Monthly Archives: November, 2014

Serendipity in Science: Personal Observation

For a scientist reading review articles about his/her research topics is a quite boring task, since review articles usually contain summaries of what are already known. The reviews have no real scientific purpose except as a source of citations and cool looking figures.

There is one reason I found review articles to be very useful to read. Frequently, the authors of the review puts in the review unpublished data or discusses the results of experiment as an “unpublished observation” or a “personal communication”. These are data not available elsewhere. These can be so-called “negative data” that current publishing policies do not favor, though I think there is no such thing as negative data in science, if experiments were done correctly, of course.

Many times negative data can be a foundation for the scientific breakthrough. Here is one example from my personal experience.

Few years ago, I was working on one project related to in vitro Foxp3 induction in naive mouse T cells. At that time, Foxp3+ T cells were very popular. Almost every second paper in immunology was somehow related to Foxp3+ T regs. For me, the interest in Tregs has to do with the fact that current theoretical frameworks on how immune system operates can not tolerate the presence of negative regulatory populations. It is a strange idea but true. Neither self-nonself nor PAMP/DAMP based immune system requires Tregs to operate, theoretically speaking, of course.

My boss then, Polly, had an idea that Tregs are T cell subset driving different type (or class) of immune response rather that inhibiting anything. Since scientists did not measure all type of responses, they saw a down-regulation of a particular known immune type response as an evidence of inhibition rather than considering that system was shifted to unknown type (cytokine) not measured in the assay (for example, IgA or IL-???).

Unlike many laboratories working on Foxp3 induction using anti-CD3/anti-CD28 antibodies, I decided to use more physiological approach of Foxp3+ T cell induction using peptide pulsed DCs and naive peptide-specific CD4 T cells. Experiments went as expected that we were able to generate peptide-specific Foxp3+ CD4 T cells. During this same time period, new T cell subset, called Th17, has been discovered and characterized. It turned out that while Foxp3 induction required TGF-beta, one could generate Th17 simply by adding IL-6 in addition to TGF-beta (TGF-beta + IL-6). It was already shown by then that presence of IL-6 drove Th17 induction and while inhibiting Foxp3+ induction.

Since I was doing an assay with Foxp3+ T cells, I have decided, for no apparent reason, to add IL-6 in my assay. I was expected to see a decrease in Foxp3 expression and increase IL-17. Strangely, when I added IL-6 to Foxp3 induction milieu (TGF-beta, peptide, DCs, CD4 T cells) I noticed that percentage of Foxp3+ T cells went up rather than go down. Th17 induction was expected. I repeated this assay multiple times and over and over I saw that IL-6 was promoting rather than inhibiting Foxp3 induction in my hands.

Now, these results went completely opposite to what everyone else were reporting in the literature. I asked my fellow postdoc to repeat the same experiments to make sure that I was not doing something strange with my culture. Again, we saw the same: IL-6 promoted Foxp3+ T cell induction.

Using IL-4 or IFN-gamma KO mice on the same background, we observed that IL-6 effect on Foxp3 induction was abolished on IFN-gamma KO but not on IL-4KO background. Indeed, using anti-IFN-gamma antibodies with wild-type CD4 T cell assay confirmed that when IFN-gamma was blocked IL-6 lost its ability to increase Foxp3 expression. Parallel experiments showed that exogenous IFN-gamma inhibited Foxp3 expression and that IL-6 inhibited IFN-gamma expression, as expected from published literature.

In the end, after 5 months of continues work, we come up of new hypothesis that could explain our observation. Our finding suggested that IL-6 promoted Foxp3 expression by suppressing IFN-gamma expression in activated peptide-specific CD4 T cells. We reasoned that other laboratories failed to see the same effect since they were using anti-CD3/anti-CD28 activation mode rather more physiological, peptide activation mode. Indeed, in our hand too, IL-6 inhibited Foxp3 expression when anti-CD3/anti-CD28 antibodies were used to activate CD4 T cells.

So, we were very confident that we found something worthy of publication in one of prestigious journals.

Then, suddenly, we started to receive reports that mice from our mouse colony started to die in higher numbers than normally observed. People had no clue what was going on. In the end, after thorough investigation that took few months, it was revealed that new type, not yet described Streptococcus was causing mice death (one of clinical signs was a cardiomyopathy). The mouse colony was shut down, newly re-derived and repopulated.

As you may have already suspected, when we repeated our experiments with IL-6 on T cells from “clean” mice, we saw that now IL-6 was inhibiting Foxp3 expression rather than promoting it and this effect was seen both times when peptide or anti-CD3/anti-CD28 were used.

