Paley’s Watch Found in Bacteria   10/31/2008    
Oct 31, 2008 — A clock with cogs, gears and ratchets that keeps accurate time – what more could William Paley wish for?  The 18th century natural theologian used the illustration of stumbling upon a watch in a heath as an example of reasoning from design to a Designer – as from watch to watchmaker.  Skeptics like David Hume challenged such reasoning of the natural theologians as a mere argument from analogy: living things are very different from mechanical machines, he argued.  One can only wonder how their debate would unfold with the discovery of a ticking watch inside one of the simplest forms of life.
    Scientists have long wondered how living things keep time.  We are all aware of our own natural cycles throughout the day.  Organisms without eyes and ears, though, like bacteria, also keep time with diurnal cycles.  How do they do it?  The secret has only been coming to light in the last few years (see 05/17/2005)  Johnson, Egli and Stewart wrote a review article in Science this week that describes what is currently known about the circadian clock present in cyanobacteria.¹  They could not help but use mechanical terms for this biological machinery.  It began right in their opening paragraph:

An endogenous circadian system in cyanobacteria exerts pervasive control over cellular processes, including global gene expression.  Indeed, the entire chromosome undergoes daily cycles of topological changes and compaction.  The biochemical machinery underlying a circadian oscillator can be reconstituted in vitro with just three cyanobacterial proteins, KaiA, KaiB, and KaiC.  These proteins interact to promote conformational changes and phosphorylation events that determine the phase of the in vitro oscillation.  The high-resolution structures of these proteins suggest a ratcheting mechanism by which the KaiABC oscillator ticks unidirectionally.  This posttranslational oscillator may interact with transcriptional and translational feedback loops to generate the emergent circadian behavior in vivo.  The conjunction of structural, biophysical, and biochemical approaches to this system reveals molecular mechanisms of biological timekeeping.

The benefit of a clockwork that is imperturbable even when buffeted by the massive intracellular changes of cell division could have provided an evolutionary driving force for convergent circadian clock mechanisms among diverse organisms.
    We now recognize KaiABC as a dynamically oscillating nanomachine that has evolved to precess unidirectionally and robustly. 

Oh, for the sight of David Hume and Charles Darwin being confronted with a ticking clock inside a “simple” cell.  We can get an idea of their reaction, though, by looking at the fact that the three authors of this review, after having described an intricate mechanism of oscillators, ratchets and feedback loops, attributed it all to evolution.  The many biochemists aware of these and other exquisite molecular machines follow suit.  In spite of overpowering evidence for design, their minds are made up: they will follow Charlie to the bitter end and die with him rather than acknowledge design.
    The Apostle Paul said in Romans 1 that the evidence for God and His attributes is clearly seen in creation, so that men are without excuse.  Each generation has evidence of sufficient clarity for its knowledge base.  For the Romans and Egyptians, the diurnal cycles of the sun, moon and stars have been more than sufficient to remove their excuses for unbelief and mistaken belief.  For today’s scientists, the diurnal cycles of nanoscopic protein clocks throughout life is more than sufficient.  The true challenge ahead is not just to delve deeper into the molecular nature of the design we already see, but to hold it up for display and preach the implications, so that it takes effect in the human mind – as Paul said, “casting down imaginations, and every high thing that exalts itself against the knowledge of God” (II Corinthians 10:5; cf. 01/17/2007).
Next headline on:  Cell Biology • Amazing Facts

FrankenTitan Comes to Life   10/30/2008    
Oct 30, 2008 — There’s electricity at Titan, the large moon of Saturn.  That can only mean one thing: life!  “Electricity Found on Saturn Moon--Could It Spark Life?” asked a headline on National Geographic News by Rebecca Carroll.  Visions of spark discharge tubes in a mad scientist’s lab arise in the imagination.  “Recently identified electrical activity on Saturn’s largest moon bolsters arguments that Titan is the kind of place that could harbor life.”
    Carroll quickly pointed out that at -350° F, any Titanian life would not resemble “life as we know it.”  Initial indications of electrical activity in the thick atmosphere of this unusual moon have been confirmed in data from the Huygens Probe that landed in 2005 (see 01/15/2005, 01/21/2005).  With that spark of imagination, the L-word leaped up from the reporter’s table:

But a new study reports faint signs of a natural electric field in Titan’s thick cloud cover that are similar to the energy radiated by lightning on Earth.
    Lightning is thought to have sparked the chemical reactions that led to the origin of life on our planet....
    Jeffrey Bada, of the Scripps Institution of Oceanography, believes the process that allowed lightning to spark life on Earth is universal and could happen in many environments—including on Titan.
    Confirmation earlier this year of Titan’s hydrocarbon lakes makes the Saturnian moon the first place other than Earth where open bodies of liquid have been found.
    Hydrocarbons are organic molecules, and the fact that they exist in large quantities on Titan suggests that life could take root there under the right conditions.

Titan’s water is currently frozen into chunks as hard as granite.  If those ice “rocks” were to melt, however, the environment could become more hospitable to the building blocks of life.
    With liquid water, the planet could host the formation of amino acids and then full proteins, which drive all biochemistry and set the stage for more complex molecules.
    “I look at Titan as a big, frozen, prebiotic casserole,” Bada said, referring to the state before the emergence of life.
    “The idea that life could be widespread in the universe, I think, is very credible.”

Creepy.  To learn about the real Frankenstein, listen to this podcast.  Truth is stranger than fiction.
Next headline on:  Solar System • Origin of Life • Dumb Ideas

1. Words demean things:  Apparently the editors of Nature have had it with certain clichés.  One editorial, published also on Nature News, pointed out the ambiguity of popular words and phrases used in scientific papers and by science reporters.  The editorial began,

   To a great extent, science is about arriving at definitions.  What is a man?  What is a number?  Questions such as these require substantial inquiry.  But where science is supposed to be precise and measured, definitions can be frustratingly vague and variable.

   As examples, the editorial reviewed the terms paradigm shift, tipping point, race, epigenetic, complexity, stem cell, consciousness and significant.  Those terms may seem intuitively obvious but in fact have multiple definitions. For the word consciousness to have meaning, for instance, there must be a physical basis for it – but none has been found.  And significant is in the eye of the beholder, despite mathematical crutches like p-values that lend a false air of confidence in scientific results.  Scientists often use a 5% confidence level as a measure of significance.  That number, though, is an arbitrary convention – and often a useless one:

   Even if a result is a genuinely statistically significant one, it can be virtually meaningless in the real world.  A new cancer treatment may ‘significantly’ extend life by a month, but many terminally ill patients would not consider that outcome significant.  A scientific finding may be ‘significant’ without having any major impact on a field; conversely, the significance of a discovery might not become apparent until years after it is made.  “One has to reserve for history the judgement of whether something is significant with a capital S,” says Steven Block, a biophysicist at Stanford University in California.

2. Class warfare:  What do we mean by a class of objects?  Take terms like species and planet: which objects belong in the class, and which are excluded?  It’s not always easy to decide, said Jeffrey Parson and Yair Wand in an essay in last week’s Nature.¹  The authors illustrate problems with these two examples.  Look at the conflict over Pluto: is it a planet, a minor planet, or a plutoid?  Depending on which properties of objects in space are considered useful to humans, it could be any one of these things – yet Pluto itself hasn’t changed.  “Plutoid” is a recently made-up word about a class of objects of which Pluto is the best-known example.  Just because the International Astronomical Union declares that from henceforth and forevermore Pluto is a plutoid, that does little more than provide a consensus for human beings and their nomenclature.  Similarly, the term species contains considerable uncertainty, as even Ernst Mayr realized when he tried to define a species as a class of organisms that can produce fertile offspring (the “biological species concept”).  Too bad that doesn’t work for the vast majority of organisms – asexual microbes and fossils.
       Some classifications can lead to false and even fatal results.  Consider the word disease, which originally just meant discomfort – or “not at ease.”  The classification of diseases has usually been centered on etiology, or causes of disease.  These fall into 3 subclasses: genetic, environmental or pathogenic.  For nearly 40 years, the authors said, doctors misdiagnosed ulcers because they could not bring themselves to believe that a bacterium, H. pylori was capable of living in the acidic environment of the stomach.  “When considering the reasons why the bacterial hypothesis was missed for such a long time (and then not readily accepted), the main problem was the misattribution of the property ‘cannot grow in the acidity of the stomach’ to the class of bacteria,” they explained.  “Re-evaluating this fundamental property involved a major mind-shift that was difficult to accept.”
       Classification is a human enterprise.  The authors gave an evolutionary spin on this skill: “Classification ... is recognized as an evolved mechanism that supports survival.”  Supposedly it helps humans get food and shelter.  They did not ask whether lions and lizards needed to evolve the mechanism to sort out their food and shelter, too.  They tried to distinguish between “categories” and “classes” by defining the former as a group of objects with shared properties, and the latter as a category that allows humans to “infer further information” consistently “over a reasonable time period.”  A little reflection, however, shows that they have simply substituted the word class for a meta-category with the same difficulties.  The information that can be inferred from a class is simply a collection of objects with shared properties – things that humans find useful.  Their final paragraph, though, revealed that they are aware of the main pitfall of classification: it happens in the mind, not in the external world.

   Taking a classification perspective on scientific discourse suggests a sequence of questions to ask when studying a domain of phenomena.  What are the properties of interest of these phenomena?  Are there stable sets of properties common to these phenomena?  Are there stable relationships in some of these sets?  And finally, and most importantly, what is the evidence or rationale that these relationships reflect the true nature of the phenomena?  This perspective has two important implications.  First, scientists should make every effort to ensure that the assumed relationships among properties are indeed correct.  Second, rather than arguing over which of several classification schemes is preferable, researchers should recognize that several correct and useful schemes can coexist.  And overall, scientists should recognize that classification happens in the mind and, as a result, it can be influenced by beliefs and emotions.  This is where science can go astray.

3. The human element:  The lead editorial in Nature last week brought these lessons home to the human species.  What does it mean to be human? the editors asked.²  The Delphic oracle may have advised Know thyself, but that is often hard to follow, they said.  Watch the editors balance their confidence in Darwin’s ability to help us know ourselves with doubts about the evidence:

   Modern science can help, but using it to uncover truths about ourselves can also be fraught with difficulty.  Consider, for example, that an important first step towards understanding contemporary human behaviour – establishing the evolutionary context in which it emerged – means piecing together odd scraps of evidence left by our hunter-gatherer ancestors tens of thousands of years ago.  The paucity of data makes it all too easy to come up with untested, and even untestable, Darwinian versions of Rudyard Kipling’s Just So Stories.

   After acknowledging that science’s just-so chickens have come home to roost, the editors resurrected an old conflict that illustrates the impossibility of speaking objectively about ourselves without wandering into politics:

   Another major challenge for researchers is being objective about a topic as philosophically, politically and ethically charged as human nature.  Take the sociobiology wars of the 1970s and 1980s.  Left-wing scholars rejected biological explanations for phenomena such as gender roles, religion, homosexuality and xenophobia, largely because they feared such explanations would be used to justify a continuation of existing inequalities on genetic grounds.  The resulting debates became hugely political.
       The combustibility of the interface between science and society is one major reason for the extraordinary fragmentation of research that tackles human behaviour.  In part because of the sociobiology battle, most social scientists still steer clear of using evolutionary hypotheses.  And even researchers who do work under the unifying framework of evolution tend to fall into distinct camps such as gene-culture co-evolution or human behavioural ecology – their practitioners divided by differences of opinion on, say, the relative importance of culture versus genes.

   The editors clearly think that evolutionary theory deserves to be a unifying theme, but have just cast doubt on the evidence behind it and the pragmatics of using it.  They attribute the problems to the complexity of our species and the lack of interdisciplinary communication.  In a belief that their magazine can help, they said they are starting a series of essays which, though they might make for “uncomfortable reading,” will try to draw lines between human evolutionary prehistory and the complex societies we live in.  The first was by Pascal Boyer about the evolution of religion.  Did it accomplish its purpose?  See our review in the 10/26/2008 entry.

It was good for Nature to point out these problems with scientific terminology.  Unfortunately, their brains are so completely sold out to Darwin they are incapable of looking in the mirror.  That’s why one moment they can be admitting the evidence is so scanty it gives ease to untested, untestable Just-So Stories about human evolution, then the next moment they give their editorial blessing to a stupid Just-So Story about the evolution of religion (10/26/2008).
    Philosophy of science is a vital topic for anyone interested in science or apologetics or both.  In philosophy of science you learn to ask questions that scientists themselves rarely ask.  Consider the important topic of classification, brought up in bullet 2 above.  Scientists too flippantly invoke class terms that are totally subjective when scrutinized.  For instance, what is a predator?  We think we understand the term, but in the class of predators you can find snails, tigers, and even the Venus Flytrap.  The differences between these objects in the class predator seem more significant than the property they share: that they eat animals.  In addition, each object belongs to multiple other classes that either distinguish it or include it: organism, vertebrate or invertebrate, plant or animal.  The class you focus on is the one that is useful at the moment.  If you are playing “Twenty Questions,” for instance, the categories initially useful to you are animal, vegetable or mineral, where animal could be anything from a flatworm to a giraffe, vegetable could be anything from algae to a redwood tree, and mineral could include diamonds and space stations.  A corollary of this idea is that classes are merely human constructs – not necessarily ways of dividing up the world as it really is, or as Plato is said to have worded it, “carving nature at its joints.”
    In his excellent lecture series on philosophy of science for The Teaching Company, Jeffrey L. Kasser used a humorous illustration.  He invented a word broccosaxodile, which he defined as “anything that is broccoli, a saxophone, or a crocodile.”  While one might question the usefulness of such a composite classification, he asked if it is any less meaningful than predator which, as we said, includes things just as diverse.  “Predator” is just a shorthand word for a composite category that we could just as well call a “snail-tiger-VenusFlytrap.”  Let’s add another example: what is a fossil?  If you immediately picture bones in rock, you are ignoring the fact that fossils can include whole insects in amber complete with their soft tissue, footprints, petrified wood, and mere impressions of jellyfish or leaves, like shadows, without any bones at all.  Fossils are not permanent, either: the dinosaur trackways in the entry below (10/28/2008) are eroding and will eventually disappear.  In that sense, a corpse in a morgue is a fossil, or the ashes of a cremated person sitting in a bottle in the heartbroken spouse’s bedroom.  (Not to be morbid, but it is almost Halloween.)
    A classification is meaningless without a context in which the term is useful to some human being for a subjective purpose.  There is nothing objective about a class if you want to think of it as referring to something that is “out there” in the world which scientists “discover” without bias.  This should be a lesson to evolutionists who think they are talking objectively when they use class terms like missing link, transitional form, ancestors, phylogenetic tree, homologous traits or innovation.  Such terms are employed for their utility – in this case, the utility of making evolutionary theory appear scientific.

Application.  Let’s apply what we’ve learned to a Biblical example some find embarrassing.  Many skeptics have ridiculed the Bible for classifying bats with birds in Leviticus 11:13-19 (see EvidentCreation.com).  OK, their point is?  This classification was amply useful to Moses, who was helping the Israelites distinguish what they were allowed to eat.  The property apropos to their circumstances was clean and unclean edible animals.  Moses, or God for that matter, was under no obligation to use modern scientific taxonomy for the purpose.  In fact, it would seem much more helpful to Israelites wandering in the wilderness to point out which of those things flying around in the dark was safe to eat.  Those of you who have camped in the desert know that swifts and bats can look very similar in the way they dart about.  Formally, we can say that the property at issue in the class being defined was “flying things” – call them “volant vertebrates” if it makes you feel better – not whether the things had fur or feathers or laid eggs.  Moreover, it would be an unfair disparagement of the mental capabilities of people who grew up in the advanced Egyptian civilization and their well-educated leader to assume they didn’t know the difference between birds and bats.  We mustn’t be chauvinistic.  They probably possessed more savvy about nature than the typical modern couch potato.

