Deep learning gets the glory, deep fact checking gets ignored

The Android client I use, Harmonic, has a shortcut to report a user, although it just prefills an email to hn@ycombinator.com.

Bioinformatically, you could compare your protein with known proteins and infer function from there, but OP's paper is specifically for the use case where we know nothing in our databases.

Time-wise it depends where in the process you start!

Do you know what your target protein even is? I've seen entire PhDs trying to purify a single protein - every protein is purified differently, there are dozens of methods and some work and some don't. If you can purify it you can run a barrage of tests on the protein - is it a kinase, how does it bind to different assays etc. That gives you a fairly broad idea in which area of activity your protein sits.

If you know what it is, you can clone it into your vector like E. coli. Then E. coli will hopefully express it. That's a few weeks/months of work, depending on how much you want to double-check.

You can then use fluorescent tags like GFP to show you where in the cell your protein is located. Is it in the cell-wall? is it in the nucleus? that might give you an indication to function. But you only have the location at this point.

If your protein is in an easily kept organism like mice, you can run knock-out experiments, where you use different approaches to either turn off or delete the gene that produces the protein. That takes a few months too - and chances are nothing in your phenotype will change once the gene is knocked out, protein-protein networks are resilient and there might be another protein jumping in to do the job.

if you have an idea of what your protein does, you can confirm using protein-protein binding studies - I think yeast two-hybrid is still very popular for this? It tests whether two specific proteins - your candidate and another protein - interact or bind.

None of those tests will tell you 'this is definitely a nicotinamide adenine dinucleotide binding protein', every test (and there are many more!) will add one piece to the puzzle.

Edit: of course it gets extra-annoying when all these puzzle pieces contradict each other. In my past life I've done some work with the ndh genes that sit on plant chloroplasts and are lost in orchids and some other groups of plants (including my babies), so it's interesting to see what they actually do and why they can be lost. It's called ndh because it was initially named NADH-dehydrogenase-like, because by sequence it kind of looks like a NADH dehydrogenase.

There's a guy in Japan (Toshiharu Shikanai) who worked on it most of his career and worked out that it certainly is NOT a NADH dehydrogenase and is instead a Fd-dependent plastoquinone reductase. https://www.sciencedirect.com/science/article/pii/S000527281...

Knockout experiments with ndh are annoying because it seems to be only really important in stress conditions - under regular conditions our ndh- plants behaved the same.

Again, this is only one protein, and since it's in chloroplasts it's ultra-common - most likely one of the more abundant proteins on earth (it's not in algae either). And we still call it ndh even though it is a Ferredoxin-plastoquinone reductase.

AI PROMPTING → AI VERIFYING (Balaji): https://x.com/balajis/status/1930156049065246851

That CERT doesn't seem to be looking for fraud, but more like errors in the bureaucracy. They request medical documents and assess them against the regular criteria, but no effort is made to find the sort of fraud criminals would engage in, like fraudulently produced documents for tests that never happened.

You still gravely misunderstand what has happened and what the conversation in physics is. I'm not just making shit up or guessing, but I do have a degree in physics. There is much more nuance to this than you'd get from Pop-Sci or even basic classes. So I'll let you in on what physicists are talking about over beers and to one another. What's going on in the papers and between them.

What you seem to misunderstand is that science is not a mechanical process. It is artistic.

You have to find new ideas and you have to challenge conventions. It is about how you challenge these ideas. It is about how you prove you are right. You're right to say that claims are one thing and proofs are another, but this is why Einstein worked on this problem rather than stating it and moving on. There's a big difference.

Let's look at Schrodinger's Cat

I hold the same belief as Einstein and this is also true for most physicists. The cat is EITHER alive or dead. Regardless of our act of checking.

Here's the big problem... and is a big part everybody misses:

A photon is an observer. The cat is an observer. The detector that releases the poison is an observer. The literal particle that is being radiated from the isotope is, you guessed it, an observer. Literally everything is an observer. An interaction necessitates observation.

So when Einstein says "Do you believe the moon only exists when I look at it?" he's talking saying he isn't special. It would be silly to think that that happens. And truth is, he's right! We can be on opposite sides of the planet and you can see the moon while I can't and vise versa. But hey, maybe I don't exist and this is all in your head! So stop arguing with yourself I guess?

MOST physicists believe what Einstein believed.

Most of us don't believe there are these infinite universes spawning to "brute force search" the universe, checking literally every possible path. This infinite multiverse is the same thing as "we all live in a simulation". Instead, we believe that we simply do not have access to this information. That is a VERY different answer. But notice something critical, how do we differentiate the two? How would we differentiate the two? Unfortunately, so far, it looks like that is not possible. But we have reasons to believe one side over another. Given everything we know so far, the universe doesn't like to just needlessly use energy.

So we're presented with two (technically more) options:

  1) There are an infinite number of universes, corresponding to all possible events as would be viewed by all possible observers. Thus, the universe is doing a brute force search on whatever its solution space is.
  2) The information is unavailable
    2 a) We can't access that information
    2 b) We don't know how to access that information

Einstein believed 2b. Most physicists sit in 2, and I'm willing to bet even Max Tegmark believes #2 is right. More people are split between 2a and 2b, but no one is really ruling either option out. Certainly we hope the answer is 2b, but until someone proves that we can't access the information, we're going to be having this debate. Of course, there's actually one more answer that will change the debate: someone proves the answer is unprovable (this actually seems to be the current likely option btw).

We should also believe 2 because we have examples of both and they're quite common.

2a) If you get into actually doing physics work you will see how complex measurements actually are. You can't actually ever directly measure something, it is always through some chain of proxies. Really, the big question with the cat here is trying to come up with a clever solution so this. Maybe we're making false assumptions. Maybe we can detect the sound of the glass cracking when it releases the poison. Maybe the cat always purrs while it is alive. Those would be ways to indirectly determine if the cat is alive or dead. But it is a thought experiment for a reason.

2b) Heat is the great example of information loss. We have time, which forces a one-way computation. We can watch particles float around and progress from time t_0 to time t_n. We know that there was a unique path and a truthful answer to how these particles moved. But if you hand someone only the data for t_0 and t_n they will be unable to tell you what trajectories those particles took! They can only do this probabilistically!

That's doesn't mean all these potential universes exist, that just means we lost the information!

Similarly, the math says a blackhole is a singularity. A point where there's infinite density in an infinitely small space. But this doesn't mean this thing definitely 100% positively unquestionably exists. That's a laughable idea. There's other explanations that have yet to be ruled out. There's other explanations that have yet to be found!

So it must be the math that is "broken". Doesn't mean it is easy to fix, but it needs to be fixed. Our physics models are incomplete. That's okay! We still have work to do.

Think about what you've said. If it were true, no progress would ever happen. Like the universe didn't suddenly change when Newton and Leibniz invented calculus! Obviously our physics models back then were wrong. The question is how wrong. As best as we can tell, we are still converging. There is noise, but you can still converge with noise. Yes, there are big problems with academia today, and they should be pushed back against (I'm not shy about doing this myself if you check my comment history), but that's different than what you're suggesting.

So here's your mistake: you think your information is complete. Really, we have barely scratched the surface here. And go ahead, prove me wrong. There's a multitude on Nobels to be awarded for proving any of these points.