As always,Jehovah gets the last laugh.

Evolutionary Studies Suggest that Atheists, Whatever They Say to the Contrary, Really Do Believe in God

Casey Luskin August 1, 2014 6:28 AM

Over the past few weeks, a theme of discussion on the Internet has been the proposal that atheists may not exist. Of course people who think they're atheists exist, but a study discussed inNature proposes that people really aren't functionally atheists because we're innately predisposed toward religion. In an article titled "Scientists discover that atheists might not exist, and that's not a joke," Science 2.0 has a nice summary:

While militant atheists like Richard Dawkins may be convinced God doesn't exist, God, if he is around, may be amused to find that atheists might not exist.

Cognitive scientists are becoming increasingly aware that a metaphysical outlook may be so deeply ingrained in human thought processes that it cannot be expunged.

While this idea may seem outlandish -- after all, it seems easy to decide not to believe in God -- evidence from several disciplines indicates that what you actually believe is not a decision you make for yourself. Your fundamental beliefs are decided by much deeper levels of consciousness, and some may well be more or less set in stone.

This line of thought has led to some scientists claiming that "atheism is psychologically impossible because of the way humans think," says Graham Lawton, an avowed atheist himself, writing in the New Scientist. "They point to studies showing, for example, that even people who claim to be committed atheists tacitly hold religious beliefs, such as the existence of an immortal soul."

This shouldn't come as a surprise, since we are born believers, not atheists, scientists say. Humans are pattern-seekers from birth, with a belief in karma, or cosmic justice, as our default setting. "A slew of cognitive traits predisposes us to faith," writes Pascal Boyer in Nature, the science journal, adding that people "are only aware of some of their religious ideas".

Boyer's article in Nature continues this line of argument: "Religious thought and behaviour can be considered part of the natural human capacities, such as music, political systems, family relations or ethnic coalitions." He continues, "religious thoughts seem to be an emergent property of our standard cognitive capacities." In a striking comment, he points out that these religious predispositions exist in humans from a very young age:

Humans also tend to entertain social relations with these and other non-physical agents, even from a very young age. ... It is a small step from having this capacity to bond with non-physical agents to conceptualizing spirits, dead ancestors and gods, who are neither visible nor tangible, yet are socially involved.

Boyer gives every sign that he himself is an atheist, writing things like, "When people proclaim their adherence to a particular faith, they subscribe to claims for which there is no evidence," or "Religious concepts and activities hijack our cognitive resources." So it's not surprising that he suggests evolution is the ultimate cause of our religiosity:

Is religion a product of our evolution? The very question makes many people, religious or otherwise, cringe, although for different reasons. Some people of faith fear that an understanding of the processes underlying belief could undermine it. Others worry that what is shown to be part of our evolutionary heritage will be interpreted as good, true, necessary or inevitable. Still others, many scientists included, simply dismiss the whole issue, seeing religion as childish, dangerous nonsense.

Here's my take. Evolutionary explanations of the origin of religion typically have two things in common: First, they're dreadfully predictable. They simply look at some aspect of religious life or faith and ask how that behavior (or belief) might aid survival by endowing us with a beneficial trait (we'll call that "X"). Second, in doing so, they utterly fail to explain the totality of religious experience and belief. Trait X might indeed aid in survival, but there's no reason why evolving Trait X would imply or necessitate evolving anything like the full-fledged religion that's so common throughout human societies today. Thankfully that's not Boyer's approach. Instead, he simply sees religion as an extension (or "hijacking") of human "standard cognitive capacities," however they might have arisen:

So is religion an adaptation or a by-product of our evolution? Perhaps one day we will find compelling evidence that a capacity for religious thoughts, rather than "religion" in the modern form of socio-political institutions, contributed to fitness in ancestral times. For the time being, the data support a more modest conclusion: religious thoughts seem to be an emergent property of our standard cognitive capacities.

At least Boyer is being honest that it's difficult as of yet to provide a full-fledged evolutionary account of the origin of religion. He argues, however, that evolutionary attempts to explain the origin of religion challenge key tenets of religion:

The findings emerging from this cognitive-evolutionary approach challenge two central tenets of most established religions. First, the notion that their particular creed differs from all other (supposedly misguided) faiths; second, that it is only because of extraordinary events or the actual presence of supernatural agents that religious ideas have taken shape. On the contrary, we now know that all versions of religion are based on very similar tacit assumptions, and that all it takes to imagine supernatural agents are normal human minds processing information in the most natural way.

So the fact that all religions think they're right and involve belief in supernatural agents mean they're all basically the same? That discounts, in a naïve way that one comes to expect from atheists, the profound differences among the world's religions. And why should our being predisposed to faith somehow mean no religion is correct? That doesn't follow at all. If anything, it would seem to support a key premise of theistic religion: that God gives us a capacity and desire to believe.

The philosopher and author Paul Copan cuts right through such arguments with clean logic. He writes:

The inventor Thomas Edison said that humans are "incurably religious." History certainly bears this out. But why have humans been so religiously inclined across the millennia and civilizations? Neo-atheists Dawkins and Dennett interpret the phenomenon this way: theology is biology. To Dawkins, God is a "delusion"; for Dennett, religious believers are under a kind of "spell" that needs to be broken. Like computers, Dawkins says, we come equipped with a remarkable predisposition to do (and believe) what we're told. So young minds full of mush are susceptible to mental infections or viruses ("memes"). Charismatic preachers and other adults spew out their superstitious bilge, and later generations latch on to it and eventually create churches and religious schools. Even if there isn't a "God gene," humans have a certain religious urge -- an apparent hardwiring in the brain that draws us to supernatural myths.

Some conclude, therefore that God doesn't exist but is simply the product of predictable biological processes. One big problem with this statement: it is a whopping non sequitur. It just doesn't follow that if humans are somehow wired to be religious, God therefore doesn't exist. This is what's called "the genetic fallacy" -- proving or disproving the truth of a view based on its origin. In this case, God's existence is a separate question from the source of religious beliefs. We need to sort out the biology of belief from the rationality of belief.

There's more to say here. We could turn the argument on its head: if God exists and has designed us to connect with him, then we're actually functioning properly when we're directed toward belief in God. We can agree that natural/physical processes partly contribute to commitment to God. In that case, the basic argument of Dawkins and Dennett could actually support the idea that religious believers are functioning decently and in order.

On top of this, we're left wondering why people would think up gods and spirits in the first place. Why would humans voluntarily sacrifice their lives for some intangible realm? Maybe it's because the physical domain doesn't contain the source of coherence, order, morality, meaning, and guidance for life. Humans, though embodied, are moral, spiritual beings; they're able to rise above the physical and biological to reflect on it and their condition. This can result in the search for a world-transcending God.

Attempts by these New Atheists to explain away theology as a useful fiction or, worse, a harmful delusion fall short of telling us why the religious impulse is so deeply embedded. If God exists, however, we have an excellent reason as to why religious fervor should exist.

