11 ms·

A lot of the commenters are trying to come up with technical solutions to the issue. It belies their incomplete study of the 'softer' sciences and the difficult

by Balgair 10y ago

A lot of the commenters are trying to come up with technical solutions to the issue. It belies their incomplete study of the 'softer' sciences and the difficulty of biological studies. Tech solutions won't work, bureaucratic solutions wont work, more data wont work. Guys, the bio side of things is incredibly complicated and trying to set controls that are achievable in your time and budget is the heart of these fields. The thing you are trying to study in the bio side of science is actually alive and trying to study you right on back. If you are going to kill the thingys, they really do want to kill you too. Look at this diagram of mitochondrial phospholipid gene/protein interactions (https://www.frontiersin.org/files/Articles/128067/fgene-06-00003-r2/image_m/fgene-06-00003-g005.jpg https://www.frontiersin.org/files/Articles/128067/fgene-06-0...). That is very complicated and that is for one of the best studied organelles in the Animalia family. There are an uncountable and evolving set of other proteins that then interact with that diagram in different ways depending on the cell-type, species, and developmental history of the organelle (to start with). All of which are totally unknown to you and will likely forever remain unknown to you up until your death. Hell, we are still figuring out the shapes of organs in our own bodies. People that have studied areas for decades spending untold millions of dollars on some of the most central questions of life have essentially nothing to say for themselves and the money spent('We dream because we get sleepy'). Trying to tease out a system that has been evolving for 4.5 billion years and makes a new generation (on average) every 20 minutes is going to be just insanely difficult. This stuff is hard, the fields know it, and we don't believe anything that someone else says, let alone what our 'facts' and experiments tell us. But we solider on because we love it and because we want to help the world.

