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Reptoid Visions?

May 25th, 2009
Strange Landscape

Strange Landscape

I see a hot misty world with cloudy white skies and rain—endless torrential rain. Large fields are drained by sinuous ditches and grazed by unicorn-like cattle making noises like coo-loo-woo, loo-hoo-hoo. It is an alien world. Here and there are strange trees, some of them broken. But across a broad shallow river is dense woodland. Here and there are groups of large rocks but in the distant mist is a city built of cyclopean stones. Is it a city or just a rocky outcrop? A city, though I do not know its name. No.

The nameless city must have been built long ago… or perhaps it has yet to be built. A race of strange grey-green reptilian creatures appear in sculptured reliefs on the monumental stones of the ancient city. They might just seem reptilian, and the greyness and greenness could be just the moss growing on them, like a patina on old bronze. Yet they look somehow human. They had the power of magic, a subtle and sophisticated technology? They abhored rectilinear structures, preferring organic shapes. Had they somehow learnt how to “grow” their buildings, their technology?

The scene is changing. The mist has thickened and the sky darkened. The sun is fading and now can only be seen occasionally through smoky black clouds. The distant city has blackened before my eyes and is now covered in soot. The reliefs can no longer be seen. The grazing creatures are falling dead on the sward. They are dead and decaying. The ditches have putrefied to an oily stinking mass of corruption. I cannot see across the broad river. It has silted up completely leaving a morass of black bubbling sewage. I get faint glimpses through the gloom and can see the trees of the forest. They have changed. They stand like stick insects at strange angles, charred and dead. Some seem to be on fire.

Some great alien civilisation has been destroyed. Or is it a future civilsation?

Book Cover: Who Lies Sleeping?

Book Cover: Who Lies Sleeping?

Second Vision

I am laying on a large slab of cold stone in a sepulchral grotto or cavern. The light that illuminated the scene is faint and green as if transmitted through sea water. The cave was of huge stones cut with the low reliefs. Though the stone was hard and cold, I feel warm, comfortable and peaceful. I am surely asleep. The green colour is getting yet darker. The smell of decay has grown overwhelming. Great gobs of mud or tar are beginning to drip from the cyclopean rocks. They are smeared with festering putrefaction. I am stiff, uncomfortable and terrified. I hear a word echoing through the cavern, gradually getting louder from the total silence: “Awake! Awake!” But I cannot. I cannot awake.

Third Vision

I am floating as if on a magic carpet, lying in the sun, warm and secure. All I have to do is imagine something and it appears. At will, I can create rainbows and firework displays, floating billiard balls dancing before me and kalaidoscopic patterns. Now I have turned over and found myself floating just above the earth which was grey and sooty. Buildings stand derelict and decaying around me. At my feet are oily puddles full of trash and rusting cans. A distorted rat-like biped suddenly scurries from behind a broken-down building. It stops when it sees me. Its eyes open wide in terror, and it jabbered horrifically, stumbling backwards. I feel sick with revulsion for the stunted horror and its disgusting world. It is disgusting, a failure of evolution. I must kill it.

Fourth Vision

I am moving through vast canyons of monumental stones. Unrecognised friends pass me with a friendly greeting. The air is warm and clear, with beautiful scents of flowers drifting in from the nearby forests. Suddenly a rat scurrying behind a stone startles me. It seems unimportant and I walk on joyfully through familiar pathways. But again a scurrying creature surprises me, then another and another. They are emerging from everywhere—loathsome, naked, skinny, rat-like dribbling things like mole rats. They are a plague of locusts or soldier ants, running beneath my feet and beginning to scramble over me. They are inundating me, biting, tearing off strips of flesh. They are staring into my face grinning malignantly. I am screaming and fall, consumed by them.

Other Visions

There have been ages when other things ruled on the earth, and they had great stone cities. Remains are rarely, but still to be, found as cyclopean stones scarcely recognisable as constructions. Their builders all died vast epochs of time before man came, but there were conditions which could revive them when the cycle of being turned once more into the correct quadrant, when their successors proved to their makers that they had forsaken all responsibility for their tenancy as guardians of the earth.

And so it is not to be thought, that man is either the oldest or the last of earth’s masters. His predecessors wait—not in the world we know but at its edges. They rest asleep—tranquil, elemental and—except when they stir—unseen. For, after the Helliconian Spring of love and lust, the son-lover begins to sere the earth and the serpent is yet poised, motionless but alert, for its the moment to strike.

It is the serpent that conquers and enjoys the fruits of the tree of life. Must it ever be so?


Table of Contents


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by Mark Beljaars

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Big Step Towards Humanity around 250,000 Years Ago

January 21st, 2010

Early humans living in the Paleolithic—2.5 million years ago to about 10,000 BC—hunted and ate in groups to have better chances of survival. A cave in Israel has been found with meat remains from 400,000 to about 250,000 years ago in the late Lower Paleolithic, the period between the barely human and the essentially human. It shows that earlier barely human hunters in the Lower Paleolithic butchered meat differently from later essentially human hunters of the Middle Paleolithic. Both were adept at hunting large game. Many people had thought the barely human beings of the earlier period could not hunt at all, and were still restricted to scavenging.

Mary C Stiner a university of Arizona anthropology professor says evidence from Qesem Cave shows the earlier late Lower Paleolithic humans focused on harvesting large game just like later late Lower Paleolithic humans. They were at the top of the food chain.

