Sunday, December 29, 2013

A gene affecting left-handedness as well as reading skill

Although many of the great apes prefer one or the other hand to perform delicate tasks, Humans are unusual in that righties greatly outnumber lefties. Left-handed people (I am one!)  show elevated rates of learning disorders such as dyslexiatend to perform better on tasks engaging the right hemisphere; and may even have different brain representations of abstract constructs like "kindness." So there has been a sense for some time that left-handedness is a marker for a grab bag of brain differences. Left-handedness is also at least partially heritable, with genetic contributions accounting for about 24% of the variance in handedness in the general population.
In September of this year, a collaboration between the Weber and Parachoni labs identified a variation in the gene PCKS6 as associated with left-handedness in individuals with dyslexia. This gene encodes a proprotein convertase, a type of enzyme which clip many different important signaling molecules. Intriguingly, PCKS6 is known to process an important set of developmental signals known as nodal proteins, and mice lacking PCKS6 develop left-right abnormalities in numerous organ systems such as the lungs and intestines. So it is plausible that similar genes are important in the developing human brain to subtly affect numerous brain functions.
It's important to note that this gene variation was only associated with left-handedness in their subjects who had dyslexia. The same gene variation did not even show the same trend in the general population. Nevertheless, the numerous changes in brain function associated with left-handedness makes this type of gene a plausible candidate for the genetic portion of the difference.

Evidence for Cassina (Black Drink) consumption at Cahokia

The Native American site of  Cahokia, the central settlement of a large polity on the Mississippi river floodplain near present-day St. Louis, supported up to 13,000 people at its peak, making it the largest pre-Columbian settlement north of Mexico. The inhabitants of Cahokia evidently had extensive trade networks (pdf link), with marine shells and shark’s teeth from the gulf coast; volcanic mica; and copper from the Great Lakes, all found at the central complex.

The natural range of two species of holly used to prepare
 cassina. The inset shows the several settlement sites which
which are associated with the Cahokia complex. 
A recent paper in PNAS suggests that the exchange with coastal tribes was not limited to durable goods. Chemical analyses of residues in ritual vessels from Cahokia have found evidence for preparation of cassina, or Black Drink, a ritual drink resembling tea which was prepared from leaves and twigs of holly trees. The species of holly used to prepare cassina grew far to the south of the Cahokia complex, with the nearest sources in Arkansas more than 550 km away. Consumption of this drink at Cahokia suggests, at a minimum,  regular trading contact over these long distances. Also, cassina was part of an entire cultural package, including special vessels for its preparation and drinking. Cahokia’s central position on the Mississippi may have been part of the spread of this ritual culture along the Mississippi watershed and beyond. Finally, the Cahokia vessels are the oldest for which boiled holly residues have been detected. This suggests the cassina culture might have even older roots along the Gulf coast.

Friday, November 29, 2013

Frying turkey fireballs

Just in time for Thanksgiving, iO9 has a collection of videos of turkey frying disasters. Boiling oil + open flame can lead to amazing fireballs.

Wednesday, November 27, 2013

Octopus swimming

Poetry in motion. Credit: UGA Aquarium

Katherine Courage at Scientific American blogs  has a nice write-up of swimming moves by octopus.  Different species of octopus will move around via jet propulsion or by walking along the sea floor, but some species can move through open water by swimming motions with their tentacles. From the written description, it sounds a bit like the breast stroke.
She has an earlier post describing an octopus-inspired robot which can propel itself using only its appendages.
As I have struggle to coordinate my four appendages into a coherent swimming motion, I do have to bow to these critters, who keep everything going swimmingly.

Bird die-offs in the Great Lakes: a side effect of ecosystem chaos

Early this year, loons on the north shores of Lake Michigan suffered a massive die-off , with thousands of the migratory birds washing ashore along Michigan's Upper Peninsula. The birds died of botulism E poisoning, a toxin produced by Clostridium bacteria. These die-offs have been recorded in the Great Lakes dating back to the 1960s, but appear to be increasing in frequency and intensity.
Loons feed heavily on Great Lakes fish en route to their
summer habitat further north. Credit: EPA
The current explanation for the die-offs is that the birds are increasingly falling victim to the ongoing disruption of the Great Lakes ecosystem. Invasive quagga mussels, which are filter feeders, are stripping the water column to such an extent that sunlight is penetrating unusually deeply. The availability of sunlight in deeper waters is thought, in turn, to  provoke algal blooms. Of the several kinds of resident algae, bird die-offs seem to match most closely with blooms of Cladophora glomerulata . These algal mats deplete oxygen from the water, promoting formation of botulinum toxin by Clostridium, which is then ingested with the algae or along with the quagga mussels, by yet another invasive species, the round goby. And the botulinum toxin becomes concentrated as it moves up the food chain, felling migratory birds and larger fish. However, although this is probably the major route by which migratory birds become ensured, Clostridium is present in several niches within the Great Lakes and may end up in the food chain through other routes.

Tuesday, November 26, 2013

How to detect life on a dying planet

In 1961, Frank Drake presented a way of calculating the probability of intelligent life outside of Earth. To summarize, he described the probability as a function of the total number of planets where life could form; the probability of life emerging; several steps involving the emergence of an intelligent civilization (essentially capable of radio astronomy); and lastly, the expected lifespan of intelligent civilizations, which Drake designated as L. This last one takes a kind of grim resonance when we think of the challenges that the products of human civilization pose to Earth's habitability in the distant future.
Mars as a model for a planet at the end of supporting life.
Credit: ESA/DLR/FU Berlin (G. Neukum)
But another limit on habitability comes from the lifespan of stars themselves. In about 3.5 billion years, our own sun will be much hotter, and Earth will be much less friendly to life, perhaps entirely lacking in plants  and therefore animals. However, a recent study suggests that surviving microbes on an Earth-like planet would still change the atmosphere in a way detectable by astronomy. Surviving methanogen bacteria and cloud-seeding microbial life could create spectral signatures visible even at stellar distances.
In a sense, searches along these lines would increase Francis Drake's Length factor in both directions, because microbes would detectably modify the atmosphere before and after intelligent life would be around.

