“The Darwiniacs play a shell game with the evidence, but the evidence is never under any of the shells.... In the end, evolutionists’ only argument is contempt.  The cultists know that if people were allowed to hear the arguments against evolution for just sixty seconds, all would be lost.  So they demonize the people making those arguments.”
—from the New York Times best seller, Godless, the Church of Liberalism by Ann Coulter (Crown Forum, 2006), pp. 243, 244.

Journals Consistently Tout Embryonic Stem Cells, Criticize Bush   07/31/2006    
This is not news.  It just bears repeating that the Big Science journals continue to push embryonic stem cell research and criticize Republicans.  The latest case in point was President Bush’s veto of the stem cell bill July 19, that led to a flurry of articles and editorials in the leading British and American science journals.
    Science July 28 tried to undermine the conservative argument that adult stem cells have a proven track record of therapies without the moral concerns.  Constance Holden in the same issue of Science reported cheerfully on every effort working to promote ES research around the obstacles of conservatives and ethicists.
    Nature included three articles on the “progress” of ES research and the “disappointment” over setbacks, including a stinging Editorial criticizing the “obduracy” of the White House on this matter.  In an article about “The lure of stem cell lines,” Nature stressed primarily the competition between countries.  Moral qualms were given minor attention, with a concession that some researchers are trying to find ways around the “emotionally charged debate” over creating human zygotes only to harvest their stem cells.  Adult stem cell alternatives were criticized for various reasons (such as lack of supply), but there was this admission in the article:

Adult-derived stem cells are the only form of stem-cell therapy to make it to the clinic so far.  For example, stem cells from bone marrow (pictured) have been used for more than 30 years to treat blood disorders.  Adult stem cells are less likely to cause tumours than embryonic stem cells, and less likely to be rejected by the immune system.

This may seem like a subtle point, but it exactly this kind of compromise that has forged America’s uneasy but workable abortion policy: abortions are legal, but in no case are taxpayers required to see their dollars fund them.  It may be tenable to argue that dissenters should not be asked to finance a practice that they find morally unacceptable.  What is not acceptable is for the president to use false pretences to stand in the way of a compromise that the Congress has sensibly endorsed.

Let’s follow their ethical argument.  If it’s OK for private parties to create embryos (the ethically debatable part), and then the taxpayers simply pay for scientists to use the embryos, is there a difference in allowing private parties to buy slaves, and taxpayers to fund using slave labor to build federal projects?  If certain people are slated for the gas chambers anyway, why not do some medical research on them and learn something that can help the country in the next war?  If people are going to have abortions anyway, should taxpayers fund organ farms where the fetuses, instead of being destroyed, could be used for research or organ transplants?  If someone else does the dirty work of stealing, robbing, or committing mayhem, is it morally acceptable for the public to utilize the products?  It should be obvious that rationalizing the results of a deed create a market for it.  Similar compromise arguments were used by slave states 150 years ago: if you don’t like slavery, go north.  If you don’t like experimenting on human subjects, move out of Germany or North Korea.  Compromise with evil never works.  America fought a bloody war to affirm the dignity of all people, and we are a better country for it.  If the creation of human embryos is a moral evil, and if abortion is a moral evil, then compromise is not an option.  Science can inform the debate, but it is not the role of scientific elitists to make ethical decisions for the rest of us.
    The editors of today’s Big Science journals are almost uniformly Darwinists, and most of them atheists.  Words like ethics and morality are terms of convenience, not eternal principles.  Not all scientists are evolutionists, but the leaders of the journals and societies are.  They didn’t used to be.  They’re like the leaders of labor unions, some of whom started out with noble motives, but who gravitate toward liberalism by some inexorable law of entropy, because governments and funding give them their power, and power corrupts.  If you thought Big Science was all about honest inquiry into the workings of nature, get over it.  They’re another brand of liberal pressure group.  Get used to it.
    By the way, private researchers are already toying with human-animal chimeras and clones, just because they can (see LifeNews for one example).  The Nobel Committee (since they considered Yasser Arafat worthy of a Peace Prize) would probably have no ethical qualms about giving their millions in prize money to the first scientist to demonstrate human cloning.  Recall how quickly moral barriers can collapse.  It was only a few years ago when conservatives feared the worst when RU-486, the “morning after pill” was announced; today, politicians were discussing whether to make it available over the counter to 18 year old girls (see BP News).  Heated debates over state lotteries eventually fizzled to where now gambling is a multi-billion dollar industry and nobody cares any more, organized crime, broken homes, exploitation of the poor notwithstanding.  Abortion?  A debate lost in 1970s.  Trying to stop it now, or even restrict it, or even to get the truth about it known, is enough to exhaust the most stalwart crusader (example on BP News).
    Tomorrow’s fears about embryonic experimentation are too chilling to imagine: races of chimeras bred for slave labor, clones created for personal legacies, brainless humans bred for spare organs, supermen bred as athletes or soldiers, female bodies bred for private sex toys, and (if embryos are merely scientific playthings), even blurrier lines about what constitutes human life and is worthy of dignity and human rights.  If embryos can be treated as experimental subjects, where will the line be drawn?  The most radical Darwinists already predict infanticide and euthanasia as neutral actions, even blessings.  The trail being blazed right now may soon become a highway.  Radical relativists do not readily give back the ground they take.  If the brave new world ahead is unthinkable, what on earth are you doing about it, for heaven’s sake?
    Some articles for thought: Apologetics Press articles by Dave Miller and Brad Harrub and another by Harrub on human cloning, stem-cell debate issues by Baptist Press and details about the presidential veto, follow-up issues on stem cells, on Agape Press, Michael Fumento in National Review about the stem-cell scam, Chuck Colson on BreakPoint about the presidential veto and crossing the great moral divide.  Alarmism?  Read the comments of David Barash in the LA Times.  He’s a psychology professor who advocates creating human-chimp hybrids just to offend Christians.  See also the commentary on this by LifeSite.
Next headline on:  Politics and Ethics

• Precious stone bones:  Two new species of plesiosaur were discovered in Australia this month, according to the BBC News.  The bones of the beasts were replaced by opal minerals that seeped in and replaced the original fossil-bearing rock.  Interpretation: one species had crests on its head, “perhaps for display or mating purposes.”  Other inferences were stated, with copious use of possibility words: suggests, believe, and might have; other times, interpretations are stated as matters of fact:

  They are thought to be of juvenile animals, suggesting the lake was a breeding and nursery ground.
      Scientists believe sea-dwelling adults returned to the shallow inland waters to breed and raise their young.
      At the time, Australia was much colder, and the inland ocean would have frozen over in places during the winter.
      Scientists believe the creatures might have evolved mechanisms to cope with the harsh climate, such as a faster metabolic rate.  They were carnivorous, feeding on fish and squid.

