Watch for the Recycle logo to find gems from the back issues!
Emergence of Genetic Code Touted 08/31/2009
In conclusion, our results show that the properties of amino acids and RNA can naturally impose a partially coded polymerization along RNA templates. We also found that the associated coding mechanism is remarkably robust against mismatches. When supplied with meaningful RNA sequences, translation systems of this kind should be capable of generating pools of proteins a small fraction of which will be functional. The feed-back action of these proteins on the translation itself may further increase its efficiency, allowing more codons to be added to its repertoire. In this evolutionary perspective, it can be speculated that a critical effect of emerging synthetases will be to establish only the [amino acid – tRNA] configurations that are fit for translation, a learning action that RNA alone cannot logically achieve.
1. Lehmann, Cibils and Libchaber, Emergence of a Code in the Polymerization of Amino Acids along RNA Templates, Public Library of Science One, 4(6): e5773; doi:10.1371/journal.pone.0005773.
OK, CEH volunteer police, time to take Apollos the Baloney Detector Dog and round up some more suspects (09/30/2007 commentary). These guys are not only charged with impersonating a scientist, but committing thought crime by being willfully ignorant and selling their ignorance publicly as science. Round up Science Daily as accomplices. Suggested sentence: watching Unlocking the Mystery of Life and reading Signature in the Cell. Public vagrancy at Rockefeller University is against the law. Ignorance is no excuse.Do fossil counts match sediment counts? The 08/25/2005 entry contains a lesson on how scientific papers can get the world wrong by calibrating each other on unreliable assumptions.
Your Throat Has Tasteful Antennae 08/30/2009
A similar signaling pathway is initiated by bitter compounds in taste cells and solitary chemosensory cells. Activated T2R receptors trigger the production of inositol 1,4,5-trisphosphate (IP3) and release of Ca2+ from internal stores. Ca2+ activates a nonselective cation channel, TrpM5, which depolarizes the cell and together with Ca2+ evokes the release of a transmitter that activates a target sensory neuron. In ciliated epithelial cells, bitter tastants signal through a similar pathway, but the functional outcome is an increased rate of ciliary beating.Their article did not mention evolution. The original article mentioned it once, but only to refer to a paper that claimed that primary cilia and motile cilia are evolutionarily related.
1. Shah, Ben-Shahar, Moninger, Kline and Welsh, Motile Cilia of Human Airway Epithelia Are Chemosensory, Science, 28 August 2009: Vol. 325. no. 5944, pp. 1131-1134, DOI: 10.1126/science.1173869.
2. Sue C. Kinnamon and Susan D. Reynolds, Cell Biology: Using Taste to Clear the Air(ways), Science, 28 August 2009: Vol. 325. no. 5944, pp. 1081-1082, DOI: 10.1126/science.1179180.
Cilia are examples Michael Behe cited as irreducibly complex structures that defy evolution and show evidence of intelligent design. In the 11 years since his first book Darwins Black Box (1996) first called attention to the amazing properties of cilia, much more was discovered about them. Behes second book The Edge of Evolution (2007) discussed them in much more detail. They are just as complex as the flagellar motor perhaps more. They are built by a complex system of molecular trucks that carry the building materials from base to tip. They use ATP to beat like oars. They coordinate their movements with neighboring cells. Now we find that they are also loaded with chemical taste sensors and connected into numerous signaling pathways. How are evolutionists going to explain all this? They cant. They dont. They just assume that natural selection can work any miracles required. Behe showed how this is contrary to evidence and common sense.How the Girl Evolved Fear of Spiders 08/29/2009
August 29, 2009 Todays Evolutionary Just-So Story is brought to you by New Scientist: Girls Are Primed to Fear Spiders. Once upon a time, while cavemen were out hunting and gathering, the women back home had to learn to avoid dangerous animals. David Rakison of Carnegie Mellon University put this all into evolutionary terms for the rest of us:
He attributes the difference to behavioural differences between men and women among our hunter-gatherer ancestors. An aversion to spiders may help women avoid dangerous animals, but in men evolution seems to have favoured more risk-taking behaviour for successful hunting.Rakison did not explain how a genetic mutation became fixed in the female of the species but was not expressed in the male. Nor did New Scientist object to the ostensibly Lamarckian explanation. Or was there some reasoned conspiracy that early men for millions of years all decided to mate with only the females who showed fear of spiders? That wouldnt make evolutionary sense. Nevertheless, the article continued, psychiatric help can assist those women who have trouble with their evolutionary arachnophobia.
Remember the T-shirts labeled Stupid and Im with Stupid? One wonders who is more stupid; the accused idiot, or the idiot who keeps hanging out with him. Rakison just told an incredibly stupid story, but New Scientist played Im With Stupid and didnt say a word about it. They even heard him mention evolutionary sense without pointing out the oxymoron. By playing along as if Stupid said nothing stupid, New Scientist wins Stupider Evolution Quote of the Week.The Darwinist hangout called Talk.Origins evolved over millions of seconds from a primitive Usenet ranting place into a nasty blog. Intelligently designed thinkers, however, may not be aware of a scholarly and civil rebuttal site called TrueOrigin.org. This website offers a large library of articles and papers answering the claims of the evolution camp. In fact, Ashby Camp, one of the organizers of TrueOrigin, has posted over 1,000 articles that support I.D. or Biblical creation science and critique evolution. The site also includes rebuttals to common TalkOrigins claims. TrueOrigin is a good place to look the next time you hear Darwinists blast away at creation science with some confident-sounding scientific claim, and need a scholarly comeback without the caricatures and personal attacks that are the trademarks of many anti-creationist sites. Use the handy search bar and you will have tons of reliable information at your fingertips.
Next resource of the week: 08/22/2009. All resources: Catalog.
Return of the Peppered Mice 08/28/2009
1. Linnen, Kingsley, Jensen and Hoekstra, On the Origin and Spread of an Adaptive Allele in Deer Mice, Science, 28 August 2009: Vol. 325. no. 5944, pp. 1095-1098, DOI: 10.1126/science.1175826.
Evolutionists get so excited about the silliest things. Even a staunch young-earth creationist like Ken Ham would yawn over this story. He readily shows in Powerpoint slides how all the variety of dogs could have easily arisen since the Flood by mutations and selection. In fact, the BBC News just reported that only three genes are involved in the wide variety of fur styles in dogs. The article said nothing about evolution.Five years ago: On 08/22/2004, creationists reported finding land dinosaurs buried with fish. A few days earlier there was a report of fossil plants found two miles under Greenland ice (08/16/2004). Meanwhile, evolutionists were struggling with the Ediacaran fossils (08/19/2004) and the African mammal fossil record (08/27/2004).
Whats Up With the Planets? 08/27/2009
1. Romeo and Turcotte, The frequency-area distribution of volcanic units on Venus: Implications for planetary resurfacing, Icarus, Volume 203, Issue 1, September 2009, Pages 13-19, doi:10.1016/j.icarus.2009.03.036.
2. Peter Huybers, Antarcticas orbital beat, Science, 28 August 2009: Vol. 325. no. 5944, pp. 1085-1086, DOI: 10.1126/science.1176186.
3. Kieffer, McFarquhar and Wohletz, A redetermination of the ice/vapor ratio of Enceladus’ plumes: Implications for sublimation and the lack of a liquid water reservoir, Icarus, Volume 203, Issue 1, September 2009, Pages 238-241, doi:10.1016/j.icarus.2009.05.011.
4. Hellier et al, An orbital period of 0.94 days for the hot-Jupiter planet WASP-18b, Nature 460, 1098-1100 (27 August 2009) | doi:10.1038/nature08245.
The history of astronomy and planetary science is a history of surprises and anomalies. Scientists build world views of how things should be, and how old they must be, and the real worlds keep astonishing them. Some people wont learn humility any other way.Feather Technology Resurrected in Printer After 40 Million Years 08/26/2009
August 26, 2009 A fossil bird feather from Germany still shows that melanosomes the cell organelles that produce iridescent colors in feathers are still visible after an alleged 40 million years. The structures were long thought to be remnants of bacteria that fed on the organic matter, but now are seen to consist of original feather material. Derek Briggs of Yale said, The discovery of ultra-structural detail in feather fossils opens up remarkable possibilities for the investigation of other features in soft-bodied fossils, like fur and even internal organs.
Meanwhile, engineers are starting to invent things based on the light-scattering properties of these structures that produce such bright colors on the feathers of birds and the wings of butterflies. New Scientist reported on the invention of magic ink by South Korean scientists. The ink works by the interaction of light with finely-patterned surface textures, rather than relying on pigments. Using nanoparticles, magnetic fields, resin and a fixer, they produce structural colors whose brilliance relies on the interference patterns produced by reflection off repetitive shapes. This is the same principle that produces the flashy colors on birds, insects, and sometimes even fossil feathers.
If you believe those fossil melanosomes have sat undisturbed for 40 million years, you probably also could believe that magic ink is really magical. Once irrationality is chosen, it knows no limits.A molecular scissors in your eye? Really? Its worth remembering from the 08/28/2003 entry how it works and why it allows you to see clearly.
Plants Use Hourglass Mechanism 08/26/2009
1. Wang, Czech and Weigel, miR156-Regulated SPL Transcription Factors Define an Endogenous Flowering Pathway in Arabidopsis thaliana, Cell, Volume 138, Issue 4, 738-749, 21 August 2009, doi:10.1016/j.cell.2009.06.014.
