[HN Gopher] Scientists discover the first new antibiotics in ove...
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Scientists discover the first new antibiotics in over 60 years
using AI
Author : taubek
Score : 152 points
Date : 2023-12-27 15:05 UTC (7 hours ago)
(HTM) web link (www.euronews.com)
(TXT) w3m dump (www.euronews.com)
| RcouF1uZ4gsC wrote:
| Tigecycline
|
| https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1426172/
|
| is a new class of antibiotics discovered around 2005 that also
| works against resistant bacteria such as MRSA and VRE.
|
| So while it is great they are coming up with new antibiotics, it
| is by no means the first in 60 years.
| PlasmonOwl wrote:
| Had the same issue on Reddit recently. Toxibaccin was
| discovered in soils in 2018. Hell I know someone who developed
| one recently at a university. It's AMAZING AI can do this, but
| it certainly doesn't destroy prior approaches. Yet.
|
| Disclaimer: spelling and name of antibiotic may be incorrect.
| It is not my field, and the spelling is phonetic from myself.
| If pressed, I will ask the scientist for the specific name.
| maxerickson wrote:
| I expect you are referencing
| https://en.wikipedia.org/wiki/Teixobactin
| 29athrowaway wrote:
| Discovered in some random dirt from Maine.
| hackernewds wrote:
| "Discovered" like penicillin? It irks me when it's
| presented as accidental, when it does go through testing
| after
| 29athrowaway wrote:
| Penicillin was also accidental? I don't understand the
| point.
| PlasmonOwl wrote:
| Maybe he conflates discovery with accident. Materials
| science searches chemical space and makes discoveries.
| There is no accident in that kind of discovery?
| maxerickson wrote:
| Seems that is a tetracycline derivative? A class of antibiotics
| generally refers to the mechanism of action, so I'd think it
| wouldn't be a new class if it is derived from an existing one.
| awwaiid wrote:
| Maybe this is a missing-comma type issue, and they mean that
| the last time that AI came up with an antibiotic was 60 years
| ago
| augustulus wrote:
| where would you put the comma to fix that?
| lacrimacida wrote:
| It's the first comma in click-bait.
| hackernewds wrote:
| now for them to make one against viruses
| pajko wrote:
| Ceftaroline
|
| https://pubmed.ncbi.nlm.nih.gov/20334458/
|
| Discovered about at the same time or later. Also works against
| MRSA.
| dvh wrote:
| I've been under the impression that we don't have new antibiotics
| because it is not economically viable.
|
| When you invent new weight loss drug you can sell millions of
| pills to anyone.
|
| If you invent new antibiotic it is immediately classified as
| "reserve antibiotic" and the sale is restricted.
| ac2u wrote:
| >it is immediately classified as "reserve antibiotic" and the
| sale is restricted.
|
| Is that so medical professionals can break it out as a means of
| last resort to save a patient and ensure the course is
| finished?
|
| If so that mightn't be a bad idea before we destroy the
| potential of new antibiotics too by having the general public
| misuse them render them useless over time.
| zbrozek wrote:
| It's probably a good idea. But doing that alone--without
| substituting market incentives with something else--means
| that there won't be new products to use in that way.
| garrisonhh wrote:
| I think the above commenter is just pointing out how the
| fundamental conflict between these two things results in
| significantly lessened incentive for pharmaceutical companies
| to put money into researching new antibiotics
| schneems wrote:
| I extremely know nothing about this field. Would a naive
| approach would to have a coordinated "crop rotation" type
| tactic where all hospitals switched to a primary antibiotic
| every C years/months do anything?
| RiDiracTid wrote:
| Empirically, many bacteria seem to be able to acquire
| resistance in a way that doesn't significantly impact
| their fitness, meaning they can basically get new
| resistances and keep old ones for almost arbitrarily
| long, so the crop rotation idea would fail massively.
|
| https://academic.oup.com/femsre/article/35/5/901/2680377
| schneems wrote:
| Good to know, thanks for the explanation!
