Evolution News and Views (ENV) provides original reporting and analysis about the debate over intelligent design and evolution, including breaking news about scientific research, academic freedom cases, and educational policy issues. ENV also covers how the rest of the newsmedia report on the debate, offering analysis and corrections to major news stories, as well as a behind-the-scenes look at how journalists and news outlets operate when they report on this issue.
September 8, 2010
NDM-1 Superbug the Result of Bad Policies, Not Compelling Evidence for Evolution's Creative Powers
Recently, the media has been discussing the micro-evolution of a new antibiotic resistant strain of bacteria, dubbed the "NDM-1 superbug." This seems to be a very sad case of one of those things that evolution is pretty good at doing -- making small, incremental improvements upon an enzyme through a step-by step process. That, plus the tendency of bacteria to collect multiple antibiotic resistances, makes this gene a real problem. However, it by no means provides evidence for the ability of evolutionary processes to produce new functions within a cell.
The problem is that antibiotics are frequently used -- and abused. Beta-lactamases, the enzymes that degrade penicillin and penicillin-like antibiotics (they are all characterized by a "beta-lactam" ring) were around before the anitbiotic era; microbial samples from the 1930s have been found that contained penicillin-resistant bacteria. The enormous populations of bacteria are then subjected to selection. Those bacteria that possessed the beta-lactamase genes survived, while those that didn't died. This resulted in many bacteria becoming resistant to penicillin. The resistance did not have to arise in every type of bacteria; those that possessed beta-lactamases could transfer the genes to those that did not, resulting in further spread of penicillin resistance. We then developed variants of penicillin, and each variant initially was successful, but eventually new variants of these beta-lactamases also arose. These variants were the result of small changes in the DNA sequence that resulted in incremental improvements in these beta-lactamases. If a variant improved survival of a microbe in an environment in which antibiotic was present (such as within a person being treated with the antibiotic for an infection) then that variant survived and spread through the microbial population.
Assurances that we have nothing to fear from Darwinism are a familiar species of evolutionary apologetics. We're told that Darwinian thinking doesn't threaten morality, religion, or belief in life's having an ultimate meaning. On the contrary, it enhances all things good and fair. Karl Giberson's recent column in the Huffington Post, "How Darwin Sustains My Baptist Search for Truth," deserves to be pinned under glass and put up on a wall as a near-perfect specimen of the genre.
Anyone who's honest with himself knows this is all propaganda and wishful thinking, but it refreshes us nevertheless to hear Darwinists themselves confess -- even trumpet -- the truth.
Darwinian scholars and journalists have been writing with what must seem, to their brethren, an alarming frankness. One occasion for the flurry of articles is the recent sensational book Sex at Dawn by Christopher Ryan and Cacilda Jetha, who present the picture of our evolutionary human ancestors as enjoying polyamory as their standard reproductive practice. Group sex was the rule for them, so there's no reason to expect marital fidelity from us, their heirs.
On the Scientific American website, psychologist Jesse Bering throws out the whole structure of sexual right and wrong with one blog post:
There are of course many important caveats, but the basic logic is that, because human beings are not naturally monogamous but rather have been explicitly designed by natural selection to seek out "extra-pair copulatory partners" -- having sex with someone other than your partner or spouse for the replicating sake of one's mindless genes -- then suppressing these deep mammalian instincts is futile and, worse, is an inevitable death knell for an otherwise honest and healthy relationship.
Dr. Bering concedes with some feeling that in evolutionary psychological terms, empathy for the jilted sexual partner also plays a role. But in general:
Right is irrelevant. There is only what works and what doesn't work, within context, in biologically adaptive terms.
