An extended review of Phillip E. Johnson's "Darwin On Trial"

by Wesley R. Elsberry

The author of the work

Phillip E. Johnson, a professor of law at the University of California at Berkeley, is also an active and eloquent anti-evolutionist. Professor Johnson has written several books aimed at providing anti-evolutionary apologetics, including one of the most cited recent anti-evolutionary works, "Darwin On Trial". Johnson has emerged as the de facto leader of a contingent of anti-evolutionists whose method of operation differs somewhat from previous anti-evolutionists. Where the ICR, CRS, and other fundamentalist anti-evolutionists have a history of promoting a Bible-based alternative to evolutionary explanation, Johnson and others have been careful to not reveal any religion-based positive beliefs, but rather approach the issues as if holding the stance of a disinterested skeptic, merely seeking to examine evolutionary theory and determine the level of confidence with which its conclusions are supported by the evidence.

This approach has been amazingly successful for Johnson. By the expedient of deflecting any questions about his personal beliefs as being irrelevant, Johnson has been able to utilize many of the very same questionable or false arguments advanced by various young-earth creationists, without suffering the embarrassment that follows when the young-earth apologetics are exposed as just sermons dressed up in tech-lingo.

Johnson's work and its influence

Johnson's work has been viewed quite differently by those who seek anti-evolutionary apologetics, and those who have long opposed the intrusion of creationism into science classrooms. To the credulous, Johnson's easy command of rhetoric and impressive credentials produce an immensely favorable impression, and the confidence that they find easy to place in Johnson is also extended to his arguments. To those who oppose the teaching of creationism as if it were science, Johnson's "Darwin On Trial" looks just like more of the same stuff that has long been published.

Anti-evolutionist apologetics are, in large part, the search for a "magic bullet" that will kill Darwinian explanations dead on contact. I use "magic bullet" not in the sense that Ehrlich used it when searching for a cure for syphilis, but rather in the sense it is used in werewolf movies. Those armed with a magic bullet can combat the evil lycanthrope directly, without having to go to the trouble of being consecrated to the task by dint of piety, or to have the strength that would allow them to contest with the werewolf directly, or even needing to know anything in a deep sense about the subject of lycanthropy. All the magic bullet user needs to know is how to point and pull a trigger.

Phillip Johnson's book of magic bullets fits the formula. Johnson fulfills the role of the sage who provides the magic bullet. He is also willing to tell you that the lycanthrope really is evil. And his rhetoric is sufficiently spiffy so that one can see that he is convinced that his magic bullets have enormous stopping power.

As long as readers of "Darwin On Trial" simply compare among themselves the shiny magic bullets found therein, little happens that would disabuse them of the efficacy of the magic bullet in practice. However, every once in a while, a reader will confidently utilize one in online discussion of evolutionary biology, and find that the lycanthrope does not keel over on contact. These magic bullets are duds in discussion.

The reason that Johnson's arguments are not effective is a matter of dispute. Johnson modestly claims that those who reject his arguments do so due to their prior commitment to materialism. (Throughout the book, Johnson uses similar pre-emptive rhetoric to attempt to claim that certain critiques do not apply, even though little or no justification is given other than the fact that Johnson is cognizant of the existence of the critique. Nor is this style of argument confined to Johnson's writing; I have heard him utilize the very same tactic in spoken presentation.) I'm sure that somewhere there exists someone whose grasp of the material is so weak that such a reason for rejection does form the sole cause for continued dismissal of Johnson's arguments. However, a more plausible class of causation may be posited: Johnson's arguments are often wrong in one way or another.

How this review is organized

I aim to accomplish several things with this review. First, I will address some common defenses of Johnson that are seen in discussion. These include the possibility that outsiders to a field of study are capable of producing significant criticism of theory within that field and the argument that aptitude in logic seen in other endeavors automatically validates argument made on the topic of current interest. I will demonstrate that practice often makes hash out of possibility, and that the employment of logical fallacies vitiates the claims that aptitude in logic must produce valid argument. Second, I will address Johnson's main point, that a fair assessment of the evidence does not support either the theory of common descent nor Darwinian descent with modification.

