[Darwins] whole argument began with a being which already possessed reproductive powers. This is the creature the evolution of which a truly comprehensive theory of evolution must give some account. Darwin himself was well aware that he had not produced such an account. It now seems to me that the findings of more than fifty years of DNA research have provided materials for a new and enormously powerful argument to design.
Astrobiologist Steven Benner thinks there could be hydrogen fish swimming in methane seas on Titan. Hes using the Huygens landing (see 01/21/2005 entry) to re-open the question of whether life requires water, or if it could have evolved to use other liquids. If life is an intrinsic property of chemical reactivity, Benner concludes, life should exist on Titan. Philip Ball at News@Nature.com asks, Are those dark patches on Titan really oceans, fed by rivers of liquid ethane? And if so, what are the fish like?
Steve, you know better (see 11/05/2004 entry). Stop grandstanding to dupe the gullible news media. This appears to be a naked ploy to arouse funding for another Titan mission: Benner said, We need to go back, with a lander that can survive for weeks, not minutes. We should go back, all right, but to learn more about an intriguing geology and atmosphere, not to prop up a dying theory. Why didnt you tell Nature that you cannot fathom a chemical basis for life that does not use DNA and proteins? Why not explain why water is unique for life? (see 12/30/2003 entry). Why not tell them that the problems with your naturalistic origin of life studies are almost bad enough to make you contemplate becoming a creationist?Editorials Lukewarm to ID, but Not as Hot to Darwin 01/31/2005
A subtle shift seems to be taking place in media coverage of intelligent-design controversies in school boards across the country. Darwinists used to be the unchallenged kings of the hill. Alternatives, whether creationism or intelligent design, were disqualified before they reached the starting gate. It also used to be open season on anti-Darwinists. No vituperative rhetoric or impugning of motives was too strong for reporters in their treatment of the villains of creationism. Several recent articles, however, show some cooling of the jets, and a little more attempt at balanced coverage by spokespersons from both sides:
Big ships turn slowly. While none of these articles endorses ID or gives Darwinism the interrogation it deserves, it does hint at a slight temperature change that can have big El Niño consequences later. At least more and more reporters are listening to ID arguments and not dismissing them out of hand. Here are some suggestions reporters should consider for their next articles:Your Motors Are Turbo-Charged 01/30/2005
Think how fast 6000 rpm is. It would redline on most cars. Yet you have motors in your body that make that speed look like slow-mo.
The Japanese have taken great interest in the cellular machine ATP synthase since its rotary operation was discovered in 1996 (see 12/22/2003 entry). Maybe its because they like rotary engines. ATP synthase is an essential protein complex that generates ATP (adenosine triphosphate), the energy currency of the cell. Found in the membranes of mitochondria and chloroplasts, it runs on an electrical current of protons, from sunlight (in plants) or digestion (in animals). It is a reversible engine: it can just as easily generate protons from the dissociation of ATP. It has five major protein parts, including a rotor, a stator, and a camshaft. The F0 domain runs like a waterwheel on protons and turns the camshaft. Three pairs of lobes in the F1 domain catalyze ATP from ADP and phosphate, in a three-phase cycle of input, catalysis, and output. Each revolution generates 3 ATP.
Hiroshi Ueno and team, reporting in PNAS,1 have invented new techniques for studying and measuring the tiny motors. Now, with the aid of a high-speed camera running at 8,000 frames per second, they have clocked the rotational speed of the entire F0F1-ATP Synthase motor at 352 revolutions per second, a whopping 21,120 rpm.
Although this molecular machine exists in all life forms, they used motors from a thermophilic bacterium. To monitor the action, the team fastened a microscopic bead to the carousel of c subunits. At 25° C, it ran at 230 rps. At 45° C, it ran at 650 rps. Extrapolating up to 60° C, the organisms optimum growth temperature, they speculate that it could be running as fast as 1,600 rps an unbelievable 96,000 rpm and that with nearly no friction and almost ideal efficiency. While they caution that reservation is needed whether these enormous numbers are actually achieved, they do say with confidence that the rotation rates they measured are much higher than earlier claims. It is intriguing to learn, they say, whether these rapid rotations are really occurring in living cells.
1Ueno et al., ATP-driven stepwise rotation of F0F1-ATP synthase, Proceedings of the National Academy of Sciences USA, 10.1073/pnas.0407857102, published online before print January 24, 2005.
We owe an apology to our readers. We have been repeating earlier reports that ATP synthase runs at 6,000 rpm. Thats like insulting the Ferrari company by watching one moving slowly in a parking lot and claiming it is rated at 10 mph. Were sorry for not giving proper credit to the Designer of this high-performance marvel. Eat your heart out, Charlie.Astrobiology: 0 Steps Forward, 3 Steps Back 01/28/2005
Astrobiology, the science in search of a subject, has major hurdles to overcome in its quest to explain everything from hydrogen to high technology. Despite being one of the most active interdisciplinary research projects around the world (see 01/07/2005 entry), a leading researcher this week conceded that several promising leads of the past are now considered unlikely. Because the biochemicals we know (proteins and nucleic acids) are so advanced and improbable under prebiotic conditions, attempts to generate them or build living systems based on them have proved fruitless. Astrobiologists are having to imagine simpler, hypothetical precursor molecules as stepping stones. If square one was the Miller experiment in the 1950s, this puts them behind square one.
Dr. Pascale Ehrenfreund leads a team of astrobiologists at Leiden University in the Netherlands. In the third presentation in a Life Detection seminar series at the Jet Propulsion Laboratory (see 12/03/2004 and 11/05/2004 entries for first two), Dr. Ehrenfreund, a specialist in complex molecules in space, who described herself as an experimentalist rather than a theorist, first put astrobiology into the larger context cosmology and astrophysics. Prebiotic molecules either had to be formed in situ on the early earth, or had to be delivered via comets, asteroids, or interstellar dust. She listed 137 molecules that have been identified in space (see Astrochemistry.net), including a number of complex carbon compounds such as polycyclic aromatic hydrocarbons (PAH). Also of interest are some 80 varieties of amino acids identified in meteorites (living things only use 22 of them). So far, this is all chemistry, not biochemistry; but if such molecules could arrive on earth by extraterrestrial special delivery, presumably they could contribute to the prebiotic soup, she speculated.
Most of the talk consisted of typical astrobiology scenarios and the details of carbon chemistry and interstellar clouds. What really got interesting were the results of her teams own specific laboratory experiments. They put thin films of amino acids (glycine and D-alanine) into a chamber made to simulate a Martian environment, complete with the UV radiation expected at the surface. The goal was to determine, even if such molecules could form in early Martian lakes, whether they could survive long enough to contribute to prebiotic chemistry. The answer was depressing: the amino acids had a half-life of only eight hours under those conditions. They repeated the experiment ten times with the same results. We have to implement that knowledge into models of regolith mixing, she said, to understand what kind of results that would give, and how long amino acids can survive.... She quickly changed the subject to future Mars missions, but other problematical facts came to light during the presentation and the Q&A session following:
The audience was polite and receptive to Dr. Ehrenfreud, who, given the challenge of the subject matter, was knowledgeable and personable. If they were expecting encouraging laboratory evidence, however, to support astrobiologys contention that life can originate spontaneously on a planet, most of what they got was, more work needs to be done.
The entire presentation can be viewed in streaming video from JPL Multimedia. As a footnote, Huygens scientists announced this week that the methane found on Titan was not produced by life, in case anyone was hoping. See the story on Space.com.
Astrobiology is a totally bogus science built on the assumptions of Darwinism and naturalistic philosophy. Its only bright side is to motivate more experimental work in chemistry, physics, geology and astronomy which is good, but assumes no other motive would do so. And its track record is abysmal. Of the biomolecules we know, Dr. Ehrenfreund said, I wouldnt really fix on this modern biochemistry thing, and on one component [like ribose or RNA]; we have done that for 50 years, and we didnt succeed to go any step further with that; so I think you have to think a little bit in a new way. So 50 years after Stanley Miller proudly announced the formation of amino acids in a laboratory flask, we now know all that was irrelevant hype. Today, the wizards of chemistry are into visualization. They ask us to envision hypothetical simpler entities, yet to be discovered, that might self-organize into self-reproducing machines.Book 01/28/2005: The Evolution-Creation Struggle by Michael Ruse (Harvard, 2005). The blurb says,
Michael Ruse, a preeminent authority on Darwinian evolutionary thought and a leading participant in the ongoing debate, uncovers surprising similarities between evolutionist and creationist thinking. Exploring the underlying philosophical commitments of evolutionists, he reveals that those most hostile to religion are just as evangelical as their fundamentalist opponents. But more crucially, and reaching beyond the biblical issues at stake, he demonstrates that these two diametrically opposed ideologies have, since the Enlightenment, engaged in a struggle for the privilege of defining human origins, moral values, and the nature of reality.Is Michael Ruse evolving? The man once ridiculed creationism as a crackpot pseudo-theory, manufactured to cover the nakedness of biblical literalism in scientific dress to get around the U.S. Constitutions separation of church and state (see also 02/18/2003 entry) now appears to giving it equal philosophical status with evolutionism.
Maybe thats what hanging around Phillip Johnson for too long does to a hardened Darwinist. To his credit, Michael Ruse has been open-minded enough to debate his opponents publicly numerous times (see 07/19/2002 entry) and appear on the air and at conferences with them. Perhaps Ruse is realizing that such friendly and intelligent folk cant be as wicked and ignorant as Richard Dawkins said they were. Maybe also he is cringing at the weak arguments being foisted by his side (see 09/03/2002 entry, for example). It seems he is starting to take Dawkins attacks against his new friends personally, and trying to find some middle ground. Ruse seems in a mental tug-of-war between Charlie and Phil. Is this part of a slow-motion Damascus experience? (see 06/12/2003 entry). Write in if you know more about this book.Bat Theory Strikes Out 01/28/2005
An international team of biologists set out to write the family history of bats, a story that is largely unknown, they admitted in Science.1 They didnt have much to go on. The fossil record is impoverished, their research confirmed, so they tried to piece together a phylogenetic story by combining all that is known about bats from molecular genetics, biogeography, and the fossil record. First, some background about bats from Nancy B. Simmons, who analyzed the research in the same issue of Science.2 They really are quite a remarkable group of mammals:
Bats, the only mammals capable of powered flight, constitute more than 20% of living mammal species. Unlike birds and other terrestrial vertebrates, most bats use echolocationa biological form of sonarto locate and track their prey. Bats are found on every continent except Antarctica, and they exploit a wide variety of food sources including insects, small vertebrates, fruit, nectar, pollen, and even blood. More than 110 bat species may coexist in some ecological communities, a number that far exceeds that of any other mammalian group. Despite their prominent position among mammals, the evolutionary history of bats is largely unknown because of a limited fossil record and incomplete phylogenies [circular reasoning]. (Emphasis added in all quotes.)It seems surprising that such a large and diverse group of mammals should be so under-represented by fossils. The researchers estimate that 61% of the fossil history is missing. Furthermore, the evolutionary history of this order has been obscured by controversial phylogenetic hypotheses. There are large bats, small bats, Old World bats, New World bats, echolocating bats and non-echolocating bats. Some theories propose that echolocation arose more than once: unlikely, says Simmons, Because bat echolocation is a complex system involving specialization of the respiratory system, ear, and brain.... Their tree requires either that it arose more than once, or some groups had it then lost it.
