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A protein folding mystery solved: Study explains core packing fractions

phys.org

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Re: A protein folding mystery solved: Study explains core packing fractions

#21

Post by daveguy »

user32489318 wrote: post #6
ChuckMcM wrote: post #2

This is the kind of cool stuff I'm going to miss during the coming dark ages. When ever I read this in a paper: "The authors acknowledge support from NIH Training Grant No. T32GM145452 (A.T.G., C.S.O., and Z.L.), NIH Training Grant No. T15LM007056-37 (J.A.L.), and the High Performance Computing facilities operated by Yale's Center for Research Computing." All of these things (the NIH and Yale's Center for Research Co…

Researchers will seek other opportunities, there are other non-US grants and support structures. While studying in EU, I knew quite a few PhDs who secured substantial financial aid from the industry directly, on their own. Yes, it will get trickier, and will steer the research in a certain direction. But I won’t call it the dark ages.

Ah yes. Industry funding. We all know how independent and dedicated to the scientific pursuit of truth industry funded research is.

It very much will be the dark ages if the only money available for research is at the mercy of industry. It probably won't be dark ages for the whole world -- just the countries that squander their research advantage. Brain drain from the US is already starting. Hopefully there will be a clear cease and desist message sent to this regime when the people vote again Nov 2026.

Re: A protein folding mystery solved: Study explains core packing fractions

#22

Post by esbranson »

ChuckMcM wrote: post #2

This is the kind of cool stuff I'm going to miss during the coming dark ages. When ever I read this in a paper: "The authors acknowledge support from NIH Training Grant No. T32GM145452 (A.T.G., C.S.O., and Z.L.), NIH Training Grant No. T15LM007056-37 (J.A.L.), and the High Performance Computing facilities operated by Yale's Center for Research Computing." All of these things (the NIH and Yale's Center for Research Co…

Well we're certainly not going to see any European institutions step up, despite their propaganda to the contrary.

Re: A protein folding mystery solved: Study explains core packing fractions

#23

Post by timr »

jibal wrote: post #14
timr wrote: post #9

Earlier quoted context omitted.

> "The authors acknowledge support from NIH Training Grant No. T32GM145452 (A.T.G., C.S.O., and Z.L.), NIH Training Grant No. T15LM007056-37 (J.A.L.), and the High Performance Computing facilities operated by Yale's Center for Research Computing." Well, NIH training grants aren't going anywhere, so far as I know, and the high-performance computing facilities may or may not be affected by a cut in indirects. If they a…

Lots of things are possible while clearly not true, and that's one of them.

Well, pretty much everything in the comment I replied to is untrue, so technically the entire comment falls in that category.

Re: A protein folding mystery solved: Study explains core packing fractions

#24

Post by trod1234 »

ChuckMcM wrote: post #2

This is the kind of cool stuff I'm going to miss during the coming dark ages. When ever I read this in a paper: "The authors acknowledge support from NIH Training Grant No. T32GM145452 (A.T.G., C.S.O., and Z.L.), NIH Training Grant No. T15LM007056-37 (J.A.L.), and the High Performance Computing facilities operated by Yale's Center for Research Computing." All of these things (the NIH and Yale's Center for Research Co…

"Solving issues through greater regulation."

Before you know, we'll have an Anti-dog-eat-dog bill, and equilization of opportunity acts. The high seas will be no longer be safe. Copper and other critical materials needed for infrastructure will no longer be available. Gasoline will go through the roof to something like $33/gallon.

Companies that once stood as steady as oak trees will vanish in the night.

Good ole rail will still be available. The only thing missing is Rearden metal.

When government forces banks to loan to people who can never pay it back. Where society becomes only about what you can do for others, and never what others can do for you. Where simply claiming you need more means you get paid more.

The inevitability of someone stopping the motor of the world is something we all must consider. It certainly won't be like in the books.

Re: A protein folding mystery solved: Study explains core packing fractions

#25

Post by dekhn »

banq wrote: post #3

The research direction has gone off track—it's overly fixated on proteins "chasing fireworks" (metaphorically trivial pursuits), while mitochondrial and other molecular pathways represent a far more substantial and impactful frontier. The academic world is mired in stagnation and decay, demanding external pressure to break its complacency.

mitochondria work by using proteins. Many mitochondrial diseases are due to misregulation of proteins. few molecular pathways are untouched by a protein at some point. Research into fundamental properties of proteins is important because it results in high impacts due to the prevalence of proteins in nearly all aspects of life.

Re: A protein folding mystery solved: Study explains core packing fractions

#26

Post by kylehotchkiss »

gilleain wrote: post #16

The 'explanation' in the article is a little thin: Why is the packing fraction 55% maximum (in globular proteins)? "The answer seems to be that the packing fraction stops increasing when the protein cores jam or rigidify." Ok, so ... > "That is, the individual amino acids that make up the protein core couldn't compress any further when the protein folded" So they can't pack any further because they 'jam'? Ohhh, from…

if allostery is the second secret to life, turning that off by compressing proteins seems inconvenient

Re: A protein folding mystery solved: Study explains core packing fractions

#27

Post by try_the_bass »

dbspin wrote: post #18
try_the_bass wrote: post #7

Earlier quoted context omitted.

