6 ms·

Proteins, Proteins Everywhere

79 points by nabla9 5y ago

323 5y ago
[flagged]
- embik 5y ago
  I think it would make sense to provide sources with those quotes from March. I’m admittedly not from the US so I had different scientists talking about the pandemic, but around here 70% vaccination was never considered enough.
  - fsagx 5y ago
    In the pandemic’s early days, Dr. Fauci tended to cite the same 60 to 70 percent estimate that most experts did. About a month ago, he began saying “70, 75 percent” in television interviews. And last week, in an interview with CNBC News, he said “75, 80, 85 percent” and “75 to 80-plus percent.” In a telephone interview the next day, Dr. Fauci acknowledged that he had slowly but deliberately been moving the goal posts. He is doing so, he said, partly based on new science, and partly on his gut feeling that the country is finally ready to hear what he really thinks. https://www.nytimes.com/2020/12/24/health/herd-immunity-covid-coronavirus.html https://www.nytimes.com/2020/12/24/health/herd-immunity-covi... https://www.medpagetoday.com/opinion/vinay-prasad/90445 https://www.medpagetoday.com/opinion/vinay-prasad/90445
    - hutzlibu 5y ago
      "and partly on his gut feeling that the country is finally ready to hear what he really thinks" When you start doing stuff like that, you stop speaking as a scientist, but as a politician.
- DisjointedHunt 5y ago
  Precisely. I'd like the scientific community to begin treating their declarations with the respectful humility science needs. Too often have i been reading headlines such as "The Universe is growing faster than it should" or "How science tells us the Pandemic will end once everyone is vaccinated". . . .or other such pop science cult rubbish. We do NOT know everything, we merely have "best fit" theories that are taught with the disclaimer that these work under specific conditions that we've observed and we have no way of gaming out all the trillions and trillions of possible outcomes in the real world. Trusting the common man with that level of transparency and then making humble "recommendations" seems a far better approach. Should we need to ram through a scientific conclusion, lets do so without making obviously uncertain statements such as "The pandemic will end once everyone is vaccinated" since that presumes a LOT.
  - _Wintermute 5y ago
    You're assuming it's the scientists making these grand claims. Unfortunately it's often the case the scientists will make some small claim with lots of caveats, a university press officer will hype it up, the media will then take that and make it into the most attention grabbing headline they can.
    - netizen-936824 5y ago
      This sorta jives with my observations, but from my experience it seems like its the general population journalists that mess things up. There's such little understanding of these complex topics and then journalists try to cram as much info into a small place and pick the things that sound most important to them. Detail gets lost and importance of some aspects overblown. This happens through multiple stages as in a game of telephone from original research all the way to average people reading or watching the news
  - otabdeveloper4 5y ago
    > How The Science tells us the pandemic will end once everyone is vaccinated Fixed it for you.
  - samus 5y ago
    > headlines such as "The Universe is growing faster than it should" or "How science tells us the Pandemic will end once everyone is vaccinated". Such headlines are the hallmark of popular science journals, who indeed seem to do damage to the credibility of science by riding the clickbait wave.
- fabian2k 5y ago
  Those statements were true for the original virus. They are not true for the current variant. And we really can't predict what new variants can do, we could have guessed that new, more transmissible variants are likely to emerge, but we can't predict the future.
  - refurb 5y ago
    So basically anything scientists tell us may or may not be true depending on how the future evolves? Come on man!
    - dekhn 5y ago
      Yes, this is absolutely the case. Public health leadership is flying in the dark about the evolution of the virus.
      - anamax 5y ago
        > Public health leadership is flying in the dark about the evolution of the virus. And yet, it says that it knows all. Which reminds me - are eggs good or bad this month?
        dekhn 5y ago
        Certainly the public health leadership never implied that it "knew all", that doesn't make sense. They make it clear they are making suggestions based on the data they have, which is ambiguous. It's not clear why you are setting yourself up for distrusting public health leadership.
        anamax 5y ago
