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Whenever morphogenesis comes up, especially with the usual "work from DNA and proteins up" approach, I feel obliged to mention Michael Levin. He also researches

Whenever morphogenesis comes up, especially with the usual "work from DNA and proteins up" approach, I feel obliged to mention Michael Levin. He also researches morphogenesis, except his approach is on a higher abstraction level. He manipulates the electrical network that cells use to communicate with each other to organize their work towards multicellular goals. Do watch his lectures, it's some really fascinating stuff. You don't need to touch genes at all to regrow limbs and organs. Neither do you need to operate on that low level to cure cancer. This whole "let's effect organism-level changes by observing and manipulating DNA and proteins" feels to me like "let's add a feature to a react web app by observing and modifying the behavior of individual transistors in the CPU". Doable given enough time, but you'd drown in complexity in the process. https://www.youtube.com/watch?v=Ed3ioGO7g10 https://www.youtube.com/watch?v=Ed3ioGO7g10

echelon 3y ago
The code is there. It's a timing and signalling problem.
hereallofit 3y ago
Piling on; I emailed Michael Levin during lockdown and he replied with answers to some high level questions and a bit of documentation. Not sure what his pace is like these days but he seems open to sincere attempts at discourse. Let's fund this instead of shitcoins, layers of indirection around POSIX.
_yb2s 3y ago
I think that analogy is very apt- the fact that we have such a hard time understanding and predicting the outcomes of bioengineering/synthetic biology suggests that we are still missing huge parts of the picture of how life works. It seems very likely to me that our views are too reductionist, and the much of the key information isn't even encoded at the level of DNA as previously assumed. The cells multicellular organisms are constructed from are all shockingly similar... "cells" are basically a solved problem for this type of life, and somewhat frozen in their functionality because major changes would disrupt the larger systems that they make up.
- deng 3y ago
  > The cells multicellular organisms are constructed from are all shockingly similar. They are not. They vary greatly in structure and function.
  - _yb2s 3y ago
    What I said was a matter of opinion, I didn't quantify it in any way, so I'm not sure how you can say that, but I will elaborate more so you have something to really disagree with :-) Sure, of course the different multicellular eukaryotes vary, but the diversity is very low compared to what we see across all life, look at Figure 1 here for example [1]. I am looking at it from the perspective of the structure of the metabolic network, as this is my area of research. There is a huge amount of diversity in the fundamental structures of metabolic networks, types of metabolites and enzymes produced, etc. across all life, but from that perspective the differences between one multicellular eukaryote and another are slight in comparison. Multicellular eukaryotes have evolved very different behaviors, shapes, sizes, etc. from a relatively conserved biochemistry. When taken out of the context of an organism in cell culture, the cells are similar enough that their behavior under diverse experimental conditions can be predicted by nearly identical metabolic models, whereas you would see nothing of the sort with distantly related bacteria- the metabolism can be massively rearranged. [1] https://www.nature.com/articles/nmicrobiol201648 https://www.nature.com/articles/nmicrobiol201648
    - deng 3y ago
      You made a broad, almost dismissive generalization from, as it turns out now, a purely macroscopic view. It's like a physicist studying galaxy filaments saying "all galaxies are shockingly similar", because the filaments show more complex structures than individual galaxies.
      - _yb2s 3y ago
        Which is exactly the point- a systems view offers a different perspective than the reductionist view.
dekhn 3y ago
I can't see any way that you could regrow a limb without "touching genes". And Levin doesn't say that in his video. At the very least, limb regrowth would require synthesis of many mRNA and their protein products, under the control of transcription factors.
- grishka 3y ago
  Yes, but you don't do that. The cells themselves do it. You only trigger that mechanism and you do it by opening and closing specific ion channels in specific patterns.
  - deng 3y ago
    The article is specifically about a difference in the mTOR protein, so in the end, a genetic difference. You will not trigger a limb regrowth in humans by opening and closing specific ion channels in our cells.
    - grishka 3y ago
      > You will not trigger a limb regrowth in humans by opening and closing specific ion channels in our cells. Levin's research begs to differ. He did successfully regrow an amputated leg in a frog.
      - deleted 3y ago
        [deleted]
      - dekhn 3y ago
        I seem to think you're interpreting that in a way that is not consistent with our current understanding of limb regrowth. This is the paper: https://www.science.org/doi/10.1126/sciadv.abj2164 https://www.science.org/doi/10.1126/sciadv.abj2164 and it clearly states they treated a frog (xenopus, a common model organism), which does not normally regenerate when it's an adult. The paper clearly states that they treated with a set of factors that they believe induced a developmental plan- implemented by the transcription of DNA, translation of RNA, and expression of proteins. The initial treatment was removed, and the effect continued. Also there's nothing about ion channels in this- the factors they used must have been actively transported- they bind to protein receptors.
joedevon 3y ago
What? Michael Levin? How about Dr. Robert O. Becker? I read about something similar in the 80s. Here's a link to one of his books, The Body Electric: https://a.co/d/fqzpaIv https://a.co/d/fqzpaIv Does Michael credit Becker for any of his work?
- joedevon 3y ago
  Googled. Yes he does! You've made my day! So happy to see someone continuing Becker's work.

