Synthetic Genetic Shakespeares

Examining the implications of science and technology


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.

Predatory Publishers and Rapid Prey Coevolution

An investigation of predatory scientific journals that publish – for a fee – anything submitted to them has uncovered something truly dumbfounding (1).  Pay-to-play predatory journals do not employ the practices such as rigorous peer reviews that are used by traditional publishers to safeguard quality.  It appears a new business model emerged when some open access publishers figured out that accepting any and all submissions was far more lucrative than the customary ways of academic publishing. 

Predatory publishing enterprises have clearly expanded recently which drew the active attention of investigatory news organizations.  Confirming quite a number of scientists have published articles in questionable venues, an examination unveiled the surprising scope of the issue.  It does seem possible some, perhaps (hopefully) many, of them were victimized by deceptive business practices (1).  However, one scientist was willing to admit using ‘lightly refereed’ outlets to publish his research in order to deliberately ‘circumvent the gatekeeping role of peer review’ (1). 

Predators Do Not Exist Where They Cannot Feed

Although it is impossible to judge how many scientists purposely publish in predatory journals, could it be that a new business service may just have found its niche?  Perhaps the perverse incentives of the publish-or-perish law of the scientific jungle is selecting the ‘fittest’ who recognize an opportunity to embellish a C. V. in order to camouflage lackluster achievements.  The pressures on researchers are not going to abate and this suggests eradicating predatory publishing may require more than alerting the scientific community to the deceptions and compiling black lists.

A Service to the Community?

Does placing work in journals with anemic or nonexistent peer review benefit anyone other than fee-pocketing publishers and researchers padding their accomplishments?  It is certainly possible to rattle off a list of researchers with ideas that were rejected initially by their peers and no doubt many geniuses are being misunderstood today.  However, even geniuses must gather enough data to narrate stories that reach credible conclusions.  Someone interested only in providing a document to enable future scientists to assess their work (1) could seek other outlets such as a blog.  To me, the bottom line is this; predatory journals are founded on deception and anyone publishing in them with knowledge aforethought is an active participant in a fundamentally dishonest and self-defeating exercise.



What Is the Harm?

Researcher Svea Eckert, noting that the industry is complex, likens the situation with predatory publishers to a poisoning of the scientific community (1).  The entire profession, the activity of peer review itself, is based on deep trust.  If we get to a point where the literature has been undermined and contaminated to such an extent it is impossible to know if published studies are ‘good, worthless or bad’ that will also, inevitably, unravel scientists’ faith in one another.  In a time of fake news and a much touted reproducibility crisis in science it will not be long before the public, bill payers for much of the research, becomes thoroughly disillusioned as well. 

Open access publishing activities on the internet have unlocked the gates to revolution.  The changes have provided novel benefits as well as opportunities for unscrupulous actors.  An ‘ecosystem of predatory publishers is churning out “fake science” for profit’ (1) and the scientific community will now be forced to adapt to it. 

Redwood logging

(1) Alex Hern and Pamela Duncan.   Predatory Publishers: The Journals That Churn Out Fake Science.  The Guardian, 10 August 2018.


In memory of Richard Knight (1898-1966)




Ticked Off – Our Out-of-Balance Environments Bite Back

Setting the Stage for Biologic Crimes

The rate of biologic crimes committed against human beings is clearly increasing in some regions.  Parasites simply take what they need from us.  In addition to the theft of our blood and tissues, a number can also act as vectors for serious diseases.  The strange thing is we have long helped some of them take advantage of us.    

In an increasing number of locations, the populations of ticks around us and the animals in our vicinity are expanding.  In addition, the geographic ranges of many tick species are enlarging (1).  Those changes place more of us at a substantially increased risk for some tick-borne diseases (1).   Certain potentially serious ailments transmitted by tick bites such as Lyme disease may already be familiar, while others like babesiosis (2) might seem exotic to most of us.  However, both diseases are increasing and will create a great deal of public health havoc in the future.  It is possible to make that prediction because environmental conditions have changed in ways that favored expansions of tick populations which act as disease vectors.  The basic equation is simple – increase the density of tick vectors and the threat of diseases they transmit often leaps up with them.             

More Than Just Infectious Diseases

If you have ever experienced an itchy mosquito bite or seen the inflammation that may follow a tick encounter, you know that the human immune system reacts vigorously to the physical breaches many parasite attacks create.  An increasing body of evidence suggests that the bite of the Lone Star tick may induce additional consequences; severe allergic responses to red meat and dairy product consumption (3, 4).  Both the number of allergy cases and apparently overlapping geographic range of the Lone Star tick in the U.S. are expanding.  A striking coincidence in distribution was one of the earliest lines of evidence suggesting these allergies were linked directly to tick bites (3, 4).  However, red meat allergy cases, also known as mammalian meat allergy, have cropped up in in other nations, suggesting more than a single tick – or other biting arthropod – species is able to produce this mysterious effect (4).      

