[HN Gopher] DNA jumps between animal species, but no one knows h...
___________________________________________________________________
DNA jumps between animal species, but no one knows how often
Author : rbanffy
Score : 171 points
Date : 2021-06-10 09:03 UTC (13 hours ago)
(HTM) web link (www.quantamagazine.org)
(TXT) w3m dump (www.quantamagazine.org)
| staticassertion wrote:
| It's almost unbelievable how DNA seems to "just work". DNA from
| one organism breaking apart and slipping into another somehow
| leads to shared expressions across horizontal species - it's
| absurd.
|
| It's like taking a random byte sequence from some binary, shoving
| it randomly into another, and the new binary gets useful new
| features.
|
| The involvement of even more complex systems like parasites makes
| it that much more insane to me.
| [deleted]
| echelon wrote:
| I think the binary example is incredibly poor and makes
| understanding this much harderr.
|
| Genes code for proteins (and promoters, etc.) and wind up in a
| chemical soup in flux. They're going to bounce around and do
| things.
|
| Their presence will be more akin to new kinds of cars or trucks
| entering a highway, and they'll have different impacts to
| traffic (kinetics, thermodynamics).
| tachyonbeam wrote:
| > It's like taking a random byte sequence from some binary,
| shoving it randomly into another, and the new binary gets
| useful new features.
|
| If you think about it for a moment, our genetic code is kind of
| designed to work that way.
|
| You get half of your genetic code from your mom, the other half
| from your dad, and somehow, all of these genes "just work"
| together. It's kind of miraculous when you think that there are
| very many genes that encode how your brain works, and how your
| liver works, your muscles, etc. Somehow, provided the baby can
| be born, a mishmash of genes from two different individuals
| almost always works out.
| dalmo3 wrote:
| > all of these genes "just work" together
|
| That's a little bit tautological since if the genes didn't
| work together they wouldn't be here after _all_ these years,
| right? Fascinating nonetheless.
| Blikkentrekker wrote:
| It should also be pointe out that about two thirds of human
| conceptions result into early embryonic death, so evidently
| it is not as smooth a ride as suggested.
| sooheon wrote:
| That seems to be the point the parent is making. Tautology
| is the the only way we can explain the way life happens to
| be -- it's because it's advantageous for it to be that way.
| czl wrote:
| "a mishmash of genes from two different individuals almost
| always works out" => different individuals of the _same_
| species (which btw is how a "species" is defined).
|
| The evolution of organisms that gene mishmash (aka sexual
| reproduction) is thought to be the result of an ongoing arms
| race between gene sequences that "try" to stay unchanged (in
| higher level species) and gene sequences that "try" to "free
| ride" (from viruses etc.) Being able to build members of your
| species from "mishmash of genes from two different
| individuals" has the effect of scrambling the DNA of each
| species member which makes attack harder.
|
| Organisms that do not do this and reproduce via cloning (aka
| Parthenogenesis) are often entirely wiped out once a pathogen
| figures out how to target their DNA -- hence the bananas
| types we eat change over time.
|
| ps: Similar evasion is used by some computer viruses: https:/
| /www.trendmicro.com/vinfo/us/security/definition/Poly...
| tachyonbeam wrote:
| > The evolution of organisms that gene mishmash (aka sexual
| reproduction) is thought to be the result of an ongoing
| arms race between gene sequences that "try" to stay
| unchanged (in higher level species) and gene sequences that
| "try" to "free ride" (from viruses etc.)
|
| Sexual reproduction means your species has a very large
| gene pool, and individuals with new combinations of genes
| can be produced very quickly. That's not just an advantage
| against viruses. It's also very useful for adapting rapidly
| and competing against other species when your environment
| changes. New threats (and new opportunities) show up all
| the time, be it dwindling or changing availability of food,
| climate change (e.g. new ice age), new predators or new
| preys, and also a group of individuals migrating to a new
| region of the world with a different climate.
| Blikkentrekker wrote:
| Probably because they do not really encode how anything works
| and because, probably by necessity, the growth of organisms
| is a swarm intelligence that is quite self-healing.
|
| In particular with coinjoined twins, it's quite remarkable
| how much the systems for body development still produce
| something that connects the inner workings, which was
| obviously not it's "purpose",but the self-healing growth
| mechanisms that corrects for errors simply leads to that.
|
| Consider the Hensel Twins who have two mouths but their
| digestive system at some point merges in a way that is
| capable of digesting. The "tubes" of their digestive tract
| actually merge at one point, but they have two stomachs.
| astockwell wrote:
| Maybe genes are declarative, not procedural har har har
| walleeee wrote:
| I'm just picking nits, but :%s/designed/evolved/g
|
| Do very much agree it's miraculous. Biological organisms are
| robust to error and chance in ways no designed system comes
| close to matching. It's awe-inspiring
| VeninVidiaVicii wrote:
| In genetics it's very common to say that things are
| designed a certain way without invoking a creator.
| burnte wrote:
| Yep, the designer is evolutionary pressures, not
| necessarily an inteligence. It's shorthand, not religious
| invokation.
| walleeee wrote:
| I didn't know this was common usage, thanks! I stand
| corrected
| burnte wrote:
| No worries, you're more right now than you were before.
| :)
| throwanem wrote:
| Don't try to think about genomics in programming terms. At best
| you'll only confuse yourself; at worst, others also. Both a
| computer program and a genome encode information, but that's
| about where the similarities end.
