Creation-Evolution Headlines
May 2004
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Thus, for the naturalist, the world is intelligible only if it starts off without intelligence and then evolves intelligence.  If it starts out with intelligence and evolves intelligence because of a priori intelligence, then somehow the world becomes unintelligible.  The absurdity here is palpable.
— William A. Dembski, The Design Revolution (IVP 2004, p. 23)
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Darwinist Chides Recklessness of Evolutionists   05/31/2004
The tendency of some evolutionists to engage in just-so storytelling was intolerable to George C. Williams, an influential Darwinian.  Throughout his life he called them to accountability.  Now elderly, he was recently honored by fellow evolutionists at State University of New York, Stony Brook.  Carl Zimmer described the event in the May 28 issue of Science.1  The article describes Williams’ attitude toward those who avoided the necessity for scientific rigor in evolutionary explanations.  (Emphasis added in all quotes.)
Williams was struck by the ad hoc way that even prominent biologists would explain an adaptation.  They’d claim that it had evolved because it provided some benefit; often, an entire population or species supposedly benefited.  Williams recalls a lecture he heard by Alfred Emerson, a zoologist at the University of Chicago, about why people age and die.  “He said growing old and dying is a good thing,” Williams says.  “We’ve evolved to do it so we get out of the way, so the young people can go on maintaining the species.”
    “I thought it was absolute nonsense,” says Williams.  Whenever people like Emerson claimed that an adaptation was for the good of a species, they never offered an explanation of how, from one generation to another, that potential benefit produced real evolutionary change.  Williams suspected that in most cases, no such explanation existed.  For him, the primary engine of evolutionary change was the one Darwin had written about in the Origin of Species: competition among individuals of the same species.  Most biologists in the 1950s simply failed to think seriously enough about how natural selection could produce adaptations, he says.
Williams has been especially harsh on the group selectionists, those who surmise that natural selection can act on groups instead of just individuals.  Zimmer points to his 1966 classic, Adaptation and Natural Selection, as the clarion call to see all adaptations as the result of “strict natural selection working on individuals.”  So how did Williams explain things?
Take a school of fish, for example.  It seems as if every individual cooperates for the good of the group, working with others to avoid predators, even if it means that individual gets devoured in the process.  Williams argued that the schooling behavior could instead be the product of individual fish trying to boost their personal chances of survival--by trying to get in the middle of the school and by watching other fish for signs of approaching predators....
    .... Williams argued that the decline of old age could be caused by pleiotropy--in other words, the harmful side effects of genes selected for advantages they offered during youth.  Just as long as the advantages of these genes outweighed the disadvantages, they would become widespread.
In other words, organisms trade off one advantage against another (see
05/11/2004 headline).  Not all group selectionists have repented, however.  Zimmer points out one ardent skeptic:
Although Williams has convinced many people of the value of his ideas, the notion that human behavior can be broken down into such finely tuned reproduction-boosting adaptations is, to say the least, controversial.  The late Stephen Jay Gould liked to call this approach “Darwinian fundamentalism,” and he credited Williams’s Adaptation and Natural Selection as “the founding document for this ultimate version of Darwinian reductionism.”
Zimmer also touches on the disappointment by some of Williams’ followers that his ideas on evolutionary medicine never really caught on.  Williams believed evolutionary theory might help doctors by helping them identify natural selection at work in their patients.  The competition between a fetus and its mother for the nutrients in the placenta, for instance, might explain the life-threatening condition called preeclampsia.  As Williams’s followers might see the situation, the mother’s blood pressure might be rising dangerously because the fetus is releasing factors into the placenta that “damage the walls of the mother’s blood vessels, thereby raising the resistance of her circulatory system,” so that it could glean more nutrients from the increased blood flow.  Participants at the meeting lamented that such “Darwinian ideas are not making a big impact” on the way doctors think.  A recent-convert doctor noted that “There’s a big barrier between people like me who are physicians and people who are in biology departments.”  Perhaps it’s just that all great ideas take time, Zimmer suggests.  (For more on evolutionary medicine, see 01/13/2003 and 06/25/2003 headlines.)
1Carl Zimmer, “George C. Williams Profile: Stretching the Limits of Evolutionary Biology, Science. Vol 304, Issue 5675, 1235-1236, 28 May 2004, [DOI: 10.1126/science.304.5675.1235].
Stephen Pinker claimed that “George Williams was instrumental in making natural selection an intellectually rigorous theory.”  There’s nothing scientifically rigorous about any of this.  The only thing Williams did was try to leash in today’s storytelling methods back to the original storytelling method.  One must not twist the plot with group selection, but only invoke individual selection, as Charlie proposed in the evolutionary Torah.  Thus, Darwinian fundamentalism must abide by the just-so storytelling method of the Mosstuh prescribed in the founding document of the Darwin Party.  We’ve said before that if you removed the personification fallacy from evolutionary theory, little would be left.  Raise your hand if you think fish plan their schooling for survival, or babies in the womb are plotting to steal from Mom.
    Medicine gets along just fine without Darwinian fundamentalism.  Pregnant mothers facing surgery are not likely to be comforted by the thought that their babies are competing with them for survival of the fittest.  (If anything, such teaching would only seem to promote abortion.)  Doctors and hospital chaplains prosper when they see the value in each individual life as a marvelous creation of a loving God.  If you care for your loved one in the hospital, better help keep the Darwin Party advocates out.  They don’t value compassion.  They value selfishness.
Next headline on:  Darwinism and Evolutionary Theory.
Young Planet Around Young Star Claimed    05/28/2004
A star estimated to be one million years old already has a planet in orbit around it, the
Spitzer Space Telescope (Hubble’s counterpart for infrared astronomy) has found.  Astrobiology Magazine says this challenges old theories.  Alan Boss (Carnegie Institute) thinks this supports his disk-instability model for planetary formation, in which gas giants can form quickly, in just hundreds or thousands of years (see 05/07/2001 headline).  If so, “that has profound implications for the prevalence of planetary systems similar to our own,” he says.  “That means you can make gas giant planets – a major component of our own solar system – in a short time scale, in even the shortest-lived disc.”
    Spitzer also found organic material in the disks of some stars, reports Jet Propulsion Laboratory.  The “raw ingredients for life” appears to be in icy bodies that might be comets.  If so, “Scientists believe these comets may have endowed Earth with some of its water and many of its biogenic, life-enabling materials.”
It also means our solar system doesn’t have to be as old as claimed even under naturalistic presuppositions.  Funny that you can have young-earth theories for other stars, but not our own.
    “Raw ingredients for life” again; sure.  Iron ore and gypsum are raw ingredients for buildings.  Once upon a time, these ingredients organized themselves into cities and factories and concert halls.
Next headline on:  AstronomyDating MethodsOrigin of Life.
Cosmos Ages a Billion Years in One Day    05/28/2004
Physicists have found that a portion of the carbon-nitrogen-oxygen reaction thought to participate in fusion reactions inside stars runs two times slower than previously thought.  The measurements were made in the Laboratory for Underground Nuclear Astrophysics (LUNA), a lab nearly a mile underground in Italy that offers more protection from cosmic rays.  The ripple effect of this discovery is that all stars age more slowly than the textbooks claim, and the universe itself may be a billion years older.  For information, see
Physics Web or Science Now.
They measured one reaction in the present.  They did not measure 14 billion years.  Notice how one small measurement can have dramatic effects.  Physics is supposed to be a “hard” science, and now the textbooks have to be rewritten about something that was thought to be pretty well understood.  What about the soft sciences, and the mushy or gaseous ones like evolutionary theory?  What discovery tomorrow might invalidate some measurement the Darwinists are trusting?
Next headline on:  CosmologyPhysicsDating Methods.
DNA: The Mystery of the Ultraconserved Elements   05/27/2004
As we proceed into the age of genomics, the DNA codes of more and more animals are coming into focus.  The genomes of humans, chimpanzees, mice, chickens, dogs, rats and pufferfish have been sequenced so far, and more are planned.  Evolutionists expected the ancestry of all living things to be traceable in the genetic code by comparing the DNA of distant vs. closely-related species, but the task has proven far more complicated than expected.  One recent finding has evolutionists really scratching their theoretical heads, as summarized in the May 28 issue of Science:
There are 481 segments longer than 200 base pairs (bp) that are absolutely conserved (100% identity with no insertions or deletions) between orthologous regions of the human, rat, and mouse genomes.  Nearly all of these segments are also conserved in the chicken and dog genomes, with an average of 95 and 99% identity, respectively.  Many are also significantly conserved in fish.  These ultraconserved elements of the human genome are most often located either overlapping exons in genes involved in RNA processing or in introns or nearby genes involved in the regulation of transcription and development.  Along with more than 5000 sequences of over 100 bp that are absolutely conserved among the three sequenced mammals, these represent a class of genetic elements whose functions and evolutionary origins are yet to be determined, but which are more highly conserved between these species than are proteins and appear to be essential for the ontogeny of mammals and other vertebrates.  (Emphasis in all quotes.)
Why is this unexpected?  According to evolutionary theory, mutations accumulate over time.  Evolutionists believe that fish, birds and mammals all diverged on the family tree and went their separate ways millions of years ago.  Why, then, are there these thousands of sequences that have not changed at all?
    Mutations, in theory, could be harmful, beneficial, or neutral.  If harmful, natural selection should weed them out.  If beneficial, natural selection should preserve them, as Darwin said in a classic passage on gradualism: “Natural selection is scrutinizing the slightest variations, rejecting those that are bad, preserving and adding up all that are good.”  But most evolutionists also consider the gray area between, the “neutral” mutations that cause neither benefit nor harm.  Exposed to mutagens in the environment over vast ages, each section of the genome should accumulate neutral mutations, resulting in genetic drift.  Presumably, the amount of drift between two species (like rats and humans) would be a function of the time since their lineages diverged, assuming a “molecular clock” ticking with a steady mutation rate.  (Is the molecular clock reliable?  See
04/20/2004 headline.)
