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Synthetic Genetic Shakespeares

Examining the implications of science and technology

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Synthetic Genetic Shakespeares

The personal blog of Tyler Kokjohn. A partial list of my scientific publications may be found on PubMed. I declare no competing scientific or financial interests regarding the topics examined in this blog. All rights reserved.

The Biohacker in the Mirror

The biotechnology revolution is being democratized – quickly.  An article published in The New York Times (1) reveals some leading researchers and entrepreneurs are becoming anxious about what citizen scientist biohackers might do with their increasing power to manipulate genetic systems. 

The laboratory resurrection of horsepox virus, a presumed extinct virus relative of smallpox, warned the scientific community impressive new technical powers are being bestowed on genetic engineers at an extraordinarily quick pace.  The New York Times article (1) maintains that experts agree biohackers seeking to do something outrageous like designing a killer virus would face high hurdles.  That assessment is comforting, but here is the real problem; 15 years ago thoughts of performing a molecular revival for something as large as horsepox virus would have been dismissed as sheer fantasy.  However, changing technology has now turned previously impossible task into published achievement.  What capabilities will scientists and biohackers have in another 15 years?  That is unclear, but the speed technology is evolving and realizations concerning the current size of the list of potential predicaments are alarming some leading scientists.

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Avoiding Self-Defeating Messages

The professional scientific community should probably approach the issues posed by biohackers carefully.  Faculty members spend a good deal of effort trying to get students interested in science.  Biohackers are a literal embodiment of self-actualization and active learning we hope to foster.  More than that, biohackers could be the informed citizen intermediaries essential to communicating the importance, possibilities and limitations of scientific research to a broader public.

The implications of new scientific capabilities such as genetic manipulation technologies sometimes distress the public.  To alleviate doubts or disarm resistance to their further investigation or use, scientists traditionally call for “dialogue.”  It is not easy to come up with ways to communicate with the larger public and those vague calls are often forgotten as a news cycle ends.  Bemoaning a disinterested public that is generally not well versed in their work, although there are exceptions, scientists have not always been anxious to go out of their way to talk to citizens.  If professional scientists fail to embrace public outreach/empowerment and recognize the biohacking community as potential allies they may accidentally telegraph a negative message: 

You need to be knowledgeable, just not too knowledgeable.  We, the authorities, will tell you what you need to know as we see fit.                           

 

Dual Use Meets Double Standard

A number of groups have taken the initiative to help people become hands-on biohackers (1).  Along the way they also instill ethics and offer guidelines for the responsible conduct of work.  Unfortunately, not all the role models have been exemplary (1), which has fueled anxieties as we imagine what ill-conceived, potentially risky experiments might be performed by impatient biohackers of the future.

Many scientists might feel relieved if biohackers could somehow be persuaded to adopt a code of conduct as similar to that of the professionals as possible.  However, professional scientists have been rather impatient themselves at times.  For example, convinced his then-radical hypothesis a bacterium, Helicobacter pylori, produced gastritis and peptic ulcers, one scientist experimented on himself by drinking a culture sample (2).  Was he chastised?  He and his collaborator ultimately won a Nobel prize for their work which overturned an entrenched paradigm.               

image-1-2

Examples of an enthusiastic rush to the clinic impelled by limited positive experimental results are not hard to find today.  Parabiosis is the surgical melding of the circulatory systems of two animals.  Experiments in which old mice were joined to younger individuals have yielded extraordinary results.  Somehow soluble factors harbored in the blood of young mice restore tissue functions in their aged associates to a more youthful state (3, 4, 5).  Uncertain whether any such measures work in humans these observations and others have helped spark a veritable gold rush to see if infusing pooled plasma samples harvested from young donors into older recipients produces any anti-aging benefits. 

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How do scientists feel about personal augmentation efforts?  When it comes to cognitive enhancement through drugs, one study suggests a good number of professionals use them to increase concentration and improve productivity (6, 7).  The practice seems safe, but there are no data from long-term safety studies in healthy consumers to give authority to that idea.  It seems scientists are as susceptible to the siren call of self-enhancement as everyone else.   

Uniquely Alone

Scientists rely on their peers for advice and criticism.  In addition, to help avoid errors or prevent unwarranted enthusiasm from driving hasty, ill-conceived experiments, professional researchers have the benefit of institutional oversight over matters of biosafety and the conduct of projects involving animals or human subjects.  Biohackers may be far more isolated.

It is important to remember that the ethical norms and practices governing biomedical research with human subjects and animal care evolved over time.  And the experiences that led to the creation of foundational documents like the Belmont Report  and the Common Rule  were sometimes hard ones.  Ethical research practices do not just happen, training and refresher courses are used to ensure investigators are well informed of risks, requirements and best practices.  Proactive support of biohacking labs (1) striving to build positive ethics foundations and promote best practices operational guidelines may be an essential public investment. 

The Human Genome Project (HGP) may provide an instructive example for accomplishing broad outreach and education goals.  Part of the funding for the HGP was dedicated to the Ethical, Legal and Social Implications Program (8) to examine several issues recognized as critical, but outside the strictly technical scope of the overall effort.  As scientists offer proposals for the Genome Project-Write (9), perhaps they will consider earmarking resources to examine the full range of implications and potential risks destined to emerge from the synthetic biology technologies they will create.     

Prohibition or Education? 

The pace of technological advances is too fast for government authorities to devise rules.  The scientists are going to have to establish the parameters for conduct and police situations as they emerge.  If the controversy over horsepox virus resurrection is any indicator, the community will likely not reach unanimous agreement on any matters.  However, despite challenges the scientific community has formulated and successfully imposed work guidelines, ethical conduct demands and safety rules in the past. 

Should everyone who ‘does synthetic biology’ be licensed and subjected to surveillance (1)?  Or will it be wiser to prohibit all biohacking performed without professional supervision?  On one hand, strict prohibitions may curtail some risks.  On the other hand, such actions seem contrary to the essential need to inform citizens about synthetic biology.  Biohackers could be important ambassadors in such efforts if their potential is recognized. 