Micro-RNAs were only discovered in the last decade. This is another example of them in action with a functional regulatory role. Darwinians will undoubtedly have a tall tale ready to explain this, but systems biology, which sees an organism as a system of interrelated and coordinated parts (see 07/21/2009), needs Darwinian storytelling like a teenage face needs a zit.Cosmic Accounting Is Wildly Inaccurate 08/26/2009
August 26, 2009 Counting faint celestial objects is admittedly hard, but the task should be within the capabilities of expert astronomers. It is, after all, as simple as counting. So much theoretical work relies on accurate counts of whats out there, they need to get at least in the ballpark. Recent indications hint that their counts have been way off.
1. Meurer et al, Evidence for a Nonuniform Initial Mass Function in the Local Universe, The Astrophysical Journal 695 (2009) 765, April 10, 2009, doi:10.1088/0004-637X/695/1/765.
Here are more reasons to be wary of the confident statements of scientists. We can police them when their work produces a cell phone or printer that works or doesnt work, but how is a layperson to judge a cosmologists assertion that dark matter constitutes 95% of reality, or galaxies evolved from mergers of mini-galaxies? Most of us cant, so we tend to give them the benefit of the doubt and trust their superior knowledge. The training theyve gone through and the knowledge theyve acquired do command respect, but its dangerous to trust scientists overmuch. There are some things they just cannot know very well. In most respects they are just like normal people: mortal, fallible, and given to overconfidence.Does Evolution Produce Winners? 08/25/2009
August 25, 2009 Referees at UCLA are calling the shots in an unusual sport: the evolution game. Mammals, birds and fish swept the medals. The losers? crocodiles, alligators, and a living fossil reptile called the tuatara. According to the judges, the more the biodiversity, the more a group wins points; the more their species go extinct or remain unchanged, the more they lose points.
Science Daily reported the scores. Our results indicate that mammals are special, judged evolutionary biologist Michael Alfaro. He and his colleagues dished out the awards to all kinds of groups kangaroos, parrots, coral reef fish, songbirds, and most of the mammals. Crawling in last place were some of the reptile groups. The tuatara, which lives on isolated places on New Zealands south island, was a big loser. There may have been a few dozen species in its heyday during the dinosaur era. Now, only one species remains. In the same period of time that produced more than 8,000 species of snakes and lizards, there were only two species of tuatara, Alfaro said.
Its not clear, though, why the rich species are being judged winners.
That is one of the big mysteries about biodiversity, Alfaro said. Why these evolutionary losers are still around is a very hard thing to explain. They have been drawing inside straights for hundreds of millions of years. Its a real mystery to biologists how there can be any tuataras, given their low rate of speciation. They must have something working for them that has allowed them to persist. In species richness, these are losers, but in another sense, this highlights how unique they are. There are incredibly disparate patterns of species richness.Another mystery is the timing. The timing of the rate increases does not correspond to the appearance of key characteristics that have been invoked to explain the evolutionary success of these groups, such as hair on mammals or mammals well-coordinated chewing ability or feathers on birds, Alfaro continued. He admitted, We need to look for new explanations.
Winners and losers, right. OK. Alfaro is just using creative writing, we understand. Or is he? He seems to really believe in his criterion for judging winners: species richness. Why not the other way around?Seven years ago this month: In evolutionary geology, you can be off by 50% or more and nobody complains. See how that happened in the 08/29/2002 entry. The previous day (08/28/2002), a geologist disputed the consensus theory of the Permian extinction.
DNA Translator More Complicated Than Thought 08/24/2009
Ribosomes, which number in the millions in a single human cell, have long been considered the black boxes in molecular biology. We know what goes in and what comes out of ribosomes, but were only beginning to learn about what is going on in between said the studys principal investigator, Jamie Cate, UC Berkeley associate professor in chemistry and molecular and cell biology, and a faculty scientist at Lawrence Berkeley National Laboratory.Ribosomes are frenetically active in all cells of the body. They take the messenger RNA transcripts from the nucleus and translate them into proteins. Two large protein-RNA subunits make up the ribosome, but hundreds of other components (proteins, cofactors and RNAs) take part in the operation. The ribosome needs to faithfully translate the genetic code coming from the DNA in the nucleus.
The mRNA dutifully delivers that code to the ribosome, which somehow reads the instructions, or data tape, as each amino acid is added to a growing protein chain.How fast is the translation work? The article said a ribosome can translate 20 codons per second an amazing rate considering how many parts are involved, bringing in raw materials, catalyzing reactions and checking for errors. Scientists used to picture a simple ratchet mechanism that kept the data tape moving. Now, they have found at least four operations in the ratchet.
We suspect that the ribosome changes its conformation in so many steps to allow it to interact with relatively big tRNAs while keeping the two segments of the ribosome from flying apart, said Cate. Its much more complicated than the simple ratcheting mechanism in a socket wrench.Much more work will be required to learn how the mechanism works in detail. Interruptions to the ribosome (such as hijacking by viruses) can cause deadly diseases. For our health, and our sense of wonder at the nano-universe, we need to learn as much as we can about cellular machinery. Cate said, Im looking forward to producing a movie of a ribosome with enough resolution and enough frames per millisecond that we can see what is happening at a molecular level.... We still have a long way to go, but were working hard. The article said nothing about evolution, nor did the original paper in Science.1
Another paper in Science discussed in detail one of the many essential proteins that begins translation by forming the first peptide bond inside the ribosome.2 Called elongation factor P (EF-P), it has a special binding site inside the ribosome and binds to both major subunits, the transfer RNA, and other ribosomal components, indicating multiple specificities in its shape for the important function it performs. During its operation, it undergoes gymnastics: it binds to L1, which results in the largest movement of the L1 stalk that has been observed in the absence of ratcheting of the ribosomal subunits. This precise movement is essential for proper positioning of the amino acids so that the first peptide bond is formed as translation begins. Essential for cell viability, EF-P is found in archaeal cells; a similar enzyme, elF-5A, operates in eukaryotes. This paper also did not mention evolution, except to state that the active components of EF-P and elF-5A are extremely well conserved (i.e., unevolved).
For an excellent animation of the whole process of translating DNA into protein, see a video at the Signature in the Cell website. Stephen Meyers book of that name contains detailed descriptions of the ribosome, along with a great deal of historical, philosophical and mathematical background information that explains how these complex protein machines are behind the reach of chance.
1. Zhang, Dunkle and Cate, Structures of the Ribosome in Intermediate States of Ratcheting, Science, 21 August 2009: Vol. 325. no. 5943, pp. 1014-1017, DOI: 10.1126/science.1175275.
2. Blaha, Stanley and Steitz, Formation of the First Peptide Bond: The Structure of EF-P Bound to the 70S Ribosome, Science, 21 August 2009: Vol. 325. no. 5943, pp. 966-970, DOI: 10.1126/science.1175800.
Darwinists need to understand two things: (1) they are flat wrong about the oft-quoted dictum that nothing in biology makes sense except in the light of evolution. These scientists needed evolutionary theory like a swimmer needs a millstone around his neck. (2) The trend in discovery in molecular biology is undermining their credibility. It has been destroying evolution for decades.Are We at the Center of the Universe? 08/23/2009
August 23, 2009 An alternative cosmology that doesnt require dark energy may have the effect of putting the Milky Way near the center of the universe. Thats not the only interpretation, but it is being considered.
Space.com reported on work by mathematicians at UC Davis who solved Einsteins field equations without dark energy. If the big bang produced ripples in space-time, it could give the illusion that the universal expansion is accelerating without actual acceleration. One potential issue with this idea is that it might require a big coincidence, Space.com said: For the universe to appear to be accelerating at the same rate in all directions, we in the Milky Way would have to be near a local center, at the spot where an expansion wave was initiated early in the Big Bang when the universe was filled with radiation. Blake Temple of UC Davis acknowledged that it may look coincidental, but may reflect local conditions from our vantage point.
Still, National Geographic News seemed alarmed by the suggestion. This violation of the Copernican Principle (the idea that all observers in the universe get the same large-scale view) would be a hard pill to swallow. It will take more work before the evidence in favor of dark energy is overthrown. Space.com, on the other hand, called dark energy a hasty fix to an inconvenient truth in the 1990s the discovery that distant supernovae were dimmer than expected and must be accelerating from us. Temple argued that dark energy looked like a fudge factor. Thats why the UC Davis team tried to find an alternative cosmology without it. Meanwhile, as Science Daily reported, most astronomers are working hard to find the mysterious dark energy.
Dark energy and dark matter continue to be offered as occult phenomena that bind the consensus assumptions of cosmology together. They serve no explanatory function. What good is it to say that Mysterious Unknown Stuff (MUST) must exist? (02/28/2008). Any storyteller can say that to prove anything. Science is supposed to observe and measure things. Let them work on that before expecting us to accept their placeholder for ignorance much longer.For an all-around Intelligent Design website, check out Access Research Network. Under the hood, the site is loaded with resourcesbooks, DVDs, recordings, articles, blogs, FAQs, news stories and much more. You can find articles by the leading lights of the ID Movement, including Phillip Johnson, William Dembski, Michael Behe, Jonathan Wells and others, and you can order all their book in their online store. Some videos and audio recordings are available at ARN and nowhere else. They even have an ID Arts section where writers, painters and sculptors have submitted works based on ID themes. Drop by and check out all the things ARN has to offer.
