36 ms·

Formal Systems in Biology

133 points by tablet 6y ago

twic 6y ago
At the end it just says: > Prior Art > Ramón y Cayal > Golgi Those guys did a hell of a lot of stuff, so sure!
fsiefken 6y ago
I was wondering if there was any work in the field of evolving 'creatures' moving in a virtual space, beyond what Karl Sims did 23 years ago. https://www.karlsims.com/evolved-virtual-creatures.html https://www.karlsims.com/evolved-virtual-creatures.html https://www.karlsims.com/galapagos/index.html https://www.karlsims.com/galapagos/index.html It would be nice if Karl Sims could open source it as it is really inspiring visual example in the field of Artificial Life, next to seeing the generations of metuselahs unfolding in Conway's game of life Another interesting article in the field of Artificial Life: https://arxiv.org/pdf/1803.03453.pdf https://arxiv.org/pdf/1803.03453.pdf
- jacobush 6y ago
  Haha, great aptronym. :)
- rzzzt 6y ago
  "Flexible Muscle-Based Locomotion for Bipedal Creatures": https://www.goatstream.com/research/papers/SA2013/ https://www.goatstream.com/research/papers/SA2013/
- newswasboring 6y ago
  Emergent Tool Use from Multi-Agent Interaction[1]. Also these agents lay a claim to being the most god damned cutest things ever. [1]https://openai.com/blog/emergent-tool-use/ https://openai.com/blog/emergent-tool-use/
- flooo 6y ago
  Colleagues in my research group are working on evolving 'creatures' in physical space, e.g. evolvable robots [0]. They address deep questions regarding the interplay between evolution/the body, learning/the brain and the environment using evolutionary algorithms and machine learning. [0] https://www.york.ac.uk/robot-lab/are/ https://www.york.ac.uk/robot-lab/are/
Jhsto 6y ago
Do you think that software should be architected as autonomous agents for it to scale infinitely? I watched an Alan Kay video [1] some time back. In the video, he had an argument about how software systems cannot scale unless the basis is the most complex "computation" system that we know -- that system being our own biological system. [1]: https://www.youtube.com/watch?v=NdSD07U5uBs https://www.youtube.com/watch?v=NdSD07U5uBs
- uoaei 6y ago
  To limit complexity in complex systems design, you need to be able to create agents which perform simple functions based on well-defined inputs. You can have a few different types of those agents interacting, and each should be discrete and be able to "survive" in an adequate "environment". Then the system, if designed correctly, can become much greater than the sum of its parts but you retain the relative simplicity to monkey around with the internals of the agents as well as the reservoirs to which they're attached, etc. Nature has seemed to become a system where iterative improvement is performed by virtue of the finite life cycle and sexual reproduction (including all the ways that DNA shuttles around the necessary source code).
bingerman 6y ago
Looks interesting, gotta take a closer look in the summer. I think it's Stanislaw (Ulam) not Stainslaw.
- qnsi 6y ago
  it should be Stanisław Ulam if we want to be hyper precise :)
ArtWomb 6y ago
A-Life 2020 is virtual this summer (Jul 13-18). For all interested in lifting the veil between its and bits ;) https://vermontcomplexsystems.org/events/ALIFE-2020/ https://vermontcomplexsystems.org/events/ALIFE-2020/
steve_gh 6y ago
Wow - takes me back to my PhD - I think I must have read everything on that list that was published before 2000. Wonderful stuff! Steve
- qnsi 6y ago
  hey Steve, What was your thesis about?
ImaCake 6y ago
I love the neuron simulator linked under McCulloch and Pitts [0]. Very fun to play around with and build your own networks. Reminds me of Conway's Game of Life and Minecraft redstone. 0. https://github.com/prathyvsh/formal-systems-in-biology https://github.com/prathyvsh/formal-systems-in-biology
ulrikrasmussen 6y ago
The first entry on this list is McCulloch-Pitts nerve nets whose expressive power were analysed by S.C. Kleene [1]. In his article he coined the term "regular events" for the class of languages that could be expressed by nerve nets/finite automata, and this is where regular expressions got their name from. If you have ever thought the name was strange, rest assured that Kleene didn't actually like it either, he just couldn't think of something better at the time: > We shall presently describe a class of events which we will call "regular events" (We would welcome any suggestions as to a more descriptive term.*) > [...] > * McCulloch and Pitts use the term "prehensible," introduced rather differently; but since we did not understand their definition, we did not adopt the term. So, had McCulloch and Pitts been a bit clearer in their seminal paper, then maybe it would have been called "prehensible expressions" :). [1] https://www.rand.org/content/dam/rand/pubs/research_memoranda/2008/RM704.pdf https://www.rand.org/content/dam/rand/pubs/research_memorand...
- jchrisa 6y ago
