Category Archives: my experience

Me on Twitter 1 year later

I joined Twitter a little over 1 year ago. Prior to this I was only on Blogger where I used to write my analysis of new research articles, specifically in immunology.

Two reasons why I choose Twitter as my primary social site:

(a) Even though I was blogging about science and writing unique quality content, very few people visited my site and even fewer left their comments. On average, my site had around 10 pageviews per day. It went up slightly to 30 pageviews when I started to regularly post my analysis (2-3 per week). Still in my view I felt it hadn’t attracted enough visitors who were interested in immunology. On Google one finds plenty of advice on how to make a site more visible and usually number 1 advice is to have current, novel and original stuff and even though I was writing original stuff it wasn’t working as I expected. So I thought maybe sending links of my posts via Twitter would increase its visibility (it did as discussed below).

(b) I have a quick mind and it is quite easy for me to come up with quick and short titles (at least I believe such things about me). So I thought Twitter can be a good venue to express my thoughts as “idea bursts”.

So I joined Twitter and began learning how to use it in a way to popularize my immunology blog. However, immediately I encountered a major hurdle on Twitter: it appeared that url links from my blogger posts were not going “public” on Twitter when attached to my tweets but were visible only to my “Followers” and I had basically none at this stage.

I searched Google to find if anyone had reported similar situation. Indeed, few discussion sites mentioned that only Twitter accounts that were popular or had many followers or were long-standing, permitted “Public” url visibility.

Basically it was a kind of catch22 situation for me: on one hand, to gain popularity and followers I needed to attach my blog post url links to my tweets, but such tweets were not visible in Twitterverse. On the other hand, my Twitter account would have not been visible in Twitterverse unless I had some followers.

So, for some time I had no idea how to solve this dilemma. Then few days later I came across an online discussion where it was mentioned that not all url links are “equal” and some url links are more popular for Twitter’s algorithm. Specifically, names of such site as BBC or NYT were mentioned. After reading this I had an “epiphany”: what would happen if I attached to my tweet a prestigious [but random] url alongside of my “non-prestigious” blog post url? Would such prestigious ulr “carry”/”boost” my non-popular url link and make it visible in Twitterverse?

It did. For a long time (2-3 months) I used to attach so called “booster” url to my tweets if I need to share my blog post links. As a “booster” url I used Nature.com home page link and it worked wonderfully.

This is how I made my Twitter account visible to Twitterverse at this stage. Later, few months later, my Twitter account “graduated” from the point of view of Twitter’s algorithm and I was able to share my blog post link autonomously without “booster” url links. I also found that attaching any photo to a tweet had the same “booster” effect.

After being an active Twitter user for more than 1 year, my experience is mostly positive. For me Twitter is one of the best places to go to find News.

However there are few things that still puzzle me about how people use Twitter.

Right now I have around 185 Followers. I myself follow around 25 people, so far. My immunology blog reached ~100 views per day since I joined Twitter. Sometimes it has more.

On Twitter I prefer to follow people who are (a) active users, (b) who write their own blog, (c) who don’t use too much of retweets, (d) tweet and share links about topics that are not yet worldwide “common knowledge”.

I especially try not to follow people who are retweeting too much. It shows that they have nothing unique to say themselves and depend on others to fill the void. I also find very puzzling the situation when people start to follow and then few days later unfollow because I did not follow them back. The fact is that I specifically state in my profile that I am tweeting mostly about immunology. If you are interested in immunology, you can follow for that purpose and not because you have an expectation of follow-follow principle, especially when you don’t tweet about immunology or science related topics.

I also have a strong opinion regarding what to tweet, retweet and even follow. Since Twitter is a public social site, we need to exercise some social oriented judgment. When I tweet or retweet anything, I do this because either I find information positive or I find information negative and of high value enough to share. But this also means that I have my own opinion about my tweets or my retweets. In other words, you need to be able to “defend” your tweet or retweets. I disapprove when people blindly retweet something and when asked to explain they have nothing to say and have no idea or opinion why they are retweeting it. This is not correct, in my view.

Of course, I don’t likes people on Twitter who ignore direct questions. This is especially true for people who have lot of followers and wrongly assume that someone with less followers does not merit their answer. This is a mistake and shows lack of culture.

I am also curious how people who follow 1000s or even 100s of people are managing their twitter feed. Right now, I follow 25 twitter account and my twitter feed has dozen tweets per hour. Imagine following 100s or even more of “active” twitter accounts and getting 100s of tweets per hour. It would be very demanding to navigate it, to sort it out and respond.

posted by David Usharauli

My path to vegetarianism

It is now almost 8 months since I became a vegetarian 🍅 🍆🍴. This transformation did not happen overnight or even in 1 year. In fact, it took me 11 years to convert this idea of being a vegetarian into practice.

From my point of view, there are few criteria (that should be met) that would allow for one’s transition from eating meat 🍗 to mostly plant diet [and some animal-derived diet, such as unfertilized eggs].