Next resource of the week: 08/15/2009. All resources: Catalog.
Appendix to The Origin: Darwin Was Wrong 08/21/2009
Why does Charlie always get off with a tender wrist slap for his crimes? If creationists proposed a theory that led medical science astray for more than a century, they would be thrown in the intellectual dungeon without possibility of parole. Darwin gets away with murder. How did these guys use Darwins theory to do their research? Nothing about their work indicated that the appendix emerged from animals lacking one. They could not explain its origin by slight, continuous, small modifications. All they did was assume the Darwinian millions-of-years timetable. Charlies only help to them was like a defense lawyer telling a crook how to lie effectively in court.On the Origin of the Tumor; come again? A year ago a Darwinist was proposing cancer as evidence for evolutionary fitness. See the 08/13/2008 entry.
Planet-Makers Ask Miracles to Evade Death Spiral 08/21/2009
The rarity of planetesimals smaller than 100 km in diameter at the end of stage 1 seems to rule out the possibility that dust aggregates somehow made it across the metre-size barrier by gradually sweeping up material from their surroundings. Instead, objects must have grown very rapidly from sub-metre-sized pebbles into 100-km-sized bodies, possibly in a single leap.To get a handle on what he just said, he is asking people to believe that pebbles grew into planets as big as Los Angeles instantaneously. That makes the punctuated equilibria theory in biology look tame by comparison.
Chambers mostly optimistic article focused on the possibility of using current asteroid size distributions as a kind of archaeological probe into the early history of the solar system. Since most surviving asteroids appear to be at least 100 km in size (though this may be an observational selection effect), some models suggest it reflects the original size distribution after stage 1 of planet formation, which he describes thusly: Dust grains coalesced into planetesimals, objects of 1–1,000 km in diameter, through an unknown process. Philosophers and logicians might enjoy a hearty debate over the difference between a miracle and an unknown process; see, for example Hugh Mclachlans discussion about miracles and science in New Scientist.
Chambers relied heavily on four papers he cited, so we looked them up. One, by Blum and Wurm,2 was supposed to guarantee that dust grains will accrete into boulders (see the 12/05/2007 where Wurm was less sanguine about this). That paper started with a less optimistic tone: The formation of planetesimals, the kilometer-sized planetary precursors, is still a puzzling process. The authors examined all the latest experiments and models, and concluded that it is possible to get pebbles up to 10cm (if charged dust particles collide below 1 m/s), but after 1 meter in diameter is reached, erosional processes dominate. In frustration they said, Due to the experimental findings discussed in the previous sections, it seems unlikely to form planetesimals by direct collisional sticking. They attempted some special pleading by invoking unusual conditions to make the particles more sticky, but then appealed to miracles to get around the giant sucking sound: However done, the formation of kilometer-sized planetesimals has to happen fast, as large bodies possess a rather short lifetime owing to their effective inward drift motion. How fast? 100 years or less. Within a century of orbit, meter-size agglomerates will meet their fate in the stellar oven. Thus, any model explaining the growth over this meter-size barrier has to be extremely fast to prevent the radial drift of the macroscopic bodies.
In the next few paragraphs, Blum and Wurm engaged in more special pleading, searching for solutions, only to conclude, We now have a somehow detailed picture of how decimeter-sized dust aggregates form, but lack a self-consistent description of the further evolution of solid bodies to the planetesimal level. Chambers borrowed his optimism from the sections that talked about the pebbles, but had to admit a big problem remains with the city-sized planetesimals: However, the transition from pebble-sized dust aggregates to mountain-sized planetesimals is problematic and remains an unresolved issue, he said. This is unfortunate, because all subsequent stages of planet formation depend on it. Then he agreed: meter-size clumps are quickly destroyed by the death spiral and collisions with neighbors. For these reasons, it seems unlikely that objects will grow larger than about one metre as a result of the gradual accumulation of dust grains. Bad news for planet builders.
But then, Chambers renewed his optimism by referencing two recent models (2007, 2008), that though still in their infancy offer hope of a solution.3,4 Both models rely in disk instability to produce large clumps almost instantaneously. Johansen et al3 recognized the problem in their abstract: How this process continues from metre-sized boulders to kilometre-scale planetesimals is a major unsolved problem: boulders are expected to stick together poorly, and to spiral into the protostar in a few hundred orbits owing to a headwind from the slower rotating gas. Only by special pleading, invoking local concentrations of matter, were they able to model the formation of minor-planet-size bodies by processes faster than those trying to destroy them. Cuzzi et al4 also understood the destructive processes at work, e.g., disruption by the ram pressure of the differentially orbiting nebula gas. Their scenario which relied on turbulence and local knots of material, was stated as a work in progress: Localized radial pressure fluctuations in the nebula, as well as interactions between differentially moving dense clumps, will also play a role that must be accounted for in future studies. Neither of these scenarios seem ready for the imprimatur of scientific theory. Chambers recognized this. Ideally, one would like observational data to test their viability, he said. Indeed. This recalls Yogi Berras quip that in theory, theory and practice should agree, but in practice, they often dont.
So far, the models and experiments are pretty glum. Thats where Chambers turned a corner and talked archaeology. Referring to a paper by Morbidelli et al,5 he argued that present distributions of asteroids can tell us about original distributions of hopeful clumps in the early solar system. But to believe this, one has to believe that asteroids were born big (the title of their paper). Only by starting out with the assumption that the original clumps were 100km in diameter could they get the size distributions to match. Here is where Morbidelli et al stated the miracle in their words: This supports the idea that planetesimals formed big, namely that the size of solids in the proto-planetary disk jumped from sub-meter scale to multi-kilometer scale, without passing through intermediate values. While were having fun with miracles, lets pile them on: the initial planetesimals had to have sizes ranging from 100 to several 100 km, probably even 1,000 km they said. Now the dust particles leaped from centimeters to the size of continents. What they said next indicates that miracles must hereafter be included in planet-building scenarios: This result sets a new constraint on planetesimal formation models and opens new perspectives for the investigation of the collisional evolution in the asteroid and Kuiper belts as well as of the accretion of the cores of the giant planets.
Meanwhile, the giant sucking sound continues. In this months Astrophysical Journal, Fred Adams and Anthony Bloch6 wrote more about Type I migration the death spiral that conveys meter-size rocks to their doom. In many planet-forming disks, the Type I migration mechanism, driven by asymmetric torques, acts on a short timescale and compromises planet formation, they said. Only by appeals to luck could they get some clumps to survive the Type I migration problem If the disk also supports magnetohydrodynamics instabilities, however, the corresponding turbulent fluctuations produce additional stochastic torques that modify the steady inward migration scenario. How many survive? The results for any given set of boundary conditions is uncertain, they admitted, but with some expected disk properties they arrived at calculations of 1% to 10% might survive; however, the fraction of surviving planets decreases exponentially with time. They did not discuss the accretion problem. They only said that unless something happens fast, by chance or miracle, dont expect to find any planets left.
For public consumption, JPL issued a feature story explaining all this in laymans terms. Without blinking an eye, the story just stated that asteroids were born big, as if that is all you need to know. Evidence is now mounting that these small space rocks quickly jumped (or grew) in size from below one meter to multi-kilometer in size, the article said and thats how they evaded the death spiral. And what is that evidence that has been mounting? Its current asteroid distributions and computer simulations (and the realization that without starting big, they would be destroyed). The only way the simulators could keep the initial asteroids from obliterating themselves was by starting them out big pebbles that somehow quickly morphed into asteroids hundreds of kilometers in size. How that happened, exactly, they couldnt say. Once their growth spurt was over, these massive celestial bodies began an epoch-sized game of demolition derby as they orbited the sun. Over the eons, and with each extraterrestrial pileup, came fewer and fewer large asteroids a fragmentation process that continues to this day. Despite the modest sizes of asteroids today, the papers authors conclude that asteroids must have been born big.
New Scientist followed suit, blessing the papers that prescribed instant planets with positive vibes. This sudden leap scenario was blessed by John Chambers as a big step forward. The only one calling for a little more caution was Scott Kenyon of the Harvard-Smithsonian Center for Astrophysics. Its a nice story and they have a lot of evidence supporting their point of view, he said, but he cautioned, according to New Scientist, that it may have been difficult to complete planet formation in a reasonable time if there were no small asteroids at the outset. Onlookers might question whether leaping over a gap is really increasing our understanding of how we got here.
1. John Chambers, Planetary science: Archaeology of the asteroid belt, Nature 460, 963-964 (20 August 2009) | doi:10.1038/460963a.
2. Blum and Wurm, The Growth Mechanisms of Macroscopic Bodies in Protoplanetary Disks, Annual Review of Astronomy and Astrophysics, Vol. 46: 21-56 (Volume publication date September 2008) (doi:10.1146/annurev.astro.46.060407.145152).
3. Johansen et al, Rapid planetesimal formation in turbulent circumstellar disks, Nature448, 1022-1025 (30 August 2007), doi:10.1038/nature06086; Received 19 December 2006; Accepted 5 July 2007.
4. Cuzzi, Hogan and Sharif, Toward Planetesimals: Dense Chondrule Clumps in the Protoplanetary Nebula, The Astrophysical Journal, 2008 ApJ 687 1432-1447, doi: 10.1086/591239.
5. Morbidelli, Bottky, Nesvorny and Levison, Asteroids Were Born Big, Icarus (July 2009), doi:10.1016/j.icarus.2009.07.011.