> This is the kind of cool stuff I'm going to miss during the coming dark ages. I really don't get this level of hyperbole. There's so much hand-wringing about funding getting cut, but it turns out it's like a 15% reduction[0]. That's not an insignificant amount, but it's not the end of the world. Taken naively, that's 15% less research that gets done. One can hope that, being a pillar of academia, the intelligent fo…

The fraud issues you mention are real and pressing... They're also completely disconnected from blanket cuts to NIH funding. There seems to be some kind of grasping for a positive in heavy cuts to essential research here. Put another way, there is zero selective pressure for 'less fraudulent' research to be cut. If anything, this applies selective pressure on publish or perish, false positive, press release style res…

> The fraud issues you mention are real and pressing... They're also completely disconnected from blanket cuts to NIH funding. There seems to be some kind of grasping for a positive in heavy cuts to essential research here. Put another way, there is zero selective pressure for 'less fraudulent' research to be cut. If anything, this applies selective pressure on publish or perish, false positive, press release style research. Harsh cuts in funding always penalise blue sky research, controversial work and anything that isn't guaranteed to bring press to the funding institution

I don't think your sweeping statements are true though, either? Every social endeavor, when allowed to grow without adequate pressure, becomes bloated, slow, and full of waste. This is almost universally true, and the exceptions tend to be things where there is heavy pressure to be lean. This pressure is more effective when it comes from within, but external pressure works, too.

If you want a process to remain efficient over time, it either needs to start that way and not change, or be aggressively pruned from time to time.

Academia should be pruning the waste and fraud itself, but is clearly not doing so aggressively enough.

I agree that the cuts, if naively applied, will cut both good research and bad. On the other hand, I think if academic research institutions are doing things naively, they're doing it wrong.

> This is absurdly reductive, and doesn't connect with the genuine issues at play incentivising good research and detecting fraud.

Of course it is! But the fact that academia seems to be utterly failing at performing even the most basic checks against fraud routinely. Of course a reductive approach is insufficient, but it would be better than the current status quo, which is to implicitly support the fraud by refusing to even look for it in the first place.

And it's honestly not any more reductive or incorrect than this:

> Harsh cuts in funding always penalise blue sky research, controversial work and anything that isn't guaranteed to bring press to the funding institution.

Re: A protein folding mystery solved: Study explains core packing fractions

#28

Post by try_the_bass »

hengheng wrote: post #13
try_the_bass wrote: post #7

Earlier quoted context omitted.

> This is the kind of cool stuff I'm going to miss during the coming dark ages. I really don't get this level of hyperbole. There's so much hand-wringing about funding getting cut, but it turns out it's like a 15% reduction[0]. That's not an insignificant amount, but it's not the end of the world. Taken naively, that's 15% less research that gets done. One can hope that, being a pillar of academia, the intelligent fo…

In any other industry, a 15% cut would be Bad News, and people would be talking about ripple effects, they would call it a "shock" and talk about the long-term consequences.

While I agree with your statement, it's also true that many industries have faced such cuts, engaged in ample hand-wringing and talk of "shocks" and "long-term consequences", and then gone on to make simple adjustments and be perfectly fine in the long run.

It's worth keeping in mind that the loudest complainers are often the ones with the most to lose; and those with the most to lose are often the ones taking advantage of waste and bloat.

To take a trivial example, look what happens any time there's a ban wave in a popular online game: people come out of the woodwork complaining about how they were unfairly banned, were a false positive, etc... and then you ultimately find out that yes, they were indeed cheating and were caught.

Complaining loudly when caught cheating or threatened with enforcement is basically human nature. The fact that people complain loudly when the gravy train runs off the rails isn't much different, and the complaints should honestly be taken with a grain of salt.

Re: A protein folding mystery solved: Study explains core packing fractions

#29

Post by try_the_bass »

agoose77 wrote: post #17
try_the_bass wrote: post #7

Earlier quoted context omitted.

> This is the kind of cool stuff I'm going to miss during the coming dark ages. I really don't get this level of hyperbole. There's so much hand-wringing about funding getting cut, but it turns out it's like a 15% reduction[0]. That's not an insignificant amount, but it's not the end of the world. Taken naively, that's 15% less research that gets done. One can hope that, being a pillar of academia, the intelligent fo…

I want to be careful about what I write given the context of what's going on, and the personal ramifications that can have. Suffice to say, it's worth considering whether the cost of a decision can be interpreted solely as how much money there is vs the wider ecosystem level consequences of said decision.

To make a counterpoint: never underestimate people's ability to make a convincing hypothetical case to connect their livelihood to "the wider ecosystem", even when that livelihood involves committing fraud.

I take a lot of these arguments with a grain of salt. As a society, we've gotten way too used to substituting plausible hypotheticals for concrete data.

Re: A protein folding mystery solved: Study explains core packing fractions

#30

Post by jibal »

timr wrote: post #23
jibal wrote: post #14

Earlier quoted context omitted.

Lots of things are possible while clearly not true, and that's one of them.

Well, pretty much everything in the comment I replied to is untrue, so technically the entire comment falls in that category.

No, everything you responded to was true, and nothing you said was true.
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