I believe all scientists should be wary of their assumptions, as these can largely determine their findings. They should also be wary of extrapolations outside the range of observation. The further the extrapolation, the less reliable the prediction. Changes in the assumptions will change the prediction. This applies in particular to boundary conditions, such as those involving initial conditions (or origins). Therefore, scientists can only speculate, imagine and guess about the origin of life.
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2001: JAN • FEB • MAR • APR • MAY • JUN • JUL • AUG • SEP • OCT • NOV • DEC
2000: SEP-OCT • NOV-DEC
Readers Object to National Geographic Ape-Man Cover 11/29/2002
In the December issue, National Geographic admits in Forum of letters to the editor, The [August 2002] issue generated plenty of mail from those who dispute evolution. The cover had featured a reconstruction of the Dmanisi skull that looked half ape, half human. One reader complained, In 50 years I have never seen GEOGRAPHIC raise the possibility that man could be a divine creation, yet the possibility of evolution is promoted as fact. Because of this your credibility is diminished for a significant percentage of Americans. A Brazilian museum curator complained about broad conclusions being formed from one teenage skull; another reader complained about linking intelligence to migratory skill. Of the six readers whose letters were printed, only one seemed to enjoy the article (but she mainly just cracked a joke about males not stopping to ask directions); three were critical, and two were neutral. Apparently some readers disputed the artists choice on how much facial hair to paint. NGs art director Christopher Sloan admitted it was the most speculative part of the reconstruction. The magazine explains the decision: Artist Mauricio Anton looked at the fossils closest living analogueschimps and humansand used a hair pattern halfway between the two.
Thus the artist made his choice on the assumption of evolution, and even then, on an arbitrary half-way point between ape and mannot 10%, not 30% not 70, 80 or 90%, but 50%even though their August story lamented that this skull throws the whole ancestry of man into a confused state of affairs. They said, Along with other fossils and tools found at the site, this skull reopens so many questions about our ancestry that one scientist muttered, They ought to put it back in the ground. In short, everything you were taught about human evolution is wrong. Why pay any attention to their artwork? Keep those cards and letters coming.Utah River Valley Shows Rapid Changes in Recent Centuries 11/27/2002
A paper in the December GSA Today (Geological Society of America) by Richard Hereford explores recent alluvial and erosional landforms in the Paria River basin of Southern Utah. The author writes, Valley-fill alluvium deposited from ca. A.D. 1400 to 1880 is widespread in tributaries of the Paria River and is largely coincident with the Little Ice Age epoch of global climate variability. He traces periods of arroyo cutting at ca. A.D. 1200-1400 and 1860-1910, interspersed with periods of alluvial deposition.
Large changes can occur within centuries. It doesnt necessarily take millions of years to see big changes in landforms. The Paria River basin is a colorful area of unique landforms and amazing hiking trails for the adventurous. For your Thanksgiving weekend enjoyment, here is a brief photo-vacation from the Creation Safari Photo Gallery into the Paria River wilderness area of the Grand Staircase Escalante National Monument:Is Darwins Tree of Life Visible in the Genes? 11/26/2002
Two papers in the Proceedings of the National Academy of Sciences online preprints (11/25) complicate the task of deducing common ancestry from genetic codes. One by Kerry L. Shaw of University of Maryland is entitled, Conflict between nuclear and mitochondrial DNA phylogenies of a recent species radiation: What mtDNA reveals and conceals about modes of speciation in Hawaiian crickets. She concludes from her comparison of phylogenies built from nuclear and mitochondrial DNA that speciation histories based on mtDNA alone can be extensively misleading.
Another paper by three Penn State geneticists is called, Overcredibility of molecular phylogenies obtained by Bayesian phylogenetics. They investigated the technique of Bayesian inference, a popular method for inferring causation, and found it too liberal compared to the more conservative bootstrap method. They write, Bayesian analysis can be excessively liberal when concatenated gene sequences are used, whereas bootstrap probabilities in neighbor-joining and maximum likelihood analyses are generally slightly conservative. These results indicate that bootstrap probabilities are more suitable for assessing the reliability of phylogenetic trees than posterior probabilities and that the mammalian and plant phylogenies may not have been fully resolved.
No kidding; the mammalian and plant phylogenies are both abominable mysteries to evolutionists. What the geneticists infer from DNA analysis often disagrees strongly with what the biologists infer from comparative anatomy, and both differ strongly from the fossil record. Dont let the popular media fool you into thinking scientists can see Darwins tree of common ancestry in the genes. These articles reveal that its not so simple, and there are many problems, contradictions, and disagreements. Follow our chain links on Darwinism for many more recent examples.Is Directed Evolution Really Evolution? 11/26/2002
Three Caltech scientists did an experiment in directed evolution, getting a genetic circuit to work by steering mutation and selection to obtain a desired result. Their paper, Directed evolution of a genetic circuit, is published in the Proceedings of the National Academy of Sciences. They feel this experiment demonstrates that directed evolution can achieve complex circuit design, even when the engineers do not understand the complex interactions of the parts. Yokobayashi et al write, We have demonstrated that directed evolution can solve a complex in vivo optimization problem involving multiple poorly understood biochemical interactions and parameters. Laboratory evolution is an algorithmic design process, ultimately amenable to automation if the screening criteria and individual operations of mutation and screening can be standardized and described.
This was an experiment in intelligent design, not evolution. Picture a large scientific research laboratory, like JPL, with thousands of egghead scientists and engineers, individually very smart and skilled. Without effective leadership, nothing might be accomplished. But give the laboratory a good director and management team, and that talent can achieve great things. The director may know very little about the details of rocket science or celestial navigation; he or she doesnt have to. An MBA may be more useful than a PhD. The director just steers the human talent toward a chosen objective, and things happen. In the same way, these researchers took an already-existing genetic code and translation system, and through intelligent design, guided the skilled molecules to achieve a predetermined function, even when they did not know the details of how the molecules actually worked. Directed evolution is a misnomer. This was an optimization experiment, and the word optimize implies goal-directed design for a purpose. The molecules were not evolving by purposeless, undirected forces like Darwinian evolution would require. They had inherent skill designed into them; they just needed to be given an assignment. So these scientists are not evolutionists; they are just good managers.Why Does Earth Still Have a Magnetic Field? 11/25/2002
Astronomy Picture of the Day asks the question:
Why does the Earth have a magnetic field? The electrical conductivity of the molten plasma of the Earths core should be able to damp the current magnetic field in only thousands of years. Yet our five billion year old Earth clearly causes magnets to point to (defined) north. The mystery is still being studied but recently thought related to motions in the Earths liquid outer core. Specifically, as portions of the outer core cool and fall inward, oceans of the liquid iron-rich magma rise outward, forced into a helical motion by the spin of the Earth. This motion, many geologists now believe, regenerates Earths magnetism.This caption accompanies a picture of a computer-generated model of the twisting motion that might generate the field.
The article doesnt mention that the magnetic field strength has been declining steadily ever since it was first measured in 1829, and has dropped 14% since then. Creationists Thomas Barnes and now Russell Humphreys have used this as evidence that the earth could not be billions of years old. Read his article and see if the helical theory will stand up to the evidence. We have other data points in the solar system for comparison: gas giants and the sun with large magnetic fields, and practically none on Venus or Mars. Just be glad earth has a good one, because it protects us from damaging radiation. Review our May 10 headline on how it acts like storm windows to give us calm skies in the midst of a rifle range of particles.Evolution and the Dogs Tale 11/22/2002
Three articles on the evolution of the dog grace the Nov. 22 issue of Science. Elisabeth Pennisi, summarizing the papers, says the reactions vary from enthusiasm to skepticism. Did dogs evolve from a single common ancestor, like the wolf, or from several? How far back was the common ancestor? Why do dogs show such diversity in size and shape? And how did the dog gain the social skills to become mans best friend? BBC News has a summary of the reports, and you can also see adaptations in Science Now and Nature Science Update (complete with dog puns, like ruff estimates and archaeological evidence for dogs is spotty). Surprisingly, dogs are better at reading our signals than chimpanzees, our closest relatives, says Nature: Distantly related dogs, on the other hand, having evolved alongside humans, seem to have converged on some of our thought processes.
