https://github.com/Svensson-Lab/pro-hormone-predictor/blob/m...

https://bioperl.org/articles/How_Perl_saved_human_genome.htm...

(And of course all the articles about excel renaming genes, and then people trying to clean up the mess…)

I see we’re being fast and loose with the term “artificial intelligence”?

https://www.rand.org/content/dam/rand/pubs/research_memorand...

See the Eukaryotic Linear Motif resource: http://elm.eu.org/elms.

— Thomas Szasz

I think that's how we still use it.

Natural language -> fully working one, I don't mean some email validators but way more complex stuff. Although, I've recently had a case which was too much even for regexes in any form or spec, then sort of grammar-based parser needed to be done from scratch.

Python will literally assign the content of your docstring (a triple-quoted string at the start of a function) to a special double underscored ("dunder") property called `__doc__` that any code can access; not just docs generators, but your own code as well (pretty dang useful for generating on-the-fly help output!).

Which also means that if you run into weird behaviour where a function doesn't do what you think it should do, you can just fire up the REPL, import that function, type `print(function_name.__doc__)` and presto, you have the documentation right there, specifically for the exact version you're using. You don't even need to leave your IDE if it comes with an integrated terminal.

Any string. Triple-quoted is just multiline strings and works anywhere.

Or even easier: `help(function_name)`!

- The python docs are there to give you the information you need.

- Passion pages are there to do a deep dive into all the crazy shit you can do with that information =D

edit: not saying it can't be done but our org isn't using auto docs

(lots of fun dunder functions in Python that make metaprogramming a lot easier, but someone needs to tell you about)

[0]: https://cardoni.net/parsing-proper-nouns-with-regex/

The harder ones I have dealt with are those looking for malformed syntax where the closing mark that might be missing could be several thousand characters after the opening mark, or the opening mark itself might be missing, across a data set that is several hundred million characters. So you need something very complex to find all the distinctive characteristics of the content that is supposed to be enclosed - while avoiding the many similar structures that give false positives. Sometimes the technically easier solution is too slow to run (look ahead and look behind, etc), so you need to pivot and use other regex features. It can take a day or two to get right.

Instead of

  [ie]*-?[A-Z]+

  [ie]?-?[A-Z]

https://regexlicensing.org/

https://stackoverflow.com/questions/1732348/regex-match-open...

Perfect

[0]: https://www.autoregex.xyz/

[1]: https://regex-generator.olafneumann.org

Regex to me, is pattern finding and abstraction taken to the extreme. I like the challenge

Now I am enlightened.

  /
  (?<=^|[ \t])
  (?
    (?
      €|EUR|\$|USD
    )
    [ \t]?
  )?
  (?
    (?
      -?
      \d{1,3}
      (?:[\.,]\d{3}|\d*)
    )
    [\.,]
    (?
      \d{2,3}
    )
  )
  (?
    [ \t]?
    (?
      (?
        €|EUR|\$|USD
      )
    ) | (?
          [ \t]|$|\n
        )
  )/x

I would've probably approached it differently, trying to first get the 'inverted' match (i.e. ignore anything that isn't a currency-like pattern) and refine from there. A bit like this one I did a while back, to parse garbled strings that may occur after OCR [0]. I imagine the approach does not translate fully, because it's pattern extraction rather than validation.

[0]: https://observablehq.com/@dleeftink/never-go-nuts

The idea of an exclusionary approach sounds interesting as well. I'll have to think about that a bit.

[0]: https://github.com/keredson/wordninja

Libraries like python's lrparsing [0] let you assign regex's (aka tokens) to variables, then build grammars by combining them using python expressions. For example:

    while_statement = Keyword('while') + '(' + expression + ')' + block
    statement = while_statement | ....
    block = Token('{') + Repeat(statement + ';') + Token('}')

On the down side, lrparsing is pure python so it's slower than python's inbuilt regex's.

[0] https://lrparsing.sourceforge.net/

We don’t need better language tools. Better parsers can, and already have, been implemented in libraries.

I’d have a look at parser combinators.

Is true though, or perhaps "state"? I know I had to come up with an algorithm because regexp alone couldn't do what I wanted (not even advanced features like lookahead, lookbehind, etc.)

https://xkcd.com/208/

A great way to do it is to split them up by concatenating them across a bunch of lines, and put a brief explanation at the end of each non-obvious part (to the right, on the same line).