Wednesday, November 20, 2013

Frederick Sanger, inventor of a major method in DNA sequencing, 1918-2013

The New York Times has an obituary of Frederick Sanger, who won two Nobel prizes for molecular biology methods.  I probably belong to the last generation to use Sanger end-termination for DNA sequencing, but his method was enough to sequence the genomes of many bacteria, and the same chemistry was used for the human genome. Really a founder of modern molecular biology.
See also an appreciation at The Curious Wavefunction.

Friday, November 15, 2013

Measuring evolutionary relationships in a folk tale

The family tree of Little Red Riding Hood stories. The Little 
Red  Riding Hood  European tales are the cluster at right 
labelled ATU 233.
Credit: Eurekalert
Since the time of Carl Linnaeus, biologists have worked on systems for classifying living beings. An ideal classification system will reflect evolutionary relationships between the organisms, so that great cats, for example, would be grouped near domestic cats, and gorillas and chimpanzees near to humans. Biologists who study these organizational principles,  collectively termed cladistics,  incorporate anatomical similarities, DNA sequences, and the fossil record with the goal of producing a "tree of life" reflecting evolutionary relationships. Drawing trees according to these rules is useful as a way of organizing data, but it may also suggest  underlying principles or relationships among the things classified. 
In last week's PLoS One, a cladistics approach was used to understand relationships among versions of a folk tale.  Jashmid Terhani at Durham University in England studied relationships between the many variations of the folk tale Little Red Riding Hood. The version in the Grimm's fairy tale, called ATU 233 in the Aarne-Thompson-Uther list of European fables,  has some plot similarities to folk tales from Africa and the far East. Quoting from Dr. Terhani's article,  "The East Asian tales also feature human protagonists (ATU 333), but they are usually a group of siblings rather than a single child (ATU 123). In most variants of the tale, they are attacked after being left at home by their mother (ATU 123), but in some cases they encounter the villain en route to their grandmother's house (as per ATU 333)." 
Figure 1 from the paper shows locations where 
Little Red Riding Hood type stories were collected.
Dr. Terhani generated a family tree using 72 variables present in the various stories. The different comparison methods yielded slightly different family trees; but the Western European tales consistently grouped together, as did the tales collected from East Asia.
The second question is whether these trees are reflecting a more fundamental resemblance between the stories grouped. A biologist looking at such a tree would be tempted to think of a single ancestor story, with an unknown assortment of elements present in the widely separated tales. But there need not be such a relationship-- a child's encounter with a hostile and brutal stranger would probably be a memorable tale  in many societies, and could have arisen independently.
The microbiologist Carl Woese encountered similar objections in the 70s and 80s, when he proposed that archaea were fundamentally different from bacteria and belonged in a separate domain of life. The resistance to Woese centered around his use of only one gene in his classification scheme. Since that time, additional support has come from many other genomic and cellular features. It's hard to think what analagous data trove would emerge to buttress analysis of folk tales.

Wednesday, November 13, 2013

Archaeopteryx, the famous early bird fossil, was adapting toward being flightless

The Munich specimen of
Archaeopteryx. Credit: Wikipedia
Archaeopteryx is a very early example of the transition between dinosaurs and birds. Ever since the first fossils of these creatures were found in southern Germany in the 1860s, the mixture of clearly dinosaur features with unambiguous feathering have prompted debate about whether this is a bird-like dinosaur or a dinosaur-like bird. But there has been general agreement that this bird was right at the earliest steps of this evolutionary process.
But an analysis described in last week's Nature suggests that this species was actually transitional toward losing flight. 
The argument, presented at a paleontology conference, goes as follows: it is known that Archaeopteryx lived on an archipelago within a tropical sea. And there are many examples of birds in isolated locales losing their flight, probably because flight requires so much energy. The most famous example of this probably the ill-fated  Dodo in Mauritania; but other examples are the grebe and the rail. Flightless birds have several differences in their skeleton compared to their flying cousins; specifically their wing bones are lighter, and the breastbone lacks a "keel" to anchor the heavy flight muscles. Finally they have more, and more symmetrical feathers. The argument, then,  is that the bones and feather imprints of Archaeopteryx fossils fall plausibly within the range of an island flightless bird.
I think that the progressive discovery of feathers on all sorts of dinosaurs  does make it seem that there was not a single pathway leading to flight. So the new theory is worth careful consideration. In the absence of a living example, the discussion of this critter's capabilities will have to remain open.

Sunday, November 10, 2013

Following salmon from the rivers into the ocean

The JSAT acoustic tags. Source: Lotek Wireless
The first encounter between juvenile salmon and the sea is a very risky time. They have to run a gantlet of predators- larger fish and birds-- before becoming safely dispersed. However, little is known about what juvenile salmon in the first few days of this critical transition. There's a nice little story about telemetry methods tracking different species of salmon using acoustic fin tags to find out what they do as they exit the Columbia river.  These tags last about 30 days and emit an acoustic signal, which can be picked up by semi-permanent listening devices set up at the fish letters and in an array around the mouth of the Columbia river. By tagging several thousand fish, they could track the aggregate movements and also get some idea of where predation was at its most intense.
A lot of the research paper involves data crunching from all of the acoustic pings recorded. The authors were able to see differences between salmon species in terms of how quickly they headed into deep water.  One trend was that the salmon of all species scattered along the north-south extent of the Columbia to a much greater extent than had been appreciated. This means that the counts of juveniles, which are important measurements of fisheries health, may be underestimated.

Thursday, November 07, 2013

A microbe which reproduces without origins of replication

Every cell needs to copy its DNA before it divided, but the mechanisms by which this is accomplished are very different between the different domains of life. DNA copying begins at so-called origins of replication,  special DNA sequence which are chemically a bit easier to pry open and also recognized by the proteins responsible for initiating the replication process. Bacteria usually have one such origin per genome, while most archaea and all eukaryotes have multiple such origins.

