612)A Collection of Posts on Charles Darwin,a Scientist Way Ahead of His Time; Dynamic vs Static Creation; Quotes of Noble Quran, Aga Khans IV and III

Chapter 30, Verse 27: He originates creation; THEN REFASHIONS IT- for Him an easy task. His is the most Sublime Symbol in the heavens and the earth(Noble Quran, 7th Century CE)

"In Islamic belief, knowledge is two-fold. There is that revealed through the Holy Prophet (s.a.s.) and that which man discovers by virtue of his own intellect. Nor do these two involve any contradiction, provided man remembers that his own mind is itself the creation of God. Without this humility, no balance is possible. With it, there are no barriers. Indeed, one strength of Islam has always lain in its belief that CREATION IS NOT STATIC BUT CONTINUOUS, that through scientific and other endeavours, God has opened and continues to open new windows for us to see the marvels of His creation"(Aga Khan IV, Aga Khan University, 16 March 1983, Karachi, Pakistan)

"THE CREATION ACCORDING TO ISLAM IS NOT A UNIQUE ACT IN A GIVEN TIME BUT A PERPETUAL AND CONSTANT EVENT; and God supports and sustains all existence at every moment by His will and His thought. Outside His will, outside His thought, all is nothing, even the things which seem to us absolutely self-evident such as space and time. Allah alone wishes: the Universe exists; and all manifestations are as a witness of the Divine Will"(Memoirs of Aga Khan III, 1954)

"Thus Islam's basic principle can only be defined as mono-realism and not as monotheism. Consider, for example, the opening declaration of every Islamic prayer: "Allah-o-Akbar". What does that mean? There can be no doubt that the second word of the declaration likens THE CHARACTER OF ALLAH TO A MATRIX WHICH CONTAINS ALL AND GIVES EXISTENCE TO THE INFINITE, TO SPACE, TO TIME, TO THE UNIVERSE, TO ALL ACTIVE AND PASSIVE FORCES IMAGINEABLE, TO LIFE AND TO THE SOUL. Imam Hassan has explained the Islamic doctrine of God and the Universe by analogy with the sun and its reflection in the pool of a fountain; there is certainly a reflection or image of the sun, but with what poverty and with what little reality; how small and pale is the likeness between this impalpable image and the immense, blazing, white-hot glory of the celestial sphere itself. Allah is the sun; and the Universe, as we know it in all its magnitude, and time, with its power, are nothing more than the reflection of the Absolute in the mirror of the fountain"(Memoirs of Aga Khan III, 1954)

The above are 4 quotes and excerpts from Blogpost Four Hundred, a collection of about 100 quotes on the subjects of Knowledge, Intellect, Creation, Education, Science and Religion:
http://gonashgo.blogspot.com/2008/09/400blogpost-four-hundred-knowledge.html


1)http://gonashgo.blogspot.com/2009/02/445darwins-evolution-life-and.html

2)http://gonashgo.blogspot.com/2008/09/404sorry-charley-church-apologizes-to.html

3)http://gonashgo.blogspot.com/2008/11/423part-3-peter-mcknight-hitting-brick_02.html

4)http://gonashgo.blogspot.com/2008/11/422part-2-peter-mcknight-religion-in.html

5)http://www.sciencenews.org/view/feature/id/39754/title/SN_Special__Darwin_turns_200

6)http://www.sciencenews.org/view/feature/id/40014/title/Darwins_Evolution

7)http://www.sciencenews.org/view/feature/id/39999/title/Evolutions_Evolution

8)http://www.sciencenews.org/view/feature/id/40006/title/Molecular_Evolution

9)http://www.sciencenews.org/view/feature/id/39974/title/Step-by-step_Evolution

10)http://www.sciencenews.org/view/feature/id/40012/title/Computing_Evolution

11)http://www.sciencenews.org/view/feature/id/40016/title/A_Most_Private_Evolution

12)http://gonashgo.blogspot.com/2009/01/441the-peter-mcknight-collection-of.html



13) February 10, 2009

Darwin, Ahead of His Time, Is Still Influential

By NICHOLAS WADE
New York Times

Darwin’s theory of evolution has become the bedrock of modern biology. But for most of the theory’s existence since 1859, even biologists have ignored or vigorously opposed it, in whole or in part.

It is a testament to Darwin’s extraordinary insight that it took almost a century for biologists to understand the essential correctness of his views.

Biologists quickly accepted the idea of evolution, but for decades they rejected natural selection, the mechanism Darwin proposed for the evolutionary process. Until the mid-20th century they largely ignored sexual selection, a special aspect of natural selection that Darwin proposed to account for male ornaments like the peacock’s tail.

