Creation-Evolution Headlines
June 2005
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“Hence it appears that whoever maintains that there is no force in the argument from final causes [design] denies the existence of any intelligent being than himself.  He has the same evidence for wisdom and intelligence in God as in a father or brother or a friend.  He infers it in both from its effects and these effects he discovers in the one as well as the other.”
Thomas Reid (1780) rebutting the arguments of David Hume (1779); cited in The Design Revolution by William Dembski, p. 229.
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Horse Evolution Tale Gets Hairier   06/30/2005    
If you thought the story of horse evolution was well understood as a poster child of Darwinism at work, consider what Weinstock et al. say in a preprint in PLoS Biology:1
The rich fossil record of horses has made them a classic example of evolutionary processes.  However, while the overall picture of equid evolution is well known [see 03/18/2003 entry], the details are surprisingly poorly understood, especially for the later Pliocene and Pleistocene, c. 3 million to 0.01 million years (Ma) ago, and nowhere more so than in the Americas.  There is no consensus on the number of equid species or even the number of lineages that existed in these continents.   (Emphasis added in all quotes.)
Tackling that challenge, the team rewrote the evolutionary history books.  Now, they put all North American horses into two species, claim they are distinct from their European look-alikes, and came earlier than the South American Hippiodon genus, which was supposed to be ancient.  This is all summarized on EurekAlert, which claims the conclusions made by comparing mitochondrial DNA “helps clarify the origins of two extinct New World horse species.” 
1Weinstock et al., “Evolution, Systematics, and Phylogeography of Pleistocene Horses in the New World: A Molecular Perspective,” Public Library of Science: Biology, Volume 3 | Issue 8 | AUGUST 2005.
Are you tired of the hype?  Every new Darwinian study overthrows the propaganda that was taught to the world for 100 years or more, but then they spin the bad news with the line, “this helps clarify the picture of evolution.”  It’s no picture; it’s a kaleidoscope of constantly shifting random bits of broken colored glass.
    These guys have no handle on what really happened to horses.  Remember?  They’re the same ones that want us to believe that our human ancestors, who were fully modern in every way, even capable of producing art that rivals Picasso, couldn’t figure out how to ride a horse for half a million years (see 01/19/2002 entry).  Now they want to tell us that all the fossil horses in North America, long thought to represent multiple branches on the Darwinian tree, are all just two species, and that “North American caballines—traditionally classified as multiple species based on their diverse size—belong to the same species.”  Any horse breeder could have told them that.  You can breed a Morgan and a quarter horse, even a Clydesdale and a Shetland (with a little help....)
    The lab work is irrelevant, because the evolutionary timeline is already a given (imagine trying to measure time with a broken clock: see 04/20/2004 entry and links in the commentary).  No amount of data is going to falsify their evolutionary belief, because this is just a game for them.  Their methodology assumes evolution, so no wonder they “prove” it!  They don’t know how fast DNA mutates, they don’t know how to classify fossils into species, and they weren’t there watching these animals move around the world.  It’s all made up to keep the Darwin Storytelling Empire in business.  Why do we trust them?  If they knew the true history of the world they would be dumbfounded, more than they already are.
    Darwinian storytellers ought to do some sweaty work on a ranch, ride a real horse (see 03/18/2005 commentary and 01/02/2003 entries), watch a sunset on our privileged planet, and learn about the real world.  Maybe it would open their eyes to consider some credible options, ones that coincide with the observations for a change.
Next headline on:  MammalsFossilsDarwinism and Evolutionary Theory
Did Old Metamorphic Rocks Form in Just 10 Years?    06/30/2005  
A discovery in Norway may collapse a geological process by five or six orders of magnitude.  A paper by Camacho et al. announced in Nature,1 yielded this comment by Simon Kelley (Open University, UK) in the same issue,2Conventional wisdom says that changes to crustal rocks pushed down deep when continents collide develop over millions of years.  But it seems that some metamorphism may be caused by tectonic events lasting only a decade” (emphasis added in all quotes).
    The gist of the story is that certain rocks called eclogites, long thought to have formed slowly over millions of years, might have formed rapidly instead, maybe in only ten.  The authors of the paper deduced that they could not have remained at the temperatures assumed for very long without losing all their argon.  Kelley explains why the mixtures in the rock suggest conflicting requirements for their formation:
The authors go on to estimate the temperature in the granulite lens during eclogite formation.  Their conclusion – less than 400 °C – is a problem for the conventional interpretation of these rocks, given that a temperature of around 700 °C is required for the formation of the adjacent eclogites.  Camacho et al. calculate that the total heating durations must have been around 18,000 years to explain the 40Ar-39Ar age profiles, but that individual fluid-flow events must have lasted just ten years to avoid significant heating of the granulite regions between the shear zones.  This model evokes a radically different picture of the conditions during eclogite formation; but any alternative explanation would have to invoke a mechanism that explains why these phlogopites retained argon despite exceeding temperatures at which the gas would normally escape.
Kelley explains why the overturning of this classic case of a slow process points out an assumption that may need just as radical an overturn: “However, the very short timescales involved will make this idea controversial, as existing work on garnet seems to indicate processes operating on a million-year timescale; but also, perhaps, simply because we geologists are attuned to thinking in millions of years, whereas the features we observe may be just the aggregations of many shorter events.”
1Camacho et al., “Short-lived orogenic cycles and the eclogitization of cold crust by spasmodic hot fluids,” Nature 35, 1191-1196 (30 June 2005) | doi: 10.1038/nature03643.
2Simon Kelley, “Geophysics: Hot fluids and cold crusts,” Nature 435, 1171 (30 June 2005) | doi: 10.1038/4351171a.
Now there was a daring and honest admission: perhaps geologists are just in the habit of throwing around millions of years, when the features they observe could just as well be “aggregations of many shorter events.”  Wow.  Think about that.  Here was a classic case of long ages from the Bergen Arcs in Norway that now must be reinterpreted.  Neither Kelley or Camacho are claiming that this formation came into being recently, but it represents, nevertheless, a monumental shift in thinking about geological processes in general.
    Dr. Terry Mortenson did his PhD thesis on the origin of old-earth thinking.  He found that most scientists until the late 18th century believed the earth was young, and that the revisions upward to millions of years were due primarily to theological and philosophical attempts to discredit the early chapters of Genesis.  Darwin, of course, later found all that extra time essential for his theory of evolution.  Today, biologists and geologists don’t dare question the vast ages because Charlie needs the time: in fact, Darwin was aggravated to a pique when Lord Kelvin robbed him of the millions of years he required (see 02/02/2004 entry).  Geologists found ways to steal those years back using radiometric dating methods, and have relaxed in complacency with their textbook geologic column, mumbling out those millions & billions nonchalantly, without much challenge (at least among the Darwin Party brethren).  But what if (as many other dating methods suggest) things are really not that old?  Follow the chain links on Dating Methods for examples.  These articles in Nature, the most prestigious scientific journal in the world, should be a wake-up call for geologists not to take vast ages for granite (which, by the way, also shows evidence of rapid formation; see 12/07/2000 entry).
Next headline on:  Dating MethodsGeology
Is Evo-Devo the Source of Endless Forms Most Beautiful?    06/29/2005  
Even staunch Darwinist Jerry A. Coyne (U of Chicago) thought this evolutionary book went overboard: Endless Forms Most Beautiful: The New Science of Evo-Devo by Sean B. Carroll (Norton, 2005), which he reviewed in Nature last week.1  (The title comes from a phrase at the end of Darwin’s Origin of Species.)  It’s a first-rate introduction to evo-devo written by an adept communicator, he feels, “but its faintly self-congratulatory message – that the most important problems in understanding the evolution of development have been solved – left me feeling uncomfortable.”
    In Coyne’s opinion, Carroll overplayed the evo-devo card.  Evo-devo assumes that gene regulation is the most important agent of evolutionary change; Coyne gives more place to gene duplication, genome duplication and ordinary old adaptive natural selection on genes and proteins.  Some of Coyne’s criticisms point out the problems inherent in all evolutionary theories.  Some examples:
  • Carroll presents his vision of the field without admitting that large parts of that vision remain controversial.  I would have appreciated a caveat or two, and non-scientists may mistakenly believe that Carroll presents the scientific consensus about evolution and development.
  • Carroll emphasizes throughout that the evolution of animal form and complexity results from three factors.
    1. The first is modularity of organization: the ground plan of bilateral animals involves repeated segments that can evolve independently....
    2. The second factor is that most animals share a small but similar set of ‘tool-kit genes’ that regulate the development of different modules.....
    3. But modularity and a shared genetic tool kit cannot by themselves account for “endless forms”, because conserved genes cannot explain diversity.  Carroll therefore repeatedly emphasizes his third thesis: that the main engine of evolution is not change in protein-coding genes but in the switches that control them.
  • The evidence for this critical hypothesis, however, rests more on inference than on observation or experiment.
  • Carroll also claims that proteins are resistant to evolutionary change: they are often involved in many pathways, and therefore a change in protein sequence, while enhancing one aspect of the protein’s many functions, could damage several others....
    But recent data cast doubt on this argument.  Humans have about 32,000 protein-coding genes, fruitflies only 13,000.  Clearly, the difference between these species involves the origin of new proteins: in fact, between 40% and 50% of our protein-coding genes have no known homologues in flies.  So one could argue that the evolution of form is very much a matter of teaching old genes to make new genes.  And, given the data, this cannot be difficult.
  • [Coyne argues for the evolutionary significance of gene duplication and adaptive selection.]  In contrast, the evidence for the adaptive divergence of gene switches is still thin.  The best case involves the loss of protective armour and spines in sticklebacks [see 06/18/2004 entry], both due to changes in regulatory elements. But these examples represent the loss of traits, rather than the origin of evolutionary novelties.
  • Carroll also gives many cases of different expression patterns of Hox genes associated with the acquisition of new structures (such as limbs, insect wings and butterfly eyespots), but these observations are only correlations. One could even argue that they are trivial.
  • Carroll’s correlations, however, do not compel us to believe that changes in these genes are the key factor in the evolution of such traits.  We now know that Hox genes and other transcription factors have many roles besides inducing body pattern, and their overall function in development – let alone in evolution – remains murky.
  • In the end, we simply don’t know the relative importance of protein and non-protein changes in creating biological diversity.   (Emphasis added in all quotes.)
Coyne ends with both him and Carroll agreeing that evidence for evolution can be distorted: “Although Endless Forms Most Beautiful is a lucid and valuable summary of evo-devo, it does proclaim a clever but still unproved hypothesis as central to the evolutionary process.  As Carroll himself notes: ‘Simplification may indeed be necessary for news articles, but it can distort the more complex and subtle realities of evolutionary patterns and mechanisms.’”
1Jerry A. Coyne, “Switching on evolution: How does evo-devo explain the huge diversity of life on Earth?”, Nature 435, 1029-1030 (23 June 2005) | doi: 10.1038/4351029a.
Is evo-devo the evil-devil among Darwinists?  Like Satan, does he twist the word of lord Charlie?  Does he distort the evidence for his own nefarious ends?  Assuredly not; both Carroll and Coyne are on the same side, trying to oust God’s design from nature and account for everything by chance and biological laws.  What anti-creationist Coyne fails to realize is that he has cast both theories, evo-devo vs. standard Darwinism, in a deadly embrace.  Carroll wrote his book because of the weaknesses of standard Darwinism, and Coyne provided only bluffing assertions that standard Darwinism is sound, while arguing that evo-devo is just a clever idea that distorts the evidence and cannot really account for the diversity of life.  To argue otherwise requires simplification; i.e., the generous use of glittering generalities to create tall tales.  Neither evolutionary hypothesis can account for the complex and subtle realities of the living world mentioned in Coyne’s review – worms, lobsters, frogs, humans, chimpanzees, fruitflies, butterflies, mice, “the Cambrian explosion, the biology of dinosaurs, the brains of humans, and the striping of zebras” – and their “eyes, limbs, hearts and other complex structures” including “fly legs, fish fins and the tube feet of sea urchins.”
    But while calling Carroll’s evidence “thin,” Coyne is just as guilty of simplification: for example, look at this paragraph (our comments in brackets):
There are other ways beside gene duplication that proteins have evolved adaptively.  These include gene conversion [left unexplained], recruitment [personification fallacy] of genes to new functions (responsible for creating the antifreeze glycoproteins that allow fish to live in frigid waters) [see 05/13/2004 entry], exon shuffling (involved in the evolution of blood clotting factors) [Whoa!  Michael Behe showed how this is an irreducibly complex system unexplainable by evolution] and the addition of transposable elements to coding sequences [as if evolutionists understand this].  Finally, and simplest of all, we have many examples of adaptive changes of protein sequence between closely related species, including differences in the coat colour of mice [see “Peppered Mice?”, 04/18/2003], the digestive enzymes of herbivores, and the haemoglobins of high-altitude birds and mammals [do we just take his word for it?  Digestive enzymes and hemoglobins were already complex, functional protein machines before evolution tweaked them, even if it could].
Endless forms most beautiful speak of a Designer, not a blind process of evolution.  The shortcomings of Coyne’s view provide an opening for the claims of Carroll’s, and vice versa, such that they strangle each other, leaving both gasping for evidence.
Next headline on:  Darwinism and Evolutionary TheoryGenetics and DNA
Small Wonder: Tubulin Visualized Up Close    06/28/2005  
Science Daily printed a neat story about microtubules, complete with a 3D visualization of how the protein components are arranged.  They are not just ropes or chains, but complex cylinders of precise parts.  Scientists are starting to get an idea of why they continually grow and shrink within the cell.  The process allows them to “explore their cellular environment to find their goals,” and is coordinated by numerous genes and protein parts.  Microtubules form the cell’s superhighway (see 04/13/2005 and 12/04/2003 entries), and are also critical in cell division for winching chromosomes into the daughter cells (see 04/30/2005 entry).
We like to keep pointing out research projects with no need for mentioning evolution, that fit within a design approach.  The cell provides plenty of examples.  Here are two more: waterwheels (12/22/2003), quality control (12/20/2003), and many, many others in the chain links on Cell Biology and Amazing Stories.  Every person, from philosopher to man on the street, should ponder such things.
Next headline on:  Cell BiologyAmazing Stories
Stupid Evolution Quote of the Week    06/28/2005  
This entry is from the BBC News, in an article about hummingbirds, the “master fliers of the bird kingdom” (see 06/24/2005 entry).  The article interviews Douglas Warrick (Oregon State), describing how evolution produces exquisite machinery by an unguided process of cobbling parts from existing stuff:
He said the hummingbird could serve as a useful model for engineers seeking to build small, flapping aeroplanes.  “You can probably learn something about building a machine from the way nature builds a machine,” he said.
    “The one big caveat is that an engineer can start from scratch – biological evolution doesn’t ever start anew.  It’s encumbered with the trappings of one’s ancestry.”
  (Emphasis added.)
The cult of Tinker Bell lives on.  Evolution is a tinkerer that dabbles with existing material and produces machines that are the envy of intelligent human designers.  What is amazing about this belief is not just that scientists keep repeating it, but that all the major news media just parrot it without question.  When the Darwinian idol finally collapses, our SEQOTW entries will provide plenty of fodder for cartoonists.
Next headline on:  BirdsDumb Stories
Nose Knows More than Math Pros Suppose   06/27/2005  
The aroma of coffee, of a steak, of cherries – these smells are all composed of dozens if not hundreds of separate molecules, yet our brains immediately recognize them each as a coherent whole.  How does the nose and the brain process all this information?  This is the subject of an article in the Caltech magazine Engineering and Science1 by Gilles Laurent, Caltech professor and neurologist, who studies olfaction and also “how single neurons perform nonlinear operations such as multiplication.”
    Unlike vision and hearing, our olfactory sense does not allow us to decompose a composite input into its constituents.  We perceive odors as single entities.  Studies on insects by Laurent and his students show that this is because individual receptors fire in patterns that are mapped like a code to a large number of unique sensors called Kenyon cells.  In insects, these cells reside in a part of the olfactory apparatus called the mushroom body (in vertebrates, it’s the olfactory cortex of the brain).  Each Kenyon cell gets a very unique set of inputs from the receptors, and thus a distinct, composite signal from a highly diverse set of inputs.  Laurent does the math to show the staggering number of possibilities for odor memory that this system permits:
The locust has 800 projection neurons connecting to 50,000 Kenyon cells.  With such a large mismatch in numbers, how are these nerve-cell populations interconnected?  When Ron Jortner, a graduate student in my lab, recorded simultaneously from both projection neurons and individual Kenyon cells to assess the probability of connection between them he found, surprisingly, that the probability was about 0.5.  In other words, each Kenyon cell seems to connect on average to half of the input population, that is, to 400 projection neurons.  The number of ways in which 400 neurons can be selected out of 800—the number of possible connection patterns—is about 10240It’s an enormous number.  To put it in context, there are about 1010 seconds in a century, and there have been about 1019 seconds since the beginning of the universe.  With 10240 possible combinations of projection neurons to choose from—assuming random connectivity—almost every Kenyon cell is likely to sample a combination of inputs that is very different from that sampled by the other Kenyon cells.  Each cell will therefore gain a picture of the state of the projection neuron population very different from that gathered by any other Kenyon cell.  It follows that the responses of individual Kenyon cells will be very specific; a given cell should respond only to particular combinations of activated projection neurons, maximally different on average from those experienced by the other Kenyon cells.   (Emphasis added in all quotes.)
Laurent noted at the beginning of the article that olfaction is a form of pattern recognition, and that “Brains solve pattern-recognition problems much better than any machine built today.”  His lab tries to figure out “how brains solve these problems.”  Most of the research by Laurent and his students is on insects, whose olfactory receptors are on their antennae.  A fruit fly has 1300 receptor neurons, with 60 different receptor types, but some moths might have several hundred thousand receptor neurons.  This gives them an amazing sensitivity to low concentrations of odors like pheromones.
    A diagram and electron micrograph on p. 44 shows what receptor neurons look like.  They have dozens of cilia projecting into the nasal cavity.  The reason dogs have superior sensitivity to smells, he explains, is that their nasal cavity contains much more surface area where the receptors project from sponge-like tissue called turbinate bone.  Dogs have ten times as much turbinate bone as humans.  He provides a fragrant illustration: “In a medium-size dog,” he says, “the turbinates have a total surface area the size of a large pizza.  In humans, they’re the size of a large cookie.”  Each receptor neuron has a single sensitivity dictated by the order of the amino acids in its multi-folded receptor proteins.  The amino acid sequences of receptor proteins show areas of both high conservation and high variability between species.  They loop seven times through the cell membrane, providing pockets where the odor molecules bind.
    Laurent describes something striking about how the receptor neurons map their inputs to ball-shaped structures called glomeruli (singular, glomerulus).  “In an amazing feat of organization during development,” a picture caption states, “each type of receptor neuron... sends its axon to the same glomerulus....”  He calls it a “surprise” that all the axons of the same receptor type (colored red in the diagram) converge so neatly to their exact counterparts.  “By implication,” he continues, “this means there are about as many glomeruli as there are receptor types.  And with the exception of the roundworm, this extraordinary organization is found in almost all the animal species that have so far been looked at.”
    From the glomeruli, the information is passed on to a smaller group of nerve cells called projection neurons, which have no axons but connect with a dozen or more glomeruli.  “With 100,000 receptor neurons converging on just 800 projection neurons, what is being computed?” he asks.  Experiments show that the precise timing of firing creates a kind of code from the multiple inputs, a pulse pattern that can be mapped and analyzed.  He likens the result to the unique arrangement that billiard balls take after the player breaks them with the cue ball; two very similar initial setups, but with slightly different angles of attack, can produce initially similar but ultimately divergent patterns of balls on the table.  (The billiard game in the nose is super-fast.  He notes on p. 48, “This happens so quickly that the representations are optimally separated within 100 to 300 milliseconds.”)  As a result, differences between very similar smells can be amplified by the system.  “That’s basically what we think is taking place in the olfactory circuit,” he says.  “The remarkable thing is that this near-chaotic process is very sensitive to the input, but very reliable nevertheless.
    To recap, the receptor proteins in the cilia of the receptor neurons react to molecules in odors.  These neurons fire their axons to the glomeruli.  The glomeruli then pass their encoded information patterns to the projection neurons.  That noise-reduced information is passed in very unique ways to the tens of thousands of Kenyon cells, which have a near infinite way to respond to the myriad possible combinations of smells.  “Kenyon cells are so specific that they only recognize one, or at most a few, odors,” a caption explains on p. 51.  He summed it up earlier (p. 46): “In other words, each odor is defined by a certain combination of receptors; the code is combinatorial.... The perception of an odor must therefore result from the brain’s interpretation of combinatorial activity patterns.”  Why, though, do a large number of receptors map to few encoders, and then those few to a large number of interpreters?  There’s a reason for everything:
It seems wasteful that hundreds of thousands of olfactory receptor neurons converge on their respective glomeruli in an amazingly precise way, but that this precision is then thrown away when seemingly disordered patterns of activation are generated in the projection neurons.  But there’s a good reason for it.  A system that amplifies small differences in signals runs the risk of also amplifying noise, in this case the noise coming from the receptors.  Noise fluctuations would make the output of the projection neurons unreliable: the averaging that results from this kind of convergent design is precisely one way to reduce such fluctuations.
(p. 49; for more on the problem of noise reduction, see 12/20/2004 entry).  The sense of smell, obviously, is “quite complex.”  It involves many more receptor types than other senses, like vision, which uses only four types of photoreceptor.  How did the code in the nose, and all the apparatus in the circuitry, come about?  Early in the article he speculated briefly about this question, but his answer assumes a remarkable convergence rather than demonstrating the evolutionary steps:
In parts of the looping receptor protein chain, the order in which the amino acids are strung together is so variable that some animals, such as the rat, have over 1,200 different receptor types.  On average, mammals have about 1,000 types, fish and birds between 100 and 200, round- worms (Caenorhabditis elegans) 1,000, and fruit flies 60.  Humans have only 600 different odorant receptor genes, but almost half of these are “pseudogenes” that no longer function, leaving us with only 350 receptor types in our nasal mucosa....
    Interestingly, when the receptor genes of mammals, flies, and worms were compared, no sequence homology was found.  In other words, the genes had probably not evolved from a common ancestor: different types of animals had come up with their own particular (but related) designs for olfactory receptors independently throughout evolutionary history.  Such convergent evolution, as it’s called, happens a lot in biological systems.  The single-lens eye design, for example, has evolved independently at least eight times in the animal kingdom.
How that happened is left as an exercise, but for Laurent, his job is in the here and now, studying the sensitive yet reliable olfactory computer: “Finding the rules of such nonlinear dynamical problems is one of our goals” (p. 49).  Concluding, he says, “Our research into olfaction some valuable insights into how such kinds of high-level synthetic representations arise from the organization and dynamics of neural circuits” (p. 51).  The nose shows that “Classifying and recognizing patterns is, after all, what our brains do best.”
1Gilles Laurent, “Olfaction: A Window into the Brain,” Engineering and Science (LXVIII:1/2), [summer] 2005, pp. 43-51 (PDF).
This article is a good companion to the next one (see 06/25/2005 entry).  The language is similar: circuitry, computation, communication, codes, signals, and information.  The lead-in photo shows a man with a very satisfied look savoring a cup of coffee, probably unaware that he is sensing a cocktail of two to three hundred compounds.  Did you have any idea how much computation and circuitry make that pleasant feeling possible?  We joke about our noses and don’t usually give them the same respect we pay the eye or ear, but each sense is more wonderful than we could possibly realize.
    Werner Gitt, in his delightful book The Wonder of Man, elaborates on some wonders of our human sense of smell.  We have between 10 and 25 million receptor cells where the odor molecules fit with the proteins like a lock and key.  Each olfactory cell measures only 5 to 15 millionths of an inch.  Past these cells waft about 12 cubic meters of air per day, as we inhale and exhale 12,000 times.  Our olfactory sense is extremely sensitive, exceeding the capabilities of most technological measuring instruments.  We can detect one ten million millionth of a gram of mercaptan, for instance, and even distinguish between left- and right-handed forms of the same molecule.  Remarkable as that is, we all know how the animal kingdom relies even more heavily on the sense of smell, marking territory with scents, using scents for sexual attraction, and navigating by their noses.  A dog has 220 million receptor cells, tenfold more than we do; think of how dogs can be trained to sniff out bombs in luggage and people trapped under rubble or avalanches, or how bloodhounds can follow the footsteps of a crook all the way from the crime scene to his shoes.  Maybe it’s good we humans don’t have that TMI problem, but our olfactory sensitivity is nothing to sneeze at.  Smells enhance the taste and flavor of our food, color our world, and influence the way we think and act in many subtle ways.  They warn us of danger, or attract us to pleasurable sensations.  “Our memory for odours is astounding,” Gitt says; “nothing can stir up old memories better than a certain scent.”  The fresh air in a pine forest, the sunshine after the rain, the fragrance of a rose, the symphony of smells at a table of great food – how impoverished life would be without a sense of smell.  Thank God for your nose.
    Laurent’s brief side trip into Fantasyland with Tinker Bell (see 03/11/2005 commentary) provided some comic relief for this intense and thought-provoking look at a system of mind-boggling complexity.  Did you enjoy the Fairy Godmother’s song, the Ballad of Convergent Evolution?
Impossible!  for a random mutation to become a neural circuit;
Impossible!  for an unguided process to produce a code so perfect.
And four DNA bases will never produce Code Morses,
Such fol-de-rol and fiddle-dee-dee of course is:
But the world is full of zanies and fools
who don’t believe in sensible rules
and won’t believe what sensible people say...
and because these daft and dewey eyed dopes
keep building up impossible hopes
impossible things are happening every day!

