I should have loved biology • Hacker News Board

Re: I should have loved biology

#111

Post by tambourine_man » Sat, Jul 09, 2022, 6:37 PM UTC

s1artibartfast wrote: post #96

bognition wrote: post #8

There is a large gap between the mechanisms of chemistry and the magic of biology that most people do not see closed until late in their education. It's a real shame that this gap cannot be closed sooner. In undergrad I took a bunch of biology and chemistry classes. It wasn't until I took Biochemistry (a senior level class) that everything came together. The biochemistry class I took was a re-telling of all the stori…

I had a similar revelation for structural biology, applying the physics I learned for bridges and buildings to microscopic proteins. They are structurally like a cathedral built by a blind and deranged architect. The fact that mechanically bend, pivot, and move like a complex machine at a micro scale to do real work is the most sci-fi thing I can conceive of. Think of a even a simple walking protein like Kinesin [1].…

> They are structurally like a cathedral built by a blind and deranged architect

That's one of the best things I read all week.

Re: I should have loved biology

#112

Post by localhost » Sat, Jul 09, 2022, 6:40 PM UTC

gilleain wrote: post #72

localhost wrote: post #60

I have a PhD in Organic Chemistry and just last week I visited my PhD supervisor's research group. My research was on understanding the mechanism of enzyme-catalyzed decarboxylation reactions. This is very detailed physical-organic reaction kinetics to seek to understand the basis for some of the remarkable acceleration that the enzyme provides (10^6) over model systems in aqueous solution. Reflecting on this, I find…

Er, hate to nitpick but photosynthesis uses magnesium, no? In the chlorophyll, at least, although other parts have haems with iron in :) (Also as with anything in biology, there is no doubt some weird organism that has like a cadmium or similar in its chlorophyll, I don't know)

You're absolutely right! I don't know what I was thinking here - I blame my supervisor :) One of the other things that my old research group did was crosslinking of hemoglobin which has iron as its central atom vs. magnesium in chlorophyll. I find it pretty amazing the structural similarity between the heme structure for metal ions in these two very different use cases.

Re: I should have loved biology

#113

Post by chongli » Sat, Jul 09, 2022, 6:40 PM UTC

czbond wrote: post #53

I was very into Chemistry and Biology until I found Computer Science. C.S. was/is fascinating, so many interesting problems. Until I found out C.S. to a majority of the world really just means coding - the most boring activity I can imagine. (to me... I have some parts of "H.D." in the ADHD, so don't downvote me). I thought C.S. would lead to a career of solving difficult Automata, algorithmic, etc problems. Nope.

Solving difficult problems is a very difficult job to get. Most employers do not want their employees solving truly difficult problems because it's too hard to replace someone capable of that. This is why the world of work has been so heavily organized around avoiding these difficult problems in favour of boring/repetitive tasks.

Re: I should have loved biology

#114

Post by brainzap » Sat, Jul 09, 2022, 6:43 PM UTC

I should have loved X but school happend.

Re: I should have loved biology

#115

Post by azalemeth » Sat, Jul 09, 2022, 6:45 PM UTC

tambourine_man wrote: post #111

s1artibartfast wrote: post #96

Earlier quoted context omitted.

I had a similar revelation for structural biology, applying the physics I learned for bridges and buildings to microscopic proteins. They are structurally like a cathedral built by a blind and deranged architect. The fact that mechanically bend, pivot, and move like a complex machine at a micro scale to do real work is the most sci-fi thing I can conceive of. Think of a even a simple walking protein like Kinesin [1].…

> They are structurally like a cathedral built by a blind and deranged architect That's one of the best things I read all week.

The other word missing is "cheap". Proteins are under a massive selection pressure: many thermodynamic reactions in fundamental bits of biology are as thermodynamically efficient as they can be, else some slightly more efficient mutant would have out-competed it aeons ago.

I became interested in biology as a physicist when I realised that all of the problems, on some level, boil down to putting a load of lego pieces in a box, shaking it up with some energy not terribly different to k_B T, and getting a fully-formed, self-replicating lego models out the other end. It's all physics. It's all utterly incomprehensibly mind-bogglingly complex with layers of complexity wrapped around each other, and far out of the realms of either physics or chemistry to compute completely. It's why I work at the intersection of the two fields.

Another famous paper, often-mentioned, related to this is "How a biologist would fix a transistor radio", essentially armed only with a shotgun. The tools of modern molecular biology may be scalpels rather than shotguns, but still, the idea is arguably the same.

Re: I should have loved biology

#116

Post by jyounker » Sat, Jul 09, 2022, 6:48 PM UTC

Banana699 wrote: post #90

bsedlm wrote: post #56

Earlier quoted context omitted.

I like to think that in life the code is also the runtime, unlike in computer technology where the hardware is the runtime.

I'm not sure there is such a fundamental difference. In biology the code is the DNA and RNA, whereas the hardware is the proteins. DNA and RNA are self-modifying and imperfectly transmitted, but those traits can also exist in computer code (to the extent that they aren't, it's because humans make sure of so, because they hate trying to understand dynamically changing things). The hardware of life is self-creating and…

> In biology the code is the DNA and RNA, whereas the hardware is the proteins.