The group of researchers came up with a family tree all right, but not without problems. Our molecular dates suggest that there are large gaps in the fossil record for most bat lineages, they state. More importantly, they exploded on the scene without apparent ancestors:
On average, the fossil record underestimates the origin of 58 bat lineages by 73% (Fig. 2). The four major microbat lineages are missing on average 56 to 86% of fossil history, with the Gondwanan clade (noctilionoids) missing the most (Fig. 2). Megabat lineages are missing a sum total of 98% of their fossil history (table S5). The terminal and internal branches are missing on average 58 and 88% of fossil history, respectively (table S5). With well over half of the Cenozoic history missing for microbat lineages and nearly all of the fossil history missing for megabat lineages, it is not surprising that Paleocene bat ancestors having transitional morphological adaptations for flight and echo-location have never been discovered.So how does one put together a family tree with so little data? The best one can. Despite the phylogenetic tree drawn for publication, the above statement was the last paragraph in the paper! Simmons says of this predicament, The scope of this big bang Eocene radiation is unprecedented in mammalian history.
1Teeling et al., A Molecular Phylogeny for Bats Illuminates Biogeography and the Fossil Record, Science, Vol 307, Issue 5709, 580-584 , 28 January 2005, [DOI: 10.1126/science.1105113].
2Nancy B. Simmons, An Eocene Big Bang for Bats, Science, Vol 307, Issue 5709, 527-528 , 28 January 2005, [DOI: 10.1126/science.1108871].
For a case study on how to spin-doctor a bad situation, read the UC Riverside press release. Youd expect lies from National Geographic, of course: Scientists Fill Blanks on Bat Family Tree. They just dont tell you what they filled it with: imagination.Medical Professionals Lambaste the Nature of Ethics 01/27/2005
Natures editorial on religion and ethics last month (see 12/09/2004 entry) motivated two medical professionals to write in and give the journal a piece of their mind.1 Apparently indignant over the editorials patronizing view of religion and its simplistic view of ethics, they made it clear that the scientific establishment is no judge of truth and righteousness.
1Correspondence, Nature 433, 355 (27 January 2005); doi:10.1038/433355a, b, c.
Medical professionals may be the awakening giant among allies in the revolution against Darwinism and the naturalistic, secularistic Big Science oligarchy. Highly intelligent, well trained and compassionate, doctors have no use for a philosophy that glorifies selfishness and survival of the fittest, even though the Darwin Party tries to wiggle its way into the medical schools (see 06/25/2003 entry). Medical doctors have devoted their lives to the unselfish care of the unfit: the weak, the sick, the poor and needy, unlike followers of eastern religions that have viewed the suffering as better off left alone to work out their karma.* Western doctors understand morals, love and purpose. If you are a medical professional, follow the lead of these two bold letter-writers, and voice your opinion. All that is needed for out-of-touch, dogmatic, disingenuous scientific oligarchies to triumph is for good doctors to say nothing.Venus Flytrap Is Snappy-Fast 01/27/2005
One tenth of a second is all the time the fly gets. The traps of the Venus flytrap, an insectivorous plant Charles Darwin called one of the most wonderful in the world, somehow responds to stimuli quickly without muscles. The entire mechanism is still largely unknown. A team of French, UK and American scientists set out to study how it works so fast. Their research, published in Nature,1, describes how the leaves are flexed into an outward curvature along two axes. The trigger hairs inside the leaves propagate a signal that causes a rapid turnover, something like turning a half tennis ball inside out. The closure has three phases: an initial slow action, a fast close, followed by a slow tightening of its grip around the prey. See also the write-up by New Scientist, which ends, Our study still leaves us baffled about one question that motivated him [Darwin] how did this mechanism evolve? (emphasis added).
1Forterre et al., How the Venus flytrap snaps, Nature 433, 421 - 425 (27 January 2005); doi:10.1038/nature03185.
Maybe it didnt evolve; did you ever consider that possibility?Design Paper Published in PNAS 01/26/2005
Can scientific progress be made from a design perspective? The Intelligent Design movement says so, but critics say ID has no place in science, which by definition must be naturalistic; judges rule that alternatives to Darwinian evolution are forbidden in public schools (see 01/13/2005 entry). The rationale is that anything else assumes God, and is therefore religiously motivated. Then how do we interpret a paper in PNAS this week,1 that is chock full of design language?
A team of Japanese and American biologists, from Caltech and University of California and elsewhere, describe the heat shock response in the cell. They not only compare this biological system to good engineering, but treat the engineering paradigm as a proper approach to the study of cellular systems: in fact, they say, Viewed from this perspective, heat shock itself constitutes an integral functional module. Such a characterization of functional modules is extremely useful, because it provides an inventory list of cellular processes. An analogy would be a list of machines and their function in a factory. For more design language, look at the abstract:
Molecular biology studies the cause-and-effect relationships among microscopic processes initiated by individual molecules within a cell and observes their macroscopic phenotypic effects on cells and organisms. These studies provide a wealth of information about the underlying networks and pathways responsible for the basic functionality and robustness of biological systems. At the same time, these studies create exciting opportunities for the development of quantitative and predictive models that connect the mechanism to its phenotype then examine various modular structures and the range of their dynamical behavior. The use of such models enables a deeper understanding of the design principles underlying biological organization and makes their reverse engineering and manipulation both possible and tractable. The heat shock response presents an interesting mechanism where such an endeavor is possible. Using a model of heat shock, we extract the design motifs in the system and justify their existence in terms of various performance objectives. We also offer a modular decomposition that parallels that of traditional engineering control architectures. (Emphasis added in all quotes.)The paper is filled with design words: engineering, robustness, feedback loops, feed-forward loops, modularity, performance, functional criteria, and the like all but the buzzphrase intelligent design. For example, Biology and engineering share many similarities at the system level, including the use of complexity to achieve robustness and performance rather than for minimal functionality.
The only mention2 of biological evolution is a passing reference in the final discussion that, in the surrounding design language, seems almost irrelevant: The formulation of such a problem aside, the physical implementation of any of its solutions seems to have been evolutionarily solved by using a number of recurring motifs... How it was solved, and who solved it, is left unexplained. Instead, the authors seem enthusiastic that a design-theoretic approach, viewing cellular mechanisms the way a computer scientist would reverse-engineer software, can be a fruitful avenue for research:
However, to understand the operational principles of a certain machine, to repair it, or to optimize its performance, it is often necessary to consider a modular decomposition of the machine itself. Such a decomposition does not necessarily require stripping the machine down to the component level but rather identifying its submodules with their predefined functionalities. A particularly successful such modular decomposition has been extensively used in the field of control and dynamical systems, where components of a system are classified in terms of their role with respect to the regulation objective. Similar decompositions exist in computer science, for example, because modularity is a basic principle of good programming.The authors make no mention of a Programmer, or state their personal beliefs about origins. But that, again, supports a principle stated frequently in the intelligent design literature: the identity of the designer is not the issue. Design detection is a purely scientific question, and the design-theoretic approach is a fruitful avenue of research.
1El-Samad, Kurata, Doyle, Gross and Khammash, Surviving heat shock: Control strategies for robustness and performance, Proceedings of the National Academy of Sciences USA, 10.1073/pnas.0403510102, published online before print January 24, 2005.
2The only other possible allusion states, Indeed, in higher level languages, a complicated programming task is usually divided into a set of modules, subroutines, or objects, with simple well defined interfaces. This results in flexible and robust programs, whose modules can be designed almost separately and, as such, are more easily evolvable. However, being in the context of computer program design, the statement implies guided evolution i.e., upgrading by intelligent design, not evolution by an undirected or Darwinian process.
Big Science went ballistic when Stephen Meyer published an ID paper in a minor journal (see 09/24/2004 entry), claiming it was a mistake to let such material pass peer review. Well, ID scientists should print this paper and wave it in the face of Eugenie Scott and Ken Miller and all the other Darwin Party hacks who claim ID is illegitimate in science. Here again and this is one of many examples we have reported (see 01/01/2005 and 12/20/2004 for recent examples) ID is not only detectable in biological phenomena, but ID itself is the most fruitful approach to doing science. This is abundantly evident in this paper, written by authors completely outside the intelligent design movement and published in a leading secular journal. Most likely unintentionally, they have underscored what the ID movement has been saying all along: regardless of ones religious beliefs (or lack of them), a reasonable inquirer into a phenomenon can detect design, and the design approach is productive for science. Its the same approach used by Faraday, Mendel, Kepler, Carver and most of the other great scientists of history. Only the Darwin Party welfare bums have a problem with it. (See 12/22/2003 entry; contrast it with the one that follows it.)Shroud of Turin Debate Reopens 01/26/2005
The shroud was from the 13th century, concluded earlier researchers, using carbon 14 dating methods. Now, other experts are claiming the methods were flawed, because the researchers dated a mended patch made by medieval monks. The BBC News reports a new claim that it is older than thought: between 1300 and 3000 years old. National Geographic News says the new tests, published in a peer-reviewed journal, greatly increase the possibility that the shroud may be as old as Christianity itself.
Well leave it to others to debate whether the Shroud of Turin dates from the time of Christ or not. Even if so, whether it was the burial shroud of Christ is a separate question. Suffice it to say that adherents on both sides had their experts, but experts are only human. Scientific results dont exist in a vacuum. Fallible humans must interpret them.Trail + Trail Mix = Health Mix 01/26/2005
Peanuts, a staple ingredient in trail mix, are rich in good chemicals, reports the BBC News. They have as many antioxidants as fruits, are high in protein and good monounsaturated fat. So take some along and go on the trail, because, according to Southwestern Medical Center, Exercise helps reduce symptoms of depression, and EurekAlert reminds us that aerobic workouts prevent disease.
