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The amount of computational power in biological systems is simply staggering. In extremely simple organisms like roundworms, there are on the order of hundreds

The amount of computational power in biological systems is simply staggering. In extremely simple organisms like roundworms, there are on the order of hundreds of neurons; for most insects you're in the 10k-1M range. A honeybee contains one million neurons, which are computational devices that we have a hard time fully and accurately mapping, and something like a billion connections between them. Each of those neurons contains the entire genome for that honeybee, around 250 million base pairs. Those code for all of the ~thousands of proteins that make up a honeybee - proteins are made up of sequences of amino acids which arrange themselves into shapes with different molecular interaction properties. Figuring out that shape given the amino acid sequence is so computationally difficult that it spawned the Folding@Home project, which is one of the largest collections of computing power in the world. The process of translating from DNA through RNA to a protein is itself substantially harder than it sounds - spend time with a bioinformatics textbook at some point to see some of the features of DNA, such as non-coding regions in the middle of sequences that describe proteins, or sections of RNA which themselves fold into functional forms. None of this is even getting down to the molecular level, where the geometry of the folded proteins allows them to accelerate reactions by millions or trillions of times, allowing processes which would normally operate at geological scales to be usable for something with the lifespan of a bacterium. The most complex systems we've ever devised pale in comparison to even basic biological systems. You need to start to look at macro-scale systems like the internet or global shipping networks before you start to see things that approximate the level of complexity of what you can grow in your garden. Nature builds things, we're playing with toys.

SkyMarshal 6y ago
Do we understand what the fundamental computational operation is in biology yet? Eg, in computers it's boolean logic, transistors with on/off gates, representing true/false or 1/0, from which all other more complex logical operations can be composed. Does biology have an equivalent? Or is your comment essentially explaining that it probably does, but is more complex and we don't understand it yet?
- slicktux 6y ago
  May I recommend the book; On Intelligence Great book on AI approach by understanding the human brain first...
- neatze 6y ago
  In terms of neural computation modeling or in terms of morphogenetic models that are fully distributed, we are not even close, in my non-expert opinion.
- roughly 6y ago
  I'm the Wrong Person to Answer This - I'm a hobbyist and a dilettante, not a scientist, but here's how I understand it: At its core, what you're seeing in all of these steps are molecular interactions - neurons fire to the rate they do because they build up sodium, potassium, or calcium ions; different chemical signaling chains are what prompt the transcription of given genes; charge affinities between the amino acids and with their environment are what create the shapes of proteins and give them their properties and capabilities. Effectively, each atom - each electron on each atom - is affecting these interactions, and that's what's driving the whole system. At the molecular level, the properties of a molecule are (effectively) determined by their structure and charge distribution - the atomic composition of the molecule, where are the electrons likely to congregate, which bonds are stronger or weaker, and where are atoms likely to be able to be added or removed. These affect how the molecule reacts with other molecules, and each reaction that changes either the structure or the charge distribution changes how the molecule will react going forward. So, the computation model is effectively a physical/structural one - how do these structures meet, compare, and combine, played out over trillions of interactions and interaction chains. (I'm consciously ignoring the quantum side, because A) I don't understand it well enough and B) the structure/charge lens seems to be basically sufficient.) It's worth taking a look at some of the cell chemical pathways to see how some of this plays out - take a look at things like the Krebs cycle, which are basically steps of interactions in which a molecule or several are modified step by step in a series of splits, joins, adds, and subtractions that allow for the next step. Part of what makes this tricky is that, while you can "zoom out" and focus on larger systems like neurons or genomes, the molecular interaction model shows up all over the place - neurons fire to the degree they do because of charge accumulation, DNA & RNA transcription are strongly affected by Weird Molecular Interactions, protein folding is at least partially a product of charge affinities, enzymes work as they do because of structure and charges. This is why a lot of these problems are enormously computationally difficult - it's a physical system, not a logical one - there's no way to isolate any layer from any other layer. (I deeply welcome corrections on any of the above, by the way - I've spent time reading on all of this, but I'm not a professional by any stretch. The above is the model I've acquired over time, not reality.)
neatze 6y ago
There is also evidence of Epigenetic Memories, memories that are genetically encoded and passed from generation to generation.
- roughly 6y ago
  So my understanding of epigenetic changes generally is that they're changes in gene expression that last beyond a single cell generation, and sometimes beyond a single organism generation. When people talk about "Epigenetic Memories," they're using a bit of a romantic term for changes in gene expression that last beyond a single generation - for instance, a mother experiences a drought or famine that causes changes that can be detected in her offspring.
  - neatze 6y ago
    This is interesting article; https://www.scientificamerican.com/article/fearful-memories-passed-down/ https://www.scientificamerican.com/article/fearful-memories-... and it is a reason I said some evidence. I am cautions my self not to be romantic about this topic, but at same time neural development is not random structure of cells and arguably brain has predispositions to behaviors. There is possibility that some genetic mutations over single generations are not strictly random, furthermore such genetic mutations specifically evolved over millions of years to introduce changes to environmental pressure. (this is only my speculation of course)
Aperocky 6y ago
The most impressive thing is that every single cell has to carry the entirety of the instruction. And somehow be able to polymorph into something like a human.
- dnautics 6y ago
  > every single cell has to carry the entirety of the instruction. I think it's more impressive that it doesn't. Quite a bit is emergent from stochasticity; the encoded parts are just how to guide the stochasticity correctly. A analogy is building a sierpinski triangle from die rolls and one instruction.
  - Aperocky 6y ago
    Still the same. We regularly compress stuff before sending it out and make programs work in multiple different environments, it could choose to install part of it on this machine and then another part because of some env variables, work almost the same way. But human is one SINGLE program, running in distributed fashion in about 30 TRILLION cell, that make us operate functionally as one single entity. That is what's impressive. What's more organization of those cell is also handled by the program. Of course, the debugging process has not been a nice one.
    - dnautics 6y ago
      That's not true. Your immune system actively randomizes its dna and reprograms itself stocastically, followed by a system of natural selection to pick winners. There is generally speaking not reproducibility, it will not "work almost the same way" between two organisms, given identical input DNA from birth.