Nothing like a magic wand named Natural Selection to do impossible things.  Just wish... and believe.  While the Darwinists are wishing upon a star in Fantasyland, design scientists are turning Frontierland into Tomorrowland.
Next headline on:  Human BodyTerrestrial ZoologyMammalsAmazing Stories
Reverse-Engineering Biological Networks Challenges Caltech Scientists   06/25/2005  
Evolutionists love to quote Dobzhansky saying, “Nothing in biology makes sense apart from evolution.”  An article in the current issue of Caltech’s magazine Engineering and Science,1 however, might change that proverb to, “Nothing in biology makes sense apart from information theory and systems engineering.”  The article makes no mention of evolution, but rather looks at biology as a model of complex information processing, computation, control, logic circuits, optimization and error correction.  “TMI, meet IST,” is the title, meaning “too much information meets the office of Information Science and Technology.”  The IST is an interdisciplinary initiative at the prestigious university that draws together mathematicians, information theorists, physicists, biologists, and social scientists with the goal of understanding how information works in complex systems – biological systems providing the guiding example.  It is organized into four new centers, the Center for the Mathematics of Information (CMI), the Center for the Physics of Information, the Center for Biological Circuit Design (CBCD), and Social and Information Sciences Laboratory (SISL), and two old ones, the Center for Neuromorphic Systems Engineering (CNSE), and the Lee Center for Advanced Networking.  “Each new center attacks a basic question,” the article explains.  “Can we find an abstract mathematical description of information that applies across disciplines?  What are the fundamental physical limits to information storage and processing?  How does nature compute and communicate information?  And how does information shape social systems?” (emphasis added in all quotes).
    Author Douglas L. Smith opens by wowing the reader with the complexity of a worm.  A tiny roundworm controls its development and biological systems in a manner that staggers the researchers with its precision and complexity.  Smith compares worm information processing to modern intelligently-designed automobiles.  A sedan can contain more than 35 million lines of code in its computers, he says; but that creates a problem for human designers – the cars are getting so complicated, “future development is actually getting stuck because they don’t know how to manage the software.”  Enter C. elegans for a little humility lesson:
But Nature controls far more complex mechanisms with ease: Consider the nematode Caenorhabditis elegans.  A lowly roundworm about the size of this comma, it grows from a single-celled egg to an adult containing exactly 959 cells.  The little fellas are clear as glass, and entire generations of lab students have spent countless hours hunched over microscopes tracking the career of each cell.  The whole process takes 24 rounds of cell division—79 of the 959 cells line the guts from mouth to anus, 302 become nerve cells, and 131 die along the way.  “Everything has been mapped precisely,” says [Jehoshua] Bruck [Moore Professor of Computational and Neural Systems and Electrical Engineering, and director of the IST], who has a framed poster of this developmental tree on his wall [the article contains this diagram].  “But we, as engineers, don’t understand how to handle all the information in that map.  We don’t understand what the principles are.”  But, somehow, the cells understand.  The egg divides, and one cell has to call heads and the other, tails.  The process involves the random diffusion of signaling molecules, but the result is very precise—you never end up with a two-headed worm.  Then the other divisions have to follow in the correct order.  “And even when every cell has a clock and the timetable,” Bruck points out, “they still need to coordinate their actions.  It’s like driving on the freeway—sometimes you need to slow down and let another car pass.”  Organisms are just information made flesh.
Sidebars in the article provide the history of information theory, from George Boole’s binary algebra to Claude Shannon’s Boolean circuitry.  Information storage and processing, guidance and control of circuits dealing with vast amounts of information under constraints of time or bandwidth, are some of the technical challenges discussed in the article.  The overlap between biological and engineered systems throughout the article is almost seamless, except for the fact that biological systems are vastly superior to anything man has invented so far.  For example,
  • But building complex machinery from molecule-sized parts is no cakewalk—how do you put all those tiny pieces in the right places?  Nature uses a program encoded in the genes.  Inspired by this, [two center members] are making DNA “tiles” that spontaneously assemble into complex patterns based on information contained in the DNA.
  • Cells do amazing things with seemingly slap-dash components.  The body heals broken bones and fights off diseases, and we walk around and we do crossword puzzles, all with flimsy, floppy protein molecules packed into cells that keep dying.  There’s nothing magical about the stuff we’re made of, so clearly the miracles are in the circuits—broadly defined—that they’re organized into.  How do these circuits work?  And what else can be done with the same components? [p. 12]
  • The goal of the Center for Biological Circuit Design (CBCD), says Paul Sternberg, Morgan Professor of Biology, investigator, Howard Hughes Medical Institute, and director of the center, “is to learn about biological circuits by trying to build them.”... There are actually three nested levels of circuitry, says Sternberg: networks of signaling molecules within a cell that handle such things as regulating metabolism or allowing an amoeba to find and engulf its prey; circuits consisting of several cells, such as the ones that coordinate our defense against infection; and the vast neuronal circuits that are responsible for, say, understanding speech.  The CBCD will initially tackle the first two, leaving the brain to the ganglion of neuroscientists on campus.
  • By biological standards, the human brain is only middlingly complex–a protein molecule can have 10 thousand atoms, a cell can contain a billion macromolecules, and the heftier E&S reader might consist of 100 trillion cells.  That’s 27 orders of magnitude of organization from an atom to a person, which is like going from the diameter of an atom to the distance to Sirius [p. 12.  For a visualization, see Secret Worlds: The Universe Within.]
  • [Sidebar] A schematic of Arnold’s cellular band-pass filter.  The sender cell emits molecules of ALH... [He describes the complex interactions of seven parts in the cascade].  Got all that?  And this is a very simple regulatory scheme, as things go.... [p. 13].
  • Says Sternberg, “...we’re just trying to get anything to work.”  It helps that the CBCD houses people who are building artificial circuits and people who are reverse engineering real ones.  “Now we say, ‘This cell has switchlike behavior—what mechanism is it using?’  It would be nice if you could say, ‘Well, there are four different ways that cells usually do that.’  It would be even better if you could say, ‘Well, there’s one way that they usually do it, let’s go test that one first.’” [p.13]
  • “Everything we do in CNSE [Center for Neuromorphic Systems Engineering] is IST-related,” says director Pietro Perona, professor of electrical engineering.  “We take neurobiological principles and use them in engineered systems, and use engineering expertise to try to understand the brain.”
The Information Age will be as monumental as was the Industrial Age in its effect on society.  Smith wraps things up whimsically:
Says Bruck, “In time, I think ‘information’ will be a first-order concept.  So in 20 years, if a high-school student asks her friend, ‘Do you like algebra?’ the other girl will say, ‘Yes,’ or ‘No,’ or ‘Yes, but I hate the teacher.’  But the other day I asked my daughter, a high-school junior, ‘Do you like information?’ and she said, ‘What?!!’”

1Douglas L. Smith, “TMI, Meet IST,” Engineering and Science (LXVIII:1/2), [summer] 2005, pp. 6-15.
OK, Intelligent Design Movement, charge!  Grab this paper and wave it in the faces of the Darwin Party, and say, “Look!  The future is information, reverse engineering, and treating biological entities as intelligently designed circuitry.  That is what ID is all about.  This entire article had as much use for Darwinism as an astronaut for a pogo stick.  Biological systems could only be understood in terms of their information content, their logic, circuitry and programming—i.e., their design.  The design is so extraordinarily complex that Caltech’s brightest stars are at square one trying to figure it out.  Darwinism is an impediment, an 18th-century, Industrial Revolution paradigm that is not up to the requirements of the Information Age.  Step aside!  ID is the future.”
    This article is one of many recent entries at the intersection of biology and nanotechnology that illustrates the power of a design-theoretic approach to science.  Although it does not mention intelligent design (and, undoubtedly, many of the participants are probably evolutionists), the content of the article plays right into the hands of the intelligent design movement.*  Look: a large interdisciplinary scientific enterprise (IST) has been organized with the goal to understand and capitalize on the information content in biology.  The same topics in this article are prevalent in the ID literature: information theory, reverse engineering, understanding and detecting design, programming, circuitry, complexity and communication.  The identity of the Designer, though an important and interesting subject,** did not enter into the discussion, and was not essential for achieving the goals of the IST.  This shows that ID is a non-religious scientific approach; it can bear fruit in a multicultural, secular setting.  Rather than bringing science to a halt, it promotes, stimulates and encourages scientific discovery—findings that will promise to revolutionize society, help cure disease, remove the drudgery of our lives and fulfill the promise of Daniel 12:4 that “many shall go to and fro, and knowledge shall increase.”  It’s past time to remove the ball and chain of Darwinian mythology and speed ahead into the Information Age—the golden age of intelligent design. 
Next headline on:  Cell BiologyTerrestrial ZoologyAmazing StoriesIntelligent Design.

*Did you catch Smith’s comment on miracles?  “There’s nothing magical about the stuff we’re made of, so clearly the miracles are in the circuits—broadly defined—that they’re organized into.”  Think about it.  By miracle he is not suggesting something like the parting of the Red Sea, but that the awe-inspiring aspect of the system is its organization, or information.  ID can latch onto this statement by reasoning that the programming, or information content, of the system cannot be generated by natural law, chance or any combination of the two (see No Free Lunch by William Dembski for rigorous proof).  This implies that something outside Nature (if defined as matter in motion) must have supplied the information.  As such, that is supernatural, or “miraculous” in that sense of the word.
**Though the identity of the Designer is not essential to progress in ID science, thinking people will surely ponder the obvious.  Looking at the circuitry in a roundworm or human brain, and watching Caltech’s best and brightest sweating to imitate the processes organisms execute flawlessly with ease, will prompt the logical conclusion: This didn’t just happen.  Someone with incomprehensible wisdom and power made this.  The attributes requisite for such an Engineer should narrow the choices sufficiently, to where preachers on Sunday could make good use of the anecdotes emerging from the CBCD Monday through Friday.  Smith said “Organisms are just information made flesh.”  Does that prompt a sermon text?
Wind Tunnel Experiments Reveal Dynamics of Hummingbird Flight   06/24/2005  
Scientists have found out that hummingbirds and insects don’t hover in the same way.  Insects support 50% of their weight on both up and down strokes, but hummingbirds support 75% on the downstroke and 25% on the upstroke.  This was published in Nature this week,1 and summarized on Science Daily.
    The latter article reminds us why hummingbirds attract our interest: 
“You would be hard-pressed to find someone who isn’t amazed by hummingbirds,” said H. Ross Hawkins, founder and executive director of The Hummingbird Society.  “Perhaps it’s their iridescent coloration and miniature size, or their ability to drop their heart rate from 500 beats per minute during the day to 40 beats per minute at night.” (Emphasis added in all quotes.)
Another bird story making the rounds this week was published in Science.2,3  Apparently, chickadees have a sophisticated signalling system in their chirps.  They can alert the flock to a size and type of predator nearby with a kind of chirping language; the number of “dee” syllables at the end of the call is code for the kind of threat.  See EurekAlert, National Geographic News, Science Now and People’s Daily Online.
1Warrick, Tobalske and Powers, “Aerodynamics of the hovering hummingbird,” Nature 435, 1094-1097 (23 June 2005) | doi: 10.1038/nature03647.
2Templeton et al., “Allometry of Alarm Calls: Black-Capped Chickadees Encode Information About Predator Size,” Science, Vol 308, Issue 5730, 1934-1937, 24 June 2005, [DOI: 10.1126/science.1108841].
3Greg Miller, “Bird Alarm Calls Size Up Predators,” Science, Vol 308, Issue 5730, 1853-1855, 24 June 2005, [DOI: 10.1126/science.308.5730.1853a].
There are few classes of animals more varied, colorful, intelligent, talented and interesting than birds.  Makes you wonder what they think when they take up people-watching.  Perhaps it’s best we don’t know what that chickadee is telling its friends when we walk by.  When a Darwinist says, like in the Miller article quoting James Hare, “The work ... shows us that even very common species that we may take for granted have evolved to have very elaborate and exacting systems of communication,” they might be chirping, check a duh, duh, duh.
Next headline on:  BirdsAmazing Stories
SETI Researchers Affirm Planetary Privilege Criteria   06/24/2005  
In the weekly SETI Thursday column on, Douglas Vakoch corroborated two claims made about the habitability of planets in the film The Privileged Planet (shown at the Smithsonian last night – see 06/09/2005 story): namely, (1) smaller stars have smaller habitable zones or “Goldilocks” zones where life can exist, and (2) planets within the habitable zone of a small star are closer in, tending to tidally lock one face toward the star – reducing the chance for habitability.  They admitted even more, that such conditions (if an atmosphere existed) would “whip up enormous wind velocities.”  They balanced that bad news with hopes that such worlds might have enough greenhouse effect to moderate the winds.  Since the discovery of Gliese 876, the smallest extrasolar planet so far, astrobiologists and SETI researchers are taking a second look at smaller M-class stars as homes for habitable planets.  None of the ones surveyed so far has a Jupiter-class planet, so the thinking is that most planets might be small rocky worlds around small, warm stars.
How much hoc can an ad hoc hawk for an ad hoc post hoc post?  An M-class star needs a Jupiter for its comet shield, remember?  And is intelligent life going to thrive on the dark side of a tidally locked world in time to build a flashlight, let alone a radio telescope?  Or is it going to bake in its sun forever on the lit side and never see the stars, dreaming of who else is out there?  Maybe there is a thin great circle on its twilight zone suitable for life.  Don’t count on a booming economy, though.
    Don’t expect sitcoms or even kid fare on the M channel.  If Goldilocks had to broadcast from such a world she would move to a nicer zone.  Like the film suggests, that leaves out 90% of the market.
Next headline on:  SETIIntelligent Design
Croc Teeth Bite Fatal Wound into Dino Phylogeny   06/23/2005  
This line sounds serious: “We have pretty much erased the record of Triassic ornithischian dinosaurs from North America, Europe and worldwide, except for South America.”  This is what William Parker said about his find of a complete Revueltosaurus fossil in Arizona that upsets the leading story of the rise of the ornithischian dinosaurs (one of two major dinosaur groups).  The fossil, earlier known only from teeth, was presumed to be a dinosaur, but now has been found to be mostly crocodilian.  What damage this does to assumptions about dinosaur evolution is explained by EurekAlert and
It is wondrous how Darwinians get their ability to build epic tales, animated features and all, on such flimsy data as a few teeth.  If they can’t even get the class of an animal right from the teeth, how can they tell us all about the age, and which ancestor begat which?  When the wrong story was assumed, for so long, and passed the peer review of children’s picture books, how much confidence does this give a reasonable observer that other figments of the story have validity?
    Dinosaur evolution theories will survive this catastrophic impact, as Darwinian tales always do; in fact, the vacancy left behind may open up more niches for rapid diversification of new plot lines.  This is known as adaptive radiation.  Any Darwinian with this positive spin rolling around in his head has evolutionary theory in a nut shell. 
Next headline on:  DinosaursFossilsDarwinism and Evolutionary Theory
Lions Guard Kidnap Victim in Ethiopia    06/22/2005  
Some news stories make you wonder about divine providence.  Netscape News reported a story of lions that rescued a kidnapped Ethiopian girl who was being beaten by seven men trying to force her to marry one of them.  In Ethiopia, men will often beat and rape a woman who resists a forced marriage; up to 70% of marriages involve such abductions, often with severe beatings.  The lions guarded and protected this woman for about half a day till she was found, then “left her like a gift and went back into the forest.”
No unwarranted claims here; just an interesting item.  The flip side is that this story should make us all angry about the lowest of beasts, sinful men, who would do such a thing.  The article says this kind of atrocity is the norm.  In this depraved culture, kidnapping and rape, with beatings, is the men’s “customary” way to force women into marriage when they resist.  For more ugliness, see what a photographer found going on in neighboring Darfur, Sudan, as reported in National Geographic News.  Let’s hear it for the lions.  If you find a Darwinist trying to excuse this “customary” behavior as an evolutionary adaptation from our ape-like past (see 07/18/2003 entry), let out a loud roar.*
Next headline on:  MammalsAmazing Stories
  *Maybe a roar-shock test will help them psychoanalyze their beliefs.
Battlefront Dispatches    06/22/2005  
Activities in the Darwin-vs-Design controversy continue generating national news:
  • War of the museums:  The Sternberg Museum in Kansas is trying to reinforce arguments for evolution, according to Voice of America news.  Proud of his T. rex display, curator Greg Liggett claims that “if the school curriculum changes to include theories such as Intelligent Design, critical scientific inquiry in Kansas classrooms might go the way of the dinosaurs.”  The Creation Museum in Kentucky, a project of Answers in Genesis, continues to take shape.
  • Reverse gear:  Larry Caldwell got Eugenie Scott of the NCSE to apologize for making libelous statements about him, according to Discovery Institute.  He threatened a lawsuit because she had written untrue and defamatory things about his attempt to allow criticisms of Darwinism in Roseville, California schools.  In addition, according to Denyse O'Leary, the California Academy of Sciences agreed to remove links to Scott’s article from their website, and publish a letter by Caldwell and a retraction by Scott in an upcoming issue of California Wild magazine where her allegations were originally made.  EvolutionNews has links to the history of the Caldwell case.
  • Web Warfare:  The American Association for the Advancement of Science (AAAS) has joined the NAS (see 06/13/2005 entry) in fighting intelligent design with internet resources.  It posted a website called “Evolution on the Front Line” to reinforce efforts to combat “efforts in Kansas and elsewhere to weaken or compromise the teaching of evolution in public school science classrooms.”
  • Townes Hall:  Nobelist Charles Townes, inventor of the maser and laser, was interviewed by UC Berkeley News.  A nominal Protestant Christian, he was tolerant of ID but not too keen on Biblical creationism.  He treats the six days of Genesis 1 as an analogy, and allows for some evolution, saying, “People who are anti-evolution are working very hard for some excuse to be against it.  I think that whole argument is a stupid one.”
  • South Carolina front:  State senator Mike Fair is advocating giving students an opportunity to hear alternatives to Darwinism in South Carolina schools, according to the The State newspaper.  The article quotes a Baptist pastor in Greenville claiming that “striving to live the Christian way of life has absolutely nothing to do with one’s view of evolution.”  Rev. Baxter Wynn continues, “It is not necessary to choose between Christianity and evolution – they are not mutually exclusive.”  Those sentiments are surely not shared by the nearby staunchly fundamentalist college that teaches young earth creationism, Bob Jones University.
  • Pennsylvania front:  A house bill in Pennsylvania may put intelligent design in the schools, according to Fox News.  The pro-ID Discovery Institute, encourages teaching the controversy, but recommends against mandating the teaching of intelligent design.
  • Philly Frenzy:  A parent wrote a letter to the Great Valley School District complaining that the textbook taught evolution, and wanted her ninth-grade daughter to opt out of the lesson.  She lost; the board voted unanimously to retain the textbook, according to the Daily Local newspaper.  This was the first complaint over evolution by this school board, but “it mirrors the controversy in Pennsylvania, and across the nation, over whether evolution should be taught alongside other, more religious-based discussions of the origins of life on Earth.”
  • Volcano eruptsYahoo News poured hot lava over creationists with its article, “US radicals blow their tops over volcano movie as Darwinism debate rages” (emphasis added).  It talked about how many customers are not buying the evolutionary line in several IMAX films (see 03/23/2005 entry), like “Volcanoes of the Deep Sea” that suggests life may have originated deep in the ocean.
    Yahoo’s piece was not a volcano, but a mud pot; better, a fumarole.  Darwinists are the ones erupting when people object to having philosophical naturalism in the form of chemical-evolution mythology crammed down their throats.  So what are the Darwin Party imagineers going to do in a free market economy?  Force the customers to watch their cartoons?  Many IMAX films are wonderful explorations into the natural world when they stick to observable facts.  Adding Tinker Bell is only distracting.
        Pastors and scientists who don’t understand the issues should keep their mouths shut.  The “Reverend” Baxter Wynn, if he was quoted accurately, appeared to be utterly ignorant of the controversy and what his Bible says about it.  His statement simultaneously commits the either-or fallacy and shouts peace, peace, when there is no peace.  Charles Townes, bless his holy heart, is a smart engineer but a weak philosopher.  His comments play right into the hands of those who would banish his Christian beliefs from public discussion.  What we need are more men like Larry Caldwell able to stand up to the lies of the dogmatic Darwinists and get them to back down.  Somebody ought to turn Liggett’s big lie back on him.
    Next headline on:  DarwinismIntelligent DesignEducationMedia
    Macroevolution Claims Investigated    06/21/2005  
    Two scientific papers recently used the word “macroevolution” in their titles.  Did they actually point to cases of natural increase in information or function?
    1. Diatoms:  A paper in PNAS by Finkel et al.1 was called, “Climatically driven macroevolutionary patterns in the size of marine diatoms over the Cenozoic.”  All it discussed was the sizes of diatoms as a function of biodiversity and ocean temperature.
    2. Island Biodiversity:  Douglas Erwin wrote a Perspectives piece in Science last week,2 entitled “Macroevolution: Seeds of Diversity.”  It is more a theoretical treatment of opposing evolutionary hypotheses (niche construction and classical gradualism) in the context of adaptive radiation on island communities, than an examination of any particular case of a plant or animal evolving into a different kind of organism.  Erwin proposes that biodiversity itself generates biodiversity: “Simply put, the reason the tropics have so many species is that they have so many species” or, “future diversity is a function of current diversity.”
          He continued by speculating that runaway biodiversification might be capped by periodic mass extinction events.  He concluded, “If periodic disturbance does provide a major control on diversity, then niche generation may be an ongoing process, more rapid during macroevolutionary transitions, but providing a regular source of new adaptive possibility until the next crisis occurs.”  Overall, macroevolution in his article was assumed, not demonstrated.

