Earlier quoted context omitted.
The point I was trying to illustrate was that neither operating systems nor genomes contain the information needed to specify their required operating substrate and environment. Perhaps it may be possible to derive or infer these requirements through simulation and analysis of the OS or genome, or perhaps not. I guess it depends on the degree to which the "code" defining the system is abstracted from its operational…
No, genome contains almost all of the information about the running environment. The epigenome is the rest. Both of these even contain information about build environment. Given high genetic mastery you would be able to figure out the conditions for the whole organism to grow, including required feedback loops. Of course, we're not even close. Generic code is somewhat close to a quine if you look right at it.
Living cells are very fast and crowded places (2012)
71–80 of 86 posts
Re: Living cells are very fast and crowded places (2012)
#72Earlier quoted context omitted.
If god was so great (or at least smarter than humans) most of it would work a lot better than it does!
Care to explain? What could be improved?
Teeth. Replacing these with a new set every 10 or 20 years would be pretty nice.
Re: Living cells are very fast and crowded places (2012)
#73Earlier quoted context omitted.
Thank you for this writeup that peels away a layer of simplification and more vividly and accurately explains what is going on. you have a way with words. The intoxicated panicked mouse will stay with me forever. That being said, I don't agree that it is a pervasive problem that simplification and abstraction is used in teaching. New concepts have to be introduced piecemeal. If a new topic was explained to an audienc…
Yes, our understanding gets more refined the more we learn. It remains messy, error-prone and incomplete. So the solution can never be to learn things 'well' or get things right first time or produce perfect teachers/videos or something like that. The solution is to go on correcting misconceptions where we are interested. Ken Shirriff's blog, mncharity's website, comments here and so on simply are part of the ongoing…
Re: Living cells are very fast and crowded places (2012)
#74I am suddenly very uncomfortable, imagining myself as a roiling blob of goo.
If it helps, consider that you are the descendant of the original "grey goo" which since pervaded the surface of an entire planet. The inheritor of a billion years of techniques in construction, alliance, deception, and warfare. A uniquely coordinated swarm of assimilating nanotechnology, poised to leap into the cosmos. ... No pressure.
Re: Living cells are very fast and crowded places (2012)
#75Earlier quoted context omitted.
If all you had was unix kernel machine code, could you really use it to engineer the hardware required for it to go inside of?
This is a bad analogy - the instructions for making everything in the cell is in the dna, so you also have the blueprints for the hardware fabrication plant.
You can't make use of DNA without all the complex machinery required to transcribe it, translate RNA and replicate it. There's a chicken and egg problem. The DNA does indeed encode the instructions to make and assemble all the rRNA, tRNA and protein sequences to do this, but you have to already have the machinery in place to do so. Kind of like compiling a compiler. You need an initial manual bootstrap, which in the case of life as we know it, took place many millions of years in the past. Just as the code for a compiler is just so much meaningless ones and zeroes without a working compiler to process it, so is DNA in the absence of the translation machinery. Without any context for how to process it, it's just a meaningless jumble of bases.
One thing to think about. If we discovered intact dinosaur remains with non-degraded DNA, could we resurrect it? We don't have the machinery since it was lost with the death of the organism. But we could potentially bootstrap it by placing it in the cell of a related species, e.g. a reptile. But if it was a completely different form of life, we wouldn't even know where to begin.
Re: Living cells are very fast and crowded places (2012)
#76Earlier quoted context omitted.
Actually it's a very misleading analogy. In biology, that's precisely what is happening: The "kernel code" i.e. our genome in fact does have all the instructions on how to build a cell, how to build tissues, how everything communicates, etc. (my education: BA in math, PhD in Biology)
The point I was trying to illustrate was that neither operating systems nor genomes contain the information needed to specify their required operating substrate and environment. Perhaps it may be possible to derive or infer these requirements through simulation and analysis of the OS or genome, or perhaps not. I guess it depends on the degree to which the "code" defining the system is abstracted from its operational…
An important point is that cells are always born of other cells. In other words, a cell replicates by dividing itself, building the parts as it goes along.
