Yahoo’s piece was not a volcano, but a mud pot; better, a fumarole.  Darwinists are the ones erupting when people object to having philosophical naturalism in the form of chemical-evolution mythology crammed down their throats.  So what are the Darwin Party imagineers going to do in a free market economy?  Force the customers to watch their cartoons?  Many IMAX films are wonderful explorations into the natural world when they stick to observable facts.  Adding Tinker Bell is only distracting.
    Pastors and scientists who don’t understand the issues should keep their mouths shut.  The “Reverend” Baxter Wynn, if he was quoted accurately, appeared to be utterly ignorant of the controversy and what his Bible says about it.  His statement simultaneously commits the either-or fallacy and shouts peace, peace, when there is no peace.  Charles Townes, bless his holy heart, is a smart engineer but a weak philosopher.  His comments play right into the hands of those who would banish his Christian beliefs from public discussion.  What we need are more men like Larry Caldwell able to stand up to the lies of the dogmatic Darwinists and get them to back down.  Somebody ought to turn Liggett’s big lie back on him.
Next headline on:  Darwinism • Intelligent Design • Education • Media

1. Diatoms:  A paper in PNAS by Finkel et al.¹ was called, “Climatically driven macroevolutionary patterns in the size of marine diatoms over the Cenozoic.”  All it discussed was the sizes of diatoms as a function of biodiversity and ocean temperature.
2. Island Biodiversity:  Douglas Erwin wrote a Perspectives piece in Science last week,² entitled “Macroevolution: Seeds of Diversity.”  It is more a theoretical treatment of opposing evolutionary hypotheses (niche construction and classical gradualism) in the context of adaptive radiation on island communities, than an examination of any particular case of a plant or animal evolving into a different kind of organism.  Erwin proposes that biodiversity itself generates biodiversity: “Simply put, the reason the tropics have so many species is that they have so many species” or, “future diversity is a function of current diversity.”
       He continued by speculating that runaway biodiversification might be capped by periodic mass extinction events.  He concluded, “If periodic disturbance does provide a major control on diversity, then niche generation may be an ongoing process, more rapid during macroevolutionary transitions, but providing a regular source of new adaptive possibility until the next crisis occurs.”  Overall, macroevolution in his article was assumed, not demonstrated.

Mere microevolution masquerading as macroevolution by mangling the meanings of messages.  Microevolution is not under dispute.  If macroevolution is a fact, Darwinists, give us an example instead of “ingenious speculation but not much rigor” (see next entry).  There should be millions of examples.  Why is this so hard to demonstrate?  A bluffing assertion is not a sign of rigor, or of vigor.  In science, it’s more a sign of rigor mortis.
Next headline on:  Darwinism • Marine Life

Evolutionary biologists agree that gene duplication has played an important role [intelligent design term] in the history of life on Earth, providing a supply of novel genes that make it possible for organisms to adapt to new environments.  The existence of diverse multigene families, particularly in eukaryotes, provides evidence that numerous events of gene duplication followed by functional diversification have shaped [intelligent design term] genomes as we know them.  But it is less certain how this panoply of new functions actually arises, leaving room for ingenious speculation but not much rigor.  Cases where we can reconstruct with any confidence the evolutionary steps involved in the functional diversification are relatively few.   (Emphasis added in all quotes.)

• Oh no:  He discredited the original subfunctionalization hypothesis of Susumi Ohno:

  The first hypothesis regarding the origin of new gene function was that of Ohno, who assumed that, after duplication, one gene copy would be entirely redundant and thus freed from all constraint.... There are a number of reasons for doubting this hypothesis  First, as the late Marianne Hughes and I showed in the case of the tetraploid frog Xenopus laevis, duplicate genes are not in general freed from all functional constraint.  Rather, purifying selection [i.e., conservation] acts to eliminate deleterious nonsynonymous (amino acid-altering) mutations even in apparently redundant gene copies.  Furthermore, there are a number of multigene families where there is evidence that positive Darwinian selection has acted to promote amino acid changes in functionally important regions of proteins.  In these families, new function clearly has not arisen as a result of random mutation alone, contrary to the prediction of Ohno’s model.

  In its place, Hughes offered the alternative hypothesis that “both functions are already present before gene duplication.”  This, however, does not explain the origin of the functions, but only their rearrangement.

• Who needs Darwin?  In a paragraph entitled “The Role of Natural Selection,” Hughes started by denying that natural selection had much to do with it:

  One theoretically attractive feature of their model of subfunctionalization, as pointed out by Lynch and colleagues, is that it can occur without the need for positive Darwinian selection, which is thought to be relatively rare at the molecular level.

  If daughter genes inherit just one of two functions, he says, “conservative or purifying natural selection will act against any mutation that eliminates function,” while the other fragment might accumulate mutations by genetic drift.  Again, this does not describe the origin of any new functions, but only the preservation of existing information.

• Gimme your best shot:  Hughes surveyed some of the best examples of Darwinian selection at the molecular level, explaining the “Babe Ruth effect.”  Even these, however, overlook the need for new functional information:

  On the other hand, some of the best-documented examples of positive Darwinian selection at the molecular level involve functional diversification among members of multigene families.... It may often be as true of molecules as it is of human beings that “a jack of all trades is master of none.”  In such cases, positive selection may actually favor the loss of one function in a bifunctional molecule if a duplicate gene is able to take up the slack.

• Dunno:  Hughes did not suggest that much is known about evolution by gene duplication, if anything; indeed, it cannot be known:

  In the case of archaeal tRNA endonucleases, there is no direct evidence whether drift alone gave rise to subfunctionalization or whether positive selection played a role.  These events occurred in the distant past; thus, the most convincing signal of positive selection, an accelerated rate of nonsynonymous nucleotide substitution is not obtainable, being obscured by numerous subsequent neutral changes.  However, the fact that subfunctionalization has occurred twice independently and by different pathways in the same gene family suggests that positive selection may indeed have been involved.  Perhaps, in the high-temperature environments occupied by these archaeal species, there is something less than optimal about the homotetrameric type of tRNA endonuclease, where the same polypeptide does double duty as a catalytic subunit and a spacer.

• Lessons learned:  Near the end of the article, Hughes made a remarkable admission about the predictive power of Darwinian biology.  He also makes his first mention of a mechanism for new function, but prefaces it with the word perhaps:

  If we have learned anything at all in a century and a half of evolutionary biology, it is that facile generalizations are dangerous.  The evolutionary process finds a way to create exceptions to every model we propose.  Thus, it seems unwise to expect that functional diversification after gene duplication follows the same pathway every time.  Sometimes, subfunctionalization may occur by drift alone.  On other occasions, as we know, positive selection is involved.  Perhaps there are even cases where a new function has arisen by Ohno’s model of resuscitation of a dead gene. 

• Somewhere in the mix:  Hughes briefly elaborated on the possibility that new function is an emergent property from the mix and match of dynamic interplays between multi-talented genes and proteins:

  In fact, as recent data on gene expression and protein-protein interaction networks make clear, all genes are multifunctional.  Even in its infancy, systems biology makes clear that protein functions are complex processes existing in multiple dimensions.  It thus seems a reasonable extension of Jensen’s original insight to propose that new protein functions arise as the multidimensional space of functional interactions is parceled out in new ways, new links in biological networks are formed, and old links are broken.

Testing this hypothesis will require work at the interface of molecular evolutionary genetics and systems biology.  We will need to be able to understand the diversification of gene duplicates in terms of the totality of each gene’s role in cellular processes.  It is a tall order given our present knowledge, but this kind of evolutionary systems biology not only will increase our understanding of how new protein functions evolve but also will shed essential light on why biological systems work the way they do.

This article sounded intriguing by its title, “Gene duplication and the origin of novel proteins,” and ostensibly set out to explain how new functions arose – but it did nothing of the sort.  All Hughes could identify by observation were degradation effects.  If genes and proteins underwent subfunctionalization, the function was already operative in the ancestor, as well as the information needed to produce function.  Did he prove that the daughter products contained more information?  No.  Did he prove that subfunctionalization actually occurred, rather than being created that way?  No.  Did he give away the store?  Yes.
    Hughes illustrated for the perceptive reader that Darwinian theory is useless and bankrupt.  It has produced little else than dangerous facile generalizations with exceptions for every proposed rule.  He has cast doubt on whether natural selection, the evolutionary mechanism that made Charlie the Philosopher-King of Science, acts as anything more than a conservative process to preserve existing information.  He tossed in for free a few falsifications of his colleagues’ speculative hypotheses.  He made up a story committing the personification fallacy about molecular Babe Ruths, without proving it has any relevance to real genes and proteins.  He demonstrated that evolutionary biology is an unending series of falsified tales, and he admitted that after “a century and a half of evolutionary biology,” almost nothing is known and everything remains to be discovered, which is “a tall order given our present knowledge” (better, lack of it).  So much for the origin of novel proteins.
    We provided extensive quotes from this paper to illustrate a recurring theme in the evolutionary scientific literature: Darwinists boast much but deliver nothing, only emptiness and confusion.  Does this vain litany of excuses and leaps in the dark deserve to be enshrined as the only valid approach to science, such that no student should be allowed to criticize it or hear any alternatives?
Next headline on:  Genetics • Evolution

When the going gets tough, the tough use their heads.  Porters around the world carry loads that would floor backpackers by balancing baskets atop their noggins or slinging sacks from their craniums.  Now a new study reveals that Nepalese porters do the job better than anyone else, hefting huge bundles while using relatively little energy.   (Emphasis added in all quotes.)