• Crest aphrodisiacs:  Another BBC News story talks about the exotic head crests on a rare species of pterosaur in Brazil.  Scientists found a younger juvenile with a less-developed crest.  Interpretation: the crest arose as a sexual display during puberty.  At least Dr. Darren Nash left the door open for doubt: “We don’t know this but we imagine they would have bobbed it around and used it to attract other pterosaurs.”  The title of the article said, however, that a flying reptile mystery was “solved.”
• Hot beef:  Earlier in the month, Live Science and other news sources reported on a study that suggested body temperature was a function of dinosaur size.  The interpretation was based on models that correlated dinosaur growth rates with maximum size as adults.  From here, it was speculated that the largest beast was 118 degrees Fahrenheit, and that temperature was the main factor setting a size limit.  The article also speculates, “Dinosaurs likely got warmer as they became adults.”

Bones are interesting, dinosaurs are fun, and gathering data is good Baconian exercise.  Most people are not content with dry accumulations of facts, however, and want a story to put them in context.  Scientists are usually happy to oblige this desire.  It’s nice when they go to the trouble to state when the facts end and the speculation begins.  All too often they leave that task to the reader – and the artist.
Next headline on:  Dinosaurs • Fossils

The discovery of self-correcting RNA transcripts suggests a previously missing link in molecular evolution.  One prerequisite of an early RNA world (devoid of DNA) is that RNA-based genomes were stable.  Genome stability required a mechanism for RNA replication and error correction during replication, which could have been similar to the newly described RNA proofreading mechanism described by Zenkin et al.  If self-correcting replicating RNAs coexisted with an RNA-based protein synthesis activity, then an early RNA-based replicase could have been replaced by a protein-based RNA replicase.  This ancient protein-based RNA replicase could have evolved to accept DNA as a template, instead of RNA, allowing the transition from RNA to DNA genomes.  In this scenario, the resulting DNA-dependent RNA polymerase retained the ancient RNA-based RNA proofreading mechanism.
    Whereas an understanding of RNA proofreading is only now emerging, DNA proofreading had long been characterized. DNA polymerases cleave misincorporated nucleotides from the growing DNA chain, but the cleavage activity resides in a protein domain distinct from the domain for synthesis.  The spatial separation of the two activities probably allowed optimization of two dedicated active sites during evolution, whereas RNA polymerase retained a single tunable active site.  This could explain how some DNA polymerases achieve very high fidelity, which is required for efficient error correction during replication of large DNA genomes.

Was blindness ever so dark as to look design in the eye, and attribute it to mindless chance?  The blind see naught but their own imaginations.  Cramer took an incredibly wondrous phenomenon (imagine! self-correcting code) and weaved a purely fictional tale about how it emerged from The Ancient Soup.  Yet this is the myth that our culture only allows to be heard by students in public schools, because any other explanation, such as design, is classified as “religion” (along with, presumably, rocket-launching Hezbollah terrorism).  In the same issue of Science was a very positive book review of a new work about Richard Dawkins, the rabidly atheistic Darwinist who subscribes to the Ancient Soup myth or something very like it: reviewer David C. Queller says, “Dawkins spills his own dirty, obscene secret, again no less powerful now that we have known it for 30 years.  All flesh is survival machinery, and the survival it promotes is that of our selfish genes.”
    If this makes you angry, then it is time to take back science from the powers of darkness, obscenity, and selfishness that swept in like a flood after Darwin.  What would the original founders of the American Association for the Advancement of Science, like Joseph Henry, think of what has become of their honorable institution?
Next headline on:  Cell Biology • Genetics • Evolution

In the classic “What the frog’s eye tells the frog’s brain,” Lettvin and colleagues showed that different types of retinal ganglion cell send specific kinds of information.  For example, one type responds best to a dark, convex form moving centripetally (a fly).  Here we consider a complementary question: how much information does the retina send and how is it apportioned among different cell types?  Recording from guinea pig retina on a multi-electrode array and presenting various types of motion in natural scenes, we measured information rates for seven types of ganglion cell.  Mean rates varied across cell types (6-13 bits • s^-1) more than across stimuli.  Sluggish cells transmitted information at lower rates than brisk cells, but because of trade-offs between noise and temporal correlation, all types had the same coding efficiency.  Calculating the proportions of each cell type from receptive field size and coverage factor, we conclude (assuming independence) that the approximately 10⁵ ganglion cells transmit on the order of 875,000 bits • s^-1.  Because sluggish cells are equally efficient but more numerous, they account for most of the information.  With approximately 10⁶ ganglion cells, the human retina would transmit data at roughly the rate of an Ethernet connection.

Auditory fibers apparently achieve their high coding efficiency via a “tuned” nonlinear filter that selectively amplifies the anticipated signal.  A similar strategy is apparently used by the mammalian rod bipolar cell to encode single photon responses.  However, this coding strategy, highly effective when the anticipated signal is sparse and well defined, may serve poorly for ganglion cells because the information of biological interest in natural scenes is so varied that highly tuned, nonlinear filters would either reject too much information or require too many cell types.
    Given the ganglion cell strategy of broad tuning and equal coding efficiency, why does the retina not send all visual information over one cell type with a high information rate?  This is possibly because the energetic cost of signaling increases nonlinearly with temporal frequency and information rate of individual axons.

