Evolutionist told his colleagues they are deluding themselves about the evidence for natural selection: see 02/16/2005.

Depressed? Believe in a Caring God     02/28/2010    
Feb 28, 2010 — “Belief in a Caring God Improves Response to Medical Treatment for Depression, Study Finds.”  That’s what Science Daily said.  The statement assumes, of course, that psychiatry knows what depression is.  Another story on Science Daily worried that “Psychiatry’s Main Method to Prevent Mistaken Diagnoses of Depression Doesn’t Work.”
    It makes sense that diagnosis must precede treatment.  The psychiatry industry’s manual, the Diagnostic and Statistical Manual of Mental Disorders or DSM (see 02/17/2010) contains the criteria for diagnosing depression.  A patient needs 5 of 9 listed symptoms to be diagnosed.  “However, these symptoms can also occur in normal responses to loss and stress.”  Because of false positives resulting from the old DSM criteria, the new DSM-IV tried to correct them with a Clinical Significance Criterion (CSC), in order to reduce over-diagnosis (some studies suggested that 33% of the population suffer from depression).  A new study, though shows that the CSC does not reduce false positives.
    Even if the dividing line between clinical depression and normal distress or sadness is fuzzy, there is no question that many people are afflicted with grief, sadness, and feelings of despair that can be debilitating.  A study of 136 adults at Rush University Medical Center tried to quantify the effect of belief in a caring God on medical treatment for depression.  Science Daily said the doctors used “the Beck Depression Inventory, the Beck Hopelessness Scale, and the Religious Well-Being Scale” to assess the depth and intensity of depression, and “feelings of hopelessness and spiritual satisfaction.”  According to the article, “the study found that those with strong beliefs in a personal and concerned God were more likely to experience an improvement.”  Therefore, “clinicians need to be aware of the role of religion in their patients’ lives.”

Articles like this might encourage some readers, but it is questionable whether “scientific” assessments by secularists can state anything meaningful on questions of this sort.  If they can’t even decide what depression is, how are they going to measure the “religious well being” of a patient who claims he or she is depressed?  Is hopelessness measured in ohms or centimeters?  There are so many variables in the human soul, and so many differences between souls, it seems hopeless to try.  Information of this sort is usually conveyed soul-to-soul, not by means of brain scans or arbitrary scales.
    Not all “caring God” beliefs are equivalent, either.  Suppose somebody believes in Elvis, or in the Force, or in Jupiter, or has false beliefs about “the man upstairs” without any basis for them other than subjective feelings.  Assuming there is a true God for the sake of argument, would you rather have depressing beliefs about a true God, or comforting beliefs in a false god?  Would you rather have a false hope that makes you feel good, or a true hope that tugs on your conscience?  Better get that question settled first.  If feeling good is your highest priority, then there is no point in reading further; you’re irrational.
    Of the possible contenders for true God who is also a caring God, not many options are available.  Buddha doesn’t care; he didn’t even want to be a god.  Hinduism has thousands of gods; which are you going to pick?  Which one really cares about you anyway, seeing you are obligated to follow your own karma?  Confucianism is a system of teachings without a personal God.  It’s doubtful readers of these pages will take seriously animism, polytheism, or any of the defunct religions of history.  Dittos for recent man-made cults like Scientology that made its founder filthy rich; who thinks for a minute that L. Ron Hubbard cares for you?
    Of the religions with a personal God, there’s Islam, but imams teach it is impossible to know Allah, because his will is capricious.  There is no peace or assurance.  A Muslim never knows if Allah is satisfied. He can only hope at death he has done enough good works to make it.  That is the problem, too, with cults and misrepresentations of the God of the Bible.  If peace with God is based on our works, there is never a way to have assurance of salvation.  Judaism, having rejected Jesus Christ, keeps looking for a Messiah that never comes.  Without a temple or sacrificial system in place, it has no assurance of pleasing God.  Post-Christian Judaism has devolved into another religion of works, rituals and moral teachings.  Jews today do not “love” God.  They try to obey him, but they don’t generally have a sense of God as a caring father.
    As a religion that tells of a caring God, Christianity stands alone and uncontested.  “For God so loved the world, that He gave his only begotten Son, that whoever believes in Him shall not perish, but has everlasting life.”  That’s the most favorite and well-known Bible verse on God’s care for His creatures (see it in every tongue), but it is certainly not the only one.  He so loved us that He did that.  Knowing that we could never reach up to Him, God reached down to us.  Knowing we could never do enough works to please Him, He did all the work himself.  While we were still sinners, Christ died for us (Romans 5).  Now he offers reconciliation as a free gift (Romans 6).  We receive that gift by receiving Christ himself (John 1).  We receive Christ by acknowledging our sin and turning from it, and confessing Him as the Lord (Romans 10).  Confessing Christ means saying He is Lord, trusting that what He did for us when he died on the cross and rose again was for our salvation.  By receiving Christ, we are born again (John 3, Romans 1-10) – saved from eternal death, and started on a new life.
    If that were not enough care for the hopeless and broken-hearted, look at what else God’s gift provides: a full pardon from all our sin (Isaiah 55); a new nature capable of pleasing God (II Corinthians 5); the Spirit of God to live within us (Romans 8); access to God at all times through prayer (Luke 18), illumination to understand his Word (John 16); a family of believers to encourage and build us up, (Ephesians 2, Hebrews 13), a real purpose for life (I Corinthians 10) and the sure hope of heaven: a new, uncorrupted creation, beyond anything we can imagine (Revelation 21).  Talk about a cure for depression!  That kind of caring God can provide a peace that passes understanding (Philippians 4), and inner joy, confidence and assurance of His care even in trials (Romans 5, II Corinthians 4).

Of course, you can play the pompous scientific elitist if you choose to.  You can reject all this, and mock belief in a caring God as superstitious nonsense.  Fine.  Depressed?  Who cares?  Tough luck.  Stuff happens.  Get over it.  Evolve, and may the farce of Darwin bewitch you – that is, till your protoplasm becomes manure for something else just as meaningless until the ultimate vanity – the heat death of the universe.
Godless philosophy, pointless for me,
None to cause us, but Cosmos–
All that is, was, and ever shall be.
From the big bang, to the slime soup,
To the heat death, dark and old:
Godless philosophy, it leaves me cold;
Godless philosophy, it leaves me cold.
Oh, and what was that issue about sense and nonsense again?  No comprendo, bud.  Get outta my way.
Next headline on:  Health • Bible and Theology

In the current study, Kanazawa argues that humans are evolutionarily designed to be conservative, caring mostly about their family and friends, and being liberal, caring about an indefinite number of genetically unrelated strangers they never meet or interact with, is evolutionarily novel.  So more intelligent children may be more likely to grow up to be liberals....
    Similarly, religion is a byproduct of humans’ tendency to perceive agency and intention as causes of events, to see “the hands of God” at work behind otherwise natural phenomena.  “Humans are evolutionarily designed to be paranoid, and they believe in God because they are paranoid,” says Kanazawa.  This innate bias toward paranoia served humans well when self-preservation and protection of their families and clans depended on extreme vigilance to all potential dangers.  “So, more intelligent children are more likely to grow up to go against their natural evolutionary tendency to believe in God, and they become atheists.”

There are so many fallacies in this article, it would be easier to quote the few statements that make sense than to list them all.  Surely any intelligent reader is shaking her or his head in disbelief right now.  This silliness gets printed in “Science Daily”?  People may joke about one another being “less evolved” but this guy is actually serious.  Clueless would be a charitable accusation.  He would need a whole additional wit to be a half-wit.
    Notice again how Darwin leads people to say dumb things while thinking themselves smart.  This week the Republicans met with Obama to discuss health care.  A number of Republicans who attended commented afterwards that liberals seem to fancy themselves smart, and think of their conservative opponents as stupid.  Some liberal TV commentators seemed actually surprised to watch the conservatives acting better prepared and more eloquent, while the liberal standard-bearers that they expected to be the IQ champs said some pretty dumb things.  A similar sociological dynamic hampers rational discussion about intelligent design: Darwin-lovers merely assume they are the smart ones, and look down their pointy elitist noses at scholars who are often their intellectual superiors.  There is no one more pitiful than a dunce with a mortarboard cap.
    Kanazawa really needs to get out more.  He is apparently suffering from chronic dementia, brought about by Darwine addiction and constant exposure to the toxic atmosphere of liberal academia.  For shock treatment, let’s help the professor out a little.

“Dr. Kanazawa, I assume you consider yourself intelligent.  You also believe you are a product of evolution, and evolution, like you said, endowed humans with the ability to think and reason.  So let’s think this through.  If liberals are the bearers of novelty, that means in Darwinian terms that they are mutants, right?  Are you sure you want to act as a bearer of mutations, since they are almost always deleterious?  It is much more probable that your mutation will lead to death than to any evolutionary progress.  Wouldn’t it be more to your advantage to become a conservative Christian, the way evolution designed you to be?  Think of the advantages.  It would increase your fitness.  It would help you and the other cooperators prevent the mutants (the atheists and liberals) from polluting the gene pool.
    As a conservative Christian possessing higher fitness, you would have to denounce Darwin, you realize.  But it would increase your chances of passing on your selfish genes, which are using humans to propagate themselves by making them believe things that aren’t true, like God.  Now, since the selfish genes are amoral, they are making all humans, including the liberals, believe things that aren’t true, correct?  That would include evolutionary theory.  Otherwise, on what basis would you judge something to be true or to be false?  If it is the novel idea that is to be preferred as true, then wouldn’t it be novel for conservative Christians in North Korea to stand out from the communist regime?  Since novelty can produce opposite things, truth is clearly not the issue at hand.  Selfish genes are just as capable of using humans to believe in evolution as it is to lead them to believe in God.  You said we are evolutionarily designed to be paranoid, and claimed that it is paranoid to believe in God, but it is equally paranoid to be an atheist.
    Your choice, therefore, is either to become a conservative Christian, which is what evolution designed you to be, or to attempt to escape the tyranny of the selfish genes, which are deceiving you into thinking evolutionary theory is true.  You can tell the selfish genes are deceiving you when they lead you to believe things that are logically inconsistent.  The escape from paranoia to sanity and higher intelligence, therefore, is for you to repent of your folly and speak in rationally-consistent terms, like intelligent design.”

This is harsh therapy, we realize, but tough love demands it.
Next headline on:  Darwin and Evolution • Politics and Ethics • Theology or Philosophy • Dumb Ideas

1. Cell-inspired electronics:  The PhysOrg article, based on a press release from Massachusetts Institute of Technology, tells how “MIT’s Rahul Sarpeshkar is now applying architectural principles from these ultra-energy-efficient cells to the design of low-power, highly parallel, hybrid analog-digital electronic circuits.”  He calls this “cytomorphic” electronics – design inspired by cells.  Think computers are reaching the pinnacle of their efficiency?  Think again:

   Essentially, cells may be viewed as circuits that use molecules, ions, proteins and DNA instead of electrons and transistors.  That analogy suggests that it should be possible to build electronic chips – what Sarpeshkar calls “cellular chemical computers” – that mimic chemical reactions very efficiently and on a very fast timescale.

   . Notice that the design imitates the architecture and the interaction strategies, not the materials.  This is good news; it means that Moore’s Law has not approached the limit, and that smaller, greener, ultra-fast supercomputers could be in everyone’s future – thanks to the living cell.
2. Bio-inspired networks:  A related story on PhysOrg reported that European researchers are trying to build bio-inspired networks to form distributed computers.  “Powerful computers made up of physically separate modules, self-organising networks, and computing inspired by biological systems are three hot research topics coming together in one European project,” the article began.  Modular elements called ubidules can explore their environment and share information with other agents.  These form a network of self-organizing networks that can help solve “scientific problems in which complexity arises from simple building blocks, such as in brains, stock markets, and the spread of new ideas.”  Modeling the complex neural networks of the brain is one example.  Another is the foraging problem: how to get distributed agents to a collection point.  A set of robots with colored beacons can converge on the solution using the distributed agent algorithms.
       Even humans can provide biological inspiration.  Computer programmers and robot designers study how social networks act as collections of agents that can learn and share to solve problems: “as in an unfamiliar shopping mall where you might locate a particular store by following a trail of people carrying distinctive plastic bags.”  Social networks also exhibit emergent self-organizational effects due to the ability of individuals to learn, share and communicate.  The challenge, then, is to make robots and computers that model the collective problem-solving ability of intelligent agents able to communicate their ideas and learn from one another.
3. See turtle run:  An amazing race happens at night on some beaches.  Baby sea turtles hatch from under the sand, and race to the water.  “Life can be scary for endangered loggerhead sea turtles immediately after they hatch,” reported Science Daily.  “After climbing out of their underground nest, the baby turtles must quickly traverse a variety of terrains for several hundred feet to reach the ocean.”  Fortunately, they are well equipped for their journey.  They have specially-designed flippers that provide “excellent mobility over dune grass, rigid obstacles and sand of varying compaction and moisture content.”  It’s so good, in fact, that researchers at the Georgia Institute of Technology are envisioning how to “build robots that can travel across complex environments.”  They built an artificial flipper to measure the stresses and strains as it pushes on sand.  Somehow, the newly-hatched turtles, who have never run the race before, know how to maintain a “balance between high speed, which requires large inertial forces, and the potential for failure through fluidization of the sand.”
       Robot designers, instead of having to calculate the number of appendages to traverse complex surfaces, could save a lot of time by imitating how these baby turtles do it.  They could “just design a robot with a flat mitt and a claw like these turtles have,” the researchers concluded.  Speaking of loggerhead sea turtles, Science Daily reported on efforts to reduce accidental captures of the endangered species.  Spanish scientists are working on rules for fisherman that can reduce the turtles getting snagged in nets – a problem that not only hurts the 20,000 turtles that are accidentally caught each year, but also hurts the fisherman who must spend time freeing and releasing them.
4. How to trap radioactivity:  To grab radioactive ions, make like a Venus flytrap.  That’s how PhysOrg said scientists at Argonne National Laboratory are strategizing.  They are designing chemical traps that snap shut on wandering ions, to sequester them and decontaminate areas of radioactive pollution.  To be successful, the strategy needs the discriminating abilities of the plant.  “Imagine the framework like a Venus flytrap,” one of the inventors said.  “When the plant jaws are open, you can drop a pebble in and the plant won’t close—it knows it isn’t food.  When a fly enters, however, the plant’s jaws snap shut.”  Experiments showed that metal sulfides with a negative charge show promise for trapping radioactive cesium ions.  “As far as we know, this Venus-flytrap process is unique,” he said.  “It also works over a large range of acidities—an essential property for cleanup at different sites around the world, where pH can range considerably.”  The article is adorned with pictures of the Venus flytrap to show how the molecular trap imitates its botanical inspiration.

Intelligent design should claim these initiatives.  Usually, there is no mention of evolution in the reports, and when it is mentioned, it is a useless appendage with no explanatory power or direction.  When you approach an observable function in nature – an adaptive flipper, an efficient network – you can imitate it on the assumption that its design, structure, and architecture were designed.  Then you design inventions to imitate that design.  Instead of the GIGO (garbage-in, garbage-out) algorithm of Darwinism, biomimetics works on the DIDO (design-in, design-out) principle.  It’s important that the D in DIDO be design, not Darwin, or else you get irrational results (see 04/26/2008 commentary).
Next headline on:  Cell Biology • Marine Biology • Intelligent Design • Biomimetics

Making Evolution Simple     02/25/2010    
Feb 25, 2010 — Getting the vast diversity of highly complex creatures seems an impossible task for evolutionary theory, but some recent stories claim it’s not so hard. 

1. Beak of the finch:  Darwin’s finches keep pecking their way into the media.  A new study claims that the wide diversity of beak shapes that have evolved can be explained by a few simple mathematical rules.  Scientists at Harvard performed a “numerical feat,” reported PhysOrg, “on perhaps the most famous icon of evolution: the beaks of Darwin’s finches.”  They grouped the 14 beak shapes into three groups that vary mainly by length and depth.  They claimed broad application of their findings: “Broadly, the work suggests that a few, simple mathematical rules may be responsible for complicated biological adaptations.”  That being said, there are caveats: “It is not possible, however, to explain the full diversity of beak shapes of all Darwin’s finches with only changes in beak length and depth.”  But another biologist was “astonished” by the simple relationships and concluded that “The mechanism that allows organisms to adapt so readily to new environments may be a relatively ‘easy’ process.”
2. Not so complex:  If you thought biology was mystifying in its complexity, you just need the take-home headline from Emory University: “Biology may not be so complex after all.”  A confident-looking young biophysicist by the name of Ilya Nemenman accompanies the opening sentence: “Centuries ago, scientists began reducing the physics of the universe into a few, key laws described by a handful of parameters.  Such simple descriptions have remained elusive for complex biological systems – until now.”  The build-up is breathtaking: what could Ilya possibly have found?  Here it is: he “identified parameters for several biochemical networks that distill the entire behavior of these systems into simple equivalent dynamics.”  In his words, in bold print, he said, “It appears that the details of the complexity of these biological systems don’t matter, as long as some aggregate property, which we’ve calculated, remains the same.”
       This is too easy, the astute reader must be thinking.  How does this explain eyes, wings and brains?  It goes on: Nemenman next compares his principles to the ideal gas law, that explains “All of the crazy interactions of these molecules hitting each other” with a simple relationship between pressure, volume and temperature.  Why would nature make the networks of chemical reactions complex when they could be simple?  He announced, “The whole behavior of the system boils down to just one parameter.”  What were all the previous biologists thinking by making everything so hard.  Yet, one might ask, how fruitful is this explanation for understanding the origin and function of biological systems?  It sounds like measuring the hum of a bumblebee is being substituted for understanding its structure, organs, senses and aerodynamics.  An organism is surely more complex than gas molecules bouncing around at random (see glittering generalities).  To be sure, the article did not discuss the origin and evolution of complexity.  But the boldness of the headline, claiming that “biology may not be so complex after all,” seems crafted to play into the hands of evolutionists who would be eager to downplay all that complexity that intelligent design theorists keep talking about.  And the article did assume evolution, asking, “is the unnecessary complexity a ‘fossil record’ of the evolutionary heritage?”
3. Driving force:  Scientists have not just proposed a driving force for evolution.  Now, announced PhysOrg, they’ve “revealed” it.  The news is that “ evolution is driven most powerfully by interactions between species, rather than adaptation to the environment.”  That surprising finding may catch some readers off guard who thought the environment was a major player in evolution.  Even more surprisingly, this announcement invokes the “Red Queen” hypothesis of continuous variation.  That flies directly in the face of the announcement two weeks ago (02/11/2010, bullet 3), that claimed the Red Queen idea only helps on rare occasions, if any.  But now, Science Daily tells us that the Red Queen is not only “correct,” but is the “driving force” behind evolution.  Nothing was stated in either article about the origin of new genetic information, structure, function, or complexity.  Presumably, a “driving force” is all you need to bring these about.