The town of Namche (at an altitude of 3500 m [11,400 ft]) near Mount Everest hosts a weekly bazaar.  Porters (Fig. 1A), predominantly ethnic Rai, Sherpa, or Tamang, typically take 7 to 9 days to travel to Namche from the Kathmandu valley.  The route, no more than a dirt footpath, covers a horizontal distance of 100 km, with total ascents (river crossings to mountain passes) of 8000 m [5 vertical miles] and total descents of 6300 m [4 vertical miles].
    One day before the bazaar, we counted 545 male and 97 female porters (and 32 yaks) en route to Namche; others passed by earlier and later in the darkness.  We weighed randomly selected porters and their loads.  The men carried loads of 93 +- 36% of their M_b (mean +- SD, n = 96 male porters), whereas the women carried 66 +- 21% of their M_b (n = 17 female porters).  The youngest porter was 11 years old, and the oldest 68; the greatest load measured was 183% of M_b, and 20% of the men carried > 125% of their M_b.  More than 30 tons of material were ported to Namche that day.

The load versus speed versus energy-cost trade-off chosen by these porters is to walk slowly for many hours each day, take frequent rests, and carry the greatest loads possible.  We observed, for example, a group of heavily loaded porters making slow headway up a steep ascent out of a river gorge.  Following whistled commands from their leader, they would take up their loads and labor uphill for no more than 15 s at a time, followed by a 45-s period of rest.  Incredibly, this group of barefoot porters was headed for Tibet, across the Nangpa glacier (altitude 5716 m [18,700 ft]), about another week’s travel beyond Namche.
    So how do they do it?  They might reduce the muscular work required to carry a load or increase their overall efficiency.  The actual mechanism is unknown at this time.

Every once in awhile we get glimpses into the suggestion that there is far more potential in the human body than most of us realize.  Those of us who have backpacked in the mountains know the strain of carrying even 40 pounds up a steep mountainside for just a couple of hours, and that at much lower elevations.  The worst feeling at a rest stop is to have some 68-year-old frail-looking grandma with a bigger pack prance right on by saying, “Mighty fine day, is it not?” as you sit there gasping for breath.
    Here we see, in Nepal, a community of men, women and children that make the impossible look routine.  They don’t shop at REI and use Patagonia gear or high-tech climbing boots; they don’t compete in the Olympics or win medals, but all of us must regard the way of life of these human mountain goats with admiration.  How much stronger and smarter could our ancestors have been?  A little humility is always in order.
Next headline on:  Human Body • Amazing Stories

Other scientists express a mix of chagrin and disdain at the amount of energy that researchers have expended on trying to separate fossil boys from girls.  Investigators need to drop their obsession with the sex of fossils and examine how individual differences in skeletal anatomy arise, contends Maciej Henneberg of the University of Adelaide in Australia.  For body weight and many skull measurements, including braincase size and facial width, individuals within each sex usually differ far more from each other than average members of opposite sexes do, he argues.
    Erik Trinkaus of Washington University in St. Louis also derides efforts to identify the sex of ancient bones.  Sex assessments always begin with the unjustified assumption that bigger bones must belong to males and smaller ones to females, he says.  And the numbers of individual specimens of A. afarensis and other ancient hominid species are too few to generate reliable estimates of male and female size ranges, in his opinion.
    Louisiana State’s Tague doesn’t go that far, but he notes that even the pelvis, the body part regarded as the gold standard for telling apart primate sexes, is surprisingly tough to read.  His work shows no consistent pattern of the pelvis being larger in females than in males.   (Emphasis added in all quotes.)

The nonsense that Darwinists get away with is atrocious and silly.  Bower’s article contained the obligatory artist’s conception of Lucy’s family life, all based on myth and unwarranted speculation.  Even though he tried to provide criticism of Lovejoy’s wacky idea, he only extended the debate between members of the Darwin Party.  Why do non-Darwinists never get a chance to provide their scientific critiques?
    Historical anthropology is out of control.  It is an endless parody of untestable speculation masquerading as legitimate research.  Science needs creationism as a check against “rampant Darwinism” as Dr. Phillip Skell called it in a recent interview (see IDURC).  He said, “The conflation of neo-Darwinism with the historical biology, and its frequent companion materialist philosophy, should be recognized and exposed for what it is, rather than disingenuously introduced as science.” 
Next headline on:  Early Man • Dumb Stories

This hypothesis is no less speculative than the one by creationists that Indians saw live pterosaurs and the Chinese saw live dinosaurs.  Evolutionists would never consider such an idea, because they have their own myths.  They are wedded to the tale that dinosaurs and pterosaurs died out long before man appeared.  Do they know this for a fact?  No; they were not there, for one thing, and their prior commitment to evolutionary theory dictates how all data are to be interpreted.  The discovery of flexible blood vessels in a T. rex recently (see 03/24/2005) shows the extent of their commitment; rather than consider the obvious, that this unfossilized material could not be 70 million years old, they adjusted their assumptions to fit their myth.
    Were the Chinese and the Lakota skilled in paleontological interpretation of disarticulated bones?  Would it not be more plausible to suggest that perhaps they saw some of these creatures before the last ones died out?  It would seem more likely that the fearsome appearance of imposing live creatures would generate better myths than would dead bones to untrained eyes.
Next headline on:  Dinosaurs

In 1952, Stanley Miller, working with Harold Urey, simulated the atmosphere of early Earth with a gas mixture of methane (CH₄), ammonia (NH₃), molecular hydrogen (H₂), and water.  When he introduced an electrical spark to represent lightning, he observed the formation of amino acids, the building blocks of proteins....
    However, by the 1960s, the validity of hydrogen-rich (and hence reducing) model atmospheres for early Earth, such as the CH₄-NH₃ atmosphere used by Miller and Urey, was under attack.  Since the 1970s, carbon dioxide (CO₂)-rich atmospheres have been favored.  Miller has shown that the production of amino acids and other organic molecules is orders of magnitude less efficient in such atmospheres.  For this and other reasons, the Miller-Urey approach to the origin of life has fallen out of favor with many researchers.  But on page 1014 of this issue, Tian et al.² argue that the early-Earth atmosphere might have been hydrogen-rich after all.
(Emphasis added in all quotes; see also 05/02/2003 entry on the history of the Miller experiment.)

1. Rinse:  Tian et al. focus on the oceans as the “birthplace of life,” but polymerization of amino acids into proteins (or nucleotides into RNA) is thermodynamically unfavorable in liquid water.
2. Salt:  Furthermore, in an early ocean as saline as that of today, the salt inhibits key prebiotic reactions.³  The bulk ocean may thus have been one of the worst places to try to originate life.
3. Toss:  After making life’s building blocks in the ocean, one needs to look elsewhere to carry the chemistry further.

These are tumultuous times in the study of the origin of life.  The early ocean may have been even less hospitable for prebiotic chemistry than previously thought, and claimed evidence for the earliest signatures of life on Earth is being strongly challenged.  Now a 30-year, albeit shaky, consensus on the nature of the early atmosphere may have to be reexamined, and the geochemical implications of an H₂-rich early atmosphere will need to be scrutinized.  This turmoil makes it a great time for young scientists to enter the field, but it also reminds us that some humility regarding our favorite models is in order.  As Jacob Bronowski noted, “Science is a tribute to what we can know although we are fallible.”

Thirty years ago, geochemists took away the primordial soup that biologists thought they needed to cook up the first life on Earth.  Now, some atmospheric chemists are trying to give it back.
    Creating the primordial organic goo used to be easy.  If you combined the methane and ammonia seen in the still-primordial atmosphere of Jupiter, passed lightninglike sparks through the mixture, and added some water, voilà, complex organic compounds such as amino acids formed.  But then in the 1970s geochemists spoiled the party by insisting that Earth’s earliest atmosphere was nothing like Jupiter’s.  Earth’s carbon would have been part of oxygen-rich carbon dioxide, and its nitrogen part of inert nitrogen gas, they said.  And hydrogen seeping from the planet’s interior would have quickly escaped to space.  That left chemists with a thin gruel indeed.