Lone star tick  

Unfortunately, more tick species are showing up in the U. S. and other regions.  An invasive species, the Asian long-horned tick, was first noted in New Jersey and has recently been discovered in several Eastern states (5).  This tick is capable of acting as a vector for several disease agents, but has not yet been linked to human illness transmission outside its original range.  Currently the tick is deemed to pose a greater threat to livestock and public health authorities have been noted as expressing they are “concerned, but not alarmed.” (5).    

Long horn tick

What Have We Done?

Basically, we humans have only been being our rapacious selves.  To meet our needs for housing and sustenance we cleared forests, plowed fields and fragmented environments extensively. Along with that we have typically extirpated or driven away top (competing) predators and depleted biodiversity.  These actions have changed ecosystems from top to bottom in ways that have inadvertently favored the proliferation of key disease agent reservoir species such as mice and deer that are also important tick hosts (1).  The simultaneous expansions of tick populations along with the reservoir host species harboring pathogens increases the risk diseases are ultimately transmitted to humans.   


What Happens Next?

Will the Asian long-horned tick invasion result in more cases of human disease?  It does seem a few ingredients (6) suggestive of more trouble ahead are in place.  This invasive species is a generalist able to exploit many animals as hosts.  Further, in its native range it is a known vector for several bacterial and viral diseases (5).  In some areas of the U.S. in which Lyme disease is rampant, habitat fragmentation, predator loss and biodiversity impoverishment would seem to be a clear harbinger of worsening future disease problems as a consequence of invasion by the new tick species (1).  However, it is uncertain how avidly the rapidly reproducing tick species will pursue human hosts in nature, whether it is competent to act as a vector for disease agents currently in local circulation and the extent to which inter-specific competition might limit its populations or capacity to interact with humans (1). 

Does the expansion in range of the Lone Star tick leave us fated to develop allergies that will force us to give up red meat whether we want to or not?  The situations are complex, dynamic and not amenable to simple predictions.  Multiple forces including climactic regimen alterations and invasions are perturbing ecosystems, but the implications for human and animal health will be revealed slowly.  However, human interventions have altered normal ecosystem function and in some ways this has already literally come back to bite us. 


(1) Aneri Pattani.   It’s High Time for Ticks, Which Are Spreading Diseases Farther.  The New York Times, 24 July 2017.

(2) Centers for Disease Control and Prevention. Babesisis FAQs

(3) Allison Aubrey.   Red Meat Allergies Caused by Tick Bites Are On the Rise.  NPR Morning Edition, 25 June 2018.

(4) Moises Velasquez-Manoff.   What the Mystery of the Tick-Borne Meat Allergy Could Reveal.  The New York Times Magazine, 24 July 2018.

(5) Donald G. McNeil, Jr.   An Invasive New Tick is Spreading in the U.S.  The New York Times, 6 August 2018.

(6) Cary Institute of Ecosystem Studies.


No Brides for Frankensteins

A recent opinion article published by The New York Times described the Facebook odyssey from callow geeks hoping to change the world to a cultural behemoth struggling with success far beyond anything they had ever imagined (1).  Or could imagine.  Facing “determined, well-funded adversaries” executing another election disinformation campaign, Facebook management is adapting by implementing a new strategy of transparency and proactive action.

It has been a long time coming.  Also published in The New York Times nearly a year ago, Kevin Roose noted the top echelon of Facebook management was distressed to discover their inventions had been turned against them (2).  Drawing parallels with Mary Shelley’s 1818 novel, Frankenstein; or, the Modern Prometheus, Roose outlined his case that Facebook had unwittingly created something it could not control.  At that time it appeared the top company leaders were beginning to realize they must assume some responsibility for the unforeseen consequences of their actions.

A Flood of Conflicted Frankensteins

Although we have reached the 200th anniversary of the publication of Frankenstein, this disturbing tale is still alive to us today (3, 4).  In fact, we could argue that as scientists explore new worlds of artificial intelligence, nanotechnology and synthetic biology the lessons of that novel are more relevant than ever.  The reality is we are experiencing a flood of persons bent on changing the world.                         

 The fictional Victor Frankenstein harkens back to the era of gentleman scientists working on their own accord.  Today’s professional scientists often work in teams with huge-scale funding and ambitions to match (5).  Translational research – work that will yield clinical tools or products to enhance human wellbeing – has been a veritable mantra for biomedical research funders for years.  The broad drive toward the immediate commercialization of the fruits of technology research has left at least one distinguished scientist wondering where such focus and pressures might lead us (6).  Many distinguished scientists at the forefront of research have direct connections to private corporations exploiting the new technologies.  The influence of potentially immense personal financial gain on public deliberations to quantify risk and benefits could be enormous.  That means citizens/rule makers seeking well-informed advice on how to proceed with new developments will have to take care to demand all conflict-of interest situations are disclosed properly.

