The editors were filled with righteous indignation in their February 9 editorial.¹ In 1944, the U.S. government had allowed John Cutler, a physician with the U.S. Public Health Service, to infect Guatemalans with syphilis and gonorrhea without their consent in order to test a prophylactic. It was all for the good, of course; who wouldn't want to use science, with its controlled experimental methods, to find a cure for devastating diseases that afflict millions?

In all, 1,308 prisoners were infected. Some of them are still alive today, having suffered ever since. In the same issue of Nature,² Matthew Walter described other examples of ethics gone awry ("Human experiments: First do harm"). But before we condemn past abusers for their "Hypocritical Oaths," the editors warned, we need to honestly assess how ethics evolve. The "barbarous experiments" in post-war Guatemala raise serious questions about how historians will judge today's "acceptable" practices.

Most unsettling is the fact that Guatemala was not an isolated case. The editors and Walter dredged up a litany of disturbing incidents from recent memory:

• In 1941, "US physician William Black infected children, including a 12-month-old baby, with the herpes virus." His work was eventually published in the Journal of Pediatrics.
• Residents of a psychiatric hospital were infected with influenza. It is doubtful any of them could have given their consent. "It might be tempting to explain away such research abuses as the work of rogue scientists," the editors said, "but the Michigan study was conducted by a leading researcher of the time, Thomas Francis Jr., and his young colleague, Jonas Salk, who went on to develop the polio vaccine."
• In 1963, "a team run by Chester Southam injected tumor cells into extremely infirm patients at the Jewish Hospital for Chronic Disease in New York without informing them that the shots contained cancer," the list continued. "Southam was later put on probation by the New York State medical licensing board, but many researchers defended the work and he was later elected president of the American Association for Cancer Research."

As for Cutler, his abuses did not end in Guatemala. He returned to the U.S. and continued subjecting American prisoners, mental patients and soldiers to infection with sexually transmitted diseases. Some of his methods, described by Walter, are sickening. He actually lied to get the cooperation of test patients:

The commission says there is no evidence that Cutler sought or obtained consent from participants, although in some cases he did get permission from commanding officers, prison officials and doctors who oversaw the patients at the psychiatric hospital. In a letter to his supervisor, John Mahoney, director of the VDRL, Cutler openly admits to deceiving patients at the psychiatric hospital, whom he was injecting with syphilis and later treating. "This double talk keeps me hopping," Cutler wrote.

Despite the failures, the work burnished Cutler's credentials. A few months after he arrived home, the World Health Organization sent Cutler to India to lead a team demonstrating how to diagnose and treat venereal diseases. In the 1960s, he became a lead researcher in the infamous Tuskegee experiment in Alabama, in which hundreds of black men with syphilis were studied for decades without receiving treatment. He flourished in the Public Health Service and later became a professor of international health at the University of Pittsburgh in Pennsylvania. He died in 2003, well before details of the Guatemala experiments were exposed.

Ethical boundaries for experiments on humans can be stated very simply. "The limits of justifiable experimentation upon our fellow creatures are well and clearly defined," Canadian physician William Osler, one of the grand old men of U.S. medicine, wrote more than a century ago. "For man absolute safety and full consent are the conditions which make such tests allowable."

Yet mysteriously, the editors claim that ethics have evolved and should evolve. Notice this convoluted statement that mixes stasis and evolution in the same sentence: "Although US standards have evolved, the concepts of informed consent and safety still underpin research on humans." On one hand they call us to engage in serious soul-searching:

What kind of work deemed as accepted today will be denounced by future generations? The question is one that all researchers should bear in mind, because history may judge them more harshly than their peers do. One example could be denial of treatment to sick people through the use of placebos in clinical trials and the ways in which some of these trials are carried out in developing nations, amid accusations of abuse of poor, uneducated participants. Broadening to other types of research, attitudes to work on embryonic stem cells may harden. And future generations may extend the protection currently in place for humans to cover other species, such as chimpanzees.

There is, of course, clear water between the Guatemalan experiments and chimpanzee research. The Guatemala research was illegal, even in the 1940s, and most of the data did not prove useful and went unpublished. Still, as with research on embryonic stem cells, there is considerable debate about the ethics of using chimpanzees as experimental subjects. In these and other cases, nations would do well to heed some of the lessons that emerged from the investigation of the experiments in Guatemala. Governments and other funders of research must exert full oversight, provide as much transparency as possible and ensure that regulations are clear, strong and evolve with the times.

Charles Darwin, however, preached that natural selection was directionless and contingent. Stephen Jay Gould emphasized that point: rewind the tape of evolution, start over, and you will likely get completely different results. Darwin also applied his concept of natural selection to the human mind and emotions. According to his view (undoubtedly shared by the editors of Nature), the ethics we call standards today had no direction or goal; they just "are" -- as are the feelings of happiness or disgust we feel comparing our values with those of 1941. By extension, the ethics of 2050, or 2100, may castigate what we praise, and may glorify what we despise.

The editors of Nature can't quite stomach the logical conclusion of their evolutionary views. Their admiration of evolution is tempered by the recognition that society needs absolutes. One cannot call past abuses "unconscionable" without a conscience. One cannot judge past abuses without a standard to judge by. Darwin's most prominent living advocate, Richard Dawkins, has admitted he wouldn't want to live in a country operating by natural selection. He prefers living in a nominally Judeo-Christian society, one that still believes in the rule of law based on unchanging ethics, that grants him the freedom to operate his business of undermining the Judeo-Christian world view.

The editors were noticeably silent about North Korea, where experimentation on human prisoners is rampant, leading to untold horrors of pain and suffering -- where the victims are expected to praise the Dear Leader for allowing them to serve him in that way. Who are the editors to accuse them? How can they know whether in some future epoch, historians will judge harshly not the North Koreans, but the editors of Nature for their barbarous, disgusting, abhorrent suggestion that what Cutler did was wrong?

Let the evolver beware.