Clearly foreseeable dangers lay just ahead and the scientific community must take steps to mitigate them.  How many professional scientists once had a chemistry set or their own home labs when they were children?  How many of us look in the mirror and recognize professional and amateur scientist biohackers have much in common?  We have now reached a stage where repeating platitudes of calling for dialogue is no longer sufficient because the synthetic biology genie is about to be released.  Active outreach efforts are no longer things scientists have the luxury to think about doing someday, but are now absolutely integral to the future success of the entire enterprise.    

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(1) Emily Baumgaertner.   As D.I.Y. Gene Editing Gains Popularity, ‘Someone is Going to Get Hurt,’ The New York Times, 14 May 2018.  https://nyti.ms/2IfT5BW

(2) Barry J. Marshall.   Helicobacter Connections.  Nobel Lecture, 8 December 2005.  https://www.nobelprize.org/nobel_prizes/medicine/laureates/2005/marshall-lecture.pdf

(3) Amy Maxmen.   Questionable “Young Blood” Transfusions Offered in U.S. as Anti-Aging Remedy.  MIT Technology Review, 13 January 2017.  https://www.technologyreview.com/s/603242/questionable-young-blood-transfusions-offered-in-us-as-anti-aging-remedy/

(4) Massimo Conese et al.   The Fountain of Youth: A Tale of Parabiosis, Stem Cells and Rejuvenation.  Open Medicine 12:376-383.  https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5662775/

(5) Gavin Haynes.   Ambrosia: The Startup Harvesting the Blood of the Young. The Guardian, 21 August 2017.  https://www.theguardian.com/society/shortcuts/2017/aug/21/ambrosia-the-startup-harvesting-the-blood-of-the-young

(6) Barbara Sahakian and Sharon Morein-Zamir.   Professor’s Little Helper.  Nature 450:1157-1159, 19 December 2007. https://www.nature.com/articles/4501157a

(7) Daniel Oberhaus.   Why Can’t We All Take Modafinil?  Vice, 1 December 2016.  https://www.vice.com/sv/article/ava7za/why-cant-we-all-take-modafinil

(8) The Ethical, Legal and Social Implications (ELSI) Program of the Human Genome Project. https://ghr.nlm.nih.gov/primer/hgp/elsi

(9) Elie Dolgin.   Scientists Downsize Bold Plan to Make Human Genome From Scratch.  Nature, 1 May 2018.  https://www.nature.com/articles/d41586-018-05043-x

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The Hybrids Among Us

A provocative article has appeared on the internet (1).  Or, more accurately, an attention-grabbing article has re-appeared.  The basic assertion is eye-catching; women retain DNA traces from every lover.  The original article was published last year and systematically critiqued by Alex Kasprak (2).  The most recent post offers nothing new.

Extrapolations, Not Experiments

Were researchers “living in denial,” making “politically correct” assumptions, and trying to “hide the evidence”?   The evidence was not concealed well since someone seems to have found it in the published scientific literature.  The idea that cells are transferred between mothers and unborn children during pregnancies and persist decades afterwards is both counterintuitive and potentially of great medical significance (3).  But, is a documented history of full term pregnancy with a male child the only way for women to end up with some foreign male cells in their brains and bodies?  Certainly not, part of the original evidence suggesting the remarkable cell exchange between mother and fetus was the realization that some women discovered to be microchimeric for male DNA had a prior history of terminated pregnancies (4).  From the start, it has been clear that even the most complete medical records do not always tell the whole story of microchimerism.                  

Patchwork

 

The direct sexual transmission of male DNA or invasive sperm hypothesis is a logical extrapolation based on some speculations (5, 6) and laboratory research findings of others.  At this point there is no firm experimental evidence any part of the competing proposed mechanism works.  To accept one of the more lurid ideas put forth we have to assume the gamete-specific surface proteins are present on cells located in the mouth, nasal passages, inner ear and behind the eyes among other sites.  Further, we have to assume those receptors act sequentially to enable close approach and fusion as they would for ovum and sperm.  The existing data reveal another problem – the exchanges between mother and gestating child are bidirectional (4) and some of mom’s cells take up residence in the baby.  Not a definitive refutation, but those findings are much harder to reconcile with an invasive sperm model.

Let’s remember how we got here – some amazing experimental results that were originally so totally unbelievable peer reviewers repeatedly rejected them (4).  So, perhaps someone will see fit to test the hypotheses that sperm are able to merge with mucosal cells of the upper GI and respiratory tract of females and transfer Y chromosomes along with all the other genes of the male donor.  It is much easier to envision an XY (male) genetic invasion following the seeding of already formed cells.  And it seems appropriate to wonder if a haploid sperm cell delivers an intact Y chromosome to the nucleus what becomes of one of the two X chromosomes that were present before that event.  However, truth can be strange and perhaps someone will demonstrate Y gene transfer through the same non-homologous end joining reactions exploited by CRISPR engineers.  If that happens some physical evidence of it should be reveal-able.  And that would be quite a find.

Invasive Hybrids Are Real

In addition to pregnancy, long-duration microchimerism is observed in twins and after solid organ transplants as well as blood/blood product transfusions (5, 6).  A body of evidence suggests that microchimerism is associated with elevated risks for autoimmune disease development.  Millions of units of whole blood and platelets are used annually for transfusions in the U.S. alone (see one estimate here).   Although it is uncertain how many transfusion procedures establish microchimerism or the implications of such events, the sheer magnitude of transfusions suggest it is important to better understand the hereditary dynamics and consequential risks associated with these life-saving interventions.           

There have been bigger, far more consequential invasion events.  Almost every cell in our bodies and those of the plants and animals surrounding us are the evolved products of ancient invasions/hybridizations (7).  A body of genetic and other evidence reveals the organelles critical to cell function, mitochondria and chloroplasts, were derived from once free-living bacteria and cyanobacteria.  The entire history of life on Earth was altered by these events.

