Friday, April 04, 2014

Natural fluorescence by chlorophyll as seen by satellite

Wired Magazine shows a cool satellite image showing chlorophyll-dependent fluorescence over the United States, based on an article which appeared in the March 25 issue of PNAS. Basically, light energy hitting the chloroplast can be successfully harvested to drive energy production; can be lost as heat; or can be reemitted as fluorescence. Chlorophyll dependent fluorescence in healthy plants
Chlorophyll-dependent fluorescence over North America.
Most of the signal is attributed to cornfields. 
accounts for 1-2% of the energy absorbed, and its intensity is thus is an indirect measure of photosynthesis. Sunlight-induced chlorophyll fluorescence is most prominent in the red and infrared portion of the spectrum.
The strong signals shown in the figure can be attributed to massive photosynthesis in North American cornfields, which exceeds that of the Amazon basin during the North American growing season.
Fluorescence by chlorophyll increases when plants are under stressed, and can be used on a laboratory scale to monitor response to drought or pathogens. Back at the satellite level, this phenomenon is also used to phytoplankton blooms in oceans.

Wednesday, March 26, 2014

3D construction of a blowfly in flight

There are a set of amazing reconstructions of the flight motion of a blowfly, available on YouTube, which show the workings of the muscles and exoskeleton. It looks like a steam engine. Very cool data visualization--  and a breakthrough in X-Ray technology to obtain the images.
YouTube #1
YouTube#2
YouTube#3

Thursday, March 13, 2014

Science of soccer ball aerodynamics

Deadspin has a great preview of the World Cup soccer ball, the Brazuca, and an analysis of whether the ball will swerve as much as the versions used in 2006 and 2010. Basically, knuckleball-like flight happens when the ball is under high drag, which occurs at low speeds.  In any soccer ball, the seams disturb the air flow and diminish drag,  making the ball's flight straight (its trajectory can be bent by spinning the ball). The South Africa World Cup ball, the Jabulani, had reduced seam depth, and therefore could "knuckle," exhibiting erratic behaviors due to high-drag flight, [YouTube] at much higher speeds than normal play balls would. The verdict on the Brazilian Brazuca ball is that its aerodynamics are likely to be to be much more like conventional balls. The blog entry has charts and imaging to make the case! Still can't wait.

Forged painting revealed by isotope analysis

The Contraste de Formes, now considered a fake.
Source: European Physical Journal 
There's a great detective story in the January issue of European Physical Journal, showing how a painting attributed to an artist can be proven to be a fake. The cotton fibers of the canvas in question showed the carbon-14 signature of the atomic age atmospheric tests, and the painting must therefore have been made after the death of the artist.
From about 1950 to 1963, testing of atomic bombs generated large amounts of carbon-14 in the atmosphere, sharply increasing the ratio of this isotope to the more common carbon-12. This atmospheric carbon-14 was taken up by living things worldwide, creating an unmistakable isotopic signature of the atomic era. This "bomb effect" carbon has been used to identify poached ivory , to give evidence for the birth of new neurons in the adult human brain, and to reveal a supposedly ancient mummy as a modern fake.
In the recent paper, the authors examined a canvas, Contraste de Formes,  in the Guggenheim collection in Venice. This canvas was purportedly one of a known series of paintings by this name painted by Fernand Leger, a cubist artist, between 1912 and 1914. Even in the 1970s, the owners of the painting had had some doubts about its authenticity.  This work was painted on cotton, not linen, and used different pigments for some colors compared to others in the series known to be from Leger. But these differences could not settle the question of whether Leger had painted it.
 In the new scientific study, the authors took a snippet of canvas and analyzed it for the carbon 14/carbon12 ratio. They found that carbon-14 was more than 40% higher than would be expected from a pre-atomic age item. Instead, the cotton plants used to make the canvas had to have been harvested in  1959 at the earliest. This final date settled the authorship question, as Leger died in 1955! The painting has to be a fake.