Exercise.  Teachers and home-school parents: here is an opportunity to introduce your precocious young thinkers to some philosophy of science.  Have them invent categories similar to broccosaxodile (above) and make lists of objects that fit.  Is the category useful in some way?  Does it allow inferring additional information?  Which members belong to other categories?
Silly categories: Make up your own silly category and defend its usefulness: vege-toy-mobiles, dirt-bike-chocolate, sister-TV-cotton (anything that is either a sister, a television, or made of cotton), etc. 
Trivial categories: Round things, small potatoes, friends, food, containers, pets, creeping things, rhyming words, oxymorons, shapes, etc.  Think of more.  In what circumstances are these useful categories?  What are examples of extremely different things that can fit in the same category?  Can you dream up a story to explain how the category evolved?
Scientific categories:  omnivore, migratory species, gene, hybrid, moon, cloud, field, particle, wave, force, reagent, network, factor, family, biome, ecosystem, riparian dweller, marine invertebrate, intelligent life, sentient being.  List some extremely different objects that fit into the same category.  Pick an object in the category and list what other categories it belongs to.  How well does the category reflect distinctions in the external world?  What kinds of observations are required to make the distinction?  Who does the observing?  When is the category useful and not useful?  Are the evolutionary stories told about these classes the only possible ways to understand them?  What does “understanding” mean without the preconditions of immaterial concepts, reason, truth, and mind?
Next headline on:  Early Man • Philosophy or Theology • Evolutionary Theory

1. Publication of the Origin was not a sudden (“revolutionary”) interruption of Victorian society’s confident belief in the traditional theological world-view.
2. The Origin did not “revolutionize” the biological sciences by removing the creationist premise or introducing new principles.
3. The Origin did not revolutionize Victorian public opinion.  The public considered Darwin and Spencer to be teaching the same lesson, known today as “Social Darwinism”, which, though fashionable, never achieved dominance.
4. Many biologists expressed significant disagreements with Darwin’s principles.
5. Darwin made little or no contribution to the renovation of theology.  His public statements on Providence were inconsistent and the liberal reform of theology was well advanced by 1850.
6. The so-called “Darwinian revolution” was, at the public opinion level, the fashion of laissez-faire economic beliefs backed by Darwin and Spencer’s inclusion of the living world in the economic paradigm.

What, exactly, are we supposed to be celebrating next year?  Ineptitude?  The gullibility of the public?  The power of fashionable ideas to distort history?  The inability of reasonable scientists with their significant disagreements to stop bad ideas at their onset?  Darwin Day can still be a worthy holiday if we make these the lessons.  We agree with Caton; first, we have to get the facts right.
Next headline on:  Darwin and Evolutionary Theory • Education

Monster Mash   10/28/2008    
Oct 28, 2008 — Just before Halloween, it’s time for tricks and treats about monsters in the fossil record.  Here’s a list of recent stories about scary beasts:

1. Dino Dance:  Are these potholes tracks or weathering marks?  PhysOrg and Science Daily were among news outlets reporting a new interpretation of formations by a grad student at the University of Utah in Navajo Sandstone near a popular photographer’s locale called The Wave.  Winston Seiler claims the round holes represent tracks of three different kinds of dinosaurs, complete with tail drag marks.  Other dinosaur tracks are known in the area; this one is unusual for the number and density of tracks, what Seiler calls a “trample surface.”  National Geographic also joined the dance party.
   Update 11/10/2008: The party dispersed when some science cops showed up.  PhysOrg reported that “A group of paleontologists visited the northern Arizona wilderness site nicknamed a ‘dinosaur dance floor’ and concluded there were no dinosaur tracks there, only a dense collection of unusual potholes eroded in the sandstone.”  One of the co-authors of the dance floor thesis agreed to work with the skeptics: “Science is an evolving process where we seek the truth,” she said.  So she turned around and changed the dance to The Shake: “This is how science works, and we’ll have to see how it shakes out in the end.”
2. Hornblower:  The unusual head crests on duckbill dinosaurs were used for shouting, claim scientists in a report on Live Science and PhysOrg.  The nasal passages on lambeosaurs and corythosaurs connected with passages in the head crest to produce resonant, bellowing calls (see diagrams on Science Daily).  The pitch of the calls probably deepened as the dinosaurs aged.  Perhaps they had a tonal language for communication, with special calls for Run for your lives!  A T. rex is coming!  Veteran dinosaur hunter Jack Horner (Montana State) noted that, “It’s difficult to infer the function of structures in an extinct dinosaur when there is so little resemblance to any living animal.”
3. Taking the plunge:  How do you interpret dinosaur tracks that gradually fade away?  The track-maker must have gone for a swim, reported Science Daily.  Debra Mickelson of University of Colorado even thinks she knows what they were doing – going out to sea to feed, 165 million years ago.
4. Migrants:  Dinosaurs weren’t the champion migrators of the ancient world, contrary to the usual view, said Phil Bell (U of Alberta) in a report on Science Daily.  How could he and colleague Eric Snively figure that out?  They calculated the energy requirements for a herd of herbivores like Edmontosaurs, and believe it would have limited their travel to 3000 km round trip – half the previous estimate.
5. Microsaur:  We tend to think of dinosaurs as mighty tyrants of the early earth, making the ground shake with every step.  Science Daily reported the finding of the smallest dinosaur ever seen.  The juvenile Heterodontosaurus (mixed teeth) had a skull less than two inches long and would have weighed less than two sticks of butter.  “It’s likely that all dinosaurs evolved from carnivorous ancestors,” said co-author Laura Porro (U of Chicago); “Since heterodontosaurs are among the earliest dinosaurs adapted to eating plants, they may represent a transition phase between meat-eating ancestors and more sophisticated, fully-herbivorous descendents.”
6. Megasaur:  A dinosaur graveyard has been found in Utah, reported Live Science.  Remains of a large number of herbivores were found, including one well-preserved skeleton and a 5-foot humerus from a brachiosaur, one of the largest dinosaurs known.  Tracks have also been found.  Another surprise was a Deltapodus stegosaur – previously known only from Europe.  How did brachiosaurs get so huge?  Another story on Live Science claims they ate high-energy foods whole, without chewing.
7. Sniffer rex:  Halloween wouldn’t be quite the same without mention of everyone’s favorite dinosaur nightmare: the Tyrannosaurus rex.  A report on Live Science claims the monsters had a good sense of smell – vital for hunting down prey.  They believe this based on the size of the opening in the skull where the olfactory bulb – an organ of smell – was located.  The article speculated on evolution of birds from dinosaurs: “Most of today’s birds have keen eyesight but lack a good nose, suggesting smell became less important at some point in birds’ ancestral history, the researchers said.”

Dinosaurs are for kids – including the grown-up kind.  Who doesn’t enjoy learning about this large and varied class of extinct animals that roamed the whole earth?  Imagining things is fun, too.  Just don’t confuse it with science.  There are limits to how much can be known about dinosaurs from their tracks and bones.  We don’t know, for instance, their favorite dance steps, to say nothing of how they decided to give up meat, reduce their noses and fly like Tweety rex.  The beasts are scary enough without the evolutionary monster tales around the campfire.
Next headline on:  Dinosaurs • Fossils • Evolution

In 1940, the American archaeologist Nelson Glueck summarized his extensive 1930s archaeological surveys in Transjordan in his book The Other Side of the Jordan, asserting that he had discovered King Solomon’s mines in the Faynan district (the northern part of biblical Edom), ~50 km south of the Dead Sea in what is now southern Jordan.  The period between the First and Second World Wars has been called the “Golden Age” of biblical archaeology when this subfield was characterized by an almost literal interpretation of the Old Testament (Hebrew Bible, HB) as historical fact.  Archaeologists such as Glueck metaphorically carried the trowel in 1 hand and the Bible in the other, searching the archaeological landscape of the southern Levant for confirmation of the biblical narrative from the Patriarchs to the United Monarchy under David and Solomon to other personages, places, and events mentioned in the sacred text.  Beginning in the 1980s, this paradigm came under severe attack, primarily by so-called biblical minimalist scholars who argued that as the HB was edited in its final form during the 5th century (c.)BC, any reference in the text to events earlier than ca.  500 BC were false.  Accordingly, the events ascribed to the early Israelite and Judean kings from the 10th-9th c. BCE were viewed as concocted by elite 5th c. BCE editors of the HB who resided in postexilic times in Babylon and later in Jerusalem.  Some of the casualities [sic] of the scholarly debate between the traditional biblical scholarship and biblical minimalists has been the historicity of David and Solomon—the latter of which is traditionally cross-dated by biblical text (1 Kings 11:40; 14:25; and 2 Chronicles 12:2–9) and the military topographic list of the Egyptian Pharaoh Sheshonq I (Shishak in the HB) found at the Temple of Amun in Thebes and dated to the early 10th c. BCE (5).
    ....The ¹⁴C dates associated with smelting debris layers from Faynan reported here demonstrate intensive 10th–9th c. BCE industrial metallurgical activities conducted by complex societies.
    The analytical approach advocated here argues for an historical biblical archaeology rooted in the application of science-based methods that enables subcentury dating and the control of the spatial context of data through digital recording tools.

Bible scholars will surely find this paper interesting.  There’s something satisfying about debunking the debunkers.  Congratulations to National Geographic News, usually a Darwinist propaganda bullhorn, for giving a fair report on the story without disparaging the Bible in the process.  Time to minimize minimalism in Biblical archaeology.  Minimalists?  Don’t need ’em in Edom.
Next headline on:  Bible • Dating Methods

Quiz question: what is an evolutionist’s favorite word?  Oh, you want a free hint?  Maybe, baby.
Next headline on:  Solar System • Stars

Snails Walk on Water   10/27/2008    
Oct 27, 2008 — Why is that scientist staring at a snail?  He’s watching a miracle: walking on water.  This is not our exaggeration: Matt Kaplan on National Geographic News entitled his article, “How Snails Walk on Water Is a Small Miracle.”  If we can figure out the trick, we might be able to make little robots do it – even if we don’t know why we would want to yet, other than it would be cool.
    Snails are small enough to be naturally buoyant, but needless to say, getting traction on water is a challenge.  The snail apparently does this by making small ripples.  The ripples are just the right size to give the snail traction without breaking the surface.  It’s a unique method of propulsion unknown till Eric Lauga, a professor of mechanical and aerospace engineering at the University of California, San Diego, decided to investigate.
    For a human to do this would require shoes as big as a football field, the article said.

  Many capabilities of animals and plants seem miraculous to us, but we sometimes use the word too carelessly.  Jesus walked on water barefoot or on sandals.  That’s a real miracle.
Next headline on:  Biomimetics • Terrestrial Zoology • Physics • Amazing Facts

Is religion a product of our evolution?  The very question makes many people, religious or otherwise, cringe, although for different reasons.  Some people of faith fear that an understanding of the processes underlying belief could undermine it.  Others worry that what is shown to be part of our evolutionary heritage will be interpreted as good, true, necessary or inevitable.  Still others, many scientists included, simply dismiss the whole issue, seeing religion as childish, dangerous nonsense.
    Such responses make it difficult to establish why and how religious thought is so pervasive in human societies – an understanding that is especially relevant in the current climate of religious fundamentalism.  In asking whether religion is one of the many consequences of having the type of brains we come equipped with, we can shed light on what kinds of religion ‘come naturally’ to human minds’

The findings emerging from this cognitive-evolutionary approach challenge two central tenets of most established religions.  First, the notion that their particular creed differs from all other (supposedly misguided) faiths; second, that it is only because of extraordinary events or the actual presence of supernatural agents that religious ideas have taken shape.  On the contrary, we now know that all versions of religion are based on very similar tacit assumptions, and that all it takes to imagine supernatural agents are normal human minds processing information in the most natural way.

Some form of religious thinking seems to be the path of least resistance for our cognitive systems.  By contrast, disbelief is generally the result of deliberate, effortful work against our natural cognitive dispositions – hardly the easiest ideology to propagate.

How otherwise intelligent people can continue to be so blind to their own biases after decades, nay centuries, of philosophers and theologians and logicians pointing them out, is stunning.  Nature has just published another in a long series of self-refuting essays.  A freshman CEH reader can probably refute this article in a sentence or two.  If not, you need to apply yourself to stopping by here more often.
    What is it about their brains that predisposes evolutionists to think this way?  You notice that we put the shoe on the other foot.  That’s fair, because to him, we are all equally evolved.  By what standard of measure can he insist that his tacit assumptions are better than anyone else’s?  By the standards of science?  Ha!  Only if he is a logical positivist – another self-refuting belief system.  If this is not obvious, go back and read Wolpert’s ideas from the 10/16/2008 entry and the commentary on logical positivism from 05/10/2007 before continuing.  If Boyer assumes that “testable predictions” render evolutionary psychology scientific, he has not learned about the dubious logic of predictive success in science.  It’s the main reason Karl Popper rejected predictive success as a criterion of science, and promoted falsification instead.  (Falsification, alas, was also later rejected as a foolproof criterion.)
    Boyer came close to recognizing the self-refuting nature of his beliefs by mentioning people who “worry that what is shown to be part of our evolutionary heritage will be interpreted as good, true, necessary or inevitable.”  (For elaboration on that point, see the 05/09/2006 commentary, bullet 5.)  He should be worried.  To what universal standard could he appeal to decide that religion is an emergent property of the brain, but science is not?  And why would he lament that atheism is hardly the easiest ideology to propagate?  At least he admitted it is an ideology.  But to what universal moral standard would he appeal to say that propagating his atheistic world view would be a good thing?  He said that science may one day find that religion contributed to fitness in ancestral times.  On what grounds, then, can he say it hijacked man’s cognitive abilities?  If it produced fitness, it is just as much an intrinsic benefit to human evolution as the brain itself.
    Boyer’s essay is plagued with other fallacies.  For one, he generalizes all religions, no matter how opposite, in a highly simplistic manner: he puts the witch doctor and the Oxford Scholar into the same “fundamentalist” bucket, also a form of ridicule.  By excepting his own reasoning from those of religious nuts, of course, he has also divided the world into us-vs-them, the either-or fallacy: i.e., you either belong to the People of Science or to the “People of Faith” (whatever that broad-brush category means).  Students want extra credit can hunt for begging the question fallacies, non-sequiturs, the post-hoc fallacy, misuse of circumstantial evidence, reductionism, subjectivity and other fallacies.
    The card-stacking fallacy is notable in this article.  He only offered three responses to the idea that religion evolved: (1) Worry by religionists that it will undermine their beliefs.  (2) Worry by evolutionists that religion, if part of our evolutionary heritage, will be seen as “good, true, necessary or inevitable.” (3) Disgust by scientists that religion is “childish, dangerous nonsense.”  Why did he not consider the possibility that theologians and knowledgeable scholars will consider his evolutionary theory or religion to be regarded as childish, dangerous nonsense?  Is that not what we have just illustrated?
    Another example of his card stacking was to list only things like ritual, metaphysical beliefs, social identity and moral codes as the characteristics of religion.  Why didn’t he mention evidence – and apologetics?  Those things may be lacking in the cultic or ritualistic religions, but the Bible is filled with historical references that can be cross-checked, and appeals to remember what the people knew to be true from evidence, reason and eyewitness testimony.  Paul and Peter claimed to be eyewitnesses of the risen and glorified Christ and emphatically denied that they were following cleverly devised fables.  They also warned people against falling for fables.  If Boyer likes prediction so much, he should consider the prediction Paul made in II Timothy 4:4 that in the last days people will “turn their ears away from the truth and turn aside to myths,” of which evolution is a prime example, because the evidence for God is clear from creation (Romans 1:18-20).  Peter, similarly, predicted the coming of belief in uniformitarianism.  He predicted that mockers would deny the evidence for creation and the flood (II Peter 3:3-9).  Do those predictions count?  Must be consistent.
    Boyer and his fellow atheistic evolutionists arrogate to themselves the chair of science, but have no floor to put it on: not a scientific floor, or a philosophical floor, or an evidence floor.  He needs the Judeo-Christian floor to be able to reason about truth, morals, and evidence at all.  Like Yoda, he speaks ex cathedra from some exalted plane above the rest of humanity, telling us about our tacit assumptions while ignoring his own (08/13/2007).  He tells others what makes them tick without understanding that what makes him tick is rebellion against his Creator.  He couldn’t slap his Father’s face without first sitting in His lap.  Pascal Boyer should sit quietly like a good boy and read Pascal.
Next headline on:  Evolutionary Theory • Human Body • Theology

The overwhelming source of O₂ on Earth is photobiological oxidation of water; neither the evolution nor the mechanism of this process are completely understood.  Apparently it arose once in a single clade of bacteria and was then appropriated via a single event, in which one cell engulfed another (endosymbiosis) to form a new symbiotic organism.  The latter became the progenitor of all photosynthetic eukaryotes, including algae and higher plants.
    The core of the oxidation machinery is photosystem II, a large protein complex containing four manganese atoms that are photocatalytically oxidized to create electron holes upstream.

