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Snapping Turtle

April 13, 2014


Out on the bike trail, my first ride of the spring: In the middle of the pavement stood this enormous turtle. Stood or sat, not sure which, but the giant thing wasn’t going anywhere–and was likely to end crushed beneath some bike tire. So I tried to pick it up.

“Snap!” What a fast pair of jaws that thing had, about two inches across. Enough to bite off three fingers. (Didn’t get video, but this gives you the idea.) So I nudged its shell with my foot, getting it to move bit by bit across the pavement, snapping all the way. Finally pointed it toward the stream. It reminded me of promoting Obamacare.

Turtles are amazing. They are one of the oldest groups of reptiles, predating the dinosaurs. Snapping turtles can stretch their head out like an accordian, really fast to grasp prey. Their eyesight is excellent–I could tell because, as I tried to get behind the turtle, it kept turning to face me down.

The turtle’s shell evolved from its rib cage; but the outer surface of the shell is skin, with large, modified scales. The rest of the turtle’s skin has smaller scales.

Like other reptiles, turtles do not age. As the turtle grows, its organs are indistinguishable from those of younger individuals, aside from size. Scientists study turtles for clues to prevent human aging. Sea turtles swim beautifully, as seen here.

Ebola Outbreak

April 9, 2014

While the world hyperventilates over the future British royal starting to crawl, the largest Ebola outbreak ever has his West Africa. Over a hundred deaths, with more than two-thirds mortality from this rapid killer. The virus hit Guinea and Liberia, including Guinea’s major city of Guekedou. Usually the virus comes from “bushmeat,” local primates and bats people eat for food. In The Highest Frontier, I imagined Ebola virions printing out from 3D printers.

What is Ebola virus; and how does it turn the body into blood pudding?

The virus particle consists of a coiled RNA molecule (not DNA, but RNA, which we usually know as a cellular copy of DNA). But many deadly viruses have RNA genomes. The Ebola virus particle fuses with the membrane of a host cell, such as a monocyte (a white blood cell). Then the viral RNA uses host ribosomes to make proteins that trick the cell into producing more Ebola virions. Furthermore, the virus makes proteins that inhibit the immune system, both adaptive immunity (antibodies) and innate immunity (interferons).

 In later stages, the newly released Ebola virions infect endothelial cells (interior of blood vessels). The endothelial cells fall away, destabilizing the blood vessels and causing massive bleeding. Various toxic shock effects occur as well.

Ebola virus is a surprisingly simple entity, with only seven genes in its genome. Amazing for all the sophisticated damage it causes, and the multiple ways of blocking the immune system.


Exercise Hormone Helps Memory

March 30, 2014

Studies connect cardio exercise with improved memory and brain function–but how? We’re just starting to see the molecular clues. Exercised muscles releas a hormone called irisin, which influences the brain’s memory center. Original report is here.

Where does irisin come from? The exercising muscles express a particular gene (that is, make messenter RNA and protein specified by the gene). The gene is called FNDC5 or Fibronectin Type III Domain Containing 5. The gene is found in humans and mice–but not invertebrates, which lack the vertebrate central nervous system. It is expressed strongly during embryonic formation of the heart. A particular peptide (short part of a protein) is cut off the FNDC5 protein; this peptide is called irision. In adults, FNDC5 expression from myocytes (muscle cells) releases irisin, whose signal is associated with converting “white fat” cells to “brown fat” with expenditure of energy.

But now, exercise is also shown to cause irisin expression and release in the hippocampus. Is this unusual, for a very particular signal molecule to have different roles in different tissues? Actually, it is very common in eukaryotic organisms (plants and animals, including us humans). Most of our proteins are multitaskers. In particular, much of brain function depends upon multitasking proteins. That is why so many single-gene birth defects have multiple effects on the body, including cognitive problems.

The hippocampus is the brain’s memory center. In the hippocampus, FNDC5 expression induces expression of BDNF (brain-derived neurotrophic factor). BDNF protects the neurons that encode memories.

So the moral is, now that spring is here (ignore the dusting of snow this morning) let’s get out and start running.

Humans Increase Speciation?

March 24, 2014


We hear a lot about the loss of species in the Anthropocene–the present geological era, in which human existenced has substantially altered the content of our biosphere and the geochemistry of our planet. Much is made of the loss of biodiversity–perhaps ten or a hundred-fold increased rate of extinction of species, from megafauna such as tasmanian tiger and dodo, to vast numbers of marine phytoplankton (photosynthetic algae and bacteria). Practically speaking, nothing can bring these species back, despite herculean attempts to reproduce one or two; the mammoth, say, or certain wild cats.

Still, there is another view that, however regrettable the losses, some new species will arise–by the intriguing process of species hybridization. I am skeptical that the new biodiversity will “make up” for the losses, especially the functional loss of keystone plants and animals that maintain whole habitats. Whenever you fell Hometree, the loss of what lived there is incalculable. And, I’m skeptical of the claim that “Climate change also tends to boost regional diversity,” since rapid change commonly decreases diversity, owing to the failure to adapt. The problem with climate change today is not change itself but rapidity, the accelerating rate of change–global change at a rate faster then ever before, and only getting faster yet.

Nonetheless, the increasing movement of species amongst different locations will generate some new species through the process of species hybridization. The primrose Primula kewensis is an example of a flowering plant that arose in Britain, from two parent species arguably less interesting than their hybrid descendant. Similarly, the human species Homo sapiens actually arose through hybridization of previously divergent hominids including Neanderthal and Denisovan.

