Conclusion: Darwins Dilemma, Creationist Propaganda and Corrupt Christians

This post is the conclusion of a four-part series. The preceding post can be found here, the introductory 1st post is linked here.




According to “many published scientists,” there is a “story being told by Darwinists” that DNA and genetics play a role in evolutionary development, protein synthesis and the ontogeny of the physical characteristics displayed by animals. In hopes of edifying the masses of wayward “Darwinists,” these same “many published scientists” point out in Darwin’s Dilemma that DNA lacks the potency and mechanical know-how required to undertake these tasks. In actuality - according to “many published scientists” - all of life is derived from non-genetic “information” that is harbored within each irreducibly complex cell. Furthermore, this “information” does not arise from earthly processes, rather these “blue prints” are “preordained” by an “intelligent source.”

Many published scientists, many published scientists and many published scientists.

At this point in the science ‘doctrine-mentry,’ piles and piles of cover pages from published articles are shown on screen. Included with these publications are those to be found in THE JOURNAL OF MOLECULAR BIOLOGY, which is visually emphasized in the film.

So, the bestowment of consecrated ‘information’ from the heavens has reportedly been shown to be a fact? Who are these “many published scientists?”

As introduced in the film, the ranks of these scientists are held by not only the Discovery Institute’s scientists, but also those from the world acclaimed Biologic Institute in Washington State. Among the “many” – which I counted as three – are Dr. Stephen Meyer, Dr. Richard Sternberg and Dr. Douglas Axe. Incidentally, did I mention that the world acclaimed Biologic Institute, like Discovery Media (the producers of Darwin’s Dilemma), is funded by the Discovery Institute? But unlike Discovery Media, the Biologic Institute is tax exempt as it is a chartable organization!

Regardless of their employers and obvious unscientific motives, if these three ‘esteemed scientists’ have conducted valid research there is no reason to discredit their work. Their individual publications should be evaluated on the merits of established protocol and peer review. For example, just because the intelligent design article credited to Meyer was published to the journal of the Proceedings of the Biological Society of Washington by then editor RICHARD STERNBERG during his last day on post doesn’t mean that the research is necessarily invalid… Of course, the subsequent statement released by the Biological Society of Washington’s Council doesn’t help Meyer’s or Sternberg’s case very much:

“The origin of biological information and the higher taxonomic categories, in vol 117, no 2, pp 213-239 of the Proceedings of the Biological Society of Washington, was published at the discretion of the former editor, Richard Sternberg. Contrary to typical editorial practices, the paper was published without review by any associate editor; Sternberg handled the entire review process. The Council…would have deemed the paper inappropriate… subject matter represents a significant departure from the nearly purely systematic content…”

As for the momentous work by Douglas Axe that was published in THE JOURNAL OF MOLECULAR BIOLOGY… Well, it doesn’t actually say anything about intelligent design, or divinely driven biological processes. The paper, titled Estimating the Prevalence of Protein Sequences Adopting Functional Enzyme Folds, essentially reports that mutational rates found in an enzyme that breaks down penicillin (beta-lactamases) are very rare. The exact rarity of these mutations, as estimated by Axe, is determined to be in a range with a high-end value of about 10 to the 74th power- very rare indeed. From this estimation of a rare mutation rate, Axe makes inferences (far reaching) to the evolution of proteins. Once these findings are sifted through the god-filter of creationists, the end result is a pronouncement in Darwin’s Dilemma that the chance of mutation is so rare as to prohibit the process of evolution from occurring. So rare, that in fact the only possible explanation for life is divine creation. Wow, now that’s an impressive leap! The total destruction of modern biology in a single paper; I’m curious as to why thousands of independent researchers the world over continue to study evolution… Must be a conspiracy!

And then, having decimated the fossil record, slandered Darwin, Simon Conway Morris, Richard Dawkins, and Stephen J Gould, AND having misrepresented the whole of modern scientific understanding, the tale of Darwin’s Dilemma comes to an end. Fin.

To draw this novel length critique of Darwin’s Dilemma to a close, let me re-emphasize that although lacking historical accuracy, scientific legitimacy and professional integrity the film’s production value and underlying truth-manipulating strategy make it a dangerous opponent to education and reason. The people behind the film are dishonest, unethical and immoral; they lie, doctor evidence and misrepresent science as a whole. In the process of attacking evolution, they falsify history and tear down the sciences of geology and chemistry.

Though they are fundamentalists and propagandists, they are also cunning and well funded… Take caution.






Axe, D. (2004). Estimating the Prevalence of Protein Sequences Adopting Functional Enzyme Folds Journal of Molecular Biology, 341 (5), 1295-1315 DOI: 10.1016/j.jmb.2004.06.058

Jack Horner on Dino-Chickens

Another short clip from a Jack Horner interview that appeared on CBS's 60-minutes last night. This one touches on the possibility of reverse-engineering chickens to create a dinosaur (or, dinosaur-like critter).

The Evo-devo clip with Sean Carroll (previous post) is from the same broadcast.



Watch CBS News Videos Online

Prime Time Evo Devo with Sean Carroll

Sean Carrol Talking Evo Devo on 60-Minutes


Watch CBS News Videos Online

Panamanian Treasure Trove

Scientists with the Smithsonian Tropical Research Institute (STRI), the Florida Museum of Natural History and the University of Oregon’s Geology Department seem to be having one heck of a good time down in Panama!

