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Smart as a Duck

July 24, 2016

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Is a duckling capable of abstract thought?
Somehow this story of true intelligence got buried beneath the convention news.

According to authors in the journal Science, experiments demonstrate the ability of newly hatched duckling to distinguish the concepts “same” and “different.”

Previously, the authors note, “pigeons and bees can be trained to discriminate whether novel images contain humans or not, or whether novel paintings are by Monet or Picasso.” Such discrimination requires extensive training between specific patterns–the pattern of a “human” shape, versus other; or the patterns of Monet versus Picasso. The discrimination of paintings does not imply artistic talent; in fact, the animals might be observing something trivial, such as the color scheme or size of objects depicted. These previous findings all required concrete objects to discriminate.

But can we demonstrate learning of an abstract concept?

Authors Antone Martinho III and Alex Kacelnik, of the Oxford Zoology department, claim to have done just that. They made ingenious use of a powerful memory tool: the imprinting of birds on their parent. Imprinting has long been demonstrated as an introductory lab in biology. The student waits for a duck egg to hatch; then the first thing the hatchling sees or hears is the student. Forever after, the hatchling follows the student as if they were its mother.

If ducklings can imprint upon a human student, what about inanimate objects? Or even an abstract concept?

In the experiment, newly hatched ducklings were exposed to pairs of objects.

In some cases, the hatchlings were exposed to pairs of objects that were identical. Other hatchlings were presented with pairs of objects that differed in shape or color.

After exposure, the hatchlings were then presented with a pair of objects of a different kind (balls versus cones). But two kinds of presentation were done: of two different objects, or two identical objects. For example, a duck was imprinted on “two spheres”, then tested on “two cones” (identical) or on “cube plus tower” (different). The duck’s preference was then measured by the number of times it stepped toward the object pair. Even though the new objects were of a different kind, the ducks still preferred (stepped toward) an identical pair, if it had imprinted on an identical pair; or a dissimilar pair, if it had imprinted on a dissimilar pair. The experiment worked either for shape or color.

When picked up by the canonical alien abductors, I wonder how many of us humans could pass this test.

 

Peacock Spiders Revisited

July 9, 2016

For something more cheerful, here’s a return of the Peacock Spider. Apparently seven new species of peacock spider have been discovered in Australia. The discovery was reported in the journal Peckhamia–a journal devoted to the biology of jumping spiders. Clearly a sign of the growing overproliferation of specialty journal, but in this case we can’t complain too much.

The Peckham society is a treasure trove of fascinating and diverse spider behavior, such as this one feasting on a fellow spider. Not the same species, so it doesn’t count as cannibalism (unless you’re a cannibal for eating a cow.)

And for the truly insatiable spider enthusiast, check out the Peckham’s video collection. To think that all this variety represents one small branch of the arachnid tree–It’s enough to give some hope for Earth’s biological world.

Oceans Rise or Fall?

July 5, 2016

Beach time of year, as good a time as any to wonder how fast the ocean is rising. In the long run, we’re locked into several feet of rise in the next century, possibly more if Antarctic glaciers accelerate.

This great figure from Discover Magazine shows how undersea “rivers” are undermining the ice shelves, accelerating their fall in unpredictable ways.

But in the near term, the ocean’s movements look surprisingly complex–giving naysayers excuses to deny the problem. For instance, the sea levels right around Antarctica will actually fall, relative to the Antarctic land mass. This happens because the mass of ice will be gone, and thus there will be less gravitational pull on the water. In addition, the land will “spring up” slightly, like the couch cushion when you get up for a snack. The net result, though, is water rising faster in farther off places like Florida and New York.

Another place ocean levels are falling is west of Mexico. The reason is weather patterns, a cyclical pattern called the Pacific Decadal Oscillation. This pattern, which takes higher math to understand, results in a decade of cooler water in the Pacific, which means denser water and lower sea level. Of course in the following period, the sea will rise double, making up for lost time.

A good reason to think about solar airplanes for your next vacation.

