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The Darwiniacs play a shell game with the evidence, but the evidence is never under any of the shells.... In the end, evolutionists only argument is contempt. The cultists know that if people were allowed to hear the arguments against evolution for just sixty seconds, all would be lost. So they demonize the people making those arguments. | |||||||||||||||||||
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Journals Consistently Tout Embryonic Stem Cells, Criticize Bush 07/31/2006
Adult-derived stem cells are the only form of stem-cell therapy to make it to the clinic so far. For example, stem cells from bone marrow (pictured) have been used for more than 30 years to treat blood disorders. Adult stem cells are less likely to cause tumours than embryonic stem cells, and less likely to be rejected by the immune system.Whether the number of adult stem-cell therapies is 65 or 9, depending on how words are defined, this statement supports the conservative contention that embryonic stem cells have no proven cures, while adult stem cells have severalor many. It must also not be forgotten that the complaints against President Bush and other conservative politicians opposing ES research is over funding. There is no ban on ES research; the debate is over whether taxpayers should pay for it. A subtext in the articles, no matter how adamant, is that the editors and scientists are aware of and sensitive to the ethical problems. This is clear in the frequent attempts to assuage the concerns of ethicists. They uniformly announce opposition to human cloning, a sister technology to ES research, and usually warn against the creation of human-animal chimeras by similar lab techniques. As an example, Nature, while discussing a possible way around the creation of embryos for destruction, said, But tampering with human embryos in this way may not address everyones ethical concerns. In the Editorial, Nature also admitted, It can be argued in good faith that not a single embryo should be destroyed in the name of medical progress. But then it justified the use of embryos from fertility clinics already slated for destruction. If the taxpayers dont fund the derivation of ES lines (non-federal funds would be required for that part), then everyone should be happy: why, look how well it works in another ethically-charged situation This may seem like a subtle point, but it exactly this kind of compromise that has forged Americas uneasy but workable abortion policy: abortions are legal, but in no case are taxpayers required to see their dollars fund them. It may be tenable to argue that dissenters should not be asked to finance a practice that they find morally unacceptable. What is not acceptable is for the president to use false pretences to stand in the way of a compromise that the Congress has sensibly endorsed.If Nature is a science magazine, and science is ethically neutral, what are UK editors doing criticizing the ethics of American politicians? Lets follow their ethical argument. If its OK for private parties to create embryos (the ethically debatable part), and then the taxpayers simply pay for scientists to use the embryos, is there a difference in allowing private parties to buy slaves, and taxpayers to fund using slave labor to build federal projects? If certain people are slated for the gas chambers anyway, why not do some medical research on them and learn something that can help the country in the next war? If people are going to have abortions anyway, should taxpayers fund organ farms where the fetuses, instead of being destroyed, could be used for research or organ transplants? If someone else does the dirty work of stealing, robbing, or committing mayhem, is it morally acceptable for the public to utilize the products? It should be obvious that rationalizing the results of a deed create a market for it. Similar compromise arguments were used by slave states 150 years ago: if you dont like slavery, go north. If you dont like experimenting on human subjects, move out of Germany or North Korea. Compromise with evil never works. America fought a bloody war to affirm the dignity of all people, and we are a better country for it. If the creation of human embryos is a moral evil, and if abortion is a moral evil, then compromise is not an option. Science can inform the debate, but it is not the role of scientific elitists to make ethical decisions for the rest of us.Opal Plesiosaurs, Flashy Pterosaurs and Hot Titanosaurs Inspire Stories 07/30/2006 ![]() Paleontologists continue to dig up bones of fascinating species of long-lost animals. When it comes to extinct species, the line between observation and interpretation becomes fuzzy, since there is no way to be absolutely sure how they behaved and what they were doing when they died. This does not prevent scientists from freely speculating on what the bones tell us.
