The ID Report

By Robert Deyes
ARN Correspondent

Put intuition aside for a moment and imagine a scenario where E.coli knockout strains that have been deleted for conditionally essential genes are rescued by proteins taken from a protein library composed of >10exp6 de novo designed sequences. The prevailing assumption- that functional proteins are constrained to a very small subset of possible sequences- would lead us to infer that finding them by a random search through sequence space would be tantamount to impossible. But a PLOS One paper published in early 2011 appears on the surface to have given us much room for thought. Scientists from Princeton's Department of Chemistry and Molecular Biology used a combinatorial library of 102-residue long proteins to rescue non-viable E.coli knockouts. The functional losses in the knockout strains affected serine, glutamate and isoleucine biosynthesis and disabled the cells' natural capacity for iron acquisition in iron-limited environments.

The E.coli knockouts were auxotrophic meaning that they exhibited a failure to grow on minimal (M9-glucose) media even after several weeks of incubation. But following transformation with the combinatorial library, several cases of successful colony growth were documented suggesting that the certain genes contained therein had successfully complemented the deletions. Sequence comparisons through formal BLAST searches showed that the rescue proteins involved, eighteen in all, were unlike any protein found in nature.

Truth be told these rescue proteins were not entirely random. Their sequences had been engineered to ensure that they would fold into a stable 3-D structure. And not just any structure. Molecular biologists are well aware that canonical sequence rules exist that must be adhered to if they are to maximize the chances of proteins folding correctly. In an alpha-helical fold, for example, polar and non-polar residues must be carefully ordered to make certain that the hydrophilic ('water-loving') and hydrophobic ('water-hating') faces of the fold emerge. The Princeton group adopted a binary code strategy of polar and non-polar residues to get 1.5x10exp6 four-helix bundles. In this singularly fundamental aspect they were designed.

What was the molecular basis that allowed rescue? From their own experiments the Princeton group ruled out the likely hood that novel pathways that bypass the adverse effects of the knockout genes had arisen since E.coli mutants that were deficient in other steps of the naturally occurring biosynthetic pathways could not be rescued. Also dismissed was the interpretation that "global alterations in metabolism had been induced by the mere expression of foreign genes" (a stress response of some kind) since none of the eighteen rescue proteins appeared to have been unfolded- a tell-tale symptom of such a global response. Mutations that minimally disrupted their structure abolished their rescue capabilities.

The evidence seemed compelling. These de novo sequences were exerting specific fonctional effects that served to avert an otherwise fatal outcome for their bacterial hosts. Still the 'design' point-of-departure raised above was without question central to this particular success story. In his book Signature In The Cell Stephen Meyer has noted how it is sequence specificity that ensures that amino acid chains fold into "useful shapes or conformations" (Ref 1). Without a library tailored for the formation of four-helix bundles, the Princeton study is unlikely to have yielded anything that would come close to salvaging the debilitated bacteria. To make matters worse, this study failed to consider in detail the cooperativity that so evidently characterizes the organismic molecular scheme. What we see here is akin to taking one piece out of a jigsaw puzzle and finding another to put in its place albeit with some considerable force of fit. Those who espouse blind evolution are still left reeling over how to explain the origin of the entire puzzle.

Importantly cells transformed with rescue proteins exhibited growth that was "significantly slower than those expressing the natural protein" (the non-knockout strains). Exponential growth occurred 24-144 hours later and reached culture densities that in some cases were as low as 12-15% of wild-type. The authors readily admit that the library proteins may "function by different mechanisms than the natural proteins they replace". Indeed assays designed to test for the deleted functions failed to show that the de novo sequences exhibited comparable enzymatic activities. The evolutionary inference given by the authors- that billions of years of evolution have driven optimal activities for faster growth- therefore appears to be nothing more than a rehash of a positively stale Darwinian fairytale. After all, if the proteins function by different mechanisms, one cannot allege that they are in any sense on the way to becoming the more efficient naturally occurring protein entities we observe in E.coli today.

For the full PLOS One article see:
Michael A. Fisher, Kara L. McKinley, Luke H. Bradley, Sara R. Viola, Michael H. Hecht (2011) De Novo Designed Proteins from a Library of Artificial Sequences Function in Escherichia Coli and Enable Cell Growth, See http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0015364

Further Reading
1. Stephen Meyer (2009) Signature In The Cell: DNA And The Evidence For Intelligent Design, Harper Collins Publishers, New York, p.99

by Denyse O'Leary
ARN correspondent

Yes, the abandonment was recounted in "E.O. Wilson's Theory of Altruism Shakes Up Understanding of Evolution" by Pamela Weintraub. Harvard biologist E. O. Wilson's 1975 Sociobiology was thought to give evolutionary psychology some respectability. Wilson, who learned his trade studying social insects, promoted the idea of kin selection - that people are genetically programmed ("bred into their bones") to behave in socially constructive ways in order to help the genes they share with others get passed on. For example, a woman looks after her sister's children to help the genes she shares with her sister get passed on. And she looks after her new neighbour from Rangoon's children to help ... hey, ... wait a minute.

So the scientific world quaked last August when Wilson renounced the theory that he had made famous. He and two Harvard colleagues, Martin Nowak and Corina Tarnita, reported in Nature that the mathematical construct on which inclusive fitness was based crumbles under closer scrutiny. The new work indicates that self-sacrifice to protect a relation’s genes does not drive evolution. In human terms, family is not so important after all; altruism emerges to protect social groups whether they are kin or not.

Um, yeah.