What is more simple: the actual biology, or the storytelling of the evolutionists?  The latter is not just simple; it’s simplistic.  It takes a simpleton to believe it.  Evolutionists are comedians.  They help us recall Groucho Marx’s line, “Who are you gonna believe?  Me, or your own eyes?”
Next headline on:  Birds • Darwin and Evolution • Amazing Facts

Who taught the spider that a chaotic pattern of curved, straight, long and short hairs created the perfect water-repellant surface?  Natural selection?  Ha!  How many spiders had to drown trying to get that right.  Biomimetics is the coolest thing in biology.  It’s interdisciplinary, too: the biologists, the physicists, and the engineers can all get together.  We’re going to see a lot of neat products coming from this very un-Darwinian, ID-friendly approach.  Your spidey raincoat and lotus windshield will keep you high and dry.  You may not want this technology in your sponge, though.  (For that, mimic a natural sponge.)
Next headline on:  Biomimetics • Terrestrial Zoology • Physics • Amazing Facts

1. Return of the hopeful monster:  Tanguy Chouard raised eyebrows in Nature News with a headline that sounds like a new movie: “Revenge of the hopeful monster.”  It discusses the revival of a heresy that would have ruffled Darwin, who always said, “Natura non facit saltum” (nature does not take leaps).  Chouard discusses evidence that nature does take leaps – big changes that can occur within a single generation.  “Experimental evidence has shown that individual genetic changes can have vast effects on an organism without dooming it to the evolutionary rubbish heap,” he said.  (The evolutionary rubbish heap is presumably where winners of the Darwin Awards go.)  But does the evolutionary Aesop fable give the edge to the gradualist tortoise, or to the saltationist hare?  Maybe both.
       Avoiding a complete overhaul of the Darwin evolution engine, Chouard tried to have his cake and eat it, too: “But small-effect mutations still matter – a lot.  They provide essential fine-tuning and sometimes pave the way for explosive evolution to follow,” he explained.  “As the molecular details unfold, theory badly needs to catch up.”
       For evidence, Chouard exhibited an evolutionary pet, the stickleback fish.  Offspring can vary substantially between armored and naked forms.  This is due to a single gene location responsible for 2/3 of the spines.  Chouard explained, “the reigning gradualist dogma regarded these as artificially protected monstrosities that would never survive the harsh hand of natural selection.”  Gradualists have argued that pleiotropy (multiple effects of single changes) means that large changes would generally be deleterious.  “How could a mutation in such a crucial gene result in anything but a hopeless monster?”  A successful large change would be tantamount to a miracle.
       The stickleback study, though, shows that “surgical strike” mutations that cause sudden changes in armor happen repeatedly.  And Lenski’s multi-generational studies on E. coli showed both saltations and gradual mutations at work, producing increases in fitness by jumps and by small steps.  The idea is “large-early, small-late” – big jumps that don’t kill the organism are fine-tuned by gradual changes.  Some of the bacteria learned to digest citrate, and then these mutants quickly swept through and overtook the population.  Lenski considered that comparable to the invasion of land by tetrapods.  (For a different interpretation, see the Behe Blog.)  “It remains to be seen,” though, Chouard added, “whether such elementary mechanisms of adaptation, often referred to as microevolution, can instruct the higher processes that constitute macroevolution, such as speciation and the emergence of biodiversity or complex organs.”  Even Goldschmidt, the hopeful-monster champion, doubted leaps that large could be made.  And Jerry Coyne cautioned generalizing results from asexual bacteria with small genomes and high mutation rates.
       So is this disjunctive theory that says evolution proceeds both by leaps and by crawls an improvement on Darwin?  Do the tortoise and the hare join hands and cross the finish line as a team?  “Large effect or small, evolution begins to look like an endless list of special cases,....” Chouard admitted.  “One reason is the general lack of knowledge about how changes in genes contribute to function and how this affects fitness.”  That sounds a pretty basic requisite for understanding evolution.  One evolutionist longed for a functional synthesis, “marrying evolutionary biology, molecular genetics and structural biology.”  Some are glad for the return of Goldschmidt’s hopeful monster hypothesis; others favor a middle ground.  “We need much more data before the issue of large versus small can be settled,” Coyne said, before the new studies can argue that “Darwin was wrong” about saltation.
       The organisms are going to be the arbiters of this dispute.  “A mutation may affect phenotype but not change fitness much,” Chouard ended.  “It may have a large effect in the context of a given genome, or in a given environment, but may have a smaller effect later in an organism’s history.”  So it seems way premature to claim that evolutionary biology has settled on a comprehensive theory of speciation, even 150 years after Darwin.  Chouard handed out promissory notes: “As researchers drill down to the molecular mechanisms driving adaptation, theory may catch up and dogmas may recede.”  Maybe Darwin was wrong.  Maybe he was right.  Maybe he was partly right.  Who knows?  He must be celebrated as the greatest biologist in history regardless.
2. Dogma must go:  Jerry Fodor, a philosopher at Rutgers, is angry at the dogmatic Darwinists who see natural selection as the be-all and end-all of evolutionary change.  But he is no creationist; he is an avowed atheist.  He discussed his book What Darwin Got Wrong, co-authored with Massimo Piattelli-Palmarini, an atheist professor of cognitive sciences at U of Arizona, on Salon.com.  Thomas Rogers, who interviewed Fodor, was surprised that a published attack on Darwin did not come from the “religious right.”  He said, “Their book details (in very technical language) how recent discoveries in genetics have thrown into question many of our perceived truths about natural selection, and why these have the potential to undermine much of what we know about evolution and biology.”  For challenging Darwin, Fodor and Piattelli-Palmarini have received “obscene and debased ” comments on blogs.
       Fodor’s beef with natural selection appears to stem from its storytelling propensity.  Why do people have traits like hair on their heads and dark hair with dark eyes?  “You can make up a story that explains why it was good to have those properties in the original environment of selection,” he said.  “Do we have any reason to think that story is true?  No.”
       Fodor argues that there is no way to tell which traits were selected because they contribute to fitness, and which traits come along for the ride.  “There isn’t anything in the Darwinist picture that allows you to answer that question.”  Why do we have toenails?  Do they serve an evolutionary purpose?  How would we know?  “It may be a case that in the environment there was some factor that favored toenails but there also may not.”  This sounds like the Stuff Happens Law.  Gene expression is too complicated, he said, to sort out fitness effects from random change: “Now the question is, how much of the evolutionary variance is determined by factors of the environment and how much is controlled by the organization of the organism, and the answer is nobody knows.”
       Fodor even argues that picking out “traits” may be meaningless.  A giraffe has a long neck.  Did nature select that trait, or is it part of the giraffe package?  “Animals can have long necks and toenails, but if you try to break such creatures apart into traits and you say, OK, ‘What selected this trait?’ and, ‘What selected that trait?’ you’ve made a mistake right from the beginning,” he said.  “The disintegration of the organism into traits is itself a spurious undertaking.”  Selection acts on the whole animal, he believes.
       An example of the storytelling habit can be seen in last week’s Science paper on whale evolution.¹  “The link between diatom diversity and observed cetacean diversity supports the hypothesis that diatom-based primary production has been an important driver of neocete evolution,” wrote Marx and Uhen.  (A “neocete” is a modern whale.)  How, exactly, did that environmental driver (diatom diversity and number) act on the genes of a pre-whale to make it a whale?  It leaves the evolution of the complex structures of the customers assumed rather than explained.  Undeterred, the authors next pulled a completely different explanatory tool off the shelf.  “Similarly, the observation that climate change also has a role to play is not surprising in light of recent research that has demonstrated substantial temperature-dependent variations in the diversity of extant cetaceans.”  But how can they disentangle that driver from other drivers, and explain why it acted the way it did on whales, but not on birds, mammals and everything else in the biosphere that was simultaneously subject to climate change?  To take Fodor’s response, “Nobody knows.”  Maybe Marx and Uhen should make a bold, Popperian prediction.  Maybe they should predict what whales will evolve into after today’s anthropogenic climate change.  Will it be as dramatic as turning a cow into a whale?  Should we find it “not surprising” if climate change has a “role to play” in driving whales back onto land, or giving them wings?  How would that role be measured?

Fodor’s courage for facing flak while seeking truth is admirable, but he doesn’t realize that his truth-seeking is incompatible with his atheism.  Truth refers to ideas that are eternal – otherwise they are not true.  How is an atheist, who is presumably a physicalist, going to employ concepts, ideas and propositions, which must be defended with honesty and integrity, without presupposing a moral and spiritual realm?  A “force” will not do.  Honesty, truth, integrity, morality presuppose a Person.  The creationists, whom he accuses of post-hoc reasoning, actually have the pre-hoc conditions for intelligibility that give their post-hoc deductions meaning.  Darwinists hawk their post-hoc stories without the pre-hoc, making them ad-hoc.  That’s when the post-hoc fallacy ensues.  Fodor should stop plagiarizing Judeo-Christian presuppositions and pay the price before taking part in the Judeo-Christian smorgasbord with its nutritious ingredients of rationality.  So he should not worry about offending the other thieves, but make amends with the smorgasbord Owner.
    It should be clear from these stories that criticisms of Darwin are not all religiously motivated.  They are substantive.  Darwinism is a collection of just-so stories funded by promissory notes with no empirical collateral.  The bank that issues Darwin notes is bankrupt.  Any theory that reduces to the Stuff Happens Law is dealing in worthless explanatory currency.  If you call Chairman Charlie and ask, “What do you know?” he doesn’t answer.  Let the dead bury their dead.
Next headline on:  Darwin and Evolution • Genetics • Intelligent Design

Evolutionary Inferences: Are They Incontrovertible?     02/23/2010    
Feb 23, 2010 — No matter what is found in plants or animals, it finds its way into an evolutionary explanation eventually.  Are these explanations driven by the data, or forced into a belief system?  Are other explanations possible?  Some recent reports might inform these questions.

1. Your inner plant:  Get in touch with your inner plant with a report from Science Daily that claims “Protein Study Shows Evolutionary Link Between Plants, Humans.”  In an experiment at Purdue, an enzyme named aminopeptidase M1 was transferred from a human to a plant.  It helped revive dying specimens.  The inference made by the scientist was this: “M1 aminopeptidase activity is such a fundamental process that it’s been conserved evolutionarily.  This protein has changed very little over time.”  The problem is that conservation is the opposite of evolution, so “conserved evolutionarily” is a bit of a conundrum.  It assumes evolution, but posits that everything else evolved since plants and humans shared a common ancestor – but this enzyme did not.  Was evolution unable to improve on this enzyme in all that time, at least along one lineage?  Is it a new evolutionary principle – a law of nature – that fundamental processes are unable to evolve?  Are there exceptions?  Or is “evolutionary conservation” a phrase that assumes what it needs to prove?  (See circular reasoning.)  Creationists explain similarities in living things as evidence of common design, not common ancestry.
2. Dinosaur tooth truth:  A new species of dinosaur has been found in Utah, reported PhysOrg.  This one, fortunately, was found head-first: two complete skulls were found.  That means the fossils can provide “fresh insight into lives of dinosaurs some 105 million years ago, including the evolution of sauropod teeth,” the article said.  Yet the “skulls were made of thin, fragile bones bound by soft tissue that were easily destroyed after death.”  Creationists often point to the fact that dinosaurs appear abruptly in the fossil record without ancestors (12/22/2009).  It would seem presumptuous to claim that the fossils can provide insight into the evolution of sauropod teeth when the evolution of sauropods themselves is the larger issue (literally).
3. The men who walked through time:  Another “out of Africa” claim made prominence in a report on Science Daily: “DNA Evidence Tells ‘Global Story’ of Human History.”  The article quotes a scientist saying, “To understand what it is to be human, it is essential to understand the human past.”  Many a theologian or preacher would shout “Amen!” but would offer a completely different history.  In fact, Dr. Robert Carter, a geneticist working with Creation Ministries International, gave a lecture at The Master’s College Feb. 20 explaining how the DNA evidence points to a single Y-chromosome and a single “mitochondrial Eve,” supporting the Biblical story (see CMI store for DVD).  In his analysis, Carter showed how the genetic evidence also supports the Flood and the Tower of Babel.  No such room was allowed for alternative interpretations in the Science Daily article, which announced triumphantly, “Overall, the reviews show just how clear it has become that all of us trace our evolutionary roots to Africa,” though admitting a couple of sentences later, “Of course, there are many things about our ancient ancestors we will never be able to know with any certainty.”
       Science Daily also claimed that the genetic evidence shows how traits like “lactose tolerance have been selected for over evolutionary time.”  Creationists would agree, but without the Darwinian ape-to-man interpretation and the millions of years.  An article in Creation Magazine (32:1, 2010, pp. 12-15; see CMI for online edition) by David Catchpoole discussed this very subject.  He showed that lactose intolerance is actually the “normal” condition, and claimed that the genetic evidence overturns evolutionary notions.
4. Island dwarfing:  Continuing with dinosaurs, another article appeared this week in PhysOrg claiming to show evidence for “island dwarfing” in Romania.  An ancient island shows smaller dinosaur fossils than elsewhere.  The question was answered with only evolutionary views: “How did the dinosaurs get to the island?  It’s not certain whether they were marooned there as the seas rose, or whether they swam or drifted there by chance later on.  Either way, this research demonstrates that once they arrived they evolved to become dwarfs.”  Yet the site contains “rich assemblages of fossil plants, insects, fishes, frogs, lizards, birds, and mammals show that the scene was rich and tropical.”  No claim appears to have been made that the other groups of animals also evolved into dwarfs.
       Yet there is a third way to interpret the evidence.  Saturday at The Master’s College, Dr. Robert Carter gave another talk about dinosaurs.  He showed evidence for dinosaurs and humans co-existing after the Flood.  He showed engravings on Bishop Bell’s tomb (CMI) and at Angkor Wat (CMI), indicating that people saw these creatures till medieval times at least.  Carter believes they were hunted to extinction as pests or trophies, or were unable to survive the climate changes after the Flood.  He pointed to the fact that all other species, including the more vulnerable crocodiles, are still doing just fine – causing grief to the evolutionary stories about causes of dinosaur extinction.  He also referred to the soft tissue and blood cells found in dinosaur bone to show that they could not have been extinct for 65 million years.  In addition to these points, scientists admitted recently that a significant number of dinosaur species could be misidentified as separate species when in fact they were varieties or the same species, or individuals of different ages.

Evolutionary storytelling is science, but evidence that supports the Bible record is not science – by definition.  Isn’t that a convenient generality and false dichotomy for Darwin and his disciples?  It allows them unlimited storytelling potential, uncontested, with no fear of contradiction.  It makes evolutionary science a kind of priesthood and everything else a heresy.  Is that how science is supposed to operate?  The evidence is out there; it belongs to everyone.  The pool of smart people in the world is not exhausted by the evolutionary biological community.
    Even some evolutionists are realizing this is a very unfair and unjust situation.  Read this book review, What Darwin Got Wrong, on Salon.com.  Author Jerry Fodor, who himself has felt the heat of academia for failing to worship Darwin unquestionably, chides the evolutionists for their dogmatism, but then accuses the creationists of post-hoc and ad-hoc reasoning.  Given his experience with the Darwin-worshipping consensus, doesn’t that charge cut both ways?  Indeed it does.  Fodor said:

Creationism isn’t the only doctrine that’s heavily into post-hoc explanation.  Darwinism is too.  If a creature develops the capacity to spin a web, you could tell a story of why spinning a web was good in the context of evolution.  That is why you should be as suspicious of Darwinism as of creationism. They have spurious consequence in common.  And that should be enough to make you worry about either account.”

Since everyone is guilty, maybe it should also make us suspicious of Jerry Fodor’s characterization of the situation.  At least here at CEH you can read both sides (with links to original sources) and decide for yourself, without having an elitist academic making summary judgments for you.
Next headline on:  Plants • Fossils • Dinosaurs • Genetics • Early Man • Darwin and Evolution • Bible and Theology

Even if this is not a “new” discovery, the re-dating of the wall earlier to the time of Solomon is significant.  Minimalist schools of archaeology have long argued that David and Solomon were small tribal clans in the Iron Age II and therefore could not have built the large cities ascribed to them.  The pictures show otherwise.  The construction is massive and sophisticated, suggesting a powerful kingdom was thriving, consistent with the Biblical account (see also the Edom findings from 10/27/2008 and the Qeiyafa inscription from 01/07/2010).
Next headline on:  Bible and Theology • Dating Methods

Carroll’s solution for the arrow of time invokes the multiverse, a controversial concept that is a current battleground in theoretical physics.  Arguably a prediction from cosmology and string theory,and to some extent quantum mechanics, the multiverse idea supposes that the Universe that we perceive is but one of a countless collection, each of which can be in a different physical state.  A case can be made that our Universe looks the way it does because it is the only one of the many possible universes that can harbour us.  For example, in another universe in which the constants of physics were slightly different from those in ours, life would not be possible.

Going further, Carroll adapts the multiverse idea to explain the directionality of time.  Universes such as ours, he suggests, continually pop into existence within the multiverse, which is itself in thermal stasis, with no sense of time.  We just happen to live in one of these baby universes, which started off in a low-entropy state and has an entropic arrow of time.

Would someone please explain how this kind of speculation differs from imagining fairies and flying pigs and aliens?  or why it should be blessed with the sacred appellation of science?  Theologians at least have some revelation to constrain their speculations about an unobserved heaven, hell and the afterlife.  This has nothing to support it.  Don’t say that these guys are acting scientifically because they are employing mathematics and laws of known physical quantities.  One could easily do the same with the aerodynamics of flying pigs, or the top running speed of gnomes.
    Emboldened by the empty promises of naturalism, evolutionists have let their imaginations run amok.  Berserk is too mild a term for it.  They presume to speak with the authority of science when telling us that baby universes just pop into existence, with some of them having matter just popping into existence, into which some of the matter coalesces into blobs of protoplasm.  Then, by faith, eyes pop into existence (the Popeye theory of evolution, 05/31/2005), allowing the cosmos to see, and brains pop into existence, allowing the cosmos to understand itself – at least in localized carbon units.
    This may be fashionable, all right, but many fashions are foolish.  It would be more honest for them to announce they are founding a new religion.  Here it is: the First Multiversalist Church of the Absurd.  Come in and worship Tyche, the goddess of chance.  Open your eyes of faith to see alternate realities.  Worship your imagination (01/17/2007 commentary) as you sing “When you wish upon a star, nature makes you what you are” (12/05/2008).  Be uplifted by our sermon, “Stuff happens” (09/15/2008 commentary).  Join in and sing our closing hymn, “Godless Philosophy” (see Darwin Hymnbook).
    Thinking beyond the known into the unknown is not wholly unwarranted.  It can provide context for understanding the known.  Considering the low entropy state of our universe, for instance, should arouse astonishment at how improbable that would be by chance.  Considering what would happen if the physical constants of the universe were not finely tuned should arouse more astonishment.  The lesson that should result from such mental excursions, upon returning to the real world, is how privileged we are to enjoy life in such a world and universe.  That should result in humble thanksgiving to the Creator.  There is little humility or gratitude in the proud hearts of the dreamers living in imaginary universes.  Pay them no mind; they are blind leaders of the blind.  Now get back to work with your eyes open, your feet on the ground, and a song of praise in your heart (suggestion).
Next headline on:  Cosmology • Darwin and Evolution • Dumb Ideas

The Brain You Use, and How It Uses You     02/21/2010    
Feb 21, 2010 — Neuroscientists continue to find out amazing things about the human brain.  In some ways we are responsible to use our brains, but in other ways the brain does things to us.  If nobody has figured out where the dividing line is for thousands of years, it’s unlikely we will today; but the following findings can shed some light on the mystery.

1. Sing for mental health.  Something about singing does a brain good.  The BBC News and National Geographic reported on work at Northwestern University that showed music helps prevent dyslexia in children and can even rewire a damaged brain.  That seems to indicate that if you did not choose to avail yourself of music therapy, the benefits would not occur.
2. Remember to forget:  New studies on memory seem to suggest that forgetting is an active process.  Old memories don’t just fade away; they are actively erased to make room for new memories.  That’s the idea in an article on Live Science reporting on work in China and at Cold Spring Harbor Labs, New York.  The researchers feel this could lead to drugs that could help patients erase bad memories, like traumatic events.  Be sure not to overdose on it.  Who knows if the brain would come back after a reboot – think of having to take all that school again.
3. Nap stir:  Speaking of a reboot, that mid-day nap might refresh your brain like a warm restart.  PhysOrg, Live Science and Science Daily all reported on findings at UC Berkeley that show naps clear the mind and boost the brain’s learning capacity.  Moms may appreciate the break when the baby takes its nap, but important things are happening in the tiny head in that interval.  Maybe Mom should take one, too.
       Participants who took 90-minute naps in a controlled experiment scored markedly better on learning tests.  One researcher put it into familiar terms: “It’s as though the e-mail inbox in your hippocampus is full and, until you sleep and clear out those fact e-mails, you’re not going to receive any more mail.  It’s just going to bounce until you sleep and move it into another folder.”  So that’s why we forget what the teacher said.  Unfortunately, the teacher doesn’t get a “Returned to sender” message from the student.  The student should not try to argue to the teacher that his napping in class is a way to enhance his learning.

