Electrochemical potential enables dormant spores to integrate enviro signals(science.org)
science.org
Electrochemical potential enables dormant spores to integrate enviro signals
https://www.science.org/doi/10.1126/science.abl7484
47 comments
'integrating' is a complex way of saying 'stuff leaks across a boundary slowly, and eventually when enough has leaked it triggers the spore to wake up'
Yeah, this feels dangerously close to claiming a woman's body is counting the months/days before they deliver a baby.
And, to be fair, I think the actual research was more about modeling how it works. Not claiming that they count, per se.
That is, just because you can model something mathematically, does not mean that the thing being modeled is the same as doing the math. Falling is not the same as calculating an equation, as it were.
And, to be fair, I think the actual research was more about modeling how it works. Not claiming that they count, per se.
That is, just because you can model something mathematically, does not mean that the thing being modeled is the same as doing the math. Falling is not the same as calculating an equation, as it were.
> That is, just because you can model something mathematically, does not mean that the thing being modeled is the same as doing the math. Falling is not the same as calculating an equation, as it were.
Interesting. The other reply to this, along with its subthread, assumes that "calculating" means "calculated using a digital computer".
Does anyone know what I do in my head when I calculate 4 + 4 is 8? Does anyone know what they do in their own head to calculate 4 + 4? Is that process the same as 2 + 2? as 38 + 153?
Interesting. The other reply to this, along with its subthread, assumes that "calculating" means "calculated using a digital computer".
Does anyone know what I do in my head when I calculate 4 + 4 is 8? Does anyone know what they do in their own head to calculate 4 + 4? Is that process the same as 2 + 2? as 38 + 153?
Few people know what happens in a computer to calculate the same. And that it is potentially very different depending on what the instructions are used to do it. :D
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> That is, just because you can model something mathematically, does not mean that the thing being modeled is the same as doing the math. Falling is not the same as calculating an equation, as it were.
This feels like a false dichotomy. The two calculations demonstrate essentially the same function, but one is performed using physical dynamics (the accumulation of something on one side of a boundary) implemented in an analog computer (overcoming an activation potential) and the other using an abstracted representation (program) implemented in a digital computer (transformations via mathematical analysis).
This feels like a false dichotomy. The two calculations demonstrate essentially the same function, but one is performed using physical dynamics (the accumulation of something on one side of a boundary) implemented in an analog computer (overcoming an activation potential) and the other using an abstracted representation (program) implemented in a digital computer (transformations via mathematical analysis).
I wanted to say "but one isn't a calculation, per se. It is a physical process that can be modeled as a calculation."
That said, I don't think I get the point you are driving to. Saying I have 1 apple and you give me another, is very akin to 1 + 1 = 2. Yet, calculating 1 + 1 = 2 in a computer is not "the same" as getting another apple in person. (And that is ignoring all of the data that is thrown away by "1 apple." How many grams/atoms/etc.?)
I grant there is a fun view of reality being a simulation. But even then, there is a difference between simulating something, with all that implies in regards to data you have thrown out, and the thing you are simulating within that simulation. They may be equivalent in some consideration, but I find it a huge stretch to claim they are the same.
That said, I don't think I get the point you are driving to. Saying I have 1 apple and you give me another, is very akin to 1 + 1 = 2. Yet, calculating 1 + 1 = 2 in a computer is not "the same" as getting another apple in person. (And that is ignoring all of the data that is thrown away by "1 apple." How many grams/atoms/etc.?)
I grant there is a fun view of reality being a simulation. But even then, there is a difference between simulating something, with all that implies in regards to data you have thrown out, and the thing you are simulating within that simulation. They may be equivalent in some consideration, but I find it a huge stretch to claim they are the same.
Your comment made me realize a chemical reaction is an analog computer computing every parameter of the chemical reaction at once.
Your comment made me realize the universe is a quantum computer calculating the position of every sub atomic particle in real time.
It might only appear real time from within the simulation.
That is precisely my point...
Indeed.
Your comment prepared me for the experience, but the ball did not drop in my case until taeric's comment (which incidentally missed your point).
To taeric: Anything IS an analog computer of itself. Doing it for real completely bypasses the need to simulate.
