[HN Gopher] I should have loved biology ___________________________________________________________________ I should have loved biology Author : h2odragon Score : 462 points Date : 2022-07-09 13:48 UTC (9 hours ago) (HTM) web link (jsomers.net) (TXT) w3m dump (jsomers.net) | UIUC_06 wrote: | I got interested in bioinformatics in the early 2000's. The | sequencing of the human genome, and of course that of many other | organisms, was a huge enabler of "systems thinking" as applied to | biology. | | It isn't really fair to blame bio teachers for not teaching this | in the 80's or even early 90's. Prior to that, it _was_ mostly | memorization. Some biologists and chemists were putting together | the basic facts that came together and gave us an "aha!" moment. | They won Nobel Prizes for a lot of that. Without Kary Mullis and | PCR in the 80's, we wouldn't know 0.01% of what we know now. | photochemsyn wrote: | Dynamic systems theory is very powerful organizing principle / | concept that makes biology make a lot more sense. It also helps | to constantly remind yourself that academic science divisions - | in particular physics, chemistry, and biology - are fairly | arbitrary and nature doesn't care much about them, and this | becomes very clear from a system-based view. | | Without a grasp of basic physical concepts like conservation of | mass and energy and the direction of entropy, life is an | impenetrable mystery. For example, imagine a river flowing | downstream with eddies on the sides - those eddies have an | upstream flow component, driven by the overall downstream energy | flow. Living cells do the same thing: they capture physical and | chemical energy from their surroundings and use their networks of | nucleic acids and proteins, and their encapsulation structures, | to reverse the normal downstream flow of entropy. | | Everything else follows pretty logically from there. How do cells | communicate with their surroundings? They take up materials, | excrete wastes, collect sensory data, engage in chemical | messaging, and so on. How do cells maintain their nucleic acid | and protein networks? By constantly repairing and rebuilding and | replicating them using inputs of energy and materials. What is | reproduction? A systems-level cellular reboot that also | introduces novelty in the form of mutations and rearrangements | (which may be useful, or not). | | For a good intro to systems-based thinking in biology: | | (2020) Systems Biology: A Very Short Introduction, Eberhard O. | Voit | | https://www.veryshortintroductions.com/view/10.1093/actrade/... | | If you want a deep dive into the modern view of the dynamic, 3D | genome, this is a great source (which also explains why just | knowing the primary sequence of a genome doesn't necessarily lead | to an understanding of disease states, failure modes, etc.): | | (2015) The Deeper Genome: Why There Is More to the Human Genome | Than Meets the Eye, John Parrington | | https://www.goodreads.com/book/show/25660581-the-deeper-geno... | ampdepolymerase wrote: | Voit looks gimmicky. Uri Alon's treatment (An Introduction to | Systems Biology) is much better. | xyhopguy wrote: | > I wanted to conjure models I could play with in my hand. I | wanted a museum where I could walk around inside the epithelium | during an immune response. I wanted to put ideas into physical | space, like on a pinboard--TLRs go here, with the other innate | armament; CD4+ T cells are there, in the adaptive world--but I | wanted it to be as searchable, copy-pasteable, shareable, and | composable as text. | | VR anyone? | causality0 wrote: | Indeed. I changed my major from biology after class became an | endless series of PowerPoint slides depicting protein chemical | reaction sequences we had to memorize. | towaway15463 wrote: | Biology would be much more interesting if it were explained from | a mechanical point of view. At the smallest scale it is a form of | nanotechnology after all. | AlbertCory wrote: | When I was in college, I took Entomology and Zoology for my bio | requirement. The first one was because the teacher had such high | ratings in the student reviews. At one time, I could name all the | orders of insects. No longer. | | It did seem like just a bunch of memorization to me then. Much, | much later, I took an Extension course in Molecular Biology, and | what a difference! I still think the diagrams they draw for | biological processes in _Molecular Biology of the Cell_ are just | stunningly beautiful, and completely blow away anything you 'll | ever see in a CS text. | | But expecting to have those revelations when you don't know how | _anything_ works yet is foolish. You have to pay your dues. | abrax3141 wrote: | Seems like the author has a limited sense of wonder. Just because | the teacher didn't say "Isn't X amazing!" He didn't realize that | it was amazing. Hint: Everything is amazing. Start looking at the | world that way and you'll do way better in everything you do. If | teachers had to tell you all the amazing things in the world they | wouldn't have time to tell you how things work - which is also | amazing. (I'm locked out of additional comments so have to | respond to my critics by edit: I'm a molecular biologist and a | computer scientist. I find the names are part of the wonder. It's | hard to describe how this can be true unless you have a wholistic | sense of what wonder means. Maybe I have an overactive sense of | wonder. ) | [deleted] | codeflo wrote: | I have to wonder where this person's school circumstances. | | For example, why was the triangle area formula only memorized and | not demonstrated to them? I thought this should be standard | everywhere in the world? Maybe they just don't remember, it | happens early (age 11-12 for me IIRC). | | Similarly, and this is from two decades ago at this point, some | basics of gene expression and cell differentiation were covered | in my later biology classes, including some of the evolutionary | steps. Details are of course fuzzy now. But I clearly remember | that learning we share so many genes and so much cell chemistry | with even basic bacteria threw me into a bit of an existential | crisis when I was 17 -- making me question what if anything is so | special about humans. | | When they were students, some people were simply unwilling to | follow any train of thought that was unlikely to be test- | relevant. The author almost admits as much: "Someone probably | told me that every cell in my body has the same DNA. But no one | shook me by the shoulders, saying how crazy that was." That's a | perfectly fine way to approach school, I'm not judging. But then | maybe don't complain that you didn't learn anything? | rjtobin wrote: | I interpret the article quite differently. The triangle example | (which as the author writes is actually an example from | "Lockhart's Lament" on American math education) isn't about | whether triangle-area-formula was ever justified to students. | It's that students aren't given the chance to really ask the | question themselves - a chance to approach math, or biology, in | the way that a mathematician or biologist does in reality: | trying to work it out for themselves, and being invited to | wonder at just how improbable textbook biological facts are | etc. | | I agree with your point that some students will be more | inquisitive, and will need less prompting to do the above | thinking themselves. But many (most?) students are not like | this, and it's a shame that many of these students could enjoy | a subject that they instead come to loathe. | blain_the_train wrote: | i feel like it's like a lisp macro, but it's more like a neural | net. is that a fair assessment? | eesmith wrote: | > I should have loved biology but I found it to be a lifeless | recitation of names: the Golgi apparatus and the Krebs cycle; | mitosis, meiosis; DNA, RNA, mRNA, tRNA. | | I should have loved biology in high school, had it been centered | on evolutionary principles, rather than (in my US classes) | seemingly disconnected materials with at most a week on | evolution. | | Because "controversy." | | I noticed this essay doesn't used the word evolution at all, | preferring "heredity." | | Evolution is what ties the fields of biology together, from | biochemistry and microbiology to anatomy, animal behavior, and | ecosystems. | | I didn't start to understand what I was missing in my biology | education until I started reading Stephen Jay Gould essays in | college. | begueradj wrote: | Unfortunately, nowadays there is more censorship in biology than | in politics | onychomys wrote: | Speaking here as a guy who started his career in organismal bio | and is now working at the cellular level, all I can say to that | is [citation needed]. | lr4444lr wrote: | This is the natural result of state standardized education. It | has its pros though, like getting a functionally literate and | numerate workforce of average people when done decently. It will | rarely serve people of the author's level of intelligence. That's | one of the cons. | bowsamic wrote: | One of my favourite course I took when studying physics at | university was "Biological Nanomachines". I find it absolutely | bizarre that trying to gain a physical intuition for biology is | not the norm. Throughout school I hated biology because it really | did just feel like rote learning. This is embarrassing but I had | such a poor understanding of what a cell was by the end of HS | biology that I still had an image in my mind of a little | conscious being that makes choices: "the cell wants to x" is | language that we can't use in a HS classroom | barry-cotter wrote: | > "the cell wants to x" is language that we can't use in a HS | classroom | | If you can't use language like that you're giving up on getting | anything through to over half of the class. Trying to impart | information to people who don't care and aren't interested is | amazingly hard. Not using agentic framing makes it harder. | Verath wrote: | During the first part of the pandemic I watched the lectures for | the Introductory Biology course [1] from MIT OpenCourseWare. I | cannot recommend those highly enough! | | Almost every lecture brought up and highlighted something really | cool and fascinating. Like how RNA sequencing over the last | couple of years has gone from expensive to almost free, and what | its uses are. Or time-lapse of bacteria adapting to antibiotics. | Or just the first lecture showing a video of someone sticking a | syringe into a cell. There were even some labs that could be done | via a normal web browser. | | For me this was so much more engaging than the biology I was | thought in high school, where we mostly learned things from | outdated books. | | [1]: https://ocw.mit.edu/courses/7-016-introductory-biology- | fall-... | feet wrote: | To anyone who watches these, watch the basic chemistry series | and organic chemistry lectures if you can find them. Follow | that up with biochemistry to get a deeper understanding of the | mechanisms of life | Daniel_sk wrote: | Modern biology is maybe able to fully disassemble the simplest | living forms - but assembling these microstructures synthetically | is still way beyond what our tools can do. It's same like a | microchip where a whole chain of small steps lead to factories | and these produced the chips. And we don't know how the original | cell/life factories looked like, we just have the cells that are | now self-assembling (they are now both the highly complex factory | and the product). We can take a cell and modify the code, but | it's hard to do it from scratch because you would need to skip | bilions of steps that lead to these microstructures. | | I have been recently thinking what is actually life - could it be | a manifestation of a fundamental physical law? And this article | had an interesting take: | https://www.pnas.org/doi/10.1073/pnas.1620001114 "How | nonequilibrium thermodynamics speaks to the mystery of life" | conradev wrote: | I enjoyed this paper on the relationship between entropy and | life - lots of overlap with that article: | | "Life and its evolution are time-oriented, irreversible | phenomena that have produced a steady increase in complexity | over billions of years. The second law of thermodynamics is the | only fundamental law in physics that distinguishes the past | from the future and so this law, and its statistical | underpinning, offer the only physical principle that can govern | any macroscopic irreversible phenomenon, including life." | | https://www.mdpi.com/1099-4300/21/12/1211/htm | telesilla wrote: | "Everywhere you look--the compiler, the shell, the CPU, the DOM-- | is an abstraction hiding lifetimes of work. Biology is like this, | just much, much worse, because living systems aren't | intentionally designed. It's all a big slop of global mutable | state". | | Brings me to wonder, could we ever create anything so marvellous | as what biology does so effortlessly. | inciampati wrote: | Because the system survives by optimizing for efficiency and | reliability. | jnwatson wrote: | It is also helpful to have a 3.7-billion-year head start. | huachimingo wrote: | Conway's Game of Life | tony_cannistra wrote: | It seems like the larger argument here (which I wholeheartedly | agree with) is that the role of skilled teacher (whether it be | human, book, YouTube, whatever) simply cannot be understated when | it comes to creating that "spark" in a learner to develop and | pursue their own passions. | | What's interesting to me, and what follows from this, I think, is | that we therefore have a lever for creating more passionate | people: create more extremely skilled teachers. | | It's obvious to me that this idea isn't new; I just wonder why | it's so deprioritized at almost every level of education. (Not | least the highest.) | Pulcinella wrote: | Money, power, control. | | Defund schools and create horrible working and learning | conditions for those who stay. Create a problem and then say | you are the only one who knows how to fix it. Prey on peoples's | fear, especially fear for their children. Sow mistrust and | bigotry in their communities. | | Unfortunately far, far too many in power who actively and | intentionally do not have the best interests of students at | heart. | | "There should be no such thing as 'good schools' and 'bad | schools.' All schools should be great." shouldn't be be a | controversial opinion, but every time I've brought it up people | get uncomfortable because parents now how precarious their | child's education can be. They've seen what has happened in | other schools and they don't want anything bad to happen to | their child's education. So even if things could be better, | they fear change and anything that could rock the boat because | they don't won't it to get worse. And they aren't wrong to be | afraid: how many times has a politician promised to fix | education and it turns out the fix is something like one more | layer of standardized testing, or cutting art classes, honors | classes, special education services to "focus on the | fundamentals" while class sizes balloon and the money from | those cut classes and services just goes _poof_? | synergy20 wrote: | On top of that, there is the "education first" mindset. When | a culture puts education first(e.g Eastern Asia countries), | it not only means they will sacrifice their limited resources | for education, it also means teachers are well respected and | well paid across the society, relatively speaking. | | Further, when a country focuses on CRT and LGBT+-education | and Equity-grading at K-12 these days, school is no longer a | place to prepare kids for a meaningful career, instead it is | a playground to raise future everyone-is-a human rights | activist or politician, we will have to rely on skillful | immigrants that actually _DO_ things to sustain the economy, | this pattern won't last very long obviously. | | It's not a teacher's problem, or school's funding problem, | it's more of a political problem to me these days(including | the recent education-unrelated law changes). I feel lost as | an independent. | JohnJamesRambo wrote: | To be fair, he wouldn't have known what DNA and RNA were which he | mentions many times in the article, if he hadn't learned the | acronym soup and the basics that biology's wonder is built upon. | localhost wrote: | 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 it sad that I never really saw how to | place this research into the much broader biological context in | which it exists. This goes back to how we teach the subject as | the linked article discusses so nicely. There is no sense of | wonder. There are no questions that are posed to the reader, just | "facts". | | Consider this question - look outside at a tree. Where did all | the carbon in the tree come from? You may have heard that carbon | fixation in plants use a process called "photosynthesis" that | involves iron ions. Where did the iron come from? If only we | taught by using storytelling techniques and posing questions to | students, perhaps we might have more engagement with science than | we have today. | jwuphysics wrote: | > Consider this question - look outside at a tree. Where did | all the carbon in the tree come from? | | I assume that you are referencing the famous 1983 interview | with Feynman, in which he playfully says that "trees come out | of the air!" For anyone who hasn't heard the interview, it's | definitely worth a listen: | https://www.npr.org/sections/krulwich/2012/09/25/161753383/t... | dkarl wrote: | > Consider this question - look outside at a tree. Where did | all the carbon in the tree come from? You may have heard that | carbon fixation in plants use a process called "photosynthesis" | that involves iron ions. Where did the iron come from? If only | we taught by using storytelling techniques and posing questions | to students, perhaps we might have more engagement with science | than we have today. | | I think that level of storytelling is already routine in | science education. It just lands differently with different | people, especially at different ages. That's why those "things | they didn't teach you in school" books are mostly full of | things they really did teach you in school, because many people | people who are hostile to a subject as teenagers are fascinated | by it later. A kid I went to high school with sent an email to | a bunch of us about 7-8 years after graduation because he was | learning some information about American history that shocked | and fascinated him, and he was really worked up about us not | being taught it in school. He thought it had intentionally been | withheld from us so we would have a rosy picture of our history | and our government, but it was all standard bits of American | history we were taught in history class. He remembered being | bored in class, so he assumed this information wasn't shared | with us, but it was, it just wasn't interesting to him at that | point in his life. | gilleain wrote: | Er, hate to nitpick but photosynthesis uses magnesium, no? In | the chlorophyll, at least, although other parts have haems with | iron in :) | | (Also as with anything in biology, there is no doubt some weird | organism that has like a cadmium or similar in its chlorophyll, | I don't know) | localhost wrote: | You're absolutely right! I don't know what I was thinking | here - I blame my supervisor :) One of the other things that | my old research group did was crosslinking of hemoglobin | which has iron as its central atom vs. magnesium in | chlorophyll. I find it pretty amazing the structural | similarity between the heme structure for metal ions in these | two very different use cases. | 3qz wrote: | dinvlad wrote: | I'd even claim that we don't really fully understand how computer | systems work anymore. Let me explain. | | When someone creates a new system, we could argue they have a | complete understanding of it, since they build everything from | the "ground up". Although even then, they use a particular level | of abstraction - not necessarily needing to