So there is never such a thing as a 'naked' genome in biology. There are things like viruses, that hijack cell machinery. There are sperm cells, that carry some DNA into an egg and use that. There is the DNA in mitochondria that rely on the host cell for some proteins.
If you trace backwards, the genome and it's substrate (the cell) have co-evolved to work together. The existing cell acts as the template for the organisation of a new cell, while reading the genome for the structure of its parts. Of course, the genome contains information about when to make the parts, and how to regulate them.
Re: Living cells are very fast and crowded places (2012)
#77> cells are extremely crowded and busy places Cells are extremely crowded and busy... and random and violent places. Molecular biology dances in a nano moshpit from hell. The Inner Life of a Cell is badly misleading. It reinforces many educationally toxic misconceptions. Yes, the graphics technology was limiting. But the video doesn't attempt to mitigate the negative impact. For instance, adding a couple of frames of…
> It's a balloon flapping madly in a hurricane, tethered to an intoxicated panicked mouse clinging to a rope Welp, my desk is now covered in coffee. Thanks for that one, I'll be stealing it ;) It may be better to think of a cell as more of a liquid crystal than anything else, considering the densities. The synapse of neurons is incredibly dense with structures and scaffolding proteins. Even most grad students still t…
:)
> liquid crystal [...] cell membrane is just a latex bodysuit for the ER
Has anyone seen an attempt to collect or catalog such analogies? "One way to think about , is ." Maybe something like http://bionumbers.hms.harvard.edu/ , but for analogical conceptual understanding, instead of rough quantitative understanding. My very fuzzy recollection is bionumbers grew out of one grad student thinking "I don't have a quantitative feel for my area", and starting to collect numbers. Could we do that for stories?
> upload your brain [...] crazy
Well, there's https://xkcd.com/793/ (clueless physicist meets unfamiliar field). But also... part of what makes science work, is fear of being embarrassed by getting it wrong in front of the community of one's peers. And to avoid that, extensively sanity checking with local peers. Trying to think clearly without those, using literature and smarts, but disconnected from the field(s), is hard. And bonus hard points for multidisciplinary questions.
Re: Living cells are very fast and crowded places (2012)
#78> cells are extremely crowded and busy places Cells are extremely crowded and busy... and random and violent places. Molecular biology dances in a nano moshpit from hell. The Inner Life of a Cell is badly misleading. It reinforces many educationally toxic misconceptions. Yes, the graphics technology was limiting. But the video doesn't attempt to mitigate the negative impact. For instance, adding a couple of frames of…
Thank you for this writeup that peels away a layer of simplification and more vividly and accurately explains what is going on. you have a way with words. The intoxicated panicked mouse will stay with me forever. That being said, I don't agree that it is a pervasive problem that simplification and abstraction is used in teaching. New concepts have to be introduced piecemeal. If a new topic was explained to an audienc…
Consider giving a briefing in the military, or to business management, or in a professional consult. Yes, you need to simplify. But distorting results, missing the point, saying things with little connection to reality, and being disorganized and incoherent, rises towards professional misconduct. Describing a foreign culture to generals, or tech to middle management, doesn't seem incomparable to describing the physical world to kids. Science education content currently gives a really wretched briefing on the physical world.
> student [...] demolishing parts of the simpler [model] that no longer fit [...] This goes on until you get to [...] becoming a researcher
But that doesn't appear to be what's happening now.
Chemistry education research describes chemistry education content as incoherent, leaving both teachers and students deeply steeped in misconceptions.
But maybe in college? First-tier astronomy graduate students are often unable tell a 5-year old what color the Sun is, without getting it wrong. First-tier medical school graduate students seem to have little grasp of cell size. These misconceptions and gaps then impair other foundational understanding. It is hard to alter misconception ecologies. Think kudzu.
But maybe researchers? Active researchers chop back their own kudzu in their specific research area. And variously trim it in areas they teach. But the ramshackleness of people's understanding increases rapidly, even within their field, as you move away from their narrow research area, and off into their kudzu forest. Where everyone else lives.