One common theme for biological hybridizations from microchimerism to fundamental cell biology might be the observation that the ideas such things could occur were first resisted by learned colleagues.  Perhaps investigators will amass sufficient evidence to establish invasive sperm are another strange-but-true reality.  Let’s see the data.    

(1) Anonymous.  2018.  Women Retain and Carry Living DNA From Every Man With Whom They’ve Made Love With.  Mind Foster, 28 April 2018.   https://mindfoster.co/1129/women-retain-and-carry-living-dna-from-every-man-with-whom-theyve-made-love-with/

(2) Alex Kasprak.   Do Women Retain DNA From Every Man They Have Ever Slept With?  Snopes.com, 26 June 2017. https://www.snopes.com/fact-check/women-retain-dna/

(3) William F. N. Chan et al.   Male Microchimerism in the Human Female Brain.  PLoS ONE 7(9): e45594.  https://doi.org/10.1371/journal.pone.0045592

(4) Marcia Barinaga. Cells Exchanged During Pregnancy Live On.  Science 296(5576):2169-2172.  http://science.sciencemag.org/content/296/5576/2169.full

(5) Evan M. Bloch et al.   Transfusion Associated Microchimerism: The Hybrid Within.  Transfusion Medicine Reviews 27(1):10-20.   https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3518667/

(6) Maureen A. Knippen.   Microchimerism: Sharing Genes in Illness and Health.  ISRN Nursing vol. 2011, Article ID 893819, 4 pages, 2011. https://www.hindawi.com/journals/isrn/2011/893819/

(7) Michael W. Gray.   Lynn Margulis and the Endosymbiont Hypothesis: 50 Years Later.  Molecular Biology of the Cell 28(10):1285-1287.    https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5426843/

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It Came From Outer Space and It Won’t Die

Discussions of panspermia – the hypothesis that life or critical precursors for it have been spread through the Universe (our galaxy at least) by comets, meteors and other agents – might be about to surge.  A recent report that hundreds of millions of viruses settle out over each square meter of Earth every day (1) may set the stage for renewed rounds of speculations. 

How is it so many viruses are afloat in the atmosphere?  The working hypothesis is dynamic weather conditions heave them to the winds (1).  But, finding such big numbers in mountain regions sparks the imagination – could some of them have floated to the Earth’s surface after a journey through outer space? 

Panspermia

 

Strange Observations

Panspermia is topical because more than just viruses are in the air.  Other perplexing recent claims that external surfaces of the International Space Station (ISS) were harboring attached bacteria have led to leaps of faith about “alien” colonizers from space (2).  The article also noted such conclusions were tentative and more work would be necessary to validate an otherworldly origins explanation (2).        

Not long before the publication of the ISS colonization claims and virus bombardment observations, we had news our solar system had been visited by the interstellar traveler ‘Oumuamua (3).  Perhaps objects like this ejected from distant solar systems seeded life forms through the galaxy or still do that today.  No word as yet whether the scientists studying virus fallout noticed any sudden increases after ‘Oumuamua whizzed past the Earth.

Taking Aim at the Claims

As the discovery of incredible rates of atmospheric virus fallout shows, examining far-out ideas is part of the fun of scientific research and sometimes worthwhile.  Unanticipated and astonishing things do happen on our lively planet. 

Reports of a strange red-colored rain in the vicinity of Kerala, India, appeared nearly 20 years ago (4).  Ruling out dust particles and lacking any mechanism to explain the sudden precipitation of so much red particulate matter led a few investigators to postulate the phenomenon had an extraterrestrial basis (4).  Correlating the unusual rain event with a putative meteor airburst and noting the red particles physically resembled cells, but did not contain DNA or RNA, the investigators suggested the red rain particles were “alternate life” seeded from outer space (4).  Papers (5, 6, 7) featuring claims that the red rain microbes replicate at extreme temperatures, 300°C or higher, added to the idea that these entities were extremely strange.  How have these observations and hypotheses held up over time?

Although previous efforts with another dye had failed, extracting red rain microbes with dimethyl sulfoxide (DMSO) enabled the (probable) demonstration of DNA by DAPI (4′,6-diamidino-2-phenylindole) binding fluorescence (8).  Not definitive evidence, but the method is solid enough to greatly diminish the notion (hope?) that red rain bugs have no DNA.

The red rain microbe growth experiments (5, 6, 7) are only partially controlled and incomplete which makes them a challenge to interpret.  Had I been a peer reviewer for these works I would have requested the authors clarify several points.  First, the nature of the red rain inoculum used for each experiment needs to be explained.  There is no indication that the experiments were conducted with pure cultures of red rain microbes.  Instead, it appears raw samples of red rain material were simply placed in growth media and incubated.  If these samples harbored other microbes/spores all results based on turbidity increases (6) would be suspect because it would not be clear if red rain microbes, terrestrial contaminants or both were growing.  If red rain bugs increased in number to produce turbidity, why was the sample shown in Figure 7 (6) not red in color?  Photographs and direct counts were shown, but there is no way to be sure what criteria were used to enumerate red rain microbes as some images seem to show possible cells with different morphologies.  The choice of growth media for some experiments – cedar oil and betadine – is odd and unexplained.  The kinetics of growth using a more familiar growth medium, Luria-Bertani broth, at 121°C (standard autoclave temp) are also unusual.  The total number of cells was very low, but the culture went through not quite 2 doublings and then plateaued.  So, are those cells viable or did they die?  If a sample was taken from that culture and the experiment repeated would any replication ensue?  That obvious test is essential, but apparently was not performed.  In addition, the authors seem to have run no controls to confirm the autoclave was really working (reached and maintained 121°C for the time periods shown) or provided any data regarding the response of well-known bacteria like E. coli for comparison.

streak plate

Ensuring pure colony isolates for testing using the streak plate method

Other claims such as the repeated assertion (6, 7) red rain cells replicate at 300°C are completely impossible to evaluate.  As a reviewer I would also have noted that one paper (6) simply stated this as a fact without any corresponding literature citations while the other (7) cites a source that actually contains no mention of such of studies at all.  Cells were subjected to a reported 370°C (max) dry heat (5) which produced physical shrinkage and color changes.  However, the actual ability of the heated cells to replicate after such treatment apparently was never confirmed by culture experiment – another incomplete effort.