understand how third- | party libraries work, or how it all translates to machine code | etc. | | Imagine now this person (or a team with equal understanding of | the system) leaves, and another team joins. How are they supposed | to "understand" it? They would have to piece together everything | very much like we're trying to do in biology. Even when the | original creators left a "plan" in the form of code, docs or even | being accessible for Q&A, they cannot possibly verbalize all the | minute details, because the complexity of the system is so large | that they would have to spend an equal amount of time on | explaining as on developing it. And that doesn't even account for | random things or reasons they themselves forgot, or never | understood in the first place. | | As a result, we're left with only a partial understanding of the | system, the level of which goes down the larger the system is. | And as more teams join and develop their own pieces and leave, | this knowledge gets diluted so much that it becomes hopeless to | even reason about the whole thing. | | So, I'd argue we can only strive to understand the most important | pieces. And, just like we see in biology, the process of their | discovery is mostly just educated trial-and-error, aided by the | tools like better diagrams to speed up the process. And maybe | that's OK, if the ultimate goal is to get to some practical | results like curing a disease or expanding the business. We can | discover the mechanisms that lead to reaching these goals, but if | they aren't relevant, then it's just going to be an academic | exercise and another data point in the trial-and-error (until | someone discovers how to use it for some new goal!). | TheCoreh wrote: | 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 is that it leads to very rigid thought | structures devoid of curiosity or contextualization: The belief | that the map is the terrain; that the universe is static, | predetermined and discretely categorized under conveniently human | terms; that scientific knowledge is either divined or | standardized by a class of bureaucrats; that things are sorted | over a "rank" of lesser to greater according to a direction | towards objective progress. | | It also generally sucks out a lot of the "fun" of learning about | the world (though I understand sometimes taxonomy/categorization | _can_ be fun in its own right). | | As an example, grammar only really "clicked" with me when I was | already in college: I was finally able to see it outside of the | "prescriptive memorization hell" that I was subjected to in | school, and instead perceive it under descriptive terms of | Computer Science. | closeparen wrote: | I sympathize, also being bad at and unhappy doing this kind of | study. But to be fair to biology, its fundamental thing is the | incredible variety of creatures in the world; their stunning | diversity as well as similarities, family resemblances, and | interactions. | repple wrote: | It seems that taxonomy is what you would like to learn only | after the subject piqued your interest, in my experience, | looking back at early school years. Prior to gaining interest, | it felt like such a drudgery. After that, however, it's like an | map to navigate the subject matter. It becomes fun in itself, | as you point out. I guess it's a level of abstraction preferred | by folks with expertise, but less so by beginners. | randcraw wrote: | I agree. I know many who were driven away from appreciating | biology due to its excess of nomenclature and memorization | thereof. It's made worse because few terms reveal much depth of | meaning about what it labels. Biology is made superficial | because the language of the subject describes only surface, no | depth. | | That's not biology's fault. No language could hope to convey | the full 'personality' of each character in a tale as rich and | complex as unfolds in Lewis' "Life of a Cell". | | But maybe biology is ripe, now that we understand enough of its | major 'characters' and their 'behaviors', for us to introduce | more abstract models of biology using concepts and language | that make for more intuitive players and their relationships. | In this way, we might tell a more comprehensible and engaging | narrative based on a much smaller set of reusable base models | -- the way that applied math expands on the concept of a | computable function or the way electrical engineering builds on | gaussian processes that model signals. | | At the very least, I would LOVE for each chapter in a molecular | bio textbook to be split into two parts -- a short overview of | the topic that follows with only the major components and | activity described, and only then, to dive into the details. | Seeing a city from high above it is an enormous help before | trying to appreciate it on foot. | joshuahedlund wrote: | If I'm an experienced programmer who is fascinated by molecular | biology and would love to transition from e-commerce to biotech, | what sorts of jobs would I look for or what would I do to prepare | for such a switch? | AndrewVos wrote: | If I wanted to learn biology as an adult, are there any books | that explain stuff in the same vain? | | Bonus points for pictures! | civilized wrote: | Pet theory: for most of human history, biology has been an | increasingly complex detective story, a notepad of mysteries | laying on a table next to an unfathomably massive evidence room | stuffed with barely organized facts. This appeals to certain | people and not to others. Only recently has it become possible to | approach it from more of an engineering perspective, which | appeals to a different set of people. | czbond wrote: | 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? | civilized wrote: | 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 | CRISPR that gave information about a wide range of proteins | in the cell, or something. They added a lot of facts to the | library. But they marketed it as if they had made a huge | stride towards understanding how the whole machine works. | That gets people like me more excited. We'd like to know how | the machine works and then use that to make it work better. | asmithmd1 wrote: | _the source code containing within it all of the instructions | required for life on Earth._ | | I would disagree, we see the object code. If we had the source, | with comments, genetic engineering would be much easier | bognition wrote: | It doesn't really make sense to talk about DNA as source code | vs object code vs whatever. | | Biology doesn't have the same clean levels of abstraction that | we've developed in computer science. DNA functionally operates | at many levels. It long term storage, local working storage, | and it is used to compute. It's a single molecule that does | everything. | | Then you have to throw in all the secondary processes that | modulate and regulate DNA replication, transcription, as well | as activation/deactivation. | | While it can be useful to lean on the abstractions we've | developed to try to understand what DNA is doing those | abstractions can only be taken so far. | asmithmd1 wrote: | Yeah, I was kind of making a joke. But to stretch the | analogy... Maybe there is a common source that is cross | compiled to different chemistries producing a seed object | code cell. | gnramires wrote: | Indeed, I classify the main difference between life | (biological systems) and technology (civilization engineered | systems) is about the structure of complexity. | | Human civilization is severely time-limited (or just time- | pressed). We can't wait millions of years running a | simulation to optimize a little widget. We need to rely very | much on high level design and comparatively little on | efficiency and optimization. On the other hand, life cannot | afford huge DNA (very costly), or energy waste (generally | disfavorable from evolution). So human built systems tend to | be of a low "Compute complexity": the computational | complexity of obtaining solutions and solving problems | themselves (like civil engineering structure problems, or | design of objects) must be fairly low. For life, systems can | be amazingly intricate, every tiniest cell a wonder that | would probably take thousands of years for civilization to | maybe be able to replicate. But it all ranges from about | 130kbp to 8Mbp[1], which would be around 16Mbit/2Mbytes at | most. So it fits (uncompressed) in a diskette (floppy). | | Even now with powerful computers, we're still mostly | constrained by cognition (specially human), you see | simplicity all around you. | | So if you look at the human world, you see (computational) | simplicity everywhere, but the natural world has undergone | trillions of generations of optimization to arrive at almost | perfect (in an almost literal way) little machines, | complicated but with a hidden amazing (size) simplicity. | | I think there's a connection to be made to algorithmic | inference as well. Originally we came up with ideas for | Universal Inference (from ideas from by Solomonoff, | Kolmogorov among others) [2][3], the most glaring candidate | was the "size prior": evidence explainable by the least | algorithmic information ought to be most likely (Solomonoff | inference). Later, there were promissing ideas around an | additional term: the "speed prior" (from Schmidhuber[4]) -- | the biological word is one where the "size prior" (simplicity | is most likely) works almost perfectly, and human | civilization is one where the "speed prior" (computationally | easy is most likely) is helpful. | | [1] https://en.wikipedia.org/wiki/Bacterial_genome | | [2] https://en.wikipedia.org/wiki/Kolmogorov_complexity | | [3] https://en.wikipedia.org/wiki/Algorithmic_probability | | [4] https://en.wikipedia.org/wiki/Speed_prior | | Side note: I think intellectually one of the ways we're | really far behind is recognizing Algorithmic Information | theory as a foundation for statistics and metaphysics. We're | very stuck making little progress on the metaphysical realm | (which physics is