Expelled Exposed.

I have not seen Ben Stein’s movie Expelled: No Intelligence Allowed, but the reviews and interviews with Stein strongly indicate that it is nonsense. For a growing collection of material relating to the movie, see Expelled Exposed, provided by the National Center for Science Education. Recent highlights include reviews by Michael Shermer and Richard Dawkins, who are in the movie, the PZ Myers expulsion episode, and a panning by none other than Fox News.

Reducibly complex bombardier beetles.

The classic creationist argument regarding “irreducible complexity” is that many multi-part biological systems cannot function without all of their parts present together in the current configuration, and thus that there is no possibility that such systems evolved through gradual intermediates. In the past, the most common examples included features at the organ level such as eyes, but with the rise of intelligent design this has shifted to more esoteric cases like bacterial flagella, the immune system, and the blood clotting cascade.

The argument is false in any case, as it overlooks the commonplace occurrence of shifts in function in evolution, in which subsets of the current system still function, but in a different way. For example, one can remove large numbers of components from bacterial flagellar systems rendering it useless for locomotion, yet the structure still functions in secretion. The point is that such complex structures could evolve through functional intermediates, but that the functions of those intermediates may have been quite different from the function of the system as it is observed now.

In other cases, the concept of irreducible complexity is refuted by simply finding cases in particular species where one or more components are missing but the system still functions in the same capacity. Some bacteria exhibit only a subset of the flagellar components found in other species but still swim. Whales lack Factor XII (Hageman factor) but their blood still clots1 (and, in fact, blood in humans with Hageman factor deficiency also still clots, though more slowly). Plenty of species lack major components of eyes found in vertebrates and cephalopod molluscs, but they see to an extent sufficient for their niches.

Bombardier beetles represent another classic creationist example of irreducible complexity that supposedly would be totally non-functional if any of the numerous components were absent. These beetles employ a mixture of hydroquinone and hydrogen peroxide which, when catalyzed, generates a strongly exothermic reaction in which a hot, repellent liquid is ejected at predators. The argument is that without all of the components present together, the defence mechanism of bombardier beetles would be useless. A typical example is given in this video, which gives an interesting overview of the complex system before concluding that the system could not work without all of the parts. In the beetle shown in this video, the liquid is heated to the boiling point of water, can be aimed with some accuracy, and is released in a series of high-velocity pulses.

It should be noted at this point that there are about 500 bombardier beetle species, divided into several tribes within the ground beetles. These are generally classified into two groups, the brachinoids and the paussoids. It is not entirely clear whether these are monophyletic, meaning that they all evolved from a common ancestor, or whether bombardier-like defence mechanisms evolved independently at least twice. For the purposes of this discussion, the details of their relationships are not particularly relevant, and instead what matters is the diversity they now display. Most of what is known about bombardier beetles comes from studies of the brachinoids (e.g., Brachinus), but this reflects only a portion of bombardier beetle diversity.

Metrius contractus is a species in the paussoid lineage that differs from other bombardier beetles in both lineages in important respects (Eisner et al. 2000). Notably, in this species the mixture of reagents is not ejected in a jet, it oozes out in a froth. M. contractus lacks the elytral flanges found in its relatives that allow it to direct the fluid forward in a jet. It does not aim the abdomen to direct the liquid, rather the excreted foam may be channeled anteriorly along grooves in the elytra (wing covers). The mixture continues to bubble after it is released, indicating that the reaction is not completed before being ejected and the solution is not boiling hot but is ejected at only about 55 degrees celcius. But the beetle survives.

Images from Eisner et al. (2000).

Crepidogaster ambraena and C. atrata are two African species of bombardier beetles in the brachinoid lineage but part of a tribe (Crepidogastrini) different from that of the brachinoids that have been studied in detail (Eisner et al. 2001). These species are similar to other brachinoids in morphological structure of the defensive system and in aiming the excretion by directing their abdomens at predators. However, they differ from the commonly described system in that their excretion is not boiling hot (about 64 degrees celcius), is more mist than jet, and is not pulsed when ejected. As a result, they are less effective than other brachinoids in terms of accuracy, the efficient ejection of liquid at high velocity, and repetitive cooling of the reaction chamber. In other words, slight changes in the structure or function of valves within the system would provide significant advantages, as they did in other brachinoids. And yet, this beetle survives as it is.