Same comment as in 04/22/2005: too little, too late.  The good news is no better than that in the Geico commercials: “I have good news and bad news.  The jury has found you guilty, you have to go into the slammer for life, your wife and kids have left you and are changing their names, your stocks went bust, and you have cancer.”
“What’s the good news?”
“I just saved $400 on my car insurance by switching to Geico.”
Everything is against the astrobiologists: the chemistry, the sources, the geology, the salt, the water, the information, the probability, the thermodynamics, the philosophy.  Does the good news really matter?  “I just saved 30% on my hydrogen when switching to the Tian et al. model.”  It would make any knowledgeable astrobiologist want to hold his head and groan, “Oh, shut up.”
Next headline on:  Origin of Life

To an evolutionist, human society acts on the same principles as cockroach society.  To evolutionary reporters, any idea that glorifies Charlie is fit to print.  As a prime example of evolutionary folly, this story speaks for itself.
[Gong.]  Next.
Next headline on:  Darwinism and Evolutionary Theory • Dumb Stories

MSNBC’s title suggests that both sides are bickering, claiming “School board members hurl insults at each other.”  But if you look into the article, the only ones hurling insults are the evolutionists; the other side is just putting up their shields.  All Connie Morris said was, after being insulted, “Had you attended, you would have been informed.  You would be sitting here as informed individuals and not arrogantly calling us dupes.”  The article claims Morris mentioned the moderates by name in print, but does not say she insulted them like the Darwinists did; she only derided evolution itself, the article says.  The evolutionists, though, called the conservatives “dupes” of intelligent design advocates and their decision based on “absolute and total fraud.”  Judge for yourself which side is acting with civility and responsibility.
    The majority conservatives had invited the pro-evolution moderates to come to the hearings, but they wouldn’t.  The Darwin Party could have contributed to the discussion, but chose to sit and pout.  If they had been listening, they would realize that the Board is taking no position on intelligent design.  The new standards are very mild.  They do not call for teaching creation or intelligent design, but only for permitting critical thinking about evolution such that it is treated like any other scientific theory, not like a sacred cow.  No advocates of a scientific theory would worry about that unless their position was weak.
Next headline on:  Darwinism and Evolutionary Theory • Education

1. Snail Trail:  John Roach in National Geographic News wrote about new painkillers and drugs being developed from toxic snail venoms.  Cone snails create an array of hundreds of unique chemical compounds (see 10/22/2003 entry).
2. Fungus Among Them:  A fungus shows promise for controlling malaria mosquitos.  It appears to be harmless to humans.  Story on Science Daily.
3. Lockjaw Therapy:  Researchers in Barcelona are discovering that tetanus toxin has therapeutic properties in treatment for neurodegenerative disorders, according to EurekAlert.

A common operational paradigm in nature appears to be control by resistance: initiator and repressor, agonist and antagonist, accelerator and brake.  Another is hormesis (see 02/12/2003 entry): i.e., that a little is good, but more is not better.  Taken together, these principles suggest that many poisons and toxins only become “evil” to our sensibilities when they get out of control.
    A dynamic community of interacting organisms needs checks and balances.  These are best understood by looking at the big picture, a view called systems biology – a perspective implicit with design reasoning.  As a corollary, relationships that could have been harmonious originally may have begun to wreak havoc when out of balance.  Regardless, there may be healthy treasures to mine in things we once considered agents of suffering.
Next headline on:  Health

Lee described Booher, 48, as “one of the finest science teachers I’ve ever been around” and said Booher would return to the classroom in the fall since he agreed to stop distributing the creationism materials.

So “Evolution Must Be Taught Exclusively.”  Anything other than 100% pure Darwin Dogma is now labeled “belief” and “religion” by fiat, no matter how scientifically sound it is, no matter how supported by reputable scientific sources.  Students’ tender eyes must be shielded from any of the voluminous damaging evidence against official dogma.  Are you mad about this?  Look at the next entry; think about all those molecular machines that are inexplicable by evolution – mechanisms that shout design with a capital D.  And they call evolution “observable scientific fact”?  How enlightened our age.
    Persecution like this is not limited to Virginia; it is happening all over the country in one of the most momentous scientific paradigm battles of the century.  Evolution is controversial, whether the Darwin Party realizes it or not.  It is tearing this country apart (see 05/24/2005, 05/13/2005 and 05/05/2005 entries, and another recent example in Utah from the Salt Lake Tribune).  It is the defining issue of the culture war.  A large majority of the public denies that evolution can explain the complexity of life, and increasing numbers of scientists are ready to cast Darwin overboard.
    Incongruously, the same Darwin Party thugs who shut out debate and forbid access to scrutiny over their incomprehensible Tinker Bell religion are usually the same people who have no problem with any leftist, radical, homosexual-activist, abortion-advocate, Marxist or new-age prophet preaching their dogma unhindered, without any opportunity to opt out.  If you’ve had enough and can’t take this any more, do something.  Start by getting informed: about the evidence, the history of science, the law, and the right strategy to combat today’s incorrigible dogmatists, the Darwinians.^*  Attend your school board meetings.  Write effective letters.  Vote.  Push back on the ACLU, the NCSE, the Dogmatists United For Separation of Reason and State, and the other pro-Darwin PACs.  Their censorship will only succeed if the citizens let it.
Next headline on:  Darwinism and Evolutionary Theory • Education

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^*Knowledge is power, but ignorance is not bliss.  It is essential that you understand the issues, the law, the science, the tactics of the Darwinists, and the art of Baloney Detecting, before leaping into the fray.  Well-intentioned but misinformed actions can do more harm than good.  Open debate is what we should seek; if it is wrong for Darwinists to mandate their views, then it is wrong to mandate creationism or intelligent design, too.  If it is wrong to censor creationism, it is wrong to censor evolutionism – that is not a desirable goal, nor will it play in the public arena.  Students of science need to know about evolution – more than the watered-down, sanitized version they are getting (see 02/11/2005 commentary for suggested curriculum).  Teaching the controversy – letting students hear all the pertinent scientific evidence for and against Darwinism and its scientific alternatives (like intelligent design), is both commendable and legally defensible in a free and pluralistic society (see example from 06/03/2005 entry).  Do your homework on the resources at the Discovery Institute before picking up the pen or microphone; if you still do not feel qualified, then support those who do.