Spatial acuity requires narrow-field cells with a high sampling rate.  Because such a type must necessarily distribute densely, its information rate should be relatively low to reduce costs.  On the other hand, encoding of high stimulus velocities requires extended spatial summation and thus a broad-field cell—plus the ability to transmit at high bit rates so as not to lose the higher temporal frequencies.  Such a cell type must necessarily be expensive, but given the extended dendritic field, this type can be sparse.  Consequently energetic considerations probably interact with other constraints to set the number of cell types and a general information rate of roughly 10 bits • s^-1 and 2 bits • spike^-1.

When our body’s capabilities are compared with machinery, the comparisons are often wonderful and amazing.  If 10 megabit-per-second ethernet-eyes don’t seem particularly cutting-edge in this age of gigabit-ethernet rates, consider that eyes are only one of millions of sensors across the body transmitting information on touch, taste, smell, and hearing as well as vision.  In its little 3-pound CPU, the brain must process that information 24 x 7 for decades.  Plus, the kind of information your brain handles is in neural-net form, not the serial data that computers process.  It is sent down tiny bundles of neurons in a package that doesn’t short out when you go swimming.

Imagine yourself in a recording studio, watching an orchestra playing a score in sync with a new movie about Robinson Crusoe.  Your brain is taking in the complex waveform of a hundred instruments and performing Fourier transforms on it such that you can make out each individual instrument.  Simultaneously, the eyes can see the rapid motions of the violinists’ bows, the action on the screen, and the static information from the studio walls and ceiling.  Millions of touch sensors are sending information on the temperature of the room, the feel of your socks, the comfort of the seat, how hungry you are, and much more.  Your tongue is reporting the mint candy in your mouth.  Your nose is deciphering complex chemical signals in the environment through a series of decoding maps.  The brain filters and focuses on information that is important for each moment.  As the intensity of the music or screen action rises, adrenaline races through your system switching on organs to be ready for action.  Next, your mind is transported to an exotic island, and you become Robinson Crusoe, using all your native senses to the hilt to survive and find your next meal.

And this all runs on potatoes! (as Dr. A. E. Wilder-Smith used to say), or on lettuce! (for the guinea pig).  Undoubtedly, if we were aware of all the factors involved in the transfer of information from the environment to the mind via our sensory apparatus, the comparison with ethernet transfer rates would seem foolishly simplistic.  In this story we have seen again that the more detail is shared about organic workings, the less there is a tendency to discuss evolution.  Scientific detail is inversely proportional to evolutionary storytelling.
    Articles like this also raise interesting philosophical questions.  What is it we are really seeing?  Clearly, the input data is being massaged.  Scientists tell us that there are not really walls and chairs and violins, but quarks separated mostly by empty space.  There are not shades of blue and beige and jade, but electromagnetic waveforms.  There are not sounds, but pressure waves in a gas.  There are not smells, but molecules.  The data points impinging on our sensors go through multiple stages of information transfer from one medium to another before arriving in our brains, with multiple rounds of filtering, processing and interpretation before and after it arrives.  What you see may be what you get, but what you get may not be what really is out there.  But then, also, unless you believe all our internal technology is nothing more than glorified mashed potatoes, you are more than what you eat.
Next headline on:  Mammals • Human Body • Terrestrial Zoology • Amazing Facts

Honey More Effective than Antibiotics    07/27/2006  
A good old nature remedy is making a comeback: honey for wounds.  An article on EurekAlert about research at the University of Bonn states that honey is more effective than antibiotics at healing cuts and wounds.  Apparently the ancient Egyptians knew about its healing power.  Honey rejects dead tissue faster, repels bacteria, promotes more rapid healing, hurts less when changing dressings, and even smells nicer.  In a day when bacteria are quickly developing resistance to antibiotics, natural alternatives like honey are again coming into their own.  You may be finding a new name in the bandage department of the drug store: medihoney.
    If you’re getting along in years, another story on EurekAlert from Johns Hopkins research said that exercise is still good for you.

The honey article states that the antiseptic property is due to glucose oxidase.  This enzyme continually generates small amounts of hydrogen peroxide from the sugars in the honey over time, enough to kill the bacteria without harming the tissues.
    It’s good to know what natural remedies are available when a long way from a hospital.  What with maggots (10/24/2003) and worms (07/13/2004), you’ll be all set.  The problem is how to get the honey away from the bees.  If you succeed, at least you can put it on the stings.
Next headline on:  Health • Biomimetics

Evolutionists widely acknowledge that regulatory genetic changes are of paramount importance for morphological and genomic evolution.  Nevertheless, mechanistic complexity and a paucity of data from nonmodel organisms have prevented testing and quantifying universal hypotheses about the macroevolution of gene regulatory mechanisms.  Here, we use a phylogenetic approach to provide a quantitative demonstration of a previously hypothesized trend, whereby the evolutionary rate of repression or loss of gene expression regions is significantly higher than the rate of activation or gain.  Such a trend is expected based on case studies in regulatory evolution and under models of molecular evolution where duplicated genes lose duplicated expression patterns in a complementary fashion.  The trend is important because repression of gene expression is a hypothesized mechanism for the origin of evolutionarily novel morphologies through specialization.

In summary, an emerging theme in evolutionary genomics is that loss is a major factor in evolution.  For example, gene duplication is quite common, and the fate of most duplicated genes is loss.  At least in several cases, DNA loss may be related to a mutational bias, where deletion mutations outnumber insertion mutations.  Here we present strong statistical support for a similar loss hypothesis for the evolution of discrete regions of gene expression.  Our data were chosen without respect to the hypothesis at hand but represents rapidly duplicating genes, which may have higher rates of expression domain loss.  Nevertheless, the methods introduced here are general and could be used to test the hypothesis in future studies by using more data from any species or multiple species.  Our results support the idea that gene duplication and loss of discrete, modular expression regions may provide a general mechanism for increased specialization over evolutionary time that may be linked with increases in genomic complexity by gene duplication.

