[HN Gopher] A Revolution in Biology?
___________________________________________________________________
A Revolution in Biology?
Author : pr337h4m
Score : 112 points
Date : 2024-06-09 18:13 UTC (4 hours ago)
(HTM) web link (www.bitsofwonder.co)
(TXT) w3m dump (www.bitsofwonder.co)
| webnrrd2k wrote:
| I'm about 55 now, and if I was high school or college age again,
| this is what I'd study. There is huge potential in future
| biological developments.
| monsieurbanana wrote:
| What if you were 33? Asking for a, huh, friend.
| throwup238 wrote:
| I'd get ready for the mid-life crisis.
| knicholes wrote:
| How?
| throwup238 wrote:
| I believe the traditional approach is a Corvette you
| can't afford and a new partner that violates the half
| plus seven rule.
| bee_rider wrote:
| I think what I'll do is get a hobby that is not too
| expensive. Like, you have to buy something overpriced to
| satisfy a midlife crisis, but at least I will try to get
| some nice headphones (not harmful at least, and with nice
| headphones you can play your music quieter, save your
| hearing) or a good bicycle (healthy!) out of it.
|
| Anything but a sports car, really. Driving around in a
| sports car is just advanced sitting, which I already do
| to much of, and they are very expensive.
| f_allwein wrote:
| By all means go back to university, even do a PhD, if you
| find a subject you're passionate about (and have the beans to
| finance it). That's what I did and it was great!
| vladms wrote:
| I find the probability of someone on the internet being able
| to give you sound advice, without knowing your situation and
| personality extremely small.
|
| For me personally it is most of the time about the balance
| between what you can afford, what would you think you would
| like to achieve and what you miss would. Reasonably, most of
| the people can't "have it all" (family, money, peace of mind,
| results, etc.).
| danielmarkbruce wrote:
| It's surprising that the main thrust of this is surprising. Do
| biologists not tend to think about electromagnetic force and it's
| implications?
| newzisforsukas wrote:
| They do but that doesn't lend to a hype topic for writing
| poorly about
|
| https://en.wikipedia.org/wiki/Developmental_bioelectricity
| spacetimeuser5 wrote:
| When in 18xx FDA or its precursor was being formed, its goal
| was to confine various "bioelectrical woo" present in medicine
| and biology at that time. And back then there was Rife's
| microscope, for example, which was able to accurately image
| living cells. Yet no-one tried to account for the cumulative
| damage/adverse effects done by FDA approved treatments in
| comparison with a potential or actual damage done by such
| "woo".
| briffid wrote:
| The most interesting for me is the offspring, reproducing a
| different structure with the same genes. I think mathematically
| this could be the missing link in evolution, where random gene
| modifications are just not probable enough to drive evolution. 3
| billion DNA pairs cannot evolve randomly, there is not enough
| time and matter in the universe to randomly try successful
| generations of life forms. However, bioelectric might be a much
| much more straightforward and fast way of driving evolution
| instead of randomly mutating DNA.
| exe34 wrote:
| > 3 billion DNA pairs cannot evolve randomly, there is not
| enough time and matter in the universe to randomly try
| successful generations of life forms
|
| the objection to the process described here is reasonable.
| thankfully this isn't how it works.
| treprinum wrote:
| > thankfully this isn't how it works.
|
| Care to elaborate what lowers this probability down to
| "computable within adolescent age" levels?
| empath75 wrote:
| You want people to explain natural selection and evolution
| to you?
| treprinum wrote:
| No, I want the computational feasibility explanation with
| some nice O(function) on biological processes. To the
| best of my knowledge, we still have no idea.
|
| Something like "the computational complexity of a beached
| fish to invent and grow a leg is O(n^2 log n) hours where
| n is the number of neural spikes in frontal cortex" or
| similar.
| exe34 wrote:
| I offer paid tuition. For PS50/h, I will learn stuff for
| you and then teach you. Prep time is typically ~3h for each
| hour I teach you. Minimum 1h lessons.