advancing more into) because of a lack of | widespread acceptance of those advanced tools for science. | Algorithmic inference gives a solid basis for comparing | metaphysical models and deep questions about the cosmos. | agumonkey wrote: | embryology made me realize that there's also an inherited | context in how genes control development, IIRC the womb | triggers some key structural changes in the very first days. | popcube wrote: | Biologist performed so many crazy experiment on fruit fly, | development biology is very interesting for reading: what | happen in each stage and all of mechanism we can understand. | czbond wrote: | I love this comment. So niche to the general population, but | deep to participants here. | jugg1es wrote: | In reference to the part where he talks about wanting it to be | easier to create 3d models in biology - the complexity of organic | molecules is very, very high. Not only are they complex, but they | change shape a lot. In fact, the more realistic a 3d | representation of an organic molecule is, the less likely that it | would help you actually understand it. Microbiology is messy. | HorizonXP wrote: | I did my undergrad in electrical and computer engineering. My | career has been focused on software. Yet, all through high school | and into university, I took biology courses. I did my masters in | medical imaging. I wrote the MCAT. | | I've always loved biology. The intricacy of the systems, and how | they work together is so fascinating and really presses the same | buttons as computing. | fastaguy88 wrote: | I think this essay applies to most of the sciences (perhaps | excluding physics), in part because it is really hard to test | whether a student was amazed by a particular insight, and much | easier to test facts. Biology is amazing. Every cell has the same | DNA, and in humans, that DNA is several meters long. In a cell | that is 25-ish microns in diameter! But chemistry is amazing too | - how do all those air molecules become uniformly distributed in | a volume? How did Avagadro figure out that number? | | The problem with teaching science is that the amazing stuff that | is accessible to a high-school student was figured out 100 - 400 | years ago, and we've learned a lot since. And for biology and | chemistry, there are all those details. (I guess math might be | worse, since we teach things that have been understood for | thousands of years, but at least the old stuff is obviously | useful.) | | I think it's really hard to teach and test on the exciting stuff. | What's exciting to me may be "who cares" to the next person. But | it's great when it works. | rob_c wrote: | Yes it's all a mixed wet bag of chemicals with probabilities but | thankfully we've spend a significant amount of time separating | and understand a lot of these molecules in isolation to try and | understand the Jigsaw of life. | | I don't normally come to the defence of the biological sciences | but why would you expect it to be anything else? | | If you're blindly reciting then either you don't understand or | haven't been tough enough to understand the parts of the puzzle. | Unfortunately this is also a consequence of modern teaching | methods I would argue but that's another problem all together... | the_only_law wrote: | I did love Biology. In fact, I think it was my first real | interest before computers or programming. | | Some aspects of the field still fascinate me, but I know if I | ever bothered to engage the interest I'd be broke. | rjsw wrote: | The Biology teachers that I had at school were a lot better | than those for other subjects, there were not many other jobs | that they could do. | User23 wrote: | This is part of why I'm grateful for my Christian faith. I view | the scientific endeavor with endless wonder, because it's | incredibly satisfying to better understand creation. I don't need | to be convinced the cell is a glorious marvel. | | It's certainly not the only way to have that intellectual | posture, but it's a powerful one. | wintermutestwin wrote: | I remember taking biology back in the 90s and thinking "this | stuff is really interesting. Even though I have minimal practical | use for this knowledge, I'm going to come back to this in a | couple years when I can explore it in VR because that would be a | far superior learning medium than a crappy textbook." | | one of these days -\\_(tsu)_/- | [deleted] | fabian2k wrote: | Biology did seem more like a recitation of facts in school to me, | but it was very different in university. I think part of it was | having a pretty bad teacher, but also the school textbooks are | just so much worse than the introductory textbooks for | university. | | I think some parts are fixable, others are difficult. A part of | the problem is that you need to cover some parts in more depth if | you want to really make sense of them. Without some basic | chemistry and thermodynamics knowledge the entire metabolic | pathways seem very arbitrary. This is probably hard to fit into | the amount of time you have in school for those subjects. | pixel_tracing wrote: | I guess I'm a prime example of this article. I originally majored | in biology (racked up enough credits so that if I wanted to I | could have a biology degree within 1 semester), then switched to | chemistry and eventually graduated with a chemistry degree and a | minor in computer science. | | My passion for biology came when I attended Human Anatomy & | Physiology. I learned about neurons and action potentials, | chemical gradients and how diffusion can cascade these changes. | These machinery like interactions made the cells come to "life." | | I then switched my major to chemistry to understand these | interactions. My favorite class was Physical Chemistry. Both of | these fields are saturated by two types: the pre-med schooler and | the academic, these two types are fighting for prestige and | status. I believe the schools mostly cater to these types so they | can get into their relevant higher ed (masters, PhD, and | medicine) schools. This ends up robbing the undergrads who are | actually interested of the material (you end up with what's | described in the article). | | In contrast computer science was a breath of fresh air :) I wish | bio and Chem fields were like that. | The_suffocated wrote: | I think this is not a biology-only phenomenon. I have the | impression that chemistry and mathematics are also not taught | well in many (if not most) high schools. Physics education in | contrast seems to be in better shape. | formerkrogemp wrote: | Let's just agree that US high school education is generally | abysmal. | ryan93 wrote: | Smart kids do incredibly well here. Who cares about average | pisa scores. Average kids anywhere don't contribute to | science or engineering | barry-cotter wrote: | If you think US high school education is abysmal where do you | think does it better? US Asians do very well compared to | other Asians, US whites to other whites, etc. | | https://www.unz.com/isteve/the-new-2018-pisa-school-test- | sco... | brnaftr361 wrote: | Is the purpose of education to make people take tests and | get high scores that bureaucrats can wave around, routing | their success? | | Or is it something a little more profound? | barry-cotter wrote: | If they can't do well on tests designed to measure skills | the students have been failed. They have not learned | skills. The US education system is quite good at teaching | skills. A large majority of countries do worse. The | skills that PISA tests are a prerequisite for almost any | more rarefied learning that is often held up as the | _real_ purpose of education. | | Being able to read for meaning, extract information, | combine knowledge from two texts, distinguish between | what is stated and what's implied, even to figure out | something _is_ implied, all of those are the kinds of | things we expect an educated person to be able to do. | PISA tests them. Trying to make people care about | academic subject matter is very difficult because most | people do not care and do not find it useful. Thus they | forget most of what they learn in school. Insofar as | education is forcing the tastes of one class on everyone | else it can burn. Most people don't care, just like most | academics don't care about sports. Forcing sports on them | would also be an injustice. | formerkrogemp wrote: | > Trying to make people care about academic subject | matter is very difficult because most people do not care | and do not find it useful. Thus they forget most of what | they learn in school. Insofar as education is forcing the | tastes of one class on everyone else it can burn. Most | people don't care, just like most academics don't care | about sports. Forcing sports on them would also be an | injustice. | | Ah, yes, we should teach less science to everyone because | that would be like forcing every academic to play sports. | Perhaps physical and science education should be provided | for every student? Education does not come at the expense | of sports. If anything, the opposite is often true. | brnaftr361 wrote: | Yeah, actually. This is projection but: | | People _are_ naturally curious. Shuffling them into the | confines of some narrow and often purposeless maze fucks | that up. That 's a considerable portion of TFA, the | institutional curricula stunted their interest in | biology. | | My curiosity was drugs, drugs lead me to biology, lead me | to chemistry, physics - but it was independent study. | Political challenges from my partner got me interested in | history and anthropology, but it was all independently | structured. | | I think if the institution gave all these little | knobheads enough autonomy to actually derive, from | themselves, some _real_ interest, they would ultimately | end up intersecting with all the sciences, it 's actually | inevitable. Instead they're just forcefed a bunch of | information they don't have a relationship with. | | Sports is biology and mechanics is molecular biology and | kinesiology and so on. It doesn't matter