A response to Shermer's Why Darwin Matters?

A Secular Questioning of Neo-Darwinism

Dr. Shermer,
"Why Darwin Matters" is the 34th book I have read on evolutionary science.  Key works I am familiar with include Gould's "The Structure of Evolutionary Theory", Robert Wright's "The Moral Animal", Michael Denton's "Evolution: a Theory in Crisis" and "Nature's Destiny", Richard Dawkins "The Ancestor's Tale" and "The Selfish Gene", Daniel Dennet's "Darwin's Dangerous Idea", Ernst Mayr's "What Evolution is", and Elaine Morgan's "Descent of Woman" and "The Aquatic Ape".
I am an a-religious (meaning that god and general religious beliefs are so obviously cultural/anthropological in origin that such questions don't even need to be asked, let alone answered) common reader.  My interest is purely secular, and I have no patience for supernatural explanations (although I have read creationist works not worth listing here).  I consider the two most important SCIENTIFIC mysteries to be 1) how did life originate, and 2) how has biological life evolved.  Both of these mysteries have rational explanations.  I just don't believe we (the scientific community) have yet arrived at those explanations.  Below I will pose specific questions that appear to me currently unanswered by science.  But first, some context.
I believe (and this is my agenda) that due to cultural/historical pressures, the scientific community is loathe to admit any doubt in the current status of evolutionary explanation, overly (in my opinion) concerned with providing the Christian/creationist/intelligent-design faction any foothold in their fight to dislodge science from its Darwinian perch.  As a result, it appears to the interested layman (me) that the scientific community is overly sensitive to questions concerning the source of speciesation and less then willing to pursue a solution to these outstanding scientific questions.  Your book is an excellent example of such sensitivity.
The fact that evolution took place is irrefutable (in my opinion), in that all organisms today are descended from organisms that existed in the past, and in many cases differ from creatures that existed in the past (they have evolved), and that as far as we know, all life is based on the same basic genetic structure.
The fact that natural/sexual selection takes place, is uncontroversial (in my mind).  Offspring generally resemble their parents, with statistical deviation taking place in any given population.  The fact that some individuals reproduce and pass along their genetic material is also uncontroversial.
What is controversial, and what a general reader such as myself, one without access to detailed and specific biochemistry, doesn't understand (or accept) is the source of genetic variation in any given population.  
In other scientific arenas I can read popular science books explaining incredibaly strange natural phenomon such as quantum mechanics and uncertainty, and while I don't have access to the mathematics I can grasp the experiments and the models that demonstrate their conclusions.  I have yet to find any such explanations, or models, that provide a scientific explanation how major changes evolve in nature, or how speciesation actually takes place.
Classic neo-Darwinism (and correct me if I am wrong) points to the following sources of variation:
1 - recombination.  While offspring generally represent their parents, often times they don't in some way.  That's why (in my opinion) sex exists at all, and why most (although not all) species sexually reproduce.  It allows some form of variation (although generally slight) in any given generation.  This variation is crucial if a species is to survive changes in the environment.  I consider genetic drift the long-term results of recombination and won't count it is a seperate source of speciesation.
2 - random mutation.  Every once in awhile, despite the incredibly conservative nature of sexual reproduction, a mutation occurs that provides changes in the phenotype.  If the change is positive, and contributes to the success of the individual, it is more likely to reproduce and pass along the new change.  
In your book you pass over quickly any issue concerning the odds of mutation resulting in complex solutions.  Your example of the sentence, "tobeornottobe" misses an important difference in using it as an analogy.  The real comparison would be to take a sentence that already works (that is, means something), something like "to be or not to be" and change it randomly one letter/symbol at a time to create another sentence that not only makes sense (that is, it survives), but actually superior to the one it replaces (that is, has a better chance of reproducing then its siblings).  If it's not better it won't be selected for and reproduced.  Now figure the odds of THAT taking place.  
Another source of variation you mention in your book is Margulis's symbiogenesis, and this sounds promising, as it provides for far greater changes in the phenotype then random mutation, but only (if I understand correctly) at the single-cell level.