| koeng wrote:
| > where random gene modifications are just not probable enough
| to drive evolution. 3 billion DNA pairs cannot evolve randomly,
| there is not enough time and matter in the universe to randomly
| try successful generations of life forms.
|
| As a biologist, I don't think this really follows. From my
| perspective of studying life, 3 billion DNA pairs can
| definitely evolve randomly - it's not even really that hard.
| Eukaryotic life just happened to get that because the fitness
| deficit from the retrotransposons weren't too bad. On the
| contrary, I can't actually see how bioelectric could drive
| evolution - only the creation of more complex structures
| jononomo wrote:
| As a biologist, how do you account for the existence of life?
| koeng wrote:
| There was an RNA molecule or molecules that could make more
| of themselves (probably really poorly, at first)
| golol wrote:
| As I understand, the worm cells act differently because the
| worm is placed in a solution which interferes with their
| electrical messaging, so it makes sense that the offspring
| growing up in the same solution would grow with the same
| defects as the parents. I think that's all there is to it.
| skywhopper wrote:
| Indeed, they do not evolve randomly. There's this thing called
| natural selection that is relatively crucial.
|
| Your interpretation of bioelectric effects as summarized in
| this article seems to have missed something. The bioelectric
| network is itself an expression of the genes involved in
| development. It's not a separate magical force.
| empath75 wrote:
| It's not any different from the nervous system, really, it's
| just that we're now recognizing that those fields are
| involved in things other than sensation, perception, etc..
| spacetimeuser5 wrote:
| >>The bioelectric network is itself an expression of the
| genes involved in development.
|
| Yes, you may need genes to express the proteins of ion
| channels and gap junctions, but there is no anatomy coded by
| genes, no genes code for how many limbs will a biosystem have
| (as reiterated by Levin). And it is this level of resolution
| that actually mattered for years before the launch of
| molecular biology and medicine.
|
| >>It's not a separate magical force.
|
| Indeed, it sort of (suppose - by up to 70%) is. If the fine
| structure constant, which defines the strength of the
| interaction between a charge and an electric field, were 4%
| less or more than its current value, the current world and
| biosphere wouldn't exist. So far physics can't explain why
| the fine structure constant has this exact value (~1/137,
| which is also unique that it is a dimenionless constant).
| (I'm not inferring anything, just presenting raw data).
| ben_w wrote:
| > I think mathematically this could be the missing link in
| evolution, where random gene modifications are just not
| probable enough to drive evolution. 3 billion DNA pairs cannot
| evolve randomly, there is not enough time and matter in the
| universe to randomly try successful generations of life forms
|
| This suggests you have not tried writing a simulated evolution
| based optimiser.
|
| They're quite easy to write, the hard part is what you mean by
| a "fitness function" (which doesn't matter for nature, it just
| is whatever it is).
|
| Such algorithms are also more than fast enough -- remember that
| for the first 3 billion years we only had single-celled life,
| and that can reproduce in 20 minutes, so we had potentially 79
| trillion generations (edit because "78.84 trillion" would be
| overselling the precision) before the first multicellular life.
| You get good results faster than that.
|
| The number of base pairs is also just a misleading statistic.
| For example: each of XXX, XXY, XYY, and Downs are found in
| around 0.1 of human births, each of which gets an extra copy of
| a chromosome. These specific changes may not be too good for
| us, but this kind of sudden massive increase is also found in
| some plants without negative repercussions.
|
| > However, bioelectric might be a much much more
| straightforward and fast way of driving evolution instead of
| randomly mutating DNA.
|
| I have no reason to expect bioelectric processes described in
| this article to be able to direct useful effects on the genome,
| for the same reasons I think it unlikely your own brain could
| by sheer willpower turn you into a werewolf.
|
| Wrong layer of abstraction.
| dang wrote:
| Related. Others?
