. His answer is Intelligent Design. But is it a sensible solution?

The Cambrian explosion

Meyer's main concern is with the Cambrian explosion 544-530 million years ago. The reason why this particular period is of great interest is that the fossil record shows the sudden appearance of many new animal forms and structures. I fact, about twenty of the twenty-six total phyla - that is, the highest (or widest) categories of biological classification in the animal kingdom - made its first appearance during the Cambrian explosion. The fossil record does not show any previous ancestor forms from which they could have evolved. They appear out of the blue. And this presents a clear problem for Darwin's theory - which was in fact also recognized by him - since his theory is one which explains incremental change, not "quantum leaps" in change. This represents the one issue on which Darwin had some doubts - from there the title. Meyer shows that it is not a question of "missing fossils", but rather that we have good reason to think that no "missing" fossils exist. The Cambrian explosion therefore presents a real challenge to Darwin's theory. 

The first biologists who became well-known for accentuating the discontinuities in the fossil record, were Stephan Jay Gould and Niles Eldredge. They proposed a theory called "punctuated equilibrium". The gaps which they accentuated were confirmed by statistical paleontology which showed that such gaps are not an anomaly; this is exactly what the fossil record tells us. The fossil record that we have (with the gaps) is a complete picture of the forms of life and it is unlikely that the many intermediate forms required by neo-Darwinism would ever be found. Although their view presented the first real challenge to neo-Darwinian theory, in the end the problem with their theory was that it did not provide an adequate mechanism to explain the gaps. So, although it focused attention on the gaps (and the deficiency of neo-Darwinism), it could not explain the origin of new body parts.

The appearance of new body structures involves a radical increase in the level of complexity of the information needed to produce them. Meyer is especially interested in this aspect of the Cambrian explosion: the Cambrian explosion is also an information explosion. Our knowledge of DNA enforces the realization that such an explosion in complexity also involves an enormous explosion in the amount of information involved. He starts this part of his discussion with the challenge presented at the Wistar Institute conference in 1966, namely that the available time since the formation of the earth is not nearly enough to produce the required complexity in biological structure through genetic mutation (which works hand in hand with natural selection; genetic mutation is the basic mechanism though which change is introduced according to neo-Darwinist evolution). One possible answer to that challenge was that functional proteins are very common in the "combinational space" i.e. the ratio of functional to non-functional biological structures produced by mutation is larger than assumed. This would reduce the necessary time periods for evolution to succeed. But this loophole was closed by Douglas Axe in a series of articles since the year 2000.

The main problem for genetic mutation is that one does not merely have to consider individual mutations; the larger context is also important. The various genes and proteins are embedded in larger "protein folds" and mutations in the first could leave the protein folds non-functional - both aspects must be taken into account. In this regard the protein folds are the smallest units of structural innovation. For evolution to work, both individual mutations and adaptations in the protein folds as a whole must be successfully achieved - and this is just not possible in any of the manners that biologists thought it would. I fact, even the "genes and proteins themselves represent complex adaptations - entities that depend upon the coordinated interaction of multiple subunits that must arise as a group to confer any functional advantage" (p253).

Meyer also discusses developmental biology where genes and proteins play an important role in embryo development. A possible Darwinian solution suggests itself in the form of mutations in key regulatory genes - but all such efforts have lead to destructive evolutions. Then there are the developmental gene regulatory networks - the many gene products, which are necessary for the development of specific animal body plans, transmit signals that influence how the various cells in an embryo develop and differentiate. There are reasons to believe that these are animal-wide systems of genetic control functions which turn genes on and off during the life of the organism. These genetic control systems have been extensively studied by Eric Davidson, who has drawn up detailed flow-diagrams which shows how such gene regulatory networks (dGRN) work. This means that building new animal body plans like those which appeared during the Cambrian Explosion, require not just new genes and proteins embedded in new protein folds, but new dGRN's. This involves significant changes on the macro-level which make classical neo-Darwinian unsuitable as the mechanism producing change (as Davidson also points out).