The inhabitants of the cave through the millennia all hunted cooperatively, brought back the best pieces of meat from their prey back to the cave, used stone knives to prepare it and fire to cook it. But earlier hunters were less efficient, less specialized at butchering, partly because their tools were not as refined. By the start of the Middle Paleolithic, the now essentially human hunters made tool marks on bones that were less varied. Besides the stone tools being better, it seems only certain hunters or skilled people cut meat to be shared among the group. Possibly some people were already specializing in butchering.

These earlier people were skilled predators and were social, but their social rules were more basic, less derived than those of the Middle Paleolithic. There was a big difference between Lower and Middle Paleolithic social behaviors, but not between Middle and Upper Paleolithic social behaviors. Neanderthals lived in the Middle Paleolithic, and they were a lot more like we Homo sapiens of the Upper Paleolithic in their more careful, even formal, distribution of meat than were the earlier hominids.

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Who Lies Sleeping? Impossible to Find—Illogical Contraption

December 15th, 2009

Dung beetle yet to achieve intelligence

Dung beetle yet to achieve intelligence

Shelby Cobras at Illogical Contraption Blog writes:

We’ve all Google searched the word dinosauroid, correct?
Of course we have.

Then tells us about the blog Tetrapod Zoology by Darren Naish that we have discussed here not long back, because Naish reviews Who Lies Sleeping?. Indeed the review is the subject of Cobras’s page at Illogical Contraption. Cobras says:

Naish calls attention to another, far more obscure book and writer—Mike Magee and his paranoid 1993 pseudoscience rant Who Lies Sleeping?

It is a viewpoint and style of assessment all the more remarkable for the fact that Cobras confesses he has not read the book:

Long story short, this book sounds amazing but is impossible to find. Shiny nickels for anyone with any sort of information on where I can get a copy.

It brings us back to his first sentence about Googling the word dinosauroid, because it is something he cannot have done, or done only with Google’s “I’m Feeling Lucky” option, because otherwise he would have found the book, right, and maybe this website, eh? Illogical Contraption writers are fond of the word shit. Maybe they’re going to tell us the story of the intelligent dung beetles.

Anyway, Mr Cobras, if you Google a bit more effectively, you ought to be able to find your way to this website, where you can order the book at a discount if you wish, but you’ll have to pay shipping. Or, you could go to Amazon and order the book where, at amazon.co.uk, you can reserve a new copy for £7.19, a whole 80p less than the normal price ot £7.99. Unfortunately, Amazon has for a long time said it is out of stock and so we get no orders from them, potential readers doubtless being put off by the anticipated delay, unless, of course, Amazon UK is not willing to order single copies. But it says they have six second hand copies from £4.

Amazon US at amazon.com have five second hand copies from $44.33, but a big saving can be had by buying them direct from us, but we require cash to be sent before we send out the books. We are too obscure to make it worthwhile getting electronic card facilities from a bank. Yeah, I know, we should get PayPal, but it had such a bad reputation a few years back, it put us off. When we recover, doubtless we’ll use it. But give us time. We’re dinosaurs, they keep telling us!

It means the fall back is to order from us direct, but as we are impossible to find, Google being too hard to use properly for the Illogical Contraptioners, we will not be getting any orders from the dung beetles—alas! they have not yet evolved to the intelligent stage.

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Wikipedia on “Reptilian Humanoid”

November 4th, 2009

It is a curious thing that Wikipedia, the amateur online encyclopedia, has a reference—in its item sub voce “Reptilian Humanoid”—to Darren Naish’s blogged critique of Who Lies Sleeping?, the book about the intelligent dinosaur (the Anthroposaur) but it does not refer to Who Lies Sleeping? itself. It might be because Wikipedia has rules forbidding “original research”, research considered beyond the scientific pale—ie not peer reviewed and accepted—but obviously has no rules against criticizing such research. It does not seem too fair (Wikipedia editors should read J S Mill On Liberty), but, more importantly, it is scientifically absurd! Indeed it is dogmatism no different from the Church allowing criticism of heresy, but refusing anyone to read anything about heresies themselves except whatever the critics cited for the purpose of refutation! And just adding the appropriate citation is not requiring any contributor to include any inadmissible claims—it is merely showing where the intelligent reader can find them.

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Common Ancestor More Human Than Chimp Like?

October 23rd, 2009

Scientists excavating in the Middle Awash region of Ethiopia have dug up the skeleton of a new species of hominid, which they have named Ardipithecus ramidus (Ar ramidus), nicknamed Ardi. Ardi is the skeleton of a likely human ancestor, the oldest hominid found to date, 1.2 million years older than Lucy (Australopithecus afarensis).

The discovery began in November 1994 with the finding of two pieces of bone from the palm of a hominid hand. In the next few weeks, 125 additional bone fragments were found. Further excavating and reconstruction went on for the next one and a half decades. The nearly complete hominid skeleton that emerged, and parts of 35 others of the same species, is 4.4 million years old. A leader of the team that discovered and studied the new fossils, Tim White of the University of California, Berkeley, says:

To understand the biology, the parts you really want are the skull and teeth, the pelvis, the limbs and the hands and the feet. And we have all of them.

