Gene duplication and molecular promiscuity

Head over to the Scientific American blog for a post that discusses a recent article suggesting a link between gene duplication and the promiscuity of enzymes involved in secondary metabolism in plants. Since gene duplication frees up one copy of the gene to "experiment", it can potentially accumulate mutations that confer the ability to bind and process more than one substrate. We should partly thank gene duplication for giving us many secondary metabolites which are used as drugs (both recreational and non-recreational), flavors and food products.

When Iron and Bacteria tragically collide: From the Middle Ages to the University of Chicago

Science brings us the bizarre, tragic but medically fascinating story of Malcolm Casadaban, a microbiologist working with plague bacteria at the University of Chicago, who died unexpectedly in 2009 of a then-unexplained cause. Obvious culprits were the plague bacteria he worked with. But the bacteria had been specially attenuated to be harmless in humans. So how could they kill?

It turned out that Casadaban had been the victim of an unfortunate double coincidence where two extremely rare causes combined to produce a lethal combination. It turns out that the plague bacteria he was working with had been rendered impotent by knocking out specific proteins which metabolize iron. More specifically they were engineered by knocking out a gene called pgm which codes for a protein allowing the bacterium to absorb iron from its surroundings. Iron is as essential to bacteria as it is to humans, and in the absence of iron-absorbing proteins the bacteria were useless as pathogens. Except that in this case they were not. Casadaban also suffered from hemochromatosis, a rare genetic disorder known for hundreds of years that causes the body to lock down stores of iron resulting in iron overload. From here it's not hard to put two and two together; when the iron-starved bacteria were suddenly introduced to Casadaban's body and its ample stores of the metal, they came to life like Frankenstein resurrected. The sudden windfall of virtually infinite stores of iron gave them the nutrient they lacked, transofrming them into a fatal force that killed Casadaban.

Very unfortunate, but utterly fascinating from a medical standpoint. The reason I find it even more interesting is that it seems to at least superfically contradict an equally fascinating story from the Middle Ages, and in the process provides a plausible explanation for what happened. There is a remarkable and horribly tragic piece of history that possibly supports the evolutionary benefit of a debilitating condition like hemochromatosis. In the Middle Ages, when the Black Death struck Europe on a terrible scale, Jews were often accused of bringing this malady into people's homes through some kind of mystic powers. Thousands of Jews were killed for the sake of this superstitious belief. And the fact that Jews as a population seemed to be less affected by the plague only encouraged the paranoia and madness. One of the reasons that's traditionally offered for this relative immunity is the hygenic kosher conditions which Jews practised which made their homes less attractive to rats. But another hypothesized factor is the higher prevelance of the hemochromatosis gene among Jews, especially Ashkenazi Jews who are widespread among Jewish communities. It seems that just like other bacteria, the plague bacterium Yersinia pestis needs iron to survive. By locking up iron stores, the bodies of Jewish individuals denied this valuable nutrient to Yersinia, which made the germ less successful in colonizing its victims. Thus hemochromatosis, while causing harm by storing excessive iron, might have compensated for that harm by serving as a defense against the deadly plague. This theory is quite controversial and may indeed be wrong, but it underscores the basic point that diseases which may seem to be presently harmful could have served a useful purpose in the past by defending against infections. Since Yersinia is largely no longer a concern in the modern world because of medical advances, we see only its ugly side.

But this seems to contradict what we have just heard. If hemochromatosis could deny iron to iron-starved plague bacteria in the Middle Ages, how could the same condition have the opposite effect on even more iron-starved bacteria in Casadaban's body? I don't know the answer, but a plausible explanation is that the ultra iron-starved, genetically engineered bugs simply evolved to be much more efficient at scavenging iron from Casadaban's cells than normal plague bacteria. We have all seen how the phosphorus-starved bacteria in the arsenic fiasco are widely thought to have evolved an ability to mop up and zealously guard phosphorus stores even more efficiently. When the going gets tough, the tough gets going, especially in the bacterial world. It is well-documented how remarkably fast bacteria can evolve their biochemical machinery to tide over unfavorable circumstances and efficiently utilize low concentrations of essential nutrients down to the last atom. It won't be suprising at all if the impotent bacteria in Casadaban's unfortunate body simply retooled to forcefully rip out iron from his cells and proliferate. A small, routine step for bacteria with giant, terrible implications for a human being.

What an unfortunate story, but it's implications are utterly sobering. It tells us how much we still don't understand about the risks of modifying genomes of simple organisms. Genetically engineered organisms can combine with naturally engineered human bodies in bizarre, unexpected and tragic ways. We may have started to come to terms with the synthetic modification of life, but we still have a long way to go before we understand how the different parts of the natural and artificial worlds dynamically interact with each other in ways that we cannot anticipate. There's miles to go before we can sleep.

Middle Ages March

As far as possible I try to avoid writing about the teaching of evolution and opposition to climate change in this country because of their overly politicized nature, but this piece in the NYT is one that no one can wisely ignore. It details a growing movement to conflate rejection of evolution with rejection of climate change that many people, and sadly especially conservatives, are spearheading. States are trying to introduce bills encouraging the teaching of “all sides” of scientific issues. Conservative politicians are advocating for students to know “all the facts”. But nobody is fooled by these thinly veiled promotions of ignorance...


...Read the rest of this post on the Desipundit blog

Coyne vs Dawkins

This year being Darwin's 200th birth anniversary, we have seen a flurry of books on evolution. Out of these two stand out for the authority of their writers and the core focus on the actual evidence for evolution that they provide; Jerry Coyne's "Why Evolution is True" and Richard Dawkins's "The Greatest Show on Earth". I have read Coyne's book and it's definitely an excellent introduction to evolution. Yet I am about 300 pages into Dawkins and one cannot help but be sucked again into his trademark clarity and explanatory elegance. I will have detailed reviews of the two books later but for now here are the main differences I can think of:

1. Dawkins talks about more evidence than simply that from biology. He also has evidence from history, geology and astronomy.

2. Dawkins's clarity of exposition is of course highly commendable. You would not necessarily find the literary sophistication of the late Stephen Jay Gould here but for straight and simple clarity this is marvelous.

3. A minor but noteworthy difference is the inclusion of dozens of absorbing color plates in the Dawkins book which are missing in Coyne's.

4. Most importantly, Dawkins's examples for evolution on the whole are definitely more fascinating and diverse than Coyne's, although Coyne's are pretty good too. For instance Coyne dwells more on the remarkable evolution of the whale from land-dwelling animals (with the hippo being a close ancestral cousin). Also, Coyne's chapter on sexual selection and speciation are among the best such discussions I have come across.