1. Immunity Tunes:  A press release from Johns Hopkins talked about how, unlike other cells, immune cells undergo a “dizzying loop of activity” to generate huge varieties of antibodies through recombination.  They liken the regulator of the recombination process to a band leader directing a jam session.  (Emphasis added in all instances.)
2. Oxygen Sensor:  “Cell’s Power Plants Also Sense Low Oxygen” announced a report from Howard Hughes Medical Institute.  In summary, “Researchers have produced the strongest evidence yet that mitochondria – the organelles that generate energy to power the cell – also monitor oxygen concentration in the cell.  If oxygen slips below a critical threshold, the mitochondrial ‘sensor’ triggers protective responses to promote survival.”  Controlling oxygen levels is important.  Both too little and too much can be deadly, not only to the cell, but to the whole organism.
3. Reverse Gear:  Nature¹ June 9 talked about the myosin monorail trains that ride the microtubule rails.  Out of the myosin superfamily of motor proteins, consisting of 18 classes, they were curious how Myosin VI is bidirectional, unlike most of its siblings.  They studied its “lever arm,” “power stroke” and “converter” but did not come up with a final model of how it works.  “Undoubtedly, this unique myosin family member has yet more surprises to reveal,” they concluded.
4. Transporters:  Aussie biologists talked about protein transport into mitochondrial membranes in Current Biology.²  Since there are two membranes, similar to those in chloroplasts (see 01/01/2005 story), there are two squads of transporters to get the cargo in and out.  Named TOM and TIM for translocons of the outer and inner membranes, these are “a series of molecular machines” that know how to sort and authenticate objects needing to pass the gates.  They envisioned an “entropic spring” mechanism that can help get the cargo passed through “no apparent input of energy.”  This type of mechanism is “an emerging theme in biology” that harnesses the disordered motion of molecules to provide binding flexibility and low energy cost to accomplish “a range of functions.”  “The TIM23 complex is a smart machine,” they say, describing its ability to grab a piece of cargo, insert it, respond to a stop-transfer signal and reject it, or pass the cargo to the next machine complex.
5. Tissue Triage:  Another paper in Current Biology³ discussed how epidermal cells repair damage.  The phylogeny of this ability was a puzzle: “Amazingly, while the eyes and hearts of Drosophila and mammals are constructed in entirely different ways and are morphologically quite distinct, their development appears to be under the control of similar master-regulatory transcription factors,” they said.  These operations on two vastly different types of organisms cannot be homologous, they suggest; they must be due to convergent evolution.  However the repair mechanism arose, it involves signaling and a cascade of coordinated events involving molecular machines.  The result?  A stitch in time, and wounds that are self-healing.  This is another “conserved repair response,” they say, meaning that it is found early in the history of life with little change since.
6. Quality Control:  A press release from Yale described a protein that “recognizes misfolded RNAs, creating a RNA quality control system for cells.”
7. Kissing Chromosomes:  A news story in Nature⁴ sheds light on a mystery of gene regulation.  We all know chromosomes come in pairs, but how do the genes on each member get expressed together when they are separated by distance?  Out of the “many strategies to orchestrate gene activation or repression” in the cell’s bag of tricks, “A three-dimensional examination of gene regulation suggests that portions from different chromosomes ‘communicate’ with each other, and bring related genes together in the nucleus to coordinate their expression.”  It’s nice that the spouses are on speaking terms.  “Such inter-chromosomal communication has been suspected for some time,” Dimitris Kioussis said, “but this is the first evidence that it actually takes place.”  Our understanding of gene regulation has changed from a linear view “to an appreciation that genes are associated with groups of proteins, forming multimolecular complexes,” he said.  We’re going to have to see the process not just in snapshots or just a movie: “Is it time to go 4D?” he jests with implicit seriousness.  No one knows how the chromosomes are brought together.  “How do genes find their appropriate location in the nucleus of a cell, and how are genes that must be expressed herded into active neighbourhoods?” he asks (see “Spaghetti in a Basketball,” 07/28/2004).  Whatever the mechanism, “These remarkable findings will puzzle us for some time to come.”
8. Inter-Agency Coordination:  Cities have fire departments, police departments, ambulances, highway patrol, disaster response teams and other agencies that sometimes have overlapping duties.  Cells do, too.  There are multiple repair mechanisms able to respond to different kinds of DNA damage.  Scientists writing in Molecular Cell⁵ discussed what is known about how they coordinate their actions during the emergency repair called TLS (trans-lesion DNA synthesis): “The process requires multiple polymerase switching events during which the high-fidelity DNA polymerase in the replication machinery arrested at the primer terminus is replaced by one or more polymerases that are specialized for TLS.  When replicative bypass is fully completed, the primer terminus is once again occupied by high-fidelity polymerases in the replicative machinery.”  It sounds like the first-aid squad knows how and when to patch up things enough to get the patient to the surgeon.
9. Texas Tech:  Scientists in Texas, publishing in Cell,⁶ found another multi-talented molecular machine.  The rotor part of the V-type ATP synthase (see 02/24/2003 entry) does more than just help acidify vesicles.  It also has “an independent function in membrane fusion,” they found.  It is essential in the process of exocytosis – what neurons do to transmit their messages.  They found that mutant embryos had severe defects in synaptic transmission of nerve signals.  (This was found in fruit flies.)  By the way, the other form of this rotary motor, the F-type ATP synthase, was called “The World’s Smallest Wind-Up Toy” by Richard Berry in Current Biology.⁷  Researchers have figured out how to make the motor turn, using magnets.  He thinks scientists are on the verge of figuring out how the F₀ rotor converts proton flow into torque.
10. Ultimate Spa:  Last but not least, scientists at the Salk Institute last month announced a surprising solution to the puzzle of how embryos start their left-right orientation.  An “embryonic body wash” operated by cilia sweeps chemical signals across the embryo: “the foundations for the basic left-right body plan are laid by a microscopic ‘pump’ on the outer surface of the embryo’s underside that wafts chemical messengers over to the left side of the body.  This sets up a chemical concentration gradient that tells stem cells how and where to develop.”  The cilia rotate at a precise 40-degree angle to generate a current over the embryo.  The original paper in Cell contains movies of the action.

Sometimes we just have to rub it in: these are just a few samples from the flood of literature coming out each week in cell biology, biochemistry and genetics (check out another example from 01/27/2003).  A little overkill is needed once in awhile, a quadruple jolt of caffeine to make the Darwinists wake up and smell the coffee.  Almost none of these papers even mention evolution, and the ones that do only assume it: e.g., Myosin VI “might have evolved to provide unique kinetic characteristics that are potentially important for a reverse-directed motor.”  Do they really expect anyone to believe that any more?
    The papers are filled, on the other hand, with design language: motors, machines, mechanisms, coordinated action, synergy, regulators, signaling, strategies and much more.  This illustrates how useless Darwinism is; with apologies to Dobzhansky, nothing in biology makes sense in the light of evolution.  Intelligent design, by contrast – whether explicit or implicit – yields profound insights.  Let ID be the golden cord to show us the way out of the dark labyrinth where Charlie misled us long ago into the lair of the Minotaur, naturalism.
Next headline on:  Cell Biology • Genetics • Intelligent Design • Amazing Stories

We stand ready to help others in addressing the increasingly strident attempts to limit the teaching of evolution or to introduce non-scientific “alternatives” into science courses and curricula.  If this controversy arrives at your doorstep, I hope that you will both alert us to the specific issues in your state or school district and be willing to use your position and prestige as a member of the NAS in helping us to work locally.   (Emphasis in original.)

Bruce Alberts is like the out-of-touch king in the Wizard of Id cartoon.  A frantic messenger runs into the castle, breathlessly shouting, “The peasants are revolting!”  Unalarmed and undeterred, the king responds, “They certainly are.”
    So he sends out his PR Philistines to mop up the rebels.  Some of his advisors know not to underestimate the field (see 02/27/2004 entry).  The NAS Goliath can boast, but he had better be a match for stones of evidence.  Observing the Philistine ranks, Brad Harrub at Apologetics Press smells fear in the air.
    The new NAS website, with all the charm of a bureaucratic office building, may please academia but will probably backfire with the public.  In the first place, its publications are old.  It is still touting its very one-sided 1999 report Science and Creationism with all its fallacies and obfuscations.  It even advertises a 1990 report “The Search for Life’s Origins,” when much of the interesting biochemistry, and much of the contradiction to evolutionary assumptions, is more recent (see 02/06/2005 and 01/28/2005 entries).  Secondly, the website is completely one-sided, offering no debate.  Nowhere are evolution critics allowed to present their case in their own words.  Readers are expected to hear all the terms of the controversy spun by the Darwin Party hacks, complete with the usual straw man, equivocation, bandwagon, extrapolation and false dichotomy fallacies.^*
    If the NAS won’t stand up to the debate plate and answer the critics instead of disqualifying them out of court, this website is going to be perceived as nothing more than a power play, and will get no respect outside the Party Faithful.  There are too many people out there who will no longer take bluffing and evasion for an answer.  Yet bluffing and evasion appears to be official NAS policy.  Quote: “Given the organizational skills, experience, and political astuteness of those who promote creationism and Intelligent Design, it is suggested that you NOT agree to enter into direct debates with the proponents if you have not been involved with such activities before” (“Teaching the Science of Evolution”).  The very next sentence says, “Cell and molecular biologists have provided some of the most compelling evidence to support the theory of evolution and should therefore be among those who raise their voices the loudest to support science curricula that help students understand the processes of evolution.”  Ha!  In a day of molecular motors and machines, that is astonishing (see 05/18/2005, 05/17/2005, 04/04/2005, 03/14/2005 and 04/30/2005 entries for recent examples).  Does this paper provide any of said evidence?  Dead silence.  If these two quotes do not illustrate bluffing and evasion, let them come clean and show us how the process of science is served by avoiding debate and making sweeping, unsupported generalizations contrary to the evidence.
    Most anti-evolution websites freely quote the very best Darwinists and critique their original sources; Creation-Evolution Headlines, for instance, frequently provides extended quotes, in context, on both sides.  Why won’t the Darwinists do better than caricature their opposition?  Anti-evolution websites are mushrooming because people are tired of Darwinian dogmatism.  We’re waiting, NAS: we want to hear the latest Tinker Bell Tale about the origin of life, the origin of complex language translation and error correction by chance, the origin of molecular machines without an engineer, and the explosion of body plans in the fossil record.  That will at least make your new website entertaining.
Next headline on:  Darwinism • Education

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*Examples:
Straw man: caricaturing the opposition as religious kooks, even when they have PhDs in science.
Equivocation: defining science as naturalism; defining evolution as change; winning the debate by definition.
Bandwagon: claiming that all scientists accept evolution (see also Big Lie).
Extrapolation: assuming that because we observe microevolution, complete molecules-to-man Darwinism is established.
False dichotomy: compartmentalizing science and religion as non-overlapping domains, yet treating evolution as if it answers the big questions of religion/philosophy.