On time scales of years to millennia, these reactions are closely coupled to the reverse process of respiration, such that net production of O₂ is virtually nil.  That is, without burial of organic matter in rocks, there would be very little free O₂ in the atmosphere.  Hence, the evolution of oxygenic photosynthesis was a necessary but not a sufficient condition to oxidize Earth’s atmosphere.

OK; how convinced are you that the evolutionary storytellers are compelled by the evidence to embrace their billions of years saga of a history they cannot observe?  It’s a magical history, in which complex oxidation machines “arise” by some unspecified natural magic.  (Note that if something “arose once,” it is not following a natural law).
    Lacking evidence, they can build models that include the natural magic built-in.  By tweaking parameters here and there, and trying to debunk contrary evidence, they can get it to work – sort of.  It continues to amaze them how finely balanced it is.
    So much for this space fantasy.  The atmosphere on Darwin’s imaginary world is too rarefied to breathe.  Let’s head back to the real world.
Next headline on:  Geology • Physics and Chemistry • Origin of Life • Dating Methods

Minding the Brain, or Braining the Mind?   10/23/2008    
Oct 23, 2008 — There’s a battle brewing over who controls your brain: nature or your mind.  Materialist scientists are recognizing that creationists are getting a foothold on this hill and “declaring war over the brain,” according to an article in New Scientist.  Psychiatrist Jeffrey Schwartz fired this salvo: “Materialism needs to start fading away and non-materialist causation needs to be understood as part of natural reality.”
    Amanda Gefter, author of the article, also took note of the book The Spiritual Brain: A neuroscientist's case for the existence of the soul by O’Leary and Beauregard.  Schwartz and Beauregard were among the speakers at an international symposium in Manhattan called Beyond the Mind-Body Problem: New Paradigms in the Science of Consciousness.  Gefter listed several fronts in the war to reclaim the mind: “Schwartz and Beauregard are part of a growing ‘non-material neuroscience’ movement,” she explained.  “They are attempting to resurrect Cartesian dualism – the idea that brain and mind are two fundamentally different kinds of things, material and immaterial – in the hope that it will make room in science both for supernatural forces and for a soul.”
    After giving adequate white space for proponents of the non-materialist view (including Angus Menuge, J. P. Moreland and the Discovery Institute), Gefter clearly wanted to throw her vote to the reigning materialist paradigm on this matter of mind.  She commented on an experiment Schwartz used to support the independent existence of mind, saying, “these experiments are entirely consistent with mainstream neurology – the material brain is changing the material brain.”
    In the middle of her article, Gefter got really serious:

Clearly, while there is a genuine attempt to appropriate neuroscience, it will not influence US laws or education in the way that anti-evolution campaigns can because neuroscience is not taught as part of the core curriculum in state-funded schools.  But as Andy Clark, professor of logic and metaphysics at the University of Edinburgh, UK, emphasises: “This is real and dangerous and coming our way.”
    He and others worry because scientists have yet to crack the great mystery of how consciousness could emerge from firing neurons.  “Progress in science is slow on many fronts,” says John Searle, a philosopher at the University of California, Berkeley.  “We don’t yet have a cure for cancer, but that doesn’t mean cancer has spiritual causes.”
    And for Patricia Churchland, a philosopher of neuroscience at the University of California, San Diego, “it is an argument from ignorance.  The fact something isn’t currently explained doesn’t mean it will never be explained or that we need to completely change not only our neuroscience but our physics.”

The attack on materialism proposes to do just that, but it all turns on definitions.  “At one time it looked like all physical causation was push/pull Newtonianism,” says Owen Flanagan, professor of philosophy and neurobiology at Duke University, North Carolina.  “Now we have a new understanding of physics.  What counts as material has changed.  Some respectable philosophers think that we might have to posit sentience as a fundamental force of nature or use quantum gravity to understand consciousness.  These stretch beyond the bounds of what we today call ‘material’, and we haven’t discovered everything about nature yet.  But what we do discover will be natural, not supernatural.”

Apparently the irony of this article was completely lost on Amanda Gefter and her materialist experts.  They were all using their minds to argue and debate about immaterial concepts.  If nothing more was happening than molecules bouncing around in their skulls, how could they even know what they were saying?
    Remember when Mom, Dad, or some other childhood mentor showed you that when you point an accusatory finger at someone else, three other fingers are pointing back at you?  Clark just lectured us on logic.  Flanagan just lectured us on definitions.  Gefter just lectured us on God-of-the-gaps arguments.  All three have just shot their little finger-guns right back into their own skulls.  Example: Gefter dismissed Schwartz’s empirical evidence that the mind can change the brain by saying, “the material brain is changing the material brain.”  OK, class, what’s the next question?  Think about it (yes, think), [Jeopardy tune plays], and the bell rings – Aha!  Who is making the material brain change the material brain?  And who is observing the change?
    Now, if you think that is just a logical trick, you have to realize that without a person doing the changing, no one would ever know a change had occurred.  This is a mind-body problem that cannot be so easily swept away.  If you could shrink yourself to the size of a cell and wander through the brain, you would no more see thought than if you wandered through Big Ben could you see time.  Time and thought live in the conceptual realm, not the material realm.  Suppose you walked through a computer chip like a pedestrian on the streets of London.  Would you see Boolean logic?  Oh, you might see certain switches light up, and perhaps you could perceive electrons in a diode or transistor junction flowing one way instead of the other.  But it is not the chip that would be sensing that logic is occurring: it would be you, the Observer.  The operation of a physical system is not the same as concept behind the system.  A system cannot tell itself the purpose of the system in a way that brings understanding.  That takes a Person.  Consider: if Amanda’s mind is not directing her argument, how could she have any free will to believe that her argument is true, and that ID is so false it should be pre-empted?  And to what is the pre-emptive strike referring, if not some well-intentioned but misguided appeal to immaterial truth and morals?
    Gefter and Flanagan dismissed this all as quibbling over definitions.  But look at the fingers pointing right back at them: they suggested that any possible concept might be enveloped within the words material or natural – even things like sentience, a quantum-gravity theory of consciousness, or any future discovery of science.  “These stretch beyond the bounds of what we today call ‘material’, and we haven’t discovered everything about nature yet.  But what we do discover will be natural, not supernatural.”  This is a rescuing device to end all rescuing devices.  No matter what the evidence, they can envelop it, like The Blob, into their materialistic worldview.
    OK, let’s push that envelope.  Suppose they find irrefutable evidence for angels.  Will they call them material?  Will they be a part of the “natural” universe?  Even God has a divine “nature.”  The word nature or natural is so slippery it can mean a dozen different things – including immaterial things like natural laws (Note: material things may obey natural laws, but laws are not material).  Materialists constantly invoke non-material things in their reasoning: mathematics, abstract logic, scientific methods to name just a few.  They also frequently make reference to unobservable entities – information, feedback, signal transduction, classification, reason, honesty and much, much more.  They help themselves to immaterial concepts and stuff them into their materialist bag, oblivious to who is doing the classifying.

God-of-the-Gaps:  J. P. Moreland, who was mentioned in Gefter’s article, has three comeback arguments to the perennial charge that Christians fill gaps in scientific knowledge with appeals to God.  Paraphrasing, he says, (1) Christians would not expect there to be many gaps.  The Biblical worldview indicates that the world runs according to predictable patterns (natural laws) most of the time.  In fact, it is only the Biblical worldview that makes sense of the concept of natural laws.  (2) Some gaps are getting wider.  Scientific discoveries about the cell and the origin of life and the fine-tuning of the universe are resisting all attempts at materialist explanations.  We should follow the evidence where it leads.  If that evidence is pointing to design, so be it.  (3) Materialists are just as guilty of the charge.  Whenever some incredibly-complex mechanism is discovered in a cell, for instance, they assume that natural selection produced it, or assume that some day in the future, a material cause will be discovered.  This is nothing more than naturalism-of-the-gaps.

The material/spiritual and natural/supernatural distinctions are false dichotomies.  They cannot stand up to a half-hour of scrutiny by a skilled philosopher.  What it boils down to is this: naturalism is anything and everything that allows a scientist (or a party animal on drugs) to avoid responsibility to their Maker.  That’s the real argument from ignorance.  They can believe in space aliens or unobservable multiverses – anything, no matter how crazy, as long as they never have to bow the knee and confess, “Thou art worthy, O Lord, to receive glory and honor and power, for Thou hast created all things, and by Thy will they exist, and were created” (Revelation 4:11).
    You can put a brain into a jar of formaldehyde, and you can throw a used computer onto a junk pile, but the concepts of mind and design, like Halloween ghosts, will always find the materialist’s haunted house and come back to join the party.
Next headline on:  Human Body • Intelligent Design • Theology, Philosophy or Religion

1. None of the structures were pennate feathers, that is, with barbs and barbules from a central vane.  The integumentary structures fell into two categories:
   1. “Shafted feathers” – Connected to the last ten tail vertebra were found two “membranous structures” consisting of parallel shafts that each branch once.  Each shaft has a thin unbranched vane of material, like a coating, along a central rachis.  The result appears as four long nearly-parallel rods that join at the base.  Collectively they are nearly as long as the skeleton of the creature.  Mark Norell (American Museum of Natural History) commented, “These seem to lack that main shaft down the middle and are just a really long collection of very long, filamentous-like structures.”
   2. “Non-shafted feathers” – These are rows of integument found outside the outline of skeleton, presumably from the skin.  They all end in parallel rows of barbs, nothing like the cross-cutting structure of bird feathers; the BBC article calls it a “fluffy, down-like covering.”  The authors stated, “the free distal barbs of Epidexipteryx arise from the edge of a membranous structure (Fig. 2b, c, d, d'), an arrangement that has never previously been reported.”
2. Some of the structures bear similarities to those on Jeholornis, a creature interpreted as being capable of powered flight (see 07/24/2002).
3. The authors allowed for the possibility that this creature was “secondarily flightless” – i.e., that it once had feathers like a bird, but lost them; if so, it was not evolving from a dinosaur into a bird.
4. The authors suggested that the feathers on Epidexipteryx were used for display, not for flight, but the LiveScience article hypothesized they “likely helped the creature balance on tree branches.”
5. The animal had a curious mosaic of traits.  National Geographic remarked, “Epidexipteryx’s anatomy seems to be a hodgepodge of features taken from a variety of animals.”  It seems to have been the “platypus” of the Jurassic – an improbable mixture of traits from different groups.
6. Since the creature had a “surprising combination of physical features” (BBC News), it should not be envisioned as a transitional form from one lineage to another.  The BBC News article complicated the evolutionary story by stating, “The discovery adds yet more complexity to the early history of the era when small meat-eating bipedal dinosaurs evolved into birds.”  The evidence, therefore, makes the explanation more complex, not simpler, in contradiction to Occam’s Razor.
7. The evolutionary date is too late to represent a pre-bird.  The BBC article said, “whereas other feathered dinosaurs [sic] date from after the appearance of the first known bird, this fossil appears to be much closer in age, so it opens a new window on the evolutionary events at the critical transition from dinosaurs to birds.”  Live Science says that the dates are uncertain; at best it was “slightly older” than Archaeopteryx.  If it was nearly contemporaneous with a fully-feathered bird that was most likely capable of powered flight, it could not be a pre-bird, bird ancestor or missing link.
8. The evolutionary link to birds is only inferential.  Live Science quoted one of the authors saying, “Although this dinosaur cannot be the direct ancestor for birds, it is one of the dinosaurs that have the closest phylogenetic relationship to birds.”
9. Mark Norell hinted that this fossil has more to say about diversity, not evolution.  “Things more primitive than this have fully formed feathers” he said.  “This is just some weirdo kind of thing this animal has.”

As scientists and others discover more and more dinosaur fossils with bird-like features, the picture of such creatures is becoming more complex, said Norell, who was not involved in the current study.
    “Just like the bird diversity we have living today goes all the way from hummingbirds to ostriches to toucans, it’s incredibly diverse,” Norell said during a telephone interview.  “Now we’re starting to see that sort of diversity extends not only in birds but also in the close bird relatives [which] were just as physically diverse as modern birds are.”

The artists’ renditions go far beyond the evidence: they’ve put vibrant colors on the alleged feathers and given the creature a whole life and personality.  The structures cannot be called feathers except by stretching the definition of the term.  The tail structures look like long rods.  The “down-like coating” could be flayed skin, given that the creature was exceptionally well preserved.  It may represent a mutant dodo-line of ancient birds that went extinct, or a member of a subclass of dinosaurs that shared the most similarities with birds without being related to them.
    Scientists should be very careful about making inferences about any complex set of data.  The bones do not jump up and announce that they were evolving into birds.  The supplementary data in the paper show nearly 300 traits that had to be compared to make a cladistic analysis.  The significance of any one of them requires a human judgment.  Which traits are you going to focus on?  Humans share traits with this fossil, too: vertebrae, teeth, radius and ulna, and many organs not visible from the bones.  It is conceivable that the scientists in another civilization might consider size, habitat, lifestyle or some other characteristic to be the overriding concern in their way of classifying things.  What kind of inferences would they draw?  Complexity, diversity and “mosaics” of traits throw simplistic schemes into disarray.  How would you rearrange your Evolutionary Tree of Tools if somebody handed you a Leatherman tool with a knife, screwdriver, pliers and scissors in a leather pouch?
    Even granting, for the sake of argument, the most generous leeway to the evolutionists and calling the structures on this thing feathers does not help their story.  Other feathered birds were nearly contemporaries.  If this was an “evolutionary dead end,” where is the highway?  A collection of dead ends may keep you busy, but is not going to get you anywhere.
Next headline on:  Dinosaurs • Birds • Fossils

Good question. In part, it was the way I was taught biology in high school.  My teachers refused to teach anything about evolution.  In fact, the only time I remember hearing the ‘E’ word in high school was when we dissected frogs.  After explaining to a room full of queasy kids how understanding the anatomy of a frog could help us understand the basics of human anatomy, the teacher paused thoughtfully and said, “Now I’m not talking about evolution here, so don’t go home and tell your parents that I’m teaching evolution”.  And that was it.  The rest of high school biology was just a collection of evidence supporting Dobzhansky’s claim that “Nothing in biology makes sense except in light of evolution”.  We collected insects and looked at pine cones, and we had a hamster that we taught to go to the bathroom through a hole in the side of its cage.  That was pretty much it.  Biology seemed more like an eccentric hobby than a coherent body of knowledge.  Mercifully, we were spared any discussion of ‘Intelligent Design’....
    I started reading more deeply in biology and realized just how flawed my early education had been.  I read Darwin and I discovered T.H. Morgan and Max Delbrück and the Phage Group.  The only advantage of coming to biology so late was that I found almost everything that I learned new and exciting.  Reading about solving the genetic code, thirty years after the fact, made me as excited as if it was happening at that moment, in a lab down the hall.  I was astounded by the calcium ATPase: a single molecule that can discriminate, with remarkable specificity, between similar divalent cations and use chemical energy to pump calcium against a 10,000-fold concentration gradient.

