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I should have loved biology

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Re: I should have loved biology

#81

Post by UIUC_06 »

I got interested in bioinformatics in the early 2000's. The sequencing of the human genome, and of course that of many other organisms, was a huge enabler of "systems thinking" as applied to biology.

It isn't really fair to blame bio teachers for not teaching this in the 80's or even early 90's. Prior to that, it was mostly memorization. Some biologists and chemists were putting together the basic facts that came together and gave us an "aha!" moment. They won Nobel Prizes for a lot of that. Without Kary Mullis and PCR in the 80's, we wouldn't know 0.01% of what we know now.

Re: I should have loved biology

#82

Post by photochemsyn »

Dynamic systems theory is very powerful organizing principle / concept that makes biology make a lot more sense. It also helps to constantly remind yourself that academic science divisions - in particular physics, chemistry, and biology - are fairly arbitrary and nature doesn't care much about them, and this becomes very clear from a system-based view.

Without a grasp of basic physical concepts like conservation of mass and energy and the direction of entropy, life is an impenetrable mystery. For example, imagine a river flowing downstream with eddies on the sides - those eddies have an upstream flow component, driven by the overall downstream energy flow. Living cells do the same thing: they capture physical and chemical energy from their surroundings and use their networks of nucleic acids and proteins, and their encapsulation structures, to reverse the normal downstream flow of entropy.

Everything else follows pretty logically from there. How do cells communicate with their surroundings? They take up materials, excrete wastes, collect sensory data, engage in chemical messaging, and so on. How do cells maintain their nucleic acid and protein networks? By constantly repairing and rebuilding and replicating them using inputs of energy and materials. What is reproduction? A systems-level cellular reboot that also introduces novelty in the form of mutations and rearrangements (which may be useful, or not).

For a good intro to systems-based thinking in biology:

(2020) Systems Biology: A Very Short Introduction, Eberhard O. Voit

https://www.veryshortintroductions.com/view/10.1093/actrade/...

If you want a deep dive into the modern view of the dynamic, 3D genome, this is a great source (which also explains why just knowing the primary sequence of a genome doesn't necessarily lead to an understanding of disease states, failure modes, etc.):

(2015) The Deeper Genome: Why There Is More to the Human Genome Than Meets the Eye, John Parrington

https://www.goodreads.com/book/show/25660581-the-deeper-geno...

Re: I should have loved biology

#83

Post by brnaftr361 »

formerkrogemp wrote: post #64
brnaftr361 wrote: post #49

Earlier quoted context omitted.

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?

Yes, yes. Education is multifaceted in its consequences. Merit depends upon objective testing. Common culture and high trust society depend in large amounts upon education and schooling. With the quality of schooling available, shortage of teachers and quality teaching personnel due to abuse and low salaries, political interference with teachers handling their own material, religious indoctrination in charter schools…

I don't think you can objectively test. When you do test you're making a singular data point that doesn't reflect ability, necessarily, but instead a coincidence of factors at a given point in time. The data point is arbitrary, even if the test is scored against the distribution.

Take, for instance, a FT-working non-trad that scores above the mean. The mean who predominately consists of students who are FT-students. Should some respect not be paid to the considerable handicaps suffered by the non-trad? How do you even begin weight that?

Of course this is multiplied a million times over in several dimensions.

Re: I should have loved biology

#84

Post by h2odragon »

atty wrote: post #39
axg11 wrote: post #25

I think what is described here comes down to the fact that we don't have much (any?) _deep_ understanding of biology. The most concrete aspects of biology are observations. For example, anatomy is very well understood because it's essentially observations of structures within living organisms, as field it has been relatively stable for a long time, hence there are well-established methods for teaching anatomy. There'…

You can have what I would consider deep knowledge of a system without the ability to manufacture it or modify it. For instance, we have pretty deep knowledge of how the sun or other stars work, but we can’t even begin to dream about creating one, or controlling one. In the same way, we know a lot of how biology works. Obviously nowhere near all of it; but we are far beyond just scratching the surface. It just turns o…

> ow the sun or other stars work, but we can’t even begin to dream about creating one

Wolfram didn't answer "how much would a solar mass of hydrogen cost" for me, but it did tell me that the solar mass is 1.988435×10^33 grams, and another search found hydrogen prices [1] in the range of US$ 250 to 1350 per MT ... So just the financing on building another sun is going to be tricky.

[1] I know it's not all hydrogen but we'll burn those bridges when we get to them.

Re: I should have loved biology

#85

Post by [deleted] »

gilleain wrote: post #73
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 must be running on slower code, as I can't quite unpack that. So the code in life is the DNA which is also the 'runtime'?

[deleted]

Re: I should have loved biology

#86

Post by jugg1es »

In reference to the part where he talks about wanting it to be easier to create 3d models in biology - the complexity of organic molecules is very, very high. Not only are they complex, but they change shape a lot. In fact, the more realistic a 3d representation of an organic molecule is, the less likely that it would help you actually understand it. Microbiology is messy.

Re: I should have loved biology

#87

Post by civilized »

czbond wrote: post #70
civilized wrote: post #21

Pet theory: for most of human history, biology has been an increasingly complex detective story, a notepad of mysteries laying on a table next to an unfathomably massive evidence room stuffed with barely organized facts. This appeals to certain people and not to others. Only recently has it become possible to approach it from more of an engineering perspective, which appeals to a different set of people.

can you expand this thought? I'm on your path but not to your destination yet. Can I summarize it as: Earlier, biology was "hunt and peck" or "observe" ... and now we're moving to a more "rigor of process & ability to create as seen in the past few decades of computer science now applying to biology" type of world?

Here's a story to illustrate. Recently there was a headline about some project at MIT that used CRISPR to figure out the function of every protein in a human cell (or something like that, I'm sure I misinterpreted it in some way). I told a friend who is an actual biologist, and he said of course they didn't literally do that, that would be impossible. So I guess what they really did was.... something-something with CRISPR that gave information about a wide range of proteins in the cell, or something. They added a lot of facts to the library. But they marketed it as if they had made a huge stride towards understanding how the whole machine works. That gets people like me more excited. We'd like to know how the machine works and then use that to make it work better.

Re: I should have loved biology

#88

Post by bonniemuffin »

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 recall the same "everything coming together" feeling, but for me it didn't happen until Applied Biochemistry in grad school.

I recall the final exam being only a single question, with a bunch of blank lined pages to write your answer, and the question was something like "You just ate a ham sandwich. What happens to it?" A good answer needed to include everything down to the molecular/chemical level and tie it together all the way up to the macro scale, and I finally felt like that class had prepared me to tell the story.

Re: I should have loved biology

#90

Post by Banana699 »

bsedlm wrote: post #56
gilleain wrote: post #55

Earlier quoted context omitted.

Great description. I would go further to describe living systems as not just distributed and so on. Also they are self-assembling and self-repairing. They are redundant - which makes them more damage resistant and 'evolvable'. Also, these complex assemblies of machines work at (mostly) room temperature and pressure. Except for extremophiles that can work down to freezing or up to boiling temperatures, or in acid or h…

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 self-repairing, but - again - this can also be easily simulated in computer hardware, to the extent that it isn't, it's because it's costly and there is no good reason for it.

Biology's difference from computers is in scope (organisms are whole factories who just happen to have computational abilities by necessity) and origin (organisms aren't designed, and this profoundly and significantly affects everything about them).

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