References:

1. Editorial, "Hypocritical Oaths," Nature 482 (09 February 2012), p. 132, doi:10.1038/482132a.

2. Matthew Walter, "Human experiments: First do harm," Nature News Feature, vol. 482 (08 February 2012), issue 7384.

The NCSE sought to ramp up its efforts on the climate front by enlarging its board of directors. Yet now our Darwin-lobbying friends have serious egg on their faces after making (not their first) unwise choice of associates. The group invited climate activist Peter H. Gleick of the Pacific Institute for Studies in Development, Environment, and Security, an ideological compatriot and neighbor in Oakland, CA, to join its board. Bad move. Gleick has just suffered a major ethical embarrassment, leading to a break with the NCSE and leaving the Darwin enforcers under a cloud.

Well, we already knew that the NCSE, which has never disavowed its link with anti-Semitic conspiracy theorist James Fetzer, has poor judgment in its choice of allies.

You've heard Gleick's name if you've followed the recent Heartland Institute dustup. Last week, news media picked up a story of purloined internal documents detailing Heartland's efforts to raise funds for its efforts to advance an idea -- climate skepticism -- that many liberals find abhorrent. The documents were mostly authentic and uninteresting, with a single exception: an incendiary memo that I could have told you was a fake.

I say that now though others beat me to the punch, by a long shot. Megan McArdle, senior editor and blogger for The Atlantic and a strong believer in human-induced catastrophic global warming, read carefully through the supposed "Confidential Memo: 2012 Heartland Climate Strategy" and pronounced it phony on a variety of technical and other grounds.

Though purportedly written for "a subset of [Heartland] Institute Board and senior staff," the memo was clearly authored by someone hostile to climate skepticism, as a read-through by anybody remotely sensitive to inflections of language would detect. The memo speaks, for example, about the institute's plans to "dissuad[e] teachers from teaching science." Whatever you think of the science behind climate skepticism, this is not how its advocates speak about their work. It's how their cruder opponents speak about them.

But the enforcers of orthodoxy on climate and evolution imagine that they've got skeptics all figured out. Many are evidently so carried away by fervor that they picture us using cartoon-villain talk of the kind that figures prominently in the memo. Whoever forged the document was speaking to, for and through that constituency.

For several days, this was catnip for the liberal media, which assumed the whole cache was genuine. Quoting the line about "dissuading teachers from teaching science" and putting the words in bold, Discovery Magazine science blogger and astronomer Phil Plait wrote,

One thing I want to point out right away which is very illuminating, if highly disturbing, about what Heartland allegedly wants to do: they are considering developing a curriculum for teachers to use in the classroom to sow confusion about climate change. I know, it sounds like I'm making that up, but I'm not.

Physicist Sean Carroll, who raised a ruckus and quit Bloggingheads.tv because the latter allowed intelligent design-proponent Michael Behe to speak for himself, commented, "'Dissuading teachers from teaching science' -- yes, people work to do this."

Meanwhile at the NCSE, Programs and Policy Director Joshua Rosenau was eating it up. Rosenau praised the still unknown person who leaked the documents as a patriot and a gentleman:

We don't know who distributed the Heartland memos, or exactly how they were obtained. But by doing so, the leaker provided a profound public service, one that we can all be grateful for. These memos provide an inside look at the climate change denial machine, revealing how they talk about their work behind closed doors.

Quickly, NCSE staff changed their own view on the matter. Gleick submitted his resignation from the board, where he was scheduled to begin serving on February 25, and the NCSE accepted his resignation.

The group's executive director tried to put the best face on it and blame climate skeptics:

"Gleick obtained and disseminated these documents without the knowledge of anyone here," NCSE's executive director Eugenie C. Scott commented, "and we do not condone his doing so." But, she added, "they show that NCSE was right to broaden its scope to include the teaching of climate science. There really are coordinated attempts to undermine the teaching of climate science, and NCSE is needed to help to thwart them."

Was it Gleick who invented the phony "memo"? He claims to have merely been passing along material from someone else:

I can explicitly confirm, as can the Heartland Institute, that the documents they emailed to me are identical to the documents that have been made public. I made no changes or alterations of any kind to any of the Heartland Institute documents or to the original anonymous communication.

This can't be a good day for Peter Gleick and I don't care to dwell on his role, whatever it might turn out to be. What this business says more generally about the ethics of the orthodoxy enforcers on climate and evolution, ruled by a dangerous passion to suppress dissent, is a different matter.

Megan McArdle asks:

Gleick has done enormous damage to his cause and his own reputation, and it's no good to say that people shouldn't be focusing on it. If his judgment is this bad, how is his judgment on matters of science? For that matter, what about the judgment of all the others in the movement who apparently see nothing worth dwelling on in his actions?

As Professor Flannery explains, Darwin's position as a child of privilege and his naturalistic worldview both in their different ways shaped his approach to the study of nature, as did Wallace's own struggling middle-class background and his less rigid understanding of science and limits. Wallace, of course, would go on to become effectively the founder of the modern intelligent-design movement.

The rogue proteins behind variant CJD, the human form of mad cow disease, have revealed their benign side. Prions, it seems, lie at the heart of a newly discovered form of near-instant evolution that provides life with a third way to adapt to potentially lethal environments. Crucially, it involves neither genetic nor epigenetic changes to DNA.

...In challenging conditions, [Yeast] can instantly churn out hundreds of brand-new and potentially lifesaving proteins from its DNA, all without changing the genes in any way.

("Prions point to a new style of evolution," New Scientist, February 16, 2012)

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MagiMold® works because of prions, special proteins that allow a cell to evolve before its DNA does. Then mutation and selection come into play and...the evolved prion-trait becomes fixed. It's more than genetic. It's more than epigenetic. It's Magi-genetic!

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From the other side of a fence on Wilshire you can see the life-size models of a mammoth caught and doomed to drown in the tar as another adult and baby mammoth look on. It's an L.A. landmark -- and a nice illustration of one problem that bedevils Darwinian theory.