During the last few months, there’s been a variety of paleontology related research coming out of the Panama Canal's spoils; I’ve seen articles on paleoclimate, paleobotany and now vertebrate paleontology.

As copied from STRI materials (PDF available HERE):

Aldo Rincón, STRI paleontology intern, unearthed a set of fossil teeth in the Panama Canal that Bruce MacFadden, curator of vertebrate paleontology at the Florida Museum of Natural History, describes as belonging to Anchitherium clarencei, a three-toed browsing horse the size of the modern donkey, living 15 to 18 million years ago.

Expanding the Panama Canal to make way for super-sized ships is providing geologists and paleontologists with rare finds. Carlos Jaramillo, STRI stratigrapher, has, in collaboration with the University of Florida and the Panama Canal Authority, organized a team of researchers and students who move in following dynamite blasts to map and collect exposed fossils.

"This is one of very few places in the tropics where we have access to fresh outcrops before they are washed away by torrential rains or overgrown by vegetation, and we expect the fossils that we have been salvaging to resolve some major scientific mysteries," said Jaramillo. "What geological forces combined to create the Panama land bridge? Were the flora and fauna of Panama before the land bridge closed similar to those of North America, or did they include other elements?"

The latest finding appears in the Journal of Paleontology, vol. 83: 489-492.

Rincón, MacFadden, Jaramillo

Good stuff…

Gregory Retallack (University of Oregon) and Michael Kirby (STRI) have also been actively publishing on materials from the Canal’s excavations. I plan to post about some of their work over the next few days - so keeping it brief for now.

Anchitherium Image Credits: FMNH

Michael Palin to Be President of RGS

REPOSTED FROM PALIN'S SITE:

Presidential News by Michael Palin on 22 May 2009 2:02pm

Eagle-eyed Palin's Travellers, or those desperate for any kind of cheap sensation, may have read or heard reports that Michael Palin (that's the real one, not the one who Twitters) has been romantically linked with the Royal Geographical Society. Well, for once, what you've read is true. I've been asked to be President of the RGS for the next three years, starting at the beginning of June. The only other time I've been President of anything was when they invented the position for me at the Campaign For Better Transport. Of which I am still President and very proud of it too.

Why did I agree to become President of such an august and celebrated body as the Royal Geographical Society ? Well, basically (and I'm quoting Monty Python here for we once invented a spokesman for the British "Well Basically" Society) because I have always been a great enthusiast for geography, as those of you who visit the site know. As well as doing everything to preserve the excellence of the RGS, I hope that I can transmit some of my enthusiasm to those who might be the geographers of the future.

This site has always encouraged travel, contact and better understanding between the people of the world. The Royal Geographical Society represents and embodies nearly 180 years of wisdom and experience of those whose lives have been dedicated to understanding our world better.I see the Presidency as a way of continuing the work I've been doing these past twenty years of travels. I shall treasure the opportunities to learn more myself and I'll let you know how it's all going. Please don't be put off by the "augustness" of the Society's title. It survives by being open to the curious and welcoming to everyone. Check out the RGS website (http://www.rgs.org/) and come and see us.

Oh and by the way, it doesn't mean I'm hanging up my boots - look out for my Kolkata (Calcutta) article in Conde Nast Traveller (October edition, I'm told). Photos by Basil Pao. And I shall be at the Palestine Literary Festival for the next few days, then off to a travel writing festival at St Malo in France to talk about Around The World In Eighty Days in a new French translation. Zut ! Alors ! It's true I shan't be planning any long TV journeys for a while, but that's more to do with Archie than the RGS ! And another grand-child due in the summer. Watch this space !

I've so much to learn about my new role that I'm not in any position to deliver heavyweight statements of intent, but I'll be putting up a press release on the site very soon. Meanwhile, keep travelling, and if you're in Ramallah next Tuesday, come and say hello.
Michael P, May 22, 2009.

Quammen on Darwin

Good write-up, swiped from Here

By ED KEMMICK – Billings Gazette

Charles Darwin, who fundamentally altered the way scientists view the world and whose ideas are nearly as inflammatory today as they were when he announced them to the world 150 years ago, was a quiet, kindly homebody who was literally sickened by excitement and dispute.
And though he is known now for one big idea, the theory of evolution by natural selection, Darwin spent his life, in the words of David Quammen, immersed "in the beautiful significance of tiny details."

Quammen [at right] is a science writer who lives in Bozeman. Having spent most of February and March delivering lectures on Darwin around the country, Quammen said he sometimes felt a little presumptuous, given that Darwin apparently never gave a single public talk on evolution.

"It was hard for him even to have a really animated discussion with one of his friends without being sick the next day," Quammen said.

Darwin is the subject of renewed interest this year because it is the 150th anniversary of the publication of "On the Origin of Species" and the bicentenary of his birth in England on Feb. 12, 1809.

Quammen is in demand because he has spent much of his career writing about evolutionary biology. He delivered a speech on Darwin at the Library of Congress in 2002, and in 2006 he wrote "The Reluctant Mr. Darwin," a short biography. He also served as general editor and wrote an introduction for a big, new illustrated edition of "The Origin" published in October.
He has lived in Bozeman since the 1970s and is now in his third and final year as the Wallace Stegner Distinguished Professor of Western American Studies at Montana State University.
He said he has been surprised "to find myself sort of a tinpot Darwin expert. ... I'm not trained as a scientist myself. I'm not an evolutionary biologist. But I've been in love with this guy and his work for a long time." ................