These are the type of experiences that make someone like me to appreciate why we do science. As to new Streptococcus we discovered, I did not have a chance to study it but I hope someone will be doing his/her PhD by studying this unusual bacteria and its unusual effects on immune system.

posted by David Usharauli

double-blind peer-review is a way to go for basic and pre-clinical studies

Today the most peer-review process in the prestigious journals is a single-blind, meaning that the reviewers know who the author(s) of the manuscript is(are) but not vice versa. Rarely, reviewers are allowed to disclose their own identities to the manuscripts’ authors, but in my experience and opinion, since reviewing is a process that require some degree of criticism and know one would prefer to be criticized by their own peers, an absolute majority of reviewers would not voluntarily disclose their own identity to the authors. So, double-open review process is less likely to be a viable option.

What is left is either currently operating single-blind or my favorite double-blind peer-review process. Current review process has two deficiencies: 1. not all editorially approved reviewers are of the same caliber, and 2. reviewers favor established names.

Double-blind evaluation would eliminate name bias favoritism.

Raising the quality of the reviewers, of course, would require conscious editorial decision. One solution would be for journal editors to send out potential reviewers names to researchers in the field and ask them to nominate the names. The names of the researchers selected to be reviewers should be published and be available for view. And I think it would helpful if the number of reviewers per submitted manuscript would be increased from current 3 to 5.

Many times I hear that double-blind peer review is impossible since the reviewer would be able to identify the manuscripts authors. Not really, in my view. The initial manuscripts will be submitted in two different formats, first regular one for the editor only and second one specific for the reviewers with no names, affiliations, acknowledgments, grant support information and statements likes “we”, “we showed before”, “as discussed in our previous” and so on. It is quite easy to accomplish. Now days scientific reagents, including commercial knockout mice strains, become so widely available that any research lab with sufficient resource can do a research indistinguishable from reagents point of view. The reviewers would not be able to identify the authors solely based on reagents and only criteria that would be left to examine will be the quality of the research manuscript itself.

Now, of course, established scientists would not like a double-blind review process since they will be the major subset that will be affected by elimination of bias and favoritism. However, double-blind review process would improve young scientists standing and would level the field to compete on the basis of objectivity and quality.

I do not even understand why there is still any discussion to implement or not double-blind review process for the scientific manuscripts. We are already using it in our clinical trials and no regulatory agency would approve any new drugs or biologicals without the results from double-blind trial. It is already overdue to introduce the similar level of scrutiny for basic and pre-clinical studies.

posted by David Usharauli

Online access to federally funded research publications must be free of charge from day 1

An absolute majority of the published scientific research are funded by tax payers’ money through the federal grants from NIH or NSF. Every scientist dreams to publish his/her work in the prestigious journals. Publication is the simplest way for a scientist to showcase the quality of his/her work.

The scientists, unlike social media followers, do not really care how many people will see their publication as long as it is seen by their colleague-scientists and could be submitted to the granting agencies. Furthermore, the absolute majority of the scientists would be OK if their research is freely avalable from the day 1 of its publication.

So, why are the journals still charging for online access to the new articles? some 30-35 years ago, when majority of scientific research were conducted at the University campuses by academic scientists, such fee for access was acceptable since Universities were able to afford multiple annual subscriptions to subject-matter journals.

However, these days, the small biotech companies conduct a big chuck of scientific research but still may lack additional funds to have annual subscriptions to many important subject-matter journals. Many times, when a new treatment fails in clinical trials, the source for a failure can be traced back to the lack of access to scientific literature at the earlier stages of treatment development.

Now days, there is 12 months delay before federally funded publication becomes open access. Can you believe that before 2007 legislation that made 12 months requirement the law, there was no such requirement at all.

But even 12 months is too long. Today research become accelerated due to improvement in computer technologies and the large data mining machinery and software. I just read news that beginning from Jan 1, 2017, Bill and Melinda Gates Foundation will require their grantees to make their research openly available immediately upon publication. Great decision, but I am still puzzled why not make it effective from Jan 1, 2015.

Journals should generate their revenue through an advertisement on their pages or through minimal submission fees. Subscription based revenue system is not viable in long run. Now days many science organizations stopped purchasing monthly hard copies of journals, including Nature and Science, and switched to online-only subscriptions to cut the cost. Eventually, the scientists will be asked to publish in a cheaper open access journals.

In the end, the prestige of any journal comes from the publication of high quality papers. Migration of high quality article submissions from today’s top journals to open access journals will raise the latter’s prestige and will benefit everyone else.

posted by David Usharauli

The best scientific journals in Immunology

As a research scientist with the focus on immunology I constantly keep myself updated with a novel developments in a basic and translational immunology. Each scientific journal usually posts new articles on specific days either (a) as an “ahead of publication”, “advance online publication (AOP)”, or (b) as a current issues.

For example, journals from the Nature Publishing Group posts new articles online usually on Sundays (more recently on Mondays) and current issues on Wednesdays. Science magazine or Cell press, on the other hand, posts new articles on Thursdays, while Journal of Experimental Medicine (JEM) and Journal of Clinical Investigation (JCI) post new articles on Mondays. Finally, Journal of Immunology, the most basic journal for immunology, posts new articles trice a week: Mondays, Wednesdays, Fridays.