Commemorating "Darwin's Legacy" for the website Skeptic.com, paleontologist and harsh intelligent-design critic Donald Prothero writes, based on his own work there, about the funny way the animals dredged up from the tar have of staying static over vast stretches of time. That is despite radically alternating environmental conditions of the kind that should stimulate some evolutionary action. The more things change the more they stay the same.

File this perhaps under "What They Say When They Think We're Not Listening":

After six years of work and publication, the conclusion is clear: none of the common Ice Age mammals and birds responded to any of the climate changes at La Brea in the last 35,000 years, even though the region went from dry chaparral to snowy piñon-juniper forests during the peak glacial 20,000 years ago, and then back to the modern chaparral again.

In four of the biggest climatic-vegetational events of the last 50 million years, the mammals and birds show no noticeable change in response to changing climates. No matter how many presentations I give where I show these data, no one (including myself) has a good explanation yet for such widespread stasis despite the obvious selective pressures of changing climate. Rather than answers, we have more questions -- and that's a good thing! Science advances when we discover what we don't know, or we discover that simple answers we'd been following for years no longer work.

This is on my mind because a colleague of ours is currently trying to wrestle several corrections to an article about evolution-related legislation from an editor whose reporter egregiously distorted Discovery Institute policy on academic freedom and mangled my colleague's words. We've been through this process with other media outlets many times before. Of course it matters because if uncorrected the article with its untruths will end up being cited as fact by Wikipedia's editors and become part of an eternal, immovable online legacy.

It can be very difficult to get these people simply to say back, accurately, what you said. As a further random illustration, I saw that Joshua Rosenau of the Darwin-lobbying National Center for Science Education blogged yesterday attempting to insinuate that this website is in sympathy with the Spanish Inquisition. He really did.

Beyond the sheer silliness, I noticed that everything Josh thinks he knows about the Spanish Inquisition he got from reading one Wikipedia article on the subject -- every single particular in his blog post, intended to demonstrate his smarts on the subject, is from there. And even that he seems to have been unable to read with the care you'd expect from a remotely thoughtful person. Leaving evolution totally to one side, he could not understand what the Spanish Inquisition set out to do or whom it targeted.

Richard Dawkins has famously attempted to christen a social movement of materialists, atheists and Darwinists called the "brights." But an absence of the very quality of which these folks want to be able to boast is what often strikes me. For many, basic reading comprehension is a stumbling block.

There are several funny things about the interview Dawkins gave the BBC to describe his new "scientific" survey (it must be true, it's "science"). One is that Dawkins thinks that the ignorance and non-practice of self-identified Christians -- about half the population of nominal Christians in the UK -- is evidence of actual non-belief. But is failure, for example, to know the name of the first book of the New Testament a good test? He was asked as a comparable matter if he, as the world's most famous Darwinist/evolutionist, knew the subtitle of Darwin's great book on evolution. He said, rather peevishly, that he did. But when pressed, he didn't. (It's "by Means of Natural Selection, or the Preservation of Favored Races in the Struggle for Life.")

He was uncomfortable having the spotlight turned on himself, of course. But as a thought experiment, let's follow up and suppose a survey that asked people if they accept the "theory of evolution." Of those saying yes, ask them the name of the famous book by Charles Darwin on the subject (not the subtitle, the actual title). How many people do you think would get the title, and get it right (On the Origin of Species). Then ask how many had read it? Rather a smaller percentage, I suspect, than those self-identified Christians who have read the Bible in full or in part.

A nice follow-up question would be to ask those who "accept the theory of evolution" if they can say what that theory is. You would get quite a collection of responses, many contradictory, I think. Ask them further if evolution was the result entirely of natural causes or if God had a role in it, and see the spectrum of concepts there. In other words, if you think Christians are ignorant, try talking to evolutionists.

A more trivial question of my youth was, "What is the longest word in the English language?" The answer (at least back then) was "antidisestablishmentarianism," which is merely the historic position of those who opposed efforts to remove the Church of England as the established church of the realm. This whole issue seems rather arcane, doesn't it? Except that for Richard Dawkins, the cause he cares about most is opposing religion -- especially Christianity -- and that makes him a passionate modern advocate of disestablishmentarianism. His heart is much more in anti-Christianity than in any scientific case for Darwin's theory of evolution.

Listen to the BBC interview here.

Image credit: Francisco de Goya, "Scene from an Inquisition," Wikimedia Commons.

Hosted ironically by an outfit calling itself the Palouse Coalition of Reason, the event included Daniel Dennett and PZ Myers with the latter doing basically a standup comedy routine mocking Darwin-doubters. "He never interacted with a single argument," our friend reports. Not once.

Well of course not.

A followup event at the University of Idaho the next night starred Darwin defenders Fred Edwords and Jen McCreight. In the Q&A, our friend alluded to some challenges to Darwinian theory and offered the view that "Good scientists are masters of the method; they aren't identified by which paradigm they pledge allegiance to."

"I was interrupted by someone and then PZ Myers chimed in (he was there as an audience member). He turned around and said to me, 'That's crap science.'" And so there you go: argument over.

You can't reason with these people -- you really can't. What made it worthwhile for our correspondent was the conversations afterward. Chatting with people from the audience, he got a chance to recommend good books to folks looking for further and better information and got into one conversation that went on over beers till midnight. That kind of human interaction is almost invariably worth the effort.

Enter the epigenome, with its codes, upon codes, upon codes. Discovery Institute's Richard Sternberg has made this the focus of his research lately and, as Casey described the other day, it's also the subject of a new book based on Sternberg's work, by Tom Woodward and James Gills, The Mysterious Epigenome: What Lies Beyond DNA.

[Editors note: CSC Fellows Michael Behe and Richard Sternberg will join Tom Woodward and James Gills to speak at a conference about epigenetics titled: Shaping Your DNA Destiny - Exploring Epigenetic Keys to Improving Your Health, Feb. 24-25 in Tampa Bay, FL.]

