Saturday, November 23, 2013

Hazy Dreams, Productive Thoughts

There has been a bug in my household, not surprising when there is a 7 year old living in the same space.  He seems to bring home new viruses each week.  This one did not hit me as hard as some of the others, but I have been tired, very tired.  The downside of each new bug is the time lost in "recovery".  I hate giving up this time to a virus, especially if I have viruses at work that need my attention.  Of course, I am referring to actual viruses in the -80°C freezer that are waiting for me to interrogate.

The upside of sleeping a little bit more each morning (instead of working out) is that I have let my mind wander to what I really want to accomplish professionally.  A few years ago, I attempted a search for a tenure track position.  To my surprise, I received several personal notes from search committee members expressing some interesting points.  What was particularly interesting is that these were notes that were in addition to the rejection letter and generally unsigned.  The notes were complementary, and pointed out what I would have needed to advance in that round.  Almost always, the missing item was NIH funding and obvious independence.  Neither is a big revelation.

As a problem solver, I have thought about this issue a great deal, not only for myself, but for future scientists.  The reality is that not every postdoc has the opportunity to submit grants to the NIH.  Seriously.  Sometimes, it is the PI who is the roadblock, other times it is a dynamic of the lab.  In the end, the actual issue is that a postdoc lives in two worlds.  One world is the lab setting based by a PI, who has a particular agenda.  The other world is the research community, which has "committee" based criteria for the postdoc deemed hirable.  Many others have discussed the inequality of academic hiring, including fantastic, well spoken, bloggers, tweeters, etc.  I cannot do this topic justice.  Instead, I will point out the math: if there is one job and 300 applicants, 299 people are not hired.  Many of them are qualified, but some criteria, fair or not, stood in the way.  This does not mean the other 299 applicants are not hard-working, accomplished scientists. So why do we treatment as losers?

I am hungry for a change, another path for the career scientist.  The biggest hurdle is knowing how to exit the current academic setting and still maintain health insurance and income.  Of course, every self-employed individual struggles with that hurdle!  The difference is that a scientist does not always have a "sellable" product.  At least, we do not understand what the sellable product really is.  In hindsight, I now realize that the postdoc effort was the sellable product.  It is the relationship between PI, postdoc, and University that needs to change, and postdocs need to demand greater ownership of their data.

Just consider what a postdoc does for the PI.  In a typical lab, the postdoc does the manual labor, trains grad students, writes protocols, research updates, papers, and lab maintenance.  This is not to say the PI does not work, on the contrary, the PI is working on administrative aspects of the lab.  Having a postdoc in the lab means more data is generated, more students are trained, and projects run smoothly.  However, there is no safety net under the postdoc, who is bound by the constraints of the PI when it comes to grants and papers.  A better system is one where the postdoc has a 3 yr contract.  Year one, the postdoc contributes 80-90% effort on the PI's project and 10-20% effort on a personal project.  This could be a literature search, small grant or crowd funded proposal, or basis of a larger project.  The second year, this changes to less effort on the PI's project and more effort on the personal project, perhaps a 60-40 split.  Finally, the third year is flipped, where the postdoc spend greater than 50% effort on a personal project.  This is what "payment" means.  Postdocs should not be service providers as much as they should be scientists.

Now, most PIs and postdocs would say that they need to give 110% for 2-3 years just to get a project started.  In that case, the payment is ownership of the data generates, meaning that as a postdoc advances each year, the postdoc acquires greater ownership of the project.  For those who say that we already have this system, I love that there are already PIs who think this way.  But it is not the norm, at least not in my experience.

After 3 years, a postdoc really is independent and should be treated as such.  Does this mean a 4th year cannot be a staff scientist?  No, it means that we need to make distinctions much earlier.  At the 4th year, academia needs to be responsible for all of the researchers in the department, meaning that postdocs are hired by the University rather than the lab.  This is a very important change that serves to add respect for a postdoctoral position.  Give all postdocs equal footing in the academic landscape and allow all to be responsible for their scientific portfolio. Open the door to allow cross effort on another PI's grant, a bit of internal freelancing.

Finally, allow these postdocs freelance space.  There are so many ways for a University to capitalize on the independent scientist, without providing them long term contracts.  The greatest reward to a University is the great science that is produced by highly creative and intelligent people.  It makes no sense to discard superdocs at the current rate.  Why not recoup the investment?

Sunday, November 17, 2013

Bidirectional Transcription, Tandem Repeats, ALS, and Competition

When I started my postdoc position at the Fred Hutchinson Cancer Research Center in 2004, I had the great opportunity to identify an antisense transcript at the FMR1 CGG repeat region (HMG, 2007).  Better yet, I was able to interact with Diane Cho as she finished her story on antisense transcripts at the DMPK locus (Mol Cell, 2005).  The only other group actively looking at antisense transcripts was the Ranum lab, who was in Minnesota at the time (Nat Gen, 2006).  We had so much to do as we navigated the skeptical mRNA-centric world.  As a consequence, we had to characterize the antisense transcripts using the tools and questions that we would use to analyze coding transcripts.  Were the antisense transcripts polyadenylated? Capped? In the nucleus or cytoplasm? Spliced or unspliced? RNA pol II or III?  There were so many preconceived notions about the extra transcription exhibited by a gene locus that we had to overcome with careful characterization.  Ultimately, we defined the appropriate way to characterize antisense transcripts at repeat regions.