Dawkins on the other hand has a fascinating account of Michigan State University bacteriologist Richard Lenski's amazing experiments with E. coli that have been running for over twenty years. They have provided a remarkable window into evolution in real time like nothing else. Also marvelously engaging are his descriptions of the immensely interesting history of the domestication of the dog. Probably the most striking example of evolution in real time from his book is his clear account of University of Exter biologist John Endler's fabulous experiments with guppies in which the fish evolved drastically before our very eyes in relatively few generations because of carefully regulated and modified selection pressure.

Overall then, Coyne's book does a great job of describing evolution but Dawkins does an even better job of explaining it. As usual Dawkins is also uniquely lyrical and poetic in parts with his sparkling command of the English language.

Thus I would think that Dawkins and Coyne (along with probably Carl Zimmer's "The Tangled Bank" due to be published on October 15) would provide the most comprehensive introduction to evolution you can get.

As Darwin said, "There is grandeur in this view of life". Both Coyne and Dawkins serve as ideal messengers to convey this grandeur to us and to illustrate the stunning diversity of life around us. Both are eminently readable.

Can natural sciences be taught without recourse to evolution?

That's the question for a discussion over the American Philosophical Society museum website. I think the answer to the question would have to be no. Now of course that does not mean it's technically impossibly; after all before Darwin natural sciences were taught without recourse to evolution. But evolution ties together all the threads like nothing else, and to teach the natural sciences without it would be to present disparate facts without really connecting them together. It would be like presenting someone with a map of a city without a single road in it.

In fact natural sciences were largely taught to us without recourse to evolution during our high school and college days. Remember those reams of facts about the anatomy of obscure animals that we had to memorize. If it wasn't the hydra it was the mouse. If not the mouse then the paramecium. I can never resent my biology teachers enough for not connecting all these animals and their features through the lens of evolution. What a world of difference it would have made if the beauty of the unity of life would have been made evident by citing the evolutionary relationships between all these exotic creatures.

In fact "Evolution" was nothing more than a set of two clumsy textbook chapters that got many of the details wrong and left countless other facts wanting. Granted, some of the teachers at least had good intentions, but they just didn't get it. Teaching biology without constantly referring to evolution is like asking someone to learn about a world without using language. Would you teach physics without recourse to mathematics? Then you should not teach biology without recourse to evolution, at least not in the twenty first century.

YEAR OF CHARLES



Two hundred years ago this day, Charles Darwin was born. The vision of life that he created and expounded on transformed humanity’s perception of its place in the universe. After Copernicus’s great heliocentric discovery, it was Darwin’s exposition of evolution and natural selection that usurped human beings from their favoured place at the center of the universe. But far from trivializing them, it taught them about the vastness and value of life, underscored the great web of interactions that they are a part of, and reinforced their place as both actor and spectator in the grand ball game of the cosmos. Not only as a guiding scientific principle but as an all-encompassing element of understanding our place in the world, evolution through natural selection has become the dominant idea of our time. As the eminent biologist Theodosius Dobzhansky put it quite simply, nothing in biology makes sense except in the light of evolution. Evolution is a fact. Natural selection is a theory that is now as good as a fact. Both evolution and natural selection happen. And both of them owe their exalted place in our consciousness to a quiet, gentle and brilliant Englishman...

...Read the rest of the post on my Desipundit blog

WHERE ARE ALL THE ENLIGHTENED MUSLIMS?

This poll result from a recent Science article should make any reasonable, rational person shudder


Copyright: Science, 2008

Neglecting the rather pleasantly heartening observation that the 'backward' Kazakhs are more enlightened than their fellow Muslims, the fact delineated in the article that there apparently are virtually no Young-Earth creationists is hardly soothing in light of these results. After taking a look at this, is it surprising that the 'moderate' Muslims are not stepping forward in large throngs to condemn their fellow Muslims' killing of innocents? The problem is not of moderates versus extremists. The problem is of mindsets that fan irrational behaviour based on rejection of world-views which are bolstered by mountains of evidence. The question we have to ask, not just of Muslims but also Christians, Jews and other deeply religious people, is whether they will truly be able to condemn their fellow religious travelers' acts of terrorism based on a reasoned and rational response? They may possibly do it for reasons of pragmatism, perhaps reasons related to political expediency or perhaps related to survival itself. But that is still a quite different stance from condemning such acts because they are as far from reason as we can imagine. Believing in evolution is not necessary for deploring these acts. But I think that a world-view as firmly grounded in reason and evidence as evolution can be a convenient yardstick to map out the general mentality of a population. Of course such surveys turn up disconcerting results in the most advanced country in the world too, namely the United States. Christians are no less ignorant than Muslims. But even in secular countries like Turkey, the Muslims seem to beat the Christians in terms of sheer numbers.

The concept of the moderate Muslim is dealt another blow by polls taken in the Muslim world regarding suicide terrorism. As Sam Harris documents in his book The End of Faith, polls regularly show that 20% of people even in Turkey answer "Yes" when asked "Is suicide bombing in defence of Islam ever justified". Given the population of Turkey, this is a huge number in terms of absolutes. Are we to believe that 14 million Turkish Muslims are Jihadi fundamentalists? That would stretch the imagination of even the most paranoid person. Indeed, probably 13.8 million out of these 14 million call themselves 'moderate' Muslims and live peaceful and pious lives. And yet they readily agree that suicide terrorism in the service of Islam can be justified at least under some circumstances. The proportion of such people in other Muslim countries is unspeakably high. There is a genuine problem here that transcends political, educational and socio-economic disparities.

Now it's also true that there is a substantial proportion of the population cited as "not having thought about evolution". To me it seems that members of this population would be of two kinds; those who basically just don't think about the topic and think it's irrelevant to their lives, and those who have given it some thought and are genuinely undecided about it. One may then think that the latter group stands a good chance of emerging as the next faction of progressive, moderate Muslims who would institute reform. But how can this happen? This latter group is going to be a weak-voiced minority in a majority that won't allow them to get an influential platform for their views. Much has been said about how Islam can only be reformed "from the inside". While this statement will always ring true, what exactly would be the source of this inside reform? It's not that there is suddenly an influential springboard which will serve as a political or social vehicle for transformation. For example, a moderate Muslim who believes in evolution and stresses its acceptance is probably not going to be elected to high public office, just like in the United States. Even if he wants to spread his message, how will he do it? The schools are mostly religious ones, with few secular ones that are going to take on the task of solidly educating their students about evolution. Even if the schools wanted to do it, there would be a pronounced backlash from many parents. Thus society itself would be largely hostile or passive to such a moderate Muslim's views.

