477-531: The Influence of Social Hierarchy on Primate Health -- Sapolsky 308 (5722): 648 -- Science

The Influence of Social Hierarchy on Primate Health -- Sapolsky 308 (5722): 648 -- Science:

Dominance hierarchies occur in numerous social species, and rank within them can greatly influence the quality of life of an animal. In this review, I consider how rank can also influence physiology and health. I first consider whether it is high- or low-ranking animals that are most stressed in a dominance hierarchy; this turns out to vary as a function of the social organization in different species and populations. I then review how the stressful characteristics of social rank have adverse adrenocortical, cardiovascular, reproductive, immunological, and neurobiological consequences. Finally, I consider how these findings apply to the human realm of health, disease, and socioeconomic status.

A review of 55 recent articles demonstrating the evolution of dominance hierarchies in primates, and drawing implications from that to humans. Evolution abounds.

476: Horsfield's Hawk-Cuckoo Nestlings Simulate Multiple Gapes for Begging -- Tanaka and Ueda 308 (5722): 653 -- Science

Horsfield's Hawk-Cuckoo Nestlings Simulate Multiple Gapes for Begging -- Tanaka and Ueda 308 (5722): 653 -- Science:

Nestlings of some brood parasitic birds evict hosts' eggs and young soon after hatching, thereby avoiding discrimination by hosts while monopolizing parental care. Eviction carries a cost, however, because lone parasitic nestlings attract a reduced provisioning rate. Here we describe a form of visual signaling used by the evicting Horsfield's hawk-cuckoo (Cuculus fugax) to obtain sufficient food. The chick displays a gape-colored patch on the wing to the host parents as they deliver food, simulating the gaping display of more than one nestling.

Coevolution of a nest parasite and it's host.

475: A Rapid Shift in a Classic Clinal Pattern in Drosophila Reflecting Climate Change -- Umina et al. 308 (5722): 691 -- Science

A Rapid Shift in a Classic Clinal Pattern in Drosophila Reflecting Climate Change -- Umina et al. 308 (5722): 691 -- Science:

Geographical clines in genetic polymorphisms are widely used as evidence of climatic selection and are expected to shift with climate change. We show that the classic latitudinal cline in the alcohol dehydrogenase polymorphism of Drosophila melanogaster has shifted over 20 years in eastern coastal Australia. Southern high-latitude populations now have the genetic constitution of more northerly populations, equivalent to a shift of 4° in latitude. A similar shift was detected for a genetically independent inversion polymorphism, whereas two other linked polymorphisms exhibiting weaker clinal patterns have remained relatively stable. These genetic changes are likely to reflect increasingly warmer and drier conditions and may serve as sensitive biomarkers for climate change.

These flies are adapting to a change in climate. We tend to think of selection and mutation as the forces of evolution, but here's a case where gene flow is causing evolution.

474: GEOCHEMISTRY: Preserved in Salt -- Hanson 308 (5722): 603c -- Science

GEOCHEMISTRY: Preserved in Salt -- Hanson 308 (5722): 603c -- Science:

The most ancient living organism is claimed to be a bacterium that has been extracted and cultured from a small bubble of fluid trapped in a Permian-aged (~250 million years ago) salt crystal, similar to the way that, for example, insects are trapped in amber. The idea is that this bacterium became entombed in a fluid inclusion in the salt crystal and remained dormant until it was resuscitated. One criticism has been that the inclusion in the salt crystal, and hence the bacterium, might be a contaminant of an uncertain and possibly younger age; the retention of younger fluids flowing through or adjacent to older rock is not uncommon.

Satterfield et al. have now determined the chemistry of the fluid inclusions in these salt crystals. Earth's ocean chemistry has changed over time, and the Late Permian oceans were depleted in Mg and sulfate as compared with today's oceans, which provides a signature that is diagnostic for this time period. The chemistry of the inclusions fits with that of Permian seawater, suggesting that the bacterium is indeed old.

250 million year old bacteria, still functional.

473: Reduced sleep in Drosophila Shaker mutants : Nature

Reduced sleep in Drosophila Shaker mutants : Nature:

Most of us sleep 7−8 h per night, and if we are deprived of sleep our performance suffers greatly; however, a few do well with just 3−4 h of sleep—a trait that seems to run in families. Determining which genes underlie this phenotype could shed light on the mechanisms and functions of sleep. To do so, we performed mutagenesis in Drosophila melanogaster, because flies also sleep for many hours and, when sleep deprived, show sleep rebound and performance impairments. By screening 9,000 mutant lines, we found minisleep (mns), a line that sleeps for one-third of the wild-type amount. We show that mns flies perform normally in a number of tasks, have preserved sleep homeostasis, but are not impaired by sleep deprivation. We then show that mns flies carry a point mutation in a conserved domain of the Shaker gene. Moreover, after crossing out genetic modifiers accumulated over many generations, other Shaker alleles also become short sleepers and fail to complement the mns phenotype. Finally, we show that short-sleeping Shaker flies have a reduced lifespan. Shaker, which encodes a voltage-dependent potassium channel controlling membrane repolarization and transmitter release, may thus regulate sleep need or efficiency.

The evolution of sleep.

472: Predicting with unpredictability : Nature

Predicting with unpredictability : Nature:

When the temporal evolution of a system cannot be studied by traditional means, random numbers can be used to generate an 'alternative' evolution. Starting with a possible configuration, small, random changes are introduced to generate a new arrangement: whenever this is more stable than the previous one, it replaces it, usually until the most stable configuration is reached. Randomness cannot tell us where the system likes to go, but allows the next best thing: exploration of the space of the configurations while avoiding any bias that might exclude the region of the possible solution. If we are able to guess the probability distribution of the configurations, then instead of conducting a uniform random search we can perform an 'importance' sampling, focusing our search on where the solution is more likely to be found.

Optimization problems are often solved using stochastic algorithms that mimic biological evolution. Although it may sound vaguely unpleasant, we come from a random search. In nature, new genetic variants are introduced through random changes (mutations) in the genetic pool while additional variability is provided by the random mixing of parent genes (by recombination). Randomness allows organisms to explore new 'designs' which the environment checks for fitness, selecting those most suited to survival. But the optimal solution is not found once and for ever. A continually changing environment means evolution is an on-going process; it does not produce the 'perfect' organism, but rather a dynamic balance of myriad organisms within an ecosystem.

Generating true randomness is a challenging task. Early attempts at stochastic simulation produced samples through processes such as dice tosses or card draws. These phenomena in principle obey newtonian mechanics, but in practice evolve unpredictably owing to their chaotic dynamics. Computers have made it much easier to produce large numbers of samples. They cannot, however, generate true random numbers.

That's in the midst of a paper talking about the development of random number generators. Math and physics rely on evolutionary biology!

Science Humor

From the letters to the editor at Nature, Nice planet, shame about the human race:

Sir:

Inspired by Stephen Baxter's Futures story "Under martian ice" (Nature 433, 668; 2005), we began to discuss the Fermi paradox: that if aliens exist, they would have visited everywhere by now, including Earth. Careful consideration led us to conclude that if they were intelligent, they would not visit this planet.

Thus — and in opposition to the anthropic principle, which argues that the Universe is the way it is because we are here to observe it — we propose the misanthropic principle as the resolution of the puzzle.

Randall D. Kamien and Madhuri Kaul

Well put. I'm tempted to write a reply, but then I'd give up my right to wear this shirt.

Basically, I'd argue that, even though we screwed up this planet, there's a lot of cool stuff. So aliens should have come here, but tried to avoid people. That's still misanthropic, but we still ought to have seen the aliens in their travels.