That last article wins Stupid Evolution Quote of the Week for beginning, “The last ancestor we shared with worms, which roamed the seas around 600 million years ago, may already have had a sophisticated brain that released hormones into the blood and was connected to various sensory organs.”  The implication is that our brains evolved from worm brains.  But this relies on evolutionary assumptions and deep time, and doesn’t help Darwin anyway; it pushes the origin of these sophisticated mechanisms closer to the goo.
    Back to reality. Who could not be fascinated by the brain?  We are aware of choosing to think and act, but there are also many processes that occur automatically in the background – re-organizing memories in sleep, re-wiring in response to music, entrainment of a new skill or idea by habit after focused concentration.  We sense that we are operating a very sophisticated computer.  We know how to use the GUI, but have no idea how the software and wiring works.  Evolutionists tend to be materialists and deny we have free will (e.g., 02/17/2010, bullet 1), but creationists typically believe we have responsibility for our choices and actions.  The debates will go on, but it’s hard to defend determinism, when you think about it.  See?
Next headline on:  Human Body • Health • Biomimetics • Amazing Facts • Dumb Ideas

Molecular Highway Motor Comes into Focus     02/19/2010    
Feb 19, 2010 — A beautiful new image of kinesin, a molecular machine that carries cargo on cellular highways, has been produced in greater detail than ever by a team at Berkeley and Brandeis Universities.  Science Daily published a picture and description of how kinesin works.  “Life’s smallest motor – a protein that shuttles cargo within cells and helps cells divide – does so by rocking up and down like a seesaw,” the article began.  The work is done using energy from ATP.
    Ken Downing described the motion: “We found that there is a pivot point, where the kinesin motor attaches to the microtubule, which acts like a fulcrum and causes kinesin to rock up and down like a seesaw as it moves along the microtubule.”  Kinesin is involved a numerous cell processes.  It’s one of the motor proteins that actually moves cargo on cellular highways.  The article said, “kinesin proteins motor along microtubules like trains on a railroad track, towing cargo to various locations within cells and assisting in cell division.”  Each rocking motion of the see-saw requires energy from ATP.
    Franck Fournio and Carolyn A. Moores, commenting on the findings for PNAS,¹ described the motors as being fuel-efficient as macromotors need to be.  “Thus the cell’s nanomachines have evolved to use ATP only when they can couple it to essential work.”  The original paper by Sindelar and Downing in PNAS² contains detailed model illustrations of how the seesaw motion links different parts of the machine to interact with structures on the microtubule.  All these interactions occur due to precisely-placed loops, linkers and pivots built out of the amino acids making up the protein parts of the machine.  Several domains of the machine undergo significant conformational changes during the motion.  Terms like “force generation” and “fulcrum” used in the paper indicate that these are true machines, just like those made by man, but on an almost unfathomably small scale – a few billionths of a meter in size.
    The authors did not describe how this machine could have evolved.  Fournio and Moores simply stated that kinesins “have evolved to” use ATP efficiently.  Sindelar and Downing said kinesin is a descendant of the myosin molecular motor family, with which it shares similarities.  They described myosin, however, as “its larger and more complex, ancient cousin,” suggesting that any evolution has been toward simplicity.

Once again we see evolution assumed in passing but contributing nothing to the understanding of a wonder of nature.  This story is all about structural architecture, function, engineering, precision, efficiency – intelligent design.  Let’s cure scientists of their bad habit of assuming evolution when the evidence for design keeps coming into sharper focus.
Next headline on:  Cell Biology • Intelligent Design • Physics • Amazing Facts

One of the main jobs of the AAAS meeting is to parcel up original research that has already been published, and often publicized, into digestible chunks.  These then reappear as news stories in papers and broadcasts around the world, turbocharged by quotes from the scientific luminaries attending the meeting.  This at least marks a change in tempo from the weekly routine, which converts original scientific findings, via a production line of embargoed press releases from journals and universities, into a steady stream of largely uncritical stories.

Hear, hear!  Great column.  He must have seen Creation-Evolution Headlines, because we’ve been preaching that sermon for years (04/18/2003, 04/01/2005, 04/05/2004, 07/19/2004, 08/13/2005, 08/10/2007, 03/20/2008, 06/25/2009).  We even showed them how to do investigative reporting (04/15/2003, 03/23/2007, 09/30/2007).  Macilwain only slipped up once by using the term scientific progress.  He should have specified that progress is not guaranteed by the passage of time, but by the quality of the evidence.  Say, where have we heard that phrase “strengths and weaknesses” before? (see StrengthsAndWeaknesses.org for a hint).
    Popular science reporting is often a wretched stench of triumphalism written by gutless wusses trying to be clever.  They treat scientists’ announcements like food from the gods to be served on golden platters to the common people.  They chew it first and barf it up on our plates, thinking it will aid digestion.  Look how they stood by the rascals of ClimateGate and lectured us on how we didn’t understand “science.”  Only lately have some of them been acknowledging that the skeptics had some valid points.
    Can you imagine what would happen if reporters actually broke rank with the pack and actually did investigative reporting on scientists?  What would happen if they brushed past the “specious authority of their jargon” and asked the hard questions, challenged their “findings”, the motivations and funding sources behind them, and the quality of the evidence?  For one thing, the public would suddenly become a lot more interested in science.  For another, the Darwinists would slither into dark corners to make their baloney in secret.  Imagine a time when an evolutionist’s pronouncement like “Cooking is what made us human” (01/21/2010) is met not by genuflections from the press but by howls and belly laughs.  It wouldn’t take long for them to get religion.
Next headline on:  Media

Flabbergast: “Primitive” Human Ancestors Were Sailors     02/18/2010    
Feb 18, 2010 — Could the headline be any more shocking if it read, “iPod found in King Tut’s tomb”?  Heather Pringle began a report in National Geographic News with, “It wasn’t supposed to happen like this.”  Stone tools alleged to be up to 130,000 years old have been found on the island of Crete.
    Since Crete is believed to have been surrounded by Mediterranean waters for five million years, this means that human ancestors thought to be too primitive to show modern behavior were intentional seafarers.  Moreover, the hundreds of stone tools found at nine locations suggest that groups of them came over to set up sustainable populations.  They did not drift out there accidentally.  This implies intent, purpose, “curiosity, and the desire for exploration.” How will this affect current theories on the origin of humans?

It’s been thought that the early humans of this time period were not capable of devising boats or even simple rafts—technology considered an expression of modern behavior.  Homo sapiens practicing modern behaviors, such as wearing jewelry and making art didn’t begin to appear until around a hundred thousand years ago.
    But the new discoveries hint that these human ancestors were capable of much more sophisticated planning, cooperation, and construction—in this case, boat building—than their simple stone tools would suggest.
“I was flabbergasted,” [Curtis] Runnels [Boston U] said.  “The idea of finding tools from this very early time period on Crete was about as believable as finding an iPod in King Tut’s tomb.”

Enough surprises like this are equivalent to a Precambrian rabbit (02/11/2010).  If evolutionists won’t pay attention to the elephant in the room, don’t expect them to notice the rabbits hopping all around their feet, let alone the pharoahs with iPods.
    A simple application of Bayes’ Theorem can assess the fate of the evolutionary hypothesis in light of this new evidence.  The hypothesis is that modern man emerged from primitive ancestors over millions of years.  The prior probability of this hypothesis has been deemed high by most evolutionary anthropologists.  The evidence is stone tools on an island requiring sophisticated seafaring skills.  The probability of the evidence is one, since it is observed.  The probability of this evidence given the hypothesis is very low.  The probability of the hypothesis has just been substantially reduced.  Therefore, the posterior probability of the hypothesis, given the evidence, being the product of the probability of the evidence given the hypothesis and the probability of the hypothesis, divided by the probability of the evidence, has been substantially reduced.  The Darwinian hypothesis is rejected.
    Using the same updating of probabilities, we can assess the likelihood of the creation hypothesis.  It states that man has always been intelligent and capable of purposeful, symbolic behavior.  An adjunct of the creation hypothesis is that human technology suffered a substantial setback during the Flood, so would have shown slow advancement wherever it is found – having had to start from scratch again.  Because the probability of the evidence given the hypothesis is high, the probability of the hypothesis given the evidence is increased.  The posterior probability of the creation hypothesis has then increased by the new evidence.  The creation hypothesis is confirmed.
Next headline on:  Early Man • Dating Methods

As a climate scientist and a contributing author to the Intergovernmental Panel on Climate Change, my heart always warms when I hear policy-makers refer to doing what “the science dictates,” as President Obama did in his remarks toward the end of the U.N.  Climate Change Treaty negotiations in Copenhagen, Denmark.  However, after the first-hand experience of the rapid crash of the Copenhagen meeting, I have changed my thinking: World leaders, please stop listening to us!  I don’t say this because I have lost faith in the verity of scientific results or the projected warming and subsequent global damages.  I say this because international policy-makers are adhering too rigidly and too literally to recommended concentration thresholds and emissions targets, and it is crippling the international policy process.

1. No free willy:  For his inaugural article to the National Academy of Sciences, Anthony Cashmore, a biologist at University of Pennsylvania, told them they have no free will.²  Apparently, he said this of his own volition, and they used their free will to elect him into the academy.  Or was he one of the elect?  Maybe it was his chemical destiny to tell the Academy they consist of “mechanical forces of nature,” who only employ free will as a “useful fiction” and operate under the “illusion of responsibility.”
       Cashmore further argued that a mistaken belief in free will is behind our criminal justice system.  Criminals are not responsible for their behavior, he said, but should be incarcerated only for pragmatic reasons.  “It is the author’s contention that a belief in free will is nothing other than a continuing belief in vitalism—something biologists proudly believe they discarded well over 100 years ago.”  Dr. Cashmore did not produce any lab results or scientific evidence to back up his belief.  Near the end, he said: “Finally, I would like to make the following point....”  But who was speaking?  Isn’t a mechanical force of nature pointless?  Should his mechanical audience choose to listen, even if they could?
2. Hunting aliens:  Gary Ruvkun, professor of genetics at Harvard Medical School, is hunting for aliens.  Space.com reported that he has an alien DNA detector he wants to use on Mars.  Reporter Michael Schirber said, “The idea isn’t too crazy,” where “too” is the operative word.  His search for extraterrestrial genomes (SETG) appears poised to be as successful as the search for extraterrestrial intelligence (SETI) has been.  Schirber quoted another scientist thinking the project is a little premature, given that no biomass has been found yet.  Meanwhile, Ruvkun is out calibrating his instrument on the acid runoff from a volcano in Argentina. 
3. Defining life: come again?:  A Dutch scientist has come up with a new definition for life.  Life, says Gerard Jagers op Akkerhuis of Wageningen University, is a hierarchy of operators.  Space.com tells about his concepts of “hypercyclic neural network” and operators with “first-next possible closure.”  Reporter Clara Moskowitz admitted, “If all this is a little heady, the scientist says he understands the idea is complex and may take some getting used to.”  After all, “Biology is often called the study of life, yet in the history of the field, experts have never agreed on just what, exactly, life is.”  One colleague has already taken issue with Jagers op Akkerhuis’ definition: “This theory and definition will confuse our biological issues even more by their circularity of reasoning,” he said.  “Recognizing something as living depends on criteria derived from known, recent living systems; a bean is a bean because it is bean shaped.”  That started an argument.
4. Play find the storyteller:  Three scientists in Canada disputed a letter-writer to PNAS³ who complained about their use of “convergent evolution” and neutral drift (instead of natural selection) to explain similar rare traits in some unrelated protozoans.  They responded in PNAS⁴ with the following retort:

   The conventional route taken by most molecular biologists is to explain complexity by positive selection.  However, we should not dismiss the purely neutral origin of complex systems like editing without evidence.  Indeed, the absence of a working model for the origin of editing through positive selection renders the neutral model even more appealing, because it is liberated from the need to justify such an absurd molecular system with “Just-So” stories.

5. Mr. Toad’s Wild Ride:  How does an amphibian hop around the world?  By developing “toadness.”  In her Evolution feature for Science Feb. 5,⁵ Elisabeth Pennisi explained, “‘Toadness’ a Key Feature for Global Spread of These Amphibians”  And what is toadness, one asks?  It’s warty skin, internal fat, ability to survive dryness, and several other traits.  They didn’t all come from the same family tree, she explained; “Instead, this quintessential ‘toad’ form has emerged multiple times on multiple evolutionary branches.”  Convergent evolution came to the rescue again, along with a new word toadness, to explain how these unique amphibians “emerged.”  Presumably, this provides understanding: “Knowing what kind of toads spread in the past should help us understand which ones will survive if accidentally transported into a new environment,” the article explained; i.e., “which taxa are likely to become invasive,” whatever that means (see 10/05/2009).
6. Tree trouble:  Two recent articles in Science illustrated the problem that evolutionary biologists have discerning phylogenetic trees in a forest of data – and dealing with their own biases.  W. P. Hanage, in “The Trouble with Trees,”⁶ didn’t quite have the stomach for Jan Sapp’s new book, The New Foundations of Evolution On the Tree of Life.  It was too non-Darwinian for him.  Nevertheless, he acknowledged debates and disputes that remain active today, and at least joined scientists to the human race: “We all carry with us intellectual baggage and preconceptions from not only our own experiences but also those of our friends, colleagues, and mentors.”
       Terry Harrison, in “Apes Among the Tangled Branches of Human Origins,”⁷ revealed that much of the hype about human evolution is based on poor and contradictory data.  Despite the hubbub over Ardipithecus last year, no clear line of descent is discernible.  The confidence of his first sentence in the concluding paragraph is quickly swallowed up with doubt:

   As paleontological exploration intensifies across Africa, our knowledge of hominoids in this critical time period will steadily grow.  Rather than just a few relictual evolutionary strands surviving to the end of the Miocene and giving rise to modern hominine lineages, as was previously thought, ape diversity in Africa during the late Miocene looks very bushlike.  The relationships between Ardipithecus and earlier hominids will remain enigmatic until the quality of the fossil evidence from the late Miocene of Africa improves, but this will eventually prove critical in resolving its affinities to later hominins.  The important questions then become: Where did Ardipithecus and the other early hominin contenders come from?  Are they truly members of the hominin lineage, or simply apes among the tangled branches that constitute the basal hominine bush?

   It appears that hominine is making its appearance in the confusing mix of paleoanthropological terms.  It’s instructive to compare the above paragraph with what scientists and journalists were saying last October (10/02/2009), when Bruce Alberts (editor of Science) proclaimed that Ardi proved that “Darwin was certainly right,” National Geographic said, “Oldest Skeleton of Human Ancestor Found,” and the BBC News called Ardi “An ancient human-like creature that may be a direct ancestor to our species.”

Who are scientists?  They are people.  They are human like the rest of us.  Why should we trust their opinions more than those of others, then?  Is it because of their training?  Their methods?  Their political power?  Like the churchmen of medieval times, scientists strut about with presumptive authority and speak with little fear of criticism from outsiders.  But the word “scientist” did not exist till 1832.  Science did not become a career profession till later, and only took on its institutional status in the 20th century.  Science is a bandwagon too small for the people wanting to ride its reputation.
    Like members of any class of human beings, whether musicians, construction workers, politicians, lawyers, realtors, athletes, or whatever, scientists include the good, the bad, and the ugly.  We should no more trust the pronouncements of a scientist a priori because he or she wears the label than we should clap for the generic musician regardless of talent.  A scientist’s pronouncements should be valued based on the evidence – not position.  We would hope that scientists have learned to be epistemically modest and committed to logic, precision (via mathematics), and careful observation, just like any reasonable human being should be.  But as the above stories show, there are some clowns in white lab coats.  Better an honest country parson than a scientist using a PhD as a pretext for saying dumb things.
    Let’s put the shrinks on the couch.  How should we classify these stories?

1. Logic derangement syndrome: espousing a self-refuting proposition.
2. Paranoid delusion disorder: imagining non-existent friends or enemies.
3. Cyclic jargonia: arguing in circles with fancy words.
4. Fictitious projection: using a just-so story to accuse someone else of telling just-so stories.
5. Transcendental verbalization: believing that inventing words leads to understanding.
6. Divination psychosis: persistent visualization of shapes and signs in uncooperative data.

No one doubts that there are severely disturbed people who need help, but it wasn’t that long ago when totalitarian dictators put the sane ones in the asylum.  Righteous, honest people in Stalin’s Russia (the ones who were not outright murdered) were given mind-altering drugs and brainwashing to try to cure them of their psychiatric disorder of believing in God.  It was intuitively obvious to the perpetrators that anyone who did not accept the regime was crazy by definition.  It happened.  It could happen again.  Many Darwinists today treat anyone who disagrees with Charlie as de facto insane.  Some of them write scholarly papers in scientific journals alleging such things.  Then they turn right around and speak of complex life “emerging” from nowhere by chance.  The have delusions of aliens emerging from primordial seas.  They envision universes exploding into existence without a cause.  They shoot at their feet with self-refuting beliefs.  Who is calling whom crazy?
    We must always be on our toes to prevent the cultural normalization of insanity.  Kipling said that part of being a man (a rational creature, by extension), is keeping your head while everyone around you is losing theirs.
Next headline on:  Bible, Theology or Philosophy • SETI • Darwin and Evolution • Health • Dumb Ideas

Observations and hypotheses these days are so intertwined it becomes hard to separate them.  Consider the suggestion that the Late Heavy Bombardment explains the Ganymede-Callisto dichotomy.  One has to assume the LHB and the long ages.  And consider the idea that tidal landslides explain the youthful surfaces of asteroids.  How many times in 4 billion years can this occur before there is no more youthful skin underneath the rubble to expose?  There is essentially no way to test these ideas without assuming the long ages of the consensus secular view of the solar system.  Science will never establish the long ages this way.  That’s the problem with assumptions.  They are assumed, not demonstrated.  Because the long ages are never allowed to become vulnerable to falsification, they become part of a self-perpetuating belief system that sometimes requires improbable contortions to maintain.  The talk about life every time water is mentioned is fact-free speculation.  It’s logic-free, too, because it would be just as corny to go off on tangents about life every time protons are found, because they also are building blocks of life.  In the TV series, Chris McKay waxed eloquent about all the ingredients for life that exist at Enceladus: a heat source, organics, and water.  We challenge him to put water, ammonia, ethane and carbon dioxide in a very cold sterile refrigerator, stir it occasionally, and wait for a very long time.  At least he could give us some experimental evidence to back up his rhetoric.  As long as one can filter out the speculative fluff in scientific stories, the rich discoveries about such varied and interesting worlds should be a delight to all who maintain a spirit of exploration.
Next headline on:  Solar System • Dating Methods • Origin of Life

Life Is Smarter Than We Know     02/15/2010    
Feb 15, 2010 — How can toads calculate?  How can cells without a brain or central nervous system figure out a balanced diet?  How can bugs navigate the wind for optimum flight time?  These are some of the questions that can arise from observations of the living world.  The more we learn about life, the more we find unexpected abilities in the most “primitive” of living things.
    The ameba seems like a lowly life form.  How smart can it be?  French scientists found out they are not only social organisms; they know how to obtain a balanced diet.  Science Daily reported that “Even single-celled organisms feed themselves in a ‘smart’ manner.”  Experiments showed that amoebas thrive best with a ratio of two parts protein to one part sugar.  When presented with a veritable grocery stand of nutrients, they went for the optimal ingredients on their own.  “Social amoebae are thus capable of solving complex nutritional challenges, quite a surprising feat for a very simple organism lacking a centralizing system,” the article said.  “The researchers are now attempting to elucidate the mechanisms involved.”
    Toads look pretty clumsy when they hop and flop, but they actually calculate the timing and impact of their landings.  Another article on Science Daily reported that experiments at Holyoke College demonstrate that “toads, like humans, are capable of anticipating when and how hard they’re going to land after a jump and activating muscles important in absorbing impact accordingly.”  This ability had only been demonstrated previously in mammals.  The observations showed that toads adjust their elbow tension according to the length of the hop.  “In addition, one major elbow muscle was always activated at a fixed interval prior to landing in all hops, regardless of distance, suggesting that toads not only gauge how hard they’re going to hit the ground, but also anticipate precisely when that will happen.”  It seems obvious that rapid feedback from eyes and other senses is involved.  This is the first time that tuned muscle activation before landings has been observed in amphibians, and “It raises questions about how widespread this ability is among other species and how important feedback from various sensory systems—e.g., vision—is for mediating this ability.”  The team plans to blindfold some toads in their next experiments to measure the dependency on visual input for this ability.
    We tend to think of birds as the champions of migration, but research in the UK shows that “the flight behavior of some insects is similar to that of migrating birds in its sophistication.”  The short story in Live Science explains that “high-flying moths and butterflies are able to select favorable winds and correct for drift, tactics that maximize the ground the insects cover and optimize their travel times.”  That certainly must be true for monarch butterflies that are currently enjoying their winter-over in some remote mountains in Mexico after their long fall migration.  There must be a lot of computing power packed in a bug brain that is smaller than a pinhead.