Thursday, March 06, 2014

Winter of 2013/2014-- ice coverage of Great Lakes nearing a record

Coverage of the Great Lakes on Feb 13, 2014. Paler shades
represent greater ice coverage. Source: NOAA
The Great Lakes system is more than 90% covered by ice right now, and is approaching the record of 95% set back in 1994. The ice is forming very rapidly now-- for example, Lake Superior was 78% covered in the last week of February, and is now at 95% coverage. The maximum ice cover of the lower lakes typically forms by the end of February, and the more northerly lakes max out a little bit later.
The ice cover on the lakes affects weather patterns over a large area, particularly to the east. Open water contributes to lake effect snow, and pulls the jet stream northward . The  winter severity of the lake system itself  is sensitive to worldwide atmospheric circulation events such as el Nino or la Nina.

Wednesday, March 05, 2014

30,000 year-old virus recovered from Permafrost

Nature has a news blurb about the isolation of a still-infectious viral particle from 30,000 year-old Siberian Permafrost. The story started with the 2012 report of the recovery of a blooming plant, which was germinated from fruits which had been cached in burrows by ancient squirrels. Researchers in France contacted the Russian field scientists and obtained soil samples from the same dig. The French team was interested in giant viruses, a recently discovered class which infects amoebas. So they basically exposed amoebas to the soil samples- and indeed, some samples contained a pathogen which killed the amoebas.
The new virus is named Pithovirus sibericum, and like other giant viruses, its genome is handled in an almost microbial fashion, with the large DNA genome not compacted, as in more familiar viruses. The DNA sequences have yielded lots of unknown sequences potentially encoding genes. It will be interesting to see how these viruses relate to the rest of the viral world, especially if there would be hints of another kingdom of life. 

Saturday, February 22, 2014

How fruit flies home in while in flight

Fruit flies are strongly attracted by the scent of fermenting fruit or wine. But, unlike photons or sound waves, odors do not travel in straight lines, but waft and form areas of high and low concentration. Thus it’s difficult for the fly to rely on scent alone to find that delicious rotting banana you left on the table. Since flies accomplish this efficiently and with a limited brain size, they’re also an interesting case from a computational point of view.
Homing in on a strawberry. 
A truly beautiful investigation of this plume-tracking behavior of fruit flies  appeared in this month’s Current Biology. The investigators  used a miniature wind tunnel and time-lapse photography to track fruit flies as they approached a piece of fruit.
To localize an odor source, flies rely on three reflex-driven behaviors. The first two are related to in-flight adjustment. Upon detecting the scent, flies turn upwind, using their eyes to help them orient themselves; and,  if they lose the trail, they exhibit a second behavior, casting about crosswind to try to pick up the scent again. Most intriguingly, all this time after sensing the odor, the flies become visually attracted to small, contrasty  objects, which in the wild would be likely to be the piece of fruit emitting the odor. In a way, all three of these make intuitive sense-- think of trying to locate the coffee stand at a crowded market hall; you see people carrying cups, and you smell coffee (and you, like the flies, are probably not welcome to feed on their drinks). So you integrate cues from both senses to locate the good stuff. 

What I also enjoyed about the article was the presentation of the data- the figures displayed the very complicated data set in a way that communicated the point effectively. I was happy to see that the lead author, Floris van Breugel, also maintains a nature photography blog.