Though the pelvis was smashed and had to be extensively reconstructed using digital technology, the discovery reveals that chimpanzees and other close ape relatives might actually have evolved more than humans did over the 7 million years since the human and ape lines diverged. No bones of the common ancestor of humans and apes have so far been found. Ardi suggests what the last ancestor shared by humans and chimps might have been like before the lineages diverged. Analysis of Australopithecus and modern African apes suggested it looked like a knuckle walking, tree swinging ape. Yet, despite being “so close to the split” relative to today, Ardi is not much like a chimpanzee, our closest living primate relative. It implies that the last common ancestor probably wasn’t either, but Ardi has features that are intermediate between the last common ancestor and australopithecines.

This skeleton flips our understanding of human evolution. It’s clear that humans are not merely a slight modification of chimps, despite their genomic similarity.

C Owen Lovejoy

Based on Ardi’s anatomy, chimpanzees may have evolved more than humans—they changed more over the past 7 million years. Ardi was 120 cm tall and weighed 50 kg, making it about twice as heavy as Lucy. It had some uniquely human characteristics, such as bipedalism and manipulative hands.

The structure of Ardi’s upper pelvis, leg bones and feet indicates it walked upright on the ground, but still could climb. Its wrist, hand and shoulder bones show that it wasn’t a knuckle walker and didn’t spend much time hanging or swinging ape style in trees. Rather, it moved along branches by palm walking, typical of extinct apes. Its foot still had an opposable big toe for grasping tree limbs but lacked the flexibility that apes use to grab and scale tree trunks and vines. Though Ardi walked upright, it was with a lurching gait due to lack of the arch in its feet, a feature that allowed later hominids, like Australopithecus and Homo, to walk smoothly. Ardi’s hand had dexterous fingers and a more flexible wrist than a chimp’s, giving it a manoueverability allowing it to grasp and catch objects on the ground and carry them while walking on two legs.

More than 150,000 plant and animal fossils have been collected from the site. The bones with the plant and animal fossils from the surrounding sediments give a clear picture of the habitat Ardi roamed in, 200,000 generations ago. It was a lush grassy African woodland with patches of denser forest and freshwater springs. Hackberries, palms and fig trees grew around much of the area, and much of Ardi’s diet might have been figs. It shared the woods with colobus monkeys, baboons, elephants, spiral horned antelopes, hyenas, shrews, hares, porcupines and other small carnivores, bats, and at least 29 species of birds like peacocks, doves, lovebirds, swifts and owls.

So hominids began standing and walking upright before climate changed Africa’s light woodland to grassy savanna. Because this hominid already walked upright while still living in woodland, the notion that human predecessors became bipedal as a way of seeing predators over tall grasses on the savanna is refuted.

The new hominid male’s canine teeth are no longer projecting or sharp like those of gorillas and other non-monogamous apes. They are short and blunt like ours. Apes like gorillas use these teeth in vicious squabbles over mates. It suggests that these animals did not fight over females. Professor Lovejoy speculates that these hominids already formed bond pairs, like humans, to raise infants together, though not necessarily for life or exclusively with one female. Lovejoy thinks Ar ramidus had developed a social system in which males were cooperative, helping females, and their own offspring, by sharing food favoring bipedality. It allows the carrying of food in the woods.

But this is all speculation, and the poor state of the pelvis in the main skeleton leaves the detail of its mode of walking open. From the evidence, different palaeoanthropologists can easily have different interpretations of how Ardi moved, and what it reveals about the last common ancestor of humans and chimps.

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Does Civilization Speed up Evolution?

October 18th, 2009

Out of Africa: 60,000 BC

Out of Africa: 60,000 BC

Are human beings still evolving? For long it was thought that human evolution had stopped when culture took over from natural selection about 50,000 years ago, in other words when we started to use our brains. But the human races emerged since then. John Hawks of the University of Wisconsin at Madison points out that, besides skin coloration, Europeans have cheekbones which slant backward, their eye sockets are shaped like goggles, and their nose bridges are high. Chinese have cheekbones facing forward, round orbits, and a low nose bridge. Australians have thicker skulls and big teeth. All of these traits have evolved while modern human beings have spread around the world after leaving Africa about 60,000 years ago, an exceptionally important time for human emergence.

Recently advances in methods of sequencing and deciphering DNA have allowed scientists to uncover genes that help people fight infectious microbes, survive frigid temperatures, or otherwise adapt to local conditions. These variants, have emerged in the last 10,000 years. Human beings are not only still evolving but the rate of evolution seems to be accelerating. What could be the cause? It is perhaps simple and obvious—more people! The larger the population the more frequent are mutations that confer some advantage in changing circumstances, first that migrating humans were continuously meeting, and now those being made by our own efforts.

Darwin himself emphasized the importance of maintaining a large herd for selecting favorable traits.

Gregory Cochran, University of Utah

Now human genetic data banks are large enough to allow scientists to test genetic ideas. The International Haplotype Map, catalogued differences in DNA from people of different descent. Geneticists, Robert Moyzis of the University of California at Irvine, and Eric Wang of Veracyte Inc in South San Francisco, were using new computational methods to mine the data for information about evolution. From the haplotype map, they found 7 percent of human genes seemed to be recent adaptations, mostly acquired in the last 40,000 years.