Link to Billings Gazette to Continue

Beautiful Data

Demonstration of the “AlloSphere,” an entirely new way to see and interpret scientific data - in full color and surround sound inside a massive metal sphere.

A 3D immersive theater that maps complex data in time and space.

Dive into the brain, feel electron spin, hear the music of the elements...

Anti-Science and Ignorance Prevail – No on Stem Cell Research

State funding for embryonic stem cell research falls to the wayside at the State’s Capital today as Reps put politics and ignorance before science, ethics and public health during a debate at the Florida State University…

Rep. Eric Eisnaugle oppossed the research because his mommy said so…

“As much of a stake she has in this, she is absolutely against using public money to fund embryonic stem cell research,” said Eisnaugle.

And Miami Representative Anitere Flores decided to make a “definitive statement” in hopes of promoting misinformation and avoiding ethical challenges. Read her letter to Science and Ethics Chair Claire Thuning-Roberson - here.


Their arguments are as baseless and ignorant as the positions themselves.

Absolutely shameful, welcome to the south ya’ll !

Copulating for Carrion

Found this personal ad on Craigslist:

The ad reads:

Copulating for Carrion,
Currently unattached chimp with a passion for Tarzan swings and coprophagia seeks mutually compatible primate for reciprocal grooming, marking territory with urine and hanging around with the troop. Must have own carrion and be willing to share. No weirdoes need respond!

Unprofessional - I know – but couldn’t resist…

But in all seriousnessness (or at least in relative seriousness), check out this article on PLoS One;

Wild Chimpanzees Exchange Meat for Sex on a Long-Term Basis

From the Abstract

"Humans and chimpanzees are unusual among primates in that they frequently perform group hunts of mammalian prey and share meat with conspecifics. Especially interesting are cases in which males give meat to unrelated females. The meat-for-sex hypothesis aims at explaining these cases by proposing that males and females exchange meat for sex, which would result in males increasing their mating success and females increasing their caloric intake without suffering the energetic costs and potential risk of injury related to hunting. Although chimpanzees have been shown to share meat extensively with females, there has not been much direct evidence in this species to support the meat-for-sex hypothesis. Here we show that female wild chimpanzees copulate more frequently with those males who, over a period of 22 months, share meat with them. We excluded other alternative hypotheses to exchanging meat for sex, by statistically controlling for rank of the male, age, rank and gregariousness of the female, association patterns of each male-female dyad and meat begging frequency of each female. Although males were more likely to share meat with estrous than anestrous females given their proportional representation in hunting parties, the relationship between mating success and sharing meat remained significant after excluding from the analysis sharing episodes with estrous females. These results strongly suggest that wild chimpanzees exchange meat for sex, and do so on a long-term basis. Similar studies on humans will determine if the direct nutritional benefits that women receive from hunters in foraging societies could also be driving the relationship between reproductive success and good hunting skills."

Natural Selection Studies Flawed?

Upcomming article at PNAS...

Repost from ScienceDaily:

Scientists at Penn State and the National Institute of Genetics in Japan have demonstrated that several statistical methods commonly used by biologists to detect natural selection at the molecular level tend to produce incorrect results.

"Our finding means that hundreds of published studies on natural selection may have drawn incorrect conclusions," said Masatoshi Nei, Penn State Evan Pugh Professor of Biology and the team's leader. The team's results will be published in the Online Early Edition of the journal Proceedings of the National Academy of Sciences during the week ending Friday 3 April 2009 and also in the journal's print edition at a later date.

Nei said that many scientists who examine human evolution have used faulty statistical methods in their studies and, as a result, their conclusions could be wrong. For example, in one published study the scientists used a statistical method to demonstrate pervasive natural selection during human evolution. "This group documented adaptive evolution in many genes expressed in the brain, thyroid, and placenta, which are assumed to be important for human evolution," said Masafumi Nozawa, a postdoctoral fellow at Penn State and one of the paper's authors. "But if the statistical method that they used is not reliable, then their results also might not be reliable," added Nei. "Of course, we would never say that natural selection is not happening, but we are saying that these statistical methods can lead scientists to make erroneous inferences," he said.

The team examined the branch-site method and several types of site-prediction methods commonly used for statistical analyses of natural selection at the molecular level. The branch-site method enables scientists to determine whether or not natural selection has occurred within a particular gene, and the site-prediction method allows scientists to predict the exact location on a gene in which natural selection has occurred.

"Both of these methods are very popular among biologists because they appear to give valuable results about which genes have undergone natural selection," said Nei. "But neither of the methods seems to give an accurate picture of what's really going on."

Nei said that for many years he has suspected that the statistical methods were faulty. "The methods assume that when natural selection occurs the number of nucleotide substitutions that lead to changes in amino acids is significantly higher than the number of nucleotide substitutions that do not result in amino acid changes," he said. "But this assumption may be wrong. Actually, the majority of amino acid substitutions do not lead to functional changes, and the adaptive change of a protein often occurs by a rare amino acid substitution. For this reason, statistical methods may give erroneous conclusions." Nei also believes that the methods are inaccurate when the number of nucleotide substitutions observed is small.