Friday, February 21, 2014

Analyzing the RNA differences between queens and workers

Over the past 30 or so years, biology has entered a second Linnaean revolution, in which our understanding of the relationships among living things has been radically re-organized, in this case driven by DNA and RNA sequencing data. Carl Woese and the identification of Archaea as a third kingdom of life is probably the most dramatic re-interpretation of the tree of life, and I would say that the bounty of viruses and non-culturable prokatyotes in metagenomc samples will eventually contribute a lot of detail.
The new information flow has been enabled by improvements in the sensitivity and throughput of next-generation DNA sequencing. Newer studies can be geared to either detect miniscule amounts of genetic material, or to capture rare variants through deeply analysis. 
This same technology can be used to investigate the relationship between genotype and phenotype. The ability to retrieve sequence from a small, focused sample makes it possible to understand the behavior of genomic material during the adpotion of alternative phenotypes. In  a paper in Molecular Ecology, Feldmeyer et al. have used this same
A queen and workers of Temnothorax ants. 
sequencing technology to analyze RNA expression differences among castes of ants in a colony. A major challenge in evolutionary biology, dating back to Darwin, is to explain the evolution of insect castes, particularly sterile workers, who contribute to the colony without possibility of direct descendants. Since they share so much of their genome, the dramatic phenotypic differences between queens and workers must arise chiefly through different gene expression, which in turn must be influenced by the food the individual receives as a larva, signals within the colony, and the environment. Social insects thus provide a great opportunity to explore the relationship between many copies of a stable genome and the range of phenotypes it can generate.
In the January issue of Molecular Ecology, Feldmeyer et al studied the ants Temnothorax longispinosus, with the overall goal of identifying RNAs which differed among the queens and various worker types. This common woodland species was chosen because some workers maintain the ability to develop ovaries and reproduce if the queen is removed. Thus the genes associated with reproductive ability would be present in a gradient from sterile workers, to fertile workers, to queens.
In the study, RNA was prepared from insects within a single colony—thus, closely related—with RNA prepared separately for each caste. Deep sequencing analysis of the RNA yielded in a very large number of previously undescribed RNA sequences. Furthermore,, the prevalence of completely novel genes was much higher  in workers, suggesting that the RNA repertoire of the worker is more derived, cladistically speaking, than the corresponding repertoire used by  the queen.

My take is that this kind of work is still in its infancy, analogous to the first naturalists to travel into the rain forests, gathering and annotating species. The next Voyage of the Beagle may be happening, with a synthesis to appear decade from now.

Wednesday, February 19, 2014

Frank Zappa has his own bacterium

A new bacterial isolate infesting vineyards turns out to be a recently emerged variant of the same bacterium which causes human acne. The new isolate is dubbed Propionibacterium Acne Zappa, in honor of Frank Zappa's song lyrics of "sand-blasted zits." In new work in Molecular Biology and Evolution,  Italian scientists have confirmed that the bacterium, which infests the bark and leaves of grapevines, is descended from the human acne-causing bacterium. It is very rare for pathogens to jump between evolutionary kingdoms, i.e. from animals to plants.
This work will appear in today's issue of Molecular Biology and Evolution.

Sunday, February 16, 2014

Bright birds and drab dinosaurs

What color were the dinosaurs? Since both reptiles and birds come in a wide variety of colors, it seems reasonable to think that dinosaur also had colored skin. Skin color is provided by melanosomes, structures within the skin cell which also block the sun's rays. So the trick to determining the color of fossil skin has been thought to lie in the shape and number of the melanosomes.
Deducing feather color from melanosome shape. Panel
(a) shows the fossil in visible light, and (b) and(.c) show
progressively higher scanning EM magnifications. 
Melanosomes are visible in (.c) as little moulds or pockets, 
indicated by the arrows. Source: Zhang et al., Nature
This line of research got a big boost in 2010 with the deduction of the plumage colors of feathered dinosaurs, by looking at the shape of their melanosomes, which in modern birds correlate  with a specific color palette.  The identification of melanosome shape is an apparently arduous procedure (see the example at left) and requires very high quality preservation in the fossil. Moreover, this approach has the limitation for example that microscopic shapes could change during the fossilization process. Still, it's remarkable how clearly the two main categories of melanosome in bird feathers can be recognized in these fossil impressions.
A new twist on skin color paleontology has recently come out in this week's Nature. Scientists were trying to systematically look at melanosomes across the animal kingdom, and found that the remarkable correlation between melanosome shape and color holds best for mammals, birds, and (by extrapolation) maniraptoran dinosaurs. Thus it would not be so easy to assign skin color to fossils from species like T-Rex, which  fall outside of these categories.