The beetles discussed above are all modern species, and none is suggested to be ancestral to any others. As such, these comparisons do not in themselves provide information on the historical sequence of changes in the evolution of the most complex bombardier beetle defences. However, the continued existence of some species lacking one or more of the features found in other species clearly refutes the argument that the complete system must arise all together in order to be functional. Much work remains to be done in sorting out how their remarkable features arose, but there is no reason to believe that they are not the product of gradual evolutionary change.



1. It is worth pointing out that whales do have the gene for Factor XII but it is pseudogenized, and that the amino acid sequence of the protein it would produce is more similar to artiodactyls than to other mammals (Semba et al. 1998).


Eisner, T., D.J. Aneshansley, M. Eisner, A.B. Attygalle, D.W. Alsop, and J. Meinwald. 2000. Spray mechanism of the most primitive bombardier beetle (Metrius contractus). Journal of Experimental Biology 203: 1265-1275.

Eisner, T., D.J. Aneshansley, J. Yack, A.B. Attygalle, and M. Eisner. 2001. Spray mechanism of crepidogastrine bombardier beetles (Carabidae; Crepidogastrini). Chemoecology 11: 209-219.

Semba, U., Y. Shibuya, H. Okabe, and T. Yamamoto. 1998. Whale Hageman factor (Factor XII): prevented production due to pseudogene conversion. Thrombosis Research 90: 31-37.

What is a just-so story?

As I and others have noted many times, facts, theories, and hypotheses are independent elements in the scientific process. Contrary to their vernacular meanings, they are not ranks indicating differential degrees of certainty in some claim.

Evolution is scientific fact, meaning that the numerous types of evidence point so overwhelmingly to shared ancestry that scientists have accepted it as true about the world, in the same provisional-but-extremely-likely sense that they accept other facts like gravity or the existence of atoms.

Evolution is also a theory, meaning that there is a cohesive body of mechanistic explanations that seeks to explain the historical fact of common descent. This includes, but is not limited to, random processes like genetic drift, quasi-random ones such as mutation, and absolutely non-random ones like natural selection.

In addition to being a fact (that species are related through common ancestry) and a theory (well supported mechanisms that explain how evolutionary change happens), evolution represents the unique historical path that living lineages have followed. Whereas there is no longer any real disagreement in biology (or indeed, in science in general) over the historical factuality of common relatedness, evolutionary biology is rife with heated debate regarding the mechanisms and their relative importance, the specific historical relationships linking related groups, and the intermediate steps that occurred in the origin of particular features. As such, hypotheses are also important in evolutionary biology, because they represent testable statements that are used to support or refute specific details of theory or path.

One of the more stinging criticisms that evolutionary biologists level at each other when they argue about evolution as path is to call a proposed account a “just-so story”. The phrase itself comes from Rudyard Kipling’s Just So Stories from the early 1900s, many of which included fantastical accounts of the origins of particular features, like the elephant’s trunk, the leopard’s spots, and the giraffe’s neck. According to Wikipedia,

A just-so story, also called the ad hoc fallacy, is a term used in academic anthropology, biological sciences, and social sciences. It describes an unverifiable and unfalsifiable narrative explanation for a cultural practice or a biological trait or behavior of humans or other animals. The use of the term is an implicit criticism that reminds the hearer of the essentially fictional and unprovable nature of such an explanation. Such tales are common in folklore and mythology.

The important criterion in whether something represents a just-so story rather than a hypothesis is a lack of testability and hence unfalsifiability. A lack of complete supporting data in itself is not an indicator that something is a just-so story, because many hypotheses also lack these prior to being subjected to testing. In other words, what matters is whether it can be tested, not whether it has already been tested, though obviously some supporting data must be provided eventually if the hypothesis is to be considered seriously.

