The baffling intelligence of a single cell: The story of E. coli chemotaxis
jsomers.net
jsomers.net
Part of our problem is the way we think. I am a person. I am not a complex adaptive system. And yet I am. I am made of entities. There is a messaging bus, the entities sense, act and interact. But I don't think of myself as a CAS or talk about We. Wecellfs?
Perhaps this a Sapir-Whorf thing. Our language limits what we can think. What is the difference between a pile of ants and an ant colony? A colony is collection of entities, but what do we call the entity that is the colony? Are the ants smart or is the colony smart.
Individuals are smart, committees are dumb.
Fundamental particles must be geniuses.
But a human isn't a bunch of individual cells, it is a cell that cloned itself many times. Those cells all have the same base code and can thus become an intelligent committee.
We're trading depth for breadth, or something like that.
10 genius clones would still take on various roles/positions in the system, requiring some optimization with respect to alignment under time/energy constraints.
Your adaptive system has a very complex model of the environment. You can model yourself as an agent in the environment, and you identify as parts of that agent. I say “parts,” because there is a ton of thinking and actions that your adaptive system performs which you do not identify as you.
I agree that, in general, we humans, downgrade the importance of external stimulus and interactions with our environment (including other people). My two cents is that this is downplayed where we live in cities and don't move too much, once you move to very distanct places and cultures (and not assuming yours is the best one) more things tick in the brain.
that said, based on the status quo we definitely don't spend enough resources on making sure we can peacefully and sustainably live next to others.
Also, I think you are talking about the corpus callosum for the 'bus' right?
Only when it comes to "left/right side analytical/creative" split, and even that mainly based in a single 2013 study, which could have all kinds of issues. Not regarding different functions in general.
Basically LSD.
It feels so weird to just... I don't know, have a different personality for a while. And when your normal self clicks back it's so relieving.
This made me appreciate what a miracle it is that my brain is fully working most of the time, and realize what a horrible disease dementia is.
How else could it be? At some level, it would inevitably be a top-level aggregation "creating a unity that doesn't really exist". The alternative would be for the whole brain to be a single elementary particle!
As described in Marvin Minsky's fascinating book "Society of Mind" ...
Complex adaptive systems can be nested. Human families, communities, societies, governments all form greater gestalts in which humans, themselves complex adaptive system are a part of.
I am a collector of theories of consciousness :) assuming your quote above is making reference to the "scale" at which "self" is understood, you might be interested in this theory:
Information Closure Theory of Consciousness (2020) https://www.researchgate.net/publication/342956066_Informati...
This reddit comment sums it up better than the paper seems to be able to: https://www.reddit.com/r/MachineLearning/comments/dco3t1/com...
> Consciousness (at least, consciousness(es) that we are familiar with) seems to occur at a certain scale. Conscious states doesn't seem to significantly covary with noisy schocastic activities of individual cells and such; rather it seems to covary at with macro-level patterns and activities emerging from a population of neurons and stuffs. We are not aware of how we precisely process information (like segmenting images, detecting faces, recognizing speeches), or perform actions (like precise motor controls and everything). We are aware of things at a much higher scale. However, consciousness doesn't seem to exist at an overly macro-level scale either (like, for example, we won't think that USA is conscious).
However I would like to mention that sometimes we do think so, as in "the will of the party", at least in some language's context.
Fun fact, when I tried to find similar sentence like "the will of Democratic/Republican Party", google returns 5 results for the former but followed by voters/members and thus not what I want, for the latter, there is no results at all. But as I find "the will of the party", I find an abstract of some paper from my area.
Maybe party is too small for this. It seems like "the will of the nation" is widely used.
[1] https://www.amazon.com/Song-Cell-Exploration-Medicine-Human/...
- The emperor of all maladies - about cancer research, for which he got a Pulitzer
- The gene - about the evolution of the field and the discoveries and what is the latest thinking
Amen. You could easily teach quite intricate biology in grade school, if you focused on a fascinating example or two. How many more people would be inspired, rather than bored?
> I discovered a very strange phenomenon: I could ask a question, which the students would answer immediately. But the next time I would ask the question – the same subject, and the same question, as far as I could tell – they couldn’t answer it at all!
> Then I say, “The main purpose of my talk is to demonstrate to you that no science is being taught in Brazil!”