Wilson has been a familiar face in the Darwin racket for nearly four decades, touted in legacy media as an eminent, impressive scholar who made evolutionary psychology into a real science - when his theory was so obviously out of touch that the simplest experience of non-Harvard life confutes it. For one thing, as agnostic philosopher David Stove points out, in human terms (as opposed to insect terms), altruism is not what needs explaining, but the lack thereof. The recent Toronto subway shutdown (a minor event, to be sure), here and here, provides a useful multicultural snapshot of what Stove means: It was the boor, the unsocial person who was "out of it", not the social person. Everyone seemed to recognize the danger of an out-of-control crowd. (We've all heard the cautionary tales, many of them true.) And the only genetics involved was the fact that we were all humans, endowed with the intelligence to see that danger and remember the tales.

Evolutionary psychology is never going to be a science because it is a discipline without a subject: Its tailless ape, who behavior requires an explanation that does not take into account conscious human awareness in real time - but looks everywhere else for an explanation instead - does not exist.

Denyse O'Leary is co-author of The Spiritual Brain.

By Robert Deyes
ARN Correspondent

In his 1987 seminal work entitled Impossibility In Medicine the American psychiatrist Jean Goodwin presented to the world the following acutely insightful vista of the brain:

"Despite many assertions to the contrary, the brain is not "like a computer". Yes, the brain has many electrical connections, just like a computer. But at each point in a computer only a binary decision can be made- yes or no, on or off, 0 or 1. Each point in the brain, each brain cell, contains all the genetic information necessary to reproduce the entire organism. A brain cell is not a switch. It has a memory; it can be subtle. Each brain cell is like a computer. The brain is like a hundred billion computers all connected together. It is impossible to understand because it is too complex. As Emerson Pugh wrote, "If the human brain was so simple that we could understand it, we would be so simple that we couldn't."" (1)

In so doing he hinted at an aspect of the brain that tied in well with a philosophical thought-chain expounded by ID philosopher Bill Dembski in his book No Free Lunch:

"Humans have designed all sorts of engineering marvels, everything from Cray supercomputers to Gothic cathedrals. But that means, if we are to believe Melvin Kooner, that a blind evolutionary process...cobbled together human neuro-anatomy which in turn gave rise to human consciousness, which in turn produces artifacts like supercomputers which in turn are not cobbled together at all but instead are carefully designed. Out pop purpose, intelligence, and design from a process that started with no purpose, intelligence, or design. This is magic" (2)

In my most recent essay Lessons From A Broken Brain I provide a high-level overview of key medical moments that helped define the hundred-billion-computer organ housed atop our bodies. The design inference shines through in the brief details I present.

On a somewhat related note there is a fascinating clip on the work of Dutch kinetic sculptor Theo Jansen who has created his own brand of beach creatures. With over twenty years of arduous work under his belt, Jansen started by pulling his 'offspring creatures' up into the wind, then gave them propellers and wings/sails to increase their running power. The commentator on this clip notes that: "through hours of experimenting and trial and error, Theo's designs are becoming more and more independent".

Jansen's own conclusion?

"What I have found about this experience of making new forms of life is that you discover all the problems that the real creator must have had creating this world"

And these are not even thinking, autonomous, reproducing beings! See Beach Creatures

Further Reading

1. No Way: The Nature of the Impossible, edited by Philip Davis and David Park. Cited in Inside The Mind Of God- Images And Words Of Inner Space, edited by Michael Reagan, Templeton Foundation Press, New York, p.61
2. William Dembski (2002) No Free Lunch: Why Specified Complexity Cannot Be Purchased Without Intelligence, Rowman & Littlefield Publishers, Inc, Lanham, Maryland, p.369

by Denyse O'Leary
ARN correspondent

In a review of a very interesting-sounding book on information systems through the ages, beginning with African drumming (James Gleick: The Information: A History, a Theory, a Flood), Freeman Dyson discusses information theory.

The story of the drum language illustrates the central dogma of information theory. The central dogma says, "Meaning is irrelevant." Information is independent of the meaning that it expresses, and of the language used to express it. Information is an abstract concept, which can be embodied equally well in human speech or in writing or in drumbeats. All that is needed to transfer information from one language to another is a coding system. A coding system may be simple or complicated. If the code is simple, as it is for the drum language with its two tones, a given amount of information requires a longer message. If the code is complicated, as it is for spoken language, the same amount of information can be conveyed in a shorter message.

and the story is not without lessons:

The information flood has also brought enormous benefits to science. The public has a distorted view of science, because children are taught in school that science is a collection of firmly established truths. In fact, science is not a collection of truths. It is a continuing exploration of mysteries. Wherever we go exploring in the world around us, we find mysteries. Our planet is covered by continents and oceans whose origin we cannot explain. Our atmosphere is constantly stirred by poorly understood disturbances that we call weather and climate. The visible matter in the universe is outweighed by a much larger quantity of dark invisible matter that we do not understand at all. The origin of life is a total mystery, and so is the existence of human consciousness. We have no clear idea how the electrical discharges occurring in nerve cells in our brains are connected with our feelings and desires and actions.

No, but we do have people who is just itchin' to stamp out doubt.

Denyse O'Leary is co-author of The Spiritual Brain.

by Denyse O'Leary
ARN correspondent

Earlier, I had mentioned the problem created by negative expert opinion, when dealing with children who are missing all or parts of their brain. A friend kindly sent me this in response, from one of the Cambridge Journals.

Note the line in the abstract below, "The relative rarity of manifest consciousness in congenitally decorticate children could be due largely to an inherent tendency of the label 'developmental vegetative state' to become a self-fulfilling prophecy."

