13 ms·

'Useless specks of dust' turn out to be building blocks of vertebrate genomes

262 points by georgecmu 5y ago

worik 5y ago
This seems to be another nail in the coffin of "DNA is Code" idea. We do not know how life organises itself. DNA is involved. We have some knowledge. But what we do not know matters much more than what we do know.
- ramraj07 5y ago
  Blowing out of proportions a bit are we? This is still dna, just in another form elsewhere. And it doesn’t uproot anything, most of the important genes are still in the main chromosomes, we just don’t have the full picture and studies like this help us inch closer towards it.
mrfusion 5y ago
So they’re saying we have chromosomes floating around in our cells? Outside the nucleaus? How do they get replicated?
- vaylian 5y ago
  The original scientific article says that mammals don't have the microchromosomes. And they are located inside the nucleus in other species.
- roflc0ptic 5y ago
  They’re saying birds and reptiles and other animals have micro chromosomes, and that mammals have incorporated these micro chromosomes into their macro-chromosomes. Per the Wikipedia page, Micro chromosomes are replicated the same way as other chromosomes - mitosis.
MichaelZuo 5y ago
"Not only are they the same in each species, but they crowd together in the center of the nucleus where they physically interact with each other, suggesting functional coherence," If there truly is some sort of functional interaction going on then this is a very profound observation. As it implies the close spacing is for some kind of mechanical/electrical mechanism within the core of every cell’s nucelus.
- 0des 5y ago
  Surely nobody was under the impression that detail stops at the nucleic level, right? It's small machines and complex systems the entire way down, ad infinitum. Our ability or inability to render or understand these increasingly small systems does not negate their existence.
  - vanderZwan 5y ago
    I agree with your general sentiment, but I don't see why we should expect "machines and complex systems" (as related to life) to exist at the level below molecules and atoms. If that was the case then we should expect otherwise identical organic molecules to have differences when they're created by living things and synthesis in the lab (ok, ok, there's chirality and carbon-14, but you get what I mean).
    - 0des 5y ago
      I get what you're trying to say, however this is a flawed assumption right up there with just getting an FTP account, mounting it locally with curlftpfs, and then using SVN or CVS on the mounted filesystem. Time and innovation are both not on your side, in this case. Complex systems are complex and extend far beyond the focal depth of our squinting.
      - WastingMyTime89 5y ago
        Wöhler proved in 1828 that there was nothing special with organic molecules by synthesising urea. I guess you could view molecular formation as a complex system involving atoms and atoms as a complex system involving quarks. That would define chemistry and particle physics as the study of said complex systems which makes sense to me. Still at that level that’s not generally viewed as the study of organisms. What we view as biology, the study of the mechanisms of life, really starts at the molecular level. If you go lower, things stop being specific enough.
est31 5y ago
It's interesting how much variation there is even within mammals when it comes to number of chromosomes, even though so much of the genome is conserved. This points to chromosomes being a major factor on the grander scales of evolution.
- gumby 5y ago
  > This points to chromosomes being a major factor on the grander scales of evolution. Or, alternatively, that chromosomal-level organization is happenstance. I agree though with your implication that it’s an interesting area of study. Perhaps there is an interesting mechanism to be learned or disproven.
  - notTheAuth 5y ago
    Check out bio electrical regeneration research If you haven’t come across it, the teams inject drugs that do nothing to cells but instigate an electrical field effect. What happens is regrowth of a limb to the correct “spec” even though that physical information is gone (limb amputated). This suggests to me an equalizing effect exists, where fields and matter feed each other just enough to reach structural equilibrium. Relativistic information network effects, proving what math objects create which field effects, and the social impacts, are going to become huge and blow away our current engineering goals of making hard silicon computers. We might be able to use nature itself as our CPU.
RyEgswuCsn 5y ago
It's a legacy codebase. The default assumption should be "DO NOT DELETE THIS". Jokes aside, I wonder if we actually know enough to safely meddle with genetic materials, e.g. with mRNAs vaccines.
- wizzwizz4 5y ago
  mRNA vaccines are barely meddling with genetic materials. We know that lots of viruses are barely harmful; mRNA vaccines are basically just: • take out most of the steps • change the payload • substitute one of the ingredients to trick the immune system. If you said CRISPR, I'd agree – but we do know enough for mRNA vaccines. To use a CS analogy, mRNA vaccines aren't Turing-complete, but CRISPR is. We understand both fairly well, but the implications of mRNA are much simpler than the vast, vast, vast implications of CRISPR.
  - what_is_orcas 5y ago
    I'm curious why you question CRISPR. I've worked with CRISPR; I've seen some very unexpected results from its use; I've also not really kept up with the science in the past few years. Do you have experience working with CRISPR? Is there a study or set of studies that concerns you, or is it the reality that negative results don't get really get published?