1st criterion is a basic interest and feeling for animals. Person must enjoy the presence of animals. Person should be willing to take care of animals (if need be). I don’t mean here just dogs or cats but any small 🐹, farm 🐔 🐖 🐑 🐮 or wild animals 🐗[including birds or fish]. Person must accept that any living animal has the right to exist free of pain. We should accept that we are not a “superior” species, but just a species with specific set of talents, as are other species with different sets of talents.

2nd criterion is any association/relationship with individuals who are vegetarians. I am fortunate to be married to a woman who is a lifelong vegetarian👫. Such an association clearly helps in various ways. Constant information sharing allows familiarization with the concept thus helping to overcome preconceived prejudices and ignorance, if any.

3rd criterion is a desire to learn to cook vegetarian meals 🍝 and feel good about it 👍. Only by experiencing food preparation and cooking, one can truly embrace vegetarianism at the dinner table. Transition to vegetarianism is a commitment  and to carry out such a commitment, one needs some level of constant incentives and enforcement. And there is no better incentive and enforcement than eating food one has spent energy in preparing. I would advise against buying vegetarian food at early stage of vegetarian transition. Such an arrangement is important, especially at the early stage until one’s vegetarian instincts become “fixed”. Also, since vegetarian diet is more nuanced in its flavor [as compared to meat-based food], it is more difficult to achieve consistent, reproducible  results with vegetarian food. By making your own food, one can overcome initial disappointment with vegetarian food bought outside [that could drive “converts” away].

Out of these 3 criteria, #3 was the hardest to achieve for me. I never liked “kitchen work”. I felt it was too burdensome. We used to constantly buy food or eat outside and then constantly complain about its quality. But now, after starting vegetarian home cooking I feel quite comfortable with time spent in kitchen and the quality of my food. I have no craving and yearning for meat as many meat-eaters think vegetarian “converts” should have. Finally, it makes me feel better that I can contribute, even if it just a little, to animal welfare and global warming causes ✌.

posted by David Usharauli

How I stumbled upon selfies back in 2004

Sometimes social culture changes and something becomes acceptable so rapidly that it’s just remarkable. I experienced at least one such event in 2004.

In early 2004, I arrived in the US to begin postdoctoral studies. At that time, I still believed that hard work was necessary and sufficient for success. So I was basically busy working in the lab. I never really developed good social skills, so standard postdoctoral work life in US was “ideal” for me. In our lab, postdocs worked alone on individual projects and we did not have much of a “party” culture.

But there was one problem. I wanted to send my photos to my family back in Georgia, showing my “life” at the workplace or at home. But how could I do it? I did have a cell phone with a silly no-resolution camera and another ordinary 1.2 mega pixel photo camera. But who was going to take my photos? I felt so “embarrassed” to take my own photos since it would have implied that I was alone and that I did not feel comfortable to ask anyone around me to take my photos for me. Basically, the concept of “selfie” was an anti-social concept for me then (and also probably for majority of people in Georgia).

But I needed photos. So, I set my camera to a 10 second timer option and started to make my selfies and sending them to my family via e-mails and hoped that no one on the other side would ask me why I was alone in all these photos. And gratefully no one did. I guess my family was “kind” enough not to make me feel “low”.

However, within a few years the selfie concept became so mainstream that no one would now question a photo where someone is pictured alone. It’s become a norm. Ultimately whether it’s good or not, I am not sure. It does give a person some “freedom” on certain occasions and sometimes I feel “proud” that I inadvertently became a”selfie pioneer” back in 2004 🙂

posted by David Usharauli

Paradox of post-publication citation

Publication records are one of the objective criterion one can use to assess scientist’s value. Of course, every scientist has a dream and desire to publish in top journals such as Nature or Science with impact factors 25 and higher .

However, absolute majority of research articles end up in society-sponsored journals. For example, Journal of Immunology, with impact factor between 3-5, is considered to be a “staple” journal in immunology. Scientist can publish his/her research article in Journal of Immunology and still feel “proud” of it.

Sure, there is enormous difference between Nature and Science and Journal of Immunology. First of all, it has to do with the branding. Both Nature and Science have huge reputation. People naturally assume that articles published there are of higher quality and reliable and indeed, on average it is absolutely true.

However, there is paradox with the regard of post-publication citations or referencing. I have frequently witnessed the fact that when scientists are presenting their work at research seminars or at scientific conferences, they are consistently citing or referring to any earlier studies as if totally equal, i.e. independent whether the referred studies were originally published in Nature, Science or Journal of Immunology (or PNAS).

In other words their confidence in reliability and quality of research results from Nature or Journal of Immunology are equal.

Logically, if you cite article from Journal of Immunology or Nature as if equal, then you accept that these journals publish equivalently valuable research results.

If so, then why are scientists still eager to publish in Nature or Science? I don’t know, that’s why it is a paradox.

posted by David Usharauli

Genuine confidence comes from experience

A lot of books are written about confidence. Confidence is a purely acquired, trained quality, not an inherited one. I remember reading a book about a true eyewitness account of one of the JFK’s speeches wherein during the process of evidently confident public speaking, JFK’s hands were trembling behind the podium. How revealing is that, just think.