Developmental Medicine & Child Neurology (1999), 41: 364-374 Copyright © 1999 Mac Keith Press

Consciousness in congenitally decorticate children: developmental vegetative state as self-fulfilling prophecy

D Alan Shewmon MD a1c1, Gregory L Holmes MD a2 and Paul A Byrne MD FAAP a3
a1 Pediatric Neurology, UCLA Medical Center, Los Angeles, CA, USA.
a2 Department of Neurology, Harvard Medical School Children's Hospital, Boston, MA, USA.
a3 Pediatrics (Neonatology) Medical College of Ohio, St Charles Hospital, Oregon, OH, USA.

Abstract
According to traditional neurophysiological theory, consciousness requires neocortical functioning, and children born without cerebral hemispheres necessarily remain indefinitely in a developmental vegetative state. Four children between 5 and 17 years old are reported with congenital brain malformations involving total or near-total absence of cerebral cortex but who, nevertheless, possessed discriminative awareness: for example, distinguishing familiar from unfamiliar people and environments, social interaction, functional vision, orienting, musical preferences, appropriate affective responses, and associative learning. These abilities may reflect 'vertical' plasticity of brainstem and diencephalic structures. The relative rarity of manifest consciousness in congenitally decorticate children could be due largely to an inherent tendency of the label 'developmental vegetative state' to become a self-fulfilling prophecy.
(Accepted November 13 1998)

The problem will be apparent to anyone who has worked with people with neurological deficits: Like any complex organ, the brain has multi levels of compensation for injuries. Now that neuroscientists can image the brain, many striking cases have come to light, demonstrating ways in which people adapt as best they can. It's no surprise that this would be especially true of children.

But it's also no surprise that dumping children in a fourth rate facility and leaving them unvisited can reliably produce a very low functioning individual in only a few years. In fact, a child of average intelligence can deteriorate under those conditions, and many have.

by Denyse O'Leary
ARN correspondent

here:

Every cell a densely populated ocean. I’d be interested to know whether wave mechanics can be used to interpret many of the behaviours of life forms.

Denyse O'Leary is co-author of The Spiritual Brain.

by Denyse O'Leary
ARN correspondent

(targeting customers of the more familiar bodice-ripper and cherry-chomp brands)

David Brooks, who used to know tripe when he saw it, now gives us this, praising pop evolutionary psychology:

Brain science helps fill the hole left by the atrophy of theology and philosophyA core finding of this work is that we are not primarily the products of our conscious thinking. The conscious mind gives us one way of making sense of our environment. But the unconscious mind gives us other, more supple ways. The cognitive revolution of the past thirty years provides a different perspective on our lives, one that emphasizes the relative importance of emotion over pure reason, social connections over individual choice, moral intuition over abstract logic, perceptiveness over I.Q. It allows us to tell a different sort of success story, an inner story to go along with the conventional surface one.

Yes. There is a name for that: fascism

Fascism, at heart, is a belief that surrendering to an emotion engendered by an idea can bring about an earthly utopia. In politics, the idea is usually appears as a messianic leader, but in current psychology, anyone with some neuroscience training can generate these visions using machines, drugs, or narratives that get published as research on human subjects.

And it is always very difficult, at best, to explain to people that, on Earth, utopia is the trade name for hell.

Anyway, Brooks unintentionally outlines the problem better than any detractor could by retailing this loathsome love story:

Harold and Erica got their first glimpse of each other in front of a Barnes + Noble. They smiled broadly as they approached, and a deep, primeval process kicked in. Harold liked what he saw, from the waist-to-hip ratio to the clear skin, all indicative of health and fertility. He enjoyed the smile that spread across Erica’s face, and unconsciously noted that the end of her eyebrows dipped down. The orbicularis-oculi muscle, which controls this part of the eyebrow, cannot be consciously controlled, so, when the tip of the eyebrow dips, that means the smile is genuine, not fake.Erica was impressed by him: women everywhere tend to prefer men who have symmetrical features and are slightly older, taller, and stronger than they are. But she was more guarded and slower to trust than Harold was. That’s in part because, while Pleistocene men could pick their mates on the basis of fertility cues discernible at a glance, Pleistocene women faced a more vexing problem. Human babies require years to become self-sufficient, and a single woman in that environment could not gather enough calories to provide for a family. She was compelled to choose a man not only for insemination but for continued support. That’s why men leap into bed more quickly than women. Various research teams have conducted a simple study. They hire a woman to go up to college men and ask them to sleep with her. More than half the men say yes. Then they have a man approach college women with the same offer. Virtually zero per cent say yes.

So Erica was subconsciously looking for signs of trustworthiness.

James Le Fanu, a British doctor who seems to have got fed up with all-rubbish all-day (a busy practice will do that), ripostes,

It would be good to think that perhaps this is all a jest, an 'argument ad absurdum' that would appeal to The New Yorker's sophisticated readership. David Brooks cannot seriously suppose this bizarre amalgam of pop psychology and cold evolutionary theorizing can really tell us anything of interest about the human psyche, let alone that it represents a "revolution in consciousness." But if he does, he would certainly not be the first to suspend their critical judgement in deference to science's claims to knowledge not possessed -- for the most salient feature of the studies he cites is how unconvincing they are even on their own terms. To take just one example already considered, Willis and Todorov's "First impressions: Making up your Mind after a 100-Ms exposure to a Face" was published in the journal Psychological Science in 2006.This study was designed to investigate the "minimal conditions" under which people infer character traits -- revealing a significant correlation between psychology undergraduates' assessment, when shown photographs of 70 amateur actors, of their "competence, trustworthiness and aggressiveness," whether viewed for just a tenth of a second or "without time constraints." This would indeed confirm the truism that people are capable of making "snap judgments," but without casting any light on the two really important questions -- the nature of the brain's astonishing feat of processing information that allows such judgements to be made and their validity -- i.e. whether those judged to be "competent, trustworthy or aggressive" really were so. So for all the ingenious ingenuity of Willis and Kosorov's experiment, we are left none the wiser.

