Rewriting All the Rules – The Arrival of Genomic Editing

Rewriting All the Rules – The Arrival of Genomic Editing

by guest blogger,
Tyler A. Kokjohn, Ph.D.

Genetic editing future

Illustration Courtesy of Jeff Ritzmann.

Humans are poised to become far more powerful.  Scientists are perfecting new tools to alter our own genomes and possibly those of all generations to come.  And it won’t stop there.  Genome editing techniques extended to other organisms and combined with strategies to disseminate modified genes through the environment will enable future genetic authors to literally re-write the DNA scripts that run entire ecosystems.

Genome editing has tremendous potential to alleviate disease and suffering.  Because scientists are still learning how genomes function, our raw engineering prowess now far outstrips any ability to predict the ultimate consequences that might follow the use of these new tools.  That leaves us in the uncomfortable situation of seeing how using genetic editing technology could provide potentially enormous benefits while recognizing going forward demands we must both court unknown risks and resolve explosive ethical dilemmas.  Appreciating the imminent intersection of issues, a group of scientists has called for informed and open discussions to ensure the coming genome engineering capabilities are used wisely and ethically (http://www.sciencemag.org/content/348/6230/36.long).

The genetic engineering technology raising the most concern is known by the cryptic designation of ‘CRISPR-Cas9′.*  Although the functional details of the system can be confusing (http://www.sciencemag.org/content/341/6148/833.full), its amazing implications are easy to grasp; human beings will soon be able to engineer their own heredity.   For example, today persons inheriting certain rare mutations in the presenilin gene are doomed to suffer early-onset dementia and death.  CRISPR-Cas9 technology may make it possible to erase the bad genetic information in that gene and change it to that found in the normal (healthy) form.  Perhaps it will ultimately become acceptable to edit the germ cells of persons to correct disease-causing mutations and thereby preempt all future problems by passing only the good gene copies on to future generations.  Such efforts and the experiments needed to reach these goals will spark intense ethical debates.

Gene editing technology can be harnessed to produce ‘guided gene drives’ (http://www.ncbi.nlm.nih.gov/pubmed/25035423) which could be deployed to modify the genetic traits of wild organisms.  In essence, this would bestow unprecedented powers to genetic engineers and allow them to restructure entire ecosystems to suit human specifications.  Perhaps editing technologies and guided gene drives will be used in the future to control or eliminate scourges like malaria by modifying mosquito vector populations.  Assessing the environmental risks associated with such manipulations will be challenging.   Although (in principle) a second guided gene drive might be employed to reverse a previously released gene drive producing undesirable impacts, undoing any consequential ecological damage may be impossible (http://www.sciencemag.org/content/345/6197/626.long).

This camel already has his nose well inside the tent and we will not have to wait long for a brave new world to arrive.  Genomic editing technology (for research purposes) is already available commercially and biotechnology companies like Editas Medicine (http://editasmedicine.com/) have been formed to develop and exploit the fast-emerging opportunities.  The tools are being perfected quickly and persistent, vague speculations that human embryos are already being modified (http://www.nature.com/news/mini-enzyme-moves-gene-editing-closer-to-the-clinic-1.17234) feeds the perception that events are literally racing forward.

Scientists, perhaps sensing an urgent need to get ahead of quickly emerging results, are calling for open dialog and meticulous investigation of safety and efficacy of gene editing in advance of its widespread use (http://www.sciencemag.org/content/348/6230/36.long).  In addition, aware that some nations prohibit or restrict germ cell engineering while others are more permissive, these experts are explicitly discouraging all efforts to modify human germline cells until the complete spectrum of issues, including ethical concerns, have been fully considered.

The pressure to use genome editing technology will be immense.  The audacious notion that human beings might re-write the book of heredity and direct their own evolution will produce intense controversy.  Perhaps the coming storm will be severe enough to halt efforts to modify human genetics except for carefully prescribed purposes.  However, it is important to remember that gene editing technology has implications that extend much further than directly manipulating human heredity.  The tools can be applied to other organisms in ways that will probably not offend sensitivities to the same degree.  Once the capacity to modify the genomes of target non-human organisms is perfected, it may be very difficult to rationalize not utilizing it.  For example, if scientists are able to modify mosquito species to prevent malaria carriage or transmission (http://www.sciencemag.org/content/345/6197/626.long), the potential benefit to human health is obvious.