Point the first: logic and necessity

The plight of the outsider

Much is made of Johnson's outsider status when critiquing biology. Johnson reasonably points out that logic is logic wherever it is utilized, and that lawyers are trained in the analysis of logical argument. Outsiders, Johnson claims, may also bring valuable insights simply because they do not have the usual biases and indoctrination. These points go to the theoretical possibility of an outsider to a field being able to make a difference, and both Johnson and his defenders are quick to point out this possibility. However, there is a significant difference between what is theoretically possible and what is actually observed. Johnson's book reduces to practice his claims of critiquing biological theory on logical grounds, and his effectiveness must be evaluated on the basis of the arguments that are realized, rather than the ones that might have been possible. It is on this basis that I have concluded that in my reading of "Darwin On Trial", Johnson's arguments typically either are wrong, insignificant, or were previously expressed by others.

What Johnson will say about himself

Let me start by documenting Johnson's claims concerning himself and his purpose in writing "Darwin On Trial".

Before undertaking this task I should say something about my qualifications and purpose. I am not a scientist but an academic lawyer by profession, with a specialty in analyzing the logic of arguments and identifying the assumptions that lie behind those arguments. This background is more appropriate than one might think, because what people believe about evolution and Darwinism depends very heavily on the kind of logic they employ and the kind of assumptions they make. (p.13, 2nd ed.)

My purpose is to examine the scientific evidence on its own terms, being careful to distinguish the evidence itself from any religious or philosophical bias that might distort our interpretation of that evidence. (p.14, 2nd ed.)

Here we find several claims from Johnson that are testimonial evidence of the efficacy of the magic bullets that he will be peddling later. Johnson attests to his prowess in logical analysis, such that he can see more clearly than those involved in the field of study what assumptions they are making. Johnson attests to his ability to evaluate actual evidence. Johnson attests to his ability to render his judgment without religious or philosophical bias.

Assigning truth values to claims: a two-way process

A question that Johnson himself asks several times in his book comes to mind: But are these claims true? There are some difficulties to be overcome. In order to perform logical analysis of a theory, one needs more than just aptitude in logic. One must also be familiar with and have a thorough understanding of the theories being analyzed. In order to evaluate evidence which supports a theory, one must be aware of all the available evidence which bears upon the theory, and also must understand how that evidence is analyzed. Because of these issues, there continues to be well-warranted concern over Johnson's outsider status. If Johnson's assumptions and the logic that he employs are based upon misunderstandings of theory, ignorance of theory, an incomplete survey of the available evidence, or misevaluation of available evidence, then his conclusions are no more than assertions without any more basis than Johnson's testimony that he believes in those assertions. This is the view that I hold after careful reading of Johnson's book; Johnson could have simply stated that he personally did not believe in either common descent or the efficacy of natural selection to account for adaptation and left it at that. Two pages would have sufficed for the remaining substance of "Darwin On Trial". Now the question is, can I substantiate this opinion of mine? I believe so, and will proceed first to the issue of familiarity.

Unfamiliarity breeds ignorance

Early in "Darwin On Trial", Johnson makes a bland assertion that casts serious doubt upon his having the requisite familiarity with the topic of interest:

Most of the professional scientific literature is available in the premier scientific journals Nature and Science, the most prestigious scientific organs in Britain and America respectively. (p.13, 2nd ed.)

Is most of the scientific literature related to evolutionary biology available in Nature and Science? Given that the journal Evolution publishes more articles each month that deal directly with evolutionary biology than Nature and Science combined, this assertion can be seen to be in serious difficulty, and with it the implication of familiarity that Johnson makes. Certain key resources in evolutionary biology, such as the Journal of Theoretical Biology, are notable because Johnson doesn't mention them at all. These are curious omissions for someone claiming to be able to provide critical and novel insights into both theory and analysis of evidence. Evolutionary biology is the subject of articles in a great many scientific journals. To highlight two journals, any two journals, as if they provide a sufficient knowledge base for coverage of the topic of evolutionary biology is simply ludicrous.