They have converged on begging, for sure; dogs have perfected this thought process to a fine art. Watching a frisbee-catching dog or a New Zealand sheepdog in action shows you how intelligent and skillful are these versatile animals. Then there are saint bernards in the snow, bloodhounds on the trail, German shepherds in the 9/11 wreckage, greyhounds on the racetrack, Alaskan sled dogs, hunters and pointers, and the all-around household mutt (poodles, however, are a grotesque collage of useless mutations). Dogs are very diverse animals, yet these articles fail to explain how the dog species evolved in the first place. Creationists and evolutionists all agree that the diversity of dogs stem from a single dog kind or common ancestor (take your pick of terms), but they are still Canis familiaris. Limited variation is not evolution. Whether dachshunds or great danes, they all still pant and bark and wag their tails and walk in circles before lying down. Evolutionists, show us the steps from worm to dog. The earliest alleged dog fossil is claimed to be only 14,000 years old, (though Nature says most dog fossils date from 7,000 years or later), yet the theoretical common ancestor, according to one researcher, goes back 135,000 years, without a trace in the fossil record. Pet dogs are found with the earliest human burials. These facts show that dogs have always been just dogs, despite their variations. Dog lovers can enjoy that special relationship with a multi-talented and friendly animal that bears the hallmarks of design. We dont need an evolutionary tale wagging the dog.Trigger for Cambrian Explosion Found? 11/22/2002
John Grotzinger of MIT told the Geological Society of America last month that he thinks he knows what triggered the Cambrian Explosion, the sudden burst of life in the near-oldest fossiliferous rocks that contain representatives of every animal phylum. While studying layers in Oman, he saw evidence of a sudden extinction at the onset of the Cambrian, dated 542 million years ago. A simple precambrian fossil suddenly disappears from the next higher layers. Evidently, some catastrophic extinction, maybe a rise in carbon dioxide in the oceans that obliterated any organisms not prepared to breathe oxygen. That cleared the playing field for an explosion of new life forms, better adapted to the changed conditions. Richard A. Kerr reports on this hypothesis, its adherents and critics, in the Nov. 22 issue of Science.
Is there a shred of evidence in this story for how complex body plans could evolve? None! Instead, only a patently illogical idea, sensible only to a doctrinaire evolutionist, that catastrophe is the mother of complexity. Evolution is the modern Phoenix myth. The more disaster, the more pressure for life to evolve even faster. Why worry about meteor impacts, then? Look at all the good they have done for this planet, like bringing a profusion of mammals out of the dinosaur graveyard. Strange, catastrophes havent brought forth life on the moon, Mercury, Venus, Mars, Jupiter, Europa, Io, Ganymede, Callisto, Saturn, Titan ....Bacteria Borrowed Each Others Photosynthesis Technology 11/22/2002
How could bacteria evolve the complex processes of photosynthesis five times separately? By technology sharing. Thats a new idea propounded by a team at Dalhousie University in Nova Scotia, reports Elisabeth Pennisi in the Nov. 22 issue of Science. They didnt have to invent it from scratch each time; they got the parts at the swap meet, via a process of lateral gene transfer.
This is an ad hoc speculation, based on evolutionary assumptions, to explain away a lack of evidence for evolution. Even if these bacteria did swap genes, It still doesnt explain how photosynthesis, an immensely complicated set of processes, proteins, genes, and regulators, could ever evolve even once in the first place. This idea is falsified by an observation mentioned in a lecture this past weekend by Dr. George Howe, retired botanist at The Masters College in California. He noted that CAM photosynthesis, a different variety of light-gathering food production used by the saguaro cactus, appears in up to 30 widely-scattered families of flowering plants. Some species in a family will have the usual kind, and some will have the CAM kind, with no phylogenetic rhyme or reason. It is inconceivable that such a complex set of hardware and software could have arisen independently even once, let alone 30 times.Neanderthals Couldnt Throw Spears 11/21/2002
A story in New Scientist claims, Neanderthals and early humans knew how to make spears - but did not know how to throw them. Instead, they had a limited hunting strategy, and used their spears merely to stab animals they had already trapped or ambushed. How do they know this, if no one has seen a living Neanderthal? Anthropologists thought that thicker bones in one arm gave evidence that Neanderthals were spear-throwers, but Steven Churchill of Duke University, NC has a different explanation. He used his students to measure the amount of force needed in throwing vs stabbing with two arms, and found that the stabbing motion produced the amount of force consistent with the amount of Neanderthal humerus thickening.
This experiment seems only designed to preserve the image of Neanderthals as brutish numbskulls who couldnt figure out how to use their arms. Does it take 20,000 years for large human being with a bigger brain than modern man to learn how to throw? Come on. We already know Neanderthals were smart and savvy, and kind-hearted. If a child can throw a spear, why couldnt a big, handsome, intelligent Neanderthal man? Who knows, maybe they got their big arms from arm wrestling, or from javelin tossing in the caveman Olympics.Are You Man or Mouse – Or In Between? 11/21/2002
An editorial in the Nov. 21 Nature states (no kidding) “Biologists divided over proposal to create human-mouse embryos.” Some scientists think they need to create human embryos using mouse stem cells to test the pluripotency of the latter (i.e., the ability to generate any cell). “But the suggestion of creating such mixed-species embryos is likely to provoke public disquiet,” Natalie Dewitt writes, “and could galvanize political opposition to all research involving human embryos.” At a forum in New York last week, scientists reached no agreement. A leading stem cell researcher, Ronald McKay, said, “I am completely opposed to putting human embryonic stem cells into any condition that will cause moral affront.” Others supported the experimentation as necessary to test the usefulness of stem cells for medical purposes.
Those inconvenient moral issues just keep getting in the way of progress. It appears they are just afraid of public disquiet or moral affront, i.e., causing a public uproar, rather than whether these activities are truly unethical or immoral. They probably dont have to worry. Sadly, much of the public seems too engrossed in the latest celebrity stories to raise an outcry over moral issues involving small clusters of cells, let alone even understand the issues. See our Sept. 23 entry on the ethical ramifications of mixing human and animal DNA.Lab to Create Artificial Life Form 11/21/2002
Its not from scratch, but controversial geneticist Craig Venter is going to create an artificial bacterium, reports New Scientist (see also CNN News). With permission from the Ethics of Genomics Group and a $3 million grant from the Department of Energy, Venters new Institute for Biological Energy Alternatives will take the simplest free-living organism, remove its DNA, and insert artificial chromosomes. These will be made up of what they think is the minimum requirement for life, which according to earlier research is comprised of 265 of its normal complement of 517 genes. The ethics committee decided this did not violate any ethical guidelines, but some are concerned about the potential for biological warfare or accidental release of a novel infectious agent. The lab believes appropriate safeguards will be taken, and the project will be valuable: The work could reveal much about the evolution of life on Earth, the article in New Scientist states.
What it will reveal is that life is irreducibly complex. 265 genes thats a lot of complex specified information, far more than the minimum complexity threshold that William Dembski uses to rule out chance as a cause, anywhere in the universe for as long as it has existed. Its also much more than the 239 protein minimum threshold for life James F. Coppedge used in Evolution: Possible or Impossible?; he calculated the chance of getting the complete set of these proteins at one in 10119850, a chance so small it would never happen at any time, in any place. Even so, Mycoplasma genitalium is a parasite dependent on its host. Rather than being an evolutionary link, it most probably is a stripped-down organism from something even more complex. Yes, this experiment will reveal much about the evolution of life on Earth; it will reveal that evolution is impossible.Architect, Contractors and Skilled Laborers Build Your Colon 11/21/2002
Don’t look for bathroom humor here; just amazement. In the Nov 21 issue of Nature, Mark Peifer waxes eloquent about this organ that is usually not brought up in polite conversation:
It is no mean feat for organisms to make and maintain their organs. The complex cellular and molecular processes involved are illustrated by two studies of the proteins that participate in producing a colon.The papers he references discuss proteins named Wnt, Myc, p21 and Eph, that are involved in the expression of genes that build the colon. This provides Peifer an analogy to a well-run construction site: “These data firmly establish Wnt signals as colon architects, identify sub-contractors such as Myc that supervise particular parts of the job, and highlight skilled labourers, such as p21 and Eph receptors, that carry out specialized tasks.”
