From Silicon to Cells: Full-Adder Circuits in Biological Computing

[@MrHichammohsen1]

Man the bit with the Buffer 5:00 really got me haha! Amazing work as usual, very much appreciated.

[@kevinknutson4596]

With the quality of your visualizations I couldn't help but think of the popular Zachtronics games and that these kinds of simple systems with their biological quirks would make amazing puzzles. Love your videos!

[@brulsmurf]

This cross-chatter might be a feature and not a bug in natural cells. This way circuits are more like a neural network that can generalize, and will work in a wide range of environments. It also gives evolution dials to rotate instead of coming up with entirely new circuits. I think this flexibility is key if you want to build and adapt complex machines with just flipping a bit here and there in the source code.

[@王沛升]

Ah yes, one of the way i explain Lactose operon and repressor function to my electrical engineer friends. Fun thing about this is that you can make things even more compact by completely abandon the need of protein using DNA codon engineering, hairpin conformation of DNA and RNAi (or other complentary oligo nucleotide). The conformation change of the DNA/RNA shape will block RNA polymerase/ribosome to do its job, and the downstream reaction or product can be observed as the output.

[@tcaDNAp]

Nothing better than a teaser for the next video to keep me thinking about this! 😁

[@CristalMediumBlue]

Hey NanoRooms! Amazing video! You need to make a video addressing the Landauer principle applied to biological computing. There are some amazing connections between information theory and biological computing that you can clarify by explaining the Landauer principle applied to biological information processing.

[@Focke42]

Full adder introduction ends at 3:02

[@AA-gl1dr]

I love this. Thank you so much.

[@markmarketing7365]

Hmmm biocomputing 😋

[@Sazoji]

could you use RNA splicing to overcome the limited logic? it wouldn't be as binary as a transcription factor, but you could make an sRNA network where hairpins knockdown transcription unless a larger sacrificial sequence is present or the folding of the hairpins is disrupted with a complimentary sequence.

[@Fixaah]

Watching this one to watch the new

[@wafikiri_]

This past half-century I've struggled to understand the nature of cognition. I almost got it ten or fifteen years ago, except for a final puzzle's piece I couldn't grasp. But a month ago, that final piece completed the puzzle. My theory of cognition not only applies to nervous systems. It is universal and also explains cognition in other systems, biological or not. Among them, microbes. What's been exposed in this video is part of the set of mechanisms allowing microbial cognition, scarce though it may be, controlling microbial behaviour.

[@Czu895]

I am an incoming freshman in college, I have just began my journey to understanding cognition. By trade I aim to be a software engineer but I am deeply interested in the other STEM fields and particularly the interdisciplinary approach of utilizing concepts from the different fields to solve complex problems. I am interested in hearing about this theory concerning the nature of cognition. Would you be willing to discuss it with me?

[@wafikiri_]

@@Czu895 Well, by nature I'm willing to share. But I also want recognition. Publishing a paper in a prestigious scientific magazine is not easy for me, however: I lack any university degree, haven't worked in any academic institution, haven't published any papers before, my paper wouldn't be reviewed by peers (for I'm peer of no scientist). I know some papers' authors got it, however: Gödel was one of them, he changed our view of mathematics forever. Another, whose name I never learnt, also did that published a short article on genetic altruism and was awarded the Nobel prize. He also changed our view of natural selection. I do not seek a Nobel prize but recognition for solving a major scientific mystery is not too much to aspire to, is it? I can guide you, however: a regular interneuron obtains most of its data from some 10,000 inputs and none of them is generally directly connected to sensory data, to any physical stimulus other than relevant concentrations of chemicals (neuroransmitters, ions); then it feeds its nervous signals to some other 10,000 neurons; and most neurons are interneurons: they all are isolated from the physical world except via nervous signals. So, the question is: what kind of data is so generic yet intrinsically meaningful in such large amounts per single neuron, and yet how the tiny contribution of a single neuron is significant enough to be so widespread? That's what I finally found out six weeks ago. Having some knowledge of mathematical structures helps. Also having philosophical motivation does. And basic knowledge of neuroanatomy and neurophysiology. But chances are it'll take anyone decades (half a century in my case) to hit the pot. So I'm writing a paper (been doing so for decades but the final revelation turns much of it irrelevant). Also, on the hindrances side, my financial status is slowly enhancing but there's many a debt to repay (fifteen years of unpaid unemployment), thus most of my efforts are not poured into the paper but on staying afloat.

[@Jack-tz7wj]

I'd recommend the paper "thermodynamics of evolution and the origin of life" by Vitaly Vanchurin

[@wafikiri_]

@@Jack-tz7wj I understand evolution"s phylogenetic enhancement of thermodynamic efficiency: natural selection uses to favour more efficient systems, cumulatively. And I am deeply aware of the various hypotheses on abiogenesis as well.

[@Jack-tz7wj]

@@wafikiri_ While this does cover that topic it's a formalism to connect these theories not a commentary on how evolution affects thermodynamic efficiency.

[@xitheris1758]

"Is there anything beyond just adding numbers using cells?" Yes. Artificial Intelligence. Or, in this case, Natural Intelligence, the basis of Human Consciousness.

[@alyosha3563]

Great video. More about synthetic biology and biomolecular computation please.

[@Czassadzeniaiczaszbierania]

Nice

[@s.m.sanbim-sifat]

I really hate when people say Biology doesn't have math. Thanks for giving me room to argue.