Saturday, February 15, 2014

Surface enhanced Raman spectroscopy to reveal Renoir's original palette

The lady in reds. Credit:
Art Institute of Chicago
The Art Institute of Chicago is presenting the results of a recent conservator's analysis of the portrait of Madame Leon Clapisson by Renoir. This portrait was undergoing routine conservation when it was discovered that edge areas of the painting, which had been protected from light by the frame, showed much stronger scarlets and purples. The conservators immediately suspected that Renoir had used carmine,  a brilliant red pigment which is very susceptible to fading, in his original color palette, meaning that the painting would originally have been much more lively.
Carmine itself is produced from the cochineal beetle, a native of the Americas which infests cactus leaves. (A neat overview of carmine production is here. ) Carmine was introduced to European artists by the Spanish, and the pigment became especially popular during the Renaissance, when it was prized for creating translucent, glowing washes. In addition to the brilliant red-pink pigment, the cochineal beetle extract can be precipitated with copper sulfate to create Indian purple.
The Art Institute has several works in its collection in which carmine-based pigments used during painting have since faded.

To confirm that carmine pigment, now faded, was used in the main body of the Mme. Clapisson portrait, Richard van Duyne of Northwestern University used surface-enhanced Raman spectroscopy, an enhancement of of Raman scattering detection optimized for anticipated low target abundances or for weak scatterers. (A YouTube overview of the method, which is widely used in forensic applications, is here).
You can see can see a reconstruction of how the original might have looked at the BBC web page here. The most apparent difference is in the background, which has  much more raspberry than the present-day painting.

Wednesday, February 12, 2014

Humped camels may have lived in the far north

Dispersal of the camelids. Credit: Jerry Mann, Wikimedia
Mammals store their fat in a variety of bodily locations, with the most common pattern being a big deposit near the belly combined with small deposits at several locations.  But there is a lot of variation, both within species-- for example, people struggling with weight gain can develop  “pear-shaped” or “apple-shaped” profiles, and Zebu cattle native to India, but not Zebu from Africa, can acquire a hump of fatty tissue behind their shoulders—and when comparing different species. Some mammal species store their fat in specialized deposits. Many marine mammals accumulate blubber under their skin, which improves their insulation. Dolphins further accumulate a “melon” of fatty tissue near their blowholes, which amplifies their echolocation clicks. 

But probably the most familiar specialized fat deposit is the fatty hump on the back of the camel.
Present day members of the camelid family include the Bactrian and Dromedary in the Eastern Hemisphere (the Camelini)  and New World camelids such as the llama and the alpaca (the Lamini). Camelids arose during the Pliestocine in North America, with later dispersals to Eurasia and to South America.  Recent fossil evidence suggests that some relatives of the present-day humped camels lived in boreal forests above the Arctic Circle . Expeditions in the  far north of Canada have identified 3.5 million year old fossil leg bones from a Paracamelus, a genus of camelid which is thought to include the ancestors of modern humped camels. The Paracemelus fossils were found in a context suggesting a lush boreal forest thick with larch trees.
Paracamelus in the high arctic. 

The two modern-day Camelini species both live in desert ecosystems, with Bactrians dominant in the high Tibetan plateau, and Dromedaries most common in desert North Africa; and it has been speculated that the camel hump would be an adaptation to these extreme environments. The recently found fossils suggest that the camel hump may instead serve as an safeguard against food shortages, which would also afflict arboreal ecosystems, as opposed to a specific feature of the desert environment. 