  This stuff got me thinking, if RegExp comes from graphs, why not use it to process graph databases. This paper is about a year old https://arxiv.org/pdf/1904.11653.pdf https://arxiv.org/pdf/1904.11653.pdf Can anyone point to open source implementations?
  - JadeNB 6y ago
    Reminder: please link to arXiv abstract pages, not directly to PDF. Wang, Han, Shao, and Li - Regular expression matching on billion-node graphs; https://arxiv.org/abs/1904.11653 https://arxiv.org/abs/1904.11653
  - uoaei 6y ago
    Is this not how SPARQL or other graph query languages work?
PaulDavisThe1st 6y ago
I'm not sure why, but I feel certain that Ilya Prigogine's work on non-equilibrium systems deserves to be on this list.
- prathyvsh 6y ago
  Thanks for the note! I have added this to research section.
ChefboyOG 6y ago
This maybe a rudimentary question, but if someone was going to study this at a university level, what would they study? I ask because I'm starting my masters in CS, but I've also been going to workshops/events at a local citizen bio lab and really enjoying it. I'd really like to go deeper into the cross-section of CS and Bio, specifically the kinds of things listed in this repo (modeling biological phenomenon as formal systems, using computation to simulate those systems, etc.) But when I look at potential programs to pursue after my CS course, I get a bit lost in all the different titles—bioinformatics, systems biology, computational biology, etc. It's hard for an outsider in the field to discern any meaningful delineation. Does anyone with experience in the field know what category of study these resources would fall under, from a university perspective?
- ljcn 6y ago
  > bioinformatics, systems biology, computational biology Of those bioinformatics is more specific (usually genomics data); the other two are overlapping and pretty non-specific terms. For example I started a Sys Bio PhD and ended up in a Comp Bio research group. A friend started the same way but ended up in control theory/microbiology. The title and even the department are somewhat arbitrary and more to do with the organisation at the university than anything else (e.g. I was in CS but my friend was Engineering I think). If you can find a good interdisciplinary course they will be familiar with people moving around depending on their interests.
- twic 6y ago
  A lot of the stuff in the repo is pretty marginal, from the point of view of mainstream molecular/cell/developmental biology, so i don't think there is a reliable systematic way to find it. In particular, that repo collects what are basically discrete maths approaches to biology: representing living things as systems of symbols rather than differential equations. I have always found that approach intuitively appealing - something about biological robustness meaning you have an opportunity to ignore a load of quantitative details and focus on the underlying structure. But in twenty-five years of being vaguely interested in it, i have never seen a really productive application of that approach, outside of treating DNA as a string of symbols. Still, perhaps 'marginal' is just another way of saying 'cutting-edge'. I think it's most likely to show up in elite research institutes where people can do slightly out-there stuff, or in explicitly cross-disciplinary institutes or programmes. The specific terms you mention have different meanings to me: bioinformatics - treating DNA, RNA, and protein sequences as text and applying computation to them, eg searching, phylogeny, structure and function prediction computational biology - various approaches to simulating cells and tissues, usually involving numerically evaluating differential equations at some level, eg how morphogens cause tissue patterning computational biophysics - computational chemistry but for large biomolecules, eg simulating how proteins work systems biology - smoke and mirrors used to obtain grants But biologists aren't really into rigorous definitions and fixed boundaries, so you might find interesting stuff within any of these.
carapace 6y ago
"What Bodies Think About: Bioelectric Computation Outside the Nervous System" https://www.youtube.com/watch?v=RjD1aLm4Thg https://www.youtube.com/watch?v=RjD1aLm4Thg https://news.ycombinator.com/item?id=18736698 https://news.ycombinator.com/item?id=18736698 and "Team Builds the First Living Robots, Tiny 'xenobots' assembled from cells..." https://www.uvm.edu/uvmnews/news/team-builds-first-living-robots https://www.uvm.edu/uvmnews/news/team-builds-first-living-ro... https://news.ycombinator.com/item?id=22040150 https://news.ycombinator.com/item?id=22040150
- Eugeleo 6y ago
  I LOVE the first talk, I think I discovered it on HN. I study bioinformatics and had no idea something like that existed.
  - carapace 6y ago
    I'd wager it's the most important and most obscure research being done today. Can you imagine being able to regrow a limb!? :-D

133 points by tablet 6y ago

twic 6y ago

At the end it just says: > Prior Art > Ramón y Cayal > Golgi Those guys did a hell of a lot of stuff, so sure!