        I'd love to have a public health leadership that is trustworthy, but it would be foolish to trust them if they're not. Feel free to point to anyone in the public health leadership who has acknowledged that things might not work as predicted or when they got it wrong. Remember "15 days to flatten the curve?" Then there's the mask flip-flop (early on, health officials said that ordinary people didn't need masks, possibly because they were trying to avoid hoarding that might interfere with having enough for medical professionals) and they're still overstating the value of typical masks. Along the same lines is the PHS response to the :Barrington Declaration". It wasn't "hey, what is their data and how did they arrive at their conclusions". It was "How do we discredit those people." Maybe they were wrong, maybe they were correct, but anyone who says that they're wrong because of who they are is doing politics, not science. Moreover, arguing that they must be evil and discredited because of their conclusion is even worse. And then there's ever popular "outdoor protests that we like are safe but the ones that we don't like will kill everyone, and that's good because those are bad people".
- refurb 5y ago
  Such a BS cop out. When I was doing my PhD, we were all training to pick apart the science. All challenges well come, as it forced our work to be airtight as possible. That’s why the final process of a PhD is your thesis “defense”. To somehow claim that we should just shut up and accept what the government says because “its based on science” is silly. Science changes, science is sometimes wrong. But we should also make clear that science results in policy and policy can be criticized without challenging science. “Yes, vaccines are effective, but no we shouldn’t force people to take them” is a policy objection, not a scientific objection.
DisjointedHunt 5y ago
Reading this story gives me SO much hope for where we are as a society at the moment. It also gives me immense reason for pause to ask how many people out there with great ideas presently do not have access to the tools outlined in the story. We need, now more than ever, an "eli5" or "get up to speed in an hour" source for these very interesting fields where all the progress of the past century is easily visualized at a high level. I get the feeling much of academia shuts down such attempts to preserve their grip on knowledge and thus their authority.
- Ovah 5y ago
  Tangent: I have years of academic studies. And yet it can be time consuming to truly understand where and how ideas came to be. I might have an equation but to understand how it was initially thought of or derived might require access to physical contemporary books. At least once I've had to resort to 18th century handwritten manuscripts. Wikipedia can be great. But I often wonder if historical scientific progress can be made even more accessible.
  - alexpetralia 5y ago
    This etiological approach is captured, for example, in the book "Inventing Temperature" by philosopher of science Hasok Chang. It chronicles the meandering, dialectical and controversial journey scientists pursue in order to discover what exactly temperature is - now elegantly captured in concise but sterile formulas. It demonstrates the process of science, as opposed to merely its output.
- netizen-936824 5y ago
  Some fields are insanely hard to get caught up that simply and quickly. There's such an immense amount of detail in biochemistry that it can quickly become overwhelming to sort through information to find what's really pertinent. I'm not saying it's impossible, but it is definitely a huge challenge
- jryb 5y ago
  > I get the feeling much of academia shuts down such attempts to preserve their grip on knowledge and thus their authority There might be fields like that, but in biology, it really just is that we've accumulated so much knowledge over the past 150 years that I genuinely can't explain modern CRISPR research to a layperson until they've taken courses in molecular biology, microbiology, chemistry, genetics and biochemistry (or the equivalent amount of self-study). The field is genuinely vast and complex, and there's no way to hide that complexity behind an abstraction without being misleading.
ralusek 5y ago
There needs to be further collaboration between computer scientists and these emerging biological platforms. Between the ability to synthesize code (RNA) and data (protein), I don't think it's been fully realized by most that they've truly entered the world of computing.
- netizen-936824 5y ago
  Don't worry, we are. But it does seem slow compared to other tech industries
- itg 5y ago
  Isn't this what the entire field of bioinformatics supposed to be about? I know a few people who left it because it doesn't pay as well (in the US) as your average software engineering job.
  - gilleain 5y ago
