6 ms·

>understandings of genes as immutable features of biology that are fixed at conception This 'understanding' has been known to be wrong for 30+ years now. Rearr

by aluren 7y ago

>understandings of genes as immutable features of biology that are fixed at conception This 'understanding' has been known to be wrong for 30+ years now. Rearrangements, microchimerism, epigenetics, chromosome organization etc. are all things that exist and modulate information transfer beyond the standard four letters or the 'environment' (whatever people think it means) and we're still only scratching the surface. I keep saying it and I'll say it again: DNA is not source code, your genes are not initial character stats in a video game. That's not how any of this works and it frustrates me whenever I read otherwise smart people making arguments that rely on premises originating from a high schooler's (or 1970's) understanding of genetics. It's even worse when the dreaded 'nature/nuture' gets mentioned.

johnchristopher 7y ago
This understanding was still taught like that in the 90's, western continental Europe.
- aluren 7y ago
  True. Most of what I've been taught after high school feels like "you've been lied to, everything you were taught in high school was wrong or grossly oversimplified and now you need to unlearn it all and relearn from scratch." Makes you wonder what the purpose of high school was in the first place.
  - davedx 7y ago
    I got the same impression from people who studied chemistry after high school too though. Some things are just simplified so our children can ramp up their understanding gradually instead of having the wild complexity of the universe thrown at them in one go.
    - thatcat 7y ago
      It makes no sense to leave things out of a description of a complex system to help someone to understand it better. Have you considered educators might not want 17 year olds to understand things that are "too dangerous"? Because that happens at a pretty basic level in chemistry.
      - iguy 7y ago
        Actually, leaving things out of a description of a complex system is the only reason we can ever understand anything!
  - johnchristopher 7y ago
    > Makes you wonder what the purpose of high school was in the first place. Oh, I have an opinion about that: Well. First and above all the first purpose of school and high school is to learn to follow authority (edit: authority in every other meanings. Tthe first authority to submit oneself to is the school). This is the first brick and if it's not assimilated in a way that suits the school the student will get thrown out of the system. A century ago there's the industrial revolution mantra: produce workers who can read and understand semi-complex or complex instructions in written and oral forms and manipulate tools (typewriters, screwdrivers, hydraulics, mechanics, machines, etc.). And now there's the "learn to learn" mantra because few things taught in the 'regular', 'normal' or 'general' school and high school cursus land jobs in the post-industrial and the information societies. Does not seem to apply to trade schools.
    - mistermann 7y ago
      This would also explain why we don't teach fundamentals of epistemology or critical thinking, even though we constantly read in the news how crucially important these skills are, because of fake news and Russian election hackers.
      - johnchristopher 7y ago
        Last time I heard about my country in OECD ranking (or was it the PISA ranking ?) it was mentioned that 1 out of 4 students out of high school was almost illiterate. They can (barely) read but they don't understand the meaning behind the words. Either it's a consequence of not teaching critical thinking or a reason we don't teach it is up to debate but the results remain.
    - __MatrixMan__ 7y ago
      > The first purpose of school and high school is to learn to follow authority. I think that depends which person at the school you ask. I am married to a low-income neighborhood high school English teacher and we talk curriculum often. Seems to me that it's about striking a balance: One side is what you said, the other side is teaching students to unite against that authority in productive ways. Too far in one direction, and you wind up with a society where none of the competent people you know have enough faith in the system to run for office. Too far in the other direction and the dominant class sees the everyone else as a threat and puts walls up. It's a difficult balance to strike, but I know a lot of teachers that work very hard at finding it.
- iguy 7y ago
  It's not called the central dogma of biology for nothing! But seriously, in my understanding it's taught that way to try to rid people of mystical pre-evolutionary notions. Once they have firmly grasped the basics they can move on to super-interesting corners where stranger things may happen, and about which people are still arguing. The physics analogy is people arriving with mistaken intuition about "when does the dead body roll out of the truck" level problems. The fact that Newton isn't the end of the story doesn't spare you from having to un-learn Hollywood/Aristotle first. Nor will your earlier confusion be any help in wrapping your head around post-Newton concepts.
