Comment by echelon | Hacker News Reader

Comment by echelon | Hacker News Reader

> I should have loved biology but I found it to be a lifeless recitation of names: the Golgi apparatus and the Krebs cycle; mitosis, meiosis; DNA, RNA, mRNA, tRNA.

You just had bad teachers. The subject is all at once beautiful, bizarre, fascinating, daunting, mysterious, majestic, labyrinthine, and awe-inspiring.

We are solutions along a physical, biogeochemical optimization gradient. We're fit to the world around us like a glove.

We're also distributed systems. Every sub-component of every single one of our cells is a computational system in flux, dynamically adjusting to trillions of inputs every single second.

Even the packing of "junk DNA" is a calculated encoding of spatiotemporal expression dynamics and far downstream behavior.

We are the universe encoding behavior unto itself. Exchanging gasses, assembling polymers, replicating, carefully kept in balance. Battling against other systems attempting to utilize the same energy gradients.

> I think we also need inspiration. There is a romance in biology, as in any other science, that a movie like Good Will Hunting could bring out. We need heroes. Whoever delivers us from this pandemic in the form of a slam dunk vaccine, or a cheap quick reliable test, should become a household name, not for their own glory but for our kids—a Feynman for them to dream about someday becoming.

Biology doesn't have the rockets or the fancy computers, but it stands to one day unlock some of the best things for humanity: a world free of diseases, long lives, and perhaps one day, even immortality.

The only reason it's not sexier is that it's still in the punch card phases. We're just starting to scratch the surface of the computers that make up ourselves.

> You just had bad teachers. The subject is all at once beautiful, bizarre, fascinating, daunting, mysterious, majestic, labyrinthine, and awe-inspiring.

This. I'd say it applies to a lot, If not all subjects.

In my experience teachers rarely explained, why we need the subject, and what's it's use. Now I see myself digging thing on my own, and realising how cool a lot of subjects are.

No. Biology is unique in the sense that life is the creation of God and is far more complex and awe-inspiring than any other subject.

Newton remarked that what colors leaves green would always be a mystery to all but our great Creator, Jesus Christ, the father.

Turns out, its chlorophyll.

https://en.wikipedia.org/wiki/God_of_the_gaps

Yes, I bite the bullet on the God of the Gaps. What I object to is materialism of the gaps. At least God has explanatory power. Materialism does not.

> God has explanatory power

For a hypothesis to have explanatory power, it must be falsifiable. Otherwise, it's compatible with literally anything and hence can explain nothing.

What observation in your mind would falsify the existence of God?

> Otherwise, it's compatible with literally anything

> and hence can explain nothing.

Could you explain your reasoning here?

An explanation for why X is true must also be an explanation of why not X is false. But God could perfectly well explain why not X is true and X is false. If God has no predictive power, if it's consistent with anything, it can't be used to distinguish between any possibilities, and hence can't explain why they should hold.

A problem: there is no requirement for explanations to be true. In fact, untrue explanations are very often preferred, if not ~mandatory.

Otherwise you can't test it, for one. It is easy to concoct all-encompassing explanations that can't be proven wrong. Here's one I just made up: instead of one god, there is a pantheon of gods. And a different one for each universe. Ours is governed by the Norse league. Prove me wrong.

https://en.wikipedia.org/wiki/Falsifiability

I think unguided natural processes plus deep time plus multiverses could also be an all-concompassing explanation that can't be proven wrong.

Even more fundamental: anything ~false built on top of Naive Realism can exist indefinitely not just undiscovered to be false, but cannot even be identified as a candidate for consideration.

Let's hope we don't have this problem here on planet Earth, and especially at a core, fundamental level(s)!

Hmm, maybe my explanation above was too ELI5, you'll have to accept my apologies if so, and you may need to explain in more detail what you're asking exactly there.

Meanwhile can you expand on your take on Naive Realism here? What's the specific issue with Naive Realism you're pointing out? (am aware there's issues)

Humans contemplate "reality" on top of various models of it, as well as various other processes (cognition) and phenomena (culture), thinking they are contemplating reality itself. And the whole world runs on this. It's kind of funny if you think about it.

I think René Magritte might have been on to you back in 1929. ;-)

https://en.wikipedia.org/wiki/The_Treachery_of_Images

(More seriously, Indirect Realism is actually several centuries old already, isn't it?)

Very nice!

And yes, it is indeed very old...old and forgotten, even by those who have knowledge of it.

But it may even be worse: what is it in the first place?

https://www.youtube.com/watch?v=EYPapE-3FRw < have an explanation by Feynman on the scientific method. (Feynman is a great teacher!)

The whole video is pretty good, and the specific point starting with "You cannot prove a vague theory wrong" is explained around 5:10.

Can you explain how this video substantiates the the claims in the comment to which I am replying?