471: Learned kin recognition cues in a social bird : Nature

Learned kin recognition cues in a social bird : Nature:

In long-tailed tits, all adults attempt to breed independently in pairs each year, but most nests fail due to depredation13, 14. Failed breeders often re-nest, but later in the season may instead become helpers14; this switch from re-nesting to helping corresponds with a seasonal change in the potential fitness benefits of each strategy15. No significant direct fitness benefits of helping have been found, but helpers preferentially care for close relatives16 and accrue indirect fitness benefits by increasing brood productivity14, 15; this kin-selected benefit represents a substantial component of inclusive fitness and is the sole source of fitness for many individuals17. Thus, helping is beneficial to both helpers and recipients, and selection should favour kin recognition6, 8. Kin-biased helping occurs in the absence of reliable spatial cues to kinship16, and a previous study suggested that long-tailed tits can discriminate between the vocalizations of close relatives and non-relatives18. Here, we describe an experiment that determines the characteristics of contact calls used in discrimination, and a second experiment that investigates the acquisition of these recognition cues.

Fitness benefits, and kin selection are parts of evolutionary hypotheses. The characteristics used and the methods of acquisition will be under heavy selection, since cheating will be good for a cheater, but horrible for the cheated.

470: IKK[alpha] limits macrophage NF-[kappa]B activation and contributes to the resolution of inflammation : Nature

IKK[alpha] limits macrophage NF-[kappa]B activation and contributes to the resolution of inflammation : Nature:

Inflammation and innate immunity involve signalling pathways leading to the production of inflammatory mediators. Usually such responses are self-limiting, but aberrant resolution of inflammation results in chronic diseases1. Much attention has focused on pro-inflammatory signalling but little is known about the mechanisms that resolve inflammation. The IkappaB kinase (IKK) complex contains two catalytic subunits, IKKalpha and IKKbeta, and controls the activation of NF-kappaB transcription factors, which play a pivotal role in inflammation2. Ample evidence indicates that IKKbeta mediates NF-kappaB activation in response to pro-inflammatory cytokines and microbial products. IKKalpha regulates an alternative pathway important for lymphoid organogenesis2, but the role of IKKalpha in inflammation is unknown. Here we describe a new role for IKKalpha in the negative regulation of macrophage activation and inflammation. IKKalpha contributes to suppression of NF-kappaB activity by accelerating both the turnover of the NF-kappaB subunits RelA and c-Rel, and their removal from pro-inflammatory gene promoters. Inactivation of IKKalpha in mice enhances inflammation and bacterial clearance. Hence, the two IKK catalytic subunits have evolved opposing but complimentary roles needed for the intricate control of inflammation and innate immunity.

469: Evolutionary biology Animal roots and shoots : Nature

Evolutionary biology Animal roots and shoots : Nature:

DNA sequence data from neglected animal groups support a controversial hypothesis of deep evolutionary history. Inferring that history using only whole-genome sequences can evidently be misleading.

Despite the comforting certainty of textbooks and 150 years of argument, the true relationships of the major groups (phyla) of animals remain contentious. In the late 1990s, a series of controversial papers used molecular evidence to propose a radical rearrangement of animal phyla1, 2, 3. Subsequently, analyses of whole-genome sequences from a few species showed strong, apparently conclusive, support for an older view4, 5, 6. Philippe et al., writing in Molecular Biology and Evolution7, now provide evidence from expanded data sets that supports the newer evolutionary tree, and also show why whole-genome data sets can lead phylogeneticists seriously astray.

Evolutionary hypotheses tested. More and better data form better hypotheses, which are in turn tested.

468: Dynamics of Drosophila embryonic patterning network perturbed in space and time using microfluidics : Nature

Dynamics of Drosophila embryonic patterning network perturbed in space and time using microfluidics : Nature:

Biochemical networks are perturbed both by fluctuations in environmental conditions and genetic variation. These perturbations must be compensated for, especially when they occur during embryonic pattern formation. Complex chemical reaction networks displaying spatiotemporal dynamics have been controlled and understood by perturbing their environment in space and time1, 2, 3. Here, we apply this approach using microfluidics to investigate the robust network in Drosophila melanogaster that compensates for variation in the Bicoid morphogen gradient. We show that the compensation system can counteract the effects of extremely unnatural environmental conditions—a temperature step—in which the anterior and posterior halves of the embryo are developing at different temperatures and thus at different rates. Embryonic patterning was normal under this condition, suggesting that a simple reciprocal gradient system is not the mechanism of compensation.

This means there must be some sort of backup system. The primary means of pattern formation evolved, then backups developed because individuals with the backup system were less likely to have offspring which developed wrong. By looking across insects it may be possible to identify the origin of the different systems and their evolution.

467: ECOLOGY: Sucrose-Free Sips Suit Acacia Ants -- Pennisi 308 (5721): 481a -- Science

ECOLOGY: Sucrose-Free Sips Suit Acacia Ants -- Pennisi 308 (5721): 481a -- Science:

The thorny acacia tree has strong allies: vicious, centimeter-long ants whose nasty bite scares off plant-eating animals and also humans. In return for defending acacias, the ants get free meals and places to live. The key to this sweet deal is the sucrose-free nectar provided by the plant, says Martin Heil, an ecologist at the Max Planck Institute for Chemical Ecology in Jena, Germany. As he and his colleagues report on page 560, a sucrose-degrading enzyme produced by the acacia customizes its nectar to appeal to the right ant partners. The defensive-minded ants that protect the tree prefer their nectar without sucrose, while other ants do not, the researchers found.

Furthermore, the acacia ants have actually decreased their own production of the same sucrose-degrading enzyme, reinforcing this particular pairing of insect with plant. The work "gives one of the first examples of a biochemical basis for behavior difference in plant-insect mutualisms," says Robert Thornburg, a biochemist at Iowa State University in Ames. "It shows that coevolutionary trends can be underlain by biochemistry."

Co-evolution at work.

466: PLANT SCIENCES: Recognition at a Distance -- Schulze-Lefert and Bieri 308 (5721): 506 -- Science

PLANT SCIENCES: Recognition at a Distance -- Schulze-Lefert and Bieri 308 (5721): 506 -- Science:

A key step in the evolution of eukaryotic immune systems was the ability to discriminate between self and nonself. Evidence suggests that animals and plants independently evolved dedicated and highly variable receptor families for recognition of nonself structures. The outcome of interactions between plants and the pathogenic microbes that invade them largely relies on a repertoire of receptors that serve as a radar system for detecting pathogen-derived nonself molecules. The function and specificity of these receptors were originally defined by genetic studies. Such studies revealed that for plants to recognize their intruders and to mount an effective resistance response, there needed to be a match between a strain-specific pathogen effector and its corresponding plant host resistance (R) gene product (1). Detection of a pathogen effector by a plant R receptor frequently leads to rapid death of plant host cells at sites of attempted invasion as part of the immune response. Most known R genes encode intracellular receptors containing a nucleotide binding site and leucine-rich repeats (LRRs) or membrane-bound surface receptors containing extracellular LRRs (2). Two new studies--by Coaker et al. (3) on page 548 of this issue and by Rooney et al. (4) in this week's Science Express--describe encounters between pathogen-secreted effector molecules and their host targets in Arabidopsis and the tomato (Lycopersicon), respectively. Although this interorganismal molecular liaison has entirely different consequences for the effector target proteins, in both cases, their manipulation holds the key to a better understanding of how plant immune receptors recognize nonself.

How 'bout that?

465: Don't Dismiss Astrobiology -- Chyba; et al. 308 (5721): 495f -- Science

Don't Dismiss Astrobiology -- Jakosky, et al. 308 (5721): 495f -- Science:

Its aim is not just to find life but, rather, to both determine and understand the distribution of life in the universe through time. One extreme possibility is that life exists only on Earth, has never existed anywhere else, and will never be present beyond Earth's orbit. At the alternative extreme, life may have originated on multiple bodies in our solar system and may be ubiquitous beyond. No matter what the answer proves to be, astrobiologists will want to know how the actual distribution of life relates to the occurrence of different planetary environments. Hence, in addition to exploring for evidence of life beyond Earth, astrobiologists study the extreme limits to life, the conditions that make environments habitable, the origin and evolution of life on Earth, the processes responsible for the occurrence of habitable environments in our solar system, and the occurrence of planets and their habitability beyond our solar system.