To demonstrate the faultiness of the statistical methods, Nei's team compiled data collected by their Emory University colleague, Shozo Yokoyama, on the genes that control the abilities of fish to see light at different water depths and on the genes that control color vision in a variety of animals. The team used these data to compare statistically predicted sites of natural selection with experimentally determined sites. They found that the statistical methods rarely predicted the actual sites of natural selection, which had been identified by Yokoyama through experiments. "In some cases, statistical method completely failed to identify the true sites where natural selection occurred," said Nei. "This particular exercise demonstrated the difficulty with which statistical methods are able to detect natural selection."

To demonstrate how small sample sizes can lead to incorrect results, the team used computer simulations to examine the evolution of genes in three primates: humans, chimpanzees, and macaques. The scientists mimicked the procedures used by the authors of a 2007 paper, which applied the branch-site method to 14,000 orthologous genes -- genes that are genealogically identical among different species -- and which found that the method predicted selection in 32 of the genes. Nei and his team also studied selection using Fisher's exact test, but this test did not detect any selection. "The results indicate that the number of nucleotide substitutions that occurred were too small to detect any selection; therefore, all of the 32 cases obtained by the branch-site method must be false positives," said Nozawa.

"These statistical methods have led many scientists to believe that natural selection acted on many more genes in humans than it did in chimpanzees, and they conclude that this is the reason why humans have developed large brains and other morphological differences," said Nei. "But I believe that these scientists are wrong. The number of genes that have undergone selection should be nearly the same in humans and chimps. The differences that make us human are more likely due to mutations that were favorable to us in the particular environment into which we moved, and these mutations then accumulated through time."

Nei said that to obtain a more realistic picture of natural selection, biologists should pair experimental data with their statistical data whenever possible. Scientists usually do not use experimental data because such experiments can be difficult to conduct and because they are very time-consuming.

A third author on the study is Yoshiyuki Suzuki, a researcher at the National Institute of Genetics in Japan. This research was supported by the National Institutes of Health.

Octopus Fossils from the Cretaceous

Cool fossil find!

New finds of 95 million year old fossils reveal much earlier origins of modern octopuses. These are among the rarest and unlikeliest of fossils. The chances of an octopus corpse surviving long enough to be fossilized are so small that prior to this discovery only a single fossil species was known, and from fewer specimens than octopuses have legs.

Everyone knows what an octopus is. Even if you have never encountered one in the flesh, the eight arms, suckers, and sack-like body are almost as familiar a body-plan as the four legs, tail and head of cats and dogs. Unlike our vertebrate cousins, however, octopuses don't have a well-developed skeleton, and while this famously allows them to squeeze into spaces that a more robust animal could not, it does create problems for scientists interested in evolutionary history. When did octopuses acquire their characteristic body-plan, for example? Nobody really knows, because fossil octopuses are rarer than, well, pretty much any very rare thing you care to mention.

The body of an octopus is composed almost entirely of muscle and skin, and when an octopus dies, it quickly decays and liquefies into a slimy blob. After just a few days there will be nothing left at all. And that assumes that the fresh carcass is not consumed almost immediately by hungry scavengers. The result is that preservation of an octopus as a fossil is about as unlikely as finding a fossil sneeze, and none of the 200-300 species of octopus known today has ever been found in fossilized form. Until now, that is.

Palaeontologists have just identified three new species of fossil octopus discovered in Cretaceous rocks in Lebanon. The five specimens, described in the latest issue of the journal Palaeontology, are 95 million years old but, astonishingly, preserve the octopuses' eight arms with traces of muscles and those characteristic rows of suckers. Even traces of the ink and internal gills are present in some specimens.

'These are sensational fossils, extraordinarily well preserved' says Dirk Fuchs of the Freie University Berlin, lead author of the report. But what surprised the scientists most was how similar the specimens are to modern octopus: 'these things are 95 million years old, yet one of the fossils is almost indistinguishable from living species." This provides important evolutionary information. "The more primitive relatives of octopuses had fleshy fins along their bodies. The new fossils are so well preserved that they show, like living octopus, that they didn't have these structures.' This pushes back the origins of modern octopus by tens of millions of years, and while this is scientifically significant, perhaps the most remarkable thing about these fossils is that they exist at all.

NEWS REPOST FROM HERE.

Reference:

Fuchs et al. New Octopods (Cephalopoda: Coleoidea) from the Late Cretaceous (Upper Cenomanian) of Hakel and Hadjoula, Lebanon. Palaeontology, 2009; 52 (1): 65 DOI: 10.1111/j.1475-4983.2008.00828.x

Symbiosis and Evolution in Aphids

Below is a hodgepodge of info discussing the symbiotic relationship between pea aphids (Acyrthosiphon pisum) and the bacteria Buchnera aphidicola as it relates to adaptation and evolution. By and large, the discussion centers on recent research by Naruo Nikoh and Atsushi Nakabachi; however several other sources are listed at the bottom of this post – including the Douglas Lab’s website which is a great place to follow-up on the latest aphid-symbiosis research.