To my engineer’s mind, a living cell was now just a complex, feedback-controlled system.  I could imagine writing equations to describe biochemical pathways, cellular functions, and, eventually, entire living cells.  Nowadays this kind of thinking would be called ‘systems biology’.  And while it is not exactly the way I approach biological problems in my lab now, it was the kind of thinking that made biology intelligible to me.

Biology teachers should have constant sorrow, too after reading this story.  This is how to turn a bright young inquiring mind into a self-contradicting smart aleck.  Can’t this blues boy realize that complex, feedback-controlled systems don’t just happen?  This man of constant sorrow can stare at intelligent design right in front of his face, like that biological machine that “can discriminate, with remarkable specificity, between similar divalent cations and use chemical energy to pump calcium against a 10,000-fold concentration gradient,” and turn right around and praise Darwin and Dobzhansky.  Step back a second and realize how insane this is.  This same dude would never step into a computer room and insult the designers, but can stare at even more complex systems and call them cobbled jumbles of time and chance.  It’s enough to make you want to yank his beard and knock on his skull and ask, “Anybody home?” (Caution: Do NOT do that to anybody except yourself, women and obsessive shavers excepted.)  The interviewer, as usual for Current Bilge, just slurps it all up like fine whine.
    Teachers: pay attention.  You cannot solve the creation-evolution controversy by ignoring it.  This does more harm than good.  Students want answers.  They are curious about evolution.  Those from religious homes may be worried about it, while those from secular humanist homes may have moms and dads ready to sue.  You cannot push this subject off.  One cannot understand modern history or science without understanding Darwin.  The next Dyche Mullins in your classroom will remember how you sloughed off the subject as if it were taboo, then a Darwin dogmatist in college will sweep him off his feet with visions of the alluring explanatory power of evolution.
    In private or home schools, the solution is simple: teach all about Darwinism – all its strengths and weaknesses, the stuff the textbooks leave out.  In public schools, the courts and the school boards have often become so paranoid they will try to persecute or dismiss any teacher who teaches scientific facts about Darwin, like they did to Roger DeHart.  Sometimes the thought police go after not what you say, but what they think your motivation is.  You have to know your principal, your state, and your school board.  Thankfully some states are passing academic freedom laws.  Many teachers have found the right way to present Darwinism honestly without dogmatism.  Who could fault that?  Science is supposed to be the opposite of dogmatism!  Don’t expect all parents and school boards to be rational, though, on this hot topic; the Discovery Institute can provide valuable help for negotiating the fine legal lines involved.  Whether public or private or home school teacher, your goal is to help students become familiar with the evolutionary theory in its historical, political and scientific contexts; to understand the arguments Darwin and his critics have made, and while at the same time to develop critical thinking skills to be able to separate dogmatic claims from scientific evidence.
    Let’s use this entry also to cogitate on the nature of science.  We tend to pigeonhole subjects into watertight categories: a scientist is someone who does science, and science is what scientists do.  Is that necessarily the case?  When Mullins is clowning around with the country band, is he doing science then, just because he is a scientist by profession?  Obviously not.  All right, then; is he doing science from the moment he steps into the Science Building on campus till the moment he goes home?  Maybe some of the time.  Not on coffee breaks.  But then, maybe some flash of scientific insight will come to him when he gazes at the swirls of cream in his cup.  Is it when he is writing a proposal or scientific paper?  Is it when he is tediously jotting down readings in his lab book while his mind is on the American League championships?  Is it anything he does because he belongs to a professional scientific society, while the bird watcher outside does not?  These questions help to dissolve prejudices about The Scientist.
    For Dyche’s view on what makes a person a good scientist, let’s look at his answer to the last question about what advice he would give a student seeking a career in biology.  Get ready for a surprise.

Advice is a tricky thing.  When I started my lab I picked out a set of mentors: three successful scientists to whom I ran with all my vexing questions.  I soon found that, no matter what the question, I always got three different (and often contradictory) pieces of advice.  One of those pieces of advice, however, usually resonated more than the others and that’s the one I would follow.  So my advice would be to get as much advice as you can from as many different sources as possible.  And remember that much of it will be bad advice, or at least bad advice for you, even if the source is an eminent and successful scientist.  You need to trust your instincts.
    As Andrew Murray once told me, “Think about all the scientists you know.  No two of them approach a problem in the same way.  No two of them run their labs the same way.  And no two successful scientists are successful for the same reason.”

Notice something interesting: this is all about intuition.  You thought that science is following the scientific method.  Here, Mullins is saying that science is all about instinct!  Then you and me are scientists whenever we listen to a lot of advice, discard the advice that doesn’t “resonate,” and trust our instincts.  You can imagine a lawyer or hunter or coach giving the same advice to his students.  What scientific method is Mullins following when he gathers as much advice as he can, then trusts his instincts?  Certainly a politician can do that.  Notice he said that no two of them [scientists] approach a problem in the same way, run their labs the same way, or are successful for the same reason.  There is no one way to do science!  A corollary is that anybody who gets good advice and trusts his instincts has just as much right to call himself a scientist as Mullins does, because there is no method, or process, or secret formula that makes what Mullins does more scientific than what any other careful investigator does.
    Oh, but you may be thinking, Mullins has a degree in science.  He passed all the educational requirements.  He joined a scientific society.  He is smart, well trained and experienced: this grants him membership in The Science Guild.  That may be all well and good, but we repeat the question: when is he doing science, and when is he not doing science?  We remind our readers that some of the greatest scientists in history never went through those qualifications.  They learned at home or from personal experience.  They were mavericks and outsiders.  Some were scorned by the Science Guild in their day – and not vindicated till after they died.  Should they be classed as non-scientists because they were outside the Guild?  Of course not.  Science only became highly professionalized and institutionalized in relatively recent times.  The word “scientist” did not even exist till William Whewell coined the term in 1832.
    Science is one of those vague words that means too little by attempting to stand for too much.  Are we to grant the same prestige to political science and economic science as we do to physics?  How about the far-out theoretical physics that still has no observational evidence?  Is psychology science?  Science of mind?  Scientology?  Clearly some distinctions are in order!
    In the original sense of the word, science means knowledge.  The word requires no set method, schooling or membership.  Knowledge welcomes all seekers and rejects some SINOs (scientists in name only).  While we should respect the degree of rigorous education that professional scientists have mastered, and the experience they have gained, and any useful or enduring findings they have made, we should keep these distinctions in mind.  When Dyche Mullins dismissively disparages intelligent design while staring it in the face in a cell, he is not doing science: he is doing ridicule.  When he falls in love with Darwin but never studies the problems and contrary arguments, he is taking things on authority.  He deserves no more respect for uninformed opinions than a cultist or gambler.  Don’t respect a scientist when he acts unscientifically, and don’t ignore a person lacking a PhD in Science when he seeks knowledge in an honest, systematic, informed way.
    A lay person with common sense on the right track may achieve more science (knowledge) than a professional pursuing a wrong track.  Being a professional scientist does not grant legitimacy to whatever that person does or says that is not observable, testable, and repeatable.  And knowledge is certainly a goal that any honest observer in search of the truth can hope to attain.
Next headline on:  Education • Intelligent Design • Evolution

Miller-Frankenstein Ghost Rises from the Dead   10/20/2008    
Oct 20, 2008 — Stanley Miller died last year, but his friendly ghost lives on.  Famous for his Halloweenish spark-discharge apparatus that brought naturalism to life, Miller subsequently began to doubt the simplistic “primordial soup” vision that took on a life of its own, making apparitions in many a textbook.  He realized that improbably atmospheric conditions—a reducing atmosphere of methane and hydrogen without oxygen—were required.  Nevertheless, the sparks in the flask made an indelible mark on the public consciousness even if Miller himself and his colleagues struggled with the harsh realities of organic chemistry.
    Miller’s ghost appeared this month in Science.¹  Jeffrey Bada (Scripps Institute) and team are awarding him posthumous honors for finding more amino acids than previously thought.  In addition, they say, volcanoes may have provided the reducing conditions for amino acid formation:

Geoscientists today doubt that the primitive atmosphere had the highly reducing composition Miller used.  However, the volcanic apparatus experiment suggests that, even if the overall atmosphere was not reducing, localized prebiotic synthesis could have been effective.  Reduced gases and lightning associated with volcanic eruptions in hot spots or island arc-type systems could have been prevalent on the early Earth before extensive continents formed.  In these volcanic plumes, HCN, aldehydes, and ketones may have been produced, which, after washing out of the atmosphere, could have become involved in the synthesis of organic molecules.  Amino acids formed in volcanic island systems could have accumulated in tidal areas, where they could be polymerized by carbonyl sulfide, a simple volcanic gas that has been shown to form peptides under mild conditions.

The tenacity with which naturalists cling to their icons would put a Buddhist monk to shame.  There are SO many problems with the Miller scenario, we weary ourselves to keep repeating them (search "Stanley Miller" in the search bar).  We”ll give them a whole earth made up of amino acids, combining and recombining at fantastically rapid rates (see online book): no life is going to happen.  Amino acids are nothing.  They are common little molecules, many of which are thermodynamically probable under certain natural conditions.  Some are found in meteorites.  It’s not the building blocks that characterize life.  It’s the way they are organized.  It’s the way they perform functions.  Organic chemists have to go to great lengths to get some of the building blocks under carefully controlled conditions.  Surely Bada et al are not suggesting that amino acids formed on land, perhaps on lava flows far from the oceans Miller required.  They can always dream up a scenario that keeps the molecules hopeful, but by the time they try to get the building blocks to join up in one-handed configuration and actually do something without a genetic code to direct them, they have to tweak the scenario to the point of absurdity.  Matter is fecund only in the imaginations of naturalists who will not permit information and direction into their world view.
    Their fascination with that phrase “building blocks of life” becomes more absurd with each announcement.  We have been told that water is a building block of life, and tailpipe soot is a building block of life.  Why stop there?  Why not call protons building blocks of life?  or quarks?  or superstrings?  The laws of chemistry militate against the formation of a functional biological apparatus.  In the lab, most of the organic ingredients for life have to be carefully shielded from oxygen.  Miller’s amino acids, even around Mother Volcano, would be subject to hydrolyzing radiation, oxidation, thermal destruction and dilution.  Astrobiologists have to imagine protected enclaves that could somehow concentrate and protect the exceedingly low yields.  Since amino acids do not polymerize in water, they have to imagine alternate waves of wetting and drying that somehow avoid washing the precious gems into the vast diluting sea (11/19/2004, 04/08/2008).  Then there need to be the right clay minerals to act as templates (but this won’t work; see 02/13/2006).  What if the next lava flow covers it up?  Sorry.  What if harmful cross-reactions dominate, as they would?  Sorry.  What if one wrong-handed amino acid joins the chain, as is immensely more probable (online book)?  Sorry.  It’s a sorry tale at every turn: improbabilities piled on improbabilities far beyond the limits of credibility.
    Don’t mistake commotion for progress.  You can listen to Robert Hazen’s cheerful Teaching Company series “Origins of Life” in which he describes in detail all the commotion in origin-of-life studies, with nothing at the end to show for it than naturalistic bluffing, hope and hype.  The characters doing OOL research look like the bad guys in Home Alone trying to burglarize life’s secrets, only to come back with bumps and bruises and burned hands.  There’s even an international organization of the burglars, ISSOL (newly renamed the International Astrobiology Society), that gathers every 3 years to pool their ignorance and share tales of woe about their latest bruises in the lab.  Its members comprise a Who’s Who (or Who Cares) of all the big names in the field.  Go ahead.  Browse the dozens of abstracts from their Summer 2008 gathering at Florence, that began with the obligatory sacrifice to Stanley Miller, and you will find everything from confident claims to frustration and dead ends, each hopeful sign falsified a few pages later.  Is this science?  What if any other group of zealots suffered this many losing confrontations with nature?
    Miller was usually more honest about the difficulties of finding how life originated than many of his disciples.  His greatest success was not in solving any of the problems, but in producing a visual propaganda tool that facilitated the dissemination of a useful lie (05/02/2003).  That’s not a legacy any self-respecting scientist should wish to have.
Next headline on:  Origin of Life • Geology

Scientists need to tell stories to nonscientists, because science stories—and you know this—have to compete with other stories about how the universe works, and how it came to be.  And some of those other stories—Bible stories, movie stories, myths—can be very beautiful and very compelling.  But to protect science and scientists—and this is not a gentle competition—you’ve got to get in there and tell your version of how things are, and why things came to be.
    We all know about creation-science movements in America.  But what you may not know is that such movements are spreading all over the world.

So Mary and her two assistants collected the dead ostrich, which was in the farmer’s backhoe bucket, and drove it back to Raleigh, and what do you know?  The former ostrich had been a pregnant former ostrich, and the bones looked pretty similar.  The next year, Mary published a paper in Science with the dinosaur bone right next to an emu bone, which looks even more like Bob’s. And since then, another T. rex, this one in Argentina, was found to have the same calcium structure—more evidence that when you look deep inside dinosaurs and deep inside birds, what you see is very, very similar.  Which gives us yet another reason to think that the robin in your front yard is an itty, bitty dinosaur.
    If your nonscience friend listens to that story, and leans in a little, and hears how scientists work with bones and dead birds in buckets, patiently looking for patterns, you have just placed a sword in her hand.  The next time somebody tells her that scientists are know-it-alls who toss off opinions, that science is an elitist plot, she would think, “welllll, but I did hear this story . . .” and the scientific method gets a little more defense, a little protection.
    But better than that, the next time your friend sees a robin, she’ll see, I hope, more than a robin.  She’ll glance at a little bird pecking for worms on the lawn, and she’ll travel 70 million years back to a time and a place that creationists say did not exist, but now, because of your story, your friend has a pregnant tyrannosaurus in her head with the unfortunate name of Bob.  Which makes robins and sparrows and chickadees and crows and all birds just a little more amazing, and a little more delightful to look at.  Which means, you win.  The creationists can’t beat delight.  You have smote them with your story.