As Harris says, the progressive position is also perceived as being theologically bankrupt; after all they are trying to argue against Muslims who are more devoutly following the Holy Book and therefore have already assumed the high ground. We have seen what has happened to progressive and secular Muslims like Salman Rushdie and Ayaan Hirsi Ali. Such enlightened Muslims are simply not in a position to stay in their respective Muslim countries and bring about reform from inside; in fact they have already been condemned by many of their fellow Muslims. Their stories would clearly discourage any potential progressive recruit from treading the same kind of path. So to me it seems that the safest strategy for a so-called progressive and moderate Muslim would be to either silently suffer and tacitly accept the trappings of his culture and society, or to completely break out and defect to more secular countries, in which case his role in own country becomes meaningless. It's a catch 22 situation in which moderates have to either accept the opinion of the majority, or become pariahs. In this light, I don't see a large-scale revival, let alone revolution, spearheaded by moderate and progressive Muslims anytime soon.

The point again is simple; as long as people have more or less blind and unquestionable faith in their Holy Book, as long as they more or less worship their favourite Invisible Man in the Sky, the distinction between moderate and extremist is bound to turn cosmetic. Moderates who may despise the details of the execution of the fundamentalists' actions may nevertheless at least tacitly agree with their stated goals. Even moderate Muslims (or Christians and Jews for that matter) would think that the world would be a better place if everyone in it was Muslim. And as long as this attitude persists, we cannot rid the world of religious fundamentalists.

WHO DESIGNED ELIZABETH HASSELBECK?

If one might believe that the ladies on The View should pontificate on evolution at all, then this quote from Elizabeth Hasselbeck should be heard. The topic of evolution comes up, and Elizabeth Hasselbeck quips that because when she sees cool handbags or shoes she asks which Italian designer designed them, so she also thinks that when she sees a person, she believes that he or she must have been designed too.



Clearly, whoever designed Elizabeth Hasslebeck could have done a better job; presumably She was too busy making her attractive. But there is a simple, honest way in which Hasselbeck could remedy her bad design and inject some order into it: read Ken Miller's Finding Darwin's God, still the clearest rebuttal to intelligent design and the old argument-from-complexity that she believes is evidence for God. Thank you.

PLEASE, DON'T STAND IN THE WAY OF THIS MAN

This is as sensible and assertive a statement about evolution that we can expect from a Presidential candidate

Do you believe that evolution by means of natural selection is a sufficient explanation for the variety and complexity of life on Earth? Should intelligent design, or some derivative thereof, be taught in science class in public schools?

Obama: I believe in evolution, and I support the strong consensus of the scientific community that evolution is scientifically validated. I do not believe it is helpful to our students to cloud discussions of science with non-scientific theories like intelligent design that are not subject to experimental scrutiny.

This is from the latest issue of Nature whose cover story is about the candidates' views on scientific issues, views that are going to be of paramount importance to the future well-being of this country. Nature asked the candidates 18 questions about science and technology, including questions about increasing funding for basic research, speeding up the track to permanent residency for talented foreign students, and pumping more funds into biomedical innovations.

Not suprisingly, McCain's camp declined to answer with specifics and Nature dug up relevant statements from his old speeches that mainly included boilerplate sound-bytes. Obama's camp on the other hand provided rather eloquent and clear answers that actually talk about facts. It's pretty amazing to hear answers that actually are filled with details about science. McCain's cast of "science" advisors looks like a Gilligan's Island outfit and includes HP chief Carly Fiorina (who thinks Sarah Palin is quite competent to be President), James Woolsey, a former CIA director and Meg Whitman, former CEO of EBay. This group seems as miscast for science as Sarah Palin is miscast for being Vice President. Obama's advisors on the other hand include some real scientists, including Dan Kammen from Berkeley and Harold Varmus from Sloan Kettering Cancer Center.

Obama would speed up the residency process for foreign students, minimize barriers between private and public R & D (this is going to be very important). And Obama is as clear about nuclear energy as anything else

What role does nuclear power have in your vision for the US energy supply, and how would you address the problem of nuclear waste?

Obama: Nuclear power represents an important part of our current energy mix. Nuclear also represents 70% of our non-carbon generated electricity. It is unlikely that we can meet our aggressive climate goals if we eliminate nuclear power as an option. However, before an expansion of nuclear power is considered, key issues must be addressed, including security of nuclear fuel and waste, waste storage and proliferation. The nuclear waste disposal efforts at Yucca Mountain [in Nevada] have been an expensive failure and should be abandoned. I will work with the industry and governors to develop a way to store nuclear waste safely while we pursue long-term solutions.

Most importantly, Obama promises to reform the political environment for scientific opinion; this would include appointing a Chief Technology Officer for the government and strengthening the President's Scientific Advisory Committee, a key source of scientific advice for the President that was abolished by the odious Richard Nixon

Many scientists are bitter about what they see as years of political interference in scientific decisions at federal agencies. What would you do to help restore impartial scientific advice in government?

Obama: Scientific and technological information is of growing importance to a range of issues. I believe such information must
be expert and uncoloured by ideology. I will restore the basic principle that government decisions should be based on the best-available, scientifically valid evidence and not on the ideological predispositions of agency officials or political appointees. More broadly, I am committed to creating a transparent and connected democracy, using cutting edge technologies to provide a new level of transparency, accountability and participation for America’s citizens. Policies must be determined using a process that builds on the long tradition of open debate that has characterized progress in science, including review by individuals who might bring new information or contrasting views. I have already established an impressive team of science advisers, including several Nobel laureates, who are helping me to shape a robust science agenda for my
administration.

This point is the most encouraging policy vision, after a 8 year tradition of bullying, manipulating, cherry picking, ignoring and roughing up science and objective facts. The cost of scientific ignorance will be progress in all its forms.

Reading this is like being immersed inside a gutter for all your life and suddenly coming up for fresh air in the bright sunlight with a gasp. This man deserves to lead this country. This country deserves to be led by this man.

THINKING ABOUT ALZHEIMER'S DISEASE AS HISTORIANS

Head slumped forward, eyes closed, she could be dozing — or knocked out by the pharmacological cocktails that dull her physical and psychic pains.

I approach, singing “Let Me Call You Sweetheart,” off key. Not a move or a flutter. Up close, I caress one freckled cheek, plant a kiss on the other. Still flutterless.

More kisses. I press my forehead to hers. “Pretty nice, huh?” Eyelids do not flicker, no soft smile, nothing.

She inhales. Her lips part. Then one word: “Beautiful.”

My skin prickles, my breath catches.

It is a clear, finely formed “beautiful,” the “t” a taut “tuh,” the first multisyllable word in months, a word that falls perfectly on the moment.

Then it is gone. The flash of synaptic lightning passes. That night, awake, I wonder, Did Pat choose “beautiful?” Or did “beautiful” choose Pat? Does she know?

This heartbreaking and sad account by a husband of his wife's early slide into Alzheimer's Disease (AD) reminds us of how much we need to do to fight this. I personally think that of the myriad diseases afflicting humankind, AD is probably the cruelest of all. Pancreatic cancer might kill you in three months and cause a lot of pain but at least you are in touch with your loved ones till the end. But this is human suffering on a totally different level.