But each test had one or two questions where you had to put together the knowledge, not just regurgitate, and that student consistently failed those question on each and every test.
Yet the student got top scores on each and every test, because the accumulated number of points was enough to get them into the top bracket.
I was so annoyed with that, asking the teacher how they could get top scores while clearly demonstrating they didn't understand the subject matter. Of course, all in vain.
edit: Great read BTW
For example, do you think we should encourage students to study for tests, or should we encourage them to just show up? After all, if you understand it intuitively why would you need to study the night before?
Also, the act of testing changes the students being measured. As does the existence of a test in the future.
Biology is just astoundingly complicated, especially micro-bio.
Lets look at the 'Central Dogma' of biology as a point to focus on a bit. It's the idea of 'information' transfer. DNA gets decoded into RNA which then gets decoded into Protiens, right? Easy peasy little discussion. You go into how DNA works a bit, it's structure, it's functions. Then you go a bit more into RNA and the various sub types, how the decoding proteins work, Slicer and Dicer, etc. You then talk about how three letter codons work to make amino acids, how you transport the mRNA out of the nucleus, etc. At each step you take a look at how the thing works and you mention some other launching off points for more research if the kids are interested. This is how a lot of education works, things like cooking, math, history, etc.
Except nearly none of what I just said about the 'Central Dogma' is considered true anymore. Sure, some of it is, but the vast majority of how proteins get made is not encompassed in it. Nearly the entirety of modern micro-biology is all about the 'exceptions' to the 'Central Dogma'. So much so that you can't really even say that there is any appreciable difference between RNA and proteins anymore. Every week, and I am not joking here, there is at least one new paper detailing some hybrid mess of RNA and proteins that has critical importance in how we understand how even the most common parts of a cell works. It's to the point that I would not call the 'Central Dogma' and outright lie, but more of a useful fiction.
Like saying that a 'for loop' is how the internet works. Yes, there are 'for loops' in the internet, yes they are critical, yes, you need to learn about them. But no, you cannot teach someone about the internet via a fascinating example or two about 'for loops'.
Understanding biology is Hard, it is the end result of 4+ billion years of literal life and death. It is not something that can be done in a few examples. Even an understanding at a 12 grade level does in fact take a full school year to get to, and even then, it's just the barest launching point into the wider field. The OP s wrong. Full Stop. You do need to learn the names of these things, you do need to get down and do the work of learning all the facts, you do need to fill your brain with these things that are going to affect you as the world gets more and more complicated, you do need to connect this incredibly vast amount of information together. It is going to affect you or the ones you love.
Edutaiment is not the way forward here. Hard work is.
> You do need to learn the names of these things, you do need to get down and do the work of learning all the facts, you do need to fill your brain with these things that are going to affect you as the world gets more and more complicated, you do need to connect this incredibly vast amount of information together. It is going to affect you or the ones you love.
Do you mean molecular biology instead, which includes the study of central dogma?
(That's a common terminology hiccup, lots of people get this wrong)
The only really important detail that wasn't in the original dogma is reverse transcriptase, and they added a dotted line to support that once it was found in physical form.
My own research centered on one subset of functions within E. coli. I was lucky that I found a carefully engineered subset of plasmids and adaptions of E.coli, that could be mathematically modelled [2] [3]. I didn't have to know the whole functioning of E. coli. I didn't have to use mathematics beyond algebra. That is, no calculus was needed. The key task was to put together the quantitative research of about half a dozen labs. Okay, I had a "mountain" of articles to read. And it took 5 years of effort. But it was only doable, because I was modelling a carefully constrained subset of cellular functions.
But of course, every neuron in the brain is bafflingly complex and we still don't know or understand how that complexity manifests itself in thought and intelligence. Given physics and the interactions of "things", every cell in the brain is more complex than the LLMs we're using today. Not to say that every cell is capable of producing the same output as an LLM of course, just that the behavior that it contributes to the overall system is that complex.
Indeed.
Biophysics of Computation: Information Processing in Single Neurons challenges this notion, using richly detailed experimental and theoretical findings from cellular biophysics to explain the repertoire of computational functions available to single neurons. The author shows how individual nerve cells can multiply, integrate, or delay synaptic inputs and how information can be encoded in the voltage across the membrane, in the intracellular calcium concentration, or in the timing of individual spikes: https://www.amazon.com/Biophysics-Computation-Information-Co...