Funny; we couldn’t find the word evolution anywhere in this article.Did Life Boot Itself Up? 11/21/2002
Gerald Joyce appreciates the problem of getting both the genetic code and self-replication to work simultaneously at the origin of life, but thinks a recent computer simulation might show how it happened. Writing in the Nov. 21 issue of Nature, he begins:
In thinking about the origin of life on Earth and, in principle, elsewhere in the Universe, many regard the ‘hard problem’ to be getting the ball rolling in the first place. It is generally thought that life on Earth began with the production of macromolecules that served as primitive stores of genetic information (genomes). Crucially, there was a need to replicate these macromolecules, both to propagate the contained information and to allow the occurrence of mutations — which, within limits, are essential for darwinian evolution based on natural selection.Another hard problem is getting a genome big enough to encode for self-replication. Manfred Eigen showed 30 years ago that error catastrophe can wipe out any sizable genome quickly if replication is not 99% accurate or better. Joyce, largely responsible for the popularity of the “RNA World” hypothesis, reminds the reader that ribozymes have been manufactured that can replicate themselves, although they have not been found in nature. Since ribozymes can both replicate and hold genetic information, perhaps that could lead to a solution of the chicken-and-egg dilemma.
Joyce points to the work of Szabó et al, who performed a computer simulation that allowed a self-replicating organism to “bootstrap” itself upward to higher complexity, if spatial isolation of the products were carefully controlled. The simulation was only done on a two-dimensional grid, so Joyce cautions that the work should not be taken too literally, although he finds it curious that even in the world of molecules, as with nations, “spatial isolation also contributes to good citizenship.” Provided the right kind of isolation were achieved, “Spatial isolation provides an opportunity for darwinian evolution to ‘discover’ solutions to problems that require molecules to interact. The results obtained by Szabó et al. show that this makes evolutionary bootstrapping possible — and perhaps it is what started our planet on the path to the complex biosphere that exists today.”
Computer simulations are unrealistic, and too prone to investigator interference. We want to see Joyce do this in the lab, using realistic mixtures and concentrations of ingredients, without any information or intervention by the researcher. The results will be predictable: the laws of thermodynamics and equilibrium will dash all hopes of spontaneous generation. Joyce not only wants the computer to be able to boot itself, he wants it to make itself. His comments commit the usual sin of personification: darwinian evolution does not discover anything, and molecules are not citizens. See our June 11 entry and commentary on previous work by Gerald Joyce, and our August entry on a more realistic computer simulation. Also, follow the Chain Links on Origin of Life for a reality check on the hopelessness of expecting life to lift itself up by its own bootstraps.Archaeoraptor: The Rest of the Story 11/21/2002
The non-dinosaur half of Archaeoraptor, “once proclaimed as a key intermediate between carnivorous dinosaurs and birds but now known to be a forgery” was a fish-eating bird, says the Nov. 21 issue of Nature.
Save your November 1999 issue of National Geographic as a collector’s item, along with the October 2000 retraction. At least it only took a year for Piltdown Chicken to be exposed, instead of the 45 years for Piltdown Man. I suppose that’s progress. National Geographic probably felt no need to dredge up their own shame today after printing the retraction, but millions of people rely on their magazine for scientific news. The hoax did not make them more reticent to make extraordinary claims; in fact, this article shows them more brazen than ever to link birds and dinosaurs, despite the fact other paleontologists disagree. They give prominence to two believers but no critics, quoting Julia Clarke saying,Planetesimal Hypothesis Requires Special Conditions 11/20/2002The really unfortunate aspect of the Archaeoraptor forgery was that it was used to suggest that other feathered dinosaur fossils were also faked, and added a layer of confusion to public understanding that shouldnt be there, said Clarke. Theres an abundant amount of evidence that the lineage leading to birds is nested in Dinosauria, she said. There are many feathered flying and non-flying dinosaur fossils from these two regions that are not forgeries.Lets have the evidence instead of the verdict, please, especially from an institution with a track record of weaving tall tales out of minuscule evidence, and rushing to judgment, as long as some data point supports evolutionary assumptions.
How do you build a solar system? Assume, tweak, and juggle. The “conventional cosmogony” that has particles slowly accreting into planets in a protoplanetary disk is full of problems, so Andrew N. Youdin (Berkeley) and Frank H. Shu (Taiwan) propose an unconventional one that, with carefully chosen parameters, might surmount the difficulties. Writing in the Nov. 20 Astrophysical Journal, they first define a planetesimals as “primitive solids of kilometer size or larger,” the presumption being these will grow into planets over time by gravitational attraction. But next, they provide a laundry list of problems with conventional planetesimal hypotheses:
Just as with biological evolution, planetary evolution requires a little bit of data and a lot of imagination. And as with biological evolution, whatever gave birth to our solar system was an unobservable, one-time occurrence that cannot be repeated. Neither biological or cosmogonical evolution is laboratory science; it is the art of storytelling, bounded only by certain laboratory constraints. We like to give our readers the unvarnished stories straight out of the science journals, before they get sanitized for the popular press and virtual reality by the animators. Notice how many parameters had to be carefully chosen to get the model to work against known forces opposing planet formation. They didn’t even get into the problems with Uranus and Neptune, and much more. Sure, one can produce a story that may or may not sound plausible, but is it true? How can they ever know? Whatever happened to Occam’s razor?Sexual Selection Has No Effect on Speciation 11/19/2002
Sorry, Charlie; sexual selection doesn’t work. Charles Darwin, in his second major work The Descent of Man proffered sexual selection as another mechanism by which new species could arise. Four UK and Swedish researchers looked for evidence to support the idea. They surveyed 480 genera of mammals, 105 of butterflies and 148 of spiders for sexual size dimorphism (e.g., larger males), polyandry in 72 mammal genera, and mating frequency in 54 kinds of butterflies. Was there any correlation with number of species? None, they reported in this month’s Biological Proceedings of the Royal Society:
In summary, we find no evidence that two measures of sexual selection, which potentially lead to variance in multi-male gene flow and sexual conflict, are associated with the degree of speciation across mammalian, butterfly and spider genera. If sexual size dimorphism and/or measures of mating pattern are predictors of the strength of sexual selection, and the level of multi-male gene flow or status of male-female conflict, we find that speciation occurs independently of sexual selection, and rather via naturally selected processes of speciation that are well recognized (Mayr 1963).They do not elaborate on what these other processes are, just passing the baton to Ernst Mayr, but that is not their focus: their point is, “Our results therefore show that speciation occurs independently of sexual selection”
It has been noted that in The Origin of Species, Darwin wrote about everything except the origin of species. He talked about artificial selection and proposed a natural counterpart, but never really solved the problem of how new species arose. He just assumed that extrapolation of variation could lead to speciation, even though empirical examples were lacking. His theory of sexual selection was another heuristic proposal, and to this day, evolutionists imagine “choosy” females and competitive males driving the accentuation of sex differences, and presumably, new species. These four scientists, surely evolutionists themselves, looked at the data objectively, and found no evidence of speciation via sexual selection. While assuming speciation occurs by other Darwinian processes, (note that “well recognized” is not the same as “established”), they deny it occurs by sexual selection. The origin of species must be happening some other way.I.D. Debaters Square Off at Hillsdale 11/19/2002
A who’s who of intelligent design proponents and critics made their views known during debates at Hillsdale College November 10-13. Jonathan Wells (pro-ID) gives his perspective on the anti-ID presentations by Larry Arnhart, Michael Ruse, Mano Singham and Niles Eldredge at the Discovery Institute website. Defending ID were Wells, Michael Behe, and William Dembski.
We encourage people to study the arguments on both sides, and have their Baloney Detector handy. It appears to us that the Darwinists are quick to oppose ID with metaphysical and religious arguments, but low on supply of scientific evidence to argue whether Darwinian evolution is actually true. Ruse, for instance, relied on negative theological arguments (for detailed treatment of this tactic, see Cornelius Hunter, Darwin’s God. Notice also his not-so-graceful sidestepping of a student’s question.) Also notable was the air of “contemptuous condescension” on the part of the evolutionists, particularly Frank Steiner, biology professor and Dean of Natural Sciences at Hillsdale – who had the last word, and ended on that kind of note. Regular readers of this column will not be impressed by what he marshaled as evidence to support his views, but may find it startling that he would quote George Orwell’s 1984 to promote the wisdom of believing in two contradictory ideas simultaneously. Does he mean evolution is doublethink? War is peace. Freedom is slavery. Ignorance is strength. One would hope his colleagues cringed at such a suggestion.Math Meets Natural Selection 11/18/2002
Sean H. Rice of Yale has published a paper in the Proceedings of the National Academy of Sciences entitled, “A general population genetic theory for the evolution of developmental interactions.” The abstract reads,
The development of most phenotypic traits involves complex interactions between many underlying factors, both genetic and environmental. To study the evolution of such processes, a set of mathematical relationships is derived that describe how selection acts to change the distribution of genetic variation given arbitrarily complex developmental interactions and any distribution of genetic and environmental variation. The result is illustrated by using it to derive models for the evolution of dominance and for the evolutionary consequences of asymmetry in the distribution of genetic variation.After an impressive array of tensor calculus functions, he concludes, “Because more individuals are far from the mean on one side than on the other, and fitness drops off nonlinearly around the optimum, there is a net selective pressure pushing the population mean away from the optimum. This is countered by directional selection pushing the mean toward the optimum (Q1). If these vectors do not point in exactly opposite directions, then there is a component of evolution along the optimum phenotype contour.” By this he means that random forces will not necessarily cancel out; an organism’s body (phenotype) might climb a peak in fitness space, even if narrow, if the fitness function allows. This is called “directional selection,” or upward evolution toward a fitness peak, as opposed to balancing selection, which would be maintaining a dynamic equilibrium.
