Ok so we had the first class meeting yesterday. It went well, although that genome review article was a bit heavy on information and it took too long to discuss. My plan for today is to organize the next discussion so we have it more structured. Along the lines of a short intro/review, and then assign students roles for discussion.

Which makes me think about a completely different thing but along similar lines. In the conflict resolution workshops I regularly facilitate we do many communication exercises. One of the most efficient ones is called 4-four part listening, in which participants are divided in small groups and they listen to a story narrated by one person in the group. These stories are usually personal experiences of conflict. The other members listen to different aspects of the story: one focuses on the facts, the other on the emotions, and the third to the values implied in the story. At the end, the story is analyzed putting together all three aspects.

So maybe that could be a good way to analyze a scientific article also: different aspects, including what is done, why is it done, how it is done, which major aspects it touches?

And most importantly, a CRITICAL reading. Of course it is easiest for those who are in the field, but even an outsider has tools to analyze a scientific article.

<Disclaimer: I am not an expert in this particular field, so these tools are limited to my general bio expertise. I have no inside knowledge, so I may miss lots of details and nuances only obvious to the specialist. However, these are my recommendations to a Bio grad student confronted with a peer reviewed specialized article.>

Above is a Youtube video about ENCODE. It is a bit longish but it can give you a quick idea of the project. And it makes this posting more colorful 🙂

Ok back to tools of critical reading. That includes but it is not limited to:

  • Background of the article/project. For example, yesterday’s gene definition article talks about the ENCODE project. One has to look up what the project exactly is, and a quick internet search immediately brought the ENCODE website up.
  • Methods- this article was, as many of you correctly noted, a review/opinion article. There is some quick reference to the methodology involved  (tiling arrays). The article says something about the methodological complexities of it and quotes several references such as Emanuelsson et al, 2007 Rozowsky et al 2007, and the original ENCODE report. A quick look at the  wikipedia article gives an explanation of the method and a whole series of references. Do you need to look them all up? Well, not right now- but if are going DEEP into a topic you have to look up the original references. Thou shall not trust a review article’s summary of a methodology. And methodology sometimes is critical. Lots of published strange data abound due to contaminated cultures, incorrectly bred mouse lines, and lack of good controls. Anybody heard of the XRMV and chronic fatigue disease connection fiasco? The arsenic life controversy? There is still people out there who doubt that prions exist.
  • The basics. Quiz yourself while reading. Consider it mental workout. When you read about concepts that you know you have seen, take a pause before going on. Splicing. Transposons. UTRs. Try to remember what you remember. Look them up if needed. Read what the article says. Things may have changed since you last studied it. Take a mental note, and try rewiring those old synapses. It is hard, I know.
  • The new stuff. Well, you have to read, double-check, and enhance your mind.
  • Afterlife of the article. If you go to the article’s official page and scroll down, you will find its official afterlife: related articles and articles that have cited it. Those can mean good things (the article is relevant and many consider it a good reference) or bad things (the article is crappy and there is a lot of comments and rebuttals). In this article’s case, there are some that cite is positively and others consider it reductionistic. To see more personal takes of articles, google the article and look for blog postings about it (once you know the field you know whose blogs’ to look for), such as this one, skeptical of it (similarly to the discussion we had in class, about possible artefacts), although the comments are quite interesting to read to. By the way I subscribed to this particular blog (Sandwalk). OMG those Monday molecule riddles! Very proud I figured B12 out. Seeing the Co atom in the middle helped. But I am digressing.Structure of vitamin B12

Well this turned out to be quite a long posting! Hope this helps for the future. Your comments are welcome!