I geek out about unusual plants. I find Welwitschia interesting because it's kind of an outlier. It's a gymnosperm, meaning it doesn't produce flowers, is wind-pollinated, and forms seeds differently than an angiosperm, but it doesn't look like other gymnosperms. Central examples of gymnosperms are conifers, with less-central examples being things like cycads and ginkgo trees, but Welwitschia looks nothing like those, or really any other plants I can think of. It's got a central meristem (growth zone) and two leaves that grow from t...
Thanks for this! Austin Vernon took a look at why the nuclear industry isn't growing and came to some broadly similar conclusions here. I think a lot of environmental groups have gotten themselves into a situation where "nuclear power is evil" is kind of taken as a given, while the techno-optimist crowd is overly sanguine about cost problems being driven by regulations and the chances of those regulations changing. in other words, there's a lot of people with different assumptions and values talking past one another in this debate. ...
The lack of context for comparable search spaces is a fair criticism. The implicit assumption (which I now realize was inappropriate not to spell out for this audience) was that your search would, at some point, involve actually making the molecules in question in order to subject them to some form of experimental characterization. The comparison of the number of possible small molecules to the amount of available terrestrial carbon was intended to make the point that achieving sizable coverage of the search space experimentally is close to a n...
I should have written 'common proteinogenic' in place of 'naturally-occurring'. Thank you for the correction.
Solving protein folding doesn't only give you the ability to know how existing proteins fold. It also gives you the ability to design new proteins.
I don't agree with this claim. AlphaFold gives you the ability to calculate how a given amino acid sequence is likely to fold. That is very different from being able to predict an amino acid sequence that performs a specific function or even has a given shape. Small modifications of known shapes or functionalities would be tractable using AlphaFold's technology, but there are other ways t...
Thanks for engaging! I think there's a real debate to be had about how public research money is spent. I put a higher expected value on continuing to fund basic cancer research than I think you do. I also am more bullish on doing working at the object level (going after specific targets) relative to the meta level (technology platforms). Maybe this is myopia on my part, working as I do in the pharmaceutical industry, but I have also spent a fair amount of time thinking about the problem.
...DeepMind beating Big Pharma at protein folding
I have a lot to say about this but I will keep it short. First, I think you're underselling the insight that cancer isn't a single disease (the Atlantic headline was shitty; of course cancer is a disease). This wasn't obvious a priori. The fact that every case of cancer is a unique and horrible snowflake means that we can't expect "a cure for cancer" any more than we can expect "a cure for car trouble". You're right, however, that some things are more likely to go wrong than others, and routine sequencing of tumors from each individ...
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. :)
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...
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...
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.
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.
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...
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.
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.
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...
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.
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...
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...
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...
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.
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.
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.
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...
"Don't screw future self" is one that has served me well for more than a decade.
Another way to think about diamandoids is to consider what kind of organic chemistry you need to put them together the "traditional" way. That'll give you some insight into the processes you're going to be competing with as you try to assemble these structures, no matter which technique you use. The syntheses tend to go by rearrangements of other scaffolds that are easier to assemble but somewhat less thermodynamically stable (https://en.wikipedia.org/wiki/Diamantane#Production for example). However, this technique gets arduous beyond 4 o... (read more)