(Paul Copan, Is God a Moral Monster?, pp. 29-30 (Baker Books, 2011) (emphases in original).)

Copan is exactly right: If God exists then we would predict that humans should have this innate tendency toward religiosity. Critics of religion will forever chase inadequate explanations for these religious tendencies. Science 2.0 gives a good example of this fruitless thinking:

If a tendency to believe in the reality of an intangible network is so deeply wired into humanity, the implication is that it must have an evolutionary purpose. Social scientists have long believed that the emotional depth and complexity of the human mind means that mindful, self-aware people necessarily suffer from deep existential dread. Spiritual beliefs evolved over thousands of years as nature's way to help us balance this out and go on functioning.

So religion evolved to help us cope with the reality that we really live in a meaningless universe? How convenient that is for those who believe we live in a meaningless universe! But why should anyone feel "existential dread" in the first place, if not for the fact that we long for something greater and beyond our mortal lives? Why is that longing for greater purpose there in the first place? This argument reduces to "religion evolved to meet a need" without, however, bothering to explain where the need itself came from.

Well, where does it come from? Perhaps the answer was given by a different Pascal -- not Pascal Boyer but Blaise Pascal. Centuries ago, he argued that if we find a "God-shaped vacuum" (a popular but apt paraphrase of his view) in the human heart, that is simply because God put it there.

Scientists discover that atheists might not exist, and that’s not a joke

By Nury Vittachi | July 6th 2014 08:03 PM

Metaphysical thought processes are more deeply wired than hitherto suspected

WHILE MILITANT ATHEISTS like Richard Dawkins may be convinced God doesn’t exist, God, if he is around, may be amused to find that atheists might not exist.

    Cognitive scientists are becoming increasingly aware that a metaphysical outlook may be so deeply ingrained in human thought processes that it cannot be expunged.

    While this idea may seem outlandish—after all, it seems easy to decide not to believe in God—evidence from several disciplines indicates that what you actually believe is not a decision you make for yourself. Your fundamental beliefs are decided by much deeper levels of consciousness, and some may well be more or less set in stone. 

    This line of thought has led to some scientists claiming that “atheism is psychologically impossible because of the way humans think,” says Graham Lawton, an avowed atheist himself, writing in the New Scientist. “They point to studies showing, for example, that even people who claim to be committed atheists tacitly hold religious beliefs, such as the existence of an immortal soul.”

    This shouldn’t come as a surprise, since we are born believers, not atheists, scientists say. Humans are pattern-seekers from birth, with a belief in karma, or cosmic justice, as our default setting. “A slew of cognitive traits predisposes us to faith,” writes Pascal Boyer in Nature, the science journal, adding that people “are only aware of some of their religious ideas”.

INTERNAL MONOLOGUES

Scientists have discovered that “invisible friends” are not something reserved for children. We all have them, and encounter them often in the form of interior monologues. As we experience events, we mentally tell a non-present listener about it. 

    The imagined listener may be a spouse, it may be Jesus or Buddha or it may be no one in particular. It’s just how the way the human mind processes facts. The identity, tangibility or existence of the listener is irrelevant.

    “From childhood, people form enduring, stable and important relationships with fictional characters, imaginary friends, deceased relatives, unseen heroes and fantasized mates,” says Boyer of Washington University, himself an atheist. This feeling of having an awareness of another  consciousness might simply be the way our natural operating system works.

PUZZLING RESPONSES

These findings may go a long way to explaining a series of puzzles in recent social science studies. In the United States, 38% of people who identified themselves as atheist or agnostic went on to claim to believe in a God or a Higher Power (Pew Forum, “Religion and the Unaffiliated”, 2012).

    While the UK is often defined as an irreligious place, a recent survey by Theos, a think tank, found that very few people—only 13 per cent of adults—agreed with the statement “humans are purely material beings with no spiritual element”. For the vast majority of us, unseen realities are very present.

    When researchers asked people whether they had taken part in esoteric spiritual practices such as having a Reiki session or having their aura read, the results were almost identical (between 38 and 40%) for people who defined themselves as religious, non-religious or atheist.

    The implication is that we all believe in a not dissimilar range of tangible and intangible realities. Whether a particular brand of higher consciousness is included in that list (“I believe in God”, “I believe in some sort of higher force”, “I believe in no higher consciousness”) is little more than a detail.

    

Starry Night at La Silla 

Creative Common license 3.0 ESO/H. Dahle - http://www.eso.org/public/images/potw1333a/

EVOLUTIONARY PURPOSES

If a tendency to believe in the reality of an intangible network is so deeply wired into humanity, the implication is that it must have an evolutionary purpose. Social scientists have long believed that the emotional depth and complexity of the human mind means that mindful, self-aware people necessarily suffer from deep existential dread. Spiritual beliefs evolved over thousands of years as nature’s way to help us balance this out and go on functioning. 

    If a loved one dies, even many anti-religious people usually feel a need for a farewell ritual, complete with readings from old books and intoned declarations that are not unlike prayers. In war situations, commanders frequently comment that atheist soldiers pray far more than they think they do.

    Statistics show that the majority of people who stop being part of organized religious groups don’t become committed atheists, but retain a mental model in which “The Universe” somehow has a purpose for humanity.

    In the US, only 20 per cent of people have no religious affiliation, but of these, only one in ten say they are atheists. The majority are “nothing in particular” according to figures published in New Scientist.

FEELING OF CONNECTEDNESS

There are other, more socially-oriented evolutionary purposes, too. Religious communities grow faster, since people behave better (referring to the general majority over the millennia, as opposed to minority extremists highlighted by the media on any given day). 

    Why is this so? Religious folk attend weekly lectures on morality, read portions of respected books about the subject on a daily basis and regularly discuss the subject in groups, so it would be inevitable that some of this guidance sinks in. 

    There is also the notion that the presence of an invisible moralistic presence makes misdemeanors harder to commit. “People who think they are being watched tend to behave themselves and cooperate more,” says the New Scientist’s Lawton. “Societies that chanced on the idea of supernatural surveillance were likely to have been more successful than those that didn't, further spreading religious ideas.”

    This is not simply a matter of religious folk having a metaphorical angel on their shoulder, dispensing advice. It is far deeper than that—a sense of interconnectivity between all things. If I commit a sin, it is not an isolated event but will have appropriate repercussions. This idea is common to all large scale faith groups, whether it is called karma or simply God ensuring that you “reap what you sow”.  

NARRATIVE PRESENCE

These theories find confirmation from a very different academic discipline—the literature department. The present writer, based at the Creativity Lab at Hong Kong Polytechnic University’s School of Design, has been looking at the manifestation of cosmic justice in fictional narratives—books, movies and games. It is clear that in almost all fictional worlds, God exists, whether the stories are written by people of a religious, atheist or indeterminate beliefs.

    It’s not that a deity appears directly in tales. It is that the fundamental basis of stories appears to be the link between the moral decisions made by the protagonists and the same characters’ ultimate destiny. The payback is always appropriate to the choices made. An unnamed, unidentified mechanism ensures that this is so, and is a fundamental element of stories—perhaps the fundamental element of narratives. 