echelon 3y ago

The code is there. It's a timing and signalling problem.

hereallofit 3y ago

Piling on; I emailed Michael Levin during lockdown and he replied with answers to some high level questions and a bit of documentation. Not sure what his pace is like these days but he seems open to sincere attempts at discourse. Let's fund this instead of shitcoins, layers of indirection around POSIX.

_yb2s 3y ago

I think that analogy is very apt- the fact that we have such a hard time understanding and predicting the outcomes of bioengineering/synthetic biology suggests that we are still missing huge parts of the picture of how life works. It seems very likely to me that our views are too reductionist, and the much of the key information isn't even encoded at the level of DNA as previously assumed. The cells multicellular organisms are constructed from are all shockingly similar... "cells" are basically a solved problem for this type of life, and somewhat frozen in their functionality because major changes would disrupt the larger systems that they make up.

deng 3y ago
> The cells multicellular organisms are constructed from are all shockingly similar. They are not. They vary greatly in structure and function.
- _yb2s 3y ago
  What I said was a matter of opinion, I didn't quantify it in any way, so I'm not sure how you can say that, but I will elaborate more so you have something to really disagree with :-) Sure, of course the different multicellular eukaryotes vary, but the diversity is very low compared to what we see across all life, look at Figure 1 here for example [1]. I am looking at it from the perspective of the structure of the metabolic network, as this is my area of research. There is a huge amount of diversity in the fundamental structures of metabolic networks, types of metabolites and enzymes produced, etc. across all life, but from that perspective the differences between one multicellular eukaryote and another are slight in comparison. Multicellular eukaryotes have evolved very different behaviors, shapes, sizes, etc. from a relatively conserved biochemistry. When taken out of the context of an organism in cell culture, the cells are similar enough that their behavior under diverse experimental conditions can be predicted by nearly identical metabolic models, whereas you would see nothing of the sort with distantly related bacteria- the metabolism can be massively rearranged. [1] https://www.nature.com/articles/nmicrobiol201648 https://www.nature.com/articles/nmicrobiol201648
  - deng 3y ago
    You made a broad, almost dismissive generalization from, as it turns out now, a purely macroscopic view. It's like a physicist studying galaxy filaments saying "all galaxies are shockingly similar", because the filaments show more complex structures than individual galaxies.
    - _yb2s 3y ago
      Which is exactly the point- a systems view offers a different perspective than the reductionist view.

dekhn 3y ago

I can't see any way that you could regrow a limb without "touching genes". And Levin doesn't say that in his video. At the very least, limb regrowth would require synthesis of many mRNA and their protein products, under the control of transcription factors.

grishka 3y ago
Yes, but you don't do that. The cells themselves do it. You only trigger that mechanism and you do it by opening and closing specific ion channels in specific patterns.
- deng 3y ago
  The article is specifically about a difference in the mTOR protein, so in the end, a genetic difference. You will not trigger a limb regrowth in humans by opening and closing specific ion channels in our cells.
  - grishka 3y ago
    > You will not trigger a limb regrowth in humans by opening and closing specific ion channels in our cells. Levin's research begs to differ. He did successfully regrow an amputated leg in a frog.
    - deleted 3y ago
      [deleted]
    - dekhn 3y ago
      I seem to think you're interpreting that in a way that is not consistent with our current understanding of limb regrowth. This is the paper: https://www.science.org/doi/10.1126/sciadv.abj2164 https://www.science.org/doi/10.1126/sciadv.abj2164 and it clearly states they treated a frog (xenopus, a common model organism), which does not normally regenerate when it's an adult. The paper clearly states that they treated with a set of factors that they believe induced a developmental plan- implemented by the transcription of DNA, translation of RNA, and expression of proteins. The initial treatment was removed, and the effect continued. Also there's nothing about ion channels in this- the factors they used must have been actively transported- they bind to protein receptors.

joedevon 3y ago

What? Michael Levin? How about Dr. Robert O. Becker? I read about something similar in the 80s. Here's a link to one of his books, The Body Electric: https://a.co/d/fqzpaIv https://a.co/d/fqzpaIv Does Michael credit Becker for any of his work?

joedevon 3y ago
Googled. Yes he does! You've made my day! So happy to see someone continuing Becker's work.