And those who are wise shall shine like the brightness of the sky above, and those who turn many to righteousness, like the stars forever and ever. But you, Daniel, shut up the words and seal the book, until the time of the end. Many shall run to and fro, and knowledge shall increase.
Since its arrival at Saturn last June (see 07/01/2004 entry), the Cassini orbiter has achieved a string of phenomenal successes, and these just 15% of the way into its tour of Saturns rings, moons and magnetosphere (see JPL press release). The prize has been publication of initial science results in Nature1 and Science2 the cover stories in both. A few of the more surprising and significant results are listed here. These papers focus on Saturns atmosphere and rings, and the moons Phoebe and Iapetus. Well have to wait for official scientific results from the Huygens probe (see 01/21/2005 entry) and the flybys of Titan.
Dating Disaster: Is Neanderthal the New Piltdown?
The legacy of Darwinian paleoanthropology has been one of dating disasters, hoaxes and misinformation. What did you expect?Iraqi Marshlands on Slow Mend 02/18/2005
The ecological disaster wrought by Saddam Husseins policy of drying up ancient marshes along the Tigris and Euphrates (see 08/18/2003 and 05/01/2003 entries) is still severe, reports Science,1,2 but groups are working hard on restoration. It may take many years and will probably never be the same. About 20% has been reflooded, with portions coming back well, but other areas are suffering from salt and contaminated water. Some bird and animal species that relied on these areas have gone extinct. The human toll from Husseins ecoterrorism is incalculable. Marsh Arabs and earlier people groups had lived in this rich ecological zone for at least 5000 years, and the rich land supported much of the population of southern Iraq.
Although other factors, such as damming upstream, had contributed to the wetlands diminution for decades, Hussein had deliberately diverted water from the regions as a political move against his enemies, a coup-de-grace that resulted in the loss of 90% of the original marsh habitat. Experts think that a sizeable portion of the area shows hope of restoration, provided the government works quickly and wisely.
1Andrew Lawler, Reviving Iraqs Wetlands, Science, Vol 307, Issue 5713, 1186-1189 , 25 February 2005, [DOI: 10.1126/science.307.5713.1186].
2Richardson et al., The Restoration Potential of the Mesopotamian Marshes of Iraq, Science, Vol 307, Issue 5713, 1307-1311 , 25 February 2005, [DOI: 10.1126/science.1105750].
The before-and-after pictures are shocking, looking like the difference between the Everglades and a desert. It wasnt the Biblical Garden of Eden, but lets hope most of this paradise can be restored. The lovers of freedom seem to be the ones leading the effort: the authors of the main paper were three Americans, one expatriated Iraqi-American, and one Iraqi national.Pot Shots at Hot Spots 02/18/2005
Say that title five times, and youll be as flummoxed as geologists reporting in Science1 last week that long-believed assumptions are wrong. They looked at three seamount chains in the Pacific, long thought to provide evidence of tectonic plates moving across stationary hot spots, and found that current theory cannot account for them:
Our findings influence our views of oceanic intraplate volcanism and absolute Pacific plate motion: (i) The textbook explanation for intraplate volcanism by fixed hot spots is either entirely wrong or insufficient to explain these phenomena. (ii) Hot spots are likely not to be stationary, but move with the convecting mantle. (iii) Non-hot spot/plume models have to be considered for explaining intraplate volcanism, whereby local lithospheric extensions are likely to be an important candidate. (iv) Furthermore, absolute Pacific plate motion, for the time period between 80 and 47 Ma, is extremely poorly constrained. It is not clear if any of the three HEB-type bends on the Pacific plate are caused by a change in plate-motion direction, and it is similarly uncertain if the plate moved NW (along an extended Hawaiian trend) or NNW as indicated by the Emperor seamount trail. (Emphasis added in all quotes.)Their three alternative explanations were only tentative: Overall, plate extension is the strongest alternative among our three options, but there are very few arguments or clues that positively identify any particular explanation.
1Koppers and Staudigel, Asynchronous Bends in Pacific Seamount Trails: A Case for Extensional Volcanism?, Science, Vol 307, Issue 5711, 904-907, 11 February 2005, [DOI: 10.1126/science.1107260].
What? The textbooks are wrong? But the pictures were so artistic, and the TV programs were so convincing, how could this be? Take your pick: current theory is either entirely wrong or insufficient to explain the observations.South American Dinosaur Find Modifies Theories 02/23/2005
A deinonychus-like dinosaur has been found in Argentina. Representatives of this group, including velociraptor, had previously only been known in the northern hemisphere and Asia. Since South America was supposedly on another land mass at the time, The new discovery demonstrates that Cretaceous theropod faunas from the southern continents shared greater similarity with those of the northern landmasses than previously thought. The new species, named Neuquenraptor, was reported in Nature1 this week; see also the summary on BBC News which says the bones are probably implying a much more ancient evolutionary history for this group of dinosaurs.
The discoverers invoke convergent evolution (homoplasy) in their phylogenetic classification of this species, stating that its a common problem:
As prompted elsewhere, homoplasy is a common problem in coelurosaurian phylogeny. In this regard, the arctometatarsalian metatarsus shows a complex evolutionary history, and the basal position of Neuquenraptor provides useful information to test the monophyly of arctometatarsalian theropods. Our analysis is consistent with recent interpretations that evolutionary transitions between the arctometatarsal and non-arctometatarsal foot occurred multiple times both in basal Coelurosauria (for example, Tyrannosauridae, Ornithomimidae) and maniraptorans (for example, alvarezsaurids, some oviraptorosaurs, derived troodontids and basal dromaeosaurids). The arctometatarsalian condition thus constitutes one of the homoplastic features most frequently evolved between Coelurosauria. (Emphasis added in all quotes.)
1Fernando E. Novas and Diego Pol, New evidence on deinonychosaurian dinosaurs from the Late Cretaceous of Patagonia, Nature 433, 858 - 861 (24 February 2005); doi:10.1038/nature03285.
Convergent evolution is a cop-out term, a non-explanation, that hides the ignorance of Darwin Party members behind jargon. We see it all the time, whether talking about plants, vertebrates, bacteria, or what have you: the magic wand of convergence does the miracles. Does it explain how similar features in very different groups converged on the same solutions? No: it multiplies the improbability that these groups would all get the same lucky mutations to develop similar structures and functions independently. This new find also pushes back the origin of this group of dinosaurs much farther back in their timescale, giving the Darwinists less time to evolve these mobile, agile hunters from their presumably less-capable ancestors. The BBC News states, Neuquenraptor argentinus is slightly different from its Northern Hemisphere relatives, having had several million years of isolated evolution. Can they tell this from a few foot bones? The story, like a weak fence, is breaking down; dont fall for linguistic tricks to whitewash the rotting timbers.Clutch Enables Your Motors to Achieve 100% Efficiency 02/23/2005
Those little ATP synthase motors (see 01/30/2005 entry) in your body and (in all living cells) made news again in Nature1 last week. Scientists in Tokyo performed an ingenious set of experiments to measure the efficiency of the F1 synthesizing domain. They attached a tiny magnet to the camshaft so that they could turn it with electromagnets at will, and they carefully measured the amount of ATP synthesized or hydrolyzed as the motor turned anticlockwise or clockwise under their control. In the hydrolysis cycle, they found that the motor did not waste ATP; each molecule was successfully hydrolyzed with perfect efficiency, to the limits of their detection.
A particular focus of their investigation was the role of the eta subunit, which is attached to the gamma camshaft. During hydrolysis, the downhill function, it did not seem to matter whether eta was present or absent. But in the uphill process (synthesizing ATP), it made a dramatic difference. Without eta, each rotation produced, on average, only one product, but with it, they got three per revolution, with at least 77% efficiency. The actual efficiency was probably higher, but was hard to measure for such small entities. In best cases, it was 100%, they said: Therefore our data point to an excellent mechanochemical coupling efficiency. In the best cases, we observed the postulated value of three ATPs synthesized per turn.
These results are consistent with the ubiquity of this strategic enzyme that fuels most of the energy consuming biological processes, they said (emphasis added in all quotes). The present work reveals the unexpected importance of the eta-subunit in the synthesis of ATP. Though its precise function remains to be discovered, it was known to play a regulatory role; now, this team suspects it acts like a structural switch or clutch to lock the enzyme into synthesis mode. Without it, the tiny motor undergoes wasteful slippage.
As a reminder to recent readers, you can find a wonderful animation of this molecular machine on the website of German biochemist Wolfgang Junge. It is labeled F0F1-ATPSynthase (animation) See also his Model Schematic.
1Rondelez et al., Highly coupled ATP synthesis by F1-ATPase single molecules, Nature 433, 773 - 777 (17 February 2005); doi:10.1038/nature03277.
By now, you expect our next observation: The authors made no reference to evolution in their paper. They are treating these devices as actual mechanical motors, with stator, rotor, camshaft, and purposeful function, achieving performance stats beyond the dreams of human engineering. Eat your heart out, David Hume.State of the Cosmos Address Offered 02/21/2005
On the occasion of the centennial of Einsteins theory of relativity, Alan Guth, the father of inflationary cosmology, with colleague David I. Kaiser of MIT, took stock of cosmological theories in the Feb. 11 issue of Science.1 How has inflation fared since its controversial but hopeful proposal in 1981?