Creationists, who seem unequipped with irony detectors, tend to dismiss all hypotheses about evolutionary path, even ones for which there is substantial supporting evidence, as just-so stories. In fact, they often demand an absurd amount of evidence and detail, such as an observable, repeatable, mutation-by-mutation demonstration of some feature evolving. When this obviously cannot be delivered (nor could its counterpart in any science), they believe this supports their unobservable, unrepeatable, vague explanation for the feature’s origins. Theirs is the ultimate just-so story, but that does not prevent them from projecting onto scientists.

As a case in point, consider the infamous bombardier beetles, which I mentioned briefly in a recent post. Along with eyes, blood clotting, the immune system, and bacterial flagella, the defence mechanism of these intriguing beetles supposedly represents an un-evolvable feature due to its irreducible complexity.

The claims made by creationists about these beetles relate to both fact and path. In terms of fact, they often suggest that the reagents used in its defensive system will explode when mixed together, and thus that their mechanism of storing them separately must have arisen fully formed. This is demonstrably false. A catalyst is required, as Dawkins showed by mixing the liquids.

With regard to path, they argue that a series of functional intermediates in the gradual evolution of the defensive apparatus is impossible in principle. This claim is also easily refuted by the presentation of plausible, testable hypotheses showing how functional intermediates could have occurred. One example is given in this video.

Now, is this the answer to how the spectacular defence system of bombardier beetles arose? I do not know, but I suspect probably not. A similar point of view is presented by Mark Isaak, who authored the Talk.Origins article Bombardier beetles and the argument of design:

The scenario above is hypothetical; the actual evolution of bombardier beetles probably did not happen exactly like that … Determining the actual sequence of development would require a great deal more research into the genetics, comparative anatomy, and paleontology of beetles. The scenario does show, however, that the evolution of a complex structure is far from impossible. The existence of alternative scenarios only strengthens that conclusion.

Are such scenarios just-so stories? No, they are hypotheses, and they are testable. For example, are the hypothetical intermediate stages found to be functional in any other species? Are the chemicals used in combination in the defence system also functional on their own elsewhere in the beetle’s body? Are there genetic differences between bombardier beetles and other Carabidae related to this system?

Without clear answers to these and other questions, the path of bombardier beetle evolution will remain an open and interesting question. However, biologists do not assume that these beetles did not evolve simply because the specific path has yet to be elucidated. And they certainly would not assume that an untestable, supernatural just-so story of cosmic proportions is the null hypothesis.

That, of course, is the difference between science and pseudoscience.

Monty Python guards Expelled.

Apparently PZ Myers was refused admission to Expelled, the pro-ID movie about how, you know, people are prevented from engaging in debate about the subject. Anyway, they decided that PZ, who is interviewed in the movie, should not see it, but they neglected to stop his guest — some guy named Richard Dawkins — from entering. I imagine the scene played out something like this as the guards were given instructions on who to let in…

Welcome Pharyngulanchers.

I see PZ has linked here in a discussion of yet more IDist nonsense regarding junk DNA. To help you find what you’re after, here is a list of relevant posts on the subject:

Junk DNA and ID redux.

Just a reminder, these are the important points under discussion:

* Proponents of ID themselves clearly suggest that “junk DNA” will mostly or all be functional.

* No unambiguous explanation has been given for why ID must assume that non-coding DNA is functional, especially since they say nothing can be known about the designer or the mechanism.

* The existence of much non-functional DNA would not necessarily refute the idea of design, as many human-designed structures have redundant, non-functional, or even counterproductive characteristics. It would, however, challenge certain assumptions about the designer and the mechanism, which again is why these must be made explicit if the junk DNA argument is to be invoked. Therefore, this is only a useful prediction if one includes details about the mechanism of design.

* The demonstration that all or most non-coding DNA is functional would not support ID to the exclusion of evolution, because a strict interpretation of Darwinian processes has always been taken to propose function as well.

* The demonstration that all or most non-coding DNA in the human genome is functional would still leave the question unanswered as to why the designer put five times more in onion genomes.

* Many functions that have been proposed or demonstrated are dependent on the process of co-option, the same process that is involved in the evolution of complex features.

* Evidence for function in non-coding DNA comes from analyses using evolutionary methods. Other approaches, such as deleting some, have not supported the hypothesis that it is functional.

