What physical ‘life force’ turns biology’s wheels? | Hacker News Reader

What physical ‘life force’ turns biology’s wheels?

quantamagazine.org

227 pointsProf_Sigmund55 comments

Truly mind blowing. A few days ago I found this animation [1] that shows it in motion

[1] https://www.reddit.com/r/educationalgifs/comments/17squg1/ho...

Smarter Every Day on Youtube has a couple of videos on this topic that are worth seeking out, especially if that animation whet your palette.

This one: https://www.youtube.com/watch?v=VPSm9gJkPxU

Imo the explanation is also done better than in the article.

This reminds me of a gem of a comment from about a month back, about a dead simple Russian guidance system from a Cold War-era missile: https://news.ycombinator.com/item?id=47389285

Actually, someone even commented in that thread about how it was similar to biological mechanisms: https://news.ycombinator.com/item?id=47390619

For explorations of simple mechanisms like this leading to complex behaviour, Valentino Braitenberg’s book Vehicles is a classic.

Would it do well on a Kindle or does it rely on illustrations?

Definitely relies on illustrations.

The author passed away 15 years ago so I will mention the PDF of the book shows up in the first few search results on Google.

Thanks!

Seconded. This book enlarged my brain.

Simple spin-scan but with a rolling airframe. The technique is still used today. It is simple only if one looks at individual components. The total package is a different beast.

https://en.wikipedia.org/wiki/RIM-116_Rolling_Airframe_Missi...

Would it not easily get sidetracked by the sun? Like a moth to a flame

Article stopped exactly where stuff got interesting.

This whole "protons entering bacterium and being pumped out" is exactly the ancestor of the mitochondria, that's what it does, except now the "outside" is the inside of the parent cell.

The respiratory complexes - the machines at the core of it all - are absolutely wild bits of natural engineering. Perhaps the most incredible and successful non-trivial natural objects in existence.

This is very similar to mitochondrial respiration with both using an electrochemical gradient of protons, the proton motive force, as an energy source.

Relevant Smarter Every Day video: https://www.youtube.com/watch?v=VPSm9gJkPxU

Stated Clearly also has a great deep dive that I've really enjoyed https://youtube.com/playlist?list=PLInNVsmlBUlSjLSj9yGEKphF0... He actually makes it as a reply to Smarter Every Day.

Holy crap this is a rabbit hole and a half. I know what I’m watching while the robot writes my code tomorrow.

Really nice 3D animations in that video. Something like this, I find quite difficult to comrehend jsut off of a text description.

What I find fascinating is the extreme efficiency of what is effectively an electric motor, reaching nearly 100% efficiency. At human scale we struggle with heat dissipation and friction

But at the same time the motor is extremely finicky/fragile in the source of energy (negentropy) it will accept, while natural life is extremely hardy and adaptable.

I wonder how much of machine-like "efficiency" is actually "overfitting" at the cost of robustness.

That is a fair point to be honest! I guess when you a 20min lifetime you can probably compromise on reliability in favour of extra efficiency

Every race, the engine of a top-fuel dragster only completes about 900 revolutions and then has to be rebuilt! https://www.motortrend.com/features/top-fuel-dragsters

The need to reproduce and repair our bodies is a big trade-off.

Electric motors are sort of like hermit crab shells - Hard and long-lasting, but they only exist because they piggyback off of a living species.

I mean, we are getting to the point where we can build self completing loops of machinery.

For more complicated organisms, robustness comes in the form of cellular turnover, and regenerative healing in response to injury, at least in youth. I wonder though if single celled organisms have or even need such a function.

Individual cells absolutely do have mechanisms to repair damage: https://pmc.ncbi.nlm.nih.gov/articles/PMC5664224/

They can even repair their own DNA: https://en.wikipedia.org/wiki/DNA_repair

Who are we to say the mechanisms of biology are “overfit”? Maybe it would be nice if our personal machinery was more robust, but that robustness comes at an evolutionary cost. The greater force that is life on earth as a system for regulating planetary energy dissipation does not care about the needs of the individual. It does not care about the fashions of the millennia. Its sights are set much farther and its history much deeper than that

Or perhaps we are "overfitting" for robustness over time and also as a group (over society) vs just individual robustness at any given moment.

We also have extremely robust livers that allow us to eat a super wide variety of food as energy inputs

For some context, a billion years at a 20 minute breeding cycle is 26.3 trillion generations.

> For some context, a billion years at a 20 minute breeding cycle is 26.3 trillion generations.

Which if you want an actual feel for the true scale of things, must be multiplied by (order of magnitude) the number of bacteriums on the planet.

Good point, forgot about that. Add another 10-20 zeros?

And when you get into things like lateral gene transfer it's not even a tree any longer.

> Which if you want an actual feel for the true scale of things

The caveat is that more zeros do nothing for our comprehension of the scale. That's the problem because most people can't comprehend how evolution is even possible. We just don't have a mental model for a trillion, it's all the same to us after a certain threshold.