Dr. Rice obviously is a whiz at math, so we hate to break the bad news, but garbage in, garbage out. If the assumptions are wrong, no amount of mathematical hand-waving is going to provide a valid conclusion. Unless you have a fitness function that is better than blind chance, you are not going to get the evolution of new organs or functions that will improve an organism, except by chance. William Dembski deals with this extensively in his latest book No Free Lunch, and proves that no fitness function is superior to blind search, because it would require additional information from the outside (i.e., cheating) to distinguish a given fitness function as better than any other – including blind search. Dr. Rice assumes that organisms are going to trend toward fitness, but how is that to be measured? If fitness is measured by survival, then it is a tautology. Recall a recent entry here by a biologist trying to explain what fitness is. First, Dr. Rice needs to define fitness in terms other than survival, then needs to find a fitness function other than chance (without sneaking in outside information) that will generate directional selection. Otherwise, all these fancy equations are just smoke and mirrors.Leonid Meteor Shower – A Biochemical Rain? 11/16/2002
NASA will have two aircraft aloft early Tuesday morning Nov. 19 to try to capture Leonid meteor dust. Why?
Researchers think meteors might have showered the Earth with the molecules necessary for life’s origin. A two-aircraft campaign, led by astronomer Dr. Peter Jenniskens of the SETI Institute and NASA's Ames Research Center, Moffett Field, Calif., will investigate this possibility. “We are looking for clues about the diversity of comets and their impact on the chemistry of life's origin on Earth,” Jenniskens said.On board will be 42 astrobiologists from 7 countries. For details on viewing the Leonids, which may provide a big meteor storm this year (the last chance for 100 years perhaps) see the Jet Propulsion Laboratory website. JPL astronomer Don Yeomans urges, “If you’re ever going to see them, this might be the year to try.”
Update 01/23/2002: The peaks were not as high as expected, but did occur on schedule. Check out this report on Space.Com about the NASA mission; they got to see the northern lights with the meteors while aloft.
Get out and enjoy natures fireworks shows whenever you can. Just don’t expect to evolve into something better. If one hits you (highly unlikely), it might punctuate your equilibrium.
DNA Translator Does the Twist 11/16/2002
A molecular protein machine responsible for translating DNA in a “primitive” cell does some pretty amazing gymnastics, scientists have discovered. Writing an extended research paper in the Nov 15 issue of Science, two biochemists from the Howard Hughes Medical Institute (Yim and Steitz) found that the RNA Polymerase (RNAP) of T7 bacteriophage is quite the contortionist. Lacking the larger genome of eukaryotes, its DNA translation equipment has to get by with less, so it performs three large conformational changes on one end, and additional shifts on the other: “The transition from an initiation to an elongation complex is accompanied by a major refolding of the amino-terminal 300 residues. This results in loss of the promoter binding site, facilitating promoter clearance, and creates a tunnel that surrounds the RNA transcript after it peels off a seven-base pair heteroduplex.” This involves seven subunits rotating 140 degrees and shifting 30 angstroms, then one subunit stretching out over twice its initial length. Then comes the grand finale:
Perhaps the most unprecedented conformational change involves residues 160 to 190, which not only extensively refold, but move about 70 Å from one side of the polymerase to the other. This region refolds from a short helix and an extended loop into a pair of antiparallel helices (H1 and H2/3). The newly formed compact structure, named subdomain H, forms part of the RNA-transcript exit tunnel and contacts the 5' end of the RNA transcript on one surface and the nontemplate DNA on the opposite surface.The other end also undergoes shape-changes to create an exit tunnel for the RNA copy of the DNA. This “massive structural reorganization” of the protein machine causes it to form a protective tunnel, positively charged on the interior, in which the delicate work of translation can occur accurately. The tunnel interior melts the DNA into two strands, shunts the non-coding strand safely to the side, brings the RNA copy elements in and binds them to the DNA template. As the machine progresses down the track, it twists and bends the DNA against its natural inclination. This then supplies the energy to open up the strands and create a “transcription bubble” where the RNA letters (nucleotides) are mated with the DNA code in the “active site”. The tunnel has just the right shape to allow the RNA elements to come in.
RNAP first has to attach to the DNA at a specific starting point called a promoter; this is the “initiation” phase. It appears that another protein called lysozyme regulates RNAP by binding to it, and preventing it from entering the “elongation phase” where all the gymnastics occur prior to the real translation work. In the initiation configuration, RNAP can produce only short chains (oligonucleotides) of RNA. The authors puzzle over whether there is a reason for this:
One might ask why the abortive synthesis of short oligonucleotides exists and why the enzyme might not be “designed” to carry out the stable RNA synthesis that occurs in the elongation phase right from the start. The initiation of RNA synthesis at a particular site that is required for specific gene expression and regulation as well as the need for de novo, unprimed synthesis necessitates binding of the polymerase at a specific DNA location, the promoter. Furthermore, the binding of T7 RNAP to both the promoter and the downstream DNA appears to be essential for opening the bubble. Because short transcripts (2 to 4 nt) cannot form stable heteroduplexes, polymerase leaving the promoter prematurely would presumably lead to bubble closure and transcript displacement by the nontemplate strand. An enzyme locked in the elongation mode conformation seems unlikely to be capable of specific initiation and bubble opening.The authors also found that point mutations in certain spots either broke the machine or made it translate much less efficiently. Eukaryotes have additional protein parts in their translation machinery that do not require the contortions done by RNA Polymerase in these ultra-miniature life-forms.
This is all so mind-boggling. It’s like these little robots can reorganize themselves, like something in an animated sci-fi movie (or a kid with an advanced Lego set). These incredibly tiny machines have moving parts that twist and turn and form tunnels and zippers and clamps and presses right on cue, and they are programmed with the know-how to handle every contingency. How could this evolve by chance? When you see such a marvelous coordination of highly-specific parts, how can you conclude anything less than that a skillful Artist and Engineer designed it? The rules have changed. Biochemists have opened the black box, and shown us what really goes on deep inside the fundamental units of life. It gets more amazing as the focus sharpens. There is essentially no mention of evolution in this paper. As we show so often, evolutionary storytelling is inversely proportional to the amount of detail available for study. (For contrast, see next headline.)Where's the Evidence for Selection? We're Still Looking 11/16/2002
Steve Olson, writing a perspective piece on population genetics in Science November 15, is “Seeking the Signs of Selection.” He’s pretty sure they will be found, now that we have the complete human genome, and faster ways to sequence genes. But it’s a daunting task (emphasis added):
About 150 anthropologists, geneticists, and pharmaceutical experts have been meeting at Cold Spring Harbor Laboratories to find the missing signs of selection in human genes that have evolved to fight diseases, a “new field, evolutionary medicine.” Olson claims there have been some prospects, like lactose tolerance and resistance to malaria conferred by the sickle-cell gene, “But beyond these well-known examples, the pickings have been slim.” He lists five samples in a table, but three are controversial or questionable, and the other two are ambiguous; is it really an improvement to have one disease like sickle-cell anemia balance another disease like malaria, so called “balancing selection”? And is the one example of “directional selection” (the classic Darwinian mechanism), i.e. lactose tolerance among pastoralists, really conclusive? Don’t adults with lactose intolerance still have babies?