Bones are interesting, dinosaurs are fun, and gathering data is good Baconian exercise. Most people are not content with dry accumulations of facts, however, and want a story to put them in context. Scientists are usually happy to oblige this desire. Its nice when they go to the trouble to state when the facts end and the speculation begins. All too often they leave that task to the reader and the artist.Self-Correcting RNA: Is It a Missing Link? 07/28/2006 ![]() A team of Russian scientists at Rutgers discovered a remarkable phenomenon: RNA that proofreads itself during its own synthesis. The work was reported in Science1: We show that during transcription elongation, the hydrolytic reaction stimulated by misincorporated nucleotides proofreads most of the misincorporation events and thus serves as an intrinsic mechanism of transcription fidelity. It has already been known that DNA transcription and translation includes a whole suite of error-correcting mechanisms, but this is the first instance of RNA self-correction. The researchers did not comment on the evolution of this capability except to state that it is likely evolutionarily conserved (i.e., unevolved in all living organisms), and that in an RNA-protein world, a proofreading and repair mechanism similar to the one described here could have allowed a large RNA genome of the last common universal ancestor to exist. This is because without an accurate proofreading mechanism even in an RNA world, duplication fidelity would have been too low for evolution: the relatively low fidelity of RNAP-catalyzed synthesis could not have been sufficient for stable maintenance of large RNA genomes in the absence of cleavage factors. Patrick Cramer (Gene Center Munich), however, writing in the same issue of Science,2 launched their final, speculative paragraph into a story of how this RNA must be a missing link. Starting with the admission that Precision can be vital, Cramer immediately invoked the E word: cells have evolved processes for proofreading and correction to shut down the propagation of errors in the DNA-to-protein pathway. Referring to the work by Zenkin et al., he said, This finding helps to explain the fidelity of gene transcription and suggests that self-correcting RNA was the genetic material during early evolution. But how, exactly, could that have come about? In his missing-link story, notice how many times Cramer used speculation words like could, probably and suggests compared to the hard requirements of reality: The discovery of self-correcting RNA transcripts suggests a previously missing link in molecular evolution. One prerequisite of an early RNA world (devoid of DNA) is that RNA-based genomes were stable. Genome stability required a mechanism for RNA replication and error correction during replication, which could have been similar to the newly described RNA proofreading mechanism described by Zenkin et al. If self-correcting replicating RNAs coexisted with an RNA-based protein synthesis activity, then an early RNA-based replicase could have been replaced by a protein-based RNA replicase. This ancient protein-based RNA replicase could have evolved to accept DNA as a template, instead of RNA, allowing the transition from RNA to DNA genomes. In this scenario, the resulting DNA-dependent RNA polymerase retained the ancient RNA-based RNA proofreading mechanism.Of course, being only a scenario for how proofreading could have evolved, Cramer offered no evidence, lab or otherwise, for such a self-correcting RNA missing link. For a discussion of problems with the RNA-world scenario, see the 07/11/2002 entry. 1Zenkin, Yuzenkova and Severinov, Transcript-Assisted Transcriptional Proofreading, Science, 28 July 2006: Vol. 313. no. 5786, pp. 518 - 520, DOI: 10.1126/science.1127422. 2Patrick Cramer, Perspectives: Molecular Biology: Self-Correcting Messages, Science, 28 July 2006: Vol. 313. no. 5786, pp. 447 - 448, DOI: 10.1126/science.1131205. Was blindness ever so dark as to look design in the eye, and attribute it to mindless chance? The blind see naught but their own imaginations. Cramer took an incredibly wondrous phenomenon (imagine! self-correcting code) and weaved a purely fictional tale about how it emerged from The Ancient Soup. Yet this is the myth that our culture only allows to be heard by students in public schools, because any other explanation, such as design, is classified as religion (along with, presumably, rocket-launching Hezbollah terrorism). In the same issue of Science was a very positive book review of a new work about Richard Dawkins, the rabidly atheistic Darwinist who subscribes to the Ancient Soup myth or something very like it: reviewer David C. Queller says, Dawkins spills his own dirty, obscene secret, again no less powerful now that we have known it for 30 years. All flesh is survival machinery, and the survival it promotes is that of our selfish genes.Eye Sends Information at Ethernet Rates 07/27/2006 ![]() Neuroscientists from Pennsylvania and New Jersey calculated the information rate of the eye. Using guinea pigs (real guinea pigs, not humans as guinea pigs), they came up with a number and interpolated it for humans: In the classic What the frogs eye tells the frogs brain, Lettvin and colleagues showed that different types of retinal ganglion cell send specific kinds of information. For example, one type responds best to a dark, convex form moving centripetally (a fly). Here we consider a complementary question: how much information does the retina send and how is it apportioned among different cell types? Recording from guinea pig retina on a multi-electrode array and presenting various types of motion in natural scenes, we measured information rates for seven types of ganglion cell. Mean rates varied across cell types (6-13 bits s-1) more than across stimuli. Sluggish cells transmitted information at lower rates than brisk cells, but because of trade-offs between noise and temporal correlation, all types had the same coding efficiency. Calculating the proportions of each cell type from receptive field size and coverage factor, we conclude (assuming independence) that the approximately 105 ganglion cells transmit on the order of 875,000 bits s-1. Because sluggish cells are equally efficient but more numerous, they account for most of the information. With approximately 106 ganglion cells, the human retina would transmit data at roughly the rate of an Ethernet connection.Their article, published in Current Biology,1 also discussed the difference between sight and sound processing: specifically, why is auditory information sent to the brain at much higher efficiency? Frog auditory nerve fibers, for instance, are reported to encode naturalistic stimuli with an efficiency sometimes reaching approximately 90% of capacity, three-fold better than optic fibers. Naturally one wonders why an optic fiber fares so poorly