* The current evidence for function, and other details about how non-coding DNA forms, both suggest that most non-coding DNA is non-functional, or at least that this is the most plausible condition pending much more evidence.

Feel free to comment, but please address these points directly.

"Fx of Junk DNA" or "Mondo hackitude-o-rama".

I do not read the intelligent design blogs, but I do read the blogs of some people who read the intelligent design blogs. Today, Afarensis points to a series of “predictions” put forward by ID proponents at the behest of William Dembski on his blog Uncommon Descent for use in an upcoming interview or something. Curious to see what ID predicts (since, as noted, I don’t read their blogs and they don’t publish in the scientific literature), I took a look.

Apparently, many ID proponents don’t know what a prediction is, or at least not what a useful, testable, scientific prediction is. For example:

“Intelligent design can predict that science will never be able to explain how this complex life arose (homochirality). This prediction has been confirmed every year for decades.”

“That after “billions and billions” of generations of any particular biological entity no new morphology will occur due to random mutations and natural selection.”

“ID predicts that many, if not all, innovative technology achievements of human kind (read agency) will have direct parallels in, or derivation from, biological systems.”

And so on.

But here is what caught my attention.

“The single most important prediction of Intelligent Design is that, although there might be the occasional degeneration of either macroscopic or microscopic structure, most structures should serve a purpose. Thus most organs should not be vestigial, and most DNA should not be “junk DNA”.”

Others concurred that 1) junk DNA won’t be junk, and 2) this is a prediction of ID, and 3) this distinguishes ID from evolutionary science.

I have been over this many times, but of course ID proponents probably don’t read my blog (or the scientific literature). Here are the salient points:

1) There is good reason to believe that non-functional DNA is common. The mechanisms of formation — primarily things like transposable element multiplications, gene duplication and pseudogenization, replication slippage, and unequal crossing over — can add DNA without any requirement that it serve a function. Actual data from genome sequences confirms that the most substantial fraction of eukaryotic DNA is transposable elements, some of which are functional, some of which cause disease, and perhaps most of which are now inactive molecular vestiges. Evolutionary biologists do not simply assume non-function out of ignorance. The default assumption for much non-coding DNA is non-function because of what we do know about how it gets there.

2) I have yet to see a convincing, or even unconvincing, argument for why ID requires that non-functional features be rare or non-existent if indeed nothing can be known about the designer. Even very sophisticated products of design by humans have their redundancies and non-functional aspects. For a fun example, consider what was discovered when parts of the source code for Windows 2000 were leaked to the internet during development. It was laced with curse words, warnings of “hacks” that had to be written in to make parts work, and just general expressions of frustration. For example:

// We are morons. We changed the IDeskTray interface between IE4″


* The magnitude of this hack compares favorably with that of the national debt.”

// Mondo hackitude-o-rama.”

These are remarks that do not code for anything. You could take them all out and nothing would happen to the function of the software. Or, taking a larger view of this analogy, your computer hard drive probably has on it all sorts of redundant, partly deleted, or perhaps even malevolent bits of code, and yet it nonetheless was a designed structure.

Here is the argument I am making. Either IDists cannot say anything one way or the other about non-function, or they must provide information about the method and motive of the designer to justify the assumption.

3) One of the basic assumptions made by hardcore adaptationists is that non-coding DNA must be functional or it would have been deleted. So, this “prediction” is not exclusive, or even original, to ID — it is based firmly in the most rigid applications of Darwinian processes.

One commenter on the ID blog said this:

As already mentioned, “junk-DNA” would completely undermine ID if it turned out to really be “junk”. But, of course it isn’t.”

I disagree on both fronts. The existence of truly non-functional DNA would not automatically indicate a conclusive refutation of intelligent design, it would only be evidence against design by a divine designer. One can have design with non-function. I also note that there presently is no convincing evidence that more than a small portion of the human genome is functional, let alone the many genomes that are much larger than that of humans.

IDists can consider “all or most non-coding DNA will have some function” their “single most important prediction” if they choose, but this is meaningless because it provides no specifics, it does not actually allow a test of ID unless they acknowledge the features of the designer, and it was already made by some evolutionary biologists decades ago.