Good old-fashioned science, the experimental kind, with controls and empirical tests, was done in these stories.  No appeals to Darwin were required.  The answers led to additional research questions.  Some of these experiments could be done in a middle school or high school.  If science restricted itself to observation and stayed out of theology (see next entry), there would be no science wars, and more young people would be attracted to careers studying the wonders of nature.
Next headline on:  Cell Biology • Terrestrial Zoology • Amazing Facts

Theodicy is the age-old conundrum of how to reconcile a just God with a world containing evils and flaws.  With respect to biological imperfections, evolution can emancipate religion from the shackles of theodicy.  No longer need we feel tempted to blaspheme an omnipotent deity by making him directly responsible for human frailties and physical shortcomings, including those we now know to be commonplace at the molecular and biochemical levels.  No longer need we be apologists for God in regard to the details of biology.  Instead, we can put the blame for biological flaws squarely on the shoulders of evolutionary processes.  In this way, evolutionary science can help return religion to its rightful realm – not as a secular interpreter of the biological minutiae of our physical existence, but rather as a respectable counselor on grander philosophical issues that have always been of ultimate concern to theologians.

Do you remember when the communist party bosses ruled the Soviet Union?  They were the only ones who ever got the microphone.  It was easy for them to tell the news media that nothing in politics makes sense except in the light of Marxism.  It was easy for them to show how flaws in capitalism were hard to explain, but made sense in terms of dialectical materialism, economic determinism and the dictatorship of the proletariat.  The glorious communist utopia was proof.  Pravda was only too happy to print the triumphant Party line.
    Like the communist party bosses, Avise feigns friendship to some religion, as long as it is well-behaved (i.e., under Party control, with the sermons censored, church activities controlled, and young people prevented from joining).  It needs to keep out of the biological minutiae of science and stick with the grand philosophical issues.  Sounds nice.  Next thing you know, they are taking over churches and turning them into museums of atheism (cf. cartoon).  This is all to help the poor dissidents, you see, who just don’t understand how communism works.  They only want to emancipate them from the shackles of capitalistic errors.  A little time in the Gulag, some mind-altering drugs, a little re-education was all for their mental health.
    Is it because there is no theologian worth his salt within calling distance that PhysOrg printed one side of the story?  Do they really think a modestly equipped seminary student would be tongue-tied with a theodicy question?  This illustrates common practice for the scientific journals and secular science reporters: like Pravda before them, they deliver one predigested view, and tell the populace how to think.  At least this article took the daring step of mentioning that a dissident belief system (intelligent design) exists.  Most mention evolutionary theory as the only answer to everything.
    Theodicy might be a problem for 19th-century deism and simplistic natural theology, but not for Biblical theology.  It was not a problem for Jesus Christ, who was certainly not oblivious to the blind, the deaf, the lepers and the lame around him.  It was not a problem for Paul, who spoke of the whole creation groaning and travailing in pain till the coming redemption of all things (Romans 8).  Nor is it a problem for modern Biblical creationists, who are eloquent in matters of sin, judgment, the worldwide Flood, and the degeneration and decay of all flesh (including the genome) because of the curse on sin.  It is not even a problem for intelligent design – why?  Because I.D. does not delve into matters of theology, like Avise does.  Intelligent design restricts its explanatory domain to design detection.  Avise is taking off on a tangent (see red herring) by claiming that if one argues intelligent design, one is duty bound to explain natural evil.  That is a non-sequitur.
    We see here a pattern that was noticed decades ago in the creation-evolution debates of Duane Gish and Henry Morris, and has been pointed out eloquently in the books of Cornelius Hunter, Darwin’s God and Darwin’s Proof: it is the evolutionists who argue theology, and the creationists who argue scientific evidence.  Notice how counter-intuitive that pattern is.  If Darwinism is the great scientific theory, and creationism the religiously-motivated pseudoscience, one would predict the opposite.  But this pattern holds up all the time.  Hunter speaks at length about theodicy, Darwin, Dobzhansky, Ken Miller, and theistic evolution to establish his argument that evolution relies on religious premises rather than scientific evidence.
    Understanding this explains why evolutionists are quick to talk theology in debate but bankrupt at explaining the origin of complex specified information observed everywhere in biology.  “We are told that complexity and even consciousness just bubbled up out of an inorganic world,” Hunter wrote.  “These are extraordinary claims and therefore they require extraordinary evidence.  Instead we have a series of unsubstantiated speculations.  These speculations are made compelling, however, by evolution’s negative theology” (Hunter, Darwin’s God, p. 174).  By negative theology, Hunter is speaking of the argument presented often by Darwin and his disciples: “God wouldn’t have done it that way.”  (Notice that is a theological argument, not a scientific argument.)
    For a daring thrill ride, let’s follow Avise’s line of thinking.  We put the blame for bad design on natural selection instead of on a beneficent Creator.  Now, we can comfort ourselves with the notion that Stuff Happens.  Corollaries include Bad Stuff Happens to Good People, and Stuff Happens at the Worst Possible Time.  Are you feeling better already?  Continue this line of thinking.  There is no reason, purpose, or goal for anything.  Stuff just happens.  Whatever happens, it is just stuff going this way or that.  Stuff, by definition, has no moral categories.  We have just destroyed morality.
    Continuing Avise’s view, we also destroyed any means of classifying things as good or evil, right or wrong, desirable or undesirable.  Why should even pleasure be good, or pain be bad?  One organism’s pleasure is another one’s pain.  We are bobbing about aimlessly on an undulating surface without gridlines or goalposts.  Nothing matters.  Stuff happens, and we all die.  Does it make any sense on Avise’s game board to pursue religion, medicine, or environmental issues?  Not at all; those presuppose good and evil.  But that’s not all; he just destroyed logic, too, despite his attempt to tell theologians that natural selection is the only logical explanation for design imperfections.  Explanation?  Logic?  No comprendo.  Avise reads from his sermon text, Nemesis 1:1 – “Brbrbrbrbrbrbr” (rubs his fingers rapidly over his lips while rolling eyes in opposite circles).
    Welcome to Avise’s dystopia: nothing makes any sense, and nothing is worth doing.  Is this the kind of solution to theodicy you expected?  It’s what you get when you force Avise, Miller and the other anti-ID propagandists to remain consistent with their worldview presuppositions.  They presume to think they can preach from their innate (created) moral sense while denying its source.  Now that you have experienced the vertigo and insanity their solution leads to, perhaps you would like to build on the rock.  Consider the logical necessity of, and the rational evidence for, a living and true God, who is rational, holy, loving, and a lot wiser than man (Jeremiah 9:23-24).
Nothing comes from nothing; nothing ever could.
Let’s start at the very beginning – a very good place to start. – Julie Andrews
Next headline on:  Human Body • Health • Intelligent Design • Genetics • Theology

Feb 13, 2010 – For a weekend when some churches are celebrating “Darwin Sunday,” our attention should be turned instead to Christian Men of Science – a book that underscores the Christian roots of modern science.  This book, subtitled “Eleven men who changed the world,” was a lifetime project of George Mulfinger, a summa cum laude graduate of Syracuse University – an atheist then, but who became a born-again Christian in graduate school.  He became a well-loved professor of physics at Bob Jones University and served on the board of the Creation Research Society.  In his spare time, he researched the lives of great Christians in science.  He excluded deists and theistic evolutionists – choosing only those who had a personal relationship with Jesus Christ – but his list includes some of the brightest scientific lights of all: Kepler, Boyle, Faraday, Maxwell and seven others.   Mulfinger uncovered many little known details about these great scientists.  His daughter, Julia Mulfinger Orozco, researched with him and completed the project after his death; son Mark Mulfinger provided the drawings.  The biographies are written in a very readable narrative form.  Published in 2001, it is an “evergreen” book, because it deals with history and biography.  The stories, inspiring for all ages, provide good role models for young people.  The book can be ordered from Amazon.
Next resource of the week:  02/06/2010.  All resources: Catalog.

For His Birthday, Darwin Gets a Scrambled Arthropod Tree     02/12/2010    
Feb 12, 2010 — If Darwin lost his tree last year (01/22/2009), it would seem any corrections or rearrangements would be academic.  Nevertheless, eight evolutionary biologists at Duke University tried rearranging one of the biggest branches on Darwin’s tree of common ancestry – the highly diverse group known as arthropods (animals with jointed appendages).  Arthropods comprise the largest number of species and the largest count of animals on the planet.  It includes the insects, spiders, crustaceans, millipedes, shrimp and much more.  The team’s results were advance-published on the Nature website right before Darwin’s 201st birthday,¹ accompanied by a press release from Duke University.
    This is just the latest in a century-long project to make sense of the arthropod family tree.  The authors admitted an “often-heated, century-long debate on arthropod relationships.”  Early attempts were based entirely on morphology (physical traits).  More recent methods have included genetic and protein comparisons, but the authors said “The molecular phylogeny of Arthropoda has proven difficult to resolve.”  The puzzles are reflected by some of the names: Paradoxopoda (paradoxical feet), Miracrustacea (surprising crustaceans) and Xenocarida (strange shrimp).  The researchers quadrupled their earlier data set for the latest phylogeny.  They claimed overall strong agreement between molecular and morphological phylogenies, but the press release stated, “Some of the relationships are so surprising that new names had to be coined for five newly-discovered groupings.”
    Even though the paper and press release present a tone of success in finally resolving the family tree, some statements indicate this is just the latest rest stop on a work in progress.  The success comes at a price; some relationships are counterintuitive or controversial.  The authors, moreover, had to select data they thought was more indicative of signal over noise.  Here are some excerpts that show any claimed success is strained:

• The remarkable antiquity, diversity and ecological significance of arthropods have inspired numerous attempts to resolve their deep phylogenetic history, but the results of two decades of intensive molecular phylogenetics have been mixed.
• More typically, analyses based on limited samples of taxa and genes have generated results that are inconsistent, weakly supported and highly sensitive to analytical conditions.
• These results provide a statistically well-supported phylogenetic framework for the largest animal phylum and represent a step towards ending the often-heated, century-long debate on arthropod relationships.
• Until recently, arthropod molecular phylogenetics relied mainly upon nuclear ribosomal DNA and mitochondrial sequences.  Our data come from the complementary DNA of single-copy nuclear protein-coding genes, which represent the largest source of data for phylogenetics.
• Uncertainty about homology at sites bracketing small insertion–deletion (indel) regions resulted in exclusion of approximately 6.5% of all sites.
• Of the six newly named groups shown in bold in Fig. 1, only two had more than 70% bootstrap support in single-gene analyses (one gene each; Supplementary Table 3).
• Bootstrap values derived for amino acids were sometimes lower than those derived from nucleotides.
• At the deepest level, our phylogeny strongly supports Mandibulata (Pancrustacea plus Myriapoda), a controversial result that is robust to expanded outgroup sampling.
• Our strong support for Mandibulata contradicts several molecular studies that have placed Myriapoda as sister group to the Chelicerata (Euchelicerata plus Pycnogonida), a grouping so contrary to morphology that it was recently dubbed Paradoxopoda.
• Although our phylogeny resolves many problems within Mandibulata, it does not resolve the status of Chelicerata, the group including Pycnogonida (sea spiders) and Euchelicerata (horseshoe crabs, scorpions and spiders).
• Xenocarida includes two unusual and morphologically dissimilar classes of crustacean, Remipedia and Cephalocarida.  We place the xenocarids and hexapods in the newly named clade Miracrustacea (’surprising crustaceans’).  Both Xenocarida and Miracrustacea are found in the maximum-likelihood trees for all four methods of analysis, although support varies.
• Bootstrap support for both Xenocarida and Miracrustacea is strong for noLRall1+nt2 and degen1 analyses (93–100%), moderately strong for codon analysis (79–89%) and weak for amino-acid analysis (17–54%).
• Our results strongly support the monophyly of Hexapoda, in contrast to mitochondrial studies that place Collembola (springtails) among ‘crustaceans’ rather than other hexapods.
• The sister group to Miracrustacea is another unanticipated group, Vericrustacea (‘true crustaceans’), which joins Malacostraca (crabs, shrimp and so on), Branchiopoda (fairy shrimp, water fleas and so on) and some members of the polyphyletic ‘Maxillopoda’, namely Thecostraca (barnacles) and Copepoda.
• Within the Vericrustacea are two other groupings not anticipated by morphology: the Multicrustacea (‘numerous crustaceans’: Malacostraca plus Thecostraca plus Copepoda) and the Communostraca (‘common shelled ones’: Malacostraca plus Thecostraca).
• Significantly, our analysis adds Mystacocarida to Oligostraca.  The mystacocarids are small, enigmatic crustaceans that live between sand grains along marine shores.  Oligostracans are a disparate, ancient clade, and there is little in their gross morphology other than reduction in the number of body segments that would suggest a close relationship among them.
• Our results differ from morphology-inspired hypotheses in uniting Pauropoda with Symphyla rather than with Diplopoda, a result that is also seen in recent analyses of nuclear ribosomal sequences.

In conclusion, our phylogenomic study provides a strongly supported phylogenetic framework for the arthropods, but the problem of reconstructing and interpreting morphological evolution within this diverse group remains.  Our phylogeny highlights the large gaps in the morphological spectrum of extant arthropods that have complicated the task of morphology-based systematists.  Our result has significant implications, as it requires taxonomists to acknowledge crustaceans as a paraphyletic grade of primitively aquatic mandibulates and to classify hexapods as a terrestrial clade within Pancrustacea.  In particular, the position of Xenocarida (Remipedia plus Cephalocarida) as the sister group to Hexapoda, and the relatively derived placement of supposedly ‘primitive’ groups such as Branchiopoda, promises to alter views on the evolution of morphology and morphogenesis in Arthropoda.

Details are necessary to show how arbitrary and contrived the practice of evolutionary tree-building is.  If this is how tree-building goes for the greatest group of animals in the world, should we be impressed with claims for any other group?  But it doesn’t matter.  Since we have already shown that tree-building is hopeless (07/25/2002) and the branching tree is a fallen icon of evolution anyway (01/22/2009), it would be charitable to call this work that the Dukes have hazarded an exercise in futility.
    They might just as well try to build a family tree for the tools in a hardware store.  Look at their capricious and arbitrary name game.  Does it help understand relationships to name a group Miracrustacea?  Are you impressed by the Latin name for “surprising crustaceans”?  What if phylogenists in a hardware store invented a group name for crowbars and screwdrivers called Xenocapulus (strange handles)?  Latin is a poor mask for vanity.
    Maybe it makes them feel good to be busy, but constructing paper trees for Darwin seems hardly a useful scientific quest.  Darwin trees aren’t good for wood, construction, shade, the environment, or anything.  Their usefulness for understanding is highly doubtful.  Scientists should do better than to obsess over vain projects that are rootless and fruitless.
Next headline on:  Terrestrial Zoology • Genetics • Darwin and Evolution

More Surprises for Darwin     02/11/2010    
Feb 11, 2010 — It’s not uncommon for theories to have to deal with anomalies, but Darwinism sure seems to get more than its share.  Here are some recent examples.

1. Fossils lie:  Fossils preserve unmistakable clues about past life, right?  Not so fast.  Nature reported that “Non-random decay of chordate characters causes bias in fossil interpretation.”¹  The way early fish decayed before burial could have changed important details about their morphology (this is from the “smelly fish” experiments, 01/30/2010).  The decay of traits is non-random and “the more phylogenetically informative are the most labile.”  Informative features of the head, in particular, tend to decay faster than the rest of the body.  The more the decay, the more the fossil looks “primitive.”  It means that fossils can be erroneously placed farther back the evolutionary tree than they should.  “Failure to distinguish between the underlying causes of character absence will lead to erroneous evolutionary conclusions.”
       The paper warned that the problem could affect interpretations of many groups: “Preliminary data suggest that this decay filter also affects other groups of organisms and that ‘stem-ward slippage’ may be a widespread but currently unrecognized bias in our understanding of the early evolution of a number of phyla.”  How come nobody thought of this before?
       Derek Briggs commented on this in the same issue of Nature.²  He summed up the problem: “Decay distorts ancestry.”  The synopsis: “Experiments with simple chordate animals show how decay may make the resulting fossils seem less evolved.  The consequence is to distort evidence of the evolution of the earliest vertebrates and their precursors.”  One immediate consequence is that the Cambrian fish found at Chengjiang, China, may actually be more complex than previously assumed.  Those famous Cambrian fossils, and those of the Burgess Shale, will have to be re-evaluated in light of the new knowledge.  This is big.  Fossils might look more primitive than they were.  Briggs pointed to this as an illustration of the most general law in science:

   Is stem-ward slippage just an isolated palaeontological example of Murphy’s law – in this case, that the most useful evidence is least likely to be preserved – relevant only to early vertebrates?  Or is it a more pervasive phenomenon?  In general, the answer is that stem-ward slippage is widespread: all fossil animals with a high proportion of missing information tend to fall out near the base of an evolutionary tree through the lack of morphological features (such as structures in the head, in the case of chordates) to ally them with more evolved groups.  And the resulting tree may be biased unless the decay sequence is random relative to the tree’s branching order – that is, the order in which characters evolved.  As well as prompting caution in interpreting soft-bodied fossils, Sansom and colleagues’ research may turn out to be important in identifying a way to assign confidence limits to the placement of these extinct forms in the tree of life.