in these comparisons, they said, then proposed an answer based on the different ganglion cell types and the difference in information fields between sight and sound: Auditory fibers apparently achieve their high coding efficiency via a tuned nonlinear filter that selectively amplifies the anticipated signal. A similar strategy is apparently used by the mammalian rod bipolar cell to encode single photon responses. However, this coding strategy, highly effective when the anticipated signal is sparse and well defined, may serve poorly for ganglion cells because the information of biological interest in natural scenes is so varied that highly tuned, nonlinear filters would either reject too much information or require too many cell types.Thats why many of the ganglion cells are of the sluggish variety. Because the dominant metabolic cost in neural signaling is associated with spiking, the cables with lower firing rates would save considerable energy. Likewise, theoretical studies predict that metabolic cost is minimized when signals are distributed over many weakly active cells. That may not be the only reason for multiple cell types. Theres a lot of processing the eye has to do. Some cells zero in on the narrow details, and others need to summarize a rapidly-changing big picture. The solution is a mixture of cell types, to optimize the benefits and trade-offs of each sensory strategy: Spatial acuity requires narrow-field cells with a high sampling rate. Because such a type must necessarily distribute densely, its information rate should be relatively low to reduce costs. On the other hand, encoding of high stimulus velocities requires extended spatial summation and thus a broad-field cellplus the ability to transmit at high bit rates so as not to lose the higher temporal frequencies. Such a cell type must necessarily be expensive, but given the extended dendritic field, this type can be sparse. Consequently energetic considerations probably interact with other constraints to set the number of cell types and a general information rate of roughly 10 bits s-1 and 2 bits spike-1.By the way, the so-called sluggish ganglion cells spiked at up to 75 times per second (though averaging 4 per second over the recording time). Some of the rapid cells spike at over 300 times per second. No wonder your eyes get tired. Incidentally, this paper did not mention anything about the evolution of these capabilities for the frog, the guinea pig, or the human. 1Koch et al., How Much the Eye Tells the Brain, Current Biology, Volume 16, Issue 14, 25 July 2006, pages 1428-1434, doi:10.1016/j.cub.2006.05.056. When our bodys capabilities are compared with machinery, the comparisons are often wonderful and amazing. If 10 megabit-per-second ethernet-eyes dont seem particularly cutting-edge in this age of gigabit-ethernet rates, consider that eyes are only one of millions of sensors across the body transmitting information on touch, taste, smell, and hearing as well as vision. In its little 3-pound CPU, the brain must process that information 24 x 7 for decades. Plus, the kind of information your brain handles is in neural-net form, not the serial data that computers process. It is sent down tiny bundles of neurons in a package that doesnt short out when you go swimming.New to Creation-Evolution Headlines? Tell us what you think: write here.Imagine yourself in a recording studio, watching an orchestra playing a score in sync with a new movie about Robinson Crusoe. Your brain is taking in the complex waveform of a hundred instruments and performing Fourier transforms on it such that you can make out each individual instrument. Simultaneously, the eyes can see the rapid motions of the violinists bows, the action on the screen, and the static information from the studio walls and ceiling. Millions of touch sensors are sending information on the temperature of the room, the feel of your socks, the comfort of the seat, how hungry you are, and much more. Your tongue is reporting the mint candy in your mouth. Your nose is deciphering complex chemical signals in the environment through a series of decoding maps. The brain filters and focuses on information that is important for each moment. As the intensity of the music or screen action rises, adrenaline races through your system switching on organs to be ready for action. Next, your mind is transported to an exotic island, and you become Robinson Crusoe, using all your native senses to the hilt to survive and find your next meal.And this all runs on potatoes! (as Dr. A. E. Wilder-Smith used to say), or on lettuce! (for the guinea pig). Undoubtedly, if we were aware of all the factors involved in the transfer of information from the environment to the mind via our sensory apparatus, the comparison with ethernet transfer rates would seem foolishly simplistic. In this story we have seen again that the more detail is shared about organic workings, the less there is a tendency to discuss evolution. Scientific detail is inversely proportional to evolutionary storytelling.
Honey More Effective than Antibiotics
07/27/2006
The honey article states that the antiseptic property is due to glucose oxidase. This enzyme continually generates small amounts of hydrogen peroxide from the sugars in the honey over time, enough to kill the bacteria without harming the tissues.Genetic Loss Is Evolutions Gain 07/26/2006 ![]() Three scientists in the University of California system found that Repression and loss of gene expression outpaces activation and gain among recently duplicated genes. Surprisingly, publishing in PNAS,1 they claim the non-intuitive hypothesis that this the mother of evolutionary invention. From the abstract: Evolutionists widely acknowledge that regulatory genetic changes are of paramount importance for morphological and genomic evolution. Nevertheless, mechanistic complexity and a paucity of data from nonmodel organisms have prevented testing and quantifying universal hypotheses about the macroevolution of gene regulatory mechanisms. Here, we use a phylogenetic approach to provide a quantitative demonstration of a previously hypothesized trend, whereby the evolutionary rate of repression or loss of gene expression regions is significantly higher than the rate of activation or gain. Such a trend is expected based on case studies in regulatory evolution and under models of molecular evolution where duplicated genes lose duplicated expression patterns in a complementary fashion. The trend is important because repression of gene expression is a hypothesized mechanism for the origin of evolutionarily novel morphologies through specialization.They found that the repression rate of genes is at least twice that of gene activation. They assume that duplicated genes will go their separate ways, and even if down-regulated by the trend toward loss, may undergo subfunctionalization i.e., come up with