Hence it appears that whoever maintains that there is no force in the argument from final causes [design] denies the existence of any intelligent being than himself. He has the same evidence for wisdom and intelligence in God as in a father or brother or a friend. He infers it in both from its effects and these effects he discovers in the one as well as the other.
If you thought the story of horse evolution was well understood as a poster child of Darwinism at work, consider what Weinstock et al. say in a preprint in PLoS Biology:1
The rich fossil record of horses has made them a classic example of evolutionary processes. However, while the overall picture of equid evolution is well known [see 03/18/2003 entry], the details are surprisingly poorly understood, especially for the later Pliocene and Pleistocene, c. 3 million to 0.01 million years (Ma) ago, and nowhere more so than in the Americas. There is no consensus on the number of equid species or even the number of lineages that existed in these continents. (Emphasis added in all quotes.)Tackling that challenge, the team rewrote the evolutionary history books. Now, they put all North American horses into two species, claim they are distinct from their European look-alikes, and came earlier than the South American Hippiodon genus, which was supposed to be ancient. This is all summarized on EurekAlert, which claims the conclusions made by comparing mitochondrial DNA helps clarify the origins of two extinct New World horse species.
1Weinstock et al., Evolution, Systematics, and Phylogeography of Pleistocene Horses in the New World: A Molecular Perspective, Public Library of Science: Biology, Volume 3 | Issue 8 | AUGUST 2005.
Are you tired of the hype? Every new Darwinian study overthrows the propaganda that was taught to the world for 100 years or more, but then they spin the bad news with the line, this helps clarify the picture of evolution. Its no picture; its a kaleidoscope of constantly shifting random bits of broken colored glass.Did Old Metamorphic Rocks Form in Just 10 Years? 06/30/2005
A discovery in Norway may collapse a geological process by five or six orders of magnitude. A paper by Camacho et al. announced in Nature,1 yielded this comment by Simon Kelley (Open University, UK) in the same issue,2 Conventional wisdom says that changes to crustal rocks pushed down deep when continents collide develop over millions of years. But it seems that some metamorphism may be caused by tectonic events lasting only a decade (emphasis added in all quotes).
The gist of the story is that certain rocks called eclogites, long thought to have formed slowly over millions of years, might have formed rapidly instead, maybe in only ten. The authors of the paper deduced that they could not have remained at the temperatures assumed for very long without losing all their argon. Kelley explains why the mixtures in the rock suggest conflicting requirements for their formation:
The authors go on to estimate the temperature in the granulite lens during eclogite formation. Their conclusion less than 400 °C is a problem for the conventional interpretation of these rocks, given that a temperature of around 700 °C is required for the formation of the adjacent eclogites. Camacho et al. calculate that the total heating durations must have been around 18,000 years to explain the 40Ar-39Ar age profiles, but that individual fluid-flow events must have lasted just ten years to avoid significant heating of the granulite regions between the shear zones. This model evokes a radically different picture of the conditions during eclogite formation; but any alternative explanation would have to invoke a mechanism that explains why these phlogopites retained argon despite exceeding temperatures at which the gas would normally escape.Kelley explains why the overturning of this classic case of a slow process points out an assumption that may need just as radical an overturn: However, the very short timescales involved will make this idea controversial, as existing work on garnet seems to indicate processes operating on a million-year timescale; but also, perhaps, simply because we geologists are attuned to thinking in millions of years, whereas the features we observe may be just the aggregations of many shorter events.
1Camacho et al., Short-lived orogenic cycles and the eclogitization of cold crust by spasmodic hot fluids, Nature 35, 1191-1196 (30 June 2005) | doi: 10.1038/nature03643.
2Simon Kelley, Geophysics: Hot fluids and cold crusts, Nature 435, 1171 (30 June 2005) | doi: 10.1038/4351171a.
Now there was a daring and honest admission: perhaps geologists are just in the habit of throwing around millions of years, when the features they observe could just as well be aggregations of many shorter events. Wow. Think about that. Here was a classic case of long ages from the Bergen Arcs in Norway that now must be reinterpreted. Neither Kelley or Camacho are claiming that this formation came into being recently, but it represents, nevertheless, a monumental shift in thinking about geological processes in general.Is Evo-Devo the Source of Endless Forms Most Beautiful? 06/29/2005
Even staunch Darwinist Jerry A. Coyne (U of Chicago) thought this evolutionary book went overboard: Endless Forms Most Beautiful: The New Science of Evo-Devo by Sean B. Carroll (Norton, 2005), which he reviewed in Nature last week.1 (The title comes from a phrase at the end of Darwins Origin of Species.) Its a first-rate introduction to evo-devo written by an adept communicator, he feels, but its faintly self-congratulatory message that the most important problems in understanding the evolution of development have been solved left me feeling uncomfortable.
In Coynes opinion, Carroll overplayed the evo-devo card. Evo-devo assumes that gene regulation is the most important agent of evolutionary change; Coyne gives more place to gene duplication, genome duplication and ordinary old adaptive natural selection on genes and proteins. Some of Coynes criticisms point out the problems inherent in all evolutionary theories. Some examples:
1Jerry A. Coyne, Switching on evolution: How does evo-devo explain the huge diversity of life on Earth?, Nature 435, 1029-1030 (23 June 2005) | doi: 10.1038/4351029a.
Is evo-devo the evil-devil among Darwinists? Like Satan, does he twist the word of lord Charlie? Does he distort the evidence for his own nefarious ends? Assuredly not; both Carroll and Coyne are on the same side, trying to oust Gods design from nature and account for everything by chance and biological laws. What anti-creationist Coyne fails to realize is that he has cast both theories, evo-devo vs. standard Darwinism, in a deadly embrace. Carroll wrote his book because of the weaknesses of standard Darwinism, and Coyne provided only bluffing assertions that standard Darwinism is sound, while arguing that evo-devo is just a clever idea that distorts the evidence and cannot really account for the diversity of life. To argue otherwise requires simplification; i.e., the generous use of glittering generalities to create tall tales. Neither evolutionary hypothesis can account for the complex and subtle realities of the living world mentioned in Coynes review worms, lobsters, frogs, humans, chimpanzees, fruitflies, butterflies, mice, the Cambrian explosion, the biology of dinosaurs, the brains of humans, and the striping of zebras and their eyes, limbs, hearts and other complex structures including fly legs, fish fins and the tube feet of sea urchins.Endless forms most beautiful speak of a Designer, not a blind process of evolution. The shortcomings of Coynes view provide an opening for the claims of Carrolls, and vice versa, such that they strangle each other, leaving both gasping for evidence.
Next headline on: Darwinism and Evolutionary Theory Genetics and DNA Small Wonder: Tubulin Visualized Up Close 06/28/2005
Science Daily printed a neat story about microtubules, complete with a 3D visualization of how the protein components are arranged. They are not just ropes or chains, but complex cylinders of precise parts. Scientists are starting to get an idea of why they continually grow and shrink within the cell. The process allows them to explore their cellular environment to find their goals, and is coordinated by numerous genes and protein parts. Microtubules form the cells superhighway (see 04/13/2005 and 12/04/2003 entries), and are also critical in cell division for winching chromosomes into the daughter cells (see 04/30/2005 entry).
We like to keep pointing out research projects with no need for mentioning evolution, that fit within a design approach. The cell provides plenty of examples. Here are two more: waterwheels (12/22/2003), quality control (12/20/2003), and many, many others in the chain links on Cell Biology and Amazing Stories. Every person, from philosopher to man on the street, should ponder such things.Stupid Evolution Quote of the Week 06/28/2005
This entry is from the BBC News, in an article about hummingbirds, the master fliers of the bird kingdom (see 06/24/2005 entry). The article interviews Douglas Warrick (Oregon State), describing how evolution produces exquisite machinery by an unguided process of cobbling parts from existing stuff:
He said the hummingbird could serve as a useful model for engineers seeking to build small, flapping aeroplanes. You can probably learn something about building a machine from the way nature builds a machine, he said.
The cult of Tinker Bell lives on. Evolution is a tinkerer that dabbles with existing material and produces machines that are the envy of intelligent human designers. What is amazing about this belief is not just that scientists keep repeating it, but that all the major news media just parrot it without question. When the Darwinian idol finally collapses, our SEQOTW entries will provide plenty of fodder for cartoonists.Nose Knows More than Math Pros Suppose 06/27/2005
The aroma of coffee, of a steak, of cherries these smells are all composed of dozens if not hundreds of separate molecules, yet our brains immediately recognize them each as a coherent whole. How does the nose and the brain process all this information? This is the subject of an article in the Caltech magazine Engineering and Science1 by Gilles Laurent, Caltech professor and neurologist, who studies olfaction and also how single neurons perform nonlinear operations such as multiplication.
Unlike vision and hearing, our olfactory sense does not allow us to decompose a composite input into its constituents. We perceive odors as single entities. Studies on insects by Laurent and his students show that this is because individual receptors fire in patterns that are mapped like a code to a large number of unique sensors called Kenyon cells. In insects, these cells reside in a part of the olfactory apparatus called the mushroom body (in vertebrates, its the olfactory cortex of the brain). Each Kenyon cell gets a very unique set of inputs from the receptors, and thus a distinct, composite signal from a highly diverse set of inputs. Laurent does the math to show the staggering number of possibilities for odor memory that this system permits:
The locust has 800 projection neurons connecting to 50,000 Kenyon cells. With such a large mismatch in numbers, how are these nerve-cell populations interconnected? When Ron Jortner, a graduate student in my lab, recorded simultaneously from both projection neurons and individual Kenyon cells to assess the probability of connection between them he found, surprisingly, that the probability was about 0.5. In other words, each Kenyon cell seems to connect on average to half of the input population, that is, to 400 projection neurons. The number of ways in which 400 neurons can be selected out of 800the number of possible connection patternsis about 10240. Its an enormous number. To put it in context, there are about 1010 seconds in a century, and there have been about 1019 seconds since the beginning of the universe. With 10240 possible combinations of projection neurons to choose fromassuming random connectivityalmost every Kenyon cell is likely to sample a combination of inputs that is very different from that sampled by the other Kenyon cells. Each cell will therefore gain a picture of the state of the projection neuron population very different from that gathered by any other Kenyon cell. It follows that the responses of individual Kenyon cells will be very specific; a given cell should respond only to particular combinations of activated projection neurons, maximally different on average from those experienced by the other Kenyon cells. (Emphasis added in all quotes.)Laurent noted at the beginning of the article that olfaction is a form of pattern recognition, and that Brains solve pattern-recognition problems much better than any machine built today. His lab tries to figure out how brains solve these problems. Most of the research by Laurent and his students is on insects, whose olfactory receptors are on their antennae. A fruit fly has 1300 receptor neurons, with 60 different receptor types, but some moths might have several hundred thousand receptor neurons. This gives them an amazing sensitivity to low concentrations of odors like pheromones.
A diagram and electron micrograph on p. 44 shows what receptor neurons look like. They have dozens of cilia projecting into the nasal cavity. The reason dogs have superior sensitivity to smells, he explains, is that their nasal cavity contains much more surface area where the receptors project from sponge-like tissue called turbinate bone. Dogs have ten times as much turbinate bone as humans. He provides a fragrant illustration: In a medium-size dog, he says, the turbinates have a total surface area the size of a large pizza. In humans, theyre the size of a large cookie. Each receptor neuron has a single sensitivity dictated by the order of the amino acids in its multi-folded receptor proteins. The amino acid sequences of receptor proteins show areas of both high conservation and high variability between species. They loop seven times through the cell membrane, providing pockets where the odor molecules bind.