|
| _Computational Boundary of a Self: Bioelectricity and Scale-Free
| Cognition (2019)_ - https://news.ycombinator.com/item?id=39244333
| - Feb 2024 (1 comment)
|
| _Brains are not required to think or solve problems - simple
| cells can do it_ - https://news.ycombinator.com/item?id=39127028
| - Jan 2024 (396 comments)
|
| _Bioelectricity, Biobots, and the Future of Biology [video]_ -
| https://news.ycombinator.com/item?id=38423588 - Nov 2023 (1
| comment)
|
| _How bioelectricity could regrow limbs and organs_ -
| https://news.ycombinator.com/item?id=38027587 - Oct 2023 (100
| comments)
|
| _M. Levin - Bioelectrical signals reveal, induce, and normalize
| cancer [video]_ - https://news.ycombinator.com/item?id=37140965 -
| Aug 2023 (1 comment)
|
| https://news.ycombinator.com/item?id=36912245 (July 2023)
|
| _Aging as a morphostasis defect: a developmental bioelectricity
| perspective_ - https://news.ycombinator.com/item?id=36264719 -
| June 2023 (1 comment)
|
| _Bioelectric networks: cognitive evolutionary scaling from
| physiology to mind_ -
| https://news.ycombinator.com/item?id=36009513 - May 2023 (1
| comment)
|
| _Bioelectric networks: from body intelligence to regenerative
| medicine_ - https://news.ycombinator.com/item?id=35763121 - April
| 2023 (1 comment)
|
| _Non-neural, developmental bioelectricity as a precursor for
| cognition_ - https://news.ycombinator.com/item?id=33902641 - Dec
| 2022 (1 comment)
|
| _Michael Levin: Intelligence Beyond the Brain (networked daptive
| morphogenesis~)_ - https://news.ycombinator.com/item?id=33217070
| - Oct 2022 (1 comment)
|
| _Plasticity without genetic change - Michael Levin [video]_ -
| https://news.ycombinator.com/item?id=32119375 - July 2022 (1
| comment)
|
| _Mike Levin on using bioelectricity to study how cells form
| (2019)_ - https://news.ycombinator.com/item?id=27819791 - July
| 2021 (21 comments)
|
| _Persuading the Body to Regenerate Its Limbs_ -
| https://news.ycombinator.com/item?id=27062477 - May 2021 (69
| comments)
|
| _The Link Between Bioelectricity and Consciousness_ -
| https://news.ycombinator.com/item?id=26435281 - March 2021 (1
| comment)
|
| _Growing Neural Cellular Automata: A Differentiable Model of
| Morphogenesis_ - https://news.ycombinator.com/item?id=22300376 -
| Feb 2020 (46 comments)
|
| _What Bodies Think About: Bioelectric Computation Outside the
| Nervous System_ - https://news.ycombinator.com/item?id=18736698 -
| Dec 2018 (16 comments)
|
| _Brainless Embryos Suggest Bioelectricity Guides Growth_ -
| https://news.ycombinator.com/item?id=16589702 - March 2018 (35
| comments)
|
| _Memory in the Flesh: Can memories survive outside the brain?_ -
| https://news.ycombinator.com/item?id=9226391 - March 2015 (12
| comments)
| grondilu wrote:
| Growing Neural Cellular Automata
| https://news.ycombinator.com/item?id=22300376, February 2020
| dang wrote:
| Added above. Thanks!
| agumonkey wrote:
| Holy ... he's been features on HN since that long ago ?? I only
| heard of him from a random partial misclick on a funny youtube
| thumbnail less than two years ago.
|
| thanks for the background
| RivieraKid wrote:
| It's incredible that the information necessary to create a human
| is just about 750 MB uncompressed. For example the very specific
| shape of the scapula bone or fear of spiders...