Inflation was invented a quarter of a century ago, Guth begins (emphasis added in all quotes), and has become a central ingredient of current cosmological research. Advances in particle physics have led to a theory, the standard model, that can account for three of the four basic forces strong and weak nuclear forces and electromagnetism but not gravity. String theorists, independently, have been working for their own unification of these forces. Guth repeats that amidst all this ferment, inflation continues to occupy a central place in cosmological research, even as its relation to fundamental particle physics continues to evolve. From there, he diverges into a primer on inflation. What some had described as a bizarre, untestable, ad hoc invention to get around serious problems in big bang models, he unashamedly portrays as a great success:
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Is Darwinism a Free Lunch Scam?
The very thing that should have made him realize Darwinism is so rotten it needs to be tossed overboard caused him, instead,to wave the magic wand of emergence and toss it into the salad bowl. Now, hes trying to sell this free lunch to his starving Darwin Party comrades. There aint no such thing. Lets hope the attendees brought their own, with meat, and that it was intelligently designed.Mars Dry Most of Its Life 02/18/2005
If Mars had liquid water, it was only briefly early in its history. Observations from the Mars Express, which just celebrated its first year in orbit, show no hint that liquid water has existed any time recently, reports Nature Science Update. Its not that H2O is rare; it is abundant at the poles, for instance, but is locked in solid ice. Apparently there was never much of a greenhouse to liquefy the water for long, despite the evidence of water-altered layers found by the Mars Exploration Rovers (see 12/03/2004 entry).
Because many scientists had envisioned a warmer, wetter Mars that could have supported life until recently, the new findings were bad news. Said one UK researcher, In a sense, weve been barking up the wrong tree for 20 years. That leaves them with a sore throat but no coon.
Early papers were released for Science1 this week. In the Feb. 17 issue,2 Richard Kerr said that now the younger, dryer side of Mars is coming out. The OMEGA spectrometer on Mars Express has detected no carbonates or clays, which should have been plentiful on a wet Mars. Instead, it has found an abundance of minerals like olivine that show no water alteration or weathering. Sulfuric acid from volcanic eruptions apparently combined with water to corrode martian rock and produce sulfates around the planet, Kerr pointed out hardly a scenario for a thriving beachfront community of living organisms. All in all, he concluded, Mars since ancient times is looking awfully cold and dry.
Thats not stopping some from putting a positive spin on the findings, and continuing to claim life might still be found there: see Space.com stories from Feb. 16 and Feb. 17.
1See six papers published online Feb. 17 on Science Express.
2Richard Kerr, And Now, the Younger, Dry Side of Mars Is Coming Out, Science, Vol 307, Issue 5712, 1025-1026 , 18 February 2005, [DOI: 10.1126/science.307.5712.1025a].
Venus was supposed to be a tropical Jurassic paradise of swamps and dinosaurs, but now it is known as a lead-raining hell (see 11/26/2003 entry). Mars was once envisioned as the home of intelligent beings who engineered advanced water projects. Then it was demoted to a land of beachfront bacteria. Now, it looks like an freezing-cold, desiccated, acidic, toxic waste dump (see 12/03/2004 entry). Mission planners had better think of a new sales pitch to get the public interested in further exploration. How about a non-evolutionary angle? It would sure be a cool place to study catastrophism. And it sure provides a nice foil to our own world, so that we appreciate and care more for our privileged planet.Introns Engineered for Genetic Repair 02/18/2005
Scientists at Purdue University are using bacterial machines to treat cancer and other diseases. These machines, called Group I introns, were thought to be useless:
Once thought of as genetic junk, introns are bits of DNA that can activate their own removal from RNA, which translates DNAs directions for gene behavior. Introns then splice the RNA back together. Scientists are just learning whether many DNA sequences previously believed to have no function actually may play specialized roles in cell behavior. (Emphasis added.)Though the function of introns is still mysterious (see 02/02/2005 entry), they appear to be highly conserved in both archaea and eukarya, suggesting they are important. Bacteria have Group I introns that do self-splicing. Eukaryotes have Group II introns that are spliced by one of the most complex molecular machines in cells, the spliceosome (see 09/17/2004 entry).
Who was it that thought many DNA sequences had no function and were genetic junk? It wasnt creationists. It was evolutionists who looked at treasuries of complex information with their distorted Charlie glasses and saw discarded leftovers of a slow, wasteful, careless evolutionary process. Now theyre having to play catch-up as the truth sinks in. Boot out the Darwin Party, the obstacles to scientific progress.New Date for Edom Fits Biblical Record 02/18/2005
The critics were wrong, and the Bible was right, according to new dates established for the kingdom of Edom southeast of the Dead Sea. This is the gist of a report from UC San Diego that found evidence of extensive copper mining in the area much earlier than previously thought. The area studied had been ignored by archaeologists because of the logistical difficulties of working in this hyper-arid region, but the UCSD team, cooperating with the kingdom of Jordan, succeeded in getting more accurate radiocarbon dates and archaeological evidence from this challenging area.
The team found evidence of two extensive periods of copper production centuries earlier than the previous dates for the Edomite kingdom (8th to 6th century B.C.). Now, as far back as the 9th to 12th centuries B.C., a new picture emerges:
In this period evidence was found of construction of massive fortifications and industrial scale metal production activities, as well as over 100 building complexes.....The results are published in the current issue of the British journal Antiquity. Another article about this discovery can be found on South Bend Tribune.
Prominent archaeologists like William Dever and Israel Finkelstein had claimed that the Biblical record was inaccurate because no such Edomite kingdom existed back in the times of David and Solomon. The Tribune article reminds us that absence of evidence is not evidence of absence. But why should not the Bible be considered evidence? It has proven correct so many times and places, and proven critics wrong so often, the burden of proof should be on the critics who would deny its accuracy. Dever himself (a friendly but vociferous rival with Finkelstein over Palestinian chronology) finds this revelation revolutionary, and says it supports the Bibles credibility about the kingdoms of David and Solomon. According to the Tribune, he still doubts the historicity of the Exodus, however. He needs to doubt his doubt.How Powerful Is Natural Selection? Biologists May Be Deluding Themselves 02/16/2005
Andrew P. Hendry (McGill University, Montreal) is no creationist; Darwinian evolution is a given in his News and Views piece in Nature1 this week. But he cautioned his fellow evolutionary biologists not to make overconfident claims about the power of Darwins most famous concept, natural selection:
Adaptation by natural selection is the centrepiece of biology. Yet evolutionary biologists may be deluding themselves if they think they have a good handle on the typical strength of selection in nature. (Emphasis added in all quotes.)Presumably, nobody does have such a handle. Darwin himself thought it was slow. Later biologists, like Kettlewell with his peppered moths, thought it was fast and strong, able to make substantial changes quickly. Hendry gives historical examples of the pendulum swinging back and forth on this issue, to the point he is not sure what to think. In 1998, Kingsolver et al. returned to the belief that selection was weak, and most estimates of selection were non-significant and centred around zero. A particularly worrisome finding, Hendry says, was that most studies did not have sufficient statistical power to detect typical strengths of selection even if it were present.
But then Hereford et al. in 2004, using the same data, came to the opposite conclusion, finding extremely strong selection overall. He based his ideas on a benchmark method: selection estimates for individual traits are standardized to allow comparison with the expected strength of selection on fitness itself. Hendry is not convinced. He repeats his warning:
These results raise some perplexing questions. Principal among them is the apparent paradox that typical studies of selection do not have the statistical power necessary to detect selection that appears unrealistically strong. Unfortunately, this paradox will not be resolved simply by accumulating more data of the same ilk, as all reviews identify problems with our current methods. How, then, are we to obtain a good handle on the true power of selection in nature?
1Andrew P. Hendry, Evolutionary biology: The power of natural selection, Nature 433, 694 - 695 (17 February 2005); doi:10.1038/433694a.
A more damaging admission by a Darwin Party spokesman could hardly be found. The entire spectrum of life, from the earliest reproducing sack of chemicals to modern human astronauts, is supposed to be the product of natural selection acting on numerous, slight modifications. Natural selection is an icon in our civilization, the stuff of myth and legend. The phrase Darwin grew to prefer, survival of the fittest (whatever fitness means; see 10/29/2002 entry) represents the most powerful force in the universe, a materialistic creator omnipotent enough to evolve not only an Earth filled with millions of diverse organisms from sponges to penguins to dragonflies to dinosaurs to horses to mushrooms to petunias to oaks but potent enough to fill unknown worlds with alien biology and weird life beyond our wildest imaginations. Natural selection is the staple of science fiction movies; it is the cardinal doctrine of the state secular religion. And now they tell us they dont even know how to measure natural selection, or to tell if it is weak or strong, fast or slow, or even detectable by statistical methods.Jurassic Park Revision #76: Bonehead Dinosaurs Not Head-Butters 02/16/2005
Pachycephalosaurs, or bone-heads, were dome-headed dinosaurs with skulls nine inches thick. Interpretation: they rammed each other like rams, or head-butted jeeps filled with hapless human tourists in the movies. Wrong, reports National Geographic in the March 2005 issue: research by Jack Horner and Mark Goodwin has shown that the thick skulls, surprisingly, could not have survived hard impacts. Moreover, the fossils show no signs of head-butting damage. Since the skull didnt make a very good crash helmet, maybe the boneheads used it for love.