    - tazjin 5y ago
      There's nothing in the comment that "questions" CRISPR, it's just pointing out that due to the larger space of possibilities more care needs to be taken with it.
      - what_is_orcas 5y ago
        I interpreted the comments about CRISPR in the parent comment to be more or less cautionary, and I used "question" as a way to say "not sure about the benefits". Sorry if I was unclear, I will work harder on my communication.
    - 5y ago
beckerdo 5y ago
A fascinating article. David Quammen's book "The Tangled Tree: A Radical History of Life" also has stories how DNA changes through more mechanisms than just mutation.
umvi 5y ago
Maybe we should use the word "use unknown" instead of "useless" when dealing with things we don't fully understand. History has humbled us countless times. I recall a recent Veritasium video wherein famous mathematicians of centuries past labelled the concept of negative numbers "useless" (because they didn't understand how they could be useful). My high school bio teacher confidently claimed that the appendix was a "useless organ".
- bruce343434 5y ago
  The video in question, for those curious: https://www.youtube.com/watch?v=cUzklzVXJwo https://www.youtube.com/watch?v=cUzklzVXJwo
- gus_massa 5y ago
  I agree, but note that the title of the research article is "Microchromosomes are building blocks of bird, reptile, and mammal chromosomes".
- ConcernedCoder 5y ago
  It is difficult to imagine a system of evolution where "useless" survives in successful iterations.
  - enkid 5y ago
    Certainly there are thing that formerly had a use but are less useful now. I'd be careful calling something useless, but if there isn't an advantage to getting rid of a feature, I see no reason it would be gotten rid of.
  - epistasis 5y ago
    Your point of view in evolution is called Adaptionism, but there are those who believe otherwise, and use the term "spandrel" to talk about the "useless" things that evolution carries along. https://en.m.wikipedia.org/wiki/Spandrel_(biology) https://en.m.wikipedia.org/wiki/Spandrel_(biology) Of course, something that is currently useless may become useful as the environment changes. Or it may not. Personally, I find a healthy sense of detachment from purpose, and certainly from any sort of teleology, is necessary to become philosophically consistent with the evidence from evolutionary biology.
deleted 5y ago
[deleted]
mcbishop 5y ago
> The exception is the platypus, which has several chromosome sections line up with microchromosomes... Even at this level, the platypus is a strange creature.
- feoren 5y ago
  One really has to wonder if we're all missing something with the platypus. Did some extremely unlikely gene transfer happen at a scale, and across taxonomic distances, that nobody has ever thought possible? There is some N where repeating the argument "it's just a quirk that they're so different" N different times starts to not feel like the simplest explanation any more. Are we absolutely certain there's no way a frisky duck-oid forced itself on an unlucky shrew-oid and in a one-in-a-billion stars-aligning miracle, managed to produce a viable offspring? (Edit: I guess they'd have to produce at least two ...)
  - pmcarlton 5y ago
    > Are we absolutely certain there's no way a frisky duck-oid forced itself on an unlucky shrew-oid and in a one-in-a-billion stars-aligning miracle, managed to produce a viable offspring? Yes.
  - antifa 5y ago
    The playpus is basically an early fork of the tree before placentas and marsupials, and the entire commit tree is squashed under Antarctica, which use to be a life filled continent connecting Australia to South America. https://youtu.be/rQRDc2SKw2I https://youtu.be/rQRDc2SKw2I
  - throwamon 5y ago
    Nah, this should be easily verifiable by simply comparing the DNA of a platypus to that of a bird. I haven't done that, but I bet I know how it would turn out.
  - mcbishop 5y ago
    Sometimes different (but related) species can reproduce... sometimes the offspring aren't sterile. Your comment makes me wonder what two most-different species have done this.
IAmGraydon 5y ago
I understand some of these words. Can someone explain this in layman’s terms?
- Doxin 5y ago
  Not a scientist so I may be wrong in places, but here goes: A chromosome is DNA folded up. What was previously thought to be specks of dust on a microscope slide turns out to be very small chromosomes. Their function is unclear. Between many birds and reptiles these microchromosomes seem to line up with the normal chromosomes fairly well. The difference is relatively speaking fairly small. In mammals however these microchromosomes are much more jumbled. These microchromosomes cluster together in the center of a cells nucleus. This means they physically interact. They touch. Now what this all means is as of yet not entirely clear. They most likely have some important function since they got preserved very well along evolution. Mammals however did something weird to these microchromosomes for unknown reasons.
greatjack613 5y ago
Ha, I though this was an article on useless crypto - https://uselesscrypto.com https://uselesscrypto.com since my skim reading of the title came up with Useless + building blocks. Little did I know.......
sydthrowaway 5y ago
The spice melange
rapjr9 5y ago
Someone should train an AI to find all the assumptions ("useless specks of dust") made in science. Then they should all be checked. Would likely result in a great leap in scientific discovery.