Synergistic Combinations of Challenges

Facebook, Twitter, Google and other digital enterprises have spawned some unforeseen and unforeseeable consequences.  But, the digital revolution is unbounded and it catalyzes and supercharges other endeavors.  Still reeling over the social media implications we see novel amalgamations of digitized DNA information and biobanks emerging in the form of ‘big data’ genetic knowledge brokers like 23andMe.  At the same time digitally-augmented researchers in the life sciences are primed to literally heave aside the rules of biology to engineer genomes at will (7), build artificial embryos that follow their own developmental conventions (8) and defy death itself by resurrecting long-extinct species (7).  The ultimate consequences of these fast evolving, synergistic endeavors cannot be predicted fully, but it is clear that we are seeing mushrooming challenges to our core ideas about what it is to be a human being.  These revolutions will breach once impenetrable boundaries and sweep away critical guideposts.  The intrepid explorers at the helms of blossoming technologies will find themselves operating far beyond any rules or regulations in virtually lawless frontiers.


No Brides for 21st Century Frankensteins         

If someone did attempt a 21st century update (4) of Mary Shelley’s work, it would likely never depict a desperate Victor Frankenstein pacifying his out-of-control creation by promising to build him a mate.  Harnessing the awesome power of present-day science, the lonesome creature could simply clone a soulmate to his personal specifications.  However, more than any specific technological devices, what is different today is the scope and diversity of tests just ahead of us.  Notwithstanding the dissimilarities, the original Frankenstein story Mary Shelley articulated over 200 years ago still reveals enduring lessons about responsibility.  The numerous ambitious, brilliant and empowered creators of today clearly continue to struggle with that quaint concept.  

(1) Kara Swisher.   The Expensive Education of Mark Zuckerberg and Silicon Valley.  The New York Times, 2 August 2018.

(2) Kevin Roose.   Facebook’s Frankenstein Moment.  The New York Times, 21 September 2017.

(3) Henk van den Belt.   Frankenstein Lives On.  Science 359(6372):137.

(4) Jon Cohen.   How a Horror Story Haunts Science.  Science 359(6372):148-151.

(5) D. Boeke et al. 2016.  The Genome Project-Write.  Science, 8 July 2016, [353(6295):126-127].

(6)  Paul Berg.  2008.  Meetings That Changed the World: Asilomar 1975: DNA Modification Secured.  Nature, 455:290-291, 17 September 2008.

(7) George Church and Ed Regis.  2012.   Regenesis. How Synthetic Biology Will Reinvent Nature and Ourselves.  Basic Books, New York.

(8) Antonio Regalado.   Artificial Human Embryos Are Coming and No One Knows How to Handle Them.  MIT Technology Review, 19 September 2017.


The Metamorphosis – Customer as Product

Some Twitter posts by one of the hosts of The Ozone Nightmare podcast drew my attention to a new partnership agreement between powerhouse pharmaceutical company GSK and 23andMe, a genetic data and research business known primarily for consumer genealogy services (1-3).  The articles Joe noticed (1, 2) explained how this new drug research collaboration hinged on utilizing the database (i.e. treasure trove) of genetic data, personal information and sample biobank amassed by 23andMe from its millions of customers.  It is possible this partnership will yield some breakthrough insights and clinical advances. 

Purchaser Becomes Product

23andMe is a direct-to-consumer genealogy and genetic testing service (4).  Their recent research agreement with GSK highlighted the fact that there was far more to this company than the ancestry determination service that likely drew in most of their customers.  Although many persons may have been surprised their DNA and personal data could be used in new and wide-ranging research involving third parties, the long term corporate goals of 23andMe were not secret (5).  In addition, customers were informed of the possibilities through terms of service (TOS) agreements and informed consent procedures – sort of (1, 2).  Most of us do not examine TOS materials carefully and it is not clear what fraction of the now millions of 23andMe customers understood the full nature of their transaction or its future implications.  However, it is clear this brilliant company has created something of immense value to researchers and drug developers.

Brave New Business Model

23andMe is one example of a two-sided genetic data and biobank business (4).  “Two-sided” refers to the fact that the company acts as the bridge between consumers and research organizations.  In the process of analyzing DNA samples mailed in for limited genetic profile testing or ancestry determinations, 23andMe has established a mass scale database of genetic markers and sample biobank.  This gigantic database and ancillary metadata are extremely valuable and 23andMe sells anonymized versions of it to third party research organizations.  Could a third party make discoveries and then market them to the millions of 23andMe customers?  Because they supply anonymized data, only 23andMe has the capacity to accomplish that.  In addition to data and biobank samples, 23andMe can also act as a matchmaker by enrolling volunteers in research studies.  The beauty of it is that by recognizing the value of a massive, correlated DNA-clinical profile database and placing itself as a strategic – and essential – biotech middleman between the consuming public and research organizations, 23andMe makes money from both sides of its business equations.                                    

23andMe is not the only organization creating biomedical information and sample databanks.  Corporate competitors exist and, more akin to academic programs, The Harvard Personal Genome Project ( in which participants agree to share their genomic data, traits and cells for free and open research has been around longer than 23andMe. 


What Are the Risks?

This brave new world holds some unfamiliar potential risks.  We have seen supposedly secure digital information sources breached, so it is natural to wonder how safe the genetic and medical data we hand over will be. The Harvard program web site explicitly notes privacy, confidentiality and anonymity are impossible to guarantee.