- In the example case of a CNN, the total weights of a kernel is of [Input Number of Channels * Input Kernel Size * Number of Filters], which can be a pretty small amount when it comes to for example a 3x3 kernel with 3 channels with 128 filters coming to a total of 3,456 parameters (3 * 3 * 3 * 128), however in the case of an ANN the same filter is strided across the entire 2D input feature map (or 3D for 3D CNNs). If the input image is of HD resolution of 1280 * 720 and the stride is 2 across both dimensions, then the number of strides is 230,400. The effective number of parameter activations is 796,262,400 (3,456 * 230,400). The reason for this example is that it is sort of a known thing for likely decades now that CNNs are inspired in part by the human visual cortex [0]. For the human visual cortex which needs to be fast, there cannot be parameter sharing across a single kernel, and likely the weights would need to be parallelized to an extent, which would theoretically imply duplicating the weights across the human brain. Thus, the advantage out here lies with ANNs.
- The neurons in the human brain would have to have a certain level of redundancy in place due to the constant cellular repair work.
- The neurons in the human brain can seemingly only be updated by Hebbian learning rather than direct updates which is in the case of the computer memory of ANNs.
- Finally, a significant part of the human brain is for non-logical but environmental reasons, such as movement and touch, and non-logical things such as fear, jealousy, lust, etc; parts which ANNs do not need to possess in the same way (eg: the fight-or-flight response of the amygdala part of the brain).
Instead of thinking in terms of a discontinuity between animals or putting humans categorically different, Bonner builds this idea of a continuum instead for both culture and learning. Of course there are differences,
https://press.princeton.edu/books/paperback/9780691023731/th...
This post of course goes deep in the rabbit hole so to speak.
[1] https://www.amazon.com/Biophysics-Computation-Information-Co...
"Quantitative modeling of bacterial chemotaxis: Signal amplification and accurate adaptation, Yuhai Tu"
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3737589/
The main points are:
* Both receptor cooperativity and accurate adaptation can be described quantitatively by simple mathematical models.
* An integrated model (the “standard model”), which contains both signal amplification and adaptation, is developed to predict responses of it E. coli cells to any time-dependent stimuli quantitatively.
* Exponential ramps induce activity shifts, which depend on the ramp rate through the methylation rate function F(a).
* Responses to oscillatory signals reveal that E. coli computes time-derivative in the low-frequency regime.
* E. coli memorizes the logarithm of the ligand concentration and the Weber-Fetcher law holds in E. coli chemotaxis.
It also goes into cooperative phase transitions in the receptor complexes as a means of signal amplification, using the same model as in Ising ferromagnetic spin-spin interactions in physics.
How close are we to being able to make a map of all atoms within a cell? There are 1E23 atoms in 1 ml of water, and an ecoli is about 500nmx500nmx1um. That means there are only about 2E10 atoms in the whole cell!
Would it be possible to somehow freeze a whole cell, then use an electron beam to knock off and identify (via mass) every atom there?
It’s stupid expensive though, and you can only really identify whole proteins. But you can do that in context, which is massive
And the scale invariance of nature is clearly visible here. The cell is "small" compared to human scale but it is as complicated as any machine existing in human scale. There is no absolute small or big in nature.
Also scale is subject to physical limitations. Bones can only carry that much weight - chemical processes are limited by - for example - maximum energy dissipation rate.
And the "in silico" experiments are probably a bit of a sleeper for people outside the field. It is really obvious how improvements in computing power will have/had a transformative impact on this field. To go from poking out random molecules and growing dangerous things in a pitri dish to fast computer simulations from DNA seems like quite a big jump in how quickly the field can learn.
there's also an absolute big, known in cosmology, far beyond the scales of galaxies, galaxy clusters, etc... it's your mom
The first is cell specialization, particularly neurons. It seems like nature really came up with a universal neuron. There aren't neurons for eyesight vs thinking, etc. They've experimented with this on frogs where they've reweired the optic nerve to a different part ofd the brain and the frog seems to see just fine. They've even added an eye and the frog seems to cope and use it just fine.
The second is the OpenWorm project [1]. This is an attempt to simulate a relatively simple organism with IIRC ~280 neurons. Despite lots of effort, the simulated version just doesn't match up to the real thing. In artificial neural networks we have a stupidly simplified model of neurons that tends to get reduced to a binary signal and an activation function. Thius can do a lot but it's clearly wholly inadequate for any realistic modelling. The protein interactions in a cell are mind-bogglingly complex.