Researchers other than the persons first reporting on red rain microbes have been able to acquire some samples for independent investigation.  This is something I thought might never happen (video).  Others have examined separate instances of colored rains and the Kerala site itself (9) detailing evidence that large-scale aerial dispersal of algal spores accounts for red rain events.  Again, these studies cannot directly refute the idea of red rain from a meteor burst, but the accumulating evidence suggests the true explanation for the 2001 event in Kerala is more prosaic. 

Still lacking seem to be efforts to obtain the ribosomal rRNA sequences that would help to identify the red rain microbes.  In addition, one aspect of the conclusion the Kerala red rain event was produced by a known species of terrestrial alga being transported in a novel way is testable by experiment.  If that idea is correct it should be possible to culture the red rain microbes using media and conditions suitable for the alga. 

Where Do We Stand?

The red rains of Kerala have spawned some unique explanations.  Research has been published at a painfully slow rate with groups reaching sharply divergent conclusions.  It is clear that some of the original extraordinary claims regarding red rain microbes have not been substantiated.  At this point it appears standard microbiological methods and gene probe experiments that could provide the most definitive evidence data have yet to be applied.  Although not conclusively falsified, the hypothesis red rain microbes discovered at Kerala are an exotic extraterrestrial life form seeded by a meteor has been steadily undermined by accumulating evidence.

The extraterrestrial origin claim for red rain microbes of Kerala may ultimately prove to be mistaken, but the panspermia theory will live on.      

 

(1) Adam Wernick.   It’s Raining Viruses, But Don’t Panic.  PRI.org, 9 March 2018.  https://www.pri.org/stories/2018-03-09/its-raining-viruses-dont-panic

(2) Paul Scott Anderson. Are Alien Microbes Hitching a Ride on the International Space Station?  EarthSky, 5 December 2017.  http://earthsky.org/space/alien-microbes-international-space-station

(3) https://www.nasa.gov/feature/goddard/2018/new-study-shows-what-interstellar-visitor-oumuamua-can-teach-us

(4) Godfrey Louis and A. Santhosh Kumar.   The Red Rain Phenomenon of Kerala and its Possible Extraterrestrial Origin.  Astrophysics and Space Science 302:175-187.   https://arxiv.org/pdf/astro-ph/0601022.pdf

(5) Godfrey Louis and A. Santhosh Kumar.   Cometary Panspermia Explains the Red Rain of Kerala.  https://arxiv.org/abs/astro-ph/0310120

(6) Godfrey Louis and A. Santhosh Kumar.   Growth Characteristics of Red Rain Microbes at Temperatures Below 100 °C.   Proc. SPIE 7819, Instruments, Methods, and Missions for Astrobiology XIII, 78190R (7 September 2010); doi: 10.1117/12.860807; https://doi.org/10.1117/12.860807

(7) Rajkumar Gangappa et al.   Growth and Replication of Red Rain Cells at 121°C and Their Red Fluorescence.  https://arxiv.org/abs/1008.4960v1  https://arxiv.org/ftp/arxiv/papers/1008/1008.4960.pdf

(8) Rajkumar Gangappa and Stuart I. Hogg.   DNA Unmasked in the Red Rain Cells of Kerala.  Microbiology 159:107-111.  http://mic.microbiologyresearch.org/content/journal/micro/10.1099/mic.0.062711-0#tab2

(9) Felix Bast et al.   European Species of Subaerial Green Alga Trentepohlia annulata (Trentopohliales, Ulvophyceae) Caused Blood Rain Kerala, India.  Journal of Phylogenetics & Evolutionary Biology 3(1).    https://www.omicsonline.org/open-access/european-species-of-subaerial-green-alga-trentepohlia-annulata-trentepohliales-ulvophyceae-caused-blood-rain-in-kerala-india-2329-9002-15-144.php?aid=40172

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Looking for Evidence of Life on Mars? Don’t Pass the Salt

“Viruses are astronomically abundant” (1)

Awakened to the fact that planet Earth is literally teeming with viruses (2) scientists have also established they play significant roles every aspect of terrestrial ecology.  Viruses are so intricately interwoven into the biotic world that some investigators hypothesize their presence could serve as a universal sign of life (1).  Cautioning that our knowledge is based entirely on the conditions currently prevailing on a single planet, scientists have offered a compelling rationale to develop “astrovirology” as a potentially important tool in the search for extraterrestrial life (1).

The staggering abundance and dynamics of viruses in our world was illuminated through a recent set of experiments which revealed hundreds of millions of them settle out of the air over every square meter of our planet every day (3).  This observation has important implications for the search for evidence of life on Mars and more.

Go Where the Water Is – Or Was

NASA scientists have adopted an overarching ‘follow the water’ strategy (4) to discover evidence of life in our solar system.  Several locations on Mars may now harbor water/ice deposits and these special regions are being safeguarded to prevent (or minimize) accidental forward contamination by terrestrial microbes during exploratory missions.   

Although Martian sites with water will be a top priority for future exploration, the red planet probably has other locations that might also hold traces of life.  Remote sensing evidence suggests extensive deposits of halite and other evaporites exist on the Martian surface (5).  Studies of terrestrial brines confirm they harbor a rich diversity of living bacteria and archaea (6) with additional work revealing under some environmental conditions microbes colonize the surfaces (6) or subsurfaces (7) of dry halite rocks.  Nucleic acid amplification experiments conducted on ancient halite samples have demonstrated the presence 16S rRNA amplicons derived from bacterial and haloarchaeal sources (8) while a complementary approach found that macromolecular remnant signatures of life may persist for millions of years within halite fluid inclusions (9).  These findings suggest the prospect the bio-signature hallmarks of microbes specialized for life in the hypersaline remnants of aquatic environments are persistent and could still be present in Martian evaporite formations.