Folks, it is time to get indignant at the Darwinists.  Again.  They continue to pull rabbits out of hats with these shenanigans of theirs, their magic words couched in jargon, published in prestigious science journals, trying to make us believe that you can get something for nothing – or worse, that trends toward loss produce gains in complexity and function.  This is like believing that shopping centers will emerge from the terrorist rockets landing in Haifa.  If such ideas should not become part of the official history of Israel, then neither should this dumb idea become part of the corpus of scientific literature.  It only happens because non-Darwinians are disqualified from participating in the discussion.  The Darwin Party’s club lounge of tantalizing speculations is making some biologists fat, lazy and corrupt (12/22/2003).  Time to unbar the doors and boot the rascals out.
    Some things can overcome downhill trends.  Fish can swim upstream.  Living things can grow against the inexorable law of entropy.  Even Jesus said that he who would gain his life must lose it.  But all these include intelligently designed mechanisms for harnessing energy against the downhill trend, or intelligent goal-directed behavior.  Darwin was supposed to get rid of all that.  We can’t let the Darwinian magicians sneak into their bag of tricks things that don’t belong there.  It’s like when a Congressman performs voodoo economics to claim his massive pork-barrel project actually saves taxpayers money.  With scientists, too, we must demand an accountant and an independent investigator.
Next headline on:  Evolutionary Theory • Dumb Ideas

The pattern is a combination of sequences that makes it easier for the DNA to bend itself and wrap tightly around a nucleosome.  But the pattern requires only some of the sequences to be present in each nucleosome binding site, so it is not obvious.  The looseness of its requirements is presumably the reason it does not conflict with the genetic code, which also has a little bit of redundancy or wiggle room built into it.

The nucleosome is made up of proteins known as histones, which are among the most highly conserved in evolution, meaning that they change very little from one species to another.  A histone of peas and cows differs in just 2 of its 102 amino acid units.  The conservation is usually attributed to the precise fit required between the histones and the DNA wound around them.  But another reason, Dr. Segal suggested, could be that any change would interfere with the nucleosomes’ ability to find their assigned positions on the DNA.

The work is done by specialists in “computational biology” – a field of study more appropriate for design thinking than for evolutionary speculating.  If Darwinists started computing the probability of evolution (see online book), they would get discouraged real fast.
Next headline on:  Genetics • Intelligent Design • Amazing Facts

Maybe there’s a bright side to this SETI business.  It keeps a lot of pesky Darwinians occupied and out of trouble.  This is fine as long as their acronym S.E.T.I. employs another: O.P.M.*
Next headline on:  SETI
*Other People’s Money

The discovery raises hopes for finding soft tissue in other regions and from other animals, including mammals, [Maria] McNamara [University College, Dublin] says, because the amphibian bone marrow was discovered in an environment vastly different form the one in which the T. rex soft tissue was found.

Never question what the scientists say; that’s how symbiosis between the media and the Gurus of Knowledge is maintained.  It helps preserve the social order.  Imagine the chaos that might ensue if unbelievers started finding soft tissue in fossils from different environments all over the world; it might throw the whole evolutionary dating scheme into a cocked hat and start a revolution.  Enforced conformity may subvert freedom of thought, but it keeps the peace.
Next headline on:  Fossils • Dating Methods • Terrestrial Zoology

Titan appears to be showing a distinct regional difference between the equator and the poles.  Being cooler, the poles may be condensing out more of the liquid methane and ethane that is believed to be constantly produced in the upper atmosphere.  The current radar SAR image strip represents only a tiny fraction of Titan’s surface, so it is impossible to say if this region with its dark patches represents much of the polar regions or not.  The last two radar passes have been exceptionally intriguing (see also the July 19 press release about the April 30 flyby).  Titan presents a few familiar landscapes, but many unique ones.  Impact craters are rare, and there are no high mountains (as detected on the smaller moons like Iapetus).  It’s going to take awhile to sort all this out.  Too much theorizing too early might spoil the fun of discovery.
Next headline on:  Solar System • Amazing Facts

• Fear Factor:  Ker Than, proposing in LiveScience that fear of snakes led to the rise of humans: “To avoid becoming snake food, early mammals had to develop ways to detect and avoid the reptiles before they could strike.  Some animals evolved better snake sniffers, while others developed immunities to serpent venom when it evolved.  Early primates developed a better eye for color, detail and movement and the ability to see in three dimensions – traits that are important for detecting threats at close range.  Humans are descended from those same primates.”  How eagles and mongooses overcame their fear of snakes without becoming philosophers was not explained.  What did a Cornell scientist think of this new idea?  “It strikes me as a very special piece of scholarship and I think it’s going to provoke a lot of thought.”
• No Problemo:  Eors Szathmary, in Science: “The uniqueness of language raises special problems.  Some see this as a fundamental impediment to a successful Darwinian approach.  I disagree.  Uniqueness presents special methodological challenges, but we should bear in mind that the origin of the eukaryotic cell, as one example, was also unique in the sense that all eukaryotes today share the same common ancestor.  This did not prohibit us from insights into the origin of, say, mitochondria....”
• Necessity our Mother:  Dolezal et al. in Science: “In creating mitochondria some 2 billion years ago, the first eukaryotes needed to establish protein import machinery in the membranes of what was a bacterial endosymbiont.  Some of the preexisting protein translocation apparatus of the endosymbiont appears to have been commandeered, including molecular chaperones, the signal peptidase, and some components of the protein-targeting machinery.”
• If It Ain’t Broke:  From Berkeley Lab: “The molecular machinery that starts the process by which a biological cell divides into two identical daughter cells apparently worked so well early on that evolution has conserved it across the eons in all forms of life on Earth.”
• Bells & Whistles:  Eva Nogales, on Science Daily: “The specialization of DNA replication initiators took place a long time ago, separating them from other members of the AAA+ superfamily of proteins while maintaining an identity among themselves that reflects the importance of the replication process.  Through the millions of years, evolution has added bells and whistles around this highly conserved central engine.”
• Abracadabra:  Bowmaker and Hunt, in Current Biology 7/11/2006, explaining how the sudden appearance of all four opsin genes is not a problem for evolution: “By applying estimates of the rate of gene divergence, it is suggested that the appearance of the four classes occurred very early in vertebrate evolution, about 450 million years ago.  This is close to the time of one of the major steps in vertebrate evolution, the appearance of jaws.... Animals have evolved their visual sensitivity to match aspects of their photic environment, and it is likely that the primary adaptive selective pressure is the spectral range and intensity of daylight.