However, what if the best approach to malaria eradication is altering or inactivating genes in ways that makes mosquito reproduction fail?  Will we then proceed to drive some species to extinction to improve the environment?  A justification for immediate use based on the idea of safeguarding human health will be compelling.  In addition, precedents on such matters would seem to have been set a long time ago.  When humans modify the environment to suit their purposes, the fate of other organisms sharing the ecosystems we exploit is sometimes given scant concern.  In fact, through the broadcast of chemical agents like DDT we can be downright indiscriminately murderous in our quest to manage the environment.  The problem is that is extremely difficult to predict the full implications of human-initiated environmental tinkering because ecosystems are complex, interconnected and dynamic entities whose functions are only dimly understood.

As an example of the complexities, think of the Monarch butterfly of North America.  A series of changes to improve agricultural economics and environmental esthetics had the unintended consequence of decimating the once vast populations of migratory Monarch butterflies (http://www.washingtonpost.com/news/energy-environment/wp/2015/02/09/the-monarch-massacre-nearly-a-billion-butterflies-have-vanished/).   The great annual migrations of this large orange and black butterfly from Canada to Mexico and back may become a thing of the past.  It is unclear whether it will be possible to reverse a tragic trend and restore the Midwestern Monarch butterfly populations to safely sustainable levels.  Are changes which have collectively driven Monarch butterflies to extinction an improvement?  The scientists who issued an urgent call to dialog and debate the development and future implementation of genomic editing technologies noted their extraordinary potential to reshape the biosphere.  The tools are powerful and if used, must be applied with the utmost of caution.  These technologies and capacities may ultimately impact the health and wellbeing of everyone and everything on our planet.

Clearly, the future discussions addressing the use of genome editing technology must involve experts.  Much of the discussion will necessarily be highly technical, but every one of us is a legitimate stakeholder in the outcome and you don’t have to be an expert to ask useful questions and influence the process.  Rather than be intimidated by the technology and conceding these far reaching decisions entirely to the authorities, recognize how your perspectives could provide critical and unbiased input to the process.  Many of the people who will elbow their way to the table are likely to have a vested interest in the use of the new technology.  You do not need a Ph. D. to know whether you value Monarch butterflies more than ensuring high fructose corn syrup will be a few cents cheaper and your perspectives on such matters may be equally as insightful and important as those with advanced degrees.  Remember, scientists are truly expert in a narrow range of subjects.  A few might well be the world’s leading authorities on creating the guide RNA components for CRISPR-Cas9 nucleases, but may never have chased a Monarch butterfly through a meadow when they were children or ever give any thoughts to such trivial matters let alone assign them an intrinsic value.  When it comes to the type of world you want for the next generation, you are the world authority.

I hope you will follow the Twitter feed of the key scientific journals, Science (@sciencemagazine) and Nature (@NatureNews), to stay informed about new developments being disseminated to the scientific community.  Be ready to post comments to those articles and the follow-on reports in the newspapers.  If you belong to any organizations engaged in conservation issues or ecological protection, ask the leaders what they are doing about this situation.  Genomic editing and gene drives are about to become reality.  How, when and where genomic modification of humans, other organisms and our biosphere is permissible will soon be under discussion.  Take part in the conversation and ensure your part of this story gets written.


D. Baltimore et al., 2015.  A Prudent Path Forward for Genomic Engineering and Germline Gene Modification.  Science 348:36-38.  http://www.sciencemag.org/content/348/6230/36.long

E. Pennisi.  2013.  The CRISPR Craze.  A Bacterial Immune System Yields a Potentially Revolutionary Genome-editing Technique.  Science 341:833-836.  http://www.sciencemag.org/content/341/6148/833.full