    In children’s stories, this can be very simple: the good guys win, the bad guys lose. In narratives for older readers, the ending is more complex, with some lose ends left dangling, and others ambiguous. Yet the ultimate appropriateness of the ending is rarely in doubt. If a tale ended with Harry Potter being tortured to death and the Dursley family dancing on his grave, the audience would be horrified, of course, but also puzzled: that’s not what happens in stories. Similarly, in a tragedy, we would be surprised if King Lear’s cruelty to Cordelia did not lead to his demise.

    Indeed, it appears that stories exist to establish that there exists a mechanism or a person—cosmic destiny, karma, God, fate, Mother Nature—to make sure the right thing happens to the right person. Without this overarching moral mechanism, narratives become records of unrelated  arbitrary events, and lose much of their entertainment value. In contrast, the stories which become universally popular appear to be carefully composed records of cosmic justice at work. 

WELL-DEFINED PROCESS

In manuals for writers (see “Screenplay” by Syd Field, for example) this process is often defined in some detail. Would-be screenwriters are taught that during the build-up of the story, the villain can sin (take unfair advantages) to his or her heart’s content without punishment, but the heroic protagonist must be karmically punished for even the slightest deviation from the path of moral rectitude. The hero does eventually win the fight, not by being bigger or stronger, but because of the choices he makes.

    This process is so well-established in narrative creation that the literati have even created a specific category for the minority of tales which fail to follow this pattern. They are known as “bleak” narratives. An example is A Fine Balance, by Rohinton Mistry, in which the likable central characters suffer terrible fates while the horrible faceless villains triumph entirely unmolested.

    While some bleak stories are well-received by critics, they rarely win mass popularity among readers or moviegoers. Stories without the appropriate outcome mechanism feel incomplete. The purveyor of cosmic justice is not just a cast member, but appears to be the hidden heart of the show.

ROOTS OF ATHEISM

But if a belief in cosmic justice is natural and deeply rooted, the question arises: where does atheism fit in? Albert Einstein, who had a life-long fascination with metaphysics, believed atheism came from a mistaken belief that harmful superstition and a general belief in religious or mystical experience were the same thing, missing the fact that evolution would discard unhelpful beliefs and foster the growth of helpful ones. He declared himself “not a ‘Freethinker’ in the usual sense of the word because I find that this is in the main an attitude nourished exclusively by an opposition against naive superstition” (“Einstein on Peace”, page 510).

    Similarly, Charles Darwin, in a meeting with a campaigner for atheism in September 1881, distanced himself from the views of his guest, finding them too “aggressive”. In the latter years of his life, he offered his premises for the use of the local church minister and changed his family schedule to enable his children to attend services.

SMALL DIFFERENCES

Of course these findings do not prove that it is impossible to stop believing in God. What they do indicate, quite powerfully, is that we may be fooling ourselves if we think that we are making the key decisions about what we believe, and if we think we know how deeply our views pervade our consciousnesses. It further suggests that the difference between the atheist and the non-atheist viewpoint is much smaller than probably either side perceives. Both groups have consciousnesses which create for themselves realities which include very similar tangible and intangible elements. It may simply be that their awareness levels and interpretations of certain surface details differ.

THE FUTURE

But as higher levels of education spread, will starry-eyed spirituality die out and cooler, drier atheism sweep the field, as some atheism campaigners suggest? Some specialists feel this is unlikely. “If godlessness flourishes where there is stability and prosperity, then climate change and environmental degradation could seriously slow the spread of atheism,” says Lawton in New Scientist.

    On a more personal level, we all have loved ones who will die, and we all have a tendency to puzzle about what consciousness is, whether it is separate from the brain, and whether it can survive.  We will always have existential dread with us—at a personal or societal level. So the need for periods of contemplative calm in churches or temples or other places devoted to the ineffable and inexplicable will remain. They appear to be part of who we are as humans.

    Furthermore, every time we read a book or watch a movie, we are reinforcing our default belief in the eventual triumph of karma. While there is certainly growth in the number of bleak narratives being produced, it is difficult to imagine them becoming the majority form of cultural entertainment. Most of us will skip Cormac McCarthy’s crushingly depressing “The Road” in favor of the newest Pixar movie.

    

POPULATION IMPLICATIONS

When looking at trends, there’s also population growth to consider. Western countries are moving away from the standard family model, and tend to obsess over topics such as same-sex marriage and abortion on demand. Whatever the rights and wrongs of these issues, in practice they are associated with shrinking populations.  Europeans (and the Japanese) are not having enough children to replace the adult generation, and are seeing their communities shrink on a daily basis. 

    Africans and South Asians, on the other hand, are generally religious and retain the traditional model of multi-child families—which may be old-fashioned from a Western point of view, but it’s a model powerfully sanctioned by the evolutionary urge to extend the gene pool. 

    “It’s clearly the case that the future will involve an increase in religious populations and a decrease in scepticism,” says Steve Jones, a professor in genetics at University College London, speaking at the Hay Festival in the UK recently.

    This may appear as bad news for pro-atheism campaigners. But for the evolutionary life-force which may actually make the decisions, this may augur well for the continued existence of humanity. (An image of Richard Dawkins and his selfish gene having a testy argument over dinner  springs to mind.)

       In the meantime, it might be wise for religious folks to refrain from teasing atheist friends who accidentally say something about their souls. And it might be equally smart for the more militant of today’s atheists to stop teasing religious people at all. 

         We might all be a little more spiritual than we think.

File under "Well said" XXXIX

Where a man can live, he can also live well.
Marcus Aurelius.

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A clash of Titans XXXIII

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A dangerous game?

Who broke Iraq? :Pros and Cons.

On making new gods II

The accompanying Commentary  reinforces the point made in part 1 of this topic.

Recently the Discovery Institute’s Stephen Meyer published Darwin’s Doubt, a book that raises many questions about the theory of evolution. As his title tells us, Darwin himself shared one of these doubts. The book has sold well, reaching #7 on the New York Timesbestseller list, #4 on the Los Angeles Times list, and #10 on Publishers Weekly.

Organisms are intelligently designed, says Meyer, who has a PhD from Cambridge University in the philosophy of science. His book is an education, demanding attentive reading but no specialized knowledge. To a large extent it uses the facts and arguments of professional biologists, some bordering on open dissent from the orthodoxy.

Darwin’s Doubt has also been subjected to a barrage of what can only be called hate. “Mendacious intellectual pornography” is among the more inventive descriptions. Hundreds of negative comments appeared on Amazon review page within hours of the 498-page book’s publication.

Donald Prothero, a geologist and research associate at the Natural History Museum in Los Angeles, typified many when he said that Meyer is a “fool,” “incompetent,” guilty of “ignorance,” in “way over his head,” with a “completely false understanding of the subject.” Further, Meyer argues “dishonestly,” promotes a “fundamental lie,” promotes a “fairy tale,” and so on.

