All of chemslug's Comments + Replies

The Moon is Down; I have not heard the clock

This is what I meant by "it's a trivial exercise in orbital mechanics, so maybe all of you do this instinctively".  I got there empirically. :)

Self-study ideas for micro-projects in "abstract" subjects?

What an "aspiring chemist" should do depends a lot on age and where they are in the educational process.  For children below high-school age, I think there are lots of great experiments you can do to illustrate principles of chemistry.  Lack of originality isn't a bug there, it's a feature.  In high school, if you think you like science, take chemistry!  There should be a lab component in most schools, so you can at least get a flavor for what working with chemicals is like.  Access to equipment like this is an underrated component... (read more)

3AllAmericanBreakfast3dMany of the coolest and most useful activities for learning are sealed off from non-professionals, or at least are expensive and time confusing to obtain certification or access. Usually for good reason. This seems like a fundamental dilemma of the role of school. To make students directly see what’s cool about different subjects, they need lots of hands-on experience. But the vast majority of their time, and most of their evaluation prior to grad school, comes from book work. Access to hands-on projects and a sense of freedom and agency is limited at best. And ultimately, that’s for reasons of safety and expense, which we can’t just criticize away. It seems then that a big learning skill is maximizing access to such applied projects. I wonder, then, if it would be better to orient school around single subjects from an earlier age. It makes more sense to give a student heightened access to mentorship, equipment, and materials if that stuff is their obsession. And for a self-studier, it seems important to figure out first what you want to obsess yourself with, and then focus on getting maximum access to applied learning environments.
Self-study ideas for micro-projects in "abstract" subjects?

There are a few problems with DIY organic chemistry.  The first one is that many of the reagents are toxic.  Some of those are volatile or readily absorbed through the skin.  Others will spontaneously burst into flame when exposed to air.  Sometimes the dangers of working with chemicals is overstated, but sometimes it's very much not.  In academic or industry labs we solve mitigate those problems with fume hoods and personal protective equipment (and no, the exhaust fan above your stove is not an acceptable substitute).  The s... (read more)

3Mary Chernyshenko3dI guess one can make soap, as an applied project. Some paper chromatography can be done without a hood, outdoors (but then one still needs to dispose of the materials safely). Gall-based inks are, in a way, on the fence between organic and inorganic (also, playing around with homemade dyes is cool, e.g. from avocado seeds, alder bark or walnut skins - the colours fade, but you can stain paper so it looks old and then draw maps of treasure on it). Cooking is instructive (although people often underestimate the dangers of vinegar "because everybody has it in their kitchen".) Also, blacklight might be fun here. But my most engaged instructors told us a real chemist develops a "sense of substance", like they often can tell things apart by their physical appearance and not even their chemical properties (given a set of familiar chemicals). There are different shades of colour, different granularities, different translucencies... it's just not something you can show at home. And separately, my botany instructors said they always make a student identify at least three species of a genus, whenever possible. For triangulation. If you give students only one species, that's how they will think of the genus as a whole. Give them two, and they will think about the differences between them, but not about the genus. But give them three, and they see the common features. Again, I don't think it's possible to show sufficient variety of chemical substances at home.
3AllAmericanBreakfast3dAlways enjoying your thoughts. Thanks chemslug. My expectation is that there are more safe and tractable micro-projects out there than the average student takes for granted. But I am also raising these questions to confirm a suspicion I have: that despite our love for the idea of "learning by doing," there are many disciplines where a long slog of paper-based learning, punctuated by a few carefully regulated experiments, has to precede any kind of creative or independent hands-on activity. LessWrong's steeped in "move fast and break things" Silicon Valley culture, which seems to inform a fair bit of the perspectives on education I see shared here. One reason why I appreciate your comments here is that you bring insight from a less-represented discipline, one with a different set of norms and requirements than we find in Programland. Do you think that most aspiring chemists would do well to figure out how to set up their own home lab, figuring out how to manage the risks and invest in some equipment? A fume hood costs a few thousand dollars, which is pricey but not completely impossible. Or is there a pretty hard norm that you don't do any serious chemistry outside a professional lab setting? At what point do chemists become qualified to design and execute their own projects?
3lsusr3dFrom the link. Wow.
What's your visual experience when reading technical material?