K. M. Esvelt et al. 2014.  Concerning RNA-guided Gene Drives for the Alteration of Wild Populations.  eLife.  http://www.ncbi.nlm.nih.gov/pubmed/25035423
K. A. Oye et al. 2014.  Regulating Gene Drives.  Regulatory Gaps Must be Filled Before Gene Drives Could be Used in the Wild.  Science 345:626-628.
http://www.sciencemag.org/content/345/6197/626.long

H. Ledford.  2015.  Mini Enzyme Moves Gene Editing Closer to the Clinic.  Discovery Expands Potential CRISPR Toolbox for Treating Genetic Diseases in Humans.  Nature 520:18.  http://www.nature.com/news/mini-enzyme-moves-gene-editing-closer-to-the-clinic-1.17234

D. Fears.  2015.  The Monarch Massacre: Nearly a Billion Butterflies Have Vanished.  The Washington Post, 9 February 2015.  http://www.washingtonpost.com/news/energy-environment/wp/2015/02/09/the-monarch-massacre-nearly-a-billion-butterflies-have-vanished/


*CRISPR-Cas9 – CRISPR stands for Clustered Regularly Interspaced Short Palindromic Repeats which were originally discovered as peculiar repeated DNA sequence patterns in some bacterial genomes.  These repeats are part of a system designed to bind specific target DNA sequences and break apart the molecules which harbor them.  The CRISPR genes are believed to form a bacterial immune system, a way for cells to remember the viruses that have infected them in the past and destroy them if they try to return. Cas9 is CRISPR associated gene 9, the protein that actually cuts DNA at specific places in the genome.  CRISPR-Cas9 allows engineers to open genomic DNA at precisely selected locations and edit the nucleotide base sequences, thereby changing the product of that gene.  In principle this technology could be used to alter germ cells to allow engineered changes to be passed to the future generations.  It is believed that all organisms which undergo sexual reproduction will be modifiable by CRISPR-Cas9 methods.

Project Core – Demarcation and Departure

Project Core – Demarcation and Departure
by guest blogger,
Tyler A. Kokjohn

Paranormal phenomena encompass a diverse array of experiences that are often considered to be entirely outside the boundaries of science.  However, the tools and techniques of scientific investigation are so powerful because they can be applied to many situations and this demarcation is not necessarily sharp.  Some cryptozoology research efforts and the search for extraterrestrial intelligence (SETI) are solidly within the scientific mainstream in terms of approach and methodology.  While the often fleeting and unpredictable nature of paranormal events complicates their study, it is possible to investigate certain aspects of them scientifically.  Project Core was created to initiate that process.

Investigations begin with a question, or as a scientist might put it more properly, a hypothesis.  The heart of the scientific method is asking questions that can be answered through direct observation or experiment.  The art of the process is ensuring that your approach and answers are unbiased and valid.  Some of the challenges are illustrated by a simple experiment I conducted in my own back yard.

The video (below) combines a series of photos taken at one minute intervals over about an hour which shows flower blooms opening up in the morning and moving to face and follow the sun.

Flowers1


How do plants respond to the environment like that?  That is a complex problem, but it is possible to reduce the scope of inquiry to an answerable question. Scientists often employ a reductionist approach to break down complicated problems into more manageable smaller pieces.  In this case the correlation between sunlight and flower opening leads to a testable hypothesis; exposure to visible light induces flowers to open.

To test my hypothesis I collected two yellow flowers in the morning before they had opened.  I placed one under a light indoors and the other inside an adjacent container (a coffee cup with a lid) which I could keep dark.  The experiment was started at 8:47 a.m. and was stopped at 9:34 a.m., when I noted almost all the flowers outside had opened up.

 

Screen Shot 2015-03-04 at 12.18.04 PM

The experimental outcomes:

Screen Shot 2015-03-04 at 12.19.14 PM

Unfortunately, it seems the original hypothesis that light exposure triggers bloom opening was not supported by the experimental evidence.  The flower blossom incubated in light opened up, but because a similar flower held in the dark (the control) also opened up, it seems light exposure had no impact on the bloom opening response.

Case closed?  Not exactly, I made a couple of mistakes.  The tricky part was trying to do my best to debunk my own investigation to discover any errors in method or logic.  To start, I reviewed the rationale for the experiment design.  Both orange and yellow flowers were available to me, but I used only yellow flowers from the same small garden area to study.  Hopefully, these actions provided experimental subjects that were as similar to each other as possible.  That means any activity differences observed during the experiment could confidently be attributed to the differences in the manipulated variables, in this case, light exposure.