    1Finkel et al., “Climatically driven macroevolutionary patterns in the size of marine diatoms over the Cenozoic,” Proceedings of the National Academy of Sciences USA, published online before print June 14, 2005, 10.1073/pnas.0409907102.
    2Douglas H. Erwin, “Macroevolution: Seeds of Diversity,” Science Vol 308, Issue 5729, 1752-1753, 17 June 2005, [DOI: 10.1126/science.1113416].
    Mere microevolution masquerading as macroevolution by mangling the meanings of messages.  Microevolution is not under dispute.  If macroevolution is a fact, Darwinists, give us an example instead of “ingenious speculation but not much rigor” (see next entry).  There should be millions of examples.  Why is this so hard to demonstrate?  A bluffing assertion is not a sign of rigor, or of vigor.  In science, it’s more a sign of rigor mortis.
    Next headline on:  DarwinismMarine Life
    Something from Nothing Dept.: Can a Divide-and-Conquer Strategy Climb Mt. Improbable?    06/20/2005  
    Darwinian evolution from the most primitive organisms to the most advanced must have produced huge increases in functional information (see 06/12/2003 entry).  Yet finding specific genetic mechanisms for just how DNA succeeded in “climbing Mt. Improbable,” as Richard Dawkins termed it in his book of the same name, has been daunting.  In a recent paper in PNAS,1 Austin L. Hughes meant to encourage his fellow Darwinists that explaining the origin of new function in proteins has been given a boost by recent findings.  In the body of the article, however, he appears to have conceded more than he affirmed.  He began,
    Evolutionary biologists agree that gene duplication has played an important role [intelligent design term] in the history of life on Earth, providing a supply of novel genes that make it possible for organisms to adapt to new environments.  The existence of diverse multigene families, particularly in eukaryotes, provides evidence that numerous events of gene duplication followed by functional diversification have shaped [intelligent design term] genomes as we know them.  But it is less certain how this panoply of new functions actually arises, leaving room for ingenious speculation but not much rigor.  Cases where we can reconstruct with any confidence the evolutionary steps involved in the functional diversification are relatively few.   (Emphasis added in all quotes.)
    To switch from gloom to hope, he described an investigation by Tocchini-Valentini et al. that examined genes for tRNA endonuclease among three branches of Archaea.  Two of them contained a single gene that combined the functions of stabilization and catalysis, but a third subdivided the functions between two genes.  They feel this is an example of subfunctionalization (see 10/24/2003 entry); i.e., a case of a multi-function gene splitting sometime in evolutionary history into separate genes that carry on the original functions separately.  Hughes was glad to hear about this report, which to him was “particularly welcome as a concrete example of how new protein functions can arise.”  Yet this would seem to be merely a case of rearranging functions rather than originating new ones, i.e., of dividing without necessarily conquering.  Did he provide any examples of new functions arising by this process?
        The rest of article only elaborates on the theme of subfunctionalization.  Hughes presented various theories, by Ohno, Jensen, Orgel and others, about how gene duplication might have shared and diversified functions among ancestral genomes (see 05/15/2005 entry for another recent example).  He talked about “gene sharing,” in which a gene might produce multiple products depending on the context: i.e., an enzyme in one type of cell, but a crystallin in the eye, but this also begs the question about where the genetic information came from.  He speculated about how subfunctionalization might produce better-adapted proteins by the “Babe Ruth effect” – analogous to how the famous baseball player performed better as either a pitcher or outfielder/hitter, but not both simultaneously – yet did not prove that subfunctionalized proteins either contained more information or did a better job.
        What is more revealing in Hughes’ commentary are statements he made about evolutionary theory, evidence and proof.  Coming from someone who accepts evolution without hesitation, these remarks cast doubt on both the methodology and achievement of an evolutionary approach to genetics:
    • Oh no:  He discredited the original subfunctionalization hypothesis of Susumi Ohno:
      The first hypothesis regarding the origin of new gene function was that of Ohno, who assumed that, after duplication, one gene copy would be entirely redundant and thus freed from all constraint.... There are a number of reasons for doubting this hypothesis  First, as the late Marianne Hughes and I showed in the case of the tetraploid frog Xenopus laevis, duplicate genes are not in general freed from all functional constraint.  Rather, purifying selection [i.e., conservation] acts to eliminate deleterious nonsynonymous (amino acid-altering) mutations even in apparently redundant gene copies.  Furthermore, there are a number of multigene families where there is evidence that positive Darwinian selection has acted to promote amino acid changes in functionally important regions of proteins.  In these families, new function clearly has not arisen as a result of random mutation alone, contrary to the prediction of Ohno’s model.
      In its place, Hughes offered the alternative hypothesis that “both functions are already present before gene duplication.”  This, however, does not explain the origin of the functions, but only their rearrangement.

    • Who needs Darwin?  In a paragraph entitled “The Role of Natural Selection,” Hughes started by denying that natural selection had much to do with it:
      One theoretically attractive feature of their model of subfunctionalization, as pointed out by Lynch and colleagues, is that it can occur without the need for positive Darwinian selection, which is thought to be relatively rare at the molecular level.
      If daughter genes inherit just one of two functions, he says, “conservative or purifying natural selection will act against any mutation that eliminates function,” while the other fragment might accumulate mutations by genetic drift.  Again, this does not describe the origin of any new functions, but only the preservation of existing information.

    • Gimme your best shot:  Hughes surveyed some of the best examples of Darwinian selection at the molecular level, explaining the “Babe Ruth effect.”  Even these, however, overlook the need for new functional information:
      On the other hand, some of the best-documented examples of positive Darwinian selection at the molecular level involve functional diversification among members of multigene families.... It may often be as true of molecules as it is of human beings that “a jack of all trades is master of none.”  In such cases, positive selection may actually favor the loss of one function in a bifunctional molecule if a duplicate gene is able to take up the slack.
    • Dunno:  Hughes did not suggest that much is known about evolution by gene duplication, if anything; indeed, it cannot be known:
      In the case of archaeal tRNA endonucleases, there is no direct evidence whether drift alone gave rise to subfunctionalization or whether positive selection played a role.  These events occurred in the distant past; thus, the most convincing signal of positive selection, an accelerated rate of nonsynonymous nucleotide substitution is not obtainable, being obscured by numerous subsequent neutral changes.  However, the fact that subfunctionalization has occurred twice independently and by different pathways in the same gene family suggests that positive selection may indeed have been involved.  Perhaps, in the high-temperature environments occupied by these archaeal species, there is something less than optimal about the homotetrameric type of tRNA endonuclease, where the same polypeptide does double duty as a catalytic subunit and a spacer.
    • Lessons learned:  Near the end of the article, Hughes made a remarkable admission about the predictive power of Darwinian biology.  He also makes his first mention of a mechanism for new function, but prefaces it with the word perhaps:
      If we have learned anything at all in a century and a half of evolutionary biology, it is that facile generalizations are dangerous.  The evolutionary process finds a way to create exceptions to every model we propose.  Thus, it seems unwise to expect that functional diversification after gene duplication follows the same pathway every time.  Sometimes, subfunctionalization may occur by drift alone.  On other occasions, as we know, positive selection is involved.  Perhaps there are even cases where a new function has arisen by Ohno’s model of resuscitation of a dead gene
    • Somewhere in the mix:  Hughes briefly elaborated on the possibility that new function is an emergent property from the mix and match of dynamic interplays between multi-talented genes and proteins:
      In fact, as recent data on gene expression and protein-protein interaction networks make clear, all genes are multifunctional.  Even in its infancy, systems biology makes clear that protein functions are complex processes existing in multiple dimensions.  It thus seems a reasonable extension of Jensen’s original insight to propose that new protein functions arise as the multidimensional space of functional interactions is parceled out in new ways, new links in biological networks are formed, and old links are broken.
    In his concluding paragraph, Hughes made it clear that the proof is left as an exercise:
    Testing this hypothesis will require work at the interface of molecular evolutionary genetics and systems biology.  We will need to be able to understand the diversification of gene duplicates in terms of the totality of each gene’s role in cellular processes.  It is a tall order given our present knowledge, but this kind of evolutionary systems biology not only will increase our understanding of how new protein functions evolve but also will shed essential light on why biological systems work the way they do.