My visual imagination is pretty much constantly on when I read chemistry papers.  There's a stereotype that you read a synthesis or catalysis paper by (1) carefully looking at the figures, (2) reading the experimental procedures, and then maybe (3) reading the text if you need clarification on a point or two.  Lots of areas of chemistry (organic, biological, materials science) benefit greatly from visualization because of the fundamental idea that structure determines function.  If you can't visualize a catalyst in 3D, it becomes much more difficult to explain things like stereoselectivity or reaction mechanism.

What is the best chemistry textbook?

If covalent vs. noncovalent bonds are something you're not familiar with, it sounds like you'd benefit from reading the chapter(s) on chemical bonding (every gen chem textbook should have one). I'd also infer from that that you won't have much of a background in thermodynamics, which rears its head when you try to understand the energy-storing and energy-releasing reactions of metabolism.

1Maxwell Peterson1moThat’s right, I don’t - I was talking to a friend about vaccines expiring and he said “things want to be in a low energy state”, which sounded like the kind of thing people say a lot and is probably right, but I didn’t, like, feel it. Thanks for your recommendations!
What is the best chemistry textbook?

When I was an undergraduate we used Atkins and Jones' Chemical Principles: the Quest for Insight (link is to a slightly older edition because it's not a field whose basic principles have changed much in the last few years).  If memory serves, it was pretty good.  I'd also recommend checking out the MIT OCW site for 5.112 (that course will do a better job of preparing you for organic chemistry than 3.091, which is more materials focused).  

It is certainly possible to start with an organic chemistry textbook as long as you have a good grasp of... (read more)

1Maxwell Peterson1moI want to learn biochemistry so I can reason about stuff that goes on in the body! I’ve started Lehninger’s Principles of Biochemistry and I mostly get it, but some of the stuff it assumes (e.g. covalent vs. noncovalent bonds) I’m not familiar with.
Thoughts on Re-reading Brave New World

Wow, that was more vehement than I was expecting.  I remember reading 1984 and Brave New World near one another, and thinking that Brave New World was significantly better.  I guess I wasn't as put off by the pro-traditionalist vibes in BNW as you were, and I remember thinking that the government in 1984 was way too capital-E Evil to be very interesting.  I'd argue that BNW is about the way things can still go wrong even when you get a lot right (ending sickness and poverty), while 1984 just seemed like Stalin's USSR with better surveillance tech.

2habryka1moYeah, I am not fully sure what made it such a miserable experience for me, and it's totally plausible there is more intellectual merit in there that I didn't successfully pick up on, but I sure really despised my time with it. Epistemic state of the above should probably be modeled as "I had a terrible time, your experience might differ".
Thoughts on Re-reading Brave New World

I know it's not perfect, but "achieve human potential" sounds like a reasonable moral axiom to start with.  A big "no thank you" to the wireheading for me.

There’s no such thing as a tree (phylogenetically)

I really enjoyed this post!  Look wistfully at pictures of Welwitschia, indeed!  I got to see some in person a few years ago when we went to the Kirstenbosch Botanical Gardens in Cape Town, and my wife was very forbearing with my gaping at the unassuming piles of green straps.

If you're interested in learning more about what the plant developmental toolbox looks like and how it's been deployed throughout plant evolution, I'd recommend David Beerling's Making Eden.  It's a pop-science book but pitched at the upper end of that range.  Merl... (read more)

Thoughts on Re-reading Brave New World

Thanks for the pointer.  There's more there than I remembered.  I originally bounced off that sequence after this post, where EY spends a lot of time worrying about whether there will be enough math puzzles to go around after the singularity.  I remember thinking that his conception of fun was so far from mine that there wasn't much point in continuing.  Maybe I should revisit that conclusion.