    I have seen a distinction made between "bioinformatics" - analysing biological data with software - and "computational biology" - using biological systems to do computing. What OP seems to be talking about is systems modelling, where you model the network of genes and proteins (genomics and proteomics) using tools partly derived from modelling of computer networks.
    - epgui 5y ago
      That's not how I would explain bioinformatics and computational biology... What people often mean when they say bioinformatics is actually computational biology: using computer software, algorithms and other such tools to analyze biological data. Bioinformatics is the development of new tools, new algorithms and new methods to do computational biology. In other words, a bioinformatician is to a computer scientist what a computational biologist is to a data scientist. Using biological systems to do computing is more in the realm of "biological computers".
- gilleain 5y ago
  Yes and no. Biological systems are similar to mechanical computers in that they are information processing systems. However, they are also self-assembling, self-repairing, wet, massively parallel, etc. Artificial biological systems are in a sense programmable, but with the difficulties of a physical system that can be error-prone and extremely complex.
Traubenfuchs 5y ago
> Meanwhile, the tragic loss of respect for scientific authority around the world Governments and their figurehead „scientists“ like Fauci have rightfully lost all our trust by contradicting the nonsense and lies they spew and moving the goalposts every other day, under the weak guise of „developing/new knowledge“.
- mdp2021 5y ago
  In fact, it's not really "scientists": scientists "search" (put together puzzle pieces, check hypotheses), they do not climb on pedestals claiming close social relation with The Truth. It's political agents looking for excuses. You appear, with that formulation, to have missed the paragraph just above: > And scientists have been attacked in new ways and with new methods by politicians who are exploiting social media and long-tested methods of indoctrination to undermine scientific authority on issues ranging from vaccines in the midst of a pandemic to the impending devastation of climate change In a stub (unfortunately), the author claimed that the role of science is under political attack. Very clearly (in some regions), there as been a devastating blow against civilization attempting through narratives for propaganda to make of science a fideistic sect, a doctrine - its opposite.
deleted 5y ago
[deleted]
- deleted 5y ago
  [deleted]
zhengiszen 5y ago
Excellent summary of the year 2021
COGlory 5y ago
>This “protein-folding problem,” as it came to be known, baffled scientists until this year, when the papers we’ve deemed the 2021 Breakthrough of the Year were published. This is a straight lie and the author should be embarrassed. There's not one scientist alive that can explain how proteins fold from their amino acid sequence. There's not one algorithm in existence that can predict it de novo. I'm so tired of seeing this lie repeated over and over. AlphaFold did not gain us any new information on how proteins fold. It just got really good at modelling them from existing data where existing data is available. Which is great. But still ultimately limited by the same categorical limitations of homology modeling. It simply has not solved protein folding. Yes it's amazing. Yes it's worthy of lots of praise. No, it did not solve protein folding, ESPECIALLY in the way that is described here.
- epgui 5y ago
  > There's not one scientist alive that can explain how proteins fold from their amino acid sequence. As a biochemist, what I understood from this editorial was totally reasonable: - scientists understand that electrostatic forces guide protein folding, and steric factors limit the conformations a protein can take - scientists understand that the primary structure determines the secondary and tertiary structures of proteins - scientists know that protein folding is aided by chaperone proteins - scientists understand how thermodynamics and entropy affect protein folding Despite all of the above, scientists cannot solve protein folding de novo. New tools now allow us to make better, cheaper predictions which are testable. Sounds reasonable to me.
  - COGlory 5y ago
    As a structural biologist, I have to ask, how did you draw that from this? > seemed possible that the three-dimensional structure of a protein could be predicted based on the sequence of its amino acids. That simply is not what AlphaFold (or any homology modeling) is doing, and certainly not: >This is a breakthrough on two fronts. It solves a scientific problem that has been on the to-do list for 50 years. And just like Fermat’s Last Theorem or gravitational waves, scientists kept at it until it was done.
yeetaccount4 5y ago
It’ll be interesting to see if this stuff could open the door to treatment options for prion diseases.