| sameoldtune wrote:
| To be fair that's just the size of the installer
| B1FF_PSUVM wrote:
| That's a good comeback, especially if you can say something
| about the site where the rest of the info is pulled from ;-)
| Angostura wrote:
| Well, the egg's cytoplasm contains quite a few of the
| frameworks
| aspenmayer wrote:
| DNA has been in development hell for billions of years, and
| yet compile/install times still vary widely between
| platforms and is not ABI compatible cross-platform.
|
| Don't get me started on the unauthorized use of proprietary
| code!
|
| https://en.wikipedia.org/wiki/Horizontal_gene_transfer
|
| We keep getting asked about "checksums" and "reproducible
| builds" and if the BDFL is going to implement them, to
| which they say: "already landed in upstream," "works on my
| machine," "notabug," and/or "wontfix" sometimes in the same
| reply.
|
| https://en.wikipedia.org/wiki/Lamarckism
|
| https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3730912/
|
| https://www.nature.com/articles/nrg.2016.106
| Terr_ wrote:
| > It's incredible that the information necessary to create a
| human is just about 750 MB uncompressed
|
| Hold up, isn't the point of this article that genes _do not_
| have all the information?
|
| The, er, _bootup environment_ of a freshly-fertilized human egg
| normally provides a _lot_ more than merely protection and raw
| materials for nine months. Likely a lot of required parameters,
| and definitely a lot of important tuning optimizations.
|
| > For example the very specific shape of the scapula bone or
| fear of spiders...
|
| There were some studies a decade back about mice inheriting
| fears of certain smells from the father, I wonder if anyone
| discovered the mechanism (or disproved the effect) by now.
| 1auralynn wrote:
| Well until they succeed in creating artificial wombs it's
| technically a much larger amount of information (e.g. the
| cellular composition of the womb, how many and what kinds of
| nutrients that flow through, etc). We are still scratching the
| surface of epigenetics too.
| tsimionescu wrote:
| It's really not. If nothing else, conditions in the uterus,
| especially in the first few months, are extremely crucial. Take
| 10 identical fertilized eggs and put them in 10 different
| people and you'll get 10 different humans, not 10 clones as
| people generally assume. And this is not just genetics of the
| mother, differences in diet and lifestyle will also
| significantly (not to mention history) impact the development
| of the fetus, especially in the early months.
| goodpoint wrote:
| > create a human *body*
| robwwilliams wrote:
| Michael Levin is coming close to the positions of both Humberto
| Maturana (autopoiesis) and of Nick Lane (proton pumping).
|
| Autopoiesis is not an easy set of concepts but one of the ideas
| is that details of structure are much less important that
| preservation of relationships that allow an entity to replenish
| its own constituents. Planarian are damn adaptable, but this is
| hardly news.
|
| Nick Lane emphasizes that DNA is subsidiary to bioenergetics and
| "proton pumping" across membranes. His recent book "Transformer"
| focuses on the Kreb's cycle and mitochondria as the crux of life
| (and autopoiesis, although he does not use this term).
|
| Lane is extremely readable. Maturana is almost inscrutable.
|
| I enjoined the target article, but am not comfortable boiling
| down development to "bioelectrics". A complementary perspective
| but I do not think this will get us farther than good old
| developmental molecular biology.
| LarsDu88 wrote:
| The language in the article is a bit overhyped. There are
| multiple examples of gradients being involved in pattern
| formation. It's just that electrical potentials are a bit of a
| newer area of study.
|
| There's the chemical gradient based on WNT signaling in fruitfly
| development, the SHH (sonic hedgehog) chemical gradient in limb
| pattern formation and body planning asymmetry. There's even auxin
| signaling in plant development.
|
| Heck, one of Alan Turing's (yes, THAT Turing) most famous papers
| from the 50s described reaction-diffusion mechanisms for pattern
| formation.
|
| Basically for evolution to invent some kind of reproducible
| pattern of something, you need to start with a gradient of
| something and tie that to gene transcription.
