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I should have loved biology

jsomers.net

271–280 of 282 posts

Re: I should have loved biology

#271
post #186

I had been putting off quantum physics and time was running out. I was worried forth semester physics at MIT was going to be tough, but then through some miracle of providence the EE department decided that a solid state chemistry chemistry class plus Into to Biology could be substituted for quantum physics. Because I had already taken a solid state chemistry class, all I had to do was take a basic introductory biolo…

I think this depends a lot on the person. For example, my brain is apparently good at completely memorizing a biology book. I fill in gaps in my knowledge (which seems to exists as a series of images and animations in my head, call it a "world" model perhaps) with what I read. It all makes sense. Maths however... It takes me seemingly endless amounts of energy to grasp things. My PhD was in Biophysics, and my colleag…

> which seems to exists as a series of images and animations in my head, call it a "world" model perhaps

This is how most things are in my mental model of almost all higher-order concepts and subject areas. Mostly for math, but also for programming/electronics, biology, chemistry, history, etc.

The thing that usually stops me from forming this kind of picture is missing a fundamental concept, or not being able to conceptualize enough of them in my limited exposure to the subject.

The thing to realize is that this isn't a thing that just happens, it's something you can build yourself as you're learning something. Since the visuospatial parts of your brain are the most powerful, it can be an enormously useful thing to do to fit subjects together and reason about them.

Anecdotally, the "easiest" math/engineering classes I had in college were the ones with robust visual representations (control systems with the transfer function block diagrams and mechanism design with a simple graphical way to design linkages where we learned the math afterward).

Re: I should have loved biology

#272

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 read a good book review[1] that moved me towards the view that figuring out how a living thing works is possible, though not necessarily easy. I highly recommend reading it, but here's a summary.

Evolution promotes fitness enhancing functionality, so we should expect biological processes to be useful for some purpose and hence not be distributed like a random graph (e.g. Erdos Reyni graphs). Indeed, if we look at biological structures, we can find that the causal networks they form are far from random. Furthermore, there are often repeated motifs present. These motifs are quite simple and seem to map neatly onto human understandable concepts (like XOR gates or autoregulators or feedforward networks etc.)

And often, the overall graphs seem like they're tree like rather than some complicated mess of feedback loops (barring autoregulation). This kind of structure is quite modular, and hence we can leverage our understanding of component parts to understand greater and greater pieces of the organism.

There are two problems with this arguement: one, that a lot of the data used for it is not nearly exhaustive. Maybe the people examining biological circuitry stumbled on the rare areas where there are repeated sub-components. Second, even if there are repeated sub components, why should we get modularity i.e. few connections, mostly local?

The former may not be an issue if there hasn't been a lot of dedicated effort towards finding human comprehensible structure in biological circuits, which there might not have been. These things are big and complicated, with many constituent parts, and teasing out the underlying structure may require loads of computation and statistical analysis, which was hard for most of the history of biology.

The latter is not adressed in the book review, or in the comments, but the review author's work makes me it plausible to me that modularity will be common in biological systems. I don't have a good summary of that, or can clearly articulate why I'm hopeful about this. But read the rest of the work of the writer of the article if you're interested in this kind of stuff (key words: natural abstractions, interfaces, selection theorems).

[1] https://www.lesswrong.com/posts/bNXdnRTpSXk9p4zmi/book-revie...

Re: I should have loved biology

#273

The obsession with taxonomy and categorization really ruins a lot of subjects in school. It kinda makes sense _why_ they are covered like this: It's really easy to “split” the syllabus into even chunks; it is a good fit for the memorization-based study techniques that are pervasive and it leads to a very “homogenous” learning experience regardless of the maturity and interests of each student. My main problem with it…

> obsession with taxonomy and categorization

Virtues of the bored

> grammar only really “clicked” with me when I was already in college

For me, it was when I took Spanish in high school. I finally had a reason to know the parts of speech.

Re: I should have loved biology

#274
post #74

Earlier quoted context omitted.

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

Smart kids do incredibly well here. Who cares about average pisa scores. Average kids anywhere don’t contribute to science or engineering

It's a harsh truth, but somebody had to say it.

Re: I should have loved biology

#275

Earlier quoted context omitted.

Don't believe the hype. Follow the math where your instincts fail you. Check out HyperPhysics if you haven't seen it. Provides a super useful map where you can see how all the concepts relate and how they fit together: http://hyperphysics.phy-astr.gsu.edu/hbase/hframe.html

>Follow the math where your instincts fail you I think that's his point. Your instincts fail you all the time when studying stuff smaller than atoms Most people don't have a gut feeling for overriding their instincts in favour of math. In fact, when you read some behavioural sciences you'll notice that overriding math with your instincts is the norm

That's the purpose of the first 2 years of a Physics education. Getting the students to the point where their understanding of the math informs their intuition, rather than the other way around. Somewhere in the second year you do some experiments that demonstrate that in quantum and relativity, their intuitions are wrong and cannot be trusted, and then you dive into the good stuff.

Re: I should have loved biology

#276
post #142

Earlier quoted context omitted.

>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…

Hold my beer... Assume an experienced rider, as learning is different. Intention is set, requiring the basal ganglia and fore brain and either a notion of free will, determinism, or whatever you fancy. The area ahead is scanned and mapped for a clear path via retina- optic nerve - visual cortex and particularly the dorsal parietal pathway. Initial organised motor signal sequences originate in pre and pre pre motor ar…

Now tell me how the mouse senses radiation

Re: I should have loved biology

#277
post #186

I had been putting off quantum physics and time was running out. I was worried forth semester physics at MIT was going to be tough, but then through some miracle of providence the EE department decided that a solid state chemistry chemistry class plus Into to Biology could be substituted for quantum physics. Because I had already taken a solid state chemistry class, all I had to do was take a basic introductory biolo…

[deleted]

Re: I should have loved biology

#278

Earlier quoted context omitted.

Do you suggest any starting material or steps on how to get started

I would love to know as well. I have always been interested in Neuroscience from the outside but have had no idea where to start.

Two that I can recommend are Eric Kandel's Principles of Neural Science, and Larry Squire's Fundamental Neuroscience.

One of the most amazing things in nature are the pentameric ligand-gated ion channels. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4412168/

Re: I should have loved biology

#279

Earlier quoted context omitted.

The thing I found about biology in my limited study of it is that if a physical effect can happen, it's almost certainly used somewhere as a functional effect. I'm regular puzzled that people think that biology is tractable. It seems to me the best we can hope for towards a complete understanding is a computational generative model.

Do you know any examples of semiconductor junctions being used in biological processes? It would be hilarious to me if there was a bacterium out there that just ”invented” a transistor or a diode for some silly reason.

Paper on biological diodes https://arxiv.org/pdf/1706.00383.pdf but it doesn't use semiconductors, but ion transport (calls it iontronics instead of solid state electronics)

Indeed the ion channels used by nerves and muscles to send electrical signals are, like, one-way valves for ions

Re: I should have loved biology

#280
post #145

Earlier quoted context omitted.

Proteins are the runtime on which DNA is executed, because they are the mechanism that "reads" DNA. But proteins are the compiled output of DNA, because they are the result of "reading" DNA. So the DNA defines the runtime environment that is necessary for DNA to run.

RNA actually has a large role to play in going from DNA to protein. Its been suspected that the first life was RNA based because RNA can actually form functional site similar to proteins to do enzymatic reactions. RNA is some of the secret sauce to many of these systems

Definitely true, and my comment was without a doubt extremely oversimplified and wrong in several respects in an attempt to explain the analogy. Thank you for giving the clarification on it.
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