Now you know why the NCSE needs a “Faith Project Director” (07/22/2006 entry, last bullet).  Whatever is needed in the presumed emergence of everything appears on cue, fully formed, by evolution.  Shine sunlight, and eyes appear.  Bring on a snake, and the human brain and binocular vision appear.  Machinery, codes, complex organs, bells and whistles – you name it – there’s nothing that Darwinian faith cannot imagine emerging by unguided processes of selection.  You should be ashamed, o ye creationists of little faith.
Next headline on:  Darwinism • Dumb Ideas

• Iron Age I:  New stars are mixed in with old ones, both at the edges of galaxies and in their centers.  Although “nuclear burning in stars is forever increasing the amount of mass in heavy elements,” two stars in the halo of the Milky Way were found to have 1/200,000 the iron abundance to hydrogen as found in the sun.  The authors conclude that this means these stars are ancient, and assume that “their very unusual mix of chemical elements provides vital information about the nature of the earliest generations of stars.”  Yet which came first, the model or the observations? 
• Iron Age II:  Not only are these halo stars surprising, but they confess that “Other ancient stars may be hiding in the centers of galaxies, where the mass density is high and conditions likely first favored star formation....”  Yet it would seem this is the place where heavy element production would be the highest.  Searching for these ancient stars in the dense cores of galaxies is “a project for the future.”
• Figure Fudging:  The only illustration in the article shows a remarkably good fit between simulations and an actual survey of galaxy distributions from the Sloan Digital Sky Survey.  Both show a web-like structure of filaments and voids.  The fine print reveals a problem: “But close examination of the nearby galaxies shows discrepancies with what the simulations might lead one to expect.  For example, our Local Group is expected to have a thousand small mass concentrations, but we infer the presence of fewer than 50 from the number of visible galaxies.”  The two-order-of-magnitude mismatch is quickly brought into conformity with model tweaking and assumption addition – or by shoving the problem into The Future:

  It is plausible that when the universe was ionized, the heating of the gas in the smallest of the dark matter concentrations was sufficient to prevent the formation of any stars, leaving dark galaxies.  But dwarf galaxies are observed.  Consistent with that knowledge, the simulations indicate that some stars formed in small mass concentrations before or shortly after the disruption by ionization (as discussed by Andrey Kravtsov and Oleg Gnedin), producing almost dark galaxies.  The challenge is to reconcile the large number of low-mass dark matter concentrations with the smaller number of observed dwarf galaxies.  Ideas are being tested by ongoing searches for the faintest nearby galaxies and the study of their properties.

• Merger Mania:  The models also show that mergers should continue to the present day.  Mergers are observed, but...

  But the patterns of heavy element abundances indicate that no major component of the Milky Way could have been assembled largely by accretion of dwarfs of the kind observed today (discussed by Eline Tolstoy).  The two large galaxies in the Local Group certainly could have formed by merging of dwarfs in the early universe; the curious thing is that the dwarfs that were left behind have to be substantially different.

• Globular 4-D Puzzle:  Observed globular clusters are not cooperating with the models, either.  Astronomers infer a great deal from the color of starlight.  For decades, the spectra of globulars led to the common conception that they are among the oldest objects in the universe (but see 10/05/2003 entry).

  Another aspect of the merging issue concerns the tight concentrations of stars known as globular clusters.  The color of a globular cluster—and likely its heavy element abundance—correlates with the luminosity of the host galaxy.  Because globular clusters generally are old, this indicates either that the globulars became attached to the present host galaxy a long time ago—which does not naturally agree with the substantial recent merging in the simulations—or that the globulars were recently attached to the host galaxy but “knew” the luminosity of the host, which seems strange (discussed by Jean Brodie).

• Local Gangsters:  Our local group of galaxies has two large spirals and many small ones.  Is this the norm?  The Millennium Simulation, one of the largest ever carried out, produced more points for debate at the meeting:

  But because the theory predicts substantial merging and accretion in nearby galaxies, which tend to destroy thin disks, a pressing issue is whether disk-dominated systems that contain old stars as well as young are as common in the simulations as they are observed to be nearby.

Also to be borne in mind is that the problems with the simulations may be highlighting the need for improved physics.  After all, the simulations invoke many parameters to describe the 4% of the universe that is made of baryonic matter, while using only a few to describe the remaining 96% in dark matter and dark energy.  It was surprising to find that we must postulate dark matter.  Dark energy was another surprise, and the dark sector may surprise us yet again.

