Merlin spends a large part of the paper trying to establish what does and does not constitute a directed mutation. Merlin, I think, fails in her attempt to properly differentiate Darwinian and Lamarckian mutations because she has not taken into account the main purpose of Darwinism as described in Part II of this essay. To recap, the entire point of Darwinism was to frame biology as to extricate itself from final causes. Therefore, any mode of genetic adaptation which fails to do so is non-Darwinian.

Explaining Away Apparent Purposefulness

Merlin, it seems, is somewhat aware of this, as she tries to explain away any apparent purposefulness within mutational mechanisms. She says,

the mutator mechanisms themselves, which provoke an increase of mutation rate in response to environmental conditions, can be shown to be an adaptive result of the population’s evolutionary history…This means that the mutator mechanism has some adaptive value for individuals or populations. In a case where a mutator mechanism happens to provoke some favorable mutation, it may be positively selected at the individual level since it may provide an advantage to some lucky individual organism and its offspring (because there is selection for the favorable mutation). But a mutator mechanism could also provide an advantage to populations since it may increase the probability that a population adapts more rapidly than others to their adverse environmental conditions. In both scenarios (i.e., individual selection and group selection), the mutator mechanism is an evolutionary adaptive outcome producing “evolutionary chance” mutations. (pg 15)

This is the classical Darwinian confusion of something being selectable versus something being produceable by natural selection. The fact that a mutator mechanism which is biased towards beneficial mutations is selectable is uncontroversial. The question of whether it could be produced by natural selection is another story. Or whether anything at all worthwhile could be produced in the absences of appropriate mutator mechanisms — that is the entire question between Darwinism and Lamarckianism! You can’t solve it by saying, “I believe it is my way!” The question is, where does the evidence show? It turns out, over and over again, that whenever we find truly beneficial mutations (as opposed to what Behe calls “trench warfare” mutations), we find that there were highly-regulated mechanisms guiding it to its result. That should give people pause, but for some reason, it doesn’t.

So now we will examine Merlin’s demarcation between Darwinian and Lamarckian mutations closer, and see if it holds up. In all cases, we will be comparing biology to the Darwinian guideline of eliminating final causes, and see if the biology supports such a guideline.

Darwinism and Changes in Mutation Rates

Merlin says that Darwinism is compatible with changing mutation rates under stress. I would argue that this is true to some extent, but not quite to the extent that Merlin thinks. It was originally thought that the reason why mutation rates increased under stress was that the cell had less energy to maintain control, and therefore things simply fell apart more quickly. While tumbling out of control, some cells happened upon a mutation that helped it adapt. This is compatible with the Darwinian view – the relationship between beneficial mutations and survival is merely happenstance, due to the inability of the cell to keep it all together in times of crisis.

However, what was later actually found in real biology, was that the increase in mutations under stress is actually an orchestrated increase in mutation rates. In times of stress, bacteria switch DNA polymerases to one which causes mutations, among other activities. In fact, if you disable certain enzymes, the beneficial mutations do not happen at all. So, rather than this happening as the result of a continuing breakup of cell processes that lead to mutations, this is actually an organized response that the cell has to stress, which relies on proper tooling to be effective.

So, while, as a theoretical point, increases in global mutation rates can be compatible with the neo-Darwinian synthesis, I would argue that the specific mechanism by which global mutation rates are actually observed to increase is actually anti-Darwinian. The machinery and orchestration, and the inability to generate proper mutations without the machinery and orchestration, have a distinctive flair of teleology.

Darwinism and Mutational Hot Spots

Merlin then says that having hot-spots of mutation is compatible with the neo-Darwinian synthesis. Again, as a theoretical point, this is true. We would expect that the physical and chemical properties of DNA would lead some sequences to be more mutable than others. But not only do we have hot-spots for mutations, these hot-spots are right where they need to be for a beneficial mutation to occur. The fact that the observed hot-spots are correlated with potentially beneficial mutations is a giant blow to the neo-Darwinian outlook, because it implies that information already present in the genome, not natural selection, is responsible for the direction of evolutionary change.