The search for remnants of natural selection in the genes is also rendered difficult by the fact that “demographic processes and random chance can mimic selection.” For example, a population might lack a gene because it migrated as a small group. Worse still, there is no one-to-one correspondence between a gene and a human trait. Jody Hey of Rutgers explains, “No one has found a variant that explains more than a couple of percent of any common disease, and all of these diseases are going to be highly multigenic” (i.e., influenced by multiple genes). The search is further clouded by the recognition that social and psychological dimensions of human behavior, such as traditions about alcohol consumption, can affect the distribution of genes. Nevertheless, Olson is optimistic: “But after years of frustration, researchers are welcoming the new data and methods that might finally yield progress.”
This entry and the one prior to it illustrate a common theme in these pages, that while evolutionists engage in guesswork and wishful thinking, the real hard evidence points to design. Here we are in 2002, with 1.4 centuries of Darwinism directing biological thought, but where is the evidence for natural selection in the genes, where it should be most obvious? We have the entire human genome sequenced, but nobody can find it. The examples he cites in his table are almost ludicrous. Surely they are nothing to crow about as evidence to support a belief in macroevolution, the origin of some new and complex function. If anything, they are relics of conservative responses by the genome to maintain the complexity it already had. “Balancing selection” (getting your enemies to fight each other) is not making you stronger. Anybody want to inherit the gene for sickle-cell anemia? That’s devolution, not evolution. It’s like getting a lucky break because a gunman missed you, and by mistake shot the carjacker who was holding you up.Man Harnesses Nature’s Tiniest Motor 11/15/2002
The Nov. 9 print issue of Science News tells about a UCLA team that is learning how to operate ATP synthase, the tiny energy-pellet manufacturing motor that is present in all living cells. Carlo Montemagno and team have attached propellers to the spinning motor and are working on ways to switch it on and off. They hope this will lead to useful applications in nanotechnology. He is taking his cue from “nature-inspired machines,” the article claims.
We’ve reported several times about ATP synthase and its marvels. The fact that nanotechnologists are able to operate these devices blurs the line between mechanical and biological worlds. This is a cogent argument against Hume’s criticism of natural theology. David Hume argued that one could not compare artificial machines with biological machines to prove the existence of God (e.g., Paley’s divine Watchmaker argument). But Montemagno is using ATP synthase as a model for nanodevices that might be made of different molecules. If a man-made motor works on the same principles as the natural one, what’s the difference? If a human engineer is required to make the artificial one, why not deduce a supreme Engineer as the Maker of the natural one?Theory of Plate Tectonics Not on Solid Ground 11/14/2002
Is geology in for a major paradigm shift? Simon Lamb comments on the new thinking going on in geology in the News and Views section of the Nov. 14 issue of Nature. Apparently some hard realities have settled in after the heady days of early plate tectonic theory:
In the late 1960s, with the advent of the theory of plate tectonics, geophysicists finally seemed to have made sense of earthquakes. The surface of the Earth is covered in a mosaic of rigid plates, and earthquakes, in this theory, occur only in narrow zones where the plates rub against each other. This was good news, because it provided a basic understanding of why there were earthquakes in the first place. But in the 1980s, there were second thoughts. The plate theory worked well in the oceans, but across the continental land masses, earthquakes seemed to occur all over the place.Lamb describes the change in heart of one geologist in particular, James Jackson, who used to believe this indicated the continents must be fluid. Now he has changed his mind and “believes that we must go back to trying to understand the motions of small plate-like blocks in the crust.” His recent article in GSA Today “is seeking to overturn more than two decades of geological thinking about the movement of the Earth’s surface.” Jackson builds on the accumulating seismic data that indicate earthquakes occur in the crust, not the mantle, so “He proposes that where these motions occur on land, we need look no deeper than the crust for their driving forces.” Though geologists debate Jackson’s ideas, one thing is clear: there is much to learn. Simon Lamb explains:
A more fundamental problem is that geologists have surprisingly little to go on when it comes to understanding the mantle, and there is an embarrassingly large gap between laboratory experiments and the behaviour of rocks under real geological conditions. To compound the problem, McKenzie and Fairhead’s results fly in the face of scores of other studies: studies conducted in northern India and elsewhere suggest much greater values of beam thickness, up to several times the thickness of the crust, plunging geophysicists into an intense argument about the significance of this discrepancy.But Jackson’s proposal that the crust acts like an elastic beam is not without its own problems. It doesn’t follow, Lamb argues, that earthquakes would be caused by strain on load-bearing regions. And Jackson’s belief that the mantle is wet “remains as speculation: if instead it’s dry, it could actually have considerable strength.” Still, Lamb commends Jackson that he “has bravely stuck his neck out and triggered a vociferous but vital debate.”
Welcome to the world of real geological science. It’s not as straightforward as those computer animations on the Discovery Channel and displays in the national parks, is it? The take-home lesson from this headline is how little they really know. As Simon Lamb admits, “Looking below the crust is not easy.” Models are built to explain certain phenomena. They gain in popularity for awhile, then sometimes collapse under the load of anomalies they can’t explain. Maybe plate tectonics theory is on the way out, or maybe it will just be modified, but never assume that what is science today will not be myth tomorrow.Fossil Proteins: A New Way to Trace Evolution? 11/13/2002
New Scientist says, “The first complete sequencing of protein from a fossil bone suggests that proteins can survive for millions of years — long enough to probe the evolution of many extinct species, including the ancestors of modern humans.” Scientists at Newcastle University sequenced osteocalcin protein from extinct bison bones in permafrost believed to be 55,000 years old. They believe this protein could survive 100 million years at freezing temperatures, and 10 million years at 50oF. This might provide a way to compare the proteins between extinct species and determine their evolutionary relationships. The paper is published in the December issue of Geology, which states, These results suggest that DNA and protein sequences can be used to directly investigate molecular phylogenies over a considerable time period, the absolute limit of which is yet to be determined.
The method is built on the assumption of evolution, so it is another case of circular reasoning. They calibrate the survivability of osteocalcin on the evolutionary belief that the extinct bison lived 55,000 years ago. But ask the obvious question: how could fragile amino acids survive anywhere near that long, or especially 120 million years as is claimed for dinosaur protein? Wouldn’t that call into question the ages that are claimed for these bones? Also, the protein amino acid of the extinct bison was identical to that of living bison, and only 1 amino acid different than that of living cattle. This caused them to make the ad hoc assumption that “osteocalcin sequences diverge slowly.” If they are calibrating a clock based on the assumption of evolution, they cannot then turn around and use it as evidence for evolution. The article only offers this dating method as a possibility for future study. It proves nothing except that there has been no evolution to speak between the extinct and living bison. But like molecular phylogeny, this method will doubtless give evolutionists another useless tool to make artificial trees while appearing to back it up with empirical measurements. Even a broken clock is right twice a day.Defective Proofreading Causes Cancer 11/12/2002
Scientists at University of Utah School of Medicine mutated genes in mice responsible for proofreading DNA, and saw 94% of them get cancer. Writing in the Nov 12 online preprints of the Proceedings of the National Academy of Sciences, they stated, “Mutations are a hallmark of cancer. Normal cells minimize spontaneous mutations through the combined actions of polymerase base selectivity, 3'-5' exonucleolytic proofreading, mismatch correction, and DNA damage repair.” They induced a point mutation in DNA polymerase delta, one of the molecular machines with a proofreading domain, and the high incidence of tumors resulted. Only 3-4% of the mice without the mutation developed cancers.
To an evolutionist, mutations are the source of new information and novelty that can be acted on by natural selection to produce eyes and brains and wings and all the other wonders of nature. But this experiment shows what is intuitively obvious, that throwing mistakes into the works causes death. It would seem more likely that nature is degenerating, not getting better, as mutations take their toll. In a perfect world where the error-correcting mechanisms work properly, there wouldn’t be any cancer. But machines break down, cars rust, and information degrades in a world subject to the Second Law of Thermodynamics. Cancer is a sign we are not evolving, but devolving. Unless it can be shown that new mutations could actually improve the proofreading capability of DNA polymerase and other error-correcting enzymes, it would be fair to conclude that the human genome is slowly degrading under the mutation load.Time Attributes Wonders of Birth to Evolution 11/11/2002
This week’s cover story in Time Magazine describes latest findings in human fetal development. Juxtaposed with high-resolution images and descriptions of the “marvelous” and seemingly “miraculous“ and “vastly complicated” process, the photo captions contain throwbacks to old embryonic recapitulation theory: “40 days: At this point, a human embryo looks no different from that of a pig, chick or elephant. All have a tail, a yolk sac and rudimentary gills. ...”