Some consistency is a virtue

Johnson's claim concerning his purpose of examining the scientific evidence without bias runs into trouble when one also reads elsewhere inconsistent statements by Johnson concerning his purpose:
My primary goal in writing Darwin On Trial was to legitimate the assertion of a theistic worldview in the secular universities. (p.165, 2nd ed.)

To have both a primary goal of legitimating a theistic worldview and a purpose of examining the scientific evidence without religious or philosophical bias might be reconciled, if one is very good at straining at gnats and the swallowing of camels. If we believe the Johnson who penned the lines of the second edition, we cannot take seriously the claim of the Johnson who penned the lines of the first that he approached the evidence without bias. However, we can confirm that Johnson does apply a bias in analysis of evidence by examination of that analysis, which is seen further on.

A logical calculus of poppycock

Johnson's training as a lawyer and his own testimony as to his prowess in analysis of logic are often cited as sufficient reason to consider his conclusions reached in Darwin On Trial to be valid. This contention is without merit: logical argument is only valid if the premises are true and the inferences are sound. The prior history of the person making the argument is irrelevant to the point of the validity of the argument itself. Logic is a field of study in itself, subject to almost as much misunderstanding as may be found in study of the field of statistics. Because even the concept of implication and its truth-table is found to be counter-intuitive to many newcomers, logic as an intellectual pursuit is more often paid lip-service to than actually mastered. Mistakes in logical argument are so common that most of them fall into categories that are named for ease in reference. Given this background, let's examine in detail some of Johnson's arguments concerning logic.

Following the will-o-the-wisp

One important phrase in logic is "non sequitur", and Johnson provides us with an example fairly early on.

In fact the stock is often highly successful at resisting improvement, often for millions of years, so there must be something wrong with the logic. (p.24, 2nd ed.)

Johnson gives us a premise, that some species persist without gross morphological change over geological time, and follows with a conclusion that the logic he just quoted is shown to be wrong thereby. The logic that Johnson refers to must, for his statement to be true, require that no lineages avoid change over those periods of time. In other words, Johnson treats the logic referred to as if it were a universal claim, as universal is used in logic. Lets look at what Johnson refers to now, to see if Johnson's characterization holds.

Darwin persuades us that the seemingly purposeful construction of living things can very often, and perhaps always, be attributed to the operation of natural selection. If you have things that are reproducing their kind; if there are sometimes random variations, nevertheless, in the offspring; if such variations can be inherited; if some such variations can sometimes confer an advantage on their owners; if there is competition between the reproducing entities; -- if there is an overproduction so that not all will be able to produce offspring themselves -- then these entities will get better at reproducing their kind. Nature acts as a selective breeder in these circumstances: the stock cannot help but improve. (quote of AG Cairns-Smith, p.24, 2nd ed.)

Cairns-Smith's logical statement can be seen to be existential in effect, not universal. The "perhaps always" of the first sentence does not imply that natural selection is acting at all times, but rather how often adaptations might be attributed to natural selection. This means that Johnson's conclusion does not follow from his premise, which is just what qualifies it as a clear example of the "non sequitur" fallacy. Anyone who cannot distinguish an existential proposition from a universal one has no business critiquing the logic of others.

Further use of "non sequitur" occurs throughout the book. A particularly egregious example comes from page 154:

What they never find is evidence that contradicts the common ancestry thesis, because to Darwinists such evidence cannot exist. (p.154, 2nd ed.)

Johnson's conclusion does not follow from his premise, since disconfirming evidence could remain unavailable for the simple reason that it will tend to be absent when common ancestry is true.

Yet another "non sequitur" example concerns the flexibility of Darwinism.