262 points by georgecmu 5y ago

This seems to be another nail in the coffin of "DNA is Code" idea. We do not know how life organises itself. DNA is involved. We have some knowledge. But what we do not know matters much more than what we do know.

ramraj07 5y ago
Blowing out of proportions a bit are we? This is still dna, just in another form elsewhere. And it doesn’t uproot anything, most of the important genes are still in the main chromosomes, we just don’t have the full picture and studies like this help us inch closer towards it.

mrfusion 5y ago

So they’re saying we have chromosomes floating around in our cells? Outside the nucleaus? How do they get replicated?

vaylian 5y ago
The original scientific article says that mammals don't have the microchromosomes. And they are located inside the nucleus in other species.
roflc0ptic 5y ago
They’re saying birds and reptiles and other animals have micro chromosomes, and that mammals have incorporated these micro chromosomes into their macro-chromosomes. Per the Wikipedia page, Micro chromosomes are replicated the same way as other chromosomes - mitosis.

MichaelZuo 5y ago

"Not only are they the same in each species, but they crowd together in the center of the nucleus where they physically interact with each other, suggesting functional coherence," If there truly is some sort of functional interaction going on then this is a very profound observation. As it implies the close spacing is for some kind of mechanical/electrical mechanism within the core of every cell’s nucelus.

0des 5y ago
Surely nobody was under the impression that detail stops at the nucleic level, right? It's small machines and complex systems the entire way down, ad infinitum. Our ability or inability to render or understand these increasingly small systems does not negate their existence.
- vanderZwan 5y ago
  I agree with your general sentiment, but I don't see why we should expect "machines and complex systems" (as related to life) to exist at the level below molecules and atoms. If that was the case then we should expect otherwise identical organic molecules to have differences when they're created by living things and synthesis in the lab (ok, ok, there's chirality and carbon-14, but you get what I mean).
  - 0des 5y ago
    I get what you're trying to say, however this is a flawed assumption right up there with just getting an FTP account, mounting it locally with curlftpfs, and then using SVN or CVS on the mounted filesystem. Time and innovation are both not on your side, in this case. Complex systems are complex and extend far beyond the focal depth of our squinting.
    - WastingMyTime89 5y ago
      Wöhler proved in 1828 that there was nothing special with organic molecules by synthesising urea. I guess you could view molecular formation as a complex system involving atoms and atoms as a complex system involving quarks. That would define chemistry and particle physics as the study of said complex systems which makes sense to me. Still at that level that’s not generally viewed as the study of organisms. What we view as biology, the study of the mechanisms of life, really starts at the molecular level. If you go lower, things stop being specific enough.

est31 5y ago

It's interesting how much variation there is even within mammals when it comes to number of chromosomes, even though so much of the genome is conserved. This points to chromosomes being a major factor on the grander scales of evolution.

gumby 5y ago
> This points to chromosomes being a major factor on the grander scales of evolution. Or, alternatively, that chromosomal-level organization is happenstance. I agree though with your implication that it’s an interesting area of study. Perhaps there is an interesting mechanism to be learned or disproven.
- notTheAuth 5y ago
  Check out bio electrical regeneration research If you haven’t come across it, the teams inject drugs that do nothing to cells but instigate an electrical field effect. What happens is regrowth of a limb to the correct “spec” even though that physical information is gone (limb amputated). This suggests to me an equalizing effect exists, where fields and matter feed each other just enough to reach structural equilibrium. Relativistic information network effects, proving what math objects create which field effects, and the social impacts, are going to become huge and blow away our current engineering goals of making hard silicon computers. We might be able to use nature itself as our CPU.

RyEgswuCsn 5y ago

It's a legacy codebase. The default assumption should be "DO NOT DELETE THIS". Jokes aside, I wonder if we actually know enough to safely meddle with genetic materials, e.g. with mRNAs vaccines.

wizzwizz4 5y ago
mRNA vaccines are barely meddling with genetic materials. We know that lots of viruses are barely harmful; mRNA vaccines are basically just: • take out most of the steps • change the payload • substitute one of the ingredients to trick the immune system. If you said CRISPR, I'd agree – but we do know enough for mRNA vaccines. To use a CS analogy, mRNA vaccines aren't Turing-complete, but CRISPR is. We understand both fairly well, but the implications of mRNA are much simpler than the vast, vast, vast implications of CRISPR.
- what_is_orcas 5y ago
  I'm curious why you question CRISPR. I've worked with CRISPR; I've seen some very unexpected results from its use; I've also not really kept up with the science in the past few years. Do you have experience working with CRISPR? Is there a study or set of studies that concerns you, or is it the reality that negative results don't get really get published?
  - tazjin 5y ago
    There's nothing in the comment that "questions" CRISPR, it's just pointing out that due to the larger space of possibilities more care needs to be taken with it.
    - what_is_orcas 5y ago
      I interpreted the comments about CRISPR in the parent comment to be more or less cautionary, and I used "question" as a way to say "not sure about the benefits". Sorry if I was unclear, I will work harder on my communication.
  - 5y ago

beckerdo 5y ago

A fascinating article. David Quammen's book "The Tangled Tree: A Radical History of Life" also has stories how DNA changes through more mechanisms than just mutation.