Answers in Genesis rightly chides Time for including these false and misleading allusions to a defunct theory, perpetrated by a fraud (Ernst Haeckel), that humans go through stages of their evolutionary past during development. If you can stomach these portions of the article and read from a viewpoint of intelligent design, you will marvel at the complexity and beauty of the programmed development process that each of us once went through.Darwin’s Finches Attacked by Parasites 11/08/2002
The BBC News reports that some of Darwin’s finches on the Galápagos Islands are being attacked by the larvae of parasitic flies. The finches were instrumental in the formulation of Charles Darwin’s theory of evolution by natural selection. Scientists are “deeply concerned.”
Oh, well, survival of the fittest, you know. Why worry; most things are extinct anyway. They say roaches will probably inherit the earth. If parasitic flies are the fittest, then long live parasitic flies*. (But those finches sure are cute.)Does Ocean Chemistry Drive Evolution? 11/08/2002
Geochemistry is getting linked to evolution, says Richard Kerr in the Nov 8 issue of Science. In his commentary of a paper in the same issue by J. A. D. Dickson, “Fossil Echinoderms As Monitor of the Mg/Ca Ratio of Phanerozoic Oceans,” he suggests the “controversial” idea that geochemical changes in the oceans might have driven major evolutionary speciation events. As mid-oceanic ridges rose and deep-sea vents spurted material from the hot crust, and erosion washed minerals into the water, life could have been alternately blessed or stressed by concentrations of minerals. Organisms creating calcium carbonate shells might have gone through a heyday followed by osteoporosis. Blooms of organisms favored by optimal chemistry could have created formations like the white cliffs of Dover or the Great Barrier Reef.
This theory really says nothing about evolution. Just like a passing wave makes a float bob up and down but not travel with the wave, certain organisms may have benefited or suffered from changes in chemistry, without evolving. Animals and plants bloom where the resources are plentiful; even humans move out of drought regions into lands of milk and honey without evolving into other species. The evolutionary talk in this article is pure conjecture (storytelling), based on a priori assumption that evolution occurred. Dickson’s paper does not even mention evolution; he only discusses the magnesium/calcium ratio in starfish skeletons. It’s a stretch for Kerr to pull an evolutionary tale out of this data, and he admits it (emphasis added):How the Elephant Got Its Snorkel 11/07/2002“It’s a really interesting idea,” says paleontologist David Jablonski of the University of Chicago, “that ocean changes could drive these major turnovers” of marine animals or even facilitate shelled animals’ bursting on the scene. The trick, he says, will be refining the patterns of evolutionary and ocean change so that cause and effect can be firmly linked. Then geophysics and life might be joined for good.Instead of another “really interesting idea” (read: pure conjecture) about evolution, how about some evidence? Why not a different conjecture? Try ours: large formations might have formed rapidly, not slowly and gradually, under different conditions.
Today’s just-so story is brought to you by National Geographic. Once upon a time, elephants lived in the water with their cousins, the manatees (sea cows). Then,
For some reason–the availability of a food source that no other creature was exploiting is one possibility–elephants, over time, developed legs that were strong enough to support their huge body weight and enabled them to become land creatures. ... elephants also evolved trunks so they could breathe with their heads underwater. To this day, elephants remain powerful swimmers.You see, children, the elephant has unique anatomy like no other mammal. Instead of a fluid-filled sack around its lungs, the elephant has connective tissue to form a strong but flexible case. “The unusual lung structure enables elephants to withstand the extreme differences in pressure above and below water without rupturing blood vessels in the lining of the lungs.” And that, boys and girls, is how the elephant got its trunk.
But teacher, why?Do Human Embryos Have a Future? 11/07/2002
The Nov 7 issue of Nature is concerned that the human embryos might be given legal protections under the Bush administration, and that this might hamper scientific research. The new Secretary’s Advisory Committee on Human Research Protections has been advised to pay particular attention to “pregnant women, embryos and fetuses,” among other groups. This language did not exist in the Clinton administration’s earlier panel, the National Human Research Protections Advisory Committee. Although the panel cannot make law, they provide input to Congress, and scientists are concerned that legislators might restrict their ability to perform experiments on embryonic stem cells or embryos left over from in vitro fertilization. Health and Human Services Director Bill Hall explained that the issue is to protect the rights of women who participate, making sure they are aware of the risks. Erika Check writes in the Nature editorial:
But some observers say that no matter what the intentions behind the change are, the move is still alarming for scientists and many other groups, such as those who wish to keep abortion legal. “It’s a dangerous precedent to characterize a cluster of cells as a human subject,” says Kevin Wilson, director of public policy for the American Society for Cell Biology.The Department of Health and Human Services has jurisdiction over the National Institutes of Health and the Food and Drug Administration.
A cluster of cells. You and I were once just a cluster of cells. That cluster of cells has all the coding and potential for full adult life. There is an unbroken chain of humanness from one generation to the next. The first step in rationalizing atrocities against a helpless group of humans is to say they’re not really human. Reductionist evolutionism has made us into just a cluster of cells; adults are just a bigger cluster. Where do they draw the line? Not even a fetus’s ability to feel pain has stopped the abortion industry from carrying out their grisly deeds all the way to term and even beyond in some cases. Here’s where the view of God and man comes to a clear dividing line: the image of God, or a cluster of cells? Human embryos have become experimental playthings for scientists who expect to be paid for their Frankenscience using American tax dollars. The reasons always sound so noble, but is it right to do wrong to do right? The principle used to be that medicine would not harm one subject to aid another; that’s why we don’t carve up scientists to give their organs to people suffering from genetic diseases. Scientists are playing with fire. These are major moral issues, with ominous implications for any helpless group of individuals. Scientists pretend they are politically neutral, even benefactors doing pure research for our good. But scientists were once a cluster of cells, too, and they kid themselves to think their positions do not involve religious, political, and even economic motivations (such as NIH funding). Science can inform the law, but scientists are not above the law. If they want unrestricted access to human experimentation, let them go to North Korea, where no such inconvenient moral stipulations will get in their way:Hubble Image 11/07/2002: The Hubble Heritage team has just released a new image of planetary nebula NGC 6369, the Little Ghost Nebula.
The heritage of Hubble has been a dynamic universe, where stars don’t just sit there and twinkle, but explode and die. Like fireworks, theyre pretty when they go.AAAS Alert: Fight Intelligent Design 11/06/2002
The world’s largest scientific organization, the American Association for the Advancement of Science (AAAS), has just issued a board resolution opposing the teaching of intelligent design in science classrooms. Calling the contemporary theory of biological evolution “one of the most robust products of scientific inquiry,” the AAAS resolution calls on members and its 272 affiliated societies to oppose the introduction of intelligent design material in schools, to educate the educators on the nature of science, and “to communicate their support to appropriate parties at the federal, state and local levels of the government.” EurekAlert explains that this board resolution resulted from concern over recent votes by school boards in Ohio and in Cobb County, Georgia that permit “teaching the controversy” about evolution. According to Alan Leshner, CEO of the AAAS, “If intelligent design theory is presented within science courses as factually based, it is likely to confuse American schoolchildren and to undermine the integrity of U.S. science education.” Leshner and five other AAAS directors have made themselves available for media interviews.
This is great news. The Darwin Party is so scared that somebody is finally calling their bluff, they have to resort to intimidation and executive order to maintain their stranglehold on education. What if they called a war and nobody showed up? What if enough people realize this is a political power play, not a search for the truth about nature? We mustn’t “confuse” the students, he says. Good grief. High school readers, are you offended that he says you aren’t smart enough to hear evidence on two sides of a question and decide which has better support? Teachers, are you offended that the AAAS has to tell you what science is? The resolution piously calls for a “fact-based, standards-based science education for American schoolchildren.” Great. Remove the evolutionary storytelling and we’ll be making progress.Search for Alien Pond Scum Is Serious Science 11/05/2002
It must be serious if NASA’s Astrobiology Institute, the National Science Foundation, and the Committee on the Origin and Evolution of Life at the National Academy of Sciences, the nation’s premier scientific organization, are all behind it. “Astrobiology is no longer a joke,” said the Astrobiology Institute Director Bruce Runegar. In a report published on BayArea.com, Robert S. Boyd of the Mercury News explained why scientists are looking for “weird life” – life based on a different genetic code (although the politically correct term is “non-terrean life”). Boyd lists about eight current projects astrobiologists are working on, from missions to Mars and Saturn to experiments on Terra (earth). He clarifies that they are not looking for little green men. Alien pond scum would do: “Even that would be a monumental discovery, proving that we are not alone in the universe.”