Computational prediction of global protein motion... suggests that enzymatic active sites tend to be placed near the hinges of the “jaws” of enzyme structures.
    Proteins self-organize into exquisitely precise structures, but the actual conformation of a protein fluctuates, and almost never coincides exactly with the average structure observed via X-ray crystallography or other methods.  Mounting evidence suggests that these induced motions play specific and essential roles in protein function....   (Emphasis added in all quotes.)

Stabilization of the transition state relative to the substrate is thought to be the key to enzymatic efficiency.  Static effects clearly play a major part via the electrostatic contribution of the positioning of polar residues.  The existence of a “dynamic effect,” however, is controversial, specifically the proposition that enzymes can channel thermal vibrational energy into modes co-directional with the reaction coordinate, thus making barrier crossing more likely.  Nevertheless, evidence is accreting to indicate a link between well-defined global motions and catalysis.

Computation of the normal modes of motion allowed the determination of the “hinges” or pivot points that separate regions of the protein moving in opposite directions, much like the end of a nutcracker.  In the vast majority of the enzymes studied, the catalytic residues were found to be located in a predicted hinge region.... This finding contributes a bioinformatic dimension to the field of functional protein dynamics and may allow improved functional annotation for the flood of newly solved protein structures.  The results also suggest an enhanced role for the global protein structure, which often has been viewed as a scaffold supporting the active site.  The study adds to the growing body of evidence that the fold determines global protein dynamics, suggesting a mechanism for allosteric signal transduction, functional impact of distant mutations, and other effects not explained by the chemistry of the active site.  In this view, enzymatic structures resemble a Pac-Man icon, with active sites located in the wedge-shaped opening, and the structure responsible for the “chewing” motion of the “mouth.”

Wonderful thoughts, devoid of evolutionary speculation.  Enzymes can no longer be viewed as floating wads of amino acid gunk, and not even as rigid tools like screwdrivers and hammers.  Now, we see them as power tools: “exquisitely precise structures” with moving parts, each part contributing to the task at hand.  This means that enzymes cannot tolerate many mutations.  Previously, biochemists thought that the active site alone was the most intolerant of mutations, but if this emerging picture of dynamic action is correct, even short sequences of amino acids distant from the active site may play vital roles in the overall function.  The game is not getting any easier for the Darwinists as Pac-Man keeps chewing through their assumptions.
Next headline on:  Cell Biology • Amazing Stories

As evolutionary theory, this is ludicrous.  Killing the owner of the uterus that is your only current chance to get your genes into the next generation (the evolutionary imperative), especially if she is caring for your current children and has a father or brothers who take exception to your uxoricide, is an excellent way to a dead end personally and genealogically.  Being the target of angry in-laws, not to mention life imprisonment or lethal injection, tends to limit one’s reproductive opportunities.   (Emphasis added in all quotes.)

The claim that works like “Murderer Next Door” are merely following data objectively in a search for truth is getting tiresome.  The very decision to seek a “scientific” validation for killing women represents a value judgment.  The fact that the claim makes no sense scientifically is almost secondary to that.

The unfortunate fact is that murder has proved to be a disturbingly effective solution to an array of adaptive problems in the ruthless evolutionary games of survival and reproductive competition.  It’s undoubtedly deeply disturbing to think that humans have homicidal circuits that get activated in certain circumstances, but that in no way implies approval or justification of murder.  Nor does it imply that murder is inevitable.  Rather, knowledge of the deep psychology of killing is required if we ever hope to prevent it.  Those who attempt to avoid this deep understanding by strident emotional appeals and cartoonish ridicule tread on dangerous moral ground.  The problem of murder can’t be solved by wishing away dark sides of human nature that we would prefer not exist.

“Anchored in evolutionary psychology” he says?  Ha.  That’s like a paper anchor in soft silt.  “Sound evolutionary biology” is an oxymoron.
    Buss’s theory is self refuting.  As an evolutionist, he cannot appeal to morality, yet look: he uses the words unfortunate, ruthless, disturbing, approval, justification, moral ground, dark sides of human nature, prefer and solved.  Each of these words rest on the assumption that we can make moral judgments between good and evil, right and wrong, and that murder is a moral problem needing a solution.  Why should murder be labeled “disturbing” or “dark” or a problem at all if it is a successful adaptive strategy?  Why, we should applaud the murderer for his evolutionary success.  Yet Dr. Buss says that it is his critics that are on dangerous “moral” ground for not comprehending his deeper understanding!  That shows how deep his understanding goes.
    Evolutionary psychologists are the gnostic gurus of naturalistic religion.  Who is Dr. Buss to offer us “knowledge” or “deep understanding” if it means that murder is hardwired into our circuits?  How is he to prove that just-so storytelling is not hardwired into his own circuits?  If we are the product of circuits that get activated by the environment, then knowledge and understanding do not even exist, and there are no problems to solve.  If people react to such foolishness with strident emotional appeals and cartoonish ridicule, well, if the shoe fits....
    Christianity teaches that murder is evil, that it is a consequence of the disobedience and rebellion against our Maker.  The Bible teaches that we are responsible to God for our actions.  Out of selfishness and lust and anger, murderers violate their conscience and act on their dark side of human nature.  Unredeemed human nature that leads to lying and murder really is dark, because it follows the lead of Satan, who was a murderer from the beginning.  All sin, including murder, incurs the righteous judgment of God, because we are each accountable for our deeds.  Evolutionary psychology gurus, on the other hand, claim that selfishness and ruthlessness are amoral, and ultimately good, because they are intrinsic factors in the mindless processes that produced our minds in the first place.  Choose you this day whom you will serve.
Next headline on:  Darwinism • Dumb Stories

It is a mystery why this particular glycosyltransferase evolved independently in roses.  The novelty of the RhGT1 enzyme therefore lies not only in its ability to catalyse glycosylation at two different sites on the anthocyanidin molecule but also in its apparent absence from other species.

Here is a small gap, but a gap nonetheless; no evidence for the evolution of this complex molecule and the enzyme that knows how to operate it – just an unconfirmed prediction from evolutionary theory.  Surprised?  Question: was evolutionary theory of any value in this investigation?
Next headline on:  Botany • Evolution

The lack of oceans of ethane and methane was a huge disappointment and surprise to planetary scientists.  They know that atmospheric methane is destroyed by the solar wind in short order – 100 million years as an upper limit (that’s only 1/45 the assumed age of Titan).  But they also expected the photolysis of methane to lead to the accumulation of hydrocarbons on the surface in the form of huge deposits of liquids.
    Another surprise is the rarity of impact craters.  What keeps the methane supplied, and what keeps the surface smoothed over for long ages, are now major puzzles for those accustomed to thinking in terms of billions of years.  Trying to get all that methane out of one volcano seems a stretch.  Even with hundreds of such vents, how long could that continue?
    The thought of a volcano erupting ice onto the surface of an alien moon, though, is pretty cool.
Next headline on:  Geology • Planetary Science

Hypocrites in the church of Darwin?  Would you trust this gang with your soul?
Next headline on:  Politics and Ethics

But it was very clear that the film was trying to situate science within the wider realm of belief.  The idea that human beings have been placed on Earth to discover the principles of the universe is not a position that stems from science; it is a metaphysical and religiously based conclusion.   (Emphasis added in all quotes.)

This was clearly an episode about power politics, not science.  Notice how the film passed two reviews that agreed there was no problem with the science; the museum backpedaled only because of the noise from barking Darwin bulldogs, most of whom have probably not even seen the film.  And what a weak excuse; it’s not that the film said anything outrageous, but rather that the Darwinistas don’t want to grant any credibility to the source.  That’s the genetic fallacy – can any good thing come out of Nazareth?  Well, come and see.
    Potts’ pot shot about the film putting the evidence into a metaphysical/religious context is absurd.  As an anthropologist studying evolutionary human origins, has he no metaphysics?  Of course he does: look at his chairing a series of lectures on “Science, Ethics and Religion” (in terms of human evolution, of course) for the AAAS recently; another example on National Geographic News shows him speculating about the evolution of modern human behavior (notice the absence of evidence).  Are these kinds of metaphysical dialogues forbidden by the Smithsonian?  Of course not.  Evolutionists shamelessly pontificate about the metaphysical/religious implications of their beliefs, right in the halls of science and before the mass media.
    For the Smithsonian to be consistent, they would have to outlaw films like Cosmos, Origins (09/29/2004) and Evolution (09/28/2001) and other pro-Darwinist films, which are replete with religious and metaphysical claims.  The inferences drawn in The Privileged Planet are understated and balanced, many of them coming from astronomers and biologists with no connections to ID.  They speak their own minds based on the evidence, something about which the Darwinians are profoundly silent.  In Darwinian movies, by contrast, the metaphysics are dogmatic and polemical, often imagineered with reckless abandon with no opportunity for rebuttal.  In sweeping generalities, Darwinians preach their philosophy of big-bang to man-as-god in homilies that would make a pope blush.  They take an inch of irrelevant fact and spin a mile with imagination, delivering their sermon outlines to animators to fill in the gaps.
    Like most institutions of Big Science, the Smithsonian has become a fundamentalist church of atheism (see next entry).  Despite the increase in its lavish facilities, it has degenerated so far from the philosophy of its first distinguished secretary, Joseph Henry, it is truly sad to see how it has been co-opted by leftist anti-religious propaganda.  Chief of the Darwinian KGB Eugenie Scott was “pleased by the swift steps the museum has taken” while other Party Faithful were even more aggressive, wanting the film canceled until they feared it would make martyrs of their political prisoners.
    As long as the news media and reporters perpetuate the false dichotomy and equivocation of “science” (Darwinian metaphysics) vs “belief” (non-Darwinian metaphysics), this pathetic war of heat will continue.  The Darwinians, the “most objectionable” fundamentalists according to Paul Johnson (see next entry), had better learn how to debate the evidence when the day comes that they can no longer take for granted their power to dominate the scientific institutions and prevent alternatives from being heard.
Next headline on:  Intelligent Design • Media

