JakeTheDog's recent activity

  1. Comment on Chinese scholar and outspoken critic directly blames Xi Jinping for severity of viral outbreak in ~news

    JakeTheDog
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    I thought that, relative to SARS and in line with "Western" standards, the CCP has reacted promptly and appropriately to the nCov? Is there any evidence of them dragging their feet and being...

    I thought that, relative to SARS and in line with "Western" standards, the CCP has reacted promptly and appropriately to the nCov? Is there any evidence of them dragging their feet and being uncooperative with global efforts?

    2 votes
  2. Comment on New Coronavirus Protease Structure Available in ~science

    JakeTheDog
    Link
    My professional (biochemistry) twitter feed has been blowing up lately with rapid releases of data on the novel coronavirus (2019-nCoV), and I thought I could give some insight to the scientific...

    My professional (biochemistry) twitter feed has been blowing up lately with rapid releases of data on the novel coronavirus (2019-nCoV), and I thought I could give some insight to the scientific front lines.

    There was also an article posted here recently about the success of AlphaFold predicting protein structure correctly, and a question about why this is important. Here's an excellent example.

    Main takeaway: because we have the structure of a key nCoV protein, and because it is very similar to the functionally-identical protein in the nCoV relative, SARS, this discovery means we can leap ahead in drug development for combating nCoV infection.

    5 votes
  3. Comment on 2020 Doomsday Clock Announcement (100 seconds to midnight) in ~news

    JakeTheDog
    Link Parent
    Yea, I totally agree that this sort of activism, if you can call it that, is an overall good. As it can put pressure on people to act. My only issue is that its authority is so misrepresented that...

    Yea, I totally agree that this sort of activism, if you can call it that, is an overall good. As it can put pressure on people to act. My only issue is that its authority is so misrepresented that it becomes a joke, and leaders that should be pressured by things like this just dismiss it outright. Not unlike how Greta Thurnberg is both raising awareness but is also making an easy target for the dismissal of climate change.

    I suppose oversimplification and overconfidence are what rub me the wrong way.

    1 vote
  4. Comment on 2020 Doomsday Clock Announcement (100 seconds to midnight) in ~news

    JakeTheDog
    Link Parent
    What? Where exactly is the science here? Predicting the future (i.e. "midnight") is not exactly a science... Unless astrology is your standard of science...

    What? Where exactly is the science here? Predicting the future (i.e. "midnight") is not exactly a science... Unless astrology is your standard of science...

    5 votes
  5. Comment on 2020 Doomsday Clock Announcement (100 seconds to midnight) in ~news

    JakeTheDog
    Link Parent
    I meant the "crazy" to be in quotes precisely because I don't accept the term but it's a cultural archetype and easy to refer to. Who knows. I rather not intrude in peoples personal lives, let...

    I meant the "crazy" to be in quotes precisely because I don't accept the term but it's a cultural archetype and easy to refer to.

    Which one, precisely?

    Who knows. I rather not intrude in peoples personal lives, let alone medical records. Point being, that mental illness does not preclude success or ensure mental health down the line.

    Anyways, this is all a derailment of my point. Which is that this clock is at best only fun speculation.

  6. Comment on 2020 Doomsday Clock Announcement (100 seconds to midnight) in ~news

    JakeTheDog
    (edited )
    Link Parent
    So what? Nobel laureates can also be indigent people with untreated mental illnesses. Winning a Nobel prize means you contributed something significant in an intellectual niche. It does not...

    So what? Nobel laureates can also be indigent people with untreated mental illnesses. Winning a Nobel prize means you contributed something significant in an intellectual niche. It does not immediately qualify one as an infallible genius across other disciplines, let alone as an oracle.

    1 vote
  7. Comment on 2020 Doomsday Clock Announcement (100 seconds to midnight) in ~news

    JakeTheDog
    Link
    How is this not grand sensationalism? Or any different than the cliche of a "crazy" person with a sandwichboard painted with "the end is near"? What bothers me here is the dressing of subjective...

