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NSF loses Kamal Shukla

January 31, 2016

Most of us know that books get published with the guidance of editors such as David Hartwell. Relatively few are aware of how progress in science is shaped by program directors at the National Science Foundation such as Kamal Shukla, who passed away last week. While Hartwell was known for promoting “hard science” in science fiction, Shukla promoted the “hard” physical and chemical foundations of biology.

An example of the research Shukla approved for funding was how the protein ubiquitin regulates gene expression (how a gene makes its product). Ubiquitin is one of many chemical tags that get attached to proteins that bind DNA. Here, Cynthia Wolberger at Johns Hopkins explains.

By understanding how ubiquitin works, we learn clues to all kinds of disease processes such as cancer. Today, Wolberger’s work is a big deal for medical research; but the start for testing her ideas came from NSF, back when NIH though it too risky.

Another researcher whose pioneering work found NSF support under Shukla was Mary Jo Ondrechen at Northwestern. Ondrechen tackles the big problems of genomics and proteomics–When you have 13,000 new protein structures determined by biophysics, how do you make sense of what they do? Massive computational programs address such questions, with results that point in countless unexpected directions. We need far-sighted shepherds at NSF to make sure such work continues.





David G. Hartwell (1941-2016) The Holobiont Mourns

January 20, 2016

Thirty years ago, a cotton-ribboned manuscript typed from four penciled notebooks about fish women had been rejected by several New York publishers. A Bryn Mawr classmate Mimi Panitch brought it to the attention of an editor at Tor. A brief note suggested we meet at a con, it might have been Lunacon. Formally dressed and pregnant with my first child, I went to meet the editor at the appointed time. A table in the bedroom was full of empty bottles. I nearly walked out, not knowing that David hosted fans all night. Instead I stayed and published most of my fiction career with David’s insightful conversations. But all beings great and small pass on, only their ripples cast wider circles. The holobiont mourns, and goes on.

Nitrogen for Mars Life

January 17, 2016


Does Mars have a nitrogen cycle? Another great story from last year, which microbiologists need to explain better.

We here about carbon all the time–a carbohydrate (sugar) gets oxidized to CO2 (problem) or else fermented and reduced to methane, CH4 (a worse problem). That’s the carbon cycle in a nutshell.

But the nitrogen cycle is far more complicated. The main form of nitrogen in the atmosphere (N2) gets fixed into ammonia (NH3), or as some prefer the ionized form, ammonium ion (NH4+). Ammonia/ammonium gets fixed into our amino acids and DNA bases. In the soil, however, bacteria just see ammonia as another thing to oxidize for energy, analogous to carbohydrates, ammonia gets oxidized. Instead of just one oxidation state, there are several, such as nitrous oxide (N2O), a serious greenhouse gas–one of the worst. Marine dead zones (of which there are several hundred worldwide) put out lots of nitrous oxide. Luckily, still other bacteria oxidize nitrous oxide to nitric oxide (NO), nitrogen dioxide (NO2), nitrite (NO3-), and nitrate (NO4-). Plants can take up nitrate, if they get it before it runs off in groundwater. Along the way still other bacteria pull off the oxygens releasing N2–completing the cycle for still other bacteria to fix the N2 back down into hydrogenated forms that make up living bodies.

If you haven’t fallen asleep by this point, you can see why microbiologists wake up at the news that Curiosity Rover may have found NO2 and nitrate (NO4-) in Martian soil. The implication is that Mars has a nitrogen cycle–perhaps abiotic (not conducted by life) and perhaps limited to small amounts, but still, if various oxidation states of nitrogen exist, they could provide a basis for microbes to get a start on metabolism providing the basis of proteins and chromosomes.

Nitrogen cycles are so complex that even here on Earth, we are still discovering new connections. Holger Daims reports a new find of “comammox” bacteria that complete the entire leg of nitrogen oxidations from ammonia through nitrate. Here they are in this micrograph, labeled yellow by fluorescent DNA probes that base-pair with just the right gene sequence.

We used to think that two or three kinds of bacteria had to get together each contributing one of the conversions in the nitrogen chain. That still happens, no doubt, but there are certain species that can actually run the whole way. Such a self-sufficient microbe might be the likeliest to get the first foothold on Mars.

Clean Gas–Not

January 12, 2016


And here’s the kind of future from which we need to save ourselves. Clean gas–that is, 330,000 car-years worth of greenhouse emissions. Leaking since October.  Say what–October? 2,000 residents displaced? Where has this news been?

And there are 400 similar facilities around the country. Meanwhile, the fracking is starting earthquakes, but the drillers refuse to follow regulations.

The problem with “natural gas” is that it’s a gas; it seeps through the smallest crack. Even a functioning well loses large quantities; no one really knows how much.  Left in the earth, to seep slowly, the methane largely gets oxidized for food by methanotrophs–bacteria that breathe oxygen to convert the methane to CO2. But the large-scale release by human technology, like the BP oil spill, are unprecedented. Time to look for geothermal heating and solar planes.


What Avatar Got Right

January 10, 2016


Charlie Jane’s Io9 post reminds me how annoying it is to defend a Hollywood blockbuster by a director who can’t pass the Bechdel test. But the post’s comments trouble me. So many miss how much real biology the film shows—and what it says about saving the one real world we’ve got.