Is that true for evolution? If that math works, it seems that any one bacterium's mutation must become universal across the globe? Evolution works but not for every instance of a beneficial mutation. I wonder what the odds are for bacteria.

It's more the probabilities, I think[1] - even in one generation, (say) 26 trillion[0] bacterium are going to experience a lot of mutations.

[0] Which is an extremely low ball number for worldwide bacterium, even billions of years ago, I think, given your average human has around 30 trillion inside them.

[1] Like "anomalies in Minecraft" series - given how many seeds there are, how many people play it, and how big the worlds are, eventually even the rarest things generate naturally.

I'm not sure why you think "any one bacterium's mutation must become universal across the globe". That's a pretty strange takeaway in the presence of a mutation that is so advantageous it lets you become a predator and hunt other bacteria or run away from predators and gain a painfully obvious survivability benefit.

The takeaway should be "mutations that confer massive benefits can become universal across the globe even if they only happen once, no matter how unlikely they are", which is obvious and intuitive.

I agree; I was talking about the math in the parent post. I think the math represents the probability of individual mutations and not of evolution.

at the scale that it operates, the flagella is more a drill than a propeller

there's a good richard feynam video about how things feel when they're that small https://www.youtube.com/watch?v=4eRCygdW--c

I could listen to him all day - great video

Another classic on how scale matters: https://en.wikipedia.org/wiki/On_Being_the_Right_Size

Visualisation of DNA polymerase enzyme copying mechanism.

https://www.youtube.com/watch?v=sKe3UgH1AKg

I have always been super annoyed by the abstraction that ATP is a magical tiny battery that transports "energy" in some nonspecific way and that cells just hand-wave absorb that magic energy.

I learned recently that the actual mechanism of the energy transfer is one of the most interesting parts of molecular biology.

ATP doesn't just store chemical energy. ATP synthase constructs the molecules by literally mashing the two halves together and mechanically twisting them. ATP can later slot into proteins, releasing that energy by mechanically moving parts of a molecular machine. It can also be split for simple heat and participate in other chemical reactions more directly.

But I find it absolutely fascinating that ATP operates as a mechanical battery. Storing actual mechanical motion in a chemical bond that can be reversed to recover the motion and transform it into work. Molecular machines are one of the most incredible things in the universe.

Protons are also called "hydrogen ions." Stuff that donates protons is called an "acid." So this is an acid chemical process but I'm not enough of a chemist to know more than that. Would welcome comments from someone who is.

Beautifully written. This doesn’t just explain the flagellar motor — it feels like watching the very “life force” behind biology running on protons and entropy. Amazing how much of life boils down to such elegant physics.

For those who remember, the flagellum was a major site of the Intelligent Design debate that gave us Christopher Rufo (via the Discovery Institute)

The general idea was that there were specific examples of "irreducible complexity" that proved that there was an intelligent designer. The project on the part of certain Christian political factions was to add a veneer of hypothesis testing to creationism. The god of the gaps retreats further

Doesn't "irreducible complexity" here mean "it wouldn't function in any reduced form", e. g. "it would not be possible to build this up in tiny parts useful for other things and then have those things transformed into these things by tiny accretions and removals over the course of the lifespans of these creatures."? The article doesn't cite anything that would suggest that this argument is any less relevant now that we understand how the system works than it was before we understood it at this level.

It does raise the question of the steps that happened to reach that functionality (not suggesting intelligent design here). I'd assume there'd be quanta of evolutionary evolvement but it isn't clear what that would look like (especially to someone like myself who is not an evolutionary biologist).

One thing to know about DNA is chunks of it can around not doing anything for long periods of time till suddenly more DNA comes in from somewhere and suddenly you have working behaviors. Things like Transposons are crazy.

Scientists collect many examples of different type of flagellum. So we can understand how it change during the evolution process. This article introduces the finding of organism structure.

this was addressed directly in TFA with a link to https://journals.asm.org/doi/10.1128/mbio.03824-24

The article states that the rotor very much evolved. But if you follow the linked evidence, various flagellar motors appear to have evolved from an original ancestor. This is exactly consistent with intelligent design and creationism. It does not demonstrate the origin of the flagellar motor in the first place. Everyone, whether creationists, theistic evolutionists, or materialistic evolutionists all agree that mutation, natural selection, genetic drift, gene flow etcetera occur. This paper advances the debate about origins no further distance. The debate is not about the survival of the "fittest", the debate is about the arrival of the fittest.

Interesting that humans and bacteria both use an electrochemical gradient to produce energy but in different ways. In humans, this happens in our mitochondria, but in bacteria this occurs across their cytoplasmic membrane. Would you agree this is a result of evolution?

Our mitochondria was bacteria.

https://allpoetry.com/The-Force-That-Through-The-Green-Fuse-...

To not use the motor is to prolong its life? So do not heat your body with the motor?

Also can work as atp generator by applying rotation ?

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