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.
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.
Williams was struck by the ad hoc way that even prominent biologists would explain an adaptation. Theyd 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. Weve evolved to do it so we get out of the way, so the young people can go on maintaining the species.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....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 Williamss 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 Williamss followers might see the situation, the mothers blood pressure might be rising dangerously because the fetus is releasing factors into the placenta that damage the walls of the mothers 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 Theres a big barrier between people like me who are physicians and people who are in biology departments. Perhaps its 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. Theres nothing scientifically rigorous about any of this. The only thing Williams did was try to leash in todays 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. Weve 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.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 (Hubbles 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 doesnt 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.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?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.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 its 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 elements. Tens 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).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. Whats most mysterious is that we dont 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 Charlies story, the genes would come to the rescue. Now this.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.
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 cant 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 youll be grinning more eventually.Human and Chimp DNA Compared 05/26/2004
Yesterdays 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 keepers 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 chimps 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
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 wasnt 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 Bonzos 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 Noahs 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.2DNA 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 dont. 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.)Hippos Sweat Their Own Sunscreen 05/25/2004
You know that reddish fluid on hippo skin that turns brown? Its 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.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.
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 its baloney, it stinks as bad in a castle as in a shack.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 dont 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.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, its not so much what you have, but what you do with what you have, that matters. Thats true for me and thee and the chimpanzee.Red Planet News; Ring World Beckons 05/25/2004
Lets 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 Europes 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 Presidents 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, its time to enjoy the ride of a lifetime.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 doesnt mean they should be done; and in a Darwinian world, who decides?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 gravitys 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 tradeoffsthey perform all of their ascribed tasks reasonably well, but no task perfectly.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 Zimmermans 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: Zimmermans 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 Wrights 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, its a wonder any journal would publish such tripe. Its only because biologists have offered their brains in sacrifice to Darwins 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. Weve 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.Cormorant Eyes Rapidly Refocus in Dives Into Murky Water 05/24/2004
Youre 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 youre 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 cormorants 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 cormorants 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.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, youll have reason to appreciate even more the elegance of their fishing expertise.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 skulls 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.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, Humanitys 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.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. Darwins 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. Sadlers 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:
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.
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 easyincrease 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 Sadlers 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 Sadlers 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 Earths 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 disciplines 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:
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.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, Cohns 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. 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. Cohns 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.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 couldnt care if it propagated itself or not. The myth of selfish genes is a misleading anthropomorphism. Only people are selfish.Giardia Spoils Evolutionists Soup 05/19/2004
In current evolutionary thinking, Giardia (the backpackers 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 dont want it to have mitochondria because it spoils their soup, he says. This thinking is deeply ingrained.Nature has a gut feeling that Giardias 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 dont want to admit it. This thinking is deeply ingrained.Fossil Water Lily Matches Modern 05/19/2004
Three Cornell botanists found fossil water lilies from the early Cretaceous that look nearly identical to modern ones, except that they are smaller. The exquisitely-detailed fossils were preserved in a New Jersey clay pit by a process of coalification. Water lilies (family Nymphaeaceae) are presumed by evolutionists to be among the earliest flowering plants (angiosperms). These ancient specimens apparently trapped beetles for pollination the same way as their living counterparts, suggesting that many modern insect–plant associations were already established by this time, (~90 million years ago). The paper is published in PNAS.1
1Gandolfo, Nixon and Crepet, Cretaceous flowers of Nymphaeaceae and implications for complex insect entrapment pollination mechanisms in early Angiosperms, Proceedings of the National Academy of Sciences USA, 10.1073/pnas.0402473101.
The paper shows fine details that make it hard to believe these impressions are that old, but that is where evolutionary theory has to put them into their mythical timeline. No evolution, again; the fossils are spitting images for modern water lilies, elaborate pollination structures and all, except smaller but size is a minor matter compared to the machinery required to produce structure. Maybe they just havent found big ones yet. These specimens exhibit precise and dramatic correspondence between the fossil floral morphology and that of modern Victoria [Amazon water lily] flowers, they announce with apparent surprise. Enough to give Charlie another bout of indigestion.Fruit Flies Fail to Exhibit Neo-Darwinism 05/18/2004
The Neo-Darwinian Synthesis is the current reigning paradigm of Darwinian evolution. It teaches that random genetic mutations provide the raw material of variation, and that natural selection acting on these variations produces all the complexity of life. A corollary is that mutation is independent of selection; i.e., that mutations do not conspire with natural selection to produce new structures and functions. Since mutations are random, it should be possible to speed up the mutation rate and thus speed up evolution.
The fruit fly Drosophila melanogaster has been used since the 1920s in experiments on neo-Darwinism. The poor bugs have been irradiated, treated with chemicals, and subjected to numerous tortures so that scientists could monitor the effects of mutations. Experiments have yielded some freaks, like four-winged flies and flies with legs where the antennae should be. One would think that, of any lab animal, fruit flies should provide some evidence that neo-Darwinism actually works. But a paper in Current Biology1 seems to indicate that most of the work in decades of experiments on Drosophila is irrelevant to the way neo-Darwinian evolution works in the wild.
It was not the intent of John F. Y. Brookfield, a geneticist at the University of Nottingham, to argue against neo-Darwinism. From all appearances, he accepts it; he begins,
The neo-Darwinian paradigm of evolutionary change assumes that mutations occur independently of any natural selection that will subsequently act on them. While such independence has been challenged in some descriptions of adaptive mutation in bacteria, it is still generally accepted to apply in multicellular organisms. It follows that, were one to examine simultaneously the process of mutation and the process of evolution, the kinds of mutational change that one would see should not be different in kind from the sorts of changes one sees occurring over evolutionary time, unless different types of mutation had systematically different phenotypic consequences: only selection can create a systematic difference between mutational and evolutionary changes.By evolutionary change, he means adaptive change. Mutational change could be neutral, producing no benefit to the organism, or it could be downhill, destructive to the species.
Brookfields topic in this paper is another question: whether mobile DNA elements can also be sources of adaptive change. In passing, though, he mentions several serious problems that neo-Darwinian theory has yet to explain.
A lack of agreement between mutation and evolutionary change was first noted in the context of dominance. In the 1920s, when the neo-Darwinian synthesis was being created, it was seen that mutations in Drosophila melanogaster are usually recessive to the wild-type allele. The paradox was that if genes are evolving, then the current wild-type allele would have been a mutant when it first arose, spreading to become the wild-type because of its advantageous phenotypic effect. Why should advantageous mutations generally be dominant, when their advantageousness depends on the particular environments that they will encounter?Brookfield describes attempts by R. A. Fisher and Sewall Wright to address this paradox. Fisher thought that dominance evolves, but Wright, whose views have been abundantly confirmed in subsequent experiments, was that mutations are recessive because they inactivate genes, so that their recessivity has a physiological, rather than an evolutionary, cause. But this seems to lead away from adaptive evolution. Turning off a gene would not create the gene in the first place. That leads to another difficulty:
Brookfield turns to focus on the possibility that mobile DNA insertions might enhance the expression pattern of a gene, and that this could lead to adaptive (evolutionary) change. He discusses recent examples of possible clues in certain fruit fly genes. In particular, a population of California fruit flies suggests the occurrence of a past selective sweep, which occurs when a new advantageous mutation arises and rapidly spreads through the population. Finding evidence of a selective sweep is difficult, he admits, and is based on circumstantial evidence. But a selective sweep is not necessarily a positive sign of evolutionary change: it has a downside:
If these apparent selective sweeps are indeed the result of mobile DNA sequence insertions, why are insertion mutations that alter the expression patterns of adjacent genes in a selectively advantageous way not more common? Why do these so rarely seem to spread through the species as a whole? One can clearly create a model in which insertions are eventually followed by imprecise excisions, leaving behind a small fragment only of the inserted sequence, or causing the loss of all the insertion, along with some flanking host sequences. Such a change might still create the advantageous phenotype, and thus one can imagine that an advantageous insertion is replaced by its deleted derivative.
The other, more disturbing, aspect of this study is that the species is responding to a very strong, man-made selective pressure, as is the case with many of our best examples of recent adaptive change in wild populations. Are these sudden man-made changes in environments typical of the environmental changes that wild populations encounter, and to which they respond through evolutionary change? Or do environments more usually change in such a gradual way that the adaptive response is qualitatively different at the molecular level. In other words, just as the mutations seen in laboratories are not typical of the mutational changes used in adaptive evolution, is it possible that the mutational changes used in adaptive evolution triggered by sudden man-made environmental changes are not typical of the mutational changes used in adaptation to the more gradual environmental changes normally encountered by wild populations?On that note, Brookfield quits. So where is the evidence for adaptive evolution resulting from mutations in fruit flies? He doesnt say. The article leaves us hanging on question marks.
1John F.Y. Brookfield, Evolutionary Genetics: Mobile DNAs as Sources of Adaptive Change? Current Biology, Vol 14, R344-R345, 4 May 2004.
Time for a joke. Wife: Why do you always answer my question with a question? Husband: Why not? Encore: Spike Jones picks up the phone in one of his skits and we only hear his side of the conversation. We hear him responding, with various inflections, You dont say? ... You dont say? .... You dont say? After he hangs up, his curious buddy asks, What did he say? Jones replies, He didnt say.Can Traits Evolve Before Need? The Case of California Chaparral Plants 05/18/2004
A biologist went to California looking for evolution in plants. He didnt find it, but believes the plants evolved anyway.