It may have helped in species recognition or for attracting a mate, the paleontologists speculate. Whatever works is cute by definition. Speculation is fun. Its especially fun when it overturns the previous speculation.Age of Modern Humans Revised, Depending on Whom You Believe 02/16/2005
The official age of the oldest anatomically modern humans is now 195,000 years, some 65,000 years older than previously thought. This announcement was made in Nature1 by Ian McDougall, Francis H. Brown and John F. Fleagle, based on revised radiometric dates calculated from sediments surrounding two human skeletons in Ethiopia. These specimens, named Omo I and Omo II, were found in the 1967 by Richard Leakey, and were then dated at 130,000 years old. The authors believe these are the earliest well-dated anatomically modern humans yet described. The earlier record was about 160,000 years.
Revisions sometimes have unintended consequences. Timelines are tied with other events, so moving one date by a third is bound to shake up other calibration points. A summary on EurekAlert explains,
Brown says that pushing the emergence of Homo sapiens from about 160,000 years ago back to about 195,000 years ago is significant because the cultural aspects of humanity in most cases appear much later in the record only 50,000 years ago which would mean 150,000 years of Homo sapiens without cultural stuff, such as evidence of eating fish, of harpoons, anything to do with music (flutes and that sort of thing), needles, even tools. This stuff all comes in very late, except for stone knife blades, which appeared between 50,000 and 200,000 years ago, depending on whom you believe. (Emphasis added in all quotes.)Fleagle agrees that there is a huge debate in the archaeological literature about the dating of the first cultural artifacts, though the accepted date hovers around 50,000 years. As modern human anatomy is documented at earlier and earlier sites, it becomes evident that there was a great time gap between the appearance of the modern skeleton and modern behavior.
Another consequence is that inferences about modernity from appearance are more subjective. Omo II was supposed to be a more primitive form, but appears from the newest dates to be nearly contemporaneous with Omo I. The team interpreted the history of rock and ash layers to arrive at the dates of the fossils, and selected feldspar crystals for potassium-argon analysis. Science Now has pictures of the skull caps.
1McDougall, Brown and Fleagle, Stratigraphic placement and age of modern humans from Kibish, Ethiopia, Nature 433, 733 - 736 (17 February 2005); doi:10.1038/nature03258.
We already knew that judgments about who is primitive and who is not are highly subjective (see 01/01/2005 entry). The labeling game amounts to a kind of paleoanthropological racism. Primitive is in the eye of the beholder. Since Mr. Omo II cant show off his intellect, the Darwin Party racists are free to categorize him as less highly evolved, like the early Darwinians used to classify non-Englishmen. Even with the new dates that make him a contemporary of Mr. Modern Omo I, Fleagle says, in effect, well, what do you know; primitives and moderns lived at the same time.National Geographic Besieged by Letters Over Darwin Article 02/15/2005
Was Darwin Wrong? the cover teased in November. Inside, printed in huge bold type, the answer was ruthless and final: NO. The evidence for evolution is overwhelming end of discussion (see 10/24/2004 entry). Not everybody liked this treatment. Over 600 letters poured in, and in the March issue, NG printed six samples chosen to reflect the variety and weight of your opinions.... Summarized, they took these positions:
Also in the March issue, decade-long editor Bill Allen announced his retirement. New editor-in-chief is Chris Johns, a photographer and author, who seems more interested in good photojournalism than confrontation. The announcement of the Allens retirement says that, under his leadership, the magazine has continued to evolve, bringing its unique perspective to ever more topical and timely storiesfrom global warming and the oil crises to obesity, evolution, and human slavery.
Chris Johns honors his predecessor but speaks vaguely of his own mission, only describing it as to make the magazine a must read. He wants to bring the photography into the digital age. In an interview on Poynter Online, he listed two of his principles as: Always be honest and tell the truth.... Be humble, there is no room for arrogance.
Without access to all the letters, we have to take it on faith that NG printed an honestly weighted sample. If so, half were strongly opposed, one was wishy-washy, and only a third were supportive. Thats impressive. If any pro-evolution letters were sent in by scientists, they didnt mention it. The two printed seemed more dogmatic than informed.Honeybees Fly with Mental Maps 02/15/2005
You can tell a honeybee to get lost, but it cant. You can even take it off its flight path, but it will find its way back. Scientists writing in PNAS1 this week described experiments by a European team that wanted to test their navigating abilities. They marked bees at feeding stations, then took them way out of the path dictated by the waggle dance back at the hive. (The waggle dance, performed by a scout, provides them with information about the direction to the food relative to the sun, the distance, and the food quality.) How did a bee behave when put in strange country? The team watched them with harmonic radar:
A sequence of behavioral routines become apparent: (i) initial straight flights in which they fly the course that they were on when captured (foraging bees) or that they learned during dance communication (recruited bees); (ii) slow search flights with frequent changes of direction in which they attempt to get their bearings; and (iii) straight and rapid flights directed either to the hive or first to the feeding station and then to the hive. These straight homing flights start at locations all around the hive and at distances far out of the visual catchment area around the hive or the feeding station. (Emphasis added in all quotes.)Thats pretty amazing navigation for a fingernail-sized creature. The scientists figured that the bees must form a map in their head to be able to choose between two goals after getting reoriented. This finding suggests a rich, map-like organization of spatial memory in navigating honey bees, they concluded.
1Menzel et al., Honey bees navigate according to a map-like spatial memory, Proceedings of the National Academy of Sciences USA, 10.1073/pnas.0408550102, published online before print February 14, 2005.
Look at how much ability is stored in a tiny bee brain. If insects werent so small (most of them) we would certainly consider them some of the most awe-inspiring creatures on earth (see Bob Jensen Photography for incredibly beautiful insect photos). Too bad some of them went bad after the initially harmonized creation.Lichens: Two Designs Are Better than One 02/15/2005
A lichen is a symbiotic organism comprised of an alga and a fungus. PNAS1 reported a study that showed that antioxidant and photoprotective mechanisms in the lichen Cladonia vulcani are more effective by orders of magnitude than those of its isolated partners (emphasis added in all quotes). Kranner et al. found:
Without the fungal contact, the alga tolerates only very dim light and its photoprotective system is only partially effective; without the alga, the glutathione-based antioxidant system of the fungus is slow and ineffective. In the lichen, this mutually enhanced resistance to oxidative stress and, in particular, its desiccation tolerance are essential for life above ground. This lifestyle, in turn, increases the chance of dispersal of reproductive propagules and ensures their joint evolutionary success.
1Kranner et al., Antioxidants and photoprotection in a lichen as compared with its isolated symbiotic partners, Proceedings of the National Academy of Sciences USA, 10.1073/pnas.0407716102, published online before print February 14, 2005.
Take out the word evolutionary, because the findings only show reproductive success. Survivability does not necessarily imply advancement in complexity; it could just as well reflect good design.Fossil Record Reliable, Study Says 02/14/2005
A University of Chicago press release declares that the fossil record is reliable. Susan M. Kidwell studied the record of bivalves as a function of their fragility and deduced that preservability of shells was only a minor factor in their observed abundance. In fact, if anything, variations having shells that seemed least likely to be preserved actually survived longer than forms with the toughest shells, she said. This does not mean the fossil record is complete; it merely means that the record is not biased toward those with the toughest shells. And because the bivalves cover such a wide range of shell types, the press release ends, these results suggest that shelly mainstays of the fossil record, such as snails, sea urchins and corals, may have comparably unbiased records, Kidwell said. Her report is published in the Feb. 11 issue of Science.1
1Susan M. Kidwell, Shell Composition Has No Net Impact on Large-Scale Evolutionary Patterns in Mollusks, Science, Vol 307, Issue 5711, 914-917 , 11 February 2005, [DOI: 10.1126/science.1106654].
Kidwell believes that this is good news for evolutionists, but only because it removes a possible source of sampling bias. But how can it be good news? It removes an excuse. Evolutionists cannot claim that the gaps are due to harder shells surviving better in the rocks. It means the gaps, the trade secret of paleontology, are real.SETI Outreach Director: Teach Evolution 02/11/2005
Evolution is the foundation of biology, geology, and astronomy, claims Edna Devore, Director of Education and Public Education for the SETI Institute. Writing in Space.Com, she finds it hard to believe evolution is controversial (see 12/14/2004 and 11/30/2004 entries). Why, just look out the airplane window; its obvious. Evolution is fundamental to modern biology, geology and astronomy. Ignoring or discarding fundamental scientific understandings of the natural world does not prepare our children well for the future, she concludes. As America strives to leave no child behind, its time that evolution is not left behind in our science classrooms.
Shes barking up the wrong tree. No informed critic is advocating ignoring or discarding evolution. Whether it can be classed with fundamental understandings of the natural world must not be merely assumed, but those on the design side of the controversy (see 01/24/2005 and 11/30/2004 entries and Evolution News blog) want evolution to be taught. You cant understand 20th century history or science without it. Charlies little world cruise makes a nice story, and Haeckels little drawings make nice cartoons to get the teens to laugh. Yes, teach evolution all of it, the good, the bad, and the ugly (see 01/17/2005, 12/30/2004, 11/29/2004, 11/19/2004 and 12/14/2004 entries, and more going back 5 years in these pages). Teach especially the parts the Darwin Party doesnt want you to know. Here; well help. Try our draft outline of a suggested eight-part comprehensive curriculum on evolution:Is Science Acting Insane? AAAS President Bemoans Constraints of Societal Ethics, Advocates Diplomacy 02/11/2005
...insanity is doing the same thing over and over and expecting a different outcome. Alan I. Leshner, president of the American Association for the Advancement of Science, reminds readers of Science1 of this proverb in order to help them face the fact that ignoring the publics values, or protesting against them, will not allow scientists to get what they want.