There are, needless to say, profounder issues involved here, of which the most salient is whether it is indeed possible to illuminate the workings of the human mind by reducing it to so many distinctive attributes that can then be investigated independently of each other.

Of course it isn't possible, but many people welcome swamp gas, having no other light. And Brooks probably really does want his fictional (whew!) profoundly unpleasant couple to be "happy."

That, however, makes the offence worse. On the plus side, Brooks has at least made clear that no one who values reason over emotion in assessing the human condition need take him seriously.

Denyse O'Leary is co-author of The Spiritual Brain.

by Denyse O'Leary
ARN correspondent

Here. He was briefly a born-again Christian as a youth, but

... my sister's husband (an aspiring psychologist whose preference for graduate school over employment my father wasn't wild about) suggested I read Beyond Freedom and Dignity by B.F. Skinner. As intellectuals go, Skinner was pretty dismissive of intellectuals -- at least the ones who blathered unproductively about "freedom" and "dignity," the ones he considered insufficiently hard-nosed and scientific.Look, he said, people are animals. Kind of like laboratory rats, except taller. Their behavioral proclivities are a product of the positive and negative reinforcements they've gotten in the past. Want to build a better society? Discern the links between past reinforcement and future proclivity, and then adjust society's disbursement of reinforcements accordingly. No need to speculate about unobservable states of mind or ponder the role of "free will" or any other imponderables. Epistemology, phenomenology, metaphysics, and 25 cents will get you a ride on the New York subway.

This was my kind of intellectual -- an anti-intellectual intellectual! I became an ardent Skinnerian.

However, that wore off, so then this:

In high school, I bought into this view, but in college, a reference to the "socio-biology" controversy on the cover of Time magazine caught my eye, and I started looking into the Darwinian underpinnings of human behavior. This train of thought culminated -- about two decades after I encountered Skinner -- in my book The Moral Animal, a full-throated defense of evolutionary psychology.

Full-throated defense of what,did you say? From the malign to the ridiculous, in one swift descent ... He ended up saying that we evolved for adultery, in Time Magazine (but could somehow help it anyway).

That's interesting. As I understand the meaning of the word "evolved", the whole point is that you can't help it. If I tell you that I evolved to have ten fingers, walk upright and see in binocular vision, the point is that I didn't and don't just choose this stuff.

The least the committed Darwinist could do (but of course he won't) is not to make nonsense of the meaning of words in common use.

He insists that Dawkins buddy Jerry Coyne misunderstands his most recent Evolution of God. Coyne thinks Non-Zero isn't a “materialist” and, amazingly enough, Non-Zero affirms that he is one. Gosh, I wonder who can be right?

Non-Zero?: He also wrote a book explaining how the universe could have arisen from the interplay between positive and negative forces, equaling zero. Bill Clinton praises it here.

Denyse O'Leary is co-author of The Spiritual Brain.

by Denyse O'Leary
ARN correspondent

Apparently you have, ... if you are not designed.

Over at MSNBC.com, Alan Boyle asked yesterday,

What would happen if we found out that we are not alone in the universe? Or, on the flip side, what would happen if we decided that we really were alone? Experts provided updated answers to those age-old questions, from a scientific as well as a religious angle, during a Sunday session at the American Association for the Advancement of Science's annual meeting. But one of the most intriguing questions had more of a personal spin: What would you ask E.T. if you had the chance?

Well, what would you ask, readers?

And, as for what would happen if we decided that we really were alone? Glad someone wondered. The underlying cultural assumption has always been that SETI searches will be rewarded, insofar as we can't be important enough to be alone. For one thing, it would imply that we are unique. Sounds too much like religion.

Still, someone bit on the question:

Suppose the search for extraterrestrial intelligence continues for a century ... and no messages are received.

Let's see, some predictions first: When the truth sinks in, science fiction takes a huge nosedive in sales and, to rescue itself, gets reclassified as fantasy. SETI folds. NASA scales back the rhetoric at media events on astrobiology and loses funding for same. After all, no one really cares about extraterrestrial bacteria, even if they are out there. They won't pay taxes for that for long, will they? No,They are the ones we have been waiting for, the ETs.

Senior astronomer Howard Smith, the biter, took the occasion to introduce his misanthropic principle:

That term plays off the widely cited anthropic principle — the idea that Earth appears to be so suited for life as we know it not necessarily because God made it that way, but simply because we wouldn't be around to see it if it wasn't.

The way Smith sees it, the misanthropic principle is a good thing. The view that we alone are responsible for our zone of the cosmos should make us feel "blessed," and more careful about not spoiling the good thing we've got here.

"The misanthropic principle is joyous," Smith said. "We should rejoice in our good fortune."

So rejoice, brother. You can get a religious message out of anything or its opposite.

Denyse O'Leary is co-author of The Spiritual Brain.

by Denyse O'Leary
ARN correspondent

From ScienceDaily (Feb. 18, 2011) this news, “Promise of Genomics Research Needs a Realistic View, Experts Urge”

Unrealistic expectations about genomic medicine have created a "bubble" that needs deflating before it puts the field's long term benefits at risk, four policy experts write in the current issue of the journal Science.

Ten years after the deciphering of the human genetic code was accompanied by over-hyped promises of medical breakthroughs, it may be time to reevaluate funding priorities to better understand how to change behaviors and reap the health benefits that would result.