    1Austin L. Hughes, “Gene duplication and the origin of novel proteins,” Proceedings of the National Academy of Sciences USA, published online before print June 13, 2005, 10.1073/pnas.0503922102.
    This article sounded intriguing by its title, “Gene duplication and the origin of novel proteins,” and ostensibly set out to explain how new functions arose – but it did nothing of the sort.  All Hughes could identify by observation were degradation effects.  If genes and proteins underwent subfunctionalization, the function was already operative in the ancestor, as well as the information needed to produce function.  Did he prove that the daughter products contained more information?  No.  Did he prove that subfunctionalization actually occurred, rather than being created that way?  No.  Did he give away the store?  Yes.
        Hughes illustrated for the perceptive reader that Darwinian theory is useless and bankrupt.  It has produced little else than dangerous facile generalizations with exceptions for every proposed rule.  He has cast doubt on whether natural selection, the evolutionary mechanism that made Charlie the Philosopher-King of Science, acts as anything more than a conservative process to preserve existing information.  He tossed in for free a few falsifications of his colleagues’ speculative hypotheses.  He made up a story committing the personification fallacy about molecular Babe Ruths, without proving it has any relevance to real genes and proteins.  He demonstrated that evolutionary biology is an unending series of falsified tales, and he admitted that after “a century and a half of evolutionary biology,” almost nothing is known and everything remains to be discovered, which is “a tall order given our present knowledge” (better, lack of it).  So much for the origin of novel proteins.
        We provided extensive quotes from this paper to illustrate a recurring theme in the evolutionary scientific literature: Darwinists boast much but deliver nothing, only emptiness and confusion.  Does this vain litany of excuses and leaps in the dark deserve to be enshrined as the only valid approach to science, such that no student should be allowed to criticize it or hear any alternatives?
    Next headline on:  GeneticsEvolution
    Supermen Living in Nepal    06/17/2005  
    There is a race of people at the base of Mt. Everest capable of feats that defy scientific explanation: the Sherpas.  They can carry up to twice their body weight under three hostile conditions that would wear out most of us in a minute: (1) high altitude, (2) long distance, and (3) steep inclines.  Somehow, the techniques they use and the adaptations their bodies have made from living in that environment have made them the supreme load carriers of the human world (they even beat out African women who routinely carry heavy loads on top of their head).  This was the subject of a research paper in Science this week.1  Science Now sums it up:
    When the going gets tough, the tough use their heads.  Porters around the world carry loads that would floor backpackers by balancing baskets atop their noggins or slinging sacks from their craniums.  Now a new study reveals that Nepalese porters do the job better than anyone else, hefting huge bundles while using relatively little energy.   (Emphasis added in all quotes.)
    The study, also reported by National Geographic News, found that Nepalese porters or sherpas routinely carry double what backpackers carry, under more extreme conditions, yet burn less energy:
    The town of Namche (at an altitude of 3500 m [11,400 ft]) near Mount Everest hosts a weekly bazaar.  Porters (Fig. 1A), predominantly ethnic Rai, Sherpa, or Tamang, typically take 7 to 9 days to travel to Namche from the Kathmandu valley.  The route, no more than a dirt footpath, covers a horizontal distance of 100 km, with total ascents (river crossings to mountain passes) of 8000 m [5 vertical miles] and total descents of 6300 m [4 vertical miles].
        One day before the bazaar, we counted 545 male and 97 female porters (and 32 yaks) en route to Namche; others passed by earlier and later in the darkness.  We weighed randomly selected porters and their loads.  The men carried loads of 93 +- 36% of their Mb (mean +- SD, n = 96 male porters), whereas the women carried 66 +- 21% of their Mb (n = 17 female porters).  The youngest porter was 11 years old, and the oldest 68; the greatest load measured was 183% of Mb, and 20% of the men carried > 125% of their MbMore than 30 tons of material were ported to Namche that day.
    The researchers measured their oxygen intake and carbon dioxide output under controlled conditions, and found that their energy utilization was “far more economical than the control subjects at all loads and more economical than the African women at all except the lightest loads.”  They marveled at watching them in their normal business hauling loads around the mountains.  How they do it is a mystery:
    The load versus speed versus energy-cost trade-off chosen by these porters is to walk slowly for many hours each day, take frequent rests, and carry the greatest loads possible.  We observed, for example, a group of heavily loaded porters making slow headway up a steep ascent out of a river gorge.  Following whistled commands from their leader, they would take up their loads and labor uphill for no more than 15 s at a time, followed by a 45-s period of rest.  Incredibly, this group of barefoot porters was headed for Tibet, across the Nangpa glacier (altitude 5716 m [18,700 ft]), about another week’s travel beyond Namche.
        So how do they do it?  They might reduce the muscular work required to carry a load or increase their overall efficiency.  The actual mechanism is unknown at this time.
    Many world mountain climbers brag if they make it up Everest, but these sherpas consider such feats all in a day’s work.  National Geographic News adds that after unloading and selling their goods, they race home for more, running down the mountain for two days, even poorly equipped and usually with very bad shoes or none at all.  They usually sleep on the trail, with nothing but rocks for pillows, even in below-freezing temperatures.  Some of their women bring their babies with them.
        See also the National Geographic story from May 2002 about the legendary Sherpas of Mt. Everest.  Many of the famous climbing expeditions on the world’s highest mountain could not have succeeded without them, it says.
    1Bastien et al., “Energetics of Load Carrying in Nepalese Porters,” Science, Vol 308, Issue 5729, 1755 , 17 June 2005, [DOI: 10.1126/science.1111513].
    Every once in awhile we get glimpses into the suggestion that there is far more potential in the human body than most of us realize.  Those of us who have backpacked in the mountains know the strain of carrying even 40 pounds up a steep mountainside for just a couple of hours, and that at much lower elevations.  The worst feeling at a rest stop is to have some 68-year-old frail-looking grandma with a bigger pack prance right on by saying, “Mighty fine day, is it not?” as you sit there gasping for breath.
        Here we see, in Nepal, a community of men, women and children that make the impossible look routine.  They don’t shop at REI and use Patagonia gear or high-tech climbing boots; they don’t compete in the Olympics or win medals, but all of us must regard the way of life of these human mountain goats with admiration.  How much stronger and smarter could our ancestors have been?  A little humility is always in order.
    Next headline on:  Human BodyAmazing Stories
    Obsessed With Sex: How Much Can Be Known About the Sexuality of Hominids?    06/17/2005  
    Bruce Bower in Science News (June 11, 167:24, p. 379) reported on the controversy about the sex life of Lucy and her mate(s).  Owen Lovejoy and Philip L. Reno (Kent State U, Ohio) have “unabashedly” put forth a hypothesis that Mr. and Mrs. Australopithecus afarensis (let’s call him Desi) had long-term relationships and stable families as they evolved along on the way to humanity.  This conclusion was based on statistical analysis of fragmentary bones which represent somewhere between 5 and 22 individuals.  They assumed that the largest femur heads were from the males and the smaller, from the females, then deduced that australopithecines displayed slightly less sexual dimorphism than gorillas do.  From there, they made presumptions about what this implied about their sex lives in the prehistoric I Love Lucy sitcom.
        Bower gave good press to Lovejoy and Reno’s hypothesis, but then surveyed the reactions of other researchers:
    Other scientists express a mix of chagrin and disdain at the amount of energy that researchers have expended on trying to separate fossil boys from girls.  Investigators need to drop their obsession with the sex of fossils and examine how individual differences in skeletal anatomy arise, contends Maciej Henneberg of the University of Adelaide in Australia.  For body weight and many skull measurements, including braincase size and facial width, individuals within each sex usually differ far more from each other than average members of opposite sexes do, he argues.
        Erik Trinkaus of Washington University in St. Louis also derides efforts to identify the sex of ancient bones.  Sex assessments always begin with the unjustified assumption that bigger bones must belong to males and smaller ones to females, he says.  And the numbers of individual specimens of A. afarensis and other ancient hominid species are too few to generate reliable estimates of male and female size ranges, in his opinion.
        Louisiana State’s Tague doesn’t go that far, but he notes that even the pelvis, the body part regarded as the gold standard for telling apart primate sexes, is surprisingly tough to read.  His work shows no consistent pattern of the pelvis being larger in females than in males.
      (Emphasis added in all quotes.)
    It’s not even clear to all researchers that Lucy was a female, to say nothing of whether the Mertzes were part of the same tribe.  Bower hopes that additional specimens will help resolve this “battle of the sexes.”
    The nonsense that Darwinists get away with is atrocious and silly.  Bower’s article contained the obligatory artist’s conception of Lucy’s family life, all based on myth and unwarranted speculation.  Even though he tried to provide criticism of Lovejoy’s wacky idea, he only extended the debate between members of the Darwin Party.  Why do non-Darwinists never get a chance to provide their scientific critiques?
        Historical anthropology is out of control.  It is an endless parody of untestable speculation masquerading as legitimate research.  Science needs creationism as a check against “rampant Darwinism” as Dr. Phillip Skell called it in a recent interview (see IDURC).  He said, “The conflation of neo-Darwinism with the historical biology, and its frequent companion materialist philosophy, should be recognized and exposed for what it is, rather than disingenuously introduced as science.” 
    Next headline on:  Early ManDumb Stories
    Did Fossils Inspire Thunderbird Legends?    06/17/2005  
    Adrienne Major thinks that the Lakota got their legend of the Thunderbird from looking at fossil pterosaurs in the badlands.  Her speculation is explored in National Geographic News.  Major thinks other world legends have their origin in fossils that ancient people observed.
    This hypothesis is no less speculative than the one by creationists that Indians saw live pterosaurs and the Chinese saw live dinosaurs.  Evolutionists would never consider such an idea, because they have their own myths.  They are wedded to the tale that dinosaurs and pterosaurs died out long before man appeared.  Do they know this for a fact?  No; they were not there, for one thing, and their prior commitment to evolutionary theory dictates how all data are to be interpreted.  The discovery of flexible blood vessels in a T. rex recently (see 03/24/2005) shows the extent of their commitment; rather than consider the obvious, that this unfossilized material could not be 70 million years old, they adjusted their assumptions to fit their myth.
        Were the Chinese and the Lakota skilled in paleontological interpretation of disarticulated bones?  Would it not be more plausible to suggest that perhaps they saw some of these creatures before the last ones died out?  It would seem more likely that the fearsome appearance of imposing live creatures would generate better myths than would dead bones to untrained eyes.
    Next headline on:  Dinosaurs
    Miller Time Party Drags On    06/16/2005  
    Astrobiologists threw a party when a team of researchers decided there was more hydrogen in the early earth’s atmosphere than thought (see “In the beginning, hydrogen: was it Miller Time?, 04/22/2005).  While this was good news for those wishing for better conditions on the early earth for chemical evolution, a few are staying sober enough to warn against letting the celebrations get carried away.
        Last month, veteran origin-of-life researcher Christopher Chyba, buoyed by the announcement, was nevertheless cautious about how much it helps the Miller scenario.  He wrote in Science:1
    In 1952, Stanley Miller, working with Harold Urey, simulated the atmosphere of early Earth with a gas mixture of methane (CH4), ammonia (NH3), molecular hydrogen (H2), and water.  When he introduced an electrical spark to represent lightning, he observed the formation of amino acids, the building blocks of proteins....
        However, by the 1960s, the validity of hydrogen-rich (and hence reducing) model atmospheres for early Earth, such as the CH4-NH3 atmosphere used by Miller and Urey, was under attack.  Since the 1970s, carbon dioxide (CO2)-rich atmospheres have been favored.  Miller has shown that the production of amino acids and other organic molecules is orders of magnitude less efficient in such atmospheres.  For this and other reasons, the Miller-Urey approach to the origin of life has fallen out of favor with many researchers.  But on page 1014 of this issue, Tian et al.2 argue that the early-Earth atmosphere might have been hydrogen-rich after all.
    (Emphasis added in all quotes; see also 05/02/2003 entry on the history of the Miller experiment.)
    Chyba described the Miller-Urey scenario in more detail, but admitted it was “probably largely wrong.”  Such a reducing atmosphere would have been hard to form or sustain.  If, however, there was a sustainable hydrogen abundance of 30% or more, as suggested by the Colorado team, conditions favoring higher production of amino acids might have existed.  Still, “Many uncertainties and problems remain,” Chyba said, and they seem serious, indeed:
    1. Rinse Tian et al. focus on the oceans as the “birthplace of life,” but polymerization of amino acids into proteins (or nucleotides into RNA) is thermodynamically unfavorable in liquid water.
    2. SaltFurthermore, in an early ocean as saline as that of today, the salt inhibits key prebiotic reactions.3  The bulk ocean may thus have been one of the worst places to try to originate life.
    3. TossAfter making life’s building blocks in the ocean, one needs to look elsewhere to carry the chemistry further.
    He suggested that meteor impacts “may also have been a major driver of organic production in an early H2-rich atmosphere,” but with all the hope and hype, Chyba advises sobriety:
    These are tumultuous times in the study of the origin of life.  The early ocean may have been even less hospitable for prebiotic chemistry than previously thought, and claimed evidence for the earliest signatures of life on Earth is being strongly challenged.  Now a 30-year, albeit shaky, consensus on the nature of the early atmosphere may have to be reexamined, and the geochemical implications of an H2-rich early atmosphere will need to be scrutinized.  This turmoil makes it a great time for young scientists to enter the field, but it also reminds us that some humility regarding our favorite models is in order.  As Jacob Bronowski noted, “Science is a tribute to what we can know although we are fallible.”
    These week in Science,4 Richard Kerr also wrote about the higher hydrogen estimate:
    Thirty years ago, geochemists took away the primordial soup that biologists thought they needed to cook up the first life on Earth.  Now, some atmospheric chemists are trying to give it back.
        Creating the primordial organic goo used to be easy.  If you combined the methane and ammonia seen in the still-primordial atmosphere of Jupiter, passed lightninglike sparks through the mixture, and added some water, voilà, complex organic compounds such as amino acids formed.  But then in the 1970s geochemists spoiled the party by insisting that Earth’s earliest atmosphere was nothing like Jupiter’s.  Earth’s carbon would have been part of oxygen-rich carbon dioxide, and its nitrogen part of inert nitrogen gas, they said.  And hydrogen seeping from the planet’s interior would have quickly escaped to space.  That left chemists with a thin gruel indeed.
    Kerr summarizes the new estimate and what it means: “Overall, hydrogen would have escaped at 1/100 the rate previously assumed, the group says.... That would make for a far more productive atmosphere than chemists have been coping with for 30 years” – allowing vast amounts of organics to form into the ocean “ to make a soup.”
        Kerr hastens to make clear that there is still disagreement.  While the announcement “is going to make the biologists a lot happier,” another doesn’t feel that Tian et al. adequately dealt with all the factors that contribute to hydrogen escape; “a more sophisticated model would show that hydrogen escaped the early Earth at least as fast as it does today.”  (Kerr does not even mention the problem with salts in the ocean.)  Is the Miller party running out of food?  He ends, “Time will tell whether too many cooks spoil the primordial broth.”
    1Christopher Chyba, “Rethinking Earth’s Early Atmosphere,” Science, Vol 308, Issue 5724, 962-963 , 13 May 2005, [DOI: 10.1126/science.1113157].
    2Tian et al., “A Hydrogen-Rich Early Earth Atmosphere,” Science, Vol 308, Issue 5724, 1014-1017, 13 May 2005, [DOI: 10.1126/science.1106983].
    3Monnard et al., “Influence of ionic inorganic solutes on self-assembly and polymerization processes related to early forms of life: implications for a prebiotic aqueous medium,” Astrobiology 2002 Summer;2(2):139-52.  They write that concentrations of salts anything like those in our contemporary oceans inhibits formation of amino acids and completely disrupts primitive membrane systems.  Conclusion: “These observations suggest that cellular life may not have begun in a marine environment because the abundance of ionic inorganic solutes would have significantly inhibited the chemical and physical processes that lead to self-assembly of more complex molecular systems.”
    4Richard Kerr, “A Better Atmosphere for Life,”, Science, Vol 308, Issue 5729, 1732, 17 June 2005, [DOI: 10.1126/science.308.5729.1732].
    Same comment as in 04/22/2005: too little, too late.  The good news is no better than that in the Geico commercials: “I have good news and bad news.  The jury has found you guilty, you have to go into the slammer for life, your wife and kids have left you and are changing their names, your stocks went bust, and you have cancer.”
    “What’s the good news?”
    “I just saved $400 on my car insurance by switching to Geico.”
    Everything is against the astrobiologists: the chemistry, the sources, the geology, the salt, the water, the information, the probability, the thermodynamics, the philosophy.  Does the good news really matter?  “I just saved 30% on my hydrogen when switching to the Tian et al. model.”  It would make any knowledgeable astrobiologist want to hold his head and groan, “Oh, shut up.”
    Next headline on:  Origin of Life
    Are Teens Like Roaches?    06/16/2005  
    A press release from University of Manchester concluded that being a teenage mother might be a good thing.  The conclusion was based on observations of the mating behavior of cockroaches.  Dr. Patricia Moore, one of the researchers, wins Stupid Evolution Quote of the Week: “Although it’s hard to compare the experiences of the female cockroach to humans, the biological mechanisms are similar and so an inappropriate apoptosis response to the ‘mistiming’ of reproduction may explain the evolution of the loss of fertility with age.”  EurekAlert reproduced the press release without any challenge.
    To an evolutionist, human society acts on the same principles as cockroach society.  To evolutionary reporters, any idea that glorifies Charlie is fit to print.  As a prime example of evolutionary folly, this story speaks for itself.
    [Gong.]  Next.
    Next headline on:  Darwinism and Evolutionary TheoryDumb Stories
    Reports Differ on Kansas Evolution Debates    06/16/2005  
    How is the debate over evolution in Kansas going?  It depends on whom you ask.  MSNBC News focused on personal attacks between board members (see also the Lexington Herald-Leader).  The Discovery Institute, by contrast, focused on the content of the new proposed standards that allows a “common-sense” approach for teaching all the science about evolution, including the problems with Darwin’s theory.
    MSNBC’s title suggests that both sides are bickering, claiming “School board members hurl insults at each other.”  But if you look into the article, the only ones hurling insults are the evolutionists; the other side is just putting up their shields.  All Connie Morris said was, after being insulted, “Had you attended, you would have been informed.  You would be sitting here as informed individuals and not arrogantly calling us dupes.”  The article claims Morris mentioned the moderates by name in print, but does not say she insulted them like the Darwinists did; she only derided evolution itself, the article says.  The evolutionists, though, called the conservatives “dupes” of intelligent design advocates and their decision based on “absolute and total fraud.”  Judge for yourself which side is acting with civility and responsibility.
        The majority conservatives had invited the pro-evolution moderates to come to the hearings, but they wouldn’t.  The Darwin Party could have contributed to the discussion, but chose to sit and pout.  If they had been listening, they would realize that the Board is taking no position on intelligent design.  The new standards are very mild.  They do not call for teaching creation or intelligent design, but only for permitting critical thinking about evolution such that it is treated like any other scientific theory, not like a sacred cow.  No advocates of a scientific theory would worry about that unless their position was weak.
    Next headline on:  Darwinism and Evolutionary TheoryEducation
    Are Natural Poisons Health Cures in Disguise?    06/15/2005  
    Three recent stories are suggesting that natural toxins may be too much of a good thing:
    1. Snail Trail:  John Roach in National Geographic News wrote about new painkillers and drugs being developed from toxic snail venoms.  Cone snails create an array of hundreds of unique chemical compounds (see 10/22/2003 entry).
    2. Fungus Among Them:  A fungus shows promise for controlling malaria mosquitos.  It appears to be harmless to humans.  Story on Science Daily.
    3. Lockjaw Therapy:  Researchers in Barcelona are discovering that tetanus toxin has therapeutic properties in treatment for neurodegenerative disorders, according to EurekAlert.
    A common operational paradigm in nature appears to be control by resistance: initiator and repressor, agonist and antagonist, accelerator and brake.  Another is hormesis (see 02/12/2003 entry): i.e., that a little is good, but more is not better.  Taken together, these principles suggest that many poisons and toxins only become “evil” to our sensibilities when they get out of control.
        A dynamic community of interacting organisms needs checks and balances.  These are best understood by looking at the big picture, a view called systems biology – a perspective implicit with design reasoning.  As a corollary, relationships that could have been harmonious originally may have begun to wreak havoc when out of balance.  Regardless, there may be healthy treasures to mine in things we once considered agents of suffering.
    Next headline on:  Health
    Virginia Teacher Chastened for Making Optional Creation Material Available   06/14/2005  
    A highly-respected and well-liked high school biology teacher in Bristol, Virginia almost lost his job recently.  His crime?  Making an optional notebook of supplementary material called “Creation Battles Evolution” available to his students.  The notebook, printed at his own expense, included evidence for creation and against evolution, from “sources ranging from the Internet to scholarly papers and quotations from scientists and scholars critical of evolution or evidence supporting it.”  Each semester for 15 years, Larry Booher had mentioned it in passing, telling the class it was optional material that would not be on the test but available for extra credit.  A reporter got wind of it and gave an anonymous tip to the school authorities.  Booher was told to stop.  The superintendent claimed the teacher had stepped over the line and ordered, “He must teach evolution exclusively – observable scientific fact, not beliefs or religion” (emphasis added).  Like Galileo, he was forced to recant: he told the Roanoke Times “he regretted handing out the material.”  The story was mentioned in the Hampton Roads Pilot, LA Times and the Richmond Times Dispatch.
        One of his former students wrote us and said he was saddened by the action, calling Booher “a teacher of great impact”  and “one of the greats in my life.”  He now values his copy of that notebook even more.  “When you can’t beat your opponent in a debate, you have to silence him, which is what they have done to a great biology teacher,” he said.  He described Booher as one of the most respected and liked teachers in the school.  He never discussed his personal views unless asked, and “made it very clear that nobody was pressured to believe anything.”  This student could not find any parent or former classmate who was happy about what the school did to Booher.  “Maybe that’s why not one parent or student complained in two decades, and it took an anonymous reporter from Charlottesville, Va (250 miles away) to make an issue of it.”
        The superintendent agreed with the assessment of Larry Booher’s reputation:
    Lee described Booher, 48, as “one of the finest science teachers I’ve ever been around” and said Booher would return to the classroom in the fall since he agreed to stop distributing the creationism materials.
        The news reports made it sound like Larry Booher had broken the law, violating a Supreme Court decision.  That decision, however, only forbade school boards from mandating equal time for creationism along with evolutionism.  It stated explicitly that teachers are free to discuss any scientific theory of origins.  Similarly, the guidelines for the congressional No Child Left Behind act targeted evolution as a controversial theory that teachers were free to discuss critically and mention alternatives.
    So “Evolution Must Be Taught Exclusively.”  Anything other than 100% pure Darwin Dogma is now labeled “belief” and “religion” by fiat, no matter how scientifically sound it is, no matter how supported by reputable scientific sources.  Students’ tender eyes must be shielded from any of the voluminous damaging evidence against official dogma.  Are you mad about this?  Look at the next entry; think about all those molecular machines that are inexplicable by evolution – mechanisms that shout design with a capital D.  And they call evolution “observable scientific fact”?  How enlightened our age.
        Persecution like this is not limited to Virginia; it is happening all over the country in one of the most momentous scientific paradigm battles of the century.  Evolution is controversial, whether the Darwin Party realizes it or not.  It is tearing this country apart (see 05/24/2005, 05/13/2005 and 05/05/2005 entries, and another recent example in Utah from the Salt Lake Tribune).  It is the defining issue of the culture war.  A large majority of the public denies that evolution can explain the complexity of life, and increasing numbers of scientists are ready to cast Darwin overboard.
        Incongruously, the same Darwin Party thugs who shut out debate and forbid access to scrutiny over their incomprehensible Tinker Bell religion are usually the same people who have no problem with any leftist, radical, homosexual-activist, abortion-advocate, Marxist or new-age prophet preaching their dogma unhindered, without any opportunity to opt out.  If you’ve had enough and can’t take this any more, do something.  Start by getting informed: about the evidence, the history of science, the law, and the right strategy to combat today’s incorrigible dogmatists, the Darwinians.*  Attend your school board meetings.  Write effective letters.  Vote.  Push back on the ACLU, the NCSE, the Dogmatists United For Separation of Reason and State, and the other pro-Darwin PACs.  Their censorship will only succeed if the citizens let it.
    Next headline on:  Darwinism and Evolutionary TheoryEducation
    *Knowledge is power, but ignorance is not bliss.  It is essential that you understand the issues, the law, the science, the tactics of the Darwinists, and the art of Baloney Detecting, before leaping into the fray.  Well-intentioned but misinformed actions can do more harm than good.  Open debate is what we should seek; if it is wrong for Darwinists to mandate their views, then it is wrong to mandate creationism or intelligent design, too.  If it is wrong to censor creationism, it is wrong to censor evolutionism – that is not a desirable goal, nor will it play in the public arena.  Students of science need to know about evolution – more than the watered-down, sanitized version they are getting (see 02/11/2005 commentary for suggested curriculum).  Teaching the controversy – letting students hear all the pertinent scientific evidence for and against Darwinism and its scientific alternatives (like intelligent design), is both commendable and legally defensible in a free and pluralistic society (see example from 06/03/2005 entry).  Do your homework on the resources at the Discovery Institute before picking up the pen or microphone; if you still do not feel qualified, then support those who do.
    Cell Wonders Accelerate   06/14/2005  
    Scientific papers on cell biology continue to uncover amazing things as techniques improve to peer into the workings of these units of life.  Here are our Top Ten from the last few weeks:
    1. Immunity Tunes:  A press release from Johns Hopkins talked about how, unlike other cells, immune cells undergo a “dizzying loop of activity” to generate huge varieties of antibodies through recombination.  They liken the regulator of the recombination process to a band leader directing a jam session.  (Emphasis added in all instances.)
    2. Oxygen Sensor:  “Cell’s Power Plants Also Sense Low Oxygen” announced a report from Howard Hughes Medical Institute.  In summary, “Researchers have produced the strongest evidence yet that mitochondria – the organelles that generate energy to power the cell – also monitor oxygen concentration in the cell.  If oxygen slips below a critical threshold, the mitochondrial ‘sensor’ triggers protective responses to promote survival.”  Controlling oxygen levels is important.  Both too little and too much can be deadly, not only to the cell, but to the whole organism.
    3. Reverse GearNature1 June 9 talked about the myosin monorail trains that ride the microtubule rails.  Out of the myosin superfamily of motor proteins, consisting of 18 classes, they were curious how Myosin VI is bidirectional, unlike most of its siblings.  They studied its “lever arm,” “power stroke” and “converter” but did not come up with a final model of how it works.  “Undoubtedly, this unique myosin family member has yet more surprises to reveal,” they concluded.
    4. Transporters:  Aussie biologists talked about protein transport into mitochondrial membranes in Current Biology.2  Since there are two membranes, similar to those in chloroplasts (see 01/01/2005 story), there are two squads of transporters to get the cargo in and out.  Named TOM and TIM for translocons of the outer and inner membranes, these are “a series of molecular machines” that know how to sort and authenticate objects needing to pass the gates.  They envisioned an “entropic spring” mechanism that can help get the cargo passed through “no apparent input of energy.”  This type of mechanism is “an emerging theme in biology” that harnesses the disordered motion of molecules to provide binding flexibility and low energy cost to accomplish “a range of functions.”  “The TIM23 complex is a smart machine,” they say, describing its ability to grab a piece of cargo, insert it, respond to a stop-transfer signal and reject it, or pass the cargo to the next machine complex.
    5. Tissue Triage:  Another paper in Current Biology3 discussed how epidermal cells repair damage.  The phylogeny of this ability was a puzzle: “Amazingly, while the eyes and hearts of Drosophila and mammals are constructed in entirely different ways and are morphologically quite distinct, their development appears to be under the control of similar master-regulatory transcription factors,” they said.  These operations on two vastly different types of organisms cannot be homologous, they suggest; they must be due to convergent evolution.  However the repair mechanism arose, it involves signaling and a cascade of coordinated events involving molecular machines.  The result?  A stitch in time, and wounds that are self-healing.  This is another “conserved repair response,” they say, meaning that it is found early in the history of life with little change since.
    6. Quality Control:  A press release from Yale described a protein that “recognizes misfolded RNAs, creating a RNA quality control system for cells.”
    7. Kissing Chromosomes:  A news story in Nature4 sheds light on a mystery of gene regulation.  We all know chromosomes come in pairs, but how do the genes on each member get expressed together when they are separated by distance?  Out of the “many strategies to orchestrate gene activation or repression” in the cell’s bag of tricks, “A three-dimensional examination of gene regulation suggests that portions from different chromosomes ‘communicate’ with each other, and bring related genes together in the nucleus to coordinate their expression.”  It’s nice that the spouses are on speaking terms.  “Such inter-chromosomal communication has been suspected for some time,” Dimitris Kioussis said, “but this is the first evidence that it actually takes place.”  Our understanding of gene regulation has changed from a linear view “to an appreciation that genes are associated with groups of proteins, forming multimolecular complexes,” he said.  We’re going to have to see the process not just in snapshots or just a movie: “Is it time to go 4D?” he jests with implicit seriousness.  No one knows how the chromosomes are brought together.  “How do genes find their appropriate location in the nucleus of a cell, and how are genes that must be expressed herded into active neighbourhoods?” he asks (see “Spaghetti in a Basketball,” 07/28/2004).  Whatever the mechanism, “These remarkable findings will puzzle us for some time to come.”
    8. Inter-Agency Coordination:  Cities have fire departments, police departments, ambulances, highway patrol, disaster response teams and other agencies that sometimes have overlapping duties.  Cells do, too.  There are multiple repair mechanisms able to respond to different kinds of DNA damage.  Scientists writing in Molecular Cell5 discussed what is known about how they coordinate their actions during the emergency repair called TLS (trans-lesion DNA synthesis): “The process requires multiple polymerase switching events during which the high-fidelity DNA polymerase in the replication machinery arrested at the primer terminus is replaced by one or more polymerases that are specialized for TLS.  When replicative bypass is fully completed, the primer terminus is once again occupied by high-fidelity polymerases in the replicative machinery.”  It sounds like the first-aid squad knows how and when to patch up things enough to get the patient to the surgeon.
    9. Texas Tech:  Scientists in Texas, publishing in Cell,6 found another multi-talented molecular machine.  The rotor part of the V-type ATP synthase (see 02/24/2003 entry) does more than just help acidify vesicles.  It also has “an independent function in membrane fusion,” they found.  It is essential in the process of exocytosis – what neurons do to transmit their messages.  They found that mutant embryos had severe defects in synaptic transmission of nerve signals.  (This was found in fruit flies.)  By the way, the other form of this rotary motor, the F-type ATP synthase, was called “The World’s Smallest Wind-Up Toy” by Richard Berry in Current Biology.7  Researchers have figured out how to make the motor turn, using magnets.  He thinks scientists are on the verge of figuring out how the F0 rotor converts proton flow into torque.
    10. Ultimate Spa:  Last but not least, scientists at the Salk Institute last month announced a surprising solution to the puzzle of how embryos start their left-right orientation.  An “embryonic body wash” operated by cilia sweeps chemical signals across the embryo: “the foundations for the basic left-right body plan are laid by a microscopic ‘pump’ on the outer surface of the embryo’s underside that wafts chemical messengers over to the left side of the body.  This sets up a chemical concentration gradient that tells stem cells how and where to develop.”  The cilia rotate at a precise 40-degree angle to generate a current over the embryo.  The original paper in Cell contains movies of the action.