Halite crystals

Do Halite Deposits Record Virus Influx?     

The recent demonstration the surface of the Earth is under a constant virus barrage (3) prompts speculation similar processes may have occurred long ago on Mars.  If that hypothesis is correct, as Martian halite deposits formed they would have received substantial inputs of virus particles through both in situ production and atmospheric settle-out processes.  That means large numbers of virions may now be entombed within surface and subsurface Martian halite deposits.  In principle, halite-entrapped virions could be recovered to provide the first unambiguous evidence an Aresian biosphere analogous to that found on the Earth today was once active on Mars.

Mars Phage

If virions are well preserved in halite deposits perhaps it will be possible to retrieve nucleic acids from them.  Recovered sequence data would provide an information bonanza about both viruses and their hosts.  The hypothesis is addressable through experiment because terrestrial halite samples are readily available for direct study.  Investigation of some subsurface salt mine sites (10) may be particularly rewarding because they may yield samples from well-stratified, comparatively ancient layers.  Did the rain of viruses (3) we see today occur in the past?  If we are lucky careful analyses of halite samples might provide an answer that question.         

The surface halite deposits of Mars may be readily accessible to future sample return and/or in situ characterization missions.  Perhaps one of the Mars Rovers has driven past some already.  If viruses are preserved in halite deposits maybe the new NASA life search mantra will be “do not pass the salt.” 

Mars rover

To Eugene L. Martin, J. D., Ph. D.  No one had more fun doing science than us.  

(1) Aaron J. Berliner et al.   2018.  Astrovirology: Viruses at Large in the Universe.  Astrobiology 18(2):207-223. https://www.liebertpub.com/doi/full/10.1089/ast.2017.1649

(2) Francisco Torrella and Richard Y. Morita.   1979.  Evidence by Electron Micrographs for a High Incidence of Bacteriophage Particles in the Waters of Yaquina Bay, Oregon: Ecological and Taxonomical Implications.  Applied and Environmental Microbiology 37(4):774-778.  https://www.ncbi.nlm.nih.gov/pmc/articles/PMC243295/pdf/aem00208-0116.pdf

(3) Adam Wernick.   2018.  It’s Raining Viruses, But Don’t Panic.  PRI.org, 9 March 2018.  https://www.pri.org/stories/2018-03-09/its-raining-viruses-dont-panic

(4) https://www.nasa.gov/vision/earth/everydaylife/jamestown-water-fs.html

(5) A. F. Davilla et al.  2010.  Hygroscopic Salts and the Potential for Life on Mars.  Astrobiology 10(6):617-628.  https://www.liebertpub.com/doi/full/10.1089/ast.2009.0421

(6) B. A. Schubert et al.  2009.  Microscopic Identification of Prokaryotes in Modern and Ancient Halite, Saline Valley and Death Valley, California.  Astrobiology 9(5):467-482. https://www.liebertpub.com/doi/pdf/10.1089/ast.2008.0282

(7) J. Wierzchos et al. 2006.  Endolithic Cyanobacteria in Halite Rocks from the Hyperacid Core of the Atacama Desert.  Astrobiology 6(3):415-422. https://www.liebertpub.com/doi/pdf/10.1089/ast.2006.6.415

(8)  S.A. Fish et al. 2002.  Recovery of 16S ribosomal RNA Gene Fragments from Ancient Halite.  Nature 417:432-436.  https://www.nature.com/articles/417432a.pdf

(9)  J. D. Griffith et al. 2008.  Discovery of Abundant Cellulose Microfibers Encased in 250 Ma Permian Halite: A Macromolecular Target in the Search for Life on Other Planets.  Astrobiology 8(2):215-228.     https://www.liebertpub.com/doi/pdf/10.1089/ast.2007.0196

(10)  Elizabeth Miller.  2017.  You Can Thank Ohio’s Tropical Sea for Your Winter Road Salt.  PBS NewsHour, 23 January 2017.  https://www.pbs.org/newshour/show/can-thank-ohios-tropical-sea-winter-road-salt

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Looking for Evidence of Life on Other Planets? Check Out the Rings of Saturn

Seeking evidence of life in our solar system by drawing on what is known of terrestrial biology, NASA scientists have followed the water.  The good news is that there are places with plenty of it around today or once had large amounts of it in the past.

Recognizing evidence of life forms, even types that are functionally analogous to terrestrial organisms, is not necessarily a simple task.  The Viking Project (1) featured two landers which executed several experiments to reveal evidence of living microorganisms.  Although some unusual chemical reactivity was observed in the soil samples, the consensus is that the Viking lander results cannot be taken as definitive evidence of living organisms.

Viking lander

 

Powerful New Techniques – Definitive Answers?

The Viking Project landers melded impressive technology with a well-executed mission plan that was completed under extremely challenging conditions.  Advances in genetic analysis technology will enable future missions to probe for life on Mars and elsewhere with more robust methods than anything available in 1976.  In principle the new generation of explorers will no longer be limited to detecting the metabolic activities of living microbes.  Genetic-based approaches may reveal the hereditary material of cells even if they happen to be inactive or are dead. 

Culture-independent methods also have significant limitations of their own and may be confounded by minute levels of terrestrial contamination.  Notwithstanding their new capabilities, investigators may once again be confronted with samples that fail to yield clear evidence of the presence of microbial life. However, if experiments can be devised and conducted such that contamination is improbable, systematic surveillance efforts using genetic methods may make it possible to be conclude that microorganisms like those now found on Earth were absent or present at extremely low amounts in the samples tested.