79 points by nabla9 5y ago

323 5y ago

[flagged]

embik 5y ago
I think it would make sense to provide sources with those quotes from March. I’m admittedly not from the US so I had different scientists talking about the pandemic, but around here 70% vaccination was never considered enough.
- fsagx 5y ago
  In the pandemic’s early days, Dr. Fauci tended to cite the same 60 to 70 percent estimate that most experts did. About a month ago, he began saying “70, 75 percent” in television interviews. And last week, in an interview with CNBC News, he said “75, 80, 85 percent” and “75 to 80-plus percent.” In a telephone interview the next day, Dr. Fauci acknowledged that he had slowly but deliberately been moving the goal posts. He is doing so, he said, partly based on new science, and partly on his gut feeling that the country is finally ready to hear what he really thinks. https://www.nytimes.com/2020/12/24/health/herd-immunity-covid-coronavirus.html https://www.nytimes.com/2020/12/24/health/herd-immunity-covi... https://www.medpagetoday.com/opinion/vinay-prasad/90445 https://www.medpagetoday.com/opinion/vinay-prasad/90445
  - hutzlibu 5y ago
    "and partly on his gut feeling that the country is finally ready to hear what he really thinks" When you start doing stuff like that, you stop speaking as a scientist, but as a politician.
DisjointedHunt 5y ago
Precisely. I'd like the scientific community to begin treating their declarations with the respectful humility science needs. Too often have i been reading headlines such as "The Universe is growing faster than it should" or "How science tells us the Pandemic will end once everyone is vaccinated". . . .or other such pop science cult rubbish. We do NOT know everything, we merely have "best fit" theories that are taught with the disclaimer that these work under specific conditions that we've observed and we have no way of gaming out all the trillions and trillions of possible outcomes in the real world. Trusting the common man with that level of transparency and then making humble "recommendations" seems a far better approach. Should we need to ram through a scientific conclusion, lets do so without making obviously uncertain statements such as "The pandemic will end once everyone is vaccinated" since that presumes a LOT.
- _Wintermute 5y ago
  You're assuming it's the scientists making these grand claims. Unfortunately it's often the case the scientists will make some small claim with lots of caveats, a university press officer will hype it up, the media will then take that and make it into the most attention grabbing headline they can.
  - netizen-936824 5y ago
    This sorta jives with my observations, but from my experience it seems like its the general population journalists that mess things up. There's such little understanding of these complex topics and then journalists try to cram as much info into a small place and pick the things that sound most important to them. Detail gets lost and importance of some aspects overblown. This happens through multiple stages as in a game of telephone from original research all the way to average people reading or watching the news
- otabdeveloper4 5y ago
  > How The Science tells us the pandemic will end once everyone is vaccinated Fixed it for you.
- samus 5y ago
  > headlines such as "The Universe is growing faster than it should" or "How science tells us the Pandemic will end once everyone is vaccinated". Such headlines are the hallmark of popular science journals, who indeed seem to do damage to the credibility of science by riding the clickbait wave.
fabian2k 5y ago
Those statements were true for the original virus. They are not true for the current variant. And we really can't predict what new variants can do, we could have guessed that new, more transmissible variants are likely to emerge, but we can't predict the future.
- refurb 5y ago
  So basically anything scientists tell us may or may not be true depending on how the future evolves? Come on man!
  - dekhn 5y ago
    Yes, this is absolutely the case. Public health leadership is flying in the dark about the evolution of the virus.
    - anamax 5y ago
      > Public health leadership is flying in the dark about the evolution of the virus. And yet, it says that it knows all. Which reminds me - are eggs good or bad this month?
      - dekhn 5y ago
        Certainly the public health leadership never implied that it "knew all", that doesn't make sense. They make it clear they are making suggestions based on the data they have, which is ambiguous. It's not clear why you are setting yourself up for distrusting public health leadership.
        anamax 5y ago
        I'd love to have a public health leadership that is trustworthy, but it would be foolish to trust them if they're not. Feel free to point to anyone in the public health leadership who has acknowledged that things might not work as predicted or when they got it wrong. Remember "15 days to flatten the curve?" Then there's the mask flip-flop (early on, health officials said that ordinary people didn't need masks, possibly because they were trying to avoid hoarding that might interfere with having enough for medical professionals) and they're still overstating the value of typical masks. Along the same lines is the PHS response to the :Barrington Declaration". It wasn't "hey, what is their data and how did they arrive at their conclusions". It was "How do we discredit those people." Maybe they were wrong, maybe they were correct, but anyone who says that they're wrong because of who they are is doing politics, not science. Moreover, arguing that they must be evil and discredited because of their conclusion is even worse. And then there's ever popular "outdoor protests that we like are safe but the ones that we don't like will kill everyone, and that's good because those are bad people".
refurb 5y ago
Such a BS cop out. When I was doing my PhD, we were all training to pick apart the science. All challenges well come, as it forced our work to be airtight as possible. That’s why the final process of a PhD is your thesis “defense”. To somehow claim that we should just shut up and accept what the government says because “its based on science” is silly. Science changes, science is sometimes wrong. But we should also make clear that science results in policy and policy can be criticized without challenging science. “Yes, vaccines are effective, but no we shouldn’t force people to take them” is a policy objection, not a scientific objection.