Leshner isnt looking forward to the next annual meeting. The theme will be Where Science Meets Society, and from the way he wrote his editorial, he dreads having to come to terms with the fact that the relationship between science and society is undergoing significant stress.... This disaffection and shift in attitudes predict a more difficult and intrusive relationship between science and society than weve enjoyed in the recent past. Whats causing the stress? Two things:
The common thread linking these examples is that science and its products are intersecting more frequently with certain human beliefs and values. As science encroaches more closely on heavily value-laden issues, members of the public are claiming a stronger role in both the regulation of science and the shaping of the research agenda.So what does he recommend?
Independence and objectivity in the shaping and conduct of science have been central to our successes and our ability to serve society. Still, our recent experiences suggest that the values dimension is here to stay, certainly for a while, and that we need to learn to work within this new context. Protesting the imposition of value-related constraints on science has been the usual response, but it doesnt work because it doesnt resonate with the public.He continues his advice: Simply protesting the incursion of value considerations into the conduct and use of science confirms the old adage that insanity is doing the same thing over and over and expecting a different outcome. Instead, Lets try some diplomacy and discussion, he says, and see how that goes for a change.
1Alan I. Leshner, Where Science Meets Society, Science, Vol 307, Issue 5711, 815, 11 February 2005, [DOI: 10.1126/science.1110260].
For fun, reread his comments, and replace each instance of science and scientists with elitism and elitists.Stupid Evolution Quote of the Week 02/10/2005
This weeks entry goes to John S. Mattick and Michael J. Gagen (U. of Queensland, Brisbane, Australia), writing in Science1 about the mathematical dynamics of networks. Notice the seamless transition from discussion of intelligently-designed human engineering to chance-based, mindless, directionless processes of evolution:
Consider, for instance, the proliferation of digital programming in such domains as computing and aviation. The increased sophistication of modern aircraft has been enabled not so much by advances in their analog components, but rather by transitions from mechanical to computational control systems, including software and optical fibers, which now constitute much of the cost. Indeed, the transition to digital technologies is a generic solution to previous limitations of analog communication and control technologies. In virtually all systems, it has been observed that explosive increases in complexity occur as a result of more advanced controls and embedded networking, most of which is invisible to the observer. In the case of biology, we suggest that the transition from an analog protein-based regulatory system to a digital RNA-based control architecture was the critical platform that enabled the evolution and development of complex organisms. (Emphasis added.)Presumably, just because the development of analog-to-digital converters in cells was invisible to the observer, an explosion in complexity resulted, transforming bacteria into whales, dragonflies, sharks, card sharks, computer programmers and aircraft pilots.
Too bad the following entry didnt make the judging in time, or it would have won: John Bohannon in Science Now opened a piece about platypus ears (see 02/10/2005 entry) with this jingle: The middle ear that endows mammals with their sense of hearing is one of the masterpieces of evolution. And it now seems that this is an instrument so nice, nature invented it twice.
1John S. Mattick and Michael J. Gagen, Mathematics/Computation: Accelerating Networks, Science, Vol 307, Issue 5711, 856-858, 11 February 2005, [DOI: 10.1126/science.1103737].
Dont let the Darwin Party charlatans get away with hiding their personification fallacies in passive-voice verbs and subjunctives. Who transitioned the cellular technology from analog to digital? How did this entity do it? Who enabled the evolution of complex organisms? Who designed the A-to-D converter? How was the digital programming done, without a Programmer? Who designed the advanced controls, to control what? Who embedded the networking? Were advances in aviation brought about by mutations and natural selection?Can Evolution Repeat Itself? 02/10/2005
A press release from University of Chicago reported today that 115-million-year-old fossil of a tiny egg-laying mammal thought to be related to the platypus provides compelling evidence of multiple origins of acute hearing in humans and other mammals (emphasis added in all quotes). The fossil apparently shows inner-ear bones in the monotreme lineage that supposedly diverged from the reptile-like ancestors of both marsupial and placental mammals.
Many paleontologists have doubted that such a seemingly complex adaptation could have originated more than once in mammals, but according to the authors of the paper, the evidence of T. trusleri [the reported shrew-size fossil] indicates that it did.They are claiming that the middle ear bones needed for acute hearing arose twice, independently, within mammals. How can this supposedly rare and unexpected evolutionary change have occurred so commonly in early mammals? the press release asks. James Hopson, one of the authors of the paper in Science,1 describes how this might have unfolded:
Recent studies of jaw and ear function in primitive mammal-like reptiles indicate that the larger angular bone may have supported an eardrum while still part of the lower jaw, Hopson said. But once the dentary bone made a new jaw hinge with the skull in the immediate predecessor of mammals, the accessory jawbones may have abandoned their job of supporting the jaw and evolved exclusively into the middle ear sound-transmitting function.Hopson adds that Only the evidence of fossils has been able to unravel this tangled history of a complex adaptation. The only fossil evidence alluded to, however, is T. trusleri and extinct mammal-like reptiles without the adaptation, compared with living mammals and the platypus. The scientific paper itself is not sure the transition is clear: because of the uncertain phylogenetic positions of these taxa with respect to true mammals (monotremes and theriiforms), none provides unequivocal support for the multiple origin of the definitive mammalian middle ear bones they only suggest the possibility of the idea. The paper also discusses uncertainty about the phylogeny of all these groups, and only provisionally builds its case based on one experts opinion, because it is in accord with the polyphyletic origin of the definitive mammalian middle ear but requires the least amount of homoplasy in comparison with other proposed phylogenetic placements of monotremes.
Martin and Luo in Science2 call this a remarkable example of homoplastic evolution (another term for convergent evolution, or the supposed independent evolution of similar structures). They call homoplasy a major feature of evolutionary morphology. This find, they say, answers a fascinating but very difficult question facing evolutionary biologists that is, whether a complex structure would be less likely than a simple structure to undergo independent homoplastic evolution. From the tone of these articles, the only thing not in question by this find is evolution itself.
1Rich et al., Independent Origins of Middle Ear Bones in Monotremes and Therians, Science, Vol 307, Issue 5711, 910-914 , 11 February 2005, [DOI: 10.1126/science.1105717].
2Thomas Martin and Zhe-Xi Luo, Homoplasy in the Mammalian Ear, Science, Vol 307, Issue 5711, 861-862, 11 February 2005, [DOI: 10.1126/science.1107202].
As always, the independent variable in this equation is Darwinian evolution. Everything else must adjust to keep the story going. Improbabilities? No problem; just create new words like homoplasy that sound scientific, and toss a little pixie dust of natural selection to corral the lucky mutations for engineering complex systems as required.Loss of Mangrove Forests Exacerbated Tsunami Damage 02/10/2005
Many seashores have a natural defense against the onslaught of a tsunami: the mangrove forest. Dense thickets of these trees that tolerate salt water and line the coasts of many subtropical islands and continents can absorb much of the energy of killer waves. It is entirely plausible that the enormity of the human death toll can be traced in large part to the destruction of large tracts of native mangrove, caused by the lure of beachfront property for hotels, fisheries and industry.
Mangrove forests help protect coastlines from erosion, storm damage and wave action by acting as buffers and catching alluvial materials, writes Nigel Williams in Current Biology.1 They also protect reefs and sea grass beds from damaging siltation and pollution. It appears that the hardest hit areas by Decembers devastating tsunamis were those with the least mangrove protection. Williams quotes Indian sources that reported that wherever mangrove forests were intact, the impact was mitigated and the lives and property of the communities inhabiting the region were saved.
Unfortunately for coastal communities, the rush to clear coastlines for industry and recreation is causing these unique ecosystems to disappear faster than the rain forests. Years ago, 75% of the coastlines of tropical and sub-tropical countries were lined with mangrove forests; now, less than half remains. The devastation of the recent disaster has awakened a new interest in this neglected yet vital marine ecosystem.
1Nigel Williams, Tsunami insight to mangrove value, Current Biology, Volume 15, Issue 3, 8 February 2005, Page R73, doi:10.1016/j.cub.2005.01.015.
The mangrove has an amazing capacity for regeneration with its floating seed pods that can cross continents like rafts, then orient themselves upright and plant themselves in shallow water. The story is told in an excellent family film about seed dispersal, Journey of Life. Mangrove forests create lush habitats for many species of animals and birds. Now, we find that they also create safety nets for humans.Watch for Falling Ants 02/09/2005
Did you know some ants are gliders? When Stephen Yanoviak (U. of Texas) was studying insects in the rain forest canopy in Peru, he was struck by the fact that ants kept landing on his arm. This launched his teams investigation into gliding ants. They took video cameras into the jungle and documented their unique mode of locomotion. They found that the bugs could rotate around and change direction in midair, even when falling like a rock. Most of the time (about 85%) the ants landed back on the tree trunk, able to crawl back up to home. They published their work on directed aerial descent in Nature,1 unsure whether the ants were escaping predators or just having fun.