That seems to be the upshot of a study by David D. Ackerly (Stanford U.) published in American Naturalist1 (see summary on EurekAlert). Ackerly wanted to test whether natural selection produced the small, tough evergreen leaves of chaparral plants. The leaves typically have thick cuticles (waxy coatings) and a particular structure and density of stomata, the pores that exchange moisture. Presumably these leaves, called sclerophylls, evolved to adapt to the drought-prone Mediterranean-type climate of southern California. Ackerly applied phylogenetic analysis and statistical techniques to the study. Of 12 species he analyzed, most showed only a small trend toward low specific leaf area, a trait characteristic of plants in Mediterranean-type (MT) climates. Only four of the 12 indicated histories consistent with adaptation through natural selection, and even then only slightly. Apparently, the plants already possessed the adaptations before the climate changed. Little, if anything, evolved:
Small leaves and low specific leaf area (SLA) have long been viewed as adaptations to Mediterranean-type climates in many species of evergreen woody plants. However, paleobotanical and floristic evidence suggests that in many cases these traits originated prior to the advent of the summer-drought climate regime. In this study, molecular phylogenies and ancestral state reconstructions were used to test the hypothesis of adaptive leaf evolution in 12 lineages of evergreen shrubs in the California chaparral. Across all lineages there was a small but significant shift toward lower SLA, but there were no trends in leaf size evolution. For individual lineages, adaptive changes were detected in only three cases for SLA and in one case for leaf size. Three of these cases of evolutionary change were observed in taxa derived from cool temperate ancestors (e.g., Heteromeles). In contrast, most lineages originating from subtropical ancestors exhibited relative stasis in leaf trait evolution (e.g., Ceanothus). The absence of change suggests that ancestors of chaparral taxa had already acquired appropriate traits that contributed to their success under Mediterranean-type climates. These results illustrate how biogeographic history may influence patterns of trait evolution and adaptation and highlight the contribution of ecological sorting processes to the assembly and functional ecology of regional biotas.What this means is that these plants already had the small, hard evergreen leaves, before they arrived in the chaparral. They did not begin as large-leaved or soft-leaved plants that got trapped in climates with dry, hot summers, some of which survived by adapting their leaves to the climate through a process of natural selection.
Moreover, Ackerly believes these plants converged on the solution of small, hard leaf size independently, before a change in climate provided them the opportunity to succeed. The functional similarities among MT ecosystems have often been cited as an outstanding example of convergent evolution, he notes, in light of the disparate phylogenetic composition of the biotas (Cody and Mooney 1978). Convergence is viewed as a strong test of the role of natural selection because no other evolutionary force is expected to produce similar phenotypes under similar conditions in independent locations and lineages. Since no one else had tested for convergence in these species with a phylogenetic approach, he did. Sure enough, he found it, but farther back in time, before the climate changed:
For the case studied here, it appears that the leaf traits of evergreen sclerophylls are highly functional in MT climate conditions but that in many lineages these traits evolved in ancestral non-MT environments. Lineages possessing such traits were apparently successful and persisted in the face of the transition to summer drought, subsequently expanding to form a dominant vegetation type in California and other MT climate regions. The maintenance of sclerophylly and related traits reflects the adaptive value of these characteristics in the face of such changes. Assuming that genetic variation has been available for these traits, the lack of substantial evolutionary change represents an adaptive pattern as the traits were maintained by stabilizing selection. The similarities in leaf traits among species in the California chaparral reflect a mix of conserved traits that arose prior to MT climates and more recent adaptive shifts in lineages derived from cooler climates. These conclusions are consistent with the evidence from biogeographic and paleontological studies (Axelrod 1989; Valiente-Banuet et al. 1998), and importantly, they are based on entirely independent data sets and methods. The results highlight the importance of both ecological and evolutionary processes contributing to contemporary patterns in the fit between organisms and their environment.Stabilizing selection means that natural selection preserved existing adaptations rather than creating new ones. The overall result seems to be: the plants did not evolve to fit the change in climate, but the climate evolved without affecting the success of the plants that were pre-adapted to MT climate.
1David D. Ackerly, Adaptation, Niche Conservatism, and Convergence: Comparative Studies of Leaf Evolution in the California Chaparral, The American Naturalist 2004. Vol. 163, pp. 654-671, The University of Chicago, 0003-0147/2004/16305-30210.
This is not evidence for evolution. It is evidence for stasis, which by definition, is non-evolution. The plants were already pre-adapted. They were able to succeed in cooler, wetter climates as well as in drought-prone Mediterranean-type climates. One would think this to be evidence of design, but Ackerly and his evolutionary friends invent hand-waving terms like conservation and stabilizing selection to hide the fact that nothing evolved. Like a buoy anchored to the seafloor, the sclerophyllic plants withstood the changing tides of climate without evolving.Does Darwinism Contribute to Sexual Deviancy? 05/17/2004
Joan Roughgarden (Stanford U.) is a transsexual biologist. Although a convinced Darwinian, she claims to have disproved Darwins theory of sexual selection (see 02/26/2003 headline). Two reviews of her book Evolutions Rainbow: Diversity, Gender and Sexuality in Nature and People (University of California Press, 2003) appeared recently, one in Nature1 and another in Science.2 The book title refers to Roughgardens position that we should no longer believe there are only two sexes, but a spectrum (rainbow) of genders. The book is part biology, and part agenda: as Sarah Hrdy describes, a passionate cry from the heart for greater understanding of sexual diversity in nature and greater tolerance for the many gay men, lesbians, bisexuals, transgenders and others who do not fit comfortably into male or female binary categories.
Apparently eager to present themselves as enlightened and politically correct, neither reviewer had anything negative to say about Roughgardens advocacy of the transsexual and transgender agenda. They were actually quite sympathetic about it, thanking her for raising biologists consciousness of the trials that transsexual and transgender individuals face in society. The thing both reviewers did not appreciate was her disparagement of Darwins theory of sexual selection.
In the Science review, Jolly takes some jabs at people of faith: The readership should, but undoubtedly wont, include the religious orthodox, who probably would not appreciate a transsexual professor of evolutionary biology quoting the Bible and the Koran. (One such quotation by Roughgarden refers to Jesus comment about eunuchs in Matthew 19:12, that some are born eunuchs, some are made eunuchs by men, and some make themselves eunuchs for the kingdom of God). Alison Jolly thinks Darwinism can easily embrace the gender revolution: what Darwinian theory needs is not so much radical revision as a simple expansion to take sexual diversity much more seriously. Sarah Hrdy seems to take a similar stance; For readers craving information about transgendered existences, or for those like me who are deeply moved by Gay Pride parades and the social transformations that they represent, this book is going to have a huge impact.
1Sarah Blaffer Hrdy, Sexual diversity and the gender agenda, Nature 429, 19 - 21 (06 May 2004); doi:10.1038/429019a.
2Alison Jolly, The Wide Spectrum of Sex and Gender, Science, Vol 304, Issue 5673, 965-966, 14 May 2004, [DOI: 10.1126/science.1097003].
Only a radical twisting of Scripture could abuse Jesus statement about eunuchs to support the transsexual/transgender agenda (see context). Are we to assume Roughgarden got religion and wants to pursue the kingdom of God? Is that the agenda of Gay Pride parades? Clearly not.The Red Queen Did Not Invent Sex 05/16/2004
A Darwinian story just died. One of the evolutionary stories for the origin of sex is the Red Queen hypothesis. Named after a character in Alice in Wonderland, it is the idea that an organism must continually change just to stay the same, like running and getting nowhere. Technically, it states that sexual reproduction is maintained because it improves a species ability to respond to a changing biotic environment. First proposed by Van Valen in 1973, it has been a favorite among competing hypotheses for the origin of sex.
Otto and Nuismer, publishing in the May 14 issue of Science,1 investigated this hypothesis with a population genetics model and found it wanting. Their abstract summarizes, Our results show that species interactions typically select against sex. We conclude that, although the Red Queen favors sex under certain circumstances, it alone does not account for the ubiquity of sex. (For more on the origin of sex, see 05/12/2004 commentary.)
1Sarah P. Otto and Scott L. Nuismer, Species Interactions and the Evolution of Sex, Science, Vol 304, Issue 5673, 1018-1020, 14 May 2004, [DOI: 10.1126/science.1094072].
How long do we have to watch Charlie shoot himself in the foot before we conclude he should not run for Sheriff?Mitochondrial Clock Untrustworthy 05/16/2004
A major assumption of the molecular clock dating method has been called into question. If so, Science Now describes the impact on current theories:
Mitochondrial Eve, the hypothetical mother of all modern humans who lived about 150,000 years ago, might be lying about her age. A key assumption in determining how long ago she livedthat molecules of mitochondrial DNA do not swap segments with one anotheris false, researchers now say. Their findings call into question a multitude of findings in evolution, early human migration, and even the relations between languages.The mitochondria in our cells, organelles that provide the ATP power supply, contain small amounts of DNA. You may have heard that we inherit this mitochondrial DNA only from our mothers. Now, scientists have found evidence that male mitochondrial DNA can be inherited, and might be mixed in with the rest of the mitochondrial DNA. Since the implications are that this is going on all the time in our cells, that would render it untrustworthy as a genealogical tracer and dating method.
An announcement about evidence for recombination in human mitochondrial DNA was published in the May 14 issue of Science.