Thursday, February 06, 2014

How bumblebees stay aloft at high altitudes

As altitude increases flight becomes much more difficult.  Air density gives less material to push against, and reduced oxygen concentrations make the exertions of flight that much more demanding. But there are rewards for going higher. Within the bees, there are fewer species at alpine altitudes, which can make these ecosystems less competitive than the lower ranges of mountains. Bumblebees, for instance, have been observed foraging as high as 5,000 meters above sea level; and some flies and butterflies live at up to 6,000 meters.
Stroke patterns of a bumblebee at 3,250m 
(green) and simulated 8,130m (blue). 
The lower- altitidue strokes are shown on 
both sides of the insect for comparison.
Source: Dillon and Dudley, Fig 2. 
But what is the upper limit of flight for a heavy insect such as a bumblebee? In a study in the February 2014 issue of Biology Letters, Dillon and Dudley tested the ability of bumblebees to get aloft in a plexiglass chamber with progressively reduced air pressure. One of their bees was still able to fly at the equivalent of 9.000 meters, which would be higher than Mt. Everest!
Dillon and Dudley analyzed film of the bees to figure out how they stayed aloft.. They found that the bees extended the range of their strokes. This is as opposed to increasing the rate of beating, which is the strategy for example used by water polo players to lift themselves out of the water. Dillon and Dudley do not speculate why the bees follow this strategy.
As for the significance of the extra capacity, they note that their test only asked that the insects get airborne. In the wild, the bees might need this ability to fly higher, or to maneuver while loaded, to evade predators.

Wednesday, January 29, 2014

Detailed mapping of the human frontal lobe


Humans and monkeys are closely related,  and even though human brains are much larger, they share a great deal of similarity in organization with those of monkeys. But humans have capabilities, especially in language and abstract reasoning, which are only modest in monkey species. It remains an ongoing question how the expanded abilities of humans are reflected in brain organization. Are human brains just bigger versions of a monkey template? Or do human brains have fundamentally new brain areas, either anatomically or by virtue of their functional connections? A recent study in Neuron by Neubert et al. [pdf link] studied this issue by using magnetic resonance imaging (MRI) to compare the brains of humans and macaque monkeys.
The frontal lobe of the human brain (source: Wikipedia).
The ventrolateral  areas, studied by Neubert et al are 44-47 and
(roughly) 10 and 11.
Neubert et al focused on the ventrolateral frontal cortex  (vlFC), because this area is associated with processes, such as language (for example, Broca's area) and cognitive flexibility, which are notably developed in humans relative to monkeys. Their study relied on two major MRI methods. To map if human brains contained new areas, not present in monkeys, they used diffusion-weighted MRI . This method extracts the magnetic resonance signals arising from differences in water diffusion, based on local tissue properties such as cell bodies, white matter fibers, or connective tissue. This type of MRI can sensitively and non-invasively reveal the neuroanatomy. 
To ask whether brain areas were differently connected in humans compared to monkeys, they used resting state functional MRI , which relies on correlated firing patterns to identify which neuronal areas are wired together.
Neubert et al. used these two methods on 25 humans and 25 macaques, and found a great deal of consistency in both the neuroanatomy and in the functionally correlated
brains. What's more, within the ventrolateral frontal cortex that they were studying, most areas in humans had a direct correlate-- anatomically and functionally-- with the macaques. They did find evidence for one area in human brain scans that did not have a direct equivalent in macaques. The lateral frontal pole region (FPl; labelled in red at the font of the brain in the image to the left), was distinctively human. It seemed to be anatomically related to area 46 (which is present in macaque, and shown in yellow in the figure) but lacking a lot of the functional connectivity of that region. 
Neubert et al. comment that the FPl is used in humans for strategic planning, multitasking, and for calibrating a correct response when many alternatives are available. 
This work is a very valuable effort to make an apples-to-apples comparison of brains in a region that is important for many of the traits that we consider most human. To really understand the significance of this area, it would be really helpful to include brain information from the nearest human relative, i.e. chimpanzees. It would also be very interesting if a specialized old-world monkey It would also be helpful to see whether niche (tree dwelling versus forest floor) or gregariousness could be correlated with the functional properties of the frontal lobes. Finally, Neubert et al noted some differences in long-range connectivity between humans and macaques from most areas in the frontal lobe. It might be that much of what we consider uniquely human might be enabled by these longer connections. 