Laurent describes something striking about how the receptor neurons map their inputs to ball-shaped structures called glomeruli (singular, glomerulus). In an amazing feat of organization during development, a picture caption states, each type of receptor neuron... sends its axon to the same glomerulus.... He calls it a surprise that all the axons of the same receptor type (colored red in the diagram) converge so neatly to their exact counterparts. By implication, he continues, this means there are about as many glomeruli as there are receptor types. And with the exception of the roundworm, this extraordinary organization is found in almost all the animal species that have so far been looked at.
From the glomeruli, the information is passed on to a smaller group of nerve cells called projection neurons, which have no axons but connect with a dozen or more glomeruli. With 100,000 receptor neurons converging on just 800 projection neurons, what is being computed? he asks. Experiments show that the precise timing of firing creates a kind of code from the multiple inputs, a pulse pattern that can be mapped and analyzed. He likens the result to the unique arrangement that billiard balls take after the player breaks them with the cue ball; two very similar initial setups, but with slightly different angles of attack, can produce initially similar but ultimately divergent patterns of balls on the table. (The billiard game in the nose is super-fast. He notes on p. 48, This happens so quickly that the representations are optimally separated within 100 to 300 milliseconds.) As a result, differences between very similar smells can be amplified by the system. Thats basically what we think is taking place in the olfactory circuit, he says. The remarkable thing is that this near-chaotic process is very sensitive to the input, but very reliable nevertheless.
To recap, the receptor proteins in the cilia of the receptor neurons react to molecules in odors. These neurons fire their axons to the glomeruli. The glomeruli then pass their encoded information patterns to the projection neurons. That noise-reduced information is passed in very unique ways to the tens of thousands of Kenyon cells, which have a near infinite way to respond to the myriad possible combinations of smells. Kenyon cells are so specific that they only recognize one, or at most a few, odors, a caption explains on p. 51. He summed it up earlier (p. 46): In other words, each odor is defined by a certain combination of receptors; the code is combinatorial.... The perception of an odor must therefore result from the brains interpretation of combinatorial activity patterns. Why, though, do a large number of receptors map to few encoders, and then those few to a large number of interpreters? Theres a reason for everything:
It seems wasteful that hundreds of thousands of olfactory receptor neurons converge on their respective glomeruli in an amazingly precise way, but that this precision is then thrown away when seemingly disordered patterns of activation are generated in the projection neurons. But theres a good reason for it. A system that amplifies small differences in signals runs the risk of also amplifying noise, in this case the noise coming from the receptors. Noise fluctuations would make the output of the projection neurons unreliable: the averaging that results from this kind of convergent design is precisely one way to reduce such fluctuations.(p. 49; for more on the problem of noise reduction, see 12/20/2004 entry). The sense of smell, obviously, is quite complex. It involves many more receptor types than other senses, like vision, which uses only four types of photoreceptor. How did the code in the nose, and all the apparatus in the circuitry, come about? Early in the article he speculated briefly about this question, but his answer assumes a remarkable convergence rather than demonstrating the evolutionary steps:
In parts of the looping receptor protein chain, the order in which the amino acids are strung together is so variable that some animals, such as the rat, have over 1,200 different receptor types. On average, mammals have about 1,000 types, fish and birds between 100 and 200, round- worms (Caenorhabditis elegans) 1,000, and fruit flies 60. Humans have only 600 different odorant receptor genes, but almost half of these are pseudogenes that no longer function, leaving us with only 350 receptor types in our nasal mucosa....How that happened is left as an exercise, but for Laurent, his job is in the here and now, studying the sensitive yet reliable olfactory computer: Finding the rules of such nonlinear dynamical problems is one of our goals (p. 49). Concluding, he says, Our research into olfaction is...giving some valuable insights into how such kinds of high-level synthetic representations arise from the organization and dynamics of neural circuits (p. 51). The nose shows that Classifying and recognizing patterns is, after all, what our brains do best.
1Gilles Laurent, Olfaction: A Window into the Brain, Engineering and Science (LXVIII:1/2), [summer] 2005, pp. 43-51 (PDF).
This article is a good companion to the next one (see 06/25/2005 entry). The language is similar: circuitry, computation, communication, codes, signals, and information. The lead-in photo shows a man with a very satisfied look savoring a cup of coffee, probably unaware that he is sensing a cocktail of two to three hundred compounds. Did you have any idea how much computation and circuitry make that pleasant feeling possible? We joke about our noses and dont usually give them the same respect we pay the eye or ear, but each sense is more wonderful than we could possibly realize.Reverse-Engineering Biological Networks Challenges Caltech Scientists 06/25/2005
Evolutionists love to quote Dobzhansky saying, Nothing in biology makes sense apart from evolution. An article in the current issue of Caltechs magazine Engineering and Science,1 however, might change that proverb to, Nothing in biology makes sense apart from information theory and systems engineering. The article makes no mention of evolution, but rather looks at biology as a model of complex information processing, computation, control, logic circuits, optimization and error correction. TMI, meet IST, is the title, meaning too much information meets the office of Information Science and Technology. The IST is an interdisciplinary initiative at the prestigious university that draws together mathematicians, information theorists, physicists, biologists, and social scientists with the goal of understanding how information works in complex systems biological systems providing the guiding example. It is organized into four new centers, the Center for the Mathematics of Information (CMI), the Center for the Physics of Information, the Center for Biological Circuit Design (CBCD), and Social and Information Sciences Laboratory (SISL), and two old ones, the Center for Neuromorphic Systems Engineering (CNSE), and the Lee Center for Advanced Networking. Each new center attacks a basic question, the article explains. Can we find an abstract mathematical description of information that applies across disciplines? What are the fundamental physical limits to information storage and processing? How does nature compute and communicate information? And how does information shape social systems? (emphasis added in all quotes).
Author Douglas L. Smith opens by wowing the reader with the complexity of a worm. A tiny roundworm controls its development and biological systems in a manner that staggers the researchers with its precision and complexity. Smith compares worm information processing to modern intelligently-designed automobiles. A sedan can contain more than 35 million lines of code in its computers, he says; but that creates a problem for human designers the cars are getting so complicated, future development is actually getting stuck because they dont know how to manage the software. Enter C. elegans for a little humility lesson:
But Nature controls far more complex mechanisms with ease: Consider the nematode Caenorhabditis elegans. A lowly roundworm about the size of this comma, it grows from a single-celled egg to an adult containing exactly 959 cells. The little fellas are clear as glass, and entire generations of lab students have spent countless hours hunched over microscopes tracking the career of each cell. The whole process takes 24 rounds of cell division79 of the 959 cells line the guts from mouth to anus, 302 become nerve cells, and 131 die along the way. Everything has been mapped precisely, says [Jehoshua] Bruck [Moore Professor of Computational and Neural Systems and Electrical Engineering, and director of the IST], who has a framed poster of this developmental tree on his wall [the article contains this diagram]. But we, as engineers, dont understand how to handle all the information in that map. We dont understand what the principles are. But, somehow, the cells understand. The egg divides, and one cell has to call heads and the other, tails. The process involves the random diffusion of signaling molecules, but the result is very preciseyou never end up with a two-headed worm. Then the other divisions have to follow in the correct order. And even when every cell has a clock and the timetable, Bruck points out, they still need to coordinate their actions. Its like driving on the freewaysometimes you need to slow down and let another car pass. Organisms are just information made flesh.Sidebars in the article provide the history of information theory, from George Booles binary algebra to Claude Shannons Boolean circuitry. Information storage and processing, guidance and control of circuits dealing with vast amounts of information under constraints of time or bandwidth, are some of the technical challenges discussed in the article. The overlap between biological and engineered systems throughout the article is almost seamless, except for the fact that biological systems are vastly superior to anything man has invented so far. For example,
Says Bruck, In time, I think information will be a first-order concept. So in 20 years, if a high-school student asks her friend, Do you like algebra? the other girl will say, Yes, or No, or Yes, but I hate the teacher. But the other day I asked my daughter, a high-school junior, Do you like information? and she said, What?!!
1Douglas L. Smith, TMI, Meet IST, Engineering and Science (LXVIII:1/2), [summer] 2005, pp. 6-15.
OK, Intelligent Design Movement, charge! Grab this paper and wave it in the faces of the Darwin Party, and say, Look! The future is information, reverse engineering, and treating biological entities as intelligently designed circuitry. That is what ID is all about. This entire article had as much use for Darwinism as an astronaut for a pogo stick. Biological systems could only be understood in terms of their information content, their logic, circuitry and programmingi.e., their design. The design is so extraordinarily complex that Caltechs brightest stars are at square one trying to figure it out. Darwinism is an impediment, an 18th-century, Industrial Revolution paradigm that is not up to the requirements of the Information Age. Step aside! ID is the future.Wind Tunnel Experiments Reveal Dynamics of Hummingbird Flight 06/24/2005
Scientists have found out that hummingbirds and insects dont hover in the same way. Insects support 50% of their weight on both up and down strokes, but hummingbirds support 75% on the downstroke and 25% on the upstroke. This was published in Nature this week,1 and summarized on Science Daily.
The latter article reminds us why hummingbirds attract our interest:
You would be hard-pressed to find someone who isnt amazed by hummingbirds, said H. Ross Hawkins, founder and executive director of The Hummingbird Society. Perhaps its their iridescent coloration and miniature size, or their ability to drop their heart rate from 500 beats per minute during the day to 40 beats per minute at night. (Emphasis added in all quotes.)Another bird story making the rounds this week was published in Science.2,3 Apparently, chickadees have a sophisticated signalling system in their chirps. They can alert the flock to a size and type of predator nearby with a kind of chirping language; the number of dee syllables at the end of the call is code for the kind of threat. See EurekAlert, National Geographic News, Science Now and Peoples Daily Online.
1Warrick, Tobalske and Powers, Aerodynamics of the hovering hummingbird, Nature 435, 1094-1097 (23 June 2005) | doi: 10.1038/nature03647.
2Templeton et al., Allometry of Alarm Calls: Black-Capped Chickadees Encode Information About Predator Size, Science, Vol 308, Issue 5730, 1934-1937, 24 June 2005, [DOI: 10.1126/science.1108841].
3Greg Miller, Bird Alarm Calls Size Up Predators, Science, Vol 308, Issue 5730, 1853-1855, 24 June 2005, [DOI: 10.1126/science.308.5730.1853a].
There are few classes of animals more varied, colorful, intelligent, talented and interesting than birds. Makes you wonder what they think when they take up people-watching. Perhaps its best we dont know what that chickadee is telling its friends when we walk by. When a Darwinist says, like in the Miller article quoting James Hare, The work ... shows us that even very common species that we may take for granted have evolved to have very elaborate and exacting systems of communication, they might be chirping, check a duh, duh, duh.SETI Researchers Affirm Planetary Privilege Criteria 06/24/2005
In the weekly SETI Thursday column on Space.com, Douglas Vakoch corroborated two claims made about the habitability of planets in the film The Privileged Planet (shown at the Smithsonian last night see 06/09/2005 story): namely, (1) smaller stars have smaller habitable zones or Goldilocks zones where life can exist, and (2) planets within the habitable zone of a small star are closer in, tending to tidally lock one face toward the star reducing the chance for habitability. They admitted even more, that such conditions (if an atmosphere existed) would whip up enormous wind velocities. They balanced that bad news with hopes that such worlds might have enough greenhouse effect to moderate the winds. Since the discovery of Gliese 876, the smallest extrasolar planet so far, astrobiologists and SETI researchers are taking a second look at smaller M-class stars as homes for habitable planets. None of the ones surveyed so far has a Jupiter-class planet, so the thinking is that most planets might be small rocky worlds around small, warm stars.