One possible way to scientifically demonstrate how mutation might work would be to take a basic, working genotype, and create a specific gene-level model that shows how random changes can be posited that changes the phenotype in a positive way, and progresses one random genetic change at a time until a new structure/system is created.  Doing so would go a long ways towards supporting this form of evolution, assuming the odds of such random changes don't prove astronomical.  (The computer simulations that are intended to show this take place are simply another over-simplified analogy, and prove nothing).
Darwin asserted that if his argument of gradual change was refuted, his theory would be refuted.  Well, I would assert that his argument of gradual change is falsified logically, as well as by the fossil record.  For example, if you were to take the gradual changes necessary to get from an original form of horse to a modern one over the 60 or so million years it took, you would find that the micro changes would be so small in any given generation (if they were all equal in size, that is gradually occurring) that they would be imperceptable to selective pressures.  This would become apparent if you measured the total difference and then divided it by the number of generations between the original and the modern.  
But that's not all that important, as Gould/Eldridge have made clear with their model of punctuated equilibrium.  What seems obvious now is that speciesation occurs one of two ways (but they are related):
1 - a relatively small group gets seperated from the larger population and becomes subjected to severe selective pressure resulting in relatively rapid change over a relatively short interval.  This happens when one tail or another of a bell curve representing the distribution in a population of a particular trait gets favored, something like size, speed, coloring, or whatever.  
2 - or, the original large population gets subjected to severe environmental pressure, and only a small percentage of a particular generation even survive, again, selection favoring one tail or another of a character distribution.
As a result, fossils of the transition are very rare, as they exist in small numbers over a small geography, and only when a population reaches stasis do enough fossils get created to be found.  Thus, few if any intermediate fossils.
So my first question: are other models of speciesation extant?  If so, what are they?
Second question: do we believe that these models of speciesation (or any other models) are capable of creating complex new biological structures/systems?  If so, do we have any specific models or detailed explanations of how these new structures/systems could come about one genetic change at a time?  And if so, do these explanations come with estimated probabilities, if chance mutation is part of the solution?  Because this didn't happen just once - it happened tens of thousands, if not millions of times in biological history.
Here is another problem with the "anything can happen given enough time" version of explanation.  If we take the Darwinian view of gradual change, where we have lots of individuals giving birth to lots of offspring any given generation, multiplying the possibility of positive mutations occurring, we are faced with the reality of any positive change getting swallowed up in the tremendously conservitive aspect of generational genetic stasis.  Unless the change is discreet, a "hopeful monster", how can a chance positive mutation propagate itself through a large population?
And if we consider the puncutated equilibrium model, we are now considering a much smaller population, with far fewer chances of generating signficant genetic change from one generation to the next, even though any positive genetic change has a better chance to be propagated in the smaller community.  Consider something like an elephant, for example, with one offspring at a time, with several years between generations.  Yet we have large mammals changing at an incredible rate (especially considering the magnitude of phenotypical change) when evolving from a land-based animal into a whale.  How did such drastic cumulative variation come about?
So my most basic question to the scientific community is this: do we really understand the source of variation?  If the answer is yes, can an explanation be provided to a general reader such as myself?  Does such an explanation already exist?  If so, can you cite it for me, point me in that direction?  Because I have yet to find it, 34 books later.
One final comment.  You equate "Intelligent Design" exclusively with religious interests.  Is it possible that something else in nature is responsible for some level of "design"?  The "design" could be local, most likely at a sub-cellular level, something that is able to take account of the environment, and the creature's place within it.  Not Lamarkian necessarily, but perhaps a distant relative.
Or it could be that some kind of complex bio-chemistry is taking place, without intent or purpose, that currently escapes our understanding.  I don't know.  Do you?
Any help you can provide would be greatly appreciated.
Anthony Wheeler

Anthony Wheeler

Humble Executive.  Literary Artist.  Altruistic Libertarian.