DisjointedHunt 5y ago

Reading this story gives me SO much hope for where we are as a society at the moment. It also gives me immense reason for pause to ask how many people out there with great ideas presently do not have access to the tools outlined in the story. We need, now more than ever, an "eli5" or "get up to speed in an hour" source for these very interesting fields where all the progress of the past century is easily visualized at a high level. I get the feeling much of academia shuts down such attempts to preserve their grip on knowledge and thus their authority.

Ovah 5y ago
Tangent: I have years of academic studies. And yet it can be time consuming to truly understand where and how ideas came to be. I might have an equation but to understand how it was initially thought of or derived might require access to physical contemporary books. At least once I've had to resort to 18th century handwritten manuscripts. Wikipedia can be great. But I often wonder if historical scientific progress can be made even more accessible.
- alexpetralia 5y ago
  This etiological approach is captured, for example, in the book "Inventing Temperature" by philosopher of science Hasok Chang. It chronicles the meandering, dialectical and controversial journey scientists pursue in order to discover what exactly temperature is - now elegantly captured in concise but sterile formulas. It demonstrates the process of science, as opposed to merely its output.
netizen-936824 5y ago
Some fields are insanely hard to get caught up that simply and quickly. There's such an immense amount of detail in biochemistry that it can quickly become overwhelming to sort through information to find what's really pertinent. I'm not saying it's impossible, but it is definitely a huge challenge
jryb 5y ago
> I get the feeling much of academia shuts down such attempts to preserve their grip on knowledge and thus their authority There might be fields like that, but in biology, it really just is that we've accumulated so much knowledge over the past 150 years that I genuinely can't explain modern CRISPR research to a layperson until they've taken courses in molecular biology, microbiology, chemistry, genetics and biochemistry (or the equivalent amount of self-study). The field is genuinely vast and complex, and there's no way to hide that complexity behind an abstraction without being misleading.

ralusek 5y ago

There needs to be further collaboration between computer scientists and these emerging biological platforms. Between the ability to synthesize code (RNA) and data (protein), I don't think it's been fully realized by most that they've truly entered the world of computing.