So George Washington Carver was right about the humble peanut: it is delicious and nutritious. And they bring good luck. Thats why JPL scientists always pass the peanuts just before every important spacecraft maneuver.Hippo to Whale: Missing Chain 01/26/2005
Despite claims to the contrary,2 whale and hippo evolution are poorly understood. Thats the gist of a paper in PNAS this week1 that tries to connect the dots between hippopotami (artiodactyls) and whales (cetaceans) and other groups of mammals. Theres lots of missing dots:
The origin of late Neogene Hippopotamidae (Artiodactyla) involves one of the most serious conflicts between comparative anatomy and molecular biology: is Artiodactyla paraphyletic? [i.e., unrelated, but similar by convergent evolution]. Molecular comparisons indicate that Cetacea should be the modern sister group of hippos. This finding implies the existence of a fossil lineage linking cetaceans (first known in the early Eocene) to hippos (first known in the middle Miocene). The relationships of hippos within Artiodactyla are challenging, and the immediate affinities of Hippopotamidae have been studied by biologists for almost two centuries without resolution. (Emphasis added in all quotes.)Their paper proposes a phylogenetic tree based on morphology; it rejects hippo relationship to pigs, and puts them as a sister group to whales, but puzzles remain: for example, the position of Ruminantia [cows] is a central question, still to be solved. Clearly, they need more fossils: Further progress in this debate is likely to come from morphological studies of paleontological data, whether known or still to be discovered (emphasis added).
1Boisserie et al., The position of Hippopotamidae within Cetartiodactyla, Proceedings of the National Academy of Sciences USA, 10.1073/pnas.0409518102, published online before print January 26, 2005.
2See, for example, 11/21/2003 and 11/18/2003 headlines. National Geographic News, reporting on this paper, calls whales and hippos close cousins, which is an odd statement, considering they conclude, There is a 40 million-year gap between fossils of early cetaceans and early hippos.
And you thought the animators on PBS and the Discovery Channel had whale and hippo evolution all figured out. From what missing links did hippos get their antibiotic sunscreen sweat? (see 05/25/2004 entry).Stupid Evolution Quote of the Week 01/26/2005
This weeks entry goes to Bill Hansson, who discussed the robber crab for Science Now. This crab has an air-adapted sense of smell similar to that of insects unusual for a crab. Accomplice for the prize is reporter Amitabh Avasthi, who explained what the crab needed to evolve:
When the ancestors of robber crabs first walked out of their watery environment to live on land, their sensory equipment needed a makeover. The olfactory receptors on the antennae of marine crabs detect soluble, water-loving molecules. A landlubbing crab must zero in on molecules that waft through the air. (Emphasis added in all quotes.)Insects have a similar electrical response to airborne scents. Avasthi dubbed this evolutionary feat the robber crabs development of a bugs nose. Hansson, whose team examined red crabs and robber crabs on Christmas island, called this a great example of convergent evolution. Then came his winning line, The robber crabs have reinvented their smell for land so remarkably that they can even smell water. All by evolution, of course.
The prize is a week-long series of lectures by George C. Williams (see 05/31/2004 entry) on how not to tell Darwinian just-so stories, followed by a friendly visit with Phillip Johnson in a courtroom.Newspaper Editorials Lead Revolt Against King Charles 01/24/2005
Some columnists and editorial writers are gaining boldness to attack the Darwin-only rule in science education. Some examples:
Want to take part in one of the biggest revolutions of modern times? Take up the pen, not the sword, and let your eloquence help bring down the idol of King Charlie the Usurper, where it can join its mates in the fantasyland section of StalinWorld.Spinach Leaf: One of Natures supreme examples of nanoscale engineering 01/24/2005
Under the peaceful summer sun, plants deal with a life-or-death situation: too much sun. Those of us with legs can take cover, but a poor spinach plant out in the furrow must deal with the excess energy or die. Since it usually doesnt die, whats its secret? A process called photosynthetic feedback de-excitation quenching, if you care to know. Scientists at Berkeley Labs discovered one key molecule in the process that helps ferry away the excess energy safely.
You can read the details in the press release, but Graham Fleming, one of the researchers, was impressed. This defense mechanism is so sensitive to changing light conditions, it will even respond to the passing of clouds overhead, he commented (emphasis added in all quotes) It is one of Natures supreme examples of nanoscale engineering. Some of the steps in the multi-step process respond in a million billionth of a second. It took special ultrafast equipment in their work on spinach leaves to discover what the molecule, a carotenoid named zeaxanthin, was doing. Science Now has a picture of the crystalline molecule under the microscope, calling it a unique safety valve. Those who want all the technical details can find the teams report in Science.1
1Holt et al., Carotenoid Cation Formation and the Regulation of Photosynthetic Light Harvesting, Science, Vol 307, Issue 5708, 433-436 , 21 January 2005, [DOI: 10.1126/science.1105833].
Think about this when you eat spinach. You are consuming a supreme example of nanoscale engineering. A can of spinach may not help you punch Brutus to kingdom come, but might help you appreciate the King who came.How To Make Instant Petrified Wood 01/24/2005
Want to petrify wood without waiting a few million years? Try this, EurekAlert teases. The recipe: pick up some pine or poplar wood chips from your local lumber store, soak them in an acid bath for two days, then soak them in silica solution for two more. Air dry, then put into argon-filled furnace at 1,400°C for two hours. Let cool in argon to room temperature. Presto. Instant petrified wood. The press release from the DOE Pacific Northwest National Laboratory states, The acid-leaching method yields an identical, positive reproduction of the wood. One of the researchers concurs; it replicates exactly the wood architecture.
Nature, however, works much more slowly, according to the report:
Yongsoon Shin and colleagues at the Department of Energy lab have converted wood to mineral, achieving in days what it takes nature millions of years to do in such places as the Gingko Petrified Forest, an hour up the Columbia River. There, trees likely felled in a cataclysmic eruption and, buried without oxygen beneath lava, leached out their woody compounds and sponged up the soils minerals over the eons. (Emphasis added.)The article adds an interesting factoid about wood tissue. The intricate network of microchannels and pores in plant matter provide enormous surfacesin wood, 1 gram of material flattened out would cover a football field, it says. Scientists are interested in creating ceramics that mimic these properties. With instant petrified wood, they might be able to separate chemicals in the lab, or filter pollutants from escaping gas.
A million years is an awful, awful, awful long time. Think about everything that has transpired since the first record of human civilization: all the wars, natural disasters, climate changes, environmental and population shifts. Now multiply that thought by a hundred that is less than one million years, let alone 10 million or a hundred million. Dont you think in all that time, with all the volcanoes going off and continents drifting around, all the weathering and erosion, all the pressure and temperature changes, nature couldnt figure out how to petrify wood a little faster, if we can do it in less than a week? Why do you think this article claims it took millions of years? Evidence? ... or maybe another reason?More Titan Results Announced 01/21/2005
A week after the successful landing on Titan, ESA held its second main press conference on the findings. The scientists were clearly upbeat about the results. The probe transmitted data for 72 minutes from the surface after its 2.5 hour descent through the atmosphere. The mesas, observed in stereo, are made of water ice about 100m high, and the channels are most likely formed by erosion from methane rain. The dark material appears concentrated in the canyons that cut through the ridges. The processed images show fluid flow in the form of rivers has been active, and also extruded water ice with possible methane springs. Even the dark regions show evidence of fluid flow.
The dark lakes or playas do not appear to have surface liquid now, although it seems evident they did in the recent past. From the surface, the stones of ice appear to have been rounded by erosion. Most of the elevated features are composed of dirty water ice with crushed ice scattered around. The eroding agent, which rains down and flows over the surface, is almost certainly liquid methane. Except for the chemistry and temperatures involved, the processes appear familiar to us on earth: condensation, evaporation, erosion, rain, rivers, wind and weather. Huygens did not sense rain on the day of landing, but the scientists suspect it rained recently, and will probably rain more, in this strange place. The rains could be seasonal. In short, dark material precipitates from the atmosphere, and is washed off the icy mesas by methane rain, where it flows down the channels to the flat areas. Its like Arizona except for the chemistry and the cold.
The Surface Science Package (SSP) worked well after landing. The probe may have settled about 10-15cm into the soil. Because the probe gives off heat from the mass spectrometer, and a 20W light bulb, scientists detected volatiles evaporating from the landing site.
From the mass spectrometer data, the team found that methane density increased during the descent and was strongest at the surface where it appears to be emitted from the soil. This was a big and important surprise. A reservoir of liquid methane must be evaporating from the subsurface. The dark seas are not from liquid ethane, but liquid methane. The scientists were pleased that many aspects of pre-Huygens models, including atmospheric composition, pressure and temperature, turned out to be quite correct.
The chemists found radiogenic argon, but not primordial argon, in the atmosphere. The methane must be primordial, it was said, because the water ice is too cold to provide a source of oxygen which would have created carbon dioxide (as on Mars). Good thing there was no free oxygen, or this world of highly flammable gases would have exploded. The haze layer exists lower than previously thought. The methane must condense, they believe; but why is it still present at all? It has to be continually renewed or else it would be long gone. Is there a reservoir inside Titan? This is a puzzle they are working on.
Where are the pools of methane? It appears the landing site is a bit of a desert. If it rains methane, the fluid appears to sink into the surface rather than remain in pools. Like dried up ponds, the flat areas appear to have liquid under the surface. How often does it rain? They could not say. The fact that liquid was evident just a few centimeters below the surface leads them to infer it must rain often.
Wow truth is stranger than fiction. What a strange and imaginative world! And think, all this is just from one small location on a sphere bigger than Mercury. It looks like our prediction won: no thick deposits of hydrocarbon precipitates were described, only water-ice geology with thin coatings of dirty snows that are easily washed off. Before gloating, we would need to know how deep the flat lakebeds are. Our opponents also need to come up with a plausible source for the methane.Daffy Duck Found in Dino Park 01/20/2005
A fossil duck from the Cretaceous has been discovered, indicating that the branch of birds including waterfowl already coexisted with the dinosaurs. A press release from NC State explains the significance of the paper published in Nature1 this week. Dr. Julia Clarke and colleagues say this means that at least duck, chicken and ratite bird relatives were coextant with non-avian dinosaurs.
1Clarke et al., Definitive fossil evidence for the extant avian radiation in the Cretaceous, Nature 433, 305 - 308 (20 January 2005); doi:10.1038/nature03150.