Plus that also lets you indent within nested parentheses, making it that much more understandable.

I'm baffled when I come across a file like this where the code itself is heavily commented, but a gnarly regex is not. Regexes are not strings, they are code -- and with their syntax, they need comments even more.

Many CoffeeScript constructs were adopted into JavaScript and TypeScript, but unfortunately, heregexes weren't among them.

Later languages have added support for the `x` flag, including C# and Rust. There is also a stage 1 proposal for JavaScript: https://github.com/tc39/proposal-regexp-x-mode

Second, not at all. An LLM can tell you how the regex works (hopefully). It can't tell you what each piece means in terms of the program's logic. Or at least not always and not reliably.

Why pay to get FDA approval, if you don't get a government granted monopoly on it afterwards?

This is one problem with using patents as the mechanism to incentivise development of medicine.

If there's an actual natural, identified substance with huge benefits to people, it's going to go gangbusters and you're going to make a lot, LOT of money selling it, even if you're doing it via roadside lemonade stand.

It feels like this claim is usually used to promote cures and treatments with extremely low quality RCTs backing their use as a sort of panacea.

I used to believe the "just do shrooms to cure depression" claims on principle until I looked into the quality of those studies, which is very low. At that point, you're just making stuff up.

Kratom, CBD, and delta-8 THC are naturally occurring bioactive substances that are newer to the US market. Both have carved out a pretty nice economic niche with a bunch of claimed health benefits.

A couple of years back, I saw a sign outside a fancy legal highs shop in Fishtown, Philadelphia touting the benefits of kratom as a pre-workout supplement. The insanity that a business was advertising an addictive opioid to healthy, opioid-naive people for better gains in the gym almost makes me want more regulation in this area.

Even synthetic research chemicals are generally legal as long as you add a "not for human consumption" label (and they aren't explicitly banned or analogous to other illegal/regulated drugs).

You can buy a 3 month supply of Lithium Orotate for like $10. I certainly wouldnt recommend self prescribing this kind of thing though.

You have to dose relatively high in order to have an effect. You’re disrupting your neural sodium-potassium pumps with it.

But it’s still pretty cheap. Hard to charge a lot for a fairly abundant element.

For example, there's a prescription engineered version of melatonin.

Melatonin is still a huge business.

Clinical trials are a significant expense in developing a drug. Kind of makes me think we should award patents not for coming up with some molecule, but instead award them for showing a molecule is safe and effective.

In any case, none of that refutes that there is a strong economic incentive for market actors to not fund FDA approval trials since any benefit will be shared by the entire market.

The substance in question is a peptide. It's not something you simply extract from a plant using a solvent. OTOH, being a peptide, it's likely easy enough to produce in a genetically engineered bacterium or yeast. Efficient extraction may remain a problem though, because you'll need to select a particular protein fragment (the peptide) from reams of other protein fragments of the bacterial / fungal cells you process.

Giving yourself an injection an hour before you eat or an hour before you are hungry isn’t going to work.

Supplements are a $50bn business [1].

[1] https://www.grandviewresearch.com/industry-analysis/us-dieta...

https://patents.google.com/?inventor=Katrin+Svensson

It would seem they are modifying peptides. Which is patentable.

Even without a patent, companies can get FDA exclusivity but for not as long as a patent grants them so unless the addressable market is huge, it’s a financially riskier bet.

This seems to be the paper, but its behind a paywall.

Anyone with access can tell me if they publish the 12mer amino acid sequence? Is there more to it (post translational modifications)

Or is it just the peptide?

Yes, the paper provides the 12-mer amino acid sequence of BRP: THRILRRLFNLC .

Regarding post-translational modifications, the BRP peptide was synthesized with a C-terminal amidation, which was critical for its bioactivity. The non-amidated version of BRP was inactive in vitro . Additionally, the paper mentions that the C-terminal cysteine (C12) was synthesized as a free thiol .

So, BRP is not just a simple peptide—it has a key post-translational modification (C-terminal amidation) that influences its function.

If you're obese, your legs are enormously strong with crazy amounts of muscle. Have you ever seen someone obese do leg presses at the gym? They can handle tons of weight.

When you lose weight, you don't need all that extra muscle. If you're carrying around 180 lbs instead of 300 lbs on your frame, all that extra muscle goes away because there's no point in keeping it. This is a good thing.

Even if you go from 200 lbs to 180 lbs, there's a level of muscle you don't need anymore.