Would a scientist make his case that way if he had real arguments? Prothero did attempt a few substantive criticisms, but inadvertently demonstrated that he had not read Meyer’s chapters that had already addressed them. Prothero, in truth, hankers after creationism as his preferred target. But Meyer’s book is devoid of creationism or biblical references. It’s all science.

Along with the attacks, we find more and more biologists recognizing that intelligent design (ID) is a serious endeavor. Meyer’s book has been praised by George Church, a professor of genetics at Harvard Medical School; Scott Turner, a professor of biology at SUNY; Russell Carlson, a professor of biochemistry at the University of Georgia and a dozen others. George Gilder, most recently the author of Knowledge and Power, calls Darwin’s Doubt “the best science book ever written.”

So what is going on? A clue was provided by Thomas Nagel’s Mind and Cosmos, published last year and the subject of a Weekly Standardcover story (“The Heretic”) by former American Spectator writer Andy Ferguson. But before discussing Nagel, who encountered his own shower of brickbats, I’ll say a little more about Darwin’s Doubt.

Charles Darwin’s Origin of Species claimed that organisms arose by random variation and natural selection, which must have been a slow business. But the fossil record shows that the major animal forms appeared without visible predecessors — an event known as the Cambrian Explosion. As the Darwinian rulebook regards such sudden changes as highly improbable, the evolutionists encounter two problems: insufficient time and missing fossils.

The Cambrian explosion occurred about 530 million years ago. More recent discoveries in China showed that the new phyla — for example arthropods, chordates, and brachiopods — appeared within a ten-million-year period. Others say the “explosive” period took only 5 to 6 million years. Compared with the reported three-billion year history of life on earth, the Cambrian explosion is the equivalent of just a few minutes in a 24-hour day. It happened in a geological blink.

The Chinese discoveries confirmed what had already been found at the Burgess Shale in British Columbia. No plausible ancestors have yet been found in lower strata, either in Canada or China. Some of the Cambrian creatures are highly complex. Among the earliest are well-preserved trilobites, with lens-focusing eyes and a 360-degree field of vision. “Not so primitive,” as Meyer writes.

Cambrian phyla were originally discovered in Wales. Darwin knew about them and realized that unless ancestors were found, his theory was in trouble. So the problem has been understood for over 150 years.

Meyer’s discussion of the problem is unrivaled in its detail and clarity. He covers the various escape routes that Darwinians have proposed. Maybe, for example, the antecedent forms lacked hard parts and so couldn’t fossilize? Awkward fact: Lots of soft-bodied organisms from the pre-Cambrian have been preserved, but they don’t get us closer to a solution.

Another chapter discusses what is known as punctuated equilibrium. The paleontologist Niles Eldredge became an expert on the ancient trilobites. At first it bothered him that they were all so similar. Then he concluded that “the absence of change” was itself significant. Stasis was “data,” not a mere artifact. With Stephen Jay Gould, he formulated “punctuated equilibrium,” which became well known. Long periods when animal forms are static, they theorized, are punctuated by periods in which new forms of animal life arise quickly — so quickly we can’t expect them to leave a record.

Years ago, speaking in a tone of subdued irony for my benefit, Donn Rosen, a curator of ichthyology at the American Museum of Natural History, wryly summarized what is involved: “Darwin said that speciation occurred too slowly for us to see it. Gould and Eldredge said it occurred too quickly for us to see it. Either way we don’t see it.”

More formally, Meyer shows that “punk eek” doesn’t work out as hoped. Not only have those fleeting ancestors not appeared anywhere, the proponents of punctuated equilibrium never came up with a mechanism that could plausibly produce so much anatomical change so quickly.

Meyer also describes how work in statistical paleontology has undermined the idea that the missing ancestral fossils are merely an artifact of incomplete sampling. If you hunt in lots of different places and keep unearthing the same old specimens, it becomes ever harder to maintain that you still haven’t looked hard enough. Maybe the missing ones never were there to begin with.

A generation ago, Colin Patterson, the senior paleontologist at the Natural History Museum in London, said in a public forum that he didn’t know of any evidence for evolution. There was some grumbling, but he knew that the crucial evidence was missing. And like Thomas Nagel today, he emphasized that he was an atheist — this was no creationist speaking.

IN THE SECOND PART of Meyer’s book, “How to Build an Animal,” the argument changes. Meyer shows that building new animal body plans requires the origin of new genetic information and “epigenetic” information (biological information stored in places outside of DNA). He shows the Cambrian explosion is not just an explosion of new forms of animal life, but an explosion of the information or instructions necessary to build them.

But to generate new information, neo-Darwinism relies on mutations — random changes in the arrangement of the chemical “bases” that function like alphabetic characters in the genetic text stored in DNA. And to build whole new animals, lots of major mutations are needed, but most are lethal.

The geneticist Hermann J. Muller, winner of the Nobel Prize in 1946, bombarded fruit flies with X-rays, which he thought would “speed up evolution.” But nothing came of it. Fruit flies not killed by the X-rays remained fruit flies. Also, mutations that occur early in embryonic development are always lethal — generating “dead animals incapable of further evolution,” as Meyer writes. Late-acting mutations may be viable, but these “do not affect global animal architectures.” Hence the Darwinian dilemma: “Major changes are not viable; viable changes are not major.”

Here Meyer also demonstrates the mathematical implausibility of the neo-Darwinian explanation for the origin of new genetic information. The speedy appearance of animals with new body plans creates a big statistical problem. Its key point is easily grasped. Guessing a one-digit number might be easy and won’t take that long. But guessing a ten or a one hundred digit number will likely take you a very long time. In biology, random mutations are equivalent to the “guesses” and the DNA and proteins are like numbers with hundreds or thousands of precisely arranged digits. The “right guess” corresponds to a DNA sequence that will produce a new protein with some heritable “adaptive” benefit for the offspring.

In all animals we find intricately folded proteins made of hundreds of precisely arranged sequences of amino acids. Meyer cites the work of molecular biologist Douglas Axe who has shown that generating even just one new protein by mutating DNA at random has a prohibitively small chance of ever occurring even on the scale of evolutionary deep time. The number of amino acid combinations that mutations much search vastly exceeds the time that is available to evolutionary history, let alone the brief period of the Cambrian explosion.

It gets worse. The improbability of a right guess, or sequence, must be multiplied over and over, because the next mutation could cancel the first. Imagine you are on a desert island with buried treasure, and X marks the spot. You hope to find the X by taking random steps. You may indeed soon step in the right direction. But you have no way of knowing which direction that is. So your second step may return you to square one. The standard Darwinian view takes no account of mutations that reverse the progress made.

In addition, proteins and genes cannot be randomly changed much at all without degrading their function. They are equivalent to small islands of function surrounded by huge seas of disorder. There is no way to “walk” from one island to another and still survive.

Yet, transitions from one body plan to another must be viable at every stage. Darwin once argued that bears may have been ancestral to whales. Consider the difficulty. A brilliant engineer might conceivably know how to assemble a whale out of molecules, amino acids, DNA, proteins, and all its other parts. No one remotely knows how to do this. But let’s posit an engineer of superhuman skill.