And biologists are still arguing about group-level selection, the idea that natural selection can operate at the level of groups as well as on individuals. Darwin proposed group selection — or something like it; scholars differ as to what he meant — to account for castes in ant societies and morality in people.

How did Darwin come to be so in advance of his time? Why were biologists so slow to understand that Darwin had provided the correct answer on so many central issues? Historians of science have noted several distinctive features of Darwin’s approach to science that, besides genius, help account for his insights. They also point to several nonscientific criteria that stood as mental blocks in the way of biologists’ accepting Darwin’s ideas.

One of Darwin’s advantages was that he did not have to write grant proposals or publish 15 articles a year. He thought deeply about every detail of his theory for more than 20 years before publishing “On the Origin of Species” in 1859, and for 12 years more before its sequel, “The Descent of Man,” which explored how his theory applied to people.

He brought several intellectual virtues to the task at hand. Instead of brushing off objections to his theory, he thought about them obsessively until he had found a solution. Showy male ornaments, like the peacock’s tail, appeared hard to explain by natural selection because they seemed more of a handicap than an aid to survival. “The sight of a feather in a peacock’s tail, whenever I gaze at it, makes me sick,” Darwin wrote. But from worrying about this problem, he developed the idea of sexual selection, that females chose males with the best ornaments, and hence elegant peacocks have the most offspring.

Darwin also had the intellectual toughness to stick with the deeply discomfiting consequences of his theory, that natural selection has no goal or purpose. Alfred Wallace, who independently thought of natural selection, later lost faith in the power of the idea and turned to spiritualism to explain the human mind. “Darwin had the courage to face the implications of what he had done, but poor Wallace couldn’t bear it,” says William Provine, a historian at Cornell University. (Read commentary by Dr. Provine on passages from "On the Origin of Species." )

Darwin’s thinking about evolution was not only deep, but also very broad. He was interested in fossils, animal breeding, geographical distribution, anatomy and plants. “That very comprehensive view allowed him to see things that others perhaps didn’t,” says Robert J. Richards, a historian at the University of Chicago. “He was so sure of his central ideas — the transmutation of species and natural selection — that he had to find a way to make it all work together.” (Dr. Richards comments on "On the Origin of Species.")

From the perspective of 2009, Darwin’s principal ideas are substantially correct. He did not get everything right. Because he didn’t know about plate tectonics, Darwin’s comments on the distribution of species are not very useful. His theory of inheritance, since he had no knowledge of genes or DNA, is beside the point. But his central concepts of natural selection and sexual selection were correct. He also presented a form of group-level selection that was long dismissed but now has leading advocates like the biologists E. O. Wilson and David Sloan Wilson.

Not only was Darwin correct on the central premises of his theory, but in several other still open issues his views also seem quite likely to prevail. His idea of how new species form was long eclipsed by Ernst Mayr’s view that a reproductive barrier like a mountain forces a species to split. But a number of biologists are now returning to Darwin’s idea that speciation occurs most often through competition in open spaces, Dr. Richards says.

Darwin believed there was a continuity between humans and other species, which led him to think of human morality as related to the sympathy seen among social animals. This long-disdained idea was resurrected only recently by researchers like the primatologist Frans de Waal. Darwin “never felt that morality was our own invention, but was a product of evolution, a position we are now seeing grow in popularity under the influence of what we know about animal behavior,” Dr. de Waal says. “In fact, we’ve now returned to the original Darwinian position.”It is somewhat remarkable that a man who died in 1882 should still be influencing discussion among biologists. It is perhaps equally strange that so many biologists failed for so many decades to accept ideas that Darwin expressed in clear and beautiful English.

The rejection was in part because a substantial amount of science, including the two new fields of Mendelian genetics and population genetics, needed to be developed before other, more enticing mechanisms of selection could be excluded. But there were also a series of nonscientific considerations that affected biologists’ judgment.

In the 19th century, biologists accepted evolution, in part because it implied progress.

“The general idea of evolution, particularly if you took it to be progressive and purposeful, fitted the ideology of the age,” says Peter J. Bowler, a historian of science at Queen’s University, Belfast. But that made it all the harder to accept that something as purposeless as natural selection could be the shaping force of evolution. “On the Origin of Species” and its central idea were largely ignored and did not come back into vogue until the 1930s. By that time the population geneticist R. A. Fisher and others had shown that Mendelian genetics was compatible with the idea of natural selection working on small variations.

“If you think of the 150 years since the publication of ‘Origin of Species,’ it had half that time in the wilderness and half at the center, and even at the center it’s often been not more than marginal,” says Helena Cronin, a philosopher of science at the London School of Economics. “That’s a pretty comprehensive rejection of Darwin.” (Dr. Cronin's comments on Darwin's text.)Darwin is still far from being fully accepted in sciences outside biology. “People say natural selection is O.K. for human bodies but not for brain or behavior,” Dr. Cronin says. “But making an exception for one species is to deny Darwin’s tenet of understanding all living things. This includes almost the whole of social studies — that’s quite an influential body that’s still rejecting Darwinism.