Always be wary when a scientist assures you he has the big picture all wrapped up and tidy, and just a few pesky details to sweep up.  Physicists boasted in the late 19th century that all the big questions were solved, and the only work left to do was improving the measurements to the sixth decimal place.  Then came general relativity and quantum mechanics, and the universe changed.  This article should be read with that in mind.  They spoke glibly about how well the large-scale models fit with the WMAP results (something we have reported earlier is far from certain: see 03/20/2006, 09/13/2005 links), but then this list of problems in near-field cosmology should have struck fear in their minds.  It seems really ominous to say that new physics are going to have to be invented to figure out the most basic objects right around us.  Then, at the end, to admit that even the large-scale model involves 96% fudge factor – and growing – well, now you understand the difference between what astronomers know and what they claim they know.  You have the observations, and you have their models.  Take your pick.
    The best early astronomers were driven by observations.  William Herschel and his son John Herschel spent incredibly long periods of time gazing into the eyepieces of their own home-made telescopes.  In more recent times, Halton Arp, Margaret Geller and John Huchra have had less use for armchair theorizing than for the hard work of observing.  It’s so much nicer to sit at a desk in the daytime and push a pencil, or punch imaginary worlds in the mind’s eye into the keyboard.  Laplace introduced a trend with his nebular hypothesis of modeling the origins of things and putting observations in the back seat.  Einstein is said to have stated that no observation can be trusted until confirmed by theory.  For shame.  Theories are man-made; observations belong to the Lord.  Choose you this day whom you will serve.
    Models can be helpful.  They have become essential tools in research.  Important questions must be raised, however, about the assumptions that go into them, and to what extent they inform us about reality.  Even in the most famous example, the physics of Newton, the classic of hard science that fueled the enthusiasm of the Enlightenment, the great Newton assumed things he could not possibly have known: that space was flat and infinite, that it was unaffected by matter, that time was constant, and that matter travels in a straight line unless acted upon by an outside force.  These are idealized definitions that he stipulated in advance.  There is no piece of matter anywhere that is not acted on by an outside force, nor could he have known with certainty that his definitions held true everywhere.  Worse, Newton assumed things called “forces” that acted mysteriously at a distance, an issue that horrified the Cartesians at the time.  Yet it worked, and worked extremely well, so Newton prevailed.  Now, of course, we know that Newtonian physics had to be replaced in the 20th century by a different model, Einstein’s, that, of course, we now know has the complete and final answer to everything.  (Scratch that.)
    Whether the finite human mind is capable of modeling this enormous universe must be constantly challenged, not merely assumed.  Just because a model works does not mean it is true.  It is a long-standing philosophical debate whether our experience, which deals only with particulars, is capable of establishing knowledge beyond our experience that is timeless, universal, necessary and certain.  It seems an inherent limitation on us that we cannot validate the system in which we are imbedded without reference to a standard outside the system.  At best, models are human playthings that must always be the slaves of the observations.  If they help improve our lives, if they help make better observations, if they seem self-consistent, let us be content with that rather than claim we “know” how the universe is put together and where it came from.  The arrogance of many modern astronomers is a character flaw that dishonors the leadership of Kepler, Herschel and many others who followed the data wherever it led, and pursued science as an attempt, however feeble, to fathom the mind of God.  It’s time to put the observations back in control and walk humbly in line.
Next headline on:  Stellar Astronomy • Cosmology • Physics • Dating Methods

• Kansas Grass Roots:  Candidates vying for school board seats in Liberal, Kansas squared off over the evolution issue: see Hutchinson News.
• Ohio Rematch:  Despite an earlier loss, Darwin critics in Ohio are hoping to bring up the issue for a vote again, reports CNS News.  The article editorializes that “Their goal is to force curriculum changes that would also allow discussion of the intelligent design theory,” when the wording of the proposed changes specifically denies this.
• McCain’s Open Mind:  Though an evolutionist himself, Senator John McCain thinks students ought to hear both sides in the debate over evolution, according to a piece in Evolution News that comments on a story reported in the New York Sun July 18.  The Sun said, “the senator mocked the idea that American young people were so delicate and impressionable that they needed to be sheltered from the concept” and compared it to cold-war efforts to shield students from learning about Marxism.
• White House Press:  President Bush’s press secretary Tony Snow entertained Wesley J. Smith of the Discovery Institute.  Smith was there to congratulate the president for vetoing the stem cell funding bill this week.
• Quilt Warfare:  In a bizarre piece of propaganda, Canadian quilt-making mom Barbara West ridiculed intelligent design on her (hopefully) intelligently-designed quilt.  According to Canmore Leader, West, whose quilt showed the earth on a pile of turtles (see humor page), won the National Award of Excellence for her design.  Casey Luskin of Discovery Institute had some smirks about this.
• Free Press:  Patrick Gavin, associate editorial page editor of the LA Examiner, gave lengthy coverage to Casey Luskin and John West about their post-Dover book Traipsing Into Evolution that critically analyzes Judge Jones’ ruling.
• WWJD:  Lita Cosner wrote for Creation Ministries International about how governments and secularists are fighting to make US schools Christ-free zones and are erring on the side of censorship.
• Conservative Backlash:  Not all pro-evolutionists are liberals.  A new group calls itself Conservatives Against Intelligent Design.  See also report on Science and Theology News.
• National Wahoo:  In the vein that everyone is someone elses’ weirdo, George Gilder of the Discovery Institute wrote a lengthy article supporting intelligent design for National Review, only to be trashed a week later by John Derbyshire on National Review.
• Evolutionary Faith:  Uncommon Descent found out that the National Center for Science Education is looking for a “Faith Project Director,”  This is odd, because the NCSE argues that evolution is built on science, and creation is based on faith.  The job duties include “developing materials pertaining to evolution and religion for print and web; representing NCSE to the faith community, in print and in person; serving as liaison between NCSE and professional theological societies and religious organizations; speaking to the press about issues involving evolution education and challenges to it; counseling teachers, administrators, parents, and others facing challenges to evolution education.” 