“Viruses are astronomically abundant” (2)

Noting viral particles are the most numerous structures on Earth derived from biological activities and their intimate involvement in fundamental ecological and evolutionary processes, a group of scientists is proposing efforts to employ them in projects to detect extraterrestrial life (2).  The total number of viruses on our planet is vast and a new study reveals that uncounted billions of them are blown from ocean waters into the air to travel far and wide.  Hundreds of millions or more settle out harmlessly around us every day (3).  On planet Earth at this point in time, wherever life is present virus particles are pervasive.  Perhaps finding viruses or their molecular traces in extraterrestrial samples would provide solid evidence something living is – or was – in them.              

Because it is possible to recognize many viruses by virtue of their odd shapes, in one sense looking for virus particles represents the ultimate culture-independent biology search method.  Samples can be examined without concern as to whether any viable organisms are present or the conditions/nutrients required for them to be metabolically active.  Whether the viruses harbor genetic materials composed of RNA, DNA, or something else, are viable, or have been inviable for years will not matter.  All methods have intrinsic limitations and one inescapable problem with looking for virus particles is that fact that most are tiny.  Still, although systematic direct searches for viruses will be laborious, including them or bio-signature proxies (2) in future missions to find evidence for life in our solar system seems well worth the effort.  It could turn out that describing viruses as “astronomically abundant” (2) could be quite accurate.

Where to Look for Extraterrestrial Viruses?

 A few places in our solar system may harbor water oceans, but a small moon of Saturn, Enceladus, may be the go-to place for life-seekers (4).  This moon has an orbital friction energy source, liquid water and precursor molecules (5).  But it also has something special – cryovolcanic geysers that spray the deep ocean materials far out into space – where it would be (comparatively) easy to sample and analyze them.  A probe would not have to land, it would only need to position itself in the outflow to collect samples from deep within the hidden ocean.  Experiments have revealed that at certain microbes are able to be active under conditions mimicking those on Enceladus (6).

EnceladusEnceladus jets

Maybe We Have Already Seen Them

The spectacular rings of Saturn harbor substantial quantities of water ice. Embedded in the E Ring, Enceladus seems to be the source of the microscopic water ice particles composing this structure.  When we look at the rings of Saturn maybe we are seeing the outer space analogue of viruses tossed about on an extremely long voyage.            

Saturn e

 

Many thanks to Dr. Curtis Suttle for bringing the PRI.org story to my attention.  To find out more about Dr. Suttle’s research visit his University of British Columbia web page.  http://www.ocgy.ubc.ca/~suttle/?p=home     

 

(1) Viking 1 & 2.  https://mars.nasa.gov/programmissions/missions/past/viking/

(2) Aaron J. Berliner et al.   2018.  Astrovirology: Viruses at Large in the Universe.  Astrobiology 18(2):207-223. https://www.liebertpub.com/doi/full/10.1089/ast.2017.1649

(3) Adam Wernick.   2018.  It’s Raining Viruses, But Don’t Panic.  PRI.org, 9 March 2018.  https://www.pri.org/stories/2018-03-09/its-raining-viruses-dont-panic

(4) Enceladus.  https://solarsystem.nasa.gov/moons/saturn-moons/enceladus/in-depth/

(5) Annie Sneed.   2016.  Excitement Builds for the Possibility of Life on Enceladus.  Scientific American, 28 June 2016.  https://www.scientificamerican.com/article/excitement-builds-for-the-possibility-of-life-on-enceladus/

(6) Meriame Berboucha.  2018.  Is There Life on Enceladus?  Forbes, 28 February 2018.  https://www.forbes.com/sites/meriameberboucha/2018/02/28/is-there-life-on-enceladus/#2539deca59fa

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Hazard Ahead – Recognizing the Signs of Ecosystem Degradation

Gigantic patches of plastic garbage now floating in the oceans (1) signal loud and clear the Anthropocene Epoch has arrived.  Additional hallmarks such as the appearance of distinct radionuclides and increases in atmospheric carbon dioxide concentrations are impossible to appreciate as directly, but can all be quantified.  However, the epoch of human stewardship of our planet is also characterized by losses.

The Vanishings

In addition to observing physical alterations such as a general worldwide decrease in the extent of ice masses and permafrost subsoils, human beings have also altered the composition and function of living communities. Despite public concern over extirpations and extinctions, disappearance stories have become commonplace news.  Recent news articles have highlighted the predicament of right whales in the North Atlantic (2) and vultures in India (3) trying to survive in the increasingly hostile environments exploited by humans.

The Big Picture Revealed by Small Things

Larger and better known species capture the most public attention when it finally becomes apparent they are endangered.  Often not considered is the fact that species do not live – or die – alone (4).  When milkweed stands are destroyed by crop-protecting herbicides, we may notice the Monarch butterflies that feed and reproduce on them vanish as well.  However, milkweeds harbor a lesser-known menagerie and these creatures will disappear from locations where their home plants are extirpated.

 

Milkweed beetle

Each visible loss should alert us a gap of unknown dimensions has appeared in the web of living species composing a functioning ecosystem.  Scientists often characterize natural systems in terms of goods and services they provide.  How many losses will it take to cause an ecosystem to malfunction to a point that the essential services we exploit begin to decline?  Are there signs we are reaching that point?

The notable declines in insect populations are particularly ominous (5, 6, 7).  These losses may reflect the cumulative impacts of practices of pesticide use combined with many factors and evidence now suggests a general decimation of insects is occurring in large areas.  The most worrisome part of insect losses is the fact that this order is such a significant part of ecosystems.

In her book Silent Spring, Rachel Carson asked readers to think about a future in which an environment mismanaged by humans could become so toxic that many species sharing our world could no longer thrive.  She illuminated how the final stage might look for us if we failed to heed the warning signs of emerging problems and take corrective actions.  Is it possible insect losses we see today are the harbingers of bigger, more obvious problems soon to come?  It may not be long before we see a patchwork of species losses become focal ecosystem function failures.  How could we end up in a silent Spring?  Perhaps we are seeing the first stages of the processes unfolding now.  Not having to clean bugs off our car windshield (6, 7) may actually be a subtle warning sign of a quietly arriving disaster.

