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New antibiotic targets IBD and AI predicted how it would work

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Re: New antibiotic targets IBD and AI predicted how it would work

#51

Post by smeej »

blauervogel wrote: post #12
smeej wrote: post #5

Earlier quoted context omitted.

It's also the case that there is a bewildering variety of things that get sort of lumped together as "IBD." Crohn's and ulcerative colitis are two of them, but there's no particular reason to assume inflammatory bowel diseases all have the same set of causes. Pretty much all of them are made worse by an e. coli infection, though, so a drug that can target just those bacteria is helpful! During my own IBD journey, I'v…

Great to hear this worked for you! What was in the the meal? And how did you decide on exactly that meal?

The meal consisted of well-boiled meat (pork/beef/chicken together, slow cooked, overnight), and carrots, zucchini, and butternut squash cooked in its juice until it mostly wasn't soup anymore.

I wanted it to be soft/easy to digest, but also nutritious. This was at least a wide enough variety of nutrients that I didn't feel miserable (just bored).

Re: New antibiotic targets IBD and AI predicted how it would work

#52

Post by smeej »

azinman2 wrote: post #17
smeej wrote: post #5

Earlier quoted context omitted.

It's also the case that there is a bewildering variety of things that get sort of lumped together as "IBD." Crohn's and ulcerative colitis are two of them, but there's no particular reason to assume inflammatory bowel diseases all have the same set of causes. Pretty much all of them are made worse by an e. coli infection, though, so a drug that can target just those bacteria is helpful! During my own IBD journey, I'v…

Which markers? What meal? Why that meal? Note it also could return; looks can be deceiving.

CRP and fecal calprotectin. The meal consisted of well-boiled meat (pork/beef/chicken together, slow cooked, overnight), and carrots, zucchini, and butternut squash cooked in its juice until it mostly wasn't soup anymore. Picked things that were very soft/easy to digest, with at least some nutritional value, because it didn't bother me. I just wanted to buy time for things to calm down.

It was meant to be an elimination diet with reintroduction, but every reintroduction attempt failed miserably for 20 months. Then, suddenly, it was fine.

I still mostly eat food I would recognize in its ingredient form instead of highly processed stuff, but if everybody's going out for pizza, I can have a couple slices and be fine. I just can't do that all the time.

Re: New antibiotic targets IBD and AI predicted how it would work

#53

Post by smeej »

jgord wrote: post #6
smeej wrote: post #5

Earlier quoted context omitted.

It's also the case that there is a bewildering variety of things that get sort of lumped together as "IBD." Crohn's and ulcerative colitis are two of them, but there's no particular reason to assume inflammatory bowel diseases all have the same set of causes. Pretty much all of them are made worse by an e. coli infection, though, so a drug that can target just those bacteria is helpful! During my own IBD journey, I'v…

Any hypothesis for why eating only one thing would solve IBD ? Would that select for a particular biota / micro-fauna environment ? or cause less mechanical / chemical inflammation ? glad it worked in your case.

I'm not a scientist on any level, so my theory only went as far as "stop irritating the thing and let it heal itself."

When they started talking about putting me on immune-suppressant drugs during a pandemic, I thought that didn't sound like a very good idea, but maybe my body could sort itself out if I gave it the opportunity.

Not a terribly sophisticated take, but it works for things like not popping blisters or picking at scabs, so it seemed worth a shot.

Re: New antibiotic targets IBD and AI predicted how it would work

#54

Post by slaterbug »

heisenbit wrote: post #36
leakycap wrote: post #34

Earlier quoted context omitted.

I think this perspective overlooks how human expertise actually works. Humans in cutting-edge research also get things wrong a lot: most hypotheses fail, most experiments don't pan out, and most novel approaches lead nowhere. When we celebrate a scientist who makes a breakthrough, we're not crediting them for being right 100% of the time. We're recognizing that they were right more often than random chance and earlie…

This is exactly how I use AI now daily: Provide it with relevant context and help me to troubleshoot some software issue. I found often it casts a wider net and provides good leads to follow up. It balances out my own bias and overall speeds up discovery of the root cause. Admittedly some benefit comes from having to explain the AI the context - half the problems are gone once one can explain them clearly.

Like a supercharged version of rubber duck debugging.

Re: New antibiotic targets IBD and AI predicted how it would work

#55

Post by smeej »

make_it_sure wrote: post #29
smeej wrote: post #5

Earlier quoted context omitted.

It's also the case that there is a bewildering variety of things that get sort of lumped together as "IBD." Crohn's and ulcerative colitis are two of them, but there's no particular reason to assume inflammatory bowel diseases all have the same set of causes. Pretty much all of them are made worse by an e. coli infection, though, so a drug that can target just those bacteria is helpful! During my own IBD journey, I'v…

i do the same, eating same thing for 2 years. While i don't have big IBD symptoms, i cannot now introduce new food, every time i try to introduce even very very small doses, i get a strange disproportionate reaction of my gut.

Gosh, I'm sorry. It does suck. For me, it was like that until it suddenly wasn't anymore. Nothing obviously changed. I kept "testing" reintroducing very small amounts of other food to try to end the elimination diet, like a bite every two months or something, and after 20 months, suddenly it went fine.

I say that just in hopes of encouraging you that healing might be right around the corner and you just might not know it yet. I certainly didn't know it was about to be over when it ended.