Thanks to Evolution News and Access Research Network for most of these leads.  Let’s get the ACLU to turn on the NCSE over separation of church and state.  Derbyshire is an arrogant hack who likens creationists to whack-a-moles.  This is a psychological disorder known as role reversal.
Next headline on:  Education • Politics and Ethics • Media • Darwinism • Intelligent Design

Is it credible to believe these fragile molecules could survive for more than a few thousand years, let alone half a million?  If and when they find DNA in dinosaur soft tissue (02/22/2006), evolutionary dating is going to be stretched to the snapping point.  But we’ve already seen that Charlie Gumby is as flexible as a cartoon superhero.
Next headline on:  Mammals • Fossils • Genetics and DNA • Dating Methods

Other news sources have not yet reported this story, but if corroborated, it should only be news to an evolutionist.  Those who hold to the Biblical creationist explanation for fossils and life deny the millions of years, so the gap is only a few thousands.  Stories about so-called “living fossils” surface once in awhile to embarrass evolutionists; see 03/31/2002 about tuataras, 03/27/2003 about salamanders, 05/30/2003 about ginkgo trees, 12/05/2003 about ostracodes, or search for living fossils in the search box above.
Next headline on:  Fossils • Terrestrial Zoology

Of course the Neanderthals don’t believe they are lacking in higher reasoning functions, because they were not invited to the panel.
    For a contrasting view of Neanderthal place in a Biblical history, see Answers in Genesis.  For earlier entries here on Neanderthal comparisons with modern man, see 06/06/2006, 02/27/2006, 01/24/2006, 09/23/2005, 05/19/2005, 02/25/2005 and 10/01/2004, or search for Neanderthal or Neandertal in the search box above.
Next headline on:  Early Man

This story signifies nothing significant.  Biodiversity naturally declines in some grasslands as forests encroach and a climax community develops.  Evolutionists would not expect noteworthy genetic change in just 150 years.  The significance of this story lies in providing another opportunity to keep King Charlie’s name before the public.
Next headline on:  Plants • Darwin

Functional redundancies, generated by gene duplications, are highly widespread throughout all known genomes.  One consequence of these redundancies is a tremendous increase to the robustness of organisms to mutations and other stresses.  Yet, this very robustness also renders redundancy evolutionarily unstable, and it is, thus, predicted to have only a transient lifetime.  In contrast, numerous reports describe instances of functional overlaps that have been conserved throughout extended evolutionary periods.  More interestingly, many such backed-up genes were shown to be transcriptionally responsive to the intactness of their redundant partner and are up-regulated if the latter is mutationally inactivated.  By manual inspection of the literature, we have compiled a list of such “responsive backup circuits” in a diverse list of species.  Reviewing these responsive backup circuits, we extract recurring principles characterizing their regulation.  We then apply modeling approaches to explore further their dynamic properties.  Our results demonstrate that responsive backup circuits may function as ideal devices for filtering nongenetic noise from transcriptional pathways and obtaining regulatory precision.  We thus challenge the view that such redundancies are simply leftovers of ancient duplications and suggest they are an additional component to the sophisticated machinery of cellular regulation.  In this respect, we suggest that compensation for gene loss is merely a side effect of sophisticated design principles using functional redundancy.

In particular, we suggest the existence of regulatory designs that exploit redundancy to achieve functionalities such as control of noise in gene expression or extreme flexibility in gene regulation.  In this respect, we suggest that compensation for gene loss is merely a side effect of sophisticated design principles using functional redundancy.
    Clues for regulatory designs controlling redundancy were obtained first in a recent study...

The model that emerges is that although many isozymes are specialized for different environmental regimes, alarm signals induced by particular stress stimuli may call for their synergistic coexpression.  Here, RBCs provide functional specialization together with extreme flexibility in gene control that could be activated when sufficient stress has been applied.  For example, in yeast, glucose serves as a regulatory input for alternating between aerobic and anaerobic growth.  Its presence is detected by two separate and independent signaling pathways, one probing intracellular glucose concentrations and the other probing extracellular concentrations.

The extent to which genomic functional redundancies have influenced the way we think about biology can be appreciated simply by inspecting the vast number of times the word “redundancy” is specifically referred to in the biomedical literature (Fig. 5, which is published as supporting information on the PNAS web site).  Particularly interesting is the abundance with which it is addressed in studies of developmental biology (Fig. 5).  In fact, it is here that concepts such as “genetic buffering” and “canalization” first had been suggested.  Furthermore, the robustness of the developmental phenotypes such as body morphologies and patterning have been repeatedly demonstrated.  So the question is, are these redundancies simply leftovers of ancient duplications, or are they an additional component to the sophisticated machinery of cellular regulation?
    In criticism, one may argue that many of the reported redundancies do not actually represent functionally equivalent genes but rather reflect only partial functional overlap.  In fact, knockout phenotypes have been described for a number of developmental genes that have redundant partners.  For these reasons, it has been suggested to define redundancy as a measure of correlated, rather than degenerate, gene functions.  Although these facts may suggest that redundancies have not evolved for the sake of buffering mutations, it has, in our opinion, little relevance to the question of whether they serve a functional role.  The interesting question is, then, can such a functional role for the duplicated state be inferred from the way the two genes are regulated?

A simple potential interpretation may suggest that although the controller is the key player performing some essential biological role, the responder is merely a less efficient substitute.  Yet, accepting the notion that redundancy could not have evolved for the sake of buffering mutations, this interpretation still is severely lacking.
    A different, and more biologically reasonable, hypothesis accounting these asymmetries is that one of the functions of the responder is to buffer dosage fluctuations of the controller.  This buffering capacity requires a functional overlap that also manifests itself in compensations against the more rare event of gene loss.  Other models accounting for this assymetry are discussed further in this work, but our main point of argument is that this complex regulation of functionally redundant, yet evolutionarily conserved genes, strongly indicates utilization of redundancy.