How much hoc can an ad hoc hawk for an ad hoc post hoc post? An M-class star needs a Jupiter for its comet shield, remember? And is intelligent life going to thrive on the dark side of a tidally locked world in time to build a flashlight, let alone a radio telescope? Or is it going to bake in its sun forever on the lit side and never see the stars, dreaming of who else is out there? Maybe there is a thin great circle on its twilight zone suitable for life. Dont count on a booming economy, though.Croc Teeth Bite Fatal Wound into Dino Phylogeny 06/23/2005
This line sounds serious: We have pretty much erased the record of Triassic ornithischian dinosaurs from North America, Europe and worldwide, except for South America. This is what William Parker said about his find of a complete Revueltosaurus fossil in Arizona that upsets the leading story of the rise of the ornithischian dinosaurs (one of two major dinosaur groups). The fossil, earlier known only from teeth, was presumed to be a dinosaur, but now has been found to be mostly crocodilian. What damage this does to assumptions about dinosaur evolution is explained by EurekAlert and LiveScience.com.
It is wondrous how Darwinians get their ability to build epic tales, animated features and all, on such flimsy data as a few teeth. If they cant even get the class of an animal right from the teeth, how can they tell us all about the age, and which ancestor begat which? When the wrong story was assumed, for so long, and passed the peer review of childrens picture books, how much confidence does this give a reasonable observer that other figments of the story have validity?Lions Guard Kidnap Victim in Ethiopia 06/22/2005
Some news stories make you wonder about divine providence. Netscape News reported a story of lions that rescued a kidnapped Ethiopian girl who was being beaten by seven men trying to force her to marry one of them. In Ethiopia, men will often beat and rape a woman who resists a forced marriage; up to 70% of marriages involve such abductions, often with severe beatings. The lions guarded and protected this woman for about half a day till she was found, then left her like a gift and went back into the forest.
No unwarranted claims here; just an interesting item. The flip side is that this story should make us all angry about the lowest of beasts, sinful men, who would do such a thing. The article says this kind of atrocity is the norm. In this depraved culture, kidnapping and rape, with beatings, is the mens customary way to force women into marriage when they resist. For more ugliness, see what a photographer found going on in neighboring Darfur, Sudan, as reported in National Geographic News. Lets hear it for the lions. If you find a Darwinist trying to excuse this customary behavior as an evolutionary adaptation from our ape-like past (see 07/18/2003 entry), let out a loud roar.*Battlefront Dispatches 06/22/2005
Activities in the Darwin-vs-Design controversy continue generating national news:
Yahoos piece was not a volcano, but a mud pot; better, a fumarole. Darwinists are the ones erupting when people object to having philosophical naturalism in the form of chemical-evolution mythology crammed down their throats. So what are the Darwin Party imagineers going to do in a free market economy? Force the customers to watch their cartoons? Many IMAX films are wonderful explorations into the natural world when they stick to observable facts. Adding Tinker Bell is only distracting.Macroevolution Claims Investigated 06/21/2005
Two scientific papers recently used the word macroevolution in their titles. Did they actually point to cases of natural increase in information or function?
1Finkel et al., Climatically driven macroevolutionary patterns in the size of marine diatoms over the Cenozoic, Proceedings of the National Academy of Sciences USA, published online before print June 14, 2005, 10.1073/pnas.0409907102.
2Douglas H. Erwin, Macroevolution: Seeds of Diversity, Science Vol 308, Issue 5729, 1752-1753, 17 June 2005, [DOI: 10.1126/science.1113416].
Mere microevolution masquerading as macroevolution by mangling the meanings of messages. Microevolution is not under dispute. If macroevolution is a fact, Darwinists, give us an example instead of ingenious speculation but not much rigor (see next entry). There should be millions of examples. Why is this so hard to demonstrate? A bluffing assertion is not a sign of rigor, or of vigor. In science, its more a sign of rigor mortis.Something from Nothing Dept.: Can a Divide-and-Conquer Strategy Climb Mt. Improbable? 06/20/2005
Darwinian evolution from the most primitive organisms to the most advanced must have produced huge increases in functional information (see 06/12/2003 entry). Yet finding specific genetic mechanisms for just how DNA succeeded in climbing Mt. Improbable, as Richard Dawkins termed it in his book of the same name, has been daunting. In a recent paper in PNAS,1 Austin L. Hughes meant to encourage his fellow Darwinists that explaining the origin of new function in proteins has been given a boost by recent findings. In the body of the article, however, he appears to have conceded more than he affirmed. He began,
Evolutionary biologists agree that gene duplication has played an important role [intelligent design term] in the history of life on Earth, providing a supply of novel genes that make it possible for organisms to adapt to new environments. The existence of diverse multigene families, particularly in eukaryotes, provides evidence that numerous events of gene duplication followed by functional diversification have shaped [intelligent design term] genomes as we know them. But it is less certain how this panoply of new functions actually arises, leaving room for ingenious speculation but not much rigor. Cases where we can reconstruct with any confidence the evolutionary steps involved in the functional diversification are relatively few. (Emphasis added in all quotes.)To switch from gloom to hope, he described an investigation by Tocchini-Valentini et al. that examined genes for tRNA endonuclease among three branches of Archaea. Two of them contained a single gene that combined the functions of stabilization and catalysis, but a third subdivided the functions between two genes. They feel this is an example of subfunctionalization (see 10/24/2003 entry); i.e., a case of a multi-function gene splitting sometime in evolutionary history into separate genes that carry on the original functions separately. Hughes was glad to hear about this report, which to him was particularly welcome as a concrete example of how new protein functions can arise. Yet this would seem to be merely a case of rearranging functions rather than originating new ones, i.e., of dividing without necessarily conquering. Did he provide any examples of new functions arising by this process?
The rest of article only elaborates on the theme of subfunctionalization. Hughes presented various theories, by Ohno, Jensen, Orgel and others, about how gene duplication might have shared and diversified functions among ancestral genomes (see 05/15/2005 entry for another recent example). He talked about gene sharing, in which a gene might produce multiple products depending on the context: i.e., an enzyme in one type of cell, but a crystallin in the eye, but this also begs the question about where the genetic information came from. He speculated about how subfunctionalization might produce better-adapted proteins by the Babe Ruth effect analogous to how the famous baseball player performed better as either a pitcher or outfielder/hitter, but not both simultaneously yet did not prove that subfunctionalized proteins either contained more information or did a better job.
What is more revealing in Hughes commentary are statements he made about evolutionary theory, evidence and proof. Coming from someone who accepts evolution without hesitation, these remarks cast doubt on both the methodology and achievement of an evolutionary approach to genetics:
Testing this hypothesis will require work at the interface of molecular evolutionary genetics and systems biology. We will need to be able to understand the diversification of gene duplicates in terms of the totality of each genes role in cellular processes. It is a tall order given our present knowledge, but this kind of evolutionary systems biology not only will increase our understanding of how new protein functions evolve but also will shed essential light on why biological systems work the way they do.
1Austin L. Hughes, Gene duplication and the origin of novel proteins, Proceedings of the National Academy of Sciences USA, published online before print June 13, 2005, 10.1073/pnas.0503922102.
This article sounded intriguing by its title, Gene duplication and the origin of novel proteins, and ostensibly set out to explain how new functions arose but it did nothing of the sort. All Hughes could identify by observation were degradation effects. If genes and proteins underwent subfunctionalization, the function was already operative in the ancestor, as well as the information needed to produce function. Did he prove that the daughter products contained more information? No. Did he prove that subfunctionalization actually occurred, rather than being created that way? No. Did he give away the store? Yes.Supermen Living in Nepal 06/17/2005
There is a race of people at the base of Mt. Everest capable of feats that defy scientific explanation: the Sherpas. They can carry up to twice their body weight under three hostile conditions that would wear out most of us in a minute: (1) high altitude, (2) long distance, and (3) steep inclines. Somehow, the techniques they use and the adaptations their bodies have made from living in that environment have made them the supreme load carriers of the human world (they even beat out African women who routinely carry heavy loads on top of their head). This was the subject of a research paper in Science this week.1 Science Now sums it up:
When the going gets tough, the tough use their heads. Porters around the world carry loads that would floor backpackers by balancing baskets atop their noggins or slinging sacks from their craniums. Now a new study reveals that Nepalese porters do the job better than anyone else, hefting huge bundles while using relatively little energy. (Emphasis added in all quotes.)The study, also reported by National Geographic News, found that Nepalese porters or sherpas routinely carry double what backpackers carry, under more extreme conditions, yet burn less energy:
The town of Namche (at an altitude of 3500 m [11,400 ft]) near Mount Everest hosts a weekly bazaar. Porters (Fig. 1A), predominantly ethnic Rai, Sherpa, or Tamang, typically take 7 to 9 days to travel to Namche from the Kathmandu valley. The route, no more than a dirt footpath, covers a horizontal distance of 100 km, with total ascents (river crossings to mountain passes) of 8000 m [5 vertical miles] and total descents of 6300 m [4 vertical miles].The researchers measured their oxygen intake and carbon dioxide output under controlled conditions, and found that their energy utilization was far more economical than the control subjects at all loads and more economical than the African women at all except the lightest loads. They marveled at watching them in their normal business hauling loads around the mountains. How they do it is a mystery:
The load versus speed versus energy-cost trade-off chosen by these porters is to walk slowly for many hours each day, take frequent rests, and carry the greatest loads possible. We observed, for example, a group of heavily loaded porters making slow headway up a steep ascent out of a river gorge. Following whistled commands from their leader, they would take up their loads and labor uphill for no more than 15 s at a time, followed by a 45-s period of rest. Incredibly, this group of barefoot porters was headed for Tibet, across the Nangpa glacier (altitude 5716 m [18,700 ft]), about another weeks travel beyond Namche.Many world mountain climbers brag if they make it up Everest, but these sherpas consider such feats all in a days work. National Geographic News adds that after unloading and selling their goods, they race home for more, running down the mountain for two days, even poorly equipped and usually with very bad shoes or none at all. They usually sleep on the trail, with nothing but rocks for pillows, even in below-freezing temperatures. Some of their women bring their babies with them.
See also the National Geographic story from May 2002 about the legendary Sherpas of Mt. Everest. Many of the famous climbing expeditions on the worlds highest mountain could not have succeeded without them, it says.
1Bastien et al., Energetics of Load Carrying in Nepalese Porters, Science, Vol 308, Issue 5729, 1755 , 17 June 2005, [DOI: 10.1126/science.1111513].
Every once in awhile we get glimpses into the suggestion that there is far more potential in the human body than most of us realize. Those of us who have backpacked in the mountains know the strain of carrying even 40 pounds up a steep mountainside for just a couple of hours, and that at much lower elevations. The worst feeling at a rest stop is to have some 68-year-old frail-looking grandma with a bigger pack prance right on by saying, Mighty fine day, is it not? as you sit there gasping for breath.Obsessed With Sex: How Much Can Be Known About the Sexuality of Hominids? 06/17/2005
Bruce Bower in Science News (June 11, 167:24, p. 379) reported on the controversy about the sex life of Lucy and her mate(s). Owen Lovejoy and Philip L. Reno (Kent State U, Ohio) have unabashedly put forth a hypothesis that Mr. and Mrs. Australopithecus afarensis (lets call him Desi) had long-term relationships and stable families as they evolved along on the way to humanity. This conclusion was based on statistical analysis of fragmentary bones which represent somewhere between 5 and 22 individuals. They assumed that the largest femur heads were from the males and the smaller, from the females, then deduced that australopithecines displayed slightly less sexual dimorphism than gorillas do. From there, they made presumptions about what this implied about their sex lives in the prehistoric I Love Lucy sitcom.