Losing muscle as you lose weight is natural and good. Now, obviously you don't want to lose so much that you become weak for your size, but that won't happen if you continue to be physically active. Your body is exceptionally good at maintaining the exact right level of muscle to meet the regular stresses it undergoes. (Provided you are eating enough protein, but that's easy.)

The side affect of muscle loss from these glp-1 agonist drugs is a serious downside that everyone should be aware of and try to mitigate if they choose to take them.

I think you've misunderstood GP. He's not saying they have too much muscle when they're overweight. He's saying that take that exact same amount of muscle, subtract a ton of fat from their upper bodies, then they have "too much muscle" as typically needed for their body mass. I don't agree with their phrasing, but the point isn't "nonsense."

It's a leap to suggest that it's "good" to lose this muscle mass. If you're obese then it's good to lose fat. It's even better to do so while maintaining muscle mass.

Every time GLP-1 drugs come up, the convo splinters off into topics that have nothing to do with anything unique to the drug. Now we're just talking about general weight loss and that it's good to exercise. Which is a trivial claim.

When people read "muscle loss" they think "oh it's going to make me weak and feeble".

Normally that’s offset by the health effects of the exercise required to gain and maintain them as well as the lack of medical conditions that prevent exercise etc. But a fat person losing weight should inherently lose muscle mass long term assuming no changes to lifestyle.

Also, if this is your stance, then GLP-1 is a red herring because you have the same issue with weight loss in general. Weight loss, without increasing resistance training, leads to muscle loss.

One insidious thing with these GLP1 drugs, is that they also seemingly affect muscles like the heart. I would not be willing to take one unless the risk of me carrying my weight far outweighed (no pun intended) the risk of the side effects. However, a lot of people seem to be treating it as some kind of miracle fad diet drug, which is concerning.

It also has other side effects like reduced elasticity on skin, etc. I suspect we'll see longer term issues in the next decade from these drugs, and I'm glad alternatives are being explored.

I can't even imagine what that's supposed to mean.

> However, when cutting weight, you can do a routine that maintains/builds muscle as you cut, to reduce the effect.

I literally talked about staying physically active.

The point is, you're going to have however much muscle your workouts and physical activity build/maintain. And you're going to lose whatever extra muscle isn't needed in your workouts. And that's fine, because you probably want well-balanced strength rather than legs that can carry around 300 lbs all day long.

None of this has anything to do with weight loss, except that simply walking around and daily movement becomes less of a workout as you lose weight because you're moving less mass. But it's not the weight loss directly that makes you lose muscle (assuming you're eating protein), it's the reduced physical strain because you weigh less so you're not needing those muscles. Do you get the distinction?

You don't need to work out even more to "reduce the effect" as you say. There's no effect. There's just working out to have whatever muscles you want. Weight loss will never lead to losing the level of muscle you need for your workout.

This is the strictly superior outcome.

But if you're going from obese to healthy, then your goal isn't to retain all your leg muscle, that's absurd. Your goal is to get to a healthy weight with overall balanced healthy muscle -- not disproportionately large legs.

Nothing is "strictly superior". What is best depends on what your goals are. Bodybuilding and not being obese any more involve wildly different measures of success.

The goal for anyone obese is to lose as much fat as sustainably possible.

For any given rate of weight loss, losing a higher proportion of body fat is always better.

This notion of "balanced" healthy muscle is one you've made up that no one else thinks of. I've been on fitness forums for well over a decade and have literally never seen a single case of this.

Correct.

> For any given rate of weight loss, losing a higher proportion of body fat is always better.

That is in direct contradiction to your previous sentence. No, losing the higher absolute amount of body fat is better. While being sustainable healthy.

> I've been on fitness forums for well over a decade and have literally never seen a single case of this.

You may be on the wrong forums then. Most forums don't think all your days should be leg days.

Okay so I don't know where I picked this up - it was a decade or more ago - but I always thought the problem was losing weight too fast is what causes bad muscle loss such as from the heart, or from leg/other muscles beyond what's no longer needed from the weight loss. Something like, you're starving yourself so your body starts drawing energy not just from your fat but from anywhere it can.

Edit: I mean someone with a healthy fat percentage body composition. Of course having to pump blood to a 300lb-140kg body is problematic for the heart, be it a mostly fat or mostly muscle body composition. My point is it's just much easier to be fat enough for it to be a problem than muscular enough without exogenous hormones or an abnormal condition.

