What do I need to change as an individual?

I can tell that I need to work on fewer-projects in more depth.

I am not sure if additional training is necessary to accomplish this, but that is the focus of my post on "What are the expectations for Individuals with an MS in Bioinformatics versus a PhD in Genomics?"?

Technique-Wise, these are the sort of things that I think I could be comfortable with:

• I am very comfortable coding in R / Python / Perl
• If I needed to get back into the lab, I could previously do a PCR and maintain a cell line
• At least previously, I had some difficulties being able to preform my own microarray experiments
• However, to be honest, I think the best fit for me would be to keep doing mostly or entirely computational work (as a Bioinformatics Specialist, Bioinformatician, etc.).
• I think I likely need to reduce the number of new patient samples that I encounter, but I am comfortable working with my own genomics data and I think I have had useful contributions using re-analysis of data deposited by other labs.
• For example, I thought this was a relatively successful story of my feedback on a pre-print being helpful
• I also have notes on my human genomics results here
• I also have on-going analysis of public cell line perturbations to demonstrate method limits for RNA-Seq analysis

Research-Wise, there are topics that I am interested in and/or have some prior experience with:

• Investigate whether a relatively simple strategy is more robust than a more complicated strategy (for example, try to identify problems with over-fitting)
• Probably a good idea to either limit the number of samples I work on at a given time and/or make sure that I have enough time for several rounds of analysis / discussion of the same dataset (which is always good for critical assessment of results)
• Perhaps place more focus on non-human genomics (and I started out doing evolutionary genomics research)?
• I have some previous virology experience, so perhaps I could study the genetics / genomics of viruses that currently infect other animals (but have not yet evolved the ability to infect people)?  This could even be part of DNA-Seq or RNA-Seq for the host.
• While I haven't done any such research from a professional standpoint, I have been comparing genomics results for my cat Bastu, and I hope to have a blog post summarizing that soon.
• If I can get agreement about some things, perhaps there is some value in shared support guidelines?
• I also truly like the idea of supporting labs with less popular research topics and/or smaller budgets (which may have a relatively greater need for shared support)
• Essentially, I am emphasizing training (indirect analysis support) and limits on projects for shared staff
• However, I don't particularly like telling other people what to do (the degree discussion is really more about having the right amount of autonomy and peer respect to perform my own analysis), even though I realize that we sometimes have obligations to society to do things that we may not find enjoyable.
• So, I think finding a solution for myself what is currently most important, but I think I have some experiences that may be useful to others.
• In general, if I were to assist with training support, I think I may be able to help with common public datasets, but I think there may need to be a rule that I couldn't help with providing analysis for a new dataset (unless a greater commitment to the project is made, where the limits on shared support would then be important)
• While helping me stay up-to-date and refreshed on details, perhaps providing local guidance (face-to-face) for a subset of content from selected on-line courses (like Coursera) may be an appropriate way for me to help, but it would be crucial that I not complete exercises for any students (which would violate the honor code, requiring students to complete their own work and demonstrate independent competence).  For example, if I did this before they started the course, perhaps I could then recommend where to learn more and get certification (as well as setting realistic expectations on the likelihood of passing the course).
• I would need a lot of practice, but outreach / optional education for the general public (such as a book club discussion that I led) can be rewarding 
• While I am less certain about my role in a professional standpoint, you can see my "speculative opinion" posts about some things that I think could be interesting

Personality-Wise, these are what I believe are my strengths and weaknesses:

• I have to be fairly independent for my current job, but I do provide a supportive role (where biological / clinical idea usually comes from PI)
• While the difference between 1 day and 2 weeks turnaround time would be an order of magnitude (for each iteration of analysis/discussion), I have received the good suggestion that I should wait at least an extra day before returning each round of results (to see if I can catch more errors by reviewing the results again the next day).
• I like the idea of helping provide a "public good," so I think I would prefer to continue working at non-profits
• Continue becoming better at more mindful when I have a prior assumption (which may or may not be true) and I may not sufficiently understand other perspectives.
• However, I appreciate those who value the need to take time to be objective and fair
• While I believe it is important to continue to make future progress, I have some concerns about responsibilities what require excellent communication (and would frequently involve relatively short interactions with individuals where I may not have the chance to correct myself)
• For example, part of the reason I work on the computer is that I bugs will stay corrected in the code (once I find them).
• In contrast, if you knew that there was an experimental protocol that required X steps and I was highly like to mess up at least 1/X steps, then that is sufficient for me to not be able to get a protocol to work (for example, I think this is why I had previous difficulty with performing my own microarray experiment).
• I think I may need to better recognize what I can fix (for myself), versus a concern about the actions of others (which may be solvable if properly communicated, or may be harder to resolve without common agreement)
• For example, there may be some room for improvement in terms of communicating myself in sensitive situations (such as disagreeing with a policy and/or a superior).  However, this is something that I am actively working on.
• Most of my family lives on the east coast of the United States (and I currently live in the west coast, in California).  As we get older, this may be something worth taking into consideration.