”The yearning to see purpose in evolution and the doubt that it really applied to people were two nonscientific criteria that led scientists to reject the essence of Darwin’s theory. A third, in terms of group selection, may be people’s tendency to think of themselves as individuals rather than as units of a group. “More and more I’m beginning to think about individualism as our own cultural bias that more or less explains why group selection was rejected so forcefully and why it is still so controversial,” says David Sloan Wilson, a biologist at Binghamton University.

Historians who are aware of the long eclipse endured by Darwin’s ideas perhaps have a clearer idea of his extraordinary contribution than do biologists, many of whom assume Darwin’s theory has always been seen to offer, as now, a grand explanatory framework for all biology. Dr. Richards, the University of Chicago historian, recalls that a biologist colleague “had occasion to read the ‘Origin’ for the first time — most biologists have never read the ‘Origin’ — because of a class he was teaching. We met on the street and he remarked, ‘You know, Bob, Darwin really knew a lot of biology.’

”Darwin knew a lot of biology: more than any of his contemporaries, more than a surprising number of his successors. From prolonged thought and study, he was able to intuit how evolution worked without having access to all the subsequent scientific knowledge that others required to be convinced of natural selection. He had the objectivity to put aside criteria with powerful emotional resonance, like the conviction that evolution should be purposeful. As a result, he saw deep into the strange workings of the evolutionary mechanism, an insight not really exceeded until a century after his great work of synthesis.



14) February 10, 2009

EssayDarwinism Must Die So That Evolution May Live

By CARL SAFINA
New York Times


“You care for nothing but shooting, dogs and rat-catching,” Robert Darwin told his son, “and you will be a disgrace to yourself and all your family.” Yet the feckless boy is everywhere. Charles Darwin gets so much credit, we can’t distinguish evolution from him.

Equating evolution with Charles Darwin ignores 150 years of discoveries, including most of what scientists understand about evolution. Such as: Gregor Mendel’s patterns of heredity (which gave Darwin’s idea of natural selection a mechanism — genetics — by which it could work); the discovery of DNA (which gave genetics a mechanism and lets us see evolutionary lineages); developmental biology (which gives DNA a mechanism); studies documenting evolution in nature (which converted the hypothetical to observable fact); evolution’s role in medicine and disease (bringing immediate relevance to the topic); and more.

By propounding “Darwinism,” even scientists and science writers perpetuate an impression that evolution is about one man, one book, one “theory.” The ninth-century Buddhist master Lin Chi said, “If you meet the Buddha on the road, kill him.” The point is that making a master teacher into a sacred fetish misses the essence of his teaching. So let us now kill Darwin.

That all life is related by common ancestry, and that populations change form over time, are the broad strokes and fine brushwork of evolution. But Darwin was late to the party. His grandfather, and others, believed new species evolved. Farmers and fanciers continually created new plant and animal varieties by selecting who survived to breed, thus handing Charles Darwin an idea. All Darwin perceived was that selection must work in nature, too.

In 1859, Darwin’s perception and evidence became “On the Origin of Species by Means of Natural Selection, or The Preservation of Favored Races in the Struggle for Life.” Few realize he published 8 books before and 10 books after “Origin.” He wrote seminal books on orchids, insects, barnacles and corals. He figured out how atolls form, and why they’re tropical.

Credit Darwin’s towering genius. No mind ran so freely, so widely or so freshly over the hills and vales of existence. But there’s a limit to how much credit is reasonable. Parking evolution with Charles Darwin overlooks the limits of his time and all subsequent progress.

Science was primitive in Darwin’s day. Ships had no engines. Not until 1842, six years after Darwin’s Beagle voyage, did Richard Owen coin the term “dinosaur.” Darwin was an adult before scientists began debating whether germs caused disease and whether physicians should clean their instruments. In 1850s London, John Snow fought cholera unaware that bacteria caused it.

Not until 1857 did Johann Carl Fuhlrott and Hermann Schaaffhausen announce that unusual bones from the Neander Valley in Germany were perhaps remains of a very old human race. In 1860 Louis Pasteur performed experiments that eventually disproved “spontaneous generation,” the idea that life continually arose from nonliving things.

Science has marched on. But evolution can seem uniquely stuck on its founder. We don’t call astronomy Copernicism, nor gravity Newtonism. “Darwinism” implies an ideology adhering to one man’s dictates, like Marxism. And “isms” (capitalism, Catholicism, racism) are not science. “Darwinism” implies that biological scientists “believe in” Darwin’s “theory.” It’s as if, since 1860, scientists have just ditto-headed Darwin rather than challenging and testing his ideas, or adding vast new knowledge.