It doesn’t hurt to look, but they have been looking for a long time, and so far come up empty. Every proposed habitat to date has proven to be hostile and dead. Venus was once thought to harbor life but turned out to be like an inferno at the surface, to the surprise of many. Likewise, the dreams of Percival Lowell (and the fears of H. G. Wells) of finding advanced life on Mars died in 1965 when Mariner 4 first imaged its dusty, cratered surface. Now, 38 years later, the red planet still shows no evidence of even microbial life, past or present; moreover, its exposure to deadly radiation makes the habitat extreme to say the least. Jupiter’s moon Europa may have water, and Saturn’s Titan may have organic chemistry; but so far, Earth is still the only known abode of life – all based on the A, G, C, T alphabet of DNA. Would weird life prove anything? It’s pretty weird already; just look at the election results.Cephalic Index: It’s All in the Head 11/05/2002
In a commentary in the Nov. 5 online preprints of the Proceedings of the National Academy of Sciences, Ralph Holloway, anthropologist at Columbia University, is surprised that a long-trusted measurement of the human head may be misleading. The “cephalic index,” a ratio of head breadth to length, was invented in the 19th century and has been used for scientific and political purposes, sometimes justifying racism or anti-immigration policies. The work of Franz Boas in 1910-1913 seemed to indicate that it was a function of environment. This supposedly neutral measurement lent itself to many biased studies about race and nationality. Holloway mentions “the debacle about Margaret Mead’s Coming of Age in Samoa” as one casualty of anthropology built on Boas’ premise. A new study of his data undercuts his conclusions. Although Holloway cautions that the new study may not be the final word, he hopes that the new data will “lead scientists, social and otherwise, to reflect more carefully on the various mantras and myths that have been collected, particularly by anthropologists of the Boasian persuasion. Science should, hopefully, march on.”
Head measurements have been used to lend a quasi-scientific respectability to racism in the late 19th and early 20th century, when Darwinism was on the rise. But even recently, Margaret Mead’s book, now discredited, was required reading for many college students and for years was held up as a model of good scientific research. (It also tended to justify free sex as normal and healthy.) Isn’t science supposed to be objective? Isn’t it based on unbiased measurement? An alarming exposé on the history and fallacy of using craniometry to justify xenophobia, racism and eugenics is Stephen Jay Gould’s The Mismeasure of Man (Gould, a staunch anti-creationist, never hesitated to lambaste his fellow evolutionists when he felt they were wrong). The Boas data have been used by evolutionary anthropologists to propose that head shape and size have been evolving since Mesolithic times, but what if the measurements are invalid? This story shows that assumptions based on faulty data, with political fallout and all, can go unchallenged for decades. Science marches on.Moonwalker Doubts Impact Theory for Origin of Moon 11/04/2002
Harrison Schmitt, Apollo 17 astronaut and geologist, doubts the popular Giant Impact theory for the origin of the moon (i.e., that an asteroid slammed into earth and the moon formed out of the debris). Speaking to the Geological Society of America last week, 30 years after his historic moon walk, he said the famous orange soil they discovered shows that the “interior of the moon is not cooperating” with the current leading hypothesis. “If the Giant Impact hypothesis is not compatible with this evidence, alternatives to it should be considered, including capture of a small, independent planet from a solar orbit near that of the Earth’s,” he said.
Good attitude, but it should go farther. Alternatives to naturalistic philosophy should also be considered.Men Are from Mars, Women Are from ... Mars 11/04/2002
Paul Davies, popular author and Australian physicist, thinks life on earth came from Mars, leading ultimately to both men and women. He shared his opinion recently in The Guardian, a UK newspaper. The evidence? Life evolved too quickly on earth otherwise.
Davies, author of The Fifth Miracle and other writings that grapple with the complexity of life, is usually pretty honest about the problems in origin of life theories. But this is really illogical. Like many evolutionary tall tales these days, there is no evidence for it, only evidence that it could not have happened the conventional evolutionary way. If you have ruled out the good, and all you have left are the bad and the ugly, which would you choose?Cell Memory “Borders on the Miraculous” 11/04/2002
Just when you thought the DNA code was mind-boggling enough, along comes the histone code. Another coding system somehow helps the cell remember itself: whether it is a blood cell, or a nerve cell, or a muscle cell. While all these cells in your body have the same genetic code, some kind of epigenetic (above-gene) code is telling it what genes need to be turned on. The Nov. 1 edition of the journal Cell has a review by Bryan M. Turner of the University of Birmingham (UK) called “Cellular memory and the histone code” that waxes enthusiastic about this cutting-edge mystery (emphasis added):
It is an obvious but easily forgotten truth that cells must have a mechanism for remembering who they are. A cell’s identity is defined by its characteristic pattern of gene expression and silencing, so remembering who it is consists of maintaining that pattern of gene expression through the traumas of DNA replication, chromatin assembly, and the radical DNA repackaging that accompanies mitosis [cell division]. The mechanisms by which around 2 m [two meters, about 6 feet] of DNA is packaged into the cell nucleus while remaining functional border on the miraculous and are still poorly understood. However, we do know more about the first stage in this packaging process, the nucleosome core particle. This structure comprises an octamer of core histones (two each of H2A, H2B, H3, and H4), around which are wrapped 146 base pairs of DNA in 1 3/4 superhelical turns (Luger et al., 1997 ). The reduction in DNA length produced by this histone-induced supercoiling is modest, but is an essential first step in the formation of higher-order chromatin structures. In recent years it has become clear that the nucleosome has an additional role, perhaps equally important and conserved, namely regulation of gene expression. Particularly exciting is the growing probability that the nucleosome can transmit epigenetic information from one cell generation to the next and has the potential to act, in effect, as the cell’s memory bank.Turner describes how the histones have tails that are exposed on the exterior of the nucleosome. It is on these tails where a variety of enzymes can rearrange some of the amino acids, providing a “rich source of epigenetic information.” So how is the code maintained and translated?
It has been suggested that specific tail modifications, or combinations thereof, constitute a code that defines actual or potential transcriptional states (Jenuwein and Allis, 2001; Richards and Elgin, 2002; Spotswood and Turner, 2002). The code is set by histone modifying enzymes of defined specificity and read by nonhistone proteins that bind in a modification-sensitive manner. In order to realize its full information carrying potential, the code must use combinations of modifications. This requires not only proteins that can read such combined modifications, but mechanisms by which they can be put in place and maintained. Recent papers have provided new insights into how specific combinations of tail modification might be generated and revealed mechanisms by which the modification of one residue can determine that of another.Turner discusses in some detail the types of reactions already known and puzzles that remain to be solved. The histone code appears quite different from the DNA sequence of letters; it is more a sequence of events: “Viewed in this light, the histone code can be seen as part of a sequence of events, possibly involving structural and catalytic proteins and RNAs, whose end result is a functionally stable chromatin state.” At times in the article the complexity of all of this seems to get to him; “To add further complexity,” begins one sentence. Near the end, Turner remarks wryly, “It is in the nature of scientific progress that simple ideas, like people, grow more complex with age.”
This is wonderful and amazing stuff. The trend of increasing complexity as more is uncovered at the basic unit of life shows no sign of abating. When you consider just how DNA in the nucleus has to be bundled safely to avoid damage during the “trauma” and “radical repackaging” that occurs during cell division, that alone is cause for astonishment. Click the link for an illustration from Eastern Michigan University showing how the six feet of DNA, so thin and fragile as to be invisible without an electron microscope, is first wrapped around the nucleosome, then supercoiled into chromatin, then bundled into chromosomes, without breaking a link anywhere (most of the time) in 60,000 genes – that’s a feat. A reader sent in this link from Technical University of Denmark – check out the great illustrations of DNA packaging, and realize that this all has to be done over and over, quickly, every time the cell divides. But now to realize that the components are actually maintaining codes and libraries, and have the mechanisms to read and act on the codes, all independently of DNA, is almost too much to fathom.Preach It, Brother: Why You Should Believe in the Big Bang 11/02/2002
The December issue of Astronomy gets downright polemical with its cover story, “Do you believe in the Big Bang? 5 reasons you should.” Both the editor (Dave Eicher) and the preacher (Jim Sweitzer) seem exasperated that only a third of the public accepts the Big Bang theory. Hearing people doubt it is “shocking” to Sweitzer, since to him it ranks with the Copernican proof that the earth revolves around the sun. He is even more aghast that belief in the Big Bang by the public actually declined in the 1990s. The current 33% figure is “smaller still than the number of supporters of evolution (53 percent), a subject steeped in controversy in recent years.”
