Entanglement of microscope and the human psych

The memory of water! The journalists were mesmerized by Benveniste's work published in Nature (1988). We told you ! Homeopaths screamed. It was basophil degranulation  experiment, wherein basophils were challenged with  allergens or ant-IgE, Upon activation, allergen - IgE  (IgE-antiIGE) complex  binds to basophil cell membrane eliciting exocytosis of histamines, proteases, chemiokines etc in the medium, which otherwise form granules in basophils. Relative presence of granules before and after the challenge can then be measured using Toluidine dye.  What was provoking in the Benvensite's study was that they performed serial dilution of ant-IgE solution upto 0.00000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000001 times to challenge basophils and and could still observe the degranulation. Following is the figure from the article:

It is clear that with that astronomical dilution, there will not be any allergen/anti-IgE in the solution. What is left is some kind of memory of anti-IgE (in the form of structure of water?), which is sufficient to elicit response. Sounds silly! It indeed was. Accompanied by the fraud-buster and the magician James Randi, the editor of Nature journal Maddox closely monitored the repetition of the experiment and found no evidence for the claims. Was it fraud? Two of the students in the lab were funded by a Homoepathy drug company. Or, was it an error of human psych?

"Seeing is believing" they say. True, but not when you  see what you want to see. I came across this incidence during my PhD days, when I was indulged into lot of in-situ experiments that involved confocal microscopy. The above study also involved microscopic counting of stained cells. What happens in a typical such experiment, we have a control sample (say uninduced B-cells or induced with water not treated by ant-IGE previously) and a test sample (induced sample) and then count the stained cells under the microscope. The problem is that we are counting cells manually through our eyes, which are not independent from our brain. Given that we know which sample is control and which is test, our brain is predisposed with certain bias (probably unintentional). This bias can interfere with the eye-brain coordination and we tend to see what we want to see. In the above experiment, for example, a student will end up counting more of unstained cells in the test samples as compared to control sample, until the experiment is done in a blind folded manner and performed by more than one student. I am not sure if that is being practiced in most of the labs, even today. Moreover, the number of cells to be counted  needs to be sufficiently large, atleast 300 or so. I have seen myself that the statistics often changed when I counted 100 cells and then added 100 more.  While this variation dropped after counting 250-300 cells. Having  said that, I often spot articles having cell-count range 20-30 cells! Wondered what limits the authors to stop counting at 20-30? Is it their laziness or does the microscope break? If that sounds crazy than I have a strong reason to argue that it is possibly the fear of losing the significance of their hypothesis (indeed, their belief). In fact, it also hints that they might have been counting the selected cells that please them. These authors also do not provide the snap-shot of colony or cluster of cells (It is possible at relatively broader resolution) and rather only provide single cells of their choice.  It goes without saying the images need to be shown from all three  X, Y and Z projections to ensure that the signal is observed from appropriate location inside the cell. Further, often the slides are prepared in a manner that squeezes the cell to omelette-like shape, which is not the native form of cells. This can potentially impact the interpretation of images, for example, of spatial co-localization studies. 

I think its time for journals to frame proper guidelines to be followed for the in-situ experiments. 

Ref: http://www.nature.com/nature/journal/v333/n6176/pdf/333816a0.pdf

On bullshit of reference letters

It was an exciting time and I was applying for faculty positions in India. There came a nonsense from NCBS, india's top research institution. They asked for not two, not three, a total of eight reference letters ! Here is the text on their web page (https://www.ncbs.res.in/faculty_positions) as of today:

"You will also have to provide the names and addresses (including email) of eight referees who can comment on your application and on your abilities."

(And guess what, they also ask for  2-3 reference letters for students who wants to attend a conference  organized by NCBS)

At first it looked strange to me. Then for a while I thought may be the top institutions may need so.  I started contacting my peers around. I easily managed assurance from  4-5 of my peers, four of them Indian. Then I contacted a senior professor in my then university of Uppsala. He said he will write for me, but  also expressed his surprise on why I am asking him despite having only casual link with him. On my elaboration of the issue, he laughed and said "they are crazy, dont even go to such people".  That spontaneous  reaction from  a successful scientist convinced me that it indeed is bullshit to ask eight reference letters. I never applied to NCBS, a fact that can be verified from NCBS too.