| zdragnar wrote:
| There's a secondary consideration as well; designing new
| chemicals is fairly easy, synthesizing them harder, and
| scaling that to commercial manufacturing very hard.
|
| Oh, and you still have to prove it to be safe and effective
| through years of clinical trials.
|
| AI is basically still only helping us with the easiest parts,
| and this particular class is drugs is essentially a limited
| resource (to avoid force-evolving stains of bacteria that are
| resistant or immune).
|
| At the end of the day, there's not as much research because
| there's a finite amount of resources to go around and there
| are easier / lower hanging fruit.
| Waterluvian wrote:
| It requires a socialized solution: to fund it for future needs
| rather than for profits.
| marcusverus wrote:
| A government which can't regulate effectively can't be
| trusted with a monopoly.
|
| Anyway, how does holding antibiotics in reserve help
| anything? Why let the bugs evolve resistance to one
| antibiotic at a time, rather than hitting them them with
| multiple antibiotics and thus raising the evolutionary hurdle
| to resistance? Was this strategy designed by the bad guys in
| a Jacky Chan movie?
| wolverine876 wrote:
| Whatever the theory, the government achieves quite a bit.
| Look at NASA, as one example, not to mention nuclear energy
| in all its applications, etc.
| travoc wrote:
| 70-80% of NASA's budget is spent on contracts with
| commercial companies, research institutions, and other
| external organizations.
| wolverine876 wrote:
| I'm not sure how that matters. The commercial companies
| also subcontract.
| stupidcar wrote:
| How would you ensure things like industrial farms use a
| more expensive multi-antibiotic approach instead of a
| cheaper single-antibiotic one without effective regulation?
| Broken_Hippo wrote:
| _A government which can 't regulate effectively can't be
| trusted with a monopoly._
|
| If only the world were as simple. But it isn't, and
| everyone knows that those with power (in general,
| governments) will never be regulated effectively enough for
| everyone - but that doesn't make them never to be trusted
| with monopoly, nor does it mean that the government's
| monopoly is bad.
|
| Sorry, I don't really want private militaries nor private
| tax collection. I'm happy the government runs things like
| IDs and drivers licenses. In fact, various department of
| motor vehicles (or whatever your local thing is called) is
| an excellent example of how a monopoly can be a good or bad
| experience. I'm originally from Indiana and the motor
| vehicle folks are great there and the service is easy to
| use - by design - but it isn't like that everywhere in the
| US. This has nothing really to do with how "effective"
| their regulation is.
|
| I'm not sure actual monopolies are better - are you really
| satisfied with your electricity provider or ISP?
| shzhdbi09gv8ioi wrote:
| Anyway what? You don't win an internet argument by dumping
| some random quote.
|
| If you have some ideas, do share them.
| sfilmeyer wrote:
| They did share an idea.
|
| > rather than hitting them them with multiple antibiotics
| and thus raising the evolutionary hurdle to resistance?
|
| It was surrounded by some rudeness and is probably a poor
| idea (but I'm no expert), but it was an idea.
| CatWChainsaw wrote:
| I don't know if multiple antibiotics helps prevent
| resistance necessarily. Resistance usually comes about when
| the dosage given allows survivors with resistance mutations
| to become the main population. I mean, I can see where
| multiple antibiotics and sub-lethal dosages that disrupt
| function in multiple ways could be enough pressure to break
| the bacteria, but sufficient dosing is important, and
| making sure a patient does their regimen properly is
| entirely the patient's responsibility. In order to prevent
| the exact same situation playing out with any new
| antibiotics, we shouldn't allow history to repeat itself.
|
| Plus the normal gut flora would be disrupted by the
| multiple antibiotics as well, so there would be more work
| involved in the recovery of the symbiotes and commensals.
| devilbunny wrote:
| > how does holding antibiotics in reserve help anything?
