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.