When all else fails, look brave. Three Harvard biologists, Ben Hunter, Jesse D. Hollister, and Kirsten Bomblies, have now sought to face the daunting new challenge with an essay in Current Biology, "Epigenetic Inheritance: What News for Evolution?"

The epigenome has no clear boundaries at this point. "Epigenetics" could refer to any heritable condition beyond DNA. Scientists now know that gene expression is controlled by numerous mechanisms, including histone tags (sometimes called the "histone code"), the "zygote code," various types of small RNAs, alternative splicing, pre- and post-transcriptional modification, and an army of transcription factors. The old "central dogma" that information flows from gene to protein has been defunct for some time, but much remains to be understood. How does the environment influence epigenetic markers? How are they passed on, and how stable are they? How do "epialleles" (a new term extending Mendel's paired gene concept) affect the phenotype?

Epigenetic marks such as cytosine methylation or histone modifications can be very dynamic and can alter gene expression in response to environmental and developmental cues without changes in DNA sequence; in some cases epigenetic changes can be heritable through meiosis. This has spurred interest -- and heated debates -- about whether epigenetic variation may play a significant role in adaptive evolution. The need to formally consider epialleles in population genetics and evolutionary theory has been emphasized ... however, more empirical data are necessary to parameterize models and assess the actual impacts of epigenetic variation on adaptive phenotypes.

It has been known for some time that epialleles at some loci are "metastable" and can change dramatically over generations. Such instability suggests it is unlikely that alternative epialleles can contribute appreciably to stable evolutionary change.

While instability speaks against the idea that individual epialleles would contribute to long-term adaptive evolution, it does beg the question why there is variation among loci in epigenetic stability in the first place. As Richards has pointed out, one possibility is that the unstable epialleles are really just phenotypically inconsequential "genomic clutter" that is reset with passing generations. On the other hand, such variation could also be part of a plastic environmental response system or, if selection can stabilize epigenetic states, then it becomes a standing supply of potentially heritable, adaptive epialleles. A particularly intriguing possible explanation when considering the role that epigenetic variation may play in long-term evolution is that it is the propensity to vary, rather than any particular allelic state, that is under selection. Simulations have shown that phenotypic variation and plasticity generated by epigenetic instability can be beneficial in variable environments, and thus instability may itself be a target of selection.

At this point, evolutionists do not know which human instinct to follow: fight or flight. The look on their faces is curiosity instead of terror.

Having realistic numbers for parameters such as allele stability, epimutation rates and reversion rates is critical for incorporating epigenetics into evolutionary theory. Studies such as the recent A. thaliana variation accumulation studies provide such vital empirical data. Moving forward, we need methods for assessing whether epigenetic marks are evolving neutrally or under selection. How do we quantify selection on methylation patterns or other epigenetic marks? What is the neutral expectation? When we observe divergence in methylation, how can we assess whether this happened under selection or via random "noise" or plasticity in the regulatory system? Having a formal body of evolutionary theory that incorporates epigenetics, as well as developing a clearer quantification of the connection between epigenetic variation and phenotypes will allow us to more rigorously ask whether or how epigenetics plays an important role in adaptive evolution. This area promises interesting new angles in the study of evolution.

Katherine Stewart at the Guardian and Kenneth Miller writing in the Huffington Post, among others, commemorated Darwin Day with what they took to be stinging rebukes of the benighted "anti-science" community, including the usual invocations of Dover-as-holy-writ and anguished prophecies that evolution skepticism lies behind widespread American science illiteracy. The latter will result in our being displaced from the leading role in international science education and research, replaced by the likes of India and China.

I'm struck again by the failure to wonder why "anti-science" views focus on some scientific questions and not others. What do Darwin, climate-change, embryonic stem-cell research and a couple more have in common? In fact, as I've written before, there are two things that unite the seemingly disparate objects of our skepticism. Above all, it is that their enforcers seek to enshrine in coercive public policy a false a picture of what being human means -- basically, no more than a clever animal -- that we know from our own experience to be untrue. That, and the observation that we keep finding defenders of orthodoxy to be caught up in propaganda and lies -- like the phony conflation of Biblical-literalist creationism with every other brand of Darwin-doubting.

Trying to worry us about our country's international status and prestige, Ken Miller writes, "Convince enough young Americans that science is a close-minded system with a particular cultural and political agenda, and we will cede leadership to emerging countries that don't share our Darwin hang-ups, and see science as the wave of the future." He takes it as a given that only an unreasonable person could ever perceive such an agenda.

It's interesting then to find one honest Darwinist, Hank Campbell of Science 2.0, frankly admitting that biology really is being twisted by beliefs that have nothing to do with science:

I was surprised, after Science 2.0 became a formal project almost six years ago, that while physicists wanted to talk about physics and psychologists wanted to talk about psychology, biologists mostly wanted to talk about religion. I assumed that was because Prof. P.Z. Myers of the University of Minnesota, best known as Pharyngula on Scienceblogs.com (and also once again on his own site), was popular. Bashing Republicans and religion was the It thing in blogging in 2006 and the bulk of Scienceblogs writers started doing the same thing because that was why their audience came. It was all about who to ridicule rather than science.

If a lot of Americans sense that some scientists and many journalists are hustling them, dodging a real debate and distracting the public with appeals to status anxiety, it should come as little surprise.

Photo credit: TranceMist, Flickr.

When scientists compared the human GULO pseudogene to its functional counterpart in the rat genome, they found that regions equivalent to exons I to VI, as well as exon XI, were absent (Inai et al., 2003). This means that the human GULO pseudogene has only five exons out of the twelve found in the functional rat GULO gene. Other features of note associated with the human GULO pseudogene included one single nucleotide insertion, two single nucleotide deletions, and one triple nucleotide deletion. Researchers also identified additional stop codons. Similar mutations have been identified in the genome of chimpanzees, orangutans and macaques (Ohta and Nishikimi, 1999).