2. Lilliputians conquered:  Speaking of fossils, another interpretation has been falsified.  The “Lilliput hypothesis” claims that life shrinks after a mass extinction.  This hypothesis has been put to use in the Permian-Triassic extinction, one of the largest in evolutionary history, to explain why gastropods were small after the event.  Now, Brayard et al, writing in Geology,³ announced the discovery in Utah of some of the largest gastropods ever found in the early Triassic.  “The occurrence of large-sized gastropods less than 2 Ma after the Permian-Triassic mass extinction refutes the Lilliput hypothesis in this clade, at least for the last ~75% of the Early Triassic.”  The paper said, “The assumption that Early Triassic gastropods (and other organisms) were generally smaller than during other periods therefore needs more substantiation....”  Nothing in the Utah fossil bed suggested unusual conditions that would have contributed to smaller or larger specimens for gastropods or other taxa.  And there’s the anomaly.  Continuing the Swift metaphor, they said, “Our large specimens from western Utah can be considered as Gullivers compared to most other described Early Triassic gastropods.”  See Science Daily for a summary and pictures of the fossils.
3. Red Queen murdered:  The Red Queen effect, a popular theme in evolutionary literature about continuous variation in response to changing environments, has been tested and found wanting.  Michael J. Benton, writing in Nature January 21,⁴ summarized work by Venditti, Meade and Mark Pagel in the same issue,⁵ saying, “Biologists have assumed that natural selection shapes larger patterns of evolution through interactions such as competition and predation.  These patterns may instead be determined by rare, stochastic speciation.”  It is obvious that any re-interpretation of speciation bears directly on theories by Darwin about the origin of species.  Now, evolutionists cannot assume that natural selection will act in any predictable away to constant selection pressure.  “So, constant speciation rate, and the Red Queen model in general,” Benton explained, “are perhaps better understood as the outcome of rare stochastic events that cause reproductive isolation, rather than a never-ending race in which species are constantly coping with a changing environment.”  That sounds closer to the Stuff Happens Law than before.
4. The naked chimpanzee:  Y-chromosome studies of the chimpanzee genome have revealed a surprise: the chimp Y-chromosome is “remarkably divergent in structure and gene content”  (Nature, Jan 28).⁶  The differences are not only more extensive than predicted; they are clustered in certain hot spots.  Science Daily took this not as a falsification of evolution, but evidence that evolution runs super-fast sometimes: “Contrary to a widely held scientific theory that the mammalian Y chromosome is slowly decaying or stagnating, new evidence suggests that in fact the Y is actually evolving quite rapidly through continuous, wholesale renovation.” See a short update on the chimp-human-similarity-meme by Jay Richards on Evolution News & Views.  Cornelius Hunter on the blog Darwin’s God considers the “rapid evolution” explanation as an appeal to magic: “we must believe that evolution magically caused rapid changes to occur right where needed to improve function and eventually create a human.”  Why, then, did PNAS report on “slow evolution” of the coelacanth genome?⁷  Why did that fish want to stay virtually unchanged for 150 million years?
5. Butterfly spotted:  Just-so story alert!  An article in PhysOrg is entitled, “How the butterflies got their spots.”  The story is of little help to evolution, though: it discusses the conundrum of how two different kinds of butterflies converged on the same wing patterns, down to the same spots, even at the gene level.  It’s “one of the most extraordinary examples of mimicry in the natural world.”  Chris Jiggins (U of Cambridge) remarked, “It’s interesting because it tells us how flexible evolution is.  If you get the same wing pattern evolving independently in different populations, do you expect the same genes to be involved?”  The expected Darwinian answer to that rhetorical question seems to be, “No.”  Mutations were found, however, to have occurred not randomly throughout the genome, but at certain “genetic hot spots” more subject to variation.
       One might have thought this would constitute a falsification of an evolutionary prediction.  Jiggins, though, turned the bug into a feature: “This tells us something about the limitations on evolution, and how predictable it is.  Our results imply that despite the many thousands of genes in the genome there are only one or two that are useful for changing this colour pattern.  It seems like evolution might be concentrated in quite small regions of the genome – or hotspots – while the rest of it does not change very much.”  It appears that evolution runs as fast or as slow as needed to keep the theory viable.

The first story is especially significant.  It means that complex animals could be inferred earlier in the fossil record than previously thought.  That muddled trace fossil might actually be the elusive Precambrian rabbit after all.  If you don’t accept that, then please explain why you accept anything by people who say that evolution runs super-fast except when it runs slowly, that evolution is predictable except when it isn’t, that evolution is a law of nature except when it is extremely flexible, that mutations are random except when they occur on hotspots, that chimpanzees are 99% similar to humans except when the differences are 70%, that Lilliputians are Gullivers, and that Red Queens are really Court Jesters.  When that Precambrian rabbit dove into the fossil hole it was shouting, “Oh dear!  Oh dear!  I shall be late! to a very important date!” at the Malice in Blunderland party.
Next headline on:  Fossils • Genetics • Mammals • Terrestrial Zoology • Darwin and Evolution

Life Masters Physics     02/10/2010    
Feb 10, 2010 — Living things, especially cells, have mastered the forces of advanced physics in ingenious ways.  This ingenuity sometimes inspires physicists to try to copy it.  Here are some recent examples:

1. Photosynthesis and quantum mechanics:  Nature reported that plants take advantage of quantum mechanics in photosynthesis.¹  “The photosynthetic apparatus of cryptophyte algae is odd – its pigments are farther apart than is expected for efficient functioning.  A study into how this apparatus works so well finds quantum effects at play.”  Grondelle and Novoderezhkin continued, showing that plants exceed humans at this skill:

   It is common knowledge that plants, algae and certain bacteria use photosynthesis to convert solar energy into a form that can be used by the organisms to live and reproduce.  But what is less well known is that the efficiency of photosynthesis might depend in part on quantum-mechanical processes.  On page 644 of this issue, Collini et al.² report evidence suggesting that a process known as quantum coherence ‘wires’ together distant molecules in the light-harvesting apparatus of marine cryptophyte algae.  This is the first time that this phenomenon has been observed in photosynthetic proteins at room temperature, rather than at much lower temperatures, bolstering the idea that quantum coherence influences light harvesting in vivo.

   Collini et al appeared surprised by their discovery: “Intriguingly, recent work has documented that light-absorbing molecules in some photosynthetic proteins capture and transfer energy according to quantum-mechanical probability laws instead of classical laws at temperatures up to 180 K,” they said.  “This contrasts with the long-held view that long-range quantum coherence between molecules cannot be sustained in complex biological systems, even at low temperatures.”  The plants’ ability to use “counter-intuitive design” employ quantum mechanical laws boosts the efficiency of light harvesting.  Grondelle and Novoderezhkin titled their article, “Quantum design for a light trap.”
2. Smart grid technology:  Continuing on the theme of photosynthesis, a commentary in PNAS by David M. Kramer (Washington State U)³ describes how plants and other phototrophs (light-loving organisms) employ a “smart grid” system to dissipate excess energy and prevent damage:

   To deal with the Promethean consequences of harvesting light, phototrophs have evolved a photonic “smart grid” that balances the delivery of light energy to its two photosystems—photosystem I (PSI) and photosystem II (PSII)—to prevent overexcitation and subsequent production of reactive oxygen species.  Like human-engineered electrical systems, the photonic smart grid can regulate energy transfer at several levels.  Unlike its engineered counterparts that have controllable power plants, phototrophs cannot down-regulate the sun.  Instead, when light capture exceeds the capacity of the system to process it, it must be dissipated or rerouted to avoid photodamage.  Chloroplasts deal with this problem by adjusting the properties of the photosynthetic antennae under photodamaging conditions.

   Kramer went on to describe how the power plant has a fail-safe mechanism.  The default state of the conformation of molecules in the photosystem is probably in the quenched mode – the safe mode.  “In this way, several different stimuli can result in similar down-regulation of the photonic smart grid.”
3. Adhesion by cohesion:  We know that post-it notes work by creating cohesive forces with tiny droplets on paper.  Beetles employ a similar trick to stick to leaves.  They are so good at it, they can cling to leaves with a force 100 times their own weight, and then instantly detach themselves.  They achieve this by controlling thousands of tiny liquid droplets in their feet.  The adhesion created by surface tension in any one drop is small, but the large number of droplet contacts adds up.
       Inspired by the success of the beetles, engineers at Cornell, with funding from the National Science Foundation and DARPA, have created a prototype adhesive that works on the same principle.  It controls the droplets with electric fields.  By reversing the fields, it can detach the device easily.  Their main problem is figuring out how to keep the droplets from coalescing, but they are making progress.  Science Daily reported that their palm-size device that employs water surface tension might make it possible for future Spider-man mimics to walk on walls.
4. Acoustical nanomechanics:  “NASA Studies Nanomechanics of Inner Ear,” announced PhysOrg.  We often take our balance for granted, but it depends on sophisticated responses of tiny hair cells to the environment (see also a second PhysOrg article on this subject).  But how do the hair cells maintain enhanced sensitivity to very small movements without being overwhelmed by large movements?  The article describes how the amplifier can be instantly switched on or off by the organism.

   The inner ear organs are designed and precisely attuned to changes in the environment: for the hearing organ, a change in the sound pressure, such as caused by a car horn, can deform the ear drum and rapidly lead to the recognition and location of the sound.  For the balance organ, movement of the head, such as unexpectedly stepping off the curb, is sensed and rapidly leads to motor reflexes to maintain equilibrium.  The more sensitive our ability is to detect these changes, the more acute our sensation.  This remarkable tuning and amplification to detect the slightest stimuli, allows us to adjust our posture.

   NASA wants to understand these mechanisms so as to help astronauts avoid vertigo in space.  They are studying the hair cells in toadfish.  “Fossil evidence, dating from at least the Devonian Period 400 million years ago, shows that the elaborate sensory structures used to sense the organism’s movement are remarkably conserved among vertebrata.  The results demonstrate an active process in the hair cells of an ancient bony fish, thus suggesting that the mechanism is ancestral, and may underlie the broad appearance of active hair cell processes in amphibians, reptiles, birds, and mammals, including humans.”  For a picture of one of the hair cells, see Science Daily.
5. Cilia got rhythm:  A paper in Nature last month tackled the problem of how cilia and flagella beat with regular oscillations.⁴  To understand it, the researchers came up with a mathematical model that employed “opposed motors and springs.”  In particular, they studied the oscillation of the flagellum in sperm cells to come up with a “sperm equation.”  This excerpt sounds like something out of an engineering textbook:

   Any oscillation can be described as a sum of sinusoidal oscillations of increasing frequency, called Fourier modes; sideways oscillations can be described by the temporal Fourier modes of tangent angles.  Power-spectrum analysis showed that experimentally observed oscillations in tangent angles were well approximated using only the first (fundamental) Fourier mode, so the sperm equation could be analytically solved using values of this mode.  Tangent angles quantify the curvature of the axoneme at a given position, and the curvature is geometrically related to the sliding distance between doublets at that position.  The sperm equation thus relates time-dependent angular movement at each position to the extent and rate of inter-doublet sliding at that position, and to the local forces that either oppose or promote further sliding.
       The model contains two adjustable parameters – stiffness and friction of the active material inside the axoneme that deforms and exerts force during bending.  It also contains several fixed parameters that Jülicher and colleagues independently measured and fed into the equation.  These include the hydrodynamic drag of the moving flagellum and its ordinary stiffness, both of which oppose active deformation, and the beat frequency.  The authors obtained an excellent fit to the data, with both internal stiffness and friction taking the negative values expected for an active material.  Importantly, a microscopic model of dynein behaviour, incorporating the force-dependent detachment concept illustrated in Figure 2, predicted negative values for stiffness and friction similar to those obtained by fitting the sperm equation.

   The authors went on to describe physics concepts like beat frequency, force-detachment relationships, piston-like movement of doublets at the base of the cilia, and sliding friction.  Your life depended on a sperm cell understanding the physics of beating its way to an egg cell – and still depends on trillions of other cilia and flagella being good physicists in the cells of your body today.
6. Bacterial flagellar switch:  A paper in Science discussed how the flagella of a bacteria can cooperate by using a stochastic switch.⁵  Several of the authors work in the Department of Physics at Oxford – not just the biology department.  “The elements of protein signaling networks are often complexes that change their activity in response to binding specific ligands,” their paper began.  “Multisubunit protein complexes often show cooperativity, with either binding or activity showing a switchlike sigmoidal dependence upon ligand concentration.”
       The authors introduced the concept of “conformational spread” to explain the switching behavior between clockwise (CW) and counterclockwise (CCW) rotation.  The description went on to discuss physical properties of the system: elasticity, a two-state Poisson process, stochastic coupling, and more.  The fact that these cellular machines can be described with the tools of mechanics not only emphasizes the physics in biophysics, but shows how human engineers envy the techniques that living things have mastered.
7. Thermodynamics: Maxwell’s demon found:  The 19th-century physicist James Clerk Maxwell knew that entropy must increase in a system, but envisioned a way to overcome it: putting an intelligent selector in the system.  A “demon” could, in principle, isolate hot and cold molecules into different compartments, for instance.  PNAS reported that bacteria could be employed to harness random Brownian motion to turn gears.⁶

   The laws of thermodynamics prohibit extraction of useful work from the Brownian motion of molecules or particles in systems at equilibrium (nonexistence of a perpetuum mobile of the second kind or Maxwell demon).  When, however, such randomly moving objects interact with certain types of time-varying external potentials or with asymmetric geometrical obstacles under nonequilibrium conditions, their motions can be “rectified” and made directional.  This phenomenon, first considered by Smoluchowski and then analyzed in detail by Feynman, underlies the operation of so-called Brownian ratchets and motors.  The examples of biological “Brownian motors” include kinesin and myosin proteins converting chemical energy into directed motion on microtubules, and bacteria propelling themselves in viscous fluid owing to the “asymmetry”/chirality of flagellar rotation.

   The authors suggest that human engineers could employee flagella as Maxwell demons to turn nanoscopic gears.  It should be noted that all the instances they listed of Brownian ratchets are found in living systems or were produced by human engineers.
8. Network engineering:  To build a better distribution network, make like a leaf.  PhysOrg announced that “Leaf veins inspire a new model for distribution networks.” 

   Following the straight and narrow may be good moral advice, but it’s not a great design principle for a distribution network.  In new research, a team of biophysicists describe a complex netting of interconnected looping veins that evolution devised to distribute water in leaves.  The work, which bucks decades of thinking, may compel engineers to revisit some common assumptions that have informed the building of many human-built distribution networks.

   The netted patterns seen in leaves may not only be the most efficient way to get cargo from here to there; it may also provide the best safety net.  The “tree network” most commonly deployed lacks the redundancy of leaf networks.  “By contrast, in the leaves of most complex plants, evolution has devised a system to distribute water that is more supple in at least two key ways,” responding to fluctuating demand and re-routing around damaged parts of the network.  Videos in the article show how water is distributed in different kinds of leaves.  The article also pointed out that the loopy network design is also found in corals and insect wings.  “These findings could seriously shake things up,” a researcher said.  “People will have to take another look at how they design these kinds of systems.”  One of the researchers is further studying how the design handles fluctuating loads, “guided by nature’s own solution in the leaf.”

Don’t you get sick of the constant credit evolution gets for engineering design?  It’s sickening because it is nonsensical.  Evolution is not an engineer.  It is not a person.  It cannot organize parts for a goal; it is completely a random, instantaneous response to immediate circumstances.  Evolutionists commit two fallacies with sickening frequency.  For one, they use evolution as an active verb, saying, for instance, that hearts evolved to pump blood.  That phrase evolved to is the fallacy: it implies goal-directed behavior.  Only intelligent agents direct things toward functional goals.  Matter in motion does not – nor do non-sentient living things.  The apparent goal-directed behavior of bacteria toward a chemical gradient or moths toward a light is an artifact of their design.  The organisms are not “deciding” to set goals and work toward achieving them.  When you see evolved to, or find design and evolution in the same sentence, red flags should go up.  The science and philosophy referees need to call a foul.
    The second fallacy evolutionists commit is kind of like the anthropic principle in cosmology: “If the universe were not finely tuned for life, we wouldn’t be here to worry about the question.”  That’s a dodge, not an explanation.  It doesn’t explain why the universe is designed or how it got that way; it is an appeal to a counterfactual.  Similarly, natural selection theory implies that if the bird did not evolve a wing, it wouldn’t be flying; if the plant did not employ quantum mechanical light traps, it wouldn’t be harvesting light.  It does not follow that the bird did evolve the wing.  That would be the logical consequence only if evolution is assumed a priori to be the only option.  But it is not.  One cannot assume what needs to be proved (circular reasoning).  Since our uniform experience is that intelligent agents do engineering, intelligent design should be the default inference to the best explanation for wings, hearts and photosynthetic systems.
    The item about Maxwell’s demon (#7 above) is noteworthy.  As the Second Law of Thermodynamics is sometimes defined, all natural systems increase in entropy.  We know that humans can overcome the law of increasing entropy (locally and temporarily) by exerting goal-directed work, such as in harnessing the chemical energy of gasoline (from sunlight) in a well-designed piston engine.  Is that natural?  If humans are natural products of evolution, then everything they do should be defined as natural.  That would mean, however, that decreasing entropy is also natural – a contradiction with the Second Law of Thermodynamics, a law of nature if there ever was one.  And what about the real-world Maxwell demons like ATP synthase motors, flagella and other Brownian ratchets that harness random thermal energy to perform useful work?  Are they natural?  It is only by making the word natural a self-contradictory concept, or by abandoning the universality of laws of nature, that a materialist can deny intelligent causes are at work in the universe and played a role in its origin.
Next headline on:  Cell Biology • Physics • Plants • Terrestrial Zoology • Biomimetics • Intelligent Design • Amazing Facts

OSU research on avian biology and physiology has been raising questions on this issue since the 1990s, often in isolation.  More scientists and other studies are now challenging the same premise, Ruben said.  The old theories were popular, had public appeal and “many people saw what they wanted to see” instead of carefully interpreting the data, he said.
O    “Pesky new fossils...sharply at odds with conventional wisdom never seem to cease popping up,” Ruben wrote in his PNAS commentary.  “Given the vagaries of the fossil record, current notions of near resolution of many of the most basic questions about long-extinct forms should probably be regarded with caution.”

So scientists saw what they wanted to see.  Next question: why did they want to see it?  The invisible hand of Charlie controls the blinders on their eyes.
    Conventional wisdom is often an oxymoron.  It afflicts those infected with sophoxymoronia (02/02/2008 commentary).  Wisdom often requires breaking from conventions, especially scientific ones, where wrong ideas reinforce one another.  Cheer for the Mavericks.  In this case, Ruben is not maverick enough.  He needs to burn his Darwin Party card and join the ID revolution.
Next headline on:  Birds • Dinosaurs • Darwin and Evolution

The reader could hardly miss the one fixed parameter that could not be altered.  Of course: as usual, it was “geologic time.”  It doesn’t matter that these delicate structures and molecules had to be str-r-r-r-e-t-ched into hundreds of thousands of years.  Boy, they sure don’t look that old.  Couldn’t it be possible that these beetles died not that long ago, maybe just a few centuries or thousands of years ago?  No; that is forbidden.  It would mean something is wrong with geological dating methods.  Whoops; we just committed a thought crime: we asked questions about “geologic time.”
    To preserve geologic time, we were just forced to accept numerous improbable notions: the pH of this environment never changed, the sun never shone, the worms never came digging, and no earthquakes or tsunamis or volcanoes in a land on the Pacific Ring of Fire disturbed this delicate microenvironment for a hundred times the length of recorded human history.  Geologic time – that unobservable, imponderable, occult substance – plays such a central role in evolutionary beliefs, everything else in science and logic must adjust to it.  Since geologic time cannot be questioned, that makes it irrational.  It should be called, “Gee, illogic time.”
Next headline on:  Fossils • Terrestrial Zoology • Geology • Dating Methods

The Evolution of Religion – or Vice Versa?     02/08/2010    
Feb 8, 2010 — A Harvard professor has evolutionized religion again.  Marc Hauser, the one who trains his little boy to adore Darwin (07/03/2007) and wrote a book on how natural selection created morality (10/27/2006), is now saying that religion is a by-product of our evolution.  “These findings suggest that religion evolved from pre-existing cognitive functions,” he wrote in Trends in Cognitive Sciences,¹ “but that it may then have been subject to selection, creating an adaptively designed system for solving the problem of cooperation.”
    The science news media, like PhysOrg and Science Daily, published this “suggestion” uncritically based on a press release from Cell Press.  Their headline reads, “Morality Research Sheds Light on the Origins of Religion.”  A key element in Hauser’s “suggestion” was that the moral sense seems uniform across cultures.  No one in these articles entertained a different suggestion: that this moral sense came from design, not evolution.  Nor did they indicate how morality could be defined or characterized apart from a religious perspective.
    Phillip Ball at Nature News announced, based on this study, “Morals don’t come from God.”  At first, this sounded like an endorsement of Hauser’s thesis, but Ball only met him halfway.  “The finding that religion scarcely influences moral intuition undermines the idea that a godless society will be immoral, says Philip Ball,” the subtitle reads.  “Whether it ‘explains’ religion is another matter.”  Ball appeared to agree that irreligion does not necessarily lead to an amoral society.  Moral dilemma tests show that people from all walks of life have a basic moral intuition – an innate ‘moral grammar’ that guides their ideas of right and wrong.  He doubted, though, that moral instinct is the place to look for the origin of religion itself.  “It seems hard to credit the idea that the immense cultural investment in religion was made merely to strengthen and fine-tune existing neural circuits related to morality,” he ended.  “Some people place more emphasis on the adaptive rationale for religious symbols and mystical beliefs, rather than morals.”  Ball just indicated that he denies propositional truths have any bearing on religious beliefs.  Any explanation must be sought in evolutionary adaptation.  He seems to admit, though, even that kind of reductionism falls short of explaining religion.  “Yet attempting to explain the origins of such a rich cultural phenomenon as religion is doomed to some extent to be a thankless task,” Ball concluded.  “For to ‘explain’ Chartres Cathedral or Bach’s Mass in B Minor in terms of non-kin cooperation is obviously to have explained nothing.”
    For earlier discussions on the evolution of religion, see 11/09/2009 and 05/27/2008.