Biomedical research has long depended on the altruistic behavior of the public and in some instances participants in clinical trials have placed themselves in danger.  Recognizing the uncertainties, the Personal Genome Project selected its participants with great care.  Persons who have purchased an ancestry service and realized only later that there was a little more to it than a traditional fee-for-service transaction will have to hope that companies live up to their pledges to employ comprehensive, proactive data security measures.     

The Genetic Information Non-discrimination Act (GINA) offers some reassurance persons discovered to carry genes with adverse impacts on future health will have some protection.  However, that legislation does not cover all contingencies and could be revised or eliminated.

So, what have you given away when you mail in that tube of saliva?  There is no way to really know, this is research and scientists are still learning.  But, even though some organizations are committing huge sums to use these new biobanks and databases, no one can foresee what the data are going to reveal or whether it be useful to you personally or anyone in the future.

The Future

The ancestry companies like 23andMe are constructing a new two-sided biotech market niche.  Still too early to gauge impacts, we should probably expect to see new innovations and combinations.  Perhaps companies will sell genetic test subscription services where customers will be screened for potentially emerging health conditions on a regular basis.  For example, periodic (prescription) colon cancer screens might provide an ideal means to assess the health and structure of the gastrointestinal tract as well as its essential microbiome.

It is also conceivable paradigm-breaking upstarts like 23andMe could soon face competition from simple point-of-care diagnostic tests based on new CRISPR-Cas systems.  Unlike single nucleotide polymorphism strategies, CRISPR-based reporter systems may be developed that are able to reveal the status of gene targets directly in a matter of minutes.  A great weakness of the current gene profile systems in wide use today is that consumers are required to surrender permanent access to their entire genomes and DNA data.  A point-of-care style test that gives a specific report on a single gene may serve the needs of a great deal of the public.  Best of all, a simple test like that could be performed in the privacy of the customer’s home.  That means no one other than the user and the persons he/she chooses would know the outcome.    


(1) Ed Cara. 23andMe is Getting Lots of Money From Big Pharma and Sharing Your Genetic Data.  Gizmodo, 26 July 2018.

(2) Paris Martineau.   How to Sign Away the Rights to Your DNA.  All it Takes is One Click.  The Outline, 26 July 2018.

(3) GSK Press Release. 25 July 2018.

(4) Henri-Corto Stoeklé et al.   23andMe: A New Two-Sided Data-Banking Market Model.  BMC Biomedical Ethics 17:19.

(5) Sarah Zhang.   Of Course 23andMe’s Plan Has been to Sell Your Genetic Data All Along.  Gizmodo, 6 January 2015.


‘Bye, Jupiter? The Ethics of Space Exploration


Benjamin Sachs (1) and his colleagues at the University of St. Andrews (2) are working to create a framework for extraterrestrial environmental ethics.  What deep philosophical questions could possibly be raised by space exploration you ask?  The basic approach toward outer space discovery and demonstration projects is about to change.  Once the exclusive realm of a few nation-states, a combination of advancing technology and private enterprise is literally democratizing space.  Poised to have a new wave of explorers and devices fan out in the solar system, some swift introspection is essential.

It’s Always All About Us

Is there any value to the Universe beyond human needs and desires?  Do we afford special consideration to any living entities we discover?  What if the living things we find are ‘only’ microbes? 

To date great efforts have been undertaken to prevent inadvertent forward contamination of Mars and other solar system sites with terrestrial microbes.  This reflects the fact that scientific curiosity has been a significant impetus for exploring solar system bodies.  Avoiding contamination reflects a basic exigency for life detection missions – scientists are interested in discovering novel, indigenous microbes, not terrestrial hitchhikers or invaders.

Finding unique life forms on Mars or other solar system sites, confirming a ‘second genesis’ took place, would be a tremendously significant scientific discovery and undoubtedly stimulate a large number of follow-up studies.  Then what?  Is there a moral duty to preserve such ecosystems?  Would discovering living residents make Mars permanently off limits for ‘terra-forming’ proposals?

If private enterprises begin to dominate space exploration, we may have to contend with situations in which the needs of the corporation do not coincide with those of the scientific community or governments.  Would a company be willing to face restrictions on terra-forming operations to keep some silly bacteria on Mars alive?  Would corporate attorneys argue that the Tellico Dam-snail darter precedent (3) applies to Mars?  In that case, since the company has already embarked on its vision of the 21st Century resurrection of Manifest Destiny, the prior claims of any lowly Aresian microbes would be void.  Hopefully, the failed litigants will find the new and improved Martian world to their liking.  If not, perhaps terra-forming companies will underwrite programs to preserve the genetic materials of the endangered species, selling it as a conscience-soothing hedge against extinction.