Most aphids host mutualistic bacteria, Buchnera aphidicola, which live inside specialized cells called bacteriocytes. Buchnera are vital to the aphids well being as they provide essential amino acids that are scarce in its diet. Now research published in the open access journal BMC Biology suggests that the aphids' ability to host Buchnera depends on genes they acquired from yet another species of bacteria via lateral gene transfer (LGT).

symbiotic bacteria Buchnera are located in specialized cells

called bacteriocytes (shown green in figure) in the aphid body cavity. [Drawing by Tomás Lazo]

Atsushi Nakabachi from Japan's RIKEN institute with his colleagues had previously uncovered two clusters of mRNA sequences from the bacteriocyte of the pea aphid Acyrthosiphon pisum that were encoded in the aphid genome, but similar to bacterial genes. Naruo Nikoh from The Open University of Japan and Nakabachi determined these sequences in full for more detailed analysis, and used real-time quantitative RT-PCR experiments to investigate the genes' expression levels in the aphid bacteriocytes.

Phylogenetic Analysis (Figure 3 - From Article)

The evidence points to LGT from bacteria to aphids. Genetic family trees show that one of the genes came from a bacterium closely related to Wolbachia, a common inherited symbiotic microbe, which infects a high proportion of insects. The aphid strain used for the study is free from Wolbachia and other closely related bacteria, but the transferred gene could be a remnant of an infection in the distant past. The evidence suggests that the aphids use these acquired genes to host Buchnera, which has lost many genes that appear to be essential for bacterial life. The association between aphids and Buchnera is over 100 million years old, and has evolved so that today neither the bacteria nor the host can reproduce without the other.

According to Nakabachi,

"the cases presented here are of special interest in that these transferred bacterial genes not only retain their functionality, but are highly expressed in the bacteriocyte that is differentiated so as to harbour Buchnera, which lack such genes."

LGT (also referred to as horizontal gene transfer) occurs when genetic material from one organism finds its way into another organism other than its offspring. Genetic engineering uses LGT deliberately, but there is increasing evidence that LGT has taken place in many organisms (usually between unicellular organisms) naturally. This has caused a major shift in how biologists view genetic family trees.

Symbiotic relationships have a great deal to teach us regarding evolution.Such interdependent relationships are not unusual in the natural world. What is unusual, report Helen Dunbar, Nancy Moran, and colleagues in a new study published [last year] in the open access journal PLoS Biology, is that a single point mutation in Buchnera's genome can have consequences for its aphid partner that are sometimes detrimental, and sometimes beneficial.

The authors probe Buchnera's and A. pisum's ability to tolerate heat. When exposed to high temperatures, Buchnera is supposed to activate special "heat-shock" genes whose products help to protect proteins from heat-related degradation. By using microarrays to assess activity of A. pisum and Buchnera genes, the researchers discovered that after a four-hour exposure to 35 °C temperature, some of their laboratory strains of Buchnera upregulated the heat-shock genes, but others did not. Further analysis showed the genetic basis for the difference: a single missing nucleotide in an adenine-filled stretch of DNA, called a promoter, that's involved in activating the heat-shock gene. Testing at a range of temperatures from 15 °C to 35 °C showed that activation of the heat-shock gene was consistently lower in the lines with the missing nucleotide than in the normal bacteria.

What does this mean for A. pisum's ability to tolerate tough conditions? To answer that, the researchers asked whether exposing juvenile aphid hosts of Buchnera with either long or short promoters to four hours of high temperatures (35 or 38 °C) affected their ability to reproduce. They found that few of the aphids with bacteria bearing short promoters reproduced after the heat treatment, while those with bacteria bearing the longer promoters had no trouble. In addition, aphids that had been exposed to the high temperatures and had the short-promoter-bearing bacteria weighed less as adults and had far fewer Buchnera inside them than did their counterparts with long-promoter-bearing bacteria.

Given these seemingly huge disadvantages to dropping a single adenine, it's hard to believe the mutation could last long in a Buchnera population. Yet, by sequencing and comparing the Buchnera associated with various A. pisum lines, the researchers discovered that the short-promoter option had arisen and been fixed twice in laboratory stock and was also found at frequencies of 21% and 13%, respectively, in bacteria in field-collected aphids from Wisconsin and New York.

Population genetic theory predicts that when a mutation is maintained in a population at high frequencies, it likely confers some benefit to its bearer. What could be the advantage of carrying a gene that causes one to lose the ability to reproduce at high temperatures?

A clue to the answer comes from the wild populations in which the mutation was not found: those living in Arizona and Utah. Could the bacterial mutation confer a competitive advantage that's only relevant in cooler climates? To find that out, the researchers performed a second test using a range of four-hour exposure temperatures. They discovered that short-promoter bacteria-bearing aphids produced progeny faster than did the normal ones when raised at 15 °C or 20 °C. Thus, though aphids containing bacterial symbionts with the heat-shock-promoter mutation fare worse than normal aphids after exposure to high temperatures, they do better under cool conditions, giving the mutation a selective advantage that causes it to be maintained in the population.

In addition to their explorations of A. pisum and its Buchnera, Moran's team also looked for and found multiple-adenine stretches related to heat-shock genes in Buchnera symbiotic with other aphid species. This offers fertile ground for further study of the intriguing interplay among aphids, bacteria, and temperature.