|
| If they have novel mechanisms of action, quite a lot. If
| it's just another entrant in a class of antibiotics for
| which we have numerous drugs (and thus resistances)
| already, probably not as much.
| UncleOxidant wrote:
| This is good example of the limits of capitalism.
| rjtavares wrote:
| The whole concept of patents already is a solution to one of
| the limits of capitalism (they're basically government
| enforced monopolies). There are interesting ideas on how to
| improve the system, hopefully we won't throw the baby with
| the bath water here.
| fasterik wrote:
| I think capitalism has plenty of solutions for this. We can
| allocate government funding for research, pass new laws that
| create tax incentives, create prize funds to incentivize
| development of specific drugs, or make advanced market
| commitments where institutions commit to buying a portion of
| a certain type of drug after it's produced.
|
| The underlying problem is the lack of political will and
| cooperation to implement these solutions.
| WorkerBee28474 wrote:
| > If you invent new antibiotic it is immediately classified as
| "reserve antibiotic" and the sale is restricted.
|
| Are there examples of this? I've heard people say this happens,
| but I've never heard a concrete example.
|
| I googled 'reserve antibiotic' and found Ceftobiprole, and see
| it's for sale for $40,000/gram, so clearly it's possible to
| charge money for a 'reserve'.
| photochemsyn wrote:
| The nature article is paywalled so it's impossible to see what
| they actually did, and the abstract is not very clear either.
| What benefit did they get from whole-genome sequencing, for
| example?
|
| Additionally, it can't be called an antibiotic until it goes
| through the necessary human clinical trials, where all kinds of
| problems can crop up - they don't seem to provide any evidence
| that their AI-enabled scan for human cell toxicity actually
| worked.
|
| Finally, the real problem with antibiotic resistance is that
| microbes always evolve resistance over time if the antibiotics
| are overused (i.e prophylactic use in industrial animal
| agribusiness, and careless prescriptions of antibiotics from
| doctors).
| throwawaymaths wrote:
| An antibiotic is an antibiotic whether or not it would kill a
| patient too.
| ycui1986 wrote:
| bleach is also antibiotic then
| hackernewds wrote:
| so is lava then
| kbelder wrote:
| Fair, but finding new antibiotics then becomes trivial.
| throwawaymaths wrote:
| Isolating a new antibiotic (even if it wouldn't work on
| humans) is typically worth a chemistry PhD. Call me when
| you get it.
| rambambram wrote:
| What is AI? I've only heard of LLM.
| catchnear4321 wrote:
| it is just the commercial name for llm and related
| technologies.
| dartos wrote:
| That's just not true. The technology that's behind LLMs have
| been in use in many disciplines for decades. (Under the names
| "machine learning," "statistics," and now AI)
|
| LLMs are just the ones that are popular right now because
| even non technical people can interact with them.
|
| In the mid 2010s it was image classification, for example.
| skellington wrote:
| Sort of. The deep-learning AI revolution started with back
| propagation techniques (80s) that made neural nets
| trainable. But since then it's taken a long time to get to
| the relatively recent architectural breakthroughs like
| transformers (2017) and modern-diffusion (2020) which lead
| to chat-gpt and dall-e. All of the big AI breakthroughs now
| are based on neural nets vs classical machine learning
| which grouped a bunch of statistical, regression, and
| optimization type models together.
|
| Modern AI is the synthesis of new techniques and old ideas
| plus huge datasets and huge computing power.
| catchnear4321 wrote:
| > LLMs are just the ones that are popular right now because
| even non technical people can interact with them.
|
| this was essentially my point, that a /s might have made
| more clear, and made cost less internet points. ai and how
| the term is used commercially are very different things.
| the latter tending to be a myopic view of the former that
| is constrained by dollar-seeking.
|
| ai is getting to be old as shit. ai hype is in its latest
| wave of commercialization. llms being the current so hot
| right now.
| jdefr89 wrote:
| It's true that AI has seen many advancements before a
| "harsh winter" comes along. You're correct this is
| sensationalized, and also, some of these technologies have
| indeed been in use for decades. But, the Transformer model
| used by the new popular LLMs is quite recent (2017 is when
| the paper originally released I believe).