But, ‘No’ May Not Last Forever

Whether or not we agree humans have a moral duty to preserve planetary and other solar system environments, there is a scientific rationale to ensure such efforts are in place.  Technology changes. New knowledge accretes and capabilities expand.  The Viking lander missions to Mars in the 1970s are a prime illustration.  Those landers were marvels of engineering for their day and they conducted direct tests to demonstrate the presence of living organisms in samples of Martian soil.  Today, using molecular probes and technologies that did not exist in 1976, scientists have capacities to detect microorganisms that cannot be cultured.  A search for life using molecular tools would likely yield quite different results from those where investigators could only study organisms that were active under the culture/incubation conditions the engineers guessed would be both good and practical to achieve.  In short, a sample confidently declared ‘dead’ in 1976 might return a different result if it was checked with the more powerful, culture-independent methods in use now.  Like archaeologists leaving portions of known sites unexcavated to await future investigators with new tools, perhaps planetary scientists will note that emerging technologies could yield new insights and take steps to safeguard pristine samples.  Perhaps the official rule-makers will mandate a go-slow approach to space body development strategies.          

Leave No Trace in Outer Space?

Sachs also wonders if humans are under an obligation to preserve the physical environments of the worlds we will explore (1).  If a body is declared (probably) dead are we then totally free to plunder it?  In the case of potentially resource-rich asteroids, will profit-making entities be allowed to literally consume them?  Should some places be deemed common heritage sites off-limits to all but the most careful expeditions?  That might be a very tough sell.

The Apollo mission lunar landing sites unintentionally illustrate a ‘leave no trace’ ethic has not been embraced by NASA Moon explorers.  Environmental conditions on the Moon will enable these artifacts of exploration to endure far into the future.  Some thoughts have been given to ensuring historic areas like these on the Moon are protected against damage or looting by future tourists (4).  While getting a selfie standing next to a flag planted by 20th century astronauts may seem like a great idea, tourist traffic might quickly obliterate the authentic footprints of the original explorers.  However, toxic dust (5) may mean large parts of the Moon will turn out to be not so hospitable to tourists and thereby prevent lunar heritage sites from being overrun.  Other locations may also remain pristine because they are simply too unpleasant for humans. 

Moon base

Changing Situations

Will the democratization of space exploration lead to anarchy?  It is not clear what changes the forces of private enterprise will produce.  Where will authority to permit or deny proposed activities be vested?  Perhaps we are entering an age with millionaires on the Moon, tycoons sovereign on Titan and plutocrats presiding over Pluto.  For those of us ordinary citizens with dreams of space exploration, the significance of moneyed interests enables us to make one solid prediction –

No matter where you go, there’s your landlord.   

Bye Jupiter  


(1) Benjamin Sachs.   Eight Questions We Should Ask About the Ethics of Space Exploration.  The Conversation, 27 June 2018.

(2) University of St. Andrews, Centre for Ethics, Philosophy and Public Affairs – Exoplanet Ethics.

(3) Teresa Sparks. TVA and the Snail Darters: A Case Study in Environmental Management

(4) Daily Mail Reporter.   Look, but Don’t Touch!  NASA Releases Set of Guidelines for Potential “Moon Tourists” to Preserve Apollo Landing Sites.  Daily Mail, 7 November 2011.

(5) The Toxic Side of the Moon.  2018.  ESA, 4 July 2018.


Unpredictable Outcomes – Percival Lowell, Clyde Tombaugh and the Discovery of Pluto

I visited the Lowell Observatory (1) at Flagstaff, Arizona, on June 29, 2018.  Now a National Registered Historic Landmark on Mars Hill just west of old Route 66, the Observatory was founded in 1894 by Percival Lowell.  Its primary mission was to study the planets of the solar system with Mars being a particular focus of attention.  We arrived just in time to take The Story of Pluto Guided Tour which culminates in the Lawrence Lowell Telescope building.  This is the site of discovery of Pluto and houses the astrograph and guide telescope actually used by Clyde Tombaugh in that effort.


The Lawrence Lowell Telescope building where Clyde Tombaugh discovered Pluto

Our tour guide gave us a lively overview of the observations that prompted a systematic search for an unseen ‘Planet X’ as Percival Lowell had designated it.  Along with the scientific aspects some history of the interesting characters in the story was provided.

The astrograph was a home-brew affair, built to handle the challenging conditions of wind and weather of Mars Hill.  The 13-inch (33 cm) objective optics features a unique triple lens arrangement designed to enable large format plates (photographs) to be exposed.  Stanley Sykes and his son Guy constructed the double-anchor point mount and a local carpenter (Mr. Mills) built the dome (2).  Clyde Tombaugh, a young man with no formal academic credentials at that time was hired to conduct the arduous search.  One of his first jobs to was to finish and paint the new astrograph (2).  Although it now sports a shiny metallic gray color, it was once (Mars?) red. 

Astrog and guide

The Lawrence Lowell astrograph and guide telescope used by Clyde Tombaugh

The Path To Pluto Via Mars

Pluto walk

An intense fascination with the planet Mars led Percival Lowell to found the Observatory that still bears his name over a century later.  Influenced by the writings of astronomers Giovanni Schiaparelli and Camille Flammarion (3), Lowell initiated his own studies of Mars and promoted the hypotheses that this world harbored a living, active biosphere inhabited by intelligent beings (3).