1Kraytsberg et al., Recombination of Human Mitochondrial DNA, Science, Vol 304, Issue 5673, 981, 14 May 2004, [DOI: 10.1126/science.1096342].
If confirmed, this calls into question many studies on presumed evolutionary history. Mitochondrial DNAs history is clearly not as clean as people had thought. Or people had wished, lamented one molecular biologist. The wishers are the dreamers in the Darwin Party, who are waking up from one of their favorite dreams to find out it was just ... a dream.New T. Rex Found; Best-Ever Skull Unveiled 05/14/2004
National Geographic News has reported the excavation of a possibly complete Tyrannosaurus Rex skeleton at a secret location, a private ranch, in Montana. The curious can monitor the interactive dig at Unearthing T. Rex.
The Carnegie Museum of Natural History in Pittsburgh has finally unveiled Samson, the best preserved skull of a Tyrannosaurus Rex, reports MSNBC News. The article says that this skull, discovered in South Dakota in 1992, may challenge scientific beliefs about the dinosaur, but does not elaborate. Maybe thats because museum curator Chris Beard leans toward the interpretation that T. Rex was not a fearsome predator chasing jeeps, but a timid, opportunistic scavenger (see Carnegie Magazine).
Tomorrows students may laugh at Jurassic Park like todays laugh at old Godzilla movies: scary, but hokey.Fish Antifreeze Provided by Pseudogene 05/13/2004
Freezing water forms crystals that can rip and tear at cells. Yet there are fish in arctic waters that can survive even below the freezing point of sea water. They accomplish this by means of special antifreeze proteins that interfere with the damaging effects of water crystals.
Scientists knew about AFP (anti-freeze protein) Type I in winter flounder, and knew its properties. They became puzzled how the fish survived temperatures lower than the protection AFP type I could provide. They suspected another antifreeze protein was at work, and found the gene that codes for it. They explain why this gene, named 5a, had escaped detection for 30 years: The two proteins differ slightly in their amino-terminal sequence and amino-acid composition. At the time of its discovery, the 5a gene was dismissed as an antifreeze-protein pseudogene, largely because the protein it encodes would have been grossly different from type I AFP and had never been detected in the flounder.
The protein is normally present in low concentrations and degrades at room temperature. At low temperatures, however, it roars into action. It becomes extraordinarily hyperactive, providing more protection against freezing than the previously-known AFP by an order of magnitude.
1Marshall, Fletcher, and Davies, Hyperactive antifreeze protein in a fish, Nature 429, 153 (13 May 2004); doi:10.1038/429153a.
Another wonderful discovery, all the more interesting for the last line: The evolutionary relationship between our 5a-like antifreeze protein and type I AFP, which also contains short tracts of alanine, remains to be solved.Cell Requires Two Keys to Let Cargo Pass 05/13/2004
For high-security environments, guards sometimes require two independent authentication methods. Before humans came up with this trick, the cells in their bodies were already using it. Itoh and Camilli explain in the May 13 issue of Nature:1
Our cells contain a series of distinct compartments that do different jobs and have different properties. The membranes that clad each of these compartments like the plasma membrane that encases the cell are defined by precise molecular compositions, which are preserved despite the continuous influx and efflux of components in transit to and from other cellular locations. Precision is the hallmark of this flow of traffic, too, which must be directed appropriately between compartments. All of this is achieved, in part, by the reversible recruitment of regulatory proteins from other parts of the cell to specific membranes or membrane regions. A growing amount of evidence hints that membrane lipids cooperate with membrane proteins to control this recruitment.They refer to work by Godi et al. in Nature Cell Biology that shows a dual-key authentication mechanism in the cell. With at least two independent, but synergistic, mechanisms, cargo is only allowed to bind to a membrane if it binds correctly to two cytosolic proteins. This can be envisioned as a kind of code:
The interaction of cytosolic proteins with both lipids and proteins on a target membrane is an efficient dual-key strategy to control their recruitment to membranes. Only when both the lipid-binding and protein-binding sites are engaged is the interaction with the membrane strong enough. The two elements of the code can be controlled independently, affording the possibility of fine-tuning the spatial and temporal regulation of recruitment.Itoh and Camilli provide no suggestions on how such a system might have evolved.
1Toshiki Itoh and Pietro de Camilli, Membrane trafficking: Dual-key strategy, Nature 429, 141 - 143 (13 May 2004); doi:10.1038/429141a.
Theres a coded message in this story. Can you decipher it?Another Impact Theory for Permian Extinction Proposed 05/13/2004
Richard Kerr was very cautious in his announcement in Science1 about a new claim about an asteroid impact near Australia causing the Permian Extinction. He went to lengths to point out that the evidence is not clear, and that many other scientists disagree. After describing the proposed impact site, he cautioned:
Not so fast, say some researchers who specialize in deciphering signs of impact lingering in rock. Theres no convincing evidence for an impact origin in the studied rocks, says impact petrographer Bevan French of the National Museum of Natural History in Washington, D.C. Everything theyre arguing was shocked [by impact] can have nonshock origins, such as volcanic activity, he argues. Despite the variety of evidence presented in this and two earlier Science papers by the same principal authors (Science, 21 November 2003, pp. 1388 and 1392), impact-triggered extinction at the P-T has yet to meet broad acceptance.
1Richard Kerr, Evidence of Huge, Deadly Impact Found Off Australian Coast? Science, Vol 304, Issue 5673, 941, 14 May 2004, [DOI: 10.1126/science.304.5673.941a].
Thats not the way it came across in the media. On a Motorola pager, MSNBC trumpeted: Scientists find suspect in great dying impact Scientists have linked Earths biggest extinction event, 250 million years ago, to a suspected impact crater off the coast of Australia.Montana Schools Not Allowed to Question Darwinism 05/13/2004
Objective origins is against the law in Darby, Montana (see 02/27/2004 headline). A policy change proposed by a local minister would have encouraged students to analyze scientific strengths and weaknesses of existing scientific theories, including the theory of evolution. It didnt lose because of a vote on the policy, or because of the threats of litigation by Americans United for Separation of Church and State. It lost because evolution supporter Erik Abrahamsen handily defeated incumbent chair Gina Schallenberger in a 4 May election, according to a news item in Science.1 The Missoulian said the election was driven by the origins debate, a rancorous battle over a controversial science policy.
1ScienceScope, Science, Volume 304, Number 5673, Issue of 14 May 2004.
Science took glee in the Darwin Party victory: Creationism Loses in Montana Town The residents of Darby, Montana, have doused one creationist brushfire by tipping the balance of its school board. (This was nothing about creationism, you recall; it was about letting the students hear about teaching students critical thinking skills. There was nothing at all about creationism, church and state, or religion in this policy proposal see 04/29/2004 headline.)Geological Column, Rev. 2004-a 05/13/2004
The geological column is not set in stone, John Whitfield discovered as he investigated the work of the International Commission on Stratigraphy (ICS), which is releasing a revised column this summer. Silurian, Devonian, Triassic: the names seem as solid and permanent as rocks themselves. But in fact, he cautions in his report in Nature,1 like fashions in hair or hem-length, the geological divisions of our planets timeline are prone to change.
Rocks, naturally, do not come with dates or names on them. The column is largely an artificial construct intended to bring some kind of universal order to the many varied assemblages of rocks and strata, and their fossil contents, around the world. Just as hair and hem lengths can vary by large margins, the dates and boundaries of the eras, epochs and periods within the column are largely a matter of convention. Sometimes those conventions fall prey to local disagreements:
Over the past 150 years, geologists have struggled to unravel Earths history. To a large extent, they have relied on significant events, such as the appearance of a specific fossil, or a reversal in the planets magnetic field, to define the boundary between two time periods. Having defined these physical boundaries, researchers then attempted to date them. But geologists in different parts of the world used different rocks as benchmarks, leading to disagreements over the exact definition of each period.Lately, however, geologists have been trying to nail down some calibration points with golden spikes. Whitfield explains,
To resolve the issue, stratigraphers are deploying golden spikes also known as global standard stratotype-section and points (GSSPs). These are locations where a good example of a worldwide event can be found, nominated by working groups within the ICS and then ratified by the IUGS [International Union of Geological Sciences]. Once a spike is set, that rock remains the boundary of a time period, even if estimates of its age change.There are now 50 golden spike points around the world, and the number is growing. But what about their dates? A method growing in popularity is to calibrate them with astronomical events, such as changes in earths orbit that led to climate changes on earth. Geologists gather clues about these changes by measuring oxygen isotope ratios and calcium carbonate concentrations in rock. Whitfield claims this method is accurate to 65 million years ago and is improving.
Geologists try to refine the dates with radiometric dating. But in the past decade, Whitfield laments, it has become clear that the results from different techniques and different labs dont agree. The solution? A global network of laboratories, all using a standard procedure, should be active in about a year. Maybe then geologists can extend their column to the entire solar system.
1John Whitfield, Geology: Time Lords, Nature 429, 124 - 125 (13 May 2004); doi:10.1038/429124a.