Not sure what you're asking here.

In re:

> Otherwise, it's compatible with literally anything and hence can explain nothing.

Feynman restates it from a different angle: he calls these kinds of things vague theories and states that they are not very useful to scientists because they can be hard to prove wrong.

Throughout he gives a bunch of examples of such vague theories that cannot be proven wrong. (eg that moogles did it, or the positions of the planets influenced when to go to the dentist, or maybe it was caused by flying saucers. )

He also points out Newtons laws which are not vague, and thus can and have been proven somewhat wrong since (see also: Einstein) .

I think further down our thread, this is in re whether saying "God did it" (or "A wizard did it" etc ) has Explanatory power:

* Why do the planets move in ellipses: "God did it"

* Why do the tides go in and out: "A wizard did it"

* How fast will an apple hit my head if dropped from precisely 10.25 meters, and will I need to wear a helmet? "Zeus knows the answer"

etc.

I mean, all technically plausible answers (maybe?), but not very useful if you're trying to understand anything. :-P

(ps. The answer to the latter should be about ~14.17 m/s ~= 50.4 km/h . Something you could go out and measure for yourself outdoors if you like! )

I think I may have noticed the problem:

> Otherwise, it's compatible with literally anything

> and hence can explain nothing.

If I'm not mistaken, what you're referring to is the fundamental unknowability of certain things, and this state often causes the mind to hallucinate "facts" like the two above. "It is unknown, therefore it is a fact that anything is possible" is plain bad thinking, but paradoxically it is very popular thinking (thus: proper thinking), even among relatively smart people.

There must be something going on here that can "explain" (in a non-incorrect fashion) all of this, it seems unlikely that we've stumbled upon never before encountered phenomena.

> I mean, all technically plausible answers (maybe?), but not very useful if you're trying to understand anything. :-P

I too enjoy building simple strawmen and knocking them down:

"Science exists, and "is correct", and I believe in it, therefore my personal opinion of fact is factual in fact".

I wonder which of these two strawmen most closely matches actual conversations that can be found on the internet. I constantly hear stories about religious people saying incredibly silly things (over and above standard silly Normative Cognition), but I rarely ever encounter it in real life. What I describe in my strawman though (essentially: scientism, the ~religion of science, etc), it is extremely common on all social media platforms, ion TV, in the newspaper, etc.

Ok, so I may have checked your comment history. You seem smart! Are you just over-thinking things horrendously? [*]

I'm just trying to talk about Falsifiability. That's the only thing I'm talking about.

If you posit an unfalsifiable ( == untestable) hypothesis, then -unsurprisingly- that hypothesis can't be tested.

Fun for teasing people if you're subtle about it, absolutely! Leaves people really confused until they catch on!

But when troubleshooting or dealing with issues in the real world, it's probably best to stick to testable hypotheses.

I'm not really sure how to explain this any better, it's really basic stuff, so I figure you already know this? (I mean it's basically how you can debug a program or fix a car too. I think Feynman learned it by fixing radios as a teenager, and when he grew up he ended up applying it to quantum mechanics.)

[*] Or - worse yet ;-) - are you a philosophy major?

Yes, I am well familiar with the things you say, I see them, and the consequences, every day.

For fun: two things to try to fit into your model:

https://en.m.wikipedia.org/wiki/Closed-world_assumption

https://en.m.wikipedia.org/wiki/Direct_and_indirect_realism

I ran into indirect realism quite a while ago, I think in neurophysiology or ethology to begin with. (A percept relating to an object is not the object itself).

Not sure why you bring up that and CWA here at this time though. Does it have something to do with falsifiability from your perspective? I think falsifiability is more of an OWA kind of thing though, isn't it? (The idea being that you never have sufficient information to know if something is true, only if it is positively false. That sounds pretty OWA to me, right?)

I'm interested to hear what you mean by "and the consequences" , because I truly have no idea what you might be seeing, and I'm really curious now. I get the impression you see people making certain kinds of mistakes?

Indirect realism is ever present, and causes many problems in the world.

It's like this:

https://www.google.com/amp/s/amp.knowyourmeme.com/memes/they...

Hmm, having been linked to a meme, I remain unenlightened. Could you expand on that just a little? What are you getting at?

Maybe you didn't engage seriously enough with the meme. Memes are very tricky!

I have a feeling you just made the stories below up.

Could you refer to an existing proof of these claims, or at least put it in some sort of a more logical form that can demonstrate that these things are necessarily true? Narrative format can make not actually true things appear true pretty easily.

Then falsify my hypothesis by coming up with some plausible materialistic mechanism to account for the existence of life.

Observer selection says a plausible materialistic mechanism for origin of life could be extremely unlikely on any given planet, and so could be an impossibly hard problem to solve.