Wow, those early birds must have evolved from dinosaurs pretty fast. This seems to require a dramatically accelerated rate of lucky mutations per year. Beware, Charlie: gambling is addictive.Some Exoplanets May Be Exostars 01/20/2005
A brown dwarf was measured with more precision, and was found to be more massive than expected. Robert Roy Britt in Space.com says this may call into question some of the discoveries of bodies orbiting other stars that were assumed to be planets. I. Neill Reid,1 writing in Nature where the measurement was announced,2 explained the implications:
Clearly, this is only one datum point, for one particular age and one particular mass. Nonetheless, there are wide potential ramifications. If this is a fair reflection of the theoretical models, then analyses of the luminosity distribution of low-mass stars and brown dwarfs in young clusters may be systematically underestimating their masses. In consequence, the turnover in the mass function would be exaggerated (that is, there would be more brown dwarfs than currently estimated), but a lower-mass cut-off might lie at higher masses, because the supposed objects of 1-2 Jupiter masses might in fact exceed 15–20 Jupiter masses (0.015–0.02 solar masses). (Emphasis added in all quotes.)See also the report on EurekAlert.
1I. Neill Reid, Astronomy: Weighing the baby, Nature 433, 207 - 208 (20 January 2005); doi:10.1038/433207a.
2Close et al., A dynamical calibration of the mass-luminosity relation at very low stellar masses and young ages, Nature 433, 286 - 289 (20 January 2005); doi:10.1038/nature03225.
There could well be planets around other stars, but its one thing to find an exoplanet. Its another thing to find a privileged exoplanet.
Calling all Darwinists: plan a vacation to StalinWorld, a theme park that celebrates the legacy of atheistic survival of the fittest!
Education: Awareness of the Intelligent Design controversy by the media is on the rise. Tuesday January 18 on Fox News, Bill OReilly interrogated biologist Dr. Michael Crane about the Dover, Pennsylvania controversy, trying to get him to explain what is so bad about considering the possibility there is a higher power that created life. Cranes argument revolved around the assumption that science cannot consider such things, and that ID belongs in the comparative religions class. OReilly responded with the possibility of theistic evolution, but hinted that stories about the past are not as scientific as subjects observable in the present. What if God really did create the world? he asked. Wouldnt that be science?
Ribosome Unties the Messenger-RNA Gordian Knot 01/19/2005
Cells needing to translate their DNA into proteins have a problem. The messenger RNAs, the molecules that carry the genetic code from the nucleus to the translating machine called the ribosome, get tied up in knots. How does the ribosome untie them before they can begin translating? Takyar et al., writing in Cell,1 explored this problem and found that the ribosome has a novel solution.
If you have seen the film Unlocking the Mystery of Life, you watched a messenger RNA molecule, nice and straight, exit the nuclear pore complex and neatly enter the ribosome, like a man reclining in a barber chair waiting to get a haircut. Unfortunately, things are not so simple. Because of chemical affinities between the bases of the RNA molecule, the bases attract other bases (base-pairing) or else fold over on themselves, forming amorphous lumps (secondary structure). Untangling this mess would be like straightening out a chain of several hundred magnets that has clumped together.
The untangling problem is not unique to messenger RNA (mRNA). DNA in the nucleus also has to be unwound. Each of the processes of replication, DNA repair, recombination, transcription, pre-mRNA splicing, and translation have their own specialized enzymes, called helicases, that latch onto the nucleic acids and work their way down the helix, unwinding them for whatever subsequent operation is necessary. Until now, though, no helicase was found associated with the ribosome. It turns out the helicase activity is built-in.
The ribosome has an entry tunnel and exit tunnel. As the mRNA strand enters, specialized proteins named S3, S4 and S5 are precisely placed to form a ring around the mRNA helix. They grab the phosphate groups on the side chains and separate the base pairs.2 Theres only room in the tunnel for a single strand. As the interior of the ribosome pulls the mRNA through, this entry-tunnel helicase, built into the walls of the tunnel, effectively melts the double strands, sending in a clean single strand for the translation machinery to work on. And how does the ribosome pull it in?
In their studies of ratcheting of the two ribosomal subunits between the pre- and posttranslocation states, Frank and Agrawal (2000) observed a reciprocal expansion and contraction in the diameter of the upstream and downstream tunnels, suggesting that these two features may alternately grab and release the mRNA during translocation of mRNA. This dynamic behavior in the downstream tunnel could also be related to its helicase function.The action seems analogous to those old Dymo labelmakers people used to use for labeling household items. You remember: as your hand clicked the machine, the tape came in one tunnel and out another. In the case of the ribosome, the entry and exit tunnels alternately expand and contract, forcing the mRNA molecule to ratchet through the system. The ratchet prevents backward motion and also is delicate enough to prevent breakage of the single strand during the unwinding process.
The placement of S3, S4 and S5 in the tunnel is critical. The researchers found that when they were mutated, the helicase activity stopped. Because it latches onto the phosphates, which are universal to RNA molecules, they can unwind any strand, regardless of the sequence of base pairs.
The authors do not speculate on how this helicase system, which is unique to the ribosome, evolved. They only note that if it did, the unwinding puzzle needed to be solved by the very first living cell:
The inescapable presence of secondary structure within mRNA coding sequences must have been one of the first problems encountered in the transition from an RNA world to a protein world and may have resulted in coupling of ribosomal helicase activity with the fundamental mechanics of translocation.How this was accomplished by a sequence of random changes, they do not explain.
1Takyar et al., mRNA Helicase Activity of the Ribosome, Cell, Vol 120, 49-58, 14 January 2005.
2It was not clear to the authors whether the helicase pulls the bases apart with the expenditure of energy. It may be that the helicase can take advantage of spontaneous separation. Base pairs tend to breathe as their weak hydrogen bonds stretch. The helicase may be able to latch onto the nucleotide during its spontaneous separation, as if saying Aha! Gotcha! and prevent the hydrogen bond from re-forming.
Again, we see an elaborate system, with only a wave of the Darwinian hand to explain it. It is a cardinal sin of evolutionists that they merely assume evolution can solve any problem the realities of chemistry, physics and the environment throw at life. They invoke hypothetical lucky mutations, never observed, that somehow appeared at the right time and place to produce irreducibly complex structures like ribosome helicase.A Proverb a Day Keeps the Doctor Away 01/18/2005
Short, pithy statements of wisdom can keep you on the right health track, according to a press release from University of Toronto. Bernard Choi offers some examples, like seven days without exercise makes one weak.
King Solomon had some pretty good ones:Are Humans Still Evolving? 01/18/2005
Science Now asks the question, are humans still evolving? Comparisons of genes and chromosomes between different people groups from Asia, Europe and Africa are challenging the view that there is one human genome. Some long stretches of DNA are inverted in some groups, and women so affected seem to have more children on average, even though the section isnt related to fertility. Oxford statistician Peter Donnelly says of these surprising findings, This could be the tip of several icebergs.
So The Human Genome may be a myth. Perhaps DNA storage is more dynamic than we expected. The story does not establish any connection to evolution by natural selection except by assuming evolution and its commonly-accepted time scale. Notice this non-sequitur: at the end, Donnelly says, If such inversions are common, then there isnt just one version of the human genome... this shows natural selection is still acting on us. Come again? Were here, we have differences, therefore we evolved? Get a grip, Pete.Remember to Exercise, and Youll Remember More 01/18/2005
Old dogs can remember old tricks and learn new ones, say researchers from the National Institutes of Health. According to an article on EurekAlert, the secret is a program of diet, exercise and stimulating environments.
Scientists got snoopy about old beagles, and found their brains could remain in tip-top shape with lifestyle adjustments. These included diets with fruits and vegetables and antioxidants, stimulating environments and social interaction with other dogs. This combination probably works for humans, too, and looks like it can stave off some of the degenerative effects of aging. This research brings a note of optimism that there are things that we can do that may significantly improve our cognitive health, said one of the researchers (emphasis added). Of the positive factors, the scientists also found that more was better.
Pack a healthy lunch in a day pack and drive off with a group of friends to a trail head in Gods great outdoors why, thats the recipe for Creation Safaris. Doesnt this picture look healthy? How about an encore? Heres proof that more is better. It doesnt have to be all strenuous, though. Relaxation can be healthy, too.Lowly Plant Inspires Waterproof Glass 01/18/2005
By adopting the lotus position, the glass in your windshield may become so water-repellant you wont need windshield wipers. Thats what an Ohio State press release says: Ohio State University engineers are designing super-slick, water-repellent surfaces that mimic the texture of lotus leaves. The leaves of the lotus, or water lily, are covered with microscopic bumps that resist water stains. Soon we may have self-cleaning glass. Everyone but the window-washing industry should be pleased.
How many generations of water lilies had to drown till the right combination of lucky heritable mutations came along? The simplest things about plants and animals are sometimes just as noteworthy as the dazzling ones.Bart Simpson Moons Saturn 01/18/2005
There was a little-known story about the Huygens landing on Saturns moon Titan last Friday (see 01/15/2005 entry). The human race sent a gift to the Titanians. Four songs recorded by two European rock musicians before launch were included along with the spacecraft. The website Music2Titan.com explains the purpose of the project:
October 1997: to enrich the Cassini-Huygens mission with a human message to potential extra-terrestrial populations, and to leave trace of our humanity to the unknown, 4 original musics [sic] composed by French musicians Julien Civange and Louis Haéri are placed on board Huygens....The 4 songs are named Lalala, Bald James Dean, Hot Time, and No Love. The lyrics of No Love include the line: What will we export there? Our dustbins, our fast-food, our knowledge, Wall Street, Che Guevara, the Mona Lisa, Bart Simpson...? According to the composer, the song raises the questions linked to the conquest and the exodus of space.
Good thing nobody was there to listen to this stuff. Can you believe it? Here was an opportunity to send a token of mans greatest art, music and intellectual achievements, and what do the Europeans send? A dustbin of human depravity (except for the Mona Lisa and Wall Street, perhaps, and whatever these mopheads considered knowledge). Dont blame the scientists for this folly: most of them probably didnt even know about it. At least Carl Sagan had enough taste to outweigh Johnny Be Good with lots of Bach and Beethoven aboard the Voyagers, and Rosetta sent along a language disk of Genesis 1-3 in 1000 languages (see 01/13/2003 entry).Simple Darwinian Theories Have to Be Abandoned 01/17/2005
Mutate one gene and a cascade of changes can result. This effect is called pleiotropy (see 10/01/2003 entry). According to an article by Stephen Strauss reporting for the Canadian newspaper Globe and Mail, The emerging richness of pleiotropy means that any simple Darwinian notion of what is going on during natural selection has to be abandoned.
Unless Darwinians can show that the positive changes outnumber the negative effects, pleiotropy seems to spell difficulty, if not doom, for neo-Darwinian theory, which relies on beneficial mutations. But if beneficial mutations are rare to begin with, how can evolutionary theory face the new problem of pleiotropy? The simplest answer, Strauss writes, is that nearly 150 years after Darwin first explained the theory of evolution, the richness of multiple effects from the same gene is such that existence itself seems problematic (emphasis added in all quotes).