Using phrases like “Darwinian selection” or “Darwinian evolution” implies there must be another kind of evolution at work, a process that can be described with another adjective. For instance, “Newtonian physics” distinguishes the mechanical physics Newton explored from subatomic quantum physics. So “Darwinian evolution” raises a question: What’s the other evolution?

Into the breach: intelligent design. I am not quite saying Darwinism gave rise to creationism, though the “isms” imply equivalence. But the term “Darwinian” built a stage upon which “intelligent” could share the spotlight.

Charles Darwin didn’t invent a belief system. He had an idea, not an ideology. The idea spawned a discipline, not disciples. He spent 20-plus years amassing and assessing the evidence and implications of similar, yet differing, creatures separated in time (fossils) or in space (islands). That’s science.

That’s why Darwin must go.

Almost everything we understand about evolution came after Darwin, not from him. He knew nothing of heredity or genetics, both crucial to evolution. Evolution wasn’t even Darwin’s idea.Darwin’s grandfather Erasmus believed life evolved from a single ancestor. “Shall we conjecture that one and the same kind of living filaments is and has been the cause of all organic life?” he wrote in “Zoonomia” in 1794. He just couldn’t figure out how.

Charles Darwin was after the how. Thinking about farmers’ selective breeding, considering the high mortality of seeds and wild animals, he surmised that natural conditions acted as a filter determining which individuals survived to breed more individuals like themselves. He called this filter “natural selection.” What Darwin had to say about evolution basically begins and ends right there. Darwin took the tiniest step beyond common knowledge. Yet because he perceived — correctly — a mechanism by which life diversifies, his insight packed sweeping power.

But he wasn’t alone. Darwin had been incubating his thesis for two decades when Alfred Russel Wallace wrote to him from Southeast Asia, independently outlining the same idea. Fearing a scoop, Darwin’s colleagues arranged a public presentation crediting both men. It was an idea whose time had come, with or without Darwin.

Darwin penned the magnum opus. Yet there were weaknesses. Individual variation underpinned the idea, but what created variants? Worse, people thought traits of both parents blended in the offspring, so wouldn’t a successful trait be diluted out of existence in a few generations? Because Darwin and colleagues were ignorant of genes and the mechanics of inheritance, they couldn’t fully understand evolution.

Gregor Mendel, an Austrian monk, discovered that in pea plants inheritance of individual traits followed patterns. Superiors burned his papers posthumously in 1884. Not until Mendel’s rediscovered “genetics” met Darwin’s natural selection in the “modern synthesis” of the 1920s did science take a giant step toward understanding evolutionary mechanics. Rosalind Franklin, James Watson and Francis Crick bestowed the next leap: DNA, the structure and mechanism of variation and inheritance.

Darwin’s intellect, humility (“It is always advisable to perceive clearly our ignorance”) and prescience astonish more as scientists clarify, in detail he never imagined, how much he got right.

But our understanding of how life works since Darwin won’t swim in the public pool of ideas until we kill the cult of Darwinism. Only when we fully acknowledge the subsequent century and a half of value added can we really appreciate both Darwin’s genius and the fact that evolution is life’s driving force, with or without Darwin.

Carl Safina is a MacArthur fellow, an adjunct professor at Stony Brook University and the president of the Blue Ocean Institute. His books include “Song for the Blue Ocean,” “Eye of the Albatross” and “Voyage of the Turtle.”



15) February 10, 2009

Genes Offer New Clues in Old Debate on Species’ Origins

By CAROL KAESUK YOON
New York Times

Charles Darwin called it the “mystery of mysteries,” a problem so significant and one he was so sure he had solved that he named his world-changing work after it: “On the Origin of Species.” So he might be surprised to learn that 150 years after the publication of his book, the study of how species originate, a process known as speciation, is not only one of the field’s most active areas of study, but also one of its most contentious.

While researchers agree that many of the recent breakthroughs would have come as a huge surprise to the grand old man, they seem to disagree about almost everything else, from what a species is to what exactly is meant by the origin of species and even whether Darwin shed any light on the process at all.

“Speciation is definitely one of the big-picture grand themes of evolutionary biology,” said Mary Jane West-Eberhard, an evolutionary biologist at the Smithsonian Tropical Research Institute in Panama. She described study of the process as “an apparent turmoil that might be misunderstood by an outsider as a caldron of doubts and uncertainties but that in fact is a vitally alive science.