6. Adams and Bloch, General Analysis of Type I Migration with Stochastic Perturbations, The Astrophysical Journal, 701 (August 2009) 1381, doi:10.1088/0004-637X/701/2/1381.
This has to be one of the most egregious lapses of scientific integrity in modern times. It is so bad, so full of special pleading and ad hoc speculation and storytelling contrary to the evidence, it is almost as bad as Darwinism and you know what that means. Elsewhere we have complained that appeals to the Stuff Happens Law are not scientific.Cambrian Explosion Still Explosive 08/20/2009In chapter 8 of his recent book Signature in the Cell, Stephen Meyer elaborated on the chance hypothesis and described when it is legitimate in scientific explanation and when it is not. Something that is one of the normal possible outcomes of a regular underlying process can be explained as an outcome of chance. But when a one-time, highly-improbable outcome that exhibits specified complexity is explained by chance (the Stuff Happens Law), it amounts to an admission of ignorance. Its a fancy way of saying, We dont know what happened or We cant explain it (p. 176).So when astronomers attribute the existence of planets to the luck of the draw, when our planet exhibits numerous cosmic coincidences that make life possible, they are using chance as an escape hatch to avoid clear evidence of design. Should we bless it with the honor of science?
August 20, 2009 Two new papers about Cambrian and Precambrian fossils did nothing to help soften the blow of the Cambrian explosion the sudden appearance of all the animal body plans in the geological blink of an eye. They essentially restated the problem for Darwin, who hoped that fossil discoveries would fill in the gaps where his required transitional forms were missing.
1. Laflamme, Xiao and Kowalewski, Osmotrophy in modular Ediacara organisms, Proceedings of the National Academy of Sciences USA, Published online August 17, 2009, doi: 10.1073/pnas.0904836106.
2. Desmond Collins, Misadventures in the Burgess Shale, Nature 460, 952-953 (20 August 2009) | doi:10.1038/460952a.
Soon to be a major motion picture! Darwins Dilemma: The Mystery of the Cambrian Fossil Record is being released next month by Illustra Media, the group that defended intelligent design in the cell with Unlocking the Mystery of Life and in astronomy with The Privileged Planet. This third film, a beautiful and powerful production, completes a trilogy of documentaries that are undermining Darwins grip on natural history and making a strong case for I.D. The Nature article above is a timely announcement. It did nothing to help protect Mr. Darwin from the impact of this new film. If anything, both articles took away whatever armor he had. The first article said that the Ediacarans were simple organisms with no transitional connection to the Cambrian animals. The second underscored the fact that virtually all animal groups alive today were present in Cambrian seas. Animals just appear, as if planted there, fully formed and loaded with biological information. In our 9 years of reporting, we have never seen any Darwinist solve this problem (search on "Cambrian explosion" in the search bar). We have only seen it grow worse for them: every new fossil discovery amplifies the concussion.Soft Squid Ink Sac Claimed to Be 150 Million Years Old 08/20/2009
August 20, 2009 The BBC News announced the discovery of a fossil squid with its ink sac still intact. The fossil, thought to be 150 million years old, was found when a rock was cracked open, revealing the one-inch-long black ink sac. The ink has been sent to Yale for analysis. An article on the Daily Mail UK shows a close-up of the ink sac and a drawing being made with the ink. Reporter David Derbyshire wrote, The odds of finding something as delicate as a squids ink sac intact after so long are put at a billion to one, but he did not explain how the odds were calculated.
Dr. Phil Wilby of the British Geological Survey (shown in a report on the Metro UK explained why this fossil was so surprising. They can be dissected as if they are living animals, you can see the muscle fibres and cells. It is difficult to imagine how you can have something as soft and sloppy as an ink sac fossilised in three dimension, still black, and inside a rock that is 150 million years old.
A group of old men were spinning their best yarns at a reunion, playing Can you top this? The prize went to old Charlie, who said, When I was a young scuba diver, I found an old Spanish galleon off the coast of Bermuda. It was dark and cold and looked downright haunted. So I slithered through an opening and got inside. Then I saw a faint glow and went toward it, and... The others leaned forward with anticipation. So what did you find, Charlie? asked Hubert. I went around a corner, down a hatch, and found this old lantern, and the light was still lit!To a Darwinist, the world is a free lunch. Is this a nutritious idea? Revisit the 08/07/2007 entry.
Evolution 2.0: Whats in the Upgrade? 08/19/2009
This mechanism, which I call combinatorial evolution, has an interesting consequence. Because new technologies arise from existing ones, we can say the collective of technology creates itself out of itself. In systems language, technology is autopoietic (from the Greek for "self-creating"). Of course, technology doesn't create itself from itself all on its own. It creates itself with the agency of human beings, much as a coral reef creates itself from itself with the assistance of small organisms.Arthur tried to make tie-ins to Darwin wherever he could. He has common ancestry, he has progress, he has a tree (or pyramid), he has building blocks, and he has emergence. He even has digital organisms producing logic circuits in silico. He fed a computer program a few simple logic circuits, some random mutations, and watched what emerged:
Once we launched the experiment we found, unsurprisingly, that most new random combinations failed to meet any needs. But after a few hundred steps, circuits started to appear that matched some elementary needs, and could be used as further building blocks. From these, more sophisticated technologies evolved. After about a quarter of a million steps, we found that the system had evolved quite complicated circuits: an 8-way-exclusive-OR, 8-way-AND, 4-bit-Equals even an 8-bit adder, the basis of a simple calculator.He did admit, of course, that the emergence of these technologies was predicated on the fact that he had defined needs for the program. These served as goals that could be rewarded. When we took away these simpler needs, these stepping-stone technologies did not emerge, and complex needs went unfulfilled.
How does Evolution 2.0 differ from Darwins kind of evolution? The primary difference is that combinatorial evolution is rare (but not absent) in biology. Living organisms, he argued, evolve primarily through incremental changes and selection. Technologies only emerge when pre-existing technologies combine in new ways. Darwinian variation and selection kick in only once a technology exists, he said. For what really counts, the formation of new species in technology, combinatorial evolution holds sway.
One phrase notably missing from his theory is intelligent design. It would seem ID would play heavily in any theory of technology, but references to human intelligence, goal-directed behavior, and purpose were referred to obliquely at best.
It sometimes seems inconceivable that such shallow logic can pass for scholarship and scientific reasoning these days. Someone needs to inform poor Dr. Arthur that he cannot derive Evolution 2.0 from Darwinism. What he calls Ev 2.0 is nothing more than human intelligent design. Humans are not omniscient. They dont create radar and iPhones ex nihilo. But they learn, they create, and they choose. They know what they want, and they can move mountains and organize materials to get it, once they find a method that works. So yes, there will be elements of progress in human technology. When the Sicilians invented the catapult, a way to inflict damage on an enemy city from a safe distance, the Romans were quick to improve on it. These were all purposeful actions by intelligent beings capable of arranging materials for ends. What on earth does that have to do with Darwinian mutation and selection? Nothing. Even the Victorian notion of progress in biology had a serious falling out in the 20th century. Our perceptive readers surely noticed Arthur cheating in his software. Just like the digital evolution charlatans, he held the strings of his marionettes so that they would do his own purposeful bidding.Faint Young Sun Paradox Resolved 08/18/2009
August 18, 2009 For decades, astronomers and geologists have worried about a paradox. Stellar evolution theory claims sunlight on the early earth would have been 20-30% dimmer than it is today, but geology shows the oceans were liquid in the earliest (Archean) rocks. For that matter, so does the book of Genesis, but that record is not usually allowed in scientific discussions. Anyway, how could the earth remained warm enough under a dim sun to keep the oceans from freezing? This has been called the faint young sun paradox. A new answer came from researchers at the Tokyo Institute of Technology and University of Copenhagens Department of Chemistry, published this month in PNAS.1
The solution involves carbonyl sulfide produced by volcanoes. Matthew Johnson of the Copenhagen group explained the scenario in the Universitys press release, The greenhouse gas that saved the world. (See also Science Daily.) Carbonyl sulfide (OCS) is the perfect greenhouse gas, he said. We estimate that a blanket of Carbonyl Sulphate [sic; sulfide] would have provided about 30 percent extra energy to the surface of the planet. And that would have compensated for what was lacking from the sun. Very convenient. But why, then, is OCS not a problem today, with all our concern about greenhouse gases and global warming? Because oxidizing conditions (free oxygen of carbon dioxide in the atmosphere) destroy OCS. In other words, OCS was plentiful when it was needed to warm the early earth, but gradually was depleted as life pumped oxygen into the atmosphere. Instead of producing the warming OCS, it would have produced cooling sulfates. This could have led to a proposed snowball earth period before the sun became warm enough to melt the oceans again. Johnson tied this in to modern political fears about global warming: Our research indicates that the distribution and composition of atmospheric gasses swung the planet from a state of life supporting warmth to a planet-wide ice-age spanning millions of years, he said. I can think of no better reason to be extremely cautious about the amounts of greenhouse gasses we are currently emitting to the atmosphere.