But a paper in this week's Nature shows that at least some archaea, when deprived of DNA origins of replication, can still copy their genomes and continue dividing. The researchers were interested in the archeal microbe Haloferax Volcanii,  because the proteins it uses to replicate its genome are very similar to those of eukaryotes (including humans). When they generated a mutant strain of Haloferax which lacked all of the origins of replication, they were very surprised to see that these origin-less bugs continued to divide-- in fact at a slightly higher rate than the normal control bugs.

How could this be? It turns out that there are other ways to copy DNA, one of which, the DNA repair pathway, adds small stretches of DNA to patch DNA breaks.  Viruses such as papillomaviruses exploit this pathway to induce cells to make many copies of the viral DNA. In brief, the viral DNA is sensed by the cell as a broken DNA piece, and the repair enzymes trying to patch it end up copying it.
It turns out that the origin-deficient  Haloferax were using this same pathway to kludge a replication strategy without DNA damage.

Now, it turns out that the choice to study Haloferax may have fortuitously made detection of this surprising end-run mechanism easier. The natural environment of Haloferax are extremely saline regions such as the Dead Sea, and the biofilms are subjected to extreme temperature fluctuations and dessication, both of which naturally cause extensive DNA damage. Thus this archeon is naturally primed to have an active DNA repair kit.

Saturday, November 02, 2013

The Chemistry of Fall Colors

Bundle up! From Prof. Shakhashiri at
We're at the point in autumn when tree leaves run the gamut from still-green, through the reds and the yellows, to already brown and falling off. I was interested to find this description of the chemistry of autumn colors from a fellow Wisconsinite. The green in leaves comes from chlorophyll, which absorbs the red and blue portions of sunlight-- corresponding fairly well to the sun's peak intensities-- and reflects the yellows and greens. Throughout the year, chlorophyll is unstable and is continuously replaced.
Basically, as fall approaches, deciduous trees begin to cut off the supply of nutrients in to the leaves, and the chlorophyll starts to fade away. The trees also recoup nutrients from the leaves, draining them of amino acids, potassium and magnesium.
As chlorophyll disappears, the color of the leaves starts to be influenced by other dye-like substances which vary from species to species. The beautiful reds of some maples, oak and sumac come from anthrocyanins, which absorb blue and blue-green light.   (Anthrocyanins also contribute to the color of red apples.) These compounds are made in the leaves during the fall, and may help with protection against free radicals  [pdf link] formed by the remaining chlorophyll when the trees are in bright sunlight.
The bright yellow seen in birch and hickory trees comes from carotenoids, which are "antenna pigments" and are present in these species throughout the year. Some recent research on Scandinavian birch has shown that the timing of t their fall colors is under natural selection  through differential infestation with a parasitic aphid.  These aphids prefer trees with bright yellow leaves in the late fall, possibly because the phloem sap becomes nutritionally richer as amino acids are withdrawn from the leaves back into the parent tree. So a tree whose leaves are yellowing in preparation for fall will attract more parasites. More parasites mean less amino acids available to the tree. Thus these trees under selective pressure to begin the color transition as late as possible in the season.

Tuesday, October 29, 2013

Botfly parasite in Wired magazine

There's a nice write up of botfly larvae, which grow within the skin of humans and other mammals, at Wired magazine.  The mother fly actually uses mosquitoes as a delivery vehicle, laying her eggs on the mosquito. When the mosquito approaches a warm body, the eggs hatch and drop off onto the host, then burrow into the skin. Not for the squeamish!

Sunday, October 20, 2013

Biomarkers to detect Alzheimer's disease before the symptoms start

Alzheimer's disease is a devastating decline of brain function, thought to be driven by the accumulation of protein debris in so-called amyloid plaques, loss of neuronal connectivity, and finally death of neurons. It seems likely that these changes begin a decade or more before the disease is first suspected.  It's a major goal of Alzheimer's research to detect the disease as early as possible, before irreversible damage to the brain has occured.
recent study from Johns Hopkins has suggested that a test for two Alzheimer's-related proteins in the cerebral-spinal fluid (CSF) may give clues that something is amiss in brain chemistry as much as 5 years before the cognitive symptoms are seen.
The new work builds on earlier observations that the CSF of patients with advanced Alzheimer's shows abnormal levels of two proteins, phosphorylated tau and beta-amyloid. These proteins are both found near sites of brain damage, so it made sense that they would be detectable in the brain fluid of these advanced patients. The new feature of the Johns Hopkins study is that these same proteins, or at least their ratios, are present in the CSF before the study population had developed symptoms of cognitive decline.
Amyloid plaques, seen here as fuzzy black blotches, in 
the brain of a person who died of Alzheimer's disease.
One of the aspects of Alzheimer's disease that was new to me  is the concept of Cognitive Reserve, that is, that some people can withstand the neuropathology similar to Alzheimer's while not showing cognitive symptoms. It is thought that the psychological flexibility or other life-long habits may improve cognitive resilience during the progression of the disease. This phenomenon makes the diagnosis of Alzheimer's disease more difficult, because each person would have a cognitive decline relative to their own baseline.  The Johns Hopkins group has seen that cognitive reserve does not associate with the proteins they measure in the CSF. Thus this approach may help reduce the uncertainty of diagnosis in patients with more advanced disease, as well as its stated goal of early detection.

Wednesday, October 16, 2013

More edible insects

The Guardian had an article this past summer saying that the foods of the future will be low on the food chain-- plants and insects. Coming from Maryland, I've always enjoyed crab, so I don't think insect
muscles wouldn't be too much of a stretch (no pun intended!) But I really can't see eating  tree grubs yet.