Sunday, January 26, 2014

Genomics and immune evasion in a transmissible dog cancer

Nature and several other news sources describe gene sequencing of Canine Transmissible Venereal Tumor (CTVT), a sexually transmitted neoplasm which has spread among dogs worldwide. Transmissible cancers are extremely rare;  usually, tumor cells transplanted from one individual to the other are quickly recognized by the immune system. The other well-known example of a transmissible tumor is the Tasmanian Devil facial tumor disease.
Evasion of the immune system by transmissible tumors.
Tasmanian Devil facial tumor (A) is not recognized as foreign
because the species has too little diversity in MCH I and II 
genes. CTVT temporarily succeeds in escaping detection
through lower MHC I expression and by secreting the
immune response suppressant TGFbeta .
Figure credit: E.P. Murchison, Oncogene 2007.
This tumor is indeed derived from one single dog, and has somehow managed to survive and propagate among all kinds of dogs. One clue to its possible evasion of the immune system is that it downregulates the major histocompatibility (MHC) genes, which are used by the immune system to distinguish self from non-self cells. It has been speculated that dogs and Tasmanian Devils both suffer increased risk of cancer-contagion via their reduced diversity of MHC genes, which makes immune surveillance much less efficient.  Similarly, human patients on immune suppressants can occasionally obtain cancer from organ transplants.

CTVT, like all cancers, accumulates genomic mutations as it divides and grows. To get more information about the population characteristics of the disease, the scientists sequenced the entire genomes of tumors obtained from widely separated dogs- one in Australia, and one in South America. These samples would give an idea of the range of genomic variation in the tumor worldwide, and give a clue about the origins of the cells. A surprise from the sequencing was the high degree of similarity of the two, widely separated tumor isolates. A molecular clock calculation suggested the cells were only separated by 460 or so years, putting the worldwide dispersal of the disease at around the same time as Christopher Columbus; and around the same time that intensive breeding of dogs for particular purposes took off.  Since the disease is sexually transmissible, the use of infected sires to breed for many litters may have amplified the disease's spread.

10 year anniversary of the Opportunity Mars Rover

Nobel Intent has a nice write-up of the Opportunity Rover, which is still exploring Mars 10 years after initial touchdown. The positive experience of Opportunity has affected NASA mission selection, science, and public relations, and this type of rover may be the paradigm for NASA surface probes for the foreseeable future.

Friday, January 24, 2014

Now showing in a galaxy near you

A supernova has erupted in a nearby galaxy, M82, and will be bright enough to be seen with amateur telescopes.  It should continue to brighten for the next two weeks, and it should be one of the brightest
Image and caption: Nature
such events for Earth observers since 1987.
The M82 galaxy is a frequent imaging target because of its unusual cigar shape, and so it might be possible to identify what lay in the region before the supernova event by going back to historical surveys of the galaxy.
Based on the early spectral readings, this supernova is thought to be of Type Ia, a class which reaches predictable absolute brightness peaks-- their brightness as seen from earth is then a function of their distance, and thus they can be used as standard candles to determine the distance of far-away objects. Because of their importance to astronomical surveying, there is a lot of interest in what exactly leads to their big explosion.  Although the parent body for this type explosion is almost certainly a white dwarf star, the details of the detonation have been hard to simulate with computer models.  The 1987 supernova was of a different type, and its parent body was probably a blue supergiant.  The different classes synthesize heavier elements to different degrees. For example with Aluminium-27 is produced at a bit more than 200 fold greater abundance by Type II supernovae compared to type Ia.

Thursday, January 23, 2014

A micro-predator limits the spread of amphibian chytrid disease

Amphibians worldwide are succumbing to a fungal infection driven by a parasitic chytrid fungus,  Batrachochytrium dendrobatidis , which infects amphibian skin,  interfering with their ability to regulate salts and causing cardiac arrest. This fungal disease is thought to be a major factor in
Possibly a frog's best friend
devastating declines in amphibian numbers in Australia, New Zealand, and Central America-- and it's still going.