epistasis 10y ago
I think there's also a lot of confusion about what the scientific literature should be. Outsiders think of journals as pre-packaged nuggets of science fact, with conclusions that you can read and trust. Scientists who publish in the journals view them as a way to communicate a body of work of "I did this, here is the result I saw. I think it might mean this." The difference between these two views can not be understated. Each group wants the literature to be useful to them, so that they can use it, and that's understandable. For most areas of science, especially in the early days of that science, it's absolutely essential that scientist's view be allowed to persist. Is it better to share early, or to wait to publish until you've tried all possible things that could potentially go wrong? I think the answer is obviously that you share the early data, and what you think it means, even if you may be wrong about it. If the goal is to advance knowledge as quickly as possible, I think that the scientist's view is probably a better idea of what a journal needs to be than what the outsiders' view is. In some fields, like fMRI studies, the field is realizing that they may need to go about things differently. And that means that a lot of the interpretations that were published earlier are incorrect. But that process of incorrect interpretation to corrected interpretation is an essential part of science.
- panic 10y ago
  Scientists and academic institutions add to the confusion with the way they promote their work. Nobody puts language like "I did this, here is the result I saw. I think it might mean this" in a press release. It's always "Breakthrough research! Is the end of cancer in sight??"
  - epistasis 10y ago
    Absolutely true, though I know of very few scientists that have been able to tamp down the game of telephone that the university's press office starts. http://www.phdcomics.com/comics.php?n=1174 http://www.phdcomics.com/comics.php?n=1174
  - nostrademons 10y ago
    A lot of this is because of the incentives that result from grant-based funding of science. Your ability to continue to do science is contingent on your ability to find someone to pay for it; it's much easier to convince someone to pay for it if you can point to headlines that say "Breakthrough research! Is the end of cancer in sight?" The old system of "gentleman science" (where only independently-wealthy heirs did science, as a hobby) had a lot of problems and wouldn't really be workable today, but one thing it had going for it was that the scientist could count on the funding being there tomorrow, and so had much less of an incentive to overstate their work.
  - averagewall 10y ago
    It doesn't help when teachers tell their students they can reference academic papers from peer reviewed journals but can't reference Wikipedia. The former is tentative and the latter is established knowledge from text books, more or less.
- ivan_gammel 10y ago
  Probably, the real problem is that "the scientific literature should be". It's not the right question to discuss today, because scientific literature is just a brief approximation of scientific knowledge and this is not what we need. Whole modern scientific system is outdated and has to be upgraded: journals, citation indexes, degrees should go away and be replaced. Science should become more formal and more digital, so that it will be easier to find and validate the results. There should be databases, search engines and digital signatures of the raw data and chains of proofs. Counting citations should be replaced with counting chains of proof produced by the scientist and included in others' works. Reliability of proof and contribution to ratings should be based on independent confirmations, which should be counted too - replication of new results should be considered an achievement too. Journals may remain, but not as a primary way to exchange scientific information - more likely, they should become the portals to the data which will link the results in databases to their human-readable interpretations.
vacri 10y ago
> Guys, the bio side of things is incredibly complicated I always find it amusing when physicists talk about how mind-blowing it is that at the quantum level, things aren't entirely predictable. Over in biology, that's the starting point for everything rather than the final frontier - you don't need ridiculously expensive tools to get to the point where you're finding unpredictable stuff.
- apathy 10y ago
  You don't need a ridiculously expensive rig to find that in physics, either: https://en.wikipedia.org/wiki/Double-slit_experiment https://en.wikipedia.org/wiki/Double-slit_experiment laser pointer plus a sharp enough carbide wheel (trained as a chemist, grad school in biostats & genetics, now mostly design experiments & clinical trials... I have physics envy, except I don't envy their funding models!)
  - Balgair 10y ago
    The double slit experiment is purely random, not unknowable. There is a large difference. In Bio, we will some day conceivably know enough to get to the point where we can build up stat models like the double slit experiment. I'd say that the double slit experiment is still leaps and bounds a better starting point than anything we have in bio and only took ~2 decades to finally parse out. Bio has been chugging along since Watson for ~8 decades before we finally got CRISPR and could really do anything about DNA.
    - apathy 10y ago
      Cre-Lox systems predate CRISPR/Cas9 or CRISPR/Cfp1 approaches by quite some time. If one exists for the system you want to study, they also tend to work better. (floxing the original mouse is, however, substantially harder) I don't think it's entirely accurate to say that conditional editing of DNA is a new thing. The ready accessibility and combinatorial possibilities, yes, but for targeted conditional knockouts, floxing mice has been a thing for about 20 years now.
    - j7ake 10y ago
jszymborski 10y ago
While we're sharing confusing pathways, here's a visualisation of _some_ of the known metabolic pathways: http://biochemical-pathways.com/#/map/1 http://biochemical-pathways.com/#/map/1
- FabHK 10y ago
  It is awesome to get a visual, visceral reminder occasionally about how much we know these days.

by Balgair 10y ago

epistasis 10y ago

I think there's also a lot of confusion about what the scientific literature should be. Outsiders think of journals as pre-packaged nuggets of science fact, with conclusions that you can read and trust. Scientists who publish in the journals view them as a way to communicate a body of work of "I did this, here is the result I saw. I think it might mean this." The difference between these two views can not be understated. Each group wants the literature to be useful to them, so that they can use it, and that's understandable. For most areas of science, especially in the early days of that science, it's absolutely essential that scientist's view be allowed to persist. Is it better to share early, or to wait to publish until you've tried all possible things that could potentially go wrong? I think the answer is obviously that you share the early data, and what you think it means, even if you may be wrong about it. If the goal is to advance knowledge as quickly as possible, I think that the scientist's view is probably a better idea of what a journal needs to be than what the outsiders' view is. In some fields, like fMRI studies, the field is realizing that they may need to go about things differently. And that means that a lot of the interpretations that were published earlier are incorrect. But that process of incorrect interpretation to corrected interpretation is an essential part of science.