You mean, the dead shall not rise again in this life?

And,practically speaking,

After all, while advances are being made in personalized medicine through the tools of pharmacogenetics, "the most powerful predictor of drug efficacy is whether a patient takes the drug."

In my own country, tens of thousands end up in the emerg every year due to beggaring around with powerful prescribed meds.

Reality check: If it's powerful enough to help you, when taken right, it's ...

In many diseases a large number of genes play a role, making meaningful predictions difficult both for individuals and in public health.

To say nothing of all the other factors, like environment and age of first onset. Now this zinger:

There's little evidence that advising people they are at genetically increased risk for disease has significant impact on their behavior, while telling others they are at less risk can promote bad behaviors.

Which is only common sense, really.

Translating scientific findings into patient care is an "inherently messy" process, as demonstrated by hormone replacement therapy and other "ideas that didn't pan out when scrutinized through the lens of evidence-based medicine."

Actually, the big problem with transhumanism is that, to achieve immortality through science and technology, you must get all traces of the human out of the process first.

Denyse O'Leary is co-author of The Spiritual Brain.

by Denyse O'Leary
ARN correspondent

Ian O'Neill tells us, “Milky way stuffed with 50 billion alien worlds” Discover (Feb 19, 2011)

Making estimates may sound trivial, but it does put the search for ET into perspective. There's at least 50 billion worlds, which have fostered the development of basic lifeforms? How many have allowed advanced civilizations to evolve?

If there are any space-faring alien races out there, "the next question is why haven't they visited us?" Borucki asked. He responded with: "I don't know."

I wonder if we'll ever know.

One problem I have with statistics that start with a current sample of one is that it strikes me as difficult to compute the odds that there are two, no matter what the sample size is. If we find a donut-shaped planet, does that mean there must be another one out there? Possibly, but if very specific and unusual conditions were required to produce it, those conditions may never have been repeated anywhere.

Very specific conditions produced life on Earth. Whether these conditions were unusual cannot be established on the magic of large numbers alone. Still, it's all good fun and great sound bites.

Denyse O'Leary is co-author of The Spiritual Brain.

by Denyse O'Leary
ARN correspondent

This from the Onion to start your day:

Anthropologists Trace Human Origins Back To One Large Goat
'Wait, That Can't Be Right,' Scientists Say
FEBRUARY 17, 2011 | ISSUE 47•07

As their colleagues huddled together and whispered behind them, researchers from Australia and Japan explained how one 6-foot-tall goat with a hominid skeletal structure spawned numerous goat-human hybrids over a period of 1.8 million years. In a series of PowerPoint slides, they then showed that our ancestors used their prehensile upper lips to perform basic agricultural tasks and stomped out crude pottery with their cloven feet, theories that team members stopped reading aloud to the assembled audience almost immediately after reaching the words "cloven feet."

"Okay, so I'm reading this now, and it says, 'After trotting out of Africa nearly 2 million years ago, our earliest ancestors used their strong hooves and hindquarters to climb up steep mountain slopes in search of delicious moss,'" said British anthropologist Oliver Cranmore, reading from the report and shaking his head. "The thing is, I think I actually wrote that part. And I remember feeling very confident and excited about it at the time. This is weird."

Wait a few months, and you'll be reading something like this in New Scientist. Oh wait, maybe weeks.

Denyse O'Leary is co-author of The Spiritual Brain.

by Denyse O'Leary
ARN correspondent

In the March edition of Scientific American, Gary Stix will explain

The Neuroscience of True Grit

When tragedy strikes, most of us ultimately rebound surprisingly well. Where does such resilience come from?

Scientific American New Issue Alert here.

Prediction: Reading this will tell us a laudable amount of neuroscience and a little about true grit. The latter is difficult to quantify because it is, if you like, a psychological wave function. What caused the Romanian rebellion against Ceaucescu to spread from street to street, after decades of the iron rod? What caused the Montgomery bus boycott, after decades of passive acceptance of segregation? What causes an abuse victim to finally have "had enough" and start fighting back?

Multiple causes, to be sure, and they can be grouped into many valid types, but there is no one, attributable cause. "I've/we've had enough of this" is in fact a focal point of many forces.

The neuroscience is sure to be absorbing and fun, but we will also be hearing from dim bulbs who think they have found a Final Cause. And can the True Grit gene be far behind? Or an "evolutionary psychology" explanation for true grit? I hear the book agents in the distance already ...

Denyse O'Leary is co-author of The Spiritual Brain.

by Denyse O'Leary
ARN correspondent

If your boss has been called into a meeting, have a look at
this:

DARWIN, DESIGN & THOMAS AQUINAS
The Mythical Conflict Between Thomism & Intelligent Design

by Logan Paul Gage

Excerpt: In a typical discussion of Darwinian evolution, Christian philosophy, and intelligent design, one is likely to hear that St. Thomas had no problem with secondary causes operating in nature and that St. Augustine knew that the Bible is "not a science textbook." Both of these assertions are true, as far as they go. But unfortunately, such platitudes only obscure deeper sources of tension between Darwinism and Thomistic thought. Here I would like to explore three intimately related sources of tension: the problem of essences, the problem of transformism, and the problem of formal causation.

The Essences of Species

First, the problem of essences. G. K. Chesterton once quipped that "evolution . . . does not especially deny the existence of God; what it does deny is the existence of man." It might appear shocking, but in this one remark the ever-perspicacious Chesterton summarized a serious conflict between classical Christian philosophy and Darwinism.

I've always thought that the Thomas Aquinas would disapprove of ID claim was manufactured by people who politely pettifog in the face of the ruthless anti-design lobby.

