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I should have loved biology

jsomers.net

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Re: I should have loved biology

#41

the source code containing within it all of the instructions required for life on Earth. I would disagree, we see the object code. If we had the source, with comments, genetic engineering would be much easier

It doesn't really make sense to talk about DNA as source code vs object code vs whatever. Biology doesn't have the same clean levels of abstraction that we've developed in computer science. DNA functionally operates at many levels. It long term storage, local working storage, and it is used to compute. It's a single molecule that does everything. Then you have to throw in all the secondary processes that modulate and…

Indeed, I classify the main difference between life (biological systems) and technology (civilization engineered systems) is about the structure of complexity.

Human civilization is severely time-limited (or just time-pressed). We can't wait millions of years running a simulation to optimize a little widget. We need to rely very much on high level design and comparatively little on efficiency and optimization. On the other hand, life cannot afford huge DNA (very costly), or energy waste (generally disfavorable from evolution). So human built systems tend to be of a low "Compute complexity": the computational complexity of obtaining solutions and solving problems themselves (like civil engineering structure problems, or design of objects) must be fairly low. For life, systems can be amazingly intricate, every tiniest cell a wonder that would probably take thousands of years for civilization to maybe be able to replicate. But it all ranges from about 130kbp to 8Mbp[1], which would be around 16Mbit/2Mbytes at most. So it fits (uncompressed) in a diskette (floppy).

Even now with powerful computers, we're still mostly constrained by cognition (specially human), you see simplicity all around you.

So if you look at the human world, you see (computational) simplicity everywhere, but the natural world has undergone trillions of generations of optimization to arrive at almost perfect (in an almost literal way) little machines, complicated but with a hidden amazing (size) simplicity.

I think there's a connection to be made to algorithmic inference as well. Originally we came up with ideas for Universal Inference (from ideas from by Solomonoff, Kolmogorov among others) [2][3], the most glaring candidate was the "size prior": evidence explainable by the least algorithmic information ought to be most likely (Solomonoff inference). Later, there were promissing ideas around an additional term: the "speed prior" (from Schmidhuber[4]) -- the biological word is one where the "size prior" (simplicity is most likely) works almost perfectly, and human civilization is one where the "speed prior" (computationally easy is most likely) is helpful.

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

[2] https://en.wikipedia.org/wiki/Kolmogorov_complexity

[3] https://en.wikipedia.org/wiki/Algorithmic_probability

[4] https://en.wikipedia.org/wiki/Speed_prior

Side note: I think intellectually one of the ways we're really far behind is recognizing Algorithmic Information theory as a foundation for statistics and metaphysics. We're very stuck making little progress on the metaphysical realm (which physics is advancing more into) because of a lack of widespread acceptance of those advanced tools for science. Algorithmic inference gives a solid basis for comparing metaphysical models and deep questions about the cosmos.

Re: I should have loved biology

#42
When I watch animations of how the cell works at a molecular level [0], I can't help but wonder how can this level of sheer complexity in dna transcription, protein production, and many other supporting functions in a single cell works in perfect harmony. It's mind boggling.

I admit that I'm biased, but I don't think this could have evolved through random processes. I'm a believer in Intelligent Design.

https://youtu.be/X_tYrnv_o6A https://youtu.be/7Hk9jct2ozY https://youtu.be/fpHaxzroYxg

Re: I should have loved biology

#43

the source code containing within it all of the instructions required for life on Earth. I would disagree, we see the object code. If we had the source, with comments, genetic engineering would be much easier

I love this comment. So niche to the general population, but deep to participants here.

Re: I should have loved biology

#44

"Everywhere you look—the compiler, the shell, the CPU, the DOM—is an abstraction hiding lifetimes of work. Biology is like this, just much, much worse, because living systems aren’t intentionally designed. It’s all a big slop of global mutable state". Brings me to wonder, could we ever create anything so marvellous as what biology does so effortlessly.

Because the system survives by optimizing for efficiency and reliability.

It is also helpful to have a 3.7-billion-year head start.

Re: I should have loved biology

#45
When I was in college, I took Entomology and Zoology for my bio requirement. The first one was because the teacher had such high ratings in the student reviews. At one time, I could name all the orders of insects. No longer.

It did seem like just a bunch of memorization to me then. Much, much later, I took an Extension course in Molecular Biology, and what a difference! I still think the diagrams they draw for biological processes in Molecular Biology of the Cell are just stunningly beautiful, and completely blow away anything you'll ever see in a CS text.

But expecting to have those revelations when you don't know how anything works yet is foolish. You have to pay your dues.

Re: I should have loved biology

#46

I did love Biology. In fact, I think it was my first real interest before computers or programming. Some aspects of the field still fascinate me, but I know if I ever bothered to engage the interest I'd be broke.

The Biology teachers that I had at school were a lot better than those for other subjects, there were not many other jobs that they could do.

Re: I should have loved biology

#48
post #42

When I watch animations of how the cell works at a molecular level [0], I can't help but wonder how can this level of sheer complexity in dna transcription, protein production, and many other supporting functions in a single cell works in perfect harmony. It's mind boggling. I admit that I'm biased, but I don't think this could have evolved through random processes. I'm a believer in Intelligent Design. https://youtu…

> I don't think this could have evolved through random processes.

It's a logical fallacy that complex processes cannot be created from random events. It certainly can, and evidence is abundant.

Biochemistry of life is an advanced form of brownian ratchet [1]. It started simple, but can get to absurd level of complexity due to selective pressure, and memory via genes. And selective pressure is nothing but maximizing for greatest replication.

There are many interesting philosophical questions inside biochemistry, but a Judeo-Christian Diety is not the most interesting.

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

Re: I should have loved biology

#49

Earlier quoted context omitted.

Let's just agree that US high school education is generally abysmal.

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?

Re: I should have loved biology

#50
Yes it's all a mixed wet bag of chemicals with probabilities but thankfully we've spend a significant amount of time separating and understand a lot of these molecules in isolation to try and understand the Jigsaw of life.

I don't normally come to the defence of the biological sciences but why would you expect it to be anything else?

If you're blindly reciting then either you don't understand or haven't been tough enough to understand the parts of the puzzle. Unfortunately this is also a consequence of modern teaching methods I would argue but that's another problem all together...

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