panic 10y ago
Scientists and academic institutions add to the confusion with the way they promote their work. Nobody puts language like "I did this, here is the result I saw. I think it might mean this" in a press release. It's always "Breakthrough research! Is the end of cancer in sight??"
- epistasis 10y ago
  Absolutely true, though I know of very few scientists that have been able to tamp down the game of telephone that the university's press office starts. http://www.phdcomics.com/comics.php?n=1174 http://www.phdcomics.com/comics.php?n=1174
- nostrademons 10y ago
  A lot of this is because of the incentives that result from grant-based funding of science. Your ability to continue to do science is contingent on your ability to find someone to pay for it; it's much easier to convince someone to pay for it if you can point to headlines that say "Breakthrough research! Is the end of cancer in sight?" The old system of "gentleman science" (where only independently-wealthy heirs did science, as a hobby) had a lot of problems and wouldn't really be workable today, but one thing it had going for it was that the scientist could count on the funding being there tomorrow, and so had much less of an incentive to overstate their work.
- averagewall 10y ago
  It doesn't help when teachers tell their students they can reference academic papers from peer reviewed journals but can't reference Wikipedia. The former is tentative and the latter is established knowledge from text books, more or less.
ivan_gammel 10y ago
Probably, the real problem is that "the scientific literature should be". It's not the right question to discuss today, because scientific literature is just a brief approximation of scientific knowledge and this is not what we need. Whole modern scientific system is outdated and has to be upgraded: journals, citation indexes, degrees should go away and be replaced. Science should become more formal and more digital, so that it will be easier to find and validate the results. There should be databases, search engines and digital signatures of the raw data and chains of proofs. Counting citations should be replaced with counting chains of proof produced by the scientist and included in others' works. Reliability of proof and contribution to ratings should be based on independent confirmations, which should be counted too - replication of new results should be considered an achievement too. Journals may remain, but not as a primary way to exchange scientific information - more likely, they should become the portals to the data which will link the results in databases to their human-readable interpretations.

vacri 10y ago

> Guys, the bio side of things is incredibly complicated I always find it amusing when physicists talk about how mind-blowing it is that at the quantum level, things aren't entirely predictable. Over in biology, that's the starting point for everything rather than the final frontier - you don't need ridiculously expensive tools to get to the point where you're finding unpredictable stuff.

apathy 10y ago
You don't need a ridiculously expensive rig to find that in physics, either: https://en.wikipedia.org/wiki/Double-slit_experiment https://en.wikipedia.org/wiki/Double-slit_experiment laser pointer plus a sharp enough carbide wheel (trained as a chemist, grad school in biostats & genetics, now mostly design experiments & clinical trials... I have physics envy, except I don't envy their funding models!)
- Balgair 10y ago
  The double slit experiment is purely random, not unknowable. There is a large difference. In Bio, we will some day conceivably know enough to get to the point where we can build up stat models like the double slit experiment. I'd say that the double slit experiment is still leaps and bounds a better starting point than anything we have in bio and only took ~2 decades to finally parse out. Bio has been chugging along since Watson for ~8 decades before we finally got CRISPR and could really do anything about DNA.
  - apathy 10y ago
    Cre-Lox systems predate CRISPR/Cas9 or CRISPR/Cfp1 approaches by quite some time. If one exists for the system you want to study, they also tend to work better. (floxing the original mouse is, however, substantially harder) I don't think it's entirely accurate to say that conditional editing of DNA is a new thing. The ready accessibility and combinatorial possibilities, yes, but for targeted conditional knockouts, floxing mice has been a thing for about 20 years now.
  - j7ake 10y ago

jszymborski 10y ago

While we're sharing confusing pathways, here's a visualisation of _some_ of the known metabolic pathways: http://biochemical-pathways.com/#/map/1 http://biochemical-pathways.com/#/map/1

FabHK 10y ago
It is awesome to get a visual, visceral reminder occasionally about how much we know these days.