”Part of the difficulty with studying the origin of species comes from the vastness of the question — how did the diversity of all life on Earth arise, from orchids to elephants to bacteria to ourselves? It is difficult, too, to try to reconstruct events — the birth of species — long past.“A decade ago, the joke was that spell-checkers regularly attempted to substitute the word ‘speciation’ with ‘speculation,’” Mohamed Noor, an evolutionary biologist at Duke University, wrote in a commentary in the journal Nature. But he added, “Speculation in this area will soon be a thing of the past.

”To support such optimism, researchers point to the recent discovery of so-called speciation genes. Most biologists define a species as a group that is reproductively isolated — it cannot interbreed or exchange genes with any other. The newly discovered genes cause reproductive isolation between two groups by causing their offspring, or hybrids, to be infertile or die. Scientists say the identities of the long-sought genes, several of which have recently been pinpointed in fruit flies, mice, fish and yeast, came as a surprise.

On Friday, Daven Presgraves, an evolutionary biologist at the University of Rochester, and colleagues published a paper in the journal Science identifying the latest such gene to be discovered. It is the second one that the team has found in fruit flies. The newly discovered gene, Nup 160, like its predecessor, Nup 96, causes reproductive isolation between the species Drosophila melanogaster and Drosophila simulans.

Unexpectedly, the genes both produce proteins that are part of a large piece of cellular machinery known as the nuclear pore complex, a gateway that controls what molecules move into and out of the nucleus. It is still unclear why, in what Dr. Presgraves describes as a blind search for genes that cause problems in hybrids, his team twice pulled out genes involved in the nuclear pore complex or why the complex might be particularly important in the evolution of reproductive isolation.

“The question is,” said Douglas Futuyma, an evolutionary biologist at the State University of New York at Stony Brook, “what the hell does this have to do with hybrid sterility?

”One reason some scientists object to the use of the term “speciation genes” is that although the genes cause reproductive isolation, it is not clear whether the genes in question caused the initial reproductive isolation responsible for the origin of the species.

To get closer to the crucial early stages of reproductive isolation, Kirsten Bomblies, an evolutionary biologist at the Max Planck Institute for Developmental Biology in Tübingen, Germany, and colleagues study hybrids that are the offspring of crosses between strains of plants within a single species. Surprisingly, even among different strains of the weed Arabidopsis thaliana, Dr. Bomblies said, “some crosses fail catastrophically.” The hybrids are “tiny, their leaves are twisted and warped, they have massive die-off of cells, and the worst cases are unable to flower.

”As with the Drosophila genes, the function of the hybrid-disrupting genes found in Arabidopsis has come as a surprise. They appear to be genes for disease resistance, suggesting that the rapid evolution of disease resistance in different strains may be the beginning of the evolution of reproductive isolation between them. The study may have significance far beyond Arabidopsis; Dr. Bomblies, who last year won a MacArthur Foundation fellowship for her research, notes that breeders have noticed the withering of different strains’ offspring in a variety of species, including wheat, tobacco, cotton and the houseplant Streptocarpus.

Loren Rieseberg, an evolutionary biologist at the University of British Columbia who was not involved with the study, said the work was important because it suggested that an entire class of genes, those involved with fending off disease, and a particular kind of natural selection — that imposed by disease organisms — could be broadly important in speciation in plants. (Read comments by Dr. Rieseberg's on "On the Origin of Species.")

The surprises now being found in the DNA of diverging species are, of course, things Darwin could never have guessed at. Having written “Origin of Species” decades before Gregor Mendel’s genetic work was rediscovered, he certainly did not anticipate such findings in his vision of the diversification of life.

“Genetics was one area where he really fell down,” said Jerry Coyne, an evolutionary biologist at the University of Chicago and the author of “Why Evolution Is True” (Penguin, 2009).

Yet the strongest pattern emerging from the study of these speciation genes is one Darwin might well have expected. The single widespread commonality is that nearly all appear to have diverged to produce reproductive isolation as a result of adaptation under powerful natural selection.

More than anything else, Darwin focused on adaptation via natural selection in the shaping of the diversity of life. The finding comes as something of a surprise to modern biologists, however, because in the absence of evidence, it was plausible that random divergence over time might also have been an important force leading groups to becoming distinct species.

“Probably the most important finding,” Dr. Rieseberg said, “is that selection is driving the process.

”The harking back to Darwin’s emphasis on selection goes well beyond studies of DNA. A particularly powerful type of selection that Darwin emphasized was sexual selection, as when females choose showy mates and male suitors violently combat one another, which can lead to the evolution of things like peacock tails or massive deer antlers.

Now new studies are providing increasing evidence that sexual selection is capable not only of producing outrageous structures but also new species, an idea of Darwin’s that Dr. West-Eberhard describes as “almost completely forgotten for nearly a century.