The third is the three-body problem. To summarize, we have a general solution for the grvity interactions of two bodies. Add one more and we don't. We have classes of solutions but no general solution. This is why JPL needs to use supercomputers to calculate flight plans with a relatively low number of bodies. We see a relatively simple set of interactions lead to massive complexity with protein folding. I imagine that it just won't be computationally viable to simulate even a single realistic cell given all th einteractions that go on. We're simply left to make estimations.
> We don’t yet have the technology to just observe all of the activity inside a living cell. That Goodsell painting above that shows the crowded cytoplasm packed with proteins is an artistic composite—backed by rigorous research to be sure—because there’s no way to capture all the different players in situ at once.
> A group at University of Illinois at Urbana-Champagne uses atomic-scale molecular dynamics simulations, in software, to understand structural details
> It’s a world that’s hard to see; sometimes you just have to imagine what’s going on down there, and back up those imaginings with the right experiments.
> One reason I’m particularly attracted to studies of E. coli chemotaxis is that it’s an early star of what’s been called “in silico” biology. It’s been the subject of many computer models.
Honest, at least.
If I knock up something in excel, and other people use that thinking it is how things are, but do not refer to the reality the model represents because there is no way to do that, how useful is the model?
Have you ever looked at old medieval beastiaries? Information is being relayed, but how useful is it?
https://alexanderadamsart.wordpress.com/2019/07/30/the-besti...
Without a means to view the underlying thing the model is meant to represent, to check and correct one's misunderstandings, how useful can the model be?
you are mixing up models and simulations. A simulation can be a great way of exploring something unknown if you understand the rules in enough granularity. Models can be judged by their ability to make accurate predictions. Electrical engineering depends on both a great deal, I expect you agree that it is useful as a field given the method of communication we're using.
For chemotaxis, while they can't observe the underlying processes directly, they result in phenomena that are observable, which can be compared with the same phenomena predicted by simulations and models (the same is true of all scientific fields).
I guess 'naming things' isn't just hard in CompSci.
So I believe intelligence arises from the cells and is an essential function of life, not only an emergent phenomena. The organs serve as division of labor amongst the cells in community for what they are already originally capable of themselves.
More musings in this direction https://sites.google.com/site/pablomayrgundter/mind
Kinda felt similar to the cell comms. I wonder what interesting distributed coordination ideas we could learn in distributed systems computing from cellular biology.
A person is billions of billions of more effective cells than an E.coli cell: still our sense of smell, drive and memory do not seem to be billions of billions times more efficient.
Or did you understand that and were wondering if we'd ever coopt the bodies mechanisms to create familiar logic gate based compute? Personally I doubt that we'd use already familiar transistors because the process requires ultra pure materials that are modified in very thin layers using gasses to scrape or place individual layers, but maybe we'd find a mechanical analogue expressible via protein, or at that point use purpose built neurons instead.
In order to evolve such a system all you need is for the separate components to be useful. A cell laying still and multiplying is useful enough, so that is the baseline. Then adding a flagella to move randomly so it can move away from its waste product and keep hitting new nutrients is also useful. From there it can start to detect waste and move when it is near waste and stop moving when it is near food. Then yo just continue such steps, not very hard to imagine compared to imagining macro evolution.
In your case, why would a flagella be useful if it's not propelling something? A flagella is only useful as a component of something, but not by itself.
I suspect the answer is that having flagella without a nose is still better than having no flagella. If so it suggests evolution isn't good at accessing groups of mutations that aren't individually beneficial.
It produces shitty flagellum, better flagellum, good flagellum.
But the problem is we don't see the intermediate forms. So right now you might see a complicated flagellum that has a lot of highly specialized parts that all need eachother, but that is merely a refinement that took place after all the pieces were already there. Like once an arch is complete, all the scaffolding that was holding it up is now vestigial and if it is removed the arch will remain standing.
That's the thing. Evolution isn't "survival of the fittest" or even "driven by more efficient anything", evolution is simply; if you die before you pass on your genes, you don't pass on your genes. Over long enough time scales, with large enough populations, with tight enough tolerances and strict enough niches, the system roughly approximates a directed iteration of more efficient parts.