Mars (2)

In his lectures, articles and books, Lowell explained how his observations of artificial canals on Mars revealed the story of a drying planet and a civilization responding with an engineering effort of gigantic scale (4).  The goings-on of the times were probably inescapable influences and several contemporaneous, large-scale canal construction projects had naturally drawn public attention in Lowell’s day.  The War of the Worlds was published a few years after Lowell began his observations and that circumstance coupled with the fact the location names employed by Giovanni Schiaparelli on his Mars maps were evocative and included linear features designated ‘canali’ (3) might have all combined to channel his thinking.

Lowell’s public lectures and 1908 book, Mars as the Abode of Life (4), ignited public interest.  His story – based on personal observations made with one of the finest telescopes in the world at that time – was compelling and it made him famous.  As a young man with a deep interest in astronomy, Clyde Tombaugh was well acquainted with the ideas of Percival Lowell and considered him a personal hero (2).  When Tombaugh sought professional advice on the planetary observations he was making with his hand-built telescope, he wrote to the Lowell Observatory.  That decision, perhaps based on perceived kinship with the late Percival Lowell, ultimately changed his life and the institution forever.  Tombaugh had no academic training, but possessed a deep love of astronomy along with a meticulous approach to work that enabled him to succeed in the grueling quest to locate Planet X predicted by the calculations of Percival Lowell.  Absent Clyde Tombaugh the discovery of the first trans-Neptunian object might have been long delayed (2, 5) and may not necessarily have occurred at the Lowell Observatory.

The Road to Redemption

Lowell extrapolated his observations of Mars surface features into evidence for an advanced civilization coping with adverse changes in planetary climate.  Further, he deduced the existence of a global canal system revealed the Aresian political environment was fundamentally different from that of Earth; the Martian engineers obviously believed in cooperation (4).     

Percival Lowell already possessed a personal fortune, so he had no financial motive to indulge the fantasies of any audience in order to sell books or pamphlets.  The Mars narrative he championed reflected personal beliefs and it made him – as well as his institution – pariahs to many in the professional scientific community (2).  A letter published in the journal Science (6) states the issues explicitly.  Lowell was accused of feeding pseudo-science to a naïve, but enthusiastic, public.  Noting Lowell’s impressive ability to communicate with the general public, the errors, misrepresentation of theories as established fact and lack of supporting data were judged worthy of censure.  Allowing that Lowell was discussing his own observations and that it is his privilege to interpret them as he saw fit, the letter author still concluded his actions were deceptive and “immoral.”

Clyde Tombaugh had the opportunity to observe Mars using the same 24-inch telescope once employed by Lowell.  Noting that he saw and drew lines like those of Lowell (5), Tombaugh pointed out that many critics were not actually planetary observers.  Despite his personal experiences and admiration of Lowell, Tombaugh recognized the realities of the canals of Mars (2, 5). 

With so much of the scientific community hostile, Percival Lowell and the Observatory staff were ‘outcasts’ (2).  When Clyde Tombaugh arrived at the Observatory over a decade after Lowell’s sudden death, the astronomers were still demoralized due to their ‘ostracism’ (2). Recognizing the discovery of a new planet would be heralded and draw immediate competition, Lowell Observatory managed their formal announcement carefully, well aware of their ‘underdog’ status (5) and the opportunity for professional reputation redemption it would provide. 

It is hard to imagine the acclaim and prestige such a discovery would bring.  Possibly one of the finest actions ever taken by the Lowell Observatory staff and leaders was the decision to give Clyde Tombaugh – the young man without formal training – full credit for his essential contributions to the successful team effort to find Planet X.  Who discovered Pluto?  To this day most of us answer ‘Clyde Tombaugh,’ although I bet he would probably have pointed out the journey began with Percival Lowell’s mathematical calculations and the work of observatory staff long before he arrived.

The Unpredictable

It is recognized that the discovery of Pluto based on Percival Lowell’s mathematical predictions for an unseen Planet X was sheer coincidence.  Almost immediately the Lowell Observatory staff and others were concerned that the estimated mass of Pluto was too small to be the cause of the perturbations in the orbits of Uranus and Neptune that launched the effort.  During the Story of Pluto Guided Tour, our presenter noted how the astronomical symbol for Pluto, could be interpreted as Percival Lowell’s initials or, more fancifully, as an enshrinement of “Pretty Darn Lucky.”  

 Hubrids 2

Driven by his personal interests, Percival Lowell carved out his place in the pantheon of astronomy.  Vilified by the scientific community of his time, Lowell and his ideas became famous among the general public.  Clyde Tombaugh considered him a personal hero.  Could it be that the discovery of Pluto was initially set in motion when Clyde started reading the writings of Lowell and emulating him?

Could works today decried loudly as pseudoscience such as The UFO Hunters program or efforts to find Bigfoot actually be seeding the next generation of scientists?  This is not a plea for skeptics to cease their critiques, I believe firmly they must continue their work, point out fallacies and show how a scientist might approach the issues.  But perhaps we will allow that some of us, possibly many of us, first start out like Percival Lowell and Clyde Tombaugh with nothing more than an intrinsic deep interest in a topic.  The scientific expertise (hopefully) will develop later.  A quote attributed to Ray Bradbury (3) sums it up –

“It’s part of the nature of man to start with romance and build to reality.” 