”A small Amazonian frog known as Physalaemus petersi provides a particularly strong example of how females’ choosiness in mates may be driving the formation of a new species. Males of the mottled brown species reach just over an inch in length and can be found singing in choruses to attract females. In some populations, the males’ song is what is called a “whine” — a kind of frog meow. But in other populations, males whine and add a squawk. Michael J. Ryan, an evolutionary biologist at the University of Texas, Austin, and colleagues have found that the difference evolved because females in one population preferred pure whine, whereas in another they preferred whine and squawk.

What is particularly interesting about petersi, though, is that the female frogs’ preference for different songs in different populations also appears to be causing the populations to begin to evolve into distinct species. When given a choice of songs from either population, females nearly uniformly prefer their own population’s song, as strictly as if the two populations belonged to two long separated species. The researchers have even gathered evidence that the populations that prefer different songs, while very closely related, appear to be beginning to diverge from one another genetically, suggesting they are moving down the path toward becoming separate species.

So if Darwin pointed out the importance of selection, and even the power of sexual selection, why the often heard claim that the “Origin” has little to say about how species originate?

The problem lies in how biologists define a species. Today, the most common definition of a species is a group that is reproductively isolated from other groups, the biological species concept set out by the evolutionary biologist Ernst Mayr in 1942. As a result, the origin of species is, necessarily, considered the origin of reproduction isolation. Yet both concepts would have been rather foreign to Darwin.

Darwin, who once wrote that species were “indefinable,” might have described a species as a segment of a branch on the ever-expanding tree of life, the same tree he drew as the only figure in the “Origin.” Or he might have said it was something more distinct than a variety and less than a genus.

And there are some biologists today who say that Darwin in all his vagueness, not modern biologists, had the definition right. David Wake, an evolutionary biologist at the University of California, Berkeley, has studied Ensatina salamanders for decades. He says their patterns of interbreeding and adaptation simply do not yield to their being divided into species as dictated by the biological species concept.

His salamanders, he said, like so many other real living things, are “much messier” than a definition like the biological species concept allows. Consider asexual species. If a species is an entity that does not exchange genes with others, then every asexual organism, every individual bacterium, for example, could be considered a separate species, hardly a useful distinction. And the complications go on and on.

So perhaps Darwin hit the mark, at least the mark he intended, when he chose his famed title.

“I think he’s not referring to how do you get two species of finch out of one,” Dr. Futuyma said of “Origin of Species.” “I think what he means is something much more embracing, something we would today call the origin of biological diversity. You could be talking about two species of finches or a human versus a giraffe or an oak tree for that matter. The world is full of species, and his book clearly embraces the whole thing.

”Darwin’s own last words in the book suggest just such a broad scope: “There is grandeur in this view of life,” he wrote, that “from so simple a beginning endless forms most beautiful and most wonderful have been, and are being, evolved.”



16) February 10, 2009

Crunching the Data for the Tree of Life

By CARL ZIMMER
New York Times


Michael Sanderson is worried. Dr. Sanderson, a biologist at the University of Arizona, is part of an effort to figure out how all the estimated 500,000 species of plants are related to one another. For years now the researchers have sequenced DNA from thousands of species from jungles, tundras and museum drawers. They have used supercomputers to crunch the genetic data and have gleaned clues to how today’s diversity of baobabs, dandelions, mosses and other plants evolved over the past 450 million years. The pace of their progress gives Dr. Sanderson hope that they will draw the entire evolutionary tree of plants within the next few years. “It’s within striking distance,” Dr. Sanderson said.

There’s just one problem. “We have no way to visualize such a tree at the moment,” he said. If they tried, they would end up with a blurry, inscrutable thicket. “It would be ironic,” Dr. Sanderson said. “We’d be saying, ‘We’ve built it, but we can’t show it to you.’

”Ever since Charles Darwin first sketched a spindly sapling in 1837, biologists have relied on evolutionary trees to understand the history of life. Today biologists draw evolutionary trees to help them track the emergence of new diseases, identify species at risk of extinction, and trace the history of disease-related genes in the human genome. Within the next few decades, biologists may figure out how the millions of species on Earth are related to one another. But for people to actually see that tree of life, the tree itself will have to evolve.

Biologists have responded to the problem by enlisting the help of computer scientists and software designers from companies like Google and Adobe to find a new way of looking at evolution. Their goal is to create a program that allows scientists and nonscientists alike to fly through evolutionary trees.

“Just like Google Earth changed the way people look at geography, a sophisticated tree of life browser could really change the way we look at the life around us,” said Mark W. Westneat, the director of the Biodiversity Synthesis Center at the Field Museum in Chicago.