This is the first study to document the mechanics and ecological relevance of this form of locomotion in the Earths most diverse lineage, the insects, they wrote. A press release on UC Berkeley News tells more about the study, with photographs of the ants and interviews with the research team. How the ants turn around in midair and control their landings is still unknown, but like many insects, they have sticky feet that enable them to cling to many surfaces. Its an amazing discovery, said Robert Dudley of the team. So ants join certain species of squirrels, lizards, frogs and even some snakes (and humans) as gliding champions this time, in the ultralight class.
1Yanoviak, Dudley and Kaspari, Directed aerial descent in canopy ants, Nature 433, 624 - 626 (10 February 2005); doi:10.1038/nature03254.
It seems unlikely that ants would lose their wings through evolution, then re-evolve this behavior as a poor substitute. Surely the power of natural selection would have favored wings evolving again to let the ants fly back home rather than forcing them to walk straight up against gravity. Why select lucky mutations for controlled descent when wings were so easy to evolve? It must have been a piece of cake if they showed up in reptiles, mammals, birds and insects. Didnt these ants have Haeckels recapitulation memory for how to evolve wings all over again? After all, walking sticks did, we are told (see 05/28/2003 entry). Ah, young disciples, Exalted Master Charlie gently scolds, One must not presume on the path Mother Nature will take. A bumbling tinkerer is She. So in her toyshop, she apparently forgot how to produce rubber-band airplanes, and decided to make miniature Buzz Lightyears, who mastered the art of falling with style.Octopus Arms Have Optimal Design 02/09/2005
The tentacles of an octopus are soft and flexible, whereas bony creatures like us have joints that, while good for moving objects around, limit our freedom of movement. Wouldnt it be cool to have both? An international team of neurobiologists, publishing in Nature,1 watched an octopus snare its food, using the flexibility of its tentacles, as expected. But then they noticed, when it needed to transfer its prey from one place to another, it employed a vertebrate-like strategy, temporarily reconfiguring its arm into a stiffened, articulated, quasi-jointed structure.
This gave them an idea. Maybe the octopus has hit on something. While the flexible arm provides a benefit for snaring objects, an articulated limb may provide an optimal solution for achieving precise, point-to-point movements, they wrote (emphasis added in all quotes). National Geographic News adds, scientists studying octopus arms conclude that they may represent the optimal design for robotic arms. Maybe the next-generation robotic arm on the Space Shuttle will resemble something from the ocean depths. One researcher remarked that a stiff arm would be likely to push a floating object away, but an arm you could use to gently wrap around an object and retrieve it, that would be useful. How to build such a device is the challenge.
1Sumbre et al., Neurobiology: Motor control of flexible octopus arms, Nature 433, 595 - 596 (10 February 2005); doi:10.1038/433595a.
Copying animal designs biomimetics is one of the hottest topics in engineering, for good reason. Here is a creature that has the capabilities of a comic book superhero. Sadly, both articles attribute this feat to evolution: octopuses have evolved the optimal design, says National Geographic, and the neurobiologists say in a wordier way,Stem Cell Research Launches into the Ethical Unknown, Full Steam Ahead 02/08/2005Fetching seems to be an example of evolutionary selection of solutions that are similar even though they are based on quite different mechanisms on morphology in arthropod and vertebrate limbs, and on stereotypical motor control in the octopus. This functional convergence suggests that a kinematically constrained, articulated limb with two segments of almost equal length is the optimal design for accurately moving an object from one point to another.This illustrates again how many countless times the scientific community and news outlets merely assume evolution is capable of any miracle needed, without telling us how the blind forces of nature could ever produce engineering design that humbles our best robotics experts.
No one knows where stem cell research will lead. Some hope for miracle cures. Some fear horrendous abuses and ethical nightmares. But states and nations, apparently more concerned over priority and prestige, are fighting to the head of the pack after the California Proposition 71 gun fired last fall.
With $3 billion in taxpayer loans at their disposal, the stealthily-named new California Institute for Regenerative Medicine is beginning to take shape, apparently unconcerned that the debate has shifted from ethics and costs to how the enterprise will operate, wrote Constance Holden in the 14 January issue of Science.1 In last weeks issue,2 she added that Prop. 71 has had a seismic effect on other states. Wait for me! seems to be the attitude of Wisconsin, New Jersey, Massachusetts, Maryland and Illinois, while other states are trying to ban research on stem cells (Science Now reports that governor Mitt Romney is trying to stop the advance in Massachusetts). The rivalry for stem cell funding is having a major shakeup on the role of the National Institutes of Health, comparable to the breakup of the Roman Empire, Holden writes.
Much of the hurry comes from a desire to beat the Asians, wrote Dennis Normile and Charles C. Mann in the same issue last week.3 Less encumbered by societal restrictions on embryonic stem cells, they remarked, scientists in the developing countries of Asia are giving Western researchers a run for their money. In Singapore, Japan, South Korea, Taiwan, China indeed, across all Asia there is little of the conflict with prevailing religious and ethical beliefs that has Western countries hesitating. No one seems to be asking whether to do it, but only how to do it. The mood in Asia is described by Normile and Mann:
Governments are ramping up funding for both basic and applied stem cell work, setting up new institutes, programs, and grant schemes, and providing incentives for private companies to join the effort. Giving these efforts a further boost, the region also has legions of lab workers willing to log long hours, and increasing numbers of expatriate scientists are returning home to work in the flourishing environment.With that kind of money and competition driving stem cell research, the concerns of a few ethicists are unlikely to be given the time of day. Although some of these enterprises specifically ban human cloning, the creator of Dolly the sheep, Ian Wilmut (Kings College, London) has been granted a license in the UK to clone early stage human embryos for medical research, reports the BBC News. Those opposed to the research said the work is unethical, unnecessary and a step toward full blown human cloning, the article says, and the ProLife Alliance stated emphatically, All human cloning is intrinsically wrong and should be outlawed. But its hard to beat the emotional appeal of proponents who argue that the procedure might help cure motor neuron disease. Meanwhile, other possible nightmare scenarios with the new biotechnology make occasional headlines, like this debate over human-animal hybrids in National Geographic News. The technology is outpacing any consensus on where to draw the line.
Ongoing successes with adult stem cells, which have no ethical problems, are getting drowned out in the fanfare over embryonic stem cells. EurekAlert reported that a new source of stem cells in umbilical cord blood shows promise for bone marrow transplants and tissue repair, for instance, and Nature Science Update just reported that in heart tissue, long thought irreplaceable, certain cardiac progenitor cells are capable in fact of regrowing heart muscle, promising hope for heart-attack survivors. A heart-warming yet heart-breaking report in World Magazine Feb. 5 describes near-miraculous cures being made with adult stem cells; trouble is, such proven advances are being passed over in the rush to fund embryonic stem cell research. The NIH, which bankrolls innovative medical research in the United States, has funded only 30 projects involving stem cells from umbilical cords, reports Lynde Langdon. In contrast, it has funded 634 projects involving embryonic stem cells. This lopsided funding of embryonic stem cell research has yet to show one successful medical benefit.
1Constance Holden, Californias Bold $3 Billion Initiative Hits the Ground Running, Science, Vol 307, Issue 5707, 195 , 14 January 2005, [DOI: 10.1126/science.307.5707.195].
2Constance Holden, U.S. States Offer Asia Stiff Competition, Science, Vol 307, Issue 5710, 662-663 , 4 February 2005, [DOI: 10.1126/science.307.5710.662].
3Dennis Normile and Charles C. Mann, Asia Jockeys for Stem Cell Lead, Science, Vol 307, Issue 5710, 660-664 , 4 February 2005, [DOI: 10.1126/science.307.5710.660].
If you thought abortion was bad, and should have been stopped at the starting gate, wait till you see what the mad scientists might do with their latest tinker toys, genetically modified human embryos. What started as moral compassion for poor women in the early debates over abortion has turned into a multibillion dollar industry, replete with lawyers and SIGs who fight any attempt to restrict their business, as concerned citizens gasp at bags full of unborn babies in trash bins, and senators investigate black markets for body parts. How many of you believe that, this time, the proponents of this new crusade really have the interests of the suffering in mind? Oh and which religious tradition, did they say, is the only one hesitating at the sight of the leaking dike?ID. Article Makes N.Y. Times 02/07/2005
Michael Behe got a full-length column in the New York Times (reproduced at Discovery.com) to present the case for intelligent design. The EvolutionNews blog says it is the second most emailed article from that days edition, and asks, Who says theres no controversy?
Which side wants to air the debate? Which side wants to shut off debate? What does that tell you?Scientist Preaches Integrity to Fellow Scientists 02/06/2005
Patrick Bateson (U. of Cambridge), concerned over reports of malpractice by scientists, wrote an essay in Science1 Feb. 4 to remind his fellow researchers about Desirable Scientific Conduct. One mustnt allow his or her affiliations or biases to influence results. Performing tainted research feeds the postmodern conception that science is a cultural construct, for one thing, and can overlook important leads. Treasure your exceptions! he says, providing a couple of examples of insights overlooked because of bias. The data point lying under the researchers thumb might be the most interesting result of the whole study. He refers to an actual incident where a Nobel Prize winner placed his thumb on a slide to cover a data point that was off the line.
Batesons advice comes down to good old-fashioned values: Desirable modes of scientific conduct require considerable self-awareness as well as a reaffirmation of the old virtues of honesty, scepticism, and integrity.
1Patrick Bateson, Desirable Scientific Conduct, Science, Vol 307, Issue 5710, 645, 4 February 2005, [DOI: 10.1126/science.1107915].