    How is this not grand sensationalism? Or any different than the cliche of a "crazy" person with a sandwichboard painted with "the end is near"? What bothers me here is the dressing of subjective opinions as some kind of objective, quantifiable fact. Nobody can predict the future, regardless of how obvious it may seem (for reference, see 2016 election predictions and also post-election fallout of how we're going back to the dark ages).

    8 votes
  8. Comment on How the stress of fight or flight turns hair white in ~health

  9. Comment on A watershed moment for protein structure prediction in ~science

    JakeTheDog
    Link Parent
    Sort of. The efficiency is acquired before the possible answers are found, by essentially simplifying the search space. First some terms: "residue" is an amino acid; a chain of amino acids make up...

    Sort of. The efficiency is acquired before the possible answers are found, by essentially simplifying the search space.

    First some terms: "residue" is an amino acid; a chain of amino acids make up a protein. A protein is like a string of beads (residues) "folded" up into a particular shape.

    There are two steps involved. First, is using their neural network, trained on the existing database of protein structures (which is big, to say the least), to predict residue-residue distances i.e. approximate the structure based on what seems to occur in nature.

    Second, they used this approximated candidate structure as a starting point for a physics-based (or a good enough approximation) simulation, essentially energy minimization, to make it realistic. Sort of like when an architect designs a crazy new building and the engineers have to make it functional/realistic for the real world.

    This pairing is optimal. The issue with step 1 is that there are no "real world" physics involved and is generally a very rough solution. And also it's based on a biased data set of preexisting structures. The issue with step 2 is that, in the absence of any concrete starting point, the search space is effectively infinite (as in it's so computationally expensive it's pointless to do).

    To be honest, this isn't really that much of an innovation (as the techniques are in regular use) but it's surprising just how good it manages to be. More than a fractional increment in accuracy, which is usually what we see.

    1 vote
  10. Comment on A watershed moment for protein structure prediction in ~science

    JakeTheDog
    (edited )
    Link Parent
    Hah, I probably should have made a top-level comment answering this in anticipation—such is the burden of knowledge (i.e. forgetting that others don't know what you know). In the simplest terms:...

    Hah, I probably should have made a top-level comment answering this in anticipation—such is the burden of knowledge (i.e. forgetting that others don't know what you know).

    In the simplest terms: knowing the structure (i.e. the "fold(s)") of a protein means we can design drugs to target the protein.

    If genes are the "blueprint", than proteins are the physical "things" that make up an object. For a car, proteins would be the tires, pedals, gears and fuel lines. Let's say this car has some sort of mechanical failure, caused by a bad gear. If a gear is missing a tooth, and you know exactly how the gear is shaped, and you know where the missing tooth is and how it should look like, then you can design a new tooth to weld onto the gear. In biology, we are the cars, a mechanical failure is the disease (or symptom), a gear is the protein, and the "new tooth" you fix the gear with is the drug.

    Right now most drugs are not so much designed as they are discovered by massive library screens, testing tens of thousands of candidate molecules by trial and error. The holy grail would be to computationally predict the ideal drug for a particular issue.

    So to answer your question: it has everything to do with tackling diseases effectively. Not only that, but also the manufacturing of valuable molecules (via synthetic biology; use bacteria or yeast to synthesize complex drugs) and new materials (think of new versions of spider silk for construction).

    I'll 1-up this by also adding that not only is the structure important, but also the dynamics. Proteins are not solid objects, many of them are floppy and move around a lot. Another tricky part is knowing how the movement is "wrong" and how to make it "move better".

    Here's one of my favorite proteins that is essentially a motor: ATP synthase. A similar protein powers a sperm's flagellum, so literally a motor.

    Here is an awesome group that does more protein animations (based on real simulations).

    2 votes
  11. Comment on A watershed moment for protein structure prediction in ~science

    JakeTheDog
    Link Parent
    I work somewhat broadly on method development, mostly specifically in mass spectrometry. I've worked on modelling a bunch of different protein systems. As awesome as these computational predictive...