Darwin drew the first evolutionary tree when he was 28. He had recently returned to England from his five-year voyage around the world aboard the Beagle, and his theory of evolution was still in an embryonic state. It occurred to him that evolution could explain the similarities and differences between species. The descendants of an ancestral species might have evolved into different forms, splitting into separate lineages “like the branching of a great tree from a single stem,” as he would later write in “On the Origin of Species.

”Darwin’s first tree is now a familiar sight in books, museum exhibits and, of course, on Wikipedia. But David Kohn, the director of the Darwin Digital Library at the American Museum of Natural History, has recently discovered 10 other trees that Darwin drew in later years. “It’s a long-term preoccupation,” Dr. Kohn said. “It feels like he’s using it to think.” While pondering how humans evolved, Darwin drew a cluster of branches to represent our common ancestry with apes and monkeys.

But during Darwin’s life, he published only a single tree. In the “Origin of Species” he included a set of branching lines, marked only by letters. “It was all at a very theoretical level,” said David Hillis, a biologist at the University of Texas. (Read Dr. Hillis's comments on Darwin's "On the Origin of Species.")

Darwin left it to other biologists to figure out what real evolutionary trees looked like. In 1879, for example, the German biologist Ernst Haeckel published a tree, complete with bark and leaves, showing humans and animals evolving from single-celled creatures.

The science of tree-building took a significant step forward in the late 1900s. Biologists set up standard rules for comparing species and figuring out who was most closely related to whom. Once they were all speaking the same scientific language, they could test each other’s hypotheses with new evidence. They also began to get new kinds evidence for their trees. It became possible to compare not just the skeleton or color patterns of species, but also their proteins and genes.

At first biologists could draw only small trees, typically with a dozen branches at most. They were held back by the fact that a group of species may possibly be related in many different ways. If a biologist adds more species to a group, the possibilities explode. “For 25 species, there are more possible trees than there are stars in the known universe,” Dr. Westneat said. “For 80 species, there are more trees than there are atoms in the known universe.

”Simply comparing every single tree would be impossible. Fortunately, mathematicians developed statistical methods for searching quickly through potential trees to find the ones that do the best job of explaining all the evidence. Computers could do millions of calculations for biologists and store a growing database of information on Web sites. Trees grew hundreds of new branches, then thousands. “We’re overwhelmed with information,” Dr. Hillis said.

Today trees with thousands of branches, sometimes called “supertrees” or “megatrees,” are starting to appear in scientific literature. Their branches reveal patterns in evolution that were missed in smaller studies.

In 2007, for example, Olaf Bininda-Edmonds, a biologist at Carl von Ossietzky University in Germany, and his colleagues published a tree of 4,500 mammals — in other words, just about every known mammal species. The tree allowed researchers to estimate the rate at which mammals have evolved into new lineages. For decades, many researchers have argued that most major groups of living mammals evolved after the dinosaurs became extinct 65 million years ago. Based on their mammal supertree, Dr. Bininda-Emonds and his colleagues argued that mammals were diversifying millions of years earlier.

Less than two years later, the mammal supertree is looking puny. In a paper to be published in the journal BMC Evolutionary Biology, Stephen Smith of the National Evolutionary Synthesis Center in North Carolina and his colleagues have created a tree containing 13,533 species of plants. Their study shows that ferns — sometimes considered as living fossils that have changed little for hundreds of millions of years — have actually been evolving faster than younger groups of plants, like conifers and flowering plants.

Plants are not just related to one another. They’re also related to us animals, fungi, bacteria and all other living things on Earth. Over the past seven years, the National Science Foundation has been financing a project known as Assembling the Tree of Life, the goal of which is “to reconstruct the evolutionary origins of all living things,” according to its Web site. Research teams are analyzing slices of the tree, while mathematicians and computer scientists work on methods to combine them into a single analysis. “You can just imagine how Darwin would have enjoyed it,” Dr. Kohn said.

Darwin would probably not enjoy trying to draw such a tree, though. “Even when the mammal supertree is printed out at two meters by two meters, the species names remain virtually unreadable,” Dr. Bininda-Emonds said. “It’s a Google Earth kind of problem. You can’t simultaneously see where Central Park is in New York, and where New York is in the United States.

”It has become clear to biologists that they are going to have to find new ways to draw evolutionary trees. “Our advances in understanding evolution are moving really fast now, but the tools for looking at these big trees are lagging behind,” Dr. Westneat said.

The future of evolutionary trees may be on display on a wall in Dr. Sanderson’s laboratory in Tucson. He and his colleagues have mounted a bank of flat-screen monitors that can show off a program they have designed called Paloverde. Dr. Sanderson can transform an evolutionary tree into a three-dimensional structure, and then use his mouse to navigate through it, zooming in on particular branches he wants to inspect.

It’s a mesmerizing sight, but Dr. Sanderson is quick to point out its limits. “My program can handle 1,000 species fairly effectively. When you get to 5,000 species, it gets very slow and not very beautiful,” he said.