While the number of online journals publishing immunology research articles went up in recent years, the absolute majority of them do not have a sufficient quality and can be easily ignored. I have no idea what type of model those new online journals follow to generate continuing stream of submissions to populate their issues. It seems that they are targeting researchers from developing countries with the emerging economies. In my opinion, if a research lab cannot generate data sufficient to publish in the basic immunology-focused journals (like, Journal of Immunology, European Journal of Immunology, International Immunology, etc), then for the sake of animal welfare, it is the best not to conduct any experiments in vivo but rather focus on in vitro cell signaling experiments.

With the respect to a high quality research, here is my list of the best scientific journals in Immunology for 2014:

1. Immunity 2. Nature 3. Science 4. Cell 5. Nature Immunology 6. Nature Medicine 7. Journal of Experimental Medicine 8. Journal of Immunology

In addition, I occasionally listen to online Seminars focused on Immunology that are archived at the Center for Cancer Research (CCR). Here is the link to watch and listen to new seminars in immunology.

posted by David Usharauli

How to hire that works

Just read a very good blog post from Science careers about some of the limitations of current hiring practices. The author correctly points out that too much emphasis on job applicant’s non-job related skills may lead to unintentional exclusion of highly talented individuals from hiring pool.

I totally agree. First of all, despite the multiple criteria employers use to screen the job candidates, only reliable tests that could measure anything with reasonable objectivity are the actual work accomplishments (in prior job positions) or the actual grades received (if evaluating college graduates). Beyond this, everything is like a toss of a coin.

When the employer starts to focus on the social or behavior characteristic of the applicants at the expense of their job skills, one inevitably ends up with workers who spend a considerable amount of time in learning or improving their “office politics” skills rather than learning or advancing the project’s needs. In general, in my view, the conformity to the preexisting work culture becomes the dominant work culture.

This culture of conformity, however, comes at the cost of the quality. People with the talent for any science field are charismatic by nature. It means that they spend a lot of time in sharpening their science skills. In most cases, they are not as polished in their inter-personal skills as their more social colleagues are. Nature rarely produces people with advanced skills in both categories. A cursory overview of biographies of the famous scientists proves this point easily (just see an upcoming movie about enigma code-breaker Alan Turing). The absolute majority of the famous scientists could be characterized as “difficult” employees in a today’s terminology.

So, how to make the best informed decision regarding a science job applicant? I have the following suggestion: the “hard” skills drive science enterprise forward and the “soft” skills maintain the status quo. So, if an employer has any particular scientific or technological issue to solve or new protocol to develop in order to move forward, then one needs to hire an individual with the best record of using the specific “hard” scientific skills. However, if one needs to just continue with the existing protocols, then preference goes to individuals with the “soft” skills.

posted by David Usharauli

Do we really train more scientists than we really need?

I want to return to this topic once more and share my opinion.

Today I read an article with the title “Postdocs speak up” in the journal Science where the authors discuss a recent meeting focused on opportunities for young scientists. The basic plot is well-known: we train far more scientists than the system (lets say the biomedical system) can absorb.

In general, I would like to point out that the title “Postdocs speak up” is quite to the point. There is definitely a perception that scientists, especially young scientists are vocal people. However, this is quite inaccurate. Science is a very conservative and hierarchical system. Postdocs who “speak up” are rare. Individualism is neither encouraged nor perceived as a positive trait. Basically, people on lower echelons (grad students, Postdocs) follow directives from people on higher echelons (Principal Investigators, etc). This is the standard. Very few PIs allow truly independent thinking. This is the evolutionary stable strategy. Postdocs in biomedical field cannot just write some code in computer and change the world. Research in biomedical science costs money and since PIs bring money, they dictate who can “speak up”.

Now, regarding the number of young scientists, I personally think that training of more scientists is an evolutionary stable strategy and we would need even more of them in the future.

Why is that? I think this trend has to do with the self-imposed reduction of productivity per scientist. We think that scientists (both in academia and industry) work 12h-16h daily. This was true in the past when access to higher education was restricted, and only a very brilliant or very dedicated person was able to complete the training necessary to become a scientist.

However, in the past 20 years, access to higher education became more affordable, not because it costs less but mainly because qualification criteria became less stringent. This change allowed people with ordinary skills, but no zeal, to receive science degrees.

Ordinary people, however, view science as ordinary work, not a vocation. They spend less time in the lab. Where before Postdocs rarely took vacation time, now people take any opportunity to spend time outside the lab. It may be called work-life balance now, but that is just a polite way of saying “I only spend minimally required time in the lab”. However, this leads to productivity decrease. The only practical solution to this dilemma is to hire more people with similar skills in order to maintain the same output with less work per person. This scenario applies equally to both academia and industry.

I predict that in the future, scientists with ordinary skills will work less and less, creating the need to hire more and more people with the similar skills.

So, we actually do need more people with PhD in biomedical sciences. Since it’s far more difficult to find people with zeal, better to train more people with less dedication.

posted by David Usharauli