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.