Hacker News Reader

Comment by MichaelZuo | Hacker News Reader

"Not only are they the same in each species, but they crowd together in the center of the nucleus where they physically interact with each other, suggesting functional coherence,"

If there truly is some sort of functional interaction going on then this is a very profound observation. As it implies the close spacing is for some kind of mechanical/electrical mechanism within the core of every cell’s nucelus.

View on HN

> As it implies the close spacing is for some kind of mechanical/electrical mechanism within the core of every cell’s nucelus.

It is interesting, but not for the reasons you may be imagining. And not a mysterious electrical mechanism.

It's well-known in the field that (e.g., in humans), chromosomes fold in on themselves in structured ways [1,2]. The functional consequence is not precisely mechanical or electrical -- rather, these folds bring regulatory domains close in 3D space to the sequences which they regulate (which may be far in 1-D sequence distance). These can be elements like "enhancers", which increase the level of transcription (DNA->RNA copying, the first step of gene expression); "insulators", which break up coherent blocks of gene regulation, etc. One of the mediating mechanisms is that regulatory proteins bind to these particular sequences; bringing them together in 3D space allows the assembly of a protein complex that actually carries out the relevant process (eg, transcription).

So, what's interesting here? There is extensive evidence of these contacts within mammalian chromosomes, but limited evidence _between_ different chromosomes. Insofar as the paper shows that mammalian macrochromosomes have homology to multiple reptile/avian microchromosomes (really, to their most recent common ancestor), it may be (speculation alert) that intra-chromosome contacts recapitulate contacts and organization seen in the ancestral microchromosomes.

(There are also "simple" interactions like wrapping of DNA on protein complexes called nucleosomes, like string on beads, but that's less interesting in this context.)

[1] https://en.wikipedia.org/wiki/Nuclear_organization#DNA_loopi... [2] https://en.wikipedia.org/wiki/Nuclear_organization#Chromosom...

Surely nobody was under the impression that detail stops at the nucleic level, right? It's small machines and complex systems the entire way down, ad infinitum. Our ability or inability to render or understand these increasingly small systems does not negate their existence.

I agree with your general sentiment, but I don't see why we should expect "machines and complex systems" (as related to life) to exist at the level below molecules and atoms. If that was the case then we should expect otherwise identical organic molecules to have differences when they're created by living things and synthesis in the lab (ok, ok, there's chirality and carbon-14, but you get what I mean).

I get what you're trying to say, however this is a flawed assumption right up there with just getting an FTP account, mounting it locally with curlftpfs, and then using SVN or CVS on the mounted filesystem. Time and innovation are both not on your side, in this case. Complex systems are complex and extend far beyond the focal depth of our squinting.

Wöhler proved in 1828 that there was nothing special with organic molecules by synthesising urea.

I guess you could view molecular formation as a complex system involving atoms and atoms as a complex system involving quarks. That would define chemistry and particle physics as the study of said complex systems which makes sense to me. Still at that level that’s not generally viewed as the study of organisms. What we view as biology, the study of the mechanisms of life, really starts at the molecular level. If you go lower, things stop being specific enough.

I genuinely don't understand what your analogy is supposed to convey, could you elaborate?

It's a reference to an old HN comment back when the creation of Dropbox was announced here. Someone commented something along the lines of "you could just" do that whole thing with the FTP server etc. It's lived on as an example of "peak HN" attitude.

So any form of disagreement with someone can be reframed as being dismissive and missing the point, and therefore "peak HN".

That's quite the non-starter for any discussion about whether an idea holds up under scrutiny.

Individual atoms and molecules are identical in a vacuum. Are they in context? They at least have quantum degrees of freedom, which is quite a lot. But whether that has functional value is tbd

A statement like "complex machines all the way down" implies precisely that molecules would be different without context because of some lower-level machinery that forms a more fundamental building block of life. This is what I am skeptical of.

There is an emerging subfield "quantum biology" that studies biological systems under quantum mechanical influence [0]. Photoreceptor systems seem to be a prominent example.