Hauser is just as religious as his lab rats; he just doesn’t advertise it.  He attends the Church of Darwin – a bigoted hate group (12/12/2009, 05/09/2006, 02/11/2006 commentary) with its own Monday School curriculum (12/21/2005), where he plays the role of High Priest Yoda (09/26/2006 commentary), accompanied by the other bishops Pascal Boyer (10/26/2008) and Daniel Dennett (02/02/2006).  James Dow accompanies on the organ (05/27/2008).
    The way to make Hauser’s belief implode and refute itself is to write a satire on The Evolution of Darwinian Storytelling.  That is what Cornelius Hunter has done on his blog Darwin’s God.  It appears that Hunter turned out the Hahvahd professor’s lights (assuming there were any to begin with).
Next headline on:  Bible and Theology • Darwin and Evolution • Dumb Ideas

There goes decades of bigoted evolutionary anthropology ranking humans by brain size (11/09/2007, bullet 3).  This has nothing to say about evolution (cf. with birds, 09/07/2005).  If evolution is the explanation for brain/body ratios going both ways, it explains nothing.  The article said that “sometimes individuals with smaller brains are favoured by natural selection,” even though selection usually favored big brains in primates.  Then again, brain size shrank in mouse lemurs, marmosets and mangabeys.  “In contrast, the study found no overall trend to increase body size, suggesting that brain and body mass have been subject to separate selection pressures in primates.”  Look how flexible evolution is; it explains everything.  If big brains are usually so favored by selection, why didn’t brain size increase in every kind of animal over time?  As a law of nature, natural selection has the strange property of producing opposite outcomes.  It’s not just Stuff Happens; its Contradictory Stuff Happens.
    Did evolutionary theory provide understanding here?  No; as usual, researchers were surprised by what they found: “The argument raised has been that the evolution of such a small brain does not fit with what we know about primate brain evolution,” they article said.  Rather than providing an explanatory framework that can make predictions, evolution is a Gumby explanation that continually gets stretched and squished to fit the data after discoveries are made (12/14/2004, 07/22/2006, 08/14/2006, 10/26/2006, 09/06/2007, 01/23/2009).
    Look at another recent example: Charles Q. Choi in Live Science told about a controversial theory that claims “The evolution of the distant ancestors of humans and other primates may have been driven by dramatic volcanic eruptions and the parting of continents.”  Wow.  Volcanos made you what you are today.  One problem with this “absurd” theory is that it has “resulted in all sorts of contradictory centers of origin.”  Moreover, Choi said that “fossils often serve as an incomplete record for what and when animals actually existed.” Keep that sentence in mind when you hear someone pointing to fossils as proof of evolution.  Satisfied?  Vote if you think evolution is increasing our understanding of nature.  For a good joke, look at the last sentence of Choi’s article.
    The obsession with brain size is misguided, anyway (08/05/2006).  As we have noted many times before, it’s quality, not quantity that counts (11/09/2007, 03/12/2008).  Was Tom Thumb any less human because of his small stature?  There have been examples of living humans doing pretty well with shrunken and damaged brains (e.g., 07/22/2009).  There’s some redundancy built in (08/28/2001).  Crows have small brains but show a lot of intelligence (05/26/2009, 08/11/2009).  Blue whales have huge brains but are not correspondingly better philosophers than humans.  We see large differences in morphology between living human tribes (Watusi vs pygmy, Inuit vs Vietnamese).  It is certainly within the range of variation for an inbred tribe, stranded on a small island, subject to local diseases, to grow physically smaller.  It doesn’t mean they were stupid or less evolved.  If we could have talked to Bilbo and Frodo on the island of Flores, we might have been impressed with their cognitive abilities.
    A small brain that performs well could be taken as a good example of miniaturization.  Human engineers pride themselves on packing more oomph in smaller devices; look how USB drives have progressed from 56k to 4GB, while getting smaller and cheaper, in a few years.  It’s not just the hardware.  The software is often more indicative of design.  There are plenty of large-brained humans walking around today with self-inflicted buggy code.  Put them in an Indonesian cave without their Bud Light and see how long they survive.
Next headline on:  Early Man • Fossils • Darwin and Evolution

Sociology of Science: the IPCC Case     02/06/2010    
Feb 6, 2010 — Climate change is off-topic for evolution news, but what is taking place in this internationally-potent paradigm is instructive.  Its troubles provide fodder for several extra-scientific disciplines: the philosophy of science, the history of science, the rhetoric of science, and the sociology of science.  Lessons from the IPCC case can inform citizens about current scientific practices in general – especially highly politicized sciences like evolution.
    What the world is witnessing in the IPCC case is astonishing – perhaps unprecedented.  Within a few months, a solid international consensus has unraveled.  It began days before a huge international conference in Copenhagen that was to impose draconian measures on world governments to curb carbon emissions.  Emails leaked or stolen revealed something rotten at the IPCC, the international clearinghouse for climate science.  Climate skeptics immediately smelled blood; their criticisms went viral on the internet.  It didn’t help that Copenhagen suffered one of its coldest winters as politicians traipsed through the snow and cold to figure out how to fight global warming.  Relevant or not, the irony was not lost on the public.
    At first, the response of the scientific community to the Climategate email scandal was to circle the wagons, underestimate the scandal’s impact, and blame the naysayers for their ignorance of the scientific facts.  But then, additional scandals came to light, exposing failures in peer review, lapses in scholarship, and evident conflicts of interest.  The disconnect between Big Science’s overconfidence and public skepticism has been growing steadily to the point where even staunch supporters of anthropogenic global warming (AGW) are calling for deep reforms.  Here are a few recent data points in the ongoing saga.

1. American opinion about global warming is cooling, reported Science Daily.
2. The BBC News, originally in the wagon circle, has lately been more open about reporting breaches of ethics that have eroded public confidence in climate science.
3. The BBC News, at first supportive of the IPCC, reported that the University of East Anglia where the scandal erupted “breached data laws” by withholding data when it was requested by skeptical scientists.  The article acknowledged that the incident caused damage to the public interest.  The university manipulated and suppressed data in a way that was “at odds with acceptable scientific practice.”
4. The journal Nature, originally in a huff over climate skeptics, has started printing some papers that are not as confident about AGW, such as this paper Jan 28 that considered degrees of climate feedback throughout the medieval period.
5. Science Daily reported that stratospheric water vapor turns out to be a “climate wild card,” affecting climate models in unexpected ways.
6. Science Magazine on Jan 29 printed an interview with IPCC head Rajendra Pachauri when calls for his resignation were heating up.  The magazine allowed him free rein to defend himself against allegations, which he did rather brusquely, but the interviewer questions seemed a little worried.
7. On Feb 2, Nature acknowledged that the IPCC has been “flooded with criticism” and took note that some of the criticisms, including data flaws and conflicts of interest, are not easily dismissable.
8. BBC commentator Malini Mehra said that “The Copenhagen Climate Accord was a failure of historic proportions that is hardly worth the paper it is printed on.”  The meetings led to a chaos of competing national self-interests.
9. BBC commentator Roger Harrabin has been growing more vocal about reform.  On Feb 1 he called for embracing uncertainty rather than pretending that the consensus science is settled.  On Feb 3 he discussed problems at the IPCC and entertained reasons why its leader should resign.
10. Richard Black’s commentaries for the BBC News have been evolving.  From initial overconfidence, he has been having to admit the scientific consensus is taking a beating.  He acknowledged on Feb 5 that skepticism is rising in the UK, noting several prominent British commentators speaking out and polls showing public discontent with the IPCC.
11. This week Science Magazine reported on the latest scandal, the misinformation about melting glaciers.  The magazine also printed an Editorial preaching about the need for integrity in science.
12. News outlets that a month ago seemed sold out to the AGW consensus are now showing some courage to give skeptical stories favorable press.  Today, Science Daily printed a story that estimates of melt from Alaskan glaciers were largely overestimated, and another Science Daily article questioned scientists’ knowledge about orbital forcing: “The notion that scientists understand how changes in Earth’s orbit affect climate well enough for estimating long-term natural climate trends that underlie any anthropogenic climate change is challenged by findings just published.”  See also the 12/19/2009 entry about cave proxies.
13. Another day, another embarrassment: PhysOrg reported that the Dutch found an inaccurate statement in the IPCC's 2007 report, claiming that half of the Netherlands is below sea level.  “No evidence could be found to show the claim had been published in a peer-reviewed journal and reports in Britain have said the reference came from green group the WWF [World Wildlife Federation], who in turn sourced it to the New Scientist magazine.”  Normally, scientific findings flow the other direction.
14. New Scientist, a cheerleader for the IPCC, nevertheless called to “Let the sunshine in” and embrace open debate, including dialogue with bloggers and skeptics.  Notice how the editorial even suggested the possibility a naked emperor on the loose:

    Some argue that the views of an untutored blogger, or even a scientist from another discipline, should never carry the same weight as those of someone with a lifetime’s expertise in a relevant field.  But if occasionally the emperors of the lab have no clothes, someone has to say so.  The wider review of science made possible by the blogosphere can improve science and foster public confidence in its methods.  Scientists should welcome the outside world in to check them out.  Their science is useless if no one trusts it.

15. AfricaGate: Now another widely-quoted factoid about global warming has come under attack: that North Africa’s crop production would drop by 50% by 2020.  The Times Online reported Feb 7 there was no basis in the IPCC report for such a claim, but it had been quoted by the IPCC chairman and by the UN Secretary-General.  “A leading British government scientist has warned the United Nations’ climate panel to tackle its blunders or lose all credibility,” the article began.

This commentary is not taking sides on AGW, since it is off-topic.  But there are important lessons here for all of science.  It goes without saying that scientists are only human, but that’s the problem: scientists are only human.  They have emotions, biases, friends, enemies, likes, dislikes, habits and weaknesses like the rest of humanity.  They are also not omniscient.  We are taught that the methods of science and peer review overcome these limitations, and produce knowledge that is reliable, progressive and relevant to nature as it really is.  Oh?  That is so 1930s.  It may still be taught in middle schools and high schools, but the philosophy of science has been quite literally revolutionized since the 1950s and 60s.  Kuhn’s book in particular launched or re-invigorated several disciplines that began to analyze scientific practice more critically:

• History of Science changed from describing science’s march of progress to a different realization: that scientific knowledge itself is historical in character – i.e., it changes over time.  Ideas claimed to be scientific facts in one generation can be fundamentally modified or overturned in the next.
• Sociology of Science: Kuhn’s description of science as a guild locked in a paradigm led to renewed attempts to examine the human element of knowledge generation: the cliques, reinforcements, shared beliefs, taboos and other non-empirical aspects that influence conclusions in scientific institutions.  Some took on the project of analyzing science scientifically, going into labs to describe the way scientists work in the way they would investigate a tribal culture.  Postmodernism overlapped with these efforts.  For sources on the history and sociology of science, see the 12/19/2009 and 04/18/2009 Resources of the Week.
• Rhetoric of Science sprang up as a discipline after Kuhn to tackle the rhetorical character of scientific claims.  How do scientists frame their theories?  How do they communicate them to the public?  To what extent do analogies, projection themes and shared language modes influence not only what scientists believe, but what direction science should go?  In addition, how is rhetoric employed in scientific controversies?  For sources on rhetoric of science, see the 11/21/2009 and 03/28/2009 Resources of the Week.

The current hubbub over climate science could calm down, with the consensus stabilizing itself again, or we could witness its collapse.  If the latter, the public image of science as objective and reliable could be severely damaged.  To be true, the IPCC is a somewhat unique case.  It is a centralized body invested with a special role for a single research domain.  Nevertheless, all the major scientific organizations and nations placed unquestioned trust in its reports, because they assumed its methods guaranteed objectivity.  Look at their initial knee-jerk reaction to skeptics.  It was not just the IPCC, but Nature, Science, PNAS, the media, and a host of non-governmental organization that treated the AGW consensus as truth and the IPCC reports as revelation from heaven (the atmosphere, that is).  Skeptics were treated as outsiders and pariahs.  The resemblance to the Darwin consensus is apt.
    Most likely, there will be some bandage reforms to the IPCC peer review process, some individuals will step down, some new regulations will be passed, and journal editors will be a little more careful for awhile.  Then old habits will return.  Remember the Hwang scandal?  Remember the calls for major reforms in peer review? (02/05/2006)  Like last New Year’s resolutions, much of that soul-searching has been forgotten.  Scientists, after all, are only human.
    Those watching this climate scandal perceptively should be alert to the degree to which non-empirical forces shape widely held beliefs in scientific institutions.  The institutions of science must be distinguished from the ideals of science.  As with labor unions, the ideals of protecting worker’s rights often get lost in the politics, corruption and self-interest of the party leadership.  Don’t think for a minute that just because Big Science owns the institutions and journals and political power when they trumpet allegiance to Darwin and hatred of intelligent design, they have an inside track on knowledge.  It’s no coincidence that the same liberal, progressive mentality that dominates Big Labor also dominates Big Science.  The Law of Nature most apropos to climate science, UN science and origins science comes from Political Science: Power Corrupts.
Next headline on:  Politics and Ethics

Old Primordial Soup Is Spoiled     02/05/2010    
Feb 5, 2010 — Don’t open it; that can of primordial soup sitting on the shelf for decades is rotten.  PhysOrg announced, “New research rejects 80-year theory of ‘primordial soup’ as the origin of life.”  In its place come new theories about tiny chemical cooking pots in the pores of deep-sea vents.  Pioneered by Michael Russell (02/15/2008) and others, these scenarios picture energy gradients and concentrating mechanisms that might have gotten life cooking deep below the sea.  National Public Radio printed a short synopsis, asking, “Is It Time To Throw Out ‘Primordial Soup’ Theory?”
    The article is clear that primordial soup is off the shelf.  “Textbooks have it that life arose from organic soup and that the first cells grew by fermenting these organics to generate energy in the form of ATP,” said team leader Dr Nick lane from University College London.  “We provide a new perspective on why that old and familiar view won’t work at all.”  One problem is that there is no energy gradient in such a view: no driving force for chemical reactions.  “Despite bioenergetic and thermodynamic failings the 80-year-old concept of primordial soup remains central to mainstream thinking on the origin of life,” said senior author, William Martin, an evolutionary biologist [Institute of Botany III in Düsseldorf].  “But soup has no capacity for producing the energy vital for life.”  There goes a ton of expensive soup down the drain.  It sure had a lot of sentimental value.

This story should make the righteous angry.  For decades – almost a century (more if you consider Darwin’s “warm little pond” story) – the Primordial Soup Myth filled biology textbooks with fallacies.  The Miller experiment, with its flasks zapped with electricity, lent itself to visualization, exaggeration and power of suggestion.  It became a veritable icon of evolution – a “useful lie” for materialists (05/02/2003).  Lee Strobel was one of countless students swayed by the Primordial Soup Myth, as he recounted in his book and film, The Case for a Creator (watch it on YouTube).  This simplistic mythoid, devoid of factoids, has now been destroyed and should be avoided, but it will take an act of Congress, an executive order and a Supreme Court decision to overcome the Law of Inertia for Falsified Theories (01/15/2010).
    With the soup gone, would you trust the same materialists to come up with a better dish?  Would you dare taste their Thicken Plot Pie? (08/22/2005).  Their new story has all the same fallacies as the old one, including the biggest: it doesn’t account for the most important element of all, the origin of genetic information (01/26/2008, and Meyer’s Signature in the Cell).
    To dispense with materialistic origin-of-life scenarios, with their “building blocks of lie,” let us propose an alternative experiment that is easily visualized and can even be tested by junior high school students.  (This was suggested by Dr. A. E. Wilder-Smith.)  Take a sardine can.  It has ideal conditions for the origin of life, because the little fishies were once alive.  It has all the molecules and nutrients life could ever want.  Do anything you want with the can, other than puncturing it or breaking its seal.  You can heat it, chill it, tap it, spin it, and expose it to electromagnetic fields.  An alternative experiment was suggested by Dr. Jonathan Wells.  Take a living cell in a test tube of sterile fluid, and puncture it.  Let the cell’s contents ooze out, then cap the tube.*  Again, you have all the ingredients for life right there.  Wait for life to emerge.
    These are the best possible conditions for origin-of-life studies.  Let the materialists succeed here before attempting to prove life could have emerged under far less favorable conditions.  We suggest it will be a lot like watching the prophets of Baal.  Give them time to cut themselves, weep and wail for the god of chance to send the fire of life.  Then, send a modern Elijah to show where the true power behind life is to be found.  He can insert a little genetic information, a little E. coli into the can perhaps, and like fire from heaven, the can will burst with life.  The only step left will be to round up the fakes and deal with them.
*Actually, a variation on this experiment was done by Louis Pasteur in the late 1800s – the famous swan-necked flask experiment that disproved spontaneous generation.  Some of his flasks, on display in France, remain sterile to this day, after well over a century, even though open to the air (source: Clermont College).  They stand as a testament to the fact that life (containing genetic information), and only life, begets life.  If materialists respect empirical evidence, let them stand in silent humility at one of the longest-running experiments in the history of science.
Next headline on:  Origin of Life • Media • Education

Many biological surfaces in both the plant and animal kingdom possess unusual structural features at the micro- and nanometre-scale that control their interaction with water and hence wettability.  An intriguing example is provided by desert beetles, which use micrometre-sized patterns of hydrophobic and hydrophilic regions on their backs to capture water from humid air.  As anyone who has admired spider webs adorned with dew drops will appreciate, spider silk is also capable of efficiently collecting water from air.  Here we show that the water-collecting ability of the capture silk of the cribellate spider Uloborus walckenaerius is the result of a unique fibre structure that forms after wetting, with the ‘wet-rebuilt’ fibres characterized by periodic spindle-knots made of random nanofibrils and separated by joints made of aligned nanofibrils.  These structural features result in a surface energy gradient between the spindle-knots and the joints and also in a difference in Laplace pressure, with both factors acting together to achieve continuous condensation and directional collection of water drops around spindle-knots.  Submillimetre-sized liquid drops have been driven by surface energy gradients, or a difference in Laplace pressure, but until now neither force on its own has been used to overcome the larger hysteresis effects that make the movement of micrometre-sized drops more difficult.  By tapping into both driving forces, spider silk achieves this task.  Inspired by this finding, we designed artificial fibres that mimic the structural features of silk and exhibit its directional water-collecting ability.