The search for the causes of Alzheimer's disease continues, and I have recently been thinking in a wild and woolly way about it from an evolutionary standpoint. While my thoughts have not been well-formed, I want to present a cursory outline here.

The thinking was inspired by two books- one book which has been discounted by many, and another which has been praised by many. The lauded book is Paul Ewald's "Plague Time" which puts forth the revolutionary hypothesis that the cause of most chronic diseases is ultimately pathogenic. The other book "Survival of the Sickest" by Sharon Moalem puts forth the potentially equally revolutionary hypothesis that most diseases arose as favourable adaptations to pathogenic onslaughts. Unfortunately the author goes off on a tangent making too many speculative and unfounded suggestions, leading some to consider his writings rather unscientific. As far as I am concerned, the one thing that the book does offer is provocative questions.

On the face of it both these hypotheses make sense. The really interesting question about any chronic disease is; why have the genes responsible for that disease endured even after so many millennia if the disease kills you? Why hasn't evolution weeded out such a harmful genotype? There are two potential answers. One is that evolution simply has not had the time to do this. The other hypothesis, more provocative, is that these diseases have actually been beneficial adaptations against something in our history. That adaptation was so beneficial that its benefits outweighed the obvious harm that it caused. While that something probably does not presently prevail, it was significant in the past. What factor could possibly have existed that needed such a radical adaptation to fight it?

Well, if we think about what it has been that we humans have been fighting the most desperately and constantly ever since we first stepped foot on the planet, it's got to be a foe that was much older than us and more exquisitely adapted than we ever were- bacteria. The history of disease is largely a history of a fierce competition that humans and bacteria have engaged in. This competition plays by the rules of natural selection, and is relentless and ruthless. For most of our history we have been fighting all kinds of astonishingly adaptable bacteria and there have been millions of martyrs in this fight, both bacterial and human. Only recently have we somewhat eroded their malign influence with antibiotics, but hardly so. They still keep evolving and developing resistance (MRSA killed 18,000 in the US in 2005), and some think that it's only a matter of time before we enter a new and terrifying age of infectious diseases.

So from an evolutionary standpoint, it's not unreasonable to assume that at least a few genetic adaptations would have developed in us to fight bacteria, since that fight more than anything else has been keeping our immune system busy and our mortality high since the very beginning. But instead of thinking about genes, why don't we think about phenotypes, about the actual effects manifested? Hence arose the hypotheses that many of the age-old chronic diseases that are currently the scourge of humanity may sometime have been genetic adaptations against bacterial infection. While the harm that is done by these diseases is obvious, maybe their benefits outweighed that harm sometime in the past.

When we think of chronic diseases, a few immediately come to mind, most notably heart disease, diabetes, Alzheimer's and cancer. But one of the best cases in point that illustrates this adaptive tendency is hemochromatosis which is an excess of iron absorption and storage, and it was this disease that made me think about AD. A rather fascinating evolutionary explanation has been provided for hemochromatosis. Apparently when certain types of bacteria attack our system, one of the first nutrients they need for survival is iron. By locking down stores of iron the body can protect itself from these bacteria. It turns out that one of the species of bacteria that especially needs iron is Yersinia pestis, the causative agent of the black plague. Now when Yersinia attacks the human body, macrophages rally to the body's defense to swallow it. Yersinia exploits iron resources in macrophages. If the body keeps iron stores from macrophages, it will keep iron from Yersinia, which however will lead to a buildup of iron in the body; hence hemochromatosis. The evidence for this hypothesis is supposed to come from the Black Plague which swept Europe in the Middle Ages and killed almost half the population. Support for the idea comes from the fact that the gene for hemochromatosis has a surprisingly higher frequency among Europeans compared to others. Could it have been passed on because it protected the citizens of that continent from the plague epidemic? It's a tantalizing hypothesis and there is some good correlation. Whether it's true or not in this case, I believe the general hypothesis about looking for past pathogenic causes that may have triggered chronic disease symptoms as adaptations is basically a sound one, and in theory testable. Such hypothesis have been formed for other diseases and are documented in the books.

But I want to hazard such a guess for the causes of AD. I started thinking along the same lines as for hemochromatosis. Apart from the two books, my thinking was also inspired by recent research that suggests that amyloid Aß peptide- a nasty aggregated protein that is a ubiquitous signature in AD brains- binds to copper, zinc, and possibly iron to generate free radicals that cause damage to neurons. Damage they may cause, but we have to note that such damage is also extremely harmful to bacteria. Could amyloid have evolved to generate free radicals that would kill pathogens? Consider that in this case it's also serving a further valuable function akin to that in hemochromatosis- keeping essential metals from the bacteria by binding to them. This would serve a 'double whammy'; denying bacteria their essential nutrients, and bombarding them with deadly free radicals. The damage that neurons suffer would possibly be a small price to pay if the benefit was the death of lethal microorganisms.

For testing this hypothesis, I need to know a couple of things:

1. Are there in fact bacteria which are extremely sensitive to copper or iron deficiency? Well, Yersinia is certainly one and in fact most bacteria are to varying extents. But since AD affects the brain, I am thinking about bacterial infections that affect the brain. How about meningitis caused by Neisseria, one of the deadliest bacterial diseases even now which is almost certainly a death sentence if not treated? Apart from this, many other diseases affect the brain if left untreated; the horrible dementia seen in the last stages of syphilis comes to mind. Potentially the brain would benefit against any of these deadly species by locking its stores of metal nutrients and generating free radicals to kill them, a dual function that amyloid could serve. I have not been able to say which one of these bacteria amyloid and AD might have evolved against. Maybe it could have been against a single species, maybe it could have been a general response to many. I am still exploring this aspect of the idea.

2. More importantly, I need epidemiology information about various epidemics that swept the world in the last thousand years or so. In the case of hemochromatosis, the causative stimulus was pinned down to Yersinia because both the disease mechanism and the pandemic are documented in detail. I cannot easily find such detailed information about meningitis or syphilis or other outbreaks.

3. In addition, while risk factors have been suggested for AD (for instance the ApoE epsilon4 gene variant), no specific genes have been suggested as causal factors for the disease. There is a clear problem with correlation and causation in this case. Also, the important role played by environmental factors such as stress and diet is becoming clear now; it's certainly not an exclusively hereditary disease, and probably not even predominantly so.

4. Most importantly, I think it is impossible to find instances of AD occurences in history for a simple reason-the disease was simply unknown before 1906 when Alöis Alzheimer first described it. Even today it is not easy to make an assessment of it. All cases of Alzheimer's before a hundred years back would have been dismissed as cases of dementia causes by old age and senility. Thus, while the causative hypothesis is testable, the effects are hard to historically investigate.