The hominids, like the primroses, were already closely related before they came together. In science fiction, Octavia Butler imagined the Oankali, extraterrestrial beings completely unrelated to humans, whose reproduction actually requires interbreeding with other life forms–and each hybridization produces a new species. On Earth, we don’t see this, although viruses (with their smaller genomes) show evidence of extensive gene exchange.

Clarification: At the level of the cell, distantly related organisms HAVE interbred–the bacteria engulfed by larger cells, evolving into mitochondria and chloroplasts. And similar assimilations occur today.

However, distantly related life forms with complex developmental body plans (such as vertebrate animals and vascular plants) do NOT hybridize unless recently diverged. If anyone knows otherwise, let me know!

Chocolate-eating Bacteria for Health

March 18, 2014

In the too-good-to-be-true category, an undergraduate researcher and her mentor report at the American Chemical Society that your intestinal bacteria digest chocolate into products that make your heart healthy.

I wish the original report were available, since the press report has it garbled, but the story apparently was reported in a talk or poster at the ACS meeting in Dallas. The press says that “stomach” bacteria are the cause, but in fact Bifidobacterium and lactic acid bacteria inhabit the intestine.

The researchers, undergraduate Maria Moore and her professor John Finley at Louisiana State say they constructed a “model digestive tract” that aims to simulate the human intestines. Placing human fecal bacteria in this model system, they added cocoa. Cocoa, the active ingredient in dark chocolate, contains antioxidant molecules such as polyphenols. The polyphenols however are in long chains that don’t get absorbed well by our intestine.

But our intestinal bacteria possess an amazing range of enzymes to break down almost any organic compound. The Bifidobacterium apparently breaks down these long-chain polyphenols into smaller ones that a human body can absorb. Antioxidants have many potential benefits including cancer prevention.

Why dark chocolate in particular? Not sure, but dark chocolate (the real stuff) has twice the cocoa content as “milk” chocolate, and half the sugar (roughly); so instead of eating sugar, the bacteria are forced to dine upon the tougher stuff that’s good for us.

Memory Molecules Move

March 6, 2014

At the recent Boskone, a panel discussed why some of us are writing science fiction on Earth, rather than some distant star. My reason is that science has multiple frontiers, in many dimensions–such as the interior of living cells. Now, scientists at Albert Einstein can watch the molecules of memory move within a neuron. The Science report is here.

Postdoc Hye Yoon Park worked with Robert Singer (and a long list of collaborators, as always) to construct a mouse in which the memory molecules can be seen. The molecules (moving white dots–click video) are messenger RNA, the RNA copies of an archival DNA gene. The gene expresses the messenger RNA to specify beta-actin protein, synthesized by a ribosome. But the amount of mRNA is what determines how much beta-actin gets made. And where the RNA goes–there goes the protein. Beta-actin transport within a neuron (nerve cell) is associated with extending the dendrites, the spine-like projections that connect to other neurons and help form memories.

So how did Park make this special mouse with fluorescence-tagged mRNA?


As usual, she used that Nobel-winning protein, GFP (Green Fluorescent Protein, originally made by a jellyfish, now made by bacteria, mice, plants, in every scientist’s lab). First, the MCP mouse (light green) was made “transgenic” by inserting the gene specifying GFP into its genome. This was done using a lentiviral vector–the research equivalent of those life-saving gene therapy vectors made from HIV (the AIDS virus, remember). The vector is constructed to contain the gene encoding GFP, located between two lentiviral integration sites. But in this case the GFP gene is “fused” (its sequence attached to) the sequence for another protein, MCP. MCP is the coat protein of a bacteriophage (a kind of virus that infects bacteria). If this starts to sound mixed up, remember this is the postmodern Franken-gene era; every useful gene gets constructed out of bits and pieces from wherever.

Now a different mouse also gets constructed (the gray one above) in which the mRNA for beta actin has some extra sequence fused, called the MBS sequence. The MBS sequence of RNA specifically binds to MCP protein.

Next–unbelievable though it may sound–the next step is actually to cross breed the two lucky mice (yes, they get to have fun the time-honored traditional way). I guess in vitro IVF could do as well, but many mouse breeders actually still do the old fashioned thing, usually picking up a male mice by the tail from one bin, and a female mouse by the tail from another bin. As a result (aside) many lab-bred mouse strains evolve low vision, because the ones that don’t see the hand coming for the tail get to breed.

Anyway, the result is the (dark green) mouse, whose neurons express both the GFP-fused MCP phage coat protein and the MBS tagged mRNA sequence that binds the fluorescent GFP-MCP protein. So wherever beta-actin mRNA goes, the GFP is sure to bind and light up fluorescent. Watch the cool video. Where the mRNA goes, and how it stores memories, is a story for another day.

X-Prize for Moon and More

March 3, 2014

The X-Prize Foundation is best known for the Ansari-funded prize for repeatable spaceflight for a hu/manned craft, in 2004. Now there’s a Google Xprize to be won for putting a rover on the moon by 2015. The design above is by Astrobotic.

But the foundation supports other kinds of prizes–including prizes in life science. The Brain-Machine prize will reward a “reliable, non-harmful interface between the digital world and the human cortex.” In other words, a cyborg; or the future Toynet world of Frontera. Other prizes reward health sensors and organogenesis. There’s even a Jurassic prize for guess what.

Suppose we combine the two fields of space exploration and artificial life? I’d like to see a self-printout prize: A prize for a rover-printer that can print out a working copy of itself. A sort of lunar cockroach–once you set down one, you’ll never need to send another.

What Xprize would you like to see?


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