Nothing about evolution prevents carrying forward explicitly negative mutations! Nothing about evolution prevents carrying completely unused functionality and features! Nothing about evolution guarantees monotonically increasing fitness!
The giraffe has a certain nerve that goes from it's brain, all the way down around it's aorta, back up it's neck, to it's tongue. It does this, because in the fish we all evolved from, such a detour was less than a centimeter longer than an "optimal" path, and as each next generation went in different directions, it's just not that big a deal. A few hundred extra calories in development, and rare instances of a negative injury outcome are just not going to get fixed, because evolution is almost never vigilant. Most higher level animals have mating behaviors that explicitly favor "wasted" energy, including the long neck of giraffes! Sexual selection has a stronger influence on most animals than evolutionary pressure.
> Also given the extremely slow process of evolution and the relatively short number of iterations it is infeasible to suggest such a solution
This is silly. The vast majority of the ground work for complex life was developed by single celled organisms that produced a new generation every half hour, there were billions of these little creatures experiencing basically any possible mutation all the time, and a water droplet with a billion short lived single cells is exactly the kind of tight tolerance, competitive atmosphere where evolution is most prominent!
Evolution is not iteration. Evolution is pruning bad branches in your breadth first tree based algorithm.
Evolution is not a slow process, it is an irregular process. The odds of a useful mutation popping up at any given time is low, but once it pops up it's there immediately. Yes, an evolutionary process could never make an iphone, but no is claiming that evolution produced the iphone. The complex systems evolution produces are things where all the changes are individually useful.
Why not? People think in such a short time and amount scale such that we cannot comprehend trillions of cells spending billions of years, iterating. Even a small change can be significant at those scales.
And my (limited) understanding is that changes that are not useful or helpful would get lost.
And additional to that, if an organism has a pump (which it needs to function properly) and that pump suddenly is no pump, it's a very bad flagellum, that organism has a very big problem. It's like if we swapped our arms for wings. Wings are cool, but we wouldn't be able to fly anyway, and we'd have serious problems as humans with no arms and hands.
Cells has many duplicates of pumps, not just one. Switching one of those to a motor to move around the liquids so the pumps can get to new molecules to absorb will be extremely beneficial to the cell, now all pumps are more efficient at just the cost of a single pump.
Yes, but it's less complex, and it in turn evolved from even simpler forms. The point is a single mutation doesn't need to create a working flagellum from scratch, it just needs to make it from what's already available. Flagella are complex structures that did not arise until after a lot of other things had already developed.
> And my (limited) understanding is that changes that are not useful or helpful would get lost.
This misunderstanding again comes from the distinction between the features and the instructions. If a mutation isn't harmful, it doesn't get reverted and in fact will spread throughout a sizeable fraction of the population. The thing is that without evolutionary pressure as more mutations occur, they will eventually break whatever the original mutation did, so the feature it coded will eventually disappear, though it can take a long time and it may change significantly before it does. There are some caveats though - a gene might code for multiple features, or may exist on a part of the DNA where further mutations are suppressed anyway, and thus even though the feature provides no advantage on its own there will still be evolutionary pressure to preserve the gene, and thus a neutral or even a slightly bad mutation might be retained indefinitely.
> And additional to that, if an organism has a pump (which it needs to function properly) and that pump suddenly is no pump, it's a very bad flagellum, that organism has a very big problem. It's like if we swapped our arms for wings. Wings are cool, but we wouldn't be able to fly anyway, and we'd have serious problems as humans with no arms and hands.
In this particular case, cells have many molecular pumps, so converting some to flagella is not a very big problem. The benefits of a shitty flagellum did outweigh the cost of losing some molecular pumps, but this is a very real limitation to what evolution can produce. Humans certainly won't evolve wings naturally without a lot of other changes happening first. But at the same time wings have evolved - in the case of birds their ancestors evolved an extremely efficient respiratory system more than 100 million years before they took flight, which helped them survive the great dying and subsequently take advantage of the oxygen rich Mesozoic era. Among these a mutation for hollow bones aided agility on the ground, among these adaptations for feathers helped with retaining body heat, among these adaptations for lunging their arms forward helped them grab prey, among these adaptations for tree climbing allowed them to become better ambushers, and it was among these that sacrificing some of their arm capabilities for shitty wings was a net gain.
So this isn't exactly 100% true. Quite often the encoding of these things can sit in our DNA not activated and then pop up out of nowhere.