Re: New antibiotic targets IBD and AI predicted how it would work

#56

Post by smeej »

m_fayer wrote: post #9
smeej wrote: post #5

Earlier quoted context omitted.

It's also the case that there is a bewildering variety of things that get sort of lumped together as "IBD." Crohn's and ulcerative colitis are two of them, but there's no particular reason to assume inflammatory bowel diseases all have the same set of causes. Pretty much all of them are made worse by an e. coli infection, though, so a drug that can target just those bacteria is helpful! During my own IBD journey, I'v…

Doctors are the only people I’ve encountered who are ready to inform you of their poorly supported contradictory conclusions with full confidence, and are fully ready to meet any pushback with gaslighting or the dreaded “difficult patient” label. They approach the phenomenon of dropping trust and respect for their profession in much the same way. It’s really frustrating. I don’t get why they feel entitled to acting t…

My favorite is the "bless your heart" head tilt that strongly implies you're just too damn stupid to follow what they're saying, when it's obvious on its face that they're contradicting themselves.

"I was correctly diagnosed with it before." "Correct." "I do not have it now." "Correct." "It is not 'in remission.' I just do not have the disease." "Correect." "But it isn't curable." "Correct." "So if it wasn't 'cured,' what did happen to it?" {head tilt} "You tell me. Follow it through. You used to have it. You do not have it anymore. It's not in remission. But it also hasn't been cured. What does that leave?" "#$%^! I don't know! That's why I'm here, asking you! As far as I know, all it leaves is contradiction and impossibility!" "Now, now. There's no need to be difficult."

(This is almost word for word the last conversation I had with my GI. I'm not exaggerating. I'm not paraphrasing. I went through it exactly like this, and she responded to me exactly like this.)

Re: New antibiotic targets IBD and AI predicted how it would work

#57

Post by smeej »

ulfw wrote: post #8
smeej wrote: post #5

Earlier quoted context omitted.

It's also the case that there is a bewildering variety of things that get sort of lumped together as "IBD." Crohn's and ulcerative colitis are two of them, but there's no particular reason to assume inflammatory bowel diseases all have the same set of causes. Pretty much all of them are made worse by an e. coli infection, though, so a drug that can target just those bacteria is helpful! During my own IBD journey, I'v…

Have you checked your Calprotectin levels?

Yes, that was one of the inflammatory markers they checked. At diagnosis, I was in the mid-400s. After medication, I was in the low-200s. After 20 months of this elimination diet, I was in the 20s.

Multiple doctors told me it would not be possible to decrease the score without medication, one of them even while holding the results in his hands proving that I had done it.

Re: New antibiotic targets IBD and AI predicted how it would work

#58

Post by smeej »

hkt wrote: post #16
smeej wrote: post #5

Earlier quoted context omitted.

It's also the case that there is a bewildering variety of things that get sort of lumped together as "IBD." Crohn's and ulcerative colitis are two of them, but there's no particular reason to assume inflammatory bowel diseases all have the same set of causes. Pretty much all of them are made worse by an e. coli infection, though, so a drug that can target just those bacteria is helpful! During my own IBD journey, I'v…

As someone with IBD who is on their fifth trip to the toilet since midnight (BST) I'd love to get the recipe. I've got a few months of steroids ahead and anything more long term and high impact is of enormous interest.

The meal consisted of well-boiled meat (pork/beef/chicken together, slow cooked, overnight), and carrots, zucchini, and butternut squash cooked in its juice in a pan until it mostly wasn't soup anymore. Salt to taste, but it's never gonna be delicious. It's tolerable. It's even fairly enjoyable once or twice. It's not a bad meal. But boy is it a tedious one after awhile.

Re: New antibiotic targets IBD and AI predicted how it would work

#59

Post by hkt »

smeej wrote: post #58
hkt wrote: post #16

Earlier quoted context omitted.

As someone with IBD who is on their fifth trip to the toilet since midnight (BST) I'd love to get the recipe. I've got a few months of steroids ahead and anything more long term and high impact is of enormous interest.

The meal consisted of well-boiled meat (pork/beef/chicken together, slow cooked, overnight), and carrots, zucchini, and butternut squash cooked in its juice in a pan until it mostly wasn't soup anymore. Salt to taste, but it's never gonna be delicious. It's tolerable. It's even fairly enjoyable once or twice. It's not a bad meal. But boy is it a tedious one after awhile.

Interesting, what was the reasoning behind it?

Re: New antibiotic targets IBD and AI predicted how it would work

#60

Post by FollowingTheDao »

KLK2019 wrote: post #2

Here is the original study published in nature microbiology. https://www.nature.com/articles/s41564-025-02142-0 Wanted to share what I thought the interesting parts. From the university press release. "To date, AI has been leveraged as a tool for predicting which molecules might have therapeutic potential, but this study used it to describe what researchers call “mechanism of action” (MOA) — or how drugs attack disea…

What????

We knew that LolCDE was a vulnerability to e coli since well before 2016 and knew inhibitors of the complex, globomycin being one of them, which they knew about since 1978

https://journals.asm.org/doi/full/10.1128/jb.00502-16

https://pubmed.ncbi.nlm.nih.gov/353012/

Is enterololin just another from of globomycin?

Is AI smart or are scientists just getting dumber?

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