Though he trusts in it, Whitfield treats this whole process something like a game, because it is. Do you see the flaw? The geological column has more to do with consensus than fact (see 12/27/2003 editorial). The geologists are confused because their evolutionary just-so stories dont agree. So they are like a group of independent Hollywood producers who want to form a consortium where they can all come to agreement on their screenplay for Planet of the Apes. And like any game, you have cheering fans. Whitfield describes how China responded when they won a golden spike: To Chinese stratigraphers, this was the equivalent of winning a bid to host the Olympics. They hoisted a six-metre-tall monument on the spot to commemorate the achievement. This means no more than getting recognition from the director of a science fiction movie. It may make them feel good, but does it tell them anything about the real world?Male Imparts More to Embryo than Just DNA 05/12/2004
A team of biologists have confirmed that male sperm RNAs are delivered to the oocyte along with the DNA. Specifically, paternal messenger RNAs are delivered to the egg. These might influence development and put the males imprint on the developing zygote. Writing in Nature,1 the researchers speculate what the finding means:
Why should spermatozoa messenger RNAs be transferred to the oocyte? Messenger RNAs encoding proteins that bind nucleic acids, such as protamine-2, are likely to be deleterious and are probably degraded following entry, and a similar fate may await other RNAs that gain access. But some may have a role in the developing zygote: for example, clusterin (also known as sulphated glycoprotein-2, or SGP-2) is delivered to the oocyte and has been implicated in cell-cell and cell-substratum interactions, enhancement of fertility rate, lipid transportation, membrane recycling, stabilization of stress proteins, and promotion or inhibition of apoptosis. These may therefore be required in the early zygote but unnecessary in the oocyte. Alternatively (or in addition), these and other unidentified molecules, such as small interfering RNAs (siRNAs), may participate in processes such as pronuclear formation, the orchestration of events leading to oocyte activation, the transition from maternal to embryonic gene control, and the establishment of imprints in early embryos.But havent cloning and parthenogenesis experiments shown the male contribution to the zygote is dispensable?
However, the success of such experiments and of somatic-cell nuclear transfer is limited, as is the production of human embryonic stem cells after somatic-cell nuclear transfer. This may be because sperm RNAs contribute to early development. Transcripts that are specific to male germ cells play a role in the differentiation of embryonic stem cells and their function may not be easily replaced.They conclude that these accessory RNAs delivered in sperm may be necessary for fertility, and may influence the developing embryo with a signature only the male can provide.
1Ostermeier et al., Reproductive biology: Delivering spermatozoan RNA to the oocyte, Nature 429, 154 (13 May 2004); doi:10.1038/429154a.
Men have been taking a beating lately (see 03/31/2004 headline), so this should provide some rebuttal. In this day of experimental families and marriages and test-tube reproduction, we need to realize that there is no substitute in a family for a man and a woman. This extends all the way up from the gametes to the sexual identity and role modeling of the whole person.Whale Flippers Inspire Aeronautical Engineers 05/11/2004
Have you seen the bumpy flippers on humpback whales, you know, the species whose males serenade their mates? Dont laugh. Scientists have found that the ungainly flippers actually have superior lift, less drag, and are less susceptible to stalling. Engineers are imitating the whale flippers for advanced aircraft and helicopter rotors, reports EurekAlert from studies at Duke University. Humpback whales maneuver in the water with surprising agility for 44-foot animals, says the press release. Test wings modeled after the flipper had 8% better lift, 32% lower drag, and could withstand stalling at a 40% steeper wing angle.
We dont need to design so many things from scratch. Biomimetics is a modern application of an ancient principle expressed by Job, ask now the beasts, and they shall teach thee (Job 12:7).Search for Evolutionary Trade-Offs Comes Up Empty 05/11/2004
Husbands and wives know a lot about trade-offs, but according to Darwinian theory, all living things are in a constant tug-of-war between competing interests. In evolutionary terms, a trade-off is a compromise between competing forces of natural selection. For instance, Simultaneously obtaining enough food to grow and reproduce while trying not to become someone elses dinner is a pervasive trade-off faced by many organisms, explains Mark McPeek (Dartmouth), writing in American Naturalist.1 How does this concept fit in with evolutionary theory?
Trade-offs are central to our conception of how the natural world is organized. Trade-offs shape the choices that individuals make (Sih 1980, 1987; Krebs and Davies 1997), influence evolutionary trajectories and mold genetic diversity (Loeschcke 1987; Rose 1991; Stearns 1992; Roff 2002), and determine which species are able to coexist with one another in the long term (Levin 1970; Tilman and Pacala 1993; Chesson 2000). Trade-offs are presumed to be caused by some genetic or phenotypic trait or traits influencing two fitness components in antagonistic ways. Understanding the mechanisms that cause trade-offs is critical for predicting their consequences (Schoener 1986; Tilman 1987).So McPeek set out to test the evolutionary trade-off hypothesis. But when he looked for a trade-off among damselflies, specifically his prediction that activity correlates to mortality from predation, he was stumped: he couldnt find it.
McPeek studied two coexisting species of damselflies that inhabit freshwater lakes. One has larvae that are much more active than the other. The active ones presumably get more food but are more exposed to predation, and suffer higher mortality. What he found, however, is that both species actually obtain the same amount of nutrition, regardless of activity. However, laboratory studies presented here show that the mechanism assumed by most theoretical and empirical studies to mediate this trade-off, namely activity simultaneously modulating foraging returns and predation risk, does not operate in this system, he lamented with apparent consternation.
In spite of no difference in the amount of food ingested or assimilated, I. verticalis larvae grew faster than Enallagma larvae because they were better able to physiologically convert assimilated food into their own biomass in the presence of mortality threats. From these studies we understand the phenotypic mechanisms determining the antagonistic patterns of relative growth and survival between these two genera, but why these patterns exist remains unclear.McPeek lays out his experimental data in exhaustive detail, but in the end, the principle he sought to verify was not found:
If the growth/predation risk trade-off has influenced the evolution of these genera, the walk and production efficiency variables should display positive correlations across species phenotypes (i.e., for the tips) and in the evolutionary contrasts. The number of walks in the presence of dragonfly predators was correlated across species with the production efficiency and growth rate in the presence of predators, but correlations among the corresponding evolutionary contrasts indicated that these variables have evolved independently; correlations among contrasts for walking and production efficiency/growth variables were all not significant, and they were not even consistent in sign (table 1; fig. 6b).His ending discussion puzzles over this negative result, and compares it with findings of other studies on evolutionary trade-offs. He really expected the vigor of the one species to exhibit a trade-off:
A trade-off implies that some character or set of characters, either phenotypic or genetic, antagonistically influence two fitness components. As this character (or set) evolves, one fitness component increases while the other decreases, hence the trade-off. Clearly, activity is not that character because activity does not influence growth rate, and they do not evolve in a correlated manner across species (table 1).A negative result is still a result, and McPeek has to leave it at that: At present it is difficult to speculate what the underlying character modulating mortality and growth may be to generate the trade-off among the damselflies, he concludes. In fact, we must entertain the possibility that this is not a trade-off in the mechanistic sense at all. In other words, no mediating phenotypic or genetic traits may have shaped the evolution of both growth rate and predation risk, he states with apparent surprise. In fact, evolutionists may have to propose an opposite principle:
Perhaps the direction of causation is also opposite from what we usually assume; these differences between the genera may not have evolved because of selection pressures to allow them to coexist (Abrams 2003), but rather these phenotypic differences may have arisen for other reasons (e.g., drift or past selective agents that no longer influence them), and the fact that these phenotypic differences promote coexistence has allowed the ecology of the system to dynamically capture these two taxa and promote their long-term persistence with their present phenotypes.This seems to suggest a force for stasis, not evolution. It gets worse; he next points to other studies that show the same thing, such as with tadpoles. We need to find the mechanism for trade-offs, he implores, to understand organizations of species with each other and with other organisms, and to understand ecology. Such differences in phenotypically mediated community dynamics cannot be correctly discerned or reliably predicted without a thorough understanding of the mechanisms shaping the phenotypes of the interacting species. So back to the drawing board.
1Mark A. McPeek, The Growth/Predation Risk Trade-Off: So What Is the Mechanism? American Naturalist2004. Vol. 163, pp. E88-E111. © 2004 by The University of Chicago. 0003-0147/2004/16305-40010, Electronically published April 26, 2004.
Notice his suggestion about past selective agents that no longer influence them as an explanation for why the evolutionary trade-off was not found. How is a past selective agent that no longer has any influence a testable scientific model? How is it different from a ghost?Former Junk DNA Now Considered Essential 05/10/2004
The term junk DNA seems to be fading with each new discovery. Helen Pearson, reporting for Nature Science Update, leads with the line Junk DNA reveals vital role: Inscrutable genetic sequences seem indispensable. They dont know what it does yet, but the assumption is it must be important for evolution to hang onto it for so long. Pearson writes,
If you thought we had explored all the important parts of our genome, think again. Scientists are puzzling over a collection of mystery DNA segments that seem to be essential to the survival of virtually all vertebrates. But their function is completely unknown.Researchers found 480 sequences that are identical between humans, mice and rats, and largely match up with chicken, dog and fish sequences too, but do not exist in invertebrates such as sea squirts and fruit flies.
Scientists can only guess what these sequences do. One idea is that they control the activity of indispensable genes. Another is that they may slice and splice RNA into different forms. Or perhaps they may control embryo growth. Pearson describes the initial reactions to the discovery that junk DNA is not junk after all:
To solve the conundrum, experts predict a flurry of studies into the enigmatic DNA chunks. People will be intrigued by this [finding], says Kelly Frazer who studies genomics at Perlegen Sciences in Mountain View, California. It is the kind of stuff that blows people away.She quotes one researcher who said, It absolutely knocked me off my chair. It was hard to believe these sections could be 100% identical. Some thought they must have contaminated their samples. The presence of exact copies in different animals suggests that even tiny changes in the sequence of these segments destroy whatever they do, Pearson surmises, and have been weeded out during evolution whereas other parts have been free to accumulate mutations.