 

Running Grows the Brain

June 23, 2016

It is old news that exercise improves the brain–at any age, from children who walk to school, to the elderly who garden. Prolonged exercise, as in running, is what we evolved to do. Running–and the intellect involved to track down animals–led early humans into a unique form of hunting, one that required memory and calculation. But what is the physiological connection? How do the heart and skeletal muscles affect the brain?

Now, researchers are beginning to figure out the molecular basis: What specific genes and proteins do the job. It took a collection of scientists from Lebanon to NYU and Harvard to come up with this alphabet soup of a project, “Exercise promotes the expression of brain derived neurotrophic factor (BDNF) through the action of the ketone body β-hydroxybutyrate.”

The researchers set mice to running on their proverbial running wheels. After thirty days running, compared with slacker mice, the runners showed increased amounts of a brain protein called BDNF. BDNF is a protein that encourages nerves to grow; a member of the same family as nerve growth factor, the protein discovered by the famous Nobel laureate Rita Levi-Montalcini (who makes an appearance in The Highest Frontier). BDNF helps maintain synapses and grows new ones in the hippocampus, cortex and forebrain; basically everywhere needed for higher function.

So what is the molecular mechanism? The authors proposed and tested a form of “epigenetics,” a mechanism by which environmental experience alters chemical tags attached to the neurons’s DNA, or to histone proteins associated with the DNA. Epigenetic markers involve enzymes called histone deacetylases (HDAC). The HDAC removes an acetyl group from a histone, a binding protein that helps “pack” DNA and determines whether its gene gets transcribed to RNA. Here, DNA is wrapped two turns around a core of eight histones (colored).

The authors did experiments that showed that inhibitors of HDAC proteins (specifically HDAC2 and HDAC3) could prevent the histone deacetylation, leaving the DNA wrapped around histones marked with acetyl groups. Acetyl groups usually code for “go ahead” and transcribe a gene. So now the gene encoding BDNF goes ahead and gets transcribed to RNA, which then gets translated by ribosomes to make BDNF protein.

What all does this have to do with mice on their running wheels? The running mice make extra ketone bodies such as D-β-hydroxybutyrate (DBHB). Ketone bodies get made by your liver after intense exercise uses up carbohydrates. Excess ketone bodies can cause problems, but as a short-term response to exercise they supercharge the brain. In particular, DBHB blocks production of HDAC2 and HDAC3 (that is what the cross-blocked vertical lines mean, in the diagram above). Since DBHB blocks the HDACs, and the HDACs block expression of BDNF, the net result is that ketone bodies induce BDNF which enhances neurons and makes more synapses.

Start running.

Lost City Of–Microbes

June 5, 2016

Atlantis of ancient ruins? Not so fast. What divers thought was an ancient Greek metropolis was actually an outgrowth of microbes. The microbes are stated to be methanogens (archaea that convert carbon dioxide and hydrogen into methane) but I think actually they are methane oxidizers.  At the bottom of the ocean, methane often arises at cold seeps, places where petroleum components and minerals seep up from subsurface volcanic activity. The minerals get oxidized by bacteria, and carbonates precipitate into odd formations.

Our Gulf of Mexico is full of cold seeps, where the methane gets oxidized by sulfate bacteria, as indicated by isotope ratios. Some of the sulfate bacteria then inhabit clams that may lose their feeding ability.  The reduced sulfate can then be oxidized to sulfides within symbiotic worms. Green dots show fluorescently labeled bacteria oxidizing sulfides within the worm. The size bar is 0.02 millimeters.

So indeed, there is a complex intricately cooperative civilization–of microbes. Meanwhile, carbonates precipitate with magnesium ion, forming dolomite. The dolomite formations date to several million years ago–even more ancient than the Greeks. As the authors state, “Exposure on the modern seabed in the shallow subtidal zone has caused confusion, as concretion morphology resembles archaeological stonework of the Hellenic period.”

 

Artificial Human

May 14, 2016

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Buried beneath reality show headlines, the NYT breathlessly informs us, “Scientists Talk Privately” about something. To wit, a group at Harvard has a secret meeting to plan to “create” an entire set of human chromosomes. Could this really be it–an Artificial Person? Without (gasp!) biological parents?

Like a rather bad Heinlein novel, there are enough contradictions to go around.