I was wondering if there was any work in the field of evolving 'creatures' moving in a virtual space, beyond what Karl Sims did 23 years ago. https://www.karlsims.com/evolved-virtual-creatures.html https://www.karlsims.com/evolved-virtual-creatures.html https://www.karlsims.com/galapagos/index.html https://www.karlsims.com/galapagos/index.html It would be nice if Karl Sims could open source it as it is really inspiring visual example in the field of Artificial Life, next to seeing the generations of metuselahs unfolding in Conway's game of life Another interesting article in the field of Artificial Life: https://arxiv.org/pdf/1803.03453.pdf https://arxiv.org/pdf/1803.03453.pdf

jacobush 6y ago
Haha, great aptronym. :)
rzzzt 6y ago
"Flexible Muscle-Based Locomotion for Bipedal Creatures": https://www.goatstream.com/research/papers/SA2013/ https://www.goatstream.com/research/papers/SA2013/
newswasboring 6y ago
Emergent Tool Use from Multi-Agent Interaction[1]. Also these agents lay a claim to being the most god damned cutest things ever. [1]https://openai.com/blog/emergent-tool-use/ https://openai.com/blog/emergent-tool-use/
flooo 6y ago
Colleagues in my research group are working on evolving 'creatures' in physical space, e.g. evolvable robots [0]. They address deep questions regarding the interplay between evolution/the body, learning/the brain and the environment using evolutionary algorithms and machine learning. [0] https://www.york.ac.uk/robot-lab/are/ https://www.york.ac.uk/robot-lab/are/

Jhsto 6y ago

Do you think that software should be architected as autonomous agents for it to scale infinitely? I watched an Alan Kay video [1] some time back. In the video, he had an argument about how software systems cannot scale unless the basis is the most complex "computation" system that we know -- that system being our own biological system. [1]: https://www.youtube.com/watch?v=NdSD07U5uBs https://www.youtube.com/watch?v=NdSD07U5uBs

uoaei 6y ago
To limit complexity in complex systems design, you need to be able to create agents which perform simple functions based on well-defined inputs. You can have a few different types of those agents interacting, and each should be discrete and be able to "survive" in an adequate "environment". Then the system, if designed correctly, can become much greater than the sum of its parts but you retain the relative simplicity to monkey around with the internals of the agents as well as the reservoirs to which they're attached, etc. Nature has seemed to become a system where iterative improvement is performed by virtue of the finite life cycle and sexual reproduction (including all the ways that DNA shuttles around the necessary source code).

bingerman 6y ago

Looks interesting, gotta take a closer look in the summer. I think it's Stanislaw (Ulam) not Stainslaw.

qnsi 6y ago
it should be Stanisław Ulam if we want to be hyper precise :)

ArtWomb 6y ago

A-Life 2020 is virtual this summer (Jul 13-18). For all interested in lifting the veil between its and bits ;) https://vermontcomplexsystems.org/events/ALIFE-2020/ https://vermontcomplexsystems.org/events/ALIFE-2020/

steve_gh 6y ago

Wow - takes me back to my PhD - I think I must have read everything on that list that was published before 2000. Wonderful stuff! Steve

qnsi 6y ago
hey Steve, What was your thesis about?

ImaCake 6y ago

I love the neuron simulator linked under McCulloch and Pitts [0]. Very fun to play around with and build your own networks. Reminds me of Conway's Game of Life and Minecraft redstone. 0. https://github.com/prathyvsh/formal-systems-in-biology https://github.com/prathyvsh/formal-systems-in-biology

ulrikrasmussen 6y ago

The first entry on this list is McCulloch-Pitts nerve nets whose expressive power were analysed by S.C. Kleene [1]. In his article he coined the term "regular events" for the class of languages that could be expressed by nerve nets/finite automata, and this is where regular expressions got their name from. If you have ever thought the name was strange, rest assured that Kleene didn't actually like it either, he just couldn't think of something better at the time: > We shall presently describe a class of events which we will call "regular events" (We would welcome any suggestions as to a more descriptive term.*) > [...] > * McCulloch and Pitts use the term "prehensible," introduced rather differently; but since we did not understand their definition, we did not adopt the term. So, had McCulloch and Pitts been a bit clearer in their seminal paper, then maybe it would have been called "prehensible expressions" :). [1] https://www.rand.org/content/dam/rand/pubs/research_memoranda/2008/RM704.pdf https://www.rand.org/content/dam/rand/pubs/research_memorand...

