Showing posts with label Data analysis. Show all posts
Showing posts with label Data analysis. Show all posts

Sunday, September 25, 2016

What is your personal experience of the difference in the way basic science research is conducted in the USA and India?


As a biomedical researcher, I consider the research I did during my Ph.D. in India to be the most rigorous by far. It was the only project where statistics were appropriately and correctly applied right from the first step, the experiment design, continuing with blinding of the samples through to data analysis.

Goal of my Ph.D. project was to figure out if prior exposure to environmental mycobacteria (NTM, Nontuberculous mycobacteria) could explain why the largest TB vaccine trial had failed to protect against adult pulmonary TB. Conducted from 1967 to 1980 on ~360000 people across 209 villages and 1 town in South India, prior exposure to environmental mycobacteria emerged as a plausible reason. Only there was no data on NTM in this environment, if yes, what species and where, in the soil/water/dust. I was just one person. How could I cover such a vast population over such a vast area? That's where statistics entered the picture, exactly where it should, in the experimental design itself. A professional statistician crunched the numbers to determine how many villages I should cover, how many houses per village, which villages, i.e., make sure I comprehensively sampled the entire trial area in as unbiased a manner as possible. Starting with this design, he carefully shepherded every step of my Ph.D. project and even blinded the samples I brought back from the field, only decoding them after I'd generated all the data. Since I don't have any other experience on basic research in India, I don't know if my experience if generalizable so I'll leave it at that. 

Moving on from differences between India and US, I'll highlight two dubious practices that are rampant in basic biomedical research the world over, at least if we go by the published literature. Overarching problem consists of two features

1. Statistics are misused, usually applied only at the back end to analyze the data after it's been generated, instead of the optimal approach which is to apply them from the beginning in the experiment design itself.

2.Definition of scientific misconduct is too narrow, completely ignoring the most prevalent practice, which isn't outright fraud but rather data selection.

Compared to basic research, rigorous statistical science applied to human clinical trials is the norm. Only very slowly is this mindset permeating into basic research to replace this ridiculous state of affairs. Last year, we saw the publication of the first randomized clinical trial in mice (1). 

The US ORI (United States Office of Research Integrity) defines Scientific misconduct as consisting of data fabrication, data falsification or plagiarism. But far more than any of these, the most prevalent practice is something that's not even on the radar, data selection, i.e., cherry-picking data. Practice is rampant. Rarely do animal model studies show data combined from different experiments. Take a look at any recent paper, even ones published in Nature or Science. Invariably a figure legend would say something along the lines of, 'Data from one representative experiment out of 3, 4 or 5 different experiments is shown'. Why not show combined data from all experiments performed? How could such a shoddy practice be the norm? Simply means intra-group variation between experiments was greater than inter-group variation within one single experiment. Either experimenters are shoddy or techniques too unrefined. Either way, cannot trust such data. And this is still the norm in basic biomedical research.  

Bibliography:
1.  Llovera, Gemma, et al. "Results of a preclinical randomized controlled multicenter trial (pRCT): Anti-CD49d treatment for acute brain ischemia." Science Translational Medicine 7.299 (2015): 299ra121-299ra121. http://stm.sciencemag.org/conten...


https://www.quora.com/What-is-Tirumalai-Kamalas-personal-experience-of-the-difference-in-the-way-basic-science-research-is-conducted-in-the-USA-and-India/answer/Tirumalai-Kamala


Sunday, May 1, 2016

What careers in science are available to people with disabilities that prevent them from working regular long hours? Is there a place in scientific research for people with conditions like fibromyalgia or chronic fatigue syndrome who are unable to consistently work long hours (or even short hours sometimes)?

In my opinion, if the person is able to work for a few hours per day on the computer,  scientific research in general and biomedical research in particular offer several opportunities for people with disabilities like fibromyalgia or chronic fatigue syndrome.

Data analysis and statistical analysis, these are two pursuits for someone whose disabilities preclude working regular hours. These days high throughput assays have become bread-and-butter in biomedical research. An enormous amount of data is generated from a single experiment. Then its hours of data analysis using specialized scientific software and statistical analysis using specialized statistical software. Such types of analyses can be done from anywhere, even home.  In industry especially where projects are done by teams, the work is often organized into an assembly-line type of process, and different parts of the project are performed by different team members. There's certainly a place in such a structure for people with disabilities who could perform such data analysis remotely, even from home.

Scientific literature mining. In industry, another place for a person with disabilities is early in the timeline for a scientific project, in helping amass the scientific justification to help with green-lighting a project. Periodically the R&D divisions of large pharma/biotech companies go through their portfolio to decide which new projects to bring on board. Business and marketing divisions determine the financial worthiness of the projects, i.e., whether the products will make money. The R&D teams work on the science side, i.e., which diseases and whether there are promising lead candidates out there that can be brought on board and developed. This takes a huge amount of scientific analysis examining the peer-reviewed scientific literature. Again, a person with disabilities could do this work remotely, even from home.

Patent examiner/researcher. Again, the work here is to scour the realm of available literature to assess if a proposed idea/invention is original or not. Scope for this job is with the federal government, research organizations and law firms.


https://www.quora.com/What-careers-in-science-are-available-to-people-with-disabilities-that-prevent-them-from-working-regular-long-hours/answer/Tirumalai-Kamala