Sounds like evolution is at play in astronomy, too.

464: Species diversity can drive speciation : Nature

Species diversity can drive speciation : Nature:

A fundamental question in evolutionary ecology and conservation biology is: why do some areas contain greater species diversity than others? Island biogeographic theory has identified the roles of immigration and extinction in relation to area size and proximity to source areas1, 2, and the role of speciation is also recognized as an important factor3, 4, 5, 6. However, one as yet unexplored possibility is that species diversity itself might help to promote speciation, and indeed the central tenets of island biogeographic theory support such a prediction. Here we use data for plants and arthropods of the volcanic archipelagos of the Canary and Hawaiian Islands to address whether there is a positive relationship between species diversity and rate of diversification. Our index of diversification for each island is the proportion of species that are endemic, and we test our prediction that this increases with increasing species number. We show that even after controlling for several important physical features of islands, diversification is strongly related to species number.

That's macroevolution at work. Speciation dynamics, coevolution, and neat biology.

463: Sexual reproduction between partners of the same mating type in Cryptococcus neoformans : Nature

Sexual reproduction between partners of the same mating type in Cryptococcus neoformans : Nature:

Although this laboratory-defined sexual cycle of C. neoformans has been known for three decades, the environmental and clinical predominance of alpha strains has posed a conundrum3. If most of the population is limited to one mating type, how would a sexual cycle occur in nature? Haploid C. neoformans alpha strains can also undergo a developmental transition involving filamentation and sporulation, known as haploid or monokaryotic fruiting4. This process resembles mating but was assumed to be mitotic and asexual. We show here that fruiting in fact represents a form of sexual reproduction between strains of the same mating type.

Fruiting and mating are both stimulated by similar environmental conditions (nitrogen starvation, desiccation, darkness and pheromones4, 5, 7), and both involve hyphal growth and the production of basidia and spores. However, the two pathways do have distinguishing features; hyphal cells produced during fruiting are mononucleate, with unfused clamp connections, whereas mating hyphal cells are dikaryotic, linked by fused clamps.

Compared with mating, fruiting is inefficient, requires prolonged incubation, and occurs in a stochastic manner at isolated points at the periphery of a growth patch, suggesting that a rate-limiting step might restrict entry into this developmental pathway. The observation that diploid alpha/alpha strains undergo more rapid and robust fruiting compared with isogenic haploid alpha strains suggested that diploidization might normally occur during fruiting. Because isolating hyphal cells to determine ploidy is technically challenging, we made use of the fact that hyphae bud to produce vegetative yeast cells (termed blastospores)4, 5, which are readily isolated by micromanipulation and grow as budding yeast cells (Fig. 1). Blastospores are uninucleate, and their DNA content presumably reflects the nuclear content of the hyphae from which they are derived (by mitosis).

Evolutionary reasoning lead to this research, because the α mating type is too common, and fruiting would impose an evolutionary cost.

462: Predation Prey plumage adaptation against falcon attack : Nature

Predation Prey plumage adaptation against falcon attack : Nature:

Several plumage types are found in feral pigeons (Columba livia), but one type imparts a clear survival advantage during attacks by the swiftest of all predators — the peregrine falcon (Falco peregrinus). Here we use quantitative field observations and experiments to demonstrate both the selective nature of the falcon's choice of prey and the effect of plumage coloration on the survival of feral pigeons. This plumage colour is an independently heritable trait that is likely to be an antipredator adaptation against high-speed attacks in open air space. …

To confirm the advantage afforded by a white rump to pigeons during a high-speed attack, we captured 756 wild and blue-barred pigeons and switched their rump-patch feathers. We then released these pigeons and monitored predation by three adult peregrine falcons. After plumage transfer, we found that capture rates were reversed (Fig. 1c). The original wild phenotype now suffered predation at the same rate as the unmanipulated blue-barred type, whereas the manipulated blue-barred type now had rates of predation as low as the unmanipulated wild type (P<0.0001). This indicates that the dorsal white rump patch is important for the survival of feral pigeons during attacks by peregrine falcons.

All feral pigeons perform the same evasive roll during predation by falcons (Fig. 1a). The protective white patch may disguise the initiation of the pigeon's evasive roll by contrasting conspicuous (white patch) and cryptic targets (grey wings and body). A fast-flying falcon primed to a conspicuous target centered on the roll might fail to detect the dodge initiated by the cryptic wings as the predator closes from behind. When pursued by predators, schools of fish in open water and many shorebirds also display their dark dorsal and light ventral surfaces in a display that alternates between a cryptic and a conspicuous signal. The use of contrasting patterns as an antipredator mechanism is widespread and may represent a case of convergent evolution. …

In the eastern part of the pigeon's native range in Eurasia, C. livia is sympatric with a subgenus of falcons, Hierfalco, that typically chase their prey in level flight. Pigeons from this region lack the white rump patch. The decline in recent decades of peregrine-falcon populations worldwide relaxed their selective pressure on feral pigeons, but this has now reversed, with falcons recolonizing many of their former haunts. Over the study period, the proportion of wild plumage types in our study population increased significantly relative to blue-barred types (P=0.01), in parallel with a steady increase in predation by peregrine falcons. This suggests that, although pigeon plumage polymorphism persists, falcon predation pressure can lead to an increase in the relative proportion of the wild pigeon phenotype.

Too cool.

461: Geobiology of a microbial endolithic community in the Yellowstone geothermal environment : Nature

Geobiology of a microbial endolithic community in the Yellowstone geothermal environment : Nature:

The endolithic environment, the pore space of rocks, is a ubiquitous habitat for microorganisms on the Earth1 and is an important target of the search for life elsewhere in the Solar System2. Photosynthetic, endolithic microbial communities commonly inhabit the outer millimetres to centimetres of all rocks exposed to the Earth's surface. In the most extreme terrestrial climates, such as hot and cold deserts, endolithic microorganisms are often the main form of life3, 4, 5. The endolithic microhabitat gives protection from intense solar radiation and desiccation, and it provides mineral nutrients, rock moisture and growth surfaces4, 5. Here we describe the discovery and identification of the constituents of an extremely acidic (pH 1) endolithic microbial community inhabiting the pore space of rocks in the geothermal environment of Yellowstone National Park, USA. Subjected to silica mineralization, such endolithic communities constitute biomarkers that can become fossilized and potentially preserved in the geological record. Remnants of these communities could serve as biosignatures and provide important clues about ancient life associated with geothermal environments on the Earth or elsewhere in the Solar System.

Understanding these bacteria and their evolution will help the search for extraterrestrial life and will clarify the fossil record of earth.

460: Researchers Make Gains in Understanding Antibiotic Resistance | Science Blog

Researchers Make Gains in Understanding Antibiotic Resistance | Science Blog:

Howard Hughes Medical Institute researchers chiseling away at the problem of antibiotic resistance now have a detailed explanation of how the drugs' main cellular target in bacteria evolves to become resistant to some of these medications. The findings are already leading to new experimental antibiotics that are being engineered to circumvent resistance, which is a major worldwide health problem.

459: Rockin' shrimp give dance signals to parasite-laden fish | Science Blog

Rockin' shrimp give dance signals to parasite-laden fish | Science Blog:

Using underwater field observations in conjunction with behavioral experiments, researchers have discovered that a small crustacean, the yellow-beaked cleaner shrimp, performs a specialized dance that affects the behavior of large, predatory client fish. This signaling represents shrimp-to-fish communication that allows both hungry cleaner shrimp and parasite-laden client fish to benefit from a non-predatory, "cleaning" interaction.

The cleaner-client relationship between the shrimp and the fish fulfills many criteria of an economic market, and in this context the shrimp's signals essentially represent "advertising." The work is reported by Justine Becker and colleagues at the University of Queensland.