    Yet there are significant segments of DNA that are 100% identical in the mammalian genomes, despite evolutionists’ belief their ancestries diverged tens of millions of years ago.  The puzzle is even more striking when fish and bird genomes show 95% or greater sequence identity with mammals in these ultraconserved elements for 300 to 400 million years.  How could this be, especially when some parts of the genomes appear to evolve rapidly?  The Darwinian explanation is that the ultraconserved regions have been subject to “purifying selection.”  This presumes that certain stretches of DNA are so important, so indispensable, that natural selection protects them from change and is vigilant about correcting mutations.  Thus, purifying selection is the converse of natural selection: instead of selecting positively for a new function, it selects negatively against change.
    Yet the authors of this paper do not seem completely satisfied with this explanation.  For one thing, not all ultraconserved elements are in the exons of active genes that code for proteins.  Many exist in introns and other regions thought to be “junk DNA.”  Why would natural selection preserve junk to a high degree of accuracy for millions of years?  The implication is that it’s not junk at all, but something vital to the regulation of gene expression.
Non-exonic ultraconserved elements are often found in “gene deserts” that extend more than a megabase.  In particular, of the non-exonic elements, there are 140 that are more than 10 kilobases (kb) away from any known gene, and 88 that are more than 100 kb away.  (See also 10/16/2003 headline.)
Indirect evidence suggests that these segments, far distant from genes, are important for regulating embryonic development or act as “distal enhancers” of the genes.  Simple scaffolding they are not.
    It is true that these ultraconserved elements do not extend to distant species, such as between humans and jellyfish or fruit flies; yet extreme conservation is apparent even among the more primitive lineages, going back to the earliest chordates.  The best that evolutionists can explain is that rapid evolution occurred in these regions in the past, then stopped in its tracks: “the bulk of the ultraconserved elements represent chordate innovations that evolved fairly rapidly at first but then slowed down considerably, becoming effectively ‘frozen’ in birds and mammals.”
    When the scientists searched for conservation in shorter segments, they found it everywhere:
A more extensive analysis of paralogs, based on a recent global clustering of highly conserved noncoding human DNA, reveals several further highly conserved intronic and intergenic elements in functionally equivalent positions relative to paralogous genes.  These were not classified as ultraconserved by our stringent criteria.  Indeed, if we merge alignment blocks of 200 bases, each with at least 99% identical columns, we obtain 1974 “highly conserved” elements up to 1087 bp long in the human.... If instead we demand at least a 100-bp exact match between humans and rodents, we get more than 5000 highly conserved elementsTens of thousands more are found at lower cutoffs; for example, there is a 57-bp exactly conserved sequence overlapping an alternatively spliced exon of the WT1 gene which is invariant in mammals and in chickens and is largely conserved in fishes (fig. S1).  The percentage of the conserved elements that overlap with a known coding region steadily rises from 14 to 34.7% as the length criteria defining these elements is reduced from 200 to 50 bp (table S6).
    If experiments with less conserved elements in recent studies are any indication, many of these shorter elements are also functional.
The scientists put these findings into three possible explanations: (1) either strong purifying selection is 20 times better at correcting mutations in these regions, or (2) the mutation rate is 20 times slower, or (3) a combination of both.  The importance of these regions must be extreme if the strong negative selection is the reason; does the conservation of active gene exons create structures that “must be extremely constraining over hundreds of bases of DNA”?  Perhaps, but questions remain for either explanation.  The article concludes on a question mark:
On the other hand, if reduced mutation rates are the explanation, then the existence of regions of a few hundred bases with 20-fold reduced mutation rates would itself be quite novel.  Although neutral mutation rates may vary depending on chromosomal location on a megabase scale, there is to our knowledge no evidence or precedent for the existence of short “hypomutable” or “hyperrepaired” neutral regions.  Finally, the answer could also be a combination of negative selection and better repair in these regions, owing to some vital role that these elements play, such as self-regulating networks of RNA processing control in the case of exonic elements and self-regulatory networks of transcriptional control for non-exonic elements.  In any case, the questions remain: What kind of elements associated with these processes would have arrived relatively early in chordate evolution and then become practically frozen in birds and mammals?  And what mechanisms would underlie this, allowing them to resist virtually all further change?
New Scientist June 3 reports an experiment the deepened the mystery: mice born without the some of the ultraconserved regions do just fine.  This announcement produced “gasps of amazement” at a scientific talk, the article says, because it was assumed if they were so conserved, they must be important for survival.  A team deleted 1000 highly conserved sequences shared between humans and mice, and found the lab mice to be virtually identical with normal mice in every measurement: growth, lifespan, metabolism, and overall development.  One of the deleted segments was over 1.6 million DNA bases long.  Perhaps backup copies exist on other chromosomes for redundancy.  The article puzzles over why some of the ultraconserved regions showed higher levels of conservation than many genes.  “What’s most mysterious is that we don’t know any molecular mechanism that would demand conservation like this,” one researcher said.
1Bejerano et al., “Ultraconserved Elements in the Human Genome,” Science, Vol 304, Issue 5675, 1321-1325, 28 May 2004, [DOI: 10.1126/science.1098119].
It was supposed to be so easy.  Where fossils and comparative anatomy failed to confirm Charlie’s story, the genes would come to the rescue.  Now this.
    The only way the Darwinians can keep their story going now is to propose that evolution is both lightning-fast and then frozen.  Somehow, brainless early chordates invented all kinds of elaborate molecular mechanisms, then put them under the Law of the Medes and the Persians; these regions of DNA could not be altered.  Thenceforth, genomes underwent fantastic degrees of evolution by natural selection, creating flying reptiles, flying birds, flying mammals and flying fish, blue whales, giraffes, lizards, peacocks and people, while these ultraconserved regions, exposed to all the natural forces affecting the other parts of the genome, remained steadfast and immovable.  Strong positive selection played fast and loose with genes, duplicating and recombining and mutating them and adding introns with seeming reckless abandon.  Simultaneously, strong purifying selection kept the ultraconserved regions virtually untouched.  All the while, genetic drift threw in a few neutral mutations at random that somehow didn’t touch the ultraconserved regions.  Ockham would slash away like a knight at this convoluted concoction of explanations.
    These findings may shed additional light on the mystery of introns, those sections of DNA that the transcription machinery cuts out and apparently discards (see 09/03/2003, 09/12/2003, 05/10/2004 and 05/19/2004 headlines).  It would seem evolutionists would predict just the important functional genes to be conserved, if anything; why would introns be conserved, unless they too are vital?  There is clearly much we don’t know yet.  While some differences between animal genes appear to be functions of their assumed ancestral distance, many others do not.  The picture is getting very complicated for the Darwin Party.  God must have had a sense of humor.
Next headline on:  Genes and DNADarwinism and Evolutionary Theory.
Exercise Your Nerves   05/27/2004
A team of neurologists from UCLA and duPont Hospital for Children in Delaware found that voluntary exercise improves regeneration of neurons, both for those who work out, and for those recuperating after injury.  The abstract in PNAS1 states:
Recent advances in understanding the role of neurotrophins on activity-dependent plasticity have provided insight into how behavior can affect specific aspects of neuronal biology.  We present evidence that voluntary exercise can prime adult dorsal root ganglion neurons for increased axonal regeneration through a neurotrophin-dependent mechanism.  Dorsal root ganglion neurons showed an increase in neurite outgrowth when cultured from animals that had undergone 3 or 7 days of exercise compared with sedentary animals.  Neurite length over 18-22 h in culture correlated directly with the distance that animals ran.  The exercise-conditioned animals also showed enhanced regrowth of axons after an in vivo nerve crush injury. Sensory ganglia from the 3- and 7-day-exercised animals contained higher brain-derived neurotrophic factor, neurotrophin 3, synapsin I, and GAP43 mRNA levels than those from sedentary animals.  Consistent with the rise in brain-derived neurotrophic factor and neurotrophin 3 during exercise, the increased growth potential of the exercise-conditioned animals required activation of the neurotrophin signaling in vivo during the exercise period but did not require new mRNA synthesis in culture.  (Emphasis added.)

1Molteni et al., “Voluntary exercise increases axonal regeneration from sensory neurons,”
Proceedings of the National Academy of Sciences USA, 10.1073/pnas.0401443101.
Couch potatoing can’t be good for you.  Use it and improve it.  The discovery that neurons can be regenerated should be good news for those who have suffered injury.  Physical therapy may be painful, but it offers hope.  Grin and bear it for as long as it takes.  Hopefully you’ll be grinning more eventually.
Next headline on:  HealthHuman Body.
Human and Chimp DNA Compared   05/26/2004
Yesterday’s entry “Humans and Chimps Compared” (see
05/25/2004 headline) dealt with outward characteristics between us and our furry fellows in the zoo, but now we have DNA to compare.  Bonzo is asking, “Am I my keeper’s brother?”  Evolutionary scientists think so, and for the first time are beginning to quantify the differences between us, at least in terms of our libraries of genetic instructions.  Initial findings are sure to provide lively debate over how to answer Bonzo.  According to a preliminary review of the ongoing genome comparison project by Jean Weissenbach published in Nature,1 (see also Nature Science Update), there are both confirmations of expectations and whopping surprises.  NSU states, “Thousands of chimp genes could significantly differ from those in humans,” and, “Chimp chromosome creates puzzles; First sequence is unexpectedly different from human equivalent.”  (The same issue of Nature also contains the first detailed analyses of human chromosomes 9 and 10.)
    For the first time, scientists have compared two whole chromosomes that have been completely mapped: human chromosome 21, and its chimp counterpart, chromosome 22.  As expected, there were many similarities: less than 1% of the sequences that could be aligned had differences in one base over another (single-nucleotide polymorphisms, or SNPs).  The actual statistical difference is not yet known accurately, however, since SNPs exist between humans also, and only one chimp’s DNA has been sampled.  What surprised the team was the “impressive” number of small-to-large sections of DNA that they believe had been either inserted or deleted (indels) as the species diverged.  Some 68,000 indels were counted, most 30 nucleotides long or less, but some up to 54,000 nucleotides.  Some of the 300-nucleotide sections could be explained as transposable elements, particularly Alu repeats, which seem to have occurred more often in humans.  Weissenbach expresses the reaction to this finding: “The number of single-nucleotide substitutions is in the range found in earlier studies, but the frequency and size of the indels are more of a surprise” (emphasis added in all quotes.)