The fact that AD is a disease of age might provide some credence to this hypothesis. Two things happen in old age. Firstly, the body's immune defenses start faltering, and this might need the body to marshall extra help to fight pathogens. Amyloid might do this. Secondly, as age progresses evolution is less worried about the tradeoff between beneficial and harmful effects because the reproductive age has already passed. So the devastating effect of AD would be less worrisome for evolution. Thus, the same AD that today is thought to reduce longevity would have ironically increased it in an age where infection would have reduced it even further.

However, if AD is an adaptation especially for old age, then it begs a crucial question; why would it exist in the first place? Evolution is geared toward increasing reproductive success, not toward increasing longevity. There is no use as such for a rather meticulously developed evolutionary adaptation that kicks in after reproductive age has passed. I think the answer may lie in the fact that while AD and amyloid do affect old people, they don't suddenly materialize in old age. What we do know now is that amyloid Aß is a natural component of our body's biochemistry and is regularly synthesized and cleared from the brain. Apparently in AD something goes wrong and it starts to suddenly agglomerate and cause harm. But if AD was truly an adaptation in the past, then it should have possibly manifested itself in younger age, perhaps not a much younger age but an age where reproduction was still possible. Consider that for evolution some dementia is much preferred to not being able to bear offspring, and so AD at a younger reproductive age would make evolutionary sense even with its vile symptoms. If this were true, then it means that the average age at which AD manifests itself has simply been increasing for the past thousand years. It would mean that AD is not per se a disease of the old; it's just become a disease of the old in recent times.

So after all the convoluted rambling and long-winded thought, here's the hypothesis:
Alzheimer's disease and especially Aß amyloid is an evolutionary adaptation that has evolved to kill pathogens by binding to key metals and generating free radicals

There are several details to unravel here. The precise relationship between metals, amyloid and neuronal damage is yet to be established although support is emerging. Which of the metals really matter? What do they exactly do? The exact role that amyloid plays in AD is of course under much scrutiny these days. And what, if anything, is the relationship between bacterial infection and amyloid Aß protein 'load' and function in the body? Which bacteria really matter?

In the end, I suggest a simple test that could validate at least part of the hypothesis; take a test-tube filled with fresh amyloid Aß protein, throw in metal ions (copper, iron, zinc, etc.), and then throw in bacteria that were thought to be responsible for major epidemics throughout history. What do you see? It may not even work in vitro- I wonder if it could be tried in vivo- but it would be worth a shot.

Now I will wait for people to shoot this idea down because we all know that science progresses through mistakes. At least I do.

GREAT IS AS GREAT DOES

Comparing which historical figure was "greater" than another one is a titillating, entertaining and often ultimately futile exercise. Yet we love to indulge in it. I myself have done it before. Sometimes such a comparison can actually give us insights into history or personality; more often it essentially boils down to demonstrating personal preferences and likings.

With such a frequently flimsy rationale for comparing personalities, one had better come up with valid cases. Comparing Churchill and FDR is fine in this context, Newton and Einstein is probably a little unwarranted (considering that they lived in vastly different times). As Silvan Schweber has demonstrated in his recent beautiful book, Oppenheimer and Einstein is a worthy comparison.

But Charles Darwin and Abraham Lincoln?? Even an amateur would have a hard time thinking of such a pointless and disparate comparison. And yet we can always trust the mainstream media for a steady supply of sub-amateurish dilettantes who get paid for entertaining their own personal quirks and musings. In this case it's Newsweek which actually has managed to turn this comparison into a cover story. The reason for the comparison? A very serious one; it turns out that both Darwin and Lincoln were born on the same day...

There are other reasons many of which are trivial; the fact that both men were riddled with depression often in their life, were workaholics, harbored doubts about their religious convictions, and were compulsive scribblers. I am pretty sure that Newsweek would have found a hundred pairs of "great" people who share such events and qualities. With such a trite and pointless comparison, I myself don't want to spend more than a paragraph on it. But what I found curious was the article's conclusions. If "greatness" were defined in terms of impact and influence of ideas, Darwin is of course the hands down winner. Or so you would think. In fact the title of the article is "Who was greater?" and that should be an easy one. But this is America, and it's that fact that makes the article more interesting. To be fair, it is well-written. That's not the criticism. The criticism is that it seems to be written by someone who on a whim thought of writing about Darwin, and then because of no particular reason thought of writing about Lincoln, and then wanted to combine the two together in some ad hoc way. And the last line makes it clear what the author's goal was all the way along- "Answer- Lincoln"

Clearly Lincoln is enormously important for Americans, with polls regularly putting him at the top of the "greatest presidents" list (although the lists are always to be taken with more than a pinch of salt, especially considering that Ronald Reagan also usually makes it into the top 5). Lincoln abolished slavery and definitely belongs on the great Americans list. But Lincoln was not a complete slavery-hater all life, as weren't many of his predecessors and contemporaries. Although this might reflect the very different outlook on this practice during those times, it does call into question Lincoln's "greatness". However, it's worth giving him the benefit of doubt and noting that at least on a relative basis he was one of the most outspoken opponents of slavery during those times. But other facts also need to be considered. It has been argued by many humanists and historians that the Civil War was unnecessary for abolishing slavery. Many diverse figures including Freeman Dyson and Ron Paul have said for example, that England got rid of slavery by buying the slaves. Perhaps this attitude would not have worked with slave-happy Southerners in white America. But did Lincoln try? Did others try hard enough?

I am not trying to put a blemish on Lincoln's stature, but considering him great begs answers to these questions. He was definitely a wise, honorable and astute man. But that does not mean his achievements go down in history unquestioned.

Now Darwin. His theory had a great impact on the whole world. It answered perhaps the single most important question that we as human beings can ask ourselves; Who are we? Where do we come from? Darwin not only discovered the answer to this question but in the process also discovered an overriding theory of unparalleled elegance and all encompassing generality that explained our origins and our journey into the past and the future. What I personally find really astonishing about Darwin is how many of his predictions came to be true. Some of his ideas were discounted, but so many of them have stood the test of time and are in fact being corroborated every single day. That he could make these predictions in spite of the absence of any knowledge of genetics, hereditary mechanisms and intact human fossils is really extraordinary.

Newsweek dug itself into a ditch by trying to compare two very different and completely unrelated people. That should have made the answer to the question "Who was greater?" very simple. In terms of influence, Lincoln changed a country but Darwin changed the whole world and our future.