Robert Krulwich does have a point.  There is a place for metaphor and narrative in science.  We use it often in our commentaries (for a recent example, see the last paragraph of the 10/17/2008 entry, below).  Good teachers, preachers and public speakers know the power of metaphor in rhetoric.  Rhetoric was one of the classical and medieval skills taught to all students.  An academic field known as rhetoric of science emerged after Thomas Kuhn’s 1961 thesis, to explore the ways in which rhetoric aids persuasion within paradigms and by challengers; the book Doubts About Darwin was built on Dr. Thomas Woodward’s PhD thesis that explored the interplay of rhetoric around the emerging Intelligent Design Movement.  Rhetoric of science departments even have their own vocabulary, and plenty of examples in the history of science to draw from.  There are cases to be made that some important scientific paradigms were won or lost by the power of rhetoric.
    This is all very interesting and fine.  Scientists ignore rhetoric at their peril.  It’s not persuasion that’s the problem; it’s propaganda.  Here is where Krulwich erred.  We often accuse the Darwinists of engaging not just in storytelling per se, but in “just-so storytelling,” which is made-up stuff.  Scientific explanations, even when aimed at Joe Six-Pack or Joe the Plumber, are supposed to be based in evidence and logic.  Often, Darwinists trade in fables concocted to save their paradigm, even when faced with incriminating evidence.
    Krulwich committed several propaganda errors in his address.  First, he divided all humanity into two classes (the either-or fallacy): scientists (e.g., those with honesty, brains and integrity, like Caltech graduates) and the rest of humanity, including scientific dunces like Phoebe on Friends, those who believe in alien abductions, Adnan Oktar, creationists and Bible believers.  He followed this with some fear-mongering about how powerful the bogeymen are: “this is not a gentle competition,” he said, giving the students a sword to conquer them.  After having consigned all non-Caltech-scientists to absurdity, it conveniently allowed him to set up a straw man to push over with very few ergs of energy.  He should read the material of the great creation scientists and best of the ID philosophers.  That’s what we do here: we take on the leading Darwinists in their leading publications.  We challenge their Goliaths.  Why does Krulwich associate creationism with the dimwits on a TV sitcom?  Let him sit down with the PhDs (some from Caltech and MIT and Cambridge) who deny Darwin, and learn a little about his own vulnerability.  Then he gave a vastly oversimplified view of science (the old truth-seeker in the white lab coat using “the scientific method,” whatever that is).  Doesn’t he realize that view went out in the 1950s?
    Finally, his sample story about robins being itty-bitty dinosaurs, besides being downright silly, sidestepped the major point of Mary Schweitzer’s work: that finding soft tissue and medullary bone in a dinosaur essentially falsifies the belief they are 65 million years old.  He swallowed the Darwine to the dregs without tasting it first or submitting it to qualitative analysis—the very thing a good scientist is supposed to do.  Consider the flaw, also, in his logic that similarities prove ancestry (see circular reasoning).  If you look deep enough into a man’s DNA and a banana’s DNA, you can find all kinds of similarities.  Darwinists pick and choose the kind of similarities they like, which they call “homologous traits” – or make up terms like “convergent evolution” and “analogous traits” to explain the others – whatever it takes to maintain their belief in Darwin’s metaphorical Tree of Life.  It’s rigged to protect their belief system from falsification.
    Overall, Krulwich gets the gong for giving advice built on half-truths.  So while we do not challenge him on the usefulness of being able to communicate scientific ideas effectively using narrative, we hope the graduating seniors of Caltech were discerning enough to smell the baloney in the hot dog.
    As for Krulwich’s line, “The creationists can’t beat delight,” this has to be one of the biggest lies of the year.  Creationists, like Louis Louis Pasteur stand amazed at the work of the Creator.  You could not find a happier group – just look at the number of praise songs they have about creation.  Compare this with the vitriol of the Darwinist People of Froth (e.g., 09/26/2005, 06/22/2007) and there is no contest.  Then, Krulwich said, “You have smote them with your story.”  In a way, he’s right.  We’re dumbfounded at the thought of a journalist telling scientists to fib, and with bad grammar at that.
    For more on the power of metaphors to mislead as well as inform, see “Metaphors Bewitch You” in the 07/04/2003 entry.
Next headline on:  Bible, Theology or Philosophy • Dumb Ideas

How Cells Thread a Needle   10/17/2008    
Oct 17, 2008 — Your challenge today is to invent a machine that can push a wet noodle through a straw.  It can’t pull it.  First it has to grab the end, then push it through without breaking it.  Oh, and there’s a catch; the straw has a plug at the far end and a constriction inside.  Give up?  Maybe you should watch how cells do it.  The mechanism was described by Anastassios Economou in Nature this week.¹
    Cells have to do this kind of thing all the time, so they have specialized machinery for the task.  The wet noodles are protein chains in their unfolded state.  The straws are narrow channels through membranes that are normally in a plugged configuration.  Just outside the straw entrance are several precisely-fitted proteins that first attract the chain and cradle it gently between two halves that swivel shut.  As one half tilts, it causes the constriction in the tunnel to open up.  The two parts then fit together like hands, and use a powered motor to gently send the noodle through.
    Economou included a schematic diagram of the five-part mechanism that pushes the proteins through.  (He included a couple of stylized hands to show how the delicate grasping and pushing is done.)  Here’s the caption:

This simplified representation is based on both earlier studies and the new findings.  In this cut-away view of the membrane, the SecA motor lies flat against the cytoplasmic side of the SecY channel (yellow), and consists of a two-domain ATP-powered engine (light and dark blue) and two ‘business-end’ domains (green and magenta; depicted as hands).  a, Initially, the channel pore is sealed by both a constriction halfway through it and a mobile plug domain (not shown) near its exit.  The pre-protein-binding domain of the motor (magenta) is in the open state, exposing an elongated corridor that connects to the entrance of the channel.  This open state is seen in structures of the isolated motor.  b, Swivelling this domain around its stem would allow it to embrace a secretory protein chain.  At this stage, a finger (green) from the second hand of SecA might be in close contact with the chain.  c, When ATP (not shown) is present, the engine conformation changes and the finger could move upwards, pushing or dragging the protein chain into the pore.  This motion, or other conformational changes, leads to the opening of the pore.

Evolution was not mentioned in this paper.  The scientists studied this process in those highly-evolved, large, complex animals known as... bacteria.
    OK, Charlie’s got a problem here.  There are half a dozen protein machines involved in this process.  They rotate, swivel and fit together in precise contact.  They are driven by ATP fuel pellets.  The machines must apply the energy precisely for function: in the right direction, in the right amount, at the right time.  Could chance produce such a complex machine?  (Bacteria, in the evolutionary fable, are among the earliest and simplest life-forms to “appear” on the early earth.)
    Do the math.  SecA contains 802 amino acid residues; SecY contains 436.  Our online book calculated that getting a 400-unit protein chain by chance would be one in 10²⁴⁰, even under unnaturally favorable circumstances.  That number is already way, way, way beyond the universal probability bound (i.e., it would never happen anywhere in the universe), and we don’t even have one protein of this multi-protein complex.  If by some wildly, radically, absurd stretch of imagination chance arrived at the right sequence for SecY (the shorter of the two proteins), it would be incredibly more unlikely to get the larger one, SecA, which is not only twice as long, but has to fit like lock and key with the first one.  Each of these protein parts is like that.  They all have to work together.  Calling this irreducibly complex is an understatement.  The machine parts don’t just happen to show up at the cell membrane by a random walk and work together for the first time.  They were designed to do what they do, and they do it exquisitely.
    Evolutionists would have us believe that natural selection tinkers with whatever parts are available, and complexity just happens.  Sooner or later, though, if you carry that logic too far, you wind up tinkering with nothing.  You could tinker with an existing radio, for instance, to make it pick up new wavelengths, but how far back can you push the tinkering metaphor back until you have nothing but a few random pieces of plastic and wire lying around?  The metaphor also suffers from implicit personification, as if the parts would even want to do such things.  Humans impose their sense of design on molecules that have no ability to plan ahead and work together, and no reason to do so.  Left to themselves, they would randomize.
    Economou has given us occasion to discuss economics.  The bankruptcy of evolutionary theory becomes more evident with each new investigation.  Trying to bail it out with public credulity is not going to make it recover.  The Darwin Party oligarchy needs to stop tinkering and tampering, remove its protectionist barricades, and let free inquiry have its way.  Intelligent design has the intellectual capital to inject into the logic markets.  Liquidity will result, knowledge banks will open up, and public confidence will stabilize the scientific institutions.  Freedom to invest in the best explanations, wherever the evidence leads, will once again usher in a prosperous era of bullish science.
Next headline on:  Cell Biology • Intelligent Design • Amazing Facts

Nonsense and Nonscience   10/17/2008    
Oct 17, 2008 — For an enterprise that prizes itself on objectivity and careful thought, science occasionally makes some outlandish claims.  Here are some things that slipped past the scientific method into the popular news media.

1. As good as it gets:  Steve Jones says men have stopped evolving.  Better enjoy what you have, because it’s not going to get any better, reported PhysOrg.  Jones said mutations may come to the rescue.  The short article contained only a small hint of doubt about all this: “That’s good news for those who like the human race just as it is, though perhaps bad news if humans need to evolve to meet some unexpected challenge down the road, the science – as yet not backed up by other research – suggests.”
2. Monster sex:  Some paleontologists seem to think they can deduce sex appeal from bones.  A particularly monstrous looking horny-headed dinosaur reported by National Geographic is a case in point.  Speaking for the male of the species, the reporter said, “Despite their less-than-cuddly appearance, researchers believe other Pachyrhinosaurs would have found the sharp adornments appealing.”
3. Close your eyes and listen to nothing:  Science Daily told about physicists who are trying to listen to dark matter.  No one has seen it, but they think maybe if they listen to the acoustic patterns of WIMPs they can hear it.  “Much of our understanding until now has been hypothetical,” the article stated in a quizzical oxymoron.
4. Buddha for peace:  What is Buddhism doing in the American Medical Association?  PhysOrg advised us on how to ease the stress of bailouts, recession, and depression: “Enter the meditative practice of mindfulness.  Born of Buddhist roots, it’s increasingly recognized as a measure to calm the mind’s chatter and elevate the brain’s thinking and organizational processes.”  Apparently the psychologists didn’t think to give Christians equal time, such as performing a controlled experiment on Philippians 4:4-8.
5. Arrrrrrgh, capitalism:  Not sure how this story got into Science Daily, but economist Peter Hayes at the University of Sunderland is trying to argue that the corporate business economy – indeed modern democracy – is a legacy of Long John Silver and Blackbeard.  No kidding: “the roots of modern democracy were not in Britain or the USA, but were the ‘corporations’ which were created on pirate ships during the golden age of buccaneering.”  Free-market economists must be shivering in their timbers.
6. God in the dock:  Apparently Live Science had no qualms about straying into theological and legal matters.  The ostensibly scientific news outlet reported that a judge in Nebraska threw out a man’s lawsuit against God.  On what grounds?  “the Almighty wasn’t properly served due to his unlisted home address.”  The plaintiff, by the way, is a state senator who “skips morning prayers during the legislative session and often criticizes Christians.”  He has 30 days to decide whether to appeal the ruling.  In a case like this, though, to whom does one appeal?

Talk is cheap.  That’s because the supply is greater than the demand.
    These stories illustrate that modern science has become a cult.  Any wild idea gets a free ride, as long as it is un-creationism and anti-Christian.  Show your Darwin Party badge at the door, recite the Standard Hate against creationism, and you can get free access to the press, who will lap up whatever you say like groupies, ask you no questions, and then pass it along unfiltered to the public.  Atheists and socialists get on the fast track to the microphones.
    Except for the last animated goodie, the stories above were all from leading science news outlets.  Remember this when we show you their latest “findings” on evolution.
Next headline on:  Dinosaurs • Evolution • Politics and Ethics • Health • Media • Dumb Ideas

“Science is truth,” chants Finagle’s Creed; “Do not be misled by facts!”  The limitations of scientific inference explored by Wolpert must hit thinking scientists like a rude awakening.  It’s like dreaming of climbing a mountain only to find oneself going up a down escalator.  The Truth about the Universe will forever remain beyond the reach of science.
    Binder ended on a confident note that science might still be converging on a close approximation of reality.  Oddly, he ended by showing that two subjects in fundamental physics are beset with shortcomings: the standard model of particle physics, and the so-far intractable problem of uniting quantum mechanics with gravity.  But then he said optimistically, in conclusion, “It is possible, though, that these various theories, along with all that we have learned in physics and other scientific disciplines, will yet merge into the best science can do: a theory of almost everything.”
    Almost is not good enough.  There will always be something else you cannot know.  Like Ken Ham quips: if you can’t know what you don’t know, you can’t know what you do know; and if you can’t know what you do know, you might know very little.  To which we add: how could you ever know whether the most important puzzle piece lies outside your world view, in the inference machine that cannot be inferred from within your system?  Maybe, for instance, the most important piece lies in theology.
Next headline on:  Cosmology • Physics • Philosophy and Theology

Selling Stem Cells to Voters   10/15/2008    
Oct 15, 2008 — If you thought embryonic stem cell research became moot after researchers found they could induce skin cells to become pluripotent, these news stories show the push is still on to open up more funds for embryonic stem cells.  A ballot measure in Michigan is a bellwether for how scientists still feel about these tantalizing objects in a Petri dish, so near yet so far due to ethical concerns.

1. Talking points:  To educate voters about a proposal on the Michigan ballot that would remove restrictions on embryonic stem cell sources, the University of Michigan issued a press release called, “Five things you should know about stem cell research.”  The goal of the article is to encourage citizens to vote yes on Proposal 2 for more access to embryonic (ES) stem cells, regardless whether “some aspects of embryonic stem cell research may pose an ethical or moral dilemma for some people.”  Summarized, here are their five selling points:
   1. Scientists agree it’s crucial to move ahead on all types of stem cell research: ES, iPS, and adult.
   2. The embryos represent the earliest stages of development.  They consist of undifferentiated blobs of cells that never grow into a fetus.
   3. Adult stem cells are only supporting actors in the quest for treatments.
   4. Induced pluripotent stem cells, though exciting, are not ready for prime time, because cancer-causing viruses are required to reprogram the cells into stem cells.
   5. Michigan scientists want access to their own embryonic stem cell lines instead of having to get them from out of state.
   In support of the second point, Sean Morrison of the university said, “The embryos that are used for research are microscopically small clumps of cells, smaller than the period at the end of a sentence on a piece of paper.  They have no specialized tissues of any type; there’s no nervous system, there’s no heart, there are no limbs.  These are clumps of cells that oftentimes in a fertility clinic don’t develop in a healthy manner and that doctors would not be willing to implant in patients.”
       The fourth point about the use of viruses for iPS cells was contradicted by an August story in Science Daily that said viral insertion is no longer necessary; a drug-like molecule can do the job.
2. Blame to go around:  Nature News showed that it’s not just ES researchers that can get embroiled in scandals.  A paper about adult mesenchymal stem cells faces retraction after other researchers could not replicate the work.  The authors are charged with manipulating images.  The one being investigated said he made “honest unintentional errors.”
3. Premises of promises:  Science Daily article last month involved studying the causes of Down Syndrome with the use of embryonic stem cells.  Researchers in London observed what happened to embryonic stem cells from genetically-engineered mice with an extra chromosome 21.  The study did not use human embryonic stem cells.  Nothing was said, furthermore, about how the study could lead to a treatment, other than hoping it might lead to clues some day.