B. dendrobatidis fungus appears to have originally been endemic to southern Africa.  A plausible hypothesis is that international trade of the south Africa toed frog, i.e.  Xenopus Laevis,  which started in the 1930s, may be behind its worldwide spread. It's a little uncomfortable to think that a laboratory organism studied by developmental biologists may have promoted such a devastating spread.

There may be some hope for control of this disease through fungus-eating protists native to the frog's home ponds. Even in heavily infected areas, amphibians in some ponds appear to remain relatively unscathed while populations in nearby ponds are decimated. A recent study of frog populations in the Pyrenees suggest that one key difference in the disease course is the numbers of rotifers, pond denizens which eat a lot of fungus. Importantly, the rotifers seem to preferentially eat the infectious stage, or zoospores, of the chytrid. Thus the fungus has trouble spreading from host to host, possibly keeping the whole amphibian population safer. If this observation is correct, then at least laboratory ponds could be stocked with rotifers or other fungus-eating protists to control chytrid.

Tuesday, January 21, 2014

Definition of life as accumulation of information

All known examples of life belong to the same biology, but across a range of scientific disciplines- astronomy, astrobiology, and synthetic biology—it is becoming conceivable that other forms of life may soon be detected or synthesized. But before we have that first life form that is truly independent of terrestrial life, it is still difficult to know what to look for—we are limited by the single known example. All of terrestrial life has shared properties. It is composed of cells, with cell membranes which enclose important contents and communicate with the outside. Living cells contain DNA and/or RNA and particular proteins. Cellular life furthermore transmits heritable information to progeny, and undergoes Darwinian evolution based on natural selection. Finally, life as we know it captures high-energy starting materials and converts them to lower-energy products to drive metabolic processes.
This single example of life has existed for multiple billions of years, out of an Earthly lifetime of something less than 5 billion years. So it works, and works well, and it might be a good template for looking elsewhere.

In a recent review in PLoS Biology, Gerald Joyce describes his ideas of a minimal definition of life, based just the information content and net information increase over time. Information would be very broadly described as the enrichment of one possible chemical configuration despite the availability of other probable configurations . Think of the DNA letter code, in which each position could be held by one of  four possible bases—a very lengthy strand of DNA, if  able to reproduce itself, would represent a process very high information content. If groups of such molecules were subject to mutations and natural selection, then the aggregate would be considered to be “accruing” information.
He gives an example from his own lab of a pair of RNA molecules which are able to reproduce one another. This is not yet life, because the investigator still must provide a template which does not change (accrue information in the above scheme). But the day might come in which a chemical system would accrue more information than is provided it by the scientist.

Monday, January 13, 2014

This is not your (great great great) grandfather's cholera

Cholera, caused by the bacterium Vibrio cholera via contact with contaminated water, affects millions of people each year. In contrast to diseases like smallpox and tuberculosis, the Vibrio strains causing cholera arose relatively recently from more benign relatives, with the first confirmed cholera epidemic occurring in 1817 in areas of present-day Bangladesh and north India. Starting with the 1817 outbreak, there have been 7 cholera pandemics, with the seventh dating from the late 60s and considered to still be ongoing.
In the modern era there have been two major disease causing strains, termed the classical and the El Tor strains, with slight differences in their epidemiology and their gene regulation of the disease-causing cholera toxin. The classical form is thought to have caused all of the first six epidemics, while El Tor, with slightly milder symptoms,  is implicated in the ongoing seventh epidemic and seems to be en route to becoming the more dominant form of the disease. Supporting the idea that the older epidemics were caused by the classical strain,  a study in the New England Journal of Medicine from last week has reported Vibrio sequences from a cholera victim from the second pandemic. The bacterial DNA was obtained from an unusual specimen-- a section of the intestine of a cholera victim from 1849 Philadelphia, which had been preserved in alcohol for 146 years.  The DNA sequences do show a great deal of similarity to the classical strain obtained from more recent epidemics.
Since the classical Vibrio strain had been on the scene for nearly 200 years, it remains to be seen why El Tor has suddenly come on the scene.There is some suggestion that the El Tor strain actively suppresses growth of the classical strain when the two are in co-culture.

