“Astrovirology” Chief Ken Stedman Guesses Earth Origins for Viruses

Stedman, Ken_0019
KEN STEDMAN

If viruses originated on Earth—which is NASA astrovirology chief Ken Stedman’s “best guess”—just why do we need a new field called astrovirology?  What would Jerry Fodor say?

Ken Stedman, whose day job at Portland State University is investigating the viruses of archaebacteria found at geothermally heated hot springs, nevertheless, thinks exploring for viruses and their biosignatures in space using state-of-the-art microscopes “needs to be done.”

But why?  Stedman says five years ago his discovery that viruses can be frozen in silica and then recover their infectivity as their glass coating dissolves, led not only to his startup company StoneStable, Inc.—which is now developing technologies to deliver vaccines that would not depend on refrigeration—but peaked his curiosity about the ability of viruses to hitch a ride in the atmosphere.

Stedman now serves as chief scientific officer of StoneStable.  He says silica is common to many planets and he obviously wonders whether viruses exist elsewhere in the universe, how far such viruses might be able to travel remaining intact, and by what means.

Stedman’s recent 12-page article: “Astrovirology: Viruses at Large in the Universe”  published in Astrobiology journal by privately held Mary Ann Liebert, Inc. caught my attention, partly because it’s behind a $50 paywall!  And partly because Astrobiology journal is such an incestuous publication with most of its editors and editorial board  tied to NASA!

The astrovirology paper’s first author is Aaron Berliner (NASA affiliation: Mars terraforming), now a PhD student at the University of California-Berkeley and the Arkin Laboratory on Martian Ecopoiesis.  Berliner’s research focus is synthetic viruses, extremophile biology, DNA nanotechnology, and making mars-in-a-jar reactors.

The paper’s other author is Tomohiro Mochizuki, an ancient virus specialist at Tokyo’s Earth Life Science Institute who has been studying viruses and microbes at the Jinata (earth hatchet) hot springs in Japan’s Izu archipelago.

Ken Stedman is a professor of biology at Portland State University’s Center for Life in Extreme Environments. Among his many honors are:  Portland State University Foundation Philanthropic Cultivation Award (2017); Oregon Museum of Science and Industry Science Communication Fellow (2017); BioMed Central Research Award (2012, Best Paper in BioMedCentral journals); BioMed Central Research Category Award (2012, Computational and high-throughput studies in genomics and systems biology);  Chair (elected), Gordon Research Conference on Archaea (2011); John Eliot Allen Outstanding Teacher Award (2003-2004) (partial list).

In addition to his position at PSU, Stedman teaches at Oregon Health and Science University.  He’s been a research fellow at Montana State University as well as at Wageningen University in The Netherlands. His post-doctoral research was with Wolfram Zillig at Max-Planck Institute for Biochemistry in Germany.  Ken Stedman has also worked in industry as a biotechnician at Sandoz Pharma, Ltd. in Switzerland and as a researcher at Genentech, Inc. in San Francisco.

His PhD is in molecular and cell biology from the University of California-Berkeley and his BSc in chemical engineering from Stanford University.

I spoke by phone recently with Ken Stedman at his lab in the Pacific Northwest, where he enjoys a view of the mountain of fire—Mount St. Helens.  Our interview follows.

Suzan Mazur: The astrovirology article you co-authored: “Astrovirology: Viruses at Large in the Universe” is currently featured in Astrobiology journal, one of 80 some publications privately published by a company headquartered in New Rochelle, New York called Mary Ann Liebert, Inc.  Mary Ann Liebert, Inc. also published the NASA Astrobiology Strategy Executive Summary, the European Astrobiology Roadmap, as well as the NASA-supported Astrobiology Primer—whose editor-in-chief is an episcopal priest, a lead author on the current NASA Astrobiology Strategy, and one of 24 religious scholars NASA/Templeton funded (2015-2017) to investigate how the religious community would respond to the discovery of life in outer space.

Astrobiology journal bills itself as “the most-cited peer-reviewed journal dedicated to the understanding of life’s origin, evolution, and distribution in the universe” and it carries the following disclaimer:

“The views, opinions, findings, conclusions and recommendations set forth in any Journal article are solely those of the authors of those articles and do not necessarily reflect the views, policy or position of the Journal, the Publisher, its editorial board or any affiliated Societies and should not be attributed to any of them.”