novel means of achieving function separate from that of the original genes (see 10/24/2003). This begs the question of how the original functions arose. Nowhere in the paper do they explain how novelty can arise, or has arisen, that produces complex function, except to speculate that animal limbs and fly halteres arose through duplication and subfunctionalization. The question of original function and expression, though, is still apt: Overall, our results raise an important question: If gene expression regions are more commonly lost than gained, why is all gene expression not eventually lost over evolutionary time? They surmise that the total expression rate will be constant through the copies; the activation event will have a common ancestry, though two repression events may occur in the daughter genes. How, though, can this create novelty? They do not explain how. They only speculate that since loss occurs, it must be another tool in the evolutionary toolkit: ...our results highlight the fact that because genes and their expression domains duplicate commonly, they must also be lost commonly. As such, the patterns of loss may be as important as gain in dictating the evolution of genomes and phenotypes. More research will be required, they admit, to see if this is the case. If this still seems like getting something for nothing, it all comes together in the last paragraph: In summary, an emerging theme in evolutionary genomics is that loss is a major factor in evolution. For example, gene duplication is quite common, and the fate of most duplicated genes is loss. At least in several cases, DNA loss may be related to a mutational bias, where deletion mutations outnumber insertion mutations. Here we present strong statistical support for a similar loss hypothesis for the evolution of discrete regions of gene expression. Our data were chosen without respect to the hypothesis at hand but represents rapidly duplicating genes, which may have higher rates of expression domain loss. Nevertheless, the methods introduced here are general and could be used to test the hypothesis in future studies by using more data from any species or multiple species. Our results support the idea that gene duplication and loss of discrete, modular expression regions may provide a general mechanism for increased specialization over evolutionary time that may be linked with increases in genomic complexity by gene duplication. 1Todd Oakley et al., Evolution: Repression and loss of gene expression outpaces activation and gain in recently duplicated fly genes, Proceedings of the National Academy of Sciences USA, 10.1073/pnas.0600750103, published online before print July 24, 2006. Folks, it is time to get indignant at the Darwinists. Again. They continue to pull rabbits out of hats with these shenanigans of theirs, their magic words couched in jargon, published in prestigious science journals, trying to make us believe that you can get something for nothing or worse, that trends toward loss produce gains in complexity and function. This is like believing that shopping centers will emerge from the terrorist rockets landing in Haifa. If such ideas should not become part of the official history of Israel, then neither should this dumb idea become part of the corpus of scientific literature. It only happens because non-Darwinians are disqualified from participating in the discussion. The Darwin Partys club lounge of tantalizing speculations is making some biologists fat, lazy and corrupt (12/22/2003). Time to unbar the doors and boot the rascals out.A Second Code Controls the DNA Code 07/26/2006 ![]() More has been discovered about the histone or nucleosome code (see 02/17/2004), a second genetic code independent of the DNA genetic sequence that directs the formation of proteins. The New York Times (see also Science Daily) reported on work by scientists at Northwestern University who found that the wrapping of DNA around nucleosomes (made of proteins called histones with varying tails of atoms) follows a pattern that regulates how genes are expressed. These patterns determine where transcription factors bind to the DNA: The pattern is a combination of sequences that makes it easier for the DNA to bend itself and wrap tightly around a nucleosome. But the pattern requires only some of the sequences to be present in each nucleosome binding site, so it is not obvious. The looseness of its requirements is presumably the reason it does not conflict with the genetic code, which also has a little bit of redundancy or wiggle room built into it.The transcription factors are prevented from binding to the wrong genes when they are wrapped around parts of the nucleosome that make them inaccessible. The news story by Nicholas Wade states that this code is highly conserved (i.e., unevolved) in all living organisms: The nucleosome is made up of proteins known as histones, which are among the most highly conserved in evolution, meaning that they change very little from one species to another. A histone of peas and cows differs in just 2 of its 102 amino acid units. The conservation is usually attributed to the precise fit required between the histones and the DNA wound around them. But another reason, Dr. Segal suggested, could be that any change would interfere with the nucleosomes ability to find their assigned positions on the DNA.Yet the phenomenon might just as well be interpreted as intelligent design instead of evolution. In fact, Wade uses the D word at the end of the article, when describing how this new code explains a mystery about DNA why there is redundancy in the number of codons that code for a given amino acid: Biologists have long speculated that the redundancy may have been designed so as to coexist with some other kind of code, he said. And this, Dr. [Eran] Segal [Weizmann Institute] said, could be the nucleosome code. See also the 07/21/2006 article on design-oriented research done at Weizmann (Rehovot, Israel). The work is done by specialists in computational biology a field of study more appropriate for design thinking than for evolutionary speculating. If Darwinists started computing the probability of evolution (see online book), they would get discouraged real fast.SETI: Shut Up and Keep Looking 07/25/2006 ![]() On Space.com, Seth Shostak of the SETI Institute answered the critics who think theyre barking up the wrong tree. Well-meaning people send him emails explaining why there is still no confirmed chitter from the cosmos after 46 years of looking. The top four include: (1) aliens use more advanced technology, (2) the Fermi Paradox means nobodys there (see 06/30/2006), (3) the aliens arent interested in us warlike primitives, and (4) the real aliens are in the Zeta Reticuli system. His basic answer: weve only begun the search. Unless you can come up with better strategy that works, pitch in and help. Weve got a lot of stars to go. Maybe theres a bright side to this SETI business. It keeps a lot of pesky Darwinians occupied and out of trouble. This is fine as long as their acronym S.E.T.I. employs another: O.P.M.