Thomas would tell them: Prove evolution. Grow a backbone.

Denyse O'Leary is co-author of The Spiritual Brain.

by Denyse O'Leary
ARN correspondent

Possibly, Richard Dawkins’s worst offense against the world of reason is the coining of the word "meme" - a "unit" of "thought" that replicates in the minds of others by neo-Darwinian natural selection. The idea itself is, of course, hardly a useful description of how people influence each other, but it serves very well as a lazy substitute for precise language.

For example, we might hear about the "hate Hilary Clinton meme", the "Islam is the religion of peace meme", or, even more inexcusably, the "religion meme". These short cuts are short circuits.

How about, in order, "Many Democrats have a strong aversion to Hilary Clinton", "Some claim that Islam is a religion of peace", and ... well, what in Hull DOES Lazybrains mean by the "religion meme"? Probably something like, "I despise traditional spiritual beliefs."

Do you see the problem here? Once Lazybrains is compelled by his Inner English Teacher to actually say what he means, he will need to defend it rationally and with evidence.

Or maybe I should save myself lots of work by just calling all this the "mental laziness meme"?

Then I wouldn't have to say what I mean, but I would at least have modelled the proposition ably.

Denyse O'Leary is co-author of The Spiritual Brain.

by Denyse O'Leary
ARN correspondent

A good laugh will help you sleep:

Brain area for empty news stories discovered

Satirical website Newsbiscuit has a cutting article making fun of the regular ‘brain scans show…’ news items that are a staple of the popular science pages.

Scientists are heralding a breakthrough in brain scan technology after a team at Oxford University produced full colour images of a human brain that shows nothing of any significance.

'This is an amazing discovery', said leading neuroscientist Baroness Susan Greenfield, 'the pictures tell us nothing about how the brain works, provide us with no insights into the nature of human consciousness, and all with such lovely colours.' ...

A couple stories like this have whizzed past recently. It sounds like I'm not the only one who gets irritated by weeknd litter box-liner.

In fairness, there are absolutely no worthwhile insights into human consciousness at present because, as Greg Peterson said, "To study the brain is to study ourselves, but in a way that makes us both subject and object. It is as if we were trying to look both in and out of the window at the same time."

Denyse O'Leary is co-author of The Spiritual Brain.

Hat tip: Stephanie West Allen at Brains on Purpose

by Denyse O'Leary
ARN correspondent

No, this isn't about what you think. For once, we are talking about frogs and newts.

A friend notes that an evolutionary biologist puzzles as follows:

"One of the most puzzling paradoxes in the evolution of toxins is why organisms evolve to be deadly - contrary to venoms, for which deadly effects have a clear benefit. Extreme toxicity occurs repeatedly, from saturniid caterpillars to dart poison frogs. Selection favors the most-fit individuals, and those should be the ones that avoid predation. Killing an individual predator does not give an advantage over simply deterring one, especially if the prey has to be handled or eaten by a predator to deliver the poison. How, then, can we explain the evolution of deadly toxicity?" (Brodie, E. D., III. 2009. Toxins and venoms. Current Biology 19: R931-R935.)

Brodie, I'm told, is a leading researcher on evolutionary arms races at the University of Virginia. He goes on to suggest a solution: "arms races between predators and prey ... drive the exaggerated evolution of toxicity in general, without resulting in deadly consequences to the primary selective agent." (R933) He suggests as an example is the predator-prey relationship between garter snakes and a newt that produces tetrodotoxin powerful enough to kill 10-20 humans or thousands of mice. But the interesting thing is that the snakes, which seem to be the "primary selective agent" for newts, in the sense of selecting them for dinner, are resistant to the toxin. Brodie attributes the newts' heightened toxicity to coevolution with the garter snakes.

My friend asks, "But how does that solve the paradox? Newts with a higher level of toxicity would only accrue selective advantage if those higher levels of toxicity protected them against the predators."

Well, I suspect the answer lies in another question: What do we think the problem is, exactly? For a Darwinist, the goal is to persuade others that natural selection is the primary source of new information in the history of life. Therefore, the problem is "coming up with a Darwinian explanation", however unsatisfactory it is. And my friend should know by now not to ask any questions if he really needs his job. (See Expelled.) Shut up, Brodie explained.

Of course, a non-Darwinist like myself would hazard a guess that no selection whatever is involved (because I don't need selection to do anything in particular and am not looking for it when it probably isn't there). If neither predator nor prey are affected by the prey's toxicity to life forms that are irrelevant to their mutual ecology (such as humans), there is no reason the prey shouldn't have as high a level of toxicity as is chemically consistent with its continued life. And for all we know, the toxin provides some hitherto unlooked for convenience for the newt.

Besides which, anyone who tried to research this topic up close and personal in the wild may now be referred to exclusively in the past tense ... Jane Goodall lives on another street, I am afraid.

Denyse O'Leary is co-author of The Spiritual Brain.

"I know this world is ruled by infinite intelligence. Everything that surrounds us - everything that exists - proves that there are infinite laws behind it. There can be no denying this fact. It is mathematical in its precision."

– Thomas A. Edison

by Denyse O'Leary
ARN correspondent

One group that isn't going along with John "end of science" Horgan's "immoral" rap about multiverse theorizing is the Templeton Foundation. A friend sends me this excerpt from a recent newsletter (which I can't currently find online):

Meanwhile, Cambridge University cosmologist and JTF Trustee John D. Barrow has just published the UK version of his new title, The Book of Universes. Barrow, a best-selling popular science author and the 2006 Templeton Prize winner, explores the underappreciated fact that Einstein's theory of relativity predicts the existence of multiple and varied universes. What might these universes be like? And what do the latest scientific findings tell us about our own universe? Barrow's Book gives readers a comprehensive overview of what we know, and what we may yet learn, about our universe, and beyond. The Book of Universes will be published in North America in March.

