[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.
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