umvi 5y ago

Maybe we should use the word "use unknown" instead of "useless" when dealing with things we don't fully understand. History has humbled us countless times. I recall a recent Veritasium video wherein famous mathematicians of centuries past labelled the concept of negative numbers "useless" (because they didn't understand how they could be useful). My high school bio teacher confidently claimed that the appendix was a "useless organ".

bruce343434 5y ago
The video in question, for those curious: https://www.youtube.com/watch?v=cUzklzVXJwo https://www.youtube.com/watch?v=cUzklzVXJwo
gus_massa 5y ago
I agree, but note that the title of the research article is "Microchromosomes are building blocks of bird, reptile, and mammal chromosomes".
ConcernedCoder 5y ago
It is difficult to imagine a system of evolution where "useless" survives in successful iterations.
- enkid 5y ago
  Certainly there are thing that formerly had a use but are less useful now. I'd be careful calling something useless, but if there isn't an advantage to getting rid of a feature, I see no reason it would be gotten rid of.
- epistasis 5y ago
  Your point of view in evolution is called Adaptionism, but there are those who believe otherwise, and use the term "spandrel" to talk about the "useless" things that evolution carries along. https://en.m.wikipedia.org/wiki/Spandrel_(biology) https://en.m.wikipedia.org/wiki/Spandrel_(biology) Of course, something that is currently useless may become useful as the environment changes. Or it may not. Personally, I find a healthy sense of detachment from purpose, and certainly from any sort of teleology, is necessary to become philosophically consistent with the evidence from evolutionary biology.

deleted 5y ago

[deleted]

mcbishop 5y ago

> The exception is the platypus, which has several chromosome sections line up with microchromosomes... Even at this level, the platypus is a strange creature.

feoren 5y ago
One really has to wonder if we're all missing something with the platypus. Did some extremely unlikely gene transfer happen at a scale, and across taxonomic distances, that nobody has ever thought possible? There is some N where repeating the argument "it's just a quirk that they're so different" N different times starts to not feel like the simplest explanation any more. Are we absolutely certain there's no way a frisky duck-oid forced itself on an unlucky shrew-oid and in a one-in-a-billion stars-aligning miracle, managed to produce a viable offspring? (Edit: I guess they'd have to produce at least two ...)
- pmcarlton 5y ago
  > Are we absolutely certain there's no way a frisky duck-oid forced itself on an unlucky shrew-oid and in a one-in-a-billion stars-aligning miracle, managed to produce a viable offspring? Yes.
- antifa 5y ago
  The playpus is basically an early fork of the tree before placentas and marsupials, and the entire commit tree is squashed under Antarctica, which use to be a life filled continent connecting Australia to South America. https://youtu.be/rQRDc2SKw2I https://youtu.be/rQRDc2SKw2I
- throwamon 5y ago
  Nah, this should be easily verifiable by simply comparing the DNA of a platypus to that of a bird. I haven't done that, but I bet I know how it would turn out.
- mcbishop 5y ago
  Sometimes different (but related) species can reproduce... sometimes the offspring aren't sterile. Your comment makes me wonder what two most-different species have done this.

IAmGraydon 5y ago

I understand some of these words. Can someone explain this in layman’s terms?

Doxin 5y ago
Not a scientist so I may be wrong in places, but here goes: A chromosome is DNA folded up. What was previously thought to be specks of dust on a microscope slide turns out to be very small chromosomes. Their function is unclear. Between many birds and reptiles these microchromosomes seem to line up with the normal chromosomes fairly well. The difference is relatively speaking fairly small. In mammals however these microchromosomes are much more jumbled. These microchromosomes cluster together in the center of a cells nucleus. This means they physically interact. They touch. Now what this all means is as of yet not entirely clear. They most likely have some important function since they got preserved very well along evolution. Mammals however did something weird to these microchromosomes for unknown reasons.

greatjack613 5y ago

Ha, I though this was an article on useless crypto - https://uselesscrypto.com https://uselesscrypto.com since my skim reading of the title came up with Useless + building blocks. Little did I know.......

sydthrowaway 5y ago

The spice melange

rapjr9 5y ago

Someone should train an AI to find all the assumptions ("useless specks of dust") made in science. Then they should all be checked. Would likely result in a great leap in scientific discovery.