*Is This Frog Marrow Really 10 Million Years Old? 07/25/2006 ![]() LiveScience reported finding intact bone marrow from fossils of frogs and salamanders. Without blinking an eye, reporter Ker Than croaked that the marrow is ten million years old. He compared it with the intact soft tissue and blood cells found in a T. rex specimen last year (see 02/22/2006, 06/03/2005, 03/24/2005), and said, The discovery raises hopes for finding soft tissue in other regions and from other animals, including mammals, [Maria] McNamara [University College, Dublin] says, because the amphibian bone marrow was discovered in an environment vastly different form the one in which the T. rex soft tissue was found.The article also surmises that many more examples of soft tissue and marrow may lie undetected in museum specimens. See also the report on National Geographic News which says the marrow is organically preserved and even maintains the original color. Never question what the scientists say; thats how symbiosis between the media and the Gurus of Knowledge is maintained. It helps preserve the social order. Imagine the chaos that might ensue if unbelievers started finding soft tissue in fossils from different environments all over the world; it might throw the whole evolutionary dating scheme into a cocked hat and start a revolution. Enforced conformity may subvert freedom of thought, but it keeps the peace.Titans Land-o'-Lakes Found 07/24/2006 ![]() The Cassini spacecraft has found features that look like methane lakes in the northern latitudes of Titan (see JPL press release). The large dark patches, some about 30 miles across with rounded edges, appear to be associated with fluid channels. Radar echoes cannot determine for sure whether the surface is liquid (dark means smooth, light means rough); the dark features could represent dry lakebeds like those found by the Huygens Probe. Still, the surfaces appear extremely flat, although some of them may show evidence of waves. Since these large, rounded dark features did not appear at equatorial latitudes, a comparison with the south pole at a future flyby will be instructive. The radar images were obtained during the T16 flyby on Saturday, July 22. Amateur enthusiasts are abuzz with excitement and interpretations at Unmanned Spaceflight, and Emily at the Planetary Society is sure they are lakes, comparing them to other lakes in the solar system. They could be calderas from cryovolcanism or just remnants of long-gone lakes. A report on Science Now says the dark areas show higher temperatures, as would be expected from liquids, and reside north of 70° where methane rains would more likely occur. Another Titan story comes from the European Space Agency. By analyzing interference patterns in the radio signal from the Huygens probe to the Cassini orbiter, researchers calculated that the surface the probe landed on is covered with pebbles 5-10cm in diameter. Also from the Saturn system, another view of Enceladus was released, paired with the moon Rhea. Taken from 2.5 million miles away, the jets of Enceladus (en-SELL-a-dus) are clearly visible (see 07/11/2006 story). A processed image was released July 21 allowing details of the outer plume to be shown feeding the E-ring. The next close flyby wont be till March 12, 2008 near the end of the prime mission (see timeline). Since Enceladus has proven extraordinarily interesting, it will doubtless become a prime target for any extended mission if the spacecraft continues its nine-year record of good health. Heads Down: Cassini is now increasing its inclination over the next few orbits (plot, the 180-degree transfer). By fall through spring, we should get unprecedented views looking down over Saturns rings from high overhead. This will provide a welcome change of view after months of seeing the rings as thin lines (example). The edge-on views have reminded us that, for all their vast extent, the rings are only about 100m thick. The new vantage point, showing the ring systems full breadth and detail of color and structure (example) is sure to inspire artists and poets as well as scientists (see overhead diagram). Titan appears to be showing a distinct regional difference between the equator and the poles. Being cooler, the poles may be condensing out more of the liquid methane and ethane that is believed to be constantly produced in the upper atmosphere. The current radar SAR image strip represents only a tiny fraction of Titans surface, so it is impossible to say if this region with its dark patches represents much of the polar regions or not. The last two radar passes have been exceptionally intriguing (see also the July 19 press release about the April 30 flyby). Titan presents a few familiar landscapes, but many unique ones. Impact craters are rare, and there are no high mountains (as detected on the smaller moons like Iapetus). Its going to take awhile to sort all this out. Too much theorizing too early might spoil the fun of discovery.Stupid Evolution Quote of the Week Judges Swamped 07/23/2006 ![]() What can editors do when too many entries come in a week? Print them all, and let the public decide:
Now you know why the NCSE needs a Faith Project Director (07/22/2006 entry, last bullet). Whatever is needed in the presumed emergence of everything appears on cue, fully formed, by evolution. Shine sunlight, and eyes appear. Bring on a snake, and the human brain and binocular vision appear. Machinery, codes, complex organs, bells and whistles you name it theres nothing that Darwinian faith cannot imagine emerging by unguided processes of selection. You should be ashamed, o ye creationists of little faith.Theory Battles Observations in Near-Field Cosmology 07/23/2006 ![]() Which is more important in science: a consistent model, or a good fit with observations? Clearly both would be the ideal. A report in Science1 this week revealed that astronomers are having trouble holding the two together. The problem is especially acute for near-field cosmology that deals with nearby galaxies. It may seem odd that astronomers feel more comfortable talking about the large-scale structure of the universe instead of our nearest neighbors, but thats essentially what Joss Bland-Hawthorn and veteran cosmologist P.J.E. Peebles said: These are exciting times for astronomy and cosmology, they crowed. On the one hand, we find that the main predictions of Big Bang inflationary cosmology are confirmed by observations of distant objects. One hand usually implies another is coming: On the other hand, nearby galaxies continue to surprise and inform us. The gloating over Big Bang certainty must be tempered by later admissions that 96% of the universe needs to be made up of unobservable stuff for the models to work: The evidence for the existence of these dark components is strong, but their properties are only loosely understood. The pair reported on meetings in Aspen, Colorado in February where problems were aired and data shared, including findings from the largest simulation of galaxy evolution ever made, the Millennium Simulation. In the spirit of the hunch that the most interesting parts of science are not the successes but the puzzles, lets look at some of the problems Bland-Hawthorn and Peebles listed in their article, where theory and observation didnt quite match up:
Yet, a discontented bystander might ask, which is the cart, and which is the horse? That question becomes especially apt when, as admitted in their last paragraph, the enormity of the fudge factors in the models is revealed: Also to be borne in mind is that the problems with the simulations may be highlighting the need for improved physics. After all, the simulations invoke many parameters to describe the 4% of the universe that is made of baryonic matter, while using only a few to describe the remaining 96% in dark matter and dark energy. It was surprising to find that we must postulate dark matter. Dark energy was another surprise, and the dark sector may surprise us yet again.Maybe the biggest surprise of all will be to someday look back and realize that there was less darkness in the real observational universe than there was in the models. 1Joss Bland-Hawthorn and P.J.E. Peebles, Astronomy: Near-Field Cosmology Science, 21 July 2006: Vol. 313. no. 5785, pp. 311 - 312, DOI: 10.1126/science.1127183. Always be wary when a scientist assures you he has the big picture all wrapped up and tidy, and just a few pesky details to sweep up. Physicists boasted in the late 19th century that all the big questions were solved, and the only work left to do was improving the measurements to the sixth decimal place. Then came general relativity and quantum mechanics, and the universe changed. This article should be read with that in mind. They spoke glibly about how well the large-scale models fit with the WMAP results (something we have reported earlier is far from certain: see 03/20/2006, 09/13/2005 links), but then this list of problems in near-field cosmology should have struck fear in their minds. It seems really ominous to say that new physics are going to have to be invented to figure out the most basic objects right around us. Then, at the end, to admit that even the large-scale model involves 96% fudge factor and growing well, now you understand the difference between what astronomers know and what they claim they know. You have the observations, and you have their models. Take your pick.Education & Political News 07/22/2006 ![]() Whats been happening in school boards about evolution and intelligent design? Here are some recent stories about politicians, reporters and ordinary citizens:
Thanks to Evolution News and Access Research Network for most of these leads. Lets get the ACLU to turn on the NCSE over separation of church and state. Derbyshire is an arrogant hack who likens creationists to whack-a-moles. This is a psychological disorder known as role reversal.Bear Tooth DNA Yields New Date Record: 400,000 Years 07/22/2006 ![]() According to a story posted on Yahoo News, Swedish scientists found intact DNA in a bear tooth claimed to be 400,000 years old. The team leader remarked, It is usually hard to find DNA that is older than 100,000 years, and work on fossilized DNA mostly focuses on material that is a few tens of thousands of years old, at most. Is it credible to believe these fragile molecules could survive for more than a few thousand years, let alone half a million? If and when they find DNA in dinosaur soft tissue (02/22/2006), evolutionary dating is going to be stretched to the snapping point. But weve already seen that Charlie Gumby is as flexible as a cartoon superhero.Chinese Living Fossil Amphibians Found 07/22/2006 ![]() World Net Daily found a story on Peoples Daily Online that 1200 specimens of an amphibian, Hynobiidaes, have been found in southwest China. The article states, These are a type of amphibian species around 300 million years old that once used to live in the dinosaur period. Other news sources have not yet reported this story, but if corroborated, it should only be news to an evolutionist. Those who hold to the Biblical creationist explanation for fossils and life deny the millions of years, so the gap is only a few thousands. Stories about so-called living fossils surface once in awhile to embarrass evolutionists; see 03/31/2002 about tuataras, 03/27/2003 about salamanders, 05/30/2003 about ginkgo trees, 12/05/2003 about ostracodes, or search for living fossils in the search box above.Neanderthal: Am I My Sequencers Brother? 07/21/2006 ![]() Associated Press reported a two-year initiative to sequence the Neanderthal genome (see MSNBC News, and also a separate report on News@Nature). A progressive creationist society headed by Dr. Hugh Ross, Reasons to Believe, is predicting the results will show Neanderthals did not evolve into modern humans. RTB has long contended that Neanderthal Man had nothing to do with the original Adam and Eve. According to the RTB article, only about 0.03% of Neanderthal DNA has been sequenced so far. Comparisons to date show Neanderthal distinctives yet some overlap with modern human DNA yet too little data to establish the amount of relatedness. There are no firm answers yet about how humans picked up key traits such as walking upright and developing complex language, according to the AP article; Neanderthals are believed to have been relatively sophisticated, but lacking in humans higher reasoning functions. Of course the Neanderthals dont believe they are lacking in higher reasoning functions, because they were not invited to the panel.Darwins Yard De-Evolves 07/21/2006 ![]() According to the BBC News biodiversity in Darwins yard at Down House in England has declined 15% since he fastidiously catalogued plant species there in 1855. This story signifies nothing significant. Biodiversity naturally declines in some grasslands as forests encroach and a climax community develops. Evolutionists would not expect noteworthy genetic change in just 150 years. The significance of this story lies in providing another opportunity to keep King Charlies name before the public.Cell Backup Systems Challenge Evolution, Show Design Principles 07/21/2006 ![]() Has an intelligent design paper been published in the Proceedings of the National Academy of Sciences?1 Read the abstract and decide whether this research supports Darwinism or design: Functional redundancies, generated by gene duplications, are highly widespread throughout all known genomes. One consequence of these redundancies is a tremendous increase to the robustness of organisms to mutations and