Scishow did an episode on this recently.
But that's the thing, this sort of implies that a complete flagellum can be spontaneously produced because it's useful, which sort of collides with the parent comment on systems evolving by combining previously useful components.
Flagella aren't useful until they are complete. So intermediate forms should be lost, right?
Would this leave us in a scenario where a single combination of several mutations at the same time suddenly gives you a complete, functional flagellum?
I suspect what you're really saying is "Will you still respect me for being a creationist". And the answer is, LOL of course not. Nobody is entitled to have their wacky ideas be respected. A lot of the "free speech" complaints are really demands that other people treat your bullshit with respect, which is an absurd demand.
But if my suspicion above is way off, please tell me. I am curious why anyone would say what you said.
Both are faith based responses to questions we cannot answer any other way. Getting caught up in absolutes thinking your interpretation is the gold standard is a sign of an unrefined critical thinking process.
This is unknown and a quite anthropomorphic view on the universe. Just because we can create things doesn't mean we ourselves were created, even in the way you're talking about in the First Mover argument.
Both are theories about the world. 'Creationism' as a theory really only became pure faith very recently as most specific claims attributable to it have been disproven or better explanations have been found. For a long time it was a perfectly cogent theory.
Not to mention, anything I present as being evidence of intelligence being more able to produce functional complexity than randomness you would reinterpret as "randomness-that-produced-something-that-look-like-intelligence producing functional complexity better than randomness-that-doesnt-look-like-intelligence".
You don't have to take evolution on faith. You can write a computer program that demonstrates that selection among almost-but-not-quite identical entities with heritable properties generates adaptive forms. Many people have.
DNA is real. Reproducing lifeforms are real. We know how they work in some detail. There's no faith required.
Accordingly, if we take a definition of "explain" which does not assume a particular interpretation of the fundamental axiom (as we should, when that axiom is the very thing under debate), my statement is perfectly valid: That actor which we cannot fathom made it so. Thus, it is.
How so? For that to happen you'd need to have the usual "evolution-is-science-and-creationism-is-religion-which-denies-science" stance, no?
There are creationist scientists, there is "creationism-proving", or at the very least allow "creationism-compatible" evidence in science, and so on. Let's reduce it even more, science hasn't been able to disprove Creation.
Believing "God did it" should not invalidate science, wanting to understand more, and actually making experiments. On the contrary, it should encourage it, as it did with many scientists who, in a way, brought us to where we are.
And as other commenters say, your computer program would prove absolutely nothing in the grand scheme of things, primarily because micro-evolution (which can easily be understood as a feature of Creation) does certainly not imply macro-evolution or abiogenesis.
You're trying to package your religion as something which it isn't. Creationism is Christian theology, not science. People know this. On some level, you know this.
It would seem you are not paying attention to what is actually being said.
You're dead wrong about this.
Macro-evolution (what I call evolutionism), on the other hand, has never been scientifically observed, explained, tested, or anything of the sort. It is an attempt at creating a fanciful story of how things came to be by extrapolating back from what we see now in entirely unrigorous, untestable, unobservable ways. It fits much more squarely in the category of History, Mythology, and indeed Theology (aTheology?) than "Science".
Really it boils down to whether you believe the laws of physics we observe now have been constant throughout time. If you do you’re called an evolutionist, if you don’t you’re called a creationist. Neither side has any proof, nor is any proof fundamentally possible.
The point being is, creationists have zero idea why they think 6,000 is some magic number in this case, other than bob said so in a book. But yea, books are written by men and men are liars. Even looking at things like RNA/DNA mutation rates in known species it's pretty damned easy to see that things have been around a whole lot longer than 6k years.
Again, please understand the underlying assumptions you are making when you concoct statements like this. Namely: DNA/RNA started as a single form and has mutated at a constant rate since then. You have no evidence to support that, and I disagree with every component of it.
Also, any guesses on why the 'modern' age is suddenly going in slow motion. Not exactly sure how you're going to pull that off without breaking chemistry completely.
And I'm not sure why you think the almighty creator of the universe would have trouble making chemistry... "work".
(Funnily, physics have come to acknowledge the same, but they call it dark matter and say it’s all very scientific, whatever it is. But this is unknown enough to be not worth much discussion.)