The story is messier inside the scientific paper. The authors needed to thread a needle getting the right balance of factors and assumptions to make this work. Heres a taste of it (the scientific jargon can be overlooked to see the amount of hedging and special pleading going on):
When the column density [atmospheric gas] increases, three types of behavior are seen. First, an increase in CO2, H2O, NH3, CS2, or O2 concentration produces a similar negative shift of 34[epsilon] and 33E (Fig. 2), because these gases generally attenuate wavelengths shorter than 202 nm (Fig. 1). In contrast, O3 and OCS shielding shift 34[epsilon] and 33E toward more positive values because they attenuate wavelengths longer than 202 nm. In contrast, an increase of O3 or OCS has the opposite effect. Finally, SO2 self-shielding produces increasing 34[epsilon] and decreasing 33E. The previous estimate of isotope effects in SO2 photolysis from self-shielding found an increasing trend in 33E (12) that is opposite to our result. The reason for the difference may be because the spectra of the isotopically substituted species were approximated by shifting the absorption peaks of the natural abundance SO2 spectrum using a set of isotope-dependent frequency shifts. These shifts were based on vibrational wavefunctions calculated using a single ab initio SO2 excited potential energy surface. However, SO2 has a score of electronic states in the relevant energy region with multiple curve crossings, giving rise to the complicated pattern seen in the experimental results. For example, three vibronic peaks of the three isotopologues are found between 200 and 205 nm (Fig. S1). First 33SO2, then 34SO2, and then 32SO2 has the highest peak intensity. Whereas the isotopologues peak positions shift linearly with distance from the band origin, the peak intensities, widths, and profiles of the vibrational structure change in a complex mass independent manner. A theoretical description of the origin of these isotope effects awaits further study....It appears clear there is much not well understood about the molecules themselves, let alone their complex, interacting effects on global warming.
Further down in the paper, they compared other greenhouse gas candidates. Carbon dioxide doesnt work, because it would require too much of it 30%, far more than present today to produce the 30% warming needed, and it also would ruin the isotopic sulfur signal in the geological record. Ammonia doesnt work, because it would photolyze too rapidly. Methane doesnt work, because the haze would have cooled rather than heated the planet. OCS (carbonyl sulfide) seemed the only candidate left standing. It would allow higher concentrations of ammonia (given that the early atmosphere was reducing), or of methane, if OCS were present in concentrations of 10 parts per million or more. Even so, the model called for more special pleading and future research:
The atmospheric models presented here are an initial attempt at predicting the [delta]33S value of aerosol sulfate for a set of atmospheric shielding scenarios. Further model studies are needed to evaluate the relative contributions of the greenhouse gases. Nonetheless, a CO-rich reducing atmosphere would have resulted in OCS-rich conditions when volcanic sulfur input was high enough. Moreover, such an atmosphere is so far the only one that can explain both the preservation of MIF [mass-independent fractionation of sulfur isotopes] and the negative [delta]33S values of Archean sulfate deposits. Hence, UV-shielding and the greenhouse effect of OCS should be considered for any model of the Archean atmosphere. These results are qualitative and remain to be confirmed by more advanced models of the Archean atmosphere and further laboratory studies.The tone of these paragraphs sounds much more reserved and tentative than the press release that triumphantly pronounced carbonyl sulfide as the greenhouse gas that saved the world.
1. Ueno, Johnson et al, Geological sulfur isotopes indicate elevated OCS in the Archean atmosphere, solving faint young sun paradox, Proceedings of the National Academy of Sciences USA, online August 17, 2009, doi: 10.1073/pnas.0903518106.
Once again, we have revealed to you the huge discrepancy between the hedging and fudging found in scientific papers and the victory speeches in the press. Beware of bluffing from scientists. Always look at the data they base their conclusions on. But even the paper announced in the title that this model solves the faint young sun paradox. It did no such thing. It was a like a string of ifs followed by a then maybe. One of the authors stood on that quicksand and preached to us about global warming. Well, if the earth goddess was smart enough to save the world when our star was weak, why isnt she smart enough to protect the earth from carbon-belching humans? Oh, but of course. It wasnt Gaia; it was Lady Luck.Is It OK When Astronomers Sell Stars? 08/17/2009
August 17, 2009 Most people have heard the ads for companies that sell you a certificate for a star they will name after you. Professional astronomers have usually been quick to discourage people from falling for the schemes that have no professional or international authority for naming stars (for instance, see this article on Wired.com). But now, according to New Scientist, an international consortium of astronomers with the Kepler Mission will be selling stars to raise money for data analysis from the spacecraft:
There are plenty of phony name-a-star things on the web, but I think we were the first scientists to use this sort of model for fundraising, and as a public outreach tool, says project leader Travis Metcalfe of the National Center for Atmospheric Research in Boulder, Colorado. Were trying to educate people about what the Kepler mission does, and to get them excited about the quest for other Earths.Since Kepler has 100,000 stars in its field of view, they hope to raise a million dollars at $10 a star to pay scientists salaries and bring them together at conferences. In return, the donor gets his or her name attached to one of the stars on Google Sky. The program was named Pale Blue Dot after Carl Sagans book of that name.
A fly on the wall listened in to the astronomers cooking up this scheme.When calculating the number of habitable planets, dont forget the sunscreen. Read about the factor SETI advocates forgot in the 08/15/2006 entry.
Twitter the ET Bandwidth Wagon 08/16/2009
Notice again that the secular SETI crowd still believes in miracles. Their word for a miraculous event is that something emerged. It doesnt matter to them that mathematics shows a chance origin of life is impossible. It just emerged, o ye of little faith.Political columnist Ann Coulter is normally out mercilessly satirizing liberals, but in her book Godless: The Church of Liberalism she spent four chapters discussing science. With her trademark wit and sarcasm, she handily dismantled Darwinism. This shows that dismantling Darwinism is so easy, even a journalist can do it (if he or she is objective; i.e., has not sworn allegiance to Darwin in advance).
Liberals hate science, Coulter says; they only use it to advance their agenda by very selective evidence and ignorance of common sense. After showing how liberals misuse and ignore scientific evidence (illustrated by their stands on criminal justice, education and abortion), Coulter unveils their absolute worst abuse of science: Darwinian evolution. Surprisingly, liberals almost ignored this major section of her book, concentrating their venom primarily on Coulters less-than-flattering portrayal of female victims used by the left to fight President Bushs war on Iraq.
If you dont need a heavy-duty book loaded with scientific terms, and want to understand scientists obsession with Charles Darwin, Godless is a good choice. Coulter reveals and explains the tight connection between Darwinism and liberal ideology. Her arguments are as unbeatable as they are humorous. The book is easily available in mall bookstores or at Amazon.com. For multitasking enjoyment, get the book on CDs (read by the author) and listen in the car while commuting. Just dont laugh so hard, or get so angry at the Darwiniacs, that you lose your concentration and earn a Darwin Award (i.e., remove yourself from the gene pool as unfit).
Next resource of the week: 07/25/2009. All resources: Catalog.
Fire Technology Began Much Earlier Than Believed 08/14/2009
This use of fire as an engineering tool is an early step in the evolution of means by which humans could more effectively control their environment. Heat treatment in Africa appears at roughly the same time as widespread evidence for symbolic behavior, signaling the development of increasingly complex cognitive ability. By enabling the manufacture of more efficient tools, heat treatment may have played a key role in allowing early modern humans to spread rapidly from the relatively benign environments of southern Africa into the colder, more hostile environments of Europe. The Neandertals in Europe apparently lacked this technique, perhaps giving the early modern humans an evolutionary advantage as they moved into Eurasia.But wait; if humans in Africa had this ability 164,000 years before the present, the next signs of symbolic ability appear starting around ~71 ka, (71,000 years), according to the paper. Thats a gap of 93,000 years nearly 10 times the length of all recorded history. Are they claiming that humans could work stone with heat on purpose, and shape spear points for hunting, but never learned anything else for nearly 100 millennia? Apparently so. And so did Science Daily, the BBC News and National Geographic News, without blinking an eye.
Brown told National Geographic the significance of this sophisticated technology for the story of human evolution. These people were extremely intelligent, he said. These are not the image of the classic cavemen, of brutish people that are stumbling around the landscape and, in spite of themselves, surviving. These are the people that [may have] even colonized the rest of the world. NG only quoted one anthropologist, John Shea of Stony Brook University, who did not think it to be evidence of a transformative event that showed modern cognitive abilities had arrived. Nevertheless, Shea praised the study, saying it will inspire people to seek out other heat-treated stone tools undetected in the African record. Shea also declined to explain what a transformative event would look like that could turn an upright ape into a thinking man.
1. Brown et al, Fire As an Engineering Tool of Early Modern Humans, Science, 14 August 2009: Vol. 325. no. 5942, pp. 859-862, DOI: 10.1126/science.1175028.
2. John Webb and Marian Domanski, Paleontology: Fire and Stone, Science, 14 August 2009: Vol. 325. no. 5942, pp. 820-821, DOI: 10.1126/science.1178014.
Dear readers, what more evidence do you need that the Darwin-drunk evolutionary shamans have gone completely nuts? Think about this. (Prerequisite: dont be automatically compliant and submissive when a scientist says something.) They are asking us to believe that our ancestors had (1) all the bodily equipment that you do (including brain size), (2) the ability to learn technology and learn from experience, (3) the foresight to understand that heat-treating stones gave improved performance in tools, which they were skilled at making, (4) were extremely intelligent, (5) created decorative objects to adorn themselves, indicating aesthetic ability, and (5) had the ability to colonize the world. OK so far? Now, get this: they want you to believe that these full-size, full-brained, fully-modern people sat around in caves and hunted game for 93,000 years never learning to talk to each other, never learning agriculture, never attempting to build a city, never learning to ride a horse, and never inventing anything better than sharp rocks. On top of that nonsense, then they want you to believe that another 50,000 to 60,000 years passed by before the first idea of agriculture and civilization popped into their intelligent heads.Brett Miller explains how NOMA works
in a perceptive cartoon at Evident Creation.