Strauss gives examples of a few more nuanced proposals for salvaging Darwinian evolution: Faced with what amounts to a growing daily confusion of genetic effects, biologists are proposing new and more highly refined theories of evolution. Some biologists hope that some mutations have only minor effects. Others are looking for examples of single mutations that might have a cascade of good effects. He ends on a hopeful note: With modern genetics increasing the supply of data about the multiple functions of genes, evolutionary biologists are increasingly confident that they are going to be able to do what Darwin promised but couldnt quite delivery [sic] -- truly explain the origin of species.
So Charlie couldnt deliver, and now, 150 years later, we are stuck with teaching his mythoid as fact without being able to subject it to critical analysis (see 01/13/2005 entry).Flying Saucer Lands on Titan 01/15/2005
The Huygens Probe successfully landed on the surface of Titan Friday morning, and appears to have remained active for an hour after impact. See the official European Space Agency site for latest scientific results. Download this 27-page Mission Description from JPL (2.0mb) for a detailed plan of the now highly successful mission.
At the day-after press conference, scientists provided some tantalizing samples from their data, including the sounds of the atmosphere recorded on a microphone (download the audio files from The Planetary Society). The principal investigator for the Surface Science Package (SSP) said they got excellent data from all 9 sensors during descent and on the surface. He won a sweepstakes for guessing the time of descent to within 7 seconds (just under 2.5 hours). Results from the Gas Chromatograph - Mass Spectrometer (GCMS) indicate a source of methane at the surface.
Eager for pictures, the media will continue to have to wait for the team to get some sleep after working through the night. But what they got produced gasps and applause: the first crude mosaic seemed to show some relief with drainage channels pouring into a shoreline, and the first color image from the landing site that showed an orange landscape and orange sky (see ESA Huygens site). The mosaic could be mistaken for an oblique aerial view of the coast of California, except that instead of a balmy beach, the scene is almost 300° below zero.
The only glitches of the mission were a missing command to turn on the Doppler Wind Experiment (DWE), and a redundant data channel that failed, losing half the possible images. However, the DWE data can be reconstructed entirely from combined data received by Earth-based radio telescopes (a remarkable capability comparable to watching a tennis court on the moon), and the imaging team got the planned number of shots; because of overlap, they should be able to reconstruct most of the panoramas they hoped for. Overall, scientific results were 100% of planned objectives and then some. That so many parts of this complex assemblage of hardware and software actually worked as hoped in an alien environment humans have never before visited is truly remarkable. This was a mission for the history books.
The treasure trove of scientific data returned from Huygens could well occupy scientists for many years. Despite lack of sleep over the last day and a half, each principal investigator seemed bristling with excitement. Some almost choked up as they described the results they got. Patience will be required for us onlookers as the experts mine the data. After years of speculation, a more accurate understanding of the atmosphere and surface of this bizarre world should emerge.
Update 01/17/2005: More science findings should be announced on Friday, Jan. 21, one week after the landing. All 369 raw images were posted by ESA yesterday. Over a third were taken after landing, and 20% were too blurry to be useful. A good 40% or so show the landscape as the probe descended about 5 meters per second. ESA also posted the sounds of Titan, including a microphone recording of winds, and a series of radar echoes that rise in frequency and tempo as the probe reached the ground with a thud. The surface texture resembles wet sand or clay with a thin solid crust, and its composition as mainly a mix of dirty water ice and hydrocarbon ice, resulting in a darker soil than expected.
Speaking of predictions, heres a chance to compare expectations of liberal evolutionists and conservative creationists. If Titan is old, it should have a layer of hydrocarbon snow half a mile thick (see 04/25/2003 and 10/16/2003 entries). If young, it should have less than an inch. Lets see whose prediction matches the findings. Lets also see if the old-agers can account for the replenishment of methane, which should have eroded away long ago if Titan had an atmosphere 4.5 billion years ago.Critical Thinking Outlawed in Georgia School District 01/13/2005
A federal judge has ordered the stickers removed from Cobb County, Georgia biology textbooks that encourage students to think critically when examining the theory of evolution (see 11/08/2004 entry), according to Yahoo News. The attorney defending the stickers tried to argue that science and religion are not mutually exclusive, and that the school board was just trying to get past the conflict and teach good science. US District Judge Clarence Cooper disagreed. He said,
By denigrating evolution, the school board appears to be endorsing the well-known prevailing alternative theory, creationism or variations thereof, even though the sticker does not specifically reference any alternative theories.... While evolution is subject to criticism, particularly with respect to the mechanism by which it occurred, the sticker misleads students regarding the significance and value of evolution in the scientific community. (Emphasis added in all quotes.)The judge must have changed his mind from November, when the Discovery Institute reported that he would not impute the motives of the parents for placing the disclaimer stickers; The Judge also held the sticker had a dual secular purpose of promoting critical thinking and reducing parental offense in light of expanded evolution coverage in the science curriculum.
The Discovery Institute blames the decision on a poor defense by the Cobb County attorney. For instance, he did not call any scientists to refute the charges, which allowed pro-Darwinist Ken Millers expert testimony to go unrebutted. Whatever changed the judges mind, the parents of six students who, along with the ACLU, sued the board over the stickers, are beaming: This is a great day for Cobb County students, said an attorney. Theyre going to be permitted to learn science unadulterated by religious dogma. Rev. Barry Lynn of Americans United for Separation of Church and State appeared on radio news programs saying he hopes this nails the lid on the coffin of this issue. Lynn lambasted those who try to diminish the value of evolution and replace it with religious dogma. An appeal, however, cannot be ruled out.
The stickers were inserted in 2002 when over 2,000 parents complained that the new textbooks taught evolution as fact, without even mentioning any alternatives. Dr. John West, speaking for the Discovery Institute called todays decision bizarre from a constitutional perspective. After ruling that the school board had a legitimate secular purpose for creating the textbook sticker, and acknowledging the fact that there are scientists who criticize modern evolutionary theory, he explained, the court nevertheless declared that the sticker is unconstitutional because some citizens might mistakenly believe that the sticker was intended to advance religioneven though the Judge admits it wasnt. He feels this shows the judge had a low view of the intelligence of his fellow citizens, because if he could figure it out, why couldnt they? To West, the only consolation is that Judge Cooper did state in his opinion that promoting critical thinking about evolution is legitimate.
Update 01/18/2005: Fox News reports that the board decided to appeal the decision. They feel that the judges decision amounts to unnecessary judicial intrusion into local control of schools.
Dogma? What religious dogma? The only religious dogma on display is that of the Judge and the ACLU who get paranoid when they think they sniff someone elses religion, whether or not any is present. They are like the drunk who thought the whole world smelled rotten when a practical joker had smeared limburger cheese in his beard. For the life of them, these attorneys, judges and Darwin-worshippers cannot see the religious dogma is their own. What is dogma, if not an insistence that other views must be excluded from free inquiry and critical thinking? This decision is disappointing, because it seemed like a slam-dunk. Anyone with common sense would agree that controversial ideas should be examined with critical thinking. It takes the convoluted arguments of Charlie worshippers to explain why their buddha needs special protection from scrutiny.Robots Dont See as Well as You Do 01/12/2005
Robot designers are still working on ways to emulate the human eye. Just when you thought digital cameras were all the rage, we learn from EurekAlert they are miserable substitutes when put into the eye sockets of robots. Robot-vision export Vladimir Brajovic explains:
Often, when we take a picture with a digital or film camera, we are disappointed that many details we remember seeing appear in the image buried in deep shadows or washed out in overexposed regions. This is because our eyes have a built-in mechanism to adapt to local illumination conditions, while our cameras dont. Because of this camera deficiency, robot vision often fails. (Emphasis added.)But cant automatic exposure meters do the same thing? No; they pick either a spot or average of the scene, and adjust all the sensors to the same level. Our individual rods and cones not only have individual light adjustments, but talk to each other about what they see, and do image processing before the signals reach the brain (see 12/30/2003 and 05/27/2003 and 05/22/2003 entries). Brajovic is trying to develop image sensors with some of these desirable capabilities.
Werner Gitt provides many more gee-whiz statistics about the eye, and other body senses, in a wonderful book, The Wonder of Man. One square millimeter of retina has 400,000 sensors. The photoreceptors are so sensitive, a single photon can activate them. The rods can react in 0.3 seconds, the cones in 0.075 seconds. Three types of cones, sensitive to different wavelengths, give us complete coverage of the visible light spectrum, with over 300 discernible hues. Unlike film, which is rated for a particular speed or sensitivity, the eyes photoreceptors are sensitive over 5 powers of 10, or 100,000 to one. The signals are transmitted on two separate channels then recombined, to avoid the problem of thermal noise. The optic nerve also filters out noise by sensing the response from multiple rods within a time limit of 0.02 second, and sending the signal along only if there is nearly simultaneous response from four or five rods scattered across the field.This Badger Ate Dinosaurs for Breakfast 01/12/2005
BBC News claims a new fossil discovery published in Nature,1 a large badger-like carnivorous mammal, ate dinosaurs for lunch. But then again, who knows what time of day the Cretaceous restaurants were open?
The fossil, another in a series of spectacular finds from the Liaoning Province in China, is creating a sensation, because it overturns an assumption that Mesozoic mammals were ecological underdogs just small, rat-sized vermin, of no account in the arena of the thunder lizards. Now, it appears some mammals were carnivores, big enough to compete with dinosaurs for food and territory. Juvenile psittocosaur bones were found in the stomach contents of the smaller of two specimens of the short-legged mammals. The bigger one was over a meter long, over twice the previous record. Paleontologists speculate they may have resembled badgers or Tasmanian devils, but their lineage does not appear to have any living descendants.
Analyzing the meaning of the find in the same issue of Nature,2 Anne Weil writes, Discoveries of large, carnivorous mammals from the Cretaceous challenge the long-held view that primitive mammals were small and uninteresting (emphasis added in all quotes.) One wonders if she has been reading Phillip Johnson lately. She continues, Have palaeontologists been asking the wrong questions?
Science Now has a picture of one of the fossils. The BBC News has an artist reconstruction of what the creature might have looked like.
1Hu, Meng, Wang and Li, Large Mesozoic mammals fed on young dinosaurs, Nature 433, 149 - 152 (13 January 2005); doi:10.1038/nature03102.
2Anne Weil, Mammalian palaeobiology: Living large in the Cretaceous, Nature 433, 116 - 117 (13 January 2005); doi:10.1038/433116b.