Thoughts on Re-reading Brave New World

Thanks for your thoughts!  I think you've put your finger on an important difference between how an individual experiences a society and what a society is capable of accomplishing.  It's the stunting in the second category that makes Brave New World a clear dystopia for me.  As for the islands, their influence on the remainder of society is clearly told to be carefully limited and controlled.  I think Huxley's inclusion of the islands as havens for the dissatisfied greatly increases the ambiguity in how the society appears to a modern r... (read more)

Holy Grails of Chemistry

I don't have any inside information about what exactly prompted the publication of these pieces, but I don't think it's unusual for practicing scientists to have some idea of what's possible if things go very, very right with their research.  They're often wrong, of course, and important discoveries are often important precisely because of unforeseen ramifications.  The Acc. Chem. Res. papers are just speculations about potentially awesome destinations for existing lines of research.

I think that the resistance to Hamming's line of questioning cam... (read more)

Thoughts on Mustachianism

Thanks for this post!

To me, the early retirement option has always seemed like it was better suited to people who had unrewarding jobs that paid better than any of the jobs they would like more (for MMM, this was programming).  On the other hand, even if you like your job it's hard to see how having substantial savings in case of layoffs or unforeseen circumstances could be a bad thing (see Richard Meadows' post on this point).  Thus, like you, I've started leaning toward the "retire in your mind" option.  I also find that the parts of my jo... (read more)

2adamzerner5moThanks for the input! Yeah. And I think I've always underestimated how many people have a job doing exactly what they want to be doing. For me, I really, really enjoy teaching and could see myself wanting to spend my life doing that. I could also see myself at the right programming job wanting to do that forever. Well, I wouldn't go that far. There is a tradeoff in play. You could go on a lot of awesome vacations with that money you'd need to retire in your mind :) As a programmer, I see some parallels here. Mainly that you get to interact and learn from other smart people when you work at a (good) company, but also that you get to solve problems that you otherwise wouldn't get to work on alone. Caveat is that if you look hard enough you can find these things in the world of open source. Hm, I think that's a good point and that there's definitely truth here. But I also think that there are things that we can learn. Covid means people can't do certain social things with their free time, but it doesn't prevent them from doing things like art or music. So if people don't take up art or music during Covid with their excess free time, that seems like reasonably strong evidence that they also wouldn't take up art or music in a non-Covid world with excess free time.
The Best Visualizations on Every Subject

For biochemistry, I think the Roche Biochemical Pathways chart is awesome, if a little overwhelming:

http://biochemical-pathways.com/#/map/1

I don't recommend using it to learn biochemistry but it's pretty great to see it all laid out in one place like that.

3ryan_b6moI feel like it being overwhelming is a feature, rather than a bug. Why doesn't such-and-such a drug work? Because it has to go through this. A good firm smack in the face with complexity helps a lot in problem solving, in my view.
The Best Visualizations on Every Subject

For the field of chemistry, I nominate The Periodic Table of the Elements.  I know it's old but it really does capture a surprising amount of information in a visually pleasing format.

[Linkpost] AlphaFold: a solution to a 50-year-old grand challenge in biology

I disagree with your assessment that structural biology is useless.  Knowing the shape of a protein can be pretty important if you want to perturb the protein's function by, say, finding or creating a small molecule that binds to it.  Crystal structures or cryo-EM structures can shed a lot of light on how a molecule binds to its target, which in turn can suggest further modifications to try and make a tighter binder.  It's not clear to me yet how easy or hard it will be to simulate ligand-protein binding using AlphaFold.  I'd lean toward 'hard' but maybe molecular dynamics simulations would dovetail well with a structure determined by AlphaFold.  

Visualizing the textbook for fun and profit

I'm very glad to see that you're learning organic chemistry!  It's a great subject for the type of exercise you've described, as it's a very visual field of study.  As you mention that visualization is a skill you're working on developing in parallel with your organic chemistry studies, I'd recommend that you get ahold of a molecular model kit.  It may sound silly, but having a physical model of a molecule in front of you can make a big difference in how long it takes to grasp why, for example, SN2 and SN1 reactions give different stereochem... (read more)

3AllAmericanBreakfast9moHaha I may take you up on that! Thank you for volunteering :D These visualization techniques are also helping with my molecular biology class. Very general purpose.
Hammertime Day 6: Mantras

"Don't screw future self" is one that has served me well for more than a decade.