What the Astrobiology journal disclaimer does not say is that most of Astrobiology journal’s editors and editorial board, and often its authors are tied to NASA.  For example, the first author on your article, Aaron Berliner, worked at NASA with senior planetary scientist Chris McKayAstrobiology’s deputy editor—to develop the Mars terraforming timeline .  You chair NASA’s astrovirology focus group and co-authored a virus paper with Sherry Cady, Astrobiology journal’s editor-in-chief.

You note in your Astrobiology journal article that one of your priorities is reaching out to the general public “regarding the ubiquity and role of viruses.” Much of what you present is, indeed, already public knowledge—referenced in six pages of end citations.

My question is why didn’t you publish your astrovirology article independently? Why publish in a journal that despite its disclaimer is seen as a propaganda arm of NASA and “the Darwinian government”—as the late, great philosopher Jerry Fodor once characterized it—a publication put together around the kitchen table of Sherry Cady and managing editor/hubby, Larry Cady, who is a fiction writer?

I mean there are red flags everywhere.  It’s like astrobiology according to the Book of Mormon.  Why did you not publish independently?

Ken Stedman: Why did we not publish independently?  The main reason we didn’t publish independently is that I promised Sherry that I would write something for Astrobiology journal.  That’s the number one reason.  A second one, and probably more important, is that even if this is a propaganda arm of NASA—those are the kinds of people that we’re trying to reach with this particular article.

Yes, I am also incredibly dedicated to the general public knowing about this and I am doing my best to inform the public, which is partly why I’m talking with you about this idea.  But I don’t see that the astrovirology article, per se, in Astrobiology journal as being outreach to the general community.  I see it as being outreach to the readers of Astrobiology journal, most of whom I think are involved with NASA.  Those are the people who read these things, and hopefully are also the ones who will be interested in following up.

Suzan Mazur:  The public is very interested in the virus narrative and NASA seems to want to control the narrative and control the technology using public funds. This is a problem.  The public doesn’t have any control over where the public funding is going or realizing profits made from spinoff companies.  The public is cut out.  I was giving you credit for posting this as an outreach to the public, but now you’re saying that that wasn’t even your intention.

You’ve got mainstream venues now picking up your astrovirology story without questioning what’s going on.  That’s dangerous. Eighty publications, and the NASA Astrobiology Strategy Executive Summary and the European Astrobiology Roadmap, etc.  There’s something deep state about this.

Ken Stedman: I would disagree with you on that.  I can mention what the editorial input was by the Cadys, and it was practically none in this case.  There were maybe two or three recommended changes in the whole manuscript and those were perfectly reasonable editorial issues that made no change whatsoever to the text, which we—Aaron Berliner and myself and Tomohiro Mochizuki—came up with.  So I think there is very little influence of NASA on this.

Suzan Mazur:  But you’re coming from NASA.  You chair NASA Astrobiology Institute’s Virus Focus Group.  Is that a paid position, by the way?

Ken Stedman:  It is a completely volunteer position.

Suzan Mazur:  I like very much that you’re investigating viruses, but I think the venue where you’re presenting your discussion of astrovirology is a bit thin on credibility at this point.

Ken Stedman:  I completely hear you on that.  One of the beefs that I actually have with the article, if I may be so blunt, is that it is not available to the public.  It’s behind a paywall, thanks to the publishers.  And I have been asked probably by 30 or 40 people, at least, to please send them a copy of the article because they are not able to access it because of the behind-the-paywall aspect.

Suzan Mazur:  Anyone can access the article for $50 but for a 24-hour view only, and only if you promise not to circulate the article in any form.

Ken Stedman:  I completely agree with you on that one.

Suzan Mazur:  And you have six pages of references.  So this story is largely already out there.  You give it a twist but a lot of this information is accessible in an online search.

You’re telling me that you wrote this story for Astrobiology journal because Sherry Cady asked you to?

Ken Stedman:  Yes.  I think there is a certain readership of Astrobiology journal that does not think about viruses and those are some of the people I would like to reach in this process.  Hopefully, to be perfectly honest, those are people who are going to start to think about viruses and are spending public money on NASA missions and on NASA experimentation.