Comet-Ocean Theory Gets Another Splash 08/13/2009
We citizens just sit here passively, listening to our shamans tell their stories of the history of the world. It has become like Muzak to our ears. We dont even pay attention to it. We may smile when one of them comes up with a witty line, like we may sip a piece of the impactors every time we drink a glass of water. We even enjoy the manufactured controversies that seem to pit one shaman against another, knowing that its all rigged, and the outcome is not in doubtEmperor Charles DearOne will always be vindicated, no matter what. Phrases from the epic tale The Darwinian Nights, like Late Heavy Bombardment and building blocks of life are so familiar, they go in one ear and out the other. It has the comforting lilt of a presumed truth. Snap out of it.The commentary of the 08/10/2005 entry about the anti-ID wars contains a historic poem by James Clerk Maxwell worth understanding. Its biting satire was written in 1874 when Maxwell perceived the materialists were taking over the science establishment. Maxwell ridiculed the rampant speculation going on, and argued in verse that the mind, will and emotions could not be subsumed within their materialistic worldview.
Evolution of the Knuckle Head 08/12/2009
The results of this study show that researchers need to reevaluate all posited knuckle-walking features and reconsider their efficacy as indicators of knuckle-walking behavior in extant and extinct primates. In this context, the absence of several posited knuckle-walking features in extant knuckle-walkers (and the presence of some of these features in nonknuckle-walkers) makes it difficult to argue that there is unambiguous evidence that bipedalism evolved from a terrestrial knuckle-walking ancestor. Instead, our data support the opposite notion, that features of the hand and wrist found in the human fossil record that have traditionally been treated as indicators of knucklewalking behavior are in fact evidence of arboreality and not terrestriality....It seems clear that evidence is no longer required for the National Academy to publish a suggestion. Whether others allowed in the debate will find their suggestion reasonable and likely remains to be seen. Ironically, in Nature this week,2 Jonathan Marks (U of North Carolina at Charlotte) wrote a letter arguing that Ape and human similarities can be deceptive. Some features can be overenthusiastically interpreted, he said, that are not directly homologous. He was talking about behavioral studies, but then he said it can also apply to comparisons of feet: They are similar, and are descended from a common ancestral structure, but they are by no means the same.
But then Marks revealed something that shows that opposite interpretations can be used as support for Darwin. He said that one can argue differences instead of similarities and still be a loyal Darwinian maybe a better one:
A genuine Darwinian approach to primate behaviour may have to acknowledge that the brains of apes (and their capabilities) may simply be different from our own, like their feet. Evolution, after all, is the production of difference. If one scholar acknowledges the adaptive divergence that has occurred between a human and a chimp over 7 million years or so of separation, and another insists that they are the same, then who is really in denial of evolution?Is it even possible to deny evolution if that is the game plan? Opposite evidence and opposite interpretations can both be used to show one is a good Darwinian. How can a Darwin skeptic even get a foothold in the debate?3
1. Tracy Kivell and Daniel Schmitt, Independent evolution of knuckle-walking in African apes shows that humans did not evolve from a knuckle-walking ancestor, Proceedings of the National Academy of Sciences, August 10, 2009, doi: 10.1073/pnas.0901280106.
2. Jonathan Marks, Ape and human similarities can be deceptive, Nature460, 796 (13 August 2009) | doi:10.1038/460796a.
3. Maybe only by pointing out that a theory that can be argued with opposite evidence and opposite interpretations is not a scientific theory at all it can explain anything, therefore explains nothing.
What a sad state of affairs when any dumb idea can get published by the National Academy and then given a favorable review by popular science reporters. You thought the thing that differentiated science from other speculations was the demand for evidence. That, sad to say, is long gone. Now, you just have to belong to the in crowd (i.e., those who have not been Expelled). Then you can put forward any suggestion you want as long as it never questions the totalitarian dictator of the world, Charles DearOne.Protein Function: Its All in the Fold 08/11/2009
August 11, 2009 Most chemical reactions involve atoms or molecules bumping into one another and exchanging electrons. Proteins, by contrast, derive their immense functional repertoire from their shapes. Several recent studies explore the amazing potential for strength, motility and catalysis that derives from the way proteins fold.
In living systems, biopolymer catalysts have evolved to accelerate specific biologically relevant transformations. In contrast, synthetic catalysts must often be designed for nonbiological transformations to be performed in abiotic solvents, pH regimes, temperatures, and pressures that are incompatible with retention of biopolymer structure and activity. Proteins, however, rely on a limited repertoire of amino acid monomers and require substantial chain lengths to achieve significant structural organization.Its clear that they did not attempt to explain how biopolymer catalysts have evolved. They also did not discuss the remarkable ability of living systems to distinguish between left- and right-handed members of chiral molecules a feature absent from non-living systems. Their work, instead, demonstrates that achieving enantioselectivity by artificial means requires intelligent design.
1. Ronald S. Rock, A new direction for titin pulling, Proceedings of the National Academy of Sciences August 5, 2009, doi: 10.1073/pnas.0906989106.
2. Maayan, Ward and Kirshenbaum, Folded biomimetic oligomers for enantioselective catalysis, Proceedings of the National Academy of Sciences, August 10, 2009, doi: 10.1073/pnas.0903187106.
A simple study of probability (see online book; also Stephen Meyers new book Signature in the Cell) would have convinced the NYU team that enantioselective catalysts made of substantial chain lengths could not have evolved. Living things needed the selectivity before life was even possible. That would leave only chance as a means getting the catalysts in the first place. Is that even conceivably possible under ideal conditions? Read chapter 3 and see.Crow Fulfills Aesop Story 08/11/2009
August 11, 2009 The fabled intelligence of the crow has been tested, and the crows passed. Bird and Emery tested an old Aesop fable and were amazed:
In Aesops fable The Crow and the Pitcher, a thirsty crow uses stones to raise the level of water in a pitcher and quench its thirst. A number of corvids have been found to use tools in the wild, and New Caledonian crows appear to understand the functional properties of tools and solve complex physical problems via causal and analogical reasoning. The rook, another member of the corvid family that does not appear to use tools in the wild, also appears able to solve non-tool-related problems via similar reasoning. Here, we present evidence that captive rooks are also able to solve a complex problem by using tools. We presented four captive rooks with a problem analogous to Aesops fable: raising the level of water so that a floating worm moved into reach. All four subjects solved the problem with an appreciation of precisely how many stones were needed. Three subjects also rapidly learned to use large stones over small ones, and that sawdust cannot be manipulated in the same manner as water. This behavior demonstrates a flexible ability to use tools, a finding with implications for the evolution of tool use and cognition in animals.Science Daily reported on the story. The BBC News report includes a video of a rook quickly solving the problem after examining the situation and appearing to think about it.
1. Christopher David Bird and Nathan John Emery, Rooks Use Stones to Raise the Water Level to Reach a Floating Worm, Current Biology, 06 August 2009, doi:10.1016/j.cub.2009.07.033.
Aesop may have been a better naturalist than we expected. OK, here are the implications for the evolution of tool use and cognition in animals. Humans evolved from crows, and apes are degenerate humans who drank too much Old Crow for millions of years.Turn your mind in knots by pondering whether evolution evolves. See the 08/04/2004 entry.
Dont Just Sit There; Do Something 08/10/2009
Most of us probably dont come anywhere near that point. Wherever that point is for your body type, you should get closer to it. With your doctors supervision, make some changes to up your activity level. Your body was made to thrive in the outdoor environment for which it was created. It goes with the territory. Walking hills and valleys keeps those systems humming.Did Evolution Create Genetic Proofreading? 08/09/2009
August 9, 2009 Protein manufacture in the cell is such a critical operation, there are numerous error-checking mechanisms the cell uses to get it right. One of the most amazing is the careful association of DNA codons with amino acids, and the proofreading or spell checking that ensures fidelity. How could spell checking evolve?
Science Daily announced that Scientists Find Early Evolution Maximized The Spellchecking Of Protein Sequences. Sounds interesting. What did they find? The answer should be in the original paper in Science.1 There, Guo, Schimmel and others from Scripps Institute claim that they found homologies between the spell-checking domains of one of the enzymes responsible for linking transfer RNA (tRNA) codons with the appropriate amino acid. In this case, it is the aminoacyl-tRNA synthetase for alanine, called AlaRS. This particular synthetase has to distinguish alanine from two other similar amino acids, glycine and serine. It does this through the use of additional factors or domains called AlaXps that provide functional redundancy by capturing mischarged tRNAAla molecules that escape the embedded editing activities of AlaRSs.2 In addition, a linker called C-Ala binds the error-correcting domains together.