These signals are evolved, and have to continue evolving to avoid dishonesty.

458: Hungry ants build a 'fibreglass' trap to put food on the rack

news @ nature.com - Amazonian ants ambush prey - Hungry ants build a 'fibreglass' trap to put food on the rack.:

Using a home-made trap, a tiny species of ant is capable of ensnaring prey much larger than itself and tearing it to pieces.

The ants (Allomerus decemarticulatus), which live in Amazonian plants called Hirtella physophora, construct a honeycomb-like structure out of their host plant's fibres from which they can stage an ambush.

We've discussed camouflage before. This is a more complicated, but the same considerations apply. The ongoing research will investigate the evolution of this behavior.

457: Low level of extinction during ice age linked to adaptability

Low level of extinction during ice age linked to adaptability:

A Johns Hopkins University graduate student may have figured out why rates of extinction were so low for many of the major groups of marine life during one of the greatest ice ages of them all, which occurred from about 330 million to 290 million years ago, late in the Paleozoic Era.

The likely answer: because those aquatic life forms that did survive during this era were singularly equipped to endure severe fluctuations in temperature and sea levels. Those that were not died in a mass extinction that heralded the ice age's onset.

"These results not only clue us in to what happened many millions of years ago, but they also have implications for understanding the modern marine ecosystem," said Matthew Powell, a doctoral candidate in the Morton K. Blaustein Department of Earth and Planetary Sciences at The Johns Hopkins University's Zanvyl Krieger School of Arts and Sciences. His paper on the topic appears in the May issue of Geology, published by the Geological Society of America.

That's natural selection at work on a massive scale.

456: Organic Materials Spotted High Above Titan's Surface | Science Blog

Organic Materials Spotted High Above Titan's Surface | Science Blog:

During its closest flyby of Saturn's moon Titan on April 16, the Cassini spacecraft came within 1,027 kilometers (638 miles) of the moon's surface and found that the outer layer of the thick, hazy atmosphere is brimming with complex hydrocarbons.

Scientists believe that Titan's atmosphere may be a laboratory for studying the organic chemistry that preceded life and provided the building blocks for life on Earth. The role of the upper atmosphere in this organic "factory" of hydrocarbons is very intriguing to scientists, especially given the large number of different hydrocarbons detected by Cassini during the flyby.

455: NASA Scientist: 'Mars Could be Biologically Alive'

NASA Scientist: 'Mars Could be Biologically Alive':

Mumma and his research colleagues have used ground-based spectrometers to carry out a simultaneous search for methane and water vapor. "Pronounced enhancements" of methane have been detected over several equatorial regions on Mars, consistent with "enhanced local release," Mumma reported.

In scientific terms, the methane line detected is "very strong indeed," Mumma noted. Using the high-tech infrared spectrometers, spectra of six narrow longitudinal bands across the face of Mars were taken. A spectra is an analysis of light broken into its rainbow of colors.

"Every one of these longitudes shows a very substantial enhancement in the equatorial zone," Mumma explained. "So this is a very intense source of methane on Mars in this region. It also requires a very rapid decay of methane…more rapid than photochemistry would allow," he added.

On Mars, the photochemical lifetime of methane is very short - roughly 300 years. Therefore, any methane now lingering within the martian atmosphere must have been released recently.

Mumma said that his data – along with what Mars Global Surveyor's Thermal Emission Spectrometer measured at the same time – suggests that "a major source" of methane over Valles Marineris is evident during the fall equinox on Mars.

Understanding the naturalistic processes which result from life on Earth helps us look for life elsewhere, and the search for life on Mars guides our understanding of the origins of life here.

Gates on IDC

Not Bill Gates, but S. James Gates, delivering the plenary at the AAAS meetings, in a talk called Einstein's Lesson for the Third Millenium:

Once, a high school student asked me two questions: "Was the only thing that Einstein did was to create theories?" and "Is all of science a theory?" I answered yes to both of these, and said, "Science is a process by which our species has obtained its most precise understanding of our home, the physical universe." Young students often think science is what you find in books, and I tell them, "That's like walking into a sculpture studio, looking down at the floor, and concluding that sculptors are people who make little piles of rock."

Several hundred years, if not thousands, have taught the scientific community that we must work in such a way as to account for our own fallibility. Thus, each generation of scientists is charged to check and recheck the scientific knowledge that's passed down to it and it's almost a unique attribute of science that we do this. Due to this cautious approach to wisdom, science casts its greatest achievements in the forms of theories. An accepted scientific theory must explain many, many facts, sometimes hundreds, thousands, or tens of thousands, but a single fact can destroy a theory.

Let me paraphrase Einstein about this. He said, "The unhappy fate of most theories is to be proven wrong shortly after being introduced. However, for those not so treated, at best nature says: 'Maybe.' "

I believe part of his legacy should guide our community in a debate that's occurring today in our nation. There is a set of suggestions, known as intelligent design, which have been offered as a scientific theory by some. We, in the scientific community, owe this discussion a respectful debate. First, to not do so would be a betrayal of our own cautiousness in approaching the gaining of wisdom. Second, historical examples show that faith-based communities do have the power to turn off science. Unless we rigorously and openly join this debate, our nation will move into the third millennium educating young ones who will be less than able to continue the progress we have seen so far.

But, for me, personally, this debate has another dimension. I spent all of my teenage years, as mentioned in the introduction, in Orlando, Florida. As many people know, the southern African American community is one with a deep tradition of religious faith. The bulk of my religious training occurred in the confines of the African American Methodist Episcopal Church. There, we were taught that faith is to be anchored on the inhuman perfection of religion. If intelligent design is accepted as science, then like all scientific theories, it is in principle possible to disprove it by the actions of human observation and thought. Thus, those who would join the inhuman perfection of religion to the human imperfection of science put both at grave peril for anyone who deeply contemplates them. Many in the AME church tradition, like me, must reject this idea that by thoughts and actions of man our faith can be called into question. This is the very greatest danger, in my opinion, of the notion of intelligent design.

I believe this debate would actually surprise Einstein, who commented so often about the practicality of Americans and America. We observe this practicality every day. If most Americans were told that a loved one were injured they would do two things: say a prayer and then pick up a cell phone. The first is a result of religion; the second is the final output of science. Most Americans see no need to choose either one or the other. And I believe Einstein would agree.

Here's another quote: "Does there truly exist an inseparable contradiction between religion and science? Can religion be superseded by science? The answers to these questions have for centuries given rise to considerable dispute and, indeed, bitter fighting. Yet, in my mind, there is no doubt that in both cases, dispassionate consideration can only lead to a negative answer." So, for our celebrant, Albert Einstein, this is not an either/or proposition.

I highlighted some interesting lines. His points are all well-taken. Treating the IDC movement as something to ignore will be a disaster. Engaging it head on has its own problems. All science suffers when people don't understand what science is and how scientists work.

His point about the unpleasant religious implications of forcing religious claims into the classroom is very apt. As always, TfK readers got that insight first.

454: Molecular fossils uncover link between viruses and the immune system

Molecular fossils uncover link between viruses and the immune system:

Researchers from the Viikki Biocenter, University of Helsinki, show that atomic structures can reveal evolutionary history of viruses in a similar fashion as fossils did for the dinosaurs and reptiles. Their article is published in the April 15 issue of Molecular Cell.

These "molecular fossils" also revealed that viruses and proteins of immune system share the same structure. One plausible explanation may be that viral building blocks served as precursors for the evolutionary more recent immune system of animals.

These results are an outcome of recent advances in structural biology, a new discipline integrating applied physics, biochemistry and biology, which have permitted detailed comparison of viral structures in atomic detail. Such comparison led to the discovery that viruses without any sequence homology may be related.

That's just wild. The evolution of viruses, and possibly of the immune system. Anyone who knows more about this, let me know.