Um, "what we know, and what we may yet learn, about our universe, and beyond" is a pretty comprehensive overview. I'd have said ambitious rather than immoral. Is it possible that cutbacks to space programs from which one can actually find out things coincide with increasingly far out theorizing?

Denyse O'Leary is co-author of The Spiritual Brain.

by Denyse O'Leary
ARN correspondent

Ken Connor, commenting on Jonah Lehrer’s New Yorker piece (December 13, 2010) on the loss of replicability of science findings over time, writes,

But now all sorts of well-established, multiply confirmed findings have started to look increasingly uncertain. It's as if our facts were losing their truth: claims that have been enshrined in textbooks are suddenly unprovable. This phenomenon doesn't yet have an official name, but it's occurring across a wide range of fields, from psychology to ecology. . . . For many scientists, the effect is especially troubling because of what it exposes about the scientific process. If replication is what separates the rigor of science from the squishiness of pseudoscience, where do we put all these rigorously validated findings that can no longer be proved? Which results should we believe?"

Which results should we believe? Which theories should we place our faith in? These are not questions that the scientific community likes to wrestle with publicly. Uncertainty tends to undermine authority, after all. Perhaps this is why some scientists go to such extreme lengths to preserve the integrity of their pet theories, even to the point of manipulating or falsifying data or suppressing information that doesn't support their desired conclusion (remember Climategate?).

What this reveals is that the "scientific" world view is a rather fragile one, in which there is little room for debate outside the accepted parameters of prevailing scientific dogmas. Those scientists with the courage to challenge these dogmas quickly find themselves blacklisted – relegated to the fringes of the profession, unable to secure prestigious positions in the community and unlikely to get their work published in prominent journals. This is hardly conduct befitting a field of study that prides itself on the objective pursuit of truth.

Actually, the problem isn’t that the claims are losing their truth. Many, especially anything to do with Darwinism, were unprovable and probably untrue in the first place, and can be kept in circulation only by the sacrifice of intellects.

Denyse O'Leary is co-author of The Spiritual Brain.

by Denyse O'Leary
ARN correspondent

From the Australian (Paul Monk, February 7, 2011), on the dangers of consensus in science:

... we are justified in being wary of foreclosing major debates based on scientific consensus, since it can be in error. Second, it shows that the way to challenge and correct scientific consensus is not through polemic or denial, but through specifying crucial variables and deductions and testing them scrupulously, in the manner of Hubble. Third, it shows that there is, nonetheless, such a thing as scientific consensus and that when handled in the manner just described, it tends to prove self-correcting. Fourth, it shows that ideally such correction will occur, as it did between Hubble and Shapley, on the basis of lucid examination of "the various possibilities". Finally, it shows that overwhelmingly human beings have always lived oblivious to the truth about the natural world and that only exacting and brilliant science has been able to discover what that truth is.

Well, foreclosing debate is a way of enshrining mediocrities and enthroning tax burdens. If that's what you want, take it and run, please.

All that said, speaking for myself, I have no idea what "the truth about the natural world is." I'm not certain of my uncertainty but am certain of one thing: Whatever the truth is, is well beyond the reach of the dullard who wouldn't know what it would be like to doubt, for example, the Darwin lobby.

Denyse O'Leary is co-author of The Spiritual Brain.

by Denyse O'Leary
ARN correspondent

A friend reminds me of this 2004 paper on the busted molecular clock:

For almost a decade now, a team of molecular evolutionists has produced a plethora of seemingly precise molecular clock estimates for divergence events ranging from the speciation of cats and dogs to lineage separations that might have occurred ,4 billion years ago. Because the appearance of accuracy has an irresistible allure, non-specialists frequently treat these estimates as factual. In this article, we show that all of these divergence-time estimates were generated through improper methodology on the basis of a single calibration point that has been unjustly denuded of error. The illusion of precision was achieved mainly through the conversion of statistical estimates (which by de?nition possess standard errors, ranges and confidence intervals) into errorless numbers. By employing such techniques successively, the time estimates of even the most ancient divergence events were made tolook deceptively precise. For example, on the basis of just 15 genes, the arthropod–nematode divergence event was ‘calculated’ to have occurred 1167 6 83 million years ago (i.e. within a 95% confidence interval of ,350 million years). Were calibration and derivation uncertainties taken into proper consideration, the 95% confidence interval would have turned out to be at least 40 times larger (,14.2 billion years).

Personally, I blame the pop science press for much of this.

Am I just too idealistic about human nature? Maybe, but I think that many scientists would not pretend to certainty as much as they do, except for the sound bites propping up the media's evolution myth - a faith statement, if ever there was one - a certainty which has nothing whatever to do with straightening out the tangles of life's history.

I used to have an editor like that. I was writing on topics unrelated to Darwinism, but his basic gist was, get me statistics, how gathered or with what reliability makes no difference.

The special punishment meted out to people like him by nature or God or whoever is that he always missed the naturally verifiable in his pursuit of the naturally unverifiable. For example, the birth rate and life expectancy of given region tells you a great deal about what you might expect of the future under normal circumstances, but he wanted me to try to find out how many women would walk out on their husbands "if they could" - a classic meaningless figure.

Authors' Graur and Martin's quotation from Douglas Adams is most apt: ‘We demand rigidly defined areas of doubt and uncertainty.’