[@xitheris1758]

Biology, in its truest sense, is a conglomerate of the Layers of Being that are unique to Life. That is, unique to systems that are capable of utilizing free energy gradients to protect themselves against entropic disintegration by acting as entropy pumps. Thus, Biology properly includes all aspects of Life: Physiology, Psychology, Sociology, Economics, and Politics. Ecology is merely Economics in which the network in question is not monospecific. The mechanisms of Politics are in Economics. The mechanisms of Economics are in Sociology. The mechanisms of Sociology are in Psychology. The mechanisms of Psychology are in Physiology. The mechanisms of Physiology are in Chemistry. The mechanisms of Chemistry are in Physics. The mechanisms of Physics are in Mathematics. The mechanisms of Mathematics are in Logic. To claim that Biology doesn't have Math is to claim that Human Beings don't have Physics, nor Chemistry, nor Physiology, nor Psychology, nor that any Human Being is capable of participating in Sociological, Economical, or Political systems. Human Beings are fundamentally made of Math. The dangers of considering oneself above or separate from the "lower" Layers of Being was known to the Ancient Greeks as hubris. Jews and Christians tout that, "Pride cometh before the fall." All long-lasting religions contain the concept. The most recent iteration may be the catchphrase that, "Facts don't care about feelings." I believe that the commonality of this mental and emotional disconnection of the Human Self from more fundamental (and thus robust) Layers of Being - largely due to uncomfortable consequences of their emergent properties - indicates a society in a state of mass psychosis, which is already causing and will continue to cause suffering that is widespread, preventable, and unnecessary. As Human Beings, our roots stretch down beyond the reaches of Biology, through Chemistry, Physics, and Math, ultimately to Logic. We need Logic, as much as trees need water. However, when wealth abounds, survival is easy, and one need not participate honestly in community to ensure survival. In such cases, defection (in the Game Theory sense) becomes beneficial for individuals. Once a critical mass has defected, the game can no longer be played by anyone. All that said, I believe that this idea, that Biology doesn't have Math, is indicative of a more serious problem in our collective ways of thinking. I'll leave it at that.

[@badoem5353]

​​​@@xitheris1758mmh, our need for logic is truly debatable tho, we're pretty hormonal af to. You could say we need a rationalization but like the previous deity-arc makes me doubt that a lot. Or: x let's kill the different acting and looking people ". Conditioned in an echo box but "logical" from that perspective.

[@xitheris1758]

@@badoem5353 Exactly. People want things to make sense, for things to have a logical basis. Whether or not the axioms are valid is a separate matter that resolves itself. Bad axioms lead to bad ideologies - those that are incompatible with human nature and/or the biosphere. Human nature and the biosphere always win in the end. Good ideologies take human nature and the biosphere into account in their axioms. As an example, it's why capitalism (for all its faults) works indefinitely, but communism can't last longer than a few decades. Capitalism includes in its axioms that human nature is inherently corrupt and of limited plasticity. Communism includes in its axioms that human nature is of infinite plasticity and is incidentally corrupt. Communist regimes may start with logical arguments, but they always become increasingly illogical as they face the futility of their attempts - to force infinite change upon nature itself. The same thing happened with the Nazis, but on the opposite end of the political spectrum. If the axioms are invalid, then the argument is illogical, even if the logical deductions themselves are sound.

[@badoem5353]

@@xitheris1758 I honestly think communism has some valid justifiable ideas but we need to reinvent the concept of money for that. Like with the arrival off full automation the living wage checks idea seems more necessary and it could provide a redestribution of wealth. I understand that we are inherently competitive and possesive but in the view of the bigger picture it would provide a bigger net benefit then what's happening now. But change is never easy ofc

[@xitheris1758]

@@badoem5353 I agree that full automation is a serious problem, potentially apocalyptic. However, redistribution of wealth never benefits the poor or needy in the end. For example, all the Covid stimulus ended up in the hands of billionaires, and now inflation is devaluing wages. Universal Basic Income doesn't work because most humans would rather live frugally and not work than live luxuriously and work hard. Once basic needs are met, most people lose motivation to work more. For example, when the Soviet Union collapsed, industries in those countries couldn't compete with Western industries. Soviet workers had their basic needs guaranteed, so they only worked because they were essentially forced to - and they didn't get to choose what work they did. When presented with freedom, they didn't know what to do with it, and because they had been conditioned to despise work, they didn't care to be competitive. Now, older and middle-aged Russians, especially men, are depressed, have no economic prospects, and are drinking themselves to death, while sending their young people to fight a hopeless imperialistic war. Work is good for people. It gives them a sense of dignity that they need to be happy. Freedom is good for people. It gives them the ability to pursue what they enjoy doing. What people enjoy doing and what they're good at doing often don't overlap. Most people will do what they enjoy rather than what they're good at. The amazing thing is that, in the long run, people who do what they enjoy (but aren't good at) are more productive than people who do what they're good at (but don't enjoy). I don't like rich people or what they do, but they'll have their way in any hierarchy - whether capitalist or communist. At least in capitalism, they get rich by making the lives of others better. The current economic system of the West resembles feudalism more than capitalism in many ways. We call ourselves capitalist countries, but we're really not. One thing I can agree with is that feudalism sucks.

[@aniketnarayan6767]

Can you do a booklist video so that we can go in depth