Suzan Mazur:  Isn’t it a bit premature to speak of astrovirology since viruses have not even been found at the level that jet airplanes fly, i.e., the stratosphere?

Ken Stedman: I would beg to differ on some of those things. People have found both microbes and viruses or things that look like viruses under those conditions.  In fact, one of our previous papers talks about viruses spread through the atmosphere.  And potentially at those kinds of levels.

Suzan Mazur:  What levels are you talking about?

Ken Stedman: Viruses and microbes that have been found at some of these levels.

Suzan Mazur:  What levels are you talking about?

Ken Stedman: I don’t know exactly at what level.  But I know that Andrew Schueger has collected samples quite high in the atmosphere.  There’s some very nice data looking at transfer of microbes from the Sahara to the Caribbean.  There’s definitely transfer that happens, exactly at what level I don’t know.

[Note: Smith, Schueger et al. in 2010 reported bacteria and fungi (not viruses) at 12.4 miles over the Pacific Ocean. ]

Suzan Mazur:  I think I know the article you’re referring to.  But viruses were not found above the jet plane level.

Ken Stedman:  So at what level is it?

Suzan Mazur: It’s below the level that jet planes fly [i.e., below the stratosphere, at the troposphere level].

Ken Stedman:  I don’t know.  That’s why I was curious.

Suzan Mazur: You’ve said “to visualize most virion morphologies, a transmission electron microscope (TEM) is required” but it’s unlikely that you’ll be able to put one “on a spacecraft in the foreseeable future.”  Can you say why?

Ken Stedman: These are very large instruments and require large amounts of power:

Suzan Mazur:  Also, Eugene Koonin has said this:

“Traditionally, microbes have been studied in isolation, but to do that, a microbe or virus has to be grown in a laboratory.  While that might sound easy, only 0.1% of the world’s microbes will grow in artificial media, with the success rate for viruses even lower.”

Doesn’t that put a serious damper on the usefulness of a TEM in space investigation of virions?

Ken Stedman:  If we’re actually going to study whatever we find there, yes, I completely agree with you.  You have to have them in culture.

We have exactly that kind of problem in my research lab right now.  We’ve discovered viruses in the absence of a host and are unable to culture them in the lab.  We’re trying very hard to find the hosts and grow them in the lab.  So, again, getting back to what we mention in the paper—putting TEM on a spacecraft to identify something morphologically as a virus, those kinds of experiments, in my opinion, need to be done.

Then, I would say, if we found something that looks basically like a lunar lander.  These viruses do look like lunar landers.

T-4 phage

There is nothing abiological we know of, or have been able to come up with, that in my opinion is credible, that would make a particle that looks like that.  Even if you don’t have a host and even if you can’t grow it in the lab.

In fact, people do give me electron microscope images quite often and say:  Does this look like a virus?  I will tell them yes or no.  At least in my considered opinion.  So, for that reason I think that getting very high resolution images of whatever particles we can find would actually be useful.

Suzan Mazur: No viruses have been found in meteorites to date.

Ken Stedman: Correct.

Suzan Mazur:  What other biosignatures are you proposing might be used to search for viruses extraterrestrially?

Ken Stedman:  There are a couple of things.  My lab has been investigating how lipid biosignatures can be used with regard to viruses.  Lipids have been found in very ancient rock and used as biosignature evidence, although all of those to date have been cellular specific.  Viruses that have lipids are few and far between and most of those virus lipids are identical to cellular lipids. But there are a few viruses that have lipids that are different from cellular lipids.  My lab is trying to find those particular viruses that have these different lipids.

There’s a published abstract online, from a paper my postdoctoral scholar and I put together a few years ago.  Basically, we’re looking for these lipids as biomarkers. Such lipids would much more likely be found in a rock record on Earth.

Another biosignature would be a morphological marker, as I’ve mentioned.  If the TEM could be carried on a spacecraft to identify known viruses, like, for example, the lunar lander shape [icosahedral head-tail morphology].  That brings up the question:  What if the virus-like particle doesn’t look like a known virus?