Another reason to reject the idea of genetic mutation according to Meyer, is the "epigenetic" revolution. This word is derived from the Greek prefix epi which means "above/beyond" and refers to sources of information which lay beyond the genes. Since 2003 it became abundantly clear that certain information regarding body plans is not derived from DNA at all - it is derived from other sources like the microtubules in the cytoskeleton of cells, the cell membranes, iron channels and electromagnetic fields in cells and the arrangement of sugar molecules on the exterior surface of cell membranes. Meyer writes: "If DNA isn't wholly responsible for the way an embryo develops - for body-plan morphogenesis - then DNA sequences can mutate indefinitely and still not produce a new body plan, regardless of the amount of time and the number of mutational trails available to the evolutionary process" (p281).

The inability of neo-Darwinism to explain the gaps in the fossil record has lead to other approaches which can be called "post-Darwinian". Such approaches became a mainstream phenomena with the gathering of the "Altenberg 16" in 2008 - scientists who believe that neo-Darwinism does not provide the evolutionary mechanisms needed to explain the origin of new biological structures (body forms). Meyer discusses some of the most important approaches in this regard. There are self-organizing models which think in terms of biological forms that arise "spontaneously ("self-organizes") through the laws of nature. Meyer shows that, although these models can account for "order" which arises mechanically (in crystals etc.), it cannot account for "complexity", which requires information - "that characterizes the digital code of DNA and the higher-level information-rich biological structures" (p306). He also discusses other approaches, for example those which focus on Hox (regulatory) genes, which can supposedly account for macro-evolution (as in Jeffrey Schwartz's Sudden Origins). He shows that these approaches have problems of their own which disqualify them as sensible explanations for the sudden appearance of new body structures in the process of evolution. 

Intelligent design?

Meyer believes that Intelligent Design can account for the sudden appearances of new life forms. He presents this solution not in metaphysical (religious) terms, but in scientific terms (he discusses the various arguments against Intelligent Design as a scientific theory). Meyer uses the method of abductive inference (to be distinguished from both inductive and deductive reasoning) according to which inference is made from past events based on present clues, facts or causes. In his view, of all the causes now in operation, the one which can best explain the Cambrian explosion, is that of (human) intelligent design. Since neo-Darwinism (as well as the other post-Darwinist models) cannot provide an explanatory cause which can account for the sudden appearance of new body structures, other possibilities should be explored - and the only one which explains the sudden appearance of new complex structures (including new dGRN's and new epigenetic information) that we know of, is (human) design. Of all the available hypotheses, this is the one, according to him, which we are forced to adopt in accordance with the method of inference to the best explanation.

Meyer argues that this approach can also predict outcomes just as any other scientific theory. In this regard he mentions the case of "junk DNA". Neo-Darwinists originally argued that the large percentage of DNA which seemed to be without any function, is a predictable outcome of the inherently random process of evolution. Intelligent Design proponents, however, predicted that some function would eventually be found for "junk DNA" - if it was designed, it must have some function. When the ENCODE project eventually confirmed that at least 80% of the genome can be assigned biochemical functions, these scientists felt vindicated. They took it as an important confirmation for their theory.

Does this confirm that Intelligent Design (ID) as a scientific theory is correct? In my view it does not. Although neo-Darwinism seemingly has serious problems in providing an adequate mechanism for macro-evolution, and ID seems to be able to account for such evolution ("designed" animal forms which appear suddenly in the fossil record), one can argue that biology as a science has just not developed the tools to deal with the complexity that is manifest in biological structures. There could be causes that we have not yet discovered and therefore not taken into account. I immediately think of the fast evolving field of quantum decoherence, where the impact of quantum effects on macro-structures is studied. It is possible that we will eventually find that evolution has a quantum component, i.e. that leaps in biological evolution have their grounds in the quantum world where they would arguably seem to be at home.