BearsAreCool 7y ago
This is new knowledge to me, where do I read about this?
- arkades 7y ago
  Every biology, molecular biology, and genetics textbook made for freshmen and sophomore bio majors. You can't pick a wrong one - this has been core material for at least two decades.
  - mehrdadn 7y ago
    Really? So like, say, Campbell Biology? That's what I've seen used in high school and colleges, and I don't recall any mention of epigenetics in it. (At least in the 7th edition one, published 2004... not sure how much it's changed since.)
    - arkades 7y ago
      So I don’t have a copy of Campbell’s underhand, but a quick google search for its table of contents brought up the ToC for 7e. Chapter 9, pg 161 covers epigenetics, p 162 gene linkages, Ch11 covers gene methylation. I’d find additional specific examples, but that’s all that’s laid out explicitly in the table of contents.
      - mehrdadn 7y ago
        Confused, are we looking at the same edition? I don't see an explicit mention in the ToC [1], and Chapter 9 is "Cellular Respiration: Harvesting Chemical Energy"... are you saying that's where they mention epigenetics? [1] https://www.pearson.ch/HigherEducation/BenjaminCummings/EAN/9780805371468/Campbell-Biology-7th-Edition- https://www.pearson.ch/HigherEducation/BenjaminCummings/EAN/...
        arkades 7y ago
        This is the ToC I found: https://www.pearsonhighered.com/assets/preface/0/1/3/4/0134812948.pdf https://www.pearsonhighered.com/assets/preface/0/1/3/4/01348...
reasonaway 7y ago
Genes do explain much of the variation between people for many characteristics. You can think of them as initial character stats that are then modified by environmental factors and random noise.
- aluren 7y ago
  Again, that's not how our modern understanding of genomics works, and hasn't been since the 1980's. There's much, much more to it than genes+environment. See all the mechanisms I've mentioned in GP. Also, you brought up 'variation between people', which can be aditionnally confounded by things that have nothing to do with DNA at all, such as the various microbiomes. It's important to note that heritability is not some kind of magic bullet that explains everything with "genes". If you want to convince a biologist that "genes" are the cause for a given phenotype, you've got to show an actual genetic causal mechanism or you've got nothing. This is, again, due to the myriad of interfering mechanisms that make "genes" very, very removed from the actual phenotype. And again, I'm not talking about the environment.
  - iguy 7y ago
    It's worth noting that there are two uses of gene here, or at least of "genetic". One of which is roughly DNA that codes for a protein, or controls such, and indeed the causal mechanisms from there to phenotype can be extremely complicated and hard to figure out. In the context of "variation between people" there's another meaning, of just whatever it is that causes inheritance. We could say many things about this (e.g. from twin studies) even before we'd discovered DNA, and non-DNA routes (like if most babies get some microbes from their mothers) would still count.
  - reasonaway 7y ago
    The complexity of how biological mechanisms work does not change basic facts about genetics. There isn't any conflict between the two. Your second point is not true for complex polygenic traits like height. Height is strongly influenced by genetics but we will likely never understand the exact mechanisms that do this.
heavenlyblue 7y ago
>> DNA is not source code It is source code, it's just that source code is self-modifying.
- aluren 7y ago
  Also the compiler is self-modifying. And the compiler flags as well. And the OS. And the chip architecture sometimes. Like, at what point do we decide that pushing the analogy further is just silly and just drop it altogether?
  - master-litty 7y ago
    I feel like my whole environment is self modifying, given the constant auto updating it wants to do :)
  - spsoto 7y ago
    I don’t disagree with you but I want to point out that it’s interesting how better software, running on an OS, running on a chip architecture, has enabled us to write better OSs and better chip which in turn allows us to write better software that allows us to repeat the cycle. Aren’t we somehow simulating how life works? Higher abstractions/constructs improve the way the lower constructs work :). Of course, just an oversimplification.
  - mannykannot 7y ago
    And yet something guides the human zygote in developing as a human. At what point do we stop focusing on refuting simplistic ideas and turn our attention to what is now known?
    - aluren 7y ago
      That 'something' you mention is called developmental biology and it's yet another level of abstraction removed from the basic cell machinery that operates around DNA. It also has nothing to do with compilers or anything computer related. At some point the analogy is just more harmful than anything else.
  - 7y ago