We now know that of the viruses found on Earth, the vast majority have very geometrically simple virions.  So those geometries are incredibly specific to viruses. If we can find something that has the appropriate geometry, that would also be a very good virus biosignature.

Suzan Mazur:  Thank you.  You cite Forterre & Prangishvili in your article suggesting that ancient viruses were already rich in morphological diversity at the time of LUCA.  And a recent article by Seligmann and Raoult on template-free RNA also reports “evidence for ancient precellular origins and recent de novo emergence of viroids.”  Could you expand on this a bit?  Are you familiar with the Seligmann and Raoult paper?

Ken Stedman:  I saw the title and abstract but have not yet had a chance to read the article. I do know the work of Forterre and Prangishvili very well.  Their interpretation is that since there is so much morphological diversity—admittedly based on many of these same geometries that I was mentioning. That you find all of this diversity in multiple different viruses and multiple different lineages of hosts and that—backwards calculation, which is always going to be a prediction—would be that there were probably multiple different morphologies.  Again, precellular or at least around a LUCA kind-of-time.

As far as the emergence of viroids, capsidless viruses—that some of them have arisen recently is a very reasonable hypothesis.  But, again, I don’t know the Seligmann and Raoult paper very well.

Suzan MazurRicardo Flores and others think that a viroid-like entity was there at the beginning because viroids don’t need protein.

Ken Stedman:  Right. That makes sense.  I think that’s very reasonable, in the absence of a time machine. It’s very hard to check those hypotheses.

Suzan Mazur: Didier Raoult argues against a tree of life, he sees all life as a mosaic.  He sees a tree of life concept as a biblical vision and Darwin as the father of intelligent design.

What is your understanding of stem-loop RNA hairpins? Do you work in that area?

Ken Stedman:  I do not work in that area but I know some things about them.  Lots of RNAs can make stem-loop hairpins. But in terms of their activities, I don’t know.

Suzan Mazur: And DNA also.  I did an interview about this last year with Georg Urtel, who was working in the lab of Dieter Braun at the time. There was a return of the hairpins in his experiment. He was working from synthetic DNA.

Ken Stedman:  Yes.  The fact that DNA and RNA can form these very interesting structures is, I think, absolutely fascinating.  One of the viruses we’re working on probably makes a very interesting double hairpin structure, but exactly what that structure looks like in a cell or for that matter in just the DNA itself, I really don’t know.

Suzan Mazur. Would you say a bit about StoneStable, your spinoff company that was started with funding from NASA?

Ken Stedman:  Our company was not started with funding from NASA. Our NASA-funded research led to the founding of the company.  It was money for virus research.  We looked at viruses in the rock record.  Looked for biosignatures for NASA.  The biosignatures we got were completely worthless, but the technology turned out to be useful for vaccine stabilization.

So, yes we did some work for NASA looking for virus fossils.  The results we got were not funded by NASA at all. It’s something that came out of the scientific process, whereby we then discovered something that is now funded by NIH.

Suzan Mazur: Would you say more about this technology that’s proved useful for vaccine stabilization?

Ken Stedman: So, we got funding from NASA to look basically for virus fossils.  The geologists will complain and say they’re not fossils, they’re just mineralized—mineral on the outside of the biological entity.  We were very interested in how old the viruses were.  In fact, going back to your question just a second ago, viruses being precellular, etc. —the direct evidence for viruses, particularly virions, is at most thousands of years old in terms of virus disease.  Regarding being able to visualize virions, it’s only been possible since the electron microscope was developed in the late 1930s.  Being able to visualize virions is very, very recent.

The question is:  How old are viruses?  There’s pretty good evidence that microbial fossils, cellular fossils are billions of years old.  But what about virus fossils?  Are they there but we just can’t detect them, at least not unambiguously—getting back to the biosignature question—or are they just not there?  Maybe they are very recent, maybe viruses haven’t been around that long.

We thought, and this is in fact what NASA funded, that if we’re going to find virus fossils, we should find the more mineral-shaped viruses and we’ll find them around hot springs.  The vast majority of my research work is studying viruses in hot springs.  I’ve been doing that for 20+ years now.