Clearly there is a lot of work ahead, Pearson says. Finding the function of the ultraconserved elements is just the tip of the iceberg. There are other vast tracts of similar so-called junk DNA whose functions await discovery.
On a related subject, Current Biology has news on introns (see 09/03/2003 headline). A dispatch by Arlin Stoltzfus begins, The evolutionary origin of spliceosomal introns remains elusive. The startling success of a new way of predicting intron sites suggests that the splicing machinery determines where introns are added to genes. New techniques show the splicing sites are not random, because observers can predict where they will be found with uncanny accuracy. The putative benefits of introns that justify their existence are still unknown. Apparently, the cell has mechanisms of targeted intron gain.
See also the May 12 BBC News report on this finding.
Researchers could have had a big head start by approaching this topic from an intelligent design perspective. Just because these stretches of DNA dont code for proteins, and just because they have unknown functions, doesnt mean they are junk. It was evolutionary presuppositions that treated them as useless leftovers of evolutionary ancestry. Now Darwinian scientists are surprised and have a lot of catching up to do. A design perspective would begin by assuming that these stretches are there for a reason. Lets find out, therefore, what they are there for.Searchers in the Dark Over Dark Matter 05/10/2004
No sooner had Sean Carroll published his essay in Nature1 that dark matter proves how insignificant we are, that Geoff Brumfiel tells us in Nature Science Update that researchers cant find the stuff. The Cryogenic Dark Matter Search II is four times more sensitive than previous searches, but came up empty. Carroll had just reiterated the common statistic that About 70% of our current Universe is dark energy and 25% is dark matter. This leaves all the stuff we have directly observed at a paltry 5% of the whole Universe. We see the light; where is the dark?
1Sean Carroll, Insignificance, Nature 429, 27 (06 May 2004); doi:10.1038/429027a.
Cosmologists love dark matter rather than light because their deeds are evolutionary. And you thought the pillar of science was observation.Botulinum Toxin Deactivated by One Slight Change 05/10/2004
A researcher at Brookhaven National Laboratory mutated a botulinum enzyme by just one amino acid, and abolished its toxicity. The mutation, a change from a glutamate to a glutamine at one position, increased the distance from a zinc atom to a water molecule by 0.6 angstrom, less than one tenth of a billionth of a meter. This was enough to prevent the botulinum enzyme from cleaving its target protein, a neurotransmitter. The modified enzyme could still bind to it, but not cleave it.
This experiment points out the specificity of enzymes. We are led to believe that evolution works by mutating things recklessly, but look how slight a change totally disarmed this enzyme. A second observation is that toxins like botulinum might have originally had a beneficial function, but became toxic through degenerative mutations. Though difficult to prove, it is an interesting suggestion that, just as with mentally ill humans, it doesnt take much to turn a benign individual into a killer. That isnt evolution. Its a breakdown in quality control. Another possibility is that botulinums function, cleaving a neurotransmitter, was originally beneficial. As reported before, many deadly poisons actually follow a hormesis curve and only become harmful above certain levels (see 02/12/2003 headline). Botox is now all the rage. In minute amounts, it is proving versatile for everything from beauty treatments to tumor reduction; see for instance this report on EurekAlert about University of Pittsburgh scientists using to ease symptoms of enlarged prostate.Caves Are Made by Bacteria 05/10/2004
Caves seem like archetypes of slow, gradual, ancient processes. Tourists have long been told that caves form slowly over many tens or hundreds of thousands of years by the slow dissolution of limestone by weak carbonic acid in water carried down from surface rainfall. That explanation took a dramatic turn in the 1970s when scientists realized that a stronger agent, sulfuric acid, might enlarge subaerial chambers much more quickly. It was a revolutionary discovery to realize that sulfuric acid could be formed by oxidation of subterranean hydrogen sulfide. Now, the same type locality where the initial studies were done, Lower Kane Cave in Wyoming, has produced another revolutionary discovery; bacteria make caves.
A trio of geologists from the University of Texas at Austin revisited Lower Kane Cave for a three-year research program. They measured very little hydrogen sulfide emitting into the air able to dissolve limestone on subaerial surfaces. Instead, they found two species of bacteria that feed on hydrogen sulfide produce more sulfuric acid. Concentrated in dense microbial mats, these bacteria essentially focus the acid on the phreatic (groundwater) limestone surfaces. Our observations show that sulfur-oxidizing bacteria colonize subaqueous carbonate surfaces, localize dissolution by generating acidity, and therefore are integral to sulfuric acid speleogenesis, they state in their revised model of sulfuric-acid speleogenesis (SAS; speleogenesis meaning cave formation). Their paper is published in the May issue of Geology.1
Although some of the hydrogen sulfide is autocatalyzed, escaping into the cave atmosphere to contribute to dissolution of subaerial surfaces as previously suggested, it appears that most of it is biogenic catalyzed by microbes that extract energy from hydrogen sulfide: cave enlargement via dissolution of the cave floor is microbially mediated, they theorize. Because these bacteria concentrate sulfuric acid formation on the cave floor and are operative where subaerial dissolution would be kinetically limited, microbial catalysis extends the phreatic depths to which porosity and conduit enlargement could occur in carbonate systems, including oil-field reservoirs and aquifers. The metabolic consequences of an active microbial ecosystem change the model for sulfuric acid speleogenesis.
See a summary of this paper on Nature Science Update, which states, Although the exact age of Lower Kane Cave is controversial, Engel says that it probably formed about 10,000 years ago. That is relatively recent; caves formed by the more common action of carbonic acid grow considerably more slowly. They claim Carlsbad Caverns is 10-14 million years old; They show just what the bacteria can achieve, given time.
1Engel, Stern and Bennett, Microbial contributions to cave formation: New insights into sulfuric acid speleogenesis, Geology, Vol. 32, No. 5, May 2004, pp. 369–372, doi: 10.1130/G20288.1.
The authors do not give any indication of how rapidly this process would occur relative to other cave-formation processes or to the old SAS model, nor do they indicate that microbial sulfide oxidation would be the only or dominant process. Nevertheless, if the dense microbial mats described by the researchers focus sulfuric acid on the rock surfaces, it seems plausible that cave formation, at least in some cases, could be much more rapid than usually assumed. Despite NSUs guesses, nobody was present even 10,000 years ago to tell us if conditions were the same back then; how much less for millions of years. If enough bacteria and the right conditions were available, why could not even large caves form rapidly? NSU claims that most caves form by standard carbonic acid solution, but look at how revolutionary the SAS model was in the 1970s. Who knows what other mechanism might be discovered?Virus: Like DNA in a Hard Plastic Shell 05/07/2004
A European team of biophysicists studied the mechanical properties of a virus and found the shell, made of protein, to act like hard plastic. Writing in PNAS,1 they described the coat of a bacteriophage they studied:
The protective proteinaceous shells (capsids) of viruses are striking examples of biological materials engineering. These highly regular, self-assembled, nanometer-sized containers are minimalistic in design, but they combine complex passive and active functions. Besides chemical protection, they are involved in the selective packing and the injection of the viral genetic material.The capsids look like oblong, geometric shapes with pointy ends. The DNA is packed inside under pressure, and the coat can withstand indentations of 30%. The measured Youngs modulus, they found, is comparable with that of hard plastic. They seemed to admire the little cases: the bacteriophage capsid is
remarkably dynamic yet resilient and tough enough to easily withstand the known packing pressure of DNA (~60 atmospheres). These capsids, thus, not only provide a chemical shield but also significant mechanical protection for their genetic contents. Viral shells are a remarkable example of natures solution to a challenging materials engineering problem: they self-assemble to form strong shells of precisely defined geometry by using a minimum amount of different proteins.The team is looking at these miniaturized packages for inspiration in the burgeoning field of nanotechnology.
1Ivanovska et al., Bacteriophage capsids: Tough nanoshells with complex elastic properties, Proceedings of the National Academy of Sciences USA, 10.1073/pnas.0308198101, published online before print May 7, 2004.
Here is observational evidence that leads to interesting questions. It shows that living things need to overcome the same kinds of physics problems that engineers face. Yet viruses are not, by definition, alive; they rely on a host for replication. How could such precision bio-nanotechnology evolve? Why do viruses exist? Did they ever have a beneficial role, considering that the vast majority are harmless? We may never be able to explain such things completely, but we can marvel at the biophysics capabilities found in nature, and deduce that such things dont just happen. Now read about the little motor that packs the contents (see 10/18/2001 headline).Hot Jupiter! Exoplanets Found Very Close to Stars 05/07/2004
Two examples of Jupiter-size planets have been found by the European Southern Observatory. They are so close to their parent stars, they orbit in less than two earth-days each. Mercury would be 17 times farther out than one of them. They belong to a new class of exoplanets scientists are terming hot Jupiters.