Bateson quotes someone who thought the results of Gregor Mendel were too good to be true, but for research done with the integrity and care he exercised, maybe it was too good for the typical Darwin Party scientist who trades in myths and stories. Its hard to know if Mendel was careless with exceptions or not; one thing is for sure, his laws of genetics have stood the test of time.Survival of the Fittest or the Luckiest? 02/06/2005
Evolutionists assume that bacteria spread because they evolve resistance to antibiotics and become more fit to survive. Thats apparently not true, says a story in EurekAlert about a study from Imperial College, London: the spread of bacteria appears to be due to chance alone.
Here are two quotes from the article by team members explaining the finding:
Dr Christophe Fraser, from Imperial College London, a Royal Society University Research Fellow and one of the authors, says: Microbiologists have assumed for some time that some disease strains spread more successfully than others. In fact we found that the variation in the communities we studied could be explained by chance. This was surprising, especially considering all the potential advantages one pathogen can have over another, such as antibiotic resistance and differences in host immunity.The team studied three pathogenic bacteria and followed the social patterns of the humans they infected. There was no clear association between success at spreading and fitness for spreading .
A related commentary by Dan Ferber in Science1 had another surprise about bacteria: they are not immortal. Reproducing strains in a culture apparently show their age. What does this mean? For one thing, the results make it unlikely that natural selection produced an immortal organism. For another, Its one of those exciting results that makes you take a fresh look at what you think you know. One observer is not sure the populations that stopped growing were aging; maybe they were taking a break for repairs. But another said the new findings put the onus of proof on anyone who claims that cells can be immortal.
1Dan Ferber, Immortality Dies as Bacteria Show Their Age, Science, Vol 307, Issue 5710, 656 , 4 February 2005, [DOI: 10.1126/science.307.5710.656a].
Would survival of the luckiest generate all the richness and complexity of the living world? This seems to be a very non-Darwinian way of looking at biology. It also seems to undermine one of the key evidences of evolution in the Darwin Partys debate arsenal: the evolution of antibiotic resistance in bacteria.Molecular Machine Parts Stockpiled in Readiness for Assembly 02/06/2005
A team from the European Molecular Biology Laboratory has done a 4D time-and-materials study of molecular machines, analyzing the process of assembly, reports EurekAlert. They found that the cell stockpiles some parts and holds them in storage, but adds the crucial elements just in time.
The researchers discovered that in yeast, key components needed to create a machine are produced ahead of time, and kept in stock. When a new machine is needed, a few crucial last pieces are synthesized and then the apparatus is assembled. Holding off on the last components enables the cell to prevent building machines at the wrong times. Thats a different scenario from what happens in bacteria, which usually start production of all the parts, from scratch, whenever they want to get something done.The authors next want to find out how long components stay around after use. Their results were published in Science1 Feb. 4; see also the brief on EurekAlert.
1Lichtenberg et al., Dynamic Complex Formation During the Yeast Cell Cycle, Science, Vol 307, Issue 5710, 724-727, 4 February 2005, [DOI: 10.1126/science.1105103].
What would you want to bet that they will find out bacteria have assembly processes just as complex as those in eukaryotes? Planning ahead for future need, machinery, assembly; that doesnt sound like the language of chance.Will Top-Down and Bottom-Up Meet in the Middle? 02/06/2005
Some difficult problems can be approached from opposite ends. Engineers needing to build a shaft through a mountain, for instance, might start digging from the bottom and the top, trying to find each other in the middle. But what if the mountain has an unanticipated impregnable layer? Or what if there is no mountain, but a lowland here, and a peak over yonder, with a canyon between them? When the middle is hypothetical, it takes faith to believe it even exists.
The origin of life is such a problem. Chemists know about chemicals, and biologists know about living cells. Is there a middle ground in which chemicals became cells? Evolutionists are convinced there is. But living systems are products of evolution, Eörs Szathmáry (Collegium Budapest), confidently states in Nature,1 and an answer in very general terms, even if possible, is likely to remain purely phenomenological: going deeper into mechanisms means having to account for the organization of various processes, and such organization has been realized in several different ways by evolution. (Emphasis added in all quotes.)
The idea is that if evolution scaled the mountain in the past, biologists should be able to find the trail by starting from both ends. The meeting point would converge at a theoretical minimal cell that is, a chemical entity satisfying three requirements for life: metabolism, a template or genetic code, and a boundary or membrane (see 08/26/2003 and 12/30/2002 entries). Szathmáry attended a meeting in Sicily this past December on Towards the Minimal Cell. A veteran theoretical biologist himself (see 02/20/2004 entry), he enjoyed the discussions by teams of biologists tackling this problem from both ends. Hints of a possible convergence were tantalizing:
Basically, there are two approaches to the minimal cell: the top-down and the bottom-up. The top-down approach aims at simplifying existing small organisms, possibly arriving at a minimal genome. Some research to this end takes Buchnera, a symbiotic bacterium that lives inside aphids, as a rewarding example (A. Moya, Univ. Valencia). This analysis is complemented by an investigation of the duplication and divergence of genes (A. Lazcano, Univ. Mexico). Remarkably, these approaches converged on the conclusion that genes dealing with RNA biosynthesis are absolutely indispensable in this framework. This may be linked to the idea of lifes origins in an RNA world, although such an inference is far from immediate. (Emphasis added in all quotes.)Szathmáry knows to be cautious because of the problems involved in the RNA World scenario (see 02/14/2004 and 07/11/2002 entries). Functioning RNA in living cells does not necessarily imply ancestry from non-living RNA molecules.
The top-down teams believe that 200 genes is the lower limit for a minimal cell. Szathmáry cautions again, however, that the minimum number could well be much higher. The conferees were not sure the top-down approach could prove fruitful:
There was general agreement that a top-down approach will not take us quite to the bottom, to the minimal possible cells in chemical terms. All putative cells, however small, will have a genetic code and a means of transcribing and translating that code. Given the complexity of this system, it is difficult to believe, either logically or historically, that the simplest living chemical system could have had these components.Well, then, how is the other team doing? They are getting frustrated:
The bottom-up approach aims at constructing artificial chemical supersystems that could be considered alive. No such experimental system exists yet; at least one component is always missing. Metabolism seems to be the stepchild in the family: what most researchers in the field used to call metabolism is usually a trivial outcome of the fact that both template replication and membrane growth need some material input. This input is usually simplified to a conversion reaction from precursors to products.Unfortunately, without all three as with the combustion triangle of fuel, oxygen and heat two factors are not enough to ignite the spark of life. Furthermore, not all are convinced that the reactions termed metabolism, template or boundary in lab experiments can be compared to those occurring in real living cells. Szathmáry briefly considers computational investigations (i.e., computer models), such as the lipid world scenario (the idea that fatty acids came first: see 04/15/2002 entry and 01/17/2002 commentary) but he finds it difficult to assess the importance of their results. So are top-down and bottom-up approaches making headway toward a grand confluence? Too early to tell, he concludes:
Clearly, there is a divide between the top-down and bottom-up approaches, and between theoretical and experimental investigations. In the future, for example, one would like to see more realistic models of the primordial genome and, conversely, an experimental approach to the lipid world. An aim in the coming years will be to bridge those gaps hence the great value of meetings such as this.
1Eörs Szathmáry, Life: In search of the simplest cell, Nature 433, 469 - 470 (03 February 2005); doi:10.1038/433469a.
In the movie Back to the Future, Doc had mere seconds to connect two ends of an electrical cable before Marty hit the wire. When they became accidentally disconnected, he slid down the cable in a desperate attempt to reconnect them, only to find they didnt quite meet. At the climactic moment, when the predicted lightning bolt sent 1.21 gigawatts of power through the wire, Doc himself momentarily became the conductor: the circuit was closed, and all lived happily ever after. How he survived to celebrate by dancing in the street well, thats Hollywood.Darwinian Funding Makes Losers Angry 02/04/2005
Evolutionists love Darwinism except when it threatens their funding. Daniel Clery complained in Science1 this week that it means the demise of physics and chemistry in UK universities. Survival of the fittest seems to be favoring the departments that provide lucrative careers. The funding shortfall for traditional chemistry and physics is due partly, of course, to the perpetual mismatch between government stinginess and scientists insatiable appetites...
But other forces are at work, too. Demand for physics and chemistry classes has been steadily falling as students are lured into more career-specific courses such as sports science, forensic science, and media studies. And the once cozy world of British academia is now a competitive marketplace in which universities must vie with each other for government research money and attract as many students as possible to maintain their income. Some researchers suspect that current funding policies are designed to weed out the weak and concentrate resources in a smaller number of superdepartments. Its a Darwinian exercise, says [Philip] Kocienski [Leeds U. School of Chemistry]. (Emphasis added in all quotes.)Clery suggests that university departments need to stop competing and start cooperating.
1Daniel Clery, Darwinian Funding and the Demise of Physics and Chemistry, Science, Vol 307, Issue 5710, 668-669, 4 February 2005, [DOI: 10.1126/science.307.5710.668].