But emblematic of modern day America, the magazine in fact leans towards saying that Lincoln was greater. The main point here, not entirely unreasonable, is that Darwin's theory is greater than the man, while Lincoln's ideas could have come only from himself. However, "Darwin's theory" involved a truly enormous amount of field work, rumination, classification and ratiocination that Darwin individually did. Evolution and natural selection may have been discovered by others, but it would have taken long efforts by many to reach such a stage. Exceptional credit belongs to Darwin simply for thinking of so many things and weaving them coherently together.

On the other hand, slavery and mistreatment of minorities did not go away in America for another hundred years after the Civil War. Lincoln made a substantial difference in the short-term, but even he could not instantly eradicate perhaps the greatest evil this country has seen. On a practical basis Lincoln did not change the face of slavery in the United States. His importance seems more symbolic than substantial; a President who put his foot down and officially declared that one of the oldest human institutions which had been taken for granted for years had always been a great moral travesty.

But far and away, what is more telling for me is that if you take a poll and ask the general public "Who was greater?", they would side even more with Lincoln. And not just because he was their president, but because in no other developed country today are there as many public opponents of "Darwinism" as in the United States. The reasons are many; religious, political and in many cases, plain ignorance of the beauty and applicability of natural selection. But whatever the reasons are, this is what it is.

And that is the real tragedy of this comparison. Not the fact that the comparison is trite and superficial. Not the fact that you are comparing apples and oranges. But the fact that the magazine's conclusions will be mirrored in a greatly amplified manner by the general population of this country.

P.S. For all the complexities of comparison, ask me who I think was the greatest American president and I will say "F.D.R." without batting an eyelid. And before that, I think we will have to go back to Jefferson to find a truly great and important president.

THE REAL PROBLEM WITH DINESH D'SOUZA IS..

...nobody knows. Nobody knows if D'Souza's real problem is self-delusion, political pandering or plain ignorance. It's probably a complex combination of all three, demonstrated colorfully as in his latest piece, "The real problem with Darwinism". Note that by saying "Darwinism" in the title D'Souza has already created the illusion that it is some dogmatic school of thought like postmodernism. D'Souza's contention is commonly trotted out by religious conservatives these days since it conveniently sets up a limp straw man which these brave defenders of truth then pummel to death.

The rest of D'Souza's piece proceeds along similar insipid lines. The opening statement sets the tone:

"The real problem with Darwinism in the public school classroom is that it is often taught in an atheist way. Textbooks by biologists like William Provine and Richard Dawkins routinely assert that evolution has done away with the need for God"

Ok, now there are two issues here. Firstly, no biology professor in his right mind would rant about atheism in a science class. However, the real important point is that a careful study of evolution must lead, and in fact beautifully leads to the conclusion that you don't need to believe in a supernatural creator of the world to understand the diversity of life. In so far as that conclusion is "atheist", teaching evolution without explicitly stating that conclusion nonetheless can lead any intelligent person to believe in atheism, at least as it applies to the creation and functioning of the world.

And as far as D'Souza's second statement is concerned, D'Souza must be confusing the good professor with someone else. At least I am not aware of any school biology textbook written by Dawkins. The least this exuberant intellectual can do is get his facts right, right?

Moving on, there is one thing on which I wholeheartedly agree with Dinesh, that Christian evangelicals have not made any dent in the teaching of evolution (although their efforts are admirable):

"Typically evangelical Christians seek to counter this atheism by trying to expose the flaws in the Darwinian account of evolution. This explains the appeal of "creation science" and the "intelligent design" (ID) movement. These critiques, however, have not made any headway in the scientific community and they have also failed whenever they have been tried in the courts. Fortunately there is a better way."

Just one thing, this ineffectiveness in getting religion across is not because of some dogmatism on the part of scientists but because of the sheer bullheadedness of the evangelicals' wayward arguments. But is there really a better way for evangelicals to forcibly impose their views upon secular education? I am all ears now...

Yes!, says our resourceful Dinesh:

"I'd like to see Christian legal groups suing school districts for promoting atheism in the biology classroom. No need to produce creationist or ID critiques of Darwinism. All that is necessary is to parade the atheist claims that have made their way into the biology textbooks and biology lectures. The issue isn't the scientific inadequacy of evolution but the way in which it is being used to undermine religious belief and promote unbelief. If the case can be made that atheism is being advocated in any way, then the textbooks would have to be rewritten and classroom presentations changed to remove the offending material. Schools would be on notice that they cannot use scientific facts to draw metaphysical conclusions in favor of atheism.

Note how D'Souza flippantly mentions the "scientific inadequacy" of evolution as if it were a given. This is about the time when sensible people give up reading but let me make a feeble effort to react before I walk away with disgust. First, prove your goddamn assertion! Don't just say that biology professors "teach atheism". I have a proposition; sit in biology classes around the country for a year, maybe you can even send undercover students to do your dirty job, and note how many professors "preach atheism". However, this is really another straw man, a favourite staple of D'Souza. As I mentioned before, a careful teaching of evolution and examination of the evidence compellingly leads to the conclusion that the world has no need for a supernatural designer to prove its existence. So now D'Souza wants to sue us even if it's the evidence and not our beliefs or opinions that lead to atheism.

And

"Schools would be on notice that they cannot use scientific facts to draw metaphysical conclusions in favor of atheism"??

No, schools don't use scientific facts to draw metaphysical conclusions in favor of atheism. All they do is draw logical conclusions based on the very much physical world. If these conclusions inevitably point to a world without design, it's not our problem that they bother your timid, paranoid minds. Grow up.

Past posts on D'Souza's dazzling erudition: 1, 2, 3

WHAT DOES MICHAEL BEHE EXACTLY TEACH?

Here's something I wonder about creationist/IDist Michael Behe- what does he say in class? He is a tenured professor of biochemistry at Lehigh University. Lehigh has a disclaimer on their site divorcing themselves from his creationist views and emphasizing nicely that the real and perhaps only reason ID cannot be taught in science classes is because it is not science. Period. (Noted by Sandwalk)

But I wonder what Behe teaches in his classes if he teaches them at all. If you are teaching a biochemistry or biology class, you cannot help but occasionally run into evolutionary concepts. In fact biochemistry is one of those disciplines which has provided significant support and credence for evolution. The discovery and analysis of homologous proteins can help trace the tree of life and biological ancestry. I wonder how Behe tackles these topics in class. Is he like a zombie who when in class has no problem saying that evolution is true, and then switches to "creationist mode" when he walks out of class? I would sure like to sit through some of his lectures.

As an aside, while the disclaimer says that he is entitled to his views, he almost certainly does not mention ID in his class, otherwise he could, and should, be fired. That's what makes me wonder even more just what is it that he exactly mentions in his classes.

AS BAD AS IT GETS: A DEBATE WITH TWO SURPRISINGLY CREATIONIST GENTLEMEN

How a debate with two friends about creationism turned into a defense of science itself...

Read the rest of the entry on Desipundit...