Of all the fundamentalist groups at large in the world today, the Darwinians seem to me the most objectionable.  They are just as strident and closed to argument as Christian or Muslim fundamentalists, but unlike those two groups the Darwinians enjoy intellectual respectability.
    Darwinians and their allies dominate the scientific establishments of the West.  They rule the campus.  Their militant brand of atheism makes them natural allies of the philosophical atheists who control most college philosophy faculties.  They dominate the leading scientific magazines and prevent their critics and opponents from getting a hearing, and they secure the best slots on TV.  Yet the Darwinian brand of evolution is becoming increasingly vulnerable as the progress of science reveals its weaknesses.  One day, perhaps soon, it will collapse in ruins.   (Emphasis added in all quotes.)

For all his worthy tirade against the Darwinists, Johnson seems to accept the big bang theory and cosmic time with uncritical gullibility.  Then he adopts a front-loading design philosophy, misreading Newton as having taught an impersonal Force.  Then, apparently after assuming the front-loaded design produced human beings, he inserts a divine intervention at the origin of language.  These strange thoughts diminish an otherwise interesting prophecy about the fall of Darwinism.
    Johnson also seems to know little about fundamentalism other than the yellow-journalism stereotype.  He defines it as stridency and closed-mindedness.  That is not what the term meant when Christian scholars like J. Gresham Machen used the word.  They were identifying what Biblical doctrines, what “fundamentals,” could not be compromised without cutting into the flesh of Christianity.  Would Johnson walk into many “fundamentalist” Christian churches today, he would see the opposite of stridency and closed-mindedness.  He would not see the image of Muslims toting AK47s and burning flags, screaming death to America.  He would not see the image of Darwinians censoring any opposition.  He would likely see humble and joyful people, singing praises to God, welcoming the stranger and asking, “How can I pray for you?”
Next headline on:  Darwinism

A simple statement of fact: there is no physics theory that explains the nature of, or even the existence of, football matches, teapots, or jumbo-jet aircraft.  The human mind is physically based, but there is no hope whatever of predicting the behaviour it controls from the underlying physical laws.  Even if we had a satisfactory fundamental physics ‘theory of everything”, this situation would remain unchanged: physics would still fail to explain the outcomes of human purpose, and so would provide an incomplete description of the real world around us.   (Emphasis added in all quotes.)

It is possible that what actually happened was the contextual emergence of complexity: the existence of human beings and their creations was not uniquely implied by the initial data in the early Universe; rather the underlying physics together with that initial data created a context that made the existence of human beings possible.  Conditions at the time of the decoupling of matter and radiation 14 billion years ago were such as to lead to the eventual development of minds that are autonomously effective.  Such minds are able to create higher-level order, such as the Hubble Space Telescope and Kurt Gödel’s incompleteness theorem, that embodies a purpose and meaning not in existence before.
    With this view, the higher levels in the hierarchy of complexity have autonomous causal powers that are functionally independent of lower-level processes.

Stored information plays a key role, resulting in non-linear dynamics that are non-local in space and time.  Brain functioning is causally affected by abstractions, such as the value of money, the rules of chess and the theory of the laser.  These abstractions are realized as brain states in individuals, but are not equivalent to them – James Clerk Maxwell’s theory of electromagnetism is not the same as any individual’s brain state.  Although such concepts are causally effective [i.e., they can lead an electrical engineer to apply them to an invention], they are not themselves physical variables.  Consequently physics per se cannot causally determine the outcome of human creativity; rather it creates the ‘possibility space’ to allow human intelligence to function autonomously.

Well, this goes to show that the debate over freewill and determinism is not argued only between theologians.  Ellis has just charmingly bluffed his way past a major logical gap in naturalism: why there is something instead of nothing, and especially why there is such astonishing complexity as in a human brain instead of nothing.  His answer: you can get something from nothing!  First, the particles emerge out of nothing.  Then, they create a possibility space out of which complexity “emerges” and takes over, becoming a new, autonomous entity, like a human mind, that can engender new levels of autonomy.  This is the old tornado-in-a-junkyard theory of the 747.  The junkyard is now to be understood as the “possibility space” of the jumbo jet.
    They just love that word emergence.  It’s the miracle word that produces any phenomenon needing explanation, from nothing.  Granting a little memory that can store information helps.  Presumably, that just emerges, too.  Can anyone demonstrate an actual new cause-and-effect space emerging from one below it and becoming autonomous?  Read Dembski’s No Free Lunch to see that it cannot be done; claims of emergence are exposed when perpetrators are seen sneaking information into the side door.
    The major flaw in this line of reasoning is to assume that possibilities yield probabilities and these, in turn, actualities – given enough time.  Like George Wald once blathered to his everlasting shame, “Time is in fact the hero of the plot.  The impossible becomes possible, the possible probable, and the probable virtually certain.  One only has to wait – time itself performs the miracles.”  No gambling addict could have more faith.  There is simply not enough time to expect the unguided emergence of just one protein molecule under the best of conditions (see online book), let alone the emergence of the simplest memory storage and retrieval system, whether in a beaver, bee, or Berkeley, to allow the hierarchy of autonomy to proceed onward and upward.
    Non-existence is extremely more likely than existence – yet here we are.  We do not need to just explain what might be, but what is.  One cannot bootstrap nothing into something.  That is equivalent to belief in magic.  The worldview that explains the something, including all the complexity of the human mind, its autonomy and its degeneration into nonsense and evil, is Christian theism.  Emergence must always be downward: the Lawgiver into the realm of law, the Creator into the realm of the created.  Which view is more in accord with physics as we observe it?  Maxwell has a lot more than electromagnetic theory to say about that.
    Out of nothing, nothing comes.  Whatever begins to exist has a cause.  If you can keep your head when all around you are losing theirs and blaming it on chance, the Universe is yours and all that’s in it, and what’s more, you’ll be a Mansoul, my son.
Next headline on:  Cosmology • Physics

A point well taken: if we cannot understand a star that looms large in our sky and is up all day, how much can we express confidence in our theories about points of light trillions of miles away?  To gain more appreciation of our sun, and our occulting moon, see the film The Privileged Planet.
Next headline on:  Solar System • Stars and Astronomy

Nice activity, surveying plants, but what’s evolution got to do with it?  This experiment continues the misperception that looking at microevolution will somehow demonstrate that bacteria can evolve into humans, given enough time, and enough small, incremental changes (see next entry and 08/20/2003 entry).  Charlie’s botanizing, though amateurish, was commendable; his storytelling was not.
Next headline on:  Darwinism and Evolutionary Theory • Botany

What if a flood of mutations struck in a short period?  Could it account for a wide range of mutational changes in the relatively recent past?  How would they know?  This result appears to undercut any remaining trust in the molecular clock, a device that was broken anyway (see 08/24/2004 entry).
    Kumar hit the nail on the head: evolutionary theory is never clean cut, and is always subject to distortion.  If evolutionists are trying to look at longtime history, good luck – because history cannot be put into a test tube.  Trying to decipher history from present observations of genes and proteins is messy business, subject to numerous assumptions that can be overthrown, such as this one.  Kumar said “The novelty of this work is that he [Lahn] used a large amount of data.”  What does this tell you about the evolutionary assumptions built on far less data?
  The Darwinists are certainly not throwing in the towel over this latest genetic earthquake.  It just illustrates that assumptions in science, trusted for decades, yielding thousands of scientific papers, can be flat wrong.
Next headline on:  Darwinism and Evolutionary Theory • Genetics and DNA

No topic in the world of science and Christianity has created the intensity of discussion and disharmony with evangelicals as the source of biological diversity.  Today’s spirited discussion often pits Christian vs. Christian and scientist vs. scientist.   (Emphasis added in all quotes.)