A few years ago, solar system models would have always put the small, rocky planets close in and the gas giants farther out. Discoveries like this have caused a major rethink of the old nebular and planetesimal hypotheses (see 05/16/2003 headline). Ideas are floating around, seriously, that gas giants could form in just hundreds of years, and if the nebula doesnt disperse fast, could be dragged into the parent star in just thousands of years. Our solar system is looking rare or unique (see 07/21/2003 headline). Are we privileged?Fossil Hummingbird, Arthropod Look Modern 05/07/2004
Science announced that a rare hummingbird fossil has been found in Germany and, though assumed to be 30 million years old, is indistinguishable from living New-World hummingbirds. This upsets the standard theory that hummingbirds evolved in the New World only. Writing in the May 7 issue,1 discoverer Gerald Mayr said,
I report on tiny skeletons of stem-group hummingbirds from the early Oligocene of Germany that are of essentially modern appearance and exhibit morphological specializations toward nectarivory and hovering flight. These are the oldest fossils of modern-type hummingbirds, which had not previously been reported from the Old World. The findings demonstrate that early hummingbird evolution was not restricted to the New World. They further suggest that bird–flower coevolution dates back to the early Oligocene and open another view on the origin of ornithophily in Old World plants.Reviewer Erik Stokstad in the same issue2 quotes ornithologist Margaret Rubega (U. of Connecticut), The amazing thing about this fossil is that its essentially a modern hummingbird. My mind is a little blown. He adds, Where the whole hovering tribe came from ... remains up in the air. MSNBC News has a picture of the fossil. It mentions that Mayr named his specimen Eurotrochilus inexpectatus, an unexpected European version of Trochilus, a modern hummingbird genus. He called his find a striking example for the complexity of evolution and animal biogeography.
The previous day, Nature announced a Cambrian fossil that shows an arthropod in the act of molting (shedding its exoskeleton). The discoverers say, Here we describe a 505-million-year-old specimen of the Cambrian soft-bodied arthropod Marrella splendens that has been visibly preserved in the middle of the act of moulting. This specimen confirms that early arthropods moulted during growth, just as they do today.
1Gerald Mayr, Old World Fossil Record of Modern-Type Hummingbirds, Science, Vol 304, Issue 5672, 861-864 , 7 May 2004, [DOI: 10.1126/science.1096856].
2Erik Stokstad, Surprise Hummingbird Fossil Sets Experts Abuzz, Science, Vol 304, Issue 5672, 810-811 , 7 May 2004, [DOI: 10.1126/science.304.5672.810a].
3Diego C. Garcia-Bellido and Desmond H. Collins, Moulting arthropod caught in the act, Nature 429, 40 (06 May 2004); doi:10.1038/429040a.
Anyone see evolution here? Is this what Charlie would have predicted? Two guesses who would have predicted the sudden, abrupt appearance of fully formed, functional organisms. (Hint: the same ones who would have predicted the salamander, the fly, the worm, the ostracode, the spider, the frog, the shark, the forams, the Cambrian fish, the cockroach, the tick, the ant, etc.)Science Bashes I.D. 05/07/2004
The Intelligent Design movement took another lashing by the journal Science,1 in the form of three book reviews by Steve Olson, a Washington DC area science writer. Olsen reviewed one pro-ID book, Darwin, Design and Public Education by John Angus Campbell and Stephen C. Meyer, and two anti-ID books, God, the Devil and Darwin by Niall Shanks, and Creationisms Trojan Horse by Barbara Forrest and Paul R. Gross. A flavor of Olsons rhetoric: Shanks... deftly skewers the scientific pretensions of intelligent design creationists. He is particularly effective in demolishing the claims of creationist William Dembski.... Olson calls the faithful to holy war:
Resistance to the teaching of evolution is not going to fade away. On the contrary, creationism appears again to be in a period of ascendancy. Science educators must try to understand and come to terms with the viewpoints and passions of those who feel threatened by the teaching of evolution in public schools. They also must be well informed to continue to resist the inclusion of religiously motivated ideas in science curricula.
1Steve Olson, Evolution and Creationism: Shapes of a Wedge, Science Vol 304, Issue 5672, 825-826, 7 May 2004, [DOI: 10.1126/science.1097382].
Saddam Hussein talked tough when he had the power to torture any opponent, but when he met his match, he cowered in a hole. Evolutionists are such cowards. If you thought for a moment they were interested in the truth, then why dont they invite Dembski to review the anti-ID books? Its always loyal D.P. (Darwin Party) comrades who get to pummel the straw men when reviewing pro-ID books, and cheer their champions when reviewing anti-ID books. Science, when touching on these subjects, is the Al Jazeera of Charlie worship. It broadcasts the weaknesses of its enemies, but hides the genocides of its imams. It rallies jihad against anyone who questions their sacred dogmas or threatens their pantheistic worldview.Feathered Dinosaur Exhibit Raises Doubts 05/06/2004
Can you trust those fossils on display in your local museum, the ones showing Feathered Dinosaurs and the Origin of Flight? No less than the respected journal Nature1 is concerned they may have been gathered and sold illegally, and are no more trustworthy than the 1999 Archaeoraptor hoax that embarrassed National Geographic magazine.
The same Utah fossil collectors who sold Archaeoraptor to the world press, Stephen and Sylvia Czerkas, now have a traveling exhibit of presumed feathered dinosaur fossils beginning to make the rounds at American museums. The exhibit is currently in a seven-month run at the San Diego Natural History Museum. Other museums, however, like the Natural History Museum of Los Angeles, do not want to be involved with questionable specimens, despite Czerkas claim that they were obtained legally.
Natures concern is concentrated on whether the fossils were smuggled illegally out of China, and that exhibiting them promotes trafficking in illegal specimens. They mention that Archaeoraptor turned out to be a forged composite from different species ... put together in China to resemble a missing link between dinosaurs and birds, but failed to ask whether any of the current Czerkas specimens might be forgeries.
1Rex Dalton, Feathered fossils cause a flap in museums, Nature 429, 5 (06 May 2004); doi:10.1038/429005a.
Here are all the enticements necessary for hoaxers: money, fame, and gullible customers. Chinese fossil scavengers know that unusual fossils that look like missing links bring a much higher price on the black market than more of the same. There is the lust for fame to be the first to discover a missing link. And there is a scientific clientele convinced that birds evolved from dinosaurs. Add to that the fact that many of these specimens arrived in the west without documentation as to their location and context, and would you believe the exhibit signs?Fish See With Electric Eyes 05/05/2004
Biologists knew that some electric fish shock their prey and others with weak electricity can navigate with it, but they didnt know till recently just how much information these fish can detect with their unique sense. French and British scientists ran some experimental tests on weakly electric fish, the African elephantnose fish Gnathonemus petersii, which sends out pulses of electricity, and the Amazonian longtail knifefish Sternopygus macrurus, which sends out electrical waves. These fish feed on aquatic larvae at night where eyes are of no use. But they have eyes of a different sort: electric eyes.
Graff et al., in their paper in the May 4 issue of Current Biology,1 showed experimentally that these fish use their electric sense for much more than just location. Their electric organs effectively provide a map of their surroundings. The electric field they generate is modulated by the dielectric properties and impedances of objects in the area: grass, stones, other fish and larvae each have their own electrical signature. These signatures are picked up by numerous sensory organs in the skin of the fish. The skin thus acts like a retina, allowing the fish to see its way in the dark. The information is so rich and varied, you could even say its analogous to 3D color vision.
Through a series of clever experiments, the scientists demonstrated that these species of fish can detect the following information about objects: size, composition, distance to objects, distance between objects, spatial patterns, 3D orientations, and similarities between different objects. They can even memorize configurations in space to create a mental map. They can do all these relying solely on their electric sense, which is alien to all other animals (They do not mention one possible exception, the duck-billed platypus.)
The authors coined a new term, electroperception, to indicate that this special sense does more than just electro-location. They compared it to the echolocation of bats and dolphins who, similarly, can discern shapes, textures, motions and distances with their special senses. Needless to say, the fishs electrical sensory apparatus requires processing for interpretation and response. They may not have the human cerebral cortex, but evolution favored the valvula cerebelli, a hypertrophied part of the metencephalon (cerebellum), which is likely to be responsible for such functions.
See also Science Now for a summary of the findings.
1Graff, Kaminski, Gresty and Ohlman, Fish Perform Spatial Pattern Recognition and Abstraction by Exclusive Use of Active Electrolocation, Current Biology Vol 14, 818-823, 4 May 2004.
This was such a great story, why did they have to mess it up with a stupid evolutionary personification at the end? Evolution cant favor anything, nor can it build a brain or a hypertrophied (enlarged) valvula cerebellum. They presented no evolutionary pathways or missing links; the comment added nothing. *Sigh*Homology for Dummies 05/05/2004
Current Biology likes to give its readers primers on various concepts. The topic in the May 4 issue is homology.1 Caleb Webber and Chris P. Ponting explain this important evolutionary term for the rest of us. The Q&A format also introduces homologys siblings: analogy, orthology, paralogy, xenology, and synteny.
Some readers may not realize that the term homology was first coined by a Christian creationist, Richard Owen, Britains foremost paleontologist in Darwins day. Owen, who despised Darwins book, defined homologous structures as similarities descended from a common archetypal body plan. The Darwinians co-opted the term to mean descended from a common ancestor. Analogous structures, by contrast, came to mean similarities not due to common ancestry, but rather to convergence (evolution toward similarity from different directions). The other words are derivatives of these key concepts. Orthology means similarities on the same branch of the phylogenetic tree; paralogy means similarity due to gene duplication; xenology means similarity arising from lateral gene transfer, and synteny can mean either genes that reside on the same chromosome, or, more generally, genes in the same orthologous order within the same genomic regions. The terms can be applied to visible structures, like vertebrate limbs and plant leaves, but are more commonly used to describe gene sequences. Now that you know the words, how are they used in practice by biologists?