Regarding the evolution we see around us all the time, I and many creationists besides me have full confidence in the idea that micro-evolution does occur. That there is a stochastic gradient decent process that hones in on time-varying local maxima over generations cannot really be denied. But that provides absolutely no answer to the questions of abiogenesis and speciation en-masse.
I will say all of science is based on faith- the faith that the human mind can perceive the universe as it truly is, using rational thought and experimental data collection. For some reason this really bothers some scientists and they like to treat science as an unquestionable objective truth, but realistically, we can't exclude any number of hypotheses, but merely state them as improbable based on our understanding.
We can certainly say that the observations look like they may have progressed at the rate we expect for the past 13 billion years, but that does nothing to exclude the possibility that around 6,000 years ago some actor we do not understand took 1 week to craft everything we observe now to be precisely how it is.
Reading your final paragraph, I believe we are more aligned than I previously thought. :)
That said, it is very rare that I hear someone describing themselves as Christian who denies the general 7 day creation story. I happen to personally believe it was seven consecutive days^, but I've heard arguments it could have been seven days with an unknown gap in-between each pair.
^ "day" being the most morally-understandable way of describing the intervals at which the creation occurred. Obviously there was no sun or even light at first, so the concept of a day itself is shaky, and I make no claims as to how many cesium-133 transitions may have occurred in that period, or how far light might have travelled in one of them once it was created, or the magnitude of the various fundamental forces' impact on matter in that period, or really anything related to our understanding of how the dynamics we currently observe may have behaved in those intervals.
But how much of the world's resources have been dominated by folks placing their faith in Eru Ilúvatar?
And I'm sure you're aware Tolkien was a devout Catholic, and described his works as fundamentally Catholic?
OTOH, English really needs another word, meaning "like intelligence, but it could be simulated by an analog computer with a good handful of of discrete components".
People tend to underestimated cells just like you do here.
I'm not thinking of simulating the whole cell. And last I heard, a DC full of computers can't fully simulate one sucrose molecule.
And even if you just look at the behavior described in the article that would still require quite a bit of components since you would need to accumulate signals and normalize them and then turn that to oscillating control signals. Computing via chemical processes like cells do makes the computations a lot simpler.
Probably, but I can only respond to the words you write and not your internal thoughts. To me a handful is 10 or less, from fingers, but I guess a handful could also be hundreds like hundreds of rice grains which makes more sense but I haven't seen anyone use handful for more than 10.
One thng I've learned from over a decade of simulating proteins and nucleic acids is that those methods, while mathematically interesting, don't provide useful data given the amount of resources they require. Instead, reduced models (effectively embeddings) and careful statistical methods are much, much more productive.
This article breaks down how the cell behaves down the the molecules. Once each part is pulled apart and examined, where did the 'intelligence' go.
The single cell, looks 'intelligent'. But, when it is all pulled apart we don't find it. It is just chemicals, reactions, physics.
Then, scale that up to multi-cellular organism, then human, its all just mechanistic, chemicals, physics. So where did the intelligence come from? Humans are also just twitching flagella.
This article just makes it a more stark idea, because a single cell appears 'intelligent', but we can pull it apart and examine the constitutive parts, the chemical, molecules.
So there is not much wiggle room for philosophy or souls. It looks intelligent, but look, we can peer under a microscope and don't see the intelligence.
No, just for a single molecule. The cell does a lot more than that. Can read this if you want to learn a bit more.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6194112/
> So there is not much wiggle room for philosophy or souls. It looks intelligent, but look, we can peer under a microscope and don't see the intelligence.
Sure, but we still can't replicate its behavior in a natural environment, just simple lab environments.
Compare with an OS kernel: individual code snippets are useless / meaningless.
Executed by some CPU or VM, each snippet can be seen to modify that machine's state.
Snippets put together may be observed, and understood as implementing some specific algorithm. Again: useless / meaningless in isolation.
Some snippets may be seen to address I/O, and so it may be assumed to be part of a subsystem that controls (or is controlled by) a peripheral device.
Now put all those parts together, and you have an intricate piece of machinery that shows flexible, adaptable, goal-oriented behaviour. Behaves in a 'smart' way (for varying definitions of 'smart').
Where did the intelligence come from? The parts' properties, how they're put together, and their interactions (among themselves & their environment).
As science progresses, I think we'll come to realize it's just that: a matter of scale & how the many parts and variables interact with their environment. No magic (but fascinating & wonderful nonetheless).