Bower gave good press to Lovejoy and Renos hypothesis, but then surveyed the reactions of other researchers:
Other scientists express a mix of chagrin and disdain at the amount of energy that researchers have expended on trying to separate fossil boys from girls. Investigators need to drop their obsession with the sex of fossils and examine how individual differences in skeletal anatomy arise, contends Maciej Henneberg of the University of Adelaide in Australia. For body weight and many skull measurements, including braincase size and facial width, individuals within each sex usually differ far more from each other than average members of opposite sexes do, he argues.Its not even clear to all researchers that Lucy was a female, to say nothing of whether the Mertzes were part of the same tribe. Bower hopes that additional specimens will help resolve this battle of the sexes.
The nonsense that Darwinists get away with is atrocious and silly. Bowers article contained the obligatory artists conception of Lucys family life, all based on myth and unwarranted speculation. Even though he tried to provide criticism of Lovejoys wacky idea, he only extended the debate between members of the Darwin Party. Why do non-Darwinists never get a chance to provide their scientific critiques?Did Fossils Inspire Thunderbird Legends? 06/17/2005
Adrienne Major thinks that the Lakota got their legend of the Thunderbird from looking at fossil pterosaurs in the badlands. Her speculation is explored in National Geographic News. Major thinks other world legends have their origin in fossils that ancient people observed.
This hypothesis is no less speculative than the one by creationists that Indians saw live pterosaurs and the Chinese saw live dinosaurs. Evolutionists would never consider such an idea, because they have their own myths. They are wedded to the tale that dinosaurs and pterosaurs died out long before man appeared. Do they know this for a fact? No; they were not there, for one thing, and their prior commitment to evolutionary theory dictates how all data are to be interpreted. The discovery of flexible blood vessels in a T. rex recently (see 03/24/2005) shows the extent of their commitment; rather than consider the obvious, that this unfossilized material could not be 70 million years old, they adjusted their assumptions to fit their myth.Miller Time Party Drags On 06/16/2005
Astrobiologists threw a party when a team of researchers decided there was more hydrogen in the early earths atmosphere than thought (see In the beginning, hydrogen: was it Miller Time?, 04/22/2005). While this was good news for those wishing for better conditions on the early earth for chemical evolution, a few are staying sober enough to warn against letting the celebrations get carried away.
Last month, veteran origin-of-life researcher Christopher Chyba, buoyed by the announcement, was nevertheless cautious about how much it helps the Miller scenario. He wrote in Science:1
In 1952, Stanley Miller, working with Harold Urey, simulated the atmosphere of early Earth with a gas mixture of methane (CH4), ammonia (NH3), molecular hydrogen (H2), and water. When he introduced an electrical spark to represent lightning, he observed the formation of amino acids, the building blocks of proteins....Chyba described the Miller-Urey scenario in more detail, but admitted it was probably largely wrong. Such a reducing atmosphere would have been hard to form or sustain. If, however, there was a sustainable hydrogen abundance of 30% or more, as suggested by the Colorado team, conditions favoring higher production of amino acids might have existed. Still, Many uncertainties and problems remain, Chyba said, and they seem serious, indeed:
These are tumultuous times in the study of the origin of life. The early ocean may have been even less hospitable for prebiotic chemistry than previously thought, and claimed evidence for the earliest signatures of life on Earth is being strongly challenged. Now a 30-year, albeit shaky, consensus on the nature of the early atmosphere may have to be reexamined, and the geochemical implications of an H2-rich early atmosphere will need to be scrutinized. This turmoil makes it a great time for young scientists to enter the field, but it also reminds us that some humility regarding our favorite models is in order. As Jacob Bronowski noted, Science is a tribute to what we can know although we are fallible.These week in Science,4 Richard Kerr also wrote about the higher hydrogen estimate:
Thirty years ago, geochemists took away the primordial soup that biologists thought they needed to cook up the first life on Earth. Now, some atmospheric chemists are trying to give it back.Kerr summarizes the new estimate and what it means: Overall, hydrogen would have escaped at 1/100 the rate previously assumed, the group says.... That would make for a far more productive atmosphere than chemists have been coping with for 30 years allowing vast amounts of organics to form into the ocean to make a soup.
Kerr hastens to make clear that there is still disagreement. While the announcement is going to make the biologists a lot happier, another doesnt feel that Tian et al. adequately dealt with all the factors that contribute to hydrogen escape; a more sophisticated model would show that hydrogen escaped the early Earth at least as fast as it does today. (Kerr does not even mention the problem with salts in the ocean.) Is the Miller party running out of food? He ends, Time will tell whether too many cooks spoil the primordial broth.
1Christopher Chyba, Rethinking Earths Early Atmosphere, Science, Vol 308, Issue 5724, 962-963 , 13 May 2005, [DOI: 10.1126/science.1113157].
2Tian et al., A Hydrogen-Rich Early Earth Atmosphere, Science, Vol 308, Issue 5724, 1014-1017, 13 May 2005, [DOI: 10.1126/science.1106983].
3Monnard et al., Influence of ionic inorganic solutes on self-assembly and polymerization processes related to early forms of life: implications for a prebiotic aqueous medium, Astrobiology 2002 Summer;2(2):139-52. They write that concentrations of salts anything like those in our contemporary oceans inhibits formation of amino acids and completely disrupts primitive membrane systems. Conclusion: These observations suggest that cellular life may not have begun in a marine environment because the abundance of ionic inorganic solutes would have significantly inhibited the chemical and physical processes that lead to self-assembly of more complex molecular systems.
4Richard Kerr, A Better Atmosphere for Life,, Science, Vol 308, Issue 5729, 1732, 17 June 2005, [DOI: 10.1126/science.308.5729.1732].
Same comment as in 04/22/2005: too little, too late. The good news is no better than that in the Geico commercials: I have good news and bad news. The jury has found you guilty, you have to go into the slammer for life, your wife and kids have left you and are changing their names, your stocks went bust, and you have cancer.Are Teens Like Roaches? 06/16/2005
A press release from University of Manchester concluded that being a teenage mother might be a good thing. The conclusion was based on observations of the mating behavior of cockroaches. Dr. Patricia Moore, one of the researchers, wins Stupid Evolution Quote of the Week: Although its hard to compare the experiences of the female cockroach to humans, the biological mechanisms are similar and so an inappropriate apoptosis response to the mistiming of reproduction may explain the evolution of the loss of fertility with age. EurekAlert reproduced the press release without any challenge.
To an evolutionist, human society acts on the same principles as cockroach society. To evolutionary reporters, any idea that glorifies Charlie is fit to print. As a prime example of evolutionary folly, this story speaks for itself.Reports Differ on Kansas Evolution Debates 06/16/2005
How is the debate over evolution in Kansas going? It depends on whom you ask. MSNBC News focused on personal attacks between board members (see also the Lexington Herald-Leader). The Discovery Institute, by contrast, focused on the content of the new proposed standards that allows a common-sense approach for teaching all the science about evolution, including the problems with Darwins theory.
MSNBCs title suggests that both sides are bickering, claiming School board members hurl insults at each other. But if you look into the article, the only ones hurling insults are the evolutionists; the other side is just putting up their shields. All Connie Morris said was, after being insulted, Had you attended, you would have been informed. You would be sitting here as informed individuals and not arrogantly calling us dupes. The article claims Morris mentioned the moderates by name in print, but does not say she insulted them like the Darwinists did; she only derided evolution itself, the article says. The evolutionists, though, called the conservatives dupes of intelligent design advocates and their decision based on absolute and total fraud. Judge for yourself which side is acting with civility and responsibility.Are Natural Poisons Health Cures in Disguise? 06/15/2005
Three recent stories are suggesting that natural toxins may be too much of a good thing:
A common operational paradigm in nature appears to be control by resistance: initiator and repressor, agonist and antagonist, accelerator and brake. Another is hormesis (see 02/12/2003 entry): i.e., that a little is good, but more is not better. Taken together, these principles suggest that many poisons and toxins only become evil to our sensibilities when they get out of control.Virginia Teacher Chastened for Making Optional Creation Material Available 06/14/2005
A highly-respected and well-liked high school biology teacher in Bristol, Virginia almost lost his job recently. His crime? Making an optional notebook of supplementary material called Creation Battles Evolution available to his students. The notebook, printed at his own expense, included evidence for creation and against evolution, from sources ranging from the Internet to scholarly papers and quotations from scientists and scholars critical of evolution or evidence supporting it. Each semester for 15 years, Larry Booher had mentioned it in passing, telling the class it was optional material that would not be on the test but available for extra credit. A reporter got wind of it and gave an anonymous tip to the school authorities. Booher was told to stop. The superintendent claimed the teacher had stepped over the line and ordered, He must teach evolution exclusively observable scientific fact, not beliefs or religion (emphasis added). Like Galileo, he was forced to recant: he told the Roanoke Times he regretted handing out the material. The story was mentioned in the Hampton Roads Pilot, LA Times and the Richmond Times Dispatch.
One of his former students wrote us and said he was saddened by the action, calling Booher a teacher of great impact and one of the greats in my life. He now values his copy of that notebook even more. When you cant beat your opponent in a debate, you have to silence him, which is what they have done to a great biology teacher, he said. He described Booher as one of the most respected and liked teachers in the school. He never discussed his personal views unless asked, and made it very clear that nobody was pressured to believe anything. This student could not find any parent or former classmate who was happy about what the school did to Booher. Maybe thats why not one parent or student complained in two decades, and it took an anonymous reporter from Charlottesville, Va (250 miles away) to make an issue of it.
The superintendent agreed with the assessment of Larry Boohers reputation:
Lee described Booher, 48, as one of the finest science teachers Ive ever been around and said Booher would return to the classroom in the fall since he agreed to stop distributing the creationism materials.The news reports made it sound like Larry Booher had broken the law, violating a Supreme Court decision. That decision, however, only forbade school boards from mandating equal time for creationism along with evolutionism. It stated explicitly that teachers are free to discuss any scientific theory of origins. Similarly, the guidelines for the congressional No Child Left Behind act targeted evolution as a controversial theory that teachers were free to discuss critically and mention alternatives.
So Evolution Must Be Taught Exclusively. Anything other than 100% pure Darwin Dogma is now labeled belief and religion by fiat, no matter how scientifically sound it is, no matter how supported by reputable scientific sources. Students tender eyes must be shielded from any of the voluminous damaging evidence against official dogma. Are you mad about this? Look at the next entry; think about all those molecular machines that are inexplicable by evolution mechanisms that shout design with a capital D. And they call evolution observable scientific fact? How enlightened our age.Cell Wonders Accelerate 06/14/2005
Scientific papers on cell biology continue to uncover amazing things as techniques improve to peer into the workings of these units of life. Here are our Top Ten from the last few weeks:
1Menetrey et al., The structure of the myosin VI motor reveals the mechanism of directionality reversal, Nature 435, 779-785 (9 June 2005) | doi: 10.1038/nature03592.
2Perry and Lithgow, Protein Targeting: Entropy, Energetics and Modular Machines, Current Biology, Vol 15, R423-R425, 7 June 2005.
3Stramer and Martin, Cell Biology: Master Regulators of Sealing and Healing, Current Biology, Vol 15, R425-R427, 7 June 2005.
4Dimitris Kioussis, Gene regulation: Kissing chromosomes, Nature 435, 579-580 (2 June 2005) | doi: 10.1038/435579a.