It is interesting that Immanuel Kant presented a problem very similar to the one outlined in Meyer's book in his Critique of the Power of Judgment (1790), in the second part called Critique of the Teleological Power of Judgment, in which he develops a scientific approach suitable for application to biological structures. In the seventh antinomy (a conflict of laws) he sets the following opposing dogmatic positions in conflict: 1. The view that everything in nature can be mechanically explained (as is the case with neo-Darwinism) and 2. that at least some biological structures can only be explained though design (in accordance with Intelligent Design). These are opposing positions which cannot be reconciled. According to Kant we can, however, defuse the conflict when we allow that both could be true - in general biological change is caused by the laws of nature, but some biological structures can only be explained if we regard them (heuristically) as if they are designed. 

According to Kant these positions can be reconciled if we allow for a supersensible (noumenal) realm as the substratum of nature in which the ground for the second type of causality (design) is situated. As such, the "whole and the parts" (i.e. the total design and its components) which have the capacity to spontaneously produce biological structures, as both the cause and the means of its own production, would be situated beyond the reach of human sensibility in the supersensible realm. In this regard Kant allows not only that the various biological products of nature, but even the whole of nature, could have been produced in this manner. According to Kant the human understanding cannot conceptualize this ground (i.e. such wholes and their relation with their parts).

In my opinion we can take the supersensible realm as empirically confirmed in the quantum realm, and the second type of causality which Kant allows (other than deterministic causality or mechanism) as the spontaneous causality typical in quantum collapse (I plan to argue this in future essays on this blog). This would mean that such "designs" are at least in part situated in the quantum realm and find expression in self-organizing (albeit not in the above-mentioned sense) biological structures. The whole-part relation which Kant refers to, finds affirmation in the various quantum states ("parts") which together form superpositions of states ("wholes") - which are in fact beyond human access and conceptualization (we only have a partial understanding thereof). One can think that complex superpositions of states could somehow incorporate the potentiality (in close integration with material biological structures) to produce the new body forms that become visible in macro-evolution.

Kant did not exclude God from such "designs" underlying biological products. He allowed for two aspects regarding these "designs" - there are the spontaneous causality (potentiality) which is grounded in the supersensible realm as well as the fundamental cause (i.e. God) beyond all of nature and even the supersensible realm in this sense. According to Kant we can think that some (non-human) understanding can think this whole-parts potentiality behind visible biological structures (i.e. the designs in the supersensible realm) which is beyond the capacity of our understanding. We can even think that some understanding (which would be God) could have intentionally designed these. Kant argues this in the final part of the Critique of the Power of Judgment. So, although we can think that the Cambrian explosion would eventually be explained in quantum terms, this will not exclude the possibility that God created the unfolding world with all the "designs" built into it. The arguments for divine design, however, go beyond this essay.


In my view Meyer did a good job in showing where and why the theory of neo-Darwinian evolution is falling short of expectations. Clearly there is a growing concern among biologists that the available mechanisms (especially genetic mutation) cannot account for macro-evolution. This is not only clear in the technical details of the arguments presented, but also in the fact that we are currently seeing a post-Darwinian revolution in biological thinking. If Meyer is correct in his assessment, we can expect that neo-Darwinism would increasingly come under pressure as the all-encompassing theory of biological explanation. Paradigms, however, do not change easily and without a viable alternative I cannot see the situation changing any time soon.

Does Intelligent Design provide an viable alternative? I do not think so. In my view it has merit in that it proposes that there are some underlying "designs" that become manifest in new biological forms. This could very well be the case. This would mean that the process of evolutionary change (genetic mutation) is not random at heart - it follows some pattern which could involve some form of order (complexity) deeply imbedded in nature as Kant proposed long ago. Although one can ascribe the origin of such "body plans" to God's active involvement in history, it is also possible that they are, at least in part, situated in the quantum realm and that the scientific community just does not as yet have the explanatory tools to account for that. They may, however, be able to do so in future. If such "plans" do exist in some form, it would nonetheless show that our universe is not merely mechanistic. And that would already be an argument that some designer, which would be God, has woven that design into the fabric of the universe at the time of the Big Bang.   

Author: Dr Willie Mc Loud (Ref.