educationdata 7y ago
I still don't buy the "There is no nature vs. nurture" statement. Maybe there's more than nature vs. nurture, or more complicated than nature vs. nurture. But totally no nature vs. nurture? Overstatement.
- aluren 7y ago
  Nature vs. nurture hasn't been a thing since the 2000's when second generation sequencing dramatically expanded the breadth of information we had about species' genomes and (along with other discoveries made at the time) made us realize there was indeed a lot more to it than this dichotomy. It's about as relevant in our modern understanding of genomics as the debate between GOTOs vs. structured programming is to our modern understanding of software engineering.
  - educationdata 7y ago
    No. It's not about whether there was "a lot" more. It's about how much it can add on top of "nature vs. nurture" to explain common social phenomena. It is very possible the new knowledge can be 100 times more complicated, but it only adds 1% more explanation power to everyday phenomena. Take physics as an example, quantum physics has "a lot" more than classical physics, but no physicists will discard classical physics as being no longer valid, or no longer useful for explaining everyday physical world, or you should always use quantum physics in engineering, etc.
    - aluren 7y ago
      Explaining common social phenomena with modern human genomics isn't a thing period. If you'd attempted to introduce some sociobiology talking points in a typical genomics conference you'd be laughed out of the room. (That's assuming the organizers would even consider your abstract for a talk in the first place.) No one really discusses 'nature vs nurture' anymore outside of a few circles that somehow still haven't gotten the memo. It's just not relevant anymore to modern fields.
      - 7y ago
aeorgnoieang 7y ago
> DNA is not source code My, admittedly weak, understanding is that the analogy is (much) more apt than not. Sure, the means by which that code is 'compiled' and 'executed' is much different than in the computers we've built, but, for one, DNA, genes, chromosomes, and all of the other various levels of organization of those units of information seem to be remarkably, amazingly stable, for many (most? almost all?) organisms, which seems to strongly imply that 'DNA is source code' is about as true as 'Earth is a sphere'. Sure, they're both only approximately true, but how approximately they're true (or not) is very important. Asimov explained this extremely well: - [Asimov - The Relativity of Wrong](http://chem.tufts.edu/answersinscience/relativityofwrong.htm http://chem.tufts.edu/answersinscience/relativityofwrong.htm) 'Epigenetics' itself seems like it might not be a particular thing among different people: - [The misunderstanding of epigenetics – Insitome](https://blog.insito.me/the-misunderstanding-of-epigenetics-a67c99ee4058 https://blog.insito.me/the-misunderstanding-of-epigenetics-a...) What epigenetics is not is anything like Lamarckian inheritance, at least not at all to the same degree. > Rearrangements, microchimerism, epigenetics, chromosome organization etc. are all things that exist and modulate information transfer beyond the standard four letters or the 'environment' (whatever people think it means) and we're still only scratching the surface. Sure, but that doesn't mean that the central dogma of biology is entirely wrong, just that it's not always and everywhere true exactly. The current best understanding of epigenetics (quoted from my second link above) is that, whatever it is, it is such that: > very little of [genetic] inheritance is perturbed by epigenetic effects
- amelius 7y ago
  To test how much this corresponds to reality, has someone cloned an organism yet with entirely synthetic DNA material?
  - ak217 7y ago
    I'm not sure what exactly you're looking for, but yes, Craig Venter's team at JCVI and later Synthetic Genomics has been building synthetic organisms starting with Mycoplasma laboratorium in 2006. Most recently, an E. coli analog was built using DNA synthesis (https://www.nature.com/articles/s41586-019-1192-5 https://www.nature.com/articles/s41586-019-1192-5). To be clear, @aeorgnoieang's response is basically correct. The central dogma holds, the epigenetic program's role is well-characterized to be relevant to development/differentiation only under normal circumstances, epigenetic imprinting effects are weak, etc. As @aeorgnoieang correctly points out, the other things you cited (microchimerism, rearrangements, chromosomal organization/spatial effects) don't actually conflict with the "DNA as source code" metaphor in any way. This is not to say that the popular understanding of these things is perfect - there are lots of misconceptions - but the way to fix that is by finding better ways to describe what we know and put it in context. A big issue is that as we learn more, media events around new discoveries make it hard to put the relative effects (of things like chimerism/mosaicism, polygenic risk factors, horizontal gene transfer, etc.) into context if you're not already an expert.