    More interesting are the protein-coding regions.  Here again, there were expected similarities yet surprising differences:
Given the broad similarities between chimps and humans, many researchers thought that changes that alter amino-acid sequences would not be very frequent.  Surprisingly, however, the consortium found that sequence differences in the protein-coding regions of genes are not a great deal less common than in non-coding genomic regions.  But some of the affected genes might be pseudogenes — defective copies of functional genes – that have arisen recently.  And, among 231 presumably functional genes that could be compared between chimps and humans, 179 have protein-coding regions of identical length; 140 of the predicted encoded proteins would differ by one amino acid or more, but probably with little or no functional impact.  Of the other 52 genes, however, 47 show more significant structural changes.
(For more on pseudogenes, see 05/13/2004 headline).  And that wasn’t the only significant difference.  The scientists found big differences in how some genes are expressed.  Weissenbach reveals some chagrin at how this complicates the answer to Bonzo’s question:
The consortium could not resist making preliminary studies of the expression of the genes on human chromosome 21 and chimp chromosome 22 as well.  Their analyses indicate that – looking at just two tissues – about 20% of these genes show significant variations in their expression.  Extrapolation from these findings suggests that if this chromosome represents about 1% of mammalian genes, there may well be thousands of genes that either encode an altered protein or are expressed differentially in humans and chimpanzees.  This will not simplify the search for the hypothetical key genetic changes that prevented us from remaining as apes.
Weissenbach points out another surprise; the FOXP2 gene, which some evolutionists had suspected (based on mutation studies in humans -- see 08/15/2002 headline) was the key mutation leading to the origin of language in humans, differs by only 2 amino acids in chimpanzees.  There must be more to language than this gene, because despite the similarity, Bonzo has a hard time carrying on a conversation with us (see 05/25/2004 headline).
    So these early findings are not yielding simple answers.  Even though analysis is just beginning, these findings do not seem to fit what Darwin predicted, as Weissenbach hints in his conclusion: “Even if the major physical, physiological and behavioural differences between the two species do not result simply from an accumulation of many small alterations, the challenge to find the most crucial changes is still ahead.”  Maybe his whimsical opening sentence has some prescient overtones: “There are good reasons to continue the endeavour to accumulate genome sequence data from the passengers of Noah’s Ark.

1Jean Weissenbach, “Genome sequencing: Differences with the relatives,” Nature 429, 353 - 355 (27 May 2004); doi:10.1038/429353a.
Here is the abstract of the report from the International Chimpanzee Chromosome 22 Consortium in the same issue:2
“Human–chimpanzee comparative genome research is essential for narrowing down genetic changes involved in the acquisition of unique human features, such as highly developed cognitive functions, bipedalism or the use of complex language.  Here, we report the high-quality DNA sequence of 33.3 megabases of chimpanzee chromosome 22.  By comparing the whole sequence with the human counterpart, chromosome 21, we found that 1.44% of the chromosome consists of single-base substitutions in addition to nearly 68,000 insertions or deletions.  These differences are sufficient to generate changes in most of the proteins.  Indeed, 83% of the 231 coding sequences, including functionally important genes, show differences at the amino acid sequence level.  Furthermore, we demonstrate different expansion of particular subfamilies of retrotransposons between the lineages, suggesting different impacts of retrotranspositions on human and chimpanzee evolution.  The genomic changes after speciation and their biological consequences seem more complex than originally hypothesized.”  (Emphasis added.)
2“DNA sequence and comparative analysis of chimpanzee chromosome 22,” Nature 429, 382 - 388 (27 May 2004); doi:10.1038/nature02564.
Did you catch that?  Weissenbach just said, “Even if the major physical, physiological and behavioural differences between the two species do not result simply from an accumulation of many small alterations...” – that indirectly but clearly says they don’t.  Now what, do you recall, did Charlie propose as a test to confirm or falsify his theory?  “If it could be demonstrated that any complex organ existed which could not possibly have been formed by numerous, successive, slight modifications, my theory would absolutely break down.”  Thank you, Charlie!  The implosion was very entertaining.  (If you think this will make evolutionists pack up and go home, you underestimate the power of the Darwin Party to change the rules.)
    It’s time to lay to rest once for all this mythoid that humans are 98.5% similar to apes.  It’s a prime example of the misuse of statistics and the use of card stacking.  Some gullible souls swallowed this bogus statistic and reasoned that chimpanzees should have the same civil rights as human children (see 05/24/2002 headline); others took it and decided humans should be lumped into the same genus with Bonzo.  Good grief.  Now at last the truth is coming to light.
    Creationists have always expected similarities as evidence of common design, and evolutionists have desperately longed for empirical evidence of common descent.  We’re barely off square one in comparative genomics.  Clearly there are many questions and puzzles ahead for both sides.  Will comparisons with other chromosomes fit this trend?  How similar would genes of other chimps be to this individual’s genome?  What similarities and differences will gorilla and orang-utan genomes reveal?  Are “pseudogenes” really evolutionary leftovers, or do they have a function? (see 05/13/2004 headline).  What is the effect of single-nucleotide polymorphisms?  How many SNPs can a genome tolerate?  Do indels have a function?  How, and how often, do they occur?  Why so many introns?  Why do Alu elements hop around the genome?  It’s too early to answer these and many other questions, but the initial findings are tantalizing.
    Now that Darwinism has been falsified (if we can connect Weissenbach’s comment to Darwin’s test literally), there are still good reasons to gather information from the passengers of Noah’s Ark
Early ManGenes and DNA
Hippos Sweat Their Own Sunscreen    05/25/2004
You know that reddish fluid on hippo skin that turns brown?  It’s not just funny colored sweat.  Japanese scientists reported in Nature1 that it acts as a sunscreen and an antibiotic.  See also the
BBC News report on this finding.
1Saikawa et al., “Pigment chemistry: The red sweat of the hippopotamus,” Nature 429, 363 (27 May 2004); doi:10.1038/429363a.
It must have been a sight watching the Japanese timidly wipe the face and back of a hippo to get their samples.  Wonder how many generations of hippos had to die of skin cancer to get this lucky set of mutations established in the population.
Next headline on:  MammalsAmazing Facts
Can a Cell Improve by Lowering Its Standards?    05/26/2004
The title of a paper in PNAS is intriguing: “Artificially ambiguous genetic code confers growth yield advantage.”  An international team claims to have created a beneficial mutation.  They removed the editing ability of a protein involved in translating the genetic code, and got it to survive in a nutrient-starved environment.  They suggest that the resulting misspellings might have provided a primitive cell with more options for evolution.
    The protein they mutated is one of the family of 20 molecular machines that hitches the correct (canonical) amino acid to its DNA template (anticodon).  One of these aminoacyl-tRNA synthetases has a hard time distinguishing between two very similar amino acids, isoleucine and valine, so an additional “editing” step corrects any “typos” that occur.  These scientists essentially removed the editor.  Then they gave the cell stronger concentrations of valine and other noncanonical amino acids, some of which are toxic.  On the one hand, the wild-type (normal) strain with the editor did better under high concentrations of toxic noncanonical amino acids.  But when starved for isoleucine, the mutated strain, without the editor getting in the way, had more options.  This apparent flexibility led the scientists to suggest that such looseness in standards could have been an advantage during the early evolution of the genetic code:
In summary, a stable and robust strain with an ambiguous code, and thus harboring statistical [e.g., non-coded] proteins, was created by irreversible ablation of the editing activity of a single tRNA synthetase.  The WT [wild-type, or normal] strain, with its full complement of editing activities, has the decided advantage of being more resistant to the potential toxicity of elevated concentrations of noncoding amino acids (for example, norvaline) (Figs. 3 and 4).  However, the editing-deficient strain with its statistical proteins has the capacity to use noncanonical amino acids to fill in at codons specifying (but starved for) particular amino acids such as isoleucine.  This capacity is advantageous in circumstances when the organism is confronted with modest concentrations of various amino acids that might have been the only available building blocks for proteins in an early environment.  The lack of both specific resources and competing species may have favored early organisms that could maximize yield and therefore maximize the chances of spreading to new resource patches that would otherwise go unused.  Thus, organisms with the capacity to generate statistical proteins could plausibly have served as intermediates in the evolution of early living systems.   (Emphasis added in all quotes)

1Pezo et al., “Artificially ambiguous genetic code confers growth yield advantage,”
Proceedings of the National Academy of Sciences USA, 10.1073/pnas.0402893101, published online before print May 26, 2004.
If lies and nonsense make you angry, you should be angry at this paper.  You should not be intimidated by the fact it was written by nine PhDs.  You should not be swayed by its presence in the journal of the prestigious National Academy of Sciences.  You should not be dazzled by the jargon.  If it’s baloney, it stinks as bad in a castle as in a shack.
    These scientists, drunk on Darwinism, are trying to make us believe that lowering your standards makes you stronger.  By analogy, firing the proofreader makes the newspaper better.  Firing the coach makes the athlete stronger.  Firing the sergeant makes the army squad better prepared for the contingencies of battle.  Baloney, baloney, baloney.
    When in a restaurant, will you maintain better health by restraining your baser appetites and restricting yourself to a well-balanced meal?  Of course.  But if you were trapped in a candy store, could you survive a little while on chocolate?  Delicious in small quantities, and better than going hungry, that doesn’t mean you should make it your daily diet.  These scientists forced normal cells to be starved for isoleucine, an essential nutrient for healthy proteins.  The normal cells did not want to eat the unhealthy ingredients that were available; they had a coach ordering them to keep off the chocolate.  But other cells, free of such discipline, engorged themselves and at least didn’t starve.  So the fatsos outqualify the hunks for the Olympics.  If you can believe that, you can believe the phony baloney premise of this paper.
    Darwinian articles often dodge personal responsibility by (1) flat-out bluffing, or (2) using passive voice verbs that cover up their own shame.  Look at this example: “The modern genetic code appeared ~3 billion years ago [Sez who?  Were you there?] .... The code itself is thought to have started in a primitive form [Who thought so?  Own up, you Darwin Party dogmatists], perhaps with codons composed of two rather than three nucleotides [where is the evidence for that?] and with different amino acids not precisely assigned to specific codons” [who made up this howler?]  It sounds pompously aloof to say “It is thought” rather than “I think this elaborate, complex system of codes and translators began from random letters in a primitive soup.”  By saying It is thought and leaving the subject undefined, the propagandist gives the reader a subliminal impression that somebody important thinks so, somebody authoritative thinks so, or that everybody who knows anything thinks so.  Don’t be fooled.