| inigojonesguy wrote:
| >Don't try to think about genomics in programming terms.
|
| At some point, some Newton person will figure it. It always
| happen.
|
| As for now, it might be interesting to understand why exactly
| the analogy between genomics and programming fails. It might
| bring interesting insights into both fields.
|
| So why not try to think about?
| throwanem wrote:
| Because the only way to imagine a useful comparison between
| these fields can be made is to be profoundly ignorant of at
| least one of them.
| sooheon wrote:
| Rather than assert the negative, can you state some
| positive facts about one or the other that makes this
| point clear?
| throwanem wrote:
| Software changes over spans of minutes to decades;
| genomes change over spans of millions of years. Software
| is written; genomes are not. The complexity of software
| is constrained by programmers' ability to comprehend it;
| the complexity of genomes is not. The environment in
| which software functions is determined by humans; the
| environment in which genomes function is not.
| techbio wrote:
| I think the environment is the confounding factor rather
| than programmer working life-span.
|
| An OS is just so much simpler than dynamically
| constrained energetic replicators in an always and
| everywhere collapsing wave function.
| only_as_i_fall wrote:
| This all seems like minor differences.
|
| Plenty of software is neither written nor comprehensible
| I can assure you of that.
|
| Like I don't think your necessarily wrong, but pointing
| out the literal differences between the two topics
| doesn't explain to me why the analogy is wrong and
| therefore doesn't support your argument.
|
| It's like saying "I'm nothing like my mother; I don't
| even have long hair"
| inigojonesguy wrote:
| I agree with you here but I get to a happy conclusion.
| The (self- or culturally imposed) constraint on
| computation to be semantically meaningful for humans does
| not apply for genomes. But this is already useful,
| because it means we at least have a hint about where to
| dig more in programming.
|
| There is Theory of Computation and there is Theory of
| Programming. Your arguments apply to TOP but not to TOC.
|
| https://pron.github.io/posts/what-we-talk-about-when-we-
| talk...
| sooheon wrote:
| Those are trivial surface level differences relative to
| the central idea of encoding, storing, replicating,
| editing digital information, which interfaces with other
| digital and analog systems.
| throwanem wrote:
| Not that there's much point to saying so, since you
| appear to be here for no other reason than to assert that
| my argument is false because you would prefer it be so,
| but here's another: software is digital; genomes are not.
| Turing_Machine wrote:
| Genomes are absolutely digital. GATC is no different from
| 1 and 0. It's just using a different base (pun intended).
|
| Files on disks have end of file markers, just like the
| start and stop sequences in DNA. Operating systems have
| cron jobs (themselves digital) that control when other
| programs execute.
| shakow wrote:
| Genomes are much more than just their sequence. Their
| spatial organisation, their methylation, their fiolding,
| their packing etc, have no equivalents in a filesystem.
| dekhn wrote:
| You mean "DNA sequences are digital" in that base pairs
| map to a sequence of enumerations.
|
| However, genomes aren't digital. They're 3D structures
| with a ton of attributes that are not trivially
| representable digitally.
| staticassertion wrote:
| FWIW all of these differences still feel extremely
| surface level. I'm no expert but I certainly am, so far,
| aware of everything you've said with regards to how they
| differ - I'm kinda hoping for more, given the strong
| assertion you made that one can not relate the two
| without being fundamentally ignorant of either topic.
|
| I also think it's somewhat ironic that you're accusing
| them of only being here to say "you're wrong" but that's
| what you've done in this thread? I only bring this up
| because I think we're all after the same thing here - to
| understand an incredibly interesting topic.
|
| I suspect most of us are really here to learn and
| discuss. You seem like you have a background in the area,
| I'm sure we would all benefit from learning about the
| differences.
|
| If it's the case that the similar is that DNA and code
| both encode information, and the differences are based on
| how they do so, it's hard to see why you think they can't
| be related at all. You've _been_ relating the two.
| throwanem wrote:
| If I've given the impression that the difference is
| merely a question of varying encodings, then I have to
| agree my arguments have thus far been lacking.
|
| The idea that a genome as expressed in nucleic acid is
| purely, and only, an informational medium, is
| fundamentally in error. It does encode information in the
| sequence of base pairs, this is true. But it is also a
| physical structure in its own right, and properties of
| that structure incidental to the encoded information have
| what recently looks to be at least as important a role in
| the process of transcription as the sequence itself.
|
| There are, for example, some sequences which will cause a
| ribosome to transcribe the surrounding genes differently
| or with varying frequency, due to the physical
| interaction between the molecules involved. (I recently
| discussed this here in the context of recent research on
| causes of eye color; it should not be too far back in my
| comment history.) We also see, for example, that both
| viral and eukaryotic DNA can be and often are transcribed
| in ways that produce different proteins from the same
| sequence, again as a result of physical constraints
| affecting the interaction with the ribosome. This is one
| reason why "junk DNA" is a bit of a misnomer, and why we
| more recently see the term fall out of use in favor of
| "noncoding DNA" - these regions carry no information in
| their own right, but nonetheless can strongly affect the
| outcome of transcription because transcription is not
| _only_ an informatic process. This isn 't true of
| software; there is no general case in which two programs
| varying only in nonsyntactic ways will be evaluated
| differently under otherwise identical conditions - we
| create programming languages as we do in part to ensure
| that _won 't_ happen, and it's also part of the reason
| why we use transistors instead of vacuum tubes or relays:
| in order to engineer that kind of variance as much as we
| can _out_ of existence. What is therefore an accidental
| property in software is an essential one in gene
| expression, and cannot be overlooked without reaching an
| inaccurate conception of how the latter process works.