SkyMarshal 6y ago

Do we understand what the fundamental computational operation is in biology yet? Eg, in computers it's boolean logic, transistors with on/off gates, representing true/false or 1/0, from which all other more complex logical operations can be composed. Does biology have an equivalent? Or is your comment essentially explaining that it probably does, but is more complex and we don't understand it yet?

slicktux 6y ago
May I recommend the book; On Intelligence Great book on AI approach by understanding the human brain first...
neatze 6y ago
In terms of neural computation modeling or in terms of morphogenetic models that are fully distributed, we are not even close, in my non-expert opinion.
roughly 6y ago
I'm the Wrong Person to Answer This - I'm a hobbyist and a dilettante, not a scientist, but here's how I understand it: At its core, what you're seeing in all of these steps are molecular interactions - neurons fire to the rate they do because they build up sodium, potassium, or calcium ions; different chemical signaling chains are what prompt the transcription of given genes; charge affinities between the amino acids and with their environment are what create the shapes of proteins and give them their properties and capabilities. Effectively, each atom - each electron on each atom - is affecting these interactions, and that's what's driving the whole system. At the molecular level, the properties of a molecule are (effectively) determined by their structure and charge distribution - the atomic composition of the molecule, where are the electrons likely to congregate, which bonds are stronger or weaker, and where are atoms likely to be able to be added or removed. These affect how the molecule reacts with other molecules, and each reaction that changes either the structure or the charge distribution changes how the molecule will react going forward. So, the computation model is effectively a physical/structural one - how do these structures meet, compare, and combine, played out over trillions of interactions and interaction chains. (I'm consciously ignoring the quantum side, because A) I don't understand it well enough and B) the structure/charge lens seems to be basically sufficient.) It's worth taking a look at some of the cell chemical pathways to see how some of this plays out - take a look at things like the Krebs cycle, which are basically steps of interactions in which a molecule or several are modified step by step in a series of splits, joins, adds, and subtractions that allow for the next step. Part of what makes this tricky is that, while you can "zoom out" and focus on larger systems like neurons or genomes, the molecular interaction model shows up all over the place - neurons fire to the degree they do because of charge accumulation, DNA & RNA transcription are strongly affected by Weird Molecular Interactions, protein folding is at least partially a product of charge affinities, enzymes work as they do because of structure and charges. This is why a lot of these problems are enormously computationally difficult - it's a physical system, not a logical one - there's no way to isolate any layer from any other layer. (I deeply welcome corrections on any of the above, by the way - I've spent time reading on all of this, but I'm not a professional by any stretch. The above is the model I've acquired over time, not reality.)

neatze 6y ago

There is also evidence of Epigenetic Memories, memories that are genetically encoded and passed from generation to generation.

roughly 6y ago
So my understanding of epigenetic changes generally is that they're changes in gene expression that last beyond a single cell generation, and sometimes beyond a single organism generation. When people talk about "Epigenetic Memories," they're using a bit of a romantic term for changes in gene expression that last beyond a single generation - for instance, a mother experiences a drought or famine that causes changes that can be detected in her offspring.
- neatze 6y ago
  This is interesting article; https://www.scientificamerican.com/article/fearful-memories-passed-down/ https://www.scientificamerican.com/article/fearful-memories-... and it is a reason I said some evidence. I am cautions my self not to be romantic about this topic, but at same time neural development is not random structure of cells and arguably brain has predispositions to behaviors. There is possibility that some genetic mutations over single generations are not strictly random, furthermore such genetic mutations specifically evolved over millions of years to introduce changes to environmental pressure. (this is only my speculation of course)

Aperocky 6y ago

The most impressive thing is that every single cell has to carry the entirety of the instruction. And somehow be able to polymorph into something like a human.

dnautics 6y ago
> every single cell has to carry the entirety of the instruction. I think it's more impressive that it doesn't. Quite a bit is emergent from stochasticity; the encoded parts are just how to guide the stochasticity correctly. A analogy is building a sierpinski triangle from die rolls and one instruction.
- Aperocky 6y ago
  Still the same. We regularly compress stuff before sending it out and make programs work in multiple different environments, it could choose to install part of it on this machine and then another part because of some env variables, work almost the same way. But human is one SINGLE program, running in distributed fashion in about 30 TRILLION cell, that make us operate functionally as one single entity. That is what's impressive. What's more organization of those cell is also handled by the program. Of course, the debugging process has not been a nice one.
  - dnautics 6y ago
    That's not true. Your immune system actively randomizes its dna and reprograms itself stocastically, followed by a system of natural selection to pick winners. There is generally speaking not reproducibility, it will not "work almost the same way" between two organisms, given identical input DNA from birth.