    Did these scientists find any evidence that their lowering of editing standards actually made their variants fitter?  No.  Did they demonstrate that the incorporation of noncanonical amino acids into the protein conferred any new functional advantage?  No.  Did they provide any empirical evidence that the genetic code began in a primitive state, without proofreading?  No.  Did they provide any historical evidence, or any analogies from present systems, that a complex, proofreading system can improve by lowering standards?  No.  Did they use certified lab techniques?  Yes.  Did they use their brains?  No.
    One thing they did do: they won Stupid Evolution Quote of the Week:  “Because they could opportunistically use whatever amino acids were available to complete a protein sequence, organisms harboring statistical proteins could have had a selective advantage in a primitive environment.  Also, by having many closely related versions of the same basic sequence, variants with a particular catalytic activity could be produced.  These microvariants might have special adaptive advantages, much in the way that one or more mutations in an enzyme can enhance its activity or broaden its specificity.  The selective advantages of more complex organisms that were able to produce their own amino acids and are dependent on higher specificity eventually forced replacement of the ancient statistical systems.  Remains of ambiguous codes are still observed in nature as in the Leu/Ser ambiguity in Candida sp. [prove it].”  Coulda, woulda, shoulda.  Gimme a break.  I thought I was in science class, not Fantasyland.
    As explained earlier (see 07/21/2003 and 06/29/2003 headlines), the aminoacyl-tRNA synthetase family of enzymes comprise an exquisite, complex system that relies on accuracy, and they know it.  They admit, “The genetic code is established in reactions catalyzed by aminoacyl-tRNA synthetases, in which each amino acid is covalently joined to its cognate tRNA.  The tRNA bears the complementary nucleotide triplet of the code corresponding to the attached amino acid.”  In cases where similar amino acids might incorrectly attach, “Certain synthetases, including isoleucyl-tRNA synthetase (IleRS), have a second active site that clears mischarged amino acids and thereby removes errors of aminoacylation.”  The existence of code-translation and quality-control systems are hallmarks of intelligent design.
    Furthermore, they admit that incorrectly attached amino acids can be toxic: “Valine is the obvious starting point because of its structural similarity to isoleucine.  However, the effects of valine are difficult to measure because of its general toxicity in minimal media, caused by feedback inhibition of the isoleucine biosynthetic pathway.”  In other words, not only are there systems to edit out the wrong amino acid, but there are feedback pathways to ensure the toxic substance does not proliferate in the cell.  They admitted that the noncanonical amino acids were toxic: “As expected, high concentrations of valine or norvaline ultimately became toxic in the editing-deficient strain but not in its WT counterpart.
    Only in a very specific environment, where the normal cell was starved and their carefully-engineered mutant was given preferential treatment, did they see it outcompete the champ.  And on this, they want us to believe that life, the genetic code, its translation machinery, molecular factories of tens of thousands of protein motors and enzymes “emerged” by chance into streamlined tunas, fast-focus cormorant eyes, human composers, and all the rich and varied life forms today.  Thereon hangs a tale: not a tale of science, but a fairy tale about a fictional place where one needs to believe six impossible things before breakfast – Fallacy in Blunderland.
Next headline on:  Genes and DNADarwinism and Evolutionary TheoryDumb Ideas.
Humans and Chimps Compared   05/25/2004
In case you had an identity crisis last time at the zoo, Current Biology can provide psychoanalysis.  The May 25 issue posted two articles side by side: one, simply entitled “Humans,”1 and the other, “Chimps.”2  Various comparisons are contrasts are drawn, including a few surprising facts, such as this statement: “Based on relative amounts of genetic variation, humans are more endangered than chimps!”
    Both articles are noteworthy for what scientists don’t know, more than for what they do; a number of controversial issues are discussed, such as whether humans are still evolving, how much humans are affecting the environment, what races mean (if anything) and how they should be defined, and whether humans should be reclassified with the chimps based on sequence similarity of genes, or on the other hand, whether humans, due to their cognitive/mental abilities, deserve to be classified in their own kingdom: “Psychozoa” (Gr., soul-life).
    Neither article questions the Darwinian assumption that humans and chimps diverged from a common ancestor 5-6 million years ago.  But neither do they dispute that the most distinguishing characteristic of humans is language.  Linda Vigilant writes in the “Chimps” article,
One defining human trait that chimpanzees lack is language.  Although some captive chimpanzees and bonobos have been laboriously taught to use sign-language or communicate using icons on a keyboard, it seems that their communicative abilities in the wild fall far short of what we do with language, and so this chimpanzee–human difference remains profound.   (Emphasis added.)
How and when this skill arose in humans is unknown and the subject of much dispute among primate zoologists.
    See also
05/26/2004 headline, “Human and Chimp DNA Compared.”
1David A. Hughes, Richard Cordaux, and Mark Stoneking, “Humans,” Current Biology, Vol 14, R367-R369, 25 May 2004.
2Linda Vigilant, “Chimps,” Current Biology, Vol 14, R369-R371, 25 May 2004.
These articles contain some interesting facts and useful information, but are imbued with the typical Darwinian fluff and storytelling about how our primitive ancestors arose in Africa millions of years ago, invented fire and language and took over the world (now read this).  Every element of the plot has its detractors willing to point out contrary evidence.  The first article wrongly repeats the mythoid that humans are 98% to 99% identical to chimpanzees in terms of genetic sequences, a phony figure (see 10/25/2002 headline).  But it does rightly point out that gene expression may be much more significant than the contents of the DNA library, as seen from comparisons with the genomes of other organisms: “In other words, it’s not so much what you have, but what you do with what you have, that matters.”  That’s true for me and thee and the chimpanzee.
    It is a legitimate biological investigation to analyze human mammalian characteristics and to draw comparisons and contrasts with our fellow creatures.  We are, as Wernher von Braun once described it, “souls cast into animal bodies.”  Animals are fun to watch and have as companions.  We have a lot in common with them, especially other primates.  But there is no evidence, and there are numerous problems, trying to relate us all to a common ancestor or reducing humans to mere genes in motion.  Language, for instance, truly is a “profound” difference, with no parallel in the animal world.  But what is language without cognition, and what is cognition without the ability to think in abstract thoughts?  Even dogs and crows have intelligence, but no animal uses logic or writes books on philosophy.  How did the laws of logic evolve?  Why would natural selection produce a physicist able to compute 23 decimal places of a cube root in his head?  Why do we care about justice?  What is the survival value of writing a symphony?  Humanness is all about soul.
    The articles also fail to recognize many other human distinctives, such as conscience, bipedalism, naked skin and enhanced touch, blushing, laughter, the moral sense, art, music and religion.  None of these can be demonstrated by a sequence of transitional forms, and none can be explained by genetic mutations and natural selection; they go far beyond the necessities of biological survival.  Understood instead as the handwork of a Designer who wants to be known by creatures made in His image, they make possible a unique realm of communication with one another and with our Maker that no animal can share.  Chimps have nostrils, but what makes us distinctively human is that our Creator breathed into our common (human) ancestor’s biological nostrils the breath of life, and man became a Psychozoa, a living soul (Gen. 2:7).  Yes, we deserve a kingdom of our own, but what’s a kingdom without a King?  Read the following passages with this view of man in mind: Isaiah 57, and I John 1-2.  They express issues and ideas no chimp will ever comprehend.
Next headline on:  MammalsEarly ManDarwinism and Evolutionary TheoryBible and Theology
Red Planet News; Ring World Beckons    05/25/2004
Let’s drop in on Mars for the latest findings.  The two
Mars Exploration Rovers are still doing splendidly; Spirit has its goal mapped out, a tour of the Columbia Hills where rock outcrops beckon geologists.  It recently crossed the 1.5 mile mark and set a single-day distance record, covering more than a football field with its autonomous guidance controls.  Its turf, Gusev Crater, turned out to be drier than expected.  Over on the far side, Opportunity has been circling Endurance Crater wondering whether to drop in for a visit.  (Scientists want to be sure that it can get out again.)
    The only surface-based evidence for past liquid water has come from Opportunity.  At several sites now, the rover detected layers and concretions that are consistent with salty water existing for a period of time.  From orbit, however, one of the most striking evidences for water flow has just become ambiguous.  The BBC News reports that the gullies streaming down some craters may have a dry explanation: rockfalls and slumping sand in the lower gravity could produce the stream-like channels, according to a paper in PNAS1.
    With rovers and orbiters in good health, more surprises are sure to come.  Some of the coolest 3D pictures are now coming from Europe’s Mars Express.  JPL hopes to catch up next year with its Mars Reconnaissance Orbiter, which, with its huge camera, “will make a more comprehensive inspection of Mars than any previous mission.”  Instead of resolving areas the size of Bonneville Salt Flats, it will detect features as small as a Yellowstone hot spring.  It will also search deeper below the surface with its ground-penetrating radar.
    Not to be forgotten, the 2001 Mars Odyssey celebrated 10,000 mapping orbits recently, and the venerable Mars Global Surveyor is still adding to its huge inventory of photographs.  All three orbiters are assisting the rover program by relaying images to earth and helping identify features of interest.
    Politically, the future is bright for Mars exploration.  At a town hall meeting at JPL today, Senator Sam Brownback (R., Kansas) and Congressman Dana Rohrabacher (R., California) invited feedback from the scientists and engineers about the President’s Moon, Mars and Beyond initiative for NASA.  Opinions were divided between the value of manned vs. robotic missions, but no one discounted the power of space exploration to inspire the next generation of adventurers.
    Far beyond Mars, the giant Cassini spacecraft is racing to home plate at Saturn.  New images are coming in almost daily at the Cassini website and also at the imaging team site.  Next highlight will be a close flyby of the little satellite Phoebe on June 11, sure to keep the world wide-eyed at the nature of this “wrong-way” moon.  Just a fuzzy ball yet, Titan is looming in the distance, the target of the daring and ambitious Huygens Probe.  Built by ESA, it will attempt to parachute below the smoggy clouds and reveal the surface for the first time.