To bring evolutionary trees up to date, biologists are working with computer scientists and other visualization experts. Dr. Westneat has been organizing meetings over the past year to bring the two cultures together. “It has the potential to move us beyond what biologists with a little bit of programming can do,” Dr. Westneat said.

Even with the help of visualization experts, biologists won’t be able to fly through the tree of life any time soon. “It’s definitely not small potatoes — it’s cutting-edge research,” said Tamara Munzner, a computer scientist at the University of British Columbia.

Dr. Munzner is working on methods to allow biologists to see details of the tree of life without losing sight of its overall shape. One of her programs acts like a fisheye lens, blowing up clusters of branches. She has also figured out how to make trees rubbery, so that a biologist can stretch some parts of it open and squeeze others down. Although a few thousand branches may slow down Paloverde, Dr. Munzner’s programs can handle millions of branches.

For Dr. Hillis, drawing the tree of life is not something to do simply because it’s there. He thinks it will become a practical tool, in the same way online databases of DNA have become practical tools for geneticists.

“What I’d really like is the entire tree of life on a small hand-held device,” Dr. Hillis said. Biologists would be able to put a tissue sample from a plant, animal or other organism in the machine, which would then scan its DNA and find its place in the tree of life, even if it’s a new species. The data could then be uploaded to a database, so that every biologist’s machine would get an updated tree. “It would be a ‘tricorder’-like device, able to identify any species on Earth in the field,” he said.

If biologists do ever succeed in drawing the tree of life, it will look profoundly different from Darwin’s sketch. Lineages do branch as they evolve, but sometimes the branches join back together. It has long been known that separate plant species sometimes produce hybrids that can no longer interbreed with their parent species. In other words, they become new species. When biologists draw the relationships of some groups of plant species, their pictures look more like webs than trees.

In other cases, genes don’t have to wait for two species to come together — they simply leap from one branch of life to another.

Viruses sometimes infect a new host species, and in the process they transfer genes from its previous host. Many species of bacteria can slurp up naked DNA or pass it to one another on tiny genetic ringlets.

“Each gene has its own evolution. It’s not inherited from mother to daughter; it’s inherited from a neighbor,” said Peer Bork of the European Molecular Biology Laboratory.

Biologists are just starting to understand how this different kind of heredity alters the tree of life. Although genes may move from one species to another fairly often, it may be rare that they become a permanent part of a new genome. Tal Dagan, a biologist at the University of Düsseldorf, has estimated their impact by analyzing hundreds of thousands of genes from microbes. She estimates that 80 percent of the genes in any microbe have been passed from one species to another at some point.

Dr. Dagan and her colleagues have not simply published their results as a table of numbers, though. “We had to have a new picture of evolution,” she said.

For Dr. Dagan, evolution is still shaped like a tree. “Most of the evolution is still going on in the branches,” she said. But over billions of years, thousands of genes have shuttled among the branches. To drive this point home, Dr. Dagan and her colleagues have drawn a dense filigree of lines between the branches of the tree of life. “You see the tree and you see the thousands of edges, and you know this is how it is,” she said.Could these sorts of evolutionary vines be added to a complete tree of life without letting visitors get lost in the complexity? “It does make things more complicated,” Dr. Munzner said.

“But it doesn’t mean it’s hopeless. My answer is, ‘Bring it on.’


”This article has been revised to reflect the following correction:

Correction: February 19, 2009 An article on Feb. 10 about efforts to create complete evolutionary trees misspelled the name of a computer program that can navigate through a three-dimensional evolutionary tree. It is Paloverde, not Paleoverde. The article also misspelled a type of tree that researchers have studied. It is the baobab, not baobob.



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http://gonashgo.blogspot.com/2009/08/500blogpost-five-hundred-is-blogpost.html
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In Shia Islam, intellect is a key component of faith. Intellect allows us to understand the creation of God: Aga Khan IV(2008)
The Qur'an itself repeatedly recommends Muslims to become better educated in order better to understand God's creation: Aga Khan IV(2007)
The Quran tells us that signs of Allah's Sovereignty are found in the contemplation of His Creation: Aga Khan IV(2007)
This notion of the capacity of the human intellect to understand and to admire the creation of Allah will bring you happiness in your everyday lives: Aga Khan IV(2007)
Islam, eminently logical, placing the greatest emphasis on knowledge, purports to understand God's creation: Aga Khan IV(2006)
The Holy Qu'ran's encouragement to study nature and the physical world around us gave the original impetus to scientific enquiry among Muslims: Aga Khan IV(1985)
The first and only thing created by God was the Intellect(Aql): Prophet Muhammad(circa 632CE)