Natural selection cannot possibly produce any modification in any one species exclusively for the good of another species; though throughout nature one species incessantly takes advantage of, and profits by, the structure of another. But natural selection can and does often produce structures for the direct injury of other species, as we see in the fang of the adder, and in the ovipositor of the ichneumon, by which its eggs are deposited in the living bodies of other insects. If it could be proved that any part of the structure of any one species had been formed for the exclusive good of another species, it would annihilate my theory, for such could not have been produced through natural selection. Although many statements may be found in works on natural history to this effect, I cannot find even one which seems to me of any weight. It is admitted that the rattlesnake has a poison-fang for its own defence and for the destruction of its prey; but some authors suppose that at the same time this snake is furnished with a rattle for its own injury, namely, to warn its prey to escape. I would almost as soon believe that the cat curls the end of its tail when preparing to spring, in order to warn the doomed mouse. But I have not space here to enter on this and other such cases. (CR Darwin, Origin of species, 1st ed., pp.228-229)

Does Johnson's use in support of "flexibility of Darwinism" make sense? I argue that it does not. Johnson says,

The problem is that the adjusting devices are so flexible that in combination they make it difficult to conceive of a way to test the claims of Darwinism empirically. Apparently maladaptive features can be attributed to pleiotropy, or to our inability to perceive the advantage that may be there, or when all else fails simply to "chance." Darwin wrote that "If it could be proved that any part of the structure of any one species had been formed for the exclusive good of another species, it would annihilate my theory, for such could not have been produced through natural selection." But this was the same Darwin who insisted that he had never claimed that natural selection was the exclusive mechanism of evolution. (p.30, 2nd ed.)

It should be noted that nobody has demonstrated the phenomenon which Darwin described as a falsifier of NS. It remains mysterious as to why Johnson should offer as an illustration of the "flexibility of Darwinism" an instance where no flexibility has been demonstrated in over a century.

How many horns does a false dilemma have?

Another phrase in logic is "false dichotomy", where one is presented two alternatives to choose from, but more alternatives may actually exist. Johnson apparently wishes to demonstrate his logical prowess by use of false dichotomy, for such appears on page 14:

The question I want to investigate is whether Darwinism is based upon a fair assessment of the scientific evidence, or whether it is another kind of fundamentalism. (p. 14, 2nd ed.)

Is it really true that these alternatives exhaust the possibilities? No. An optimistic or pessimistic assessment of the evidence can be considered unfair and yet not lead to a conclusion that the result comports to "fundamentalism". Johnson's dichotomy excludes significant possibilities, which is just the same error that he claims to be trying to correct with his anti-materialistic arguments.

Arguments made of flax

"Strawman" is a term for a logical fallacy which is common enough to have passed into general usage. A strawman is easily knocked down, and thus the strawman fallacy consists of constructing an argument, attributing it to one's opponent, and then rebutting it. The fallacy in a strawman argument is that one's opponent does not make the argument which is rebutted, but rather a different and less easily attacked argument. Can we find evidence of such in "Darwin On Trial"? Not only can we find such, but this one is even directed toward Darwin himself:

In the long term the biggest problem was the fossill record, which did not provide evidence of the many transitional forms that Darwin's theory required to have existed. (pp.33-34, 2nd ed.)

What Darwin had to say about the fossil record and what we should find therein does not require any more examples of transitions than we actually observe. Darwin's famous passage explaining the various factors as to why the fossil record is incomplete covers both geological and biological causes, and accords well with more modern treatments, such as Eldredge and Gould's 1972 exposition of punctuated equilibria.

If another example of the strawman fallacy is wanted, one can read on from almost any point and expect to find one. Here's one from Johnson's chapter on mutations:

But now we must deal with another fallacy, and a supremely important one. That evolution by macromutation is impossible does not prove that evolution by micromutation is probable, or even possible. (p.37-38, 2nd ed.)

