Giant virus, contamination, Svante Pääbo and the Neanderthal Genome, and Sydney Brenner on funding and scientific publishing

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That giant virus

OK, sure, I know, Pithovirus, that giant virus they thawed out of the 30,000 year-old Siberian permafrost, is a pathogen specific for amoebas, blah blah blah. But I can’t help wondering what else is going to turn up as the warming Earth releases creatures from the melting of ice frozen many thousands of years ago.

Pithovirus. Credit: Julia Bartoli & Chantal Abergel

Pithovirus. Credit: Julia Bartoli & Chantal Abergel

And I’m not alone. Carl Zimmer mentioned the possibility in his Matters column. Last year a different giant virus was found in a human patient with pneumonia. Vincent Racaniello gives details of this case at his Virology Blog.

At Climate Progress, Ari Phillips is worried too.  And, he notes, so are the researchers themselves, although they are mostly concerned about more recent pathogens that might resurface as the frozen tundra thaws, very serious pathogens such as smallpox.

Pithovirus, the new giant virus, really is a giant, 1.5 micrometers, 25% bigger than any virus previously found. As big as some bacteria, visible in an ordinary microscope. And it’s not like most viruses in other ways, either. It’s got a DNA genome, but it’s small. Pithovirus doesn’t reproduce in typical viral fashion by taking over the cell nucleus, as Ed Yong tells us at Nature News. It violates the usual viral profile in other ways, too. The standard in present-day viruses is to smoosh up the genome to make it as tiny as possible. This guy lets its DNA sprawl, although there is still lots of empty space in its baggy body.

For a primer on giant viruses, see Marcia Stone’s post at Small Things Considered from last November. The existence of these creatures, she says, requires redrawing the Tree of Life.  There’s an argument that giant viruses may be descended directly from lifeforms that existed before the fabled LUCA, the hypothetical last universal common ancestor of all cellular life presently on Earth.

Contamination

Zimmer quotes a researcher not involved in the Pithovirus work as speculating that the find might not be genuine after all, that the sample might have been contaminated with young viruses. Since I’m a virological ignoramus, I won’t argue that point, except to note that in that case why does Pithovirus seem to be unlike any other virus ever seen?

However, I don’t want to distract from the fact that contamination of samples can be an enormous problem in many fields of research. Contamination is on my mind because I have just reviewed Svante Pääbo’s new memoir Neanderthal Man: In Search of Lost Genomes for the Genetic Literacy Project.

Left, H. neanderthalensis. Right, Svante Pääbo   Credit: Frank Vinken

Left, H. neanderthalensis. Right, Svante Pääbo Credit: Frank Vinken

This engaging book is obsessed with contamination, although that’s not obvious at first. It briefly describes how the grand old man of ancient DNA became a scientist. It also, as you may have heard, describes Pääbo’s life as a bisexual, although that’s brief too, and the very antithesis of salacious. The memoir is all about sex, but it is not sexy.

Instead, Neanderthal Man is devoted–and devoted is definitely the word–to the years-long ancient DNA project to sequence the Neanderthal genome. Pääbo and his far-flung team did that to an accuracy that exceeds most of the contemporary genomes being sequenced today. The sequencing project was about sex in the sense that its real aim was to discover the aftermath of sex: whether bits of the Neanderthal genome survive in us.

If the book is mostly about doing the Neanderthal genome, doing the Neanderthal genome was mostly about contamination–or, rather, trying to bypass contamination. That meant fishing genuine Neanderthal DNA out of a soup of DNA from other creatures, bacterial and human–extraneous DNA that had, over 40,000-plus years, soaked into every Neanderthal bone they worked on.

Before I read Neanderthal Man, I thought I knew something about contamination of ancient DNA. In fact, though, I had no clue. No matter how well informed you are about genetics, Svante Pääbo will teach you things.

Funding

Neanderthal Man also got me wondering about the role of the funding process in smoothing the way for good work, innovative work. Pääbo works at the Max Planck Institute for Evolutionary Anthropology in Leipzig; in fact, he helped design it. The Max Planck Society funds a staggering 82 such institutes, most in Germany.

In organization the Max Plancks are a bit like the Howard Hughes Medical Institutes–designed around individual researchers who have enormous freedom, and part of that freedom is freedom from having to write grant proposals.

The principle is the same even though the funding sources are different.  HHMI’s money came originally from the estate of a very rich man. Most of the Max Planck budget “is derived from the coffers of the public sector,” which I assume means German taxpayers. Even so, when Pääbo found he needed $5 million more than originally planned to pay for additional sequencing, the money was forthcoming. (In fact, as I recall, the Society gave him more.)

Obviously there is no such possibility with public money here in the US. But there are costs, certainly, to the government funding system we’ve developed here. The Nobel laureate Sydney Brenner rails against some of them in an interview much blogged-about this week.

Sydney Brenner delivering his Nobel Prize banquet speech, 2002. Credit: Hans Mehlin

Sydney Brenner delivering his Nobel Prize banquet speech, 2002. Credit: Hans Mehlin

Brenner argues that with present-day funding practices, Fred Sanger, who won two Nobel Prizes, would not have been able to support his work on the biochemistry that underlies most of today’s biological research. That’s  because he went a decade between publications. Bioinformaticist Mick Watson disputes that at Opiniomics, arguing that if he was working today, Sanger’s findings would have been handed over to a private company  “where the technology would be developed free of the pressures of academic research.” Seems to me there would be plenty of pressure at a private company, although of course not pressure to publish.

Brenner has proposed a funding alternative that he calls the Casino Fund, organized along the HHMI/Max Planck lines of support for an excellent individual researcher who then puts together lab and team to suit. Every organization that gives money to science should take 1% of it and write it off, Brenner declares. “You give it to people like me, to successful gamblers,” he argues. But “all the business people stand up and say, how can we ensure payback on our investment? My answer was, okay make it 0.1%. But nobody wants to accept the risk.”

Brenner also has a lot to say about the scientific publishing industry, none of it complimentary. For takes on this, largely in agreement with him, see Retraction Watch (and many comments), In the Pipleline, and the Mermaid’s Tale.

 

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