| jfengel wrote:
| "Deep learning" and neural networks in general were a thing
| long before they were applied specifically to language models.
|
| It's still not "intelligence" but it does use techniques
| inspired by brains and have some of the same advantages in
| "seeing" patterns.
| Dalewyn wrote:
| "AI" is what we used to call algorithms, macros, and
| applications not too long ago.
|
| Marketing.
| gumballindie wrote:
| Amazon goes as far as to call my heating fan's temperature
| control ai. Probably why it doesn't work and it randomly
| turns on and off.
| graypegg wrote:
| I don't think you should be seemingly in the negatives for this
| comment. :( It's a totally valid question, and the whole
| industry has introduced so many new words, acronyms and private
| definitions. It feels unfair to punish someone for not
| following them all.
|
| AI is "artificial intelligence". That's a pretty intentionally
| vague term. It doesn't imply any specific technological
| implementation, but it does imply the device/software makes
| decisions autonomously that would otherwise need a human to
| intervene. There's a million holes in that definition, and
| that's why the adjective "AI" kind of sucks when used on its
| own. It's also worth noting it's been used in sci-fi for eons.
| It's also been used to describe non-playable characters in
| video games for a long time, which obviously didn't have the
| sort of "AI" we think of now.
|
| LLMs are neural networks that work with "tokens" from text. So
| a big statistics-based predictive AI. There are more complex
| implementations that can consume other kinds of content as
| well, but "LLM" almost always refers to a neural network that
| consumes small chunks of text called tokens, and outputs more
| tokens based on that input. The magic we see with LLMs happens
| because given enough data, language itself builds up a
| surprisingly good model of "thinking".
|
| There's some really good explanations in the sibling comments!
| I'm no expert, and I think someone can probably correct me here
| if I messed up something there.
| pfisherman wrote:
| The headline is sensationalized.
|
| They did a virtual screen of a large compound library.
|
| QSAR / QSPR / Virtual Screening has been around since the late
| 1950s.
|
| The secret sauce here was the large experimental dataset - on the
| order of 10^5 compounds - they generated to train the model.
|
| Maybe the explainability part is kind of novel for a neural
| network based approach; but not clear that you couldn't identify
| substructure classes better with a pure bioinformatic approach.
| wolverine876 wrote:
| The OP says something different:
|
| _" The insight here was that we could see what was being
| learned by the models to make their predictions that certain
| molecules would make for good antibiotics," James Collins,
| professor of Medical Engineering and Science at the
| Massachusetts Institute of Technology (MIT) and one of the
| study's authors, said in a statement._
|
| ...
|
| _" What we set out to do in this study was to open the black
| box. These models consist of very large numbers of calculations
| that mimic neural connections, and no one really knows what's
| going on underneath the hood," said Felix Wong, a postdoc at
| MIT and Harvard and one of the study's lead authors._
|
| > not clear that you couldn't identify substructure classes
| better with a pure bioinformatic approach.
|
| Lots of things aren't clear, but what supports your particular
| claim? Has it ever been done? And is it addressed in the
| article?
| hedora wrote:
| They're saying that traditional computational drug discovery
| pipelines do all the stuff the authors are claiming.
|
| So, yes, it's been done at scale for decades.
|
| The article makes all sorts of incorrect claims. For example,
| it says it has been 60 years since the last antibiotic was
| discovered, and that this works enables computational
| screening of antibiotics for the first time.
|
| Here's work from 2022 that used conventional computational
| screening to discover a novel antibiotic:
|
| https://phys.org/news/2022-10-discovery-antibiotic-
| resistant...
| wolverine876 wrote:
| These claims on HN, about every OP, really lack credibility
| for me. Either HN commenters are the only smart people in
| the world or we are misleading each other. At the same
| time, we are dissuading each other from engaging in a world
| of intellect, knowledge and innovation.