5Friedberg et al., Trading Places: How Do DNA Polymerases Switch during Translesion DNA Synthesis? Molecular Cell, Volume 18, Issue 5, 27 May 2005, Pages 499-505, doi:10.1016/j.molcel.2005.03.032.
6Heisinger et al., The v-ATPase V0 Subunit a1 Is Required for a Late Step in Synaptic Vesicle Exocytosis in Drosophila, Cell, Volume 121, Issue 4, 20 May 2005, Pages 607-620, doi:10.1016/j.cell.2005.03.012.
7Richard Berry, ATP Synthesis: The Worlds Smallest Wind-Up Toy, Current Biology, Vol 15, R385-R387, 24 May 2005.
Sometimes we just have to rub it in: these are just a few samples from the flood of literature coming out each week in cell biology, biochemistry and genetics (check out another example from 01/27/2003). A little overkill is needed once in awhile, a quadruple jolt of caffeine to make the Darwinists wake up and smell the coffee. Almost none of these papers even mention evolution, and the ones that do only assume it: e.g., Myosin VI might have evolved to provide unique kinetic characteristics that are potentially important for a reverse-directed motor. Do they really expect anyone to believe that any more?NAS Enters the Evolution Web Wars 06/13/2005
MSNBC News reports that Scientists take evolution fight online: National Academies sets up Web site to defend theory. (See also Wired News.) The Evolution Resources website of the National Academy of Sciences, nationalacademies.org/evolution, contains online books and articles, but the most recent entry is an address by outgoing NAS president Bruce Alberts (see 03/24/2005 entry) seeking to rally academy members to fight the advance of creationism and intelligent design:
We stand ready to help others in addressing the increasingly strident attempts to limit the teaching of evolution or to introduce non-scientific alternatives into science courses and curricula. If this controversy arrives at your doorstep, I hope that you will both alert us to the specific issues in your state or school district and be willing to use your position and prestige as a member of the NAS in helping us to work locally. (Emphasis in original.)The most recent technical report offered is a teachers guide to using evidences of microevolution in the Hawaiian Islands as a case study in evolution and the nature of science.
The MSNBC article written by Reuters quotes only pro-evolutionary sources. It misrepresents the goals of anti-evolutionists, saying bluntly that some U.S. religious groups want to be taught in schools only if their own views of a divine creator get equal credence. It also calls alternatives non-scientifically based, and quotes the NAS saying, The theory of evolution is one of sciences most robust theories, and the National Academies have long supported the position that evolution be taught as a central element in any science education program. The article also carries a link to the staunchly anti-creationist NCSE (National Center for Science Education).
Bruce Alberts is like the out-of-touch king in the Wizard of Id cartoon. A frantic messenger runs into the castle, breathlessly shouting, The peasants are revolting! Unalarmed and undeterred, the king responds, They certainly are.Enzymes Chew Like Pac-Man 06/10/2005
Evidence is growing that many enzymes have moving parts. They act like scissors, clamps and little pac-mans. When precisely-folded chains of amino acids emerge from the ribosome, they fold into unique shapes with the aid of chaperones. But those shapes are not static globs. They move, say Dmitry A. Kondrashov and George N. Phillips, Jr. (U. of Wisconsin). Writing in Structure,1 they describe some of the molecular mastication mechanics of these amazing machines:
Computational prediction of global protein motion... suggests that enzymatic active sites tend to be placed near the hinges of the jaws of enzyme structures.Proteins are so tiny, the motions are very hard to observe. The authors describe the various techniques that try to shed light on the central question: do these motions contribute to enzyme function? It appears they do:
Stabilization of the transition state relative to the substrate is thought to be the key to enzymatic efficiency. Static effects clearly play a major part via the electrostatic contribution of the positioning of polar residues. The existence of a dynamic effect, however, is controversial, specifically the proposition that enzymes can channel thermal vibrational energy into modes co-directional with the reaction coordinate, thus making barrier crossing more likely. Nevertheless, evidence is accreting to indicate a link between well-defined global motions and catalysis.After the technical jargon, they lighten up and explain this for the rest of us with some everyday comparisons:
Computation of the normal modes of motion allowed the determination of the hinges or pivot points that separate regions of the protein moving in opposite directions, much like the end of a nutcracker. In the vast majority of the enzymes studied, the catalytic residues were found to be located in a predicted hinge region.... This finding contributes a bioinformatic dimension to the field of functional protein dynamics and may allow improved functional annotation for the flood of newly solved protein structures. The results also suggest an enhanced role for the global protein structure, which often has been viewed as a scaffold supporting the active site. The study adds to the growing body of evidence that the fold determines global protein dynamics, suggesting a mechanism for allosteric signal transduction, functional impact of distant mutations, and other effects not explained by the chemistry of the active site. In this view, enzymatic structures resemble a Pac-Man icon, with active sites located in the wedge-shaped opening, and the structure responsible for the chewing motion of the mouth.What this means is that the whole protein all the amino acids, even those distant from the active site, are involved. It is possible that they contribute to orienting the substrate into the active site and stabilizing it once it makes contact, like a vise grip. Moving parts might also contribute to the release of the substrate after catalysis is complete. The structure might strip off solvents before the substrate reaches the active site, resulting in more efficient catalysis. Even short fragments distant from the hinge might contribute an essential part of the overall function.
Viewing enzymes as dynamic machines opens up new avenues for investigation, they envision. The specific sequences in all the parts of the enzyme would require closer scrutiny; they might have moving parts as well. At least, it is an idea to chew on, they conclude; The relative importance of topology and sequence for protein dynamics and function needs to be investigated, in order to add more teeth to the masticating view of enzyme dynamics.
1Dmitry A. Kondrashov and George N. Phillips, Jr, Molecular Mastication Mechanics, Structure, Volume 13, Issue 6, June 2005, pages 836-837, doi:10.1016/j.str.2005.05.004.
Wonderful thoughts, devoid of evolutionary speculation. Enzymes can no longer be viewed as floating wads of amino acid gunk, and not even as rigid tools like screwdrivers and hammers. Now, we see them as power tools: exquisitely precise structures with moving parts, each part contributing to the task at hand. This means that enzymes cannot tolerate many mutations. Previously, biochemists thought that the active site alone was the most intolerant of mutations, but if this emerging picture of dynamic action is correct, even short sequences of amino acids distant from the active site may play vital roles in the overall function. The game is not getting any easier for the Darwinists as Pac-Man keeps chewing through their assumptions.Is It Justifiable to Speculate About the Evolution of Murder? 06/10/2005
Sharon Begley, writing in the Wall Street Journal May 20, was pretty angry that an evolutionary psychologist tried to give an evolutionary explanation for why men murder women. She called the theory by Dr. David Buss (U. of Texas, Austin) a just-so story and bad science. In his book, The Murderer Next Door: Why the Mind Is Designed to Kill, Buss had portrayed murder of women as an adaptive strategy for some males to leave more offspring than competitors. Not only is this theory offensive and wrong, Begley charged, it it is a ludicrous idea even in evolutionary terms:
As evolutionary theory, this is ludicrous. Killing the owner of the uterus that is your only current chance to get your genes into the next generation (the evolutionary imperative), especially if she is caring for your current children and has a father or brothers who take exception to your uxoricide, is an excellent way to a dead end personally and genealogically. Being the target of angry in-laws, not to mention life imprisonment or lethal injection, tends to limit ones reproductive opportunities. (Emphasis added in all quotes.)Why would this adaptation, she continues, work only in humans but not other species? She quotes Jaak Panksepp, who counters, Only a few species [like insects] kill their mating partners, and the killing is usually done by females. He called the ideas of Buss ugly evolutionary icing with no basis. Begley ends by discounting the scientific objectivity of such storytelling:
The claim that works like Murderer Next Door are merely following data objectively in a search for truth is getting tiresome. The very decision to seek a scientific validation for killing women represents a value judgment. The fact that the claim makes no sense scientifically is almost secondary to that.And now, the rebuttal. Dr. Buss wrote back in an attempt to justify his position scientifically. He was dismayed to see Begleys sarcastic, emotional and misleading depiction of his theory, saying the issue demands sober scientific analysis. Attributing murder to poverty, pathology, exposure to media violence, poor parenting cannot explain its predictability in certain circumstances, he said. By comparison, he claimed, My book presents the most comprehensive and scientifically cogent theory of why people kill, anchored in evolutionary psychology. In addition, The books theory is based on sound evolutionary biology, anchored in the clear logic of reproductive competition, he continued.
He continued by arguing that the only way to deal with murder was to understand its evolutionary basis:
The unfortunate fact is that murder has proved to be a disturbingly effective solution to an array of adaptive problems in the ruthless evolutionary games of survival and reproductive competition. Its undoubtedly deeply disturbing to think that humans have homicidal circuits that get activated in certain circumstances, but that in no way implies approval or justification of murder. Nor does it imply that murder is inevitable. Rather, knowledge of the deep psychology of killing is required if we ever hope to prevent it. Those who attempt to avoid this deep understanding by strident emotional appeals and cartoonish ridicule tread on dangerous moral ground. The problem of murder cant be solved by wishing away dark sides of human nature that we would prefer not exist.This high-visibility debate in the Wall Street Journal seems destined to sharpen the acrimony between those evolutionists and non-evolutionists over the question whether evolutionary psychology has any scientific validity.
Anchored in evolutionary psychology he says? Ha. Thats like a paper anchor in soft silt. Sound evolutionary biology is an oxymoron.Roses Are Red, Darwinists Are Blue 06/09/2005
Roses have a special pigment molecule, a particular form of anthocyanin, responsible for all the rich red-to-blue shades in the petals that delight gardeners and attract pollinating insects. This molecule is different from the pigments in every other flowering plant; it is glycosylated at two positions instead of one.2 A single enzyme does the job at both points. Without the glycosylation reaction at both ends, the molecule is unstable and cannot be soluble in water in the vacuoles of the cells in which it operates.
A team of Japanese scientists investigated how this double-glycosylation reaction system might have evolved. They could find no intermediate. Reporting in Nature,1 they said that while other flowers use derivatives from a singly-glycosylated form, this is evolutionarily precluded in roses by their different glycosylation pattern, which may be unique to members of the Rosaceae (emphasis added in all quotes). They also stated with puzzlement,
It is a mystery why this particular glycosyltransferase evolved independently in roses. The novelty of the RhGT1 enzyme therefore lies not only in its ability to catalyse glycosylation at two different sites on the anthocyanidin molecule but also in its apparent absence from other species.They prepared a phylogenetic tree based on this type of pigment-preparing enzyme family, but it ended up with the rose family on a branch all by itself.
1Ogata et al., Plant biochemistry: Anthocyanin biosynthesis in roses, Nature, 435, 757-758 (9 June 2005) | doi: 10.1038/nature435757a.
2Glycosylation replaces an OH (hydroxyl) group with a glucoside. This is performed by an enzyme called a glycosyltransferase, in the case of roses, RhGT1.
Here is a small gap, but a gap nonetheless; no evidence for the evolution of this complex molecule and the enzyme that knows how to operate it just an unconfirmed prediction from evolutionary theory. Surprised? Question: was evolutionary theory of any value in this investigation?Ice Volcano Seen on Titan 06/09/2005
Planetary scientists are reporting the possible discovery of an ice volcano on Saturns large moon Titan. A large circular feature, 18 miles across, appears to have a caldera at the top, is surrounded by stress fractures, and appears warmer than the surroundings (warmer, relatively speaking: the mean surface temperature is -290° F). The infrared pictures are somewhat indistinct due to the smoggy haze that obstructs views of the surface.