Change Log:

11/14/2019 - public post
11/15/2019 - public post
11/21/2019 - fix typos + add waiting a little longer to return results
1/7/2020 - add link for on-line course notes
4/30/2020 - update cat link for blog post versus GitHub

10/7/2020 - add note about computational emphasis

Democratizing Scientific Research

Today, I came across a very interesting blog post by Christina Agapakis (via a GenomeWeb article). This post focuses on efforts to "democratize scientific research.” For the most part, the article discusses a post on another blog and the efforts by a group called DIYbio, which stands for “do-it-yourself biology.” She also emphasizes the need to make formal changes in the way institutions conduct scientific research, and I particularly liked some of her suggestions for improvement:

"What if there were more opportunities for high-paying technical jobs in science for people without advanced degrees? What if there were more biotech vocational programs to learn the skills you would need to work in these jobs? What if it were easier and cheaper for groups of scientists and engineers everywhere to turn ideas and hypotheses into technology and knowledge? What if there were real ways for knowledge to become power for that kid living in South Central LA?"

In regard to the issues brought up directly in her post, I think Christina is a little too harsh on DIYbio. I do agree that the organization's efforts are probably not sufficient to help intelligent individuals “[living] in a community plagued by violence and poverty” reach their full potential, and it is probably reasonable to assume that most of the participants are “white, middle class, and primarily male.” However, I think DIYbio positively contributes to the production of new ideas and products that would not otherwise be feasible. To be fair, Christina does say that DIYbio has helped promote “scientific participation and enthusiasm” and could be a useful model for developing programs for underprivileged individuals, but her opinions about DIYbio are mostly negative. She also claims that DIYbio perpetuates “the myth of the Victorian Gentleman Scientist,” who “[pursues] a 'pure' science not because of an interest in money and free of any state control but because of a deep curiosity with the power of the natural world.” I certainly agree that the Gentleman Scientist is an undesirable model for scientists that is unlikely to produce practical research and does not provide a reasonable venue for research for anyone without prior financial security. However, I honestly didn’t get that vibe from reading over the DIYbio website, although I should admit that my knowledge is limited because I hadn't heard of DIYbio before today.

In general, I am a big supporter of anything that removes politics from scientific research because I think personal and professional bias compromises the objective judgment that is so critical to good science. I think this requires fair assessment of scientific progress that emphasizes the impact of a specific result (and the effectiveness of the methods to achieve that result) and limits the role of authority as much as possible. For example, I think it would help if the peer-review process for scientific journals was a double blind process. Currently, the reviewers know the author names and institutional affiliations, but the authors do not usually know the identity of their reviewers. I know some exceptions to the latter case but not the former case (please correct my ignorance if you know of some examples). Of course, this would not be a perfect solution. Some reviewers may be able to recognize the work done by established scientists due to biological systems and methods employed in previous publications, and well-connected scientists will probably be friends with some reviewers and can give them a heads up that they have submitted an article for peer review. This is slightly tangential to the topic of DIYbio, but my ideas are relevant to the broad concept of "democratizing” scientific research by formal changes in institutional policies.

There is also a very interesting (and long) response to Christina’s post that does a good job discussing how “[it] is entirely possible to develop high level expertise outside of the formal system” and also noting that certain avenues of research (like “programming and electronics’) are much more feasible for the everyday scientist than research in biology or chemistry. Materials for biological research can be harder to acquire and more prone to regulation. For certain types of biological research, such as biomedical research, it is also relatively difficult to bring therapeutics to the market without a formal research position, in part due to the need to run clinical trails and gain FDA approval. The author of the comment specifically mentions over-regulation. I agree that some regulation is definitely unnecessary and hinders scientific progress (for example, I personally think the FDA should only limit the use of drugs due to toxicity without also considering effectiveness, and instead allow physicians to decide on the own if the treatment is effective and superior to alternative methods), but I do think that there is some rationale for not allowing everyone access to stuff like anthrax.

In short, I think informal biology research is a good thing that can benefit society (as acknowledged in Christina’s concluding paragraph), and I also think it would also benefit society to employ formal institutional changes to encourage individuals from varied backgrounds to conduct scientific research.