All this language is just confusing. In a chemical gradient sense, molds and yeasts solve tough problems all the time, but it's not much more than physics
(Good point and agreed, but who am I to pass up meme potential. ;)
1) It's a poorly defined word that means different things to different people
2) The word "mechanism" perfectly describes what it is
At the end of the day it's just using the detection of food, to switch from "tumble" (try a random direction to find food) to "run" (assume we're near, or in, a patch of food, and move forward to consume more).
But also we're in a context where acknowledging the intelligence of other life forms is pretty radical so distinguishing them as 'lesser' than human would be precisely opposite of the point. The baseline world view is that human intelligence is magically different than other animal intelligences.
It's also seems odd to call it "baffling" when they 100% understand how it works!
dude, I am an analog computer with a good handful of discrete components and I'm definitely intelligent
All it requires is mutations, time and selection pressure.
The Blind Watchmaker is still a good read.
I understand there would be limitations in the lifespan of the monkey and such, but in a hypothetical case, would that work?
So, a better (but still not great) question, would be, if a monkey bangs on keys forever would they ever produce any kind of story at all?
But, that's still not good enough, because evolution is iterative, and would pick out very short stories that worked a bit, and that page kept getting duplicated out to new monkeys who would start typing from the end of that story
Therefore, to attribute such a well-ordered and well-balanced being which has unity to the jumbled hands of innumerable, lifeless, ignorant, aggressive, unconscious, chaotic, blind and deaf natural causes, the blindness and deafness of which increase with their coming together and intermingling among the ways of numberless possibilities, is as unreasonable as accepting innumerable impossibilities all at once. If we leave this impossibility aside and assume that material causes have effects, these effects can only occur through direct contact and touch. However, the contact of natural causes is with the exteriors of living beings. And yet we see that the interiors of such beings (like a Single Cell) , where the hands of material causes can neither reach nor touch, are ten times more delicate, well-ordered and perfect as regards art than their exteriors. Therefore, although tiny animate creatures, on which the hands and organs of material causes can in no way be situated, indeed they cannot touch the creatures’ exteriors all at once even, are more strange and wonderful as regards their art and creation than the largest creatures, to attribute them to those lifeless, unknowing, crude, distant, vast, conflicting, deaf and blind causes can result only from a deafness and blindness compounded to the number of animate beings.(from light of Quran)
The convergent evolution of pitcher plants is an example of this. There are a number of features that evolve to the same functionality in plants, and many of them have to work together to become fully functional. Yet we see in plants separated by vast distances and millions of years of separation that traits that are useless alone encode themselves and then will will have near spontaneous usefulness when some other gene evolves.
The laws of large numbers are not things the human mind really grasps well at all.
In a given teaspoon of ocean water in the top layer, there are millions of bacteria (in soil there can be up to 1 billion). Each one lives for a day or two before it either divides or is consumed, with a handful of mutations at each round of division. So ~200 divisions a year, for three billion years, with selection stochastically whittling out the few good mutations the crop up now and then, in a diversity of changing ecosystems and you end up with where we are today. Oh, and the occasional horizontal gene transfer for extra spice.
Obviously that is a large hand wave -- the numbers above are from today's environment; early on the biotic density was lower. But the large numbers swamp things. The only real mystery is how things initially got started. But again, it is hard to imagine the time scale involved and the wide variety of environments that exist over the time to imagine the happy accident where the first self-replicating molecule just happen in the right environment that was stable enough for long enough for that self replication to gain traction.
Evolution producing a complicated, half non-working, incomprehensible, "everything interacts with everything else in a chaotic and unpredictable to us way", is the EXPECTED outcome.
It's similar to how many big programming projects become spaghetti messes of half integrations and barely functional parts hooked together half-hazardly where every feature relies on a bit of code nobody understands. It's an "iterate on the stuff that works" process, except the machinery inside a cell is way more effective and tolerant of such a regime than our stupidly strict programming languages and computers.
We're still quite far from replicating this kind of tech.
Well, if the Roomba could exchange genetic information with the surrounding population and adapting to a changing environment would give the appearance of intelligence and design.
Creationists can't see the forest for the trees.
Perhaps I’m misunderstanding you, but to me it seems like you have no argument with evolutionists. Your beliefs seem to permit evolution. I think your disagreement is actually with people that see evolution as evidence for atheism.