Web4

April 22, 2018 – Earth Day

(1) Charles J. Moore.   Choking the Oceans With Plastic.  The New York Times, 25 August 2014.  https://www.nytimes.com/2014/08/26/opinion/choking-the-oceans-with-plastic.html

(2) Sarah Gibbens.   Bad Breeding Season Spells Trouble for Endangered Whale.  National Geographic, 27 February 2018. https://news.nationalgeographic.com/2018/02/north-atlantic-right-whales-calving-season-extinction-spd/

(3) Express News Service.   Tamil Nadu Gets Vulture Shock. The New Indian Express, 16 April 2018.  http://www.newindianexpress.com/states/tamil-nadu/2018/apr/16/tamil-nadu-gets-vulture-shock-1802061.html

(4) Tyler Kokjohn.   The Little Things Count.  Arizona Wilderness Advocate, Issue 3, Summer 2003.  http://www.azwild.org/newsletter/2003_03_kokjohn.shtml

(5) Nathan Donley.   Missing All the Monarch Butterflies?  They Face a New Pesticide Threat on the Horizon.  The Kansas City Star, 19 March 2018. http://www.kansascity.com/opinion/editorials/article205889654.html

(6) Gretchen Vogel.   Where Have All the Insects Gone?  Science, 10 May 2017.  http://www.sciencemag.org/news/2017/05/where-have-all-insects-gone

(7) Tom Spears.   Canada is Actually Running Short of Bugs.  The London Free Press, 24 September 2017.  http://lfpress.com/2017/09/24/canada-is-actually-running-short-of-bugs/wcm/480e50f6-df5f-4974-9b74-0586ab7c6e47

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Gene Drives – Will Conqueror Biomolecular Bots Dictate a New Book of Life?

Declining vulture populations have received some recent news coverage. The number of human rabies cases in India is not known which makes it difficult to establish clear correlations between vulture population losses and human rabies increases. However, the notion some ecological changes yield unanticipated consequences and potential health risks still holds.

JayVay

Gene Drives – Will Conqueror Biomolecular Bots Dictate a New Book of Life?
By Guest Blogger,
Tyler Kokjohn, Ph.D.

 A new DNA engineering technique known by the strange name CRISPR-Cas9 allows scientists to edit the genomes of living cells with unprecedented ease and precision (1).  The method has only been in wide use for a few years, so it is hard to envision all the breakthroughs it will foster.  However, it is already clear the implications will extend far beyond the laboratory and clinic.

Conqueror WormThe CRISPR-Cas9 DNA editing system is versatile, but scientists have extended its capabilities by creating powerful new forms of this technology which function as gene drives (2).  A gene drive disperses genetic alterations or DNA cargo rapidly through a population by overruling the normal patterns of inheritance.  A recipient of a gene drive receives the complete genetic information needed to synthesize the enzymes and guide…

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It’s Raining Viruses

Our planet teems with viruses.  Earth’s atmosphere has been recognized to harbor virus particles, but a group headed up by Dr. Curtis Suttle has now performed some experiments revealing the total numbers are stunning (1).  They estimate that 800 million virus particles settle out onto each square meter of the planet daily.  You may view this paper here.

Umbrella

Your Numbers May Vary

The prevailing wisdom holds that some viruses produced near the surfaces of terrestrial or marine sites become airborne due to weather events.  It is also conceivable that they are actively produced in situ through infection of viable microbes suspended in the atmosphere.  Dr. Suttle’s group quantified virus fallout in a mountain region of Spain.  Assuming that area has substantially better air quality than many parts of the globe, it seems a safe bet that their estimate could turn out to be conservative.  Also, local weather patterns, season and the proximity of potential virus reservoirs such as productive coastal ocean waters will undoubtedly influence the virus seeding and settle-out rates.

Should I Be Worried?

Large scale weather patterns influence planetary ecology through the mobilization of key dust-borne mineral nutrients (2).  Satellite imagery confirms that small dust particles – and presumably bacteria and viruses as well – swept high into the atmosphere by storms are able to traverse impressive distances over our planet.  The body of evidence suggests quite a few viruses are in the air around you. 

Does this mean we are in danger?  Most of the viruses in the world do not produce human disease.  In addition, we are able to fend off the vast majority of would-be microbe and virus invaders with a combination of effective physical barriers and immune responses.  The figure below shows some of the bacterial and fungal agents suspended in the air a few feet above ground level at Glendale, Arizona.  This sample of 1,000 liters was taken on a clear day with light breezes.  Only a fraction of the total microbes actually present in the air sample were revealed in this assay because not all the cells would grow on this agar medium under the incubation conditions employed.  An adult will inspire that volume of air in around 2 hours.

Phoenix Air Sample

Viewing viruses solely as adversaries is probably too limited an appraisal of their ecological roles.  The interior and exterior surfaces of our bodies are colonized by large, metabolically active and diverse microbial populations.  Eight hundred million viruses falling onto each square meter of the planet is certainly an impressive number, but we may absorb 50 times more than that every day through our intestines (3).  The normal microbial flora conveys important health benefits leading to speculations that these viruses are helpful as well.  The problem is that we simply do not know much about the Universe of viruses lurking in and all around us.

Phage attack

So, Where Do They Come From?

The dynamics of disease epidemics produced by even the best understood viruses puzzle us at times.  For example, recent appearances of avian influenza in the U.S. Midwest were hard to track back directly to waterfowl reservoirs (4) or biosecurity shortcomings.  For years the most economical explanation was that a wind-borne spread process must have accounted for some transmission.  Maybe that notion no longer seems so far-fetched.

Mars

Could viruses have arrived on Earth through a Panspermia process after being seeded into space from Mars or the clouds of Venus through mechanisms unknown?  Or maybe they have come from much further by hitchhiking on matter such as ‘Oumuamua traversing interstellar space (5).  The current evidence suggests our viruses are most likely home-grown, but perhaps a future Mars rover mission will deploy a capture device or carefully sort through some dust piles just to see what exactly is blowing around and settling out. Maybe we will find that virus traces (6) still reign over the red planet.    