other stresses. Yet, this very robustness also renders redundancy evolutionarily unstable, and it is, thus, predicted to have only a transient lifetime. In contrast, numerous reports describe instances of functional overlaps that have been conserved throughout extended evolutionary periods. More interestingly, many such backed-up genes were shown to be transcriptionally responsive to the intactness of their redundant partner and are up-regulated if the latter is mutationally inactivated. By manual inspection of the literature, we have compiled a list of such responsive backup circuits in a diverse list of species. Reviewing these responsive backup circuits, we extract recurring principles characterizing their regulation. We then apply modeling approaches to explore further their dynamic properties. Our results demonstrate that responsive backup circuits may function as ideal devices for filtering nongenetic noise from transcriptional pathways and obtaining regulatory precision. We thus challenge the view that such redundancies are simply leftovers of ancient duplications and suggest they are an additional component to the sophisticated machinery of cellular regulation. In this respect, we suggest that compensation for gene loss is merely a side effect of sophisticated design principles using functional redundancy.The three authors, all from the Weizmann Institute in Rehovot, Israel, speak freely of the evolution of this phenomenon in their paper; they also, interestingly, refer to design and design principles just as often: In particular, we suggest the existence of regulatory designs that exploit redundancy to achieve functionalities such as control of noise in gene expression or extreme flexibility in gene regulation. In this respect, we suggest that compensation for gene loss is merely a side effect of sophisticated design principles using functional redundancy.They call these cases of functional redundancy responsive backup circuits (RBCs). Interestingly, they found some cases where one RBC is regulated by another RBC. Though often the two backup copies were differently regulated, they could become coregulated under certain environmental conditions. The team also found that some of these functionally redundant genes are found all the way from yeast to mammals; this is sometimes called evolutionary conservation but actually describes stasis, not evolution. The authors do not deny that these backup systems evolved somehow: For a single cell, the ability to quickly and efficiently respond to fluctuating environments is crucial and offers an obvious evolutionary advantage, they postulate, suggesting that accidental duplication of genes was co-opted for this purpose. They do not get into any details of how this might have happened, however, and their analysis seems more interested on the complexity and design benefit of the systems. Their criteria for functional backups were stated thus: Two lines of evidence could indicate a functions direct benefit from existing redundancy: first is the evolutionary conservation of the functional overlap, and second is a nontrivial regulatory design that utilizes it. How many such systems exist in nature they could not say, because there have not been enough studies. Many functionally equivalent copies of enzymes (isozymes) are known. The genes that produce them are often regulated by different pathways. Under stress, however, some can become coregulated to provide robustness against environmental irregularities or damaging mutations. The model that emerges is that although many isozymes are specialized for different environmental regimes, alarm signals induced by particular stress stimuli may call for their synergistic coexpression. Here, RBCs provide functional specialization together with extreme flexibility in gene control that could be activated when sufficient stress has been applied. For example, in yeast, glucose serves as a regulatory input for alternating between aerobic and anaerobic growth. Its presence is detected by two separate and independent signaling pathways, one probing intracellular glucose concentrations and the other probing extracellular concentrations.They searched the literature and found several interesting ones that are described in detail in the paper. In all these cases, the common denominator is that one of the two duplicates is under repression in wild type and that that repression is relieved upon its partners mutation. This raises an interesting question one that could have been asked by someone in the intelligent design movement. They even answer a possible objection with a design principle: The extent to which genomic functional redundancies have influenced the way we think about biology can be appreciated simply by inspecting the vast number of times the word redundancy is specifically referred to in the biomedical literature (Fig. 5, which is published as supporting information on the PNAS web site). Particularly interesting is the abundance with which it is addressed in studies of developmental biology (Fig. 5). In fact, it is here that concepts such as genetic buffering and canalization first had been suggested. Furthermore, the robustness of the developmental phenotypes such as body morphologies and patterning have been repeatedly demonstrated. So the question is, are these redundancies simply leftovers of ancient duplications, or are they an additional component to the sophisticated machinery of cellular regulation?Along that line, they found that the amount of upregulation of one gene was often dependent on the regulation of the other. This suggested to them that the sum of the expression of the two copies is nearly constant as a buffer against noise in the system. When one line gets noisy, due to a mutation, the other responds with more signal. They call this dosage-dependent linear response. In some cases during development, the responsive overlap decreases as the organism grows. In short, The abundance of redundancies occurring in genes related to developmental processes, and their functional role as master regulators (Fig. 5) may be taken to suggest their utilization in either the flexibility or robustness of regulatory control. Some examples they give are even more complex. RBCs may also be implicated in the resistance of some organisms to multiple drugs. In some cases, each isoform can compensate equally for the other; in others, one of the forms is the main (the controller) and the other acts as the backup (the responder), only coming into play when the primary goes sour. One of the most profound and insightful of these recurring regulatory themes, they exclaim, is that, although both genes are capable of some functional compensation, disruption of the responder produces a significantly less deleterious phenotype than disruption of the controller. In evolutionary terms, why would the backup copy be better? A simple