Sorry, Charlie, you cant have it both ways. If the law of the jungle is right for biology, then what is, is right. After all, dont the physicists say nature selected the universe we were born in? And dont the chemists say nature selected the building blocks of life? So even if it means philosophical suicide, you can choose your path, but you cant choose the consequences. You cant appeal to the nobler motives, because they are illusions in your view, so give it your best shot on the Malthusian dogpile (see 02/03/2005 entry).Selecting Corn Oil Genes Produces More Corn Oil, but What Else? 02/04/2005
Breeders have been trying to squeeze more corn oil out of corn for over a century, one of the longest-running scientific experiments ever. They have made pretty dramatic gains in yield, from 5% to 20%, in 100 generations, says William G. Hill in Science.1 Now also, geneticists have the tools to look for which genes are evolving. The story is not all that clear, however, both for corn and for similar studies trying to beef up poultry (if youll pardon the expression).
Do lots of small genetic changes add up (the infinitesimal model suggested by Darwin), or do single nucleotide polymorphisms (SNP) produce dramatic changes? Maybe both, maybe one or the other, or maybe something else. Its not clear how to define a small genetic change, for one thing, or how to isolate one change from effects on other genes.
The continuing responses to selection, therefore, are not likely to be due mainly to continuing tiny changes in gene frequency predicted by the infinitesimal model; instead they may be due to the fixation of genes, including those arising by mutation after selection started, which have appreciable effects while segregating. The biological processes leading to oil concentration or chicken growth are obviously highly interactive, but genes that contribute to selection response must differ in effect when averaged over all other segregating genes. (Emphasis added in all quotes.)The experiments to which Hill refers did not provide unambiguous evidence that small genetic mutations (quantitative trait loci, or QTLs) added up, even in this clear-cut case of artificial selection. He leaves it as an exercise: We have yet to discover how such QTLs work, but several of the SNPs associated with oil concentration were at candidate loci, so there are opportunities to find out. So this is an ongoing challenge for geneticists: identify the genes and the molecular changes in them that cause these many small but important differences in quantitative traits. Nevertheless, he is sure that this century-long experiment will illuminate how evolution works: It is these small differences that generate variability in populations, providing fuel for change through the action of natural and artificial selection.
1William G. Hill, A Century of Corn Selection, Science, Vol 307, Issue 5710, 683-684, 4 February 2005, [DOI: 10.1126/science.1105459].
Excuse me, but after a hundred years of forcing selection to go one way, which nature does not do, are you saying that corn still only produces corn oil, and not something else? Are you hinting that breeders have hit a plateau at 20%? That with all the tools of genetics to look for a known effect, they are not sure which genes are producing it?Book Review 02/03/2005: From Darwin to Hitler by Richard Weikart, reviewed by Johannes L. Jacobse at TownHall.com:
Jacobse puzzles over why so many intellectuals in Germany allowed Hitler to rise to power with so little objection. The answer, Weikarts book explains, is that Darwinian ethics had so permeated German thinking by that time that the Nazi platform of promoting fitness and weeding out the unfit did not seem all that unusual. Neither Weikart nor Jacobse blame all the Nazi atrocities on Darwinism, yet believe the connection is incontrovertible:
Why were the Jews the target of Nazi genocide? Weikart says the historical evidence is inconclusive, although it appears that Hitler drew more from a popularized street Darwinism than from the scholarly tracts of intellectuals. Although anti-Semitism was always a feature of Darwinian social dogma, Hitler made it the centerpiece of Nazi social policy.The book review explains in more detail how the Darwinian world view took over Germany, and how Darwinian ethics fed directly into the German social and intellectual scene leading up to Hitler. Richard Weikart is a professor of history at California State University.
In an online article by professor Weikart, Does Darwinism Devalue Human Life?, he discusses Darwinian ethics in relation not only to Hitler, but to modern trends in medical research and social policy. Read the first two paragraphs to get hooked.Age Estimate for Oldest Glacier Revised Way Down 02/02/2005
Deposits from Antarctic glacial ice thought to be 8.1 million years old have been re-dated at not more than 310,000 years old, and maybe as little as 43,000, reports a team writing in the Feb. issue of Geology.1 Ng (MIT), Hallet, Sletten and Stone (U. of Washington) analyzed cosmogenic helium-3 and calculated the rate of sublimation of the ice to arrive at the new age estimate for glacial till (leftover rock debris from glacial melt or ice evaporation). Such rapid recent growth of the till contradicts previous interpretations that it is older than 8.1 Ma at an adjacent site, where it encloses volcanic ash of this age, they say (emphasis added in all quotes). We question whether the ash provides a valid age constraint for the ice. Earlier geologists had dated the ash fall as a time constraint on the glacial till, but this team says it may accumulate much more rapidly than assumed. Our results show that the ash may not be a reliable stratigraphic indicator.
1Ng et al., Fast-growing till over ancient ice in Beacon Valley, Antarctica, Geology, Vol. 33, No. 2, pp. 121–124, doi: 10.1130/G21064.1.
This team may not have the last word, either. Readers should learn from this story that even among secular geologists, interpretations can contradict one another by orders of magnitude. This is not just a story about dating methods, but also feeds into the debate about global warming. Their paper begins, The recent history of East Antarctica is key to understanding the response of large ice sheets to climate forcing. Beware political decisions based on advice from geologists who read present data and weave stories about things that happened millions of years ago, as if it will help forecast future events. Considering revisions this large, politicians might be better off forecasting climate from analysis of layers in a calfs liver.Bird Brain No Longer an Insult 02/01/2005
Birds can perform amazing tasks beyond the reach of cats and dogs, begins an article in the BBC News. So pay a little respect. You can still call your boss a bird brain, but had better quickly explain why that is a compliment. See also the longer article on MSNBC News.
In a related article, Jessica Ebert wrote in Nature1 that bird-brain terminology is undergoing a reformation. The century-old naming convention of brain parts in birds resulted from a belief that birds were primitive, possessing simple brains capable only of instinct. The distinction between bird and mammal brain capabilities is artificial, scientists now realize: Signalling molecules and neurotransmitters operate similarly in the brains of birds and mammals. And researchers agree that birds can learn: crows can pass on tool-making skills, for example. A consortium of neurobiologists has revamped the nomenclature to give bird brains the respect they deserve.
1Jessica Ebert, Reformation of bird-brain terminology takes off, Nature 433, 449 (03 February 2005); doi:10.1038/433449b.
Can your pet cat or dog sing? Fly? Talk? Migrate across the world? Solve a puzzle as fast as a bird? Dont let the small size fool you. Birds are compressed packages of extreme design that are a wonder to behold. The diversity of skills found among birds is mind-boggling. A dinosaur couldnt figure all this out if it wanted to, even if it knew how to select those rare lucky mutations.Genes Evolving Downward 02/02/2005
Those assuming the evolution of eukaryotic genomes has progressed upward in complexity may find the following abstract from PNAS1 startling:
We use the pattern of intron conservation in 684 groups of orthologs from seven fully sequenced eukaryotic genomes to provide maximum likelihood estimates of the number of introns present in the same orthologs in various eukaryotic ancestors. We find: (i) intron density in the plant-animal ancestor was high, perhaps two-thirds that of humans and three times that of Drosophila; and (ii) intron density in the ancestral bilateran was also high, equaling that of humans and four times that of Drosophila. We further find that modern introns are generally very old, with two-thirds of modern bilateran introns dating to the ancestral bilateran and two-fifths of modern plant, animal, and fungus introns dating to the plant-animal ancestor. Intron losses outnumber gains over a large range of eukaryotic lineages. These results show that early eukaryotic gene structures were very complex, and that simplification, not embellishment, has dominated subsequent evolution. (Emphasis added in all quotes.)In their paper, Harvard biologists Scott Roy and Walter Gilbert used the maximum-likelihood phylogenetic method instead of maximum parsimony, and feel it provided a better ancestral tree. In fact, they used the same data as other scientists who used parsimony, and got very different results. They are emphatic about their conclusions:
These results push back the origin of very introndense genome structures over a billion years to the plant-animal split. Indeed, ancestors at the divergences between major eukaryotic kingdoms as well as the ancestral bilateran appear to have harbored nearly as many introns as the most intron-dense modern organisms. This is a sharp repudiation of the common assumption that intron-riddled gene structures arose only recently.This bias toward intron loss instead of gain appears to be a general trend among eukaryotes, they conclude. What does this mean? The only way to rescue an evolution toward improvement with these results is to suggest that introns are bad, like parasites, and that over time, eukaryotes got better at ridding themselves of them. They reject that and other notions, assuming instead that It seems much more likely that different selection or mutation regimes for introns along different lineages are driving the observed instances of gene streamlining. Although intron function and evolution is still largely unknown, they leave only an admission of ignorance of what their results mean only that geneticists had better re-examine their assumptions:
These results contradict the assumption that genome complexity has increased through evolution. Instead, species have repeatedly abandoned complex gene structures for simpler ones, questioning the purpose and value of intricate gene structures. These results suggest a reconsideration of the genomics of eukaryotic emergence.
1Scott W. Roy and Walter Gilbert, Complex early genes, Proceedings of the National Academy of Sciences USA, 10.1073/pnas.0408355101, published online before print February 1, 2005.
Introns and the complex molecular machines that process them (spliceosomes see 09/12/2002 and 09/17/2004 entries) are still mysterious, but does anyone see a neat picture of evolution here? Why would some introns be ultra-conserved (see 05/27/2004 entry), and others be removed? Evolutionary theory is not helping explain introns or spliceosomes, and may be missing entirely the picture of what is going on. Why not approach the data from the perspective of intelligent design and entropy? The complexity was apparently present from the start. Where did it come from? The notions of ancestry in this picture are fictional. The assumed trees are filled with gaps. What seems apparent is devolution, not evolution.Teachers Getting Reluctant to Teach Evolution 02/01/2005
Cornelia Dean in the New York Times worries that, to stay out of trouble, more and more biology teachers are avoiding the discussion of evolution.