> [paraphrased:] a balancing act of introducing and dismantling increasingly detailed and intricate models
What does "teach friction" mean? Does it mean teaching kindergarten kids what can make them slip and fall? And behavioral and engineering strategies for avoiding that? Sock nubbies need to be on the bottom? Or does it mean teaching them, years later, algebraic plug-and-chug of Arrhenius' law of large objects sliding on pig fat? And for the pig fat model, should they develop a feel for reasonable sliding numbers? Should they be able to judge how well unfamiliar situations match the model?
Imagine being in a 19th-century one-room schoolhouse with a book or two. You might aspire to teaching plug-and-chug, on models students won't use in the real world. Imagine being in a 2017 classroom. You have plug-and-chug. You might aspire to teaching numeracy and transferable knowledge (can be applied to unfamiliar problems), but it would be hard, given the constraints you face. Now imagine a 2037 classroom. The kids have had AR their entire lives. Hybrid computer-human systems have dropped the currently ghastly-high cost of pulling together insights from very large numbers of busy and expensive domain experts. So what could you aspire to?
Might we aspire to a hands-on deep-and-broad understanding of the physical world? It's straightforward to teach early primary students bits of foundational knowledge that graduate students should have, but often don't. It's currently too expensive to scale that. Even considering the positive feedback of getting things "right". But costs are declining. Maybe we'll hit a new regime, as bizarrely unfamiliar, as say expecting peasants to learn to read?
Re: Living cells are very fast and crowded places (2012)
#79Earlier quoted context omitted.
Thank you for this writeup that peels away a layer of simplification and more vividly and accurately explains what is going on. you have a way with words. The intoxicated panicked mouse will stay with me forever. That being said, I don't agree that it is a pervasive problem that simplification and abstraction is used in teaching. New concepts have to be introduced piecemeal. If a new topic was explained to an audienc…
> you have a way with words. The intoxicated panicked mouse will stay with me forever. I like "random walk on a leash" too. Powerful and descriptive.
Re: Living cells are very fast and crowded places (2012)
#80> cells are extremely crowded and busy places Cells are extremely crowded and busy... and random and violent places. Molecular biology dances in a nano moshpit from hell. The Inner Life of a Cell is badly misleading. It reinforces many educationally toxic misconceptions. Yes, the graphics technology was limiting. But the video doesn't attempt to mitigate the negative impact. For instance, adding a couple of frames of…
You don't have to teach everyone everything. This is a misguided belief of the modern western education system that evolved from Christian roots. As Bruce Lee would say - I cannot teach because I don't believe in systems or methods. So how do I learn? Only when I look for the cause of my ignorance. The masses don't spend their time looking for the cause of their ignorance.
Leaving aside the question of whether atoms should be taught, if we do spend time teaching such, it would be nice to succeed at teaching it, which we currently aren't.
But bigger picture, I speculate that the unpleasantness and lack of utility, are caused by how atoms are taught, rather than by the subject of atoms. Perhaps taught much better, atoms might hang together with lots of other things (interwoven finger gesture), creating fun and powerful insight into the world.
> You don't have to teach everyone everything.
There's an old idea that the way to learn history, is to start with whatever interests you. Because history is such an interconnected tapestry, that it doesn't matter which tread you start on. If you like tiddlywinks, you'll soon encounter materials, and trade networks, and game evolution, and social partitioning, and... everything.
Science and engineering are also richly interwoven webs. So why can't you do something similar? Because our science and engineering expertise is too scattered, insufficiently disseminated and integrated. And with past tech, that was too expensive to change.
With better tech, and a lot of societal effort, that might change. So "anyone could learn about anything". Rather than almost immediately hitting a story of "Ah, that touches on several areas. And I'm sorry, textbooks handle all of them badly. You might spend a few months getting up to speed on the research literature in each area, but even then... Well, you really have to move across the country for long in-person conversations with one of a few professors (crazy busy) or their students, and then do that again for each other area. But... have you considered just giving up and crushing your interest now?"