In the current issue of Philosophy Now, Joel Marks declares himself a born-again amoralist. He used to be a moral atheist, but now, having divested himself of earlier illusions, he chirpily goes for what he calls "hard atheism" and, "In fact, I have given up morality altogether!" On the science backing up his position, he comments:
Late last year, the eminent Christian philosopher and proponent of intelligent design, William Lane Craig, crossed swords in debate with the avid apologist for Darwinian evolution, Francisco Ayala, of the Biologos Foundation. The debate was chaired by philosopher of physics Bradley Monton of the University of Colorado, an ID sympathizer, though a convinced atheist himself. Monton is the author of the book, Seeking God in Science: An Atheist Defends Intelligent Design. A fascinating ID the Future interview with Professor Monton can be downloaded here.
Following Dr. Ayala's opening statement, Dr. Craig commenced his presentation by carefully setting out the definition of ID as the study of legitimate design inferences. Craig stipulated that, were Ayala to attempt to refute the inference to design with respect to biological systems, he would need to do one of two things. Either Ayala would need to directly challenge the legitimacy of the explanatory filter (presumably by demonstrating that it incorporates false positives) or demonstrate that the systems featured in biology do not meet the criteria of the explanatory filter. Setting aside the discussions pertaining to the tenability of universal common ancestry, Craig set about to argue that Ayala's attempts to disqualify ID on scientific grounds were doomed because he had failed to demonstrate, in his published work, that the dual forces of random mutation and natural selection, are causally sufficient to account for macroevolution. He also argued that Ayala's more numerous attempts to disqualify ID on theological grounds are completely irrelevant to the process of drawing a design inference from biological phenomena, because none of the arguments for ID aspire to show that the designer possesses the qualities of omnibenevolence or omnipotence. After all, Craig argued, a design inference is still warranted with respect to a medieval torture rack, regardless of the malevolent purposes of the system's design. Questions pertaining to the nature of the designer are for natural theology, not for the scientific research program of ID. This is what distinguishes the modern concept of ID from the Watchmaker argument of William Paley's Natural Theology.
Here come more threats to academic freedom, not unlike those seen by intelligent design proponents and Darwin skeptics. Over the years we've covered many, many cases like this where someone who expresses doubt about Darwinian evolution is harassed, fired, denied tenure, and so on.
"The significance of this is a threat to academic freedom and it's also a threat to academic science," Siegel said. "If scientists have to produce work that meets a certain view to keep their jobs, researchers are going to stop publishing negative findings for fear of being fired."
No, they will simply stop researching period in the subject areas that get them in trouble. The average scientist can find lots of fruitful areas of research that won't get her in hot water with the pointy-headed elites who's all-seeing academic eyes keep a watch out for anything that is out of line with the current orthodoxy. And journal editors will avoid publishing controversial papers for fear of reprisal. If you are already overwhelmed in your job, you are unlikely to take on a risky paper. Better to just steer clear of such areas.
But of course we all know that Academia (may it last forever in all its gloriousness) doesn't drum people out because their views differ from the established consensus.
"If 100 people conclude one thing and another person concludes something completely different, then it's natural for his credibility to be called into question," Maxwell said.
There is little doubt that hostage-taker James Lee's virulent
Social Darwinism was the product of a tragically disturbed man. But can an
entire culture fall for the pernicious ideology of Social Darwinism, especially
its scientific and political elites? Unfortunately, the answer to that question
is an unequivocal yes, as I have documented in my book Darwin Day in America, and as the new documentary "What Hath Darwin Wrought?"
persuasively shows. Perhaps the most jarring fact about the troubling views of
James Lee is that similar views have been espoused over the past century by
leading scientists, politicians,
and thinkers. Ideas do have consequences, and not just for seriously disturbed
individuals like James Lee.
Hawking Not Needed to Explain His New Book, Says Universe
Universe
Reached today for comment about Stephen Hawking's new book, the Universe said that Professor Hawking should receive no credit for the ideas.
"You humans naively assume that 'physicists' exist, who discover theories," said the Universe. "But I did it all. Me. The transitory entity known to you as 'Stephen Hawking' is merely an epiphenomenon of the laws of nature, otherwise known as Me, the Universe itself. Mindless physical stuff, the only thing that ever really existed, or ever will exist."