The Dr. Credibility principle.

The title “Doctor” and the abbreviated prefix “Dr.” come from the Latin for “teacher”, and are traditionally bestowed on those who have earned a doctoral degree, the highest academic degree attainable. The suffix Ph.D. is an abbreviation for Philosophiæ Doctor (L. “Teacher of philosophy”), with “philosophy” from the Greek for “love or pursuit of wisdom”. The Ph.D. is awarded in most academic disciplines, including science (in many cases, the D.Sc., or Doctor of Science, is awarded as an honour for special accomplishment). Medical professionals may also hold the title “Doctor” even though they may do little or no teaching, with common suffixes being M.D. (Medicinae Doctor, or Doctor of Medicine), D.V.M. (Doctor of Veterinary Medicine), D.D.S. (Doctor of Dental Surgery), and so on. It is also possible to obtain the title “Doctor” in areas such as homeopathic medicine or chiropractic. In other words, the title alone does not provide much information about what the individual’s qualifications are. However, one can reasonably argue that the prestige attached to it comes from the fact that individuals such as medical doctors and scientists who hold the title are typically ranked among those with greatest prestige.

For the past several years, i.e., since completing my Ph.D. degree, my official title has been “Dr.” and not “Mr.”. Some people become upset if you call them “Mr.” (or “Ms.”) instead of “Dr.”, but I generally try not to make too much of this. In academic settings, I think a good rule is that people who do not hold the degree, or colleagues in formal settings, should address those with the degree by their official title of “Dr.”. On the other hand, in informal settings with colleagues who hold the same title, or with students with whom one is familiar (e.g., graduate students in one’s own group), using the title simply becomes awkward and first names are appropriate. I will admit that it did take me some time to get used to calling my advisors by their first names, and I have since observed this in several of my students. Outside of academic settings, I generally don’t correct people if they call me “Mr.”, and I don’t introduce myself with the title. I believe most of my colleagues take a similar approach, though of course there is some variation.

Two recent discussions on science blogs have prompted this post, in case you were curious as to why I was bothering to tell you this. Both relate to what I am calling the “Dr. Credibility principle”, which is an attempt to gain undeserved credibility simply through invoking the title.

The first is the example of Dr. Sharon Moalem, author of the book Survival of the Sickest. It appears Dr. Moalem has been misrepresenting his credentials, making it seem as though he has obtained a medical degree, when in fact he has not (though he his a med student). PZ Myers has already discussed the book, which seems to be largely based on non-scientific and pseudoscientific arguments. I had a feeling that this would be so right away. Why? Because he used the title “Dr.” on the cover.

You see, scientists almost never use the prefix “Dr.” on their book covers. It doesn’t matter if it is a popular book or a technical one. If you have science books, go see for yourself. We just don’t do it. In fact, I am willing to extend the “Dr. Credibility principle” to claim that whenever you see someone making a big deal out of their title, especially on a book cover, you can usually bet it is because the content of the book cannot stand on its own without a deflecting appeal to authority. Yet, as noted, those with real authority, and because of whom the title has some prestige, do not use it in that way.

The second case is the Discovery Institute’s public relations gimmick of having “scientists” sign the following “Dissent from Darwinism” statement:

We are skeptical of claims for the ability of random mutation and natural selection to account for the complexity of life. Careful examination of the evidence for Darwinian theory should be encouraged.

As I tell my students, this is so benign that I could easily sign it, and I suspect any biologist could. I too am skeptical of claims that random mutation and natural selection account for everything. And careful examination of the evidence should be encouraged in all sciences, always. Nevertheless, as John Lynch has demonstrated, people with qualifications in evolutionary biology don’t sign this list because it is obviously intended to confuse the uninitiated.

Compare this with a statement that many biologists (though only those with the name Steve or its derivatives) are only too happy to put their names on:

Evolution is a vital, well-supported, unifying principle of the biological sciences, and the scientific evidence is overwhelmingly in favor of the idea that all living things share a common ancestry. Although there are legitimate debates about the patterns and processes of evolution, there is no serious scientific doubt that evolution occurred or that natural selection is a major mechanism in its occurrence. It is scientifically inappropriate and pedagogically irresponsible for creationist pseudoscience, including but not limited to “intelligent design,” to be introduced into the science curricula of our nation’s public schools.