by aluren 7y ago

johnchristopher 7y ago

This understanding was still taught like that in the 90's, western continental Europe.

aluren 7y ago
True. Most of what I've been taught after high school feels like "you've been lied to, everything you were taught in high school was wrong or grossly oversimplified and now you need to unlearn it all and relearn from scratch." Makes you wonder what the purpose of high school was in the first place.
- davedx 7y ago
  I got the same impression from people who studied chemistry after high school too though. Some things are just simplified so our children can ramp up their understanding gradually instead of having the wild complexity of the universe thrown at them in one go.
  - thatcat 7y ago
    It makes no sense to leave things out of a description of a complex system to help someone to understand it better. Have you considered educators might not want 17 year olds to understand things that are "too dangerous"? Because that happens at a pretty basic level in chemistry.
    - iguy 7y ago
      Actually, leaving things out of a description of a complex system is the only reason we can ever understand anything!
- johnchristopher 7y ago
  > Makes you wonder what the purpose of high school was in the first place. Oh, I have an opinion about that: Well. First and above all the first purpose of school and high school is to learn to follow authority (edit: authority in every other meanings. Tthe first authority to submit oneself to is the school). This is the first brick and if it's not assimilated in a way that suits the school the student will get thrown out of the system. A century ago there's the industrial revolution mantra: produce workers who can read and understand semi-complex or complex instructions in written and oral forms and manipulate tools (typewriters, screwdrivers, hydraulics, mechanics, machines, etc.). And now there's the "learn to learn" mantra because few things taught in the 'regular', 'normal' or 'general' school and high school cursus land jobs in the post-industrial and the information societies. Does not seem to apply to trade schools.
  - mistermann 7y ago
    This would also explain why we don't teach fundamentals of epistemology or critical thinking, even though we constantly read in the news how crucially important these skills are, because of fake news and Russian election hackers.
    - johnchristopher 7y ago
      Last time I heard about my country in OECD ranking (or was it the PISA ranking ?) it was mentioned that 1 out of 4 students out of high school was almost illiterate. They can (barely) read but they don't understand the meaning behind the words. Either it's a consequence of not teaching critical thinking or a reason we don't teach it is up to debate but the results remain.
  - __MatrixMan__ 7y ago
    > The first purpose of school and high school is to learn to follow authority. I think that depends which person at the school you ask. I am married to a low-income neighborhood high school English teacher and we talk curriculum often. Seems to me that it's about striking a balance: One side is what you said, the other side is teaching students to unite against that authority in productive ways. Too far in one direction, and you wind up with a society where none of the competent people you know have enough faith in the system to run for office. Too far in the other direction and the dominant class sees the everyone else as a threat and puts walls up. It's a difficult balance to strike, but I know a lot of teachers that work very hard at finding it.
iguy 7y ago
It's not called the central dogma of biology for nothing! But seriously, in my understanding it's taught that way to try to rid people of mystical pre-evolutionary notions. Once they have firmly grasped the basics they can move on to super-interesting corners where stranger things may happen, and about which people are still arguing. The physics analogy is people arriving with mistaken intuition about "when does the dead body roll out of the truck" level problems. The fact that Newton isn't the end of the story doesn't spare you from having to un-learn Hollywood/Aristotle first. Nor will your earlier confusion be any help in wrapping your head around post-Newton concepts.