    Educators will want to contact the Cassini outreach department to get a copy of Ring World, a beautiful DVD animation made especially for planetaria, and stunning on a wide-screen TV.  It gives viewers a theater-style visual overview of the entire Cassini/Huygens mission to Saturn and Titan.  Highlights from the film are downloadable in QuickTime format.
1Shinbrot, Duong, Kwan, and Alvarez, “Dry granular flows can generate surface features resembling those seen in Martian gullies,” Proceedings of the National Academy of Sciences USA, 10.1073/pnas.0308251101 (published online May 28).
These are great days of planetary exploration.  We can feel somewhat like the townspeople of 1804 felt as Lewis and Clark left St. Louis to explore terra incognita and started sending back samples from upriver.  It will take years to sort out all the data and figure out what it means.  For now, it’s time to enjoy the ride of a lifetime.
Next headline on:  MarsSolar System
Stem Cell Cover-Up?    05/24/2004
Stem cells, most have heard, hold promise for many life-saving cures.  Michael Fumento in
Insight Magazine claims that while adult stem cells have shown many positive results, the media and science establishments tend to hype the benefits of embryonic stem cells while glossing over the ethical and moral problems they present.
    Recently, Nature1 published an editorial about the ethical controversy in Korea, in which a lab working on therapeutic cloning pressured female students to donate their eggs for the study.  Noting that to some, “the idea of creating a human embryo and culturing it for several days to obtain stem cells that would be needed to grow such grafts is morally reprehensible,” the editorial says the last thing cloning research needs now is further ethical controversy.  “If the air is not cleared quickly, the consequences for Korean science – and for research into therapeutic cloning internationally – could be severe.  It will be a tragedy if one of the greatest scientific stories of the year ends up being remembered, in South Korea especially, as one that lost the trust of the people.
1Editorial, “Ethics of therapeutic cloning,” Nature 429, 1 (06 May 2004); doi:10.1038/429001b.
Nature seems to miss the point.  It is more concerned about whether the women were coerced than whether creating human embryos just to destroy them is morally reprehensible or not.  While some techniques may really help those with debilitating genetic diseases, we cannot assume scientists all operate from pure motives.  Fame and fortune seduce many a mortal.  Just because some things can be done, that doesn’t mean they should be done; and in a Darwinian world, who decides?
Next headline on:  Politics and EthicsHealth
Plant Evolution Modeled in Computer   05/24/2004
Simulation games are popular on computers.  Darwinian biologists seem to like them, too.  What they cannot go back in time to observe, they sometimes try to recreate in silico, inside the silicon chips of a computer.  Karl J. Niklas (Cornell) tried to simulate plant evolution, and wrote about it in Annual Review of Earth and Planetary Sciences.1  He feels his contribution was to demonstrate that plants had to be multitasking specialists: they optimized competing interests in a dynamic environment, rather than achieving perfection with any one structure.  This involved tradeoffs; a horizontal stem might provide the best light-gathering stance, for instance, but puts the plant at the burden of having to fight gravity’s leverage:
Indeed, when viewed with a biophysical or engineering perspective, none of the basic biological tasks plants perform can be maximized without decreasing or imperiling the performance of another necessary task.  In this sense, the relationships among organic form-function generally involve optimization rather than maximization.  But differently, single-tasked devices can perform their ascribed functions perfectly, at least in theory.  In contrast, multitasked devices, whether organic or inorganic, invariably involve compromises and tradeoffs—they perform all of their ascribed tasks reasonably well, but no task perfectly.
(Emphasis added in all quotes; for more on evolutionary tradeoffs, see
05/11/2004 headline.)
The origin of land plants “sparked one of the most dramatic bursts of diversifying evolution in the history of life,” he claims, indicating the motivation for this project.  In just 46 million short years from the Silurian through the Devonian, these pioneering plants had “diversified phyletically and structurally to encompass all of the major land plant lineages and the full spectrum of organizational grades represented in present-day floras, with the exception of flowering plants.”  He lists 11 innovations they introduced, from branching stems to leaves to stomata with guard cells to seeds and wood.  They employed sexual reproduction with alternation of generations and diversified into an enormous number of morphologies, from mosses and ferns to pines and giant redwoods.  “Why plant evolution was so rapid during the Late Silurian-Devonian time interval remains problematic,” he admits.  “Lessons drawn from evolutionary theory provide limited insights”  Thus, computer modeling to the rescue.
    For his model, Niklas used a principle proposed by Sewall Wright in 1931: the fitness landscape, a “heuristic device” that visualizes evolution as “a series of walks over fitness landscapes with adaptive hills and maladaptive valleys.”  On this landscape, Niklas placed his digital plants and gave them four competing problems to solve: (1) water conservation, (2) mechanical stability, (3) spore dispersal, and (4) light interception.  He defined the fitness of each combination and set the plants on their “adaptive walk” on the fitness landscape (peaks on the fitness landscape imply high fitness and good adaptation, and valleys imply poor adaptation and low fitness).  First, he used a stable fitness landscape, then he ran it again with a dynamic landscape, which would reflect a more realistic environment changing over time.  He found that overall fitness levels dropped considerably in the dynamic fitness landscape.  How does one decide when to vary the landscape?  “Unfortunately, there are no a priori rules for how or when a particular landscape changes,” he says.  “Therefore, the number of permutations of shifting landscapes is literally astronomically large.”  So he looked to the fossil record for guidance, and also tried to learn from repeated trials what seemed to match natural history.
    In a brief aside, he compared his results to the predictions of Zimmerman’s telome theory – the idea that all of the diverse morphologies of plants can be reduced to the action of five developmental processes – planation, overtopping, reduction, recurvature, and webbing – acting on branched points (telomes) and unbranched points (mesomes).  But telome theory is far from a complete story:
The telome theory has been criticized, and rightly so, for a variety of reasons (Niklas 2000, Kaplan 2001).  One obvious problem with the theory is its vagueness regarding the developmental mechanisms responsible for overtopping, planation, etc.  Indeed, these terms are descriptive rather than explicative in nature.  Another criticism is that the telome theory never explains why certain morphological transformations occur as opposed to others, nor does it stipulate the sequence of processes foreshadowing the appearance of a particular morphology.  Why should planated and webbed lateral branch systems evolve?  Are the leaves of ferns or seed plants functionally adaptive in terms of light interception or some other biological requirement?  Did these megaphylls [broad leaves] evolve as the result of the simultaneous operation of reduction, overtopping, planation, and webbing, or did planation and webbing occur after reduction and overtopping?  Questions such as these can be answered retrospectively (and only in small part) by examining the fossil record, but the telome theory sheds little light on them.
So why use it?  Because the terminology is useful: “Zimmerman’s ideas are nevertheless useful because they provide a lexicon of terms for the morphological transformations observed in the fossil record and for those identified by the computer simulations presented here.  In turn, these simulations suggest the adaptive significance of the transformations envisioned by the telome theory.”
    Niklas produced some digital plants that succeeded in adapting to his fitness landscape, but warned against overinterpreting the results.  In his concluding “Caveats and Desiderata,” he said,
Computer models such as the ones presented here are heuristic tools.  They provide an opportunity to test assumptions about how a particular biological or physical system operates or behaves.  Their validity can be evaluated by comparing predicted with observed behavior.  When observation and prediction disagree, the assumptions upon which a model rests are either incorrect or incomplete.  However, the obverse is not true.  When predicted and observed behavior agrees, the assumptions upon which a model rests cannot be said to be sufficient and necessary.  The reason is simple — model can describe the behavior of a system for the wrong reasons.  This caveat is important, because the only rigorous test of a computer model is to experimentally manipulate the system it purports to describe and to see if the model predicts the outcome for each manipulation.
Niklas did not perform any such rigorous experimental tests with real plants.  He explains why, but still claims his model had merit:
Unfortunately, we cannot experiment with history.  We can only observe it.  For this reason, the most conservative interpretation of the simulations presented here is that six general properties emerge logically (mathematically) from the assumptions made about early vascular plant evolution.  These properties are as follows: (a) the number of equally fit morphological variants is predicted to increase as the number of functional tasks subject to selection increases; (b) the relative fitness of these phenotypes decreases as the number of tasks increases; (c) therefore, morphological diversification is easier on complex as opposed to simple fitness landscapes; (d) constraints on how morphology can be developmentally altered do not a priori limit the number of equally fit variants that can be reached by adaptive walks; (e) however, the relative fitness of these variants is significantly lower than the phenotypic optima that can be reached by unfettered adaptive walks; and (f) adaptive walks on shifting fitness landscapes (used to mimic changes in the focus of selection) identify morphological optima that often differ significantly from those on stable fitness landscapes (used to mimic constant selection).
He points to a few living vascular plants as confirmations of these general predictions, and concludes that the six properties also make biological sense.  Feeling thus justified, he concludes,
Computer simulations of morphological evolution are still very much in their infancy, especially in terms of constructing morphospaces and understanding the developmental mechanisms that permit or confine phenotypic transformations in them (see Thomas & Reif 1993, McGhee 1999, Niklas 2003).  However, as conceptual tools, they provide opportunities to explore the logical consequences of popular metaphors for evolution, such as Sewall Wright’s adaptive walks on fitness landscapes, and by so doing, quantify the possible biological structure and dynamics of opportunistic historical events that distinguish some evolutionary episodes as more adaptive than others.

1Karl J. Niklas, “Computer Models of Early Land Plant Evolution,” Annual Review of Earth and Planetary Sciences, May 2004, Vol. 32, pp. 47-66 (doi:10.1146/annurev.earth.32.092203.122440).
You can prove anything on a computer.  This is so oversimplified, so narrow-minded, so dumb, it’s a wonder any journal would publish such tripe.  It’s only because biologists have offered their brains in sacrifice to Darwin’s image that they cannot see the illogic of their own positions.  Niklas came close, and had a gem of insight here or there,2 but failed to see the worthlessness of his simulation.  His fake plants evolved because he made them evolve.  We’ve seen this so many times before with other computer models.  It is not evolution, it is intelligent design.  These modelers set the fitness goals, define the criteria for success, and reward the ones that get there.  Natural selection has no such guiding intelligence.

2(One perceptive insight he shared was that agreement with predictions does not necessarily make the assumptions of one’s model sufficient and necessary.  But then, contrary to his requirement for rigorous experimental testing, he failed to deliver any.)