The Discovery Institute has managed to find only 700 signatories since 2001. The NCSE’s list, which is meant only as a parody, has 860 Steves.

Most of the individuals who have signed the Discovery Institute’s list have degrees in engineering (see the Salem conjecture), chemistry, physics, or computer science, though several at least have biological training, albeit in physiology or molecular biology. Some of them are not scientists of any sort. The only unifying feature appears to be that they hold a Ph.D. in something. Once again, it’s the “Dr. Credibility principle”: If one has the title, one must be an authority on the issue under discussion.

The Dr. Credibility principle finds it most extraordinary application in the Orwellian-entitled Physicians and Surgeons for Scientific Integrity. Who can join, you ask? “Any person with an M.D., D. O., D.D.S., D.M.D., D.V.M. or equivalent degree may become a physician/surgeon member of PSSI”. Personally, I don’t think anyone should take a medical doctor, dentist, or veterinarian as an authority on biology any more than they should let biologists like me prescribe drugs or perform a root canal. The only possible explanation is that this is another misguided appeal to authority. Unfortunately, many people are liable to buy into it, especially in groups like anti-evolutionists, where authority seems to trump data regularly.

Let me say it clearly. Having the title “Dr.” does not make anyone an authority on anything except, one would hope, the field in which they obtained a degree. Anything else is just playing doctor to gain undue credibility.

Huckabee is right for all the wrong reasons.

Over at Pharyngula, PZ points to an interview with former Arkansas Governor and presidential hopeful Mike Huckabee. As a Canadian, I have long been amused by Huckabee for reasons you can see here. The prospect of this guy becoming president is unnerving, but then so is the fact that our neighbours saw fit to elect (or at least, not not-elect) Bush. Twice.

Here is what Huckabee has to say about evolution. I have omitted the bit about teaching non-scientific alternatives in science class that preceded it, because it’s too silly to repeat (he says “all views”, but presumably he means “one other view” only).

Because, frankly, Darwinism is not an established scientific fact. It is a theory of evolution, that’s why it’s called the theory of evolution.

He’s right. “Darwinism” — a term used mostly by creationists, but also historically (e.g., Wallace) and to an extent today (e.g., Dawkins), especially in Britain — refers to natural selection as a mechanism of evolution. And it is a theory. In science, a theory is an explanation for an observed or inferred condition of the natural world that is well established through multiple lines of empirical evidence (i.e., a fact). Darwin’s theory of natural selection is one explanation for the fact that species are related through descent, which in turn has been well established in science for well over a century on the basis of fossils, biogeography, embryology, morphology, and genetics. Darwinian natural selection is not the only available explanation, and therefore represents a subset of modern evolutionary theory. That natural selection happens is an established fact (witness antibiotic resistance), but what its role is in causing large-scale evolution remains a subject of discussion among biologists.

So “Darwinism,” in the sense of meaning that the majority of evolution occurs via natural selection, is indeed not an established fact, it is a theory. Huckabee’s words are correct, even if his intent is terribly muddled. Scientific theories explain facts. If there is no established fact, then there is no theory needed.

I invite Gov. Huckabee to read more about this in a recent paper that is freely available here.

News stories of interest.

In keeping with my recent minimalist approach to the blog, here are some links to stories by others that I think you may find interesting.

US ‘doomed’ if creationist president elected: scientists (PhysOrg)

I think this is a great line:

The logic that convinces us that evolution is a fact is the same logic we use to say smoking is hazardous to your health or we have serious energy policy issues because of global warming,” University of Michigan professor Gilbert Omenn told reporters at the launch of a book on evolution by the National Academy of Sciences (NAS).

Evolutionary idea
Scientists rally to explain and defend the cornerstone of biological study
(Houston Chronicle)

An interesting piece (especially given the venue), and I am happy to say that it makes a note of the new journal Evolution: Education and Outreach, which I hope you’re all planning to read.