FINNISH SCHOOL SHOOTING AND DARWINISM

A gunman has shot seven others in a tragic Finnish school shooting. For once the perpetrator was "captured" alive. Apparently he posted a YouTube video of himself before the shooting:

"The video shows a picture of a building by a lake and two photos of a young man holding a gun. Going by the username Sturmgeist89, the person who posted the video calls himself a "social Darwinist" who would "eliminate all who I see unfit". "Sturmgeist" means storm spirit in German."

Clearly we need to stop teaching Darwinian evolution in schools; that's the kind of freaks it engenders. Clearly we also should stop practising capitalism; in a socialist society Paris Hilton would never have had the kind of wealth she has to splatter herself all over the press.

MILES TO GO BEFORE...

A recent and highly promising trial of an HIV vaccine has failed and shown depressing results. This setback reminds us of how complex a problem HIV/AIDS is, with so many daunting scientific, economic, political and sociocultural ramifications...

Read the rest of the post on Desipundit...

WHY IT'S HARD TO ARGUE WITH THEM

It's obvious that both global warming and evolution are supported by reams of evidence, yet why are people so loathe to accept this? There are of course many many reasons and answers to this question, some of which I have discussed on this blog. But on a public basis, what I think is quite key is the simple fact that it's easy to dissent, but relatively difficult to justify. By "difficult" I certainly don't mean that it's actually difficult to justify the evidence for global warming or evolution. In fact that's extremely simple because the evidence is right there in front of us.

But what's dificult is to justify and explain viewpoints from a public debate standpoint. Consider a global warming debate in which a dissenter throws around a 10 second general objection, for example, "Computer models can be unpredictable because they are built on assumptions". This statement is much easier for the lay public to understand because it represents a pretty general fact that is true in many cases. Now it's the climatologist's turn to defend himself. This is going to take much more time because he or she would have to explain how it's true that computer models can be unpredictable, but how researchers take this uncertainty into account, run multiple simulations, weed out fudge factors, do statistical analyses coming up with multiple scenarios, and assign degree of confidence to predictions. This knowledge is surely out there, but it's quite obvious that the climatologist is going to take more than the 10 minutes alloted response time to explain this. And with good reason; although the punchlines of science can be simple, actually explaining science often takes time, and that too with good reason, since science wants to do as thorough a job of analysing the data and drawing conclusions as it can.
But the lay public often does not see this. What they think is that the climatologist is unable to answer the dissenter's objections in 10 minutes. They take this to mean that he cannot defend himself. In the public's eyes, the dissenter has scored points.

A similar example exists for evolution, where actually the argument should be much simpler, but unfortunately it's not. Some dissenter (or god forbid, ID guy) will say something like "The bacterial flagellum is too complex to have arisen through chance". Not withstanding the fact that this statement is just plain wrong ("change" is not operating here), we have to admit that the bacterial flagellum does at least look complicated for the layman. But now, when the biologist has to answer this objection, he needs to demonstrate how each part of the flagellum has counterparts in other organisms, how even "half a flagellum" can actually work, and how the flagellum has actually arisen as a result of a mix-and-match kind of strategy adopted by natural selection. He would also have to explain the experiments leading to these conclusions. The explanation is elegant and extremely persuasive, but naturally it will take more than the allocated 10 minutes, leading laypeople to believe that perhaps the disssenter has a point.

The reason why this situation is unfortunate is because the burden of proof is always put on the scientist, when it is actually on the dissenter who has to prove his point. But the public often does not understand this, because they don't understand the weight of scientific evidence that strengthens the scientist's positions. Understanding this evidence itself will take some reading and exploring, but what they want is a 10 minute (or less) answer. Unfortunately for the public, the very fact that something can take more time to explain means that it may be dubious. Needless to say, this is absurd for obvious reasons.

In addition to this problem, such dissenters also are usually good at rhetoric, since unlike scientists, they have spent most of their time practising it in the absence of actual evidence to support their claims. Scientists are often not very good at rhetoric since don't feel a need to be a good at that, and rightly let the evidence speak for itself. But that means that in public debates, where the public is unfortunately more easily swayed by rhetoric, they are inherently pitted on the hard side.

A similar situation also exists for people in non-scientific fields. Noam Chomsky has made the good point that he is always on the losing side in a short television debate, because the objection of the dissenter is a 10 second statement which reflects what's expressed by the conventional media. Since it's already there in the papers and on TV, people already know this, so all he has to do is to state it. On the other hand, when Chomsky needs to counter his point, he needs to reference and cite non-conventional and minority sources that the public has not heard of. Clearly, this is a more time-consuming task. Unfortunately, Chomsky has only 10 minutes to respond, so he cannot do this convincingly in those few minutes. The result is that the public goes away with a false impression that Chomsky is wrong and the dissenter is right.

This situation is rife throughout the media. It is inherent in every interview that TV channels do and every talk show where guests are invited to present their views. In each and every one of these cases, there is a potential and many times actual risk of the public getting the wrong impressions simply because someone does not have enough time to make their views clear.

There is no clear-cut solution to these problems except to educate the public through means other than the 10 minute segment shows. In that respect, the books written by Chomsky or climatologists or evolutionists and many others serve an absolutely essential and admirable function. But the public also should be informed about this very point; that they should not trust debates held in a studio that last for 30 minutes, with 10 minutes alloted to each speaker. Because in such a case, they are almost always going to get a biased impression, no matter how convincing it seems.

IT'S NOT ABOUT THE SCIENCE

A pretty amazing debate has been going on in the webpages of Amazon.com. But first, a little about what it is about. The webpage is the one displaying Michael Behe's "Darwin's Black Box", a book that has stirred up unnecessary muck, although not unpredictably. Behe is a biochemist with some credible credentials, but incredible assertions. He is the infamous guy who popularised the concept of "irreducible complexity" in the late 1990s. Behe's contention simply put was (and is) that the biological world is so complex, that only a designer could have made it. That's because if we considered any one of the tiny, fundamental units of life, such as an eye, it is quite clear that taking away any one of the myriad parts that comprise the eye would render it completely non-functional. Thus, it is inconceivable (to Behe) that the eye could have actually evolved gradually, and that all the parts should have been put together, already formed, by some intelligent designer. Enter ID, creationism in a dapper although embarrassingly ostentatious outfit.

