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Biologist's perspective: this paper is not about the biology. The simulation performed here has zero biological interest - the point of the paper was to show ho
by jryb 7y ago
Biologist's perspective: this paper is not about the biology. The simulation performed here has zero biological interest - the point of the paper was to show how efficient and scalable their software is. This article about the paper is terrible, but honestly I feel like they should be given a pass - it's hard to justify to a lay audience that understands neither DNA nor memory bandwidth why you would choose to study something that is of no use to the field.
There's an inherent tension when doing a method development paper - if your result is too fantastical it's hard to know whether it's an artifact of your (potentially faulty) technique, and if the thing you're studying is well-understood then it serves as a good control, but it's less interesting. I suspect they chose the latter path since it requires no validation via existing methodologies.
- stochastic_monk 7y agoI'm not familiar with this method, but NAMD and CHARM are a great way to inspect biological systems at greater resolution than experimental methods can measure. There was really cool work on fibrinogen about a decade ago showing how it provides elasticity. Reference: https://www.ks.uiuc.edu/Highlights/?section=2008&highlight=2008-02 https://www.ks.uiuc.edu/Highlights/?section=2008&highlight=2...
- dekhn 7y agoThat's a PR narrative twisted to make the results sound much more useful than they really were :(
- phkahler 7y agoMaybe the problem is that these scientists aren't doing science, they did some engineering. That's great, but it doesnt fit their publishing model.
- thatcat 7y agoWhat is the engineer publishing model?
- phkahler 7y agoOne engineering model is to put the code on github under an open source license so people can use it. But please dont just put it out there and walk away. If you want to develop a useful piece of software, find a way to maintain it. Another model is to offer it for sale as a product. Either way, engineers dont really care about publishing, we care about making useful things and Shari g how-to.
- thatcat 7y agoMost engineering fields have journals and publish their research in the same manner as scientists. Whether they care about publishing or not is related to whether their position is in academia or industry.
- dekhn 7y agoI agree this paper isn't really useful for biology. LANL maintains team of pseudo-biologists who scale up MD simulations and publish papers like this periodically (https://www.lanl.gov/projects/karissa/Ribosomes.html https://www.lanl.gov/projects/karissa/Ribosomes.html shows some previous work). I wish this was a field where you could just apply more CPU and get better results (I say that with multiple papers published under my name which claim exactly that) but I'm skeptical. The force fields we use are far too approximate (point charges, assumption of transferrability) and it really does seem like we don't actually need most of this information to answer the questions we want to answer- those can be answered using more parsimonious techniques.
- vo2maxer 7y agoI don’t see how this would be of “zero biological interest.” Is it because presently it is not that useful or because it will never have any applicability?
- jryb 7y agoBecause what they were examining is already very well understood.