Look hard for any justification of the use of human embryos in these articles.  What is it about human embryos that continues to drive scientists’ passion to own them?  If iPS cells and adult stem cells can provide essentially everything they wanted to accomplish for human treatments, and if mouse embryos can be studied for theory, why this insatiable lust for human embryos?  Were you impressed by any of their rationalizations?
    Consider some background issues.  First of all, there is still only hype to hope for cures from ES cells.  All the actual treatments are coming from adult stem cells.  Second, fraud is a general concern in scientific ethics and does not bear specifically on stem cell research.  Any case of fraud, even in celestial physics, deserves to be investigated.  The researchers in the adult stem cell case claim they made innocent mistakes.  Even if proven blameworthy, they did nothing on the scale of the Hwang scandal (02/05/2006).  In that case, the gold rush to be first drove the Korean scientists to stretch the truth.  Adult stem cell research, however, has been showing success for years.  The “me first” motivation was lacking.
    To the heart of the matter: look at the U of Michigan’s five selling points for Proposal 2 on the November 4 state ballot.  What can you find there other than greed and selfishness?  The scientists cannot point to anything that ES cells will do to help humans, other than make their unethical work easier and pad their resumes.  To show this, let’s rephrase their points to sell Nazi-style human experimentation on imbeciles.  Imagine yourself in the 1930s listening to eugenicists advocate Proposal 2X that would loosen up restrictions on human research that “some people” might find morally objectionable:

Five Things You Should Know About Imbecile Research
1. Scientists agree it is crucial to move ahead on imbecile research.
2. The imbeciles are not fully developed.  They have no skills as philosophers or artists, nor will they ever be implanted in a university classroom.
3. Volunteers with average IQs are only supporting actors in the quest for treatments.
4. Volunteers with average IQs are not ready for prime time, because it is difficult to get them to sign the release documents without coercion.
5. Michigan scientists want access to imbeciles without having to go to Germany.

Notice how the press release downplayed the moral issues.  It emphasized the word some: “But some aspects of embryonic stem cell research may pose an ethical or moral dilemma for some people.”  Who are the some people, if not the dimwitted citizens of Michigan who don’t understand that some university professor stands to make a lot of money or win a Nobel Prize?
    Embryos are just “microscopically small clumps of cells,” Morrison tells us (the reductionist fallacy).  If size is the issue, then all of us are mere specks of dust compared to the planet we live on.  Embryos have no specialized tissues or organs, he said, ignoring the fact that they have the complete genetic code to build those organs.  Children do not have their secondary sexual characteristics, either, if complete development is the criterion for humanness.  The ES cells are going to be thrown away by fertility clinics anyway, he argued.  God help us when utility becomes the standard for human worth.  The comatose, mentally retarded, elderly and disabled will have reasons to fear The Science Lab with that kind of ethic.
    Only Judeo-Christian morality, that deems human life sacred because we were created in the image of God, can save science from the Law of Unintended Consequences if all restrictions are eventually lifted from embryonic stem cell research.  Arguing that fertility clinics should send their discarded embryos to science labs begs the question whether they should have been created in the first place, and removes the Judeo-Christian barricade to the slippery slope.  Suppose, for comparison, we applied the pragmatic utility argument to aborted fetuses.  “Women are going to get abortions anyway,” advocates could argue; “wouldn’t it be better to get some scientific benefit from the discarded babies?”  A macabre market for fetal body parts would be created.  More women would get abortions, because Planned Parenthood could lure its victims with the line that they would be helping Science.  Abortions would skyrocket, and human life would be cheapened.
    ES research advocates lure citizens to bite the bill by dangling the loaded word “science” in front of it.  Those little cells in the Petri dish seem abstract, tiny, and impersonal.  But though they have no limbs or hearts or brains yet, they are completely human.  They contain all the genetic instructions for a full-grown human being.  That embryo has the potential to be a concert violinist, a charity worker, a businessman creating hundreds of jobs, a mother, a president, or a scientist some day.  You were once an embryo.  Would you have wanted your zygote to be discarded or cut up?  Whatever the Creator has allowed or disallowed in His own sovereign plan for the biological fate of humans is His business; it is not man’s to usurp.  Oh, but you don’t believe in God?  Then to whom are you going to grant the power to decide who gets the right to life?  Dread giving that power to any man: his next victim could be you.
    Civilization has, for the time being, reacted against the dark days of eugenics that classed some humans as imbeciles to justify treating them as subhuman.  Dehumanization has always been a halfway house to eradication.  We must regard any attempt to dehumanize human beings as opening a Pandora’s Box of terrors.  The Judeo-Christian padlock keeps it closed.  If scientists desire complete freedom to work on their fellow human beings as objects instead of persons with inherent dignity, we have the perfect place for them to set up their ES lab: North Korea.
Next headline on:  Cell Biology • Politics and Ethics

In evolutionary terms, tooth-like structures – such as the denticles that appear as a ubiquitous feature on the body armour of early vertebrates – might have preceded the advent of jaws proper.  The staggering histological diversity of such structures has led to byzantine systems of classification of vertebrate hard tissues, and in turn to serious differences of opinion.  The acrimony of these debates has scaled linearly with the lack of experimental embryological evidence about the underlying process.

The presence of denticles on the body of early jawed vertebrates led to speculation that, early in vertebrate evolution, embryonic ectoderm moved into the mouth and initiated organized tooth rows there.  In contrast to this ‘outside-in’ view of events is the ‘inside-out’ theory.  This theory holds that the evolutionary origins of teeth started in the mouth or pharynx and are linked to the presence of embryonic endoderm.  An outward migration of cells, or a co-option of a pharyngeal tooth-forming program in a part of the outer body surface, would have to occur to explain the presence of denticles on the outer covering of sharks and other more basal vertebrates.
    Both theories hinge on the idea that there is an inherent difference in the inductive power of ectoderm and endoderm, and that migration of one or the other is the crucial factor in tooth formation.  Implicit in this is the notion that tooth and denticle anatomy reflects embryonic origins – that is, that actual tooth or denticle histology can reveal which embryonic tissue was the key source.

....the authors show that there is no relationship between ectodermal and endodermal origin and the shape or nature of the resulting teeth – at least at the point when such teeth become visible.  The enamel of teeth can be of ectodermal, endodermal or mixed origin.  This is a dramatic finding.  It means that one cannot infer relative distributions of ectoderm and endoderm from tooth or denticle anatomy even in a living species, let alone in a fossil.

Nonetheless, Soukup and colleagues’ study removes the basis for theories depending on ‘co-option’ processes that would require migration of epithelial cells, and redirects future research.  We need to study the molecular co-option of tooth or denticle genetic programs, a process that might have occurred several times independently in the history of jawed vertebrates.  Which gene-regulatory regions are involved in switching on key regulators of tooth or denticle initiation in both epithelial and mesenchymal tissue?  How, where and when did these genomic regions evolve?  Are the same regions driving expression in ectoderm and endoderm?  Are the regions involved in patterning denticle fields also used for organizing feathers and hair?  And where are the ‘atoms of information’ that initiate, position and shape a tooth or denticle, and make its internal structure different from that of a dermal bone?

Ha!  This is rich.  Look carefully: did you find any explanatory power for evolution in this story?  No; it was all hand-waving and misdirection.  He waffled: it might be outside-in, it might be inside-out, but whoa!  The paper found both are wrong, so maybe it’s downside-up, upside-down, or over the rainbow.  For all this time, we listened to those grandiose tales of How the T. rex Got Its Teeth and other fables, and they never told us there was nothing empirical to back them up.  They can’t even look down in the mouth and find out what’s going on in a developing salamander right now.  How many years has it been since Charlie proposed natural selection as the explanation of all explanations?  All we see are questions and empty speculations.
    Making up words is not explanation.  Look at what Georgy did.  He’s got miracle-words everywhere.  He spoke of the “advent” of jaws.  That sounds downright churchy.  Jaws became flesh, and dwelt among fish.  It’s surprising the Darwin Party doesn’t celebrate Bite-mas in their Byzantine classification temple.  It must be hard to celebrate when “the acrimony of these debates scales linearly with the lack of experimental embryological evidence about the underlying process” of evolution.  Since the acrimony requires robust armor, you can bet the lack of evidence must be huge.  This is an inverse relationship: less evidence, more acrimony.  Do the new math.  In the set of scientific explanations, this means evolution is the empty set.
    There’s plenty more miracles in their story.  While divining the pudding (10/09/2008), they see the ectoderm moving into the mouth, where “it initiated tooth rows there.”  Well, great.  Who did the initiating?  Did it initiate the program on purpose?  Was it following a master plan?  No; they would say.  It was just another miracle of chance that worked.  Isn’t scientific explanation wonderful; the Stuff Happens Law is always there when you need it.
    Next, we are told that the “evolutionary origins of teeth started in the mouth... and are linked to the presence of embryonic ectoderm”.  It evolved because it evolved.  Then, as part of the hand-waving calisthenics, “An outward migration of cells, or a co-option of a pharyngeal tooth-forming program” would have to occur because, according to the puddingoscopy readout, evolution needs to explain both shark skin and shark teeth.  Tooth-forming program?  Who was the programmer?  Whence come the “atoms of information” that flow into teeth or into denticles?  Does information have any meaning without an observer?
    The workout turns intense with extreme jawboning exercises: “We need to study the molecular co-option of tooth or denticle genetic programs, a process that might have occurred several times independently in the jawed vertebrates.”  Wow; that’s real miracles fer ye, o ye of little faith.  What is co-option, if not a sleight-of-mind personification of intelligent design?  It’s the old the Tinker Bell defense.  The evolution fairy decided that jaw ectoderm needed a little bite, so zap! a tooth was born.  Do you have any idea how complex a mouth full of teeth is?  Each tooth has roots, blood vessels, dentin, enamel, a precise shape for its function, and a matching tooth on the other jaw, to say nothing of genetic programs to assemble them at the right time and replace baby teeth with permanent teeth.  To assume that they will just “occur” (note the miracle word) not once but several times independently is absurd.  Since Georgy needed every trick in the evolutionary explanation cookbook, he even threw in a little Haeckel recapitulation theory for taste: “Implicit in this is the notion that tooth and denticle anatomy reflects embryonic origins – that is, that actual tooth or denticle histology can reveal which embryonic tissue was the key source.”  That’s ontology recapitulates phylogeny, in case you missed it.  But Mr. Scientist, Sir, we’re kind of tired of “notions.”  When are we going to get your scientific explanation?  (Notions are found in fabric stores near the sewing machines.  If you use notions without strong empirical fabric, whatsoever you sew you shall also rip.)
    The real howler of miracle-words was mentioned so surreptitiously you might have missed it.  He spoke of the “inductive power of ectoderm and endoderm”.  Clearly, Georgy was not talking about logical induction here.  He was talking about some mystical power in tissue cells that could induce them to evolve into teeth.  If there is a more blatant case of pulling a rabbit out of a hat (in this case, a hard tooth out of squishy cells), then clap wildly for the magic show.  This is circumlocution pretending to be scientific explanation.  It’s as comical as Moliere’s satire on Aristotelian explanations when the doctor in one of his plays explains why opium induces sleep – because it has a “dormitive virtue.”  In the same way, this Doctor Koentges put his readers to sleep by hypnotizing them to envision tooth evolution occurring as a result of the “inductive power” of ectoderm or endoderm cells.  To put it simply, he is saying, “evolution occurs because of the evolution-inducing power of material substances.”  Pray tell how this improves on animism.
    The Darwinists are so clever.  They hide their miracles in highfalutin words.  They shield their faith with cryptic jargon.  These are the same people who turn around and accuse religious people (especially the dastardly creationists) of using God-of-the-gaps logic whenever they can’t explain something.  Creationists and ID advocates, we are told, bring science to a halt by just appealing to faith and saying, “God did it, I believe it, that settles it.”  Come now.  Let’s play “find the hypocrite.”
    Reality check time.  Turn off the reruns of the Darwin Charade Parade, stop looking at the cheerleaders (09/29/2008 commentary), and examine what’s left.  Speculation.  Dramatic findings that long-held theories are falling by the wayside.  New unanswered questions.  Byzantine systems of classification (is this the Dark Ages?).  A rare honest admission that “one cannot infer relative distributions of ectoderm and endoderm from tooth or denticle anatomy even in a living species, let alone in a fossil,” meaning that any hope of reconstructing the evolution of teeth is doomed from the start.  More vaporware.  More futureware.  This, folks, is the magic of evolutionary explanations: it’s all bombastic oratory about change we can believe in, without a plan or a policy that will work in the hard, cruel world of reality.  That’s why you have to believe in it.  Wishful thinking, if strong enough, eases the pain when you hit bottom.
    When in doubt, look tough.  “Cracking such hard technical nuts will require strong intellectual teeth as well as robust body armour,” Koentges said, “given the vigour of opinion on this subject.”  He hasn’t seen anything yet.  Just when he thought this was only intramural warfare, the Visigoths showed up over the horizon (05/09/2006)  Unlike the obese and lazy Darwin Party animals, they don’t use plastic teeth and cardboard armor.  They look disciplined, determined, and armed to the teeth.  For combat over the truth of the tooth, they’re prepared for a bite to the finish.  General Dawkins rallies his troops out of their drunken stupor, bluffing that the Visigoths are a pushover because they trust in “faith” instead of “science.”  Better have some bite behind the bark; and remember, let not the one who puts his armor on boast like the one who takes it off.
Next headline on:  Mammals • Marine Biology • Terrestrial Zoology • Evolutionary Theory

Plants Have Thermostats   10/13/2008    
Oct 13, 2008 — Plants, being stuck in the ground, have few options when it gets hot.  They may not be able to move into the shade like animals, but they know how to cope.  They have a built-in thermostat that acts like a fire prevention department.  Science Daily tells the story.
    Researchers at Michigan State identified a protein named bZIP28 that lives in the cell around the endoplasmic reticulum (ER), a bundle of tubes and tunnels that acts like a protein assembly, storage and distribution center.  This little protein acts something like a firehouse dog on a leash, tied to the walls of the ER.  When the temperature reaches a certain point, the leash is cut, and the dog runs off into the nucleus, where he barks, so to speak, and sets off a chain reaction.  “The bZIP28 protein is anchored in the endoplasmic reticulum, away from its place of action,” an MSU biochemist said.  “But when the plant is stressed by heat, one end of bZIP28 is cut off and moves into the nucleus of the cell where it can turn on other genes to control the heat response.”
    Researchers found that cells without the firehouse dog died when the temperature rose above a certain level.  Another researcher on the team remarked, “We’re finding that heat tolerance is a more complex process than was first thought.”

Science makes progress when researchers leave the shrine of Darwin and examine the details of plants and animals with design in mind.  Now that we are beginning to unravel the complexities of just one subsystem of plants, the heat response, we might be able to engineer it to allow desirable plants to grow in arid climates for the good of the people.  This is how science should be done.
    On a somewhat related note, Science News printed a feature story about growing farms in the city.  Why not?  Rooftops and special greenhouse skyscrapers could turn jungles of steel into generators of fresh air, flowers and food.  Hydroponics allows growing many plants in water without soil.  Imagine getting fresh tomatoes from the building next door instead of a thousand miles away.  Even barges and abandoned buildings could be put to use, while farmland can get a Sabbath rest or be returned to its native forest ecology.  Upward farming: once the engineering and cost challenges are worked out, this could become a sensible green trend to help humans and their plant friends co-exist.
Next headline on:  Plants • Genetics • Amazing Facts

If it could work, then this is an answer to one way to build an omnidirectional beacon.  It would be an example of an ‘almost natural’ signal that would get captured in a survey of the universe by an emerging technology, that’s us, and finally recognized in a database by some curious grad student.