GULO and Common Descent

The GULO pseudogene -- particularly the identical base deletion in exon X at position 97 -- has long been used as an argument for establishing the validity of common descent.

Since 2003, ID proponents have been citing the claim of Inai et al. that parallel substitutious have occurred in the human and guinea-pig lineages. Inai et al. calculated the probability of attaining identical substitutions in those two lineages at the number of sites observed to be 1.83 x 10^-12, hypothesizing the phenomenon of mutational hotspots to account for this occurrence. This claim, however, is no longer tenable. As I mentioned, researchers used the rat sequence as a norm to compare the primate and guinea-pig sequence. It is more likely though that the rat GULO gene has mutated such that it is not representative of the ancestral sequence, rather than the convergence of the primate and guinea-pig sequence. This becomes clear when we consider a broader range of taxa (see here and here).

Inconsistent Use of Statistics

It is interesting to note that the argument for common ancestry based on common mutations affecting a segment of DNA is based on a form of reasoning that is uncannily similar to the specified-complexity criterion employed by advocates of design. Given the premise that mutations occur essentially at random, the inference to common ancestry is preferred over the chance hypothesis. Notice that the inference is justified not solely on the basis of high improbability (attaining the same specific mutations in multiple lineages is no more improbable than any other combination of mutations of the same number).

If the specific mutational combination occurred only once, however -- that is, before the divergence of the two lineages -- one no longer needs to explain how the same specific improbable combination of mutations occurred more than once. In this case, if we assume that there is no function for the pseudogene, as well as other assumptions (e.g. no hotspot mutations), then the common ancestry hypothesis seems preferable. If the event cannot be accounted for by common ancestry, then something fundamentally non-random must account for the phenomenon (this is what led Inai to postulate the existence of genomic hotspots where certain kinds of mutations occur with greater frequency). If Darwinists are happy to employ this kind of reasoning in their own defence of evolutionary theory, why do they object so vehemently to its use by advocates of ID?

After I had raised concerns about the prohibitive improbabilities facing the occurrence of many of the macromolecular functionally interdependent systems found in living systems, the renowned evolutionary biologist and philosopher Massimo Pigliucci wrote to me on an Internet forum,

No evolutionary biologist I know...actually attaches probabilities to specific evolutionary events of the type you are talking about. There is no way to do that. Similarly, there is no way to attach probabilities to the set of physical laws regulating our universe, for the simple reason that we have no sample population to draw from (which is why typically you estimate probabilities).

What's more, as Jonathan Wells observes in the appendix of The Myth of Junk DNA, the GULO pseudogene argument is circular. Balakirev and Ayala (2003) and Khachane and Harrison (2009) take pseudogene similarities as evidence of function. When such similarities are explicable by reference to common descent, then it is taken as evidence for common descent. When such similarities are not explicable by common descent, on the other hand, it is taken as evidence of function. Moreover, there are many well documented cases of deep molecular convergence (for a catalogue, see Fazale Rana's contribution -- chapter 21 -- to The Nature of Nature). Again, when these instances are explicable by common descent, it is taken as evidence of shared ancestry. When these instances are not explicable by common descent, it is evidence of convergent evolution -- and thus the efficacy of the neo-Darwinian mechanism. This is classic circular reasoning.

Signs of Function?

There is actually some evidence to suggest that concentrations of ascorbic acid in the human fetus and in the neonate is not wholly explicable by the mother's intake of vitamin C in her diet. For example, a study conducted by Andersson et al. (1956) documented, over a period of five years, no more than two reports of infantile scurvy in malnourished South African Bantu infants. It was found that ascorbic acid plasma concentrations were comparable among infants who had been well nourished.

A further study, by Adlard et al. (1974), found substantially heightened vitamin C concentrations in the fetal human brain as compared to that of the adult. This concentration was found to fall with increased gestational age.

Salmenpera (1984) examined the levels of plasma vitamin C in infants who had been breast-fed as compared with controls who had been supplemented with vitamin C. They reported that the concentration of plasma vitamin C was the same or higher in the former compared to the latter. In fact, the concentration was roughly double the maternal concentration. The author reported, "Surprisingly, the infantile plasma concentration, which was already high compared with maternal concentration, continued to rise despite the decreasing concentration in milk ... the significance of this phenomenon is unknown."

Some researchers have actually suggested that the loss of a functional GULO may have provided a selective advantage for early man. For example, Calabrese (1982) wrote,

Considerable controversy exists over the role of ascorbic acid in maintaining health and resisting a wide variety of diseases including cancer. It has been contended that the evolutionary loss of ascorbic acid synthesis capability in man has enhanced the occurrence of numerous chronic diseases and was essentially a maladaptive alteration which initially was well tolerated because early man lived in a habitat which supplied foods with amounts of vitamin C equivalent to what they normally may have synthesized. However, as humans migrated into habitats with less availability of vitamin C, the adverse aspects of the loss of ascorbic acid synthesizing capability came to be demonstrated (1,2). In contrast, this paper proposes that the loss of an ability to synthesize ascorbic acid in humans, far from being a neutral or totally negative mutation, may have been a critical preadaptation which markedly enhanced the survival of earlv man with a G-6-PD deficiency living in a malarial infested environment [emphasis added]

It is proposed that the loss of ability by humans to synthesize ascorbic aicd may have markedly enhanced the survival opportunities of early man living in a malarial infested environment. This hypothesis is based on biomedical evidence which indicates that glucose-6-phosphate dehydrogenase (G-6-PD) deficient individuals display enhanced sensitivity to ascorbic acid induced hemolysis which has been fatal at sufficiently hiqh doses and that the G-6-PD deficient trait has been selected for in malarial environments.