The El Tor biotype has some variation over its shorter time on the world stage, and this may augur a continued evolution of the disease. Detailed analyses of bacterial DNA from the 7th (current) pandemic show 3 major genetic groupings from isolates collected over the past 4 decades, suggesting 3 sequential waves of emergence of this biotype from their origin in the northeast corner of the Indian subcontinent. By careful phylogenetic analysis, they provide evidence for intercontinental routes of transmission separated into three epochs, suggesting that the disease strains follow boom-and-bust behavior. Thus, disease-causing Vibrio is probably still evolving in the Bay of Bengal region and may yet give rise to more variant cholera epidemics in the near future.

Saturday, January 11, 2014

How much has life reshaped Earth?

Earth has hosted life for much of its geological existence, and living things have changed much of Earth's geological properties-- from local patterns of erosion to the composition of the atmosphere, living things put their visible stamp on Earth. A recent interview with Tilman Spohn in Astrobiology  magazine asks whether life has transformed Earth even more deeply, by affecting the process of continental drift.
The focus of the question is the extent to which biological weathering at the surface can change the contents of the underlying mantle on which the continents float. Living things such as lichen or bacteria accelerate the breakage of rocks, generating sediments, which are eventually washed to sea. At sea these sediments can accumulate in subduction zones, places where the earth's surface dips down toward the lower layers.
What makes this important is the enormous water content of weathered rock sediments. Water carried down into the mantle would soften the mantle, increasing the overall churn. In computer simulations, an increase churn of mantle rocks leads to increased continental movement and breakage.

So, if life has sufficiently changed (or is still changing) which rocks get weathered, and how fast, these changes would alter the entire face of the planet-- encouraging more tectonic plates and motions.  

Saturday, January 04, 2014

A link between Stonehenge and Orkney monument cultures

Science magazine has a pair of articles (and a segment in their weekly podcast) summarizing new interpretations of the Stonehenge site. I could not find a lay summary in English (German is here).
The extant Stonehenge is part of a repeatedly re-built burial complex, on a site that was evidently sacred for up to  6,000 years, predating the arrival of Neolithic culture in the area.
The new data suggest cultural connections linking the greater Stonehenge site to the Stones of Stenness
The Ring of Brodgar on Mainland, the largest 
of the Orkneys. 
Credit:Patrick Dieudonne/Robert Harding World Imagery/Corbis
and the Ring of Brodgar, structures in the Orkney islands which predate the major Stonehenge construction by several centuries. Michael Pearson has been excavating houses in Durrington Walls, a short distance from Stonehenge, which he believes housed the people who made both structures. The newly unearthed houses show construction methods identical to those used in far older buildings on the Orkneys. Combined with the similarity of
Neolithic sites around Stonehenge. 
the stone circles, the workers who built Stonehenge likely had at least familiarity with the older Orkney culture.
It has already been discovered that the cattle tended in the Durington Walls village came from Wales, and that artifacts in the barrows at Stonehenge come from as far away as the Italian Alps. So with people from the Orkneys in the mix, the emerging picture of the Stonehenge area is one of a very cosmopolitan meeting place. The Ring of Brogdar itself appears to be part of a vast complex and thus plausibly puts the Orkneys as the original heart of an interconnected Neolithic British culture.

This blog goes to 11

The Onion has a good parody of high-energy physics: scientists at Nabisco announce the synthesis of the highly unstable Quadriscuit, a hyper-wafer which cannot be accounted for by classical Fig Newtonian physics.
I'm still trying to understand candy corn, myself. There's some spooky action at a distance going on in there.