The explanation in the “out of Africa” scenario, is that humans began to encounter utterly new selective forces as they migrated, adjusting to novel foods, predators, climates, and physical conditions. Our own growing inventiveness increased the pressure to change.

The faster our ingenuity alters our habitat, the quicker we have to adapt in response.

Robert Moyzis

Migration of Humans from Africa as indicated by genes

Migration of Humans from Africa as indicated by genes

Moreover, using a computer simulation, they tested what would have happened if humans had evolved at the same modern rate since we diverged from a common ancestral ape 6 million years ago. It predicted that the difference between humans and chimpanzees would be 160 times bigger than it is. In other words we must be evolving faster now than we were 6 million years ago.

Some of the selective pressures on the migrating humans are now obvious. Because people with dark skin cannot efficiently make vitamin D from ultraviolet radiation in northern latitudes where the light is weak, they are susceptible to bone deformities like rickets. So, the skin pigment, melanin, originally present in humans emerging from tropical Africa, decreased people’s fitness to reproduce as they moved north. Consequently, two dozen different mutations which inhibited melanin production in the skin have been selected in Europeans and Asians in the last 20,000 years. The loss of melanin also led to the emergence of blue eyes:

No one on earth had blue eyes 10,000 years ago.

John Hawks

Perhaps the biggest sudden change came with the human transition to farming after they evolved as hunter gatherers. Keeping domestic animals like goats, sheep and particularly cows provided milk as a source of food, but when humans first settled into farming around 10,000 years ago, they were unable to digest lactose, the main sugar in milk. Then about 8,000 years ago, a mutation arose in northern Europe enabling some of them to consume milk without the lactose making them sick. Today the gene is present in 80 percent of Europeans but in only 20 percent of Asians and Africans. Even so, the 20 percent among Asians and Africans suggests a considerable genetic movement in only 8000 years, unless the mutation arose more than once.

Following the settling of the hunter gatherers, the next development was the formation of towns then cities in quick succession, and with the concentration of people into confined spaces came all the diseases of modern life. In these crowded, filthy towns and cities, pathogens spread uncontrollably causing epidemics of smallpox, cholera, typhus, and malaria, new diseases. Here was an intense selective force. People began with little immunity, and many must have died, but some had some immunity and were able to live longer. Better able to reproduce, their genes were selected until enough people were able to survive the unhealthy conditions. They developed degrees of immunity, but so too the diseases evolved, and the battle went on until recent times with the development of medicine.

Human sperm was also affected by the new conditions. More choice of sexual partners was available in the close life of towns and cities. Woman began having sex with more than one man in less than the day long viability of sperm in the female vagina. So, the genes of the man with sperm that was more vigorous or mobile or abundant or longer lived was more likely to be selected and emerge in the woman’s children. Now sperm is different from sperm of a few thousand years ago. New mutations in genes for sperm production are present in every ethnic group studied. Moreover, it suggests that religious fundamentalists are wrong in claiming women are naturally loyal to one man. The genetic adaptations suggest otherwise, even if some are blind to the reality of society.

Regarding the human brain, about a hundred fast changing genes are associated with neurotransmitters, including serotonin, a mood regulator, glutamate, involved in general arousal, and dopamine, which regulates attention. Around 40 percent of the new neurotransmitter genes have emerged in the past 50,000 years, mostly in the past 10,000 years.

Moyzis says that confrontations in hunter gatherer societies are usually settled when one of the parties just walks away. “It’s easy to join another group.” Not, though, in settled farming communities. “You can’t just walk away.” Anyone who stood and fought was likely to be killed, while those less easily aroused did not get into such dangerous situations, a selective pressure in favour of those with an amicable temperament. The glutamate pathways involved in arousal adapted.

In settled communities, ability to add up and memory became important for keeping track of herds and bartering. Most recently, in the last 2000 years, Chinese rulers have screened people to be government administrators using standard tests. Those with the abilities were chosen and got jobs in the Mandarin system, the Chinese civil service, giving them a guaranteed income able to support multiple wives and many children who would often inherit their father’s numerical and literary skills. Those who failed the tests remained as illiterate hard worked peasants in the rice paddies. This is selection akin to the selection of strains in animals.

Probably for thousands of years in some cultures, certain kinds of intellectual ability may have been tied to reproductive success.

Robert Moyzis

Jews of eastern European descent, the Ashkenazim, might be another example. They are unusually intelligent and successful in life. The reason might be that for a millennium they were persecuted in Europe and were forbidden by Christians to earn an income in a respectable job. So they took disreputable jobs as moneylenders, usury being nominally a sin for Christians. They became adept at handling and using money and also became financial administrators to the nobility—each noble had “his Jew”. They also had to remain alert for persecution, and ready to respond if it looked likely. Jews who could not manage it died or were killed, so the selective pressure on them was great, and those who were successful had to be clever. Together with a mutually supportive social life, the Jews who emerged into modern times evolved great mental abilities.

A mutation called DRD4 arose 50,000 years ago, according to sequencing studies, just as humans were spreading out of Africa. It makes a receptor in the brain less able to bond to dopamine, apparently causing ADHD (Attention Deficit Hyperactivity Disorder) in children. It is called the “migratory gene” because it arose just as humans had started to leave Africa, and it gets more common the farther from Africa they get. It is present in only 20 percent of Europeans and Africans, but in 40 percent of north Americans natives and 80 percent of some South American natives.