Summary and Conclusion

The GULO pseudogene may or may not turn out to harbour some sort of function. With more and more papers coming out documenting a myriad of functions associated with pseudogenes, such a future finding should not come as a surprise. The hypothesis of limited common descent seems to me, for the time being, a reasonable one. Perhaps it is the case that all taxa belonging to the Primate Order are related by descent. Extending this inference to universal common descent, however, runs into substantial scientific problems. Whichever scenario turns out to be correct, it has no bearing on the question of the respective scientific merits of neo-Darwinism and intelligent design to account for the complexity of life.

Kettlewell's evidence soon became the classic textbook demonstration of natural selection in action -- commonly illustrated with photos of peppered moths resting on light- and dark-colored tree trunks.

By the 1990s, however, biologists had discovered several discrepancies in the classic story -- not the least of which was that peppered moths in the wild do not usually rest on tree trunks. Most of the textbook photos had been staged.

In the 2000s the story began disappearing from the textbooks. British biologist Michael Majerus then did some studies that he felt supported the camouflage-predation explanation. But before he died of cancer in 2009, he only managed to publish a report of his study in the Darwin lobby's in-house magazine Evolution: Education and Outreach. Now four other British biologists have presented his results posthumously in the Royal Society's peer-reviewed Biology Letters. In an accompanying supplement, the authors presented their version of what they call "the peppered moth debacle." And a debacle it certainly is, but not in the way they think.

According to Charles Darwin, natural selection has been "the most important" factor in the descent with modification of all living things from one or a few common ancestors, yet he had no actual evidence for it. All he could offer in The Origin of Species were "one or two imaginary illustrations." It wasn't until almost a century later that Kettlewell seemed to provide "Darwin's missing evidence" by marking and releasing light- and dark-colored moths in polluted and unpolluted woodlands and recovering some of them the next day. Consistent with the camouflage-predation explanation, the proportion of better-camouflaged moths increased between their release and recapture.

Throughout the 1970s and 1980s, however, researchers reported various problems with the camouflage-predation explanation, and in 1998 University of Massachusetts biologist Theodore Sargent and two colleagues published an article in volume 30 of Evolutionary Biology concluding "there is little persuasive evidence, in the form of rigorous and replicated observations and experiments, to support this explanation at the present time." (p. 318)

The same year, Michael Majerus published a book in which he concluded that evidence gathered in the forty years since Kettlewell's work showed that "the basic peppered moth story is wrong, inaccurate, or incomplete, with respect to most of the story's component parts." (p. 116) In a review of Majerus's book published in Nature, University of Chicago evolutionary biologist Jerry Coyne wrote: "From time to time, evolutionists re-examine a classic experimental study and find, to their horror, that it is flawed or downright wrong." According to Coyne, the fact that peppered moths in the wild rarely rest on tree trunks "alone invalidates Kettlewell's release-and-recapture experiments, as moths were released by placing them directly onto tree trunks."

In 1999, I published an article in The Scientist summarizing these and other criticisms of the peppered moth story, and in 2000 I included a chapter on peppered moths in my book Icons of Evolution. Then, in 2002, journalist Judith Hooper published a book about the controversy titled Of Moths and Men. Hooper accused Kettlewell of fraud, though I never did; my criticism was directed primarily at textbook writers who ignored problems with the story and continued to use staged photos even after they were known to misrepresent natural conditions.

By then, what had previously been a fairly limited scientific dispute over the cause(s) of industrial melanism had become a debacle. Sargent and I were demonized, and Majerus and Coyne were persuaded to reaffirm the peppered moth story as the prime example of Darwinian evolution in action. Majerus also embarked on the study that was just recently reported in Biology Letters.

In that study, conducted over a seven-year period from 2001 to 2007, Majerus performed release-and-recapture experiments in an unpolluted woodland near his home with 4,522 light-colored and 342 dark-colored moths, using methods he considered superior to Kettlewell's. He found that dark-colored moths (which were less camouflaged in this situation) had only a 91% survival rate compared with light-colored moths. He also observed 135 moths in resting positions, of which 35.6% were on tree trunks.

Yet during the seven years of Majerus's study, thousands of peppered moths must have passed through the woodland near his house, so 135 moths were a tiny fraction of the total. Furthermore, as he himself acknowledged in a 2007 lecture in Sweden, his results might have been "somewhat biased towards the lower parts of the tree, due to sampling technique."

Indeed. If peppered moths normally rest high in the upper branches, as several researchers concluded in the 1980s, then doing statistics on those visible to an observer on the ground (even one who climbs part-way up some trees, as Majerus did), is bound to suffer from sampling bias. Imagine someone looking over the side of a boat and concluding that most fish in the sea live within ten feet of the surface.

The correct question to ask is not whether peppered moths ever rest on tree trunks, but whether peppered moths normally rest on tree trunks. It's possible they do, but finding 48 moths resting on tree trunks over the course of seven years does not answer that question -- especially when tree trunks are the primary location where you are looking for moths.

Majerus titled his 2007 lecture "The Peppered Moth: The Proof of Darwinian Evolution." He summarized the results of his seven-year study, but he explained that the real proof of Darwinian evolution is the following:

Darwinian evolution is a logical fact, and had to be even in 1859. Consider Darwin's four observations and three deductions, upon which selection theory is based.

• Organisms produce far more offspring than give rise to mature individuals.
• Yet, population sizes remain more or less constant.
• Therefore, there must be a high rate of mortality.
• The individuals in a species show variation.
• Therefore, some variants will succeed better than others, and those with beneficial characteristics will be naturally selected to produce the next generation.
• There is a hereditary resemblance between parents and offspring.
• Therefore, beneficial traits will be passed to future generations.

Given these four observed facts and three simple, logical deductions, selection cannot NOT happen.

In any case, Darwinian evolution requires much more than the selection of beneficial traits, and much more than a shift in the proportions of light- and dark-colored moths. It requires the descent with modification of all living things from one or a few common ancestors. Darwin did not write a book titled How the Proportions of Two Pre-existing Moth Varieties Can Change Through Natural Selection; he wrote a book titled The Origin of Species by Means of Natural Selection.