BearsAreCool 7y ago

This is new knowledge to me, where do I read about this?

arkades 7y ago
Every biology, molecular biology, and genetics textbook made for freshmen and sophomore bio majors. You can't pick a wrong one - this has been core material for at least two decades.
- mehrdadn 7y ago
  Really? So like, say, Campbell Biology? That's what I've seen used in high school and colleges, and I don't recall any mention of epigenetics in it. (At least in the 7th edition one, published 2004... not sure how much it's changed since.)
  - arkades 7y ago
    So I don’t have a copy of Campbell’s underhand, but a quick google search for its table of contents brought up the ToC for 7e. Chapter 9, pg 161 covers epigenetics, p 162 gene linkages, Ch11 covers gene methylation. I’d find additional specific examples, but that’s all that’s laid out explicitly in the table of contents.
    - mehrdadn 7y ago
      Confused, are we looking at the same edition? I don't see an explicit mention in the ToC [1], and Chapter 9 is "Cellular Respiration: Harvesting Chemical Energy"... are you saying that's where they mention epigenetics? [1] https://www.pearson.ch/HigherEducation/BenjaminCummings/EAN/9780805371468/Campbell-Biology-7th-Edition- https://www.pearson.ch/HigherEducation/BenjaminCummings/EAN/...
      - arkades 7y ago
        This is the ToC I found: https://www.pearsonhighered.com/assets/preface/0/1/3/4/0134812948.pdf https://www.pearsonhighered.com/assets/preface/0/1/3/4/01348...

reasonaway 7y ago

Genes do explain much of the variation between people for many characteristics. You can think of them as initial character stats that are then modified by environmental factors and random noise.

aluren 7y ago
Again, that's not how our modern understanding of genomics works, and hasn't been since the 1980's. There's much, much more to it than genes+environment. See all the mechanisms I've mentioned in GP. Also, you brought up 'variation between people', which can be aditionnally confounded by things that have nothing to do with DNA at all, such as the various microbiomes. It's important to note that heritability is not some kind of magic bullet that explains everything with "genes". If you want to convince a biologist that "genes" are the cause for a given phenotype, you've got to show an actual genetic causal mechanism or you've got nothing. This is, again, due to the myriad of interfering mechanisms that make "genes" very, very removed from the actual phenotype. And again, I'm not talking about the environment.
- iguy 7y ago
  It's worth noting that there are two uses of gene here, or at least of "genetic". One of which is roughly DNA that codes for a protein, or controls such, and indeed the causal mechanisms from there to phenotype can be extremely complicated and hard to figure out. In the context of "variation between people" there's another meaning, of just whatever it is that causes inheritance. We could say many things about this (e.g. from twin studies) even before we'd discovered DNA, and non-DNA routes (like if most babies get some microbes from their mothers) would still count.
- reasonaway 7y ago
  The complexity of how biological mechanisms work does not change basic facts about genetics. There isn't any conflict between the two. Your second point is not true for complex polygenic traits like height. Height is strongly influenced by genetics but we will likely never understand the exact mechanisms that do this.

heavenlyblue 7y ago

>> DNA is not source code It is source code, it's just that source code is self-modifying.

aluren 7y ago
Also the compiler is self-modifying. And the compiler flags as well. And the OS. And the chip architecture sometimes. Like, at what point do we decide that pushing the analogy further is just silly and just drop it altogether?
- master-litty 7y ago
  I feel like my whole environment is self modifying, given the constant auto updating it wants to do :)
- spsoto 7y ago
  I don’t disagree with you but I want to point out that it’s interesting how better software, running on an OS, running on a chip architecture, has enabled us to write better OSs and better chip which in turn allows us to write better software that allows us to repeat the cycle. Aren’t we somehow simulating how life works? Higher abstractions/constructs improve the way the lower constructs work :). Of course, just an oversimplification.
- mannykannot 7y ago
  And yet something guides the human zygote in developing as a human. At what point do we stop focusing on refuting simplistic ideas and turn our attention to what is now known?
  - aluren 7y ago
    That 'something' you mention is called developmental biology and it's yet another level of abstraction removed from the basic cell machinery that operates around DNA. It also has nothing to do with compilers or anything computer related. At some point the analogy is just more harmful than anything else.
- 7y ago

educationdata 7y ago

I still don't buy the "There is no nature vs. nurture" statement. Maybe there's more than nature vs. nurture, or more complicated than nature vs. nurture. But totally no nature vs. nurture? Overstatement.