|
| That's just one example, and it's true that processes
| like these can be modeled in software to variously
| imperfect degrees of fidelity and that information-
| theoretical models can be useful in understanding some
| aspects of how they work. But that's not the same thing
| as them working similarly enough that understanding one
| very well suffices to reason about the other. I
| definitely can see how it's easy to assume otherwise!
| It's an assumption I shared, before my own yearlong
| exposure to the field at a sufficient level of detail to
| start to understand what I hadn't understood about it
| before, and considerable reading and study thereafter.
|
| Unfortunately, I was there to provide engineering support
| to people doing that work, not to do it myself, and the
| knowledge I've derived from that experience apparently
| does not extend so far as producing a concise and
| positive statement of the fundamental difference between
| the two fields of study - I spent considerably more time
| teaching informaticists how to program, formally and
| otherwise, than I spent learning about bioinformatics.
| That leaves me able to recommend little beyond seeking
| out similar experience of your own, which I _do_
| recommend if the depth of your interest suffices
| -although I do also have to say working in academia as a
| nonacademic has very little else to recommend it.
|
| I know there are some folks on HN with formal knowledge
| and training greatly exceeding my own, and some of whom
| have probably also had experience teaching the basics in
| an accessible way. Perhaps one of them might give a more
| useful answer here than I've been able to.
| staticassertion wrote:
| Thanks, this was much more interesting to read, and
| educational for someone with a software background, which
| I think kind of goes to show that discussing analogs is
| actually a reasonable way to approach the unknown :)
| ABCLAW wrote:
| >some sequences which will cause a ribosome to transcribe
| the surrounding genes differently
|
| Not to be a negative nancy here, but if we're being
| precise, ribosomes do not transcribe. They translate.
|
| Under the fairly reductive central dogma of biology: DNA
| -> RNA (Transcription) RNA -> Protein (Translation)
|
| Transcription and translation are separate mechanics that
| don't occur in the same area of the cell, and both use
| very different complexes to mediate the rates of each in
| different physical environments.
|
| I don't disagree with any of the substantive points being
| made, but I think the proper terminology only adds to
| your argument so I found it strange that it was left out.
| throwanem wrote:
| It's one of the drawbacks of being an autodidact; I
| pretty much always have to check to be sure I'm not
| confusing these two similar terms, and I didn't stop to
| check this time. Thanks for the correction.
| inigojonesguy wrote:
| Again I agree with you, because I had a similar
| experience. But, again, my conclusion is different than
| yours.
|
| You write that we should not talk about biochemistry as
| computation, as far as I understand. Instead I'd say that
| we have not studied enough how nature does computation
| without programmers or even human friendly semantics.
|
| Is still computation, involving space and physics. Too
| complex to efficiently simulate it (for now) but not big
| enough so that the emerging behaviour is simple, like for
| a gas.
| dekhn wrote:
| ribosomes don't transcribe genes.
| techbio wrote:
| I love this. It's a little black and white, but the
| comparison is as between video game worlds and the real
| world. Only enough to fool the willing eye.
|
| I use a variation of this form as 'persons whos science
| and religions conflict don't know enough about either
| one'.
| burning_hamster wrote:
| As a bioinformatician, I cannot wait to use this quote on
| someone.
| throwanem wrote:
| As an enthusiastically former staff engineer at a
| bioinformatics institute, I'm happy to have been of help!
| Please feel free to do so without attribution; if nothing
| else, it'd be a shame at this late date to have my
| opinions of the caste system in academia disturbed by the
| novel experience of receiving credit for my contributions
| to the work of people with letters after their names. :D
| airhead969 wrote:
| Department chairs > PIs >~ profs > visiting profs >
| assistant profs >~ visiting asst profs > postdocs > grad
| students > employees > undergrads > high-school interns
|
| Dedicated grant-writing staff are gold, literally and
| figuratively.
|
| (I worked at a biomedical informatics shop.)
| dekhn wrote:
| I'm profoundly ignorant in neither (PhD in biophysics,
| software engineer for 20 years). Genomics and programming
| analogies are cool, but the most important thing is that
| understanding that molecular structures can encode
| information in a replicable way, and the discovery of
| application of entropy to data storage and transmission,
| demonstrates that information is a universal concept,
| that the genome is a data storage system, and the enzymes
| that operate it are operating on information, in a
| computational way. To me that's a pretty useful
| comparison.
| uhhhhhhhhhhhhhh wrote:
| So when DNA gets pushed through a ribosome and the base pairs
| are used as instructions to build proteins that is not
| computation? Sounds turingmachine (or at least, machinelike)
| to me
| staticassertion wrote:
| I can only use the models that I have, accurate or otherwise.
| I hope I'm not confusing others, I'm not pretending to be an
| expert in DNA.
|
| > Both a computer program and a genome encode information,
| but that's about where the similarities end.
|
| FWIW this is a very significant similarity to me.