Children with the mutation are restless, seek novelty and take risks. Some conjecture that these traits were favourably selected as the humans migrated farther because they inclined those with such a gene to explore new frontiers. The trouble is that such traits are more likely to get people killed than to make them successful explorers. Wang says, “having the trait of focusing on multiple directions might have been a good thing. People focused in one direction might get eaten”. In fact the opposite seems more likely. The traits are like the symptoms of the toxo parasite, thought to be involved in schizophrenia, and found in the environment of some predators like cats. Prey that get infected by the parasite get confused and become easier prey for the predator!

Some scientists are not happy with the idea that our brains might be evolving, and might have evolved differently in the different races of humanity. It offers ammunition for racist theories. Yet must the science be hidden because of ignorance and bigotry? It is up to our own societies to teach what is correct, and to combat prejudice and hatred. Racialist theories are not objective, but are based on biased choices of what skills matter. In different environments, different skills evolved. Groups of people like the Jews or the Chinese mandarins might have succeeded in particular societies, but should society collapse and revert to chaos and people having to scratch a living from the fields, who is to say that the mandarins or the Jews would remain successful. Farm laborers might then be the survivors. The idea of any absolute racial superiority is absurd. Even genetically, intelligence is not a single trait but a suite of abilities, and each ancestral environment favored a different set of them.

In any case, at present ethnic groups are intermingling freely, and the children of future generations are thoroughly mixing their DNA in a vast genetic reshuffling.

Adapted from Kathleen McAuliffe, “They Don’t Make Homo Sapiens Like They Used To”, Discovery Magazine, February 9, 2009

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Dollo’s Law in the War of Science and Religion

October 16th, 2009

An organism never returns to its former state.

Dollo’s law, Louis Dollo, 1905

Land animals returned to the water becoming streamlined, but they did not turn back into fish. Birds leant how to fly, but some returned to flightlessness, remaining nevertheless unquestionably birds. As Dollo’s law states, although species can seem to go backwards in evolution, they do not reverse their previous evolutionary steps. Joseph W Thornton of Oregon, et al, have shown that there are molecular reasons for this. It is that mutations that happen after the mutations that allowed the evolutionary change, prevent it from being reversed, unless all the other mutations are reversed in the right inverse sequence. It makes evolution like a ratchet. Essentially having moved in a direction, it cannot step backwards unless the change was very simple.

Creationists have tried to make something of this molecular confirmation, and extension of Dollo’s law. Michael Behe, a creationist biologist much loved by creationists as being a rare specimen of his type has used the well funded Discovery Institute to air his own views, which seem to be that evolution is rendered impossible by Thornton’s findings. Thornton replied at Karl Zimmer’s request. Here is the gist of the reply, somewhat simplified by removal of a few technical words. The original is available at Kar Zimmer’s blog at Discovery Magazine (not Institute!).

Joe Thornton answered Michael Behe’s criticism of evolution based on his paper in Nature. Behe’s interpretation of the work was incorrect. He claimed the findings supported his argument that adaptations requiring more than one mutation could not evolve by evolutionary processes. The many errors in Behe’s Edge of Evolution, in which he makes this argument, have often been pointed out, though Christian fundamentalists will not listen.

Behe ignores the fact that adaptive combinations of mutations can and do evolve by pathways involving neutral intermediates. He says, if it takes more than one mutation to produce even a crude version of the new protein function, selection cannot drive acquisition of the adaptive combination. But the evolutionary path to the new function is not blocked nor does evolution run into a brick wall, as Behe alleges. Neutral mutations do not harm the ancestral function, so can remain in populations unchanged for a long time, until a new mutation yields a new function and is subject to selection. It is what is observed in the evolution of the glucocorticoid receptor (GR) Thornton and coworkers studied.

Multiple mutations are required for the GR to evolve its specificity for the hormone cortisol. Some of the mutations that trigger the change in function are harmful in isolation, but others are harmless, having no effect on the function of the protein. Once they are in place the protein can tolerate the other mutations that shift and then optimize the new function. So, there were pathways from the ancestral protein to the new function that passed only through harmless or beneficial intermediate states. Even some mildly harmful intermediates will work under some genetic conditions, but with a lower probability. A path to a new function that involves neutral intermediates is subject to evolutionary mutation, drift, and selection, so evolution can explain the evolution of GR’s new function. Behe ignores the importance of neutral pathways in protein evolution.

Examining whether the mutations that allowed the evolution of GR’s new function could be reversed in a later version of the GR, restoring the ancestral conformation and function, the later version of the protein could no longer tolerate ancestral amino acids at key sites, though they had earlier been present in the protein. It was because harmful mutations had occurred after the shift in function that clashed with or would not support the ancestral conformation. But, when these mutations are reversed first, before the function-switching mutations, the ancestral structure and function can be restored.

Reversing the harmful mutations alone does not enhance the ancestral function, but sometimes has no effect, being just the flip-side of the harmless ones—reversal of a harmful mutation is a harmless mutation for reverse evolution. Several pathways lead back to the ancestral sequence that pass only through steps that are neutral or beneficial with respect to the protein’s functions. So, all pathways to the ancestral sequence and structure are not blocked, as Behe says they are. The chance effects of genetic drift could allow the protein to float along such paths, allowing time for the function-shifting mutations to be reversed. However, selection alone would not be sufficient to drive the protein deterministically through the neutral steps. If selection for the ancestral function were imposed, reversal to the same sequence and conformation as the ancestor would be unlikely, though not impossible.