    1Menetrey et al., “The structure of the myosin VI motor reveals the mechanism of directionality reversal,” Nature 435, 779-785 (9 June 2005) | doi: 10.1038/nature03592.
    2Perry and Lithgow, “Protein Targeting: Entropy, Energetics and Modular Machines,” Current Biology, Vol 15, R423-R425, 7 June 2005.
    3Stramer and Martin, “Cell Biology: Master Regulators of Sealing and Healing,” Current Biology, Vol 15, R425-R427, 7 June 2005.
    4Dimitris Kioussis, “Gene regulation: Kissing chromosomes,” Nature 435, 579-580 (2 June 2005) | doi: 10.1038/435579a.
    5Friedberg et al., “Trading Places: How Do DNA Polymerases Switch during Translesion DNA Synthesis?” Molecular Cell, Volume 18, Issue 5, 27 May 2005, Pages 499-505, doi:10.1016/j.molcel.2005.03.032.
    6Heisinger et al., “The v-ATPase V0 Subunit a1 Is Required for a Late Step in Synaptic Vesicle Exocytosis in Drosophila,” Cell, Volume 121, Issue 4, 20 May 2005, Pages 607-620, doi:10.1016/j.cell.2005.03.012.
    7Richard Berry, “ATP Synthesis: The World’s Smallest Wind-Up Toy,” Current Biology, Vol 15, R385-R387, 24 May 2005.
    Sometimes we just have to rub it in: these are just a few samples from the flood of literature coming out each week in cell biology, biochemistry and genetics (check out another example from 01/27/2003).  A little overkill is needed once in awhile, a quadruple jolt of caffeine to make the Darwinists wake up and smell the coffee.  Almost none of these papers even mention evolution, and the ones that do only assume it: e.g., Myosin VI “might have evolved to provide unique kinetic characteristics that are potentially important for a reverse-directed motor.”  Do they really expect anyone to believe that any more?
        The papers are filled, on the other hand, with design language: motors, machines, mechanisms, coordinated action, synergy, regulators, signaling, strategies and much more.  This illustrates how useless Darwinism is; with apologies to Dobzhansky, nothing in biology makes sense in the light of evolution.  Intelligent design, by contrast – whether explicit or implicit – yields profound insights.  Let ID be the golden cord to show us the way out of the dark labyrinth where Charlie misled us long ago into the lair of the Minotaur, naturalism.
    Next headline on:  Cell BiologyGeneticsIntelligent DesignAmazing Stories
    NAS Enters the Evolution Web Wars    06/13/2005  
    MSNBC News reports that “Scientists take evolution fight online: National Academies sets up Web site to defend theory.”  (See also Wired News.)  The Evolution Resources website of the National Academy of Sciences,, contains online books and articles, but the most recent entry is an address by outgoing NAS president Bruce Alberts (see 03/24/2005 entry) seeking to rally academy members to fight the advance of creationism and intelligent design:
    We stand ready to help others in addressing the increasingly strident attempts to limit the teaching of evolution or to introduce non-scientific “alternatives” into science courses and curricula.  If this controversy arrives at your doorstep, I hope that you will both alert us to the specific issues in your state or school district and be willing to use your position and prestige as a member of the NAS in helping us to work locally.   (Emphasis in original.)
    The most recent technical report offered is a teacher’s guide to using evidences of microevolution in the Hawaiian Islands as a case study in evolution and the nature of science.
        The MSNBC article written by Reuters quotes only pro-evolutionary sources.  It misrepresents the goals of anti-evolutionists, saying bluntly that “some U.S. religious groups want to be taught in schools only if their own views of a divine creator get equal credence.”  It also calls alternatives “non-scientifically based,” and quotes the NAS saying, “The theory of evolution is one of science’s most robust theories, and the National Academies have long supported the position that evolution be taught as a central element in any science education program.”  The article also carries a link to the staunchly anti-creationist NCSE (National Center for Science Education).
    Bruce Alberts is like the out-of-touch king in the Wizard of Id cartoon.  A frantic messenger runs into the castle, breathlessly shouting, “The peasants are revolting!”  Unalarmed and undeterred, the king responds, “They certainly are.”
        So he sends out his PR Philistines to mop up the rebels.  Some of his advisors know not to underestimate the field (see 02/27/2004 entry).  The NAS Goliath can boast, but he had better be a match for stones of evidence.  Observing the Philistine ranks, Brad Harrub at Apologetics Press smells fear in the air.
        The new NAS website, with all the charm of a bureaucratic office building, may please academia but will probably backfire with the public.  In the first place, its publications are old.  It is still touting its very one-sided 1999 report Science and Creationism with all its fallacies and obfuscations.  It even advertises a 1990 report “The Search for Life’s Origins,” when much of the interesting biochemistry, and much of the contradiction to evolutionary assumptions, is more recent (see 02/06/2005 and 01/28/2005 entries).  Secondly, the website is completely one-sided, offering no debate.  Nowhere are evolution critics allowed to present their case in their own words.  Readers are expected to hear all the terms of the controversy spun by the Darwin Party hacks, complete with the usual straw man, equivocation, bandwagon, extrapolation and false dichotomy fallacies.*
        If the NAS won’t stand up to the debate plate and answer the critics instead of disqualifying them out of court, this website is going to be perceived as nothing more than a power play, and will get no respect outside the Party Faithful.  There are too many people out there who will no longer take bluffing and evasion for an answer.  Yet bluffing and evasion appears to be official NAS policy.  Quote: “Given the organizational skills, experience, and political astuteness of those who promote creationism and Intelligent Design, it is suggested that you NOT agree to enter into direct debates with the proponents if you have not been involved with such activities before” (“Teaching the Science of Evolution”).  The very next sentence says, “Cell and molecular biologists have provided some of the most compelling evidence to support the theory of evolution and should therefore be among those who raise their voices the loudest to support science curricula that help students understand the processes of evolution.”  Ha!  In a day of molecular motors and machines, that is astonishing (see 05/18/2005, 05/17/2005, 04/04/2005, 03/14/2005 and 04/30/2005 entries for recent examples).  Does this paper provide any of said evidence?  Dead silence.  If these two quotes do not illustrate bluffing and evasion, let them come clean and show us how the process of science is served by avoiding debate and making sweeping, unsupported generalizations contrary to the evidence.
        Most anti-evolution websites freely quote the very best Darwinists and critique their original sources; Creation-Evolution Headlines, for instance, frequently provides extended quotes, in context, on both sides.  Why won’t the Darwinists do better than caricature their opposition?  Anti-evolution websites are mushrooming because people are tired of Darwinian dogmatism.  We’re waiting, NAS: we want to hear the latest Tinker Bell Tale about the origin of life, the origin of complex language translation and error correction by chance, the origin of molecular machines without an engineer, and the explosion of body plans in the fossil record.  That will at least make your new website entertaining.
    Next headline on:  DarwinismEducation