Interestingly, this actually leads to a quantitative approach to deciding the question of Darwinism or Lamarckianism. Dembski’s Active Information concept could, at least in theory, be used to determine this. You could set up colonies of bacteria, and give them stressors. In one group, you let their mutational machinery do the work, and in the other, you knock out the mutational machinery, but simulate truly random mutations at the same estimated mutation rate using a source such as radiation. If the natural cells produce adaptive mutations at a significantly better rate than than the radiated cells, then it shows that they have positive Active Information. According to the No Free Lunch theorems, this would indicate final causes, and thus be in violation of Darwinism.

The fact is, modern biology shows that cells are pre-loaded with scads of information about how they can be best mutated. One can deny this if they wish, but they do not do so based on the data we have at hand.

Semi-Directed Mutations

While I can see where the above two categories of mutations might cause some people to not be able to differentiate between the Darwinian and Lamarckian versions of mutation theory, I am completely bewildered when it comes to semi-directed mutations. Semi-directed mutations are mutations which satisfy all of the following criteria:

• A stress condition increases a cell’s mutation rate
• The mutation rate is increased in a localized area only
• The area that the mutation rate is increased in includes the area of the beneficial mutation

Now, I can understand if we only had one or two known mutations that fit this profile, how someone might think they were flukes. If, for most of the time, the localized mutation rate area did not match the location of the likely beneficial mutation, then we would be warranted to think that on rare occasion these might align, and produce what we need. However, what we are seeing is that the cell often times focuses its mutations precisely on the genes, or sets of genes, which need mutating. In bacteria, this is often done by increasing transcription rates using a mutagenic DNA polymerase.

In your immune system this is done, at least in part, by a deaminase attaching to the antibody gene to cause mutations. This deaminase is targeted by a non-coding DNA element, which points it not only to the correct gene, but the correct *part* of the correct gene. It would make no sense to mutate the part of the antibody which attaches to the cell, but only the part which attaches to the antigen. And, in fact, that is precisely the part that gets mutated. The region which attaches to the cells suffers almost no mutations whatsoever.

Merlin’s complaint about this process is that it doesn’t single out a single, specific mutation to accomplish the result. In the case of the immune system, the localization of the mutation rate increases the likelihood that a beneficial mutation will occur by well over 6 orders of magnitude. So how does one reconcile that with the idea of “evolutionary chance” mutations?

So, sure, it doesn’t target the exact mutation. If by “Darwinian” one means “organisms aren’t omniscient”, then, sure. Nobody thought they were. But what the data points to is that the adaptations that organisms undergo are well-regulated. They don’t seem to be accidents for any usable meaning of the word. In fact, they appear to be quite purposeful.

So, if the purpose of keeping the term “Darwinism” or “The Modern Synthesis” is to save face for an idea, then, sure, keep it to keep anyone from getting embarrassed. But one can only call this Darwinian, or non-teleological, by completely removing any real meaning from these concepts. It comes down to, as one commenter put it on this forum, being like redefining the meaning of “is”. Sure, you can do that, but if you do, it isn’t because you are trying to be precise, but rather because you are trying to obfuscate the obvious.

Now, in the next posting, we will dive into a class of mutations which Merlin seems to be unaware of, but which are definitively within her own category of directed mutations.

Our next debate features famed atheist Christopher Hitchens, author of God is Not Great: How Religion Poisons Everything, and Dr. David Berlinski, author of The Devil’s Delusion: Atheism and Its Scientific Pretensions.  The question being debated: What are the implications of a purely secular society?  It promises to be a formidable clash of titans.  In addition to being highly entertaining and witty, these two men have a serious message they want to communicate.

The Does Religion Poison Everything? Debate begins at 7 p.m., September 7.

The luncheon, reception, and debate all take place at the Sheraton Birmingham Hotel:

For those of us who cannot make the debate, the DVD can be ordered here.

Dr. Berliski is a Senior Fellow of the Discovery Institute.