Taken together, the existence of harmless and harmful mutations indicates that neutral paths to specific adaptive combinations of mutations are opening and closing during evolution. If the clock could be turned back and history allowed to run again, a different path probably will be followed, and different protein forms would evolve by the natural processes of evolution.

Behe’s second error is to confuse reversal to the ancestral sequence and structure with re-acquisition of a similar function. Restrictive mutations make selection alone insufficient to drive the protein back to the same form as that found in the ancestor. But nothing in the results implies that, if selection were to favor the ancestral function again, the protein could not adapt by evolving a different, convergent, underlying basis for the function. Indeed, directed evolution experiments in the laboratory have shown that mutation and selection alone can cause steroid receptor proteins to rapidly evolve sensitivity to new hormones. Some of the mutations involved are different from those that occurred during the historical evolution of ancient proteins.

The work shows re-evolution of the underlying ancestral form is unlikely, but it says nothing about the re-evolution of the ancestral function. Chance processes play a key role in determining which adaptive forms actually evolve under selection, but this does not mean, as Behe alleges, that no adaptive form can evolve.

Finally, Behe erroneously supposes that, if each of a set of specific evolutionary outcomes has a low probability, then none will evolve. This is like saying that giantkilling in sport is impossible—that Torquay United could never defeat Tottenham Hotspur at soccer. According to Behe’s reasoning, the fact that it happened means it was willed by God. Or in human history, countless possibilities could emerge from our present state, making the probability of the one that actually does evolve extraordinarily low. Yet some such state will happen. Having emerged, its prior probability seems negligible, making it an impossible event, according to Behe. Yet one of the impossible futures will happen. That one was not impossible. That our present biology did not evolve deterministically simply means that other states could have evolved instead. It does not imply that it did not evolve.

Consider your own life history as an analogy. When young, you run out of coins for the electricity meter in your flat one cold winter night, so go down to the pub to get warm and get change for later. There you meet your future wife! If you’d had change, or the night was not cold, or you’d gone to bed, or to another pub or the cinema, you would never have met the woman for good or ill you married. We can all relate chance events that affected how our lives turned out. The probability of anyone’s particular life is extraordinarily small, but it happened! The present is one of many possibilities, so there is no difficulty reconciling the nature of evolutionary processes with the complexity of biological forms. As history unfolds, potential pathways to different futures are constantly opening and closing. Evolutionary processes allow living forms to move along these pathways to a unique end—but it is one out of many that could have taken place.

Behe’s argument has no scientific merit. It is not a scientific argument, but mere prejudice and dogma. It is scientific ignorance, based on ignorantly or deliberately misunderstanding the fundamental processes of molecular evolution, and failing to understand probability. He confuses contingency, ignores the role of genetic drift, and he wrongly thinks that low probability excludes any evolution though when many events are possible, one is inevitable, even if it is no change!

Creationists and those too dishonest even to call themselves creationists are keen to get into debates with evolutionary scientists to be able to claim:

Look, an evolutionary biologist who actually does scientific research is arguing with me. Let’s teach this controversy in public schools!

but there is no scientific controversy about whether natural processes can drive the evolution of complex proteins. Thornton concluded that his work ought not be misinterpreted by those who would like to pretend that there is a genuinely scientific controversy. All there is is the inevitable war of science and religion.

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Gracilization: evidence of humans domesticating themselves

October 16th, 2009

“Gracilization” — that is, “a worldwide thinning of the human skull” starting around 40,000 years ago. Why was it that, millenniums before the agricultural revolution, our ancestors became progressively lighter-boned and smaller? A crucial clue: The fossil record and contemporary breeding experiments alike confirm that domestication, whether accidental — as in the evolution of the dog from the wolf — or deliberate, induces pedomorphism, or the retention of juvenile features into adulthood. “Gracilization . . . occurred because early modern humans were becoming tamer,” Wade writes. “And who, exactly, was domesticating them? The answer is obvious: people were domesticating themselves.

Source: latimes.com

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Mothers and Others

September 13th, 2009

The two species of ape, homo sapiens and pan troglodytes (humans and chimpanzees) share about 98 percent of their DNA, but the question of just how big a gulf exists between humans and apes continues to perplex us. If some apes have mastered language, tools, deceit and war, what makes humans unique? Are we more intelligent?

Michael Tomasello, an evolutionary biologist, says the question of human and ape intelligence is not always clear. Scientists at the Max Planck Institute gave cognitive tests to adult chimpanzees and orangutans, and to human two year olds. The apes matched the children in their understanding of the physical world, but apes were better than adult humans at remembering patterns of numbers. The human children performed better on tests that measured social skills, like social learning and communicating. Social skills set the humans apart, and human mothers care for their children longer allowing social skills to develop.

Natalie Angier gave in the New York Times (March 2009) a new account of the theory that mothers caring for their children pushed along human coöperation and socialization. Primatologist, Sarah Blaffer Hrdy, thinks (Mothers and Others: The Evolutionary Origins of Mutual Understanding) the social skills of infants are what makes us human. Human babies are dependent on their elders for such a long time that humanity had to evolve shared child care, and this spirit of coöperation spread through human society.