Then you give him the bad news. In making the bear-to-whale transition, the ever-modifying creature has to continue living, breathing, and reproducing even as those changes are taking place. That would be like telling a naval architect that he has to redesign an army tank into a submarine, but at every transition the vehicle has to function as a weapon of war. By the way, it must also be able to give birth to baby submarines.

IN THE THIRD PART of his book, Meyer outlines his positive case for intelligent design. Ironically, here he uses the same principle of scientific reasoning that Darwin used in the Origin. Darwin subscribed to a principle of scientific reasoning known as the Vera Causaprinciple. This asserts that scientists should seek to explain events in the remote past by causes “now in operation.” Meyer applies this to the question of the origin of the information necessary to produce new forms of animal life. He argues that the only known cause of the origin of the kind of digital information that arises in the Cambrian explosion is intelligent activity. He quotes the information theorist Henry Quastler who stated that “the creation of information is habitually associated with conscious activity.” Thus, he concludes, using Darwin’s principle, that intelligent design provides the best explanation for the Cambrian information explosion.

If a correct scientific theory is pursued, we expect new knowledge to comport with the theory. Yet recent discoveries, especially in molecular biology, were not foreseen and have weakened Darwinism. For example, Darwin’s German contemporary and supporter Ernst Haeckel viewed the cell as a simple lump of “protoplasm.” Now we know that it is a hi-tech nano-factory complicated beyond comprehension. A cell can also reproduce itself, something no man-made machine has yet been able to do.

It is said that intelligent design makes no predictions, but it does, and one has been dramatically confirmed. William Dembski, the author of several ID books, predicted in 1998: “On an evolutionary view we expect a lot of useless DNA. If on the other hand organisms are designed, we expect DNA as much as possible to exhibit function.” The “junk DNA” theory has been supported by most leading biologists, including NIH Director Francis Collins.

But Dembski’s view was confirmed last year by prestigious science journals, including Nature. They published papers on the ENCODE project, challenging the view that DNA contains mostly a record of the “errors” in the Darwinian process. ENCODE reported last year that over 80% of DNA in the human genome “serves some purpose, biochemically speaking.” Earlier, 98% had been considered junk.

Meyer also reviews the “Rules of Science” decreeing what is permitted if an investigation is to be called scientific. “Methodological naturalism” is the main one today: Only material causes are permitted. That rule is the basis for Darwinian accusations that ID is creationism. ID does admit non-material causes, thereby flouting the (recently imposed) rule obliging scientists to adhere to naturalism all the way.

Yet science itself abounds with non-material entities. Information is non-material and if it is essential for building organisms, how is it transmitted to the three-dimensional world of matter? There’s an obvious parallel, Meyer points out. How are the decisions we make in our own conscious minds transmitted to the world of physical matter? We know every day that we can transform our mental decisions into physical acts. We choose to lift our arm, and it lifts.

Neuroscience hopes to explain this materially — to show how the brain’s nerve endings translate into consciousness, thence into acts. But one may predict that they will keep looking for a long time, because the gulf separating matter and consciousness is greater than that separating us from the remotest galaxy. That doesn’t mean that mind is too remote, unreal, or can be excluded from science. Mind is within us and nothing can be closer. Without it, the very ideas, theories, and arguments of science wouldn’t exist.

If our own minds can disturb matter in ways that cannot be explained by materialists, is it not possible that some larger or more encompassing Mind can impact the world of nature? No, say the materialists. Why not? Because, in their philosophy, matter is all that exists. That’s why they call themselves materialists. And that is why Thomas Nagel’s book is so significant. His book is subtitled “Why the Materialist Neo-Darwinian Conception of Nature Is Almost Certainly False.” Incidentally, Nagel has also gone out of his way to praise Stephen Meyer.

Even though Nagel is a prominent philosopher with an endowed chair at New York University, his book was reviled by prominent evolutionists — so much so that the New Republic called them “Darwinian dittoheads.” In Britain, the Guardian newspaper called Mind and Cosmos “the most despised science book of 2012.” Maybe Meyer will win that honor in 2013.

Materialism, sometimes called naturalism, is the belief that matter — molecules in motion — is all that exists. Everything else: mind, consciousness, spirit — must somehow be reduced to the orchestrated firing of neurons. It was this bleak philosophy that Nagel challenged.

The point is that if matter is all that exists, then something like Darwinism must be true, because highly complex organisms are real; not just men but mice, and on down to bacteria. How did they get here, in a purely material world? They must have accumulated themselves, bit by accidental bit, over a very long period. Which is close to being a re-description of Darwin’s theory. Darwin wrote in a notebook that he was a materialist himself, but hardly dare say so openly. His theory of evolution by natural selection was his attempt to confine science to an exclusive reliance on material causes.

It follows that those Darwinists who are also materialists — most of them are — can take this philosophy as their backstop and relax. They don’t have to master or rebut ID arguments. They don’t even have to listen to them. Their science is already built into their philosophy. But if Nagel’s doubts about materialism hold up (and few laymen really accept materialism in the first place, because it denies free will and we know that consciousness is real), then the idea that there never was much to support Darwinism may one day be accepted. It was extrapolated from the observed facts of variation; it was assumed but has never been demonstrated.

This much is clear: The Darwinists cannot live with ID as their enemy. They can easily co-exist with creationism, but that came from the Bible, which can be dismissed in our secular age. They rage at ID, on the other hand, because it challenges them in what they have seen as their strong suit: Science.

On Higher education V

On Higher EducationVI

Jehovah's servants Champions of civil liberty.

Jehovah’s Witnesses were unlikely champions of religious freedom.
BY SARAH BARRINGER GORDON

One of the most momentous cases on the Supreme Court docket as war raged globally in 1943 was about a single sentence said aloud by schoolchildren every day. They stood, held their right hands over their hearts or in a raised-arm salute and began, “I pledge allegiance to the flag…” To most Americans the pledge was a solemn affirmation of national unity, especially at a time when millions of U.S. troops were fighting overseas. But the Jehovah’s Witnesses, a religious sect renowned for descending en masse on small towns or city neighborhoods and calling on members of other faiths to “awake” and escape the snare of the devil and his minions, felt otherwise. They insisted that pledging allegiance to the flag was a form of idolatry akin to the worship of graven images prohibited by the Bible. In West Virginia State Board of Education v. Barnette, Walter Barnett (whose surname was misspelled by a court clerk) argued that the constitutional rights of his daughters Marie, 8, and Gathie, 9, were violated when they were expelled from Slip Hill Grade School near Charleston, W.Va., for refusing to recite the pledge.

In a landmark decision written by Justice Robert Jackson and announced on Flag Day, June 14, the Supreme Court sided with the Witnesses. “To believe that patriotism will not flourish if patriotic ceremonies are voluntary and spontaneous instead of a compulsory routine is to make an unflattering estimate of the appeal of our institutions to free minds,” Jackson said. “If there is any fixed star in our constitutional constellation, it is that no official, high or petty, can prescribe what shall be orthodox in politics, nationalism, religion, or other matters of opinion or force citizens to confess by word or act their faith therein.”