453: Ancient enzyme guides healthy eating in mammals

Ancient enzyme guides healthy eating in mammals:

An ancient enzyme in the brains of mammals acts as an innate nutritionist of sorts, guiding them to make healthy choices about what to eat, according to new work published in the April issue of Cell Metabolism. The molecular mechanism is likely to be important in all mammals, including humans, that eat a varied diet comprised of meat and vegetables, the researchers said.

David Ron, of the New York University School of Medicine, and his colleagues found in mice that an enzyme known as GCN2 kinase sets off a cascade of events that relays information to the brain about the amino acid content of foods, enabling the animals to adjust their intake in favor of a more balanced meal. The same enzyme in yeast also acts as an amino acid sensor, earlier work has shown.

"This ancient pathway in mice recognizes drops in blood amino acid levels that occur following consumption of food with an imbalanced composition," said Ron. "That recognition culminates in a behavioral response that limits consumption of the imbalanced food and favors, by default, a more balanced diet."

The new findings confirm and extend a recent report by Dorothy Gietzen at the University of California, Davis, detailing the same pathway in rats. …

The findings reveal that the ancient amino acid-sensing pathway affects feeding behavior by activating a brain circuit that biases consumption against imbalanced food sources, the researchers said.

While the findings are in mice, "there's no reason to believe that the same mechanism isn't at work in humans," Ron said.

Why isn't there any reason to doubt that it works in people, too? Common descent. Following the evolution of this gene will reveal a lot about metabolism in different groups. Different species can synthesize different amino acids, and need different amounts of others. Understanding how they detect deficiencies and how the gene has adapted to different circumstances will reveal a lot about the history of modern species.

452: Open-System Coral Ages Reveal Persistent Suborbital Sea-Level Cycles -- Thompson and Goldstein 308 (5720): 401 -- Science

Open-System Coral Ages Reveal Persistent Suborbital Sea-Level Cycles -- Thompson and Goldstein 308 (5720): 401 -- Science:

Sea level is a sensitive index of global climate that has been linked to Earth's orbital variations, with a minimum periodicity of about 21,000 years. Although there is ample evidence for climate oscillations that are too frequent to be explained by orbital forcing, suborbital-frequency sea-level change has been difficult to resolve, primarily because of problems with uranium/thorium coral dating. Here we use a new approach that corrects coral ages for the frequently observed open-system behavior of uranium-series nuclides, substantially improving the resolution of sea-level reconstruction. This curve reveals persistent sea-level oscillations that are too frequent to be explained exclusively by orbital forcing.

This research relies on understanding the evolution of the corals, and it reveals important information about forces driving the evolution of life.

451: Who Killed the Elephants? -- Pasotti 2005 (411): 1 -- sciencenow

Who Killed the Elephants? -- Pasotti 2005 (411): 1 -- sciencenow:

At least 12 kinds of elephants and mammoths used to roam the African, Eurasian, and American continents. Today, only two species of elephants are left in South Asia and sub-Saharan Africa. One theory for this dramatic demise holds that rapid climate shifts at the end of the most recent major ice age, some 10,000 years ago, altered vegetation and broke up habitats, causing the death of those unable to adapt to the new conditions. Another hypothesis blames prehistoric humans, whose improved weapons and hunting techniques allowed them to wipe out whole herds of elephants and mammoths (Science, 8 June 2001, p. 1888).

To help resolve the debate, archaeologist Todd Surovell of the University of Wyoming, Laramie, and colleagues tested two assumptions. If humans caused the elephant and mammoth extinctions, Surovell reasoned, the timing of the die-offs in specific regions should match human expansion into those regions. On the contrary, if the extinction of these mammals were due to climate change, elephants and mammoths should remain in regions already colonized by humans and would only begin to die off once climate change occurred.

The team tested both theories by analyzing where and when elephants and mammoths were killed. In all, the study included 41 archaeological sites on five continents. The researchers found that, as humans migrated out of Africa, they left a trail of dead elephants and mammoths in their wake. The creatures disappear from the fossil record of a region once it became colonized by humans. Modern elephants survived in refuges uninviting to humans, such as tropical forests, says Surovell, whose team reports its findings online this week in the Proceedings of the National Academy of Sciences.

Evolutionary hypotheses about humans guided this research. Understanding why African and Asian elephants survived will reveal a lot about their evolution.

450: PLANT BIOLOGY: Closing the Wound -- Hurtley 308 (5720): 326c -- Science

PLANT BIOLOGY: Closing the Wound -- Hurtley 308 (5720): 326c -- Science:

In the normal cut and thrust of everyday life, nonfatal injuries are common, and organisms rely on rapid repair mechanisms to stanch the loss of fluids. Adolph et al. have studied the invasive tropical green alga Caulerpa taxifolia, which lives as single polyploid multinucleated cells. In the early 1980s, Caulerpa invaded the Mediterranean, and its mechanism of wound repair may have contributed to its high growth rates. When the algal cells are mechanically broken, a gelatinous material consisting of cross-linked proteins rapidly plugs the wound and results in two cells, each with a full genomic inheritance. Polymer formation depends on the enzymatic unmasking of caulerpenyne, the dominant secondary metabolite of the alga. Its 1,4-bis-enoylacetate moiety is transformed into a dialdehyde, which reacts with nucleophilic groups of algal proteins, forming a life-saving plug. -- SMH

Angew. Chem. Int. Ed. 44, 10.1002/anie.200462276 (2005).

Evolution of a novel wound healing technique. It's allowing the species to invade a new habitat, a perfect example of "survival of the fittest."

449: Molecular motors cooperate in moving cellular cargo

Molecular motors cooperate in moving cellular cargo, study shows:

Researchers using an extremely fast and accurate imaging technique have shed light on the tiny movements of molecular motors that shuttle material within living cells. The motors cooperate in a delicate choreography of steps, rather than engaging in the brute-force tug of war many scientists had imagined.

“We discovered that two molecular motors – dynein and kinesin – do not compete for control, even though they want to move the same cargo in opposite directions,” said Paul Selvin, a professor of physics at the University of Illinois at Urbana-Champaign and corresponding author of a paper to appear in the journal Science, as part of the Science Express Web site, on April 7. “We also found that multiple motors can work in concert, producing more than 10 times the speed of individual motors measured outside the cell.”

Dynein and kinesin are biomolecular motors that haul cargo from one part of a cell to another. Dynein moves material from the cell membrane to the nucleus; kinesin moves material from the cell nucleus to the cell membrane. The little cargo transporters accomplish their task by stepping along filaments called microtubules.

Common descent explains the similarities in cellular structure. Evolutionary biologists will use the details of the structures to understand the evolution of microtubules.

448: The Structure of a Retinal-Forming Carotenoid Oxygenase -- Kloer et al. 308 (5719): 267 -- Science

The Structure of a Retinal-Forming Carotenoid Oxygenase -- Kloer et al. 308 (5719): 267 -- Science:

Retinal and its derivatives participate in numerous cellular activities; they are crucial for vision and the immune system and are therefore of nutritional importance. Retinal-forming carotenoid oxygenases constitute a sequence-related family of more than 100 currently known members. The family was discovered through a 9'-cis-epoxycarotenoid oxygenase that participates in the biosynthesis of the important plant hormone abscisic acid. A prominent family member is ß-carotene-15,15'-oxygenase from animals, which cleaves ß-carotene symmetrically to two molecules of retinal. Another member is ß-carotene-9',10'-oxygenase, cleaving ß-carotene asymmetrically to form apo-10'-ß-carotenal, which is thought to be converted to retinoic acid, a key actor in developmental processes. The family includes the retinal pigment epithelial protein RPE65, mutations of which cause Leber's congenital amaurosis, a severe blinding disease. In plants, the genome of Arabidopsis thaliana codes for as many as nine family members, several of which have been established as carotenoid oxygenases. Some of these genes yield products regulating growth and development. Other plant members catalyze the biosynthesis of pigments. Cyanobacterial retinal-producing members have been proposed and recently identified in Synechocystis. Here, we report the crystal structure of the Synechocystis enzyme at 2.4 Å resolution, revealing the reaction geometry and establishing a solid base for modeling all other family members.