The flowers I tested were cut and that meant they were physiologically different from the ones out in the yard with functioning root systems.  However, I synchronized my experiment with the bloom opening behavior of the rooted flowers.  The cut flowers, including the one in the dark, had also opened at the same time of day.  In addition, the fact that cut flower blooms opened suggests that all the necessary systems functioned like those active in the rooted plants.  If the cut flowers did not open or did so in a very different time frame it would be a lot more difficult to make a convincing case for functional physiological equivalence.  So it appears my reductionist approach using cut flowers mimicked reality closely enough to be useful.

The work began with an obvious correlation between light exposure and bloom opening.  However, even the most apparently clear-cut correlations do not necessarily reveal the true underlying causes.  To avoid falling prey to the logical fallacy ‘with this, therefore because of this,’ deceptive correlations are rooted out by subjecting them to additional confirmatory tests.   However, these tests must be done carefully and their results interpreted skeptically.

There are problems with my study because I was too lax with the self-criticism from beginning to end.  I set up and performed the experiment improperly, but failed to notice the error until after the work was completed.  Suppose I wanted to submit a manuscript describing this work and my conclusions to a scientific journal for publication.  Before it is published, it goes through a peer review in which it is evaluated by anonymous experts chosen by the journal editors.  Editors rely on peer reviewers to expose shortcomings in approach or execution.

It is not hard to imagine if I had not noticed the errors and submitted my work for publication, an alert reviewer would probably returned a polite, but devastating, critique of the work and results to the journal editor and me.

The author has failed to test his central hypothesis that light exposure induces closed flower blooms to open.  Unfortunately, the collection of flowers seems to have taken place after dawn when all the blooms had already been exposed to indirect light.  Perhaps this exposure was sufficient to catalyze petal motion.  If so, the observation that a flower incubated in the dark could open is easily explainable as nothing more than experimental artifact.  To answer the question, the investigator will need to collect flowers at night and take precautions to ensure the dark controls are incubated without any light exposure.    

Without this system of external checks, you can see how easy it would be to make and publish errors.  In this case, I did not have a true controlled experiment because of an unnoticed oversight in how I performed the work.  That small mistake was the difference between being able to reach a scientifically valid conclusion or not.             

With experience a person can get better at developing controlled experiments, but a more insidious danger, confirmation bias, sometimes confounds investigators.  Humans are natural story tellers.  Accepting the experimental results at face value it was easy to conclude that light exposure has nothing to do with bloom opening.  That idea is so seductive because it seems to fit all the observations so well.  The problem is that the way I did the work makes it impossible to reach any experimentally-validated conclusion at all about the impact of light on bloom opening.  I quit being skeptical too soon.  Believing the results of a single shoddy experiment, I then built a tidy global narrative as to how the whole process worked.  But note how I began by investigating one hypothesis (light exposure induces bloom opening) and ended up answering a different one (light exposure has nothing to do with bloom opening). These subtle shifts and circular logic traps can be extremely hard to recognize because few stories appeal to us more than the ones we create ourselves.  Poor experiment design is troublesome, but lethal confirmation bias may emerge at any point in the investigation process.  Even liberal applications of Occam’s Razor may not prevent biased investigators from extracting preconceived answers out of uncorroborated correlations and poorly executed experiments.  If a mainstream scientist is skillful or simply lucky, he or she recognizes any errors and corrects them before proceeding to publication.  If not, a peer reviewer will probably be delighted to expose them.

Creating and evaluating hypotheses by confronting them with data demands proficiency, patience and determined ruthlessness.  Hypotheses for which no properly controlled, reproducible supporting evidence can be developed must be modified, put aside or rejected.  The process is sometimes so tricky that scientists do not trust themselves to do it properly every time.  That’s why they employ peer review to check their work.