But, publications and grant applications were not easy to obtain. Most reviewers hated the notion of antisense transcript. A major assumption was that the transcripts we identified were "spurious", a term that I have come to realize is tossed around to mean: NOT REAL.  My other favorite critique was the statement "you do not know if the antisense transcript causes disease".  All of the genes we characterized had a repeat expansion associated with disease.  I find it incredibly short sighted to think that the antisense transcript somehow was independent of the sense "disease-causing" transcript when both harbored an expansion from the same region.

A representation of strand-specific interrogation of transcripts at a CAG repeat region

As a consequence, it is difficult to publish noncoding transcriptional activity at a locus.  Basically, the transcriptome is an uncharacterized frontier, largely due to lack of interest by genomics field and lack of research funding for the transcriptional regulation field.  The tenuous relationship between the transcriptomics field and what seems like the rest of science is best depicted by the public distain for the ENCODE Project.  I would rather not spend time on discussing the merits of either side of the argument, rather I want to focus on what I have seen, touched, sequenced, characterized, and understood about bidirectional transcription at unstable tandem repeat loc.

To date, only a few gene regions have been characterized well enough to understand the consequence of a repeat expansion.  This includes the FMR1, SCA8, DMPK, FRDA, SCA7, HTT, loci, plus a few more.  However, there are ~30 known unstable tandem repeat regions associated with neurodegenerative, developmental disorders, and muscular dystrophy.  The repeats are tri, tetra, penta, hexa, and dodeca repeat regions found near promoters, introns, and exonic regions of gene loci.  A quick glance of any human gene of interest on the UCSC browser reveals higher transcriptional activity near repeat regions as demonstrated by deposited ESTs.  Note, this activity is in both directions.  Comparison of the human genome and other organisms, such as mouse, reveal that in many cases, there are overlapping genes at the repeat regions.  A huge question is whether the antisense transcripts we have identified are actually remnants of genes no longer in play due to the formation of a true repeat region or whether the antisense transcripts represent regulatory elements, not yet fully appreciated.  

Ideally, I would like to continue to explore bidirectional transcription with the goal to provide a clearer picture of the transcriptional activity at tandem repeat gene loci.  This is primarily due to the number of diseases associated with repeat expansions.  When a repeat region expands, additional and potentially toxic RNAs are generated.  These transcripts could also be utilized as locus-specific biomarkers for the associated disease pathogenesisWith an increased focus on therapeutic agents, such as ASOs that target expanded sense transcripts for degradation, it is imperative that we understand what transcripts are generated from expanded disease-associated alleles.   

Unfortunately, as a senior scientist in some one else's lab, I did not have my own funding.  The years of work to break down the barriers to even recognize antisense transcripts are perhaps wasted for my career, as I could not hang on long enough to acquire funding.  However, there is some light at the end of the tunnel.  The Amyotrophic Lateral Sclerosis (ALS), community seems to have embraced bidirectional transcription, as well as another controversial topic, Repeat-associated Non-ATG (RAN) translation.  RAN translation was first described by Laura Ranum, another pioneer in bidirectional transcription at repeat regions.   In fact, the ALS community is incredibly competitive about the sense, antisense, coding, non-coding, toxic, non-toxic, RNAs and transcripts and the C9ORF72 gene.  It is a thrill to read each paper, each perspective, and each interpretation.  There seems to be little room of critique of antisense transcripts in their world, instead they seem to be focused on using every bit of evidence they can find to characterize the molecular mechanisms underlying this disease.  

Make no mistake, I do not support some of the underhanded competition that has occurred in this field.  Even I have been taken advantage by a few members of the C9ORF72 community, but I stand firm that the outcome will benefit the patient community, so it is worth it.  I have faith that the researchers are close to having viable and realistic therapeutics for ALS, something that is truly needed.  But I chuckle at how easily authors have claimed to "demonstrate" bidirectional transcription at C9ORF72, such as the Petrucelli Lab, where the evidence is basically in vitro analysis of transfected constructs or Edbauer Lab, where evidence of antisense translation is the proof.  This is liberating for the field, where scientists with expertise in disease characterization do not have to spend 3-5 years characterizing the transcript boundaries, localization, and processing prior to addressing impact on disease.  

There is time and space for researchers such as myself, who can more quickly address the RNAs generated at the locus.  I hope the recent body of work at the C9ORF72 locus will make it easier to address bidirectional transcription at the remaining 20+ unstable tandem repeat genes, all associated with equally devastating disease. Nonetheless, I wish that I could have a conversation with the reviewers of my grants, papers, and research proposals and ask them why they rejected the validity of bidirectional transcription.  What did they gain by blocking progress?  There was never a consequence for them, instead the ultimate burden is on the individuals who harbor repeat expansions and suffer from disease.  These individuals continue to wait for someone to be interested in their gene mutation.  It pains me that I came so close to being able to advance understanding of the gene loci associated with 20+ unstable repeat regions, but the road block of grant review did not see these diseases as important.