Sources: Eureka Alert, PhysOrg and Douglas Lab

Nikoh, N., & Nakabachi, A. (2009). Aphids acquired symbiotic genes via lateral gene transfer BMC Biology, 7 (1) DOI: 10.1186/1741-7007-7-12

Dunbar, H., Wilson, A., Ferguson, N., & Moran, N. (2007). Aphid Thermal Tolerance Is Governed by a Point Mutation in Bacterial Symbionts PLoS Biology, 5 (5) DOI: 10.1371/journal.pbio.0050096

Trilobites, Paleoecology and Anomalocaris

The “Explosion,” as the Cambrian Diversification is commonly referred, occurred approximately a half-billion years ago and is represented by the rapid appearance of about fifty phyla of animals. Present day scientists through the study of numerous fossils, as well as, genetic research have identified this uprising from the Kingdom Animalia and have come to the astonishing conclusion that the entire event lasted, at the very most, a mere ten million years. Most would agree that this seems an extremely minute quantity of time to permit such an all-encompassing radiation, which is one reason why this event is not only a topic of current research, but also one of heated debate.

A linear representation of animal evolution would certainly have a spike near the geologic time of the Cambrian Explosion. All present day phyla (i.e. body-plans, or animal “designs”) arose during that time (with the exception of Bryozoa) including that of the most abundant animal, and second most abundant organism (following only bacteria) on earth today, the arthropods.

One of the groups to rise from the Cambrian is the Phylum Arthropoda. Today the most common arthropods are the insects, but in pre-history, deep in geologic time, the title of most abundant arthropod may quite possibly have gone to the class Trilobita.

Trilobites are without a doubt one of the most easily recognized fossils in modern times, their abundance and variety have played a key role in paleontology as they act as wonderful index fossils. Variation in trilobites covers a wide range of morphological deviation, but most hold a few key characteristics in common. These common morphological characteristics include the division of the trilobite exoskeleton into three distinct regions, those being the head, (cephalon), the main body (thorax) and the tail (pygidium). These regions, especially the cephalon, have distinct sub-features that aid in the identification of individual trilobites, some of which are diagramed below in Figure 1.

FIGURE 1

Trilobites were structurally similar to many modern day arthropods; they possessed jointed appendages and hard exoskeletons, which fortunately - in conjunction with the process of molting - provided us with numerous high quality fossils today. The trilobites ranged in size from mere millimeters to over two-feet in length. They occupied primarily calm, deep waters were there was an abundance of fine silts which they plowed through with their flattened cephalons in order to search out rich debris to be used as a food source. Some trilobites however were most certainly predators, and many may have occupied other niches as well. They appeared (or they apparently appeared - some evidence suggests that they may have earlier origins) early in the Cambrian, reached their zenith in the late Cambrian and then began diversifying up till the Permian during which time they became extinct. There have been estimates of greater than 20,000 species of these incredibly successful Paleozoic marine arthropods - making classification rather tedious at times with new finds occurring on a regular basis. Luckily, some fossils retain sufficient detail as to render their classification relatively certain; however fossils don’t always readily describe the ways in which organisms interacted within their ecosystems.

This is one reason why Jennifer Dunne, et al, conducted research focused towards delineating the food-webs and niche interactions of species identified from the Chengjiang and Burgess Shales. From the Author’s Summary of Compilation and Network Analyses of Cambrian Food Webs,

“Our analyses show that for most aspects of network structure, the Early Cambrian Chengjiang Shale and Middle Cambrian Burgess Shale food webs are very similar to modern webs. This suggests that there are strong and enduring constraints on the organization of feeding interactions in ecosystems. However, a few differences, particularly in the Chengjiang Shale web, suggest that some aspects of network structure were still in flux during early phases of de novo ecosystem construction.”

In another paleoecology related story, Mariel Schotenfeld from the University of Massachusetts Amherst has challenged the widely held idea that Anomalocaris preyed on trilobites.

Anomalocaris

From upcomming G.S.A. agenda: “The Cambrian animal Anomalocaris is hypothesized to have eaten trilobites and other biomineralized prey. The lack of broken or abraded teeth on the plates comprising examination of the mouth apparatus of Anomalocaris suggests that it may not have had the ability to break the exoskeletons of any hard-shelled animal. SEM – EDS of the mouth apparatus from Burgess Shale specimens, indicate that the 32 plates are composed of organic carbon, suggesting they were originally unmineralized cuticle.

Mechanical properties of these plates were analyzed using CAD modeling and Finite Element Analysis. Poisson's ratio and Young's modulus of potential Anomalocaris plates, as well as density and fracture strength used for the FEA analyses, were estimated using a range of modern-day arthropods. Two end-member values were used both to approximate the range of strengths exhibited by Anomalocaris' cuticle, and also to encompass the range of exoskeleton strength likely exhibited by trilobites. The hardest skeletal values are from wet lobster (Homarus americanus) crusher claw cuticle; these are most likely to deform in a brittle manner. The softest are from adult dung beetle (Copris ochus) cuticles. In order to bite and successfully break the calcified cuticle of a trilobite, Anomalocaris' mouth plates would have needed to withstand forces that are greater than those required to fracture a trilobite exoskeleton. Results demonstrate that the teeth-like structures of the mouth plates should have deformed or broken when less than 90 N of force was applied perpendicular to the plates.

Additionally, documented trilobite malformations were compared to modern and extinct arthropod malformations. Abnormal trilobites previously attributed to predation of Anomalocaris might also be interpreted as molting failures or genetic mutations; such malformations occur with similar frequency in modern marine clawed lobsters, brachyuran decapods, and limulids. Furthermore, there is no direct evidence for Anomalocaris' feeding habits such as gut contents.”