| throwanem wrote:
| One might with equal merit say that, because I know English
| orthography, I can also read Linear A.
| staticassertion wrote:
| I'm not sure what it is you think I'm trying to say, but
| much of your point seems to be "don't talk about things
| you don't understand", which I have no interest in
| abiding. I like talking about things I don't understand,
| and I've enjoyed the posts from you and others on the
| topic, even if I'll only ever be a layman.
| throwanem wrote:
| Talking about things you don't understand is no problem
| by me! What I'm trying to point to here is the hazard of
| making assumptions about something one doesn't
| understand, and then trying to reason about the thing
| based on those assumptions.
| staticassertion wrote:
| Oh sure, yeah I mean it's all in good fun. I wouldn't try
| to actually establish any serious thought other than
| "this is wild".
| faeyanpiraat wrote:
| I think a working analogy here would be that source code
| (dna) gets compiled (physics/chemistry) into an
| executable (living organism with even more dna) which
| gets executed by the os (phys/chem again) to produce
| changes on some data (organism interacts with the
| environment), and on and on..
|
| The details are of course endless and they aren't
| interchangeable between the two fields, but the analogy
| is still there..
| throwanem wrote:
| Sure, but is it meaningful? What predictions does it
| enable that are sufficiently borne out by reality to make
| it seem likely that less easily testable predictions on
| the same basis may likewise prove sound?
|
| I mean, I can as well say that chalk and cheese are alike
| in that both have mass, occupy space, and leave a streak
| behind when you rub them on something. It is a true
| statement, but what does it help me predict about either?
| ABCLAW wrote:
| I think the only real takeaways on the coding/biology
| comparison are applying base-level informatic systems
| ideas to explain some biological developments, and in
| reverse looking at biological system mechanics as
| inspiration for designed systems.
|
| I don't think the 'chemistry is an OPERATING SYSTEM'
| level of handwaving is sufficient to glean insights, but
| understanding general systems-level interactome patterns
| of how proteins interact does help provide knowledge
| about how natural and designed systems can self-regulate,
| how they fail, how they can be structured, etc.
| throwanem wrote:
| Sure, at that level it makes sense. The trouble seems to
| be that in order to know that that's the level at which
| it makes sense, you need to know considerably more about
| informatics than is the default among programmers who
| like to indulge in this kind of speculation. Kind of a
| Dunning-Kruger problem, maybe; there certainly was a time
| when I likewise didn't know what I didn't know.
| andrewflnr wrote:
| The closest programming analogy for a new gene is probably
| dropping a new listener/sender on a message bus. It can send
| messages independently in response to messages that were
| already on the bus before it arrived. If there's a little bit
| of a shared language (which there is here, since the bus is
| chemistry itself), that can lead to new behaviors of the system
| without necessarily breaking anything.
| vikingerik wrote:
| Well, survivorship bias. We only see the results where it
| worked, we don't see the enormous number of attempts where it
| didn't.
| kbenson wrote:
| It's less so when you know about some evolutionary programming
| techniques, such as using Lisp with a subset of the code that
| defines behavior in a tree structure that allows for parts of
| that tree to be swapped in and out from other programs using
| the same design whike still yielding an executing program.
| Combined with a fitness function you can "breed" programs for a
| task.
|
| As I understand it there are attributes of Lisp and attributes
| of the program structure (such as putting much of the logic in
| that tree structure with defined split points) which makes this
| much more feasible than otherwise.
|
| My guess is that DNA has evolved similarly, where the ways in
| which it splits and the mechanism in which it is interpreted
| and executed help, and also the organisms we're talking about
| (us and the other complex ones) have iterated to a design
| that's more amenable to bits being swapped. That is large
| chunks of us may be more similar to a lisp program with
| attributes that make it easy to swap parts than to a bunch of
| object bytecode with absolute and relative jumps all over.
|
| Note: A lot of this is poorly remembered from a survey of AI
| class two decades ago, so it bears someone with a stronger
| background verifying I'm not making a complete hash of it.
| Rapzid wrote:
| What I'm very interested in ATM(just now after reading this
| topic) is how the process of evolution really works. Not the
| selection so much, but the actual mutations.
|
| The last I ever learned about it, and perhaps the common
| belief, is that random-ish gene mutations account for it. 4
| billion years doesn't seem like enough time to account for all
| that unless changes are heavily weighted towards doing
| something somewhat useful. Like there is a system at play..
| Lego blocks vs bits. IDK.
| TheEzEzz wrote:
| This is crazy from the perspective of "old fashioned binaries",
| but less so in the context of neural networks. You can do all
| sorts of splicing and dicing of the bits in neural networks
| (their weights) and end up with useful networks. Dropout, for
| example, specifically trains a network to be resilient to
| having swaths of the network removed, and makes individual
| features in the network resilient to having a random selection
| of other features present or not-present. If I remember right,
| the original dropout paper even analogizes this to how genes
| have evolved to be resilient to this type of random pairing.
| Dylan16807 wrote:
| A program has to run those sequences mostly in order. Rather
| than swapping around blobs of binary it's more like each gene
| being its own small program, and things working is much less
| surprising in that context.
| [deleted]
| yyyk wrote:
| Not having access to the journal article, I wonder how much of
| this can be explained by retroviruses inserting their DNA, which
| is well established to be inheritable (e.g. when the retrovirus
| managed to infect sperm or egg in humans).