Nussbaum allowed David Wilcox (Eastern U) to get away with a horrendous straw man argument.  Wilcox puts words into an imaginary student’s mouth when facing evolution in biology class: “Why do I have to learn this stuff – don’t you know that God hates science?”  Good grief.  Has anyone outside an insane asylum ever said that?  In response, Wilcox triumphantly touts theistic evolution as the winner with this half-truth: “God doesn’t hate science – he invented it.  We try to get them to see that evolution happened and it’s not so scary... that evolution is the way God did it.”  Well, if Nussbaum’s intent was to make this proponent of “evolutionary theism” make a fool of himself, he succeeded.  Runner-up was Ken Miller again with this borderline blasphemous straw man: “Their [the creationists'] God is like a kid who is not a very good mechanic and has to keep lifting the hood and tinkering with the engine.”  Who’s he kidding?  It’s the Darwinists who worship Tinker Bell (see 03/11/2005 commentary).
   Other than that, Nussbaum’s article is fairly balanced, though gloomy.  He seems to see the most light in the two compromise views that will never work, theistic evolution (an oxymoron) or non-overlapping domains (a false dichotomy).  The main flaw in the article is the covert treatment of evolution as science instead of religion.  That is the hidden assumption in much of secular reporting.  It must be exposed for what it is: a big lie.  Therapy requires mastering the Baloney Detector, then reading all the chain links on Darwinism and Evolutionary Theory in these pages.  Follow-up treatment can include digesting our online book.
    The evangelicals who are not gloomy and conflicted are the young-earth creationists and intelligent design people.  Most of them are vibrant, motivated, excited, passionate, interested, and devoted.  Maybe they’re onto something.  Read this, especially the first bullet item.
Next headline on:  Evolution • Theology

I am a public high school biology teacher, and I do an unusual thing.  I teach my students more than they have to know about evolution.  I push them to behave like competent jurors – not just to swallow what some authority figure tells them to believe – not even me – but rather to critically analyze, with an open mind, the evidence set before them....
Teenagers, not surprisingly, find this approach exhilarating.   (Emphasis added in all quotes.)

Evolution can be taught skillfully and poorly.  Anti-evolution can be taught skillfully and poorly.  Reporting on either can be done skillfully or poorly.  Here are two examples for you to evaluate.
    No reputable anti-evolutionist wants students to become afraid of the controversy over evolution and become tempted to shut up.  No reputable pro-evolution teacher should want the class to be indoctrinated, nor have a student feel browbeaten for having honest questions about evolution.  Cowan seems to have hit the sweet spot.  Can anyone really doubt that learning to think critically is going to help the next generation of scientists?
    The only losers in the Darwin Wars, when fought fairly, are the indoctrinators who don’t want the students to know about Haeckel and Piltdown and the other dirty laundry in the textbook.  Watch the film Icons of Evolution, including the Q&A in the bonus features, for a fuller defense of the “teach the controversy” approach.  And teachers: feel free to use our eight-part, non-religious curriculum (see 02/11/2005 commentary) for supplementary material the textbook left out.  Watch those young eyes perk up....
Next headline on:  Education • Evolution

Unambiguous indicators of gender in dinosaurs are usually lost during fossilization along with other aspects of soft tissue anatomy.  We report the presence of endosteally derived bone tissues lining the interior marrow cavities of portions of Tyrannosaurus rex (MOR 1125) hindlimb elements, and hypothesize that these tissues are homologous to specialized avian tissues known as medullary bone.  Because medullary bone is unique to female birds, its discovery in extinct dinosaurs solidifies the link between dinosaurs and birds, suggests similar reproductive strategies, and provides an objective means of gender differentiation in dinosaurs.   (Emphasis added in all quotes.)

The existence of avian-type MB in dinosaurs has been hypothesized but not identified.  In part, this could be because of taphonomic bias [i.e., fossil-hunters not expecting to find it], because the death and fossilization of an ovulating dinosaur would be comparatively rare.  Additionally, MB in extant birds is fragile, the spicules separating easily from the originating layer (fig. S1).  Dinosaur MB may separate and be lost from overlying CB in a similar manner during diagenesis [i.e., the hardening of sediment into rock].

This is incredible.  How can these scientists ignore the obvious?  There’s no way this bone could be so old, but all they can think about are connecting homology dots between dinosaurs and birds by circumstantial evidence.  Did they see the dinosaur laying eggs?  No.  Did they prove this is medullary bone?  Perhaps.  Does it prove an ancestral relationship if the dinosaur did have medullary bone?  No.  Does that matter?  Not much.  What really matters about this story is the age of the specimen.  If this specimen is only a few thousand years old, none of this dino-bird homology matters: this blows apart the entire tale of dinosaur evolution.  Belief in millions of years and the rest of the evolutionary timeline takes a staggering blow.
    Look at them strain at a gnat about medullary bone, but swallow a camel about the age.  Instead of expressing shock and anguish, instead of repenting in dust and ashes for spreading lies about dinosaur ages for the past century and a half, they grin and say, “We’ll ah’ll be.  Ain’t it amazin’ how these soft tissues survived for sempty millon yeers.”  It makes one think their brainwashing is so complete they would say the same thing if face to face with a living dinosaur.  Absurd?  Not at all: they already do it with living fossils much “older” in their time scheme.
    Folks, consider the facts in this story.  Soft tissues from a bone of T. rex, everyone’s favorite monster, were found in Montana.  The specimen preserves fine microscopic detail and even pigment.  The material is still flexible and not fossilized.  We know that medullary bone in living birds is “fragile, the spicules separating easily from the originating layer.”  The initial reaction by the scientists was disbelief, because no known process could preserve soft tissues like this for so long.  (And what a thought to consider that this monster might have been alive just a few thousand years ago!)

Though this is a spectacular example, we should not think that it is an isolated case.  Many insects from around the world have been found preserved in amber (fossil tree resin), with even hairs and veins in the wings preserved in exquisite detail.  Some still contain bacteria in the guts and DNA fragments have been extracted.  Often the specimens are indistinguishable from living species, yet claimed to be millions of years old.  Yet we know that tree resin weathers rapidly and is usually not produced in quantities that can extend for meters and entomb frogs and large insects, which would normally float and decay before being preserved.  On what grounds can evolutionists claim such fossils are ancient?  (For more information on fossil amber, get the presentation “Amber – New Insights” by Dr. Harald Binder, available at Access Research Network.)

The only way anyone can claim these dinosaur bones are tens of millions of years old is by prior commitment to a belief system that demands forcing all evidence into a long, drawn-out process of evolution.  The young-earth creationists have a great opportunity here.  They and anyone still unbrainwashed about geologic time, and all who respect hard evidence, should hammer away relentlessly at the credulity of the Darwinists, demanding that they explain how a specimen like this could survive even one hundredth of that much time.^*  If you see this bone on exhibit at the North Carolina Museum of Natural History, be nice, but come prepared with good questions and reputable background information.  Don’t take bluffing and evasion for an answer.  Undoubtedly, after enough exasperation, they will probably provide the docents a manual on how to deal with those pesky visitors who won’t buy the script, but keep demanding, “Just the facts, ma'am.”^**
Next headline on:  Dinosaurs • Birds • Fossils • Dating Methods

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^*Here’s an opportunity also for an unbiased lab.  Take an ostrich specimen with intact medullary bone, put it into similar conditions, and monitor the rate of decay.  It may years or even decades to get some valid data, but it should be possible to set some upper limit on how long the tissues could be expected to survive.
^**For an example of the impact that polite questioning can have, see the May Scientist of the Month story.

Dekker says he’s puzzled by the outcry but chalks it up to a “Pavlov reaction” to ID.  “Many scientists associate it with conservative Christians, Kansas, and George Bush—so it has to be bad,” he says.  He hopes the debate will get more serious after the impending publication of a collection of 22 essays about ID and related themes, most of them by Dutch scientists, which he has co-edited.  Van der Hoeven has agreed to receive the first copy of the book at a ceremony in The Hague next week.   (Emphasis added in all quotes.)