Unfortunately for what Johnson claims that we have to deal with, this argument appears to be novel to himself. That is, there aren't any biologists urging people to accept a micromutational view as "proved" simply because macromutation is improbable.

Not all is true, therefore all is false

Having demonstrated several errors on Johnson's part, I could suggest that the reader consider whether, since some of Johnson's argumentation is erroneous, that perhaps all of his argumentation may be considered erroneous. This tactic is used by Johnson himself:

If our hypothesis is that mammals evolved from therapsids only once (a point to which I shall return), then most of the therapsids with mammal-like characteristics were not part of a macroevolutionary transition. If most were not then perhaps all were not. (p.79, 2nd ed.)

This is a very interesting approach to handling the physical evidence. With reasoning like this, Johnson's skepticism has nothing to fear from the data. Whether this can be considered to constitute "fair assessment" of that evidence may be left to the reader's judgment.

A small shell game swapping analysis of logic for analysis of evidence

Another point concerning evaluation of the physical evidence that Johnson's quoted statement concerning the reptile-to-mammal transition is that Johnson doesn't actually evaluate that evidence, but rather simply critiques descriptions or high-level summaries of what the physical evidence shows. To be sure, many scholars rely upon such statements, but typically only use such as an auxiliary support for other evidence and argument. Johnson's goal is to sow doubt concerning the factuality of common descent, and dismissal of the evidence of the therapsids in documenting possible ancestry for mammals on the basis of rhetoric alone leaves much to be desired.

Prof. X says Y. Or did he?

Simple misrepresentation can lead to faulty logical constructs, and Johnson is good enough to provide us with an example:

When disconfirming evidence cannot be ignored completely, it is countered with ad hoc hypotheses. Douglas Futuyma's textbook tells college students that "Darwin more than anyone else extended to living things ... the conclusion that mutability, not stasis, is the natural order." So he did, and in consequence paleontologists overlooked in the fossil record the prevalence of stasis. Stasis could not come to public notice until it was dressed up as evidence for "punctuated equilibrium," which sounded at first like a new theory but turned out to be a minor variant of Darwinism. (p.154, 2nd ed.)

Unfortunately for Johnson's argument, the "stasis" that Futuyma refers to is not the same stasis that is the subject of punctuated equilibria. The very sentence before the one quoted makes this clear:

The concept of a changing universe had been replacing the long-unquestioned view of a static world, identical in all essentials to the Creator's perfect creation.
The stasis that Eldredge and Gould refer to is the tendency for periods of gross morphological change to be short compared to the time in which no such change is discernible. These are separable, separate, and distinct concepts. When someone has to stoop so low as to equate "fixity of species" and morphological stasis to make a false point, one has to wonder not only about familiarity with the material, but also one may legitimately begin to suspect that such distortions are undertaken deliberately.

Johnson and ad hoc rhetoric

Beyond the simple fact of misrepresentation, there is the further issue that Johnson claims punctuated equilibria to be an "ad hoc" hypothesis. But punctuated equilibria was developed from the basis of another theory, that of allopatric speciation of peripheral isolates. As such, PE is a theory of general utility, not an ad hoc means of escaping from unfavorable evidence, or even lack of evidence, as anti-evolutionists so often claim. It is notable that Eldredge and Gould provided fossil evidence in their 1972 essay which introduced the concept of PE, which nicely counters the assertion that PE means evolution occurs "too fast" to ever be seen.

The casting of aspersions

Sometimes Johnson is simply artful in the casting of phrases to make it seem that he has demonstrated something of interest, when examination of the instance in detail reveals something far more prosaic.
The Academy thus defined "science" in such a way that advocates of supernatural creation may neither argue for their own position nor dispute the claims of the scientific establishment. (p. 8, 2nd ed.)