Avatar is the only film I know that shows an ecosystem in its full dynamics; the way it really works. There is divergent evolution—the six-legged creatures with the common body plan. Even the Hollywood humanoids have their “missing link,” the prolemuris with its half fused arms. May seem hokey—but evolution actually does work that way, more often than you think. Ever looked at a peacock spider, or maybe a nudibranch? Did you know we’re cousins? Google-image nudibranchs, then imagine laughing if a film depicted humans evolving from a world of that.

Avatar’s ecosystem actually works like our real one: All the life forms compete, yet collaborate. Animals fight to the death by day, then sleep together in a heap by night. Plants savagely compete for the light—while below ground, their roots share miles of fungal internet. The Pandora network interconnecting all the plants; something like that really exists, called mycorrhizae.

And above all, Who is going to save the planet? If not someone like Jake, then who?

Suppose you rewrote the film where Neytiri or Tsutey saves their own world. How would they go about it?

Of course, Neytiri could do it. But to do so, she’d have to learn as much about the Western oppressor as Jake does about the Navi, either the weapons or the Western legal system and media. In real life, that’s how people get “saved.” Either a Western visitor adopts the local ways (Lawrence of Arabia, or Gertrude Bell) or an oppressed leader learns Western ways. Gandhi got a British education, and his nonviolence used the Western media, skillfully and deliberately. In Avatar, even Neytiri has to do that at the end, by saving Jake’s original body. In real life, the “native” leaders who do that become a bit Western; they can never completely go back.

In real life, “uncontacted peoples” can barely survive contact, lest most of them die of our diseases. That’s why our laws—Western style laws and governments—protect them from us. The Nicobarese are off limits because the Indian government says so. Fifty or so groups in South America are protected the same; not perfectly, but we’re trying. In effect, we “protect” them the same way we protect wild animals in game preserves.

What alternative do you suggest?

After I watched Avatar, I turned to the guy next to me who’d seen it six times. I asked if he knew there were parts of Brasil that looked like Pandora. He said, “I’ve never been outside Ohio. Have you?”

Isn’t all of Earth one last game preserve—and we are the Uncontacted? What Jake or Neytiri will save us? Look in the mirror, Western savior.

A Virus Has Ribosomes?

January 3, 2016


Sorry for the long absence, thanks to writing my NSF grant –the one that keeps my lab in business. (If you drill down you’ll find my current award “Kenyon 1” in Ohio.) I had thought I could put it off for a year–but my group has grown to 20+, with three major projects (E. coli on aspirin,  bacterial neurotransmitters, high pH evolution) plus my Antarctic metagenomes, so besides completing Evolving Science 4E (almost) the grant had to get in. I won’t say what I proposed to NSF, except we already have a clinical lab inquiry for our early data, but that’s a story for another day.

My New Year’s resolution is to complete at least one blog story per week, plus make progress on Blood Star before all the science comes true already (see plant virus gene therapy).
Today’s post is perhaps last year’s biggest story you never heard, the giant Mollivirus recovered from 30,000 years-old tundra in Siberia.

Thirty thousand years, remember? Woolly mammoths, saber-tooth tigers, and three species of humans still roamed the Earth. And amebas full of viruses. Some ameba froze to death, still infected by a giant virus called Mollivirus which remained infective.  French students at the lab of Chantal Abergel and Jean-Michel Claverie incubated the tundra sample with live amebas (and a bunch of antibiotics to get rid of bacteria), then looked for where the amebas died. Previously, similar frozen samples have released Pandoravirus and Pithovirus. Can smallpox and 1918 influenza be far behind?

The new virus shows remarkable complexity in its reproduction cycle. First the ameba has to engulf the virus (by phagocytosis) which is large enough to resemble a tasty bacterium. That’s the selective pressure for ameba-host viruses to be giant: If too small,  the ameba won’t engulf them. Once engulfed, the virus escapes the phagosome and invades the ameba’s nucleus where it sets up a virus factory. The factory starts churning out new virions. But interestingly, each virion packs unidentified fibrous material (see above). Maybe like packing peanuts? To make the whole package bigger and more attractive to the next predatory host?

Beyond that, the most intriguing point: Possibly for the first time, we have a virus that packs ribosomal proteins. Transfer RNA (tRNA to carry amino acids to the ribosome) has been found before, even specified by viral genes–Mollivirus has those genes too. But never the protein components of ribosomes. If a virus actually made working ribosomes, that would pretty much tip the scale to say, This “virus” is an honest-to-goodness cell. So far, we don’t know if (1) the Mollivirus-packed ribosomal proteins form ribosomes (probably not); (2) the ribosomal proteins “moonlight” serving other tasks for the virus, similar to how lysine tRNA serves as a reverse-transcriptase primer for HIV (AIDS virus); or (3) they’re just more packing peanuts to plump the virion.

Stay tuned for the French group’s next ancient virus discovery.

Water Flows on Mars

September 29, 2015

After years of hints, NASA finally calls it: Water flows on Mars. Not anything like Niagra Falls, but enough to see signs of channels forming. In the past, evidence had accumulated for water channels a billion years ago. But now, we see signs of water “days” ago.

The time-lapse animation of Palikir Crater, above, shows streaks that lengthen during the Martian summer. The streaks fade as it gets colder; presumably the water sublimes or freezes.

Where does the water come from? Calculation show that it can’t come from the Martian atmosphere, which is too thin to precipitate more than a few microns deep. Does it come out of the ground?

If water does come up and flow, even brine (salty water), would it contain life?
We already have evidence that life existed on Mars three billion years ago, more or less. The fossil mats that Nora Noffke analyzed look just as convincing as similar fossils on Earth. Unless some catastrophe sterilized the entire planet, one would think living descendants remain today.




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