Thursday, January 14, 2016

Decoding Incan Khipus

Close up of Khipu cords dangling from the main strand. From the Khipu database project

The New York Times ran an article on January 2nd about progress in understanding the Incan recording system- the khipu (or Quipu) system of knots. These constructions involve knotted ropes all attached to a main cord, with the color of the rope, the type and position of the knot, and possible other factors contributing to the final meaning of the object. A scribe would "read" a khipu by running fingers along the length of the dangling strands.
Since colonial times it has been known that the Inca sent khipus via messenger to communicate throughout the empire, so they presumably had content beyond the number code which researchers have deduced. But the lack of context for the extant khipus has hampered any inferences about these additional meanings. The Times article discusses the 2013 discovery of 34 khipus in place in the ruins of a garrison area in the Inca military base of Incahuasi (or Inkawasi).  These chips were found next to storage areas for specific goods-- one khipu near a storage area for peanuts, and another near where chili peppers were stored, and so forth. This context may allow researchers to see if "peanut" appears as a unique feature in the khipu from that storage area, and whether an analogous marking might designate the "chili pepper" khipu. 
One hint that this might be correct is that in some locations several khipus  were tied together, and the tied-together ones yielded very similar number counts. One could imagine several people keeping inventory during the day and returning their khipu to a central figure for reconciliation. This type of cross-checking was hinted at by an Inca writer, Guaman Poma, in 1609.
Ultimately, the understanding of the information encoded in these objects would require many more examples, found in good context, as with these 34. 

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

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, March 01, 2014

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.