The saga of the Big Bang is the scientific origin story for all of modern astrophysics and the language by which astronomers explain nearly all they see with their telescopes. It is to an astronomer what evolution is to a biologist – and even more unpopular with the public. So, ladies and gentlemen of the jury, if you’re on the fence about the theory, read on – the following five exhibits will prove beyond a reasonable doubt that the universe was created in the Big Bang.This should be good. Here are the five reasons:
Astronomy should be ashamed to print this simplistic, high-school pep talk. It reminded us of a Sydney Harris cartoon; we couldn’t find a copy on the Web to show you, so we’ll have to use word pictures. Harris portrays an outdoor Pentecostal-style revival meeting in progress, but the preacher and the crowd are modern cosmologists. The preacher is waving his textbook overhead, and with great fervor, delivers his sermon, punctuated by responses from the spirit-filled audience:Two For the Price of One: Did Transfer RNA Arise From Complementary Genes? 11/01/2002“Brothers and sisters, at the time of 10-33 secondsThe banner behind the stage reads, BELIEVE.
The latest (Oct 27) issue of Molecular Cell has a novel theory on how transfer RNA evolved. In a letter to the editor, Charles Carter and William Duax revive the 1995 Rodin-Ohno hypothesis that suggests complementary strands of DNA can code for different proteins. To understand this, we need to back up and learn a little about transfer RNA. DNA translation, you may recall, starts when enzymes unwind a strand of DNA to expose a gene, and a messenger RNA molecule forms by base-pairing with the exposed DNA nucleotides (the “letters” A, C, T, and G). The resulting messenger RNA molecule (mRNA), like a long computer tape bearing the code for a protein, exits the nucleus and approaches a ribosome. There, individual transfer RNA molecules (tRNA), each carrying a specific amino acid on one end and a three-letter RNA codon on the other, mate with specific parts of the mRNA by base-pairing, and the amino acids on the other end join together into a protein chain. This much is elementary biochemistry, illustrated beautifully with computer animation in the film Unlocking the Mystery of Life. The process is actually much more complicated, requiring a host of helper enzymes at every step.
There seems to be no natural attraction between an amino acid and its own transfer-RNA, so something must bring them together. It is as if there were two languages, and neither party understands the other except when there is an interpreter to bridge the gap. This essential task is done by a special group of enzymes which match the different tRNA’s and amino acids. One part of each such enzyme fits just its own particular kind of amino acid and no other. Another part of the enzyme interacts with its own type of tRNA. In plain language, it can be pictured as follows: the enzyme grasps its amino acid and its tRNA and fastens them together. (p. 147)In the Molecular Cell article, Carter and Duax recognize the challenge that this complex arrangement presents to evolutionary theory (emphasis added):
The fidelity of protein synthesis resides almost entirely in the 20 aminoacyl-tRNA synthetases (aaRS), which acylate their cognate tRNAs with the appropriate amino acid. The origin of codon-dependent translation presents a challenging intellectual problem in biology, owing to the apparently irreducible complexity represented by their simultaneous appearance. Key to the conundrum is that contemporary aaRS divide into two classes each with ten enzymes (Eriani et al., 1990 ), whose respective architectures have quite unrelated homologies (Cusack et al., 1990 ). Moreover, catalytic domains in class I and II aaRS:tRNA complexes from corresponding subclasses have complementary shapes that recognize nonoverlapping surfaces on the tRNA acceptor stems (Ribas de Poublana and Schimmel, 2001 ). Pairwise binding between classes may therefore have protected tRNAs early in evolution, and the class division likely dates from the dawn of biology.Drawing from an analogy with a gene found in a freshwater mold that seems to code for two different proteins, depending on whether the primary strand of the gene or its complementary strand is translated, Carter and Duax propose that genetic complementarity is behind the origin of the two classes of aaRS enzymes: one class evolved off the primary “sense” strand of DNA, and another class evolved off the complementary “antisense” strand. From the original primordial split, the 20 aaRS enzymes arose: “Two synthetases, coding from that repertoire, might similarly have sufficed to produce recognizable protein folds. Subclass speciation via gene duplication then would have enriched the coding repertoire.”
Let’s think about this. Imagine a string of Morse Code dots and dashes that carries a message: for instance,How Complex Organs Like the Placenta Evolved 11/01/2002
An article in the Nov. 1 issue of Science hints that Darwinists are on the defensive against creationists. Virginia Morell starts out (emphasis added):
It’s one of the oldest riddles in evolutionary biology: How does natural selection gradually create an eye, or any complex organ for that matter? The puzzle troubled Charles Darwin, who nevertheless gamely nailed together a ladder of how it might have happened—from photoreceptor cells to highly refined orbits—by drawing examples from living organisms such as mollusks and arthropods. But holes in this progression have persistently bothered evolutionary biologists and left openings that creationists have been only too happy to exploit. Now a team of researchers presents a model system for studying the evolution of complex organs—in this case, the placenta—that Darwin could only dream about.She reports on the work of David Reznick on placentas in a kind of guppylike fish. Reznick, of UC Riverside, chose this genus because some member species have placentas and some don’t, and some appear to have intermediate stages. What is it about the placentas of this genus that can help the Darwinists find ammunition against the creationists?
Placentas serve as a decent stand-in for eyes and other complex organs such as the heart or kidney whose histories evolutionary biologists have never been able to trace, Reznick and colleagues argue. By definition, complex organs are composites of independently derived features; for instance, the human eye focuses light and also perceives color. In the case of the placenta, the organ provides nutrients for the fetus while simultaneously managing waste products and regulating gas exchanges. Evidence of the intermediate steps for acquiring such organs is missing from the fossil record, enabling creationists to claim they were “created” de novo.So how did Reznick answer this one of “thorny evolutionary questions” with guppy placentas? First, he and colleague Mark Springer developed a phylogenetic tree for the genus, which indicated to him that placentas evolved three times among different species of the fish. Then he correlated the tree with “dates of geological events that probably led the species to diverge.” He found that the shortest time interval between a species with a placenta “and its last common ancestor without one was 750,000 years–a period in keeping with the 400,000 years other researchers have calculated for the evolution of the eye. Despite this relatively short period, ‘it’s not a problem for evolution to create this kind of complexity,’ says [Stephen] Stearns [of Yale].” Another Yale biologist cautions that Reznick has not proved that this little guppy placenta is a complex organ, and Reznick admits it. But at least these guppies might provide a glimpse of how it happened. “We can’t ask how this kind of adaptation evolved with mammals because it only happened once over 100 million years ago,” he says. Morell agrees: “But like the evolution of the eye, the evolution of the mammalian placenta is lost in history.”
Reznick’s paper in the same issue of Science is entitled “Independent Origins and Rapid Evolution of the Placenta in the Fish Genus Poeciliopsis”, co-authored by his colleague Mark Springer and by Mariana Mateos of the Monterey Bay Aquarium. It states that the fish placenta is really a “follicular pseudoplacenta” that only appears to have some functional similarities to the mammalian placenta.
Did Reznick or Morell or the others provide any independent evidence on how a complex organ like a placenta evolved? No! Their only arguments beg the question: i.e., evolution happened, so it must have happened. The phylogenetic tree assumes evolution. The geologic dating assumes evolution. The whole answer assumes evolution! Did they provide any detailed analysis of how a fish without a placenta could evolve one by slow, gradual steps, where each step provided an advantage? Did they prove that the guppy placenta has complexity comparable to a mammalian placenta or an eye? Did they explain why some guppies get along just fine without it? They did none of these things. They just assumed it happened, and since it happened in a relatively short time period according to their own evolutionary assumptions, it must not be a problem for evolution to evolve placentas or any other complex organ. Their reasoning also depends on the broken molecular clock hypothesis and phylogenetic trees that exist only in the imagination of the investigator. Somehow geologic events (asteroid impacts?) spurred these little fish to evolve complex organs by some unknown, magical means, while leaving their cousins without them. And they did this trick not just once, but three times! If this is the best reasoning that the Darwin Party can come up with against creationists, and if this is the best that one of the most eminent scientific journals in the world can find to print, their days are numbered.