Friday, October 11, 2013

Collagen from dinosaur fossils-- some insight into a mechanism for preservation

Historically, fossil dinosaur bones have been considered to be entirely mineralized, that is, that they are faithful replicas of the bones but don't contain bone per se. However, in 2005, the laboratory of Mary Schweitzer fortuitously observed what looked to be soft-tissue blood vessels and even blood cells in a Tyrannosaurus leg bone. Schweitzer's lab has since worked on recovering and identifying proteins , specifically collagen, in fossilized dinosaur bones. However, many in the field find it hard to believe that 65 million-year-old proteins would survive the fossilization process, and I would say a substantial
A cartoon of collagen structure indicating major binding
or interaction sites of other proteins (shown in color). 
The protein sequences detected in fossil extracts
 all correspond to "protected" amino acids in the
 groove of the triple helix. Three out of 11 successful
reads corresponded to integrin binding sites (green).
additional group, while not actively hostile to her assertions, is at a minimum awaiting confirmation by other labs and methods. The chief issue of concern is that protein (and bone protein especially) is much more complicated chemically than RNA and DNA, making it hard to believe it could be detected in a sample millions of years old. First, in contrast to RNA and DNA, there is no way to reliably amplify protein fragments. Secondly, proteins like collagen are cross-linked, and this chemical modification complicates detection of the cross-linked portions.

Schweitzer has more recently collaborated with collagen expert Joseph Orgel in a very recent paper in the open-access jounal PLOS One, which at least offers an explanation for which protein fragments their detection methods are registering. Collagen, the major protein in bones, is wound into incredibly tough three-stranded helical fibrils, and would be as good a candidate as any to survive fossilization processes. And there are patterns to the portions of collagen detected by their experiments. Collagen fragments detected in analysis of two different fossil dinosaur bones seemed to derive from the same place in the collagen fibril, consistent with the idea that those regions are better preserved than others. Secondly, the  fragments from both species correspond to sections of collagen known to lie in the interior of the triple helix. By being shielded here, the authors hypothesize, these fragments were more likely to be preserved in sufficient amounts to be detected.
I would say that while these two factors could explain detection of fossil collagen, the same shielding and similarity effects would also apply to contaminating avian or even reptilian collagen. And it wouldn't take much modern protein contamination to drown out a 65 million year-old signal. So for myself, I still find this a tantalizing possibility, but still scientifically ambiguous.

Thursday, October 10, 2013

The social side of online gaming

Massively-multiplayer online role playing games, or MMORPGs, are popular time sinks involving very
The popular image of a gamer
long sessions in front of a computer. Popular stereotypes of gamers involve socially awkward, indoor-dwelling males subsisting on junk food and Mountain Dew.  But these stereotypes do an injustice to a huge and diverse community.  For example, World of Warcraft has 8 million subscribers including lots of folks who wouldn't fit that stereotype.
However, a lot of the scientific literature on MMORPGs examines addiction issues. Studies of huge numbers of the huge numbers of leisure players have been largely left to the marketers.
I think there's a scientific opportunity being missed here. Just as biological extracts of willow bark led to the isolation of aspirin, the strong pull and elaborate societies created online within MMORPGs are telling us something about what attracts and holds people's-- all people's-- attention. This is both a sociological phenomenon and a psychological one. The human species is tremendously, even uniquely social, and from infancy on the human brain responds preferentially to socially meaningful cues. MMORPGs are so successful because they tap into the human affinity for belonging, interaction, cooperation-- and tribalism. These games in themselves are of course creations of humans,  and their attractiveness comes in part from their large numbers of users, which makes them difficult subjects for study. The social science of online gaming will have to devise more reproducible instances which are still interesting enough to trigger the social immersion of the commercial games.

Friday, October 04, 2013

Science Magazine issue on science communication: quality control for manuscripts

Quantification of the flawed manuscript submission study. On
the left, categories of target journals. Green represents the
DOAJ list, which is suggested in the article not to vet journals  
sufficiently(see text and link). Beige represents journals on a 
blacklist maintained by Jeffrey Beale. Of the target journals,
very few of the journals which rejected the paper came from 
Beale's list, while many of the DOAJ journals did
 recommend rejection. 
This week's Science has several articles about improving communication of scientific results.  Scientific journals are in the process of a revolution driven by the world-wide web, and there are many new entrants into the field. Since scientists are under pressure to constantly publish, the dramatic increase in titles creates a possible risk to publication standards.

 An article by John Bonahan in the Science special issue focuses on quality control in open-access journals. To test how well the new journals were doing in handling manuscripts, Bonahan deliberately submitted a highly  flawed manuscript  to 304 open-access journals, and was flabbergasted to find the manuscript was accepted 157 times. Of the accepting journals, a disproportionate number came from a name and shame list maintained by Jeffrey Beall of journals which he believes are acting unprofessionally (this category would also include hidden billings and unclear copyright behaviors). However, many others which appear in the Directory of Open-Access Journals (DOAJ) also accepted the paper.
Remarkably, Beall found that four of these journals went ahead and  published the faulty manuscript even after it had been withdrawn.
This is remarkable and indicates a system of scientific discourse in distress. It is important to point out that print journals, which are not covered in this study, are also fallible, and in particular have had issues with more subtle problems like data fabrication. In fact, the blog Retraction Watch contacted Bonahan regarding his faulty manuscript study, and he said print journals were not targeted because their turnaround for manuscripts was too slow to get good numbers for his study! I think the manuscript study is thus best taken as evidence of systemic stress rather than flagging a particular publishing model as especially flawed.

Update: the Chronicle of Higher Education is more critical of the study design. I still think what Bonahan found is pretty appalling even within the limitations.

Hollow raptor teeth: evidence for a venomous bite?

A diagram of the Sinornithosaurus skull showing
grooved teeth (labelled vg) and a sinus above the
palate(labelled sff for subfenestral fossa), both of which
suggest a venomous bite.
Credit: Gong et al., 2009
The National Geographic site has an older article about evidence that at least some dinosaurs were venomous. The species in question,  Sinornithosarus, belongs to the feathered raptor dinosaurs, among which were the ancestors of birds.
Sinornithosaurus has long, spiky fangs on its upper jaw, which resemble the fangs of  "rear-fanged" snakes. These fangs additionally have grooves, and the space above the palate appears to have room for a venom gland. One important detail about these long, narrow teeth is that the creature's bite could not have been very forceful lest the teeth break (and in fact a the tip of a raptor tooth has been recovered in the fossilized wing bone of a Pterosaur). Thus this skull looks like it belonged to a creature with a bite-and-hold predation style.
This idea has remained somewhat controversial.  Grooves occur in teeth of non-venomous animals, where they can can be involved in sucking or grooming behaviors, and certainly the possibility of selective tooth wear during fossilization has to be considered. Regardless, even close relatives to Sinornithosaurus do not have these tooth grooves. So it may be that this venomous lineage was an evolutionary dead end.