First of all, what’s so unique about making a human genome–something trillions of our own body cells do every day? The NYT informs us, the scientists will “use chemicals to manufacture all the DNA.” Mm-hm. So my own cells are made of what, if not chemicals? Cosmic ray particles, maybe?

What we call “chemicals” presumably means bulk processed petrochemical products stored in 1-kilo bottles obtained from Sigma-Aldrich or Thermo-Fisher. And “manufacture” means a concrete-slab factory, where mostly male persons “fabricate” things, as opposed to a bit of meat within a female that uses its own DNA copying enzymes.

But suppose, continues NYT, we could “use a synthetic genome to create human beings without biological parents?”

Project leader George Church (who started out as a bacterial molecular biologist) assures us we’ve got it wrong. “They’re painting a picture which I don’t think represents the project,” Church observes. The project is “not aimed at creating people, just cells.”  Again, this claim represents a surprisingly parochial view of what constitutes the “natural” human reproductive process. We can argue endlessly over whether a fertilized egg or embryo constitutes a human being, but there can be no doubt that most of our bodies at some point developed from a single cell that became a few more cells.

The technology exists to replace the nucleus of an egg cell with a new nucleus. Could a “synthetic” set of human chromosomes replace the chromosomes of an egg cell?  What about a skin cell transformed into an egg, something also near possibility?

Of course, no article about artificial  human life is going to get away without mentioning Einstein. The crowning awful possibility: “Would it be O.K., for example, to sequence and then synthesize Einstein’s genome? If so how many Einstein genomes should be made and installed in cells, and who would get to make them?”

Please–Enough already Einstein. Myself, I’d rather recreate Mileva Marić, the physicist whom Einstein got pregnant and married, and who probably co-created his most famous works.

So why create a synthetic human genome? We don’t know, given the “secret” nature of the Harvard meeting, but let’s give them a break and assume they just want a more efficient way to “construct” a genome out of various parts and see what it does in a cell. Cell culture is a lot more efficient than running after mini-humans (mice), as some of my students can attest. Nevertheless, we approach ever nearer the day when any skin cell could become a human.

 

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Sharers of Hawaii Make Super Corals

April 24, 2016

In  A Door into Ocean, the Sharers tend their entire planet, lifeshaping each apparently wild form of life to restore balance. The corals on the floating trees get helpful microbes, while the seaswallowers get lifeshaped (engineered) to resist the invaders’ poisons. Is that where we’re headed? Already our wilderness managers radio-tag every vertebrate in sight, monitoring populations like a zoo. But Hawaiian biologists are going one step farther: actively breeding corals to withstand global warming, the climate change now inevitable. Unnatural selection? Perhaps, but perhaps better than no corals left?

Ruth Gates and Madelein Van Oppen are trying just that. Gates noted some exceptionally hardy corals in Hawaii that seemed to withstand heat and acid, the two big causes of coral death. She and Van Oppen obtained grants from Paul Allen’s Ocean Challenge program. Their mission: to build Super Corals  for the Future.

After a massive coral bleaching episode, Gates found regions where occasional corals bloomed surrounded by dead ones. Even the survivors’ symbiotic algae were okay. So now she propagates these survivors, and investigates their genes, trying to find out how to make corals hardier.

Does the Super Coral project represent future promise, or only vain hopes? Coral grows slowly; it’s hard to see how a few engineered polyps could propagate throughout the ocean. Rising temperatures and falling pH are happening so fast, faster than ever recorded in Earth’s history. Mitigation projects should not lull us into thinking we can ignore a rate of change that will eventually boil our planet. But perhaps on the way, we might save a few corals.  Gates says, “Our project is acknowledging that a future is coming where nature is no longer fully natural.”

Surprisingly, we find corals even in regions where biologists had thought their growth impossible. Most recently the muddy mouth of the Amazon was shown to host corals, along with sea fans, fish, and sponges. Considering how much traffic the Amazon gets, we biologists might be surprised and just a bit embarrassed to have overlooked such riches. Surely it’s worth the investment to see how much life we can save, while the world’s populations make their leaders keep the world worth saving.

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