Your comment prepared me for the experience, but the ball did not drop in my case until taeric's comment (which incidentally missed your point).
To taeric: Anything IS an analog computer of itself. Doing it for real completely bypasses the need to simulate.
This is the explanation of why the brain is an analog biochemical computer
By this, though, you have to then consider mere half life decay as a calculator. Such that the definition becomes pointless.
> Such that the definition becomes pointless.
This is a subjective, normative claim. As such it doesn't hold much water.
This is a subjective, normative claim. As such it doesn't hold much water.
Analog vs digital computing can do the same thing (in the functionalist sense) even though they are not implemented in the same media nor representation. They exist at two different levels of abstraction, but still represent the same process. Under the tenets of functionalism and related philosophies, this statement is the same as saying that the two computations are the same fundamentally.
Conceivably, I could build a slalom course for balls to roll down hills such that it "computes" a function by giving the answer as the number of balls in a particular bin at the bottom of the hill, given some input configuration of balls at the top of the hill. You could conceivably do this with any well-behaved function over the integers, given the appropriate slalom course. How is setting the slalom course different from writing a computer program?
I am claiming the difference is only in representation and physical implementation (balls in an analog slalom course vs binary numerical program in an electromechanical digital computer).
Physical processes are used to compute things all the time. Have you ever studied an internal combustion engine? Sensors and circuits are physical components that are used to implement feedback loops that determine ("compute") a set point or steady-state phenomenon within the engine. The function of the engine is to run, and it does so with analog computations, free of digital interface.
Do you then say that the engine has not actually computed an appropriate setting given its (physical, analog) programming? If not, then what has it done? One may answer that it has simply fulfilled its physical inevitability via deterministic processes -- but this explanation applies equally to the digital computer as it is still a physical machine performing physical processes to reach an end state.
I've gone through this enough times with myself that I can't see it another way, but if you have an alternative view feel free to share.
Conceivably, I could build a slalom course for balls to roll down hills such that it "computes" a function by giving the answer as the number of balls in a particular bin at the bottom of the hill, given some input configuration of balls at the top of the hill. You could conceivably do this with any well-behaved function over the integers, given the appropriate slalom course. How is setting the slalom course different from writing a computer program?
I am claiming the difference is only in representation and physical implementation (balls in an analog slalom course vs binary numerical program in an electromechanical digital computer).
Physical processes are used to compute things all the time. Have you ever studied an internal combustion engine? Sensors and circuits are physical components that are used to implement feedback loops that determine ("compute") a set point or steady-state phenomenon within the engine. The function of the engine is to run, and it does so with analog computations, free of digital interface.
Do you then say that the engine has not actually computed an appropriate setting given its (physical, analog) programming? If not, then what has it done? One may answer that it has simply fulfilled its physical inevitability via deterministic processes -- but this explanation applies equally to the digital computer as it is still a physical machine performing physical processes to reach an end state.
I've gone through this enough times with myself that I can't see it another way, but if you have an alternative view feel free to share.
My argument is that you can perceive them to do the same things. Even though they are, in fact, doing something else.
And this, in large, rests on your perception ignoring everything else about what happened in the process. When eating my food, did I slowly subtract all of the grams from the input of food that I was given? In a perception of the event? Yes. Would you say that I was slowly counting away at the grams of food? I was never even cognizant of the number of grams, so that is an odd take. Even if an outsider could have been aware of how many grams something is and that I would stand up on finishing. It does not make sense to call that counting, as you are advocating in this thread.
Regarding the brain as a computer. This is an interesting one, as it is classically accepted and appeals heavily to the way we built up the idea of a modern computer. My take is that, if it is a calculator in that sense, it is only calculating on the simulation that it is building of and for itself. And that it is its own self interpretation that allows this view.
And this, in large, rests on your perception ignoring everything else about what happened in the process. When eating my food, did I slowly subtract all of the grams from the input of food that I was given? In a perception of the event? Yes. Would you say that I was slowly counting away at the grams of food? I was never even cognizant of the number of grams, so that is an odd take. Even if an outsider could have been aware of how many grams something is and that I would stand up on finishing. It does not make sense to call that counting, as you are advocating in this thread.