Why am I so hostile to that requirement? First of all, I never liked the concept to reference letter as prerequisite for an application to be screened or processed at first place. Well, what if someone's PhD or post-doc or both PIs turned out be assholes and don't bother about these automated request flooding in their inbox? Secondly, is there any "bad" reference letter at all? They are always good, isn't it? Why to have such a formality then? Thirdly, should not good profile be speaking itself about the candidate? The Irony is that most institutions (even in the west) ask for such requirement through their automated online application system. ONly when all the reference letters reach them, they consider the application complete. I am not against the reference letters, but considering these letters as one of criteria  for the completion of the application is nonsense. A candidate with good record deserves to be interviewed with or without reference letters at first place. Then comes the role of reference letters to 'only ensure' the suitability of the candidate for the  position. Remember,  I did not invoke a very subjective matter of  judgements through reference letters. How do someone judge us from reference letters given that most of them are generally good? Does the profile of peer matter? How do they read between the lines? How to they insulate the professional comment made from personal opinions? Without invoking these non-trivial issues, the requirement of such letters to complete the application itself looks ridiculous. And then you think asking for eight letters will make you special. Yes, it does but not in scientific excellence but in advertising your arrogance in a stupid form.

Free-riding in Science

Free-riders are the individuals who intend to enjoy the success on others’ credits.  Often,scientific community suffers from ethical issues, which might be a direct or indirect consequence of free-riding. I express different scenarios of free-riding and discuss how it could be alarmingly dangerous for scientific community.

Nowhere do we see the extent of intellectual freedom that is entertained in scientific research. This positively feeds the science by attracting innovative brains willing to take up challenges. Intellectual discussions leading to ideation followed up by  co-operation and flawless execution serve as a central dogma in scientific operations. However, real world is never perfect and rather operates in noisy manner. Certain individuals have tendency to exploit the system for their self-interest by their clever but rather apparent tricks. We term these individuals as free riders and discuss how these could create panic atmosphere locally in the individual lab and sometimes globally spread across the whole department or unit of a scientific institution.

When the student is free-rider

This, probably, is the most common scenario among the three. Students interested in job and salary rather than science are common in scientific community. In the lack of scientific interest and enthusiasm, these students are merely free-riders of their colleagues and PI.  Sliding in the authorships with the insignificant or sometimes no contribution is not something unheard. A soft and over-generous PI could also escalate such free-riding. Do such freee riders suffer? I personally know the sufficient number of examples, where they did not. Once a free-rider is able to manage a decent CV and land him/herself to a faculty position, where is the suffering? A free-riding student transform into a free-riding PI and virtue continues. 

When the PI is free-rider

It might sound weird to some because of the fact that it is difficult to make out whether it is free-riding or the smartness of the PI. While the same might sound quite familiar to others who came across such individuals repeatedly.  A PI can be termed as free-rider when it thrives inappropriately onto students and collaborators  rather than on own ideas and efforts.  However, being a commander of the unit, PI could often escape or go unnoticed by many.  Moreover, a PI could cover up the free-riding by the weight of publications and other scientific accomplishments which themselves are inappropriately credited.  Though it is hard to distinguish the trade-mark features in the every-day behavior of PI being free-rider, it becomes apparent if followed closely for a reasonable duration.  Number of publications per year speaks a lot. Its not totally unheard of  a PI having 30-40 publications per year on average, which suggest that he/she submits paper on weekly basis and that too in their leisure time because they are part of important national/international committees, editors of journals, directors of institutes or grant agencies.  Several other traits could  in fact differ person to person and sometimes  strikingly contrasts to each other.  For example, such a PI could be highly communicative to certain ‘useful’ students to extract the ideas and getting the things done and later on not crediting the student appropriately for the same. Credit then either is taken by the PI itself or by a beloved student of PI if nepotism operates. In contrast, the PI could also be a highly non-communicative; a sign of incompetence; leaves the students on their own and eventually takes the credit as corresponding author of the work initiated, executed and written solely by student (s). Such student-PI relationship is often a suffering for the student and sometimes for the PI when the student turns out to be a bold and fearless ‘punisher’. A PI may also feed on some of collaborators and surprisingly on completely unknown people. Collaborators might sense the free-riding and may not collaborate with the these free-riders for long.  Such PIs, thus, rotate their collaborators and generally do not have long term collaborators.  Interestingly, free-riding PIs might also demand authorships on the articles they review by personally contacting the authors. Though, there is no estimate for such scientific misconducts due to lack of  public declarations, based on surveys it is often seen that a significant percentage of scientists do not mind crediting non-contributing authors(Roger Croll, The Noncontributing Author: An Issue of Credit and Responsibility, Perspectives in Biology and Medicine, 27, 3. 1984). Ever-increasing trend of more authors per article also helps free-riding PIs to slide in easily. Moreover, having the power to hire and fire, it is unlikely that a PI gets punished by the student. 

When the PI and the student both are free-riders

Though rare, the most dangerous scenario is when PI and student(s) both are free-riders. The situation might get panic and tense due to regular bashing and severe lack of productivity. I have seen scenario, where students trapped in such situations, move to other labs after wasting a couple of years. Students have such options of volatility, PIs don't and are left with no options than waiting for a good student.              