The length of the human childhood is such that others in the social group were drawn in as assistant mothers into helping, out of necessity, and this calmed the antagonism individual apes previously had towards each other. As Angier describes, a human mother is rarely unwilling to hand her child to someone else she knows, but gorilla and chimpanzee mothers live with a constant fear of infanticide. Chimpanzee and gorilla mothers are capable of rearing their offspring pretty much through their own powers, but human mothers are not.

Human beings evolved as coöperative breeders, says Dr Hrdy, a reproductive strategy in which mothers are assisted by people of either sex who help care for and feed the young. Most biologists would concur that humans have evolved the need for shared child care, but our status as coöperative breeders, rather than our exceptionally complex brains, helps explain many aspects of our temperament. Our relative pacifism[!], for example, or the expectation that we can fly from New York to Los Angeles without fear of personal dismemberment. Chimpanzees are pretty smart, but were you to board an airplane filled with chimpanzees, you “would be lucky to disembark with all 10 fingers and toes still attached”, Dr Hrdy writes.

Our capacity to coöperate in groups, to empathize with others and to wonder what others are thinking and feeling, probably in response to the selective pressures of being in a social group, and the need to trust and rely on others and be deemed trustworthy and reliable in turn. Babies became adorable and keen to make connections with every passing adult gaze. Mothers became willing to play pass the baby. Mother chimpanzees and gorillas jealously hold on to their infants for the first six months or more of life. Other females may express real interest in the newborn, but the mother does not let go. You never know when one of those females will turn infanticidal, or be unwilling or unable to defend the young ape against an infanticidal male.

By contrast, human mothers in virtually every culture studied allow others to hold their babies from birth onward, to a greater or lesser extent depending on tradition. Among the !Kung foragers of the Kalahari, babies are held by a father, grandmother, older sibling or some other member of the social group maybe 25 percent of the time. Among the Efe foragers of Central Africa, babies spend 60 percent of their daylight hours being carried by somebody other than their mother. In 87 percent of foraging societies, mothers sometimes suckle each other’s children!

Dr Hrdy objected to the dogma, especially among laypeople but also some anthropologists, that humans evolved their extreme sociality and coöperative behavior to better compete with other humans.

I’m not comfortable accepting this idea that the origins of hypersociality can be found in warfare, or that in group amity arose in the interest of out group enmity.

Humans have indeed been violent and militaristic for the last 12,000 or so years, when hunter gatherers started settling down and defending territories, and overpopulation set in. Before then, there were not enough people around to wage wars. The average population during the hundreds of thousands of years of human evolution that preceded the Neolithic Age may have been around 2,000 breeding adults.

What would humans have been fighting over? They were too busy trying to keep themselves and their children alive.

Dr Hrdy also argues that our human ancestors became emotionally modern long before the human brain had reached its current average volume of 1,300 cubic centimeters, which is about three times the size of a chimpanzee brain—in other words, that we became the nicest apes before becoming the smartest. You don’t need a bulging brain to evolve coöperative breeding. Many species of birds breed coöperatively, as do lions, rats, meerkats, wolves and marmosets, among others. But to become a coöperatively breeding ape, and to persuade a bunch of smart, hot tempered, suspicious, politically cunning primates to start sharing child care and provisionings, now that took a novel evolutionary development, the advent of trust.

To explain the rise of coöperative breeding among humans, Dr Hrdy collates much new research in anthropology, genetics, infant development, and comparative biology. Recent research has overturned the older idea that humans are a patrilocal species—husbands remain with their clan and wives move into their husband’s clan. Instead, young mothers in many traditional societies have their own mothers and other female relatives close at hand, and who better to trust with baby care than your mom or your aunt?

New studies have shown the importance of postmenopausal women to gathering roots and tubers, the food that is the staple of hunter gatherer diets, not freshly killed game. Other anthropologists have made the startling discovery that children have entertainment value, and that among traditional cultures without television or internet access, a baby is the best show in town.

But even in the area of social skills some apes might offer humans a lesson. Chimpanzees in the wild live in a violent, male dominated society. Their close relatives the bonobos, however, are matriarchal and relatively peaceful. To keep that peace they have a novel solution, as Hannah Holmes (The Well Dressed Ape: A Natural History of Myself) explains. Bonobos…

…rarely encounter a conflict they can’t resolve by copulating.

The impact of shared motherhood on human evolution was profound. With their helpers, women could give birth to offspring with ever longer childhoods—the better to build big brains and strong immune systems—and at ever shrinking intervals. The average time between births for a chimpanzee mother is about six years. For a human mother, it’s two or three years. As a result of our combined braininess and fecundity, humans have managed to colonize the planet, exploit, marginalize or exterminate all competing forms of life, and build a vast military industrial complex in the US, if nowhere else. Did the anthroposaurs have the same experience?

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More Clever Birds!

August 12th, 2009

Steve Connor, Science Editor of The UK Independent, reports (6 August 2009) that rooks, members of the crow family (corvids), could work out how to raise the water level in a narrow necked laboratory flask by dropping in stones until they could reach a tasty worm floating on the surface. One of Aesop’s fables describes how a thirsty crow was able to drink from a half-full pitcher after raising the water level by adding pebbles. It seems that it had a basis in real life.