David Berlinski describes himself as “a secular Jew and an agnostic.”  He has written a number of books on mathematics, but he is best known for his appearance in the Ben Stein film “Expelled” as well as for his irreverent assault upon the New Atheists in his book, The Devil’s Delusion: Atheism and Its Scientific Pretensions.  Mr. Berlinski, whose immediate family was saved during the Holocaust by the “American Schindler” Varian Fry, resides in Paris.  He possesses a Ph.D. from Princeton University and formerly taught philosophy and mathematics at Stanford University and the University of Paris.

Christopher Hitchens, an atheist and polemicist, is best known for his controversial book, God is Not Great: How Religion Poisons Everything, and, most recently, for his memoir, Hitch 22, which has been on The New York Times Best Seller List since its release last month.  Hitchens has been a columnist for The Atlantic, Slate, and Vanity Fair, and has debated his views around the English-speaking world.  Hitchens is one of the so-called “New Atheists”, along with other notables like Richard Dawkins.

Miller brought up the traditional arguments which he has become so renowned for, alleging that Behe’s claims regarding irreducible complexity were false on the basis that 10 proteins homologous to a complement of those present in the flagellar system could be found in the Type-III Secretary System. When Behe attempted to explain why such a discovery offered no traction to neo-Darwinism, Miller insisted that he only respond to the question which was being asked (which was, apparently, the legitimacy of Miller’s substantially tweaked definition of irreducible complexity, rather than the causal mechanism of evolution and its explicative powers to produce the powerful illusion of design in biological systems).

Pennock, meanwhile, repeatedly confused the concept of a theoretical basis for design detection (which ID proponents are unanimously in agreement on) and a theory of design implementation (which we are currently lacking unanimity on).

Here’s the debate:
Part 1
Part 2
Part 3

Following Dr. Ayala’s opening statement, Dr. Craig commenced his presentation by carefully setting out the definition of ID as the study of legitimate design inferences. Craig stipulated that, were Ayala to attempt to refute the inference to design with respect to biological systems, he would need to do one of two things. Either Ayala would need to directly challenge the legitimacy of the explanatory filter (presumably by demonstrating that it incorporates false positives) or demonstrate that the systems featured in biology do not meet the criteria of the explanatory filter. Setting aside the discussions pertaining to the tenability of universal common ancestry, Craig set about to argue that Ayala’s attempts to disqualify ID on scientific grounds were doomed because he had failed to demonstrate, in his published work, that the dual forces of random mutation and natural selection, are causally sufficient to account for macroevolution. He also argued that Ayala’s more numerous attempts to disqualify ID on theological grounds are completely irrelevant to the process of drawing a design inference from biological phenomena, because none of the arguments for ID aspire to show that the designer possesses the qualities of omnibenevolence or omnipotence. After all, Craig argued, a design inference is still warranted with respect to a medieval torture rack, regardless of the malevolent purposes of the system’s design. Questions pertaining to the nature of the designer are for natural theology, not for the scientific research program of ID. This is what distinguishes the modern concept of ID from the Watchmaker argument of William Paley’s Natural Theology. Read More>>>

John Lennox is Professor of Mathematics in the University of Oxford, Fellow in Mathematics and the Philosophy of Science, and Pastoral Advisor at Green Templeton College, Oxford. He is also an adjunct Lecturer at Wycliffe Hall, Oxford University and at the Oxford Centre for Christian Apologetics and is a Senior Fellow of the Trinity Forum. In addition, he teaches for the Oxford Strategic Leadership Programme at the Executive Education Centre, Said Business School, Oxford University.

http://science-and-values.blogspot.com/

Merlin’s paper spends a lot of time dealing with the synthetic theory as defined by its original exponents – as well it should, since modern biology owes many of its intellectual underpinnings to these originators. Merlin described the writings of Fisher, Haldane, Simpson, Dobzhansky, and others as “canonical”, and deservedly so. They were the pioneers of how to marry genetics and Darwinism, and the fact that their work survived so well past the discovery of DNA is a testament to their intellectual power.