[0] https://quantum.ch.ntu.edu.tw/ycclab/wp-content/uploads/2015...

I guess my issue was more with the implication that we'll find more fundamental building blocks of life.

Are you more comfortable with the implication that we won't?

Comfortable or uncomfortable doesn't even enter the discussion. You can't go down much further without entering the domain of high-energy physics. Which is not the domain of life.

How so?

It's hard for structure to form in burning hot plasmas. But hell, we only know about ourselves. That's the flaw in all the dogmatic thinking about what life is. Life is after all, just structured computation, and computation is just action, and action..just the passage of observer time:

https://www.youtube.com/watch?v=Q_CQDSlmboA

Before we go into the discussion of whether life may or may not be able to exist in hot plasmas (which is fine, in a speculative hypothetical physics kind of way), the point is that we are talking about the building blocks of our form of life. Which is not the kind that exists in hot plasmas.

I'm reminded of an early machine learning experiment where a system self-trained to perform a certain task on a piece of dedicated hardware did so unexpectedly. The researchers "knew" the solution but wanted to learn how their project solved it.

At some point, the sensing for analog effects became the most efficient way to achieve the result by exploiting flaws or unique properties in the individual components, sort of like that inductance backdoor where a particular set of instructions in a certain circuit leaks into another until it's energized enough to trigger it like a relay. Anyway, the result was unintuitive but worked.

Anyway, there's no doubt that after millions and millions of years, there are natural principles at the quantum and atomic levels that biologics are taking advantage of that we're basically only at the "allegory of the cave" level of understanding.

The micro is very much relative.

I don't completely understand what you are saying; the information encoded at the nucleic level does not have any analogy at the sub-molecular level (IE there is no biological information stored using subatomic particles or quantum tricks), nor do there seem to be any functional contributes to non-information molecular mechanisms.

I interpreted the parent comment as: Artifacts of the virtual machine that physics / biology / chemistry "executes" on (i.e. the universe and potentially minute physical properties we aren't aware of) may be reflected at the macro-scale in the "output" (life).

That doesn't make any sense from a scientific perspection, and reality is not a virtual machine that physics executes on.

What would be the difference?

> reality is not a

A. You don't know this, because it's (quite possibly) unprovable

B. Charitably, it was meant as a metaphor

I assume they were referring to emergence.

https://en.wikipedia.org/wiki/Emergence

Yes, if the word 'complexity' falls then emergence is inevitable to be mentioned alongside.

> there is no biological information stored using subatomic particles or quantum tricks

This is correct, but only because "biological information" is utter gibberish without meaningful interpretation, from you not the comment that you criticize.

The more general statement was that people's horizon seems to be severely limited (except that the comment phrased it in an acceptably ironic mood). You practically proved them right

There are some known subparts of the nucleus, in particular the Nucleolus [1], and that link discuss a few additional subparts.

I'm not an expert in biology, so I don't know if this is a new part, or it's a part that we already know but in mammals is made by small areas of the big chromosomes and in this animals this areas are on their own.

[1] https://en.wikipedia.org/wiki/Nucleolus

Edit: nucleolus -> nucleus

> There are some known subparts of the nucleolus, in particular the Nucleolus

I think you meant "known subparts of the nucleus", right?

Thanks. I fixed it now, because my typo made the sentence very confusing.

Reminds me of…

The Vermin only teaze and pinch

Their Foes superior by an Inch.

So, Nat'ralists observe, a Flea

Hath smaller Fleas that on him prey,

And these have smaller yet to bite 'em,

And so proceed ad infinitum:

Thus ev'ry Poet, in his Kind

Is bit by him that comes behind.

-Swift

> -Swift

Taylor or Jonathan?

> Flea

> prey

> bite'em

> ad infinitum

What is this telling us about former pronounciation rules?

> , in his Kind

this feels like it's only there to force the rhyme

Reply on news.ycombinator.com