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I should have loved biology

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Re: I should have loved biology

#161
post #57

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 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 went through biochem, but didn’t fully understand just how gigantic & complicated proteins are until I started learning about computational protein folding.

Some years back, there seemed an opportunity to create an educational web interactive, a full-scale 3D folding sim, with hands-on direct manipulation, by aiming for plausible-not-correct folding. The simulation literature having built up lots of shortcuts for slashing computation costs, which sacrificed correctness but not plausibility. So one might variously knead a protein, alter it and its environment, and watch it flail. I wonder if anyone ever got around to it?

Re: I should have loved biology

#162
post #39

Earlier quoted context omitted.

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…

Gotta budget for some extra hydrogen to burn the bridges.

Re: I should have loved biology

#163
A lot is discussed here about cellular life. There are equally fascinating things about complex societal life systems. For example most people fascinated about life in this thread are likely highly paid programmers looking for a hobby. Most actual biologists who work on this for a living are worried about meeting their ends and paying mortgages that they likely have no time to wonder about amazing aspects of their day to day work.

Re: I should have loved biology

#164
post #142

Earlier quoted context omitted.

The two questions I really remember from my neuroscience grad program are: "You discover a mouse that can sense radiation. How does it do it?" "You are riding a bicycle. Explain." We had to do it in 2 pages, NSF grant rules on spacing and margins.

>You are riding a bicycle. Explain Oh man, where do I even start? Sensory input from the inner ear to balance, the networks that handle feedback from afferent signals from the periphery, efferent pathways to control motor movement. I don't even know all the details but it's mind bogglingly complex. Do I explain the molecular basis of action potentials? The modulating effects of inhibitory feedback within the networks…

[deleted]

Re: I should have loved biology

#165

Earlier quoted context omitted.

Except it seems like a way harder question!

... it'll be fun if you start from what happens when the enter key is pressed- the mechanics and electronics involved in submitting that URL (and some chemistry and physics behind what your eyes see on the screen), the physical transmission of the signal from your computer to through the interwebs and some error correction protocols to ensure your signals are still useful. Maybe toss a line or two in about the comple…

Going over quantum electrodynamics to explain how to make microcircuits would be fun, that was our first class specific to electrical engineering for me some 30 plus years ago.

Re: I should have loved biology

#166
The author references and includes illustrations from a really beautifully done book called "The Machinery of Life". I immediately bought it after seeing those pictures. Does anyone else have recommendations for beautifully illustrated biology books/textbooks?

Re: I should have loved biology

#167

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…

> If only we taught by using storytelling techniques and posing questions to students

The sciences are a richly interwoven tapestry of stories, so the question arises, might it be taught like that?

I suggest the bottleneck is that crafting such stories is very very expensive, and very poorly incentivized.

To see this, try taking an existing story, and sampling the neighborhood. In some way broaden or retarget it. Take the "tree carbon source" story. Perhaps make it rough quantitative, say flow vs time of day, as in a "plants consume O2 too - rainforests are only net producers for a couple of hours around noon" story. Or vs lifetime. Or use ocean primary producers, and sketching dissolved gas flows - how recently was consumed CO2 part of the atmosphere? Or sketch a global daily-or-seasonal "inhale/exhale" graphic. Or deep-time context - when did such fixation begin historically, and how has it changed since? Or flow residence times for different biomes? Or a correct telling of "treed sunlight released as campfire redshifted light and heat". Or ...

My experience has been, that if you ask simple, obvious, important-for-integrated-understanding accessible-down-to-K questions, you're pervasively dropped in primary literature searches. If you're lucky, the secondary research literature will catch you. Tertiary literature, like professional "everything about X" too-big-for-a-doorstop tomes are sometimes of helpful, but online are generally unavailable or copyright violations. Sometimes phython/mathematica/R/etc scientific code is regrettably required. Education and outreach content is generally useless - because of scope and focus limitations, when not incoherent and incorrect. And there's much effort, even by the American Chemical Society, to kill off sci-hub. Which will make this all even less plausible.

So I suggest the absence of accessible powerful integrated stories (aka science education that doesn't suck), is a failure of the science research community, not the "science" education community. Because only they have the expertise to create them. Or at least, a failure of research funding to incentivize it. And thus a collective failure to appreciate the magnitude of awesome being left on the table. Assuming sufficient awesome might overcome indifference.

Which is less than clear. "The Sun is yellow" is very popular story. From preK to the most used intro astronomy college textbooks. It's pervasive among even first-tier astronomy graduate students. Also to be found on astronomy education research's lists of most common misconceptions in astronomy education. We've known Sun color for at least a century, had detailed limb tint numbers for decades, and now years of intensive work on stellar atmospheres for occultation, and "science" education content has managed to remain uncoupled from all of it. Getting it right would permit weaving with stories of blackbodies and planetary energy flow and color vision and more. Perhaps someday someone will pay someone enough to care, or finally become sufficiently embarrassed to change. But if anyone expects that will happen this decade rather than next, or the one after, I'd really appreciate to hearing why.

On a more upbeat note, it's been noted that almost all (US) professors in the sciences have been through a small number of institutions. So maybe imagine someone with too much money funding a dozen awesome scientific storytelling programs, and waiting a decade or three?

Or maybe creating good science stories might be promoted as a hobby, for people who were in the sciences but left and so have time on their hands? Sidestepping the massive resource allocation challenge by making it unpaid work.

Re: I should have loved biology

#168

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…

This happens so much in education, and specifically academics. A lot of theoretical explanations without stepping back from theory and going back to reality once in a while to ponder about the implications. I passed a lot of courses by memorizing theoretical concepts without truly understanding it. I feel that's wasteful because I'm not advocating for longer lectures, but rather more effective teaching methods (at least they would be for me). Understanding a concept is very different than proving a theorem.

Re: I should have loved biology

#169
post #70

Earlier quoted context omitted.

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 C…

I believe the parent refers to this [1,2,3] study. Indeed, this was about targeting many (11,923) genes with Perturb-seq (CRISPR screen with single-cell RNA-sequencing readout). There are two human cell lines used in the study (K562 and RPE1). For functional annotation, authors focused on 1,973 targeted genes that had strong transcriptional phenotype after the perturbation. As there's some correlation structure, that's what they studied, annotating clusters of individual perturbations using public databases (like STRING [4]) and literature. Seems like a lot of great work has been done here though stating that we now know all the functions of all the genes might be a bit of a stretch indeed.

[1]: https://news.mit.edu/2022/crispr-based-map-ties-every-human-... [2]: https://www.cell.com/cell/fulltext/S0092-8674(22)00597-9 [3]: https://gwps.wi.mit.edu/ [4]: https://string-db.org/

Re: I should have loved biology

#170
post #168

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…

This happens so much in education, and specifically academics. A lot of theoretical explanations without stepping back from theory and going back to reality once in a while to ponder about the implications. I passed a lot of courses by memorizing theoretical concepts without truly understanding it. I feel that's wasteful because I'm not advocating for longer lectures, but rather more effective teaching methods (at le…

I was told that this was so that they could craft cirriculums that stretch decades when it could be taught much quicker. Doing so would be deterimental to the labor market in academia.
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