SETI researchers still do not get it.  They employ exactly the types of scientific reasoning used by the Intelligent Design community to justify the design inference as scientific.  ID claims that intelligent causes can be separated from natural causes by means of a design filter – design is the last-resort inference when chance and natural law have been ruled out.  Would not the SETI people do the same?
    In fact, they would probably work hard to rule out natural law first.  They would see whether an altered Cepheid belongs to a new class of naturally pulsating stars.  Natural law would probably be their default hypothesis.  The astrophysicists would go to work on theories to explain the Cepheids that don’t fit the current theory.  Only as a last resort would the improbable hypothesis of an intelligent cause be considered.  The same is true for the neutrino beams.
    Even so, this article makes it clear that SETI researchers would feel justified in inferring intelligence from natural phenomena.  So do forensic scientists, cryptographers, and archaeologists.  There is nothing new, really, in the ID approach.  People have employed ID reasoning ever since ancient Sumer and beyond.  ID just formalized the logic behind the way we separate intelligent causes from natural causes.  The identity of the designer is not the question.  A coroner may have no clue who the murderer was when deciding a crime victim did not die of natural causes.  A cryptanalyst may not be able to read the message or know its purpose when determining that a string of bits is too improbable to have originated by chance.  The reasoning is the same in any field where design principles are used: whether studying the contours of a possible stone tool, the marks on a cliff in an unknown language, or the information content in DNA.  The ID Movement is really a call for fairness.  What’s good for SETI should be good for biology.
    SETI has no recourse in counter-claiming that the aliens evolved by natural causes.  You can’t tell anything about the aliens from the content of their message.  Even if they were to tell us they evolved, how could we know they were telling the truth?  Jill Tarter would have no way to tell that demons were not out there lying to her for the fun of watching her trip over herself on the way to the phone to tell the world she had found another case of the evolution of intelligence.  Liars can be clever.  “We are here to serve man,” their cookbook says.  More likely, though, the whole world would just miss the message.
    This illustrates another important ID principle.  The Design Filter can leak false negatives, but never false positives.  A false negative means that something might be designed but we didn’t detect it.  Modern art doesn’t look designed sometimes, and a murderer might have committed such a perfect crime that the coroner thinks it was a natural death.  In the same way, could SETI know whether all Cepheid variables have been tweaked by aliens?  No way.  The aliens could be in cahoots.  They could have a standard of tweaking Cepheids that misleads us novices on earth into thinking that the stars are just obeying a natural law.  We would not see the design that is there: that’s a false negative.  The Design Filter is impervious to false positives, however.  If the stringent criteria for design are met, a scientist can be certain it was designed.  Once natural law and chance are ruled out, and a match to an independently specified pattern is found, it clinches the case: the phenomenon was designed.
    ID has set the criteria so high, it’s overkill.  ID’s standards are much higher than those stated in the Science News article.  If it is fair for SETI to theoretically infer design from a few neutrinos, and if an archaeologist is allowed to infer design from a sharp-edged rock, and a court of law can convict a felon based on evidence that is beyond reasonable doubt, then all scientists should be willing to consider the overwhelming evidence for design in astronomy and biology.  They should not rule out the design inference due to prejudice.  Design detection is as neutral as an input in computer software passing a series of if-then statements.  The identity of the designer is downstream from that decision node. 
Next headline on:  SETI • Intelligent Design • Astronomy • Physics

“Beaver are an essential ecosystem engineer,” said co-author Steve Zack of the Wildlife Conservation Society.  “Beavers help repair degraded stream habitats and their dams and associated ponds recharge local water tables and create wetlands.  With our changing climate likely to mean increasing droughts in the West, managing ways to allow watersheds to act more like sponges will be a challenge.  Beaver are a powerful tool to be considered for that, and the associated benefits to other wildlife add to their value.”

The article includes a picture of a beaver dam in Lundy Canyon along the eastern Sierra.  For a little visual vacation, your trusty reporter has posted a picture he took in August a few miles south of there along McGee Creek.  Note the lush habitat all around the pond.  Can you spot the beaver house?
Quiz questions: (1) What is the plural of beaver?  (2) What are the young called?  (3) How big was the largest beaver in the fossil record?*
Next headline on:  Birds • Mammals

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*Answers: (1) Both beaver and beavers are acceptable.  (2) Kits.  (3) The North American Giant Beaver, one of the largest rodents that ever lived, grew as large as a grizzly bear and probably weighed 300 pounds or more.

Deep Life Is Right at Home in Total Darkness   10/10/2008    
Oct 10, 2008 — It seems every year scientists find organisms thriving in environments thought too inhospitable for life.  A new word was coined for these organisms: extremophiles – lovers of the extreme.  Two recent discoveries push the envelope of extreme environments almost to the deep limit.

1. Pressurized fish:  The bottoms of the deep ocean trenches of the Pacific have never been photographed – till now.  It took Oceanlab, a robotic submarine, five hours just to reach bottom – 7700 meters down, almost five miles below the surface.  It is completely dark down there.  The pressure is so high – 8000 tonnes per square meter – it would be like 1600 elephants piled on a car.  The temperature is freezing.  Imagine the astonishment of scientists finding schools of snailfish happily feeding in social groups.  The picture is there on Science Daily.
       The director of Oceanlab said, “It’s incredible.... We thought the deepest fishes would be motionless, solitary, fragile individuals eking out an existence in a food-sparse environment,” but they were agile, not fragile.  “The images show groups that are sociable and active – possibly even families – feeding on little shrimp, yet living in one of the most extreme environments on Earth.”
2. Gold strike:  Science Daily also reported one-of-a-kind microorganisms living in a gold mine 1.74 miles below ground.  These organisms are not part of a food chain.  The subsist entirely on hydrogen and sulfate produced by radioactive decay of uranium.  They live in total darkness, with no oxygen.  The genome of this microbe shows that it shares many genes with Archaea, many species of which also live in extreme environments like hot springs.  This species appears to live in solitary confinement in the crust of the earth where no nutrients from the biosphere reach it.
       The microbe was named Desulforudis audaxviator.  Its genome was found to be a superset of the raw essentials.  It has 2,157 protein-coding genes, more than the 1500-some-odd genes of streamlined bacteria.  This surprised the scientists: “The genome was not as streamlined as might be expected of an organism living in what is presumably a very stable environment.”  It “contained everything needed for the organism to sustain an independent existence and reproduce, including the ability to incorporate the elements necessary for life from inorganic sources, move freely, and protect itself from viruses, harsh conditions, and nutrient-poor periods by becoming a spore.”  Apparently this is the only species living in the habitat of a deep gold mine in South Africa.

“One question that has arisen when considering the capacity of other planets to support life is whether organisms can exist independently, without access even to the sun,”says [Dylan] Chivian [Berkeley Labs].  “The answer is yes, and here’s the proof.  It’s sort of philosophically exciting to know that everything necessary for life can be packed into a single genome.”

“Evolution has equipped the versatile spelunker with genes....” Oh, please.  No fairy tales while we are trying to appreciate the wonders of creation.  It’s like stocking fool’s gold in a gold mine, or dousing a deep-battered fish dinner with ipecac.
Next headline on:  Marine Biology • Cell Biology • Genetics and DNA • Origin of Life • Amazing Facts

Exactly why turtles evolved their shell remains a mystery, Joyce says.  A full shell might offer added protection and stability.  And the proof could be in the pudding – their body plan is the world’s oldest, changing little over 200 million years.  “For some reason just being a turtle is an idea that came along and just really works,” he says.

Joyce’s comment is so worthy of the SEQOTW prize, he gets to share it with Gill Bejerano (see next entry).  Can you believe what the Darwinists get away with in science these days?  If we are to understand this article, chance came up with an idea (stop right there).  Does your pet rock ever come up with ideas?  How about the dust devil sweeping over the highway?  Furthermore, this idea came by pure chance.  Here we have the Darwinians resorting to the Stuff Happens Law again (see 09/15/2008 commentary).  Then they tell us that such ideas, emerging by chance, are so good, so wondrously engineered, that “for some reason” naturalism knows what, chance decides they “work” very well.  So here Lady Luck is not only an inventor but the judge of the invention.
    How do we know this is a great idea?  Well, they say, the proof is right there: in the pudding.  This opens up a whole new method of divination (07/26/2008 commentary) for the Darwinian soothslayers (Note: sooth means truth).  We’ll call it puddingoscopy.  Lady Luck looks into her pudding and finds proof, Joyce says.  The angle of the folds and bubbles, the color and texture, or some other attributes of unknown character, provide her with clues.  An “idea” flashes into her mind.  Her imagination tells her it will “work.”  She fleshes out the details, records it in genetic information, and there it remains: a best-seller for 200 million years.
    What we’re witnessing here is not the origin of turtles, but rather the origin of new chapters in Darwin’s Just-So Storybook (09/30/2008).  This one, “How the Turtle Got Its Shell,” is always printed in hardback: perhaps for protection and stability.  “For some reason, just being a turtle is an idea that came along and just really works.”  “Just”?  In science, plagiarizing intelligent design for Lady Luck should be considered very unjust.  CEH declares a citizen’s arrest (see 09/30/2007 commentary).
Next headline on:  Fossils • Terrestrial Zoology • Evolution • Dumb Ideas

“Evolution is a lot of fun,” said Bejerano, who plans to continue the investigation into what the ultraconserved segments might be doing.  “You answer one question, and five others pop up.  But one of the most rewarding things to me is the fact that we’re developing a growing appreciation for how much these regions actually matter.”

Would you count on an evolutionist to know what makes sense?  Their pet theory can be falsified right before their eyes, and instead of weeping in remorse, they call it fun.
    Suppose van Helmont called it fun when Francesco Redi showed that mice do not spontaneously arise from straw.  “Spontaneous generation is a lot of fun.  You answer one question, and five others pop up.”  Nobody denies that Fantasyland is fun.  It’s just that we appreciate it for its escapism, not for how much it actually matters.
Next headline on:  Evolutionary Theory • Genetics • Dumb Ideas

Are We Getting Biased Science?   10/07/2008    
Oct 7, 2008 — Much more scientific research is being done than ever gets reported, say three researchers in a story reported by Science Daily.  High-impact journals tend to report selectively from a large field of medical and laboratory research.  As a result, “only a small proportion of all research results are eventually chosen for publication, and these results are unrepresentative of scientists’ repeated samplings of the real world.”  This gives a very distorted view of scientific research, they said.  They feel it is a “moral imperative” to fix the way scientific research is judged and disseminated.

There is a strong likelihood that the Darwin-loving mainstream journals give inordinate publicity to evolutionary papers.  If the journals printed a true sample of the actual laboratory research that goes on, the science-to-Darwin ratio (like the signal to noise ratio) would probably shoot way up.  Science would sound much sweeter and clearer without the constant noise of evolutionary static.
    This is the Darwin Party’s pump-and-dump scheme.  They artificially inflate the value of evolutionary research, then dump it on the unsuspecting public who think they are getting unbiased science.  This devalues science for everyone.
Next headline on:  Politics and Ethics

The pictures don’t look convincing.  If they prove to be tracks, it doesn’t help the evolutionists, anyway.  Worms and millipedes are already highly-complex organisms.  Imagine how much genetic information is required for an animal to walk with multiple legs.
    Without the bodies of the track-makers visible, no claims can be made these represent transitional forms.  It appears the authors have not ruled out other more mundane explanations.  This claim needs much better evidence.
Next headline on:  Fossils • Dating Methods

It’s always error-prone to try to rescue a theory with ad hoc appeals to imponderable substances.  The Oxford team may be off the wall, but their off-the-wallness is only a matter of degree from the consensus theory of dark energy.  This article also points out that astronomers don’t know as much as they claim they do.  The uniform distribution of matter and the Copernican Principle are shown to be assumptions – not observations.
Next headline on:  Cosmology

Living Better Bioelectrically   10/04/2008    
Oct 4, 2008 — Electric eels are inspiring a new generation of fuel cells.  Science Daily reported that a remarkable fusion of engineering and biology may lead to tiny electronic devices that run on biology’s own energy currency, ATP.  “Engineers long have known that great ideas can be lifted from Mother Nature, but a new paper by researchers at Yale University and the National Institute of Standards and Technology (NIST) takes it to a cellular level.”
    The voltage-generating cells in an electric eel are called electrocytes.  They work by pumping sodium and potassium ions in and out of the cell membrane through specially designed channels or gates (see 01/17/2002).  The cells are then stacked in series, to build up voltage, and in parallel, to build up current.  The result?  An electric eel can generate 600 volts – enough to knock a horse off its feet (see National Geographic).  Electric eels and other forms of electric fish use their powers primarily at lower levels for navigation (05/05/2004), communication, and even courtship (see 06/20/2007, bullet 5).
    The Yale-NIST team is using a “systems biology” approach (08/21/2003), considering the overall context of function, to understand and build on biological technology.  Of seven types of channels in the cell membrane, the specifications of each are being examined: reaction time, density in the membrane, and more.  “Nerve cells, which move information rather than energy, can fire rapidly but with relatively little power,” the article said, whereas “Electrocytes have a slower cycle, but deliver more power for longer periods.”  Tweaking the specs in engineering models allow bio-engineers to optimize voltage production for human applications.
    The article not only ignored evolution completely, it seemed positively fixated on design.  “Applying modern engineering design tools to one of the basic units of life, they argue that artificial cells could be built that not only replicate the electrical behavior of electric eel cells but in fact improve on them,” the body of the story began.  David LaVan, NIST engineer, put it this way: “Do we understand how a cell produces electricity well enough to design one—and to optimize that design?”  This is reverse engineering – which implies intelligent design.  An engineer has to see and appreciate design to want to emulate it.
    In this case, engineers don’t have to copy the design with their own components made from scratch, as with gecko-foot tape (see 12/06/2006, 06/20/2007.)  They can take parts from existing off-the-shelf technology and adapt it for human-designed applications.  They can use engineered proteins to build membranes.  They can tailor bacteria or mitochondria (cellular powerhouses) to produce ATP for energizing the reactions.  They can modify electrocytes to produce continuous electrical current instead of pulses.
    An interesting question comes to mind.  If an extraterrestrial engineer were to land in the lab and study the eel and the biological electronics designed by humans, would it know where the evolution stops and the intelligent design begins?

Answer: yes, it would know that evolution stopped at the science door and intelligent design produced the whole show.  Evolution as a concept would be the trash can for explaining mistakes and degeneration.
    “Nerve cells ... move information rather than energy.”  Did you catch that?  Your body is wired for the intranet as well as for power.  Let CEH help empower you to get good information flowing.
Next headline on:  Marine Biology • Biomimetics • Physics • Intelligent Design

Bangin’ Around to Get Something New Under the Sun   10/03/2008    
Oct 3, 2008 — You’ve heard of the Big Bang, and the Cambrian Explosion.  Now, to get the solar system started, astronomers have added a Little Bang to move things along in the naturalistic path from nothing to everything.  Science Daily, Space.com and PhysOrg all reprinted a press release from the Carnegie Institution claiming that a nearby supernova led to our solar system.
    Alan Boss thinks he’s gotten the devil out of the details.  A nearby supernova, you see, was needed in the model for two reasons: to get our sun’s birth cloud to gravitationally collapse, and to seed it with isotopes like iron-60, whose short-lived daughter radionuclides are found in some meteorites.  These two requirements did not work well together.  “Until this study,” Boss explained, “scientists have not been able to work out a self-consistent scenario, where collapse is triggered at the same time that newly created isotopes from the supernova are injected into the collapsing cloud.”  By fine-tuning the explosion in his computer model, Alan Boss and team found a way to keep the right ingredients together.
    Students of solar system cosmogony may not have realized that the supernova-shock model was so plagued with difficulties.  A 10-year-old conundrum regarding the need to heat by compression at the same time the cloud cools by radiation “has left serious doubts in the community about whether a supernova shock started these events over four billion years ago or not,” one astronomer commented.  But now, Boss has hope again.  “This is the first time a detailed model for a supernova triggering the formation of our solar system has been shown to work,” he admitted.  “We started with a Little Bang 9 billion years after the Big Bang.”