These folks are interested in retinal because it occurs in animals and plants, and in the cyanobacteria which may be ancestral to modern plant chloroplasts. This particular retinal may inform us on the evolution of photosynthetic plants.

447: Anthropology: The earliest toothless hominin skull

Anthropology: The earliest toothless hominin skull:

The site of Dmanisi in the Eurasian republic of Georgia has yielded striking hominin, faunal and archaeological material as evidence for the presence of early Homo outside Africa 1.77 million years ago, documenting an important episode in human evolution. Here we describe a beautifully preserved skull and jawbone from a Dmanisi hominin of this period who had lost all but one tooth several years before death. This specimen not only represents the earliest case of severe masticatory impairment in the hominin fossil record to be discovered so far, but also raises questions about alternative subsistence strategies in early Homo.

The evolution of social behavior. This individual was probably fed by relatives. Nifty.

446: New material of the earliest hominid from the Upper Miocene of Chad

New material of the earliest hominid from the Upper Miocene of Chad:

Discoveries in Chad by the Mission Paléoanthropologique Franco-Tchadienne have substantially changed our understanding of early human evolution in Africa. In particular, the TM 266 locality in the Toros-Menalla fossiliferous area yielded a nearly complete cranium (TM 266-01-60-1), a mandible, and several isolated teeth assigned to Sahelanthropus tchadensis and biochronologically dated to the late Miocene epoch (about 7 million years ago). Despite the relative completeness of the TM 266 cranium, there has been some controversy about its morphology and its status in the hominid clade. Here we describe new dental and mandibular specimens from three Toros-Menalla (Chad) fossiliferous localities (TM 247, TM 266 and TM 292) of the same age. This new material, including a lower canine consistent with a non-honing C/P3 complex, post-canine teeth with primitive root morphology and intermediate radial enamel thickness, is attributed to S. tchadensis. It expands the hypodigm of the species and provides additional anatomical characters that confirm the morphological differences between S. tchadensis and African apes. S. tchadensis presents several key derived features consistent with its position in the hominid clade close to the last common ancestor of chimpanzees and humans.

Filling in the tree of life, tying the early human clade to the rest of the apes. Evolving Thoughts has, surprise surprise, some thoughts.

445: Evolutionary biology: Channels of resistance

Evolutionary biology: Channels of resistance:

The softshell clam (Mya arenaria) occurs around the Atlantic coast of North America. The clams can become contaminated with saxitoxin, the cause of paralytic shellfish poisoning in humans and economic losses to the shellfish industry. The toxin is produced by 'red tide' algae and finds its way into the clams when the algae are ingested. V. Monica Bricelj et al. (Nature 434, 763–767; 2005) show that clams from areas subject to recurrent red tides are relatively resistant to the toxin and tend to accumulate it in their tissues. But clams from unaffected areas have low resistance when exposed to the toxin in the laboratory. These differences were mirrored by the sensitivity of isolated clam nerve-trunks exposed to the toxin in vitro.

To investigate the underlying molecular mechanism, Bricelj et al. sequenced the genomic region encoding a putative voltage-gated sodium channel. Such channels sit in cell membranes and regulate ion flow. The authors found a single mutation that correlated with resistance to the toxin, and that results in replacement of a glutamic acid by aspartic acid at a site previously implicated in the binding of saxitoxin. When introduced into a channel from rat brain, this mutation did not affect ion conductance. But the sensitivity of the channel to saxitoxin was greatly reduced owing to a large decrease in the binding affinity of the toxin at the channel pore.

Saxitoxin produced by red-tide algae probably acts as a potent selective agent on the clams, leading to genetic adaptation, the target of selection being genetic variation at a single site in an ion channel.

This is a similar mechanism to the garter snake's response to newt toxin. Evolution at work. Testable evolutionary hypotheses, being tested.

444: Bivoltinism as an Antecedent to Eusociality in the Paper Wasp Genus Polistes -- Hunt and Amdam 308 (5719): 264 -- Science

Bivoltinism as an Antecedent to Eusociality in the Paper Wasp Genus Polistes -- Hunt and Amdam 308 (5719): 264 -- Science:

To learn the evolutionary trajectories of caste differentiation in eusocial species is a major goal of sociobiology. We present an explanatory framework for caste evolution in the eusocial wasp genus Polistes (Vespidae), which is a model system for insect eusocial evolution. We hypothesize that Polistes worker and gyne castes stem from two developmental pathways that characterized the bivoltine life cycle of a solitary ancestor. Through individual-based simulations, we show that our mechanistic framework can reproduce colony-level characteristics of Polistes and, thereby, that social castes can emerge from solitary regulatory pathways. Our explanatory framework illustrates, by specific example, a changed perspective for understanding insect social evolution.

Testable evolutionary hypotheses. Computer simulations show that this mechanism is feasible, and research on wasps will reveal whether it explains the evolution of true sociality in the wasps.

443: Ipr1 gene mediates innate immunity to tuberculosis

Ipr1 gene mediates innate immunity to tuberculosis:

An estimated eight million people are infected each year with the pathogen Mycobacterium tuberculosis, and more than two million die annually. Yet only about 10% of those infected develop tuberculosis. Genetic variation within host populations is known to be significant in humans and animals, but the nature of genetic control of host resistance to tuberculosis remains poorly understood. Previously we mapped a new genetic locus on mouse chromosome 1, designated sst1 (for supersusceptibility to tuberculosis 1). Here we show that this locus mediates innate immunity in sst1 congenic mouse strains and identify a candidate gene, Intracellular pathogen resistance 1 (Ipr1), within the sst1 locus.

Did you see how they just slipped between people and mice? Like it made perfect sense? That's evolution at work. The same gene in both species, and it has the same effect. In addition to making people susceptible to disease, it may have effects on various cellular mechanisms.

442: Developmental biology: Reproduction in clusters

Developmental biology: Reproduction in clusters:

Homeobox genes have some quirky features: they huddle together and tend to be expressed in the order that they appear in their cluster. A new cluster, specific to reproductive development, has now been discovered.

The survival of animal species depends upon the proper development of germ cells: oocytes and sperm. In mammals, this process is tightly coordinated with the development of non-reproductive cells nearby, such as Sertoli cells, which nourish developing sperm cells1. Changes in the delicate interactions between reproductive and non-reproductive cells are often a source of decreased fertility, so the appropriate regulation in time and space of the underlying genetic determinants must be essential. Writing in Cell, MacLean et al.2 describe how they identified a new set of these genetic determinants — a cluster of homeobox genes that are expressed during the development of germ cells. The clustering of these genes may help to determine their spatial and temporal regulation.

Hox genes are conserved through much of Animalia, and help explain the development of novel structures within existing body forms. Very neat.

441: Stirring the primordial soup

Stirring the primordial soup:

Circumstantial evidence for the central position of RNA in the origin of life can be found in 'relic' pieces of RNA that hold a few of the most important functions in the cell. Perhaps the most convincing observation is that, in the synthesis of proteins on the ribosome, the key chemical event — peptide-bond formation — is catalysed solely by RNA, suggesting that primacy lies with RNA rather than protein. A major impediment to full acceptance of an 'RNA world' is that, although it can easily be imagined that a pure RNA machine (a proto-ribosome) can make proteins, there is no equivalent RNA machine to make RNA (a ribopolymerase). All the RNA we know is made by protein, leading to perhaps the original 'chicken-and-egg' problem of which came first.

Taylor proposes a model of the transition from free-floating RNA to encapsulated RNA, which may resolve the problem. Testable evolutionary hypotheses. Hurray!