Majerus went on to say that "there are a tremendous number of examples of Darwinian selection in action." And indeed there are: beak changes in Galápagos finches, for one. Natural selection happens; I've never met anyone who doubts it. The question is whether natural selection can produce new species, organs and body plans. This question is not answered by shifts in the proportions of pre-existing varieties of the same species. Even if the camouflage-predation explanation for industrial melanism were undisputed, it would not get us any closer to "proving" Darwinian evolution.

Since there are other, better examples of natural selection, why do Darwinists go to such lengths to defend the peppered moth story? And why do they practically bite themselves in two vilifying its critics?

The answer, I think, can be found in the conclusion of Majerus's 2007 lecture. "The rise and fall of the peppered moth," he said, "is one of the most visually impacting and easily understood examples of Darwinian evolution in action, [so] it should be taught. It provides after all: The Proof of Evolution." It doesn't matter that the camouflage-predation story is scientifically disputed. It doesn't matter that the story doesn't come close to demonstrating the origin of a new species, much less the descent of all species from a common ancestor. What matters is that the peppered myth is a useful tool for indoctrinating students in Darwinian evolution.

In 1999 Canadian textbook-writer Bob Ritter, who knew that peppered moth pictures were staged but used them anyway, defended his practice on the same grounds. "You have to look at the audience," he was quoted as saying in the April 5, 1999, Alberta Report Newsmagazine. "How convoluted do you want to make it for a first time learner?" High school students "are still very concrete in the way they learn," said Ritter. "The advantage of this example of natural selection is that it is extremely visual."

It's no wonder that science education is in trouble.

Instead of celebrating dogmatism, it would be a truer testament to the best of Darwin's legacy to promote academic freedom. As the great man himself said:

A fair result can be obtained only by fully stating and balancing the facts and arguments on both sides of each question.

Academic Freedom Day events may be as simple as having a table on your local college campus where people can sign the Academic Freedom Petition and find out more about academic freedom on evolution. Or events can be more elaborate like holding a screening of Expelled: No Intelligence Allowed or Icons of Evolution. See here for more ideas on what you can do to celebrate Academic Freedom Day.

Here are some articles that you might want to read and promote as a way to educate people about the importance of academic freedom on evolution.

What does Discovery Institute advocate for science education policy? As a matter of public policy, Discovery Institute opposes any effort to require the teaching of intelligent design by school districts or state boards of education. Instead of mandating intelligent design, Discovery Institute seeks to increase the coverage of evolution in textbooks. It believes that evolution should be fully and completely presented to students, and that they should learn more about evolutionary theory, not less, including about its unresolved issues. In other words, evolution should be taught as a scientific theory that is open to critical scrutiny, not as a sacred dogma that can't be questioned. Read our full policy here: Discovery Institute's Science Education Policy.

Need a comprehensive overview of the debate over evolution? Looking for resources to share with friends and colleagues to help them better understand what intelligent design is, what it isn't, and how it differs from Darwinian evolutionary theory? Download this briefing packet: The Theory of Intelligent Design: A Briefing Packet for Educators.

What are students being taught about evolution in today's classrooms? Here is an updated review of the most popular textbooks used in high school biology courses across the country: (Not) Making the Grade: An Evaluation of 22 Recent Biology Textbooks and Their Use of Selected Icons of Evolution. You can also listen to an interview with report author Casey Luskin on this ID the Future Podcast.

Whether you are a teacher, a student, or a parent, here's a book that will help you understand what Darwin's theory of evolution is, why many scientists find it persuasive, and why other scientists question the theory or some key aspects of it. Get your own copy of Explore Evolution: The Arguments For and Against Neo-Darwinism.

More academic freedom and science education resources:

Darwin Day Poll Shatters Stereotypes: Democrats Favor Freedom to Discuss Evolution's Strengths and Weaknesses More than Republicans

Should We Teach Scientific Criticisms of Neo-Darwinism? Many Authorities Say YES!

Rick Santorum, the Santorum Amendment and Intelligent Design

Podcast: Law Professor David DeWolf on the History of the Santorum Amendment

The Constitutionality and Pedagogical Benefits of Teaching Evolution Scientifically

Podcast: The Best Way to Teach Evolution: Treat It Like Science

The play works as a lighthearted approach to serious, controversial matters. Listen for yourself here.

As Professor Fuller explains more fully in the first part of his recent ID the Future podcast interview with David Boze, Darwin, like Peter Singer, would see little if any ontological difference between man and animal, who on a naturalistic view share a common history and thus nature. Man, for Darwin, could only be a momentary and unforeseen bump on an evolutionary road to nowhere in particular. Thus, Fuller's Darwin would not today accord man special rights in the political realm compared with, say, nonhuman animals, such as great apes. Conversely, Fuller's Lincoln is and always was enthusiastic about man as a being uniquely made in the image of God, specially dignified in the world, and thus entitled to privileged status within any system of rights.

The difference, of course, is natural selection, which stands against the idea that there is discoverable purpose in the world, in life generally, or in one's own existence. If you experience having purpose in your life, it is made up, not found.

Fuller makes clear the moral poverty of this anemic view. For the individual who takes natural selection seriously, personal decision-making can't amount to much more than the maximization of individual pleasure and minimization or avoidance of individual pain, or some other sort of hedonic calculus. For the body politic, policies that take natural selection seriously will increasingly restrain human life and freedom in the face of, e.g., competing animal and ecological interests, since even the "line" between subject (e.g., conscious agents) and objects (e.g., rocks, trees) is arbitrary if natural selection has produced all life. That is, if natural selection is in, then purpose is out, and the line between "us" and "them" will be naturally seen as endlessly malleable, if not dissolvable at will.

The slope is not merely theoretical. It is real and slippery enough to allow descent into the crazy world of plant rights. Fuller doesn't take us all the way there in his play, but Stanley Fish has foreseen it, and it is at best a little spooky.