    Straw man: caricaturing the opposition as religious kooks, even when they have PhDs in science.
    Equivocation: defining science as naturalism; defining evolution as change; winning the debate by definition.
    Bandwagon: claiming that all scientists accept evolution (see also Big Lie).
    Extrapolation: assuming that because we observe microevolution, complete molecules-to-man Darwinism is established.
    False dichotomy: compartmentalizing science and religion as non-overlapping domains, yet treating evolution as if it answers the big questions of religion/philosophy.
    Enzymes Chew Like Pac-Man    06/10/2005  
    Evidence is growing that many enzymes have moving parts.  They act like scissors, clamps and little pac-mans.  When precisely-folded chains of amino acids emerge from the ribosome, they fold into unique shapes with the aid of chaperones.  But those shapes are not static globs.  They move, say Dmitry A. Kondrashov and George N. Phillips, Jr. (U. of Wisconsin).  Writing in Structure,1 they describe some of the “molecular mastication mechanics” of these amazing machines:
    Computational prediction of global protein motion... suggests that enzymatic active sites tend to be placed near the hinges of the “jaws” of enzyme structures.
        Proteins self-organize into exquisitely precise structures, but the actual conformation of a protein fluctuates, and almost never coincides exactly with the average structure observed via X-ray crystallography or other methods.  Mounting evidence suggests that these induced motions play specific and essential roles in protein function....
      (Emphasis added in all quotes.)
    Proteins are so tiny, the motions are very hard to observe.  The authors describe the various techniques that try to shed light on “the central question: do these motions contribute to enzyme function?”  It appears they do:
    Stabilization of the transition state relative to the substrate is thought to be the key to enzymatic efficiencyStatic effects clearly play a major part via the electrostatic contribution of the positioning of polar residues.  The existence of a “dynamic effect,” however, is controversial, specifically the proposition that enzymes can channel thermal vibrational energy into modes co-directional with the reaction coordinate, thus making barrier crossing more likely.  Nevertheless, evidence is accreting to indicate a link between well-defined global motions and catalysis.
    After the technical jargon, they lighten up and explain this for the rest of us with some everyday comparisons: 
    Computation of the normal modes of motion allowed the determination of the “hinges” or pivot points that separate regions of the protein moving in opposite directions, much like the end of a nutcracker.  In the vast majority of the enzymes studied, the catalytic residues were found to be located in a predicted hinge region.... This finding contributes a bioinformatic dimension to the field of functional protein dynamics and may allow improved functional annotation for the flood of newly solved protein structures.  The results also suggest an enhanced role for the global protein structure, which often has been viewed as a scaffold supporting the active site.  The study adds to the growing body of evidence that the fold determines global protein dynamics, suggesting a mechanism for allosteric signal transduction, functional impact of distant mutations, and other effects not explained by the chemistry of the active site.  In this view, enzymatic structures resemble a Pac-Man icon, with active sites located in the wedge-shaped opening, and the structure responsible for the “chewing” motion of the “mouth.”
    What this means is that the whole protein – all the amino acids, even those distant from the active site, are involved.  It is possible that they contribute to orienting the substrate into the active site and stabilizing it once it makes contact, like a vise grip.  Moving parts might also contribute to the release of the substrate after catalysis is complete.  The structure might strip off solvents before the substrate reaches the active site, resulting in more efficient catalysis.  Even short fragments distant from the hinge might contribute an essential part of the overall function.
        Viewing enzymes as dynamic machines opens up new avenues for investigation, they envision.  The specific sequences in all the parts of the enzyme would require closer scrutiny; they might have moving parts as well.  At least, it is an idea to chew on, they conclude; “The relative importance of topology and sequence for protein dynamics and function needs to be investigated, in order to add more teeth to the masticating view of enzyme dynamics.”
    1Dmitry A. Kondrashov and George N. Phillips, Jr, “Molecular Mastication Mechanics,” Structure, Volume 13, Issue 6, June 2005, pages 836-837, doi:10.1016/j.str.2005.05.004.
    Wonderful thoughts, devoid of evolutionary speculation.  Enzymes can no longer be viewed as floating wads of amino acid gunk, and not even as rigid tools like screwdrivers and hammers.  Now, we see them as power tools: “exquisitely precise structures” with moving parts, each part contributing to the task at hand.  This means that enzymes cannot tolerate many mutations.  Previously, biochemists thought that the active site alone was the most intolerant of mutations, but if this emerging picture of dynamic action is correct, even short sequences of amino acids distant from the active site may play vital roles in the overall function.  The game is not getting any easier for the Darwinists as Pac-Man keeps chewing through their assumptions.
    Next headline on:  Cell BiologyAmazing Stories
    Is It Justifiable to Speculate About the Evolution of Murder?    06/10/2005  
    Sharon Begley, writing in the Wall Street Journal May 20, was pretty angry that an evolutionary psychologist tried to give an evolutionary explanation for why men murder women.  She called the theory by Dr. David Buss (U. of Texas, Austin) a just-so story and bad science.  In his book, “The Murderer Next Door: Why the Mind Is Designed to Kill,” Buss had portrayed murder of women as an adaptive strategy for some males to leave more offspring than competitors.  Not only is this theory “offensive and wrong,” Begley charged, it it is a ludicrous idea – even in evolutionary terms:
    As evolutionary theory, this is ludicrous.  Killing the owner of the uterus that is your only current chance to get your genes into the next generation (the evolutionary imperative), especially if she is caring for your current children and has a father or brothers who take exception to your uxoricide, is an excellent way to a dead end personally and genealogically.  Being the target of angry in-laws, not to mention life imprisonment or lethal injection, tends to limit one’s reproductive opportunities.   (Emphasis added in all quotes.)
    Why would this adaptation, she continues, work only in humans but not other species?  She quotes Jaak Panksepp, who counters, “Only a few species [like insects] kill their mating partners, and the killing is usually done by females.”  He called the ideas of Buss “ugly evolutionary icing with no basis.”  Begley ends by discounting the scientific objectivity of such storytelling:
    The claim that works like “Murderer Next Door” are merely following data objectively in a search for truth is getting tiresomeThe very decision to seek a “scientific” validation for killing women represents a value judgment.  The fact that the claim makes no sense scientifically is almost secondary to that.
    And now, the rebuttal.  Dr. Buss wrote back in an attempt to justify his position scientifically.  He was “dismayed” to see Begley’s “sarcastic, emotional and misleading depiction” of his theory, saying the issue “demands sober scientific analysis.”  Attributing murder to “poverty, pathology, exposure to media violence, poor parenting” cannot explain its predictability in certain circumstances, he said.  By comparison, he claimed, “My book presents the most comprehensive and scientifically cogent theory of why people kill, anchored in evolutionary psychology.”  In addition, “The book’s theory is based on sound evolutionary biology, anchored in the clear logic of reproductive competition,” he continued.
        He continued by arguing that the only way to deal with murder was to understand its evolutionary basis:
    The unfortunate fact is that murder has proved to be a disturbingly effective solution to an array of adaptive problems in the ruthless evolutionary games of survival and reproductive competition.  It’s undoubtedly deeply disturbing to think that humans have homicidal circuits that get activated in certain circumstances, but that in no way implies approval or justification of murder.  Nor does it imply that murder is inevitable.  Rather, knowledge of the deep psychology of killing is required if we ever hope to prevent it.  Those who attempt to avoid this deep understanding by strident emotional appeals and cartoonish ridicule tread on dangerous moral ground.  The problem of murder can’t be solved by wishing away dark sides of human nature that we would prefer not exist.
    This high-visibility debate in the Wall Street Journal seems destined to sharpen the acrimony between those evolutionists and non-evolutionists over the question whether evolutionary psychology has any scientific validity.
    “Anchored in evolutionary psychology” he says?  Ha.  That’s like a paper anchor in soft silt.  “Sound evolutionary biology” is an oxymoron.
        Buss’s theory is self refuting.  As an evolutionist, he cannot appeal to morality, yet look: he uses the words unfortunate, ruthless, disturbing, approval, justification, moral ground, dark sides of human nature, prefer and solved.  Each of these words rest on the assumption that we can make moral judgments between good and evil, right and wrong, and that murder is a moral problem needing a solution.  Why should murder be labeled “disturbing” or “dark” or a problem at all if it is a successful adaptive strategy?  Why, we should applaud the murderer for his evolutionary success.  Yet Dr. Buss says that it is his critics that are on dangerous “moral” ground for not comprehending his deeper understanding!  That shows how deep his understanding goes.
        Evolutionary psychologists are the gnostic gurus of naturalistic religion.  Who is Dr. Buss to offer us “knowledge” or “deep understanding” if it means that murder is hardwired into our circuits?  How is he to prove that just-so storytelling is not hardwired into his own circuits?  If we are the product of circuits that get activated by the environment, then knowledge and understanding do not even exist, and there are no problems to solve.  If people react to such foolishness with strident emotional appeals and cartoonish ridicule, well, if the shoe fits....
        Christianity teaches that murder is evil, that it is a consequence of the disobedience and rebellion against our Maker.  The Bible teaches that we are responsible to God for our actions.  Out of selfishness and lust and anger, murderers violate their conscience and act on their dark side of human nature.  Unredeemed human nature that leads to lying and murder really is dark, because it follows the lead of Satan, who was a murderer from the beginning.  All sin, including murder, incurs the righteous judgment of God, because we are each accountable for our deeds.  Evolutionary psychology gurus, on the other hand, claim that selfishness and ruthlessness are amoral, and ultimately good, because they are intrinsic factors in the mindless processes that produced our minds in the first place.  Choose you this day whom you will serve.
    Next headline on:  DarwinismDumb Stories
    Roses Are Red, Darwinists Are Blue   06/09/2005  
    Roses have a special pigment molecule, a particular form of anthocyanin, responsible for all the rich red-to-blue shades in the petals that delight gardeners and attract pollinating insects.  This molecule is different from the pigments in every other flowering plant; it is glycosylated at two positions instead of one.2  A single enzyme does the job at both points.  Without the glycosylation reaction at both ends, the molecule is unstable and cannot be soluble in water in the vacuoles of the cells in which it operates.
        A team of Japanese scientists investigated how this double-glycosylation reaction system might have evolved.  They could find no intermediate.  Reporting in Nature,1 they said that while other flowers use derivatives from a singly-glycosylated form, “this is evolutionarily precluded in roses by their different glycosylation pattern, which may be unique to members of the Rosaceae” (emphasis added in all quotes).  They also stated with puzzlement,
    It is a mystery why this particular glycosyltransferase evolved independently in roses.  The novelty of the RhGT1 enzyme therefore lies not only in its ability to catalyse glycosylation at two different sites on the anthocyanidin molecule but also in its apparent absence from other species.
    They prepared a phylogenetic tree based on this type of pigment-preparing enzyme family, but it ended up with the rose family on a branch all by itself.
    1Ogata et al., “Plant biochemistry: Anthocyanin biosynthesis in roses,” Nature, 435, 757-758 (9 June 2005) | doi: 10.1038/nature435757a.
    2Glycosylation replaces an OH (hydroxyl) group with a glucoside.  This is performed by an enzyme called a glycosyltransferase, in the case of roses, RhGT1.
    Here is a small gap, but a gap nonetheless; no evidence for the evolution of this complex molecule and the enzyme that knows how to operate it – just an unconfirmed prediction from evolutionary theory.  Surprised?  Question: was evolutionary theory of any value in this investigation?
    Next headline on:  BotanyEvolution
    Ice Volcano Seen on Titan    06/09/2005  
    Planetary scientists are reporting the possible discovery of an ice volcano on Saturn’s large moon Titan.  A large circular feature, 18 miles across, appears to have a caldera at the top, is surrounded by stress fractures, and appears warmer than the surroundings (warmer, relatively speaking: the mean surface temperature is -290° F).  The infrared pictures are somewhat indistinct due to the smoggy haze that obstructs views of the surface.
        The discovery, announced in Nature,1,2 might explain the origin of the methane observed in Titan’s atmosphere.  The paper states that “a widespread methane ocean does not exist” on the surface.  Instead, cryovolcanism might provide a mechanism that could resupply the methane from below.  See also press releases from the Cassini website, JPL and the BBCNews@Nature remarks that scientists were disappointed to find that Titan is as dry as a bone.
    1Louise Prokter, “Planetary science: Shades of Titan,” Nature 435, 749-750 (9 June 2005) | doi: 10.1038/435749a.
    2Sotin et al., “Release of volatiles from a possible cryovolcano from near-infrared imaging of Titan,” Nature 435, 786-789 (9 June 2005) | doi: 10.1038/nature03596.
    The lack of oceans of ethane and methane was a huge disappointment and surprise to planetary scientists.  They know that atmospheric methane is destroyed by the solar wind in short order – 100 million years as an upper limit (that’s only 1/45 the assumed age of Titan).  But they also expected the photolysis of methane to lead to the accumulation of hydrocarbons on the surface in the form of huge deposits of liquids.
        Another surprise is the rarity of impact craters.  What keeps the methane supplied, and what keeps the surface smoothed over for long ages, are now major puzzles for those accustomed to thinking in terms of billions of years.  Trying to get all that methane out of one volcano seems a stretch.  Even with hundreds of such vents, how long could that continue?
        The thought of a volcano erupting ice onto the surface of an alien moon, though, is pretty cool.
    Next headline on:  GeologyPlanetary Science
    Scientists Confess Their Sins    06/09/2005  
    One-third of scientists engaged in unethical behavior over the last three years, according to a report in Nature.1,2  These include falsification, fabrication and plagiarism as well as a host of questionable research practices.  It’s not so much a problem of high-profile cases of fraud as much as everyday, mundane, “corrosive” ethical lapses that are endangering the integrity of science.  See also the summary on MSNBC News
    1Meredith Wadman, “One in three scientists confesses to having sinned,” Nature 435, 718-719 (9 June 2005) | doi: 10.1038/435718b.
    2Martinson et al., “Scientists behaving badly,” Nature 435, 737-738 (9 June 2005) | doi: 10.1038/435737a.
    Hypocrites in the church of Darwin?  Would you trust this gang with your soul?
    Next headline on:  Politics and Ethics
    Smithsonian Reversal Over ID Noticed by Big Science    06/09/2005  
    Both Nature1 and Science2 noticed the Smithsonian’s flip-flop over co-sponsoring The Privileged Planet at their Natural History Museum this month (see 06/01/2005 entry).  Both noted the quandary that the Smithsonian found itself in.  They could not back out because of a contract, but under pressure from evolutionists, did not want to appear to endorse intelligent design.  This led them to return the $16,000 fee so that they would not appear to be cooperating with the Discovery Institute, and to remove their co-sponsorship while allowing the event to go forward.
        Nature noted that email from “researchers and the public” prompted the backtracking, titling its news item, “Evolution row makes museum ditch donation” (even though the film is not about evolution).  Science said the Smithsonian’s compromise, permitting the film to be shown privately but without their co-sponsorship or taking a fee, allowed the Institution to avoid the appearance of endorsing the film on the one hand, while on the other avoiding giving the “Discovery Institute yet another martyrdom story.”
        Both articles agreed that Discovery Institute had done nothing wrong in scheduling the film.  It was a routine procedure they followed.  Science said that museum spokesperson gave the film a clean review, even though museum policies “preclude events with a religious, political, or commercial message.”  A second review, after the hubbub, also concluded that “the film fell within the museum’s guidelines for such events.”  Their basis for claiming the film violated their scientific research policy was explained by anthropologist Richard Potts, chair of the museum’s human origins program:
    But it was very clear that the film was trying to situate science within the wider realm of belief.  The idea that human beings have been placed on Earth to discover the principles of the universe is not a position that stems from science; it is a metaphysical and religiously based conclusion.   (Emphasis added in all quotes.)
    The Smithsonian frequently accepts donations for use of their auditorium.  After the complaints by evolutionists, however, the Smithsonian is reviewing its policies to avoid confusion in the future.
    Update 06/24/2005: The event apparently went off smoothly without acrimony or dissent; here is an eyewitness report from Salvador Cordova.
    1Geoff Brumfiel, “Evolutionist row makes museum ditch donation,” Nature 435, 725 (9 June 2005) | doi: 10.1038/435725a.
    2Yudhijit Bhattacharjee, “Smithsonian Gives Grudging OK to Film Backing ID Argument,” Science, Vol 308, Issue 5728, 1526, 10 June 2005, [DOI: 10.1126/science.308.5728.1526a].
    This was clearly an episode about power politics, not science.  Notice how the film passed two reviews that agreed there was no problem with the science; the museum backpedaled only because of the noise from barking Darwin bulldogs, most of whom have probably not even seen the film.  And what a weak excuse; it’s not that the film said anything outrageous, but rather that the Darwinistas don’t want to grant any credibility to the source.  That’s the genetic fallacy – can any good thing come out of Nazareth?  Well, come and see.
        Potts’ pot shot about the film putting the evidence into a metaphysical/religious context is absurd.  As an anthropologist studying evolutionary human origins, has he no metaphysics?  Of course he does: look at his chairing a series of lectures on “Science, Ethics and Religion” (in terms of human evolution, of course) for the AAAS recently; another example on National Geographic News shows him speculating about the evolution of modern human behavior (notice the absence of evidence).  Are these kinds of metaphysical dialogues forbidden by the Smithsonian?  Of course not.  Evolutionists shamelessly pontificate about the metaphysical/religious implications of their beliefs, right in the halls of science and before the mass media.
        For the Smithsonian to be consistent, they would have to outlaw films like Cosmos, Origins (09/29/2004) and Evolution (09/28/2001) and other pro-Darwinist films, which are replete with religious and metaphysical claims.  The inferences drawn in The Privileged Planet are understated and balanced, many of them coming from astronomers and biologists with no connections to ID.  They speak their own minds based on the evidence, something about which the Darwinians are profoundly silent.  In Darwinian movies, by contrast, the metaphysics are dogmatic and polemical, often imagineered with reckless abandon with no opportunity for rebuttal.  In sweeping generalities, Darwinians preach their philosophy of big-bang to man-as-god in homilies that would make a pope blush.  They take an inch of irrelevant fact and spin a mile with imagination, delivering their sermon outlines to animators to fill in the gaps.
        Like most institutions of Big Science, the Smithsonian has become a fundamentalist church of atheism (see next entry).  Despite the increase in its lavish facilities, it has degenerated so far from the philosophy of its first distinguished secretary, Joseph Henry, it is truly sad to see how it has been co-opted by leftist anti-religious propaganda.  Chief of the Darwinian KGB Eugenie Scott was “pleased by the swift steps the museum has taken” while other Party Faithful were even more aggressive, wanting the film canceled until they feared it would make martyrs of their political prisoners.
        As long as the news media and reporters perpetuate the false dichotomy and equivocation of “science” (Darwinian metaphysics) vs “belief” (non-Darwinian metaphysics), this pathetic war of heat will continue.  The Darwinians, the “most objectionable” fundamentalists according to Paul Johnson (see next entry), had better learn how to debate the evidence when the day comes that they can no longer take for granted their power to dominate the scientific institutions and prevent alternatives from being heard.
    Next headline on:  Intelligent DesignMedia
    Historian Predicts Downfall of Darwinian Fundamentalism    06/08/2005  
    In the upcoming June 20 issue of Forbes magazine, British historian Paul Johnson attacks the fundamentalism of Darwinists, and predicts its demise:
    Of all the fundamentalist groups at large in the world today, the Darwinians seem to me the most objectionable.  They are just as strident and closed to argument as Christian or Muslim fundamentalists, but unlike those two groups the Darwinians enjoy intellectual respectability.
        Darwinians and their allies dominate the scientific establishments of the West.  They rule the campus.  Their militant brand of atheism makes them natural allies of the philosophical atheists who control most college philosophy faculties.  They dominate the leading scientific magazines and prevent their critics and opponents from getting a hearing, and they secure the best slots on TV.  Yet the Darwinian brand of evolution is becoming increasingly vulnerable as the progress of science reveals its weaknesses.  One day, perhaps soon, it will collapse in ruins.
      (Emphasis added in all quotes.)
    The entire article has been reprinted by the Discovery Institute.
    For all his worthy tirade against the Darwinists, Johnson seems to accept the big bang theory and cosmic time with uncritical gullibility.  Then he adopts a front-loading design philosophy, misreading Newton as having taught an impersonal Force.  Then, apparently after assuming the front-loaded design produced human beings, he inserts a divine intervention at the origin of language.  These strange thoughts diminish an otherwise interesting prophecy about the fall of Darwinism.
        Johnson also seems to know little about fundamentalism other than the yellow-journalism stereotype.  He defines it as stridency and closed-mindedness.  That is not what the term meant when Christian scholars like J. Gresham Machen used the word.  They were identifying what Biblical doctrines, what “fundamentals,” could not be compromised without cutting into the flesh of Christianity.  Would Johnson walk into many “fundamentalist” Christian churches today, he would see the opposite of stridency and closed-mindedness.  He would not see the image of Muslims toting AK47s and burning flags, screaming death to America.  He would not see the image of Darwinians censoring any opposition.  He would likely see humble and joyful people, singing praises to God, welcoming the stranger and asking, “How can I pray for you?”
    Next headline on:  Darwinism
    The Cause of a Teapot: Can Physics Explain Design?    06/08/2005  
    George F. R. Ellis (U. of Cape Town) wrote a Concepts piece in Nature1 this week that asks fundamental questions about ordinary things, particularly, can we get from fundamental physics to complex hierarchical structures through a chain of cause and effect?
    A simple statement of fact: there is no physics theory that explains the nature of, or even the existence of, football matches, teapots, or jumbo-jet aircraft.  The human mind is physically based, but there is no hope whatever of predicting the behaviour it controls from the underlying physical laws.  Even if we had a satisfactory fundamental physics ‘theory of everything”, this situation would remain unchanged: physics would still fail to explain the outcomes of human purpose, and so would provide an incomplete description of the real world around us.   (Emphasis added in all quotes.)
    But Ellis does not end on that depressing note.  Admitting that meaning, though inexplicable from fundamental physics, did come into being, he claims that physics can illuminate the cause-effect structure of the universe.  It does so by creating a playing field where emergent properties like human intelligence can create their own cause-effect realities.  In the right context, he claims, higher levels of order can emerge and become autonomous:
    It is possible that what actually happened was the contextual emergence of complexity: the existence of human beings and their creations was not uniquely implied by the initial data in the early Universe; rather the underlying physics together with that initial data created a context that made the existence of human beings possible.  Conditions at the time of the decoupling of matter and radiation 14 billion years ago were such as to lead to the eventual development of minds that are autonomously effective.  Such minds are able to create higher-level order, such as the Hubble Space Telescope and Kurt Gödel’s incompleteness theorem, that embodies a purpose and meaning not in existence before.
        With this view, the higher levels in the hierarchy of complexity have autonomous causal powers that are functionally independent of lower-level processes.
    He admits that a key to making this work is the ability to store information, yet he fails to define the term:
    Stored information plays a key role, resulting in non-linear dynamics that are non-local in space and time.  Brain functioning is causally affected by abstractions, such as the value of money, the rules of chess and the theory of the laser.  These abstractions are realized as brain states in individuals, but are not equivalent to themJames Clerk Maxwell’s theory of electromagnetism is not the same as any individual’s brain state.  Although such concepts are causally effective [i.e., they can lead an electrical engineer to apply them to an invention], they are not themselves physical variables.  Consequently physics per se cannot causally determine the outcome of human creativity; rather it creates the ‘possibility space’ to allow human intelligence to function autonomously.
    Even beaver dam building and the dances of honeybees, he says, might have emerged late late in the expanding Universe, “made possible but not causally determined by the underlying physics and chemistry of matter.”  To figure out how the hierarchy of complex structures can arise is the challenge of physics, he says: i.e., how “top-down causation and memory effects allow autonomous higher levels of order to emerge with genuine causal powers” of their own.  The meager attempts to do this with complexity theory, chaos theory and the like only take us “a small step on this road.”
        A photo of a teapot adorns his article.  The caption reads, “Intelligent design: no physics theory is able to explain a teapot.”  Lest one think he would dare give aid and comfort to the Intelligent Design movement, he makes it clear which side he is on: “Darwinian processes of selection,” he asserts, “guided the physical development of living systems, including the human brain.”
    1George F. R. Ellis, “Physics, complexity and causality,” Nature 435, 743 (9 June 2005) | doi: 10.1038/435743a.
    Well, this goes to show that the debate over freewill and determinism is not argued only between theologians.  Ellis has just charmingly bluffed his way past a major logical gap in naturalism: why there is something instead of nothing, and especially why there is such astonishing complexity as in a human brain instead of nothing.  His answer: you can get something from nothing!  First, the particles emerge out of nothing.  Then, they create a possibility space out of which complexity “emerges” and takes over, becoming a new, autonomous entity, like a human mind, that can engender new levels of autonomy.  This is the old tornado-in-a-junkyard theory of the 747.  The junkyard is now to be understood as the “possibility space” of the jumbo jet.
        They just love that word emergence.  It’s the miracle word that produces any phenomenon needing explanation, from nothing.  Granting a little memory that can store information helps.  Presumably, that just emerges, too.  Can anyone demonstrate an actual new cause-and-effect space emerging from one below it and becoming autonomous?  Read Dembski’s No Free Lunch to see that it cannot be done; claims of emergence are exposed when perpetrators are seen sneaking information into the side door.
        The major flaw in this line of reasoning is to assume that possibilities yield probabilities and these, in turn, actualities – given enough time.  Like George Wald once blathered to his everlasting shame, “Time is in fact the hero of the plot.  The impossible becomes possible, the possible probable, and the probable virtually certain.  One only has to wait – time itself performs the miracles.”  No gambling addict could have more faith.  There is simply not enough time to expect the unguided emergence of just one protein molecule under the best of conditions (see online book), let alone the emergence of the simplest memory storage and retrieval system, whether in a beaver, bee, or Berkeley, to allow the hierarchy of autonomy to proceed onward and upward.
        Non-existence is extremely more likely than existence – yet here we are.  We do not need to just explain what might be, but what is.  One cannot bootstrap nothing into something.  That is equivalent to belief in magic.  The worldview that explains the something, including all the complexity of the human mind, its autonomy and its degeneration into nonsense and evil, is Christian theism.  Emergence must always be downward: the Lawgiver into the realm of law, the Creator into the realm of the created.  Which view is more in accord with physics as we observe it?  Maxwell has a lot more than electromagnetic theory to say about that.
        Out of nothing, nothing comes.  Whatever begins to exist has a cause.  If you can keep your head when all around you are losing theirs and blaming it on chance, the Universe is yours and all that’s in it, and what’s more, you’ll be a Mansoul, my son.
    Next headline on:  CosmologyPhysics
    Understanding the Sun – Not    06/07/2005  
    Exclusive  The star we understand best should be the closest – our own – right?  Despite a revolution in solar observations, there is much we don’t know about Ol' Sol.  That was the flavor of a talk by Dr. Alan Title (Stanford) at the Jet Propulsion Laboratory on Monday.  At one point, he showed a picture of magnetic loops extending far from the solar surface without dissipating, and growing and combining from small to large scales, and remarked, “Anybody familiar with basic E&M [electromagnetic theory] knows that that is impossible.”  Other mysteries involve the rotation of the convecting layer, lack of symmetry between the poles, and even the origin of the magnetic field.  The bottom line was that we have more questions than answers over the last decade.
        In the Q&A, someone asked if lessons learned from solar astrophysics are getting to the stellar astronomers.  The answer was a qualified yes.  It could be better but is fairly good, he said; but if we can’t understand convection in our own star, that’s a warning and a challenge to postulating about the fluid mechanics of other stars.
        Another question was whether we still learn anything useful from solar eclipses.  Yes, he said (although the discoveries tend to be more fun these days).  We can put coronagraphs in orbit, but they are hard to keep steady.  “The moon is a very good occulting disk,” he said.
    A point well taken: if we cannot understand a star that looms large in our sky and is up all day, how much can we express confidence in our theories about points of light trillions of miles away?  To gain more appreciation of our sun, and our occulting moon, see the film The Privileged Planet.
    Next headline on:  Solar SystemStars and Astronomy
    Darwin Is Alive and Well at Down House    06/07/2005  
    Chris Darwin, that is – the great, great grandson of Charles, and his fellow descendants Erasmus, Sarah, Allegra, Randal Keynes, and Leo Darwin Vogel.  The family members are retracing his footsteps in the fields around his old house by inventorying the plants, reports the BBC News.  The survey will help show if the flowering plants have evolved over the last 150 years.
    Update 06/16/2005: Chris Darwin described for the BBC two trips he took to the Galápagos islands to retrace the footsteps of his famous great great grandfather.  Chris chuckled that he must not have his predecessor’s genes, because he failed basic biology class.
    Nice activity, surveying plants, but what’s evolution got to do with it?  This experiment continues the misperception that looking at microevolution will somehow demonstrate that bacteria can evolve into humans, given enough time, and enough small, incremental changes (see next entry and 08/20/2003 entry).  Charlie’s botanizing, though amateurish, was commendable; his storytelling was not.
    Next headline on:  Darwinism and Evolutionary TheoryBotany
    Another Darwinian Assumption Overturned: Results “Too Radical”    06/07/2005  
    Evolutionists are stunned at a study in comparative genomics performed by University of Chicago researchers that overturns a common belief about natural selection.  EurekAlert summarizes the finding: “The new data show that if more mutations show up at a gene, that gene tends to accept a higher percentage of those mutations.”  This means that mutations accepted into a genome are not strictly a function of natural selection, but of mutation rate.
        Mutations accepted into a gene can be synonymous or non-synonymous.  Synonymous mutations (Ks) swap an amino acid with a similar one, such that the protein can still function.  Non-synonymous mutations (Ka) change the shape of the protein and thereby can be acted on by natural selection.  Scientists have assumed that the percentage of non-synonymous mutations accepted during evolution remains constant.  Bruce Lahn, author of the paper in Trends in Genetics, commented on the assumption: “This theory has been the workhorse of molecular evolution.  Thousands of scientific papers have been published based directly or indirectly on this notion.”  The new study shows, instead, that “the faster the speed of new mutations, the greater the percentage of those mutations accepted.”
        Several statements in the press release make this finding sound revolutionary:
    • “We’ve discovered a striking phenomenon that challenges a paradigm of molecular evolution that has been around for several decades,” said lead author Bruce Lahn, Ph.D., assistant professor of genetics at the University of Chicago and Howard Hughes Medical Institute investigator.  “As such, it may cause a significant shift in the field.”
    • Lahn cannot explain the mechanism of his findings and expects many will question this novel finding.  “It’s too radical,” he said.  “People just don’t want to believe it, but the data are there.”
    • “Lahn and his associates have found a most striking result, one that is totally unexpected,” said geneticist James Crow, professor emeritus of genetics and zoology at the University of Wisconsin-Madison.
    • Sudhir Kumar, an associate professor of molecular evolution at Arizona State University, agreed.  “It goes against strict theory, but evolutionary biologists know that nothing’s clean cut.  There’s always distortion because we’re looking at longtime history.
      (Emphasis added in all quotes.) What this means is up in the air.  James Crow ended with a look to the future: “I hope that further work will provide an explanation of what now is a major puzzle.”
    What if a flood of mutations struck in a short period?  Could it account for a wide range of mutational changes in the relatively recent past?  How would they know?  This result appears to undercut any remaining trust in the molecular clock, a device that was broken anyway (see 08/24/2004 entry).
        Kumar hit the nail on the head: evolutionary theory is never clean cut, and is always subject to distortion.  If evolutionists are trying to look at longtime history, good luck – because history cannot be put into a test tube.  Trying to decipher history from present observations of genes and proteins is messy business, subject to numerous assumptions that can be overthrown, such as this one.  Kumar said “The novelty of this work is that he [Lahn] used a large amount of data.”  What does this tell you about the evolutionary assumptions built on far less data?
      The Darwinists are certainly not throwing in the towel over this latest genetic earthquake.  It just illustrates that assumptions in science, trusted for decades, yielding thousands of scientific papers, can be flat wrong.
    Next headline on:  Darwinism and Evolutionary TheoryGenetics and DNA
    Evangelical Christians Split on How to Handle Evolution   06/03/2005  
    A dismal picture of controversy dividing Christian brother against brother, with no resolution in sight, is painted by Paul Nussbaum in the Philadelphia Inquirer.  He says evangelical Christians are not monolithic in their opposition to evolution, but as divided as much of the rest of the nation.  He quotes a spokesperson for the American Scientific Affiliation, a group of scientists who lean toward theistic evolution and old-earth creationism, saying:
    No topic in the world of science and Christianity has created the intensity of discussion and disharmony with evangelicals as the source of biological diversity.  Today’s spirited discussion often pits Christian vs. Christian and scientist vs. scientist.   (Emphasis added in all quotes.)
    The article touches on some of the approaches for integrating Christian faith and evolution, including young-earth creationism, intelligent design, theistic evolution, and the view that science and religion represent non-overlapping realms of truth.
        One evangelical certainly not conflicted over evolution is Lee Strobel, former atheist and now host of Faith Under Fire and author of The Case for a Creator.  Interviewed by Christianity Today, Strobel argues that no compromise is necessary; science backs up faith. 
    Nussbaum allowed David Wilcox (Eastern U) to get away with a horrendous straw man argument.  Wilcox puts words into an imaginary student’s mouth when facing evolution in biology class: “Why do I have to learn this stuff – don’t you know that God hates science?”  Good grief.  Has anyone outside an insane asylum ever said that?  In response, Wilcox triumphantly touts theistic evolution as the winner with this half-truth: “God doesn’t hate science – he invented it.  We try to get them to see that evolution happened and it’s not so scary... that evolution is the way God did it.”  Well, if Nussbaum’s intent was to make this proponent of “evolutionary theism” make a fool of himself, he succeeded.  Runner-up was Ken Miller again with this borderline blasphemous straw man: “Their [the creationists'] God is like a kid who is not a very good mechanic and has to keep lifting the hood and tinkering with the engine.”  Who’s he kidding?  It’s the Darwinists who worship Tinker Bell (see 03/11/2005 commentary).
       Other than that, Nussbaum’s article is fairly balanced, though gloomy.  He seems to see the most light in the two compromise views that will never work, theistic evolution (an oxymoron) or non-overlapping domains (a false dichotomy).  The main flaw in the article is the covert treatment of evolution as science instead of religion.  That is the hidden assumption in much of secular reporting.  It must be exposed for what it is: a big lie.  Therapy requires mastering the Baloney Detector, then reading all the chain links on Darwinism and Evolutionary Theory in these pages.  Follow-up treatment can include digesting our online book.
        The evangelicals who are not gloomy and conflicted are the young-earth creationists and intelligent design people.  Most of them are vibrant, motivated, excited, passionate, interested, and devoted.  Maybe they’re onto something.  Read this, especially the first bullet item.
    Next headline on:  EvolutionTheology
    Who Wins and Loses in the Darwin Wars?   06/03/2005  
    Sandra Lilley, writing in MSNBC News, pictures sad-faced students, whose scientific inquisitiveness has been stifled by the controversy over evolution.  The article starts with a touching photo of a young girl, a look of wonder in her eyes, examining a toy human skeleton.  “Science is becoming a political ‘hot potato’ for some students,” she describes, “transforming what should be a dynamic, fascinating topic into a total turn-off” (emphasis added in all quotes).  “And some students are choosing silence over losing a prom date.”
        Lilley quotes only pro-evolution spokespersons (some nominal Christians) who express the opinion that the next generation of scientists is being threatened by creationists and politicians raising a ruckus over evolution, leaving students bewildered over a conflict they don’t understand, preferring to avoid the subject as a result.
        The only evidence offered for evolution in the article is from Ken Miller: “If a child becomes a pharmacist and someone develops a resistance to a drug, that is evolution,” he said.  Miller argues that society will be at a disadvantage if we don’t teach evolution, which he equates with basic science.
        A different point of view was offered by high school science teacher Doug Cowan (Port Orchard, Washington), writing for the Christian Science Monitor.  In his experience, he claims, students become stimulated over his non-sectarian “teach the controversy” approach. 
    I am a public high school biology teacher, and I do an unusual thing.  I teach my students more than they have to know about evolution.  I push them to behave like competent jurors – not just to swallow what some authority figure tells them to believe – not even me – but rather to critically analyze, with an open mind, the evidence set before them....
    Teenagers, not surprisingly, find this approach exhilarating.
      (Emphasis added in all quotes.)
    He finds that the students “perk up” when he points out that “contrary to their large and monolithic biology textbook, some highly credentialed scientists insist that there are limitations to Darwin's theory.”  When he displays some of the alleged evidences for evolution that have been found fraudulent (Piltdown Man, Haeckel’s embryos), “the sleepy looks in the classroom usually vanish.”
        Cowan, however, is not on an anti-evolution crusade.  He also lays out all the “reputable evidence for evolution,” the “pillars of evolutionary theory” such as bacterial resistance, finch beaks and genetically altered fruit flies, then challenges the class to reason whether these observed microevolutionary changes can be extrapolated into macroevolution.
        By maintaining a neutral stance, letting them examine all the evidence and make up their own minds, Cowan says his approach is on firm legal footing.  Students and parents alike seem to appreciate his method.  Students feel liberated to weigh the evidence for themselves.  “The job of the scientist, I explain, is to find the best explanation to a problem, not just to defend his or her own position at all costs.”  For support, he quotes Charles Darwin: “A fair result can be obtained only by fully stating and balancing the facts and arguments on both sides of each question.”
    Evolution can be taught skillfully and poorly.  Anti-evolution can be taught skillfully and poorly.  Reporting on either can be done skillfully or poorly.  Here are two examples for you to evaluate.
        No reputable anti-evolutionist wants students to become afraid of the controversy over evolution and become tempted to shut up.  No reputable pro-evolution teacher should want the class to be indoctrinated, nor have a student feel browbeaten for having honest questions about evolution.  Cowan seems to have hit the sweet spot.  Can anyone really doubt that learning to think critically is going to help the next generation of scientists?
        The only losers in the Darwin Wars, when fought fairly, are the indoctrinators who don’t want the students to know about Haeckel and Piltdown and the other dirty laundry in the textbook.  Watch the film Icons of Evolution, including the Q&A in the bonus features, for a fuller defense of the “teach the controversy” approach.  And teachers: feel free to use our eight-part, non-religious curriculum (see 02/11/2005 commentary) for supplementary material the textbook left out.  Watch those young eyes perk up....
    Next headline on:  EducationEvolution
    Soft T-Rex Tissue Claimed Bird-Like; Age Ignored   06/03/2005  
    More details about the soft tissue found in a T. rex thigh bone (see 03/24/2005 story) were published in Science this week.1  Mary Schweitzer’s team claims to have found evidence of medullary bone [MB], a type of mineralized and vascularized bony tissue found only in certain birds during ovulation as a buffer against calcium loss.  The abstract and summary posted in a press release from North Carolina State says it’s a girl, and she’s pregnant:
    Unambiguous indicators of gender in dinosaurs are usually lost during fossilization along with other aspects of soft tissue anatomy.  We report the presence of endosteally derived bone tissues lining the interior marrow cavities of portions of Tyrannosaurus rex (MOR 1125) hindlimb elements, and hypothesize that these tissues are homologous to specialized avian tissues known as medullary bone.  Because medullary bone is unique to female birds, its discovery in extinct dinosaurs solidifies the link between dinosaurs and birds, suggests similar reproductive strategies, and provides an objective means of gender differentiation in dinosaurs.   (Emphasis added in all quotes.)
    Understated in the report is how these soft tissues could have survived for so long.  The paper in Science says only:
    The existence of avian-type MB in dinosaurs has been hypothesized but not identified.  In part, this could be because of taphonomic bias [i.e., fossil-hunters not expecting to find it], because the death and fossilization of an ovulating dinosaur would be comparatively rare.  Additionally, MB in extant birds is fragile, the spicules separating easily from the originating layer (fig. S1).  Dinosaur MB may separate and be lost from overlying CB in a similar manner during diagenesis [i.e., the hardening of sediment into rock].
    National Geographic admitted briefly that “all obvious gender indicators vanish when soft tissues decay during fossilization” but emphasized the gender-identification and phylogenetic angles of the story.  The BBC News article showed a picture of the bones, but said nothing about their assumed ages.  The NC press release did not explain the 70-million year figure, but merely asserted it.  Betsy M. Bennett, Directory of the NC Museum of Natural Sciences, stated emphatically, “We’re pleased to be able to provide a way for the public to see for themselves evidence that after millions of years, soft tissue can actually be preserved in dinosaur bone.”
        Another paper published in Science Express announced the sequencing of the genome from a cave bear, thought to have been extinct for 40,000 years.  In the BBC News write-up, a scientist predicted, “I don’t think we can extract DNA from dinosaurs, I think they are too old.”  It will be interesting to see if Mary Schweitzer’s team finds any in the T. rex bone, where blood vessels, and possibly blood cells, were seen.
    1Schweitzer et al., “Gender-Specific Reproductive Tissue in Ratites and Tyrannosaurus rex, Science, Vol 308, Issue 5727, 1456-1460, 3 June 2005, [DOI: 10.1126/science.1112158].
    This is incredible.  How can these scientists ignore the obvious?  There’s no way this bone could be so old, but all they can think about are connecting homology dots between dinosaurs and birds by circumstantial evidence.  Did they see the dinosaur laying eggs?  No.  Did they prove this is medullary bone?  Perhaps.  Does it prove an ancestral relationship if the dinosaur did have medullary bone?  No.  Does that matter?  Not much.  What really matters about this story is the age of the specimen.  If this specimen is only a few thousand years old, none of this dino-bird homology matters: this blows apart the entire tale of dinosaur evolution.  Belief in millions of years and the rest of the evolutionary timeline takes a staggering blow.
        Look at them strain at a gnat about medullary bone, but swallow a camel about the age.  Instead of expressing shock and anguish, instead of repenting in dust and ashes for spreading lies about dinosaur ages for the past century and a half, they grin and say, “We’ll ah’ll be.  Ain’t it amazin’ how these soft tissues survived for sempty millon yeers.”  It makes one think their brainwashing is so complete they would say the same thing if face to face with a living dinosaur.  Absurd?  Not at all: they already do it with living fossils much “older” in their time scheme.
        Folks, consider the facts in this story.  Soft tissues from a bone of T. rex, everyone’s favorite monster, were found in Montana.  The specimen preserves fine microscopic detail and even pigment.  The material is still flexible and not fossilized.  We know that medullary bone in living birds is “fragile, the spicules separating easily from the originating layer.”  The initial reaction by the scientists was disbelief, because no known process could preserve soft tissues like this for so long.  (And what a thought to consider that this monster might have been alive just a few thousand years ago!)
    Though this is a spectacular example, we should not think that it is an isolated case.  Many insects from around the world have been found preserved in amber (fossil tree resin), with even hairs and veins in the wings preserved in exquisite detail.  Some still contain bacteria in the guts and DNA fragments have been extracted.  Often the specimens are indistinguishable from living species, yet claimed to be millions of years old.  Yet we know that tree resin weathers rapidly and is usually not produced in quantities that can extend for meters and entomb frogs and large insects, which would normally float and decay before being preserved.  On what grounds can evolutionists claim such fossils are ancient?  (For more information on fossil amber, get the presentation “Amber – New Insights” by Dr. Harald Binder, available at Access Research Network.)
    The only way anyone can claim these dinosaur bones are tens of millions of years old is by prior commitment to a belief system that demands forcing all evidence into a long, drawn-out process of evolution.  The young-earth creationists have a great opportunity here.  They and anyone still unbrainwashed about geologic time, and all who respect hard evidence, should hammer away relentlessly at the credulity of the Darwinists, demanding that they explain how a specimen like this could survive even one hundredth of that much time.*  If you see this bone on exhibit at the North Carolina Museum of Natural History, be nice, but come prepared with good questions and reputable background information.  Don’t take bluffing and evasion for an answer.  Undoubtedly, after enough exasperation, they will probably provide the docents a manual on how to deal with those pesky visitors who won’t buy the script, but keep demanding, “Just the facts, ma'am.”**
    Next headline on:  DinosaursBirdsFossilsDating Methods
    *Here’s an opportunity also for an unbiased lab.  Take an ostrich specimen with intact medullary bone, put it into similar conditions, and monitor the rate of decay.  It may years or even decades to get some valid data, but it should be possible to set some upper limit on how long the tissues could be expected to survive.
    **For an example of the impact that polite questioning can have, see the May Scientist of the Month story.
    Kansas Debate Over ID Reverberates in Holland    06/03/2005  
    “Is Holland becoming the Kansas of Europe?” asked Martin Enserink in Science this week.1  All that education minister Maria van der Hoeven wants to do is have some public debate about intelligent design, but the suggestion has caused an uproar among scientists who claim she wants to take Holland back to the Dark Ages.  On the contrary, van der Hoeven explains, she thinks it will promote dialogue between Christians, Jews and Muslims who are all united over the notion of a creator.
        The education minister is not a card-carrying member of the intelligent design movement, and explains she is not trying to impose or ban anything.  She was apparently impressed by the arguments of Cees Dekker, “a renowned nanophysicist at Delft University of Technology who believes that the idea of design in nature is ‘almost inescapable.’”
        While trying to encourage discussion, she has had to spend much time defending herself over this “tempest in a teacup” as she called it.  Why are scientists “scolding her” and saying it is “not her business to get involved in biology”?  One possible reason is that the news from Kansas “has made us all a bit more sensitive.”  Another may be the rumblings within the country: “Even in Holland, there are plenty of people ready to castrate Darwin,” said biochemist Piet Borst.  He thinks that “Vigilance is important” on this issue.  Dekker and van der Hoeven are taking this in stride.
    Dekker says he’s puzzled by the outcry but chalks it up to a “Pavlov reaction” to ID.  “Many scientists associate it with conservative Christians, Kansas, and George Bush—so it has to be bad,” he says.  He hopes the debate will get more serious after the impending publication of a collection of 22 essays about ID and related themes, most of them by Dutch scientists, which he has co-edited.  Van der Hoeven has agreed to receive the first copy of the book at a ceremony in The Hague next week.   (Emphasis added in all quotes.)
    Enserink ends with the reaction of John Calvert, supporter of ID in Kansas, to the idea of a debate over ID in Holland.  “I think it’s a dynamite idea,” he said.
    1Martin Enserink, “Is Holland Becoming the Kansas of Europe?”, Science, Vol 308, Issue 5727, 1394, 3 June 2005, [DOI: 10.1126/science.308.5727.1394b].
    This is another remarkable story on the growing influence of the intelligent design movement around the world, even in liberal Holland where the words George Bush, conservative Christianity and Kansas produce Pavlovian barks.  Enserink points out that Holland is “not quite Kansas—after all, this is the country that legalized euthanasia and invented gay marriage.”  Yet even there a small but committed cadre of scientists, politicians and laymen find the arguments for intelligent design compelling, and they want the debate to be heard.  They are not castrating Darwin.  His impotence is his own (see next two headlines).  Dutch scientists are justly proud of their layman forerunner, the staunch Christian creationist from Delft, Antony van Leeuwenhoek – the father of microbiology – who helped lead science out of the Dark Ages (if there ever was such a period).  He demonstrated how creation-oriented science can be the best in the world, full of vitality and motivation and excellence.  When all the Darwinists can do is scream “Dark Ages,” you know their sunset is coming.  But when it is sunset on one side of the worldview, it’s sunrise on the other.
    Next headline on:  EvolutionEducationIntelligent Design
    He’s Ba-a-a-ck: Lamarck Puts Pressure on Darwin – and ID, Too?    06/03/2005  
    To historians of evolutionary theory, Lamarck is a 19th-century loser.  His hypothesis of “inheritance of acquired characteristics,” according to high school textbooks and common knowledge, was debunked by experiment, and overturned when Darwin proposed natural selection as a mechanism for evolution.  Why, then, does Massimo Pugliucci (Dept. of Ecology and Evolution, State University of New York at Stony Brook, NY) give Lamarck good press in a book review in Nature?1  Why does he put Darwin on defense, charging that a “broader view of inheritance puts pressure on the neo-darwinian synthesis”?
        Pugliucci favorably reviewed the book Evolution in Four Dimensions: Genetic, Epigenetic, Behavioral, and Symbolic Variation in the History of Life by Eva Jablonka and Marion J. Lamb (Bradford Books, 2005), a “lamarckist” polemic:
    The authors argue that there is more to heredity than genes; that some hereditary variations are non-random in origin; that some acquired information is inherited; and that evolutionary change can result from ‘instruction’ as well as selection.  This may sound rather revolutionary, even preposterously close to lamarckism.  But Jablonka and Lamb build on evidence from standard research in evolutionary and molecular biology, and their case should be examined on its merits, rather than being dismissed by a knee-jerk reaction.   (Emphasis added in all quotes.)
    He quickly quenches any alarm that he or the authors want to revive the kind of lamarckism that taught direct inheritance of acquired characteristics, or “direct adaptive feedback from the soma to the germ line” – for example, that a lumberjack’s strong arms would be inherited by his baby boy.  “That version of lamarckism is dead,” he assures us, “killed off by our understanding of molecular biology, and nobody is attempting to revive it.”  But that first meaning of lamarckism is not all that Lamarck taught:
    The second meaning is actually closer to the core of Lamarck’s ideas, which are rarely, if ever, read by modern biologists.  The suggestion is that some heritable, adaptive changes come not from natural selection, but from the action of evolved internal systems that generate non-random ‘guesses’ in response to environmental challenges.  Examples are not hard to find, contrary to the assumed wisdom of standard neo-darwinism.  Consider the existence of ‘hotspots’ that make mutations in certain regions of the genome much more likely than in others.  Or the impressive ability of some bacteria to increase the mutation rate of a specific gene involved in the metabolism of a given amino acid when that amino acid becomes scarce in the environment.
    Pugliucci acknowledges that “Jablonka and Lamb are surely taking a gamble in labeling their position as lamarckist,” but he sides with them in one shocking point: “they are correct to point out that no modern biologist is a darwinist in the sense Darwin would have understood – not least because Darwin included a lamarckian mechanism of the first (now frowned upon) type in his theory, as he had no solution to the problem of heredity” (see 10/14/2003 entry).
        Having disabled the alarm, Pugliucci now offers the neo-lamarckism of Jablonka and Lamb as the evolutionary answer to the intelligent design movement:
    If one accepts this bold, expanded version of heredity and evolution, it turns out that evolution can proceed very rapidly and phenotypic modification can precede genetic changes.... Indeed, changes at the genetic level will often simply stabilize adaptive modifications that are initiated through phenotypic plasticity [i.e., acquired characteristics], epigenetic control mechanisms, or behavioural and symbolic means [i.e., social/language communication from parent to offspring].  This is a framework that would greatly help to solve old problems in evolutionary biology, such as the origin of novel structures [see 08/20/2003 entry], and even the appearance of what ‘intelligent design’ proponents refer to, rather nonsensically, as ‘irreducible complexity’.  This wouldn’t require the abandonment of neo-darwinism, but rather its expansion beyond what Ernst Mayr contemptuously labelled ‘bean-bag genetics’.
    So Pugliucci offers not an either-or choice of lamarckism vs. neo-Darwinism, but an expanded synthesis beyond that thesis-antithesis dichotomy.  For empirical support, he points to the “partial failure of the originally ultra-reductionist, gene-centred approach that gave us genomics,” saying that “the interesting stuff is going on at the level of large gene networks” [see 01/10/2003 entry], “not of individual genes, partly because there is widespread functional redundancy in the genome.”  Presumably, this pool of functionality can be drawn on by environmental cues to optimize solutions to problems (see next headline).
        Realizing his viewpoint will probably anger the hard-core selectionists, like Richard Dawkins (04/23/2003) and George Williams (05/31/2004), he draws on a defense, in closing, that has been used by several intelligent design proponents as strategic realism about changing the minds of the old guard:
    The clamour to revise neo-darwinism is becoming so loud that hopefully most practising evolutionary biologists will begin to pay attention.  It has been said that science often makes progress not because people change their minds, but because the old ones die off and the new generation is more open to novel ideas.  I therefore recommend this and the other books I mentioned on the future of evolutionary theory to the current crop of graduate students, postdocs and young assistant professors.  They’ll know what to do.