440: BIOCHEMISTRY: Subunit Arithmetic

BIOCHEMISTRY: Subunit Arithmetic - Science -- Editor's Choice {08 April 2005; 308 (5719)}:

The largest and least well-described (in structural terms) of the five respiratory enzyme complexes in mammalian mitochondria is the NADH:ubiquinone oxidoreductase, also known as complex I. Only recently has it been determined that the number of distinct subunits is 46, in comparison to 30 and 14 for the corresponding complex I orthologs in plants and bacteria, respectively. Applying a comparative genomic analysis using both nuclear and organellar sequence data, Gabaldón et al. show that complex I in the eukaryotic ancestor of the fungi, plants, and metazoa had grown to 35 subunits from the simpler bacterial/archaeal core, having added subunits that came along as the endosymbiont was acquired and stabilized and gaining new recruits from the host. In the subsequent eukaryotic radiation, more subunits have been added to and subtracted from all over the complex, as judged by the three-dimensional maps generated from biochemical and electron microscopic studies. This piecemeal aggrandizement contrasts with the modular assembly of existing multisubunit enzymes into the prokaryotic complex I.

Understanding the evolution of mitochondria. Very cool. Note the description of "piecemeal aggrandizement," which is to say, not designed.

439: Biodiversity in Sri Lanka and the Western Ghats -- Helgen et al. 308 (5719): 199b -- Science

Biodiversity in Sri Lanka and the Western Ghats -- Helgen et al. 308 (5719): 199b -- Science:

We read with interest the Report "Local endemism within the Western Ghats-Sri Lanka biodiversity hotspot" by F. Bossuyt et al. (15 Oct. 2004, p. 479), which documents patterns of diversification in selected vertebrate and invertebrate lineages from Sri Lanka and the Western Ghats region of western India. Although these two areas have long been united as a single biogeographic unit (1), and more recently as a biodiversity "hotspot" (2), Bossuyt et al. highlight the distinctive faunal histories of the two regions and caution against treating them as a single unit for conservation purposes.

A hierarchal pattern of biogeography? Almost as if historical events had driven some sort of process, a process involving descent and modification. What name should we give this? Evolution? Yes, let's.

438: STRUCTURAL BIOLOGY: "D" Is Not for Diversity -- Garboczi 308 (5719): 209 -- Science

STRUCTURAL BIOLOGY: "D" Is Not for Diversity -- Garboczi 308 (5719): 209 -- Science:

our structural understanding of γδ TCRs is limited because, until now, the only structures available have been those of a Vδ domain from a human γδ TCR (4) and a γδ TCR expressed by human γδ T cells in the bloodstream (5). These structures reveal the domains of γδ TCRs and a putative antigen-binding site, but not how a γδ TCR binds to its antigen. Unlike antibodies and αβ TCRs, γδ TCRs have few known ligands. For a molecular understanding of γδ T cell function, we need to know the antigens that γδ TCRs bind and how they are recognized. This requires determining the structure of a γδ TCR in a complex with its antigen. The best-known antigens for mouse γδ TCRs are the nonclassical MHC proteins known as T10 and its close relative T22 (6). Now, Shin et al. (2) demonstrate that there is a substantial population of mouse γδ T cells bearing surface TCRs that carry a full-length D gene segment (Dδ2) and bind to the T22 molecule. In a complementary study, Adams et al. (3) determine the crystal structure of a γδTCR/T22 complex. Their structure reveals how G8, one of the γδ TCRs studied by Shin et al., binds to the T22 molecule--G8 uses amino acid residues encoded by the Dδ2 gene.

Unlike αβ TCRs that recognize and bind to antigenic peptides complexed with MHC molecules, γδ TCRs do not recognize peptides. In fact, their recognition of T22 molecules does not depend on the cellular antigen-processing machinery that generates antigenic peptides.

I'm confident that that text is all in english. It relates to the evolution and structure of the immune system in humans and mice. Common descent, evolutionary hypotheses, etc.

436-437: CELL BIOLOGY: GSK-3ß and Microtubule Assembly in Axons -- Zhou and Snider 308 (5719): 211 -- Science

CELL BIOLOGY: GSK-3ß and Microtubule Assembly in Axons -- Zhou and Snider 308 (5719): 211 -- Science:

Two papers recently published in Cell (3, 4), together with other recent work, suggest that glycogen synthase kinase 3ß (GSK-3ß) is a crucial player in the regulation of axon morphogenesis downstream of phosphatidylinositol 3-kinase (PI3K) signaling. First purified in 1980, GSK-3ß is a serine/threonine kinase that mediates the inactivation of glycogen synthase. Surprisingly, GSK-3ß has emerged as a key regulatory kinase in the nervous system with involvement in processes ranging from neural development to mood stabilization to neurodegeneration.

These are studies on the shared microtubule arrangements of neurons. More on microtubules back here. This is common descent, and it generates evolutionary hypotheses about these proteins.

435: Estimating Duration and Intensity of Neoproterozoic Snowball Glaciations from Ir Anomalies -- Bodiselitsch et al. 308 (5719): 239 -- Science

Estimating Duration and Intensity of Neoproterozoic Snowball Glaciations from Ir Anomalies -- Bodiselitsch et al. 308 (5719): 239 -- Science:

The Neoproterozoic glaciations supposedly ended in a supergreenhouse environment, which led to rapid melting of the ice cover and precipitation of the so-called cap carbonates. If Earth was covered with ice, then extraterrestrial material would have accumulated on and within the ice and precipitated during rapid melting at the end of the glaciation. We found iridium (Ir) anomalies at the base of cap carbonates in three drill cores from the Eastern Congo craton. Our data confirm the presence of extended global Neoproterozoic glaciations and indicate that the duration of the Marinoan glacial episode was at least 3 million, and most likely 12 million, years.

This isn't evolution per se, though an easy case can be made that species changes 600-700 million years ago were the first tip off that something happened. This is a neat example of science at work. A hypothesis generates an unlikely prediction (a prediction unlikely to be true if the hypothesis is false, but likely to be true of the hypothesis is true). That prediction comes true, and the hypothesis itself is considered more likely.

434: An Off-and-On Switch for Controlling Animals?

The New York Times > Science > An Off-and-On Switch for Controlling Animals?:

[R]esearchers at Yale have done Galvani one better. They can make fruit flies walk, leap or fly by shining a laser at the insects, setting off certain neurons inside them.

It's possible, at least in theory, that this method could someday be developed into a sort of animal remote control. But its biggest promise is as a scientific tool that may shed light on the function of different kinds of neurons. The ability to switch on particular neurons may allow scientists to discover clues about a range of disorders, from Parkinson's disease to drug addiction.

Dr. Susana Lima and Dr. Gero Miesenböck, the authors of the study, engineered a light-sensitive trigger that could be attached to neurons of flies.

The researchers began their work by transplanting a gene related to the structure of certain pain-sensing neurons in rats. Dr. Lima and Dr. Miesenböck added genetic on-switches to the rat gene so that it would become active only in a particular type of neuron in a fly.

To turn the transplanted rat channels into light-sensitive triggers, Dr. Lima and Dr. Miesenböck then took advantage of the way the altered neurons produced electric impulses. Unlike fly neurons, the altered cells could produce electric impulses only in the presence of a molecule called ATP.

Very cool. Using the shared architecture of rats and flies, shared because of common descent, they are learning to control fly neurons. By controlling that, they hope to have similar control over vertebrate neurons, curing diseases like Parkinson's.

Kline in the news

This was supposed to be at Thoughts from Kansas.

433: Space Explosions May Have Initiated Extinction on Earth | Science Blog

Space Explosions May Have Initiated Extinction on Earth | Science Blog:

Scientists at NASA and the University of Kansas say that a mass extinction on Earth hundreds of millions of years ago could have been triggered by a star explosion called a gamma-ray burst. The scientists do not have direct evidence that such a burst activated the ancient extinction. The strength of their work is their atmospheric modeling -- essentially a "what if" scenario.