However, while these works should be deservedly referenced and pondered regarding what is and is not included in the synthetic theory, there are a few possibilities which should also be considered:

1. Being fallible humans, not everything that they say will necessarily be consistent with their theory as described
2. Being early pioneers, not all of their conceptions will be adequately thought out
3. Again, being early pioneers, it was not clear which parts of the theory would be important to other disciplines, and useful for building knowledge
4. Finally, just as “Darwinism” doesn’t refer to the theory as Darwin himself described it, the modern synthesis, having been formulated essentially two generations ago, has itself migrated a little from where it was originally conceived
5. Many theories are organized around a core idea, and it is good to see whether it is the core idea being challenged or merely a peripheral theory.

Judging these requires looking to later literature as a guide to not only where the synthetic theory started, but also where it went and why it went there.

So, while Merlin viewed her job as defining what the original synthetic theorists meant, and then evaluating supposed neo-Lamarckian features of biology on those terms, I think a better set of goals would be to evaluate these features in comparison to the synthetic theory as currently described and used in the evolutionary sciences today. If Wright, Shapiro, Jablonka, and Lamb have indeed found something revolutionary, it matters little whether it would have been revolutionary to Simpson and Dobzhansky – it matters much more whether or not it is revolutionary in the context of the modern debate.

Having said that, I think that, for the most part, the definitions have not changed that much. One of the key tenets of the neo-Darwinian view of evolutionary change, both then and now, is that the needs of the organism do not affect the likelihood that a mutation is beneficial. According to neo-Darwinism, beneficial mutations are purely capricious – that is, there is nothing to guide a mutational process to a beneficial destination.

Why Are Haphazard Mutations Important to Neo-Darwinian Theory?

It is important to take a moment and reflect on why this tenet is important to the neo-Darwinian outlook of biology – an issue which Merlin does not directly address. Underlying the neo-Darwinian revolution is the desire to eradicate final causes from biology. Quoting Simpson, Ernst Mayr said that Darwin “has swept out such finalistic teleology by the front door”. In order to do this, Darwinists invoke natural selection as the sole driver of adaptive change. Therefore, if natural selection is in the driver seat, then the mutations themselves must not be more than accident. Otherwise, it would be the mutational mechanism (a mechanism internal to the organism itself), not natural selection, being the driving force of evolutionary change. Since the driver would be internal to the organism, this would leave a door for final causes to creep back into the study of biology. Therefore, neo-Darwinists are careful to keep that door shut as best they can.

So that is why mutational mechanism is important for Darwinists – if the mutational mechanism directs change in a certain direction, then natural selection is no longer the primary creative force in biology.

The Neo-Darwinian Influence Across Multiple Fields

This can be seen in the numerous theories that have been built off of neo-Darwinism. Modern phylogenic studies, for instance, build phylogenetic trees under the assumption that complex traits should only have arisen only once, since the ability for them to arise more than once by chance is nearly zero. This logic works only if the generation of the trait is accidental. If it instead driven by a mutational process geared towards that type of change, then this is no longer a valid criteria for selecting among potential phylogenies.

Likewise, molecular biologists look for evidence of positive selection in genomes by looking for gene sequences that diverge rapidly from a common ancestor. However, this is invalidated if the driver of beneficial mutations is actually the mutational process itself.

A good review of the use of chance in modern evolutionary biology is Gunther Eble’s On the Dual Nature of Chance in Evolutionary Biology and Paleobiology.

Why Subtle Shifts in Mutation Theory Can Be Revolutionary

It is unfortunate that Merlin didn’t go beyond the classic texts on synthetic theory precisely because then it would be clear why this question of the origin of mutations is revolutionary – it is revolutionary because so many fields and disciplines within evolutionary biology use the assumption of accidental mutations whose sole guide is natural selection as a foundation for their field. If this assumption is removed, then this would require the reorganization of many fields around new theoretical bases. It is this, much more than any congruence or incongruence with classic texts, which makes the overturning of the neo-Darwinian assumption about mutations revolutionary.

Since so many disparate pieces of the modern picture of biology are built on the neo-Darwinistic view of mutations, even subtle shifts in this view are likely to have a profound effect across all of biology.