Nathan Emery of Queen Mary, University of London, and Christopher Bird of Cambridge did the studies. Four different rooks quickly discovered the trick. The only other animal to perform a similar task was an orang-utan, which spurted water into a tube until it could reach a floating peanut. It seems rooks and crows have comparable intelligence to primates at using tools.

A large number of studies on both corvids and apes, have found that the crow’s performance is on a par with or better than apes’. Not only can they think through complex problems requiring the use of tools, but they can imagine the consequences of their actions. They do not learn the trick by trial and error, but create novel solutions to problems that they have never encountered before.

Only great apes and humans have been thought to be able to think ahead, yet these birds have brains the size of walnuts and do not use tools in the wild. Hand reared crows however can fashion a simple tool out of wire to help them retrieve food from an empty container, and separate studies of wild crows in New Caledonia have shown they can make similar tools to retrieve grubs from tree holes.

Dr Emery added:

We believe that intelligence in rooks and other crows evolved primarily to solve social problems, as almost all crow species live in large social groups, but they also mainly form pair bonds, like human marriages, and some of their cognitive abilities appear to have evolved to help them predict what others are going to do next, so-called mind reading.

Published in the journal Current Biology.

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Crows as Clever as Great Apes

July 20th, 2009

James Owen, National Geographic News, 9 December 2004

Anyone who has watched crows, jays, ravens and other members of the corvid family will know they’re anything but birdbrained. For instance, jays will sit on ant nests, allowing the angry insects to douse them with formic acid, a natural pesticide which helps rid the birds of parasites. Urban-living carrion crows have learned to use road traffic for cracking tough nuts. They do this at traffic light crossings, waiting patiently with human pedestrians for a red light before retrieving their prize. Yet corvids may be even cleverer than we think.

A new study suggests their cognitive abilities are a match for primates such as chimpanzees and gorillas. Furthermore, crows may provide clues to understanding human intelligence. Published in the journal, Science, the study is authored by Nathan Emery and Nicola Clayton, from the departments of animal behavior and experimental psychology at Cambridge University, England.

They say that, while having very different brain structures, both crows and primates use a combination of mental tools, including imagination and the anticipation of possible future events, to solve similar problems. They write:

Studies have found that some corvids are not only superior in intelligence to birds of other avian species, perhaps with the exception of some parrots, but also rival many nonhuman primates.

Large Brains

Increasingly, scientists agree that it isn’t physical need that makes animals smart, but social necessity. Group living tends to be a complicated business, so for individuals to prosper they need to understand exactly what’s going on. So highly social creatures like dolphins, chimps, and humans tend to be large-brained and intelligent. The study notes that crows are also social and have unusually large brains for their size:

It is relatively the same size as the chimpanzee brain.

Crows and apes both think about their social and physical surroundings in complex ways, using tool use as an example. Like apes, many birds employ tools to gather food, but it isn’t clear whether chimps or crows appreciate how these tools work. It may be that they simply discover their usefulness by accident. However, studies of New Caledonian crows, from the South Pacific, suggest otherwise. New Caledonian crows manufacture two very different types of tool for finding prey. Hooks crafted from twigs are used to poke grubs from holes in trees, while they also cut up stiff leaves with their beaks, carefully sculpting them into sharp instruments for probing leaf detritus for insects and other invertebrates. A New Caledonian crow in captivity learned how to bend a piece of straight wire into a hook to probe for food. Such sophisticated tool manufacture and use is unique in non-human wild animals, according to Jackie Chappell, a UK-based zoologist who has studied the birds. Emery and Clayton compare the crow’s handiwork to minor human technological innovations. And because different New Caledonian crow populations make these tools to slightly different designs, some scientists take this as evidence of some form of culture, as has been suggested in chimpanzees.

Imagination?

Other corvids may use memories of past experiences to plan ahead. A previous study of Western scrub jays by Emery and Clayton suggests jays with past experience of pilfering food caches collected by other jays can then use this knowledge to protect their own caches. Lab experiments showed that if a habitual thief was observed while burying its own cache, it would later go back and move it when no other bird was looking. Meanwhile, “innocent” jays did not exhibit the same cunning.

The researchers also argue that such behavior suggests Western scrub jays are able to second guess another’s intentions, or, to put it another way, get into another bird’s mind. In which case, this could be evidence for imagination. Emery and Clayton write:

Western scrub jays may present a case for imagination because the jays needed to have remembered the previous relevant social context, used their own experience of having been a thief to predict the behavior of a pilferer, and determined the safest course of action to protect the caches from pilferage.

Studies to assess similar cognitive abilities in apes have been inconclusive, according to John Pearce, professor of psychology at Cardiff University in Wales. The Western scrub jay study is some of the best evidence going that one animal can understand what another is thinking.

Pearce believes we can gain insights into the basic mechanisms of human intelligence through the study of animals. He says language is generally considered to be one of the major divisions between human and animal intelligence, which makes Western scrub jays especially noteworthy.

What’s so interesting is that while Western scrub jays may not have language, the research shows they’ve got many of the intellectual abilities that humans have. This suggests that many of our intellectual abilities which we think we need language for perhaps we don’t in fact need language for. That then makes us try to understand these abilities in a different way.

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