Low muscle mass is associated a broad swath of illnesses, low activity, and generally poor health.

Muscle mass's power as a predictor is not the same as it's utility as an intervention.

Something being a good a good predicative indicator does not mean it is an effective intervention.

"Building muscle" is an intervention and has extremely well-documented mechanisms that have a causal role in improving health.

Our bodies like to have a balance of everything.

"Muscle mass is a huge predictor of mortality"

In biology, most such predictors work only up to a point. Massively muscular people don't live to be 120. Bodies don't work in a straightforward fashion, and there are other effects to consider. For example, activation of the mTOR pathway, associated with tissue growth, is associated with shorter lifespan, and mTOR inhibitors like rapamycin seem to be modestly prolonging lives of many species.

Well, you lose weight all over. You lose fat in your arms and your shoulders don't need to be quite as strong. You lose weight on your face and your neck muscles don't need to be quite as strong. You lose more in your legs, but you're supposed to lose muscle mass all over.

> Someone relying on a GLP-1 drug is often someone who isn't very active at all.

Sure, but that's a completely separate issue. It doesn't have anything to do with weight loss. Being in good strong physical shape is great, but nobody should expect weight loss to magically result in strength. That's like thinking you can stop going to the gym but won't lose any of the muscle you'd previously built up. It's got nothing to do with weight loss though. It's got to do with the fact that you're not working out.

Yes, that puts you at risk. That's why you should exercise, even if it just means daily walks.

The point is, you're not winding up with too little muscle because you lost weight. If you're winding up with too little muscle, it's because you're not being physically active enough. If you're physically active, you won't lose the muscle that you still need even as you lose weight.

Imagine someone eating only candy and pastries, but because they eat so huge amounts, they actually get a half-decent amount of protein. Then they decrease portion size with the help of appetite suppresants.

> Provided you are eating enough protein, but that's easy.

If you're trying to lose weight eating only candy and pastries, then we're having an entirely different conversation...

Sure, but what if I want it? Maybe I want to jump extra high, or want to be able to lift things 120lbs heavier than I could before?

It's natural but that doesn't make it good. In particular, muscle loss can cause heart problems because the heart is a muscle. The body's catabolic processes don't distinguish between different kinds of muscle.

https://en.wikipedia.org/wiki/Aerobic_exercise#Health_effect...

Obviously it’s not a problem if an obese person’s quads shrinks 2x because they lift 2x weight every day.

They can't handle reps. It's almost as if muscle has several different properties that are important beyond just "mass."

I started drinking a protein shake once a day and the random mysterious injuries stopped.

[0] https://www.barbellmedicine.com/blog/where-should-my-priorit...

See this article: https://www.healthline.com/nutrition/high-protein-diet-plan#...

> The Recommended Dietary Allowance (RDA) of protein is 0.8 g per kilogram of body weight (g/kg/bw), or 0.36 g per pound of body weight (g/lbs/bw).

> However, the authors of a 2019 review suggest that this number is often misinterpreted as the ideal number. It’s only the minimum amount of protein required to prevent nutrient deficiencies and muscle loss in most healthy individuals.

> A 2017 study found that participants who ate a high protein diet of 1.34 g/kg/bw (0.6 g/lbs/bw) for more than 75% of the 6-month duration experienced significantly more weight loss than the group who followed the RDA requirements.

> A 2016 review found that eating up to 2 g/kg/bw (0.9 g/lbs/bw) may help promote strength and prevent muscle degeneration.

etc.

You’re 100% right though, the key to retaining muscle mass while in a caloric deficit is consuming sufficient protein, or even over-consuming protein. In starvation situations muscle is next up after fat when getting consumed for energy but it seems like for the most part the muscle mass deterioration during significant weight loss periods is a natural side effect of the process and lifestyle required to accomplish it.

https://pmc.ncbi.nlm.nih.gov/articles/PMC5421125/

Secondary to that, the body needs some amount of glucose. The best option for that is stored glycogen. When those stores run out the body can enter ketosis which reduces but does not eliminate the need for glucose. Fat consists of three fatty acids joined by a glycerol part. Most of the energy is in the fatty acids, but the glycerol can serve as a limited supply of glucose. However that is not really sufficient, so to get more glucose, and the other option is breaking down protein.