The team found that most of the domains of AlaRS are highly-conserved (i.e., unevolved) in all three kingdoms of life including the modular arrangement of AlaRS itself. That makes sense, else we would all be dead. In their wording, strong selective pressure retains these editing activities throughout evolution. But they did find C-Ala is only loosely conserved. From this they wove a story of how this spell checking arrangement came to be:
This phylogenetic analysis implies that all three forms of AlaXp evolved in the ancestral community. This phylogeny also suggests that AlaXp-II is derived from AlaXp-I. The editing domain of ThrRS is closest to AlaXp-I, thus suggesting an early separation that split the original editing enzyme into two different specificities, one for tRNAThr and the other for tRNAAla. Most importantly, the phylogenetic analysis indicates that the editing domain of AlaRS appeared concurrently with the ancient, most-developed, and largest free-standing editing enzyme, the C-Ala–containing AlaXp-II. Thus, C-Ala may have been instrumental in bringing together editing and aminoacylation domains on one tRNA to ultimately (through fusion) create AlaRS (fig. S6).In the simpler words of the Science Daily summary, the results show that two separate functionsalanine adding and editingwere joined together in a single enzyme during early evolution, in a way that greatly enhances these activities. The findings provide a glimpse into how enzyme functions have evolved.
1. Guo, Chong, Beebe, Shapiro, Yang and Schimmel, The C-Ala Domain Brings Together Editing and Aminoacylation Functions on One tRNA, Science, 7 August 2009: Vol. 325. no. 5941, pp. 744 - 747, DOI: 10.1126/science.1174343.
2. There are three classes of AlaXp. Three types (Ia, Ib, and II) of free-standing genome-encoded AlaXps are widely distributed in all three kingdoms of life and act in trans to clear tRNAAla mischarged with Ser or Gly (7, 8, 31, 32). Type Ia AlaXp lacks the Gly-rich motif near the N terminus of the editing motif of type Ib and type II AlaXps (33). However, unlike types Ia and Ib AlaXps that are composed of just the editing domain, type II AlaXp has the C-Ala domain (Fig. 1A).
They found no such thing. They found living organisms with spell-checking and proofreading that works on a phenomenally accurate scale much better than the output of professional typists. Then they made up a story out of thin air about how the parts of the machinery were brought together during an evolutionary history that was never to be doubted. They ignored the error catastrophe that would have brought life down to a crash before the proofreading was already working. They expected us to believe that selective pressure acts like a designer substitute to work miracles. And they expected us baloney-detectors to swallow their line as if they found how all this came about. Dont fall for it any more than if they compared engine parts from a Mazda and a Ford and told you they found a glimpse of how they emerged from the dirt, or if they compared the spell checking algorithms in Internet Explorer and Firefox and described how they had a common ancestor in an earthquake.Paper View: A Geology Paradigm Suffers a Paradox 08/07/2009
August 7, 2009 A pair of geologists found a paradox in a paradigm. That paradigm is the belief that ancient ocean levels rose and fell in cycles as ice sheets retreated and advanced, and the cause of the cycles was periodic changes in earths orbit. They modeled this process and couldnt get it to work. They couldnt get the sea level to rise as high as the evidence shows it did. And it would have required enormously high fluctuations in atmospheric carbon dioxide to get rid of the ice sheets each time.
Horton and Poulsen [U of Michigan, Ann Arbor], writing in Geology,1 called their paper the Paradox of late Paleozoic glacioeustasy. Time out for definitions: eustasy refers to global sea levels as measured from a static reference (like the center of the earth); glacioeustasy is, by extension, the global sea level during ice ages. In theory, the earths cyclic orbital variations over long time scales2 force ice ages to advance and retreat. In the Paleozoic, when the land terrain was generally lower, large ice sheets could form and melt over vast areas, producing cyclothems, or sedimentary deposits alternating between strata buried under water (subaqueous) and under air (subaerial). Sounds plausible, but how accurate is this picture scientifically? How well is it understood? After all, Horton and Poulsen began by saying that this paradigm has been used to explain our planets past: Models of Euramerican cyclothem deposition invoke orbitally driven glacioeustasy to explain widespread cyclic marine and nonmarine late Paleozoic sedimentary sequences. Presumably, a geologist doesnt just want to catalog the rocks, but explain how they got that way.
Things get messy real quick when fitting the field data into the paradigm. It appears global sea levels would have had to alternate by 100 meters or more to produce the beds. Their model, however, couldnt get the water to rise more than 25m. And only by adjusting the model with enormous fluctuations in atmospheric carbon dioxide could they get the ice sheets to melt away. These results present a potential paradox: while our model is able to simulate widespread Gondwanan glaciation, it is unable to reproduce significant orbitally driven glacioeustatic fluctuations without very large magnitude carbon cycle perturbations.
Their Introduction describes the paradigm: from 326 to 267 million years ago (mya), conditions primed the late Paleozoic paleoenvironment for glaciation.3 The continents were joined into a supercontinent called Gondwana, and carbon dioxide levels were low. Ice sheets formed and grew when orbital changes cooled the atmosphere; they retreated when warm times returned. The ice sheets of Gondwana left not only direct geological evidence of continental glaciation, but also indirect sedimentary signatures of their waxing and waning, they said. The presence of North American deposits that appear cyclic has been used to infer that late Paleozoic depositional environments were largely controlled by glacioeustasy. If that is the explanation, though, the fluctuations in global sea level were very large: up to 200m much larger than the inches or feet that alarmists of global warming warn us about today. Can sea level changes of that magnitude be forced by orbital cycles? Thats what Horton and Poulsen wanted to find out. Remember, the plausibility of a hypothesis has nothing to do with its credibility, and vice versa. Science wants to run the numbers.
The next section of the paper described the methods and results of their model. A global model, of course, requires dependence on other models, like at atmospheric general circulation model (GCM) ... coupled to a three-dimensional ice sheet model. They also had to rely on models of topographic elevations of a continent Gondwana that no longer exists.4 And, they played with carbon dioxide levels consistent with proxy estimates. The growth and extent of the resulting ice sheets reflected the level of atmospheric CO2 as expected, but they couldnt get it to melt except at the higher concentrations. They said increases in excess of 2000 ppm were required to cause substantial melting of Gondwanan ice sheets. (Note: current levels are about 384 ppm amidst all the hubbub about global warming.) In addition, the causative factors seemed inadequate. The dynamic response of continental ice sheet volume to our prescribed transient orbital insolation variations is modest, they said. That means that orbital forcing does not have that great an effect. It certainly did not produce global sea level rises of 100 meters or more. And it contradicts other studies that claim to find correlations between recent ice ages and orbital periods, like a recent paper in Science.5 (See summary on Science Daily).
In their discussion and conclusions, they evaluated possible resolutions of the paradox. Perhaps Orbital changes were linked to the carbon cycle through a positive feedback like they believe was operative during the greener Pleistocene epoch. Even so, the model required extreme concentrations of carbon dioxide to get the ice sheets to retreat completely between cycles (ablation). But what in nature would generate such high concentrations in the Paleozoic?
Our simulation of late Paleozoic glacial conditions presents a paradox. While our simulation of large (>100 m sea-level equivalent) continental ice sheets is in good agreement with sedimentological evidence of Gondwanan glaciation, our orbitally driven ice-volume changes are ~10 m, much smaller than the late Paleozoic glacioeustatic variations implied by both cyclothems and isotopic analyses. The absence of significant continental-scale ice sheet ablation in the face of changing orbital insolation poses a significant challenge to our current understanding of late Paleozoic ice sheet dynamics.More bad news. What does this do to the more recent Pleistocene glacioeustasy theory? It was supposed to be better understood because ice core data admittedly shows some agreement with orbital and atmospheric factors.6 But even here, The cause of Pleistocene glacial-interglacial cycles is still debated, they said, but is generally thought to be due to a combination of orbitally controlled insolation forcing and greenhouse gas fluctuations. But those are the same factors used for the Paleozoic model. They didnt work there. How do we know the same factors would produce Pleistocene cycles?
To save the Paleozoic paradigm, they appealed to ignorance. Unlike the Pleistocene, late Paleozoic pCO2 levels are not well constrained. Maybe somehow the levels fluctuated wildly back then; however, the temporal resolution of this record remains coarse, so there is no way to know with any accuracy. Furthermore, a mechanism by which atmospheric pCO2 concentrations could repeatedly fluctuate by ~2000 ppm over orbital time scales is not known. Methane clathrates under the sea could discharge a great deal of greenhouse gas quickly; However, the long recharge rate of clathrates would prevent repeated discharges on orbital time scales. So that idea is no help. Is it possible that the sea levels rose and fell independent of carbon dioxide concentrations? An energy balance model (EBM) reproduced the cycles, they noted. But then they discounted it:
Simulations using an energy balance model (EBM) coupled to an ice sheet model indicate that orbital insolation variations alone can produce repeated ~100 m sea-level fluctuations (Hyde et al., 1999). We cannot say with certainty why our results differ from those using an EBM; however, we suspect that differences in the paleoboundary conditions and/or the treatment of ablation and precipitation rates in the calculation of mass balance over the ice sheet might be responsible. For example, unlike our model where precipitation over Gondwana is explicitly calculated, EBM precipitation rates are based on prescribed modern precipitation rates (Hyde et al., 1999). Predictions of equilibrium ice sheets made using GCM–ice sheet models with fixed (nontransient) orbital conditions have also been used to infer large late Paleozoic glacioeustatic fluctuations (of as much as 245 m; Horton et al., 2007). However, our new results indicate that these estimates are too large. The reason is straightforward: in the fixed-orbit experiments, there is no preexisting ice sheet to influence the final mass balance. In contrast, in our transient experiments, the preexisting ice sheet (simulated during the previous orbital step) has a substantial influence on local conditions due to temperature-elevation and ice-albedo feedbacks. Orbitally driven insolation changes are not large enough to overcome these local ice sheet effects; consequently, orbital changes produce only small ice-volume fluctuations.Time to assess the situation. Horton and Poulsen believe they experimented with a reasonable model, but they could not replicate the paradigm. This may have potential implications for the late Paleozoic climate system and for ice sheet dynamics in general. Maybe the model is the problem. Any model has limitations; it is only a simulation of a process in which multiple factors interact in complex ways. Still, if there were an orbital signature, it should appear in the simulation. Their main obstacle was getting rid of the ice sheets once they formed (in some runs, the ice sheets reached the latitudes of modern-day Buenos Aires). The Pleistocene paradigm invokes additional processes to get rid of the ice quickly between cycles: including subglacial sediment destabilization (MacAyeal, 1993; Clark and Pollard, 1998), reorganization of the oceans thermohaline circulation (Maslin et al., 2001), and the removal of coastal sea-ice buttressing (Rignot and Thomas, 2002). Future runs including those factors may have better luck. But theres a disturbing alternative interpretation: Alternatively, our lack of large glacioeustatic change could also indicate that the Pleistocene Northern Hemisphere glacial-interglacial cycles may not be a good analogue for late Paleozoic glaciation. The two epochs are not comparable, in other words. This has a more disturbing side effect: in which case non-uniformitarian processes (e.g., very large perturbations of the carbon cycle) may have driven late Paleozoic glacioeustatic fluctuations. To rework a phrase: the (almost-present) Pleistocene was not the key to the past Paleozoic.