"Hawking, and that other guy -- what's his face, Dawkins -- have been stealing my royalties for years. I've got some lawyers working on that."
"Anyway, I don't know why Hawking and Dawkins, or Harris and Dennett and the rest of that crew, go on and on about 'God' not existing, when they don't exist either. 'Noted atheist authors,' blah, blah, blah. What a load. Physics is everything, and ultimately, the only thing."
"I wrote this article, for instance. Interviewed myself. Wrap your minds -- which you don't possess, actually -- around that, you bits of unreal cosmic debris."
In the previous post, I discussed a recent paper in Trends in Genetics, "Causes and evolutionary significance of genetic convergence," which notes that that genetic convergence is not uncommon, even though only a "restricted number of substitutions" at the genetic level can create novel phenotypic traits. This data not only shows that functional genotypes are rare, but it also poses a much deeper problem for evolutionary thinking--one that challenges the very basis for constructing phylogenetic trees.
A line that's being widely offered on James Lee, who took hostages at the Discovery Channel on Wednesday before being shot and killed, fastens on his debt to Al Gore's Inconvenient Truth. The connection to Darwin, pushed heavily in Lee's list of demands, goes on being ignored. (No surprise.) But there's even more to the Darwin angle than I previously realized.
Lee's manifesto has otherwise been dismissed as mostly "a big bag of crazy." Not so fast. Lee was obviously disturbed, but the document he left behind makes sense in its weird way -- providing that you've dipped a bit into the ideas of his guru. No, not Al Gore. Daniel Quinn, whose book My Ishmael Lee insisted must become the focus of daily programming on the Discovery Channel. With Quinn, evolution and natural selection are a theme that, in turn, helps makes sense of James Lee's writing.
What seems crazy falls into place. For example, what is it that Lee had against farmers? ("All human procreation and farming must cease!" On his MySpace page, he denounces Genesis 1 as "obviously written by a totalitarian farmer.") It's very simple.
In Quinn's telling of history, agriculture was the beginning of the end for humans. Or rather, our accustomed "Totalitarian Agriculture." Here he is in a video interview talking about it with Alan D. Thornhill, then a professor of ecology and evolutionary biology at Rice University, now -- rather interestingly -- science advisor to the director of the Bureau of Ocean Energy Management, Regulation, and Enforcement, part of the U.S. Department of the Interior. Agriculture allowed the human population to grow and grow, since to feed more people, all you have to do is grow more food. Before that, human beings followed natural selection. We lived in tribes -- a social form that is itself a product of natural selection, he emphasizes. This, and the more natural non-Totalitarian Agriculture, put an automatic cap on the number of us that could survive.
On August 21 Karl Giberson, physics professor at Eastern Nazarene College and one of several engaged in the ever-interesting juggling act of defending "faith and science" by means of a Darwinian apologetic, now has added to his litany of misconceptions a boorish attack on Al Mohler in The Huffington Post, "How Darwin Sustains My Baptist Search for Truth." Since David Klinghoffer has provided an excellent summary of the issues involved in an earlier post to this site, Karl Giberson v Al Mohler on Darwin: The Grudge Match, they need not be restated here. The point here is to address Giberson's principal objection, namely, Mohler's assertion that "Darwin did not embark upon the Beagle having no preconceptions of what exactly he was looking for or having no theory of how life emerged . . . ." Giberson wants to dismiss Mohler's comments as merely an effort "to undermine evolution by suggesting that it was 'invented' to prop up Darwin's worldview."