Dean quotes someone who claims the practice of avoiding the topic was widespread, particularly in districts where many people adhere to fundamentalist faiths. But why would teachers fear discussing it because of that? Its open season on fundamentalist faiths (loaded words for Bible-believing Christians). Most teachers have no problem with attributing everything bad in the world to Christianity. Maybe the students from those districts are better at asking the hard questions that give Darwin Party biology teachers stomach aches (see 06/14/2004 commentary).Initial Science Results from Cassini, cont.
1Nature Vol 433 No 7027 pp669-784, 17 Feb 2005; 3 papers, 1 review article.
2Science, 307:5713 (25 Feb. 2005); 11 papers, 3 review articles.
For anyone who was intrigued by the Voyager discoveries back in 1981, these are great days indeed. The Saturn system is a far more dynamic and complex panorama than anyone could have expected. Did you enjoy getting this much detail in this entry? If so, write us and let us know whether the effort to summarize all this material was helpful and interesting; thanks to those who have written in already.State of the Cosmos, cont.
According to inflationary cosmology, the universe expanded exponentially quickly for a fraction of a second very early in its historygrowing from a patch as small as 10–26 m, one hundred billion times smaller than a proton, to macroscopic scales on the order of a meter, all within about 10–35 sbefore slowing down to the more stately rate of expansion that has characterized the universes behavior ever since. The driving force behind this dramatic growth, strangely enough, was gravity.... Although this might sound like hopeless (or, depending on ones inclinations, interesting) speculation, in fact inflationary cosmology leads to several quantitative predictions about the present behavior of our universepredictions that are being tested to unprecedented accuracy by a new generation of observational techniques. So far the agreement has been excellent.One such prediction, he claims, is that the universe should be nearly perfectly flat, or balanced between expansion and contraction. Guth points to the WMAP measurements (see 02/14/2003, 03/06/2003 and 05/02/2003 entries) as confirming this prediction that solved the flatness problem (the observation that the universe was very nearly flat), a conundrum of pre-inflationary models. Another prediction is that the universe should be homogeneous and isotropic on large scales, which again, he says, is found to be the case. Before inflation, cosmologists had to reckon with the horizon problem:
Without inflation, this large-scale smoothness appears quite puzzling. According to ordinary (noninflationary) big bang cosmology, these photons should never have had a chance to come to thermal equilibrium: The regions in the sky from which they were released would have been about 100 times farther apart than even light could have traveled between the time of the big bang and the time of the photons release. Much like the flatness problem, inflation provides a simple and generic reason for the observed homogeneity of the CMB: Todays observable universe originated from a much smaller region than that in the noninflationary scenarios. This much-smaller patch could easily have become smooth before inflation began. Inflation would then stretch this small homogeneous region to encompass the entire observable universe.Guth points to small-scale perturbations, or ripples, in the cosmic microwave background (CMB) as also supportive of his inflation idea, mainly because other proposals have been ruled out. While full class of inflationary models can make a variety of predictions, he says, the simplest model fits the data beautifully (see 06/18/2003 and 06/12/2001 entries for contrary views).
With such an admirable track record behind him, Guth turns to how research on inflation has progressed. Some have questioned that, once started, inflation could have ever stopped again: the eternal inflation problem. Others wonder how ordinary matter would have arisen when inflation effectively dropped the temperature to zero and diluted the density of ordinary matter to negligible quantities. Particles were created, he explains by oscillations that set up resonances between quantum fields: Large numbers of particles would be created very quickly within specific energy-bands.... This dramatic burst of particle creation would affect spacetime itself, as it responded to changes in the arrangement of matter and energy.
Guth also discusses how inflation fits in with brane cosmology (see 04/26/2002 entry) and string theory, insisting it is compatible with either. He seems to like the latter, because it produces a story of two lovers who need each other:
The union of string theory and cosmology is barely past its honeymoon, but so far the marriage appears to be a happy one. Inflation, from its inception, was a phenomenologically very successful idea that has been in need of a fundamental theory to constrain its many variations. String theory, from its inception, has been a very well-constrained mathematical theory in need of a phenomenology to provide contact with observation. The match seems perfect, but time will be needed before we know for sure whether either marriage partner can fulfill the needs of the other. In the meantime, ideas are stirring that have the potential to radically alter our ideas about fundamental laws of physics.In fact, with brane theory, there seems to be a happy threesome in the offing. The milieu of proposals, each with its suite of variables (some 10500 possible inflating/vacuum states in string theory, for instance) leaves the reader with a sense of an infinite combination of possibilities with little hope for picking the right one to build the universe we know:
Although the rules of string theory are unique, the low-energy laws that describe the physics that we can in practice observe would depend strongly on which vacuum state our universe was built upon. Other vacuum states could give rise to different values of fundamental constants, or even to altogether different types of elementary particles, and even different numbers of large spatial dimensions! Furthermore, because inflation is generically eternal, one would expect that the resulting eternally inflating spacetime would sample every one of these states, each an infinite number of times. Because all of these states are possible, the important problem is to learn which states are probable. This problem involves comparison of one infinity with another, which is in general not a well-defined question. Proposals have been made and arguments have been given to justify them, but no conclusive solution to this problem has been found.Guth explains that no one has been able to explain why our universe took the initial state it did: i.e., whether its state was determined or random. Maybe the escape clause is to believe that all possible states exist, and we observe the one that produced observers (the anthropic principle). Guth seems surprisingly warm to this idea that produced a privileged planet by chance:
Another possibility, now widely discussed, is that nothing determines the choice of vacuum for our universe; instead, the observable universe is viewed as a tiny speck within a multiverse that contains every possible type of vacuum. If this point of view is right, then a quantity such as the electron-to-proton mass ratio would be on the same footing as the distance between our planet and the sun. Neither is fixed by the fundamental laws, but instead both are determined by historical accidents, restricted only by the fact that if these quantities did not lie within a suitable range, we would not be here to make the observations. This ideathat the laws of physics that we observe are determined not by fundamental principles, but instead by the requirement that intelligent life can exist to observe themis often called the anthropic principle. Although in some contexts this principle might sound patently religious, the combination of inflationary cosmology and the landscape of string theory gives the anthropic principle a scientifically viable framework.(See also 02/05/2002 entry on multiple universes.) One particularly shocking example of anthropic parameters is the energy density of the vacuum (see 09/30/2004 entry) which, according to naive estimates, could be up to 10120 times as high as that which is observed, even with dark energy (see 02/28/2004 entry). Puzzles like the anthropic principle reinforce the necessity of asking cosmological questions:
There are both positive and negative contributions, but physicists have been trying for decades to find some reason why the positive and negative contributions should cancel, so far to no avail. It seems even more hopeless to find a reason why the net energy density should be nonzero, but 120 orders of magnitude smaller than its expected value. However, if one adopts the anthropic point of view, it was argued as early as 1987 by Weinberg that an explanation is at hand: If the multiverse contained regions with all conceivable values of the cosmological constant, galaxies and hence life could appear only in those very rare regions where the value is small, because otherwise the huge gravitational repulsion would blow matter apart without allowing it to collect into galaxies.Guth repeats the usual precision cosmology rhetoric that our instruments are nailing down the values of fundamental cosmic properties (see 09/20/2004 entry). But inflation is not such a precise quantity; in his conclusion, he admits that much work needs to be done (see 12/21/2000 and 05/30/2001 entries):
Even with the evidence in favor of inflation now stronger than ever, much work remains. Inflationary cosmology has always been a framework for studying the interconnections between particle physics and gravitationa collection of models rather than a unique theory. The next generation of astronomical detectors should be able to distinguish between competing inflationary models, whittling down the large number of options to a preferred few.Hopefully, those detectors will also solve some remaining major puzzles such as the nature of dark matter and dark energy, which combined are said to make up 96% of the universe, leaving a mere 4% that we observe (see 06/20/2003 and 12/17/2003 entries). Whatever its origin, dark energy, much like dark matter, presents a fascinating puzzle that will keep cosmologists busy for years to come. (See also 06/04/2002 entry, and 11/02/2002 entry and commentary.)
1Alan H. Guth and David I. Kaiser, Inflationary Cosmology: Exploring the Universe from the Smallest to the Largest Scales, Science, Vol 307, Issue 5711, 884-890, 11 February 2005, [DOI: 10.1126/science.1107483].
We had to show you in their own words what these MIT eggheads are saying. Guth, whose name stands for Grand Unified Theory Huckster, has been propounding his framework for 25 years now, and has become famous for it. But what is inflation, other than an untestable, ad hoc proposal invented to get around insurmountable obstacles in the Big Bang cosmology of the 70s? Astronomers were well aware of the flatness problem and the horizon problem; with a sweep of the hand and some abstruse math, con artist Guth in his magic show wagon said no problem, well just stretch the universe and the problems will no longer be visible. A viewer objects that he has just diluted the particles to negligible density. No problem again; well pick the right vacuum state to make quantum fields resonate, such that their energy produces new particles out of nothing. Another viewer objects that one cannot determine the conditions by chance to rig the outcome. Well, then, the huckster chimes, if it were not so, we would not be here arguing about it now, would we? Hmmmmm?Teach Evolution, cont.
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