where you start, | you track into that shit. Passion the latitude it lends | to the people possessed by it is what allows us to push | deeper and deeper. Not stunting intellectual growth by | conditioning people into a state of repulsion at the | premise of learning. | formerkrogemp wrote: | Yes, yes. Education is multifaceted in its consequences. | Merit depends upon objective testing. Common culture and | high trust society depend in large amounts upon education | and schooling. With the quality of schooling available, | shortage of teachers and quality teaching personnel due | to abuse and low salaries, political interference with | teachers handling their own material, religious | indoctrination in charter schools, and the amount of | students requiring remedial classes in college. Of | course, more data and parameters can be considered, but I | don't think anyone can consider the broad state of | secondary and primary education in the US as "healthy" or | "improving." | brnaftr361 wrote: | I don't think you _can_ objectively test. When you do | test you 're making a singular data point that doesn't | reflect ability, necessarily, but instead a coincidence | of factors at a given point in time. The data point is | arbitrary, even if the test is scored against the | distribution. | | Take, for instance, a FT-working non-trad that scores | above the mean. The mean who predominately consists of | students who are FT-students. Should some respect not be | paid to the considerable handicaps suffered by the non- | trad? How do you even begin weight that? | | Of course this is multiplied a million times over in | several dimensions. | chongli wrote: | _" The science of government it is my duty to study, more | than all other sciences; the arts of legislation and | administration and negotiation ought to take the place | of, indeed exclude, in a manner, all other arts. I must | study politics and war, that our sons may have liberty to | study mathematics and philosophy. Our sons ought to study | mathematics and philosophy, geography, natural history | and naval architecture, navigation, commerce and | agriculture in order to give their children a right to | study painting, poetry, music, architecture, statuary, | tapestry and porcelain." | | -- John Adams in a letter to his wife Abigail_ | | I'm sure many people would love to have their children | study the arts and humanities and develop profound | insights into human nature and life itself. | Unfortunately, many people are stuck studying mathematics | and other subjects like it in the hopes of having a | decent career. | brainzap wrote: | I should have loved X but school happend. | cercatrova wrote: | Not sure where the author went to school, but when I was in | school, this is in fact how we learned biology, as well as | mathematics and chemistry. Maybe our teachers were good, but we | derived facts like the area of a triangle through geometric as | well as algebraic means, and same for biology. | planarhobbit wrote: | For most of us, these great awakenings come with age. They are | rich, sublime flashes of clarity and intellect to be enjoyed | (first and foremost) and nourished (thereafter) with more such | awakenings. The simplest of deductions lead us to wonder how, | what, and if. This is the tunnel through which some people end up | believing, through disbelief and astonishment, that there is a | grand design at play and that it is a thing of beauty and wonder. | agumonkey wrote: | There were animations of DNA -> protein translation, it felt very | much like good old (map f list) :) | pflanze wrote: | Previous discussion (Nov 2020): | https://news.ycombinator.com/item?id=25136422 | SilasX wrote: | Low effort comment, but, wow. This article is a super thorough | version of the shower thought that, biology is a lot cooler once | you reframe it as the study of naturally occurring self- | replicators. | popcube wrote: | this is all the selfish gene want to talk about | 8bitsrule wrote: | Exactly how I feel about it. I grew up in a town in the middle of | a wilderness, surrounded in all directions by dozens of miles of | amazing things in lakes, swamps and forests. What did we learn | about them in the classroom? _Nothing_ , seldom even mentioned. | Then I learned to drive. | | What do I remember from HS bio? Lists and lists of lists, uglenas | and pseupodas. Way to kill the buzz. | czbond wrote: | I was very into Chemistry and Biology until I found Computer | Science. C.S. was/is fascinating, so many interesting problems. | | Until I found out C.S. to a majority of the world really just | means coding - the most boring activity I can imagine. (to me... | I have some parts of "H.D." in the ADHD, so don't downvote me). | | I thought C.S. would lead to a career of solving difficult | Automata, algorithmic, etc problems. Nope. | chongli wrote: | Solving difficult problems is a very difficult job to get. Most | employers do not want their employees solving truly difficult | problems because it's too hard to replace someone capable of | that. This is why the world of work has been so heavily | organized around avoiding these difficult problems in favour of | boring/repetitive tasks. | the_only_law wrote: | Hah yes, an unfortunate realization was that programming as a | career strips away many of the things that made me interested | in the first place. | axg11 wrote: | I think what is described here comes down to the fact that we | don't have much (any?) _deep_ understanding of biology. The most | concrete aspects of biology are observations. For example, | anatomy is very well understood because it's essentially | observations of structures within living organisms, as field it | has been relatively stable for a long time, hence there are well- | established methods for teaching anatomy. | | There's a huge gap between the fundamental units of biology | (biochemistry) and the resulting emergent behaviour (living | things). We don't have a good bottom-up system to predict the | emergent behaviour so we're mostly left with observing from the | top down and poking/prodding sub-systems, hoping to gain some | insight. | | When so much of biology is observation without deep insight, it | shouldn't be a surprise that biology is difficult to teach, and | even more difficult to find beauty in for new students. | shpongled wrote: | I would argue that depends on your definition of deep - we are | certainly getting better at developing both genetic and | chemical tools that allow us to probe specific pathways/sub- | systems of biology, and read out the resulting perturbed | phenotype(s). | | > There's a huge gap between the fundamental units of biology | (biochemistry) and the resulting emergent behaviour (living | things). We don't have a good bottom-up system to predict the | emergent behaviour so we're mostly left with observing from the | top down and poking/prodding sub-systems, hoping to gain some | insight. | | I think this is just about the last thing that we will ever | solve/figure out. | | There are just a mind-boggling number of parameters, feedback | loops, dynamic modifications, interactions, etc that are | effecting cellular state (let alone organism state) - something | that I think many CS oriented folks ignore when talking about | "DNA as source code" (perhaps if program behavior depended on | the size of indents, font, variable names, how many lines of | code you wrote, the proximity in source location of different | functions, etc). | randcraw wrote: | Yeah, I think programmers would better appreciate the | complexity and subtlety of biology much better if they had to | _evolve_ their programs rather than code them up explicitly. | (I say this as someone with degrees in both subjects.) | AlecSchueler wrote: | > (perhaps if program behavior depended on the size of | indents, font, variable names, how many lines of code you | wrote, the proximity in source location of different | functions, etc) | | I think I've seen all of those functionalities implemented in | esoteric programming languages! Nice comparison. | marcosdumay wrote: | What you haven't seen is a CD-ROM sized program with no | abstraction, encapsulation, or modularization, all | implemented on a language that has all of those. | | Oh, and that is being interpreted by more than one | incompatible interpreter at the same time. | onychomys wrote: | > There's a huge gap between the fundamental units of biology | (biochemistry) and the resulting emergent behaviour (living | things). | | And then a very similar gap between the fundamental units of | one small branch of biology, ecology, where the fundamental | units are living things and the emergent behavior is everything | you see outside your window! We have a lot of math that | explains how things act and evolve together and it's all just | the tiniest little smidge of what actually happens. | ramraj07 wrote: | Hard disagree. We understand biology for the most part. The | issue is in the exact implementations. | | An analogy would be like understanding how a computer works. We | know how chips are made, the physics behind them. We know how | bits are stored and processing steps are executed. We also know | generally how operating systems work. We have the full compiled | code as assembly instructions. But we don't have the source | code of the OS. We just use crude tools to figure out The | details of the OS and how it works on particular subsystems but | because of the crude nature of the tools the knowledge we gain | is ambiguous at times. | randcraw wrote: | Biology is incomparable to computers, or to any other man- | made machine. In computers the components interact in well- | defined separable and independent roles. In a biological | organism, all components depend heavily on not just one or | two other components, but many. The role we impute for each | mechanism often interfere and/or collaborate with other | seemingly unrelated mechanisms, often in hierarchical and | nonlinear fashion. That's why the function of even simple | biological subsystems is so challenging