    To get a sense of the futility of this model, imagine my writing a simulation about the evolution of computers.  I define fitness scores for screen visibility, mouse responsiveness, keyboard ergonomics and other factors I deem worthy, then start some high-tech devices evolving and reward those that succeed in terms of outward conformance to my specifications.  Maybe I wind up with a variety of objects that look like palmtops, laptops and desktops.  But I describe nothing about programmers or users, nor the thinking required to make a computer.  Is such a result worth anything more than a cheap science-fiction game for kids?
    Let’s understand something important here.  Plants have DNA.  They are adapted because they have complex, specified information in their genes.  Watching little digital organisms evolve branches and leaves and other structures might be cute, but says absolutely nothing about how the genetic information and developmental pathways achieved the structures, and more importantly, says nothing about the intricate cellular processes, like photosynthesis and cell division and sexual reproduction and regulation of stomates originated and employed the morphologies.  Niklas halfheartedly admitted as much.  He should know that plants at the cellular level are fantastically complicated factories of molecular machines.  Which is more intricate: the cover of your computer or the chips and software inside?  If I only pay attention to the morphology of the external parts, I have missed the whole point of what is required to make a computer, or a plant.
    The “fitness landscape” metaphor is only a metaphor, but it is actually a more accurate metaphor than a ramp.  Early evolutionists mistakenly pictured Darwinism like a ramp, on which organisms marched onward and upward.  “Progressivists” viewed natural selection as a “fitness ratchet” leading inevitably to bigger and better things.  Knowledgeable evolutionists today realize this view was simplistic.  There are peaks and valleys of fitness (whatever that is; see Fitness for Dummies, 10/29/2002).  Picture marbles rolling around on a surface constantly in motion, with peaks and pits forming and reforming at random locations.  Real marbles might roll uphill for short periods, but gravity will ensure they tend to inhabit the valleys and pits most of the time.  The gravity in the fitness landscape is the second law of thermodynamics – the inviolable trend toward entropy.  Evolutionists want us to believe that natural selection will overcome this entropic gravity and force the marbles to the tops of the peaks.  Trouble is, even if they got there and stayed there, they would be stuck, unable to evolve further without dropping down into the valley again and losing what fitness they had.  Now realize that the adaptive peaks are like Devils Towers and Space Needles: the exquisite engineering seen in whale flippers and cormorant eyes and spider silk and the other things the biomimetic engineers marvel at are so improbable as to be unthinkable for undirected processes to achieve (despite Richard Dawkins’ claims that chance and natural selection can “climb Mt. Improbable” another fallacy “proved” by worthless computer simulations).  No matter, it’s just a metaphor, and metaphors bewitch you.  Engineering doesn’t emerge without design except in the imagination of evolutionists.
    Niklas said, “Unfortunately, we cannot experiment with history.  We can only observe it.”  When was the last time you observed history?  If you watched a historical event like 9/11, you observed it in the present.  Did you observe the fall of the Roman empire, or the building of Stonehenge?  Did Niklas observe the origin of land plants?  We don’t observe history.  We believe eyewitness accounts and examine artifacts.  Even recordings (artifacts viewed in the present) can have biases, and there were no videotapes of the origin of plants, anyway.  We can observe fossils as they are in the present, but can only infer how they got there; piecing scattered fossils into a sequence is even more fraught with difficulties (see 05/21/2004 headline).  There is no observable history of evolution.  There is a story imposed on the artifacts seen in the present.  An eyewitness account from a credible witness that can be corroborated by observation is superior to a story weaved out of personal bias and propped up by circumstantial evidence.
    By the way, there is a credible eyewitness account that fits the evidence.  It will tell a biologist all he needs to know about the emergence of plants and how they achieved their high levels of adaptive fitness.  It explains not only the outward morphology, but the programming and developmental constraints that maintain fitness.  It’s in that best seller in your hotel room drawer.  Let’s start at the very beginning, a very good place to start.  (Nothing comes from nothing; nothing ever could.)
Next headline on:  PlantsDarwinism and Evolutionary TheoryNext dumb story.

Cormorant Eyes Rapidly Refocus in Dives Into Murky Water   05/24/2004
You’re hang gliding over a lake, and you spot a fish below.  From your hovering position, you drop into a rapid, steep dive headfirst into the water.  Whoops; your eyes just went out of focus, and you lost your fish in the murky depths.  Too bad you’re not a cormorant.
    Cormorants (a kind of waterfowl) are able to adjust the lenses of their eyes from air-focus to water-focus in a split second, according to an article in Current Biology May 25.1  Four Israeli scientists bedazzle us:
Cormorants (Aves; Phalacrocoracidae) are active fliers, yet they forage by pursuit diving and capture of fish with the bill.  In air, the cormorant’s cornea provides most of the total refractive power of the eye.  Underwater, however, corneal power is lost, as the cornea is now bathed in liquids of similar refractive index.  The retention of a sharp image, while performing precise visual tasks underwater, requires that the cormorant’s optical system compensates for the loss of refractive power of the cornea.  In addition, the underwater photic environment differs markedly from the aerial one, with the image quality undergoing a rapid deterioration through scatter and absorption.  Upon submergence, cormorants compensate for the loss of corneal power (>55 dioptres, D) and rapidly (>1000D/sec) attain a state of emmetropia, i.e. they are well focussed, by marked changes in the shape of their very flexible lens.  (Emphasis added in all quotes.)
The scientists somehow acquired accurate measurements of the birds’ optical acuity in air and in murky water.  The birds’ vision is as good as that of fish, seals and whales who spend most of their time underwater.  Cormorants, however, need outstanding vision in water as well as air.  “The requirements to perform precise visuo-motor tasks in two optically different media, and the uniqueness of the lenticular system of these birds,” they note with some admiration, ”make the vision of pursuit-diving birds a model of vertebrate capacities at the extreme.
1Strod, Arad, Izhaki and Katzir, “Cormorants keep their power: visual resolution in a pursuit-diving bird under amphibious and turbid conditions,”
Current Biology, Vol 14, R376-R377, 25 May 2004.
Strod and Arad work at the Hula Valley Nature Preserve in northern Israel; perhaps that is where they made some of the observations.  TV nature programs sometimes show these birds in action.  Next time you see one, you’ll have reason to appreciate even more the elegance of their fishing expertise.
    Once again, this excellent intelligent-design paper was marred by a worthless insertion of the E word, probably because Current Darwin-Worship wouldn’t print it otherwise: they conclude, “Low turbidity levels are commonly encountered in natural water bodies and thus are of crucial importance in our understanding of the evolution, sensory ecology, and micro-habitat selection in aquatic organisms.”  This, as usual, means that nobody understands how these optical marvels evolved, but the Darwin Party hopes to some day.  I wonder if the authors really buy that promissory note.  So how many billion cormorants died of starvation till they got their optics right?  Sorry, 990 dioptres per second isn’t good enough; let’s bump it up to 1000 and make sure all the less fit go extinct.  For sure.  We don’t need such evolutionary whistling in the dark.  Cormorants knew the tune from the top, and in the right key, too; see sharp or be flat.
Next headline on:  BirdsAmazing Facts
Early Humans Refused to Be Classified    05/24/2004
We humans like to classify things, and when we classify ourselves, we sometimes get into trouble.  We create groups of “us” and “them” that breed conflicts.  A fight of sorts is going on between paleoanthropologists, reports Science News1 May 22, over what to make of some skulls found in a cave in Romania.  The skulls are blurring the neat categories most anthropologists had made to distinguish primitive and early modern humans.
    The discovery last June, an Indiana Jones-like adventure involving cave diving into a tomb-like chamber and finding bones of cave bears and human skulls, has the makings of a good movie.  But now that the skulls are in the lab, scientists are scratching their own skulls figuring out where to fit them in the human lineage.  The problem is that they display both “primitive” and “modern” traits: modern cheek bones and no brow ridges, but heavy-set jaws and massive teeth.  Named Oase (wah-see) after the cave in which they were found, the skulls also contain multi-ridged third molars larger than those of Neanderthals.  These bones and another found in Portugal that displays “a potpourri of traits from both species” are causing some anthropologists to suggest that all these varieties of early humans interbred.  That threatens to overturn favorite theories about human evolution:
The Oase skull’s strange combination of modern and archaic characteristics underscores scientific confusion about how to define anatomically modern humans, [Erik] Trinkaus [Washington U at St. Louis] adds.
    “Paleontologists have created an artificial [anatomical] Rubicon that the Oase fossils violate,” he says.  “The blend of traits on these specimens contradicts the existence of a straightforward evolutionary process [during the Stone Age] in which modern humans came out of Africa and replaced everyone else.”
  (Emphasis added in all quotes.)
    In more serious jeopardy is the practice of classification itself.  “One way to make sense of fossils such as the Portuguese child and the Oase skull is to stop assuming that each ancient Homo species existed on a separate branch of an evolutionary tree, says Trenton W. Holliday of Tulane University in New Orleans.”
1Bruce Bower, “Humanity’s Strange Face,”
Science News Week of May 22, 2004; Vol. 165, No. 21, p. 328.
Is it possible to be racist with long-dead humans?  There is a great deal of variation among people groups living today (Watusi and pygmy, etc.), yet they are all 100% human and it is very unPC to discriminate between them.  Variation within a species can be quite pronounced.  Anthropologists seem to be too quick to sort bones into evolutionary lineages without considering the environmental influences on anatomy, such as diet: chewing tough meat might accentuate brow ridges and teeth, for instance.
    This long-fumbling practice of classifying human bones into separate species so as to weave a tale of evolution should be scorned for its phony discrimination.  It’s not science; it is dogma looking for support.  Primitive, my tooth.  These deceased brethren could probably outrun and outsmart any modern paleoanthropologist on the trail of a cave bear.  That takes brains, physical fitness, and complex DNA that is anything but primitive.  Maybe the new paradigm is that humans have been devolving from highly intelligent, skilled, artistic hunters into lazy, obese, foolish storytellers.