Giberson's complaint is easily addressed from his own standpoint. Since he seems to privilege the historians on this issue (rejecting Mohler's comments as those of "a theologian and not a historian" is an odd dismissal since Giberson isn't a historian either!), what have the subject specialists said on this matter? As will become evident, it really is very much a question of worldview. The central issue at hand isn't whether or not Darwin embarked upon the Beagle "in search of evolution" but whether or not his mental attitude was prepared for it and what the nature of his attitude really was. In other words, had Darwin already formed a mental template of how natural phenomena would be interpreted once he encountered them on the Beagle? The issue certainly isn't Genesis but the genesis of Charles Darwin (1809-1882). The historians tell us three major things in this regard.
If someone opposed to abortion were to take hostages at an
abortion clinic, you can be sure the newsmedia would tenaciously track down and
publicize every anti-abortion association and comment of the criminal in
question. But when a gunman inspired by Darwinism takes hostages at the offices
of the Discovery Channel, reporters seem curiously uninterested in fully
disclosing the criminal's own self-described motivations. Most of yesterday's media
reports about hostage-taker James Lee dutifully reported Lee's eco-extremism
and his pathological hatred for humanity. But they also suppressed any mention
of Lee's explicit
appeals to Darwin and Malthus as the intellectual foundations for his
views. At least, I could find no references to Lee's Darwinian motivations in
the accounts I read by the New
York Times, the Los
Angeles Times, the Washington
Post, ABC, CNN,
and MSNBC.
Lee obviously was mentally disturbed, and the vast majority of Darwinists today
would not defend his violent actions, just as the vast majority of those in the
pro-life community would not embrace violence against abortion clinics. But the
complete absence of Lee's Darwinian motivations from many, if not most, news
reports is noteworthy.
Bruce Chapman has an insightful bit of commentary about today's tragic events at the Discovery Channel offices.
It was both scary and pathetic at the Discovery Channel in Maryland today when an environmental terrorist took hostages in an attempt to force the television network to show more programs on Malthus and Darwin and to rail against over-population and global warming.
Oddly missing from initial news accounts was any mention of Darwin. But, in James J. Lee's manifesto, emerges this clear demand: "Develop shows that mention the Malthusian sciences about how food production leads to the overpopulation of the Human race. Talk about Evolution. Talk about Malthus and Darwin until it sinks into the stupid people's brains until they get it!!"
We are thankful that James J. Lee, the hostage-taker who invaded the Discovery Channel building today in Maryland, did no physical harm to his hostages, who have now been safely freed. Lee, a radical environmentalist, was shot and killed. While expressing relief that police action averted a greater possible tragedy, it's worth noting the contents of the late Mr. Lee's reported manifesto, a list of demands he published online, directed at the cable channel. Demand number 7 reads:
Develop shows that mention the Malthusian sciences about how food production leads to the overpopulation of the Human race. Talk about Evolution. Talk about Malthus and Darwin until it sinks into the stupid people's brains until they get it!!
For the sake of the planet, Lee urges the sterilization of "filthy" human beings and suggests airing "forums of leading scientists who understand and agree with the Malthus-Darwin science and the problem of human overpopulation."
Somehow it's not surprising that he was an opponent of religion as well. Demand number 4:
A recent article in Trends in Genetics, "Causes and evolutionary significance of genetic convergence," addresses the apparently "convergent" appearance of genes or gene sequences and how unguided evolution can explain this. The paper defines convergence as the "independent appearance of the same trait in different lineages." Thus, genetic convergence is the independent appearance of the same genetic trait in different lineages. The article starts by explaining how widespread convergent evolution is:
In public debates (and personal discussions) with Michael Shermer and Massimo Pigliucci, I've met an argument, advanced by both skeptics, which opens interesting and largely unexplored territory in the ID vs. naturalism controversy. In a new article, the science writer and astronomer John Gribbin steps into the same territory, a speculative region familiar to fans of science fiction, not to mention philosophy students with time on their hands and imaginations liberated (perhaps) by alcohol. Back in my early teens, when I lived on a steady diet of science fiction and first saw Stanley Kubrick's masterpiece 2001: A Space Odyssey, I could have discussed these ideas well into the night. A short blog post will have to suffice today.