Dunne, J., Williams, R., Martinez, N., Wood, R., & Erwin, D. (2008). Compilation and Network Analyses of Cambrian Food Webs PLoS Biology, 6 (4) DOI: 10.1371/journal.pbio.0060102

19 Leopold Leadership Fellows Named by Woods Institute

Woods Institute Names 19 Leopard Fellows;

Congrats;

Kevin Arrigo, Department of Environmental Earth System Science, Stanford. Role of polar marine microalgae in global biogeochemical cycling.

Brendan Bohannan, Department of Biology, University of Oregon. Microbial biodiversity; response of microbial communities to environmental change.

David Breshears, School of Natural Resources, University of Arizona. Dieback of woodlands in response to severe drought.

Anne Chin, Department of Geography, University of Oregon. Dynamics of dryland rivers affected by urban development; dynamics of headwater mountain streams.

Simon Donner, Department of Geography, University of British Columbia. Effects of climate change and land use change on ecosystems.

Victoria Fabry, Department of Biological Sciences, California State University-San Marcos. Impact of ocean acidification on marine ecosystems.

Margot Gerritsen, Department of Energy Resources Engineering, Stanford. Optimization of environmentally friendly oil production processes, carbon sequestration and tidal energy systems.

Gretchen Hofmann, Department of Ecology, Evolution and Marine Biology, University of California-Santa Barbara. Impacts of ocean acidification on marine populations.

Madhu Khanna, Department of Agricultural and Consumer Economics, University of Illinois at Urbana-Champaign. Economic mechanisms for encouraging voluntary corporate environmental initiatives; environmental and economic implications of biofuel mandates, subsidies and tariffs.

David Lea, Department of Earth Science, UC-Santa Barbara. Implications of paleoclimate data for understanding and predicting climate change.

Laura Meyerson, Department of Natural Resources Science, University of Rhode Island. Identification of native plant populations at risk of extinction from invasive plant species.

Paige Novak, Department of Civil Engineering, University of Minnesota. Contamination of water and wastewater by estrogen compounds.

Dov Sax, Department of Ecology and Evolutionary Biology and Center for Environmental Studies, Brown University. Species extinction; evaluation of "assisted migration" as policy.

Karen Seto, School of Forestry and Environmental Studies, Yale University. Impacts of urban growth.

Whendee Silver, Department of Environmental Science, Policy and Management, UC-Berkeley. Land use management effects on climate change; impact of tropical reforestation.

U. Rashid Sumaila, Fisheries Centre, University of British Columbia. Economics of fishing and impacts on marine conservation policies.

Jeanne VanBriesen, Department of Civil and Environmental Engineering, Carnegie Mellon University. Drinking-water safety.

Jianguo "Jingle" Wu, School of Life Sciences and School of Sustainability, Arizona State University. Urbanization and its ecological effects in Arizona; biodiversity and ecosystem function in Mongolia.

Luis Zambrano González, Department of Zoology, Instituto de Biología, Universidad Nacional Autónoma de México. Dynamics of freshwater fish populations.

Stem Cells the Vatican and Monty Python

Pope Benedict: ''all Catholics, especially legislators, jurists and those responsible for the common good of society' to promote human life from conception to death”

Philadelphia Archbishop Cardinal Justin Rigali: ''This action is morally wrong because it encourages the destruction of innocent human life, treating vulnerable human beings as mere products to be harvested''

United States' Bishops' Conference: ''a sad victory of politics over science and ethics''

Osservatore Romano: “immoral and superfluous''


So in lay terms…

Academic Freedom Act Cartoon in Florida Newspaper

The Gainesville Sun posted an editorial and political cartoon criticizing the Education Academic Freedom Act bill filed in Florida.

Also blogged at Florida Citizens for Science.

Way to go Mary Bahr!







From Letter:

Imagine our society without computer networks, electronics, chemistry and modern medicine. Both our lives and economy would be greatly diminished. Biotechnology has created nearly 600 new businesses in medicine, the environment and agriculture in Florida with jobs that pay almost twice the State average. State economic adviser Enterprise Florida has labeled biotechnology a High Impact Industry and recommends legislators make sure we “provide students with the needed skills to work in biotechnology companies and market Florida as a hub for life science research and business development.”


Unfortunately At least one legislator has ignored Enterprise Florida’s advice. State Sen. Stephen Wise, of Clay County, is attacking science in Florida with his Critical Analysis bill SB 2396. Similar bills have been used to introduce Intelligent Design Creationism into science classrooms. Senator Wise recently reported in the Florida Times Union he wishes to do exactly that.


Leaders ranging from a Republican federal judge to the Pope have declared Intelligent Design a religious belief, not a scientific theory, making its introduction into a science classroom unconstitutional. In addition to irresponsibly putting our struggling school districts at risk of millions of dollars in law suits, Senator Wise is attacking the scientific basis of Florida’s Biotechnology economic expansion.