The reason that we thought we’d find mineralized viruses in and around hot springs is because the super-heated water, which comes up at depth, will go through all the minerals.  It will leach out those minerals because it’s superheated.  Once it gets to the surface, that superheated water, which is now saturated in minerals, cools down.  As it cools down all of those minerals start precipitating out of the solution.  They will precipitate on whatever is there.

We work on viruses at hot springs, so we know there are viruses at hot springs.  We know that the minerals will precipitate on those viruses.  Now what we need is a way to detect those viruses that the minerals have precipitated on.

So instead of going to the hot springs, which are very complicated, at least chemically, we decided to basically make an artificial hot-spring-like condition in our research lab together with a virus with a very well known morphology—the bacteriophage HT4—the morphology that looks kind of like a lunar lander with the icosahedral head on top of a tail.

Suzan Mazur:  Which is most viruses.

Ken Stedman:  Exactly.  Well, there’s a paper that just came out in Nature that said that may not be true.  But we thought that if we’re going to find something, we should see mineralization of bacteriophage HT4.  And if we’re going to continue to see this amazing morphology while minerals are precipitating on it, we should do it under controlled conditions in the lab.

So, again, funded by NASA, we looked at these conditions and we saw beautiful coatings of silica that were detectable in the transmission electron microscope coating bacteriophage HT4 for up to about three days.  After three days, they became completely unrecognizable blobs. Fossils older than three days were not detectable even using TEM.

Suzan Mazur:  Are you saying that some sort of protective coating could be used by viruses coming from space to Earth?

Ken Stedman:  Right, if there was an appropriate condition to coat them.

Suzan Mazur:  Are you thinking silica or something else?

Ken Stedman:  In this case we used silica, which is common to many planets.

Suzan Mazur:  Would that be protection enough traveling through space?

Ken Stedman: That was one of the next things we did.  We looked at those viruses to see if they were protected under those kinds of conditions.  But there are two different ways of thinking about protection.  One would be protecting the shape, the morphology.  The other one is protecting infectivity.

What the graduate student working on this found was that when you did this silica coating, which is basically glass, once you coat a virus in glass it loses its infectivity.  The big surprise was that this coating is reversible.  When the coating comes off, the virus regains some of its infectivity.

Suzan Mazur:  But you don’t know what can happen to viruses with the radiation  actually out there.

Ken Stedman:  Right. One of the things my student did was even under these controlled conditions in the lab he found that after two months even with the nicely coated viruses, all infectivity was gone and could not be recovered.  So it was literally a process of months, not the—what is the minimum transit time from Mars to Earth?  A lot longer than months.  At that point I would say silica coating will not protect viruses for a long enough time to transfer from one planet to another.

But while two months is clearly not enough time in terms of a virus hypothetically traveling from Mars to Earth, two months is plenty of time to get a vaccine from a distribution center on Earth where it’s being produced to people living in the backlands worldwide where these vaccines might be needed. So that’s the foundation of the company.

Suzan Mazur:  What’s your best guess as to where viruses or RNA or viroid-like entities originated?  Do you think it happened on a comet, an asteroid, on Earth?  Where do you think it happened?

Ken StedmanMy best guess is it happened on Earth probably under very similar conditions in which cellular life was also developing, at about the same time. [emphasis added]

Suzan Mazur:  How do you feel about public funds being allocated to scientific investigation by the scientific establishment with the public essentially cut out of the picture, which has its roots post-WWII?  As science and technology historian David F. Noble once pointed out to me, the way they kept the public out was through peer review.  This is another beef that I have about Astrobiology journal. Noble regarded peer review as censorship, a way to control the narrative.

Ken Stedman:  I wouldn’t go quite that far.  One of the things that I do is I try and communicate my science to the public as much as possible.  Because I completely agree that if public money is being used to fund research that I do, I am obligated to tell the public about it.

Suzan Mazur:  But the situation is much stickier than that.  In 1980, there was an amendment to the Patent Act—the Bayh-Dole amendment—where companies ever since have been able to approach universities where 90% of the research is publicly funded, and where companies can lay down money for monopoly rights. Noble characterized the Bayh-Dole amendment as “the biggest give-away in American history.”

I think these issues of democracy and science that David F. Noble championed need to now be seriously revisited so that the public is cut in not out of the decision-making regarding allocation of public funds to science as well as the resulting profit.

 

 

 

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