Denyse O'Leary is co-author of The Spiritual Brain.

by Denyse O'Leary
ARN correspondent

Or sea slugs?

Like, humans had 100, 000 genes, which proved we were a big-brained ape, then 30, 000, a bit more than a worm. Oh but wait, the fern has 250,000 genes and someone who has never kept a fern can be confident that they’re mostly junk. Now, ten years on, here's the kind of thing we hear:

Since the human genome was sequenced, we know more about our own history, and the lines between us and other species have blurred, Cole-Turner said. A comparison with the Neanderthal genome revealed that Neanderthals likely mated with our ancestors, since between 1 percent and 4 percent of some modern humans' DNA came from Neanderthals. Even the genome from the first amphibian to be sequenced, the African clawed frog, showed surprising similarities to the human genome. “

[ ... ]

"Now that we have the sequence for the whole genome, including the 98 percent (considered junk), we find that at least half of it is functional. It is even difficult nowadays to say what a gene is," said Robert Plomin, a research professor at the Institute of Psychiatry at King's College London.

[ ... ]

"It's not chaos. It is tractable. We can understand all the nuts and bolts of a living system; there are just so many moving parts it's just hard to describe," he said.

- Wynn Parry, MSNBC News, 2/3/2011

I wonder what the next “just-a-“spin” will be? Any guesses?

Denyse O'Leary is co-author of The Spiritual Brain.

by Denyse O'Leary
ARN correspondent

Here's Kathy Weston (Science, February 04, 2011) on, among other things, the surprising importance of networking - unless you have already got a Nobel prize:

My initial conviction -- essential for anyone who wants to make it as a scientist -- that I could really make a difference, maybe even win a few prizes and get famous, eroded when I realized that my brain was simply not wired like those of the phalanx of Nobelists I met over the years; I was never going to be original enough to be a star. This early realization, combined with a deep-seated lack of self-confidence, meant that I was useless at self-promotion and networking. I would go to conferences and hide in corners, never daring to talk to the speakers and the big shots. I never managed, as an infinitely more successful friend put it, "to piss in all the right places."

[ ... ]

What could I have done to check my descent into mediocrity? I should have put aside my fears of looking dumb and got on with the networking stuff anyway. And -- very importantly -- I should have found myself a mentor. Every scientist needs someone in a position of power who has faith in his or her abilities, to provide advice and do a bit of trumpet-blowing on his or her behalf. I should have taken more scientific risks, gone for bigger stakes, and thought harder about direction. Finally, I should have followed my instincts and quit my job before it quit me -- but I was hampered by an exaggerated terror of being labeled a failure. (In fact, none of my friends and family seems to care a hoot about my fall from grace, and of course I should have known that all along.)

Much food for thought here, on women in the competitive world of science.

Part of Weston's difficulty was that, like most women, she simply couldn't ignore relationships, on the theory that if she was a big success, they would take care of themselves. This puts me in mind of Cordelia Fine's timely dismissal of research on supposed innate differences between men and women. Yes, most such claims are easily debunked - but the anomaly remains, and Weston depicts the outcome astutely.

All that said, science writer is a great career choice - if you like writing. Of course, if you write sympathetically about ID theorists, you must live with a troll monitor around your neck, but in some places, that's a distinction.

Denyse O'Leary is co-author of The Spiritual Brain.

by Denyse O'Leary
ARN correspondent

Here:

Srivastava had been hooked by a different sort of lure - that spooky voice, whispering to him about a flaw in the game. At first, he tried to brush it aside. "Like everyone else, I assumed that the lottery was unbreakable," he says. "There’s no way there could be a flaw, and there’s no way I just happened to discover the flaw on my walk home."

And yet, his inner voice refused to pipe down. "I remember telling myself that the Ontario Lottery is a multibillion-dollar-a- year business," he says. “They must know what they’re doing, right?”

Oh yes, Mohan, that’s something you can count on for sure. The government knows what it's doing. Or someone else knows what they’re doing. Or anyway ...

Oh, go ahead, losers. Believe everything is due to chance and buy those darn tickets. Maybe we'll finance a hospital out of it. Still, ...

Denyse O'Leary is co-author of The Spiritual Brain.

Denyse O'Leary
ARN Reporter

Here is the "Edge World Question Center", a leading materialist think tank, with 2011's Question:

THE WORLD QUESTION CENTER

James Flynn has defined "shorthand abstractions" (or "SHA's") as concepts drawn from science that have become part of the language and make people smarter by providing widely applicable templates ("market", "placebo", "random sample," "naturalistic fallacy," are a few of his examples). His idea is that the abstraction is available as a single cognitive chunk which can be used as an element in thinking and debate.

The Edge Question 2011

WHAT SCIENTIFIC CONCEPT WOULD IMPROVE EVERYBODY'S COGNITIVE TOOLKIT?

The term 'scientific"is to be understood in a broad sense as the most reliable way of gaining knowledge about anything, whether it be the human spirit, the role of great people in history, or the structure of DNA. A "scientific concept" may come from philosophy, logic, economics, jurisprudence, or other analytic enterprises, as long as it is a rigorous conceptual tool that may be summed up succinctly (or "in a phrase") but has broad application to understanding the world.

[Thanks to Steven Pinker for suggesting this year's Edge Question and to Daniel Kahneman for advice on its presentation.]

164 contributors, many whose names you will recognize, participated.

Any thoughts of your own? Go here to comment.

(Note: Interesting, how many key words from medicine easily come to mind, yet medicine has slowly been moving away from a materialist paradigm, as Mario Beauregard and I noted in The Spiritual Brain. )

Hat tip: Stephanie West Allen at Brains on Purpose