to decipher. Context | and interdependency are everywhere. That's why the | oxymoronicism of a biologist "fixing a radio" rings so true. | dinvlad wrote: | > Context and interdependency are everywhere. | | Very much applicable to software as well :-) Modern systems | are so complex there're very few people (if at all) who | understand everything in them, even though they were man- | made over time. | Balgair wrote: | Having done a _lot_ of biology, I 'd disagree that we | understand biology. | | My background is neuro, so take that into account. But in | neuro, we've nearly no idea about the larger parts of how it | all works. Sure, yeah, electrically active neurons, we have | that down. But the non electrically active parts? I mean, | we're still debating about how much of the brain is glia. | Like, we can't even agree on how to count. Don't get me | started on synapses. | dinvlad wrote: | I don't even think we understand software, much less | biology :-) We can only hope to understand the pieces that | are most relevant to the business domain we're trying to | solve (like curing a disease or expanding an online | business). The complexity of both types of systems is just | increasing exponentially over time, so there's little hope | (or even need) to understand the whole thing. The challenge | is, of course, to understand what's relevant in the first | place. | | And just like in software, we can only hope to come with | the right levels of abstraction and disregard the | irrelevant parts at each level of understanding. | atty wrote: | 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 out that modifying a working complex | system is pretty hard. | h2odragon wrote: | > 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 1.988435x10^33 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 we'll burn those bridges | when we get to them. | PebblesRox wrote: | Gotta budget for some extra hydrogen to burn the bridges. | P-NP wrote: | 6th paragraph: Someone should have said this to me: Imagine a | flashy spaceship lands in your backyard. The door opens and you | are invited to investigate everything to see what you can learn. | The technology is clearly millions of years beyond what we can | make. This is biology. -Bert Hubert, "Our Amazing Immune System" | nitwit005 wrote: | I suspect most biology majors would be plenty interested in these | topics. The barrier tends to be the foundational knowledge they | have to get through, like statistics and organic chemistry. | | I presume the author now has that foundation, so it's | unsurprisingly much easier to approach. | Pulcinella wrote: | Yeah it doesn't help that things like HS Chemistry and Chem 101 | classes aren't really Chemistry, it's all the things to you | need to know to get started doing and learning Chemistry. | | It would be like if we saved learning how to read and write or | learning Arabic numerals and basic number sense until early | high school. | pgrepds wrote: | I disagree that biology, or by proxy any other science, should be | written in such a way that a non-expert in the field should | understand everything without consulting wikipedia or any other | source. Studying a natural sciences includes learning a certain | vocabulary and grammar. The reason for this is simple. We agree | on certain definitions, words and sentences, to minimise the | possibility of ambiguities and misconceptions. This is a very | important aspect of any science. | | In the same sense, abstracting things is important. Abstraction | gives us the opportunity to apply the results from one seemingly | foreign field to another. | | It is not the task of science to create enthusiasm for the result | for people outside the field in technical articles or textbooks | as this post tries to endorse. | | The excitement for a certain topic should be given by the | teachers and, to be honest, this was also always the case in my | experience, but I might have been very lucky. | | Furthermore, the vast generalisation "Instead, we're told that if | you ever find yourself wanting the area of a triangle, here's the | procedure" couldn't be further from what I've experienced. I've | never been given a "procedure" in math without being taught why | and how it works. | bognition wrote: | 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 stories you learned in molecular biology but | with the tools you acquire in organic chemistry. | | Equipped with those tools I relearned the Krebs cycle and | photosynthesis as real chemical reactions that make sense rather | than a chain of facts to be memorized. | | The class left me with a deep and profound reverence for life. | Every process in a cell has a mechanism that can understood with | chemistry. However, the magic of life exists where those | processes come together and interact in incredibly complicated | ways. | | It's seductive to think that we should be able to tease apart | this complicated processes and figure out how "life" works, and | maybe someday we will. However, it's easy to underestimate the | level of complexity and interconnectedness in these systems. | | Many of us understand how hard it can be to debug a distributed | system. Imagine trying to reverse engineer a distributed system | with tens of thousands of interconnected services and messaging | queues that all just sort of evolved and were not built with | clean engineering practices. | gilleain wrote: | Great description. | | I would go further to describe living systems as not just | distributed and so on. Also they are self-assembling and self- | repairing. They are redundant - which makes them more damage | resistant and 'evolvable'. | | Also, these complex assemblies of machines work at (mostly) | room temperature and pressure. Except for extremophiles that | can work down to freezing or up to boiling temperatures, or in | acid or high pressure environments. | | Also enzymes catalyse stereospecific reactions, or can use | light to drive proton gradients across a lipid membrane, or | reduce nitrogen gas. I've always found it funny the sci-fi | obsession with 'nanomachines' when living systems are basically | composed of exactly that. | bsedlm wrote: | I like to think that in life the code is also the runtime, | unlike in computer technology where the hardware is the | runtime. | Banana699 wrote: | I'm not sure there is such a fundamental difference. In | biology the code is the DNA and RNA, whereas the hardware | is the proteins. DNA and RNA are self-modifying and | imperfectly transmitted, but those traits can also exist in | computer code (to the extent that they aren't, it's because | humans make sure of so, because they hate trying to | understand dynamically changing things). The hardware of | life is self-creating and self-repairing, but - again - | this can also be easily simulated in computer hardware, to | the extent that it isn't, it's because it's costly and | there is no good reason for it. | | Biology's difference from computers is in scope (organisms | are whole factories who just happen to have computational | abilities by necessity) and origin (organisms aren't | designed, and this profoundly and significantly affects | everything about them). | jyounker wrote: | > In biology the code is the DNA and RNA, whereas the | hardware is the proteins. | | This distinction isn't as clear as you think. The active | parts of ribosomes (the machines that translate mRNA into | proteins) are catalytic RNA. There are organisms that use | RNA to store templates (RNA viruses). | towaway15463 wrote: | The code is a serialized record of the hardware. It has to | be translated from codons to amino acids before being | assembled. | gilleain wrote: | I must be running on slower code, as I can't quite unpack | that. So the code in life is the DNA which is also the | 'runtime'? | MereInterest wrote: | 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. | bsedlm wrote: | yes exactly. you've explained this much better than I did | feet wrote: | 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 | [deleted] | ip26 wrote: | 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 | evolved spontaneously. There's just endless complexity there. | | There's 574 amino acids making four separate interlocking | chains in a single globin, plus the heme, all just to bind 4 | oxygen molecules. It's simultaneously elegant but hugely | complex, far above any discussion of the rna sequencing. | | It's a big part of the "gap" between chemistry and biology IMO. | gilleain wrote: | I worked for a professor (James Milner-White) who was | interested in early protein evolution and I remember a | conversation we had about the possibility that proteins could | have evolved from large to small. | | Not sure if it was from a published paper, but the idea was | that early proteins might have been large - say several | hundred residues - but mostly disordered. | | The smaller, more ordered 'domains' would then have evolved | within these larger chains. Recombination and deletion would | then have pruned down the disordered parts to leave more | efficient smaller proteins. | | No idea if that idea makes sense or has any research behind | it, but it's quite a neat theory. | ngc248 wrote: | wow ... it makes sense ... more of a top down approach. | feet wrote: | Its actually top down _and_ bottom up at the same time. | All of biochemistry operates on the basic rules of | physics which determine how the chemistry happens with | feedback from the surroundings /system as the top down | part | randcraw wrote: | Knowledge Distillation is a related concept in deep NNs, as | are the concepts behind the compression of data in signal | processing. | MereInterest wrote: | There was a paper a few years ago about a similar effect in | artificial neural networks [0]. The gist was that a large | network can contain many subnetworks, and the number of | subnetworks grows much faster than the size of the network | they are contained in. They were able to find a subnetwork | in a randomly weighted network with equivalent