Sunday, September 29, 2013

Humans and hornets don't mix

I missed this news item last week that a very aggressive type of hornet, the Asian giant hornet or Vespa mandarin, has increased in numbers in its native southern China to the point that this year they have become a public health hazard.  The venom of these hornets is very toxic to mammals, with laboratory a single sting can kill a mouse. And they will swarm humans-- here is a case report of a man with 100 stings who suffered multiple organ failure and died.The increase of human-hornet contact in China this fall seems to be a consequence of a series of very mild winters increasing hornet populations combined with increasing human incursions into hornet habitat.
The Asian giant hornet. Source:Wikipedia
The venom of these hornets has a few components of interest to pharmacists and scientists. Mandaratoxin, also known as Antigen 5, poisons presynaptic sodium channels, thus in the context of a sting interferes with neuromuscular junctions. Hornet venom also contains Vespakinin-M, an analog of bradykinin, which causes blood vessels to dilate.

The chief reason these hornets are such a health concern is the quantity of venom they inject-- nearly a milligram of venom with each sting, nearly double that of the nearest hornet competitor. Definitely a bug to be avoided.

Update: a summary of this year's hornet attacks in China. 

One officer away from nuclear war

There's a really interesting article in Jalopnik about a moment in the Cuban Missile Crisis when a Soviet sub nearly launched its nuclear-tipped torpedo at an American vessel. Soviet protocol required unanimous agreement between the three control officers before such a launch, and in this instance only a single officer refused. It's long-past history, but still pretty scary stuff.

Wednesday, September 25, 2013

Life in earth's harshest environments

Part of what interests me about the possibility of bacterial life outside of earth is the amazing versatility of microorganisms in Earth's harshest environments.  My personal favorite are the bacterial colonies which grow on nuclear fuel rods. Pretty much anywhere that has been carefully looked at has a detectable microbial presence.
In that light, it's not surprising that deep, anoxic, hypersaline basins on the Mediterannean sea floor are also teeming with life.  These pools form in isolated spots on the seafloor where tectonic activity exposes a rock layer rich in salts. The salts dissolve, generating a shallow depression and imparting high density to the dissolving water. Thus it is stagnant, anoxic, and very, very salty. What is a surprise is that eukaryotic organisms such as protists and fungi seem to also have found a home in this area. It will be interesting to find out what energy source is ultimately powering this community.

Monday, September 23, 2013

Detecting signs of life on far-away planets

Astrobiology has an interesting discussion of how the newest generation of telescopes could be used to detect signs of life even on extremely remote and distant planets. Earth-- the only known example of a planet supporting life-- has been extensively remodeled by its biosphere. The changes to Earth, especially to its atmosphere , (for example its high levels of atmospheric oxygen) might be detectable even at galactic distances by a sensitive enough telescope.

Recent exoplanets with earth-like sizes and properties.
Credit: Astobiology
The astrobiology article discusses the hypothetical detection of  ozone in the atmosphere of a planet orbiting a red dwarf star. Ozone is created when ultraviolet rays hit oxygen-- so the ozone signal, which could conceivably be seen by telescopes, would be both a function of oxygen on the planet and the ultraviolet production of its star.

A second discussion from last year focused on how to look for photosynthesis on a far-away planet. On our planet, photosynthetic organisms can harvest the sun's light from near-infrared wavelengths to about  400 nm (violet). In planets harboring large amounts of photosynthetic organisms, the starlight reflected from the planet's surface would be reduced in the wavelengths used. Other labs have actually modelled this effect on Earthshine. Teresstrial green plants are dominant enough that the spectrum of reflected sunshine shows a big bump in wavelengths that these plants don't use. Thus reflectance increases greatly between 670 nm and 800 nm

Thursday, September 19, 2013

Mars Curiosity-- after a year, no sign of methane

The scientific team operating the Mars Curiosity rover has now published their year-long search for methane without any positive results. Detection of methane near the surface of Mars would have been a "smoking gun" for ongoing life on that planet, and indeed some earth-based observations have suggested large scale releases of methane reaching Mars' atmosphere. So it does put a pretty strong limit of how much life could be there right now. But it is still an open possibility whether there was life a long time ago.

Wind tunnel to test airworthiness of the feathered dinousaurs

Fossil discoveries over the last decade have shown that many dinosaurs had feathers, including
Yutryannus huali, a 30-ft long relative
of T-Rex. Credit: The Mirror
dinosaurs which were obviously not flight-worthy (see picture). So in the fossil finds that appear more and more bird-like, it's still an ongoing question about whether and when that evolutionary lineage achieved flight. One especially old fossil and candidate ancestor, Microraptor  had respectable feathering on all four limbs plus the tail. This early bird-like dinosaur, if it could fly, would suggest that ancestors of birds had four wings, before two-winged forms arose. But there are no present-day examples of four-winged flying creatures, so whether and how this critter flew is a real puzzle. So several groups have made scale models and examined their aerodynamic properties.
A scale model of Microraptor
(from Alexander et al.)
In 2010, Alexander et al. made a foam model, based on a bones from an individual Microraptor fossil, and even trimmed modern bird feathers to recapitulate the fossil plumage.  They then tweaked the angle of attack for the wings or tail and launched it from a catapault to compare flights.
Alexander et al. found that their Microraptor model was at a minimum, a very stable glider, but probably not capable of  active flight.
More recently, Dyke et al. , tested their own model in a wind tunnel. Similarly to Alexander et al., Dyke et al.  concluded that Microraptor probably could glide fairly well. Their results support the idea that the ancestors of birds employed four feathered limbs.
This conclusion validates a 1915 prediction by William Beebe that the lineage leading to modern birds included a 4-winged ancestor. Beebe based his prediction on his observation of long leg feathers in some modern bird breeds-- and by a close look at the famous early bird fossil, Acheropteryx.