|
| Retroviruses could be a mechanism for the DNA jump - though we'd
| have to ask how they got a portion of an host's DNA - or they
| could be an alternative mechanism which would explain why the
| surrounding 'junk' DNA is identical without requiring a
| speculative 'DNA jump', all three fish species could have been
| infected by the same retrovirus.
| LatteLazy wrote:
| I was amazed when I learnt that viruses could move DNA from host
| to host. But then it makes perfect sense. It must make evolution
| so much more efficient.
|
| It made me wonder whether viruses (or similar participants) would
| be vital to complex life evolving on other planets?
| flobosg wrote:
| You don't need to look that far: Syncytin, a protein involved
| in placental development, is derived from an ancient
| retrovirus[1]. In other words, a virus made mammals possible.
|
| [1]: https://whyy.org/segments/the-placenta-went-viral-and-
| protom...
|
| EDIT: If I recall correctly, endogenous retroviruses are
| involved in brain development as well.
| bjornlouser wrote:
| "When herring are exuberantly spawning, the surrounding water can
| turn milky with the amount of sperm they release."
| uhhhhhhhhhhhhhh wrote:
| "Organic non-vegan almond-milk substitute"
| failwhaleshark wrote:
| _You must cut down the mightiest tree in the forest with..._
| williesleg wrote:
| I'm gonna look like a mermaid now for sure!
| nemo44x wrote:
| > Graham thinks that these sequences are "definitive proof" that
| a small chunk of a herring chromosome made its way into a
| smelt's. "If anybody wants to dispute this," she said, "you know,
| I don't see how they possibly could."
|
| I think the problem here is she is presenting something that is
| unfalsifiable and therefore problematic. I think it would then be
| on her and her team (or someone else who cares enough) to prove
| that it is possible somehow. Devise an experiment (a very clever
| one I'm sure) of some type that proves that DNA can be passed on
| this way somehow.
| failwhaleshark wrote:
| Distant past hybridization or would there be an accumulation of
| mutations unless that segment were well-conserved?
| nashashmi wrote:
| That explains why Chinese animals and humans have similar eyes. I
| thought it must have been some bacteria that caused the change.
| doubtfuluser wrote:
| I know too little about biology, but given the sheer number of
| species in the world, does this one single instance really prove
| this? How likely is it to see this between any two (unrelated)
| species in the world?
| staticassertion wrote:
| The article sites several instances.
| flir wrote:
| https://www.pnas.org/content/111/18/6672 - an example from the
| plant world. I suspect (no evidence!) it's one of those things
| where the more you look the more you find - in plants, at
| least.
| flobosg wrote:
| It's very unlikely, but not impossible.
|
| Here's a plant-to-insect example, discussed a few months ago:
| https://news.ycombinator.com/item?id=26600298
| graderjs wrote:
| This is why we can't nuke mosquitos. They are invaluable in H
| gene transfer and aid our evolution and aid evolving our immune
| systems to handle many pathogens. People don't know this and want
| to nuke mosquitos because itchy. But it will ruin many things.
| failwhaleshark wrote:
| ? I don't see the function of mosquitos except as niche
| opportunists to increase the universe's entropy faster by
| breeding and killing other critters. They may be incidentally
| useful as food, but the biomass can be filled by less harmful
| to higher lifeforms insects.
|
| Speaking of mosquitos, with all of the intense rain, southeast
| Texas is more akin to the deep South with enormous quantities
| of flying insects, i.e., moths, beetles, and tons of mosquitos.
| I setup the largest bug zapper I could find for one night, and
| it decimated about 2 lbs / 1 kg of insects in a pile so large,
| it clogged it and left the table it was on completely full of
| carcasses. IOW: the area needs more birds, if the cats and
| previous lack of flying insects would stop killing them.
| alwaysdoit wrote:
| I guess you're going to volunteer to feed them the human blood
| they need to reproduce, then?
| graderjs wrote:
| Willingly make my donation nightly.
|
| The mosquito "needle" is highly evolved. Less painful than a
| thumb blood sample. Don't push them off prematurely and you
| get less itch, IMHO. Don't scratch and you get less itch,
| too.
| rightbyte wrote:
| > But it is very surprising, even weird, that both fish do so
| with the same AFP gene
|
| Maybe that constellation of a gene is the "obvoius solution" and
| both fish will likely develop it by chance? Why assume the genes
| jump over ...
| permo-w wrote:
| Do you think these scientists are stupid?
| foxhop wrote:
| Part of science is questioning other peoples hypothesis,
| results, and analysis. This is how science works.
| snakeboy wrote:
| Yes, but speculation about the most obvious questions from
| someone who hasn't done any work to investigate whether
| it's already been addressed doesn't progress science
| either.
|
| Here's the 2nd paragraph from the linked article (which is
| already a source someone created to help non-experts
| understand the main ideas):
|
| > It isn't surprising, then, that herrings and smelts, two
| groups of fish that commonly roam the northernmost reaches
| of the Atlantic and Pacific Oceans, both make AFPs. But it
| is very surprising, even weird, that both fish do so with
| the same AFP gene -- particularly since their ancestors
| diverged more than 250 million years ago and the gene is
| absent from all the other fish species related to them.