Some of the new questions Anne Weil is asking turn the evolutionary story of the Cretaceous upside down:DNA Translators Cannot Tolerate Editor Layoffs 01/12/2005Hypotheses developed to explain the evolution of mammalian size often focus on dinosaurs. The most frequently repeated speculation is that Mesozoic mammals were forced to remain small by a combination of heavy predation pressure from dinosaurs and the saturation of ecological niches by large reptiles. Are the mammals from the Lujiatun beds large because the dinosaurs are small? This question may be premature, as the fossil deposits are under active excavation and description of the fauna is not complete. Yet the two new specimens of Repenomamus prompt a reversal of the question, if only in speculation: how might mammals have influenced dinosaur evolution? It seems likely that small dinosaurs experienced predation pressure from mammals. Indeed, in describing the diminutive S. changii, which lies evolutionarily at the base of a lineage closely related to that of birds, Xu et al. express surprise that, although the avian lineage continued an evolutionary trend towards small size, closely related dinosaurian lineages became larger again. Maybe these small dinosaurs got larger or got off the ground to avoid the rapacious mammals.So evolutionary theory can explain anything, no matter what the bones. But if early mammals were already large and carnivorous, where is the evolution? No problem; just throw in a few new subplots to the never-ending story. Animals just got larger and smaller according to who was eating whom. The old speculation game is alive and well (read about Doug in the 09/18/2003 commentary).
Weve explained elsewhere about the family of molecular machines called aminoacyl-tRNA synthetases (see 05/26/2004 entry and its embedded links). Their job is to associate each word of DNA code (codon) with its corresponding piece of a protein (amino acid). In a very real sense, they translate the DNA code into the protein code. One amazing capability of these machines is that they proofread their work. They can differentiate between similar molecules, and edit out incorrect pieces inserted by mistake. Scientists from Scripps Institute writing in PNAS1 thought they would watch what happened when they gave one of these translators a mutation that diminished this editing ability. It wasnt pretty:
The genetic code is established in aminoacylation reactions catalyzed by aminoacyl-tRNA synthetases. Many aminoacyl-tRNA synthetases require an additional domain for editing, to correct errors made by the catalytic domain. A nonfunctional editing domain results in an ambiguous genetic code, where a single codon is not translated as a specific amino acid but rather as a statistical distribution of amino acids. Here, wide-ranging consequences of genetic code ambiguity in Escherichia coli were investigated with an editing-defective isoleucyl-tRNA synthetase. Ambiguity retarded cell growth at most temperatures in rich and minimal media. These growth rate differences were seen regardless of the carbon source. Inclusion of an amino acid analogue that is misactivated (and not cleared) diminished growth rate by up to 100-fold relative to an isogenic strain with normal editing function. Experiments with target-specific antibiotics for ribosomes, DNA replication, and cell wall biosynthesis, in conjunction with measurements of mutation frequencies, were consistent with global changes in protein function caused by errors of translation and not editing-induced mutational errors. Thus, a single defective editing domain caused translationally generated global effects on protein functions that, in turn, provide powerful selective pressures for maintenance of editing by aminoacyl-tRNA synthetases. (Emphasis added.)In short, removing the editing created big problems. The poor bacteria were stunted and vulnerable to malfunctions. When the translator could not maintain high fidelity by editing out mistakes, crippled proteins were produced, and the organism became a sitting duck for the harsh realities of survival.
Update 01/26/2005: This paper generated a commentary in PNAS by Randall Hughes and Andrew Ellington of the University of Texas.2 They agreed that over the long run, there has been and will continue to be tremendous selective pressure to maintain the current genetic code. But they surmise that, since not all the substituted amino acids produced fatalities, evolution might take advantage of them. Taking advantage of protein misfolding might at first seem to be an improbable event, they admit, but this phenomenon is conceptually similar to other ways in which organisms take evolutionary advantage of even inclement environments. Like citizens under siege scrounging for food, they envision a cell under stress with a general need to explore a larger genetic space or a larger protein folding space or both. Maybe the cell has already planned for such things through experience. To the extent that organisms have encountered environmental stress intermittently over evolutionary time, they write, it may even be advantageous to establish some sort of regulatory feedback between stress and phenotypic exploration. In the end, though, they agree that the cell works hard to prevent such errors and possesses exquisite means to eliminate typos. That means it will be difficult to find ways to change the genetic code in lab organisms: simple substitutions will be an uphill battle.
1Bacher, Crécy-Lagard and Schimmel, Inhibited cell growth and protein functional changes from an editing-defective tRNA synthetase, Proceedings of the National Academy of Sciences USA, 10.1073/pnas.0409064102, published online before print January 12, 2005.
2Randall A. Hughes and Andrew D. Ellington, Mistakes in translation dont translate into termination, Proceedings of the National Academy of Sciences USA, February 1, 2005, vol. 102, no. 5, pp. 1273-1274.
Notice that they implied that natural selection had strong motivation to preserve the editing function of these machines. They did not say natural selection had the ability to originate these machines. That supports creation, not evolution. Hughes and Ellington added nothing but speculation: namely, the Darwinian plot line that stress is good, because it forces organisms to evolve or perish. But they only gave examples of mechanisms that are already in place to respond to stress. They did not show how a mindless cell would think to itself, Y'know, I really ought to come up with a disaster plan.We Were Wrong About Isochrons, Geologists Say 01/12/2005
An isochron (a word meaning "equal time") is supposed to be a line connecting points on a graph that represent the same age, or the same age difference. If your rain gutter barrel fills fast and the bucket in your garage fills slowly, for instance, you can figure the time the rain started if you know their individual fill rates; the line connecting those two points on a graph would be an isochron. If you found another bucket and its fill rate also fell on the line, it would imply it started filling at the same time. As straightforward as this method is at home or in the lab, can it be misleading when extrapolated millions of years into the past, when the initial and intervening conditions were not subject to observation?
When geologists date rocks, they seek to identify minerals that are isochronous, though they may decay at different rates. A hidden assumption was that the initial isotope ratios were fixed at the time the rock formed. Not so fast, say four geologists from the UK, Wisconsin and California, writing in Geology:1
The determination of accurate and precise isochron ages for igneous rocks requires that the initial isotope ratios of the analyzed minerals are identical at the time of eruption or emplacement. Studies of young volcanic rocks at the mineral scale have shown this assumption to be invalid in many instances. Variations in initial isotope ratios can result in erroneous or imprecise ages. (Emphasis added in all quotes.)This realization questions a fundamental tenet in isochron geochronologythat the initial isotope composition of the analyzed phases is identical. Since variations in these ratios are now known, it creates the possibility that it may compromise geochronological interpretations.
Sources of variation in initial ratios include: (1) rocks forming over multiple stages instead of one, (2) crustal contamination, (3) partial assimilation of parent isotopes, and (4) magma recharge. These sources of error can, in principle, be identified, they claim, by examining cross-sections of the rock from core to rim, provided that the components involved are isotopically distinct. But unless identified via independent checks, isochron ages can be fictitious, they warn. They give an example of how rubidium-strontium data points may result in a good isochron fit, even though the age obtained is meaningless. One case produced an order-of-magnitude difference between the argon age and the rubidium-strontium age, even with a valid isochron.
To date a rock via isochrons, the geologist has to know that the rock had (1) slow diffusion and (2) rapid cooling. But then, The cooling history will depend on the volume of magma involved and its starting temperature, which in turn is a function of its composition. They give examples where it is evident that open-system processes during crystallization must be invoked to impart isotopic heterogeneity to the mineral population; i.e., to explain away differences in age between two methods by claiming the rock was open to the environment during its lifetime. They admit, though, that if the initial variation is systematic (e.g., due to open-system mixing or contamination), then isochrons are generated that can be very good based on their fit to the graph, but the ages are geologically meaningless.
The authors assert that these sources of error might still be useful. They describe ways how fictitious isochrons might, if true ages are known from other methods, lead to interpretations of how the rocks were formed. They claim that it is highly unlikely that open-system processes that affect the isochrons of one method would affect another method the same way. Their summary, however, consists primarily of cautions:
1Davidson, Charlier, Hora, and Perlroth, Mineral isochrons and isotopic fingerprinting: Pitfalls and promises, Geology, Vol. 33, No. 1, pp. 29–32, doi: 10.1130/G21063.1.
Now, wait just a rockhounding minute. Isochrons have been touted by the uniformitarians as a fail-safe method for dating rocks, because the data points are supposed to be self-checking (Darwin-lover Ken Miller used this argument in a debate against Henry Morris years ago.) Now, these geologists, publishing in the premiere geological journal in the world, are telling us that isochrons can look perfect on paper yet give meaningless ages, by orders of magnitude, if the initial conditions are not known, or if the rocks were open systems at some time in the past. That sounds like what young earth creationists have been complaining about all along. But then, these geologists put a happy face on the situation. Its not all bad news, they say, because if the geologist can know the true age by another method, he can glean some useful information out of the errors. But if they were wrong about the isochron method, what faulty assumptions are going to turn up some day about other methods, in a future issue of Geology? Their confidence that they can know anything about what happened 200 million years ago is about as reassuring as the surgeon who told his patient, I have good news and bad news. The bad news is that we removed the wrong kidney. The good news is that your other kidney is doing just fine.Dover, PA Administrators Will Read ID Statement 01/11/2005
In a compromise aimed at relieving recalcitrant teachers, the Dover, Pennsylvania school board decided that administrators will read a four-paragraph statement about evolution and intelligent design (ID) to high school students for any teachers that want to opt out of the new policy (see 11/04/2004 headline). The decision, according to the York Daily Record, was made partly because of a lawsuit entered by 11 teachers that claim that intelligent design is not science. Supporters of the ID policy claim they only want students to hear that there are alternatives to Darwinism. The one-minute statement will say,
The Pennsylvania Academic Standards require students to learn about Darwins Theory of Evolution and eventually to take a standardized test of which evolution is a part.The newspaper report ends by quoting an open letter from a biologist and a philosopher about why ID is not science but rather a form of creationism propped up by a biased and selective view of the evidence. Evolution, by contrast, they claim is based on and supported by an immense and diverse array of evidence and is continually being tested and reaffirmed by new discoveries from many scientific fields. They compare the theory of evolution to theories of relativity and continental drift, which no one questions. They say that evolution promises great medical discoveries (see 01/13/2003 entry), and that students need dependable scientific knowledge to gain admission to colleges and universities and compete for good jobs.