The evidence suggests professional astronomer peers held the work of Percival Lowell in generally low esteem.  The passage of time has revealed his overall claims regarding the planet Mars were indisputably untrue.  Still, they might have captured the imagination of the young Clyde Tombaugh and set the stage for him to make some amazing discoveries.

(1) The Lowell Observatory.

(2) Clyde W. Tombaugh and Patrick Moore.   Out of the Darkness.  The Planet Pluto.  Mentor Books.

(3) William Sheehan and Stephen James O’Meara.   Mars.  The Lure of the Red Planet.  Prometheus Books.

(4) Percival Lowell.   Mars as the Abode of Life.  Reprinted (2000) by Bohn Press.

(5) David H. Levy.   Clyde Tombaugh. Discoverer of Planet Pluto.  Sky Publishing Corporation.

(6) Eliot Blackwelder.   Letters – Discussion and Correspondence – Mars As The Abode of LifeScience 29:659-661, 23 April 1909.

For younger readers –

Tony Simon.  1965.  The Search for Planet X.  Scholastic Book Services.


CRISPR At-Home Diagnostics – The Questions to Come

Move over, biohackers.  A biotech company has plans to put CRISPR technology into the homes of consumers for DIY medical diagnosis (1).  “Dr. Google” and WebMD, take note, CRISPR-based diagnostic tests may make you obsolete (1).

CRISPR, the Ultimate Diagnostician

CRISPR technology has drawn attention primarily because it enables the precision alteration of genomes.  However, the capacity to locate specific nucleic acid sequences also means it could seek out and reveal viruses and other invaders.  Highly specific, potentially able to allow fast, sensitive and unambiguous identification of pathogens that are difficult or dangerous to culture, CRISPR technology might be the future of infectious disease diagnosis.  Can the amazing capacities of CRISPR be translated into at-home diagnostic tests?      

The Sharpest Double-Edged Sword

The article (1) mentioned malaria and Zika virus as potential CRISPR-based diagnosis targets.  Zika virus infection is an emerging global concern posing particular risks during pregnancy (2, 3).  In general, Zika virus and its close arbovirus relatives are difficult to culture and diagnosing illnesses caused by them is challenging in the earliest stages.  Assuming the technology lives up to its potential, the speed, sensitivity and specificity offered by a validated CRISPR test method might be a huge advance.  How might an at-home test for Zika virus infection perform in the real world? 

Because of its potential to produce devastating birth defects and Guillain-Barré syndrome, concern about Zika virus infection is warranted.  And the virus is sneaky; a majority of infected persons, possibly up to 80% (2), never exhibit signs or symptoms of infection.  Zika virus is transmitted by mosquito bite, but it can also be passed by sexual contact months after initial exposure.  The Centers for Disease Control and Prevention (CDC) has criterion-based recommendations for Zika virus testing (3).  Current nucleic acid-based tests are effective only for about 2 weeks after onset of symptoms.  After that point the virus is typically cleared from circulation and clinicians will then rely on tests that reveal patient antibodies.  Again, most patients never show any signs or have any symptoms after being infected with Zika virus.

A Future Scenario

A male traveler spent time in an area where Zika virus was circulating.  Immediately after returning home, he and his wife decided they would like to start a family.  However, he knows it is possible to transmit Zika virus to his wife through sexual relations for up to 6 months after infection.  A validated at-home Zika virus CRISPR infection blood test kit is available and he used it.  The test was negative for Zika virus.

Is he OK to try to start a family immediately or is he better off waiting for 6 months?

The DIY Passage to the Future

Here are some questions that impact the decision – did he ever have any signs (rash, fever) or symptoms (feeling unwell, muscle aches) that might indicate Zika virus infection?  When did he have them and when did he perform the DIY Zika virus test?  Timing is everything here because if the new CRISPR diagnostic test uses blood it will probably have a limited reliable detection window just like the current nucleic acid tests. Perhaps the coming CRISPR at-home Zika virus test system will be extremely sophisticated and combine nucleic acid surveillance with antibody screens.  Hopefully, the at-home kits will include information to enable users to understand how the procedure(s) works, explain that under some circumstances the different formats return apparently contradictory findings and point out critical limitations that impact final interpretation of results.  Again, if you look at the CDC guidelines for Zika virus testing (3) you will see how and when to apply them involves several factors.  So, back to the scenario; are you ready to make the call?  What if it was your baby on the line?   



Maybe the future for a case like this one lies in methods able to assess semen samples which could give patients the most accurate sense of risk for Zika virus transmission through sexual contact.  Even the most powerful tests will have limitations and it will be interesting to see how Mammoth Biosciences and others approach the CRISPR diagnostics at-home market.  If the “internet makes us freak out about our health” (1) imagine what is going to happen when a diverse population of consumers are empowered with their own personal medical testing capabilities.   