    I work somewhat broadly on method development, mostly specifically in mass spectrometry. I've worked on modelling a bunch of different protein systems. As awesome as these computational predictive methods are, nothing beats good ol' fashioned empirical analysis with wet-lab techniques.

    One of the major issues is that, despite there being a lot of different techniques you can use to acquire data on protein structures—all with their own strengths and weaknesses—there are some serious limitations that may be impossible to overcome by any one technique. I say "impossible" because the chemistry and/or physics of the protein is simply not compatible with the technique (like large and "floppy" proteins for X-ray crystallography).

    So, the current frontier of the field is to solve protein structures using data obtained by several different techniques in parallel, and then computationally combine the data to model the structure.

    The usefulness of the purely computational approach, as you share here, is that a) predicting a set of 1000 new sequences you just obtained is way easier and faster than going the empirical route, so it's a good first pass and, b) predicted structures can also be combined (and/or validated) with empirical methods.

    5 votes
  12. Comment on A watershed moment for protein structure prediction in ~science

    JakeTheDog
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    If anyone has any questions—I'm an enthusiastic researcher in this field (not specifically AI/ML but structural biology) and I'd be happy to answer!

    If anyone has any questions—I'm an enthusiastic researcher in this field (not specifically AI/ML but structural biology) and I'd be happy to answer!

    3 votes
  13. Comment on What's your favorite food that tastes good and is good for you? in ~food

    JakeTheDog
    Link
    Plain Greek yogurt + frozen fruit + muesli + ground chia seeds or hemp hearts + cocoa. It's essentially a dessert (that serves as a light meal) that is rich in protein, fat and dietary fibre and...

    Plain Greek yogurt + frozen fruit + muesli + ground chia seeds or hemp hearts + cocoa. It's essentially a dessert (that serves as a light meal) that is rich in protein, fat and dietary fibre and the sugars are locked in with the fiber. Plus a bunch of other nutrients with whatever else you add (like the chia seeds or hemp hearts).

    2 votes
  14. Comment on What's your favorite food that tastes good and is good for you? in ~food

    JakeTheDog
    Link Parent
    Depends on the brand. Most often they are absolutely packed with sugar.

    Depends on the brand. Most often they are absolutely packed with sugar.

    4 votes
  15. Comment on Which Tech Company Is Really the Most Evil? in ~tech

    JakeTheDog
    Link Parent
    Yea, but it's not like Slate is bastion of quality and rigor to begin with...

    Yea, but it's not like Slate is bastion of quality and rigor to begin with...

    2 votes
  16. Comment on Supreme Court unanimously dismisses B.C. appeal of Trans Mountain in ~news

    JakeTheDog
    Link Parent
    That's a really nice explanation, thanks for the level-headed response. Can you speculate as to what will likely happen to Alberta in the next decade or so? It seems like they're fucked either...

    That's a really nice explanation, thanks for the level-headed response.

    Can you speculate as to what will likely happen to Alberta in the next decade or so? It seems like they're fucked either way—the expansion of the oil industry is at a literal impasse and adopting a new resource export is unlikely (renewables to support themselves but that's it). I ask because the current government appears to be all-in on oil but that may not be a sustainable strategy, wheras the previous gov (NDP) seemed to be more concerned about diversifying? Do you think Alberta's economy will wither if this continues? I know of some people thinking of joining the industry there, so I'm somewhat concerned.

    1 vote
  17. Comment on Supreme Court unanimously dismisses B.C. appeal of Trans Mountain in ~news

    JakeTheDog
    Link
    How come Alberta isn't pushing any substantial investment in other energy sources? They have already sold a ton of oil, made a ton of money (IIRC Edmonton and Calgary have high median incomes, and...

    How come Alberta isn't pushing any substantial investment in other energy sources? They have already sold a ton of oil, made a ton of money (IIRC Edmonton and Calgary have high median incomes, and growing, and the province has a big savings from the tax?) and the future is renewables anyways. Seems like they're in as good of a position as any to pivot.

    3 votes