|
| HN is a forum of intellectual curiosity. The near-universal
| critiques are the opposite of that.
| COGlory wrote:
| I don't know what to tell you. New antibiotics are
| discovered pretty often. They aren't brought to market,
| but they certainly are discovered. This headline is just
| wrong.
| Jensson wrote:
| > These claims on HN, about every OP, really lack
| credibility for me.
|
| Do you trust journalists that much? Have you ever read an
| article about something you are an expert on? You
| shouldn't trust articles that much. I trust HN
| discussions much more since there are plenty of people
| who will weigh in when things are wrong or
| misrepresented, unlike these articles.
|
| Edit: Gell-Mann Amnesia effect, that was what this is
| called. Don't trust the media just because you aren't an
| expert.
| wolverine876 wrote:
| You've lept to a conclusion about what I trust and then
| how that putative trust drives my reasoning. I'm not the
| imaginary person you are addressing.
|
| > I trust HN discussions much more since there are plenty
| of people who will weigh in when things are wrong or
| misrepresented, unlike these articles.
|
| Why are those people, with no responsibility, little
| expertise, etc., more trustworthy than other people? It
| seems like the common bias of social media - for some
| reason, people trust strangers with no credibility, which
| exposes them to the enormous amount of misinformation and
| just BS that now floods our world. If the article author
| or a professor wrote the same thing in a HN comment, it
| seems like you'd believe it.
| Jensson wrote:
| > Why are those people, with no responsibility, little
| expertise, etc., more trustworthy than other people?
|
| I don't trust them, I trust the discussion in aggregate.
| The discussion includes people on all sides in a healthy
| forum. If you are on a subreddit you are in an echo
| chamber so many voices will be missing, but HN has good
| representation of experts and people from all sorts of
| fields so I trust these discussions to unearth better
| truths than what a typical journalist can.
|
| > If the article author or a professor wrote the same
| thing in a HN comment, it seems like you'd believe it.
|
| No, if they wrote the article in a comment with that
| headline it would get comments saying why it is wrong,
| just like here. The ability for people like you to object
| is why I trust it more.
| wolverine876 wrote:
| Do you see what social media has wrought? How can you
| trust the herd mentality? Is there a greater source of
| misinformation, disinformation, and ignorance in the
| history of humanity? (No.)
|
| Regarding things I already know - or even OPs I've read
| but which most commenters have not - HN is mostly
| misinformation.
|
| I participate in HN, obviously - only because I've found
| nothing better (a complement to it, in a way, and maybe
| there's no known way to improve).
| Jensson wrote:
| I'm not sure what you mean? There are commenters here who
| are wrong, yes. But the discussion in aggregate usually
| have some people who are correct. Those people are
| missing in these articles, these articles are mostly just
| a person who is wrong about a lot of things. There are
| some nuggets of truths in them but you can't trust any
| sensational headlines to be representative of what
| actually happened.
|
| If you are saying that most discussions here on HN have
| zero people who are right, then I strongly disagree. It
| is very rare for there to be no truths in HN discussions.
| On reddit however it is very common for me to see not a
| single reasonable post to be found.
| wolverine876 wrote:
| How do you know which comments are accurate? Plenty of
| research shows that, without expertise yourself, people
| are awful at that judgment.
| timr wrote:
| Worked in the space of AI QSAR/QSPR. Parent comment is
| correct in all respects. Science journalism is abysmal
| and hyperbolic, and that's why you see people tearing
| into headlines like this. I don't know "euronews.next",
| but...let's just say that it doesn't inspire a great
| sense of journalistic integrity?
|
| For greater context, in the drug discovery world,
| "explainability" of QSAR/QSPR has been a longstanding
| goal. It's (rightly) not considered sufficient to have
| "black box" models that make predictions -- it's too
| expensive and risky to carry drug candidates into the lab
| based on the output of an algorithm, so subject-matter
| experts want to know _why_ the algorithms are making the
| predictions that they make.