potential interpretation may suggest that although the controller is the key player performing some essential biological role, the responder is merely a less efficient substitute. Yet, accepting the notion that redundancy could not have evolved for the sake of buffering mutations, this interpretation still is severely lacking.Their next subsection is called Regulatory Designs. What emerges from their discussion of how each gene can regulate its partner is a complex picture: in one case, redundancy is embedded within a more complex interaction network that includes a unidirectional responsive circuit in which the controller (dlx3) also represses its own transcription, whereas the responder (dlx7) is a positive autoregulator. More examples like this are described. They predicted, and found, that RBCs could also regulate downstream processes from variation and fluctuations arising from nongenetic noise. The net result is that by using these functional backup systems, the organism has more robustness against perturbations, yet more flexibility in a dynamic environment. What is the fruit of this research? Why should scientists look for these regulatory designs in the cell? They offer an intriguing example. It is known that one form of human muscular dystrophy occurs when a member of an RBC suffers a mutation. Studies of this pair in mice, however, shows that the other member can respond by upregulating its expression. It is thought a similar response might occur in humans. Inspired by the compensatory effect demonstrated by this RBC in mice, its artificial induction in humans by means of gene therapy has been suggested. Although such modalities have not yet been realized, they suggest a fruitful possibility. 1Kafri, Levy and Pilpel, The regulatory utilization of genetic redundancy through responsive backup circuits, Proceedings of the National Academy of Sciences USA, 10.1073/pnas.0604883103, published online before print July 21, 2006 This is really a remarkable paper filled with inspiring possibilities. If we can just think design instead of years of mindless mutations, we might find cures for debilitating diseases. This paper has much of the obligatory evolutionspeak, but what does Darwinian thinking really contribute? Nothing. Although the researchers paid lip service to the evolutionary explanation that members of RBC pairs might have arisen through gene duplication, and that the coregulation might have provided a selectable fitness advantage, such language is really nothing more than the usual aftermarket sales pitch on the designed product. The real heart of their argument was that design exists, it is functional, and we can learn from it in ways that could help mankind. The future of design-theoretic science looks bright.Likely, Evolution May Be a Fact, Presumably 07/19/2006 ![]() When reading evolutionary science papers, one gets the feeling there are more than the usual number of words indicating conjecture, doubt and uncertainty. We decided to check this out in the July 11 issue of Current Biology. Scans for the words perhaps, probably, might, possibly, likely, may, apparently, seem and presumably and their derivatives were conducted on two papers dealing with evolutionary research and two papers of similar length on cell biology research that did not concern evolution. On average, the two evolutionary papers had 3.7 times as many conjecture words than the non-evolutionary ones. Some examples:
Theres the shell game (see top right quotation). Evolutionists preach about science and criticize faith, but look at their research. This is why Colin Patterson, in a moment of frankness, asked his evolutionary colleagues if they could point to one thing about evolution that they knew was true. All he got was silence.Evolutionists Idolize Darwin Daddy 07/18/2006 ![]() What is it about Charles Darwin? Evolutionists seem to hold this one 19th-century scientist in higher regard than any other man in history. In print or debate, they sometimes criticize anti-evolutionists for attacking Darwinian evolution, arguing that evolutionary theory has come a long way since Charles Darwin published On the Origin of Species by Natural Selection in 1859. One would think if evolutionists really believed this, they would pick up and move on, focusing on the work of the latest and greatest proponents, rather than exalting a Victorian individual whose views have been largely superseded. Yet their own fixation on the bearded father of evolution is a running theme in their own literature. Consider these three examples from the most recent issue of Current Biology (07/11/2006):
1Florence Maderspacher, The captivating coral the origins of early evolutionary imagery, Current Biology, Volume 16, Issue 13, 11 July 2006, pages R476-R478, doi:10.1016/j.cub.2006.06.019. 2Nigel Williams, Darwins champions fight back, Current Biology, Volume 16, Issue 13, 11 July 2006, pages R479-R480, doi:10.1016/j.cub.2006.06.035. 2Lynne Cassimeris, Q & A, Current Biology, Volume 16, Issue 13 , 11 July 2006, pages R480-R481, doi:10.1016/j.cub.2006.06.015. Can you think of any scientist in history that gets this kind of attention? Einstein scores high points, maybe, and perhaps Newton, but certainly no other scientist, no matter how great his or her achievement, gets the gushy worship that Pope Charlie gets from his devoted foot-kissers. There is no annual Einstein Day or Newton Day, but Charlies birthday is becoming an international event. Even in Darwins old age, his groupies would stand in awe in his presence at the Shrine of Down House, and grown men would crumble in the presence of the god as biographer Janet Browne described the new cult (see 02/13/2004 commentary). This is not even weird science. Clearly, its religion. No wonder creationists, intelligent design advocates, theologians and pastors often target the cult of Darwin (see op-ed piece by Albert Mohler), because evolutionists themselves have placed Charlies fatherly image on their own standards. If he falls, who is there (09/02/2004) to stand against the attacking Visigoths? (07/14/2006) Richard Dawkins? Bring it on.Cell Untangles Its Own DNA 07/17/2006 ![]() DNA is packed like spaghetti in a basketball (07/28/2004), but must constantly be accessed by transcribers, duplicators and other molecular machines. Scientists at the Karolinska Institute, according to EurekAlert, have found a complex of protein machines that know how to untangle DNA. Machines that can keep DNA from separating too early (cohesins) and keep DNA coils compact (condensins) have been studied extensively, but these scientists looked more at another mechanism. When they artificially perturbed DNA strands, the machines went to work fixing the damage: The research group has studied the third, less well understood, protein complex, known as the Smc5/6 complex. This protein complex was found to bind to locations on th |