Supernatural forces are a lazy explanation and don't offer any true insight. They have been invoked time and time again, and there has always been a natural explanation for phenomena that were once attributed to God(s). It's an intellectual dead end.

I disagree. I think that life is a unique case.

What you consider "Life" is just an awe-inspiring amount of complexity that has irked out an existence in the small, brief gradient of temperature our universe has permitted.

The clouds of Jupiter, when viewed from a planetary scale, have a similar amount of [apparent] complexity.

We simply bias familiar complexity due to our evolutionary pathway.

A planet-sized fungal-like Gaia creature that "eats" clouds by atmospheric manipulation and is able to seed it's lower planetary orbit with proto-replicative molecules would scuff at such a self-centered bias.

Can you think of anything that might distinguish the complexity of life from the complexity of the clouds of Jupiter? Or do you think life is simply a nonsense concept?

>Or do you think life is simply a nonsense concept?

yes!

Just as Carl Sagan likened consciousnesses as an emergent phenomenon that happens somewhere between the neuron count of a worm and a dog an a certain ape; " Life " is a word we use for a MASSIVE AMOUNT OF COMPLEXITY.

we are not a single species in a vacuum - we are clearly, nearly obviously, the product of our environment, literally.

We are a biosphere, stuck in a gravity well, fed by the sun: without Sol (gravity really under the hood), we cannot afford the fight on the second law of thermodynamics. We use it to locally displace some entropy and get us a lil complexity, even if temporarily.

life is just some magnitude of complexity. its an illusion.

we are not special.

we came from tidally-stirred, protein-packed, slurry pools of eventually-replicative molecules. probably packed tightly into some mineral for a backbone at first; eventually crossing the line from a repeating geologic/acid formation and more of a proto-algaeic-slime of a chain of molecules that depend on each other.

shit is moot. once you have replication - even if that seems like a massive gap to you (not to me), you have a resource-competing-selfish entity. It will then innately, by its own merit of existence, compete against itself for its own resources and be subject to random mutations due to ionizing radiation. ionization radiating is pretty universal, so no leap there.

the molecules would be subject to increasing selective pressure.

Darwin's theory.

either we here, or we aint.

the universe, time, and pretty much everything is dominated by bacteria like molecules, i am sure.

"intelligence (as we know it)" - (the ability to arrive at the same state from different inputs) is a mini-max point in many evolutionary pathways that we can easily see felines arriving at in our absence.

we are nothing special.

No, life is not simply anything that is very complex.

I think it's far more likely that we're the simulation of some super intelligence than the creation of a mythological deity worshiped by ancient goat herders.

But to each simulant, their own programming. Unicuique suum.

You realize that those two ideas are identical, right? RIGHT??

Can you copy paste in your implementation of equals()? My spider senses tell me there is a bug contained within.

What do we call the people who created the simulation? Is it unreasonable that they would give us stories to impose their own morals on us? Maybe they have a punishment or a reward for you depending on your qualities, such as getting to live in the host universe or getting stuck in an undesirable environment.

I’m more partial to God being Humans that survived the flood (being real and caused by an asteroid exploding over ice caps) and have been chilling underwater, occasionally popping their UAPs up and poking around. But I don’t hold that view too firmly.

> In my experience teachers rarely explained, why we need the subject, and what's it's use.

That's exactly the opposite of being "beautiful, bizarre, fascinating, daunting, mysterious, majestic, labyrinthine, and awe-inspiring".

OP's article lists the Krebs cycle as an example, to me the Krebs Cycle is a prime example of how not to teach biology.

Most high schools and every biology course uses the cycle as a milestone of learning, but usually teaches it by pure rote learning, words that have no meaning. Oxaloacetate turns into citrate via the citrate synthase and Acetyl CoA (I had to look this up; of course I learned it three times by heart and forgot immediately after the exam). Most of my teachers taught it like this, a meaningless collection of words and steps that you have to rote learn.

Except for my microbiology professor! We spent a semester learning about the basics of biochemistry, why reactions have to happen the way they happen, until we all had a relatively clear logic. We learned the Krebs cycle at the end, as a special kind of application and use case of the inherent logic. We want to 'reactivate' NAD+ into NADH, so we need an H+. But look at our Malate! There's a nice H dangling there in the OH group. Hs are taken off by dehydrogenases because they de- the hydrogen, so surely our helper is called the malate dehydrogenase. And it is! What happens to an O that has it's H taken away? the most usual outcome is a double-binded O. Which is why our oxaloacetate looks the way it does. If you know what malate looks like you know what oxaloacetate looks like. (And so on).

Of course you can't explain the entire cycle and its terms this way, as names like malate are there for historic reasons, but it gets you far closer to the inherent beauty of the thing. It's just a pity it's usually taught by rote.

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