Aspects of paranormal phenomena can be reduced to experimentally tractable questions.     The Project Core survey is best viewed as a departure point to construct hypotheses to be confirmed or refuted through additional work.  Some potential lines of inquiry are already clear.  We invite you to explore the questions posed in the Project Core survey as well as develop new testable hypotheses, the ultimate peer review.

The inherent challenge of paranormal phenomena investigation suggests that many attempts to describe and comprehend them may be deemed crude and unsatisfactory.  We should anticipate needing to systematically eliminate biases, refine ideas and explore alternative approaches as new data and insightful constructive criticisms dictate.

Intruders Foundation Consent Forms: Consent or Exploitation?

It comes as no surprise to me that an alien abduction book-writing hypnotist’s consent form reads more like an amateurish cover my ass form. But that’s because I’m from here. What happens when an actual scientist the likes of whom alien abduction researchers have been screaming at for years to take this subject seriously does so and reads these consent forms? Well, your answer is below. And it begs the question: Do these abduction researchers really want scientists and the mainstream to take their work seriously or is that smoke and mirrors because they assume such people will not anyway? It’s easy to yell “Take me seriously!” or demand disclosure from the government when you know it’s not going to happen. Then you get to look like a hero of the people and profit from that.

This begs another question and another: Are these researchers really researchers? If there are no standards, no ethics, only the defense of misused tools like hypnosis and book reviews… speeches about the coherence of cherry-picked data… should this be considered a field of study to begin with?

–Jeremy Vaeni

Intruders Foundation Consent Forms: Consent or Exploitation?
by,
Tyler Kokjohn

Jack Brewer’s recent blog post on The UFO Trail regarding access to confidential hypnosis tapes exposed far more than a thoughtless violation of research confidentiality standards.  The Intruders Foundation consent form Jack published with his essay is shocking and virtually nothing like an informed consent form that would be employed for biomedical research.

First and foremost it served as notice that Budd Hopkins had claimed all publication rights to every utterance and any created entity of interest he could collect from his subjects.  Any privacy or confidentiality issues for the participant were apparently entirely secondary matters.  Worse, possible psychological issues emerging following participation were fully foreseeable adverse events – the document clearly informs the subject of that.  But then Budd simply washed his hands of them. In effect, subjects assumed risks that were never adequately explained and if anything went wrong were left on their own.

Unfortunately, risk is an unavoidable part of some biomedical research.  Potential foreseeable risks are managed through a comprehensive informed consent process to provide full, detailed information in advance to all subjects.  Written informed consent documents provide potential subjects with information about the nature of the research, how it will be used, the risks incurred and the rights of all participants. Potential adverse events must be described in sufficient detail and in an understandable fashion so that every subject knows completely what might go wrong BEFORE agreeing to participate.  Adverse events are mitigated through meticulous followup care during and after the study term if necessary.  No research may commence until the investigator has devised an appropriate and complete written informed consent form and obtains full institutional approval for it as well as a detailed written plan to recognize and mitigate all adverse events arising from the investigation.  The investigator and institution are responsible for completely informing all individuals of the attendant risks involved and assume full responsibility for the welfare of the subject and any/all needs that emerge as a consequence of participation in the study.  Attempting to insulate oneself from lawsuits through the invocation of a vague disclaimer or withholding vital information to thwart informed decision-making by possible participants is never permitted.

The evidence suggests Budd Hopkins realized serious problems might develop from his investigations – and he took steps to try to avoid the trouble they might cause him. After taking pains to highlight his own incompetence and lack of medical training, he persisted in rooting around where he effectively admitted he had no business whatsoever.  Holding himself legally blameless for all consequential damages, he was seemingly disinterested in mitigating any injuries he induced.

The implications are far reaching. If Budd Hopkins knew his work could create serious issues, it would seem that others using similar methods must have had analogous experiences with the induction of adverse events.  In other words, hypnosis investigators know this or reasonably should know of the potential for investigations to produce trouble in their subjects.  Authors Philip Klass, Jim Schnabel and Kevin Randle et al. had the situation well figured years ago, but were ignored. Recognizing this is no parlor game and what really can happen is something many hypnotists probably hope no one else ever figures out.  Anyone contemplating taking part in research is well advised to read and consider the informed consent documents carefully before participating.