Well, that just makes our planet even more privileged than ever to have had such a fine-tuned explosion nearby to gently deliver our baby sun.  Better not expect this to have happened so delicately around other stars.  Alan Boss, you may recall, rocked the astronomical community a few years ago by proposing his heretical disk-instability model for the origin of planets, as opposed to the conventional slow gravitational accretion model, which was struggling with the problem of planetary migration (see 03/21/2006).
    Why this evolutionary fascination with explosions?  It’s all they have, folks.  In the absence of a designing intelligence, they have to look at what remains: chaos, chance and violence.  From bangs and booms and flotsam and jetsam the most graceful and elegant examples of design known to man just magically “emerge” by chance.  And they call creationists stupid-stitious.
    At least creationists have more fun.  They are in church praising God, the supreme Architect of our fine-tuned universe, using their whole being – body, mind and emotions – in joyful celebrations with highly-skilled musicians employing finely-crafted instruments, singing out with all their might the glories of One who knows how to employ controlled energy toward purposeful ends:

O Lord my God, when I in awesome wonder,
Consider all the worlds Thy hands have made;
I see the stars, I hear the rolling thunder,
Thy power throughout the Universe displayed.
Then sings my soul, my Savior God, to Thee:
How great Thou art!  How great Thou art!

Meanwhile, in dreary laboratories, morose naturalists, their minds lost in imaginary worlds, trying in vain to get their brains to emerge from a series of explosions, drone on:

Talkin’ to myself and feelin’ old,
Sometimes I’d like to quit,
Nothin’ ever seems to fit;
Bangin’ around,
Nothing to do but frown;
Reinin’ in my models always gets me down.

Next headline on:  Cosmology • Astronomy • Solar System

Reducing Human Behavior to Natural Laws   10/02/2008    
Oct 2, 2008 — Can human behavior be reduced to natural laws that science can study in a morally neutral way?  Darwin sought to incorporate all aspects of the living world, including behavior, in natural laws that were amenable to scientific explanation.  Evolutionary biologists and neuroscientists continue in that tradition today.  Consider two recent examples in the literature that described how human behavior evolves.

1. One nation, under Darwin:  PhysOrg published a short article 9/24/08 about how a strong leader can benefit society.  “In a study that looks at the evolutionary role of leaders in society, the researchers explored how having a leader in charge – with the power to punish – works better than spreading responsibility through the entire group.”  They said that a leader who punishes cheaters and freeloaders increases the cooperation and riches for everyone.
       The article talked about how strong leadership benefits the “greater good,” but failed to mention if the model applies equally well to tyrants.  The lead author, who holds the Canada Research Chair in Culture, Cognition and Evolution, was probably not thinking about the exquisite methods of punishment of leaders like Stalin or Kim Il Sung.  Natural laws, however, are indifferent to morals.  It could be argued that their strong leadership did accomplish their national goals quite effectively.  In fact, political scientists often point out that dictatorships are the most efficient forms of government – much more so than democracies and republics with their inevitable delays from long debates, power struggles and drawn-out campaigns. 
2. Evolutionary utopia:  Another study was aware of the possibility of mass murder.  “Cultural boundaries have often been the basis for discrimination, nationalism, religious wars, and genocide,” began a paper in Science last week.¹  “Little is known, however, about how cultural groups form or the evolutionary forces behind group affiliation and ingroup favoritism.”  This shows right off the bat that they were looking for evolutionary forces, not moral or intelligent causes, behind such effects.  In fact, the paper remained fairly dispassionate about favoritism (which could entail genocide).  Note the word meaningless in their next sentence: “Hence, we examine these forces experimentally and show that arbitrary symbolic markers, though initially meaningless, evolve to play a key role in cultural group formation and ingroup favoritism because they enable a population of heterogeneous individuals to solve important coordination problems.”  So it’s also a paper on the evolutionary emergence of meaning.
       The paper approached human poopulations amorally.  A sample population might involve two races at war, communists vs capitalists, or identical people with red shirts and blue shirts – it doesn’t matter, as long as what happens as they interact is explainable in terms of “evolutionary forces.”  The authors were not looking for the thoughts and philosophies and morals of the individuals as having any explanatory power; it’s all about how a population evolves.  Presumably this could explain ant behavior as well as human behavior.
       The symbolic markers that were a key element in their model were extremely generic: “This process requires that individuals differ in some critical but unobservable way and that their markers be freely and flexibly chosen.”  Once the markers are identified, “markers become accurate predictors of behavior.”  A natural law is born:

   The resulting social environment includes strong incentives to bias interactions toward others with the same marker, and subjects accordingly show strong ingroup favoritism.  When markers do not acquire meaning as accurate predictors of behavior, players show a markedly reduced taste for ingroup favoritism.  Our results support the prominent evolutionary hypothesis that cultural processes can reshape the selective pressures facing individuals and so favor the evolution of behavioral traits not previously advantaged.

   What do they mean by “meaning”?  They asked this question later in the paper: “How does symbolic meaning emerge in the absence of fiat?  (Fiat, presumably, involves intelligent causation.)  Their evolutionary theory produces meaning out of meaninglessness: “Interestingly, mixing players with different expectations, which creates the original problem, also creates a potential solution,” they answered.  “It does so by producing small amounts of covariation that can feed back into the system and accumulate dynamically.”  This is meaning at its most rudimentary, biological, content-free level.  Any covariation that becomes self-reinforcing becomes a measure of meaningfulness.  If the players on the game board start cooperating around an arbitrary symbolic marker, no matter if they are computer soldiers in a war game, bacteria in a petri dish or human slaves, then meaning has “emerged” in this dispassionate world of evolutionary explanation.  One only has to follow the dynamical outcome.  In their experiments on human subjects playing contrived games, “These results indicate that players showed a general tendency to couple behaviors and markers,” they continued.  Notice how content-free and values-free the generalized laws were described: “This tendency, however, was strongest when a player hit upon a successful behavior-marker combination, and it was further reinforced and amplified in the marker-maintained treatment when the marker was not prevented from acquiring meaning.”  Meaning, here, is not meaning in the traditional sense of semantics.  It is self-reinforcing behavior linked to a symbolic marker that brings out the unobservable differences in a population.
       Ostensibly, all the researchers were trying to do is understand why humans tend to rally around symbols.  Why do people cheer for their flag when the flag initially was just a piece of colored cloth?  Moral principles, values, propositions, philosophies and theologies have nothing to do with it, from their perspective.  It’s just the way evolutionary forces produce outcomes.  Notice how generic the language is:

   These results show how the evolution of cultural groups can reconstitute the social environment and produce selection for an ingroup bias that was not initially advantageous.  If selective pressures of this sort were common in past human societies, a plausible outcome would arguably be a relatively inflexible bias leading individuals to prefer others similar in some symbolic dimension.  This idea is consistent with much research showing an astonishing willingness for subjects to exhibit ingroup favoritism when groups are based on trivial, short-lived distinctions. 

   They performed more experiments to see if the favoritism might have been biased beforehand.  They ran correlation coefficients, charted measurements on graphs, and did other scientific things.  Conclusion: evolutionary forces are sufficient to explain what happened.  Trivial groups evolve into cultural groups.  Any symbolic markers, however trivial and meaningless, provide rallying points for unobservable differences between individuals in populations to express themselves.
       In their final paragraph they put this all into perspective.  Think of how many complex human situations, how many battles, cross-town rivalries, special-interest clubs, fads and cultural revolutions are now explainable in terms of simple evolutionary laws:

   The research on intergroup processes indicates that people have a willingness to show ingroup favoritism, and in particular this holds even when groups are trivial and evanescent.  This research tradition has generally examined neither the evolutionary mechanisms behind group formation nor the impact of these mechanisms on ingroup favoritism.  We implemented an experiment in which the significance of groups had to arise, if at all, endogenously, thus providing an evolutionary foundation for ingroup favoritism.  In this setting, trivial groups remained trivial under certain circumstances, but under other circumstances they developed into cultural groups composed of individuals who shared both behavioral expectations and symbolic markers signaling group affiliation.  Ingroup favoritism was strongly associated with cultural groups but not with trivial groups.  Our experiments made exclusive use of coordination games, which serve as a kind of generic proxy for strategic settings with multiple equilibria.  Many strategic settings are characterized by multiple equilibria, and thus the dynamical processes examined here have potentially broad significance.  The mechanisms implicated in the evolution of human prosociality, for example, often produce multiple equilibria, and so cooperation is a behavioral domain with considerable scope for the path-dependent evolution of groups with different norms and expectations.  In this sense, cooperation can be analogous to coordination.  Even more generally, whenever people have a shared interest in distinguishing among themselves in terms of their unobservable information, whatever that means in a given situation, the logic behind the evolution of cultural groups holds.

If any of you were swayed by the claims in these papers, you need a serious deprogramming session, kind of like soldiers being deloused after returning from a jungle.  If you don’t see yet how these articles are logically self-refuting and morally pernicious, please, get on your thinking cap.  You will need it because the evolutionists just removed it.  They said you don’t need it any more because you are just a victim of evolutionary forces.  Somehow they are immune to the evolutionary forces acting on them, because they belong to the Yoda Order of the Disinterested and Detached Scientifically Wise Wizards.  This is an ingroup favoritism they must maintain, as evolutionists on a higher plane than the rest of us, lest we on the playing field look at them and accuse them of writing their papers only because evolutionary forces made them do it.  That would be their undoing.  It is vital, therefore, that they maintain their illusion of objectivity.
    Undoubtedly they could point to plenty of examples of strongly-held group loyalties around meaningless markers: skin color, favorite food, team flags, arbitary national allegiances (for instance, whether the Sicilians should have allied with Rome or Carthage), and whether to join the Lions Club or the Loyal Order of Moose.  People have an innate ability to identify with fellowships, wear the uniform, and rally behind the standard of their favorite group identity, no matter how profound or silly.  Watch political conventions and observe the crazy ecstasy of crowds cheering on their standard-bearer.  Think about Lincoln demoting indecisive generals and choosing strong, ruthless generals willing to punish non-cooperators and get the job done.  A defender of the two studies above might argue, doesn’t it make sense to try to understand these human tendencies scientifically?  The authors might deny our charge of promoting themselves to the Yoda Order of the Wise.  They might say, “We are humans like the rest of you.  We acknowledge we have these tendencies ourselves.  We’re not making moral judgments.  We feel that by investigating scientifically, with controlled experiments, what makes us act the way we do, how group loyalties emerge, and why we look to strong leaders, we can avoid some of the pitfalls of ignorance about these matters and approach problems in ways more likely to avoid conflict and bring about peaceful solutions.  By understanding our social dynamics, we can try to make the world a better place.  Once we understand the evolutionary tendencies that influence our actions, we can learn to control them, and thus avoid some of the racism and genocide that has plagued human history.  Why are you criticizing this?  What’s the matter with you?  Aren’t you the pernicious ones who would interfere with the progress of science?”
    Such criticisms make some sense from a Judeo-Christian perspective.  They make absolutely no sense from an evolutionary perspective.  The claims and questions in the previous paragraph borrow heavily from Judeo-Christian presuppositions and values: honesty, fairness, truth, beauty, peace, understanding, morality.  Remember, the evolutionist believes everything consists of particles in motion obeying natural laws (which cannot be construed as laws in a designed or moral sense, but only as patterns in experience).  It’s as if these researchers burglarized the Judeo-Christian house, stole all the tools and utensils and furniture, raided the refrigerator, then took it to Darwin’s house and served up a feast for their friends they never could have cooked up out of their own resources.  That’s why their explanation is not just dumb, but pernicious.  They’re bloomin’ thieves.
    Now if they want to become Christians, we can talk.  We can reason.  We can discuss the pros and cons of their propositions, some of which may be partly accurate (though ignoring the intellectual aspect of human behavior is bound to produce error).  We can let them recast their theory, provided they strip out all the evolution talk and reference their sources.  Since Jews and Christians believe humans are made in the image of God, it is possible for people to use their eyes to study the eye, their hands to study the hand, and their minds to study the mind.  Animals and plants do not do such things.  Your cat may look in the mirror, but it does not come up with a theory of cat behavior and write it up in a scientific journal.  Cats do not have self-awareness, abstract reasoning ability, language, ontology, epistemology, moral philosophy and all the other prerequisites for explanation.  Animals don’t explain things; they just operate.  They may memorize patterns and learn behaviors that reward actions, but they do not deal in concepts.  They do not ponder meaning in life and ultimate reality. 
    As human beings with an imago Dei (image of God), we have the mental and spiritual resources to operate in the conceptual realm.  At the same time, we have physical natures we share with the animals (stomachs, kidneys, vertebrae, etc.).  But in what organ does self-awareness and abstract reasoning reside?  Our dual nature produces confusion to evolutionists, but the spiritual and intellectual (non-physical) nature is uniquely human.  We are persons.  This is what allows humans, and humans alone, to observe and explain their own behavior.  As created beings, we can observe (and sometimes laugh at) those behaviors that reflect our shared properties with animals: talking like a crow, following the herd, strutting like a peacock, loafing like a sloth, and pigging out at the dinner table.  It is the fallacy of reductionism to suppose that our physical nature entails our spiritual nature.  Honesty, truth, courage, explanation, morality – these and many other qualities that make a man a man instead of a mouse refer to eternal realities.  What is true or moral unless it refers to that which is unchanging, permanent, universal, necessary, and certain?  You can’t get that from randomly moving particles, patterns in experience, or any combination of the two.
    The fallacy in evolutionary explanations for human behavior is worse than reductionism.  It ignores the most important aspects of humanness.  We praise those people who subject their physical appetities and natural propensities to their spiritual values: the soldier who ignores his pain to rescue a comrade, the student who suppresses his desire to go to a party to finish a term paper, the leader who suppresses his fear to confront an evil, the young person who waits for marriage, the voter who studies the issues instead of following the party line, the man or woman who reasons instead of reacting to fleshly passions.  “Are you a man or a beast?” – the question emphasizes the point.  Our humanity consists in reasoning, planning, believing, choosing and acting based on concepts and values often contrary to what the flesh wants.  Only humans can exercise self-control.  You have to have a self to control it.  A dog or horse or dolphin will do amazing feats to be rewarded by its trainer, but that is not self-control; it is trainer control.  The animal gets an immediate reward.  Does your dog plan for retirement and write up a will?
    Ignoring the key distinguishing marks of humanity to explain human behavior by mystical “evolutionary forces” as if we are pinballs in a game is completely misdirected if not silly.  It is also self-refuting.  It’s like explaining books from the chemistry of paper and ink, and then writing a book about it with a stolen Judeo-Christian pen.  Add to those sins the evolutionists’ complete lack of moral judgment.  Their explanation draws no distinctions; to them, if cooperation is achieved, that’s good (notice that they cannot completely erase the concept of good).  The evolutionary forces and laws care nothing about the means by which cooperation is achieved.  Stalin is the moral equivalent of Reagan.  Let the prisoners in the Gulag weep in silence.  Let them abandon any appeal to their fellow man or to heaven for justice.  Justice!  That word is completely absent from the Darwin Dictionary.
    These researchers, because they retain a shadow of that image of God, continue to trade in concepts.  They cannot do that as consistent evolutionists.  If they want to be consistent, let them screech and scratch and watch each other’s behinds (see National Geographic for an edifying exploration of that).  The moment they want to appeal to explanation as if it might be true, they deserve to be sued for worldview plagiarism.  In court, the bailiff will make them swear on the Bible to tell the truth, the whole truth, and nothing but the truth, so help them God.
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From an evolutionary perspective, the result of this study is a no-brainer.  Imagine what could have or did happen to all of the organisms that lost their wits along with their glucose when running from predators.  They were obviously a light snack for the animals able to use lactate.

This is the same Gerald Weismann that won SEQOTW two months ago for updating Darwin with On the Origin of Tumors by Natural Selection (08/13/2008).  This time, Weissmann was absolutely right.  From an evolutionary perspective, it was a no-brainer.
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