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First of all, why is a Lander writing this? What qualifies him to reconstruct the history of CRISPR? He doesn't do CRISPR research. Historical reviews are alway
by Gatsky 11y ago
First of all, why is a Lander writing this? What qualifies him to reconstruct the history of CRISPR? He doesn't do CRISPR research. Historical reviews are always written by the people that actually did the research because A) who else really knows what happened and B) we are interested in their perspective. So Lander's qualification is what exactly? That he's an important person who knows what DNA is?
The article itself also absolutely stinks. First an ad hoc justification why this article is important consisting of nothing more than platitudes about science, then evocative descriptions of the weather in Santa Pola, progressively more brief descriptions of other sicentists' work followed by a long section at the end which could be a slightly edited version of the closing remarks from the Broad Institute's patent attorney in their dispute against the other CRISPR developers.
This in particular, stinks:
"The history also illustrates the growing role in biology of “hypothesis-free” discovery based on big data. The discovery of the CRISPR loci, their biological function, and the tracrRNA all emerged not from wet-bench experiments but from open-ended bioinformatic exploration of large-scale, often public, genomic datasets. “Hypothesis-driven” science of course remains essential, but the 21st century will see an increasing partnership between these two approaches."
What 'growing role'? Biology has always been largely hypothesis-free. Which hypothesis was being tested when DNA was discovered? They were trying to fit a model to the data, not testing out their ideas about how DNA should look. Penicillin was discovered by accident, where was the hypothesis there? And the importance of bioinformatic exploration? How does this: "Using his word processor, Mojica painstakingly extracted each spacer and inserted it into the BLAST program to search for similarity with any other known DNA sequence" support the importance of bioinformatics? Manually pasting 4500 sequences into BLAST? Surely this is an example of progress DESPITE any substantial bioinformatics.
I can't see why this was written except to further the agenda of the author and his institute, and to color history to support their legal claims. I can't see how this was published except through nepotism, eminence based science and the kind of shameful arrogance and entitlement that only academics have the luxury to cultivate. Maybe Lander thought he was setting the record straight, but that isn't his privilege.
- noname123 11y ago>Biology has always been largely hypothesis-free. I think Dr.Lander is talking about having open infrastructures and databases cataloging human genome variations; that allow everyone explore the datasets to find new patterns. You are right searching through BLAST is easy. However, maintaining and updating entries into the NCBI BLAST databases is not. Genomes are sequenced, assembled and submitted to NCBI every day. Cataloguing the variations in different strains of the different species, and identifying real novel evolutionary variations compared to just noises to existing reference genomes is not an easy task (1000 Genomes, dbSNP, malaria genome network, etc.) It is analogous to saying, Googling is easy but building and maintaining a search engine is not. I get what you are saying that some important discoveries are made by accidents, but the open data and intuitive platforms need to be there for the inspirational late night "Showerthought" googling-that-leads to-insight to happen in the first place.
- Gatsky 11y agoMy point is that his justification of why his article is important - that it demonstrates how science is done these days, including the importance of bioinformatics - seems pretty phoney to me.
- skosuri 11y agoWow, This is a lot of anger. I for one appreciated the viewpoint (taken with an eye that it is his view). Anyways, for what it's worth, Lander's lab has done a bunch with CRISPR's so your initial premise is flat out wrong [eg., http://www.ncbi.nlm.nih.gov/m/pubmed/24336569/ http://www.ncbi.nlm.nih.gov/m/pubmed/24336569/ ]. Second, I remember when they figured out that they were targeting phage. I was working with some Cyanobacteria that had a bunch of crispr loci as well. I do remember distinctly it being one of the first times that a whole new bio came from large part from informatics. (Another being lncRNA ultra conserved elements). Anyways, I really don't get the viciousness of this response.
- Gatsky 11y ago"Lander's lab has done a bunch with CRISPR's" http://www.ncbi.nlm.nih.gov/pubmed/?term=CRISPR+AND+Lander+ES%5BAuthor%5D http://www.ncbi.nlm.nih.gov/pubmed/?term=CRISPR+AND+Lander+E... There are 5 citations. 2 are reviews. 2 are original research: one in Jan 2014, another in Nov 2015. A similar search for Jennifer Doudna reveals 44. Feng Zhang has 43. Maybe he's been doing years of CRISPR work in secret, but I don't think my premise is 'flat out wrong' - he isn't the person to write the definitive history of CRISPR. Second - the human genome project is surely the key example of an entire field that could not have been birthed without informatics - Celera genomics doing the shotgun assembly showed everyone how important it was beyond a doubt. This all happened in 2000. Lander is saying this isn't enough to convince us all how important bioinformatics is. In 2016, when bioinformatics is so ubiquitous, he finds the need to cite Mojica copy pasting 4500 sequences manually from microsoft word into a BLAST search in 2003 as another seminal example to make sure we all get it? This doesn't strike you as even a little disingenuous or ad hoc? I guess we have different ideas about how problematic it is if someone tries to rewrite history while it's still happening.
- kmonad 11y agoI see you are worried about unfairness resulting if this article's view of history were to become the established view. Who would you think are most likely to get the short end of the stick here? Is an emphasis of the importance of bioinformatics directly detrimental to anyone? Genuinely asking.