|
| edit: I am more sympathetic to this behavior when the topic
| is more politically contentious, since it may be
| unreasonably difficult for a layman to know the biases of
| the authors and the source may indeed be trying to slide
| something under the rug. But here we're talking about fish
| genetics. There's no culture war or red vs. blue divide
| here (I hope!)
| vlovich123 wrote:
| Not my field but another seemingly plausible explanation,
| at least to me, exists. The common ancestor did have this
| gene and most other descendants lost the gene because it
| wasn't needed and was selected against.
| odyssey7 wrote:
| I can't see the scientists being harmed by a layperson's
| curious engagement. Every scientist was once a curious
| layperson.
| snakeboy wrote:
| I didn't say it harms scientists. I said this example
| doesn't progress science. Curious laypersons are well and
| good. I would recommend they start by reading the linked
| Quanta article :)
| garmaine wrote:
| Do you think this comment was helpful?
| throwanem wrote:
| It isn't an assumption; the null hypothesis here is that that
| _doesn 't_ happen. Genes coding for cryoprotective proteins
| have indeed, as you suggest, evolved independently among
| various species. The resulting genes, despite all producing
| proteins similar enough to do the necessary job, are "radically
| different" and "highly diverse." [1]
|
| What's different in this case is that, in three otherwise very
| distantly related species of fish, we find their antifreeze
| proteins are coded for by the _same_ genes:
|
| > But, the isolated occurrence of three very similar type II
| AFPs in three distantly related species (herring, smelt and sea
| raven) cannot be explained by this mechanism. These globular,
| lectin-like AFPs have a unique disulfide-bonding pattern, and
| share up to 85% identity in their amino acid sequences, with
| regions of even higher identity in their genes. A thorough
| search of current databases failed to find a homolog in any
| other species with greater than 40% amino acid sequence
| identity. [1]
|
| In light of the fact that all other genes known to code for
| these proteins are very distinct both from this one and from
| one another, that three species should have a near-identical
| sequence coding for a near-identical protein suggests rather
| strongly that this version of the gene arose in one species and
| was then acquired by the other two, i.e., that horizontal gene
| transfer has occurred among these vertebrates.
|
| [1] https://pubmed.ncbi.nlm.nih.gov/18612417/
| teachingassist wrote:
| > that three species should have a near-identical sequence
| coding for a near-identical protein suggests rather strongly
| that this version of the gene arose in one species and was
| then acquired by the other two
|
| We'd strongly expect the amino acid sequence to be similar
| both by "convergent evolution" (each case evolved
| independently with the same motivation) and "lateral
| transfer" (one case evolved and then shared DNA across
| species), so this wouldn't typically distinguish those two
| cases.
|
| The sibling answer about structure of introns and exons is a
| more convincing answer, in my opinion. I don't think we would
| expect to see that in convergent evolution, but we would in a
| copy-paste job.
| throwanem wrote:
| On what basis do you hold any such expectation? The paper
| explicitly contrasts its subject with several examples of
| convergent evolution producing functionally equivalent, but
| proteomically and genomically highly distinct, outcomes -
| which is typical of convergent evolution in general.
|
| That said, I agree that the similarity of adjacent
| noncoding sequence is also a strong indicator that
| convergent evolution isn't causative here.
| teachingassist wrote:
| > On what basis do you hold any such expectation?... The
| paper explicitly contrasts its subject with several
| examples of convergent evolution producing functionally
| equivalent, but proteomically and genomically highly
| distinct, outcomes
|
| On the basis that the protein is the function here.
| (antifreeze protein). There might only be one good, or
| best local maximum, solution for this problem at the
| protein level. So, we would expect natural selection
| might converge on that one solution. And, the results of
| two runs would not be nearly as different as they are in
| cases where natural selection is optimizing for a system
| process.
|
| Obligatory coding comparison:
|
| If I asked two programmers to code a webshop, I would
| expect the underlying code to look substantially
| different - if the code looked the same, I'd take it as
| evidence of copying.
|
| If I asked two programmers to code "If A then B", I would
| expect the underlying code to look substantially the
| same, whether or not they copied.
|
| A specific antifreeze protein is the second case: both
| the code and the outcome. It's not part of a system which
| would have more freedom of variation in its solutions.
| throwanem wrote:
| Preventing crystallization of water is the function. And
| again, on what basis so presume? Trivial literature
| review would have sufficed to reveal that there is a
| whole, mostly very nonhomologous, _class_ of these
| proteins, not just the one. [1] It is precisely for this
| reason that near identity observed in the proteins used
| by these three unrelated fish species is surprising.
|
| As I have already noted this morning, it is at best
| pointless to attempt to reason out genomics based on
| first principles drawn from computing. Thank you for
| taking the time to demonstrate the kind of error that
| invariably results!
|
| [1] https://en.m.wikipedia.org/wiki/Antifreeze_protein
| teachingassist wrote:
| Even with all this 'trivial literature review', there
| still remains the possibility three fish might have
| randomly walked [or non-randomly walked] into the same
| solution with the same local maximum, which couldn't be
| distinguished from lateral transfer just by looking at
| the protein structure.
|
| "A doesn't always happen this way" isn't evidence, at
| all, for B happening. Your logic is faulty.
|
| Thank you for appreciating my sense of humour. As someone
| who has worked in a genomics lab, I think coding
| analogies are perfectly fine. The analogy is not in
| error.