Jehovah’s Witnesses were unlikely champions of religious freedom. The sect’s leaders denounced all other religions and all secular governments as tools of the devil, and preached the imminence of the Apocalypse, during which no one except Jehovah’s Witnesses would be spared. But their persistence in fighting in the courts for their beliefs had a dramatic impact on constitutional law. Barnette is just one of several major Supreme Court decisions involving freedom of religion, speech, assembly and conscience that arose from clashes between Jehovah’s Witnesses and government authorities. The Witnesses insisted that God’s law demanded they refrain from all pledges of allegiance to earthly governments. They tested the nation’s tolerance of controversial beliefs and led to an increasing recognition that a willingness to embrace religious diversity is what distinguishes America from tyrannical regimes.

The Witness sect was founded in the 1870s, and caused a stir when the founder, Charles Taze Russell, a haberdasher in Pittsburgh, predicted the world would come to an end in 1914. Russell died in 1916; he was succeeded by his lawyer Joseph Franklin Rutherford, who shrewdly emphasized that the Apocalypse was near, but not so near that Witnesses didn’t have time to convert new followers, which they were required to do lest they miss out on salvation. This “blood guilt” propelled in-your-face proselytizing by Witnesses in various communities on street corners and in door-to-door visits. Soon the sect developed a reputation for exhibiting “astonishing powers of annoyance,” as one legal commentator put it.

Rutherford ruled the Witnesses with an iron fist. He routinely encouraged public displays of contempt for “Satan’s world,” which included all other religions and all secular governments. At the time, the number of Witnesses in the U.S.—roughly 40,000—was so small that many Americans could ignore them. But in Nazi Germany, no group was too small to escape the eye of new chancellor Adolf Hitler, who banned the Witnesses after they refused to show their fealty to him with the mandatory “Heil Hitler” raised-arm salute. (Many Witnesses would later perish in his death camps.) In response, Rutherford praised the German Witnesses and advised all of his followers to refuse to participate in any oaths of allegiance that violated (in his view) the Second Commandment: “Thou shall have no Gods before me.”

With conflict looming around the world in the 1930s, many states enacted flag salute requirements, especially in schools. The steadfast refusal of Witnesses to pledge, combined with their refusal to serve in the military or to support America’s war effort in any way, triggered public anger. Witnesses soon became a ubiquitous presence in courtrooms across the country.

The relationship between Witnesses and the courts was complicated, in part because of the open disdain Rutherford and his followers displayed toward all forms of government and organized religion. Rutherford instructed Witnesses not to vote, serve on juries or participate in other civic duties. He even claimed Social Security numbers were the “mark of the beast” foretold in Revelations. The Catholic Church, said Rutherford, was a “racket,” and Protestants and Jews were “great simpletons,” taken in by the Catholic hierarchy to “carry on her commercial, religious traffic and increase her revenues.” Complaints about unwelcome public proselytizing by Witnesses led to frequent run-ins with state and local authorities and hundreds of appearances in lower courts. Every day in court for Rutherford and the Witnesses’ chief attorney, Hayden Covington, was an opportunity to preach the true meaning of law to the judges and to confront the satanic government.

In late 1935, Witness Walter Gobitas’ two children—Lillian, 12, and Billy, 10—were expelled from school in Minersville, Pa., because they balked at the mandatory recital of the Pledge of Allegiance, and a long court battle ensued. When Gobitis v. Minersville School District (as with Barnette, a court clerk misspelled the family surname) made its way to the Supreme Court in the spring of 1940, Rutherford and Covington framed their argument in religious terms, claiming that any statute contrary to God’s law as given to Moses must be void. The Court rejected the Witnesses’ claim, holding that the secular interests of the school district in fostering patriotism were paramount. In the majority opinion, written during the same month that France fell to the Nazis, Felix Frankfurter wrote: “National unity is the basis of national security.” The plaintiffs, said Frankfurter, were free to “fight out the wise use of legislative authority in the forum of public opinion and before legislative assemblies.”

In a strongly worded dissent, Justice Harlan Stone argued that “constitutional guarantees or personal liberty are not always absolutes…but it is a long step, and one which I am unwilling to take, that government may, as a supposed educational measure…compel public affirmations which violate their public conscience.” Further, said Stone, the prospect of help for this “small and helpless minority” by the political process was so remote that Frankfurter had effectively “surrendered…the liberty of small minorities to the popular will.”

Public reaction to Gobitis bordered on hysteria, colored by the hotly debated prospect of American participation in the war in Europe. Some vigilantes interpreted the Supreme Court’s decision as a signal that Jehovah’s Witnesses were traitors who might be linked to a network of Nazi spies and saboteurs. In Imperial, a town outside Pittsburgh, a mob descended on a small group of Witnesses and pummeled them mercilessly. One Witness was beaten unconscious, and those who fled were cornered by ax- and knife-wielding men riding the town’s fire truck as someone yelled, “Get the ropes! Bring the flag!” In Kennebunk, Maine, the Witnesses’ gathering place, Kingdom Hall, was ransacked and torched, and days of rioting ensued. In Litchfield, Ill., an angry crowd spread an American flag on the hood of a car and watched while a man repeatedly smashed the head of a Witness upon it. In Rockville, Md., Witnesses were assaulted across the street from the police station, while officers stood and watched. By the end of the year, the American Civil Liberties Union estimated that 1,500 Witnesses had been assaulted in 335 separate attacks.

The reversal of Gobitis in Barnette just three years later was remarkably swift considering the typical pace of deliberations in the Supreme Court. In the wake of all the violence against Witnesses, three Supreme Court justices—William O. Douglas, Frank Murphy and Hugo Black—publicly signaled in a separate case that they thought Gobitis had been “wrongly decided.” When Barnette reached the Supreme Court in 1943, Harlan Stone, the lone dissenter in Gobitis, had risen to chief justice. The facts of the two cases mirrored each other, but the outcome differed dramatically. Most important, in ruling that Witness children could not be forced to recite the pledge, the new majority rejected the notion that legislatures, rather than the courts, were the proper place to address questions involving religious liberty. The “very purpose” of the Bill of Rights, wrote Justice Robert Jackson, was to protect some issues from the majority rule of politics. “One’s right to life, liberty and property, to free speech, a free press, freedom of worship and assembly, may not be submitted to vote….Fundamental rights depend on the outcome of no elections.” Jackson’s opinion was laced with condemnation of enforced patriotism and oblique hints at the slaughter taking place in Hitler’s Europe. “Those who begin in coercive elimination of dissent soon find themselves exterminating dissenters,” Jackson wrote. “Compulsory unification of opinions achieves only the unanimity of the graveyard.” Religious dissenters, when seen from this perspective, are like the canary in the coal mine: When they begin to suffer and die, everyone should be worried that the atmosphere has been polluted by tyranny.