| wolverine876 wrote:
| > Science journalism is abysmal and hyperbolic
|
| Do you see the irony? What better describes social media?
| Personally, I see plenty of good, valuable, useful
| science journalism; it's got plenty of flaws, like any
| human endeavor - including social media comments.
|
| But attacking journalism is normalized, and thus people
| know they can do it without being questioned and get some
| social media likes from it. It would be interesting to
| see the same responses turned on individual social media
| comments - what flaws could we find? :)
|
| > For greater context, in the drug discovery world,
| "explainability" of QSAR/QSPR has been a longstanding
| goal. It's (rightly) not considered sufficient to have
| "black box" models that make predictions -- it's too
| expensive and risky to carry drug candidates into the lab
| based on the output of an algorithm, so subject-matter
| experts want to know why the algorithms are making the
| predictions that they make.
|
| Ironically, that's what the OP is about; that was the
| point of their research.
| timr wrote:
| > Do you see the irony? What better describes social
| media?
|
| Social media is not one thing. You've got multiple people
| in this thread who know the subject, in detail, telling
| you that the headline is wrong. These aren't youtube
| video comments.
|
| > Ironically, that's what the OP is about; that was the
| point of their research.
|
| Yes, I know. That's why I wrote that. The research is
| about a relatively obscure technical problem. The
| headline made it sound like a revolutionary breakthrough
| in antibiotic development.
| wolverine876 wrote:
| > Social media is not one thing.
|
| Fair enough, but science journalism is not just one
| thing.
|
| > You've got multiple people in this thread who know the
| subject, in detail, telling you that the headline is
| wrong.
|
| That appears on every HN discussion of anything. It's not
| a signal of wrongness or rightness, any more than the
| color of the banner at the top - if it's orange, the OP
| must be obviously wrong!
| hedora wrote:
| It turns out there's usually a group of HN commenters
| that specialize in whatever the topic is and are more
| qualified to discuss the technical contributions than the
| person that paraphrased a university press release.
| Maxion wrote:
| I would recommend reading the actual paper, and not the press
| release. The main novelty here and what the paper is about is
| their method, not the discovery of the antibiotic.
| pfisherman wrote:
| Chemprop is not new, it has been around since at least 2020.
| la64710 wrote:
| Exactly , it seems the overall process of sorting and filtering
| vast amount of data remains the same only that the AI component
| is an additional tool to the toolchest to accelerate the
| process.
| hoc wrote:
| I would have expexted a more generative approach than the one
| they present.
|
| While this speeds up the screning process quite a lot you might
| as well feel like someone might just have thrown something out
| that might actually turn out useful and you can't backcheck
| without resorting to testing everthing.
|
| When I read the headline I was expected something more along "a
| network that knows what processes we have and therfor could
| imagine what compounds we could come up with" combined with that
| "inverse" network that predicts weaknesses of bacteria. Then
| those two would be matched and we would have to figure out the
| missing steps how to actually build the compound coming from that
| "black box" prediction.
|
| The benefit would be that we would be presented with something
| that could exist but we hadn't thought of because of our
| processes and limited resources.
|
| While I value the speedup and cost effect I'd think we could do
| much better here in exploiting the "creative" and powerful
| numerical inverse potential of ANNs especially in this area and
| outsmart those evolutionary skills of bacteria that way.
| stainablesteel wrote:
| your approach is a lot more complex, but they satisfy a lot of
| optimal criteria with a simpler approach, which i actually
| think is more impressive and also a much better target to hit.
| in fact i think they could have even achieved the same results
| using a much simpler exploratory method.
|
| a lot of biology, as well as where its been exploited, relies
| on specific binding, along with this comes the hope that what
| you test won't inadvertently show off-target effects. Through
| looking at what's already available for information you can
| actually use the lack something existing within a human system
| as a probabilistic edge over the future success of their
| application. in a regard its like an artistic rendering that
| makes use of negative space, its an impressive direction.
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