|
| In the fruit fly example it's a chemical trigger that reaches the
| nucleus via wnt signaling. In the flatworm example, it's a
| membrane polarization gradient that drives the gradient rather
| than a chemical one.
|
| I'd imagine the patterns you can create from electrical
| depolarization are simpler than the ones you can get from
| chemicals interacting as you lose many of the interesting
| interactions you get from reaction-diffusion
| spacetimeuser5 wrote:
| With such apparent speed and quality of research thought we will
| never have anatomical compiler, let alone electroceutocals and
| anthrobots, on a routine basis at least in the next couple of
| hundreds of years.
| dash2 wrote:
| > They've done things like getting frogs to develop extra limbs,
| and getting them to develop an eye in their gut, or an eye in
| their tail that they can actually see out of.
|
| I have two contradictory reactions to this. 1. "Isn't science
| amazing!" 2. "Poor froggy, how horrible."
| fngjdflmdflg wrote:
| >the impact of Levin's work is a shift away from genes as the
| only determinant of structure
|
| Nobody was making the claim that genes are the only determinant
| of structure though. A trivial example is the mother's hormones
| affecting her child's development in utero. To cause a shift away
| from genes would require showing that the bioelectric network is
| not itself caused by genetic factors. Otherwise while it may be
| useful as a tool to develop treatments for developmental diseases
| it does not change that genes are the ultimate cause of the
| bioelectric network itself (except as when directly manipulated
| by scientists).
|
| Quoting Levin himself:
|
| >Evolution was using bioelectric signaling long before neurons
| and muscles appeared, to solve the problem of creating and
| repairing complex bodies.[0]
|
| It sounds like to me from this quote that bioelectric networks
| are not something outside of genetics but just another important
| biological system.
|
| It's hard to pin down what the author is really getting at in the
| first place. For example these two lines:
|
| >genes are great, and they do contain much of the necessary
| information for building our bodies. But they don't contain all
| of it >[...] >Levin's point is that genes are like machine code,
| and modern-day programmers never think about machine code--they
| think about higher-level software constructs like objects,
| modules, and applications.
|
| Yet machine code really is what is being executed by the
| computer. Nobody would say that the computer is really running
| c++, for example, or that c++ is a new "determinant of structure"
| of the program. It is completely subsumed by machine code.
|
| The author is the entire time equating a set of instructions (the
| genome) to a biological system (the "bioelectric network").
| However it does not make sense to equate these things in the way
| the author has done it (at least not without a lot more
| elaboration). The genes do not really _do_ anything except get
| copied and transcribed into mRNA while the bioelectric network
| clearly is doing something. So it really seems more like the
| author should be comparing proteins with the bioelectric network.
| But I think here the problem becomes much more obvious - there is
| no other way besides proteins for biological organisms to do
| work. So it is obvious that the bioelectric network is somehow
| formed by the work of proteins, and the proteins are themselves
| caused by genes. The human body has within it many systems: the
| circulatory system, the respiratory system, the endocrine system,
| the nervous system, the muscular system etc. These all exist at
| "higher levels of abstraction" than genes and some of them, like
| the endocrine system, play a role in development. But it wouldn't
| make sense to say that these system are "in competition" with the
| genome. Even though we can use the circulatory system to
| transport a drug to the body that changes the structure of the
| body.
|
| Another major difference is that genetics are continually showing
| their influence because the body is continually creating proteins
| from the genome. It sounds from the article that this bioelectric
| network is really only relevant at the developmental stage (if I
| am wrong here then I feel the article should have made that more
| explicit).
|
| Ultimately I feel the article is arguing a bit against a strawman
| of "genes as the only determinant of structure" and is also
| making too vague of a claim about genes having a new competitor,
| so to speak.
|
| [0] https://link.springer.com/article/10.1007/s10071-023-01780-3
___________________________________________________________________
(page generated 2024-06-09 23:00 UTC)