Saturday, November 2, 2013

Reveal, Reclaim, Reform The 3 R's in Modern Science

On the blog front, I have been suffering from a bit of paralysis.  My intent for this blog is to focus on my field of interest: transcription, transcription regulation, and transcriptomics. However, my focus has been diffuse and scattered lately.  In the past few weeks, I have been caught off guard by the number of bloggers, columnists, and science writers who have been critical of the waste, fraud, and misconduct in science. 

Let me clarify: I am not taken back by the comments that have been made.  Instead, I am surprised to see more scientists be open about what is happening in academic science.  In the past 4-5 years, when I openly expressed my concerns about the state of academic science, I was accused of not being a team player or worse, not being competitive.  Seemingly, by pointing out the failings of academic science, I was seen as someone who could no longer compete with my peers.  The hesitation to be as corrupt as my competitors suggested I was not a strong scientist. 

What troubles me most is how my silence enabled continued misconduct.  Now I feel compelled to share my experiences and support those who dare to challenge the status quo.  It is time to “reveal” the bad behavior of scientists so that collectively we can decide how to recognize and discourage underhanded behavior.

Misconduct is not a new problem, thus pointing my finger at individual scientists is hardly productive.  Instead, I want to speak up to say misconduct, whether deliberate or careless, gender and ethnic disparity in career advancement and funding, as well as exploitation of students, technicians, and postdocs are all important topics that should no longer be ignored.  I witnessed this behavior at every level of my training from undergraduate to project scientist.  Like most trainees, I tried to steer clear of those who were blatant frauds, but eventually ended up in an area where inappropriate behavior was considered smart and competitive.

During my second postdoc, I was surprised by the number of graduate students and postdocs who could relate multiple, unique, and individual stories of scientific misconduct by their PIs, collaborators, or lab mates.  Worse, I met a number of newly minted (and inbred) postdocs who supported underhanded approaches to double salaries, honorary authorship, and un-reproducible results.  Their objective was to increase authorship and grant funding.  I encountered the attitude that most of our work is obsolete in 5 years, so why worry about the integrity of science? Keep your head down and worry about the paycheck and the number of publications on your CV, it is the only way up the career ladder.

Initially, I was outraged.  When I witnessed a postdoc who sabotaged the research going on around her, I encouraged one of the victims to speak up.  To my disgust, the victim was reprimanded and later fired, for revealing a problem in the lab.  The saboteur was rewarded for being competitive and given a raise.  The rest of the lab was told to never speak up again, as it will not be tolerated.  It was then that I felt defeated.  Once again, the whistle blower was punished.

Scientific misconduct is most insidious when it is from a person of power, who controls references, publications, grant and paper reviews.  As a result, we cannot put all of the responsibility on those who have been victimized.  However, this power is reduced when their misconduct is revealed.  As members of the scientific community, it is our responsibility to speak up for those who do not have voices.  Of course, keep in mind that graduate students have a department chair, and committee members to look out for them.  Technicians, undergraduates, postdocs, and senior scientists do not have this type of support under our current system, where the University has a vested interest in the PI’s career rather than the careers of those in the lab. 

We need to “reclaim” our voices, expertise, and experiences.  Too many postdocs leave their field of research taking with them all of the knowledge they amassed from undergrad to postdoc.  As a result, experiments are never published, shared, or further explored.  What a waste of time and effort.  How do we capitalize on this obviously untapped source of knowledge? Macro or micro-blogging coupled with open-notebooks or mandatory raw data sharing is probably the best way to establish an area of expertise. 

A little chatter about the relative levels of scientific integrity at different Universities, departments, and lab groups should be expected.  I know this makes some people uncomfortable, but our silence only aids the misdeeds of others.  We should have a greater fear of tarnishing our reputations than fear of not getting funding.  We should have greater pride in publishing sound, reproducible data than pride in a mega-paper in Science, Nature, or Cell.  

I challenge everyone who became a scientist to satisfy curiosity and to advance a particular scientific question to reclaim positions as mentors, investigators, and experts.  Grant funding and academic positions are very slim for early career investigators, but that does not mean we must stop being scientists.  There are other outlets, including using social media to advance a scientific question.  We may not have the means to perform experimentation, but we can read, evaluate, and question the published work of those in our fields.  Ultimately, to blog, tweet, and comment our critiques of the work is the best type of peer review, as it gives us the opportunity to have on-going conversations about the science.  In doing so, we will reveal who among the authors understood the experimentation and experimental question from those who were mere middle-managers, assembling the story.  Our voices are the strongest tools we have to work against the rise in scientific fluff, particularly un-reproducible or highly improbable research. 

Better yet, as outside voices, we can champion good science, even if it is not published in a top-tier journal.   Good science should be publically acknowledged, and social media provides an excellent platform.  Furthermore, social media is a platform that provides all of us the opportunity to establish an expertise in a field of study.  Ultimately, using our voices to share our knowledge is the best way to “reform” science, as we know it.