This figure (below), from Massimo Pigliucci, helps to describe the issue:
Both Pigliucci and Shermer have grasped that causation by a higher intelligence does not necessarily entail causation by a benevolent God -- and the former possibility, they think, might follow as a reasonable inference from physical evidence. This was the point, incidentally, of Richard Dawkins's speculations, at the end of the movie Expelled, about extraterrestrial intelligence possibly causing the origin of life on Earth. These physical effects might appear to us as "magic," meaning inexplicable by our current science. Arthur C. Clarke's famous Third Law -- "Any sufficiently advanced technology is indistinguishable from magic" -- is the wonderfully pithy bumper sticker version of the argument.
Evolutionary biologists make poor historians, especially when it comes to Charles Darwin. So intent on preserving the reputation of St. Charles, evolutionists typically do their best to paper-over Darwin's less-than-savory views on issues like race or the application of natural selection to society. British biochemist and theistic evolutionist Denis Alexander runs true to form in a newly posted interview at BioLogos. In the interview, Alexander does his best to disassociate Darwin from the idea of "survival of the fittest," noting that the phrase was coined by Herbert Spencer rather than Charles Darwin, and that it was then picked up by nasty politicians like Kaiser Wilhelm and Adolf Hitler, who used it to promote their noxious views.
Alexander is correct that Spencer coined the phrase "survival of the fittest," and that the idea was adopted by the Kaiser and by Hitler. But he neglects to mention one other important figure from history who embraced the term: Charles Darwin himself. As I point out in my book Darwin Day in America, Darwin eventually described "survival of the fittest" as "more accurate" than his own term of "natural selection," and he employed the phrase repeatedly in the fifth and sixth editions of On the Origin of Species as well as in other works.
Many years ago I interviewed Eric Hoffer (1898-1983), and may have been the last journalist to do so. Widely known as the Longshoreman Philosopher, he was for years a member of the dockers' union in San Francisco, but his views were not those of your typical stevedore. He had published The True Believer in 1951, and more books after that. Impressed by the breadth of his mind and the unconventional nature of his opinions, I wrote and asked if I could come and interview him. That was in 1980. He invited me to come.
He had written that "when God died in the middle of the 19th century there was immediately set in motion a process which tended to reverse the separation of nature and human nature." Darwinism, and the intellectual currents of his day, "aimed to reduce human nature to nature." Biologically, man was now seen as nothing more than "a superior monkey." Politically, he was an automaton who could be manipulated by a Mao or a Stalin.
Hoffer's refusal to join the parade of thinkers who accepted that man was little more than a boastful ape was perhaps his finest hour as a philosopher. It showed him at his most independent. And his perception of the unique qualities of man encouraged him to ponder man's Creator.
Out of the blue, when I arrived in San Francisco, I asked Hoffer whether he believed in evolution. His reply was immediate: "It's easier to believe in God."
The Darwinian model of evolution holds that one of the key mechanisms of evolutionary innovation is the duplication of genes and the subsequent divergence of one of the duplicate copies to undertake a new functional role. Because a probability of a single gene stumbling upon a significantly different (yet functionally advantageous) sequence is so small, the idea is that, following a duplication of a gene, one copy is able to retain the original function, while the other is free to explore the vast sea of combinatorial possibilities in search of some novel function.
It is widely believed that a duplicate gene has no phenotypic cost or advantage associated with it - that is, it is selectively neutral. In such a state, it is thought that the gene is free to mutate, independent of selection constraints or pressure. When a previously protein-coding gene incurs deleterious mutations such that it no longer codes for a useful polypeptide, the gene is rendered a "pseudogene".
One recent paper, which recently appeared in the open-access journal, PLoS Genetics, by Kuo and Ochman, entitled "The Extinction Dynamics of Bacterial Pseudogenes", offers a potent challenge to this view. According to the paper's abstract:
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