Anecdotally, a friend of mine was on a diet and exercise regime, then at some point he switched to Mounjaro to reduce cravings, while keeping the same diet and exercise regime (he's a data geek so he documented things pretty well), and his muscle gain maybe slowed a tiny bit, but didn't reverse on Mounjaro.

Sample size of one, but at least it's not zero.

I cycle frequently and the impact of the weight loss and added strength has made me feel much faster this year (and it's still rainy/cold season).

I can't find any evidence that GLP-1 are catabolic to muscle mass. There is no evidence I can find that GLP-1s do anything above what calorie restriction does.

There is a linear relationship between calorie restriction and fat loss down to under 10% body fat. There is so much wrong information on calorie restriction from studies done on people who were literally starving with already very low body fat %. Then apply that to people with 25% body fat is just wrong.

Westerners trying to lose weight don't have this problem. I think part of the obesity epidemic is this insane idea that calorie restriction is bad. Everyone kind of understands the thermodynamics of calories in / calories out. Everyone even kind of understands the benefits of fasting. At the same time though there is this nonsense that if you restrict calories too much you start burning all this muscle mass. It is patently absurd.

Add up the calories of what a 250lb bodybuilder is eating for contest prep to lose fat and you will see they are "starving" too.

It seems that there's nothing unique about semaglutide, and %FFM loss is just a function of how rapidly you lose weight.

The most rapid losers on semaglutide have the same %FFM loss (30%) as bariatric patients, for example.

And if you don't want to lose weight that fast, you can just temper the dose (unlike with bariatric surgery).

What worries me is if what if in 20 years of use, something with insulin gets blown out?

There is a chance it could be a drug for life like testosterone. We know though how devastating obesity is on health so it is really going to be up to the individual to take the risk. Not really my business at that level.

I think it's extremely probable that the most rapid losers are running the largest calorie deficit and also the largest protein deficit.

I would have said just eat protein and work out when I was in my teens, 20s and early 30s too.

I am 48 and not on testosterone, yet. I actually can't recover at this point from workouts that burn enough calories vs working out less but more calorie restriction in terms of fat loss. Even 60 minute walks cause me to be more hungry to be able to recover from than what I can restrict without walking.

I am at the final death throws of natural and not being on TRT basically. I have been pushing TRT out since my late 30s but have gone way too far.

I think the TRT threshold probably be when you can't outrun calorie restriction by working out. For me, that has probably been since 43 or 44. By 46 for sure.

Personally, I don't need GLP-1s. So many people though do.

In the end, it really is just metabolic math. As a former wrestler who did some insane weight-losing in my youth, the muscle mass loss is due to extreme calorie restriction. Besides, just sitting around starving is not a good way to become healthier in the long run, and that's where the muscle loss will be worst. To be a true journey towards better health, dieting should be accompied by at least a lot of walking and some light weight training, in the minimum.

And don't forget your supplements, kids (addressing general readership), because our foods are less nutrient dense in 2025, so find out if some supplements help energy levels on the downslope. Me and my teenagers have taken a sip / mini-gulp of a product called 'Orgain' daily for a month or so, and I have found my energy better, while having less cravings. An entire little 11oz single-size drink is way too much for me (too many vitamins, makes me sleepy), having 'just a little bit' is not at all scientific, but we seem to be thriving on that little bit of supplementation.

And, as always, avoid those processed sugars, kids! Whole sugar cane is very, very good for us, but only in moderate doses. Processed sugar is the crack cocaine of sugar cane, as opposed to just chewing a leaf of the coca plant.

High school wrestling though might push things too far.Many of those guys under heavyweight do not have the bodyfat % to be restricting so much so are actually losing muscle mass.

I know Jordan Burroughs diet that I have seen seemed like maximum micro nutrients for the calorie because how else can you eat to be a 4 time world champion at 74kg?

I am probably half an inch taller than Burroughs and 163lbs is impossible. It is too far. Way too far.

You can lose muscle mass without drugs just by eating poorly (and not doing adequate movement)

[1] https://newatlas.com/disease/obesity/gold-nanoparticles-obes...

But might destroy your bone marrow's ability to create blood cells[1].

1. https://www.mayoclinic.org/diseases-conditions/aplastic-anem...

Losing a ton of weight, especially very quickly, is extremely catabolic. Any substance that prevents this would by definition be an anabolic substance.

[1] https://finance.yahoo.com/quote/NVO/

[0]: https://www.reddie.co.uk/2024/08/30/the-year-of-ozempic-an-i...