The authors seem to be eager to dismiss charges that the terminology provides an ostentatious distraction from evolutionary assumptions. No, it is truly useful, as a famous biologist once said:
Differentiating between homology and analogy is not mere pedantry2: homology allows Darwinian evolutionary theory to be applied accurately across the biosciences. And, as Theodosius Dobzhansky (19001975) famously remarked, Nothing in biology makes sense except in the light of evolution.With that understood, the authors point out occasions where lack of understanding of the ancestry can trip up the observer. Sequence similarity, for instance, is not the same thing as homology: Sequence similarity is a quantity that is agnostic of evolution. In contrast, homology is a property that describes evolutionary history. In other words, sequences can look homologous but not really be related in the family tree. Even evolutionary scientists goof on this point sometimes:
Just as with bird wings and bat wings, perceived similarities between sequences need not be due to a common evolutionary origin. Research papers sometimes wrongly quote values of percent homology. In these cases percent identity is meant, as two genes either have a common ancestor or they do not. The only appropriate use of percent homology is when separate portions of a gene have distinct evolutionary histories, for example as a result of a gene fusion event.That raises the next obvious question; How can one be sure beyond reasonable doubt that two similar sequences are homologous? To answer it requires a little high school algebra. Hang on:
Using statistics you can estimate how likely it is that randomly composed sequences yield alignment scores that are at least as high as that obtained between the real sequences in question. For example, the BLAST program reports an Expect (or E) value for each alignment (with score x), which is the number of times sequences are expected, with scores >=x, to crop up in a search just by chance. As E gets closer to zero, the more confident one should be in a prediction of homology. Many users cautiously consider only those alignments with E-values lower than 10-3 as substantiating evidence for homology.Now that thats clear, what about proteins? They can have similar folds; does that indicate homology? Not necessarily. They warn that once again we are faced with similarities: we cannot be sure that just because two proteins fold up in the same way it means they arose from a common ancestor. Nevertheless, spatial coincidence of active or binding sites, or unusual structure, can boost the odds of a homology prediction being correct. Then there is the puzzle of convergence:
What about convergent evolution? As far as we can tell, the convergence of gene sequences is extremely rare. It is, by far, easier for Nature to duplicate a gene than invent similar genes on two separate occasions. By contrast, independent invention of protein structure is often suggested to have occurred, yet for most of these cases the evolutionary provenance is unclear.Next, they describe how orthology, paralogy and xenology are best illustrated with a phylogenetic tree, and draw one to make it clear. However, they caution, lineage-specific gene deletion, pseudogenisation, duplication, conversion and rapid sequence divergence can all confuse phylogenetic tree reconstruction. Better leave that to the experts. They provide examples of confusion that can arise from gene duplication and deletion.
Note that these relationships [orthologs, paralogs etc.] are defined with respect to evolution, and not function. Nevertheless, they are useful in predicting function as the more recently two genes shared a common ancestor, the more likely it is that they have retained similar functions. Moreover, orthologous genes that have been spared by natural selection from deletion or duplication over many millions of years are also likely to share overlapping functions.Well, that about wraps up this lesson. One more issue is the need for such jargon. How useful are these words, really? Why not invent a new term that avoids evolutionary assumptions altogether?
Do we need new terms (neologies)? Some would say that we do. They argue that we should coin terms to describe similarities in sequence or structure, for example between biological molecules regardless of whether these arose by divergence from a common ancestor. Only definitions that are useful will survive, they suggest, while those that are not will be dropped (a linguistic mimicking of purifying selection). We believe that there is too much bewilderment already in the use of homology, orthology and paralogy, so introducing yet more terms appears to be asking for trouble. Moreover, the terms in current use are sufficient, when applied appropriately, to qualitatively describe the consequences of gene duplication (homologs), speciation (orthologs), intragenome duplication (paralogs) and horizontal transfer (xenologues), which are four of the major evolutionary forces acting on genes.Coincidentally, the same week, Nature3 posted a story about a case of apparent convergent evolution. The abstract states, Swift-swimming, open-ocean hunters such as mako sharks and tunas need a big engine. Despite their long separation in evolutionary terms, the internal drive systems adopted by these fishes are much the same.... after 400 million years of separate evolutionary trajectories, these two high-speed predators have converged on solutions to the problem of swimming fast that go from skin to skeleton. Dont forget that certain extinct marine reptiles with similar body shapes that probably also converged on these solutions independently.
1Caleb Webber and Chris P. Ponting, Magazine: Genes and homology, Current BiologyVol 14, R332-R333, 4 May 2004.
2Pedantry, n., pedantic presentation or application of knowledge or learning. Pedantic, adj., or, relating to, or being a pedant. Pedant, n., 2. a. one who parades his learning. b. one who is unimaginative or who unduly emphasizes minutiae in the presentation or use of knowledge. Pedantic can also mean: narrowly, stodgily, and often ostentatiously learned: e.g., ontogeny recapitulates phylogeny.
3Adam P. Summers, Fast Fish, Nature 429, 31 - 33 (06 May 2004); doi:10.1038/429031a.
Well, now Im more bewildered than ever. Didnt they just say that we need the evolutionary terms with their evolutionary baggage so that we can describe evolutionary forces in evolutionary terms? This has me going around in so many circles Im getting dizzy.Origin-of-Life Researcher Leslie Orgel Interviewed 05/05/2004
The May 4 issue of Current Biology1 contains an interview with organic chemist Leslie Orgel of the Salk Institute, who in 1974 published the book The Origin of Life on Earth with Stanley Miller of spark-discharge fame (see 05/02/2003 and 10/31/2002 headlines). He considers his biggest mistake not thinking of the RNA World scenario first (see 02/20/2004 headline) His greatest ambition is I would like to understand in chemical detail how RNA or some simpler polymer capable of evolution through natural selection established itself on the primitive Earth. Asked if he had a scientific hero, and why, he replied tersely: Charles Darwin, for all the obvious reasons.
1Q&A: Leslie Orgel, Current Biology Vol 14, R331-R332, 4 May 2004.
Isnt this pathetic? An intelligent individual wastes 40 years of his life trying to pay homage to Charlie by filling in the biggest blank (see 08/15/2003 headline) in his idols creation myth (see 02/15/2004 headline), and has nothing to show for it (compare 08/26/2003 headline). As if the RNA World fiction is going to save his faith (see 07/11/2002 and 06/18/2002 headlines). Is his career any different than that of a sorcerers apprentice seeking to please his wizard (see 02/13/2004 headline), or a promising lad deciding to become a priest of Marduk, devoting his life to figuring out what patterns in a liver lead to success on the battlefield? Sad. Well leave it as an exercise to determine what he meant by his genuflection, Charles Darwin, for all the obvious reasons.Io, Io, Its Off to Work We Go 05/04/2004
The innermost large moon of Jupiter, Io is the most volcanically active body in the solar system. About the size of our moon but no more than a speck of light in small telescopes, it caused a sensation when Galileo first glimpsed it and the other three major satellites of Jupiter in 1610. Back then, it upset tradition about the hierarchy of the heavens; today, it is upsetting tradition about the age and composition of planetary bodies. The volcanos were first observed by the Voyagers in 1979, and have been monitored with earth instruments since then, but were most clearly and dramatically revealed by the Galileo spacecraft between 1995 and 2003. Now that its seven-year orbital tour of the Jupiter system is history, planetary scientists are trying to come to grips with the startling findings from all four large moons. The May issue of Icarus is devoted to the puzzles of Io, whose volcanos dwarf those on earth. Io After Galileo provides a status report, a state of the moon address, before its off to work they go for more data mining and problem solving.
Most of the articles are descriptive of the dramatic and colorful volcanos seen in the photographic images: Tupan Patera, a lava lake 47 miles across and half a mile deep; Tvashtar Catena, a chain of craters that displayed a 240-mile-high plume and 30-mile-long fire fountain; Thor, an eruption that reached 310 miles high; Amirami, the largest lava flow in the solar system; mountains towering up to 36,000 feet (Everest is 29,000); and much more. The fact that such activity could exist on a small moon that should be mostly frozen by now is calling into question traditional theories about the dynamics of planetary interiors. Ios lavas, for instance, are generally much hotter than the basaltic lavas on earth. It appears they contain heavy elements like iron and magnesium (called ultramafic lavas). Theory demands that the heavy elements sink into the interior; how can these heavy elements erupt out onto the surface? What drives the incessant heat flow that is as active at the poles as at the equator, and shows no cooling down during the night?
The first-order explanation is that Io is tidally pumped by its orbital resonance between Jupiter and Europa. Like a rubber ball repeatedly squeezed, Ios tides generate heat and that heat has to come out. Volcanic activity was actually predicted on this principle shortly before Voyager 1 arrived. The problem is that there is more heat flow by an order of magnitude than most models of tidal flexing predict. Veeder, Matson, Johnson, Davies and Blaney1 have made the problem worse in their paper by recalculating the heat flow from thermal anomalies and adding in the extra amount detected from polar sources, arriving at a weighted average of 2.5 watts per square meter well above that predicted by most theories of tidal dissipation in Jupiter and Io. Considering all the heat emitted by cooling lavas over the entire surface, Matson in an earlier paper had set an upper bound of 13.5 watts per square meter. This is nearly five times the heat coming out of Yellowstones thermal basins.