performance | to a trained network of a much smaller size. | | [0] https://arxiv.org/abs/1911.13299 | randcraw wrote: | Nice. Sounds like these self-assembling subnets could be | the basis for a viable model explaining the mechanisms | behind early evolution. | charlie0 wrote: | Skynet? | mncharity wrote: | > 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? | go_elmo wrote: | Lovely life lesson shared. It also blew my mind how much | complexity handling non formal, discrete systems adds. Just | samoling root development takes years and endless hours of | tedious, non automatable work. No wonder the field progresses | orders of magnitudes slower. Also, add chaos theory, quantum | mechanics, differential equations and enzyme molecules to the | distributed system to make it a bit more realistic. | s1artibartfast wrote: | I had a similar revelation for structural biology, applying the | physics I learned for bridges and buildings to microscopic | proteins. They are structurally like a cathedral built by a | blind and deranged architect. The fact that mechanically bend, | pivot, and move like a complex machine at a micro scale to do | real work is the most sci-fi thing I can conceive of. | | Think of a even a simple walking protein like Kinesin [1]. What | is not shown in the video is that this is all happening in a | hurricane of molecules battering it from all sides. Each part | of the structure is being pushed, pulled, bent, robot made out | of sticks and rubber bands. | | https://www.youtube.com/watch?v=y-uuk4Pr2i8 | tambourine_man wrote: | > They are structurally like a cathedral built by a blind and | deranged architect | | That's one of the best things I read all week. | azalemeth wrote: | The other word missing is "cheap". Proteins are under a | massive selection pressure: many thermodynamic reactions in | fundamental bits of biology are as thermodynamically | efficient as they can be, else some slightly more efficient | mutant would have out-competed it aeons ago. | | I became interested in biology as a physicist when I | realised that all of the problems, on some level, boil down | to putting a load of lego pieces in a box, shaking it up | with some energy not terribly different to k_B T, and | getting a fully-formed, self-replicating lego models out | the other end. It's all physics. It's all utterly | incomprehensibly mind-bogglingly complex with layers of | complexity wrapped around each other, and far out of the | realms of either physics or chemistry to compute | completely. It's why I work at the intersection of the two | fields. | | Another famous paper, often-mentioned, related to this is | "How a biologist would fix a transistor radio", essentially | armed only with a shotgun. The tools of modern molecular | biology may be scalpels rather than shotguns, but still, | the idea is arguably the same. | AinderS wrote: | > It's why I work at the intersection of the two fields. | | Sounds fascinating. May I ask which field that is/what | type of work you do? | ciconia wrote: | > 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. | | In high school I really hated biology and chemistry. It was | just a bunch of abstract stuff. What made me (re)discover | biology was taking up gardening. To me gardening is like | _applied_ biology. After a while you really start to get a | sense of how it all works and just how unbelievably complex | life systems are: photosynthesis, the carbon cycle, the | different water cycles, how soil life affects the plants that | grow in it, and how incredibly resourceful plants are in | interacting with their environment (not to mention insects and | other creatures higher up the food chain...) | mkr-hn wrote: | The more I understand about biology, the more bizarre it is | that people try to beat it down to simple, obvious, narrow, and | globally consistent binaries to serve their ideological | purposes. | dizzant wrote: | While retaining the typical high school separation between | math, biology, chemistry, and physics, but given control over | the curricula taught in those courses, do you think it is | possible to teach a single very high-level concept such as the | Krebs cycle in full complexity at a high school level (i.e. | starting from algebra and very limited science education, | completed in four full-time years)? This seems like a foothold | for a potentially interesting restructuring of how we educate | children, oriented toward depth in a few things to enlighten | future breadth. I ask specifically about feasibility, since | that seems like a necessary prerequisite to a discussion of | beneficial value. | robbiep wrote: | I majored in biochemistry as well. I was so unbelievably | hooked. The ground up principles. It led me to medicine | bonniemuffin wrote: | I recall the same "everything coming together" feeling, but for | me it didn't happen until Applied Biochemistry in grad school. | | I recall the final exam being only a single question, with a | bunch of blank lined pages to write your answer, and the | question was something like "You just ate a ham sandwich. What | happens to it?" A good answer needed to include everything down | to the molecular/chemical level and tie it together all the way | up to the macro scale, and I finally felt like that class had | prepared me to tell the story. | thanatos519 wrote: | I love it! Much like the "I type a URL into my browser and | press enter. What happens?" tech interview question. | dataflow wrote: | Except it seems like a way harder question! | Infinitesimus wrote: | ... 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 complexities of | running a large data center and how your response time | varies based on some sorcery. | | Then you go the extra mile and weave a tale of electrons | wrestling with their universe of invisible | electromagnetic wave overlords that determine their fate | while they embark on a treacherous journey to convey | information thousands of kilometers across with | blistering speed. Tell them of the aged electron saw a | family member get attacked by a stray cosmic ray and the | fright of the pack when one simply tunneled out of | existence... | Koshkin wrote: | > _it 'll be fun_ | | Not during an interview, though. The interviewer would | see it as trolling (at best), and you would fail the | interview. And for a good reason! Because as an engineer | (and an intelligent person in general) you must be able | to separate what is essential from the non-essential for | the subject in question. For instance, the physics or the | physiology of the process of pushing a key on a keyboard | is probably not what the question was about, nor do those | things in fact have much to do with typing, even (which | you can do on a touchscreen or using the mouse). | feet wrote: | When we start looking at life at the level of physics, | chemistry, and biochemistry, the absolute beauty of the | system begins to appear. The complexity is on a scale | that's difficult to imagine or even unimaginable even to | those trained in the fields, and there is a feeling of | wonder that words can't capture | Balgair wrote: | 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. | feet wrote: | >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? I feel | like all of that barely scratches the surface of the insane | complexity of neuronal networks | | And how does one even begin to talk about our desire and | internal drive to do things like ride a bicycle | _dain_ wrote: | Or the physics of the bicycle itself! It can stay up even | without a rider. | imaltont wrote: | I feel the same way about just math in general, and all the | sciences that derive a lot of their knowledge and systems from | it. You start learning math as just high level/abstracted away | things where you just have to memorize that this thing does | that and in this case do this instead, especially derivation I | remember they showed us the formula with dy/dx, but they never | showed us any proofs of why or how that lead to the different | outcomes, we just had to memorize. | | Meanwhile, later when you get to higher education, math just | kind of explode into this creative problem solving field with | loads of interesting problems and ways to reason about them, | but you almost have to relearn it/properly learn the basics | over again when you get there, because you never learned why or | how the basics works, just the input and output of the basics. | pgrepds wrote: | I had the opposite experience. My teacher took extra care to | explain to us why and how certain things worked in math. The | reason I loved math so much, and still do, is because I never | had to memorize anything. I just had to understand how it | worked. In biology, however, it was very different. I had to | memorize facts instead of understanding them. | khaledh wrote: | When I watch animations of how the cell works at a molecular | level [0], I can't help but wonder how can this level of sheer | complexity in dna transcription, protein production, and many | other supporting functions in a single cell works in perfect | harmony. It's mind boggling. | | I admit that I'm biased, but I don't think this could have | evolved through random processes. I'm a believer in Intelligent | Design. | | https://youtu.be/X_tYrnv_o6A https://youtu.be/7Hk9jct2ozY | https://youtu.be/fpHaxzroYxg | kosherhurricane wrote: | The coolest thing about biology is that it's not just in every | cell of your body, but every cell on life on earth. | | But the funny thing about that is that the genes for say the | 'helicase' looks like it was made by a copy machine, churned | out by the millions, for every life on earth. But if you look | very carefully, it's not a copy made from a master copy, but | copied from each other. There are small mistakes made by this | 'copy machine', so that you can trace the different generations | of the copy of the 'helicase' based on what mistakes have been | accumulated. You dig further, and you can map out different | generations and make a tree like diagram. The further away from | each