This is really a remarkable paper filled with inspiring possibilities.  If we can just think design instead of years of mindless mutations, we might find cures for debilitating diseases.  This paper has much of the obligatory evolutionspeak, but what does Darwinian thinking really contribute?  Nothing.  Although the researchers paid lip service to the evolutionary explanation that members of RBC pairs might have arisen through gene duplication, and that the coregulation might have provided a selectable fitness advantage, such language is really nothing more than the usual aftermarket sales pitch on the designed product.  The real heart of their argument was that design exists, it is functional, and we can learn from it in ways that could help mankind.  The future of design-theoretic science looks bright.
Next headline on:  Cell Biology • Genetics • Intelligent Design

There’s the shell game (see top right quotation).  Evolutionists preach about science and criticize faith, but look at their research.  This is why Colin Patterson, in a moment of frankness, asked his evolutionary colleagues if they could point to one thing about evolution that they knew was true.  All he got was silence.
    Four papers from one journal, of course, cannot represent a statistical sample, but maybe this anecdotal evidence can interest someone in performing a larger study on the comparative numbers of conjecture-words between evolutionary papers and research papers on observable, testable lab science.
Next headline on:  Evolution

• Darwin Iconography:  Florence Maderspacher, the magazine’s reviews editor, wrote about how the “tree of life” imagery from Darwin’s book needs to be revised.¹  Revisiting the one diagram in the Origin, she explained how a coral, rather than a tree, represents the image that guided Darwin’s development of his theory.  (This is the historical revision presented in a new book by Horst Bredekamp, Darwin’s Coral.)
      The aroma of Maderspacher’s review exudes not primarily from the debate about the path of evolution as understood today, however, as much as the desire to accurately preserve the old man’s vision.  “Bredekamp offers fascinating insights into how Darwin’s thinking developed,” she says in one place, and speaks of his sketches “that allow us to watch Darwin think” in another.  The medium-length review, which ends with the theme of accuracy in “evolutionary iconography,” mentions Darwin’s name 50 times.
• Darwin Goliath Squad:  An editorial called “Darwin’s Champions Fight Back” begins, “Researchers are building their response to the attack by creationism on evolution as interest in Darwin memorabilia continues to grow.  Nigel Williams reports.”²  As the subtitle suggests, the article discusses both the counterattack against creationism and the growing interest in Darwin collections.  Williams first summarizes the work by “Darwin’s champions” against creationism in the UK, including the international joint statement (see 06/19/2006), and statements by the Royal Society, Nottingham University and the press.  Then Williams’ attention turns affectionately to Charles Darwin:

  But in spite of this battle, Darwin memorabilia and other material are attracting growing interest.  The world’s largest collection of editions of Charles Darwin’s works was bought last month by Britain’s Natural History Museum for nearly £1 million, the most expensive acquisition in the museum’s 125 year history.  Antiquarians, Chris and Michele Kohler collected about 3,500 items, filling four rooms of their house, over 20 years.  The collection includes almost everything Darwin published from 1829 onwards.
      The museum’s director said: “This acquisition makes the museum the ultimate Darwin resource.  Darwin brought about a revolution in how humans think about themselves and the natural world.  Combining this collection with our existing holdings gives us an unprecedented insight into how the theory of evolution developed, and how Darwin worked.”

  Williams follows with the story of a “lovely letter” by Darwin to a Victorian clergyman who had questions about his evolutionary theory.  In the letter, Charles Darwin gently helps Rev. William Denton overcome his doubts.  “As in The Origin of Species,” Williams explains, “he uses specific examples to make his point.  For example, he discusses the origin of deafness in cats and why pigs in Florida are black.”  The “striking” letter is expected to fetch £20,000–30,000.
      Williams sees the rise in interest over Darwin as timely: “With the bicentenary of Darwin's birth and the 150th anniversary of the first publication of The Origin of Species due in the next few years, researchers hope that these events will help provide a prop to garner public interest and support and also help stem the anti-evolutionary tide.  This short article mentions Darwin 16 times.  Another project is raising funds for the 2009 Darwin Bicentennial.  The BBC News reported on a project to build a full-scale replica of the H.M.S. Beagle, the ship that launched Charles Darwin to fame.
• Darwin Daddy-O:  “Who’s your daddy,” cartoon pops ask, when junior needs to show a little respect.  Well, Lynne Cassimeris (Lehigh U) is no smart aleck.  In her interview in the same issue,³ she knows who’s in charge:

  Do you have a scientific hero?
  Darwin is quickly becoming my scientific hero because he synthesized so many observations into one coherent theory of evolution by natural selection.  His theory is beautifully logical and explains so much of what we see in biology.

  Speaking of affection, here’s how Cassimeris responds when someone takes Darwin’s name in vain:

  Speaking of evolution, your colleague Michael Behe is one of the leading proponents of ‘intelligent design’: care to comment on what it’s like to be in a biology department that includes an ‘ID’ proponent?
  An article in the student newspaper falsely accused me of taunting Mike with chants of “Darwin’s your daddy”, so I guess that’s another reason why Darwin is my science hero – he’s my daddy too.

  Cassimeris went on to praise Behe in a backhanded way.  “Mike’s ideas led all of us to think more about evolution and how important it is to our own fields and to biology education,” she said.  “Before Mike’s book, evolution was something that many of us took for granted and didn’t consider all that much.... So, I have to credit Mike with inspiring me to think about evolution much more than I had before.” 

Can you think of any scientist in history that gets this kind of attention?  Einstein scores high points, maybe, and perhaps Newton, but certainly no other scientist, no matter how great his or her achievement, gets the gushy worship that Pope Charlie gets from his devoted foot-kissers.  There is no annual Einstein Day or Newton Day, but Charlie’s birthday is becoming an international event.  Even in Darwin’s old age, his groupies would stand in awe in his presence at the Shrine of Down House, and “grown men would crumble in the presence of the god” as biographer Janet Browne described the new cult (see 02/13/2004 commentary).  This is not even weird science.  Clearly, it’s religion.  No wonder creationists, intelligent design advocates, theologians and pastors often target the cult of Darwin (see op-ed piece by Albert Mohler), because evolutionists themselves have placed Charlie’s fatherly image on their own standards.  If he falls, who is there (09/02/2004) to stand against the attacking Visigoths? (07/14/2006)  Richard Dawkins?  Bring it on.
Next headline on:  Darwin • Intelligent Design

The research group has studied the third, less well understood, protein complex, known as the Smc5/6 complex.  This protein complex was found to bind to locations on th