Tuesday, September 17, 2013

The bubonic plague bacterium grows by suppressing inflammation in the lungs

There's a nice Open Access article in PNAS from 2011 which investigates how Y. pestis, the bacterium which causes bubonic plague, can overtake the lungs so quickly. Y. pestis is a fairly recent evolutionary descendant of a larger family of Yersina bacteria.  Many of these bacteria can jump to humans from their mammalian reservoirs, but Y. pestis is by far the deadliest. Y. pestis is very unusual in that infected lungs do not get inflamed for up to 36 hours after infection.
In the paper at the link, Price et al. show that Y. Pestis  strongly  suppresses the lung inflammatory response-- so that not just the plague bacterium, but other resident bacteria start to proliferate like crazy. They were not able to identify which gene or genes of Y. Pestis are responsible for this, but since they have close relative strains of Yersina bacteria, they should be able to figure it out soon. The anti-inflammatory action doesn't work in Y. Pestis mutants which lack the secretory pathway, suggesting that some combination of the known secreted toxins is important to suppress the immune system.
The authors also speculate about why Y. Pestis might have this ability while its recent ancestor does not. Y. Pseudotuberculosis  is mainly a food-borne disease, meaning it may be present in large numbers in a prey animal and therefore ingested to successfully infect its next target. Y. Pestis may have been under selective pressure to successfully infect starting from extremely small numbers, such as would be available from a flea-bite. A strong suppression of the immune system would help these bugs reach critical mass-- a feature not required in the ancestor.

Thursday, September 12, 2013

What our telescopes can't see

There's a really thoughtful opinion piece in the New York Times written by Pippa Goldschmidt, a former astronomer who worked at telescopes high in the mountains of Chile. Although the physical beauty of the night sky is still a huge motivation for her, her scientific activities-- operating the telescope, analyzing images-- became progressively more divorced from that sense of encounter.  This ambivalence was heightened by her realization that the Chilean desert at the foot of the mountain was the site of horrific political repression-- in this second way, her studies interfered with her sense of groundedness.
As the title of my blog would suggest, the visual encounter for me has always been the pinnacle, the reason why science is worth all the work and tears. Keats perceptively equated this experience to his happiness reading Chapman's translation of Homer. But looking into the lens does come with consequences for engagement with the real world.

Monday, September 09, 2013

Portable X-ray fluorimeter as an archaeology field tool

I came across this mention of archaeologists using a portable X-ray fluorimeter device to measure trace metal contents in artifacts out in the field. This device can detect small levels of metals, such as Zinc, Rubidium and Strontium, which vary among rocks originating in different volcano systems, thus narrowing down the region in which a rock could have originated.
Watch out where you're pointing that, bucko
For example, obsidian-- volcanic glass-- was highly prized throughout the ancient world because it can be honed into very sharp blades. Obsidian was traded extensively across North America, and an obsidian blade found in present-day Oklahoma might have originated as far away as northern present-day Mexico.  A precise "fingerprint"of the rock helps the archaeologists deduce trading networks, in this case probably involving the Mississippi river and its tributaries.
This X-ray device has a number of advantages, including being non-destructive, fast, and not needing too much sample preparation. However, the device is not yet as sophisticated of the Star Trek "tricorder." It does better with samples of size greater than 1 cm, and is more sensitive toward some metals over others-- thus, even when properly calibrated and operated, it can't always uniquely identify the volcanic source of a specimen.  Still, it's much faster than the Vulcan mind-meld.

Cooking with Cicadas

The last few cicadas are still up in the trees, so I thought I should point out that they are edible. In fact, lots of insects have edible portions and new ones remain to be investigated. Enjoy!

Saturday, September 07, 2013

Heaps of snail shells: Evidence for human occupation of Llanos de Moxos 10,000 years ago

The Llanos de Moxos region of northern Bolivia is a flat tropical savannah, covering about 90,000 square miles, at the eastern edge of the Andes mountains and pierced by major tributaries of the Amazon. The climate in the Llanos de Moxos is extremely harsh, cycling between extreme dryness and flooding. The ecosystem is similar in appearance to the Florida Everglades, dominated by aquatic vegetation, sedges and grasses. Because of frequent inundation, trees are restricted to occasional hillocks termed forest islands.
Aerial view of Llanos de Maxos, showing forest islands 
surrounded by  grassy floodplain. The forest islands are about
 300 feet long, and their ground level is raised about 3 feet
 above the surrounding plains.Credit: Lombardo et al.   
Though the climate in Llanos de Moxos is very harsh, this region has been received a lot of attention because of evidence that it supported a large pre-Colombian population of fishers and farmers called the Earth Mover culture. These inhabitants are thought to have raised massive earthworks to channel the flood waters and to improve agricultural output. But it has been very difficult to find conventional evidence for human habitation, such as rock tools or burials,  in this area. This might be because suitable rock for making tools has always scarce throughout this ecosystem, and because the harsh climate favors rapid decomposition of other types of evidence of human activity.  So archaeologists studying ancient inhabitants of this area have had to rely on other kinds of evidence.

Pomacea snails Note the flap, 
or opercula, blocking the shell opening
to protect the snail from drying out.
Credit: snailbusters
One of the major foodstuffs within the Llanos de Moxos is the Pomacea family of freshwater snails, more commonly known as apple snails. These molluscs thrive in tropical wetlands, and are in fact an invasive species problem in Florida and in Hawaii. The pre-Colombian peoples of the Llanos de Maxos ate huge numbers of these snails, leaving middens (essentially rubbish heaps) containing tons of snail shells alongside their earthworks.

All of these concepts came together in an unexpected way during a study of several forest islands in Llanos de Moxos published in the August, 2013 issue of PLoS One. Forest islands serve as refuge areas even today during floods, so the authors of the study had begun excavations in three of these hillocks to look for evidence of the Earth Mover culture.  On all three hillocks, they did find a layer with artifacts that resembled those of the Earth Mover culture. However, as they dug deeper, they found that the entire centers of these 300-foot mounds were made up of middens full of snail shells. The shell-rich layer extended downward for more than 2 meters, below the present day water table. Radiocarbon dating showed that the deepest part of these shell middens were more than 10,000 years old! These shells were therefore laid down long before the Earth Mover culture was present.