This is another remarkable story on the growing influence of the intelligent design movement around the world, even in liberal Holland where the words George Bush, conservative Christianity and Kansas produce Pavlovian barks.  Enserink points out that Holland is “not quite Kansas—after all, this is the country that legalized euthanasia and invented gay marriage.”  Yet even there a small but committed cadre of scientists, politicians and laymen find the arguments for intelligent design compelling, and they want the debate to be heard.  They are not castrating Darwin.  His impotence is his own (see next two headlines).  Dutch scientists are justly proud of their layman forerunner, the staunch Christian creationist from Delft, Antony van Leeuwenhoek – the father of microbiology – who helped lead science out of the Dark Ages (if there ever was such a period).  He demonstrated how creation-oriented science can be the best in the world, full of vitality and motivation and excellence.  When all the Darwinists can do is scream “Dark Ages,” you know their sunset is coming.  But when it is sunset on one side of the worldview, it’s sunrise on the other.
Next headline on:  Evolution • Education • Intelligent Design

The authors argue that there is more to heredity than genes; that some hereditary variations are non-random in origin; that some acquired information is inherited; and that evolutionary change can result from ‘instruction’ as well as selection.  This may sound rather revolutionary, even preposterously close to lamarckism.  But Jablonka and Lamb build on evidence from standard research in evolutionary and molecular biology, and their case should be examined on its merits, rather than being dismissed by a knee-jerk reaction.   (Emphasis added in all quotes.)

The second meaning is actually closer to the core of Lamarck’s ideas, which are rarely, if ever, read by modern biologists.  The suggestion is that some heritable, adaptive changes come not from natural selection, but from the action of evolved internal systems that generate non-random ‘guesses’ in response to environmental challenges.  Examples are not hard to find, contrary to the assumed wisdom of standard neo-darwinism.  Consider the existence of ‘hotspots’ that make mutations in certain regions of the genome much more likely than in others.  Or the impressive ability of some bacteria to increase the mutation rate of a specific gene involved in the metabolism of a given amino acid when that amino acid becomes scarce in the environment.

If one accepts this bold, expanded version of heredity and evolution, it turns out that evolution can proceed very rapidly and phenotypic modification can precede genetic changes.... Indeed, changes at the genetic level will often simply stabilize adaptive modifications that are initiated through phenotypic plasticity [i.e., acquired characteristics], epigenetic control mechanisms, or behavioural and symbolic means [i.e., social/language communication from parent to offspring].  This is a framework that would greatly help to solve old problems in evolutionary biology, such as the origin of novel structures [see 08/20/2003 entry], and even the appearance of what ‘intelligent design’ proponents refer to, rather nonsensically, as ‘irreducible complexity’.  This wouldn’t require the abandonment of neo-darwinism, but rather its expansion beyond what Ernst Mayr contemptuously labelled ‘bean-bag genetics’.

The clamour to revise neo-darwinism is becoming so loud that hopefully most practising evolutionary biologists will begin to pay attention.  It has been said that science often makes progress not because people change their minds, but because the old ones die off and the new generation is more open to novel ideas.  I therefore recommend this and the other books I mentioned on the future of evolutionary theory to the current crop of graduate students, postdocs and young assistant professors.  They’ll know what to do.

They’ll know what to do, all right: they’ll chuck Chuck and baptize Jean-Baptiste into the dustbin of discredited prophets, and embrace intelligent design.  Like Sutherland in the next article below, Pugliucci and his champions believe that specified complexity and optimization can emerge spontaneously, without purpose or direction, as long as there is a need.  But that fallacy is not just with neo-Darwinism and its reductionist genomics; it is with any theory that fails to include information as a fundamental property of the universe.  No combination of chance and natural law will produce information.  Think of a blank DVD and one containing microscopic pits encoding the latest Star Wars movie: they have the same mass and physical properties.  It is the information content that makes all the difference when you insert them into a DVD player.  Similarly, to believe that the information content in the genome and in all the gene networks and epigenetic controls to which Pugliucci refers could have arisen by naturalistic means cannot be done without assuming naturalism at the outset.  All our common experience teaches that information arises only from intelligent causes.
    What this book review does, despite its dismissive ridicule of intelligent design, is strengthen the strategic posture of ID.  It advertises the weaknesses of the Darwin camp to the enemy.  The “clamor to revise neo-darwinism” has risen to a fever pitch within the Darwin camp, and can no longer be ignored, except by the Old Guard who have grown deaf with age.  The phrase “irreducible complexity” has rattled the evolutionary generals:
“Quick: we need a counterattack,” they strategize.  “How’s the neo-Darwinian antidote working?”
“Too weak,” the technician responds [see 10/14/2003 entry]; “Their weapons have developed immunity to it, and we’ve found it incapable of protecting our own soldiers.  It’s not as potent as we thought it was.”
“Anything else in our strategic arsenal?”  [See 07/23/2004 entry.]
“Nothing new, General.  Most of our weapons were forged in the 19th century.”
“Well, then, did anything work well before Chairman Charles?”
“We could resurrect an older weapon used with partial success from time to time, even by Darwin,” a lieutenant responds [see 10/14/2003 and 07/02/2004 entries].  It was invented by General Lamarck.”
“We can’t use that; it’s broken.  Everybody knows that.”
“We’ve got to do something, General.  Let the young recruits try it and see if they can get parts of it to work this time.”
    The intelligent design strategists, like Gideon spying around the tents of Midian (see Judges 7), are listening in on all of this.  Can a loaf of barley bread overturn ten thousand tents?  It can, either when the tents are made of wind held together by fog, or when there is supernatural power in charge.  It appears the I.D. camp has both advantages.
Next headline on:  Darwinism and Evolutionary Theory • Intelligent Design

The use of optimization has allowed biologists to move from merely describing patterns or mechanisms to being able to predict, from first principles, how organisms should be designed.  Optimality models are based on three elements: the choices available; what is being optimized; and the constraints.
    Physiologists have used optimization to answer a wide range of questions about animal morphology.  For example, optimization has been invoked to predict the design of a bone of given weight that minimizes the risk of breaking or buckling; the speed at which it is most efficient to switch from running to walking; and the gut design that provides the highest energy gain from a given diet.  The prediction of the triplet code as the most parsimonious means of coding 20 amino acids using the four bases of DNA is another successful example of this methodology.   (Emphasis added in all quotes.)

A considerable strength of using optimization is that once we understand why organisms are as they are, then it should be possible to understand how they will respond to new conditions.  Optimization can therefore be used to understand behaviour, and to predict population dynamics, in new environments, such as those resulting from habitat loss or a rise in sea level.
    There are increasing calls for biology to be predictive.  Optimization is the only approach biology has for making predictions from first principles.  The wider adoption of these ideas right across biology should reap ample rewards.

Sorry, Bill.  You can’t get the blood of design from a turn-up of natural selection.  Necessity is the mother of invention only when intelligence guides the process.  The only thing nature is good at optimizing is entropy.  The optimization approach will only make sense when design scientists oust the naturalistic usurpers from biology.
Next headline on:  Evolution • Dumb Ideas

Why should the Darwinists be alarmed at this decision by the Smithsonian to co-sponsor the film?  It’s a private showing.  The film makes a pretty mild proposition that there are aspects of our universe that seem inexplicable by chance, and that there might be some grand design or purpose behind it.  Five scientists at the American Museum of Natural History already agreed that our solar system appears special (see 04/04/2005 story).  One of the founders of the Smithsonian, the great American physicist Joseph Henry (see July 2004 Scientist of the Month) would be pleased.
    Most of the critics who are up in arms act like they haven’t even see the film.  As for the Amazing Randi, the most amazing thing about him right now is his inconsistency.  He exposes those who fool others, but fails to see how he is fooling himself (see 10/06/2000 story).  His tactic is bound to backfire and only give the film more publicity.  Randi should stick to what he is good at: fighting faith healers and psychic surgeons.  Would he have offered the Smithsonian money to stop Michael Faraday and Joseph Henry from doing stage demonstrations?  Doubt it.  Come on, all you materialist skeptics; skepticism is good to a point, but sometimes you need to aim your baloney detectors at yourselves.  Instead of censorship, how about some debate about the scientific facts?  Since Randi doesn’t appear up to debunking what cannot be debunked, because it is reinforced in the film by many respectable scientists he himself respects, he is making a pseudoscientist of himself.  Now the promoters of the film have a new advertising angle: Come see the film The Amazing Randi doesn’t want you to see!
Next headline on:  Intelligent Design • Media

Planetary science is not exactly batting a thousand these days, even without curve balls.  Looks like she didn’t accept the date when sports dropout McFly proposed, “Amalthea, you are my density... er, I mean, my destiny.”
Next headline on:  Solar System

Even if Mars had lots of water, and even if its atmosphere was able to shield out the harmful radiation reaching the surface, it would not necessarily have had life.  This just erodes the hopes of astrobiologists even further.  About the only lively thing going on is the occasional dust devil passing by (see movie taken by Spirit).
Next headline on:  Mars • Geology