The scientists calculated that gamma-ray radiation from a relatively nearby star explosion, hitting the Earth for only ten seconds, could deplete up to half of the atmosphere's protective ozone layer. Recovery could take at least five years. With the ozone layer damaged, ultraviolet radiation from the Sun could kill much of the life on land and near the surface of oceans and lakes, and disrupt the food chain.

Dr. Bruce Liebermann, also of KU, started the idea that the Ordovician extinction was triggered by a gamma ray burst. This research is inspired by evolutionary biology, and generates testable hypotheses. Ongoing space missions will gather vital data, and paleontological data will test claims about past events.

432: Early Earth atmosphere hydrogen-rich, favorable to life

U. of Colorado study shows early Earth atmosphere hydrogen-rich, favorable to life:

A new University of Colorado at Boulder study indicates Earth in its infancy probably had substantial quantities of hydrogen in its atmosphere, a surprising finding that may alter the way many scientists think about how life began on the planet.

Published in the April 7 issue of Science Express, the online edition of Science Magazine, the study concludes traditional models estimating hydrogen escape from Earth's atmosphere several billions of years ago are flawed. The new study indicates up to 40 percent of the early atmosphere was hydrogen, implying a more favorable climate for the production of pre-biotic organic compounds like amino acids, and ultimately, life.

This isn't proof, but it's encouraging to find support for our predictions. This is research inspired by evolution and supportive of evolutionary hypotheses.

431: RNA Polymerase IV Directs Silencing of Endogenous DNA -- Herr et al. 308 (5718): 118 -- Science

RNA Polymerase IV Directs Silencing of Endogenous DNA -- Herr et al. 308 (5718): 118 -- Science:

An RNA polymerase in plants which evolved to control repetitive DNA and certain transoposons. Evolutionary hypotheses, common descent. They compare rice and Arabidopsis and generate a phylogeny showing the evolution of the novel polymerase.

430: Phage Stimulated by Antibiotic Exposure

Mike the Mad Biologist: Phage Stimulated by Antibiotic Exposure (Huh?!):

A recent paper in Applied and Environmental Microbiology demonstrated that exposure to the antibiotic norfloxacin to E. coli O157:H7 resulted in increased transcription of gene products associated with Stx phage. I'll take the time to explain this in English. O157:H7 is a strain of E. coli that can caused lethal food poisoning, and is also found in cattle (where it doesn't cause disease). Some of the really nasty compounds that cause disease ('shiga toxins') are encoded by genes found in bacterial viruses, or phage. Essentially, when the bacterium is exposed to antibiotics, the cell produces more toxins.

That means that more virulent E coli result from inadequate antibiotic treatment.

429: Deadly newt no match for highly evolved garter snake | Science Blog

Deadly newt no match for highly evolved garter snake | Science Blog:

An evolutionary arms race between predatory garter snakes and their newt quarry is turning out to be something of an illusion. At the molecular level, another battle rages. And in this second, miniature realm, it's the newt who's the aggressor.

Biologists at Indiana University Bloomington, Utah State University and the University of Utah present evidence in this week's Nature that a toxin produced by the rough skinned newt, Taricha granulosa, has forced several evolutionary changes in the garter snake Thamnophis sirtalis or, more specifically, in the snake nerve cell protein that endures the toxin's attacks.

Evolutionary hypothesis tested. New information added to genes. Cool biology.

416-428: Mad Biology

Thanks to Mike the Mad Biologist for this breakdown. Others are encouraged to do the same.

So it's that time again, when the Mad Biologist downloads more interesting science articles that I'll never get around to reading. As before, this is not an all-inclusive list, just some stuff I found interesting. Hopefully, Josh will get around to posting this on the Evolution Project. For those of you too dim to figure it out, evolution is really important for understanding microbiology.

Nonhomogeneous Model of Sequence Evolution Indicates Independent Origins of Primary Endosymbionts Within the Enterobacteriales (gamma-Proteobacteria), Herbeck et al. (2005) Mol. Biol. Evol. 22: 520.

This paper uses non-standard molecular models to reconstruct the evolutionary history of insect bacterial endosymbionts.

The evolution of groups of cooperating bacteria and the growth rate versus yield trade-off, Kreft et al. (2005) Microbiology 151: 637.

One of the issues this article addresses is why bacteria haven't evolved multicellularity.

Osteocalcin protein sequences of Neanderthals and modern primates, Nielsen-Marsh (2005) PNAS 102: 4409.

So there's no microbiology. I think anytime you can do protein chemistry on 75,000 year old molecules and relate it to evolution, it's pretty cool.

Integrons in Xanthomonas: A source of species genome diversity, Gillings et al. (2005) PNAS 102: 4419.

The integration of gene cassettes into Xanthomonas has resulted in ecological differentiation within this genus.

A mechanism for the association of amino acids with their codons and the origin of the genetic code, Copley et al. (2005) PNAS 102: 4442.

This article discusses the evolution of the genetic code.

Detecting amino acid sites under positive selection and purifying selection, Massingham et al. (2005) Genetics 169: 1753.

This article describes a technique for determining which amino acids in a protein are under selection.

Evolution of genomic content in the stepwise emergence of Escherichia coli O157:H7, Wick et al. (2005) J. Bacteriology 187: 1783.

This article describes how a nice, run-of-the-mill E. coli evolved into a highly virulent pathogen (and I've mentioned O157:H7 before).

Escherichia coli strains belonging to phylogenetic group B2 have superior capacity to persist in the intestinal microflora of infants, Nowrouzian et al. (2005) Journal of Infectious Diseases 191: 1078.

One group of E. coli descended from a common ancestor persist longer in infants.

Antimicrobial-resistant and extraintestinal pathogenic Escherichia coli in retail foods, Johnson et al. (2005) Journal of Infectious Diseases 191: 1040.

Population genetic analyses indicate that retail foods are an important vehicle for community-wide dissemination of antimicrobialresistant E. coli and extra-intestinal pathogenic E. coli (such as those that cause urinary tract infections).

Evolutionary origins and sequence of the Escherichia coli O4 O-antigen gene cluster, D'Souza et al. (2005) FEMS Microbiology Letters 244: 27.

"Sequencing of the E. coli O4 O-antigen gene cluster revealed a similar gene order and high levels of similarity to that of E. coli O26; indicating a common ancestor. These lateral transfer events observed within O-antigen gene clusters may occur as part of the evolution of the pathogenic clones."

Tackling the population genetics of clonal and partially clonal organisms, Halkett et al. (2005) Trends in Ecol. and Evol. 20: 194.

A summary of how to do population genetics in clonal organisms. I have a feeling I'm going to be disappointed with this article...

Falsifications and corroborations: Karl Popper's influence on systematics, Helfenbein et al. (2005), Molecular Phylogenetics and Evolution 35: 271.

"In this paper, we provide the reader with a concise summary of Popper s ideas relevant to systematics, review the systematic literature invoking or declining Popper s importance to the field, and make a recommendation for the future course of philosophical thinking in systematics. We try to make clear various authors interpretations of Popper's work and how those interpretations have impacted systematic thought." Hey, we are supposed to doctors of philosophy after all...

Nucleotide substitution and recombination at orthologous loci in Staphylococcus aureus, Hughes et al. (2005), Journal of Bacteriology 187: 2698.

Genes related to pathogenesis have undergone recombination, suggesting that recombination plays a significant role in the evolution of pathogenesis.

415: Water Found on Mars

APOD: 2005 April 1 - Water on Mars:

Can you help discover water on Mars? Finding water on different regions on Mars has implications for understanding its complex geologic history, the possible existence of past life and the sustenance of potential future astronauts. Many space missions have taken photographs of the surface of the red planet, and some of them might show a subtle clue pointing to water on Mars that has been missed. By close inspection of images, following curiosity, applying scientific principles, applying knowledge about features on the Martian surface, and applying principles of planetary geology, such clues might be brought to light.