Heres the upshot: they found a paradox, and couldnt resolve it. This undercuts a paradigm that was thought to be fairly well understood. They only explanation left was non-uniformitarian something that runs against the grain of the whole science of geology. It reduces to the Stuff Happens Law (09/15/2008). The consequences are enormous, but the solution lies in the nebulous future: The resolution of this late Paleozoic paradox is fundamental for understanding the processes that drive glacioeustatic cyclicity and late Paleozoic climate change (Poulsen et al., 2007; Peyser and Poulsen, 2008), and is relevant to our current understanding of the climate-cryosphere system.
This can only imply one thing: jargon and math and computer skills notwithstanding, geologists, planetary scientists and atmospheric scientists understand very little of this at all. Politicians should take note.
1. Daniel E. Horton and Christopher J. Poulsen, Paradox of late Paleozoic glacioeustasy, Geology, August 2009, v. 37 no. 8 p. 715-718, doi: 10.1130/G30016A.1.
2. These include rates of precession, obliquity, and eccentricity that can combine into long-term cyclic fluctuations. Presumably, this affects insolation (the amount and angle of sunlight hitting the land masses) and therefore the climate, although other non-orbital factors could be involved (e.g., volcanic outgassing).
3. These glacial cycles are different from those in the Pleistocene when mountains were much higher.
4. Skeptics might ask if this hypothetical continent really did exist, if its existence is model-dependent on the interpretation of the very cyclic deposits examined in this paper.
5. Clark et al, The Last Glacial Maximum, Science, 7 August 2009: Vol. 325. no. 5941, pp. 710-714, DOI: 10.1126/science.1172873. 6. See 02/05/2008 and 08/08/2006 about whether orbital forcing mechanisms match the geological record.
Time for a refresher course on our Guide to Evolution (right sidebar). The First Law of Scientific Progress and Maiers Law are, as you can see, not just jokes, but standard ways of doing business in the halls of academia. Getting grants, writing computer models, and publishing them in scientific journals is all fine and good, but when the ultimate explanation is Stuff Happens, are we any better off? When the authors throw up their hands and task future researchers with the obligation to figure this out, has our understanding of Planet Earth increased? When the answer is Stuff Happens, and we dont know why it happens, what is the probability the answer is outside the box?Animal feats from six years back in the archives: the fiber-optic sponge (08/20/2003), the animal that walks on water (08/13/2003), the animal that sees with its ears (08/07/2003), and the tiny high jump champion with a 7-G leap (08/01/2003).
Mars Looks More Hostile to Life 08/06/2009
1. Lefevre and Forget, Observed variations of methane on Mars unexplained by known atmospheric chemistry and physics, Nature 460, 720-723 (6 August 2009) | doi:10.1038/nature08228.
Join the Search For Terrestrial Intelligence in Astrobiology. Go to IsThereIntelligentLifeInAstrobiology.com and run the SFTI@Home program now. Expect a long wait.Frank & Honest
Would you ever expect New Scientist to allow room for miracles and say they do not necessarily contradict laws of science? Read the surprising opinion piece by Hugh Mclachlan, professor of practical philosophy at Glasgow Caledonian University, UK, who says, We deceive ourselves if we imagine science has established that only scientific explanations are valid or that scientific explanations can take only one particular form.
Pterosaur Fuzz May Have Boosted Flying Finesse 08/05/2009
The trend in evolutionary explanation is for the subject matter to become more complex, and the storytelling to become more convoluted.Readers Digress
Michael Ruse, the Darwin-worshiping ex-Quaker shunning his childhood roots, always looking for a clue while denying the Cluegiver, frames a false dichotomy between Heraclitus vs Parmenides, Plato vs Aristotle, organism vs machine, Gaia vs Medea in his analysis of James Lovelocks Gaia hypothesis only to combine them at the end into a wobbly idol with feet of iron and clay. His essay is on Chronicle.com. The questions he poses, and the philosophers answers through history, are worth being educated about. Youll have more fun reading William Dembskis apt little spoof on methodological counterintuitiveness.
Spleen Scores, Darwin Loses 08/04/2009
That last silly line with Evolution as the clever wizard should be enough to vent your spleen. Evolution got medicine into this mess. Dont let Evolution become the hero of the story. Evolution is a wizard, all right: the blunderful Wizard of Flaws (09/05/2008).Do astronomers know how spiral galaxies form? Revisit the 08/01/2002 entry, where a prominent theorist speculated that maybe the spiral structure comes from nothing. How scientific is that?
Cosmologist Has a Sobering Thought: We Are Forever in the Dark About Dark Energy 08/03/2009
This means that we cannot pin down the geometry of space-time. We are then caught in a vicious circle: to know the geometry of the universe we need to pin down dark energy. Yet to determine how much dark energy there is, we need to know the geometry. Knowing one without the other is futile and a recipe for disaster.Ferreira unraveled the hype behind COBE, WMAP and the other instruments and studies that seemed to support the standard model. He was brutally honest about how little we actually know. He talked about new findings that shook my faith in the notion that the universe is flat. He ended his confession on a mildly optimistic note. Happily all is not lost: new experiments are being designed to probe the deepest recesses of the cosmos, he said. New probes and small projects are chipping away at our ignorance. Getting a handle on the geometry of space-time is just going to take a bit longer than we originally thought.
Cosmologists are the biggest hype marketers in the universe. How many books have been written promoting a golden age of precision cosmology? How many speeches have been given? How many dazzling planetarium shows? Ferreira is not the only evangelist that preached to us, repent and believe the big bang gospel (e.g., 11/02/2002).Dino Protein Confirmed 08/02/2009
August 2, 2009 An independent study of bone marrow contents from a T. rex that was reported in 2007 to contain fragments of protein has confirmed the claim, reported Science Daily. Seven peptides from collagen, and apparently traces from hemoglobin, were detected. The findings are scheduled to be published in the Sept. 4 issue of Journal of Proteome Research. For a previous report on dinosaur protein see the 04/30/2009 entry.
As the evidence for original protein in these dinosaur bones grows, the discussion of how it could last for 65 million years goes strangely quiet.Fertile Crescent Disappearing 08/01/2009
August 1, 2009 The birthplace of civilization and empire, the Fertile Crescent, is drying up. New Scientist posted a worrisome story that modern Iraq is in dire straits as dams upstream in Turkey are threatening to reduce the Tigris and Euphrates rivers to a quarter of their natural levels. This is happening in a land already parched by drought. The marsh lands in lower Mesopotamia are again threatened after a brief period of hope they could be restored from Saddam Husseins ecological terror (see 05/01/2003 and 06/06/2006). Scientists estimate the fertile lands of Mesopotamia where empires first thrived will be gone this century.
Sumer, Akkad, Ur, Kish, Babylonia, Assyria so many great empires rose and fell here. The Bible is filled with stories of events in Mesopotamia. Great kings and armies strode through this region. Great cities emerged and collapsed, forgotten in the dust till unearthed by archaeologists. Its hard to imagine the lush land between the rivers becoming a desert. Perhaps politics will turn, treaties will change the situation, and the rivers can continue to bring life to the vast Iraqi desert; perhaps not. Geography is not guaranteed. If empires had not risen here, they would have elsewhere. Nothing on the planet is forever. Whatever happens, we can hope that freedom in the resurrected Iraq will allow archaeologists to continue to bring evidence to light about the first civilizations that arose in this area.Remember the hard time scientists and politicians gave President Bush over his policy on embryonic stem cells? The 07/31/2006 entry should be remembered now that researchers are treating numerous diseases with induced pluripotent stem cells from adult tissue that have all the pluripotency of embryonic cells (05/03/2009) Meanwhile, embryonic stem cell research has yet to produce one hope of a cure after three years since that article; its only achievement has been the biggest scandal in modern science history (02/05/2006).