This distinction isn't as clear as you think. The active parts of ribosomes (the machines that translate mRNA into proteins) are catalytic RNA. There are organisms that use RNA to store templates (RNA viruses).

Re: I should have loved biology

#117

Post by pgrepds » Sat, Jul 09, 2022, 6:50 PM UTC

I disagree that biology, or by proxy any other science, should be written in such a way that a non-expert in the field should understand everything without consulting wikipedia or any other source. Studying a natural sciences includes learning a certain vocabulary and grammar. The reason for this is simple. We agree on certain definitions, words and sentences, to minimise the possibility of ambiguities and misconceptions. This is a very important aspect of any science.

In the same sense, abstracting things is important. Abstraction gives us the opportunity to apply the results from one seemingly foreign field to another.

It is not the task of science to create enthusiasm for the result for people outside the field in technical articles or textbooks as this post tries to endorse.

The excitement for a certain topic should be given by the teachers and, to be honest, this was also always the case in my experience, but I might have been very lucky.

Furthermore, the vast generalisation “Instead, we’re told that if you ever find yourself wanting the area of a triangle, here’s the procedure” couldn't be further from what I've experienced. I’ve never been given a “procedure” in math without being taught why and how it works.

Re: I should have loved biology

#118

Post by MereInterest » Sat, Jul 09, 2022, 6:51 PM UTC

gilleain wrote: post #67

ip26 wrote: post #57

Earlier quoted context omitted.

I went through biochem, but didn’t fully understand just how gigantic & complicated proteins are until I started learning about computational protein folding. There’s several levels of abstraction just between rna/ribosomes and functional proteins… that’s one of the most shocking complexities to me, most pieces of life are rather elegant when you come to understand them but it’s hard to imagine how complex proteins e…

I worked for a professor (James Milner-White) who was interested in early protein evolution and I remember a conversation we had about the possibility that proteins could have evolved from large to small. Not sure if it was from a published paper, but the idea was that early proteins might have been large - say several hundred residues - but mostly disordered. The smaller, more ordered 'domains' would then have evolv…

There was a paper a few years ago about a similar effect in artificial neural networks [0]. The gist was that a large network can contain many subnetworks, and the number of subnetworks grows much faster than the size of the network they are contained in. They were able to find a subnetwork in a randomly weighted network with equivalent performance to a trained network of a much smaller size.

[0] https://arxiv.org/abs/1911.13299

Re: I should have loved biology

#119

Post by chongli » Sat, Jul 09, 2022, 6:51 PM UTC

brnaftr361 wrote: post #49

barry-cotter wrote: post #35

Earlier quoted context omitted.

If you think US high school education is abysmal where do you think does it better? US Asians do very well compared to other Asians, US whites to other whites, etc. https://www.unz.com/isteve/the-new-2018-pisa-school-test-sco...

Is the purpose of education to make people take tests and get high scores that bureaucrats can wave around, routing their success? Or is it something a little more profound?

"The science of government it is my duty to study, more than all other sciences; the arts of legislation and administration and negotiation ought to take the place of, indeed exclude, in a manner, all other arts. I must study politics and war, that our sons may have liberty to study mathematics and philosophy. Our sons ought to study mathematics and philosophy, geography, natural history and naval architecture, navigation, commerce and agriculture in order to give their children a right to study painting, poetry, music, architecture, statuary, tapestry and porcelain."

-- John Adams in a letter to his wife Abigail

I'm sure many people would love to have their children study the arts and humanities and develop profound insights into human nature and life itself. Unfortunately, many people are stuck studying mathematics and other subjects like it in the hopes of having a decent career.

Re: I should have loved biology

#120

Post by adrian_b » Sat, Jul 09, 2022, 6:58 PM UTC

Pulcinella wrote: post #36

ta988 wrote: post #9

There are additional factors that make molecules in cells not subject to pure diffusion rules. Charge depending on the pH of the area ( even if in such a crowded space it is likely not really a pH anymore), and molecular interactions. Proteins (and virtually any other molecules but proteins and to a lesser extent nucleic acids are particularly good at that) can stick or be repulsed by their overall composition (exter…

Yeah see the art of David Goodsell. I believe he said the concentrations of the various biomolecules are roughly accurate based on calculations he does before starting painting. Cells are incredibly crowded. The human body being 60-70% water is usually presented in pop-sci as “wow we are mostly water!” but that’s actually very concentrated for chemical reactions. You usually don’t perform reactions that concentrated…

All the living cells spend continuously a lot of energy as long as they are still alive for avoiding the appearance of precipitates inside the cell, e.g. by pumping out of the cells the ions of calcium and sodium and pumping inside the cell the ions of magnesium and potassium, because the former are much more prone to produce precipitates than the latter.

This continuous ion pumping is a major component of the energy consumption of a living being when it is idle, apparently doing nothing.