Uncontrolled free-riding

In the age of big data collaboratory science, if a PI is part of a consortium, his/her students easily make to articles coming out of consoritum with or without any contribution.  PIs do not mind including students without significant contribution because they need to shape their students' career too. There is no mechanism to assess the constribution of each author as of now. As more and more such consortia projects stem in future, such free-riding will not be under any control unless a robust mechanism is introduced. 

Rational irrrationality

The last time I had good taste of rationally correct arguments in general public was at Roorki railway station on way back to Chandigarh from my home town Lucknow. I got down to the station to  stretch my body and look around the course of life. Suddenly I heard an old man  dressed like a 'Sadhu' (saint) wearing saffron clothes preaching an innocent guy. From the outlook, I was convinced that he must have been  infiltrating some religious nonsense into a budding brain. Out of curiosity, I moved nearer to the site to a distance just enough to hear the conversation. The first few words I heard were 'dharam' (religion), 'pooja' (worship) and 'daan' (donation), further solidifying my doubts. Hold on, before jumping on to the conclusion, I quickly  learned that it wasn't routine religious preaching, but a fair criticism of the same. He was criticizing how religion (he was peculiar about Hindu, but that's irrelevant here) harasses innocent poor people. I have had heard of religion being divisive,  preaches to compromise, promotes helplessness and slavery, stagnate the rational thinking and blah blah blah. Here was a different point. Being a Sadhu, he knew the physical, emotional, psychological and financial expenditure to fulfill the rituals of religion. He cited the examples of rituals followed on the occasions of marriages, or someone's death in very detail, followed by his interpretation on how this is affecting the society, well for the bad. Delivered in his very desi accent, the whole conversation appeared very effective. Loud horn from the train engine and I was back to my seat.

I miserably fail to understand the major limitations in being rational. Is it the childhood training? Is it society and religion? Is it education? This sadhu had defied all. He dint look educated and appeared indulged into religious rituals. Yet, he appeared rational. May be he was an outlier, let's buy that. However, what explains the rational poverty, if at all,  in the society I live in, which is educated at the highest level? Is it really lacking or people suppress their own rationality in self-interest to benefit from the system. Or is it a feedback between the two, which throws this strange combination of being highly educated, but irrrelational individuals? Let me not declare that this indeed is the case. Let us assume that this might be the case for the sake of discussion. Rationality means acting by reason. Reason is developed to connect and act as per reality of cause and effect in the nature. If the rationality is based on beliefs and assumptions that have little to do with the cause and effect relationship, it can  have dire consequences. The highly educated people, therefore, are expected to have good sense of rationality because of their understanding of cause and effect.  Why do I, then, see educated but irrational individuals in my proposed assumption? One explanation could be their context dependent rationality. After all,  we are not practicing our rationality all the time and on trivial and mundane issues of private nature we might not invoke it. However, the real test of rationality is in social context. How would someone sound irrational in social interactions, meetings and administrative deeds? Well the principle of such seemingly irrational outlook might underlie in the concept of rationality itself. They still follow the reasoning and they are still rational, but TO THEMSELVES, i.e., some kind of personalized version of rationality, known as instrumental rationality in the dictionary of philosophy.  This type of rationality is concerned with the opting and implementing actions that maximizes the possibility of outcome that are priortized higher in one's objectives.The rationality we should bother about is the other one, possibly more relevant in the the context, known as epistmatic rationality, which deals with the achieving accuracy in once understanding based on evidence and implementing the logically correct, cognitionally unbiased and truth centric acts. This type of rationality mitigates the falsehood and self-interest based actions, which have some scope in instrumental rationality.The epistamic rationality can be a subtype of broader and pervasive instrumental rationality, wherein we insulate our deeds from falsehood and self-interest and project our goals accordingly. Here is the news: What we see in the society is , presumably, the Gaussian distribution of the balance between the two. The Gaussian curve would tend to be  more skewed towards instrumental rationality as we increase the competition among individual for resources. That's because instrumental rationality associates with the individual's  survival. Competition is intrinsic in Indian societies. Right from school days, we are expected to compete, rather than co-operate,with our colleagues.

Therefore, one can predict that if resources are limited and individuals have higher ambitions, the epistmatic rationality will have little scope and the instrumental rationality will prevail. I work in such a place, that sadhu does not.