other the two helicases are, the more mistakes have been | accumulated. | | You keep doing that for every life on earth, and you get | something like this [1]. | | And then you dig further and realize that there is no Hand of | God there, and creationism is a primitive explanation for | something people didn't understand, like how lightning was God | being angry. | | [1] | https://www.sciencedirect.com/science/article/pii/S235234091... | kosherhurricane wrote: | > I don't think this could have evolved through random | processes. | | It's a logical fallacy that complex processes cannot be created | from random events. It certainly can, and evidence is abundant. | | Biochemistry of life is an advanced form of brownian ratchet | [1]. It started simple, but can get to absurd level of | complexity due to selective pressure, and memory via genes. And | selective pressure is nothing but maximizing for greatest | replication. | | There are many interesting philosophical questions inside | biochemistry, but a Judeo-Christian Diety is not the most | interesting. | | [1] https://en.wikipedia.org/wiki/Brownian_ratchet | eesmith wrote: | Your references are all computer animations, smoothed and | simplified. I'll quote liberally from | https://freethoughtblogs.com/pharyngula/2008/02/03/buffeted-... | on an animation of "Inner Life of a Cell" by Harvard | Biovisions: | | > Here's the central problem: molecules don't behave that way. | What is portrayed is wonderfully precise movement; it looks | like the molecules are all directed, purposeful, and smooth. | Take for instance the behavior of kinesin, that stalk-like | molecule seen marching in a stately way down a tubule, with two | "feet" in alternating step, towing a large vesicle. That's not | how it moves! We have experiments in which kinesin is tagged -- | it's towing a fluorescent sphere -- and far from a steady | march, what it does is take one step forward, two steps | forward, one step back, two steps forward, one back, one | forward ... it jitters. On average it progresses in one | direction, but moment by moment it's a shivery little dance. | Similarly, the movie shows the monomers of tubulin zooming in | to assemble a microtubule. No! What it should show is a wobbly | cloud of monomers bouncing about, and when one bumps into an | appropriate place in the polymer, then it locks down. I made | this same criticism in my review of Mark Haw's excellent book, | Middle World, which does get it right. For purposes of drama | and minimizing complexity and confusion, though, the animators | of that video have stripped out one of the most essential | properties of systems at that scale: noise, variability, and | the stochastic nature of chemical interactions. | | > That's particularly unfortunate, because it is the seeming | purposefulness of the activity of the cell that has made that | clip so popular with creationists. It fits with their naive | notions of directed activity at every level of the cell, and of | their denial of the central role of chance in chemistry and | biology. | al2o3cr wrote: | So you look at everything that we've been able to figure out, | things we didn't know about even a few decades ago, and you | conclude "WELL I CAN'T SEE THE REST OF THE PUZZLE RIGHT NOW SO | I GUESS MY IMAGINARY FRIEND DID IT" | | So goddamn stupid that it's just sad. | cercatrova wrote: | This is known as the God of the gaps argument [0] | | [0] https://en.wikipedia.org/wiki/God_of_the_gaps | khaledh wrote: | Ok let's stay scientific. What are the odds of forming a | single enzyme (necessary for life) composed of a chain of | roughly 200 amino acids, each is drawn from a pool of 20 | possible amino acids? 20^200, right? The estimated number | of atoms in the entire universe is 10^80 atoms. Can you | explain what process would consistently keep winning the | protein lottery with those kind of odds? | eesmith wrote: | That's not how evolution works. You've omitted natural | selection. Quoting from "The Failures of Mathematical | Anti-Evolutionism" by Jason Rosenhouse at | https://skepticalinquirer.org/2022/05/the-failures-of- | mathem... | | > However, this argument is premised on the notion that | genes and proteins evolve through a process analogous to | tossing a coin multiple times. This is untrue because | there is nothing analogous to natural selection when you | are tossing coins. Natural selection is a non-random | process, and this fundamentally affects the probability | of evolving a particular gene. | | > ... Modern proponents of intelligent design (ID) are | usually too sophisticated to make such an error. Instead, | they present a superficially more sophisticated | probability-based argument. Their idea is best | illustrated by example. ... ID proponents argue that it | is the combination of improbability and matching a | pattern that makes them suspect that something other than | chance or purely natural processes are at work. They use | the phrase "complex, specified information" to capture | this idea. In this context, "complex" just means | "improbable," and "specified" means "matches a pattern." | ... | | > The argument likewise founders on the question of | complexity. According to ID proponents, establishing | complexity requires carrying out a probability | calculation, but we have no means for carrying out such a | computation in this context. The evolutionary process is | affected by so many variables that there is no hope of | quantifying them for the purposes of evaluating such a | probability. | | Back in the 1990s, the newsgroup talk.origins put | together a long index of creationist claims. Your example | is http://www.talkorigins.org/indexcc/CB/CB010.html | | > The calculation of odds assumes that the protein | molecule formed by chance. However, biochemistry is not | chance, making the calculated odds meaningless. | Biochemistry produces complex products, and the products | themselves interact in complex ways. | | > The calculation of odds assumes that the protein | molecule must take one certain form. However, there are | innumerable possible proteins that promote biological | activity. Any calculation of odds must take into account | all possible molecules (not just proteins) that might | function to promote life. | | > The calculation of odds assumes the creation of life in | its present form. The first life would have been very | much simpler. | | > The calculation of odds ignores the fact that | innumerable trials would have been occurring | simultaneously. | | It links to further discussion at | http://www.talkorigins.org/faqs/abioprob/abioprob.html | ("Lies, Damned Lies, Statistics, and Probability of | Abiogenesis Calculations") | | Richard Dawkin's book "Climbing Mount Improbable" "is | about probability and how it applies to the theory of | evolution. It is designed to debunk claims by | creationists about the probability of naturalistic | mechanisms like natural selection." (quoting | https://en.wikipedia.org/wiki/Climbing_Mount_Improbable | ). | | Five copies of the book are available to borrow right now | for free (with an account) from archive.org, at https://a | rchive.org/search.php?query=%22Climbing+Mount+Impro... . | | All of these explain why your probability calculation is | not meaningful. | bilsbie wrote: | It really makes you realize how much room for improvement there | is in education. | thanatos519 wrote: | I didn't even take biology because I thought the physics/math end | of the stack was the ultimate truth. I was not even wrong! | ta988 wrote: | There are additional factors that make molecules in cells not | subject to pure diffusion rules. Charge depending on the pH of | the area ( even if in such a crowded space it is likely not | really a pH anymore), and molecular interactions. Proteins (and | virtually any other molecules but proteins and to a lesser extent | nucleic acids are particularly good at that) can stick or be | repulsed by their overall composition (external charges, | hydrophobicity) but they can also stick to each other. Biology is | fascinating but you can't isolate it long from chemistry and | physics if you want to understand it. | Pulcinella wrote: | Yeah see the art of David Goodsell. I believe he said the | concentrations of the various biomolecules are roughly accurate | based on calculations he does before starting painting. Cells | are incredibly crowded. The human body being 60-70% water is | usually presented in pop-sci as "wow we are mostly water!" but | that's actually very concentrated for chemical reactions. You | usually don't perform reactions that concentrated in a lab | whether it's biochemistry, organic chemistry, inorganic, | analytical, etc. It's a wonder all this stuff doesn't just gunk | up and precipitate out of solution. | | https://ccsb.scripps.edu/goodsell/ | oldsecondhand wrote: | > It's a wonder all this stuff doesn't just gunk up | | It does gunk up but it takes a few decades. | [deleted] | adrian_b wrote: | All the living cells spend continuously a lot of energy as | long as they are still alive for avoiding the appearance of | precipitates inside the cell, e.g. by pumping out of the | cells the ions of calcium and sodium and pumping inside the | cell the ions of magnesium and potassium, because the former | are much more prone to produce precipitates than the latter. | | This continuous ion pumping is a major component of the | energy consumption of a living being when it is idle, | apparently doing nothing. | ta988 wrote: | It is a big part of the communication, regulation and | sensory system of cells. A lot of receptors are linked to | ion channels for example. That's also the reason why there | are pumps to bring the ions back on the other side too. | popcube wrote: | yes, biology education in schools are terrible. remembering so | many things actually is important, students keep reminding new | thing even they in master degree...but the fun of science do not | show in text book. ___________________________________________________________________ (page generated 2022-07-09 23:00 UTC)