Dr. Sniegowski and Dr. Weisberg (authors of this open letter), your assignment is to write on the blackboard, 500 times, I will not tell a lie (see 11/30/2004 entry). Then you must read all four years of back issues of Creation-Evolution Headlines. Anyone who cannot find anything wrong with this letter must also read the back issues before continuing. Selective evidence? Bias? Religious motivation? Such hypocrisy is laughable. How many times do we need to go over this? Go back and read 11/30/2004, 09/29/2004, 08/18/2004, 05/07/2004, 02/27/2004 and the rest of the chain links on Darwinism or Intelligent Design.Iapetus Cracked Like a Nut 01/07/2005
Saturn has a moon named for the two-faced Roman god Janus, but the real two-faced moon is the larger Iapetus. Since Jean Dominique Cassini discovered the moon in 1671 and noticed its varying brightness, scientists have been mystified by its two hemispheres, one as black as coal, the other white as snow. Investigators were sure they would figure it out when Voyager 2 flew by in 1981. They didnt. Investigators were hopeful they would figure it out when Cassini flew by less than two weeks ago on December 31, 2004. They didnt. In fact, they were thrown another curve: a ridge that wraps around the equator that gives the moon the appearance of a cracked walnut (see imaging team picture and caption). This is no ordinary crack; the ridgeline forms a mountain range 800 miles long and 13 miles high in places three times the height of Mt. Everest. For a global perspective, see this 3D image and this composite of the dark hemisphere. The landslide at the right of the previous image slumped from a 9-mile scarp of an impact basin, and flowed tens of miles across a crater floor.
For decades, scientists have tried to prove one of two models for Iapetus black-and-white contrast: either the dark material erupted from the inside (endogenic) and spread over the surface, or was splattered onto the moon from the outside (exogenic). Since the dark material covers the leading hemisphere (the side facing the orbital motion, like a windshield), the exogenic model has been slightly favored, but planetary scientists could not understand a source for the material that would not have also plastered the inner moons, unless it was dust blown off from an impact on Phoebe (see 06/14/2004 headline) but the spectra didnt match. The new hi-resolution images from Cassini, taken seven times closer than Voyager, still favor the exogenic model, because the dark regions have feathery edges and are distributed around the equator, not the poles. The pictures seem to rule out a liquidy or mushy ooze spreading out from the interior, but scientists cannot eliminate the possibility that dusty debris erupted from cracks or geysers. Could geological processes related to the equatorial ridge be related to the dark material? If so, what drove those processes on a frozen moon?
The ridge is a geological feature unique in the solar system. It seems to cut right through more ancient craters. The albedo difference divides the leading and trailing hemispheres, but this ridge divides the northern and southern hemispheres. Are they related? Since Iapetus is far out (literally and figuratively), Cassini wont get another chance to observe it at close range till 2007. That encounter, in September of that year, will be much closer and provide 100 times better resolution. The JPL press release says scientists are hoping to determine whether Iapetus was volcanically active in the past odd for an icy-cold moon far from any tidal influences. Two weeks ago, scientists had a major mystery to solve at Iapetus; now they have two.
Planetary science is the art of building skeet for observations to shoot down. Next episode in this exciting sport comes this Friday, when the Huygens Probe parachutes to the surface of Titan.Astrobiology: Follow the Money 01/07/2005
To date, astrobiology remains, as George Gaylord Simpson once quipped, an area of study without a known subject. Yet it is one of the hottest research areas within NASA. A renowned origin-of-life researcher from Scripps Institution of Oceanography, Dr. Jeffrey Bada, found out why when he read the new book The Living Universe: NASA and the Development of Astrobiology by Steven J. Dick and James E. Strick (Rutgers, 2004). His book review appears in Science:1
Today, it seems nearly everyone is an astrobiologist. A decade ago, I knew essentially none. Why this sudden obsession with a field that encompasses so many diverse areas in both the physical and life sciences? So far, life has not been found to exist away from Earth, although the surge in interest in astrobiology suggests there is intense optimism within at least parts of the science community that this singularity will change in the future. But scientific curiosity alone likely cannot explain the explosive growth of astrobiology. After reading The Living Universe: NASA and the Development of Astrobiology, I came to the conclusion that one of the fields attractions was moneyand lots of it. (Emphasis added in all quotes.)Following the money trail, Bada found that exobiology (astrobiologys older relative) got over $5 million in funding from NASA, leading up to the 1976 Viking missions. After they failed to detect life on Mars, exobiology funding dwindled, but in the mid-1990s, NASA administrators Wesley Huntress and Daniel Goldin envisioned astrobiology as a means of integrating biological sciences into the space exploration program while also revitalizing places such as ARC [Ames Research Center] and providing a solid funding base for academic research. In 1995, the NASA Astrobiology Institute was inaugurated. Fortuitously, the next year, the Martian Meteorite ALH84001 hit the newspapers with supposed evidence for life. Bada says, Among scientists and the general public alike, this claim generated intense interest inas well as controversy aboutthe possibilities of life beyond Earth. All of a sudden, astrobiology was the hottest topic around.
And where there is interest, there is money. The scientific community raced to get a piece of the action, and today the Institute comprises 16 funded nodes with five-year budgets of between about $5 million and $12 million. Today, there are astrobiology journals, astrobiology conferences, and astrobiology international meetings. They may not have found evidence for life out there, but astrobiology has become a field with a life of its own, he quips. The field has indeed exploded. It is a huge public-relations boon not only for NASA, but for the European Space Agency (ESA). To be sure, NASA did not invent exobiology or astrobiology speculations about life in outer space go back eons but the terms became NASA funding buzzwords and mission drivers. The assumption is that the public will be more jazzed over finding something that crawls instead of hearing about more craters, rock, ice, and dust.
The Huygens Probe is now a week away from landing on Titan. No scientist expects to find life at nearly 300° below zero, but astrobiologists have capitalized on their fad by portraying Titan as the early Earth in a deep freeze. They tantalize school children with hopes that complex prebiotic carbon compounds might be found on the surface, that could be the building blocks of life. When the Mars rovers found hints of past liquid water (see 01/05/2005 headline), it buoyed astrobiologists hopes that evidence for past life might be found in a future mission, such as the Mars Science Laboratory or Mars Sample Return. If Mars proves lifeless, the last hope in our solar system will be Europa, where an ocean of liquid water may persist under the miles-deep ice crust. Astrobiology has a big stake in these efforts, Bada warns. Finding evidence for life on another body in our solar system would give the field the justification it requires in order to remain an active, well-funded area of research.
1Jeffrey L. Bada, A Field with a Life of Its Own, Science, Science, Vol 307, Issue 5706, 46, 7 January 2005, [DOI: 10.1126/science.1106678].
For astrobiology not to be viewed by historians as a giant boondoggle, its adherents had better find something soon. But even if they dont find it on Mars or Europa, their search extends to the stars, where they can speculate endlessly. Missions like Kepler, the Space Interferometry Mission and Terrestrial Planet Finder are motivated largely by the search for lifes origins (which being interpreted, always means a naturalistic origin by chemical evolution; see 06/23/2003 headline). Similarly, SETI, the search for extra-terrestrial intelligence, thrives on the premise that life evolves wherever the conditions are favorable. It, too, is an area of study without a known subject.Why You Breathe Deep to Sniff a Flower 01/06/2005
It may sound like a 747 when your uncle blows his nose, but scientists at Imperial College found nose airflow to be more complicated than the aerodynamics of a jumbo jets wing, according to a press release by the reporting the Biotechnology and Biological Sciences Research Council . They made a 3D model of the nasal passages and studied colored liquid and beads as they flowed through. The press release comments, The fluid dynamics of the nose is one of the most complex in the body, even more so than the flow of blood through the heart, with anatomical structures that cause eddies, whirls and recirculation.
Dr Denis Doorly, the other principal researcher [with Bob Schroter], said, People are used to the flows around an aeroplane being complicated but that is in some ways simpler than understanding the flows inside the nose. The geometry of the nose is highly complex, with no straight lines or simple curves like an aircraft wing and the regime of airflow is not simply laminar or turbulent. (Emphasis added in all quotes.)This leads to the answer to the question posed by the title of this entry:
The research has mapped the flow of air around anatomical landmarks in the nose, such as the conchae and has discovered why we need to breathe deeply to smell a flower. Our sense of smell relies on a sample of air reaching the olfactory bulb at the top of the nose and that requires a sharp breathe [sic] and a high velocity shot of air to reach it. The Imperial scientists have found that the geometry of the nose causes the air to eddy around in the vicinity of the bulb so you can smell the flower.One of the results of the study may be to design better ways to unblock a stuffy nose. Come to think of it, the sneeze response is usually pretty effective, and pretty amazing, too. It involves coordination between the lungs, the eyes, the brain, the nose and the diaphragm.
Sniffing must be true for all mammals. Watch your dog sniff in puffs of air when trying to smell an object. If the olfactory bulb were always exposed to every breath, it might overwhelm the brain with TMI (too much information). This way, it allows the user to focus on a smell when it wants to. So not only is the olfactory bulb offset from the breathing passage, it sits where the air forms an eddy, allowing it to get multiple readings for higher resolution. Remember the 11/07/2001 headline, also, that reported you have a code in your nose. Who designed the fluid dynamics of this system? Charlie? Eheu! (see 10/10/2002 headline).ID Blog Opens 01/05/2005
The Discovery Institute, an Intelligent Design think-tank in Seattle, has initiated a new blog, Evolution News & Views, that analyzes how evolution is presented in the media (see mission statement). One of the first entries concerns how a PBS station in New Mexico censored the showing of the film Unlocking the Mystery of Life after it had been approved (see Discovery Institute response and article on World Net Daily).
Next headline on: Intelligent Design
Bird Studies Overthrow Evolutionary Assumptions About Population Genetics
Its the Type III civilizations that are the interesting ones (see II Corinthians 12).Gecko Has Self-Cleaning Feet 01/04/2005
Imagine self-cleaning, reusable tape. No matter where you stick it, you can remove it and stick it on another surface, no matter how dirty, and it always acts like new. The tokay gecko has achieved such a feat on its feet, according to a physicist and a biologist from Lewis and Clark College, Oregon, publishing in PNAS.1 The abstract sets up the problem:
A tokay gecko can cling to virtually any surface and support its body mass with a single toe by using the millions of keratinous setae on its toe pads. Each seta branches into hundreds of 200-nm spatulae that make intimate contact with a variety of surface profiles. We showed previously that the combined surface area of billions of spatulae maximizes van der Waals interactions to generate large adhesive and shear forces. [see 09/05/2003 headline]. Geckos are not known to groom their feet yet retain their stickiness for months between molts. How geckos manage to keep their feet clean while walking about with sticky toes has remained a puzzle until now. Although self-cleaning by water droplets occurs in plant and animal surfaces, no adhesive has been shown to self-clean. In the present study, we demonstrate that gecko setae are a self-cleaning adhesive. (Emphasis added in all quotes.)How do they do it? The authors did a force analysis on the gecko spatulae, the surface, and contaminant particles. They found that with the small size of the spatulae, contaminants are more likely to stick to the surface than to the spatulae. (The spatulae look like split ends on a broom straw, with the setae represented by the straws). As a result, the gecko feet possess a passive self-cleaning mechanism that is intrinsic to the structure of the setae and spatulae. Furthermore, the spatulae have an anti-self property that keeps them from sticking to each other.