    1Massimo Pugliucci, “Expanding evolution, ” Nature 435, 565-566 (2 June 2005) | doi: 10.1038/435565a.
    They’ll know what to do, all right: they’ll chuck Chuck and baptize Jean-Baptiste into the dustbin of discredited prophets, and embrace intelligent design.  Like Sutherland in the next article below, Pugliucci and his champions believe that specified complexity and optimization can emerge spontaneously, without purpose or direction, as long as there is a need.  But that fallacy is not just with neo-Darwinism and its reductionist genomics; it is with any theory that fails to include information as a fundamental property of the universe.  No combination of chance and natural law will produce information.  Think of a blank DVD and one containing microscopic pits encoding the latest Star Wars movie: they have the same mass and physical properties.  It is the information content that makes all the difference when you insert them into a DVD player.  Similarly, to believe that the information content in the genome and in all the gene networks and epigenetic controls to which Pugliucci refers could have arisen by naturalistic means cannot be done without assuming naturalism at the outset.  All our common experience teaches that information arises only from intelligent causes.
        What this book review does, despite its dismissive ridicule of intelligent design, is strengthen the strategic posture of ID.  It advertises the weaknesses of the Darwin camp to the enemy.  The “clamor to revise neo-darwinism” has risen to a fever pitch within the Darwin camp, and can no longer be ignored, except by the Old Guard who have grown deaf with age.  The phrase “irreducible complexity” has rattled the evolutionary generals:
    “Quick: we need a counterattack,” they strategize.  “How’s the neo-Darwinian antidote working?”
    “Too weak,” the technician responds [see 10/14/2003 entry]; “Their weapons have developed immunity to it, and we’ve found it incapable of protecting our own soldiers.  It’s not as potent as we thought it was.”
    “Anything else in our strategic arsenal?”  [See 07/23/2004 entry.]
    “Nothing new, General.  Most of our weapons were forged in the 19th century.”
    “Well, then, did anything work well before Chairman Charles?”
    “We could resurrect an older weapon used with partial success from time to time, even by Darwin,” a lieutenant responds [see 10/14/2003 and 07/02/2004 entries].  It was invented by General Lamarck.”
    “We can’t use that; it’s broken.  Everybody knows that.”
    “We’ve got to do something, General.  Let the young recruits try it and see if they can get parts of it to work this time.”
        The intelligent design strategists, like Gideon spying around the tents of Midian (see Judges 7), are listening in on all of this.  Can a loaf of barley bread overturn ten thousand tents?  It can, either when the tents are made of wind held together by fog, or when there is supernatural power in charge.  It appears the I.D. camp has both advantages.
    Next headline on:  Darwinism and Evolutionary TheoryIntelligent Design
    Something from Nothing Dept.   06/02/2005  
    How do you get optimization by chance?  In a Concepts piece in Nature this week,1 William J. Sutherland (U. of East Anglia, UK) suggested that the constraints of the environment will drive living systems toward optimal solutions.  He thinks that’s how “selective forces” shaped your teeth and jaw, for instance.  Economists and engineers use optimization theory, he reasons, so why not biologists? 
    The use of optimization has allowed biologists to move from merely describing patterns or mechanisms to being able to predict, from first principles, how organisms should be designed.  Optimality models are based on three elements: the choices available; what is being optimized; and the constraints.
        Physiologists have used optimization to answer a wide range of questions about animal morphology.  For example, optimization has been invoked to predict the design of a bone of given weight that minimizes the risk of breaking or buckling; the speed at which it is most efficient to switch from running to walking; and the gut design that provides the highest energy gain from a given diet.  The prediction of the triplet code as the most parsimonious means of coding 20 amino acids using the four bases of DNA is another successful example of this methodology.
      (Emphasis added in all quotes.)
    Though the concept has its critics, Sutherland gives a few more examples of how the optimization approach might have shaped biological systems by natural selection.  But intelligent design (ID) is clearly not what he has in mind; he gives Darwin the credit: “Darwin’s theory of natural selection provided an obvious mechanism for explaining optimization in biology: more efficiently designed individuals will leave more offspring.”2  The optimization approach will be fruitful, he concludes:
    A considerable strength of using optimization is that once we understand why organisms are as they are, then it should be possible to understand how they will respond to new conditions.  Optimization can therefore be used to understand behaviour, and to predict population dynamics, in new environments, such as those resulting from habitat loss or a rise in sea level.
        There are increasing calls for biology to be predictive.  Optimization is the only approach biology has for making predictions from first principles.  The wider adoption of these ideas right across biology should reap ample rewards.