Lombardo et al. make several arguments that these ancient shell-rich deposits are the result of human activity. First, the layer also contained animal bones and charcoal, which are commonly found in human middens elsewhere. The archaeologists also detected chemical compounds associated with human feces within the layers. Furthermore, the snail shells themselves were overwhelmingly specimens of large edible Pomocea snails, and the vast majority of these had had their opercula removed. Thus something had eaten all those snails. Although many animals in this region do feed on apple snails, no known predator creates middens of this size. The authors thus conclude that only human activity could have led to such a large deposit.

Lombardo et al speculate that the hillocks formed over centuries of use. Once a midden became large enough,  silts would begin to accumulate around its margins, its crest would no longer be flooded, and trees could grow, further increasing the attractiveness of that spot for the inhabitants. Much later, the Earth Mover culture would find the same spots to be useful for their seasonal activities.

A last item is the extreme age of these midden deposits, with the deepest layers dating to 10,5000 years ago. The very first humans are thought to have arrived in the Americas around 14,000 years ago. This does not leave a lot of time for the culture which created these shell middens to have established itself at this  remote location of the upper Amazon. As Lombardo et al comment elsewhere, either these groups were extremely adept at exploiting this harsh ecosystem or they arrived extremely soon after the Americas were populated. Alternatively, perhaps the 14,000 year date for first peopling of the Americas needs re-examination.

Wednesday, September 04, 2013

Why are bats such good reservoirs for spill over of viral diseases?

This is a follow up to my earlier post summarizing evidence that the virus which causes the lethal disease Middle Eastern Respiratory Syndrome (MERS)  is harbored by bats. 

A number of viruses which cause deadly disease in humans--  including the rabies and  Ebola virus families, as well as the more recently identified MERS and Nipah viruses-- have been found in wild bats. Bats are thought to serve as a continuing wildlife source-- a reservoir-  for outbreaks of these viral diseases. Because of the public health risk of these diseases, it's important to understand the role of bats with respect to these and potential new viruses, so that human or livestock outbreaks can be controlled. A couple of recent reviews covering bat biology have started to describe why the life cycle of these animals is conducive to harboring viruses.

A 2012 review by Wood et al. lists several details about bats that may make them very good reservoirs for viruses which might affect humans. First, as the only flying mammals, bats combine the mobility of birds with a mammalian immune system. This means that viruses can be spread from bat to bat, or "spill over" from bats into other mammals, over a much larger range compared to, say, mice. Moreover, different bat species will occassionally share roosting locations, and individual bats occasionally switch colonies, increasing the possible viral exchange even more. And. depending on the dominant bat species, these colonies can be densely packed with animals. For example, nursing mother Mexican free-tailed bats can reach 4000 pups per square meter. Finally, it is possible that bat hibernation suppresses their immune system enough that contagion could slowly spread during the winter months.

Cover your mouth when you sneeze!
Photo credit: Morning Bray
A really fascinating more recent study by Amman et al. picks up on specific behaviors of Egyptian fruit bats which might explain cycles of human Marburg virus disease. In a large region of sub-Saharan Africa, outbreaks of human Marburg virus disease have been repeatedly traced to gold mines with large colonies of Egyptian fruit bats. Interestingly, even among miners who worked in the mines year-round, human outbreaks showed two seasonal peaks: mid-June through mid-September, and mid-December through mid-March. Strikingly, population surveys of Marburg virus in the bats in one such colony, showed that the peak seasons for human outbreaks corresponded to the peak frequency of juvenile bats (ages 4-7 months) with active infections. No other age group had peaks which matched the seasonal pattern of transmission to humans.
With a bit more detective work, they found another correlation which might explain increased juvenile rates of infection. Egyptian fruit bats tend to breed in synchrony, and these seasons of human disease and juvenile bats with infections correspond to the highest frequency of juvenile bats being initially weaned. Weanlings are less socially prominent, and have to cluster together at less desirable territory at the edges of the colony-- sometimes directly underneath the main adult mass. Thus a new, synchronized cohort of previously uninfected young bats is exposed to the virus, and some of them will develop active infections. Amman et al. did not speculate if juvenile bats, as inexperienced hunters, would further be more likely to encounter humans. But certainly all of the other elements are in place.

So the ultimate source of viruses causing outbreaks of several diseases lies within bat colonies, but there is still a lot to be learned. In many cases, sick humans were not directly exposed to bats, suggesting that these viruses may pass from bats through intermediaries before ultimately infecting humans. Secondly, bats (and other mammals) harbor many viruses which are not threatening to humans. What makes a particular virus capable of jumping species, and which of those are a threat to cause disease? Finally, it's not understood why, for many of these viruses, infected bats seem neither to clear the infection nor to succumb to them. The answer to this may lie in the specifics of their immune system.

A few other observations are needed to keep perspective on this topic. The first is that, of the approximately 4500 mammalian species, there are more than 1000 species of bats (and nearly 2000 species of rodents, another frequent recipient of the "vermin" tag). It's almost certainly a mistake to ascribe all of these dangerous diseases to all bat species. Secondly, the upswing in these outbreaks is largely due to humans (e.g. miners) coming into bat habitat rather than an invasion of the bats. And finally, even in disease prone areas, bat colonies give a lot of perks to nearby humans, including controlling insect populations, pollinating plants and dispersing fruit seeds.

Sunday, September 01, 2013

Genome post is up at Carnival of Evolution

My genome post about potential selective pressures on orchid genome size is up at the Carnival of Evolution at evoanth.

Sabine Hossenfelder on Should You Write a Science Blog

Via John Hawks, a nice essay on why science blogging matters at Back Reaction.

Advice number 1: Don't start blogging unless you have the time.
I would rephrase it to say, blogging takes a log of time---  don't blog unless it's worth it to you.

Thursday, August 29, 2013

What is the survival advantage of a larger genome?