Today, the Witnesses still proselytize, but their right to do so is well established thanks to their long legal campaign. Over time they became less confrontational and blended into the fabric of American life.

In the wake of the Barnette decision, the flag and the Pledge of Allegiance continued to occupy a key (yet ambiguous) place in American politics and law. The original pledge was a secular oath, with no reference to any power greater than the United States of America. The phrase “under God” was added by an act of Congress and signed into law by President Dwight Eisenhower on Flag Day, June 14, 1954. Eisenhower, who had grown up in a Jehovah’s Witness household but later became a Presbyterian, alluded to the growing threat posed by Communists in the Soviet Union and China when he signed the bill: “In this way we are reaffirming the transcendence of religious faith in America’s heritage and future; in this way we shall constantly strengthen those spiritual weapons which forever will be our country’s most powerful resources in peace and war.”

Eisenhower’s political instincts for the ways that religion functioned in American life were finely honed: Support for the amendment to the Pledge of Allegiance was strong, including an overwhelming majority of Catholics and Protestants as well as a majority of Jews. According to a Gallup survey, the only group that truly opposed the change was the smattering of atheists. In a country locked in battle with godless communism, a spiritual weapon such as an amended pledge that was not denominationally specific made sense. Only after the intervening half-century and more does the “Judeo-Christian” God invoked in the pledge seem less than broadly inclusive.

Sarah Barringer Gordon is the author of The Spirit of the Law: Religious Voices and the Constitution in Modern America.

Darwin and Hitler.

unsettling "Settled science"

Tom Wolfe and the "Kudzu" of "Settled Science"
Evolution News & Views

Writing in Commentary, Andrew Ferguson offers a fantastic review of Tom Wolfe's takedown of Darwin, The Kingdom of Speech.

On Jerry Coyne's review in the Washington Post:

The reviewer was Jerry Coyne, a biologist from the University of Chicago and a volunteer border cop who patrols the perimeter where science and popular culture meet, making sure that scientists are accorded the proper deference. The Kingdom of Speech is deeply transgressive in this way. Wolfe makes sport of scientific pretensions generally and neo-Darwinian pretensions specifically, and Coyne, a neo-Darwinist to the soles of his Birkenstocks, isn't going to let a mere journalist, or even a Grand Old Man of Letters, get away with it.

Fact-check: Coyne wears specially custom-handmade cowboy boots, not Birkenstocks. He must own closets full. We know because he spends a great deal of space on his evolution blog detailing this with accompanying photos of the boots both under construction and on his feet. Only imagined dialogues between a cat and a dog receive more attention. Even Wolfe would have a hard time spoofing Coyne. Otherwise this is spot-on.

More:

[Coyne] charges him with ignorance and unreason and, above all, presumption. Among scientists, this is a common reaction to an uppity layman. In their better moods, even scientific fundamentalists will tell you the glory of science lies in the endless empirical testing and revision of theories, the back-and-forth of assertion and rebuttal, the stuttering, incremental advance toward truth, the openness to dissent and new ideas. And most often that's what science is. Let an uncredentialed outsider sneak into the lab, however, asking rude questions about one theory or another, and -- wham! -- the back-and-forth is shut down and something called "settled science" rises in its place to keep the amateurs at bay.

In neo-Darwinism, the "settled science" has spread like kudzu, as more and more areas of human life, from morality to music, are recast as nothing more than the consequence of natural selection.

"Settled science" as kudzu infestation. A brilliant image.

On the role of human exceptionalism, and careerism, in the evolution debate:

You don't hear much about [Alfred Russel] Wallace anymore, and you hear even less about [Max] Muller, while their contemporary Darwin became, of course, one of the most famous men who ever lived. Human exceptionalism has a lot to do with their relative reputations. Wallace embraced it and so did Muller; indeed, they thought it was self- evident. Darwin didn't. And most scientists, especially fundamentalists like Jerry Coyne, have inherited Darwin's materialism as dogma. It's a good deal for scientists. After all, if everything we consider uniquely human is a consequence of purely materialistic processes, then the guys who study materialistic processes for a living hold the key to every human question. It's nice work if you can get it.

Marx had this much right: Ideas are strongly influenced by the way people choose to make a living. The practice of materialist science is self-confirming. The notion that scientists with a lifetime invested in drawing materialist conclusions would readily give fair consideration to ideas challenging the way they make their living is a joke.

Putting The Kingdom of Speech into the context of Wolfe's earlier books:

The Kingdom of Speech is popular intellectual history of the most exhilarating kind. Its closest antecedents came along nearly 40 years ago, both of them also by Wolfe. The Painted Word laid waste the world of abstract art, and From Bauhaus to Our House attacked the absurdities of modernist architecture. In all three of these books, Wolfe lampoons the reigning orthodoxy of our intellectual elites...

In conclusion:

Wolfe joins a small and hardy band of writers and other high-brows who take joy in staring down the bullies of scientism: Marilynne Robinson, David Berlinski, Wendell Berry, Thomas Nagel, a few others.


Berlinski, Nagel, Wolfe -- that is excellent company to be in. Read the rest here.

Power to the PC police?:Pros and cons.

A clash of Titans XXXII

Truth is dangerous III

Darwinism can't win even with loaded dice.

Researchers Ran a Massive Yearlong Experiment to Get Bacteria to Evolve. Guess What Happened?

Evolution News & Views

It's a struggle out there. You have to be fit to survive. When the pressure is on, nature favors the ones who can take the heat.

It's a theme that has been drummed into our heads since school. It's a cultural meme. Social Darwinists used it to justify atrocities -- see the new documentary The Biology of the Second Reich. Today's kinder, gentler Darwinists downplay the violence in the struggle for existence, yet the fact as they see it is inescapable: environmental circumstances select random genetic mutations that confer fitness, i.e., survival, by allowing organisms to adapt.

That in a nutshell explains the development of complex life forms. We're assured there are gobs of evidence for it, too.

Looking into a recent paper in PNAS about evolutionary fitness tradeoffs, you have to feel sorry for a team of five evolutionists from UC Irvine who did their level best to produce clear evidence for the favored story. They began with a startling revelation:

Despite the centrality of adaptation to evolution, surprisingly little is knownabout the diversity of mutations that contribute to adaptation or about their phenotypic and fitness effects (1). There are, in fact, only a few well-known examples linking genotype, phenotype, and adaptation in nature (2-4). (Emphasis added.)

Those references are worth a glance. Reference (1) is to H. Allen Orr (2005), "The genetic theory of adaptation: a brief history,"where he states, "Here I survey the history of adaptation theory, focusing on the rise and fall of various views over the past century and the reasons for the slow development of a mature theory of adaptation."