The fact that this operates by a mechanical, passive property rather than an active cleaning process gave the authors hope that man can invent a similar self-cleaning adhesive. Thus, the self-cleaning and anti-self conditions may represent a sweet spot in the evolutionary and engineering design spaces for adhesive nanostructures.
1W. R. Hansen and K. Autumn, Evidence for self-cleaning in gecko setae, Proceedings of the National Academy of Sciences USA, 10.1073/pnas.0408304102, published online before print January 3, 2005.
Question: why is this paper classified under Evolution? Anyone see any evolution here? Evolution is not an engineer. Without all the structural properties present simultaneously, the gecko would quickly die of clogged feet that could not cling to anything. These guys said nothing about how this intricate and effective structure could have evolved by a chance process. Lets keep Charlie out of it.Theologians Wrestle with Gods Role in Disasters 01/03/2005
As international rescue efforts accelerate in the aftermath of last weeks tsunamis in Asia (see Caltech for the geological story, and Nature News for the earthquakes affect on Earths rotation), commentators and theologians are beginning to ask the why? questions. The liberal Archbishop of Canterbury is doubting the existence of God, according to the UK News Telegraph. From a Jewish perspective, Rabbi Daniel Lapin, writing in World Net Daily, argues that its not Gods fault, but mans, for living in quake-prone areas. On his blog, Biola professor John Mark Reynolds answers the critics who try to use the disaster as an opportunity to attack theism. Creationist writer Carl Wieland writes for Answers in Genesis about how this incident raises the age-old questions about death and suffering, as does Dr. David Miller on Apologetics Press. Dr. Kelly Hollowell, also on World Net Daily, compares this disaster with Noahs flood. To be fair, the fearfulness of any disaster needs to be balanced against the sum total of factors that make Earth a privileged planet as an abode for life. Perhaps the best philosophers are the relief agencies like World Vision, who are focusing their energy not on talking, but on helping the victims.
Sooner or later, everyone needs to come to grips with the big questions about suffering. Actually, this disaster, which will undoubtedly go on record as one of the biggest in modern history, is a trifle compared to the global flood in the days of Noah described in the Bible (Genesis 6-9). From orbit, these tsunamis would not even register as bathtub ripples. The Flood killed all but Noah and his family, and reshaped the whole planet (see Dr. Walt Browns geological treatment of the Biblical Flood).Anthropologist Claims Humans, Neanderthals, Australopithecines All Variations on One Species 01/01/2005
According to a news story in the UK News Telegraph, all fossil hominids, including modern humans, Australopithecines, Neanderthals and the recent Indonesian hobbit man, belong to the same species: Homo sapiens. Reporter Robert Matthews wrote about Maciej Henneberg (U of Adelaide) and his argument, based on skull sizes and body weights for 200 fossil specimens, that all known hominid bones fit within the range of variation expected for a single species. Henneberg made the startling claim in the Journal of Comparative Human Biology, where he said, All hominims [sic] appear to be a single gradually evolving lineage containing only one species at each point in time.
Henneberg still believes humans were evolving, but his analysis points out several important shortcomings in the science of paleoanthropology that should make the thoughtful reader wary of its practitioners. (1) There is a huge range of variation possible within a single species. (2) It is difficult to assign any human bone to one or another species. Notice what this led Henneberg to state: There is no precise way in which we can test whether Julius Caesar and Princess Diana were members of the same species of Homo sapiens (emphasis added in all quotes). Consider what that means when judging bones of alleged human ancestors. You could tell any story you want. (We like the one that Caesar and Diana were different species.) (3) The article reminds everyone that paleoanthropologists often bicker about the meaning of their discoveries (see 12/21/2004 headline). Geoffrey Harrison (Prof. emeritus, Oxford) said it best: Clearly there is a need to be more aware of the possibility of variation but that is not the inclination today. It has been a problem because the discoverers have usually put so much effort into finding the evidence, so they want it to be important. (4) There are too few bones to make any conclusions. Henneberg said there are fewer than 30 Neanderthal specimens available for study. (5) Neanderthals could be considered fully human. The article refers to Henneberg stating, in effect, that What evidence there is, however, is consistent with Neanderthals being from the same species as modern humans. Christopher Stringer (Natural History Museum, London) adds that Neanderthals were not significantly different from us in skull or body size. The argument they are a different species is, of course, only a hypothesis... (italics added).Cellular UPS Gets Right Packages to Chloroplasts 01/01/2005
If all your packages were sent correctly over the holidays, consider the job a plant cell has getting 3000 proteins into a chloroplast. Mistakes are not just inconvenient. They can be deadly, or at least bring photosynthesis to a halt. To guarantee proper delivery of components, plant cells have a remarkable shipping system, described in Current Biology by two UK biologists, Paul Javis and Colin Robinson.1 Part of the challenge is getting polypeptides past the double membranes of the chloroplast. A remarkable crew of enzymes and molecular machines puts a shipping label (transit peptide) on each amino acid chain, reads it, routes it to the correct destination, and then removes it:
Over 90% of the ~3000 different proteins present in mature chloroplasts are encoded on nuclear DNA and translated in the cytosol [cell fluid outside the nucleus]. These proteins are synthesized in precursor form each bearing an amino-terminal targeting signal called a transit peptide and are imported into the organelle by an active, post-translational targeting process (Figure 1). This process is mediated by molecular machines in the outer and inner envelope membranes, referred to as translocon at the outer envelope membrane of chloroplasts (Toc) and translocon at the inner envelope membrane of chloroplasts (Tic), respectively. Upon arrival in the stroma [chloroplast interior], the transit peptide is removed and the protein either takes on its final conformation or is sorted to one of several internal compartments in a separate targeting process. (Emphasis added in all quotes.)The authors believe, like most evolutionists, that plastids (including chloroplasts) arose when a primordial cell engulfed another and took over its light-harvesting machinery, a process called endosymbiosis (see 10/01/2004, 09/09/2004, 08/06/2004 and 10/07/2003 headlines, and refutation by Don Batten). They believe the former cell that became the chloroplast retained only a stripped down version of its genetic code, and most of the DNA instructions for building these 3000 chloroplast proteins got transferred to the nucleus. Yet this means that a tremendous amount of machinery had to be developed to get the proteins to their destinations:
Chloroplasts are complex organelles comprising six distinct suborganellar compartments: they have three different membranes (the two envelope membranes and the internal thylakoid membrane), and three discrete aqueous compartments (the intermembrane space of the envelope, the stroma and the thylakoid lumen). One of the consequences of this structural intricacy is that the internal routing of chloroplast proteins is a surprisingly complex process. While envelope proteins may employ variations of the Toc/Tic import pathway to arrive at their final destination, proteins destined for the thylakoid membrane or lumen employ one of four distinct targeting pathways (Figure 1). Thylakoid membrane proteins are targeted by the signal recognition particle (SRP)-dependent and spontaneous insertion pathways, whereas lumenal proteins are targeted by the Sec and Tat pathways....Each of these pathways is an assembly-line process involving multiple proteins dedicated to these tasks. Several points brought out in the article make it challenging to perceive of a smooth transition from endosymbiosis to todays complex shipping and handling pathways (numbering ours):
The Tat pathway manages the remarkable feat of transporting large, folded proteins without collapsing the delta-pH, and we currently know very little about this mechanism. Most membrane proteins use a possibly spontaneous insertion mechanism that just does not make sense at the moment why do these proteins need so little assistance from translocation apparatus, when membrane proteins in other organelles and organisms need so much? And how do these thylakoid proteins avoid inserting into the wrong membrane? We have gone some way toward understanding the rationale for the existence of all these pathways, but the thylakoid may still have surprises in store.By contrast, another paper in the same issue of Current Biology2 makes confident claims that the endosymbiosis theory has been demonstrated with diatoms (see 10/01/2004 and 07/21/2004 headlines about diatoms). They suggest that it was dangerous for genes to remain in the plastids, because of free radicals generated by the photosynthesis machinery, and because of higher mutation rates, and thats why most of them wandered to the nucleus.
1Paul Jarvis and Colin Robinson, Mechanisms of Protein Import and Routing in Chloroplasts, Current Biology, Volume 14, Issue 24, 29 December 2004, Pages R1064-R1077, doi:10.1016/j.cub.2004.11.049.
2Nisbet, Killian and McFadden, Diatom Genomics: Genetic Acquisitions and Mergers, Current Biology Volume 14, Issue 24, 29 December 2004, Pages R1048-R1050, doi:10.1016/j.cub.2004.11.043.
If you survived this mind-numbing description of chloroplast protein transport, you probably gasped at the complexity of it all. On a general level, getting a protein from one place to another sounds simple (thats the way the authors of the second paper made it sound). But look how many players are involved, how many checks and balances, how many protection mechanisms and signals are required to get the packages delivered accurately. And this is all just to get the chloroplast to start to get ready to begin to commence doing its job: harvesting light for photosynthesis (and thats another story: if this one was over your head, run for cover).Stupid Evolution Quote of the Week 01/01/2005
The authors of the second paper in the previous story compared endosymbiosis to mergers of companies, apparently unaware they were comparing undirected natural processes with intelligently planned decisions by human minds:
Imagine you are running a successful small business converting carbon dioxide into sugar. Suddenly, you are taken over by a bigger company. They commandeer your intellectual property, relocate it to head office, and to add insult to injury they ship your own tools back to you and expect you to keep making sugar. Such a business takeover is the perfect analogy for the endosymbiotic origin of plastids. The small business is a photosynthetic cyanobacterium, the aggressive takeover merchant is the eukaryotic host, and the intellectual property is the cohort of genes encoding the machinery for photosynthesis, most of which have now been relocated from the endosymbionts genome to the host nucleus. (Emphasis added.)
1Nisbet, Killian and McFadden, Diatom Genomics: Genetic Acquisitions and Mergers, Current Biology Volume 14, Issue 24, 29 December 2004, Pages R1048-R1050, doi:10.1016/j.cub.2004.11.043.
At least they admitted genes are intellectual property. Adding insult to injury is also intelligent design, of the mischievous kind. Encoding, machinery, synthesis; these words do not belong in the Darwin Dictionary. They were plagiarized from the creationist world view encyclopedia. Plagiarism is also intelligent design of the mischievous kind.