Harvard to Investigate Origins of Life, etc

Here are news items with my comments in square brackets:

Harvard to Investigate Origins of Life, ABCNEWS/ Associated Press Aug. 16, 2005 - Harvard University is joining the long-running debate over the theory of evolution by launching a research project to study how life began. The team of researchers will receive $1 million in funding annually from Harvard over the next few years. The project begins with an admission that some mysteries about life's origins cannot be explained. "My expectation is that we will be able to reduce this to a very simple series of logical events that could have taken place with no divine intervention," said David R. Liu, a professor of chemistry and chemical biology at Harvard. The "Origins of Life in the Universe Initiative" is still in its early stages, scientists told the Boston Sunday Globe. Harvard has told the research team to make plans for adding faculty members and a collection of multimillion-dollar facilities. Evolution is a fundamental scientific theory that species evolved over millions of years. It has been standard in most public school science texts for decades but recently re-emerged in the spotlight as communities and some states debated whether school children should also be taught about creationism or intelligent design. The theory of intelligent design says life on earth is too complex to have developed through evolution, implying that a higher power must have had a hand in creation. Harvard has not been seen as a leader in origins of life research, but the university's vast resources could change that perception. "It is quite gratifying to see Harvard is going for a solution to a problem that will be remembered 100 years from now," said Steven Benner, a University of Florida scientist who is one of the world's top chemists in origins-of-life research. ... [The references to "the long-running debate over the theory of evolution … whether school children should also be taught about creationism or intelligent design," "intelligent design says life on earth is too complex to have developed through evolution" and "with no divine intervention" is a dead give-away that Harvard (which up till now has shown little or no interest in origin of life research) is reacting to the rising tide of scepticism about evolution. As Phil Johnson observed, "If Darwinists are to keep the Creator out of the picture, they have to provide a naturalistic explanation for the origin of life." (Johnson P.E., "Darwin on Trial," 1993, p.103). Antony Flew's abandoning of atheism for deism because, "It has become inordinately difficult even to begin to think about constructing a naturalistic theory of the evolution of that first reproducing organism" (Philosophy Now) would not have gone unnoticed among the Harvard secular elite. It is also a tacit admission that, more than a half-century since the Miller-Urey experiment (1953), materialistic-naturalistic science has no explanation of the origin of life. Note that the proposition there was "no divine intervention" in the origin of life is "science", and so can be taught in schools, but the counter-proposition that there was divine intervention" is dismissed as "religion" and so cannot be taught in schools!]

Study: Most Wild Chimps Are Southpaws, ABCNEWS/ Associated Press … RANDOLPH E. SCHMID AP Science Writer The Associated Press Aug. 16, 2005 - When it comes to fishing tasty termites out of their mounds, wild chimpanzees don't have the right stuff. Most, in fact, are southpaws. A three-year study of 17 wild chimps in Gombe National Park, Tanzania, found that 12 of them used their left hands when using sticks to probe for termites. Four were right-handed and one was listed as ambiguously handed. "Contrary to previous claims, wild chimpanzees show population-level handedness in tool-use," reported the research team led by William D. Hopkins of the Yerkes National Primate Research Center at Emory University in Atlanta. Population-level handedness indicates a preference for one hand in a large group. Hopkins' findings are reported in Tuesday's issue of Proceedings of the National Academy of Sciences. The paper also looked at previous studies of chimpanzees and found that others had noted a left-handed preference when using sticks to fish for termites, but there had been reports of a right-handed preference when cracking nuts. Scientists have long debated whether nonhuman primates exhibit handedness. Because the hands are controlled by opposite sides of the brain, the finding could indicate that this brain division had begun as long as 5 million years ago, prior to the split between humans and chimpanzees. Richard W. Byrne of the University of St. Andrews in Fife, United Kingdom, who has reported on hand-preference in mountain gorillas doing complex tasks, said: "It now looks as if whatever gives a population skew to manually skilled behavior has its roots deep in the shared ancestry of humans and all other African great apes." ... A larger question concerns the evolution of language, Hopkins said in a telephone interview. Most people, right and left handed, use the left hemisphere of the brain to process language, he explained. The argument has been made that if humans developed language after the split from apes, and language is related to handedness, then there shouldn't be handedness in apes, he said, "This reinforces the view that the whole historical link between language and handedness is probably not a correct one and people need to rethink those ideas," Hopkins said. ...
Study: Chimps show hand preference, CNN, August 16, 2005 … Chimpanzees in captivity show a right-handed preference for some tasks, but researchers have wondered if this because they are raised by humans, who are mostly right-handed. ... Humans are still far more likely than chimps to be right-handed. It could be there was a genetic mutation favoring right-handedness in humans, the researchers said. Or it could be that this is a reflection of the unique organization of human brains, they added.[If chimps were predominantly right-handed like humans, it would be hailed as evidence of our close relationship. Therefore, the opposite handedness in chimps from humans is evidence of a more distant relationship. This also indicates that the language ability in humans arose after the chimp-human split. This reminded me of what Gould pointed out about the differences between humans and chimps:

"The genetic differences between humans and chimps are minor, but they include at least ten large inversions and translocations. An inversion is, literally, the turning around of a chromosomal segment. Each hybrid cell would have a set of chimp and a corresponding set of human chromosomes. Egg and sperm cells are made by a process called meiosis, or reduction division. In meiosis, each chromosome must pair (lie side by side) with its counterpart before cell division, so that corresponding genes can match up one to one: that is, each chimp chromosome must pair with its human counterpart. But if a piece of human chromosome is inverted relative to its counterpart in chimps, then gene-by-gene pairing cannot occur without elaborate looping and twisting that usually precludes successful cell division." (Gould S.J., "Ever Since Darwin: Reflections in Natural History," [1978], Penguin: London, 1991, reprint, p.55)

Each of those "ten large inversions and translocations" would presumably mean a new species (for the "meiosis" reason that Gould gave), so while I accept that humans and chimps share a common ancestor, there are probably at least ten species in between them and us.]

Cloning a world away, Roger Highfield, Daily Telegraph, 10 August 2005. ... In the light of cloned mice, goats, horses, pigs, deer, carp and fruit flies, the creation of Snuppy by South Korea's king of cloning, Prof Wook-Suk Hwang, shows that there is no fundamental reason why humans cannot be cloned, though experiments to date underline how risky and inefficient the process is. ... Early cloning attempts relied on sea urchins, salamanders, frogs and other creatures which have big eggs that are conveniently delivered as spawn. These cold-blooded pioneers were used to explore the biology of development to shed light on whether creatures were fully formed at the moment of fertilisation, and just grew, or if they developed from a single cell to the complex arrangement of billions in an adult. Nuclear transfer was first used almost a century ago by the great German embryologist Hans Spemann, who used a delicate hair from Margrette, his baby daughter, as a noose to manipulate a newly fertilised salamander egg. ... Evidence that all of the cells of an adult contained the recipe to make an individual was obtained in the 1950s by John Gurdon at Oxford University, who was trying to clone the African clawed frog Xenopus laevis. He went on to create 30 albino frogs, cloned by nuclear transfer from the cells of an albino tadpole into the eggs of normally pigmented frogs. One of his pupils, Chris Graham, wanted to develop nuclear transfer for mice and this marked the start of efforts to clone mammals that culminated in 1986 in the work of Steen Willadsen, an inventive Dane working in Cambridge. His lambs were the first mammals to be cloned beyond any doubt by nuclear transfer and his work would provide much of the impetus that drove Prof Ian Wilmut to create Dolly at the Roslin Institute, near Edinburgh. Over the years, Hollywood has invested millions in cloning fantasies. ... Copies of Adolf Hitler starred in the 1978 movie of another Ira Levin novel, The Boys From Brazil. ... Based on Prof Hwang's experience with Snuppy (although, admittedly, there are technical reasons why dogs are hard to clone) to ... clone a baby would mean obtaining more than 1,000 fresh human eggs, which are in very short supply, and using them to create 1,000 cloned embryos. If the Snuppy example holds true, these would then be implanted in 123 women. Of those surrogate mothers, all but one would risk the hurt and turmoil of the pregnancy failing, of miscarriages and deformed foetuses. Another common problem with nuclear transfer is unusually big offspring. Prof Wilmut also fears the psychological effects on a clone. In short, despite Hollywood's efforts to make it look easy, even a totalitarian dictator would find it tough to indulge a narcissistic cloning fantasy. ... [I did a major assignment on cloning in a molecular biology unit 3-4 years ago, and my conclusion then was that humans, who are particularly difficult to clone, apart from the ethical, social, economic and legal reasons (a cloned human, unlike a dog, could sue its creators), would never be cloned. It is nice to see this now being increasingly acknowledged. Indeed, so many are the problems of cloning, it is unlikely that even the original idea of cloning identical lines of high-quality farm animals (to replace the hit and miss of selective breeding) is an economic proposition.]