Regarding the brain as a computer. This is an interesting one, as it is classically accepted and appeals heavily to the way we built up the idea of a modern computer. My take is that, if it is a calculator in that sense, it is only calculating on the simulation that it is building of and for itself. And that it is its own self interpretation that allows this view.
> And this, in large, rests on your perception ignoring everything else about what happened in the process.
In statistical learning theory we colloquially refer to this as "averaging over the noise" which is, functionally, a very useful feature for a computing system to have.
> Would you say that I was slowly counting away at the grams of food?
No, I would say that the process of digestion slowly converted molecules of food into molecules of other stuff + heat. But that isn't even the relevant quantity in this instance, instead the relevant quantity is available energy for use in other parts of your body. In this framework both can be said to have been "computed" (there is a lot of information content in physical reality, so there is plenty to spare to represent both quantities through the same process), but I regard it as a failure of imagination to merely assume that I mean to say that counting integers is the same as collecting a quantity of something.
> I was never even cognizant of the number of grams, so that is an odd take.
Why do you need to be cognizant (aware) of something for it to have occurred? That presents as egocentric hubris to me. You will certainly experience something (having more energy to do other stuff) but you shouldn't expect that a priori and any subsequent experience is only incidental. Phenomenological experience is purely receptive, ie, only works with what it can receive.
> It does not make sense to call that counting, as you are advocating in this thread.
I am not calling it "counting", I am calling it "computing". I have been clear and consistent on that. Probably your definition of "computation" conflates the two, but the two are only synonymous in cases of digital computing.
> My take is that, if it is a calculator in that sense, it is only calculating on the simulation that it is building of and for itself.
This is what I mean by "abstract representation". The brain builds up a model of the world, dividing it into self and other. But there are more fundamental operations underpinning that process, and by now it is common parlance in the neurosciences to regard functional neuronal sub-circuits as "computing" things, even though we have no direct access to their inputs nor outputs. "We" as in "self-aware, sentient, cognitive beings with a functional world model" experience the representations which are built up on those more fundamental computations, and simulate the outside world, and that's the closest thing to "digital" computation that can be said to occur in our minds because of the relatively abstract nature of the representations.
In statistical learning theory we colloquially refer to this as "averaging over the noise" which is, functionally, a very useful feature for a computing system to have.
> Would you say that I was slowly counting away at the grams of food?
No, I would say that the process of digestion slowly converted molecules of food into molecules of other stuff + heat. But that isn't even the relevant quantity in this instance, instead the relevant quantity is available energy for use in other parts of your body. In this framework both can be said to have been "computed" (there is a lot of information content in physical reality, so there is plenty to spare to represent both quantities through the same process), but I regard it as a failure of imagination to merely assume that I mean to say that counting integers is the same as collecting a quantity of something.
> I was never even cognizant of the number of grams, so that is an odd take.
Why do you need to be cognizant (aware) of something for it to have occurred? That presents as egocentric hubris to me. You will certainly experience something (having more energy to do other stuff) but you shouldn't expect that a priori and any subsequent experience is only incidental. Phenomenological experience is purely receptive, ie, only works with what it can receive.
> It does not make sense to call that counting, as you are advocating in this thread.
I am not calling it "counting", I am calling it "computing". I have been clear and consistent on that. Probably your definition of "computation" conflates the two, but the two are only synonymous in cases of digital computing.
> My take is that, if it is a calculator in that sense, it is only calculating on the simulation that it is building of and for itself.
This is what I mean by "abstract representation". The brain builds up a model of the world, dividing it into self and other. But there are more fundamental operations underpinning that process, and by now it is common parlance in the neurosciences to regard functional neuronal sub-circuits as "computing" things, even though we have no direct access to their inputs nor outputs. "We" as in "self-aware, sentient, cognitive beings with a functional world model" experience the representations which are built up on those more fundamental computations, and simulate the outside world, and that's the closest thing to "digital" computation that can be said to occur in our minds because of the relatively abstract nature of the representations.
In this, then, we are talking past each other. If you want to define computing as the process of doing something, than I fully agree with you. This thread was hinged on the original headline's wording of it being them "counting" things happening. Is why I asked if you would say a woman's body was counting the months/days. That, I argue, is silly.