The final paper by Keszthelyi, Jaeger, Turtle, Milazzo and Radebaugh2 is entitled A post-Galileo view of Ios interior. In proposing their mushy magma ocean model, in which the interior has no solid core but is mushy all way through, they seem to be meekly standing up with bulls-eyes painted on their backs, waiting for the inevitable criticisms: how can the tall mountains exist? How does the model prevent runaway melting? How do you stop the magma from escaping too fast? How do you prevent differentiation? More complex models will be required, they meekly admit, and Such future work may show that the mushy magma ocean model will need to be further refined, or even rejected. They point to previous critiques: Stevenson (2002) predicts that a mush zone >20 km deep would be unstable over geologic timescales. Another issue is that, if the temperature of the mantle were to change significantly on a time scale of less than 106 [one million] years, then our model for stresses in the lithosphere would be inaccurate (McKinnon et al., 2001). Hey, its only a model, a useful starting point for future discussions. So Io, its off to work we go.
1Glenn J. Veeder, Dennis L. Matson, Torrence V. Johnson, Ashley G. Davies and Diana L. Blaney, The polar contribution to the heat flow of Io, Icarus Volume 169, Issue 1, May 2004, Pages 264-270, doi:10.1016/j.icarus.2003.11.016.
2Laszlo Keszthelyi, Windy L. Jaeger, Elizabeth P. Turtle, Moses Milazzo and Jani Radebaugh, A post-Galileo view of Ios interior, Icarus Volume 169, Issue 1, May 2004, Pages 271-286; doi:10.1016/j.icarus.2004.01.005.
One model they never seem to consider is that Io might not be as old as they assume. Did you catch the phrase geologic timescales? Thats code for 4.6 billion years. If the model does not fit geologic timescales then the model must be tweaked till it does. 4.6 billion years is the golden parameter, the figure that must not be altered, because Darwinian evolution depends on it.New Institute 05/04/2004
Dr. D. James Kennedy announced this week that his Coral Ridge Ministries (Ft. Lauderdale, Florida) is launching a new initiative dedicated to defending Biblical creation: the Creation Studies Institute. Their May newsletter indicates that Tom DeRosa, known for his creation expeditions that have uncovered dinosaur bones (see 01/29/2003 headline), will head the new ministry which will provide radio programs, conferences, field expeditions, newsletters and an interactive website. The newsletter tells Tom DeRosas testimony, From Atheist to Creationist, and also updates the story of Tom Vail and his Grand Canyon book (see 01/08/2004 headline). It ends with a commentary by Dr. Kennedy entitled, Darwins Crumbling Idea.
Dr. James Kennedy, a nationally-known TV pastor, has been a strong supporter of Biblical creation for many years. Its amazing how many ministries his organization operates, but unlike some media ministers, Kennedy never let all this go to his head: he still has a heart for one-on-one evangelism and concern for the individual soul. Many pastors seem afraid of science or consider creation/evolution a side issue (see why the church must emphasize creation), but Kennedy understands the deleterious effects of Darwinism in our culture* and the importance of confronting it. Tom DeRosa has a long track record of hands-on field work and leadership with people, and understands both sides of the creation-evolution issue from personal experience. This should be an effective collaboration.How Climate Influenced the Dead Sea and History 05/03/2004
The Dead Sea, the lowest lake on earth (1368 ft below sea level), figures prominently in the Bible. Near this body of water, Lot settled and the cities of the plain were destroyed. David wandered here, battles were fought nearby, and Herod built a fortress at Masada overlooking the lake. Later, Moslems and Crusaders left marks of their conquests in the region. Did the Dead Sea preserve a record of climactic changes that affected not only the Great Rift Valley in which it resides, but also the whole land of Israel? Students of Biblical history will be interested in two papers about the Dead Sea published in the May Bulletin of the Geological Society of America.
The first paper by R. Bookman (Ken-Tor) et al.1 reconstructs a curve of lake levels during historic times. Currently, the Dead Sea is at a record low due to diversion of Jordan River waters for irrigation. This has exposed historic shorelines for analysis. The team took radiocarbon dates of organic material at three sites around the lake to discern periods when the lake shore rose and fell. They then correlated the lake levels with cultural changes occurring in Palestine at those times:
Highstands occurred in the second and first centuries B.C. and the fourth century A.D. during the Roman and early Byzantine periods, respectively, in the eleventh and twelfth centuries A.D. during the Crusader period, and at the end of the nineteenth century A.D. The rises mark a significant change in the annual rainfall in the region, which likely exceeded the instrumentally measured modern average.The team estimated that high-water levels correspond to annual Jerusalem rainfall rates of 26 inches per year or more, and low-water levels to droughts of 18-20 in/yr or less. Thus Dead Sea lake levels are indicators of overall climate in Palestine. The oldest part of the curve is the least certain, but seems to indicate a high water level during the patriarchal period:
The oldest sediments described (unit I, Fig. 5) correspond to a lake level higher than 411 mbsl dated to 2140–1445 B.C. (3703 ± 37 and 3220 ± 36 radiocarbon yr B.P., Table 1). At that time the lake level was falling from an earlier highstand (prior to the fifteenth century B.C.), but no indicator for the absolute lake-level elevation was found at our sites. However, unit I may correspond to a distinct shore ridge identified in a western location in the Nahal Darga fan delta (Fig. 1C ) at 370 mbsl, where its age was estimated at 3000–4000 yr B.P.The second paper by David-Novak et al.2 examined debris flows in the canyons around the Dead Sea. Unusually strong storms in 1995 and 1997 allowed them to calibrate, for the first time, the rainfall conditions necessary to trigger a debris flow in an arid environment. The 1995 storm, in which a convective cell hovered over the area and dumped rain at rates nearly 2 inches per hour, was the most severe and resulted in debris flows in all the canyons under the heaviest rain; the 1997 storm was milder and more localized to the plateau, and only resulted in three debris flows.
Since rainfall measurements were available for these storms, they were able to interpolate an estimate for the rainfall rate necessary to trigger a debris flow, and found the threshold to be approximately 30mm/hr for at least one hour (1.2 inches per hour). Surprisingly, they found evidence for prehistoric debris flows was rare. They estimate only zero to three debris flows occurred during the last 3000 years, but they admit that it is possible that some deposits, mainly at the larger basins, were formed by multiple flows that are currently indistinguishable.
Although Debris flows are major processes of sediment transport in arid regions, particularly in areas of high relief, their rarity has made it difficult to measure the rainfall necessary to trigger them. Fortunately, at Nahal Arugot and Nahal David on the western slopes of the Dead Sea, rain gauges and a stream flow measurement station were available for the intense storms of 1995 and 1997.
1R. Bookman (Ken-Tor), Y. Enzel, A. Agnon and M. Stein, Late Holocene lake levels of the Dead Sea, Geological Society of America Bulletin Vol. 116, No. 5 (May/June 2004), pp. 555–571, doi: 10.1130/B25286.1.
2 Hagit Ben David-Novak, Efrat Morin and Yehouda Enzel, Modern extreme storms and the rainfall thresholds for initiating debris flows on the hyperarid western escarpment of the Dead Sea, Israel, Geological Society of America Bulletin Vol. 116, No. 5 (May/June 2004) pp. 718–728, doi: 10.1130/B25403.2.
Bible study is enhanced by considering the environment in which the great sagas of history took place. How did the geology, climate, zoology, botany, mineralogy, topography and hydrology affect culture, or influence decisions of kings and tribal groups? Availability of water, for instance, is a primary deciding factor for settlers, and strongly influences the locations of cities and roads. Of particular interest is the story of Abraham and Lot. Anyone looking at the Dead Sea shores today would wonder why Lot would find the place attractive; today, it is hot, dry and nearly devoid of vegetation. Yet when Lot viewed it, it was well watered everywhere (before the LORD destroyed Sodom and Gomorrah) like the garden of the LORD, like the land of Egypt as you go toward Zoar (Gen. 13:10). Was this desert once a garden?Tufa Mounds Formed Instantaneously, Geologically Speaking 05/01/2004
Tufa towers have been found forming in Big Soda Lake, Nevada, at the rate of 30mm/year. Now more than 3 meters tall, that means they could have reached their current height in only 100 years. Rosen et al., who reported this in the May issue of Geology,1 warn that care should be taken when trying to determine the significance of variations in isotopic or chemical compositions of tufas that may have been caused by mixing with groundwater, because The exceptionally fast growth of the tufa mounds indicates that large tufa deposits may form almost instantaneously in geologic time. They point out that similar structures have been used as proxy for paleoclimate throughout the world such as in Spain. They conclude,
The presence of large, fast-growing tufa mounds in a modern closed-basin lake indicates that care must be taken when evaluating the growth rate of ancient tufa mounds for paleoclimate or signatures and paleohydrologic information. In particular, if overgrowth and/or recrystallization such as described here occur, there is ample possibility of obtaining a mixed signature from tufa that may not be representative of either groundwater recharge sources or local surface water. In such cases, caution must be exercised in elucidating the paleoclimate or paleohydrologic signature.
1Rosen, Arehart and Lico, Exceptionally fast growth rate of 100-yr-old tufa, Big Soda Lake, Nevada: Implications for using tufa as a paleoclimate proxy, Geology Vol. 32, No. 5 (May 2004), pp. 409–412, doi: 10.1130/G20386.1.
Large tufa mounds are found around the world. Some notable examples are at Mono Lake and Searles Dry Lake in California. Before assuming these structures took long ages to form, or can tell us about past climates, we should take note of these geologists surprising findings.