jchrisa 6y ago
This stuff got me thinking, if RegExp comes from graphs, why not use it to process graph databases. This paper is about a year old https://arxiv.org/pdf/1904.11653.pdf https://arxiv.org/pdf/1904.11653.pdf Can anyone point to open source implementations?
- JadeNB 6y ago
  Reminder: please link to arXiv abstract pages, not directly to PDF. Wang, Han, Shao, and Li - Regular expression matching on billion-node graphs; https://arxiv.org/abs/1904.11653 https://arxiv.org/abs/1904.11653
- uoaei 6y ago
  Is this not how SPARQL or other graph query languages work?

PaulDavisThe1st 6y ago

I'm not sure why, but I feel certain that Ilya Prigogine's work on non-equilibrium systems deserves to be on this list.

prathyvsh 6y ago
Thanks for the note! I have added this to research section.

ChefboyOG 6y ago

This maybe a rudimentary question, but if someone was going to study this at a university level, what would they study? I ask because I'm starting my masters in CS, but I've also been going to workshops/events at a local citizen bio lab and really enjoying it. I'd really like to go deeper into the cross-section of CS and Bio, specifically the kinds of things listed in this repo (modeling biological phenomenon as formal systems, using computation to simulate those systems, etc.) But when I look at potential programs to pursue after my CS course, I get a bit lost in all the different titles—bioinformatics, systems biology, computational biology, etc. It's hard for an outsider in the field to discern any meaningful delineation. Does anyone with experience in the field know what category of study these resources would fall under, from a university perspective?

ljcn 6y ago
> bioinformatics, systems biology, computational biology Of those bioinformatics is more specific (usually genomics data); the other two are overlapping and pretty non-specific terms. For example I started a Sys Bio PhD and ended up in a Comp Bio research group. A friend started the same way but ended up in control theory/microbiology. The title and even the department are somewhat arbitrary and more to do with the organisation at the university than anything else (e.g. I was in CS but my friend was Engineering I think). If you can find a good interdisciplinary course they will be familiar with people moving around depending on their interests.
twic 6y ago
A lot of the stuff in the repo is pretty marginal, from the point of view of mainstream molecular/cell/developmental biology, so i don't think there is a reliable systematic way to find it. In particular, that repo collects what are basically discrete maths approaches to biology: representing living things as systems of symbols rather than differential equations. I have always found that approach intuitively appealing - something about biological robustness meaning you have an opportunity to ignore a load of quantitative details and focus on the underlying structure. But in twenty-five years of being vaguely interested in it, i have never seen a really productive application of that approach, outside of treating DNA as a string of symbols. Still, perhaps 'marginal' is just another way of saying 'cutting-edge'. I think it's most likely to show up in elite research institutes where people can do slightly out-there stuff, or in explicitly cross-disciplinary institutes or programmes. The specific terms you mention have different meanings to me: bioinformatics - treating DNA, RNA, and protein sequences as text and applying computation to them, eg searching, phylogeny, structure and function prediction computational biology - various approaches to simulating cells and tissues, usually involving numerically evaluating differential equations at some level, eg how morphogens cause tissue patterning computational biophysics - computational chemistry but for large biomolecules, eg simulating how proteins work systems biology - smoke and mirrors used to obtain grants But biologists aren't really into rigorous definitions and fixed boundaries, so you might find interesting stuff within any of these.

carapace 6y ago

"What Bodies Think About: Bioelectric Computation Outside the Nervous System" https://www.youtube.com/watch?v=RjD1aLm4Thg https://www.youtube.com/watch?v=RjD1aLm4Thg https://news.ycombinator.com/item?id=18736698 https://news.ycombinator.com/item?id=18736698 and "Team Builds the First Living Robots, Tiny 'xenobots' assembled from cells..." https://www.uvm.edu/uvmnews/news/team-builds-first-living-robots https://www.uvm.edu/uvmnews/news/team-builds-first-living-ro... https://news.ycombinator.com/item?id=22040150 https://news.ycombinator.com/item?id=22040150

Eugeleo 6y ago
I LOVE the first talk, I think I discovered it on HN. I study bioinformatics and had no idea something like that existed.
- carapace 6y ago
  I'd wager it's the most important and most obscure research being done today. Can you imagine being able to regrow a limb!? :-D