    1William J. Sutherland, “The Best Solution,” Nature 435, 569 (2 June 2005) | doi: 10.1038/435569a.
    2Of course this is obvious.  How do you know the individual is efficiently designed?  Because it left more offspring.  Why did it leave more offspring?  Well, obviously, it must have been more efficiently designed.  This circular argument, is an example of a tautology, or a statement of the obvious, like “deaf people can’t hear, because they are deaf.”  Natural selection falls into this tautology trap any time fitness is defined in terms of fecundity (see 10/29/2002 entry).
    Sorry, Bill.  You can’t get the blood of design from a turn-up of natural selection.  Necessity is the mother of invention only when intelligence guides the process.  The only thing nature is good at optimizing is entropy.  The optimization approach will only make sense when design scientists oust the naturalistic usurpers from biology.
    Next headline on:  EvolutionDumb Ideas
    ID Film To Be Aired at Smithsonian   06/01/2005  
    The intelligent-design film The Privileged Planet will be shown at the Smithsonian on June 23.  See story on The Ames Tribune.  Pam Sheppard at AIG has a report also.  Following the showing at the National Museum of Natural History, the film will air on PBS stations around the country.
    Update 06/02/2005: The Smithsonian appears to be backpedaling.  Although they have not canceled the showing, they are now claiming the content of the film is “not consistent with the mission of the Smithsonian Institution’s scientific research,” reports the Washington Post.  Yet all the arrangements were made on the up and up two months ago, with no objections made even though staffers previewed the film twice.  They are apparently taking heat from some opponents of intelligent design.  The Post article reveals that The Amazing Randi (a well-known skeptic) offered the Smithsonian $20,000 not to show the film.  For updates on this developing story, visit the EvolutionNews blog; it contains links to recent news reports, and also has copies of the original documents from the Smithsonian about the film showing. Update 06/24/2005: The event apparently went off smoothly without acrimony or dissent.  Here is an eyewitness report from Salvador Cordova.  See also the 06/09/2005 entry.
    Why should the Darwinists be alarmed at this decision by the Smithsonian to co-sponsor the film?  It’s a private showing.  The film makes a pretty mild proposition that there are aspects of our universe that seem inexplicable by chance, and that there might be some grand design or purpose behind it.  Five scientists at the American Museum of Natural History already agreed that our solar system appears special (see 04/04/2005 story).  One of the founders of the Smithsonian, the great American physicist Joseph Henry (see July 2004 Scientist of the Month) would be pleased.
        Most of the critics who are up in arms act like they haven’t even see the film.  As for the Amazing Randi, the most amazing thing about him right now is his inconsistency.  He exposes those who fool others, but fails to see how he is fooling himself (see 10/06/2000 story).  His tactic is bound to backfire and only give the film more publicity.  Randi should stick to what he is good at: fighting faith healers and psychic surgeons.  Would he have offered the Smithsonian money to stop Michael Faraday and Joseph Henry from doing stage demonstrations?  Doubt it.  Come on, all you materialist skeptics; skepticism is good to a point, but sometimes you need to aim your baloney detectors at yourselves.  Instead of censorship, how about some debate about the scientific facts?  Since Randi doesn’t appear up to debunking what cannot be debunked, because it is reinforced in the film by many respectable scientists he himself respects, he is making a pseudoscientist of himself.  Now the promoters of the film have a new advertising angle: Come see the film The Amazing Randi doesn’t want you to see!
    Next headline on:  Intelligent DesignMedia
    Jupiter Moon Throws Curve Ball    06/01/2005  
    The little inner moon of Jupiter, Amalthea, isn’t dense enough.  A press release from Jet Propulsion Laboratory says that data from the Galileo spacecraft “shakes up long-held theories of how moons form around giant planets.”  Density of moons is supposed to decrease with radius around Jupiter, meaning that Amalthea should be the most solid.  Instead, it appears to be a loose rubble pile less dense than water.  An alternative theory, that it formed farther out and migrated or was captured, is also implausible.  “Amalthea is throwing us a curve ball,” one scientist said.  The original paper was published in Science May 27.1
    1Anderson et al., “Amalthea’s Density Is Less than That of Water,” Science, Vol 308, Issue 5726, 1291-1293, 27 May 2005, [DOI: 10.1126/science.1110422].
    Planetary science is not exactly batting a thousand these days, even without curve balls.  Looks like she didn’t accept the date when sports dropout McFly proposed, “Amalthea, you are my density... er, I mean, my destiny.”
    Next headline on:  Solar System
    Mars Dry Areas More Extensive than Thought    06/01/2005  
    If Mars had oceans or lakes, it wasn’t for long, at least in the Syrtis Major region.  Results of observations of the thermal emission imaging system (THEMIS) aboard the 2001 Mars Odyssey reveal about four times as much olivine as previously recognized in the Nili Fossae adjacent to the Syrtis volcanic shield.  Olivine quickly degrades in the presence of water.  Philip R. Christensen, principal investigator, who published the results in the June issue of Geology,1 believes eruptive volcanoes were the primary source of the olivine-rich basalts, not intrusive processes like dikes or sills.
        The report on Mars Daily says the area studied is 11 times larger than the big island of Hawaii.  Co-author Victoria Hamilton said that finding this much olivine in a “very old region of Mars” was intriguing, and suggests that this area of Mars, at least, “has not seen much water.”
        Nevertheless, other areas look like something flowed.  Mars Express released an image of Ares Valles (near where the Mars Pathfinder rover landed) that looks like an extensive flood plain.  Perhaps volcanic heat melted frozen groundwater for a brief flooding episode some time long ago.
    Update 06/06/2005: News@Nature reported that this could explain the methane.  Rather than coming from living organisms, the methane could emerge from the olivine in a process called serpentinization.  Chris Oze (Dartmouth) said, “I’d love to see bugs, but you can’t just go on hope.  You have to consider the geological options.”  Apparently, it would not require that much olivine to do the job, and now there’s probably more around than first expected.
    1Hamilton and Christensen, “Evidence for extensive, olivine-rich bedrock on Mars,” Geology, Vol. 33, No. 6, pp. 433–436, doi: 10.1130/G21258.1.
    Even if Mars had lots of water, and even if its atmosphere was able to shield out the harmful radiation reaching the surface, it would not necessarily have had life.  This just erodes the hopes of astrobiologists even further.  About the only lively thing going on is the occasional dust devil passing by (see movie taken by Spirit).
    Next headline on:  MarsGeology

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    (a registered nurse in Alabama, who found us on

    “WOW.  Unbelievable.... My question is, do you sleep? ... I’m utterly impressed by your page which represents untold amounts of time and energy as well as your faith.”
    (a mountain man in Alaska).

    “Just wanted to say that I recently ran across your web site featuring science headlines and your commentary and find it to be A++++, superb, a 10, a homerun – I run out of superlatives to describe it! ... You can be sure I will visit your site often – daily when possible – to gain the latest information to use in my speaking engagements.  I’ll also do my part to help publicize your site among college students.  Keep up the good work.  Your material is appreciated and used.”
    (a college campus minister)

    Featured Creation Scientist for June

    Leonhard Euler
    1707 - 1783

    Let’s take a look this month at a true story of a very interesting individual, one whose name will ring a bell for anyone who has studied higher mathematics, because his name is associated with dozens of theorems, proofs, algorithms, constants and laws.  Though not a scientist by training, he contributed immeasurably to science by advancing its language (mathematics) and its toolkit of operations.  According to math professor Howard Anton, he “made major contributions to virtually every branch of mathematics as well as to the theory of optics, planetary motion, electricity, magnetism, and general mechanics.”  His name was Leonhard Euler (pronounced oiler), a true genius who was also a committed Christian all his life.

    Euler was so smart it’s almost scary.  In his thick textbook Calculus, Howard Anton includes brief biographies of famous mathematicians; his entry on Euler sounds like an episode from Ripley’s “Believe It or Not” –

    Euler was probably the most prolific mathematician who ever lived.  It has been said that, “Euler wrote mathematics as effortlessly as most men breathe.” .... Euler’s energy and capacity for work were virtually boundless.  His collected works form about 60 to 80 quarto sized volumes and it is believed that much of his work has been lost.  What is particularly astonishing is that Euler was blind for the last 17 years of his life, and this was one of his most productive periods!  Euler’s flawless memory was phenomenal.  Early in his life he memorized the entire Aeneid by Virgil and at age 70 could not only recite the entire work, but could also state the first and last sentence on each page of the book from which he memorized the work.  His ability to solve problems in his head was beyond belief.  He worked out in his head major problems of lunar motion that baffled Isaac Newton and once did a complicated calculation in his head to settle an argument between two students whose computations differed in the fiftieth decimal place.

    This gives us cause to ponder the possibilities inherent in the human brain.  It makes us wonder what initial abilities the Creator gave to man that have been degenerating since the creation, only to surface occasionally to above-average levels in rare geniuses like Euler.  It also makes us wonder how any theory of evolution could ever produce such a superabundance of potential, far more than needed for mere survival.  The ability to perform abstract, symbolic reasoning in the human mind, unknown in the animal kingdom, provides strong evidence for the special creation of man.  Nothing comes from nothing.  A mind as gifted as Euler’s could only come from a bigger Mind, one that is all-knowing and infinite in wisdom and knowledge.

    Did Euler’s genius make him an aloof braggart or freakish savant?  Not at all.  He was a gracious and unselfish person, a loving father of a large family, a teacher, a diplomatic gentleman and a man of deep faith and conviction.  People loved and respected him.  He was a hard worker and a lover of the truth.  There are no indications he thought highly of himself, but that he pursued his area of expertise in the desire to advance knowledge and aid the sciences.  But when it came time to defend his faith, he was prepared, like Pascal, to take up the challenge.

    Leonhard’s father was a pastor who also enjoyed mathematics.  After home- schooling the boy for his elementary years, Paul Euler sent his son to the University of Basel, Switzerland (their home town), hoping he would follow in his theological footsteps.  Though faithful to his Calvinistic upbringing all his life, Leonhard’s interest and proficiency in geometry convinced his father a change of career was warranted.  Tutored under Johann Bernoulli, Leonhard by age 16 had a Bachelor of Arts and a Masters in philosophy, and by 18 was doing mathematical research and producing original work that continued unabated for the next six decades.  His career took him beyond the University of Basel to the St. Petersburg Academy of Sciences in Russia, and for 25 years to the Berlin Academy of Sciences, then back to Russia.  In this brief biography, we are more interested in the beliefs and personal life of this amazing individual, who singlehandedly was responsible for about a third of all mathematical output of the 18th century.

    Christian living was a practical reality, not a Sunday formality, to Euler.  Dan Graves, in his excellent chapter on Euler in Scientists of Faith says, “Despite his turn to math, Euler retained his firm Calvinist beliefs throughout life, holding daily prayer and worship in his home and sometimes preaching.”  Unable to find work in Switzerland, Leonhard moved to St. Petersburg, Russia where, at age 26, he met and married another Swiss emigrant, Katharina Gsell, his bride for 40 years. Graves describes their family life: “Katharina bore him thirteen children, whom he loved dearly.  He often carried on his work with children sitting on his lap or clinging to his back.”  But Dan Graves also illustrates a theme we have seen often in these biographies, that the individuals we know primarily for their intellectual achievements were real human beings who often had to overcome severe trials and misfortunes.

    Not only did Euler lose sight in one eye at age 28 while straining on a particularly difficult problem, he lost sight of his other eye at age 59 in great pain, as Graves describes: “An operation to restore the better of the two was successful, but infection invaded both eyes.  After horrible agony he permanently lost his sight.  He later said that only his faith in God enabled him to bear those days of torment.”  As stated earlier, however, some of his greatest work was yet to come, fully half his lifetime output, as Euler wrote out his complex derivations on “the black slate of his mind.”  Taking this disability in stride, he said, “Now I will have less distraction.”

    Additional trials came from political and philosophical enemies.  In his thirties, Euler moved from an unstable political situation in Russia, when spies were everywhere and purges were the rule, and worked under the Prussian emperor Frederick the Great.  There he served 25 years and added immensely to the prestige of the Berlin Academy of Sciences.  But his patron Frederick, an Enlightenment skeptic, sneered at the Christian faith of his niece’s tutor.  In response, Euler wrote Letters to a German Princess, in which he gently combined piety with the sciences.  The book became a best-seller in seven languages, but Frederick was not impressed.  Voltaire, the French Enlightenment anti-Christian deist, joined in mocking Euler’s Biblical world view.  Euler corresponded with apologetic works defending Christian doctrine against Voltaire, Leibniz, Wolff and other Enlightenment skeptics, until the interference and opposition by Frederick became intolerable and he had to uproot again.  At age 59, he moved back to St. Petersburg to accept a position under Catherine II (the Great).  The Russians welcomed him as a returning hero.  But that was the year, 1766, when he became totally blind.  In 1771, his house burned down and he escaped with his life and his manuscripts.  Two years later, his wife died.

    Undeterred by misfortune, upheaval and disability, Euler continued his work. With only his mind’s eye, he worked through detailed algorithms and dictated them to his sons.  Dan Graves said that his work actually became clearer and more concise.  An online biography at Ryerson Polytechnic Institute states that “He was apparently able to do extensive and complex calculations in his head, remembering every step so that he could recite them for his sons to record. ... he published more than 500 books and papers during his lifetime, with another 400 appearing posthumously”.  Another online biography claims that his death in 1783 left a vast backlog of articles that the St. Petersburg Academy continued to publish for nearly 50 more years.  Dan Graves tallies his publications at 886, which he claims have only recently been brought together, and constitute the size of a large set of encyclopedias.  The Encyclopedia Britannica says the compilations began in 1911 and are still continuing!  That’s an incredible volume of writing for anyone, let alone technical writing, especially for a blind man!

    What is contained in all this prodigious output?  Just about anything and everything dealing with mathematics.  Euler’s work transformed the look of homework around the world: the convention of using the letter pi for the ratio of the circumference to the diameter of a circle, the letter e for the base of the natural logarithm, the Greek letter sigma for the sum of a series of numbers, and the letter i for the unit of imaginary numbers.  The theory of infinities and continuity.  Important work on our present understanding of functions, including the highly-used f notation such as y = f(x).  Greater perfection in differential and integral calculus, including many new techniques for solving indefinite integrals and the introduction of the well-known integral sign.  More simplicity in analytical operations.  Advances in the theory of linear differential equations.  The properties of integers and the theory of numbers, leading to the foundations of pure mathematics.  Euler’s criterion.  Euler’s constant.  Euler numbers.  The list goes on.

    In addition, Euler tackled numerous theoretical and practical physical problems, including work on the basic principles of mechanics, optics, acoustics and astronomy.  The Encyclopedia Britannica says,

    Euler devoted considerable attention to developing a more perfect theory of lunar motion, which was particularly troublesome, since it involved the so- called three-body problem–the interactions of Sun, Moon and Earth.  (The problem is still unsolved.)  His partial solution, published in 1753, assisted the British Admiralty in calculating lunar tables, of importance then in attempting to determine longitude at sea.  One of the feats of his blind years was to perform all the elaborate calculations in his head for his second theory of lunar motion in 1772. ... Euler and Lagrange together are regarded as the greatest mathematicians of the 18th century; but Euler has never been excelled either in productivity or in the skillful and imaginative use of algorithmic devices (i.e., computational procedures) for solving problems.

    Phenomenal as his intellectual achievements were, we should see beyond them the heart of a faithful Christian, strong enough to defend his faith against the most powerful skeptics of his day, yet humble enough to depend totally on the Lord for comfort in the midst of suffering.  We should see in his popular writings and textbooks for elementary schools a desire to help the young.  We should see in his Letters to a German Princess a belief in the unity of knowledge and virtue.  We should see a loving father taking time to play with his children, the fruit of such love being evidenced years later in his sons’ willingness to help transcribe his mental output during his 17 years of total blindness.  We should see an active senior working tirelessly till the day of his death at age 76.  We should be reminded that steadfast faith in the Word of God is not a hindrance, but rather a stimulus, to the advance of knowledge.  We should see that a mind in touch with its Creator, whether its physical windows are open or shut, can be a beautiful and powerful thing.

    Are you enjoying this series?  Please write us with your comments, and tell a friend!

    If you are enjoying this series, you can learn more about great Christians in science by reading our online book-in-progress:
    The World’s Greatest Creation Scientists from Y1K to Y2K.
    Copies are also available from our online store.

    A Concise Guide
    to Understanding
    Evolutionary Theory

    You can observe a lot by just watching.
    – Yogi Berra

    First Law of Scientific Progress
    The advance of science can be measured by the rate at which exceptions to previously held laws accumulate.
    1. Exceptions always outnumber rules.
    2. There are always exceptions to established exceptions.
    3. By the time one masters the exceptions, no one recalls the rules to which they apply.

    Darwin’s Law
    Nature will tell you a direct lie if she can.
    Bloch’s Extension
    So will Darwinists.

    Finagle’s Creed
    Science is true.  Don’t be misled by facts.

    Finagle’s 2nd Law
    No matter what the anticipated result, there will always be someone eager to (a) misinterpret it, (b) fake it, or (c) believe it happened according to his own pet theory.

    Finagle’s Rules
    3. Draw your curves, then plot your data.
    4. In case of doubt, make it sound convincing.
    6. Do not believe in miracles – rely on them.

    Murphy’s Law of Research
    Enough research will tend to support your theory.

    Maier’s Law
    If the facts do not conform to the theory, they must be disposed of.
    1. The bigger the theory, the better.
    2. The experiments may be considered a success if no more than 50% of the observed measurements must be discarded to obtain a correspondence with the theory.

    Eddington’s Theory
    The number of different hypotheses erected to explain a given biological phenomenon is inversely proportional to the available knowledge.

    Young’s Law
    All great discoveries are made by mistake.
    The greater the funding, the longer it takes to make the mistake.

    Peer’s Law
    The solution to a problem changes the nature of the problem.

    Peter’s Law of Evolution
    Competence always contains the seed of incompetence.

    Weinberg’s Corollary
    An expert is a person who avoids the small errors while sweeping on to the grand fallacy.

    Souder’s Law
    Repetition does not establish validity.

    Cohen’s Law
    What really matters is the name you succeed in imposing on the facts – not the facts themselves.

    Harrison’s Postulate
    For every action, there is an equal and opposite criticism.

    Thumb’s Second Postulate
    An easily-understood, workable falsehood is more useful than a complex, incomprehensible truth.

    Ruckert’s Law
    There is nothing so small that it can’t be blown out of proportion

    Hawkins’ Theory of Progress
    Progress does not consist in replacing a theory that is wrong with one that is right.  It consists in replacing a theory that is wrong with one that is more subtly wrong.

    Macbeth’s Law
    The best theory is not ipso facto a good theory.

    Disraeli’s Dictum
    Error is often more earnest than truth.

    Advice from Paul

    Guard what was committed to your trust, avoiding the profane and idle babblings and contradictions of what is falsely called knowledge – by professing it some have strayed concerning the faith.

    I Timothy 6:20-21

    Song of the True Scientist

    O Lord, how manifold are Your works!   In wisdom You have made them all.   The earth is full of Your possessions . . . . May the glory of the Lord endure forever.   May the Lord rejoice in His works . . . . I will sing to the Lord s long as I live; I will sing praise to my God while I have my being.   May my meditation be sweet to Him; I will be glad in the Lord.   May sinners be consumed from the earth, and the wicked be no more.   Bless the Lord, O my soul!   Praise the Lord! 

    from Psalm 104

    Maxwell’s Motivation

    Through the creatures Thou hast made
    Show the brightness of Thy glory.
    Be eternal truth displayed
    In their substance transitory.
    Till green earth and ocean hoary,
    Massy rock and tender blade,
    Tell the same unending story:
    We are truth in form arrayed.

    Teach me thus Thy works to read,
    That my faith,– new strength accruing–
    May from world to world proceed,
    Wisdom’s fruitful search pursuing
    Till, thy truth my mind imbuing,
    I proclaim the eternal Creed –
    Oft the glorious theme renewing,
    God our Lord is God indeed.

    James Clerk Maxwell
    One of the greatest physicists
    of all time (a creationist).

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