First, there is no bar to advocates of supernatural creation arguing or disputing anything they want. What is asserted is that the arguments that have been advanced do not fit the criteria of scientific argument. Second, the advocates of supernatural creation in question have abandoned making an argument for their own position not only under the definition of science as seeking natural explanations, but also under a definition of science that merely asserts that claims will be empirically testable, as Johnson's quotation of Duane Gish on p. 114 demonstrates.

We do not know how God created, what processes He used, for God used processes which are not now operating anywhere in the natural universe. This is why we refer to Divine Cration as Special Creation. We cannot discover by scientific investigation anything about the creative processes used by God. (Quote of D Gish, p.114, 2nd ed.)

Johnson's excoriation of the Academy for excluding SciCre by definition falters on the simple fact that even those who advance SciCre abdicated from use of scientific investigation. The Academy simply re-stated what the SciCre proponents had told them.

Point the second: The main event

Professor Johnson responded to the criticism of Stephen Jay Gould by stating that he was disappointed that Gould had not addressed his major points. The problem with this is that in logical argument, messing up on smaller points early on robs larger conclusions later of any force, and Gould had pointed out a bevy of smaller incorrect points. As I have noted before, these errors do more than simply vitiate logical arguments based upon them; they also erode any confidence that we may have placed in testimonial statements concerning aptitude, talent, or familiarity that were made. Johnson's larger points are that common descent is not a proven concept and that natural selection is not proven to be capable of effecting the adaptive change necessary for common descent to proceed via natural processes. Johnson apparently wants to utilize a standard of proof from criminal law and apply it to scientific theories: proof beyond a reasonable doubt. Let me argue this from a civil law perspective for a moment and give a different standard: proof via preponderance of the evidence. In those cases where Johnson claims that evidence disconfirms natural selection or common descent, he is uniformly incorrect. Johnson mishandles available evidence or ignores evidence in order to falsely conclude disconfirmation. There's the assertion; now for the documentation...

Johnson's criticisms due to evidence are found in several chapters in Darwin On Trial. I intend to demonstrate that by errors both of misunderstanding and omission, Johnson fails to produce examples of actual disconfirming evidence. What evidence is available, when examined fairly, accords closely with common descent and natural selection.

The fossil record and natural selection

When dealing with the fossil record, Johnson takes as disconfirming data the current observed ratio of transitional sequences to non-transitional, based upon the assertion that under Darwin's views we should expect many more.

Darwin's theory predicted not merely that fossil transitionals would be found; it implied that a truly complete fossil record would be mostly transitionals, and that what we think of as fixed species would be revealed as mere arbitrary viewpoints in a process of continual change. (p.48, 2nd ed.)

Johnson's assertion is false. We can tell that it is false because we can read Darwin's own words and find that Johnson's summary fails to represent what Darwin said. Johnson never went to the trouble of attempting to derive an expected ratio of transitional fossils to non-transitional fossils from what Darwin actually said. Let me demonstrate by example the derivation of an expectation of the ratio of transitional fossils to non-transitional fossils from what Darwin wrote. Darwin stated that natural selection would work intermittently, and often only at long intervals.