| throwanem wrote:
| Happily, the paper does not only do that! Too, there are
| several comments peripheral to this thread which discuss
| the paper's findings outside the proteome.
|
| Far be it from me to suggest that anyone in a Hacker News
| thread has failed to do even the most basic of reading in
| a field outside their own, but I will say that the paper
| is linked in one of my earlier comments, should you
| perhaps like to renew your acquaintance with its
| contents.
| teachingassist wrote:
| > Happily, the paper does not only do that!
|
| Yes, happily! Since, as I was saying in my first comment:
| I didn't agree with this part of the paper's abstract
| being relevant evidence, or your take on it; but I agreed
| with it in other aspects.
| throwanem wrote:
| Yes, and your disagreement appears to proceed from an
| attempt to reason purely from first principles, with no
| sign of apprehending either the clear evidence that
| convergent evolution on proteins which prevent water from
| crystallizing into ice in no other case has produced
| anything like such genomic or proteomic similarity as in
| the case under discussion, or the infinitesimal
| probability of that happening by coincidence.
|
| I'm not averse to the idea that I may be wrong on any of
| those points, but thus far I'm not seeing anything
| substantive to suspect I am likely to be so. These are
| just assertions that you're making, and while your
| reasoning itself is not unsound, the premises from which
| it follows as yet lack anything resembling
| substantiation, which is sorely needed given that those
| premises so contradict all available evidence.
|
| ...and, in response to your prior edit, this is coming
| from someone who has _also_ worked in a genomics lab.
| Even if I hadn 't, what point to claiming authority on
| that basis?
| teachingassist wrote:
| > no sign of apprehending
|
| I apprehended it perfectly well; I'm still in
| disagreement, since my argument is unaffected.
|
| > so contradict all available evidence
|
| It doesn't, and that's what you have missed. What I said
| is logically harmonious with all available evidence.
|
| By observing three fish with the same solution for
| antifreeze, we know that three fish have the same
| solution for antifreeze. This immediately contradicts any
| claim that all unrelated species have different solutions
| for antifreeze, which makes them worthy of study. It's a
| "black swan".
|
| As such, whatever mechanism has caused this has not been
| seen to work this way elsewhere. Therefore, saying "this
| mechanism is not seen to work this way elsewhere" is not
| remarkable as evidence.
|
| It's now a neutral statement which matches our
| expectation, and can't therefore be evidence against the
| mechanism. It's certainly not evidence for another
| mechanism.
|
| I could just as well say "I have only observed horizontal
| transfer in N other cases, and this is not one of those N
| cases, therefore it is not horizontal transfer". That
| would be wrong, but has equal logical merit as your
| claim.
| throwanem wrote:
| All of which still ignores how wildly unlikely it is that
| such a high degree of similarity occurs by chance.
|
| The paper doesn't claim causality either, but only
| argues, in my view pretty convincingly, that lateral gene
| transfer is a likelier explanation for the observed
| similarity than any other including convergent evolution.
| You haven't argued otherwise, but only that convergent
| evolution in this case is not _implausible_ - which is
| true, but answers no claim that anyone is actually
| making.
|
| There's no point in that that I can see, so if you want
| to keep on doing it, I'm afraid you'll need to do so in
| the absence of an interlocutor, or at least of an
| interlocutor who is me.
| teachingassist wrote:
| > All of which still ignores how wildly unlikely it is
| that such a high degree of similarity occurs by chance.
|
| It is wildly unlikely that I should exist through the
| process of evolution, to waste my afternoon on this
| argument, and yet: here I am :) Have a nice day.
| teachingassist wrote:
| > Even if I hadn't, what point to claiming authority on
| that basis?
|
| Oh, this was a direct response to the fact that you
| repeatedly implied that I was ignorant and hadn't done
| basic reading in the field. You were wrong about that as
| well.
|
| Someone disagreeing with you is not always a sign of
| ignorance.
| throwanem wrote:
| It's not _that_ you disagree with me that leads me to
| that surmise, but _how_. You have a good one too!
| erdewit wrote:
| Also, the article mentions that the introns - the "junk" DNA
| around the DNA that encodes the actual protein - is 95%
| similar.
| nerdychristie wrote:
| There are a few reasons convergent evolution is really unlikely
| here.
|
| 1) This particular gene isn't the obvious solution - there are
| many, highly diverse antifreeze proteins, not to mention other
| mechanisms of freeze resistance (glycerol production, for
| example).
|
| 2) Even if it were, the genetic code is redundant, meaning that
| there are often several 3-base codons that code for a given
| amino acid. So even if the exact amino acid sequence is what
| mattered, the odds of using the exact same coding to obtain
| that sequence is unlikely.
|
| 3) The similarity extends beyond the coding region. It includes
| stretches of DNA in between and flanking the gene's code
| itself. These are stretches of DNA that normally mutate at a
| much higher rate than the coding region itself, and they aren't
| under the selective pressure of making a working protein, so
| there's no real evolutionary explanation for how they'd end up
| so similar.
| RocketSyntax wrote:
| viruses and bacteria doing crispr like stuff since the dawn of
| time. there's a whole microbiome that could affect human embryos
| JunkDNA wrote:
| I was on one of the teams that refuted the claims of horizontal
| gene transfer in the original human genome paper. The bar for
| establishing a true case of horizontal transfer in vertebrates is
| high. It's really improbable given the required sequence of
| events laid out in the article. It's one thing for some DNA to
| get picked up by random cells in the organism (happens with viral
| infection all the time). Getting to the germline cells and
| becoming inherited is a whole other story given that vertebrates
| have evolved mechanisms to guard against this specific scenario.