Biotechnology, which promises a more sustainable future, strategies to counteract climate change, medical benefits to prolong and enrich lives and high paying jobs, rests on the framework for modern biology known as the Scientific Theory of Evolution. Our new State Science Standards call for thorough examination of all aspects of science, but critical analysis does not include falsely claiming a religious belief as a scientific theory. Confusing Florida students about the nature of science will not lead to informed citizen scientists required for a prosperous future for Florida. Oppose Critical Analysis Bill SB 2396


Mary Bahr,


Gainesville

Cross Dressing Lizards

Young male lizards in South Africa imitate females to fool aggressive older males into leaving them alone, in an example of transvestism in the natural world, researchers have found.


The lizards not only avoid fights but gain access to females under the nose of their more macho rivals, the South African and Australian researchers discovered.




They found that young male Augrabies flat lizards delayed displaying the extravagant coloration of sexually-mature males until they were able to defend themselves adequately.


"Experienced males will chase and bite their young rivals," said associate professor Martin Whiting of Johannesburg's University of the Witwatersrand.


"By delaying the onset of colour to a more convenient period, these males, termed she-males, are making the best of a bad situation."


Australian National University associate professor Scott Keogh said opting to become transvestites for a period offered young males a dual advantage.


"They can avoid potentially dangerous bouts with dominant males and still have access to normally inaccessible females," he said.


But, as with large hands and an Adam's apple in the human world, there is a flaw in the lizards' transvestite transformation.


Dominant males can detect transvestite's male hormones with their sensitive tongues, even if they are taken in by their female appearance.


University of Sydney researcher Jonathan Webb said this meant the she-males needed to be nimble to avoid advances from dominant males smitten by their fake female allure.
"Males are fooled by looks, but not by scent," he said.


"She-males are able to maintain this deception by staying one step ahead of a prying male, and thereby avoiding a nosey tongue that might give the game away."


The research was published in the journal Proceedings of the Royal Society.



Source: here

Federal Government and Science - Harold Varmus

Harold Varmus on John Stewart - Federal Money for Research, Science under Bush...

The Daily Show With Jon StewartM - Th 11p / 10c

Harold Varmus

Daily Show Full Episodes
Important Things With Demetri Martin

Political Humor
Joke of the Day

Darwin - The Musical

Charles Darwin the musical.

Evolution and National Security - An Analogy to Nowhere

Exploring new models for problem solving is a good thing, but I’m inclined to think that someone may be taking this analogy a bit too far…

My initial impression is that with enough creative coaxing evolution’s lessons on national security are about as meaningful as evolution’s lessons on learning to play the guitar - though admittedly I haven’t read the book.

There is a video lecture available on YouTube here.

+ + +

FROM SCIENCE DAILY HERE;

Take A Darwinian Approach To A Dangerous World: Ecologist Preaches 'Natural' Security For Homeland Defense

In nature, the threat level is always at least orange: Predators and plagues are an unrelenting menace to the well-being (and successful reproduction) of every living thing.
So does your body make every gulp of air take off its shoes before entering your lungs to ensure that it's not smuggling pathogens?

Of course not, says Rafe Sagarin, an assistant research professor of marine science and conservation in Duke University's Nicholas School of the Environment, and it would be ridiculous to try. If you didn't suffocate first, the microbes would simply find another way to get in. That's what natural threats do.

Sagarin, an ecologist who's normally more concerned with the urchins and starfish in tide pools, got to thinking about these things as a Congressional science fellow less than a year after the 9/11 terrorist attacks. He saw Washington building an expensive new shell, erecting large barriers around buildings and posting guards and cameras in every doorway.

"Everything was about more guards, more guns, and more gates," he said. "I was thinking, 'If I'm an adaptive organism, how would I cope with this?' "Pretty simply, as it turns out. "If they're checking every trunk, I'll put the bomb in the back seat."

Sagarin thinks this way because he's a biologist, not a cop. And, he says, it's a mode of thinking—informed by Charles Darwin's insights into life's struggle for survival and fecundity—that more security analysts would be wise to adopt.

At the annual meeting of the American Association for the Advancement of Science in Chicago, Sagarin has organized a 90-minute symposium on the subject, to be held Friday morning, Feb. 13.

Sagarin is also the editor of "Natural Security: A Darwinian Approach to a Dangerous World" (University of California Press, 2008), which convened a national committee of experts from related fields like biology, anthropology, and virology, as well as security, psychology, and math to think about ways that Homeland Security could act more like an immune system and less like a tough-talking Texas sheriff.

In nature, a threat is dealt with in several ways. There's collectivism, where one meerkat sounds the alarm about an approaching hawk, or camouflage, where the ptarmigan hides in plain sight. There's redundancy, like our wisdom teeth, or unpredictable behavior, like the puffer fish's sudden, spiky pop.

Under the unyielding pressure of 3.5 billion years of evolution, the variety of defenses is beyond counting. But they all have a few features in common. A top-down, build-a-wall, broadcast-your-status approach "is exactly the opposite of what organisms do," Sagarin says.

An immune system, for example, is not run by a central authority. It relies on a distributed network of autonomous agents that sense trouble on the local level and respond, adapting to the threat and signaling for backup without awaiting orders from HQ.

Sagarin's brand of "natural security" may take some getting used to. "Organisms do not try to get rid of risk in their environment," he says. "They learn to live with it."

The total elimination of risk is far more costly than the organism could bear, and probably futile, since the threats adapt. But by being responsive and adaptable and not putting every last bit of its budget into defense, an organism stands a far better chance of being able to handle an unforeseen risk in an escalating arms race, he says.

"Almost everything organisms do is, in some way, about security."