Next headline on:  Early Man
Do Fossils Show a Worldwide Record of Evolution?   05/21/2004
The fossil record provides the acid test for evolutionary theory.  Everyone who walks a real dog by a poodle knows that small-scale variation occurs among living species, but non-evolutionists get understandably annoyed when Darwinians extrapolate the observed variations to encompass all of life: as if to say, because finch beaks vary, therefore humans had bacteria ancestors.  Darwin’s bold hypothesis connected all living things into a branching tree of life.  He claimed that, ultimately, whales and oaks and kangaroos and seashells could trace their ancestry to single-celled organisms.  The only way to connect this hypothesis to actual earth history is to examine the fossil record.  Does the record of the rocks show a sequence of life evolving from simple to complex?
    Those who assume so might be disturbed by a paper in the Annual Review of Earth and Planetary Sciences1 by Peter M. Sadler (UC Riverside).  The annual reviews are a good place to catch up on the state of the art of this or that discipline.  Sadler’s review concerns quantitative biostratigraphy, the attempt to correlate global fossil data.  Things are looking up in this field; fossil data are becoming more available in large databases, and computers are making the number-crunching easier.  He takes the reader through the latest computer algorithms that attempt to correlate fossils from tens, hundreds, or thousands of sites around the world into a unified, global time sequence.  Though his lengthy paper never questions evolution (and hardly mentions it), and while written with a tone of scholarly confidence, it gives a distinct impression that biostratigraphy is more art than science.
    Imagine an ideal record where everything that had died left a fossil, and these fossils accumulated upward, layer upon layer, since the beginning of life.  If evolution had occurred, each species would have a first appearance in the record (a first-appearance datum, or FAD), and when it went extinct, it would exhibit a last-appearance datum, or LAD.  These “horizons” would form a vertical timeline for each species, which could be correlated with similar ones around the world.  Assume it were also possible to reliably date each layer.  Tracing the history of life, then, would be a piece of cake; actually, a layer cake, because the layers would preserve a clear sequence, from oldest at the bottom, to youngest at the top.  The fossils they contain, if evolution had occurred, would clearly exhibit increasing complexity as each new phylum, order, class, genus and species appeared through time.
    Alas, as with most things in life, the situation is far from being so simple.  Sadler points out a number of difficulties that make global correlation of fossil-bearing strata a challenge:
  • Imbalance:  Most of the record consists of seashells.  “Richly fossiliferous sections are more common in the marine invertebrate record,” he notes.  (Marine invertebrates actually comprise about 95% of all known fossils.  That means all the large mammals, land plants and dinosaurs make up a tiny fraction of the record).  In a few studies, he claims, biostratigraphers can produce sequences of some marine invertebrates to resolutions of 10,000 to 50,000 years, though resolution is usually much lower.

  • Gaps:  “Relative to marine Cenozoic correlation problems, nonmarine instances suffer from a lack of continuous sections,” he says (emphasis added in all quotes.)  Instead of showing a continuous record of evolution, the record is discontinuous or jerky, riddled with gaps.  (Stephen Jay Gould once remarked that the near universal presence of gaps in the fossil record is the “trade secret” of paleontology.)  Many sites display “isolated faunas” that do not overlap with other sites.  Sadler explains how the gaps affect biostratigraphy:
    Biology demands that the global abundance of a species cannot fall to zero within its temporal range.  Unfortunately, species distributions are patchy, the patches may shift, few individuals are fossilized, and fossils may be overlooked.  Consequently, the local taxon ranges observed in single stratigraphic sections reflect local conditions and do include gaps.  More critically, and for the same reasons, gaps of unknown extent occur at the ends of observed ranges.  Thus, local horizons of highest and lowest finds of a species do not correspond to the global FAD and LAD.  The discrepancies vary from place to place, and locally observed taxon range charts contradict one another in detail concerning the sequence of range-end events.
    For these and other reasons, Sadler warns that it is “crucial to acknowledge that local first and last appearances are also uniquely troublesome as recorders of calendar events: The local stratigraphic horizons at which they are observed do not reliably reproduce the true global sequence of origination and extinction events.  Discrepancies must be expected because local appearances and disappearances are likely to be migration events and probably displaced by lapses in fossilization.”

  • Reworking:  Many fossils have been transported or reworked, destroying the temporal sequence information.  (Some of the best-known fossil sites, such as Dinosaur National Monument, La Brea Tar Pits, and Petrified Forest present this difficulty.)  The biostratigrapher cannot assume the apparent FAD-LAD horizons represent the true history of the fossils, because many processes can disrupt the correlation of fossils with strata: floods can transport fossils from one location to another, burrowing animals can rework the deposits, or deposits can fall into a cave or be washed down well bores into older strata.  Moreoever, it is not always easy to tell when or how much reworking has occurred.  “Severe caving may require abandoning FADs altogether,” he says.  Marine microfossils are especially subject to reworking.  The sometimes “cryptic” signatures of reworking may go “unrecognized,” and their impact on the record may be significant.  Yet the biostratigrapher needs to rely on databases that are contaminated by this problem: “Large integrated databases will combine taxa that are prone to reworking with those that are not.  Decisions about the likelihood of reworking, or the most palatable assumptions concerning reworking, currently force a dichotomous choice between methods that seek maximal ranges and those that seek probable ranges.  No method yet embodies a satisfactory theory of reworking that can obviate this unfortunate choice,” he laments, yet the computer models often assume that little or no reworking occurred.

  • Decreasing Information with Age:  The farther back in time, the less reliable the inputs: for instance, “Paleozoic instances include less radiometric, paleomagnetic, and stable isotopic data.”  The known instances usually do not overlap.  “The large Paleozoic correlation problem in Table 1 includes many pairs of sections that do not overlap in age.  They must be stacked in the correct order and impart to the problem a significant component of seriationSeriation is the essence of the problem when the data are isolated faunas.”

    Considering these difficulties, is it even possible to produce a global correlation of fossils into a time sequence?  Sadler apparently feels the problem is tractable and current work is promising, but the use of simplifying assumptions is unavoidable.  Some are reasonable (e.g., a FAD must precede its LAD, and proven coexistences must be honored).  Also, certain geological events provide a means of independently correlating fossiliferous strata.  A volcanic ash fall, for instance, might be traceable across a large region, or magnetic reversals or global climate changes can provide clues.  In addition, paleontologists try to hitch the data to milestones obtained via radiometric dating (although these are usually not applicable to the sedimentary strata that contain fossils).  Putting it all together is easier said than done:

    The way to improve the resolving power of the geologic calendar is obvious but not easy—increase the number of events and thus reduce the average time intervals between them.  There is no shortage of species to add.  The real problem is to keep all the appearance and extinction events in their correct sequence.  The difficulty increases dramatically with the number of species for three reasons: First, the number of possible sequences of appearance and extinction events grows faster than exponentially as a function of the number of species (Figure 1).  Also, events that are separated by smaller time intervals are more likely to be preserved in contradictory order from place to place.  Finally, as the list of species grows it must include more provincial organisms that will be missing from many locations.
        The bulk of Sadler’s paper concerns various clever mathematical algorithms biostratigraphers have developed to approach this huge puzzle.  Some make use of the principles of operations research.  Some employ heuristic algorithms or manipulate matrices with iterative processes to try to converge on a solution.  Each method is best suited to its own data type, each makes its own assumptions, and each has its shortcomings.  Consequently, he cautions the reader not to expect too much:
    The true global sequence of FADs and LADs is not knowable in detail and the locally preserved sequences of highest and lowest finds are incomplete and contradictory.  The practical and tractable problem is to find a hypothetical sequence of FADs and LADs that enjoys the lowest net misfit with all observations in local range charts and isolated faunas, or requires the smallest net adjustment of all observed ranges.  It is an optimization problem.
    Sadler freely admits that contradictions are inevitable.  Much of his paper concerns dealing with misfits: how to measure misfits, and how to minimize them.  Some of these misfits are those that contradict the expectations of evolution.  One of the criteria for success seems to be how well the result of an algorithm agrees with the “correct” phylogenetic sequence: “Procedures for fitting the best LOC [line of correlation on the graph] include deterministic regression techniques ... and heuristic search algorithms from evolutionary programming,” he explains.  Congruence with evolutionary phylogeny seems to define Sadler’s “best-fit” or “optimal” sequences.  In the opening, he indicates that evolutionary sequence information takes priority over geological dating information:
    Geologic time correlation proceeds by constructing a global calendar of past events in which the appearances and extinctions of fossil species dominate the entries.  Other events include changes in ocean chemistry, reversals of Earth’s magnetic field, and the deposition of volcanic ash beds, some of them dated by radiometric methods.  The challenge is to merge incomplete inventories of physical events and partly contradictory faunal successions from many local thickness scales (measured stratigraphic sections) onto a single calendar that correctly sequences all the events and scales the time intervals between them.  Because correctly sequenced events serve the purpose of correlation, with or without knowledge of their numerical ages, sequencing is the fundamental task and the focus of this review.  Numerical estimates of age are available for very few events, especially in the older periods of the Phanerozoic.  Furthermore, estimates of the relative size of time intervals between events rest largely upon questionable assumptions about rates of sediment accumulation and biological turnover.  Consequently, scaling and calibration tasks are best attempted after the optimal sequence of events has been determined.
    In the conclusion, titled “The Remaining Challenges,” Sadler reveals his discipline’s dependence on evolutionary theory, and drops hints that it needs to be more of a two-way street:
    Paleobiologists can extract considerable information about the phylogenetic sequence of taxa by analyzing the morphology of fossils, without recourse to stratigraphic information.  But these insights do not yet aid the correlation task as much as they might.  To date, more effort has been committed to questions concerning the place of stratigraphic information in cladistic analyses of morphology than to the possibility that the resulting cladograms provide independent evidence of sequence that can improve biostratigraphy.
    How this avoids circular reasoning he does not explain.  Instead, he suggests how evolutionary systematists can help – by revealing, for instance, “the order of FADs that best fits the morphologic information.”  But even with their assistance, he sees three “looming challenges” posed by modern stratigraphic databases:
    1. Deciding on a single method:  “First it is desirable to integrate more data types into a single method.  Every method, regardless of the data to which it is suited, must seek a sequence of events.  Consequently, the best way to suit all the data is to invert the problem, working through a suite of permutable sequences and achieving iterative improvements as judged by the fit between the sequences and the data.”
    2. Speed vs. Completeness:  “But the second challenge is to manage considerably larger data sets without loss of speed.  The flexibility of the inverse approach sacrifices speed.  The fastest algorithms are those that are tailored to specific data types and work forward from the data to the best solution.