Plantinga's goal in this book is to show that there is only "superficial conflict but deep concord between science and theistic religion." So it makes sense that he would start with biological evolution, since this is the part of science where many perceive a conflict. The way Plantinga handles the meaning of "random" and "Darwinism" is complicated, so I'm going to postpone discussion of these matters until the next installment and focus here on his broader argument.

Plantinga gets quickly and clearly to the central point of the alleged conflict between evolutionary theory and Christian theism. It reduces almost entirely to the question of whether the origin and history of life is guided or unguided. A teleological view of evolution can be reconciled with Christian theism. "What is not consistent with Christian belief," he writes, "is the claim that this process of evolution is unguided -- that no personal agent, not even God, has guided, directed, orchestrated, or shaped it." According to Plantinga, this is not a claim or a finding of science per se (more on that in the next installment); nevertheless, "there is a veritable choir of extremely distinguished experts insisting that this process is unguided" (p. 12).

Therefore, Plantinga spends ample time responding to the arguments of a few prominent soloists in the choir. First up: Richard Dawkins. However one judges evolutionary theory in general, Dawkins unambiguously claims, as the subtitle of The Blind Watchmaker puts it, that "the evidence of evolution reveals a universe without design." If Dawkins's claim is true, Plantinga notes, then the Christian belief that God "has created human beings, and created them in his own image," is false. So, what of Dawkins's argument?

Despite the promise of the subtitle to deal with "evidence," Dawkins's arguments in The Blind Watchmaker aren't dense with data from biological research. They are largely of the Darwinian storytelling variety. Dawkins spends a lot of time describing how something like the mammalian eye could have evolved in an unguided Darwinian fashion from an earlier organism that lacks such an eye. The series must be continuous and each step, of course, must either confer on its possessor some survival advantage, or at least not exact a large cost in terms of survival. If one has an active imagination and is content with unrealistically Lego-like, bottom-up treatments of organisms, it's easy to conjure up a series of such steps.

Plantinga does an admirable job of analyzing and summarizing Dawkins's basic argument, and even manages to compress several of Dawkins's key questions into one Big Question:

(BQ) Is there a path through organic space connecting, say, some ancient population of unicellular life with the human eye, where each point on the path could plausibly have come from a preceding point by way of a heritable random genetic mutation that was adaptively useful, and that could plausibly then have spread through the appropriate population by way of unguided natural selection?

There's nothing wrong with an argument that comes to a modest conclusion; but Dawkins claims to have shown that the evidence of evolution reveals a universe without design. As a result, he's guilty of severe overreach. This is especially obvious when Plantinga reduces Dawkins's larger argument to its logical core. It ain't pretty. In The Blind Watchmaker, Dawkins seems to be arguing

p is not astronomically improbable

P.

Since Dawkins is a smart guy, though, surely he wouldn't offer such a terrible argument, would he?

Well, smart people make terrible arguments all the time. Still, Plantinga pursues the possibility that Dawkins is drawing on some unstated premises that, when stated, might make his argument a little less bad. I think this is the correct approach, since these premises are very much in evidence throughout Dawkins's writings.

The first is Dawkins's refrain that since we're seeking to explain organized complexity, we can't just postulate it, as we would do with a designer. As Dawkins says, "Invoking a supernatural Designer is to explain precisely nothing."

This is similar to the old "Who designed the designer?" retort. It is, in my opinion, one of the silliest arguments around. And Plantinga shows just that. First of all, even if X would need to be designed by something more complex than X, that doesn't disqualify one from inferring that X is designed. If that were a reliable rule of reasoning, then we could never invoke design. The possibility of a follow up question to an answer doesn't show that the answer is a bad one, especially when one is simply trying to offer a proximate rather than an ultimate explanation.

At some point, of course, the regress of explanation must stop at an ultimate explanation. That's true for everyone. The theist thinks God is the necessarily existing thing on which everything else depends. The materialist has an alternative candidate for ultimate explanation. But Dawkins doesn't come close to considering these sorts of possibilities and defending the materialist alternative. He really seems to think that the very possibility of a follow up question disqualifies design as a real explanation.

The second hidden premise in Dawkins's argument could be his claim that the existence of God is stupendously unlikely. If we add that assertion to Dawkins's argument above -- p is not astronomically improbable, therefore P -- then it makes more sense. If God (or intelligent design generally) is extremely unlikely, and the organized complexity in biology is extremely unlikely give chance alone, then something like Darwinism has to be true. It's the only show in town. If there are three options, and two are extremely unlikely, then perhaps all one needs to show is that the third option is not astronomically improbable. And Dawkins has done that.

Plantinga observes, briefly, that if this is Dawkins's argument, then it depends very little, if at all, on scientific evidence. It's an eliminative argument based on Dawkins's intuitions about what is probable and plausible. We're left with Dawkins's personal intuitions because his arguments for God's improbability are weak. His main argument depends, again, on this idea that anything that designed a biological object would have to be more complex than that biological object. I think what Dawkins has in mind is something like this: If it's unlikely that a bacterial flagellum could have arisen by chance or the Darwinian mechanism, then any agent that designed the flagellum would be even less likely.

Plantinga finds a fatal problem here. Dawkins defines complexity as the property of something that has parts "arranged in a way that is unlikely to have arisen by chance alone." But God is immaterial and so doesn't have parts in this sense. According to Dawkins's own definition of complexity, therefore, God is not complex. One can make a similar point without invoking God. It doesn't follow that because an agent can produce organized complexity, that the agent is complex. (Frankly, I don't think it makes sense to refer to any agent as "complex.") Organized complexity might very well be a reliable sign of an intelligent agent. So Dawkins's argument against the improbability of God's existence, and, a fortiori, the improbability of intelligent design, fails.

The take-home lesson, Plantinga concludes, is "that Dawkins gives us no reason whatever to think that current biological science is in conflict with Christian belief." Plantinga, in contrast, gives us plenty of reasons to agree.