(1) Kristen Houser. At-Home CRISPR Kit Will Diagnose You Better Than WebMD.  Futurism, 27 April 2018.  ly/2MRf4O6

(2) Shamez N. Ladhani et al.   Outbreak of Zika Virus in the Americas and the Association with Microcephaly, Congenital Malformations and Guillain-Barré Syndrome.  Archives of Disease in Childhood 101(7):600-602.

(3) Centers for Disease Control and Prevention. Testing Guidance for Zika Virus. \

(4) Centers for Disease Control and Prevention. Men and Zika.


A Wild Ride Comes to an End

June 22, 2018

In a few days I will wrap up my final set of experiments.  Having been engaged in research nearly 40 years this is a big personal milestone.    

It’s been quite a journey.  From restriction mapping the DNA of human tumor virus BK, cloning the recA gene analogue of Pseudomonas aeruginosa, hunting bacteriophages to using hard-core biochemistry to examine Alzheimer’s disease, it was never boring.  I have always had a great deal of good luck in my life and at each step along my path I discovered helpful mentors and good colleagues. 

I have included a few waypoint pictures.  Not everything resulted in publications indexed on PubMed.  Truth be told, some of the more interesting projects involved what is loosely termed the paranormal – UFO’s, cryptids, alien abductions, etc.  Are such efforts beneath the dignity of true scientists?  It depends on the scientists.  However, I am able to report that along these often ridiculed trails I met some fascinating people, had tremendous amounts of fun and learned more than I ever dreamed possible.

Being able to live this life has been a privilege.



Tau tangles in the neurons of an AD patient



A red Cyclops from an alkaline lake



Dinosaur bone



UFO Hoax



UNL-1, a bacteriophage with a novel UV damage reactivation phenotype



The Triassic Trees of Dobell Ranch

June 13, 2018

If you have seen a petrified wood specimen featuring bright red, purple, orange-yellow colors, chances are good it came from Northeast Arizona.  Petrified wood may be found in many locations, but only a few spots produce specimens with such vibrant colors.  Larry Jensen and I visited the Dobell Ranch dig site located near Holbrook, Arizona, to find out how the petrified wood samples we have seen in rock shops and shows are collected.  The picture below of a polished petrified wood cross-section table top was taken at the Tucson Fossil and Gem Show.

Pet wood table

Rhonda Dobell runs a curio shop not far from what is probably the petrified wood capitol of the world, Holbrook, Arizona.  I am not sure how long she has been excavating and selling petrified wood from this land, but was informed the ranch has been held by the Dobell family since 1932.  A sizeable selection is available for customers at her roadside curio stand and the active dig site is nearby (an easy drive) with a lot more items of every size.

Pick and choose

 Part of the offerings at the Dobell Dig Site

What she sells is the real deal; petrified wood cleaned of dirt and extraneous deposits of debris in an otherwise unmodified state.  In some instances the gross external morphological features were so well preserved it is hard to believe that you are not looking at a tree.  To convince yourself, simply try picking up one of them.  Or take a look at the Big Sky country around you and imagine where you have to trek in these parts to get such a thing.


Rhonda’s granddaughter waits for some work

The petrified wood is excavated from a deep, soft overburden.  These logs dating from the Triassic period (ca. 200 million years ago) were apparently buried quickly in sediments and volcanic ash and then fossilized/colored by quartz and other minerals.  Quite a bit of the original matrix complete with what look like polished river rocks surrounds the petrified wood. 

Dobell dig

I am not sure how deep the covering deposits run, but pits I estimated to be up to 30 feet deep were being worked at the time of our visit.  Pictured below is a log in the excavation process. Rhonda pointed out another log lies directly beneath.  A photograph from a different vantage point with Rhonda’s granddaughter provides some perspective.

Excavation  Perspective

An interesting feature of some of the petrified logs was that the fossilization process sometimes preserved hollows and voids, some retaining signs of apparent termite damage.  For the giant undergoing excavation, Rhonda showed us exactly where she knows (through tapping) a hollow area will be found. 


You will not need to dig out your own specimens, the hard work and basic preparation has already been done by the Dobells.  However, as you pick up, roll over and haul heavy specimens, likely under a merciless sun, you are going to discover something else.  Getting all those beautiful petrified wood pieces demands expertise and a lot of back-breaking labor.  It won’t take long to realize how much hard work Rhonda and her family have put into their business.  Bring plenty of water with you to drink and to pour on the rocks to get a better sense of the colors that would be brought out by polishing.

Specimen tumbling

Specimen for tumbling

The Dobell Ranch abuts the Petrified Forest National Park and a short drive will take you to the park entrance.  Next to the Visitor Center you can see quite a number of impressive specimens exposed on the surface and get an overview of the harsh badlands that compose the region.

PFNP overlook

Petrified Forest National Park

We inhabit an amazing world.  No humans ever saw these trees of the Triassic when they were alive, but we have a very good idea what some of them looked like so long ago.


An image gallery of Dobell Dig Site specimens courtesy of Larry Jensen









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