On the other hand, I do believe that natural selection will always act very slowly, often only at long intervals of time, and generally on only a very few of the inhabitants of the same region at the same time. (CR Darwin, Origin of Species, 1st ed., p.153)
Darwin addressed geographical distribution of fossils as a factor.
One other consideration is worth notice: with animals and plants that can propagate rapidly and are not highly locomotive, there is reason to suspect, as we have formerly seen, that their varieties are generally at first local; and that such local varieties do not spread widely and supplant their parent-forms until they have been modified and perfected in some considerable degree. According to this view, the chance of discovering in a formation in any one country all the early stages of transition between any two forms, is small, for the successive changes are supposed to have been local or confined to some one spot. Most marine animals have a wide range; and we have seen that with plants it is those which have the widest range, that oftenest present varieties; so that with shells and other marine animals, it is probably those which have had the widest range, far exceeding the limits of the known geological formations of Europe, which have oftenest given rise, first to local varieties and ultimately to new species; and this again would greatly lessen the chance of our being able to trace the stages of transition in any one geological formation. (CR Darwin, Origin of Species, 1st ed., p.306)
In his famous section on the imperfection of the geological record, Darwin gave several further reasons to doubt that we would ever have a complete record of past life.
I have attempted to show that the geological record is extremely imperfect; that only a small portion of the globe has been geologically explored with care; that only certain classes of organic beings have been largely preserved in a fossil state; that the number both of specimens and of species, preserved in our museums, is absolutely as nothing compared with the incalculable number of generations which must have passed away even during a single formation; that, owing to subsidence being necessary for the accumulation of fossiliferous deposits thick enough to resist future degradation, enormous intervals of time have elapsed between the successive formations; that there has probably been more extinction during the periods of subsidence, and more variation during the periods of elevation, and during the latter the record will have been least perfectly kept; that each single formation has not been continuously deposited; that the duration of each formation is, perhaps, short compared with the average duration of specific forms; that migration has played an important part in the first appearance of new forms in any one area and formation; that widely ranging species are those which have varied most, and have oftenest given rise to new species; and that varieties have at first often been local. All these causes taken conjointly, must have tended to make the geological record extremely imperfect, and will to a large extent explain why we do not find interminable varieties, connecting together all the extinct and existing forms of life by the finest graduated steps. (CR Darwin, Origin of Species, 1st ed., pp.340-341)

Given these views of Darwin, we can derive an expectation of the ratio of transitional to non-transitional fossils found. I include in the following only those factors which yield a differential expectation of discovery of transitional fossils displaying the action of natural selection.


where EFR is the "expected fossil ratio",
NSTP is the "natural selection time proportion",
NSPP is the "natural selection population proportion",
AP is the "area proportion",
SEVR is the "subsidence vs. elevation variation ratio",
FSDP is the "formation to species duration proportion",
ETF is the "expected number of transitional fossils",
and OFS is the number of "observed fossil species".

Now, we can assign some estimated numbers to the variables listed above. Because Darwin said "often only at long intervals", NSTP should be small. Let's assign a relatively large "small" value of 0.1. Since Darwin said that natural selection operates on only a very few inhabitants at a time, NSPP should be smaller still than NSTP. Let's assign a value of 0.01. For AP, the area proportion between the geographic extent of a widely ranging species and its local variety, a value of 0.1 is probably an overestimate, but let's leave it at that for the moment. For SEVR, Darwin's text would indicate a value of 0.25 or less would be reasonable. FSDP is something best estimated by a geologist, but Darwin probably felt it to be under 0.5. Replacing values, we find that

EFR = 0.1 * 0.01 * 0.1 * 0.25 * 0.5
EFR = 0.0000125 = 1/80,000

David Raup has estimated the number of catalogued fossil species at 250,000. This allows us to generate an estimate for number of transitional sequences expected under Darwin's own views as:

ETF = EFR * OFS = 0.0000125 * 250,000 = 3.125

Roger Cuffey's 1974 paper on paleontologic evidence listed references for at least 139 fine-grained species to species transitional sequences. According to an expectation derived from Darwin's own words and values from the real world, it can be seen that the fossils have been rather more forthcoming that one would expect, not less. Johnson's assertion of the opposite is not credible and flies in the face of both Darwin's views and real-world data.

Molecular evidence and common descent

When considering the molecular evidence, Johnson failed to account for many different lines of evidence that have been documented, such as homeobox genes and repeated sequences in unexpressed regions. Johnson counts "molecular equidistance" as a factor that tends to place natural selection in doubt. Johnson's further discussion makes it clear that he does not understand how the molecular evidence is analyzed, and he falsely concludes that this is a problem with natural selection. The phrase "linkage disequilibrium" is notably absent from Johnson's review of the molecular evidence, and yet provides direct confirmation of the action of natural selection in modern populations. I go into some detail concerning molecular sequences here, thoroughly picking apart the error that Johnson passes on from Denton.