If you are merely arguing that we can all be symbolically described, and that a woman's body is computing the baby, I'm fine with that and agree. If you are then arguing that this symbol of a baby is akin to a computation that you can represent somewhere else, and that another process that computes the same symbols is the same. I'm also still fine. I'd still reject that the body is counting or computing in the other representation's terms. But, again, that does not seem to be what you thought we were discussing.
If you are merely arguing that we can all be symbolically described, and that a woman's body is computing the baby, I'm fine with that and agree. If you are then arguing that this symbol of a baby is akin to a computation that you can represent somewhere else, and that another process that computes the same symbols is the same. I'm also still fine. I'd still reject that the body is counting or computing in the other representation's terms. But, again, that does not seem to be what you thought we were discussing.
Article mentions "short nutrient pulses result in step-like changes" which implies a discrete event, not like continuous leakage.
I wonder about distribution of the sizes of those pulses.
If all the pulses are basically the same size, then a trigger over the total is indistinguishable from "counting" the number of pulses.
Otherwise, yeah it's not really like "counting" at all.
I wonder about distribution of the sizes of those pulses.
If all the pulses are basically the same size, then a trigger over the total is indistinguishable from "counting" the number of pulses.
Otherwise, yeah it's not really like "counting" at all.
I'm pretty sure (having read the same two paragraphs as anyone else) that the pulses were caused artificially in the experiment. The pulses let them demonstrate that the spores can passively soak up potassium to a certain threshold, then activate. The interesting part being that the process doesn't cost the spore energy.
This is more like measurement than counting, imho. Something of an osmotic thermostat, ionostat perhaps.
This is more like measurement than counting, imho. Something of an osmotic thermostat, ionostat perhaps.
Stuff leaks across the boundary in a stimulus dependent manner though. So it's basically setting dStuff / dt = Stimulus. Monitoring stuff-levels then allows it to monitor area under stimulus curve. Quite fascinating if you ask me.
Nothing wrong with that, after all that’s how the good ol’ 555 timer works!
That's in the sense of mathematical integration; e.g. integrating op-amp, etc.
Bacteria count sheep in their sleep. Brilliant!
_Electric_ sheep, even!
This is a beautiful piece of Science! And please ignore those fighting about the title edits..
a strong contender for best headline of the year
To be fair, I took it from the author and did some modifications. I think it was very clear how he described it. https://twitter.com/kaitochondria/status/1578083629334294529...
Thanks for the Twitter thread. That's a more digestible introduction to the paper.
Would be nice to read the whole article
Seems like that is another different article about the paywalled one
Check at the bottom: "More information: Kaito Kikuchi et al, Electrochemical potential enables dormant spores to integrate environmental signals, Science (2022)"
Spore op-amps?
Please change the headline to "Electrochemical potential enables dormant spores to integrate environmental signals" per Hacker News guidelines.
From the guidelines:
> Otherwise please use the original title, unless it is misleading or linkbait; don't editorialize.
From the guidelines:
> Otherwise please use the original title, unless it is misleading or linkbait; don't editorialize.
That's past 80 characters, and I don't really think this is an interesting place to enforce the rules here — did your instincts tell you that HN readers are about to be bait-and-switched by the editorialized title?
Counting is very different from integrating.
Lots of stuff in biology integrates continuous signals. Discrete counting of discrete events is quite rare.
In many senses you can compute with things that count discretely: Peano Arithmetic is undecidable. Yet unbounded dense linear orders (i.e. the theory of the rationals) are decidable, so you can't embed "program X halts" into them.
Lots of stuff in biology integrates continuous signals. Discrete counting of discrete events is quite rare.
In many senses you can compute with things that count discretely: Peano Arithmetic is undecidable. Yet unbounded dense linear orders (i.e. the theory of the rationals) are decidable, so you can't embed "program X halts" into them.
"Dormant spores tally wakeup stimuli via EC potential"?
Full disclosure: an important part of my job is fitting git commit messages to the 50 character rule.
Full disclosure: an important part of my job is fitting git commit messages to the 50 character rule.
So too us and our actions are decisions.
That title is fucked. I prefer the English one.