There are holes as big as empty space in Behe's whole framework. In one fell swoop, he pushes so many issues under the rug that the rug can no longer bear the presence of all of them, and splits wide open. Behe makes a general philosophical argument, gives it a fancy name, and simply proclaims that it is true by default, the classic demonstration of the "argument from ignorance". He does not look at any contradictory evidence, and even when it is overwhleming, deems it insufficient without any justification. Most importantly, Behe offers not one iota of positive evidence for his own assertions, including the stupendous lack of explanation for the complexity of his intelligent designer who designed such a complex world. Science only partially progresses by elimination of alternatives. It needs solid positive proof to be useful and real. Also, a scientific theory does not collapse only because some detail in it is simply challenged. There are many details in evolution that are debated by scientists. But that does not mean that they don't believe in evolution itself, because there's monumental evidence from a stunning variety of scientific disciplines in support of the truth of evolution. In fact, it is staggering how many different questions in different fields seem to come under the purview of evolution as their answers are revealed everyday. In this context, I have to say that the efforts of Behe and his cronies to discredit evolution are an abomination upon science, and display at most a juvenile understanding of the scientific method.

But needless to say, Behe has been the poster boy for creationists in the last decade, who want to furtively bring creationism to the schools under the guise of scientific jargon. Behe deliberately has chosen the field of biochemistry for his crusade (and crusade is the right word, because his spiels are all based on faith), because he wants to enter creationism through the backdoors of hard science. Most of his creationist patrons probably don't even understand what he says, but no doubt dance with glee when they hear him citing scholarly notions and hijacking them to support his purpose.

Behe was also an apologist for the creationists in the infamous Dover creationist trial of two years ago, where twelve parents of school children had brought a suit against the teaching of creationism in science class. Behe was a defendent for the creationists, and among others, Kenneth Miller the Brown University Professor was an expert witness for the plaintiffs. One of Behe's arguments in Darwin's Black Box is that the immune system is too complex to have evolved by natural selection, ergo, it must have been, by default, designed. During the Dover trial, Behe was shown more than fifty peer reviewed journal publications that dealt with the evolution of the immune system. Not only could he not refute them, but he confessed that he had not read any of them. In the end, the attorney for the plaintiffs as well as the judge roundly scolded Behe and his ilk, and cited their "breathtaking inanity" for simply touting that complex structures arose by the work of an intelligent designer, and for implying that there surely could not be any need to actually study where they came from. In an embarrassing moment for Behe, the plaintiffs' attorney said that while serious scientists were engaged in studying the evolution of the immune system and finding new therapies for diseases, Behe and his sympathizers were not only misleading the public, but were doing absolutely nothing to advance the future of science and medicine. In fact, I feel more pity than anger for Behe, who is clearly an intelligent and educated person, and yet wants to waste his time advancing crackpot causes and not actually making a difference by doing scientific research.

The most vocal opponent of Behe has been Brown University professor Kenneth Miller, and I would strongly recommend his book "Finding Darwin's God" for anyone who wants a good understanding of evolution (including a clear refutation of the belief that evolution is a product of chance), as well a very spirited and convincing reply to Behe's assertions of irreducible complexity. The bacterial flagellum, probably the only example of a true motor in nature, is an astounding factoid of life's complexity. Without doing any research, Behe had again simply proclaimed that it was irreducibly complex. However, Miller showed that there are several examples of other flagella in nature, which show some of the components of the bacterial flagellum and yet work, even if not as well; what is most bothersome that Behe has frequently either not just been aware of the literature, or more believably has shown deliberate ignorance of it. This principle extends to all those other systems which Behe claims are irreducibly complex. The bottom line is, yes, many complex structures in nature can be shown to be made up of independently functioning partial components, and we can follow an evolutionary history for the presence of all these components. For those which are not, there is no reason whatsoever to believe that they were designed by any Yahweh or Zeus.
The humble and yet stunning eye was always one of the favourite targets of creationists, and they used to cite Darwin's own quip about his incredulity at the eye's functioning:

"To suppose that the eye with all its inimitable contrivances for adjusting the focus to different distances, for admitting different amounts of light, and for the correction of spherical and chromatic aberration, could have been formed by natural selection, seems, I freely confess, absurd in the highest degree."

They also conveniently ignore what he said next:

"Reason tells me, that if numerous gradations from a simple and imperfect eye to one complex and perfect can be shown to exist, each grade being useful to its possessor, as is certainly the case; if further, the eye ever varies and the variations be inherited, as is likewise certainly the case and if such variations should be useful to any animal under changing conditions of life, then the difficulty of believing that a perfect and complex eye could be formed by natural selection, though insuperable by our imagination, should not be considered as subversive of the theory."

There it is; The Reluctant Mr. Darwin demolished irreducible complexity a hundred and fifty years ago.

So, if Darwin himself laid to rest all such troubling questions about irreducible complexity more than a century ago (it is truly remarkable to discover how prescient- and right- the man was), why is there a 85 comment debate on the Amazon.com webpage showcasing Behe's book? The debate is in the comments section of a certain J.M. Ridlon, who seems to know evolution inside out. Incidentally, and again it should not be surprising, the book has received four stars and 575 reviews, which means that most of the reviews have been favourable. This can mean several things; firstly, that sensible people simply did not comment. But what I am more certain about is that most of the reviews were probably written by intelligent folks, probably and unnecessarily fence-sitters, who got impressed with Behe's scientific exposition and felt convinced that at the least, there were serious flaws with evolution. It's very sad if such a thing happened. To these of course we can gently say only one thing; read a good book. Start with Climbing Mount Improbable, that alone will suffice and help you understand evolution a little better.

On the other side of the debate is a cabal of dissenters who keep asking Ridlon to prove with complete certainty all the assertions that he makes. What surprises me is that even these dissenters seem to be intelligent and well-read, and yet they show a deliberately woeful ignorance of the scientific method. However, after trudging through the 83 comments and being highly impressed with Ridlon's knowledge of evolution, it becomes clear; these dissenters don't really want to prove evolution wrong and creationism right. In fact, the comments clearly show that they steer clear from trying to affirmatively expound upon creationism; not surprising since they don't have a shred of evidence for the existence of an intelligent designer. All they do is take potshots,some quite learned sounding ones, at evolution. And then it becomes clear; they want to create "reasonable doubt" about evolution to then allow creationism to be also taught as an "alternative theory" in classes. As it is with many other creationists, they want educators to "teach the debate" where there is none, and they are mustering every effort they can to try to actually convert their arguments into a true debate. After every comment, J.M. Ridlon has given a detailed response, showing how their arguments are wrong.

But now, I have a suggestion for him; J. M. Ridlon, don't bother. These folks are just out to make a political point, not a scientific one. This is not science, it is the manifestation of the dredges of human nature. So no matter how much you convince them about the known certainty of evolution, all they will do is ask, "But, are you one hundred percent certain?". When you, as a good scientist will say that of course not, but that does not tarnish evolution, they will simply turn Bill O'Reillyesque and shout "That's it! That means the whole theory is wrong. We are right, you are wrong!" Now, do we watch Bill O'Reilly except when we want some 'white noise' in the background to help us sometimes fall asleep? Then, J. D., I suggest that you do the same about this comment-fest. It's not about science.