Did double whammy of volcano and asteroid wipe out dinosaurs?, Steve Connor, The Independent 17 August 2005 ... 16 August 2005 Volcanic eruptions may have triggered the demise of the dinosaurs. Many scientists believed that an asteroid caused the mass extinction 65 million years ago. However, a new study points to a more complex event that began with a series of eruptions which took place in what is now north-western India. The Deccan Traps in Maharashtra state are flows of lava resulting from huge outpourings of molten rock and ash. A mile deep, they cover about 200,000 square miles. Vulcanologists have long thought the eruption, dated to about 65 million years ago, could have caused the extinction. However, the Deccan Traps resulted from a series of eruptions that occurred over perhaps a million years. This would have given the global climate plenty of time to adjust. But the study shows a major part of the eruption occurred over a short period. Scientists from the Institut de Physique du Globe de Paris calculated that at least 2,000ft of lava was deposited in 30,000 years, which could have greatly altered global climate. They have also shown that the Traps were erupting when the asteroid crashed into what is now Mexico. This was a spectacular and almost unprecedented double whammy for Earth. Mike Widdowson, a vulcanologist, said it seems the end of the dinosaurs may have begun with climate change brought about by the eruptions and ended with the asteroid. "The eruptions pre-conditioned the global environment toward a catastrophic tipping point before the impact occurred. The asteroid was the coup de grâce," he said. ... [Another article on this that makes it clearer that the K/T mass extinction that took out the dinosaurs was an "almost unprecedented double whammy for Earth", in a short period of global warming caused by the greenhouse effect of volcanic emissions, then a sudden period of global cooling by the asteroid impact's `nuclear winter'. Since without this `one-two punch' we would not be here, I regard this as another fine-tuned event by an Intelligent Designer (who I assume is the Christian God), in preparing the Earth for man. I will add this also to section PC 8.3.1.1.1 "Preparing Earth for Life and Man ... Pruning the Tree of Life ... The Cretaceous-Tertiary (K/T) extinction " to the outline of my planned second book "Progressive Creation"]