netizen-936824 5y ago
Don't worry, we are. But it does seem slow compared to other tech industries
itg 5y ago
Isn't this what the entire field of bioinformatics supposed to be about? I know a few people who left it because it doesn't pay as well (in the US) as your average software engineering job.
- gilleain 5y ago
  I have seen a distinction made between "bioinformatics" - analysing biological data with software - and "computational biology" - using biological systems to do computing. What OP seems to be talking about is systems modelling, where you model the network of genes and proteins (genomics and proteomics) using tools partly derived from modelling of computer networks.
  - epgui 5y ago
    That's not how I would explain bioinformatics and computational biology... What people often mean when they say bioinformatics is actually computational biology: using computer software, algorithms and other such tools to analyze biological data. Bioinformatics is the development of new tools, new algorithms and new methods to do computational biology. In other words, a bioinformatician is to a computer scientist what a computational biologist is to a data scientist. Using biological systems to do computing is more in the realm of "biological computers".
gilleain 5y ago
Yes and no. Biological systems are similar to mechanical computers in that they are information processing systems. However, they are also self-assembling, self-repairing, wet, massively parallel, etc. Artificial biological systems are in a sense programmable, but with the difficulties of a physical system that can be error-prone and extremely complex.

Traubenfuchs 5y ago

> Meanwhile, the tragic loss of respect for scientific authority around the world Governments and their figurehead „scientists“ like Fauci have rightfully lost all our trust by contradicting the nonsense and lies they spew and moving the goalposts every other day, under the weak guise of „developing/new knowledge“.

mdp2021 5y ago
In fact, it's not really "scientists": scientists "search" (put together puzzle pieces, check hypotheses), they do not climb on pedestals claiming close social relation with The Truth. It's political agents looking for excuses. You appear, with that formulation, to have missed the paragraph just above: > And scientists have been attacked in new ways and with new methods by politicians who are exploiting social media and long-tested methods of indoctrination to undermine scientific authority on issues ranging from vaccines in the midst of a pandemic to the impending devastation of climate change In a stub (unfortunately), the author claimed that the role of science is under political attack. Very clearly (in some regions), there as been a devastating blow against civilization attempting through narratives for propaganda to make of science a fideistic sect, a doctrine - its opposite.

deleted 5y ago

[deleted]

deleted 5y ago
[deleted]

zhengiszen 5y ago

Excellent summary of the year 2021

COGlory 5y ago

>This “protein-folding problem,” as it came to be known, baffled scientists until this year, when the papers we’ve deemed the 2021 Breakthrough of the Year were published. This is a straight lie and the author should be embarrassed. There's not one scientist alive that can explain how proteins fold from their amino acid sequence. There's not one algorithm in existence that can predict it de novo. I'm so tired of seeing this lie repeated over and over. AlphaFold did not gain us any new information on how proteins fold. It just got really good at modelling them from existing data where existing data is available. Which is great. But still ultimately limited by the same categorical limitations of homology modeling. It simply has not solved protein folding. Yes it's amazing. Yes it's worthy of lots of praise. No, it did not solve protein folding, ESPECIALLY in the way that is described here.

epgui 5y ago
> There's not one scientist alive that can explain how proteins fold from their amino acid sequence. As a biochemist, what I understood from this editorial was totally reasonable: - scientists understand that electrostatic forces guide protein folding, and steric factors limit the conformations a protein can take - scientists understand that the primary structure determines the secondary and tertiary structures of proteins - scientists know that protein folding is aided by chaperone proteins - scientists understand how thermodynamics and entropy affect protein folding Despite all of the above, scientists cannot solve protein folding de novo. New tools now allow us to make better, cheaper predictions which are testable. Sounds reasonable to me.
- COGlory 5y ago
  As a structural biologist, I have to ask, how did you draw that from this? > seemed possible that the three-dimensional structure of a protein could be predicted based on the sequence of its amino acids. That simply is not what AlphaFold (or any homology modeling) is doing, and certainly not: >This is a breakthrough on two fronts. It solves a scientific problem that has been on the to-do list for 50 years. And just like Fermat’s Last Theorem or gravitational waves, scientists kept at it until it was done.

yeetaccount4 5y ago

It’ll be interesting to see if this stuff could open the door to treatment options for prion diseases.