4 ms·

Wow, 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

by skosuri 11y ago

Wow, 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 ago
  I 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.
  - Gatsky 11y ago
    The actual or perceived importance of bioinformatics is safe. My point was that holding up CRISPR as an example of why bioinformatics is important is a bizarre thing to do (this is most definitely not news to anybody working in the life sciences), and only makes sense I think as a kind of half-hearted attempt to justify the writing of an article which otherwise is very easily construed as being of dubious intent.
- skosuri 11y ago
  1. You said, "He doesn't do CRISPR research." If you are going ad hominim, it's usually better if you get your facts right. 2. FWIW, I think you are largely rewriting history by your comment. The dominant feeling I remember about the HGP at the time was that it wasn't worth it and we didn't learn any new bio. This feeling is still widespread... And biology has always been "hypothesis free"??? Really? Anyways, both of these points were largely ancillary imo to the early history of the field that I thought was an interesting viewpoint.
  - Gatsky 11y ago
    We're just two guys arguing on the internet now, but here we go again. 1. To me, just having your name on a paper does not equal 'doing research in the field'. In the cases of these 2 papers, he is neither the senior author, nor does the first author come from his lab. He doesn't actually cite any of his own papers in the review, after all. 2. I'm not rewriting history because I'm talking about what people think about bioinformatics in the present because of the human genome project. Lander's point is that CRISPR informs our opinion about bioinformatics today, and I'm disagreeing this is a valid point etc etc see above. I agree with you that at the time HGP happened the reaction was lukewarm. But whatever you want to say about the impact on humanity, it is indisputable that the HGP has enabled so much science that relies on bioinformatics, and elevated bioinformatics to a key part of modern life science. Not going to get into the hypothesis free argument here, but the issue is essentially that in biology it is often impossible to specify all the necessary details of the model you are hypothesising about, which means that hypotheses have poor generalisability and reproducibility. This means that any progress we make isn't by virtue of falsifying hypotheses, but more by observation and investigation of phenomena which may have been observed by chance. Just the act of making a hypothesis does not make a science 'hypothesis driven' - those hypotheses actually need to contribute in a material fashion to the accumulation of knowledge or more importantly, insight.

by skosuri 11y ago

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 ago
I 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.
- Gatsky 11y ago
  The actual or perceived importance of bioinformatics is safe. My point was that holding up CRISPR as an example of why bioinformatics is important is a bizarre thing to do (this is most definitely not news to anybody working in the life sciences), and only makes sense I think as a kind of half-hearted attempt to justify the writing of an article which otherwise is very easily construed as being of dubious intent.
skosuri 11y ago
1. You said, "He doesn't do CRISPR research." If you are going ad hominim, it's usually better if you get your facts right. 2. FWIW, I think you are largely rewriting history by your comment. The dominant feeling I remember about the HGP at the time was that it wasn't worth it and we didn't learn any new bio. This feeling is still widespread... And biology has always been "hypothesis free"??? Really? Anyways, both of these points were largely ancillary imo to the early history of the field that I thought was an interesting viewpoint.
- Gatsky 11y ago
  We're just two guys arguing on the internet now, but here we go again. 1. To me, just having your name on a paper does not equal 'doing research in the field'. In the cases of these 2 papers, he is neither the senior author, nor does the first author come from his lab. He doesn't actually cite any of his own papers in the review, after all. 2. I'm not rewriting history because I'm talking about what people think about bioinformatics in the present because of the human genome project. Lander's point is that CRISPR informs our opinion about bioinformatics today, and I'm disagreeing this is a valid point etc etc see above. I agree with you that at the time HGP happened the reaction was lukewarm. But whatever you want to say about the impact on humanity, it is indisputable that the HGP has enabled so much science that relies on bioinformatics, and elevated bioinformatics to a key part of modern life science. Not going to get into the hypothesis free argument here, but the issue is essentially that in biology it is often impossible to specify all the necessary details of the model you are hypothesising about, which means that hypotheses have poor generalisability and reproducibility. This means that any progress we make isn't by virtue of falsifying hypotheses, but more by observation and investigation of phenomena which may have been observed by chance. Just the act of making a hypothesis does not make a science 'hypothesis driven' - those hypotheses actually need to contribute in a material fashion to the accumulation of knowledge or more importantly, insight.