Building a Virtual Microbe, Gene by Gene by Gene, Carl Zimmer The New York Times, August 16, 2005, Michael Ellison has a dream: to reconstruct a living thing inside a computer, down to every last molecule. It is, he said, "the ultimate goal in biology to be able to do this." It's a dream that Dr. Ellison, a biologist at the University of Alberta, shares with other scientists, who have imagined such an achievement for decades. Understanding how all of the parts of an organism work together would lift biology to a new level, they argue. Biologists would be able to understand life as deeply as engineers understand the bridges and airplanes that they build. "You can sit down at a computer, and you can design experiments, and you can see the performance of this thing, and then you can figure out why it's done what it's done," Dr. Ellison said. "You're not going to recognize the full return of the biological revolution until you can simulate a living organism." In the past few years this fantasy has become plausible and now Dr. Ellison is part of an international team of biologists who are now trying to make it a reality. They have chosen to recreate Escherichia coli, the humble resident of the human gut that has been the favorite species for biology experiments for decades. "We picked the simplest organism about which we know the most," Dr. Ellison said. Scientists may know more about E. coli than they do about any other species on earth, but that doesn't mean that creating a virtual E. coli will be a snap. Many mysteries remain to be solved, and at the moment even a single E. coli may be too complex to recreate in a computer. But the effort is still worthwhile, some scientists argue, because it would become a powerful tool for drug testing, genetic engineering and for understanding some of life's deepest mysteries. Discovered in 1885, Escherichia coli soon proved easy to raise in laboratories. Its popularity boomed in the 1940's when scientists figured out how to use it to pry open the secrets of genes. In the 1970's scientists figured out how to insert foreign DNA into E. coli, turning them into biochemical factories that could churn out valuable compounds like insulin. ... Research on E. coli accelerated even more after 1997, when scientists published its entire genome. Scientists were able to survey all 4,288 of its genes, discovering how groups of them worked together to break down food, make new copies of DNA and do other tasks. Some scientists speculated that before long they might understand how all of the pieces of E. coli worked together. Such speculations were not new. In 1967, Francis H. C. Crick, the co-discoverer of DNA, and the Nobel Prize-winning biologist Sydney Brenner had called for "the complete solution of E. coli." But the call went unheeded for over 30 years. After all, E. coli contains an estimated 60 million biological molecules. Simulating all of them at once was an absurdly difficult task. But by the late 1990's, it began to look plausible, although not necessarily easy. Despite decades of research, many of E. coli's genes still remain a mystery - "probably around 1,000 genes," Dr. Thomas said. "There's a lot more we need to know about E. coli before we can build a really solid model." ... As knowledge of E. coli grows, scientists are starting to build models of the microbe that capture some of its behavior. "This field is moving forward very aggressively," said Bernhard Palsson of the University of California, San Diego. Dr. Palsson models E. coli's metabolism. ... Meanwhile, researchers at the laboratory of Philippe Cluzel at the University of Chicago have been focusing their efforts on making E. coli swim. The microbe swims with several spinning tails, each driven by a motor revolving 270 times a second. If the tails turn counterclockwise, they all wrap into a bundle that can propel E. coli forward. If the microbe makes the motors turn clockwise, on the other hand, the tails fly apart and send E. coli into a tumble. By alternatively swimming and tumbling, E. coli can navigate through its tiny world. It "decides" which way to spin its motors based on the information it gets from sensors that stud its outer membrane. "It's a big information-processing network," said Thierry Emonet, a research scientist at the University of Chicago. To understand this microbial computer, Dr. Emonet and his colleagues have created a virtual E. coli that can sense its surroundings and decide how to swim. They simulate the chemical reactions that carry signals from sensors to motors, and then track the path a virtual E. coli takes through three-dimensional space. ... Dr. Emonet said he hoped that his model would allow scientists to understand other sorts of decisions made by cells. Cells "decide" to divide in response to certain signals, for example, and runaway cell division can lead to cancer. Understanding the simple decisions of E. coli may help researchers understand the decisions of more complex cells like those in our own bodies. "If you can't understand how a single E. coli is able to find food by passing information from the outside to the inside, there's very little hope for understanding a system like cancer," Dr. Emonet said. A full-blown model of E. coli would be able not only to swim, but eat food, fight off invading viruses, make copies of its DNA, and do many other tasks all at the same time. Scientists agree that building a multitasking model would be a daunting job. "Technically, that's incredibly more difficult," Dr. Thomas said. Dr. Ellison and his colleagues have decided to take the first steps toward creating a full-blown model. They want to begin by simulating a simplified E. coli. "We're going to strip E. coli down to about one-quarter of its original size," Dr. Ellison said. Dr. Wanner is working with colleagues in Japan to make this minimal E. coli. "We're trying to knock out groups of 100 genes at a time," Dr. Wanner said. They hope to produce a stripped-down E. coli with only around 1,000 genes within two years. .... The researchers hope to use the model to recreate an entire E. coli, complete with genes, enzymes, membrane channels and other parts. There is one major catch, however. Even a stripped-down E. coli is so complex that no existing program can simulate it. "Our gamble in this is that computers are getting more powerful, so we build the framework and within 5 or 10 years the computers will be able to deal with this," Dr. Ellison said. "Assuming the speed of computing keeps increasing, I don't see why it's not possible," said Dr. Emonet ... But, like some other scientists, he has some reservations about its usefulness. "Even if we could make a simulation of everything inside E. coli today, that does not mean we would understand it," he said "The trick is to build the thing in steps and check that you understand the phenomena one at a time." A full-blown model of E. coli is still worth the effort, many scientists argue, because of its potential benefits. Scientists could
adapt the E. coli model to more complex human cells to simulate how they react to different drugs. "Then you can really do genetic engineering," Dr. Ellison said. "I mean where you can actually design an organism or change it in massive ways. When people talk about genetic engineering today, it's really kind of a joke because they mean, 'I moved a gene from one organism into another organism, and I'm going to pray that it works.' " A virtual E. coli could allow scientists to see in advance how major changes to the microbe would affect it. "That opens up a huge amount of opportunity," Dr. Ellison said. ... [Personally I doubt that they could ever completly model an entire bacterium like E. coli. And even if they did, the simulation would be so complex that no human mind could understand it. But it will be interesting if they work out its the information content. The "motor revolving 270 times a second" that is controlled by "a big information-processing network" is none other than the bacterial flagellum! It will be particularly interesting if they can work out the information content of that!]

Stephen E. Jones, BSc (Biol)
"Problems of Evolution"