| burning_hamster wrote:
| I just read the PLOS one paper. The arguments they brought
| forth were strong. If this had been my paper, I would have been
| livid if I had been rejected. However, given the fragmented and
| buggy state of bioinformatics tooling and databases at the
| time, I can easily imagine how their extraordinary claims did
| not the cross the "beyond reasonable doubt" threshold. From a
| reviewer's perspective, a couple matching disulfide bridges and
| a negative Southern alone might not have convinced me either.
| Glad it worked out for her in the end though.
| ak217 wrote:
| The issue with the evidence in that paper is that they used
| primers to amplify the specific genes of interest. That
| introduces a strong assumption at the start of their
| analysis: specifically, that these genes appeared in the
| genomes by some HGT process instead of independently being
| duplicated internally in each genome from another gene shared
| among the species. Whole genome sequences were not available
| for these species at the time. A modern, more complete
| analysis would look into homologs across whole genomes and
| try to reject that hypothesis, which is much less
| extraordinary than animal germline HGT.
|
| That's precisely why the authors published the new Cell paper
| https://www.cell.com/action/showPdf?pii=S0168-9525%2821%2900.
| .. with stronger evidence from whole genome sequence to
| support the HGT hypothesis. I'm still trying to wrap my head
| around Figure 2 there, so I'm on the fence.
| attractivechaos wrote:
| The Trends in Genetics (not Cell) paper seems plausible. I
| don't study fish genetics or evolution. As I remember, fish
| genomes tend to have more genome-wide duplications and
| losses in comparison to other vertebrates. One possibility
| is that some fish lose AFPs because they don't need them -
| i.e. the observation could be caused by loss of function
| instead of gain of function due to HGT. I have to admit
| that the chance of gene losses across multiple fish
| lineages is pretty tiny but it is at least associated with
| a known mechanism.
|
| Anyways, an interesting article.
| dekhn wrote:
| My understanding is that inherited HGT in vertebrates is now an
| established mainstream position and that it was mainly the low
| quality of the original sequences that prevented people from
| refuting this point (specifically in humans). A lot of the
| stuff published in 2001 about human genomes was later shown to
| be of dubious quality, massively overstating the value of the
| data to make strong conclusions.
| Pyramus wrote:
| So did you know about the paper in question and if so how
| convinced are you of the claims/evidence in this specific case?
| pgt wrote:
| When "vertebrates have evolved mechanisms to guard against this
| specific scenario", it hardly sounds "improbable."
| muyuu wrote:
| well, not when the protection is against any form of DNA
| contamination and not specifically foreign DNA intrusion
|
| the fact that random large mutations typically lead to an
| inviable zygote should be enough evolutionary pressure, it
| doesn't need to be specific protection against the entry of
| external DNA
| elmomle wrote:
| The sequences we're discussing aren't really random,
| though. Presumably the chance of viability with such a
| sequence incorporated, though still low, is much higher
| than if it were a truly random sequence.
| faeyanpiraat wrote:
| Are you sure?
|
| Having one foreign sequence which have some specific
| features (to keep the originating organism viable) could
| have a chance of never being compatible with the target
| organism.
|
| Having a completely random sequence by definition have
| some chance of being compatible.
|
| The question is which scenario has a higher chance of
| success.
| enkid wrote:
| This is a case I could see going either way. Random
| mutations are probably much smaller and closer to the
| original, and therefore potentially more viable. Yes,
| it's random, but most of the time it won't have a major
| effect on the proteins the DNA generates. On the other
| hand, if we are talking about transferring segments,
| there's the potential of that DNA to create actively
| harmful proteins.
| [deleted]
| nszceta wrote:
| Mr. Hands was on to something
| shireboy wrote:
| As someone with no business even commenting on this topic, I'll
| ask anyway: is it possible that a virus could do this? My (again,
| naive) understanding of CRISPR is that it uses a virus to inject
| DNA fragments into an organism's cells in a way that they become
| usable. Is there any chance that a naturally occurring virus
| injected this sequence into the fish in such a way that they both
| incorporate it into their offspring, at which point natural
| selection takes over?
| failwhaleshark wrote:
| In which direction? Host-to-virus and virus-to-host (germline)
| HGT.
|
| Virus-to-virus HGT: happens all of the time.
|
| Retrovirus-to-host: endogenous retroviruses are ~8% of the
| human genome.
|
| Host-to-virus: I don't know.
|
| The other issue would be the size of the payload.
|
| It seems like a big stretch, but so is life.
|
| I doubt any of this is realistically-possible except in
| externally-fertilized species where either something weird
| happened between gametes of different species or a retrovirus
| infected the gametes. Hybridization may also be an explanation.
| flobosg wrote:
| Some info on antifreeze proteins from a structural biology point
| of view: https://pdb101.rcsb.org/motm/120
| airhead969 wrote:
| Germline hxfer? Maaaaaybe a faint possibility because of how most
| fish procreate but never gonna happen in critters that have
| direct sexual contact.
___________________________________________________________________
(page generated 2021-06-10 23:01 UTC)