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Comment by captainmuon | Hacker News Reader

This reminds me of something I always wanted to ask. Are the majority of molecules in the body "named" or "purposeful" molecules, like haemoglobin, vitamins, water, lipids, DNA, etc., or is there a lot of random stuff, where just some atoms are arranged arbitrarily? Ignoring for a second the trival thing that you can make really long polymers, you have mutations in DNA and so on - I would could those into the first case. What is the ratio of "encyclopaedic" molecules (discovered or not) to "random stuff" (useless or not)?

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Everything has a name, but it is generally a “systematic” name[1] rather than a one-off descriptive name. Even DNA is a systematic name for the monomer (de-oxy-ribose-nucleic-acid is one of the defined nucleic acids bound to a ribose sugar missing an oxygen at the 2-position carbon).

Biology uses an enormous space of small molecule structures (to say nothing of proteins, which have their own naming schemes) and few have names you might recognize generally, but all have useful systematic names that biologists and chemists can quickly parse.

As a twist, most systematic naming schemes don’t produce unique labels, so there’s often multiple ways to say the same thing, and different discipline subcultures have different biases in this regard.

Edit: re-reading OP, another interpretation is that they’re asking what percent of molecules in the body aren’t involved in biology. The answer to that is probably something that approximates 0%. At the end of the day, the combined interaction of all of this chemistry is what biology is, and everything is more or less everywhere. (…concentration is everything.)

[1] https://en.m.wikipedia.org/wiki/Systematic_name#In_chemistry

> what percent of molecules in the body aren’t involved in biology. The answer to that is probably something that approximates 0%.

I think the answer might be different (and more interesting) if constrained to human biology. What percentage of the variety of “stuff” in our bloodstream/tissues, that came in from our air/water/food and then maybe got metabolized a bit, is now of a form entirely inapplicable to anything going on — or that could even potentially go on — in a human body? How much is pure “waste to be excreted” from the human perspective, with both no use in keeping it around, but also no danger in keeping it around?

(I know that this is at least what allantoin is for the species that make it; but we’re not one of those.)

I presume a lot of toxins that get inactivated by the liver end up in such a form.

Depending on your definition of "no use in keeping it around." Apparently it's fairly useful as a moisturizer and as a skin protectant. You're still correct, of course, in the sense that it's not metabolically useful, but it's kind of amusing to me that it's got these other cosmetic effects that are in some sense useful.

Not everything can nor does have a "name". First, there are kinds of molecules which we have not yet imagined yet, for which we do not yet have an IUPAC naming system. One could be devised, however that's an ongoing task.

Think of the endohedral fullerenes — metal atoms stuck inside of buckyball cages — those have really only been directly in chemists' sights for 30 or so years. [0]

Another pair of extrema are 2D materials and network solids, which are effectively massive molecules. Again, we don't have a great naming system for them, even if we could properly catalogue all of the bonds (and enclosed species). And more practically, one is probably better off with a set of atomic coordinates to describe them.

[0] https://en.wikipedia.org/wiki/Endohedral_fullerene

I mean, sure.

One example, we're discovering thousands of new proteins in human cells because we collectively assumed short protein chains wouldn't fold into anything functional: https://blogs.sciencemag.org/pipeline/archives/2020/03/11/ne...

"Mitochondria is the powerhouse of the cell", right? So it's supposed to be in a cell, right? Well, mitochondria seem to just hang out in blood, running just fine. Nobody knows why. There is even evidence they move between cells: https://blogs.sciencemag.org/pipeline/archives/2020/02/03/fr...

The cell is packed full of different species of RNA. We keep discovering new types of RNA, performing various unknown signaling tasks: https://blogs.sciencemag.org/pipeline/archives/2019/10/03/en...

As always, we don't know what we don't know. At the high school level, the textbooks will present a complete, sensible model of cell biology, because a textbook that lists off a thousand molecules each labeled with "Not sure what this does" would not be a very emotionally satisfying textbook.

The more I learn about biology, the more scared I am of taking drugs. The wikipedia article on any given drug will tell you it bonds to receptor so-and-so and produces effect A and side effect B etc etc. Well sure, it does that, but it's not like it's a guided missile. The molecule ghosts through the cell membrane and rattles through the metabolic machinery, bouncing off transcription proteins, sticking and unsticking, until a few million out of the untold sextillion you ingested manage to find the target and bond. (Temporarily! All human drugs must not bind too tightly, or else they disable that receptor, and you die)

I have mild seasonal allergies. When the complaints from my coworkers about my persistent cough get loud enough, I take a Loratadine pill from the bottle on my desk, and fifteen minutes later, they go away. How on Earth does it do that? The immune system is a vast, poorly understood, constantly introspective machine. After a billion years of cellular warfare it has defenses on defenses on defenses all made specifically to not be disabled. And yet Loratadine reaches through the ranks of spinning buzzsaws and turns it off like flicking a switch. How?

And, why? It shuts off just the seasonal allergies. Why do I have a specific cellular pathway that makes me cough occasionally when I inhale pollen? It's certainly not disabling the entire immune system, or I would be rapidly eaten from the inside out by my gut bacteria, or the thousands of fungal species coating my skin and mucus membranes. Just the pollen receptors. It boggles the mind.

http://biochemical-pathways.com/#/map/1

I couldn't give you a ratio but I'd think it's quite a high ratio. There probably aren't many molecules that don't have either a chemical (i.e. have some function in a pathway) or physicochemical influence.

Not saying you're wrong, but why do you think that? I'd have thought the same thing about DNA, but I keep being told most DNA is junk (although I wouldn't be surprised to find out later we just don't know what it's for).

https://www.discovermagazine.com/health/our-cells-are-filled...

It looks like even the portion of DNA that isn’t metadata could also be there so mutations and damage are less likely to occur in critical portions.

I think this because:

(a) Access for all but the smallest molecules to cells is tightly regulated by e.g. membrane transport proteins.

(b) similar to a, tissue where exchange with the outside world can occur, such as the intestine and lungs, are even more regulated and heavily guarded by the immune system. Apart from small molecules with the right lipofilicity, some minerals, potentially small peptides, or entities with other mechanisms of entry like viruses, nothing gets in (excluding endocytosis by e.g. immune cells).

(c) Anything entering the circulation will be processed by the liver eventually, where all kinds of enzymes target a broad range of structural motifs to break down molecules into 'non-foreign' building blocks to be reused.

(d) I can't think of any molecules not belonging to a particular known class. There is water, elemental ions, carbohydrates/sugars, peptides/proteins, lipids, and RNA/DNA, and small molecules (e.g. intermediate products). All of these except a subset of small molecules and heavy metals can be either broken down into 'known' parts or disposed of (not completely though; over time waste builds up which is likely part of why we age). Now if there are many inert small molecules, they would show up in all kinds of analytical tests. Inert or not, we can classify all of them chemically. There is a lot of stuff for which we don't know the exact function of course, and as these systems are highly complex and dynamic, functionality can be broad and context dependent.

By the way, the term junk DNA has various meanings in different contexts. In the context of non-codig DNA, this "junk" e.g. plays a role in epigenetic regulation as it influences physical accessibility for transcription. Also, DNA is relatively stable and unlikely to interfere with other cellular processes in the same way that random small molecules would.

I could definitely be wrong though. I'm almost done with my biomedical engineering masters, but over the years I turned to software and all the chem and bio knowledge is becoming rusty very quickly. It's also a field in which knowledge doesn't age well as it has been growing quite fast.

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