The discovery, announced in Nature,1,2 might explain the origin of the methane observed in Titans atmosphere. The paper states that a widespread methane ocean does not exist on the surface. Instead, cryovolcanism might provide a mechanism that could resupply the methane from below. See also press releases from the Cassini website, JPL and the BBC. News@Nature remarks that scientists were disappointed to find that Titan is as dry as a bone.
1Louise Prokter, Planetary science: Shades of Titan, Nature 435, 749-750 (9 June 2005) | doi: 10.1038/435749a.
2Sotin et al., Release of volatiles from a possible cryovolcano from near-infrared imaging of Titan, Nature 435, 786-789 (9 June 2005) | doi: 10.1038/nature03596.
The lack of oceans of ethane and methane was a huge disappointment and surprise to planetary scientists. They know that atmospheric methane is destroyed by the solar wind in short order 100 million years as an upper limit (thats only 1/45 the assumed age of Titan). But they also expected the photolysis of methane to lead to the accumulation of hydrocarbons on the surface in the form of huge deposits of liquids.Scientists Confess Their Sins 06/09/2005
One-third of scientists engaged in unethical behavior over the last three years, according to a report in Nature.1,2 These include falsification, fabrication and plagiarism as well as a host of questionable research practices. Its not so much a problem of high-profile cases of fraud as much as everyday, mundane, corrosive ethical lapses that are endangering the integrity of science. See also the summary on MSNBC News
1Meredith Wadman, One in three scientists confesses to having sinned, Nature 435, 718-719 (9 June 2005) | doi: 10.1038/435718b.
2Martinson et al., Scientists behaving badly, Nature 435, 737-738 (9 June 2005) | doi: 10.1038/435737a.
Hypocrites in the church of Darwin? Would you trust this gang with your soul?Smithsonian Reversal Over ID Noticed by Big Science 06/09/2005
Both Nature1 and Science2 noticed the Smithsonians flip-flop over co-sponsoring The Privileged Planet at their Natural History Museum this month (see 06/01/2005 entry). Both noted the quandary that the Smithsonian found itself in. They could not back out because of a contract, but under pressure from evolutionists, did not want to appear to endorse intelligent design. This led them to return the $16,000 fee so that they would not appear to be cooperating with the Discovery Institute, and to remove their co-sponsorship while allowing the event to go forward.
Nature noted that email from researchers and the public prompted the backtracking, titling its news item, Evolution row makes museum ditch donation (even though the film is not about evolution). Science said the Smithsonians compromise, permitting the film to be shown privately but without their co-sponsorship or taking a fee, allowed the Institution to avoid the appearance of endorsing the film on the one hand, while on the other avoiding giving the Discovery Institute yet another martyrdom story.
Both articles agreed that Discovery Institute had done nothing wrong in scheduling the film. It was a routine procedure they followed. Science said that museum spokesperson gave the film a clean review, even though museum policies preclude events with a religious, political, or commercial message. A second review, after the hubbub, also concluded that the film fell within the museums guidelines for such events. Their basis for claiming the film violated their scientific research policy was explained by anthropologist Richard Potts, chair of the museums human origins program:
But it was very clear that the film was trying to situate science within the wider realm of belief. The idea that human beings have been placed on Earth to discover the principles of the universe is not a position that stems from science; it is a metaphysical and religiously based conclusion. (Emphasis added in all quotes.)The Smithsonian frequently accepts donations for use of their auditorium. After the complaints by evolutionists, however, the Smithsonian is reviewing its policies to avoid confusion in the future.
Update 06/24/2005: The event apparently went off smoothly without acrimony or dissent; here is an eyewitness report from Salvador Cordova.
1Geoff Brumfiel, Evolutionist row makes museum ditch donation, Nature 435, 725 (9 June 2005) | doi: 10.1038/435725a.
2Yudhijit Bhattacharjee, Smithsonian Gives Grudging OK to Film Backing ID Argument, Science, Vol 308, Issue 5728, 1526, 10 June 2005, [DOI: 10.1126/science.308.5728.1526a].
This was clearly an episode about power politics, not science. Notice how the film passed two reviews that agreed there was no problem with the science; the museum backpedaled only because of the noise from barking Darwin bulldogs, most of whom have probably not even seen the film. And what a weak excuse; its not that the film said anything outrageous, but rather that the Darwinistas dont want to grant any credibility to the source. Thats the genetic fallacy can any good thing come out of Nazareth? Well, come and see.Historian Predicts Downfall of Darwinian Fundamentalism 06/08/2005
In the upcoming June 20 issue of Forbes magazine, British historian Paul Johnson attacks the fundamentalism of Darwinists, and predicts its demise:
Of all the fundamentalist groups at large in the world today, the Darwinians seem to me the most objectionable. They are just as strident and closed to argument as Christian or Muslim fundamentalists, but unlike those two groups the Darwinians enjoy intellectual respectability.The entire article has been reprinted by the Discovery Institute.
For all his worthy tirade against the Darwinists, Johnson seems to accept the big bang theory and cosmic time with uncritical gullibility. Then he adopts a front-loading design philosophy, misreading Newton as having taught an impersonal Force. Then, apparently after assuming the front-loaded design produced human beings, he inserts a divine intervention at the origin of language. These strange thoughts diminish an otherwise interesting prophecy about the fall of Darwinism.The Cause of a Teapot: Can Physics Explain Design? 06/08/2005
George F. R. Ellis (U. of Cape Town) wrote a Concepts piece in Nature1 this week that asks fundamental questions about ordinary things, particularly, can we get from fundamental physics to complex hierarchical structures through a chain of cause and effect?
A simple statement of fact: there is no physics theory that explains the nature of, or even the existence of, football matches, teapots, or jumbo-jet aircraft. The human mind is physically based, but there is no hope whatever of predicting the behaviour it controls from the underlying physical laws. Even if we had a satisfactory fundamental physics theory of everything, this situation would remain unchanged: physics would still fail to explain the outcomes of human purpose, and so would provide an incomplete description of the real world around us. (Emphasis added in all quotes.)But Ellis does not end on that depressing note. Admitting that meaning, though inexplicable from fundamental physics, did come into being, he claims that physics can illuminate the cause-effect structure of the universe. It does so by creating a playing field where emergent properties like human intelligence can create their own cause-effect realities. In the right context, he claims, higher levels of order can emerge and become autonomous:
It is possible that what actually happened was the contextual emergence of complexity: the existence of human beings and their creations was not uniquely implied by the initial data in the early Universe; rather the underlying physics together with that initial data created a context that made the existence of human beings possible. Conditions at the time of the decoupling of matter and radiation 14 billion years ago were such as to lead to the eventual development of minds that are autonomously effective. Such minds are able to create higher-level order, such as the Hubble Space Telescope and Kurt Gödels incompleteness theorem, that embodies a purpose and meaning not in existence before.He admits that a key to making this work is the ability to store information, yet he fails to define the term:
Stored information plays a key role, resulting in non-linear dynamics that are non-local in space and time. Brain functioning is causally affected by abstractions, such as the value of money, the rules of chess and the theory of the laser. These abstractions are realized as brain states in individuals, but are not equivalent to them James Clerk Maxwells theory of electromagnetism is not the same as any individuals brain state. Although such concepts are causally effective [i.e., they can lead an electrical engineer to apply them to an invention], they are not themselves physical variables. Consequently physics per se cannot causally determine the outcome of human creativity; rather it creates the possibility space to allow human intelligence to function autonomously.Even beaver dam building and the dances of honeybees, he says, might have emerged late late in the expanding Universe, made possible but not causally determined by the underlying physics and chemistry of matter. To figure out how the hierarchy of complex structures can arise is the challenge of physics, he says: i.e., how top-down causation and memory effects allow autonomous higher levels of order to emerge with genuine causal powers of their own. The meager attempts to do this with complexity theory, chaos theory and the like only take us a small step on this road.
A photo of a teapot adorns his article. The caption reads, Intelligent design: no physics theory is able to explain a teapot. Lest one think he would dare give aid and comfort to the Intelligent Design movement, he makes it clear which side he is on: Darwinian processes of selection, he asserts, guided the physical development of living systems, including the human brain.
1George F. R. Ellis, Physics, complexity and causality, Nature 435, 743 (9 June 2005) | doi: 10.1038/435743a.
Well, this goes to show that the debate over freewill and determinism is not argued only between theologians. Ellis has just charmingly bluffed his way past a major logical gap in naturalism: why there is something instead of nothing, and especially why there is such astonishing complexity as in a human brain instead of nothing. His answer: you can get something from nothing! First, the particles emerge out of nothing. Then, they create a possibility space out of which complexity emerges and takes over, becoming a new, autonomous entity, like a human mind, that can engender new levels of autonomy. This is the old tornado-in-a-junkyard theory of the 747. The junkyard is now to be understood as the possibility space of the jumbo jet.Understanding the Sun Not 06/07/2005
Exclusive The star we understand best should be the closest our own right? Despite a revolution in solar observations, there is much we dont know about Ol' Sol. That was the flavor of a talk by Dr. Alan Title (Stanford) at the Jet Propulsion Laboratory on Monday. At one point, he showed a picture of magnetic loops extending far from the solar surface without dissipating, and growing and combining from small to large scales, and remarked, Anybody familiar with basic E&M [electromagnetic theory] knows that that is impossible. Other mysteries involve the rotation of the convecting layer, lack of symmetry between the poles, and even the origin of the magnetic field. The bottom line was that we have more questions than answers over the last decade.
In the Q&A, someone asked if lessons learned from solar astrophysics are getting to the stellar astronomers. The answer was a qualified yes. It could be better but is fairly good, he said; but if we cant understand convection in our own star, thats a warning and a challenge to postulating about the fluid mechanics of other stars.
Another question was whether we still learn anything useful from solar eclipses. Yes, he said (although the discoveries tend to be more fun these days). We can put coronagraphs in orbit, but they are hard to keep steady. The moon is a very good occulting disk, he said.
A point well taken: if we cannot understand a star that looms large in our sky and is up all day, how much can we express confidence in our theories about points of light trillions of miles away? To gain more appreciation of our sun, and our occulting moon, see the film The Privileged Planet.Darwin Is Alive and Well at Down House 06/07/2005
Chris Darwin, that is the great, great grandson of Charles, and his fellow descendants Erasmus, Sarah, Allegra, Randal Keynes, and Leo Darwin Vogel. The family members are retracing his footsteps in the fields around his old house by inventorying the plants, reports the BBC News. The survey will help show if the flowering plants have evolved over the last 150 years.
Update 06/16/2005: Chris Darwin described for the BBC two trips he took to the Galápagos islands to retrace the footsteps of his famous great great grandfather. Chris chuckled that he must not have his predecessors genes, because he failed basic biology class.
Nice activity, surveying plants, but whats evolution got to do with it? This experiment continues the misperception that looking at microevolution will somehow demonstrate that bacteria can evolve into humans, given enough time, and enough small, incremental changes (see next entry and 08/20/2003 entry). Charlies botanizing, though amateurish, was commendable; his storytelling was not.Another Darwinian Assumption Overturned: Results Too Radical 06/07/2005
Evolutionists are stunned at a study in comparative genomics performed by University of Chicago researchers that overturns a common belief about natural selection. EurekAlert summarizes the finding: The new data show that if more mutations show up at a gene, that gene tends to accept a higher percentage of those mutations. This means that mutations accepted into a genome are not strictly a function of natural selection, but of mutation rate.