The issue of self-citation

Ever wondered where the greatest Indian scientists of present times are hiding? Well, they are not hiding, they are just not there. Scientific excellence is measured by the quality and quantity of research articles published in international journals (let's count national journals also to minimize the risk of sedition charges).  There needs to be some comparisons drawn with other countries. It would possibly be unfair to compare India with top 20 countries ranked as per their H-index (http://www.scimagojr.com/). Accordingly, as of today, India holds 22nd position  and just above is Russia and just below is Brazil. Taking Russia for comparison, I suppose, would still be brutal. Let's take Brazil here for comparison. I will also take couple of asian countries: Singapore and Pakistan (a developed and a developing country). Well for some excitement. Let us assess through following criteria:

1. Total citable documents
2. Citations/document
4. Number of international collaborations

1. Total citable documents

The wow plot of indian science. Isn't it? One could simply argue that india and brazil being disproportionately more populous as compared to Singapore would certainly show greater number citable documents. However, the accelerated publication  observed in last 10 years for india and Brazil looks remarkable. Even greater acceleration observed in last 5-6 years for india as compared to Brazil is the "wow" I mentioned. Here is the news: this wow trend is projected by the bureaucrats  of indian science in every other general public lecture on indian science. In general, Fractional Count  or FC (number of authors belonging to that particular country) for each article is calculated and sometimes further down weighted for some research journals like that of astrophysics for balancing reasons. Nevertheless, FC or weighted FC would essentially be number of articles with some adjustments like the ones mentioned above that, I suppose, would only change the trend quantitatively and not qualitatively. Some studies also attempt to normalize #articles by per capita expenditure to claim the better performance of indian science. Well, on those lines, one can also argue to  normalize it further by the purchasing power of currency. For example, the PhD salaries in Singapore and Brazil are five and two times higher than that in India. Let's, for the time being, buy that Indian science performs better when scaled to per capita expenditure. The values of per capita expenditure in R & D in India is USD 39 and for Pakistan it's USD 13. Later, in this post these values will be revoked.

2.  Citations/document

This is an important criteria that directly reflects how relevant a particular article is. Following plot clearly suggests that not Singapore, but Brazil also outperforms India. Papers published in recent times would still not be sufficiently cited and, therefore, the trend of last 10 years can be ignored for this analysis. Moreover, closeness of India and Pakistan might worry nationalists! But hold on riot is yet to come.

One important factor, which is ignored in the above plot is the tendency of scientist to cite their own papers, known as self-citations. This reminds me an incident, where one of my senior colleague in IGIB (in the year 2005) was asked by the reviewer of an ordinary journal to delete ref # 1-12 (or so) from the article because these were  not directly relevant in the context. Coincidentally these were  also self-citations. Clearly, it would be interesting to replot the the ciations/document after subtracting the self-citations. Here it is:

Even a layman would appreciate that a more  appropriate assessment of scientific performance should be measured through its quality like the plot above rather than quantitative measures that count the bulk of documents while ignoring the underlying relevance. In this regard, India is hardly better than Pakistan, a country that we unanimously considered inferior to ours wrt science and education. Remember the per capita expenditure for pakistan is 13 USD, one third that of India. Contrary to this observation, at my present institution, I have seen many many numbers and plots that claim bloom of indian science. It is also being claimed through articles like this one: http://scroll.in/article/777202/science-research-in-india-is-flourishing-despite-funding-cuts-and-indifference-says-new-study , which was recently floated around scientific community in India. It says:

"The new study, while taking stock of prevailing problems, suggests that the negative perception is partially because of a lack of media interest and studies the impact of Indian publications in comparison to the countries with similar spending on science research."

Does Paki media broadcasts, advertises and encourages their science to achieve the same level of citations/article as of India? Chutzpah!

he same article also claims:

This, coupled with, “good collaborative ties” of Indian researchers with the rest of the world, ensures a steady stream of output in the face of budget cuts and abysmal spending, even as the country constantly tries to punch above its weight.

This can be again be directly challenged as following:

4. Number of international collaborations

International collaborations can arguably be considered as one of the criteria to judge the scientific accomplishment for following reasons:

• It helps collating sufficient evidence of the scientific claims
• Helps training the manpower in cutting edge techniques
• Helps in converging different ideas. Two heads are better than single.  
• Many great scientific discoveries were achieved through collaborations. Discovery of Higgs bosons is an example.

Here is the plot:

You see the riots? Pakistan is a way ahead of India and Brazil and in fact the difference has expanded in last 5 years. When it comes to science, India seems more conservative and shy than the one who is labeled. Recall the similar or probably worse purchase value of currency and lower (by 1/3) per capita expenditure on R&D of Pakistan as compared to India.

It is also notable that I am comparing with pakistan and did not even talk about Singapore's performance. The problems with most of the scientometric studies is that the authors tend to project numbers, controls and plots to their convenience. Ideally, I could have sat to work on the issue in a more comprehensive manner, the question is whether it is worth. If we count the articles published in top journals in last 5 years from India, it will be on our finger counts and probably will not go to double digits. Isn't that sufficient to guess the quality?

PS: All the data and plots were obtained from http://www.scimagojr.com/