(1) Jim Robbins.   Trillions Upon Trillions of Viruses Fall From the Sky Each Day.  The New York Times, 13 April 2013. https://nyti.ms/2IRy6Rx

(2) Francie Diep. Saharan Dust Feeds Atlantic Ocean Plankton.  Scientific Americanhttps://www.scientificamerican.com/gallery/saharan-dust-feeds-atlantic-ocean-plankton/\

(3) Giorgia Guglielmi.   Does a Sea of Viruses Inside Our Body Help Keep Us Healthy?  Science, 21 November 2017.  http://www.sciencemag.org/news/2017/11/does-sea-viruses-inside-our-body-help-keep-us-healthy

(4) Tom Polansek.   U.S. Bird Experts Mystified by Avian Flu Spread.  Reuters, 13 March 2015.  https://www.reuters.com/article/us-health-birdflu-tracking/u-s-bird-experts-mystified-by-midwest-avian-flu-spread-idUSKBN0M92FN20150313

(5) https://www.nasa.gov/planetarydefense/faq/interstellar

(6) Aaron J. Berliner et al.   Astrovirology: Viruses at Large in the Universe.  Astrobiology 18(2):207-223.  https://www.liebertpub.com/doi/pdf/10.1089/ast.2017.1649

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Never Sell the Clones

Sunday evening, March 11, 2018, 60 Minutes aired a story about how cloned ponies have infiltrated polo in Argentina (1).  A multi-faceted account reported by Lesley Stahl, it is well worth your time.

An accident involving a prized pony may have started it all.  Before the animal was euthanized, the owner, a champion polo player and noted pony breeder directed a veterinarian to preserve skin cell samples.  In 2006 he was anticipating the day might come when it would be possible to resurrect his lost pony.  His foresight paid off.

Several animal species have been cloned and the technology is generally available.  However, the work is complicated and expensive making the cloning of companion or champion animals a game for the well-funded (2).  Using cells harvested from several of their best horses the polo breeders have created more than 100 clones.  These activities are legal and permissible under the rules of polo.   

ponies

Nature vs. Nurture Again

Does having the right genes make a champion polo pony or are a good environment and proper training the most important factors?  The 60 Minutes program reveals the clones are raised in a truly extraordinary environment featuring special diets, expert care and superb training.  Despite some subtle physical differences, the discussion that the clones possess the aptitudes and dispositions of their progenitors is quite interesting.  No claims are made that the clones are totally identical to their ancestors – some spontaneous mutations, mostly inconsequential, will always be present.  In addition, the clones are produced in surrogate mares.  That means the gestational environment will be close, but not identical to, the conditions for the originals.  Environmental conditions exert some influence over gene expression and development.   

Couldn’t expert breeders accomplish the same thing as the high-tech cloners?  In one sense they already did exactly that – the clones were derived from ponies created by just such methods.  The other consideration is that the clones beg the question as to which animals are the best – that decision was already made and carried forward into the future through cloning.  But, can anyone be sure that donor animals selected possessed the best polo pony genetic profile there ever can be?

The ultimate test for polo ponies is success on the field of competition.  In a championship match of clones vs. breeders, the clones prevailed by the narrowest of margins (1).  Perhaps this reflects the fact that the human riders also play a significant role in the competition.  In a situation where both horses and riders are top flight, it would appear cloned ponies did not offer any huge competitive advantage.

As is the case for ponies produced in the traditional ways, the value of clone-sired foals is based on the pedigree of their ancestors.  Cloned ponies are mated with champion stock and the foals may command a high price – sold for a reported maximum price of $250,000 (1).  The pony breeder/cloner interviewed noted something interesting about the fate of the cloned animals.  They are never sold.  The reason is simple, if you marketed them it would not be long before everybody had the same miracle stock.  End of mystique and/or competitive advantage.   

The Future                             

The amount of tissue needed to clone a champion polo pony is small and perhaps misappropriation of clones will become a problem.  Or the issues of safeguarding clones might get even more complex.  It may become necessary to update the definition of clone (3) yet again as scientists begin developing more powerful genetic manipulation technologies (4).  For example, what if new technologies allow someone to take the genomic sequence of a champion and simply introduce all the genetic changes that turn an ordinary animal into a proven top performer?  Is that clone infringement?  As the cloners should understand, each new technology opens up new possibilities.  The cat-and-mouse intrigues of elite Olympic athletes attempting to gain advantage (5) suggests that competitive forces might spur the emergence of a genomics high technology race in the polo pony world of the future.

Never Sell the Clones

For now, polo pony foals derived from champion stock are valuable.  However, it is uncertain how much genetic variability exists in breeding stocks.  Perhaps there is a magic genetic profile that only the champion animals possess.  It may not take long to determine if that is true.  Refusing to sell clones is a brilliant, if potentially temporary, business strategy.  In the future persons unable to purchase a genetic champion pony may be able to construct one of their own.       

 

Thanks to Carol Rainey for making certain I saw the 60 Minutes story on polo pony clones.   http://www.carolrainey.com/

 

(1) Lesley Stahl.   The Clones of Polo.  60 Minutes, (CBS News), 11 March 2018.  https://www.cbsnews.com/news/the-clones-of-polo/

 (2) Matt Stevens.   Barbra Streisand Cloned Her Dog. For $50,000, You Can Clone Yours.  The New York Times, 28 February 2018.  https://nyti.ms/2COao5l

(3) National Human Genome Research Institute.   https://www.genome.gov/25020028/cloning-fact-sheet/

(4) D. Boeke et al. 2016.  The Genome Project-Write.  Science, 8 July 2016, [353(6295):126-127]. http://science.sciencemag.org/content/353/6295/126.full

(5) Bret Stetka.   Have We Reached the Athletic Limits of the Human Body?  Scientific American, 5 August 2016.  https://www.scientificamerican.com/article/have-we-reached-the-athletic-limits-of-the-human-body/

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