The huge variation in genome sizes.  (Note that the X-axis
 is logirithmic.) Source: Wikimedia.
The amount of genomic DNA varies at least 40000-fold across eukaryotic species. But species with a lot of nuclear DNA content do not necessarily seem more complex than those with a small genome-- for example, amoebas have genomes much larger than those of humans. What's more, sequencing data show that the DNA of organisms with large genomes does not include large numbers of "extra" protein coding genes absent in their relatives with small genomes.  Instead, the difference among closely related species is made up chiefly by DNA sequences which do not code for proteins. 

 The high degree of variability  in genome sizes among closely related species is an instance of "the C-value enigma."  It costs a lot of energy to maintain DNA, to repair it when it's damaged, and to handle it accurately during cell division and sexual reproduction, and these costs would be expected to translate into a survival disadvantage, driving species over time toward very compact genomes. And there are real costs to having large genomes. Among plants, for example, there is a strong correlation between the size of the genome and the duration of meiosis. Plants with larger genomes are also more sensitive, in aggregate, to DNA damage via radiation, and they do less well in ecosystems with heavy metal pollution.  Is there some type of counterbalancing survival advantage to having and maintaining all that extra DNA? If so, what is it?

An 2009 paper by Leitch et al.  illustrates this enigma with respect to orchids. Genome sizes in this plant family vary more than 150-fold. (For comparision, genome size variation across all mammals is about 4 fold.) Leitch et al gathered data from 300 different orchid species and crunched the numbers to see if they could discern correlations between genome size and other traits of the plants.  The first trend that Leitch et al noticed was that the genome sizes of most orchid species, across all subfamilies, clustered at a fairly small size, comparable to the sizes observed for mammals. Larger genomes were much rarer.

Genome size (reported as 1C,  or the 
DNA content of unfertilized seeds) of
orchids, separated by lifestyle:
 terrestrial (top) or epiphytic (bottom).  
Genomes larger than 15 ph are observed 
exclusively in land-dwelling orchids.
Next, Leitch et al. noticed a striking difference when genome sizes were plotted according to the plant lifestyle. All of the large genomes they observed belonged  to ground-dwelling orchids.  Epiphyte orchids in this study (which grow  on other plants for physical support) exclusively had genomes at the small end of the range for all species. This pattern held even within orchid subfamilies containing species with both lifestyles. This difference in size distributions suggests that either a large genome is selected against in plants with an ephiphytic lifestyle, or that some advantage might be available for plants with large genomes and terrestrial lifestyle. 
Referring to data from other plant studies, Leitch et al. hypothesize that having a larger genome is disadvantageous for epiphytic orchids. One possible disadvantage that they consider is the known correlation between larger genome sizes and larger plant cell sizes.  Larger cells-- specifically, larger guard cells forming the pores on the bottom of leaves-- would make larger air pores, leading to more rapid exchange of gas but also to increased water loss. Perhaps epiphytic orchids, which must conserve water, have undergone selection for smaller guard cells and thus smaller genomes. Alternatively, phosphorous-- a key component of DNA-- is scarce in the epiphytic niche, and could become a source of selective pressure. Thus the study of Leitch et al. ends up by documenting a specific instance in which larger DNA genomic content appears to be a survival disadvantage. 

The model of Frank et al. Increases
 in atmospheric CO2 levels would
 tend to favor plants with larger guard cells
on their leaves. 
Another approach to understanding the relationship between genome sizes to evolutionary processes is to examine the fossil record. There is a really fascinating example of this in a 2012 paper by  Frank et al.  Frank et al speculated that larger guard cells, by promoting gas exchange,  would be advantageous during evolutionary intervals in which atmospheric carbon dioxide was high. To evaluate this, they collected measurements of guard cell volumes from 400 million years of the fossil record, and remarkably did find a correlation between this simple geometric measure and measures of atmospheric CO2.  Since genome size correlates with guard cell size, its possible that genomic size contributed to evolutionary processes on this longer time scale.
Frank et al. are careful to add this disclaimer to their work: "Our goal is not to identify, nor does it require, a mechanism for change in or evolution of plant genome size. However, an understanding of the selective forces involved requires a model that tells us what to expect from a given set of assumptions, so to this end, we describe a simple model to accompany our findings." With this caveat, their paper provides conceptual support for large genomes as a structural, rather than strictly genetic, trait. 

Wednesday, August 28, 2013

Ramblin' man

John Hawks reviews data that Homo Erectus hominins were in China as early as 1.6 million years ago. I guess wanderlust is in our bones!  The more precise dating is obtained using paleomagnettic measures.

Many other animals dispersed from Africa in this epoch (lower Pliestocene), and it could be that the hominins were following the availability of familiar game.

Tuesday, August 27, 2013

Evidence for Neanderthal manufacture of leatherworking tools

The lissoir tool as used to burnish hides.
Credit: Abri Peyrony and Pech-de-l'Aze projects
There is considerable controversy about the social abilities and cultural achievements of Neanderthals.  In western European sites, tools and ornaments have been found in Neanderthal contexts, but it was not clear if these items were indigenous to the Neanderthals or somehow learned from anatomically modern humans. In today's PNAS, Sorressi et al.  report bone tools for burnishing hides, excavated from Neanderthal sites dating to before the arrival of anatomically modern humans. These new finds thus strengthen the the argument that Neanderthals had their own toolmaking culture.

Sequoias are used to this

Fire scars (arrows)  in a sequoia cross-section show 
that this tree survived repeated wildfires over
 its 500 year lifespan.
National Geographic has a nice write-up of how sequoias handle wildfires like the current Rim Fire near Yosemite valley. As the cross-section shows, these giants have seen it all, from droughts to wildfires.  During the Medieval Warm period, a prior very warm and dry period in the Sierras, a given sequoia would experience wildfires at intervals of 10 to 15 years.

Monday, August 26, 2013

Tame dogs-- and feral scientists

Via John Hawks, I had missed this during last summer: there are several big scientific groups interested in when and where dogs were first domesticated. It is clear that there were dogs in human society about 10,000 years ago, but more recent claims are pushing the start of domestication back to as far as 35,000 years ago. A very interesting-- but still contentious-- topic!