Mutations accepted into a gene can be synonymous or non-synonymous. Synonymous mutations (Ks) swap an amino acid with a similar one, such that the protein can still function. Non-synonymous mutations (Ka) change the shape of the protein and thereby can be acted on by natural selection. Scientists have assumed that the percentage of non-synonymous mutations accepted during evolution remains constant. Bruce Lahn, author of the paper in Trends in Genetics, commented on the assumption: This theory has been the workhorse of molecular evolution. Thousands of scientific papers have been published based directly or indirectly on this notion. The new study shows, instead, that the faster the speed of new mutations, the greater the percentage of those mutations accepted.
Several statements in the press release make this finding sound revolutionary:
What if a flood of mutations struck in a short period? Could it account for a wide range of mutational changes in the relatively recent past? How would they know? This result appears to undercut any remaining trust in the molecular clock, a device that was broken anyway (see 08/24/2004 entry).Evangelical Christians Split on How to Handle Evolution 06/03/2005
A dismal picture of controversy dividing Christian brother against brother, with no resolution in sight, is painted by Paul Nussbaum in the Philadelphia Inquirer. He says evangelical Christians are not monolithic in their opposition to evolution, but as divided as much of the rest of the nation. He quotes a spokesperson for the American Scientific Affiliation, a group of scientists who lean toward theistic evolution and old-earth creationism, saying:
No topic in the world of science and Christianity has created the intensity of discussion and disharmony with evangelicals as the source of biological diversity. Todays spirited discussion often pits Christian vs. Christian and scientist vs. scientist. (Emphasis added in all quotes.)The article touches on some of the approaches for integrating Christian faith and evolution, including young-earth creationism, intelligent design, theistic evolution, and the view that science and religion represent non-overlapping realms of truth.
One evangelical certainly not conflicted over evolution is Lee Strobel, former atheist and now host of Faith Under Fire and author of The Case for a Creator. Interviewed by Christianity Today, Strobel argues that no compromise is necessary; science backs up faith.
Nussbaum allowed David Wilcox (Eastern U) to get away with a horrendous straw man argument. Wilcox puts words into an imaginary students mouth when facing evolution in biology class: Why do I have to learn this stuff dont you know that God hates science? Good grief. Has anyone outside an insane asylum ever said that? In response, Wilcox triumphantly touts theistic evolution as the winner with this half-truth: God doesnt hate science he invented it. We try to get them to see that evolution happened and its not so scary... that evolution is the way God did it. Well, if Nussbaums intent was to make this proponent of evolutionary theism make a fool of himself, he succeeded. Runner-up was Ken Miller again with this borderline blasphemous straw man: Their [the creationists'] God is like a kid who is not a very good mechanic and has to keep lifting the hood and tinkering with the engine. Whos he kidding? Its the Darwinists who worship Tinker Bell (see 03/11/2005 commentary).Who Wins and Loses in the Darwin Wars? 06/03/2005
Sandra Lilley, writing in MSNBC News, pictures sad-faced students, whose scientific inquisitiveness has been stifled by the controversy over evolution. The article starts with a touching photo of a young girl, a look of wonder in her eyes, examining a toy human skeleton. Science is becoming a political hot potato for some students, she describes, transforming what should be a dynamic, fascinating topic into a total turn-off (emphasis added in all quotes). And some students are choosing silence over losing a prom date.
Lilley quotes only pro-evolution spokespersons (some nominal Christians) who express the opinion that the next generation of scientists is being threatened by creationists and politicians raising a ruckus over evolution, leaving students bewildered over a conflict they dont understand, preferring to avoid the subject as a result.
The only evidence offered for evolution in the article is from Ken Miller: If a child becomes a pharmacist and someone develops a resistance to a drug, that is evolution, he said. Miller argues that society will be at a disadvantage if we dont teach evolution, which he equates with basic science.
A different point of view was offered by high school science teacher Doug Cowan (Port Orchard, Washington), writing for the Christian Science Monitor. In his experience, he claims, students become stimulated over his non-sectarian teach the controversy approach.
I am a public high school biology teacher, and I do an unusual thing. I teach my students more than they have to know about evolution. I push them to behave like competent jurors not just to swallow what some authority figure tells them to believe not even me but rather to critically analyze, with an open mind, the evidence set before them....He finds that the students perk up when he points out that contrary to their large and monolithic biology textbook, some highly credentialed scientists insist that there are limitations to Darwin's theory. When he displays some of the alleged evidences for evolution that have been found fraudulent (Piltdown Man, Haeckels embryos), the sleepy looks in the classroom usually vanish.
Cowan, however, is not on an anti-evolution crusade. He also lays out all the reputable evidence for evolution, the pillars of evolutionary theory such as bacterial resistance, finch beaks and genetically altered fruit flies, then challenges the class to reason whether these observed microevolutionary changes can be extrapolated into macroevolution.
By maintaining a neutral stance, letting them examine all the evidence and make up their own minds, Cowan says his approach is on firm legal footing. Students and parents alike seem to appreciate his method. Students feel liberated to weigh the evidence for themselves. The job of the scientist, I explain, is to find the best explanation to a problem, not just to defend his or her own position at all costs. For support, he quotes Charles Darwin: A fair result can be obtained only by fully stating and balancing the facts and arguments on both sides of each question.
Evolution can be taught skillfully and poorly. Anti-evolution can be taught skillfully and poorly. Reporting on either can be done skillfully or poorly. Here are two examples for you to evaluate.Soft T-Rex Tissue Claimed Bird-Like; Age Ignored 06/03/2005
More details about the soft tissue found in a T. rex thigh bone (see 03/24/2005 story) were published in Science this week.1 Mary Schweitzers team claims to have found evidence of medullary bone [MB], a type of mineralized and vascularized bony tissue found only in certain birds during ovulation as a buffer against calcium loss. The abstract and summary posted in a press release from North Carolina State says its a girl, and shes pregnant:
Unambiguous indicators of gender in dinosaurs are usually lost during fossilization along with other aspects of soft tissue anatomy. We report the presence of endosteally derived bone tissues lining the interior marrow cavities of portions of Tyrannosaurus rex (MOR 1125) hindlimb elements, and hypothesize that these tissues are homologous to specialized avian tissues known as medullary bone. Because medullary bone is unique to female birds, its discovery in extinct dinosaurs solidifies the link between dinosaurs and birds, suggests similar reproductive strategies, and provides an objective means of gender differentiation in dinosaurs. (Emphasis added in all quotes.)Understated in the report is how these soft tissues could have survived for so long. The paper in Science says only:
The existence of avian-type MB in dinosaurs has been hypothesized but not identified. In part, this could be because of taphonomic bias [i.e., fossil-hunters not expecting to find it], because the death and fossilization of an ovulating dinosaur would be comparatively rare. Additionally, MB in extant birds is fragile, the spicules separating easily from the originating layer (fig. S1). Dinosaur MB may separate and be lost from overlying CB in a similar manner during diagenesis [i.e., the hardening of sediment into rock].National Geographic admitted briefly that all obvious gender indicators vanish when soft tissues decay during fossilization but emphasized the gender-identification and phylogenetic angles of the story. The BBC News article showed a picture of the bones, but said nothing about their assumed ages. The NC press release did not explain the 70-million year figure, but merely asserted it. Betsy M. Bennett, Directory of the NC Museum of Natural Sciences, stated emphatically, Were pleased to be able to provide a way for the public to see for themselves evidence that after millions of years, soft tissue can actually be preserved in dinosaur bone.
Another paper published in Science Express announced the sequencing of the genome from a cave bear, thought to have been extinct for 40,000 years. In the BBC News write-up, a scientist predicted, I dont think we can extract DNA from dinosaurs, I think they are too old. It will be interesting to see if Mary Schweitzers team finds any in the T. rex bone, where blood vessels, and possibly blood cells, were seen.
1Schweitzer et al., Gender-Specific Reproductive Tissue in Ratites and Tyrannosaurus rex, Science, Vol 308, Issue 5727, 1456-1460, 3 June 2005, [DOI: 10.1126/science.1112158].
This is incredible. How can these scientists ignore the obvious? Theres no way this bone could be so old, but all they can think about are connecting homology dots between dinosaurs and birds by circumstantial evidence. Did they see the dinosaur laying eggs? No. Did they prove this is medullary bone? Perhaps. Does it prove an ancestral relationship if the dinosaur did have medullary bone? No. Does that matter? Not much. What really matters about this story is the age of the specimen. If this specimen is only a few thousand years old, none of this dino-bird homology matters: this blows apart the entire tale of dinosaur evolution. Belief in millions of years and the rest of the evolutionary timeline takes a staggering blow.Kansas Debate Over ID Reverberates in Holland 06/03/2005
Is Holland becoming the Kansas of Europe? asked Martin Enserink in Science this week.1 All that education minister Maria van der Hoeven wants to do is have some public debate about intelligent design, but the suggestion has caused an uproar among scientists who claim she wants to take Holland back to the Dark Ages. On the contrary, van der Hoeven explains, she thinks it will promote dialogue between Christians, Jews and Muslims who are all united over the notion of a creator.
The education minister is not a card-carrying member of the intelligent design movement, and explains she is not trying to impose or ban anything. She was apparently impressed by the arguments of Cees Dekker, a renowned nanophysicist at Delft University of Technology who believes that the idea of design in nature is almost inescapable.
While trying to encourage discussion, she has had to spend much time defending herself over this tempest in a teacup as she called it. Why are scientists scolding her and saying it is not her business to get involved in biology? One possible reason is that the news from Kansas has made us all a bit more sensitive. Another may be the rumblings within the country: Even in Holland, there are plenty of people ready to castrate Darwin, said biochemist Piet Borst. He thinks that Vigilance is important on this issue. Dekker and van der Hoeven are taking this in stride.
Dekker says hes puzzled by the outcry but chalks it up to a Pavlov reaction to ID. Many scientists associate it with conservative Christians, Kansas, and George Bushso it has to be bad, he says. He hopes the debate will get more serious after the impending publication of a collection of 22 essays about ID and related themes, most of them by Dutch scientists, which he has co-edited. Van der Hoeven has agreed to receive the first copy of the book at a ceremony in The Hague next week. (Emphasis added in all quotes.)Enserink ends with the reaction of John Calvert, supporter of ID in Kansas, to the idea of a debate over ID in Holland. I think its a dynamite idea, he said.
1Martin Enserink, Is Holland Becoming the Kansas of Europe?, Science, Vol 308, Issue 5727, 1394, 3 June 2005, [DOI: 10.1126/science.308.5727.1394b].
This is another remarkable story on the growing influence of the intelligent design movement around the world, even in liberal Holland where the words George Bush, conservative Christianity and Kansas produce Pavlovian barks. Enserink points out that Holland is not quite Kansasafter all, this is the country that legalized euthanasia and invented gay marriage. Yet even there a small but committed cadre of scientists, politicians and laymen find the arguments for intelligent design compelling, and they want the debate to be heard. They are not castrating Darwin. His impotence is his own (see next two headlines). Dutch scientists are justly proud of their layman forerunner, the staunch Christian creationist from Delft, Antony van Leeuwenhoek the father of microbiology who helped lead science out of the Dark Ages (if there ever was such a period). He demonstrated how creation-oriented science can be the best in the world, full of vitality and motivation and excellence. When all the Darwinists can do is scream Dark Ages, you know their sunset is coming. But when it is sunset on one side of the worldview, its sunrise on the other.Hes Ba-a-a-ck: Lamarck Puts Pressure on Darwin and ID, Too? 06/03/2005
To historians of evolutionary theory, Lamarck is a 19th-century loser. His hypothesis of inheritance of acquired characteristics, according to high school textbooks and common knowledge, was debunked by experiment, and overturned when Darwin proposed natural selection as a mechanism for evolution. Why, then, does Massimo Pugliucci (Dept. of Ecology and Evolution, State University of New York at Stony Brook, NY) give Lamarck good press in a book review in Nature?1 Why does he put Darwin on defense, charging that a broader view of inheritance puts pressure on the neo-darwinian synthesis?