If you are in a science field, the most dreaded task is giving presentations or articulating your opinions in front of your esteemed peers. You are continuously thinking: am I voicing something clever or stupid? How is my presentation perceived? Dull or exciting? You seek validation from number of questions asked to gauge the audience engagement level. Even the most seasoned scientists are nervous about it. My former science boss, for example, Polly Matzinger, probably the most brilliant mind in immunology since Niels Jerne, said to get GI tract upsets prior to every presentation, even though she would go on to mesmerize the audience afterwards.

Many science laboratories with 6+ postdoctoral researchers usually run science journal clubs to share recent research development in the field. If you are a PhD student or postdoc and your lab does not have such system, find a way to establish it. Go and ask your supervisor about it. In my opinion, journal clubs are must for young scientists. It is the only venue available where you do not have a personal standing in the work and can discuss and debate research results objectively, thus sharpening your skills as a thinker, not a doer.

I remember my first journal club presentation. I had no idea how to choose a paper for a journal club. I chose the paper that was published 2 years earlier, a clear indication of my lack of understanding how science research operates. I thought I had a confidence but this confidence was clearly based on ignorance rather than experience. I just have chosen the paper because I thought it was telling something “new”. I had no prior experience in lab environment and I did not receive any formal PhD training prior to my postdoctoral research. Honestly, it took me close to 3 years before I started to understand the principles of scientific reasoning relevant for the successful journal clubs.

I even started a blog, called NIHilist’s Immunology where I post my analyses of new research in immunology so young scientists who want to learn the principle of scientific reasoning can go and view my discussions and if it make sense to adopt them for their own purpose. I wish I had opportunity when I was doing my first steps in science.

A true measure of confidence comes when you are convinced and are able to convince others. Such feedback reinforcement happens only with the experience and multiple efforts, not naturally or out of blue.

posted by David Usharauli

Two myths I used to believe

Myth # 1. All scientists are brilliant or even clever or competent

If you grow up in a developing country where only way to “experience” science is through old books and occasional science journals published in English, you could easily start to imagine that people with a pipette in their hands who are working in the bio-hoods, with the richly stocked lab shelves in the background, are all professionals, basically geniuses in their field, especially if they are working in countries like USA (since you constantly hear that science awards, like Nobel Prize, are given to scientists for discoveries carried out in the USA).

You read or watch on TV the young people in the lab coats discussing how they love and enjoy doing science and how they want to make the difference. You actually believe that it is true until….

Until you end up as a postdoc yourself in a science lab in one of the most prestigious academic centers. Suddenly you realize you have no idea why some of the members of the lab have chosen to be here in the first place. They do not participate in science discussions, journal clubs, seminars or ask any questions. You wonder if they are capable of scientific reasoning and rationalization. Maybe not. They are just sitting there and after 5:00 pm leave for home. Nothing related to science excites them. And without excitement and true interest in experimental results, it is absolutely impossible for someone to do a 12 hour workday. Why are they occupying positions that could go to persons who at least are eager and excited about science?

I do not believe anymore that if someone is working in a science lab, even in the best labs, that they are smart, bright or even clever or competent. I do not believe in CV/Resumes either. I do not believe in personal interviews because it never works.

I only believe in how a person describes what he/she has done. In my experience people with a genuine interest in their science work have a wider vocabulary describing their own work and frequently use synonyms to easily adapt to the level of their audience, in contrast to people who are in science from reasons other than science itself.

Myth # 2. Private sector is more efficient than Government

I remember when I was working in the academic environment (that was a part of federal government), we had one scientist who joined the lab from the industry (one of the biotech company). He used to mention that he become disillusioned about the biotech industry since it allowed too much wastefulness. He was telling us how many of the company’s employees were not doing anything all day long, spending all of their time in the tea room in idle conversation with colleagues. Honestly, I did not believe him then. I was asking how come a private company was tolerating such behavior, did the company not care about its employees’ productivity? Why would the company keep such people? He would just laugh at me and tell that the company knew about these people but was doing nothing.

Now I know that he was absolutely correct. There is no difference between private, governmental or academic efficiency in science. Every lab has people who do nothing and this is tolerated. If you ask me why it is the case, I have no idea. I just know that it is true. It appears that majority of people prefer to pretend rather than have a constructive confrontation with their bosses, employees or colleagues. Many times, employers compensate the lack of productivity from such “do nothing” employees by dumping extra burden on other employees or hiring more people. Of course, in the long run, this will not work. No wonder that the company the guy came from to our lab does not exist anymore.

posted by David Usharauli

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

Fake it to Make it

I love science. I love to debate.

When I first started my science career in immunology in early 2004 at NIAID, my boss, Polly Matzinger said to me something like this “David, pretend that everything is OK”. I just smiled at her. I had no idea what she meant. I never asked her.

After more ten (10) years in science, I may now know the answer.

In this blog, niaIDEAlist’s Report, I am going to write about my experience in science, my opinions about current scientific research and data, as well as about notable science news.

posted by David Usharauli