aluren 7y ago
Nature vs. nurture hasn't been a thing since the 2000's when second generation sequencing dramatically expanded the breadth of information we had about species' genomes and (along with other discoveries made at the time) made us realize there was indeed a lot more to it than this dichotomy. It's about as relevant in our modern understanding of genomics as the debate between GOTOs vs. structured programming is to our modern understanding of software engineering.
- educationdata 7y ago
  No. It's not about whether there was "a lot" more. It's about how much it can add on top of "nature vs. nurture" to explain common social phenomena. It is very possible the new knowledge can be 100 times more complicated, but it only adds 1% more explanation power to everyday phenomena. Take physics as an example, quantum physics has "a lot" more than classical physics, but no physicists will discard classical physics as being no longer valid, or no longer useful for explaining everyday physical world, or you should always use quantum physics in engineering, etc.
  - aluren 7y ago
    Explaining common social phenomena with modern human genomics isn't a thing period. If you'd attempted to introduce some sociobiology talking points in a typical genomics conference you'd be laughed out of the room. (That's assuming the organizers would even consider your abstract for a talk in the first place.) No one really discusses 'nature vs nurture' anymore outside of a few circles that somehow still haven't gotten the memo. It's just not relevant anymore to modern fields.
    - 7y ago

aeorgnoieang 7y ago

> DNA is not source code My, admittedly weak, understanding is that the analogy is (much) more apt than not. Sure, the means by which that code is 'compiled' and 'executed' is much different than in the computers we've built, but, for one, DNA, genes, chromosomes, and all of the other various levels of organization of those units of information seem to be remarkably, amazingly stable, for many (most? almost all?) organisms, which seems to strongly imply that 'DNA is source code' is about as true as 'Earth is a sphere'. Sure, they're both only approximately true, but how approximately they're true (or not) is very important. Asimov explained this extremely well: - [Asimov - The Relativity of Wrong](http://chem.tufts.edu/answersinscience/relativityofwrong.htm http://chem.tufts.edu/answersinscience/relativityofwrong.htm) 'Epigenetics' itself seems like it might not be a particular thing among different people: - [The misunderstanding of epigenetics – Insitome](https://blog.insito.me/the-misunderstanding-of-epigenetics-a67c99ee4058 https://blog.insito.me/the-misunderstanding-of-epigenetics-a...) What epigenetics is not is anything like Lamarckian inheritance, at least not at all to the same degree. > Rearrangements, microchimerism, epigenetics, chromosome organization etc. are all things that exist and modulate information transfer beyond the standard four letters or the 'environment' (whatever people think it means) and we're still only scratching the surface. Sure, but that doesn't mean that the central dogma of biology is entirely wrong, just that it's not always and everywhere true exactly. The current best understanding of epigenetics (quoted from my second link above) is that, whatever it is, it is such that: > very little of [genetic] inheritance is perturbed by epigenetic effects

amelius 7y ago
To test how much this corresponds to reality, has someone cloned an organism yet with entirely synthetic DNA material?
- ak217 7y ago
  I'm not sure what exactly you're looking for, but yes, Craig Venter's team at JCVI and later Synthetic Genomics has been building synthetic organisms starting with Mycoplasma laboratorium in 2006. Most recently, an E. coli analog was built using DNA synthesis (https://www.nature.com/articles/s41586-019-1192-5 https://www.nature.com/articles/s41586-019-1192-5). To be clear, @aeorgnoieang's response is basically correct. The central dogma holds, the epigenetic program's role is well-characterized to be relevant to development/differentiation only under normal circumstances, epigenetic imprinting effects are weak, etc. As @aeorgnoieang correctly points out, the other things you cited (microchimerism, rearrangements, chromosomal organization/spatial effects) don't actually conflict with the "DNA as source code" metaphor in any way. This is not to say that the popular understanding of these things is perfect - there are lots of misconceptions - but the way to fix that is by finding better ways to describe what we know and put it in context. A big issue is that as we learn more, media events around new discoveries make it hard to put the relative effects (of things like chimerism/mosaicism, polygenic risk factors, horizontal gene transfer, etc.) into context if you're not already an expert.