Pugliucci favorably reviewed the book Evolution in Four Dimensions: Genetic, Epigenetic, Behavioral, and Symbolic Variation in the History of Life by Eva Jablonka and Marion J. Lamb (Bradford Books, 2005), a lamarckist polemic:
The authors argue that there is more to heredity than genes; that some hereditary variations are non-random in origin; that some acquired information is inherited; and that evolutionary change can result from instruction as well as selection. This may sound rather revolutionary, even preposterously close to lamarckism. But Jablonka and Lamb build on evidence from standard research in evolutionary and molecular biology, and their case should be examined on its merits, rather than being dismissed by a knee-jerk reaction. (Emphasis added in all quotes.)He quickly quenches any alarm that he or the authors want to revive the kind of lamarckism that taught direct inheritance of acquired characteristics, or direct adaptive feedback from the soma to the germ line for example, that a lumberjacks strong arms would be inherited by his baby boy. That version of lamarckism is dead, he assures us, killed off by our understanding of molecular biology, and nobody is attempting to revive it. But that first meaning of lamarckism is not all that Lamarck taught:
The second meaning is actually closer to the core of Lamarcks ideas, which are rarely, if ever, read by modern biologists. The suggestion is that some heritable, adaptive changes come not from natural selection, but from the action of evolved internal systems that generate non-random guesses in response to environmental challenges. Examples are not hard to find, contrary to the assumed wisdom of standard neo-darwinism. Consider the existence of hotspots that make mutations in certain regions of the genome much more likely than in others. Or the impressive ability of some bacteria to increase the mutation rate of a specific gene involved in the metabolism of a given amino acid when that amino acid becomes scarce in the environment.Pugliucci acknowledges that Jablonka and Lamb are surely taking a gamble in labeling their position as lamarckist, but he sides with them in one shocking point: they are correct to point out that no modern biologist is a darwinist in the sense Darwin would have understood not least because Darwin included a lamarckian mechanism of the first (now frowned upon) type in his theory, as he had no solution to the problem of heredity (see 10/14/2003 entry).
Having disabled the alarm, Pugliucci now offers the neo-lamarckism of Jablonka and Lamb as the evolutionary answer to the intelligent design movement:
If one accepts this bold, expanded version of heredity and evolution, it turns out that evolution can proceed very rapidly and phenotypic modification can precede genetic changes.... Indeed, changes at the genetic level will often simply stabilize adaptive modifications that are initiated through phenotypic plasticity [i.e., acquired characteristics], epigenetic control mechanisms, or behavioural and symbolic means [i.e., social/language communication from parent to offspring]. This is a framework that would greatly help to solve old problems in evolutionary biology, such as the origin of novel structures [see 08/20/2003 entry], and even the appearance of what intelligent design proponents refer to, rather nonsensically, as irreducible complexity. This wouldnt require the abandonment of neo-darwinism, but rather its expansion beyond what Ernst Mayr contemptuously labelled bean-bag genetics.So Pugliucci offers not an either-or choice of lamarckism vs. neo-Darwinism, but an expanded synthesis beyond that thesis-antithesis dichotomy. For empirical support, he points to the partial failure of the originally ultra-reductionist, gene-centred approach that gave us genomics, saying that the interesting stuff is going on at the level of large gene networks [see 01/10/2003 entry], not of individual genes, partly because there is widespread functional redundancy in the genome. Presumably, this pool of functionality can be drawn on by environmental cues to optimize solutions to problems (see next headline).
Realizing his viewpoint will probably anger the hard-core selectionists, like Richard Dawkins (04/23/2003) and George Williams (05/31/2004), he draws on a defense, in closing, that has been used by several intelligent design proponents as strategic realism about changing the minds of the old guard:
The clamour to revise neo-darwinism is becoming so loud that hopefully most practising evolutionary biologists will begin to pay attention. It has been said that science often makes progress not because people change their minds, but because the old ones die off and the new generation is more open to novel ideas. I therefore recommend this and the other books I mentioned on the future of evolutionary theory to the current crop of graduate students, postdocs and young assistant professors. Theyll know what to do.
1Massimo Pugliucci, Expanding evolution, Nature 435, 565-566 (2 June 2005) | doi: 10.1038/435565a.
Theyll know what to do, all right: theyll chuck Chuck and baptize Jean-Baptiste into the dustbin of discredited prophets, and embrace intelligent design. Like Sutherland in the next article below, Pugliucci and his champions believe that specified complexity and optimization can emerge spontaneously, without purpose or direction, as long as there is a need. But that fallacy is not just with neo-Darwinism and its reductionist genomics; it is with any theory that fails to include information as a fundamental property of the universe. No combination of chance and natural law will produce information. Think of a blank DVD and one containing microscopic pits encoding the latest Star Wars movie: they have the same mass and physical properties. It is the information content that makes all the difference when you insert them into a DVD player. Similarly, to believe that the information content in the genome and in all the gene networks and epigenetic controls to which Pugliucci refers could have arisen by naturalistic means cannot be done without assuming naturalism at the outset. All our common experience teaches that information arises only from intelligent causes.Something from Nothing Dept. 06/02/2005
How do you get optimization by chance? In a Concepts piece in Nature this week,1 William J. Sutherland (U. of East Anglia, UK) suggested that the constraints of the environment will drive living systems toward optimal solutions. He thinks thats how selective forces shaped your teeth and jaw, for instance. Economists and engineers use optimization theory, he reasons, so why not biologists?
The use of optimization has allowed biologists to move from merely describing patterns or mechanisms to being able to predict, from first principles, how organisms should be designed. Optimality models are based on three elements: the choices available; what is being optimized; and the constraints.Though the concept has its critics, Sutherland gives a few more examples of how the optimization approach might have shaped biological systems by natural selection. But intelligent design (ID) is clearly not what he has in mind; he gives Darwin the credit: Darwins theory of natural selection provided an obvious mechanism for explaining optimization in biology: more efficiently designed individuals will leave more offspring.2 The optimization approach will be fruitful, he concludes:
A considerable strength of using optimization is that once we understand why organisms are as they are, then it should be possible to understand how they will respond to new conditions. Optimization can therefore be used to understand behaviour, and to predict population dynamics, in new environments, such as those resulting from habitat loss or a rise in sea level.
1William J. Sutherland, The Best Solution, Nature 435, 569 (2 June 2005) | doi: 10.1038/435569a.
2Of course this is obvious. How do you know the individual is efficiently designed? Because it left more offspring. Why did it leave more offspring? Well, obviously, it must have been more efficiently designed. This circular argument, is an example of a tautology, or a statement of the obvious, like deaf people cant hear, because they are deaf. Natural selection falls into this tautology trap any time fitness is defined in terms of fecundity (see 10/29/2002 entry).
Sorry, Bill. You cant get the blood of design from a turn-up of natural selection. Necessity is the mother of invention only when intelligence guides the process. The only thing nature is good at optimizing is entropy. The optimization approach will only make sense when design scientists oust the naturalistic usurpers from biology.ID Film To Be Aired at Smithsonian 06/01/2005
The intelligent-design film The Privileged Planet will be shown at the Smithsonian on June 23. See story on The Ames Tribune. Pam Sheppard at AIG has a report also. Following the showing at the National Museum of Natural History, the film will air on PBS stations around the country.
Update 06/02/2005: The Smithsonian appears to be backpedaling. Although they have not canceled the showing, they are now claiming the content of the film is not consistent with the mission of the Smithsonian Institutions scientific research, reports the Washington Post. Yet all the arrangements were made on the up and up two months ago, with no objections made even though staffers previewed the film twice. They are apparently taking heat from some opponents of intelligent design. The Post article reveals that The Amazing Randi (a well-known skeptic) offered the Smithsonian $20,000 not to show the film. For updates on this developing story, visit the EvolutionNews blog; it contains links to recent news reports, and also has copies of the original documents from the Smithsonian about the film showing. Update 06/24/2005: The event apparently went off smoothly without acrimony or dissent. Here is an eyewitness report from Salvador Cordova. See also the 06/09/2005 entry.
Why should the Darwinists be alarmed at this decision by the Smithsonian to co-sponsor the film? Its a private showing. The film makes a pretty mild proposition that there are aspects of our universe that seem inexplicable by chance, and that there might be some grand design or purpose behind it. Five scientists at the American Museum of Natural History already agreed that our solar system appears special (see 04/04/2005 story). One of the founders of the Smithsonian, the great American physicist Joseph Henry (see July 2004 Scientist of the Month) would be pleased.Jupiter Moon Throws Curve Ball 06/01/2005
The little inner moon of Jupiter, Amalthea, isnt dense enough. A press release from Jet Propulsion Laboratory says that data from the Galileo spacecraft shakes up long-held theories of how moons form around giant planets. Density of moons is supposed to decrease with radius around Jupiter, meaning that Amalthea should be the most solid. Instead, it appears to be a loose rubble pile less dense than water. An alternative theory, that it formed farther out and migrated or was captured, is also implausible. Amalthea is throwing us a curve ball, one scientist said. The original paper was published in Science May 27.1
1Anderson et al., Amaltheas Density Is Less than That of Water, Science, Vol 308, Issue 5726, 1291-1293, 27 May 2005, [DOI: 10.1126/science.1110422].
Planetary science is not exactly batting a thousand these days, even without curve balls. Looks like she didnt accept the date when sports dropout McFly proposed, Amalthea, you are my density... er, I mean, my destiny.Mars Dry Areas More Extensive than Thought 06/01/2005
If Mars had oceans or lakes, it wasnt for long, at least in the Syrtis Major region. Results of observations of the thermal emission imaging system (THEMIS) aboard the 2001 Mars Odyssey reveal about four times as much olivine as previously recognized in the Nili Fossae adjacent to the Syrtis volcanic shield. Olivine quickly degrades in the presence of water. Philip R. Christensen, principal investigator, who published the results in the June issue of Geology,1 believes eruptive volcanoes were the primary source of the olivine-rich basalts, not intrusive processes like dikes or sills.
The report on Mars Daily says the area studied is 11 times larger than the big island of Hawaii. Co-author Victoria Hamilton said that finding this much olivine in a very old region of Mars was intriguing, and suggests that this area of Mars, at least, has not seen much water.
Nevertheless, other areas look like something flowed. Mars Express released an image of Ares Valles (near where the Mars Pathfinder rover landed) that looks like an extensive flood plain. Perhaps volcanic heat melted frozen groundwater for a brief flooding episode some time long ago.
Update 06/06/2005: News@Nature reported that this could explain the methane. Rather than coming from living organisms, the methane could emerge from the olivine in a process called serpentinization. Chris Oze (Dartmouth) said, Id love to see bugs, but you cant just go on hope. You have to consider the geological options. Apparently, it would not require that much olivine to do the job, and now theres probably more around than first expected.
1Hamilton and Christensen, Evidence for extensive, olivine-rich bedrock on Mars, Geology, Vol. 33, No. 6, pp. 433–436, doi: 10.1130/G21258.1.
Even if Mars had lots of water, and even if its atmosphere was able to shield out the harmful radiation reaching the surface, it would not necessarily have had life. This just erodes the hopes of astrobiologists even further. About the only lively thing going on is the occasional dust devil passing by (see movie taken by Spirit).