Here’s another teachable moment with your child in the garden.  We should never take simple things for granted.  It’s clear that the spider can teach humans their design principles, but who taught them to the spider?  Be sure to explain to the child that storytelling with tautologies is not an acceptable response (10/29/2002).
Next headline on:  Terrestrial Zoology • Physics • Biomimetics • Amazing Facts

Universe Has a Run-Down Feeling     02/03/2010    
Feb 03, 2010 — There’s 30 times more entropy in the universe than thought, according to Dr. Charley Lineweaver at the Australian National University.  PhysOrg said that Lineweaver and a PhD student Charles Egan measured the entropy of the universe.  It looks like it is feeling pretty run down. 

“We considered all contributions to the entropy of the observable universe: stars, star light, the cosmic microwave background.  We even made an estimate of the entropy of dark matter.  But it’s the entropy of super-massive black holes that dominates the entropy of the universe.  When we used the new data on the number and size of super-massive black holes, we found that the entropy of the observable universe is about 30 times larger than previous calculations,” said Mr. Egan.
    “Contrary to common opinion, the maintenance of all the complicated structures we see around us -- galaxies, stars, hurricanes and kangaroos -- have the net effect of increasing the disorder and entropy of the universe.  But to be fair, their contributions are negligible compared to the entropy of super-massive black holes,” added Dr Lineweaver.

Hurry!  You only have billions of years left to evolve!  Whether evolutionists will yawn, or will question the measurements of the entropy of unobservable entities, remains to be seen.  Still, it’s a reminder that the universe will run down over time.  It will take something able to work outside the universe and time to stop the inevitable.  For three great Christian physicists who took part in the energy conservation revolution of the 19th century, see our biographies of Maxwell, Joule, and Thomson.
Next headline on:  Cosmology • Physics

Building a Cell: Staggering Complexity     02/02/2010    
Feb 2, 2010 — “The living cell is a self-organizing, self-replicating, environmentally responsive machine of staggering complexity.”  Thus began a special section on “Building a Cell” in Nature last week.¹  The section with five papers explores what is known about gene regulation, cell organization and signalling.  It’s an opportunity, as well, to see what scientists think about what they are seeing.  “This Insight offers a hint of the most exciting research on the regulation of cellular organization and function,” the editors said, inviting the readers in for a look.

1. Chromosome segregation: staggering machinery:  Bloom and Joglekar started out the series with a look at how cells divide the daughter chromosomes during cell division.²  “All organisms, from bacteria to humans, face the daunting task of replicating, packaging and segregating up to two metres (about 6 x 10⁹ base pairs) of DNA when each cell divides,” their attention-getting abstract began.  “This task is carried out up to a trillion times during the development of a human from a single fertilized cell.”  Scientists may understand the strategy for replication, “But when it comes to packaging and segregating a genome, the mechanisms are only beginning to be understood and are often as variable as the organisms in which they are studied.”
       Yet the seemingly unlimited ways different organisms accomplish this must meet stiff requirements for precision: “chromosome segregation must be executed with high fidelity so that the mother cell and the daughter cell that arise from division receive precisely the same DNA content,” they said.  Everything has to be done just right.  The cell has to be able to tell the chromosomes apart: which ones are the copies, and which ones are just look-alikes?  Where does each chromosome belong on the spatial template, like band members on a football field half-time show?  And where is the drum major calling the signals?  Here’s a take-home sentence: “Finally, the segregation machinery must function with far greater accuracy than man-made machines and with an exquisitely soft touch to prevent the DNA strands from breaking.”
       Bloom and Joglekar talked “machine language” over and over.  The cell has specialized machines for all kinds of tasks: segregation machines, packaging machines, elaborate machines, streamlined machines, protein translocation machines, DNA-processing machines, DNA-translocation machines, robust macromolecular machines, accurate machines, ratchets, translocation pumps, mitotic spindles, DNA springs, coupling devices, and more.  The authors struggle to “understand how these remarkable machines function with such exquisite accuracy.”
       The paper reads like a description of an alien spaceship filled with machinery carrying out amazing coordinated functions that visitors can only partially grasp, but know everything is obeying laws of physics: e.g., “Although DNA is not covalently linked to spindle microtubules or motor proteins, it may act as a spring in its capacity to absorb force and therefore prevent molecular motors from travelling too fast.”  Another example: “A different way of organizing polymers is to anchor many chains to a substrate (Fig. 1c).  In the field of polymer physics, this is an important strategy for regulating forces between polymers (for example in polymer brushes) and the environment, and for creating methods to switch rapidly from attraction to repulsion.  One type of brush is a Velcro-like structure, in which a highly oligomerized protein is attached to a subcellular site.”  Sure enough, such a strategy was discovered recently in a bacterium, with finesse: “Polymers of the C. crescentus protein PopZ assemble into a higher-order filamentous network that functions as an anchor for chromosome capture,” they said.
       On two occasions they referred to evolution: (1) Speaking of how cells package the chromosomes to avoid breakage while making certain essential genes accessible during cell division, they said, “Several diverse protein machines have evolved to carry out these processes.”  They did not say how they evolved.  (2) Speaking of how certain genes are deactivated by histone modifications, they said, “DNA wrapping around the histone may impart a topological block to transcription.  In this model, nucleosome chirality at the centromere, as well as the path of DNA as it enters and exits the nucleosome, may have evolved to inhibit transcribing polymerases from inactivating the centromere, which would otherwise lead to chromosome loss.”  Presumably, if the cell had not “evolved” all this machinery “to” do these exquisite, coordinated functions, it would not exist today.
2. Alternative splicing: staggering information and control:  Nilson and Graveley contributed a review article for the series about how alternative splicing expands the genome.³  This refers to the fact that a compact library of genes can be read in different ways, to generate more information in less space.  It would be like a software library with modules that can be joined in various ways to produce a variety of outcomes.  Like the other papers, this one has plenty of “wow factor” –

   The collection of components required to carry out the intricate processes involved in generating and maintaining a living, breathing and, sometimes, thinking organism is staggeringly complex.  Where do all of the parts come from?  Early estimates stated that about 100,000 genes would be required to make up a mammal; however, the actual number is less than one-quarter of that, barely four times the number of genes in budding yeast.  It is now clear that the ‘missing’ information is in large part provided by alternative splicing, the process by which multiple different functional messenger RNAs, and therefore proteins, can be synthesized from a single gene.

   A realization has been growing that alternative splicing, once thought unusual, is common.  Here’s a “spectacular example,” they noted: a gene in a fruit fly can produce 38,016 distinct messenger RNAs, “a number far in excess of the total number of genes (~14,500) in the organism.”  This means that there is far more information encoded in the genome than earlier believed: “the number of functionally distinct proteins that could be encoded by the genome is staggering.”  They said it now appears that “alternative splicing is one of the main sources of proteomic diversity in multicellular eukaryotes.”
       This raises obvious questions about oversight and control.  What tells the fruit fly which one of the 38,000 protein products is needed at a particular time from that particular gene?  “The biochemical mechanisms that control splice-site usage, and therefore alternative splicing, are complex and in large part remain poorly understood,” they said.  “It is clear that there cannot be specific and distinct factors dedicated to each of the more than 100,000 alternative splicing decisions that occur in human cells; several genomes worth of regulatory proteins would be required if this were the case.”  Apparently, a small number of proteins are involved in alternative splicing events.  But what regulates the regulators?  “How can this handful of splicing regulators be responsible for controlling the plethora of alternative splicing events that occur?”  Again, this is “far from understood.”  The complexity truly is staggering when just the known mechanisms are listed:

   The number of mechanisms that are known to be involved in splicing regulation approximates the number of specific splicing decisions that have been analysed in any detail.  These mechanisms range from straightforward ones, such as steric blocking of splice sites or positive recruitment of the splicing machinery, to more complicated ones, such as formation of ‘dead-end’ complexes, blocking of splice-site communication or facilitation of splice-site communication.  Even these mechanisms are poorly understood at a detailed biochemical level (for example, what distinguishes dead-end complexes from productive complexes remains unclear).
       The picture becomes even cloudier when splicing (and alternative splicing) is viewed not as a static process but as a highly dynamic process encompassing a large (yet to be defined) number of kinetic steps.  It is now clear that many factors can have marked effects on splicing patterns; these include transcription rate, core-splicing-machinery levels, intron size and competition between splice sites.

   So the kinetic factors add another dimension to the effects of alternative splicing.  Add to this the effects of chromatin structure (the “histone code”) and staggering seems an understatement.  Had enough yet?  “Last, before leaving the mechanistic aspects of alternative splicing, it should be noted that we have understated the complexity of the mechanisms involved.”  At this point, when the reader is about to collapse from overload, they keep rubbing it in: “it is clear that context affects function, and this adds a layer of complexity to the already complex field of alternative and regulated splicing.”
       Surely these authors would not think this all evolved, would they?  Actually, they did.  In a confusing section about “bioinformatics,” a word that connotes intelligent design, they suggested that alternative splicing provides “evolutionary plasticity” – a more fluid environment in which mutations could cause significant evolution over point mutations on a gene.  But at the current time, these are only suggestions, if you can “envisage” them:

   These examples show the high level of evolutionary plasticity that alternative splicing provides.  Because small changes (that is, point mutations) in either exons or introns can create or destroy splicing control elements, it is easy to envisage that splicing patterns are constantly evolving: advantageous mutations would rapidly be selected for, and deleterious mutations would be selected against.  Indeed, we speculate that ‘non-conserved’ changes in splicing patterns might underlie the observed phenotypic variations between species and between individuals within species.  Recent studies have provided insight into the way in which human exons have evolved and the extent of alternative splicing differences between humans and chimpanzees.  Additional studies along these lines are likely to improve the understanding of how alternative splicing contributes to speciation and phenotypic diversity.

   Thus, the real “understanding” is only a promissory note dependent on future research.  Will anyone remember to check back in a decade and see how the promissory note paid off?  Or will this be an example of a misuse of the power of suggestion?
       The authors are not ignorant of the questions this research raises about final causes.  “Another crucial question is how many mRNA isoforms are functionally relevant?  Teleology suggests that if an isoform exists, it is important (similarly to the way in which ‘junk’ DNA is now considered to be treasure),” they noted, as if smarting from the realization that the “junk DNA” paradigm has imploded.  “But this idea [teleology] is hard to prove and is difficult for some to accept.”  First of all, we don’t know how many isoforms [products of alternative splicing] are functional, and “the question of how many alternative splicing events are functionally relevant is destined to remain unanswered for some time.”  A number of tantalizing possibilities appear on the horizon. 

   Another outstanding question is whether there is a decipherable ‘splicing code’.  Will a computer be able to predict reliably the splicing patterns in a cell or organism?  Despite the numerous variables (known and unknown) involved in splice-site choice, rapid progress has been made in this area.  But it is not clear when or whether this Rosetta stone of splicing will emerge....
       Much remains to be learned about the mechanisms of alternative splicing and the regulatory networks of alternative splicing.  It is clear that researchers are only beginning to understand the diversity and details of the mechanisms that are used to regulate alternative splicing, as well as the factors involved.  Recent technological advances, particularly in genomic analysis, suggest that the next few years are likely to be filled with many exciting and unanticipated discoveries that could rapidly reveal the mysteries of the field.

3. Endocytosis: Master Plan Association:  Cells are not isolated entities.  They interact profoundly with their environment.  One way they do this is through endocytosis: the orderly capture of material from outside the cell membrane to the inside.  The authors of the third entry in Building a Cell⁴  wrote that endocytosis, long understood as mere intercellular trafficking, is being “integrated at a deeper level in the cellular ‘master plan’ (the cellular network of signalling circuits that lie at the base of the cell’s make-up).”  By deciphering this level, the “endocytotic matrix,” scientists “might uncover a fundamental aspect of how a cell is built.”
       Their are two major types of endocytosis.  One uses clathrin (see 10/07/2003), the other does not.  Clathrin is a unique 3-legged protein that links up to form a kind of geodesic-dome net around the cargo coming in through the cell membrane (watch the “Flight of the Clathrin Bumblebee” animation from Harvard).  Other pathways envelop the cargo in lipids, without the clathrin.  By containing the cargo in a vesicle, the cell can control it, like shipping containers arriving at a dock.  The cargo can contain nutrients or signals from the environment.  A new finding coming to light is that the signals are reciprocal.  This hints that more is going on than once thought:

   Recent studies, however, have uncovered a wealth of evidence that endocytosis has a much wider impact on signalling, including the finding that signalling pathways and endocytic pathways are regulated in a reciprocal manner, and the finding that several molecules have roles in both endocytosis and signalling (see refs 3, 4, 5 for reviews).  The emerging model is that the net biochemical output of signalling pathways largely depends on topological constraints.  These constraints are imposed by the association of signalling molecules with membranes, which in turn is regulated by endocytosis and by cycles of endocytosis and recycling to the plasma membrane (that is, endocytic and exocytic cycles (EECs)).  This set-up allows signals to be decoded by the cell according to precise kinetics and at spatially defined sites of action.  And, not surprisingly, it translates into endocytosis having a large impact on almost every cellular process.  In addition, evidence is emerging that the endocytic machinery has molecular functions that are not immediately reconcilable with membrane trafficking, leading researchers to question whether these ‘non-canonical’ functions are ‘moonlighting’ jobs or whether they point to deeper levels of integration of the endocytic matrix within signalling circuitries and cellular programs.

   Moonlighting jobs: what a suggestive analogy.  But if the moonlighting is even part of a bigger master plan, that’s even more suggestive of unforeseen complexity at deeper levels.  “Here we summarize the current understanding of how endocytosis is embedded in the cellular master plan, and more specifically its connections to signalling,” they said, launching into the discussion.  They seem to like that “master plan” metaphor: “We review endocytosis at the level of the circuits involved, highlighting how the integration of endocytosis and signalling determines the net biochemical output of a cell.  Then, we analyse how endocytosis affects the execution of complex cellular programs.  And, last, we speculate on how endocytosis might have evolved to become a pervasive component of the cellular master plan.”  How did the E-word evolved sneak into the master plan?  We shall see.
       Sparing our overwhelmed readers the details of signalling, circuits and I/O, we note that the authors make “a plea for systems biology” to pull all this data together – i.e., a big-picture perspective.  We note the authors mentioning “microtubule motors” that propel the vesicles along highways to their targets, such as the nucleus.  Yet the average speed of the motors seem inadequate to explain how the signals traverse large distances to reach their targets as rapidly as experiments show.  Are there “traveling waves” of protein activation?  We don’t yet know.  The system also has to account for degradation and recycling of some parts.  Recent findings show endocytosis intimately involved in such diverse activities as mitosis, cell-cycle progression, and transcription, as well as in signaling.  The roles for endocytosis described by the authors seems endless: asymmetrical cell division, cytokinesis (the last part of cell division), genetic reprogramming, tumor suppression, transcription.  They wonder again whether the endocytosis mechanisms are “freelancing” these jobs or are part of a bigger picture.
       Trying to get a grip on how all these roles might have evolved, they explored three analogies: (1) the moonlighting hypothesis (endocytic proteins carry on dual functions), the (2) autogenous hypothesis (it all started with membrane budding), and (3) the “Roman-road” hypothesis (it emerged for one function but found uses for others later, like Roman roads built to transport armies proved useful for commerce).  The autogenous hypothesis imagines the nucleus evolving from an endosome (endocytotic vesicle).  “Eukaryotic cells would thus have evolved as a consequence of the acquisition of a novel cellular property, the capacity to carry out endocytosis, putting this process at the centre of the eukaryotic cell master plan.”  Putting have evolved and master plan in the same sentence seems strained.  It gets even more strained when motors enter the picture: “As a consequence, several functions must have co-evolved with endocytosis,” they said: “For example, the evolutionary development of endocytosis must have co-evolved with that of the cytoskeleton, because membrane dynamics requires cytoskeletal scaffolds and molecular motors.”  How that happened was left as an exercise.  The Roman-road discussion became even more personified and mixed with intelligent-design lingo:

   Different passengers can be envisaged on these endocytic routes: commuters, hitch-hikers, hijackers and ticket holders.  Commuters are the regular passengers (cargo and associated machinery) for which the system was initially designed.  Hitch-hikers are molecules that parasitize the system (that is, they hitch a free ride) for a purpose not associated with endocytosis, without altering the functioning of the system.  Hijackers are hitch-hikers that sidetrack the system for their own purposes, causing it to malfunction, for example pathogens and, probably, cancer proteins.  Ticket holders are hitch-hikers that have evolved to ‘pay the fare’, by acquiring a new endocytosis-associated role (and therefore contributing to the functioning of the endocytic system), while retaining their original role.  Their new endocytic function might be unrelated to their original role to the extent that they seem to be moonlighting, thus bringing us back to the first proposed hypothesis [moonlighting].

   How useful these metaphors are to really understanding the “master plan” of the cell is debatable.  But it appears that intelligent design is the key to unlocking the mystery of endocytosis, regardless of what the authors think about evolution.  Why?  Because it is apparent there is a master plan:

   The evidence that we have reviewed here clearly indicates that endocytosis and signalling are two sides of the same coin and should be conceptualized as a single cellular process that is central to the eukaryotic cellular master plan.  Unravelling the logic of the ‘endocytic matrix’ therefore seems to be indispensable to any attempt to reverse engineer the cellular master plan in order to understand how a cell is ‘built’.

   Remarkably, their concluding suggestions for further research incorporate both intelligent-design and evolutionary concepts.  On the one hand, they recommended “complete understanding will be obtained only by integrating an additional level of complexity: information from ‘omics’ approaches and ‘top-down’ modelling,” as if there really is a master plan.  But then they said we might be able to reproduce the evolutionary history of endocytosis.  “Finally, scientists have traditionally devoted considerably more energy to understanding how things are than to how things came to be the way they are.  Re-evolving an endomembrane system in vivo, starting from prokaryotes, is a formidable task, but if it is successful, it will enormously improve understanding of the master plan of eukaryotic cells.”  Go figure.  They used the phrase “master plan” eight times, but spoke of its antithesis, evolution, 14 times.  We can only hope that with understanding – however scientists arrive at it – will come healthful benefits, like the ability to fight disease.
4. Chromatin remodelling: glimpses of a higher code:  Combinatorial assembly is a key phrase in the fourth paper in the series.⁵  If that sounds like coding, that’s because it is.  Ho and Crabtree wrote,

   Before mammalian genomes were sequenced and genome-wide analyses of chromatin function became possible, ATP-dependent chromatin remodelling was thought to be largely a permissive mechanism that operates to allow the binding of general transcription factors.  However, the discovery that a large number of non-redundant genes are involved in chromatin remodelling and the ability to carry out more rigorous genetic analyses is enabling the specialized and instructive functions of these complexes to be defined.  These functions arise partly from the combinatorial assembly of the complexes.  The assembly of complexes from products of gene families suggest that biological specificity is produced in much the same way that letters produce meaning by being assembled into words.  But the mechanisms by which these chromatin-remodelling “words” are “translated” into specific biological functions are still unclear, and new ways to probe complex chromatin structure might be needed before we can improve our mechanistic understanding.