    3. Reworked fossils.  As quoted above, “No method yet embodies a satisfactory theory of reworking that can obviate this unfortunate choice” between maximal ranges and probability ranges (that is, choosing between incorporating all the data into the model vs. using the data that produce the expected result).
    .  Are biostratigraphers stuck in a rut?  He ends, “As in the past, answers to all these challenges might be discovered by recognizing analogies with problems in other disciplines and adapting their numerical methods.”
    1Peter M. Sadler, “Quantitative Biostratigraphy: Achieving Finer Resolution in Global Correlation,”
    Annual Review of Earth and Planetary Sciences, May 2004, Vol. 32, pp. 187-213 (doi:10.1146/annurev.earth.32.101802.120428).
    It must be acknowledged that Sadler neither doubts evolution nor intended to cast doubt on evolution in this paper.  A casual reading would lead one to think that everything is fine and the Darwinians are making great progress.  But, if read perceptively, without evolutionary assumptions, it is quite revealing.  Where is the proof of the pudding?  Where is the evidence in the fossil record to prove Charlie right?  Sadler exposes to view what a huge “optimization” problem he has on his hands.  The best he can do is try to keep the “contradictions” and “misfits” to a minimum.
        As with everything else in evolutionary theory, the tweak space is greater than the data space.  Only massive inputs of questionable assumptions keep the story intact.  A story of evolution clearly doesn’t jump out of the data, as if it were an intuitively obvious fact that only an obscurantist would deny.  No; instead of supplying the Darwin Party with the proof they desire, he needs to ask them for help as he stumbles through a contradictory, unmanageable, confusing, formidable task.  It’s reminiscent of the impossible dream the molecular phylogenists face trying to keep Charlie’s imagined tree of life connected to reality (see 07/25/2002 and 06/13/2003 headlines).  In the end, they must assume evolution to prove evolution.  Instead of taking the evidence where it leads, they apply similar heuristic “optimization” approaches to handling overwhelming and contradictory inputs, where “optimal” means “mostly agrees with Charlie, if we neglect the misfits.”
        Notice that “gap” is a loaded word.  What if it is a brute fact that the data are discontinuous?  Then that is the true sequence; there are no gaps.  A gap is only a gap if you assume evolution.  Why not face the evidence squarely: living taxa are discontinuous, and fossil taxa are discontinuous.  They appeared abruptly, and some died abruptly.  If it weren’t that such an admission destroys Darwinism, that would be what the textbooks would matter-of-factly present.
        Skeptical readers are encouraged to put aside “questionable assumptions” about “rates of sediment accumulation and biological turnover,” and to study this article without Darwin-tinted glasses on.  Look at the fossil data as objectively as possible.  What is found?  Multitudes of non-overlapping “isolated faunas” without clear “seriation” information.  A preponderance of seashells.  Unknown effects of reworking.  Fossil graveyards.  Myriads of dead organisms buried in water-laid rock strata all over the world.  Sadler suggests a solution in his ending sentence; biostratigraphers might have better success by looking outside the box and adapting the techniques of other disciplines.  Most likely he did not intend to consider some disciplines that the ruling Darwin Party has placed off limits.  Too bad; what if that’s where the true solution is waiting to be found?
    Next headline on:  GeologyFossilsDating Methods
    Evolution of Jaws: A Hox on Storytelling   05/19/2004
    Lampreys are jawless fish, unlike Jaws and his kin.  M.J. Cohn found that Hox genes are expressed in a lamprey in the first pharangeal arch.  Noting that fish with jaws do not express Hox genes in the first pharangeal arch [PA1], from which the jaws develop, Cohn hypothesized that jaw evolution proceeded with a retreat of Hox expression from this arch.  But an international team publishing in Nature1 found another lamprey with no Hox expression in the arch.  They conclude, “Cohn’s finding is not a general feature within the lamprey group and is therefore unlikely to be related to jawlessness.”  Instead, “ the lack of Hox expression in the lamprey PA1 may reflect the fact that in both lampreys and gnathostomes [jawed creatures] the rostral-most pharyngeal arch forms highly specialized structures that are morphologically distinct from those of more posterior arches” (emphasis added).  The presence or absence of Hox expression in PA1 is “therefore not functionally relevant to jawlessness,” they say.
    1Takio et al., “Evolutionary biology: Lamprey Hox genes and the evolution of jaws,”
    Nature (20 May 2004); doi:10.1038/nature02616.
    Let us understand that evolution cannot advance by losses.  A lamprey is not going to get a jaw by turning off genes.  Is Cohn asking us to believe that there were jaw-making genes that the lamprey decided to turn off?  Clearly not.  But to evolve by losses is like the merchant who lost money on every sale but thought he could make it up in volume.  A jaw is a “highly specialized structure” made of many parts that must fit together.  Cohn’s hypothesis was just a tall tale based on circumstantial evidence and belief in evolution.  At least he was ambidextrous; he could wave his hands and whistle in the dark at the same time.
        It’s getting monotonous to report evolutionary just-so stories that have proven false.  Can we get some positive evidence for a change, instead of jawboning?
    Next headline on:  Fish and Marine LifeDarwinism and Evolutionary Theory
    Selfish Genes Turn Cooperative   05/19/2004
    Nature1 has reported evidence that transposons help to regulate gene expression.  Transposons are genetic material that insert themselves into the DNA of a host, and were thought to represent “selfish genes” that only had their own propagation in mind, “without regard for the consequences.”  Some new studies on the L1 retrotransposon, which makes up about 17% of the human genome (mainly within non-coding introns), have shown, however, that they may do us some good.
        The studies “suggest that the insertion of L1 elements into introns can also diminish cellular gene expression in a graded fashion,” the News and Views piece says.  “In the words of Han, Szak and Boeke, such L1 insertions provide a ‘molecular rheostat’ with which to govern gene activity — and their bioinformatics analysis establishes that the mechanism is widely used.”  (For more on the molecular rheostat concept, see
    01/10/2003 headline).  If the transposons were truly selfish, “responding individually to darwinian natural selection” “without regard for the consequences,” it has “long been a mystery” what keeps them “at bay.”  If the new studies “unveil a major control mechanism,” part of the solution may be to recognize synergy instead of selfishness.
    1Frederic Bushman, “Gene regulation: Selfish elements make a mark,” Nature 429, 253 - 255 (20 May 2004); doi:10.1038/429253b.
    How can a gene be selfish?  A gene has no concept of self.  It couldn’t care if it propagated itself or not.  The myth of selfish genes is a misleading anthropomorphism.  Only people are selfish.
        On the other hand, genes are not altruistic, either.  The metaphors of rheostats, regulators and molecular machines imply intelligent design and programming.  That is not an anthropomorphism, because machines are not personal.  Consequently, one doesn’t have to demonstrate anything about the designer to see the evidence that a product was designed.  But observing that the design works so well (i.e., your senses are working as you read this thanks to the regulation provided by transposons), it wouldn’t hurt to ponder the subject a little.
    Next headline on:  Genes and DNA
    Giardia Spoils Evolutionists’ Soup   05/19/2004
    In current evolutionary thinking, Giardia (the backpacker’s bane, a water-borne intestinal parasite that causes cramps and diarrhea) is an oldie.  Once long ago, early cells supposedly engulfed bacteria that became specialized into modern mitochondria.  “Until a few months ago, Giardia was thought to represent a throwback to the time before this union,” reports Nature,1 because the organism apparently did not contain mitochondria.  Recently, however, scientists had found the genes that code for mitochondrial proteins.  “But the real bombshell came last November,” Jonathan Knight reports, when a team found the proteins clustered in little sacs they dubbed mitosomes, or mitochondria-like bodies (see
    11/12/2003 headline).  Some scientists want more evidence before giving up their evolutionary trees.
    This attitude frustrates people such as William Martin, who studies molecular evolution at Heinrich Heine University in Düsseldorf, Germany.  He is convinced that the best and simplest explanation for the data is that Giardia once had mitochondria.  Some people, he argues, refuse to accept this because they have spent too many years working on the opposite assumption.  “They don’t want it to have mitochondria because it spoils their soup,” he says.  “This thinking is deeply ingrained.”
        The thinking has its roots in the concept of the Archezoa, Martin argues, the group that was conceived to bring together a range of single-celled eukaryotes thought to lack mitochondriaGiardia was the granddaddy, having branched off on its own before any other eukaryote, according to evolutionary trees built using sequences of RNA from ribosomes, the organelles in which proteins are made....
    But one by one, the Archezoa all proved to have either a set of mitochondrial genes in their nuclei, \ or relics of mitochondria such as mitosomes or hydrogenosomes.
      (Emphasis added.)
    Nature has a “gut feeling” that “Giardia’s status as the earliest branching eukaryote has also been questioned” by these discoveries.  Maybe some day, someone will discover “a new member of the Archezoa, sans mitochondria or mitosomes, lurking in the oxygen-starved muck at the bottom of a lake.”  But even then, “Some recent evolutionary trees that take into account the variable rates at which different DNA bases mutate paint a much muddier picture of the early branches.”
    1Jonathan Knight, “Giardia: Not so special, after all?” Nature 429, 236 - 237 (20 May 2004); doi:10.1038/429236a.
    Need we remind anyone that a mitochondrion is among the most complex organelles in a cell, home of the elaborate molecular machine named ATP synthase? (See 02/13/2004 and 09/18/2003 headlines).  So here again is a familiar pattern: the earliest, most “primitive” organisms are already busily using advanced technology.  Darwinists can point to no precursors.  The ones they surmised were precursors turned out not to be; they are either just as complex, or parasites that degenerated from earlier complex organisms.  Another familiar pattern: evolutionists don’t want to admit it.  “This thinking is deeply ingrained.”
        A group of evolutionary biologists was standing by the rail on a Darwin Party cruise aboard the HMS Beagle 3.  They were all moaning from having eaten spoiled soup, made with bad leaves from the wrong tree.  Captain FitzBehe walked up to a green-faced patron who just fed the fish.  “What’s the matter, Chuck?” he asked with a slap on the shoulder.  “Weak stomach?”  “No, captain,” the evolutionist struggled to reply.  “I’m throwing it farther than anybody else.”
    Next he