References (2-4) surely must represent what, in the authors' opinions, constitute the best "well-known examples linking genotype, phenotype, and adaptation in nature." What are they? #2 is about stickleback fish that gained or lost body armor, but the authors admit, like these ones do, that "the genetic and molecular basis of morphological evolution is poorly understood." #3 is about mice with varying coat colors due to a single mutation that allows light-colored mice to survive better on light backgrounds and dark-colored mice to survive better on dark backgrounds (a kind of "peppered mice" story). #4 is about a gene in butterflies that affects wing pattern mimicry. So these are their best examples linking genes to adaptation. What became of Darwin's finches and peppered moths?

Moving right along, the UC Irvine team next offers an excuse for this lack of evidence:

In nature, this connection is often complicated by factors such as varying selection pressures or underlying genetic heterogeneities. Although the task is difficult, the general inability to connect phenotype to genotype in the context of environmental adaptation has been a major failing in the field of evolution.

So they are here to fix that epic fail. After listing four complicating factors in their study, they say this in the last sentence of the paper:

Given the breadth of these complexities in a well-controlled experimental system, it is no wonder that the mapping of genotype, phenotype, and fitness continues to be a daunting task in natural populations.

In a moment we will see what they did and what went wrong, but first pause to be astonished.This is the theory that is so well-established by mountains of evidence, we are constantly told, that any criticism of it must be stifled as ignorant, and only this theory must be allowed to be considered scientific. They have just told us otherwise. "Surprisingly little is known" about it, and the best examples they could produce are all instances of trivial variations among existing species. If they had better examples, they surely would have brandished them proudly instead of giving excuses about how hard it is to find genetic evidence for adaptation.

The Experimental Test

Their experiment should have been ideal for testing the genetics of adaptation: 2,000 generations of E. coli bacteria subjected to heat. "In total, we performed >800 fitness competitions, making this one of the largest studies of its kind." The games are on! Evolve or perish! Long live the fittest!

Their "large-scale experiment" started with an "ancestral strain" of E. coli bacteria that they replicated 115 times and subjected to high temperatures (42.2 °C, or 108 °F) for 2,000 generations. "At the end of the experiment, fitness was measured at 42.2 °C for a single clone from each of 114 lineages; on average, fitness increased ∼40% during the yearlong experiment" (meaning, there were still some that hadn't died of heat exhaustion).

The hunt was on for genetic mutations that conferred ability to take the heat. "We sequenced the genome of these 114 clones, identifying 1,258 mutations relative to the ancestral genome," they say. To decide which mutations most likely had something to do with fitness, they identified two "adaptive pathways," both affecting RNA polymerase (RNAP). Clones could survive with one or the other mutation, but not the two together: "mutations in the two pathways were strongly negatively associated." (This is called negative epistasis; more on that later).

Their challenge of linking genetic mutations to fitness, though, was only beginning.

Our thermal stress experiment has identified many putatively beneficial mutationsthat lead to higher fitness under thermal stress. However, we still do not know the phenotypic consequences of these mutations or their relationship with fitness. Do the apparently distinct adaptive pathways converge on similar phenotypes? Or might the two pathways ... lead to alternative phenotypic solutions to a common selective pressure?

Here we begin to address these questions by measuring a complex phenotype: the magnitude of fitness tradeoffs across a thermal gradient. Evolutionary tradeoffs, which are defined as reduced fitness in a nonselected environment, are of great interest in their own right; they are widely observed and frequently assumed to govern and constrain trait evolution.

The operative word there is "assumed." For example, all these mutations may have been neutral, with no phenotypic consequences. Or, mutations for better survival in heat might have had negative consequences for surviving cold (an evolutionary trade-off), with no overall gain in fitness. "Whatever the cause, tradeoffs have rarely been linked to specific genetic variants" -- another embarrassing revelation.

Paltry Results

In this ideal setup (one of the largest of its kind, remember), they were not even looking for a glamorous innovation, like a wing or an eye. Just connecting a particular mutation to a functional phenotype would have been rated a great success, even if all it meant was shifting the germ's optimum temperature range by a few degrees. Trade-offs notwithstanding, so what if the fittest germ in the hot tub would shiver in the cold bath? They would at least be able to connect "genotype, phenotype and adaptation" together -- the kind of evidence neo-Darwinians need and want.

They found that half the clones shifted their thermal range upward by a few degrees (losing ability to survive cold -- the trade-off), and others survived the heat without losing ability to survive cold. Then they found two independent mutations in the RNAP gene that appear relevant to those shifts, as long as they don't occur together. Success? Not so fast.

For one thing, they don't know why those mutations had that effect. They suggested that they might slow RNAP down when its tendency under heat stress is to speed up, thus improving its likelihood to finish a protein synthesis, but this was not clear. Also, to their surprise, the ancestral strain could sometimes bounce back from doom through the "Lazarus effect" (resurrection from the dead) -- but they don't know how that effect works.

Surprisingly, however, w_a [absolute fitness] of the ancestor was negative (w_a = −0.290) but not significantly <0 .00="" 45.0="" able="" and="" at="" fig.="" nbsp="" s1="" s2="" strong="" style="border: 0px; margin: 0px; outline: 0px; padding: 0px;">This unexpected behavior

 was caused by the occasional sudden recovery of populations whose densities had initially declined markedly, a phenomenon known as the "Lazarus effect".

So how is Lazarus coming out of the grave? They don't know. Maybe there is some "preadaptation" to heat in these bacteria:

At the upper end of the thermal niche, most (>95%) of the clones persist at 45 °C, signaling an expansion of their niche at least 2 °C beyond that of the ancestor (Fig. 1B). This observation contrasts with a previous study in which only one of six 42 °C-adapted lines expanded their upper thermal limit but suggests a degree of "preadaptation" to temperatures beyond the clones' immediate experience. Above 45 °C the analyses become complicated by the Lazarus effect, in whichdeclining populations suddenly recover, presumably due to major effect mutations. Indeed, the ancestral clone, which is habituated to laboratory conditions of 37 °C, does not persist at 43 °C but often recovers at 45 °C (Fig. S2). We do not yet know the molecular processes underlying the Lazarus effect, but two seem possible: either the fitness effects of mutations change as a function of the intensity of stress or the mutation rate increases under high stress (33, 34). We do not yet know which of these two mechanisms predominates.

Complicating matters even more are things like "negative epistasis" (mutations that counteract each other) and "antagonistic pleiotropy" (unintended consequences of a "beneficial" mutation on other parts of the genome).

In short, it was hard to find anything beyond a "suggestion" or a "scenario" that these bacteria improved their fitness in any way by genetic mutations, other than the gross observation that some of the clones managed to survive at 45 °C. But even the ancestor could do that sometimes through the "Lazarus effect." The authors also ignored the possibility that E. coli have ways to generate their own mutations under stress. That would be supportive of intelligent design, as would the notion that bacteria contain "a degree of preadaptation" to temperatures beyond their immediate experience.

Some experiment. What we learn from this paper is that under ideal conditions, with the best methods, scientists have a devil of a time trying to establish neo-Darwinian theory in a scientifically rigorous way. A look at their references shows a debt to Lenski's methods that similarly produced paltry results on one of the longest-running experiments in history trying to demonstrate evolution in a lab.

Is this a theory that deserves to rule the world?