   The authors did not use the phrase “histone code” but the concept is related.  Apparently the combinatorial assembly of histone modifications is a means of storing cellular information independent of the genetic code.  An important question is whether the code is heritable.  The answer: we don’t yet know.  They said, “At present it is not known whether chromatin remodelling can transmit the memory of cell fate from one generation to the next.  With mounting evidence of the transience and reversibility of chromatin modifications (such as the presence of histone demethylases), the view that chromatin configuration is fixed after being established is giving way to the view that the chromatin landscape can be altered in response to both extrinsic signals and intrinsic signals, such that de-differentiation through nuclear reprogramming is possible.”  That possibility is clearly of interest for stem cell research.  On the other hand, “If their program of action is transmitted from one generation to another, then uncovering the mechanisms that direct remodellers back to their appropriate sites of action after each cell division will be crucial for understanding how the specificity and the memory of chromatin-remodelling action are achieved during development.”  One thing is clear from recent research: “For these reasons, the roles of ATP-dependent chromatin remodelling may be wider, yet more precise and programmatic, than was previously thought.”
       What did these authors think about evolution?  All they said was brief and speculative.  They assumed evolution without saying anything about how it took place.

   ATP-dependent chromatin-remodelling complexes seem to have evolved to accommodate the major changes in chromatin regulation that occurred during the evolution of vertebrates from unicellular eukaryotes (Box 1).  As an example, complexes of the SWI/SNF family, which is one of the most-studied families of chromatin-remodelling complexes, have lost, gained and shuffled subunits during evolution from yeast to vertebrates.  In particular, the transition to vertebrate chromatin-remodelling complexes involved the expansion of several of the gene families encoding the subunits and the use of combinatorial assembly, which together are predicted to allow the formation of several hundred complexes.  But what is the advantage of combinatorial assembly?

   This statement says little more than “it evolved during the evolution of” this or that.  Moreover, the wording that said evolution involved the expansion...and the use of combinatorial assembly, by using subjunctive and passive verbs, shields the statement from any explanatory utility.  <1>Who or <1>what came up with “the use of combinatorial assembly”  How?  Why?  Evolution, a mindless and passive process, cannot shed light on such questions.
       Certainly, the authors avoided elaborating on what they meant.  But they did elaborate on their last question, “what is the advantage of combinatorial assembly?”  It’s much like the advantage of alternative splicing (see #2 above): it allows for orders of magnitude more information to be derived from the same compact code.  It means that both alternative splicing and chromatin remodelling use the same strategy of combinatorial assembly to yield vast quantities of functional information.  One of their figures illustrates how “Combinatorial assembly of chromatin-remodelling complexes produces biological specificity.”  They said, “Current evidence indicates that many vertebrate chromatin-regulatory complexes are assembled combinatorially ... thereby greatly expanding the potential for diverse gene-expression patterns compared with unicellular eukaryotes.”
       This expansion of compact information is particularly evident in the “diverse patterns of gene expression [that] occurs in the development and function of the brain,” they noted; therefore, “it may be no accident that an extraordinary diversity of neural phenotypes is emerging from genetic studies of the subunits of chromatin remodellers in the nervous system,” they said.  No accident; does that comport with a blind Darwinian mechanism?
5. Cell skeleton: epigenetic information:  The final paper in the series concerns the cytoskeleton. Did you know those soft squishy entities we call cells have a skeleton?  It’s true: “The ability of a eukaryotic cell to resist deformation, to transport intracellular cargo and to change shape during movement depends on the cytoskeleton, an interconnected network of filamentous polymers and regulatory proteins,” wrote Fletcher and Mullins,⁶ (see 01/14/2008).  That’s old news.  What’s new, they continued, is that “Attention is now focused on how cytoskeletal networks generate, transmit and respond to mechanical signals over both short and long timescales.”  An important insight is emerging from this work, they said: “long-lived cytoskeletal structures may act as epigenetic determinants of cell shape, function and fate.”  Not all the information about a living cell is stored in DNA.  That’s what epigenetic (above the gene) means.
       These authors put cell research into a historical context.  Years of detailed research has brought us to a time when we need to step back and look at the big picture.

   In a 1960 lecture, cell and developmental biologist Paul A. Weiss encouraged his audience to think of the cell as an integrated whole “lest our necessary and highly successful preoccupation with cell fragments and fractions obscure the fact that the cell is not just an inert playground for a few almighty masterminding molecules, but is a system, a hierarchically ordered system, of mutually interdependent species of molecules, molecular groupings, and supramolecular entities; and that life, through cell life, depends on the order of their interactions”.
       This statement may be more relevant today than it was 50 years ago.  Despite tremendous progress, fundamental gaps remain between our understanding of individual molecules and our understanding of how these molecules function collectively to form living cells.  The sequencing of genomes outpaces characterization of the cellular components they encode and far exceeds our ability to reassemble these components into the types of complex system that can provide mechanistic insight into cellular behaviour.  An even more difficult task is to connect the behaviour of cells in culture with that of more complex living tissues and organisms.

   Notice how this statement relates to the quote by Dr. Daniel Robinson at the top right of this page.  Understanding is not going to come merely from studying fragments; it’s going to require grasping the big picture of how all these hierarchical complex organizations fit together.
       With that sermon in mind, Fletcher and Mullins delved into the details of the cytoskeleton.  “The cytoskeleton carries out three broad functions: it spatially organizes the contents of the cell; it connects the cell physically and biochemically to the external environment; and it generates coordinated forces that enable the cell to move and change shape.”  The word skeleton is a bit of a misnomer, they noted; “it is a dynamic and adaptive structure whose component polymers and regulatory proteins are in constant flux.”
       Once again, the concepts of combinatorial assembly come to mind.  They use a simple analogy that invokes images of intelligent design – more or less:

   The proteins that make up the cytoskeleton have many similarities to LEGO, the popular children's toy.  Both consist of many copies of a few key pieces that fit together to form larger objects.  Both can be assembled into a wide range of structures with diverse properties that depend on how the pieces are assembled.  And both can be disassembled and reassembled into different shapes according to changing needs.  But only the cytoskeleton fulfils all of these functions through self-assembly.

   It appears that we are looking at a system that is both the toy and the player.  From a few simple building blocks, many diverse structures and functions are built.  The authors wonder “how molecules collaborate to form functional cytoskeletal structures” that both provide stability to the cell and response from the environment.  Does “self-assembly” really explain such things?  Or is it a place-holder for ignorance about processes beyond our comprehension?
       Many wonders about the protein parts, like the microtubules, which form highways for intracellular traffic, are discussed in this paper, which space does not allow to recount.  Here’s one sample: “A microtubule can switch between two states: stably growing and rapidly shrinking.  This ‘dynamic instability’ enables the microtubule cytoskeleton to reorganize rapidly and allows individual microtubules to search the cellular space quickly, up to 1,000-fold faster than a polymer that is sensitive only to changes in the cellular concentration of its constituent subunits or to the actions of regulatory proteins.”
       Microtubules, intermediate filaments, and actin filaments with their cross-bridges form intricate, dynamic networks that give spatial organization to the cell interior.  The pieces are not independent: “the polymers of the cytoskeleton are intricately linked together,” they said.  “The organization of these links and the resultant architecture of the cytoskeletal networks has a central role in transmitting compressive and tensile stresses and in sensing the mechanical microenvironment.  On the hubs and highways of this network, motor proteins do their work – carrying cargo, pulling, harnessing, constructing, and responding to signals.  Interestingly, “Some cytoskeletal structures can span distances much larger than that of the typical cell,” such as in filopodia, forming communication channels between cells.  The same physical constraints must be obeyed that engineers consider when building bridges:

   Microtubules are the stiffest of the three polymers and have the most complex assembly and disassembly dynamics.  The persistence length of microtubules, a measure of filament flexibility that increases with stiffness, is so large (~5 mm) that single microtubules can form tracks that are almost linear and span the length of a typical animal cell, although microtubules are known to buckle under the compressive loads in cells.  During interphase, the part of the cell cycle during which cells prepare for division, many cells take advantage of this stiffness by assembling radial arrays of microtubules that function as central hubs and ‘highways’ for intracellular traffic.  During mitosis, the part of the cell cycle during which cells separate chromosomes into two identical sets, the microtubule cytoskeleton rearranges itself into a high-fidelity DNA-segregating machine called the mitotic spindle.  The ability of the mitotic spindle to find and align chromosomes depends, in part, on the complex assembly dynamics of individual microtubules.

   Another example shows that biology speaks the same language as engineering:

   When shear stresses are applied to actin-filament networks, as well as to networks of intermediate filaments or extracellular-matrix filaments such as collagen and fibrin, the networks stiffen and resist additional deformation, as a result of filament entanglement (in which the displacement of one filament is impeded by another filament) and the entropic elasticity of individual filaments.  When a rigid crosslinker such as scruin is added to randomly organized actin filaments and shear stress is applied, the magnitude of the elastic modulus (a measure of the resistance of the network to deformation) increases significantly, and the network retains the stress-stiffening behaviour attributed to the entropic elasticity of individual filaments.  When the more flexible crosslinker filamin A is added to randomly organized actin filaments together with the molecular motor myosin, the rigidity of the network increases to more than that of an entangled filament network, and the network stiffens nonlinearly as though it were subject to external stress.  These studies demonstrate the importance of the entropic elasticity of filaments in the mechanical properties of networks without specific filament orientation.

   You get the idea.  Young’s modulus, compressive forces, shear stresses and other physics terms pervade the paper – as if we were reading a treatise on architecture.  But it’s not just the architecture.  These systems are integrated with other systems in a hierarchical, unified whole – the living cell.  When things go wrong, the results can be as catastrophic as an earthquake.  “And mutations in the genes encoding intermediate filament proteins are associated with many diseases in humans ... including a predisposition to liver disease in the case of some keratins, amyotrophic lateral sclerosis (also known as Lou Gehrig’s disease) in the case of a neuronal class of intermediate filament called neurofilaments, and progeria (a hereditary form of premature ageing) in the case of improperly assembled nuclear lamins.”
       The authors commented on one other interesting and important development: epigenetics.  Evidence is emerging that the cytoskeleton determines part of a cell’s “memory” that is inherited through cell division.  “Given that cytoskeletal structures are often highly dynamic, with specific factors that promote disassembly and recycling of the cytoskeletal building blocks competing with factors that assemble and stabilize them, is it possible for mechanical inputs to be recorded?” they asked.  Because the time lag for disassembly of a network exceeds the cell cycle, it appears that a hysteresis signal persists through the division: “the result can be a persistent structure that affects the behaviour of a cell over a longer timescale than the initial signal.”  It can provide a memory independent of DNA.  But this memory is not in the particulars, but rather than in the interactions: “In contrast to molecular motors, for which the relationship between force and velocity is immediately reversible, the observation that there is more than one growth velocity for a given force suggests that actin-filament network growth depends on history.  The cytoskeletal structure and the process by which it is built can record mechanical interactions, whereas a single filament could not.”  What are the implications?  A cell’s fate will depend not only the DNA it inherits, but on the structure of the parent cells: “To the extent that the cytoskeleton is intricately involved both mechanically and biochemically in cellular processes such as cell division and motility, long-lived cytoskeletal structures could create variability in cell behaviour and may guide variation towards certain phenotypes,” i.e., cell fate.  The details of this idea have “just begun to be explored in detail.”
       The authors ended by noting that, “Until not long ago, eukaryotic cells were thought to be distinguished from bacteria and archaea by the presence of a cytoskeleton.  But the discovery of cytoskeletal polymers even in comparatively simple cells of small size and genome are revealing the central importance of internal organization for cell function.”  They speculated briefly on the origin of the polymers of the cytoskeleton, but the description was only about possible homologous structures in bacteria.  “More than 35 actin-like proteins have been identified in bacteria, but most remain to be characterized,” they said.  This begs the question about where the bacteria got their cytoskeletons.  They must do a good job, because we still have them with us.

We hope you have enjoyed this tour inside the cell.  Review articles like those in this series, unlike single papers that focus on one detail, are valuable for pulling together many recent findings into a coherent picture.  And what a picture!  Systems upon systems, structures upon structures, codes upon codes: the language of networks, signals, responses, interactions, and communication – the details of which underscore the complexity of the whole.  Whoever described a cell as an “undifferentiated blob of protoplasm” should be placed in the Dodo cage.  Dr. Mullins sure knows better now.  His paper was the least concerned about evolution.  We hope he will smell the coffee, trust his instincts, and wake up to thoughts of design (10/21/2008).
    Evolutionists have to be the most incorrigible ideologues that ever walked this planet.  No one else in the history of mankind has had this much access to the details of life’s complexity.  Yet despite staring at this complexity with the highest resolution ever attained, and despite employing the language of engineering to describe it, they continue to say “it evolved.”  They attribute “machinery [that] must function with far greater accuracy than man-made machines” to blindness and accident.  To add insult to injury, some of them forbid anyone from thinking anything else!
    This is one area where the Master Plan has broken down.  The broken parts require complete overhaul, wipe, reinstall of new software, and reboot.  It was costly to provide that overhaul, but it can be downloaded free.  In the big picture, though, we can see that, all along, it was the Master Plan behind the Master Plan.
Next headline on:  Cell Biology • Genetics • Intelligent Design • Darwin and Evolution • Amazing Facts

SETI, Miracles, and Comfort     02/01/2010    
Feb 1, 2010 — Would knowledge that the universe is filled with aliens bring you comfort?  Or are you more comfortable thinking humans are alone in the universe?  Seth Shostak, director of the SETI Institute, was interviewed briefly by Bill Hemmer on Fox News this morning, where only one answer to this idea was assumed.
    Shostak came on the program to talk about the recently-publicized views by astronomer Paul Davies that alien life may be among us in forms we cannot recognize (see PhysOrg and Breitbart News for examples).  Shostak agreed with Davies that scientists may be missing it, because we are attuned to look for DNA as evidence of life.  But aliens might be made of other stuff – QNA, ZNA or something we don’t know, he quipped.
    Shostak went on to opine that since life appeared quickly on Earth after its formation, that suggests that life is easy to evolve.  He leapt from that suggestion to opine that life might be easy to evolve on other planets, too – i.e., that life is not a miracle, but will appear as a natural consequence anywhere the conditions are right.
    In the respectful dialogue, Hemmer interjected the option that even if alien life is found, it doesn’t necessarily mean it wasn’t created.  After all, many people believe that life on Earth is a miracle.  Shostak responded (paraphrasing), “Well, that would be comforting, wouldn’t it?”  He said a termite in a mound might feel special until it looked out and found termite mounds all over the place.  The short interview left off on that note.

Let’s see if we have this straight.  According to Shostak, (1) a scientist is allowed to defend a conclusion on a single data point; (2) it’s OK to believe in unobservables, as long as they are materialistic; (3) assumptions count as data, (4) theology brings naïve comfort, but materialism brings realistic unexceptionalism, and (5) don’t believe in miracles – rely on them (Finagle’s Rule #6).
    CEH has often challenged Shostak’s ideas (e.g., 04/01/2008, or search on Shostak in the search bar for more), but this is nothing personal; he appears to be a likeable chap and is only human.  His ideas, though, can be considered representative of many in the secular science community, particularly in the astrobiology and origin-of-life tribal cultures.  Since he often writes about them in colorful language for the media, he places himself in the dunking booth (e.g., 07/16/2009).  Our arguments, therefore, aim at the dunking lever, not the man (08/08/2008).  If he gets dunked in the process, well, we will be glad to offer him a towel with the word LOGIC printed on it.
    Shostak portrays himself a scientist, but what has he just done?  He has defended philosophical materialism with its own assumptions.  He said, in short, life evolved materialistically because it evolves materialistically, and we know this because we evolved materialistically, because we are here.  This is worse than defending astrology with horoscopes, because there is zero evidence to back it up.  He assumed life emerged materialistically on an unobserved primitive earth, and since that assumption pulled itself up by its own bootstraps, he walked around in the boots and said it means life emerges materialistically everywhere – and that it means life is not miraculous.  Yet the improbability of chemicals coming together into systems with coded operating systems, able to reproduce themselves accurately, is so extreme, it makes belief in theological miracles tame by comparison.
    Then he made the bizarre assertion that the belief life is a miraculous creation brings some people “comfort.”  Do you see the disgusting elitism in that remark?  It characterizes many in academia, and in progressivist politics, too.  It’s the underlying attitude that “We’re smart, and lay people (especially those who believe in a Creator) are stupid.  Their beliefs in miracles (and other fairy tales) may give them comfort, like drunkards guzzling their Southern Comfort, but we sober-minded, rational, objective scientists are the Patrons of Truth and Knowledge and Wisdom.”
    This is not only patronizing nonsense, it is logical nonsense.  Those who disagree with his materialism could just as logically make the argument that SETI believers would find comfort in a universe filled with aliens.  In fact, a theist could turn the tables and argue that Shostak and his ilk have a strong emotional need to find comfort in alien life, otherwise there is the disturbing implication that life might be somehow special, and therefore might have been created.  No theist need be disturbed by the discovery of life on other worlds.  A materialist, though, would find its absence disturbingly hard to explain.  Who needs comfort but a disturbed mind?
    Finally, if Shostak employs inference without evidence to explain unobservables, he should allow others to make inferences about unobservables from evidence.  Without evidence for QNA, ZNA and other unknown bases for alien life, nor any evidence it exists, he allowed Paul Davies and himself to speculate unfettered about the possibility of life-as-we-don’t-know-it living among us – and throughout the universe – as long as it matches one’s world view.  Have a little fun with that kind of liberty.  Speculate that when the aliens are detected, their first message will be that it has been revealed to them that humans are depraved sinners, so they are on the way as missionaries to bring us the gospel.
    But even the material stuff physicists talk about is often inferred only by its effects.  We can’t see quarks or neutrinos, but their presence is inferred by secondary effects in expensive colliders and by the comfort it gives physicists in the elegance of their theories.  It is just as common for scientists in other scientific fields to infer intelligent causes from their effects – in forensics, cryptography, archaeology, and yes, Dr. Shostak, even in SETI itself (12/03/2005).  If you permit yourself the liberty to infer intelligent causation from communications from sentient beings without evidence for it, then allow that right to others who infer intelligent causation in the DNA of sentient beings in front of their observing eyes, right here on this planet.  If you allow yourself the liberty to believe in miracles, then don’t deny that liberty to those who define miracles not as wildly improbable chance occurrences, but as the visible effects of intelligent agents, whom we know from uniform experience are able to direct and constrain the laws of nature with goals and willful intent.  Fairness, after all, can be a very comforting thing.  So is logical consistency.  Your towel, sir.
Next headline on:  SETI • Origin of Life • Bible and Theology

No, this is not going to get our Dumb award; it is fine for human beings to look to nature for inspiration for their art and music.  There is a long-standing tradition of using and imitating the sounds of nature in composition.  Respighi incorporated the songs of a nightingale in his tone poem, The Pines of Rome.  Ferde Grofe used a wind machine in Grand Canyon Suite: Cloudburst.  More recently, fluegelhornist Jeff Oster used sonified electromagnetic waves from Saturn’s magnetosphere in his piece, Saturn Calling.  Undoubtedly you can think of other examples.  Centuries ago, Johannes Kepler sensed a “music of the spheres” in the orderly laws governing planetary motion.
    What this reminds us of, though, is that music is a product of a human soul.  No one else we know is making music – no aliens, no animals (at least in the production of music for aesthetic purposes), and surely not supernovas.  Maybe angels sing – if they do, it’s because they also are sentient beings with emotions.  Finding aesthetic beauty in the sounds and workings of nature is a trademark of human nature.  It’s not purely logical, like Dr. Spock might call curious, though it overlaps with logic.  It incorporates the body and soul, the intellect and the emotions.  But we would add to this story: the only way to be grateful dead is to be right with God, both before and after your physiology attains room temperature.  What more could you ask for in life?
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