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Nature, in Code: Biology in JavaScript

edX · École polytechnique fédérale de Lausanne · 3 HN comments

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Learn JavaScript programming by implementing key biology concepts in code, including natural selection, genetics and epidemics.

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Before I start: My comment is not about the person, I don't know anything about him, only about one specific section in the linked article. Also, I'm making this a question rather than a strong opinionated statement, because I am in no position to provide the latter. That means I'm ready to stand corrected and post my observation for discussion.

I skipped to where I thought I see something about something "sciency", and I found the section when you skip to

> Just to clarify here for our readers, obviously, you’re poking holes in Darwin’s Theory of Evolution but you’re saying it only tells the story up to a certain point...

I don't understand what he is talking about. I mean, where is that "controversy"? I can only see what's in that article, I don't know what else he may have said or written elsewhere. I only took biology classes on edX the last few years (the most important one was [0]), and nothing he says in that section is "controversial". Genetic drift and small populations are part of the teaching, if you go to edX's course "Nature, in Code: Biology in JavaScript" [1] you even get to simulate just that numerically, population bottlenecks, genetic drift, and more. I recognize everything he said from the courses I took, or from lecture videos on Youtube (by biologists and geneticists, specifically, e.g. this one: [2] - very funny guy too).

Going only by what I see in that article, in that section, I can only assume he is making a mistake in declaring some imagined and made-up "controversy" where none exists.

What am I missing?

To me his statements are like somebody trying to defend their "controversial" point of view that the earth is on a course around the sun, making very defensive statements because they think, for whatever reason, they are saying something incredibly controversial.

[0] https://www.edx.org/course/introduction-biology-secret-life-...

[1] https://www.edx.org/course/nature-code-biology-javascript-ep...

[2] https://www.gresham.ac.uk/professors-and-speakers/professor-...

heurist
Neutral theory is controversial in that it is unproven (or was when I last read about it 6 years ago). It is still a legitimate topic of research.
p1esk
To me, the main controversy is that evolution seems to work too well. Almost as if some "intelligent designer" guided it.
ItsMe000001
But "intelligent designs" work less well!

The only ever work for very specific things. On a larger scale there again is no design anywhere, see for example the economic principles, the "invisible hand". As soon as humans tried to "design" such larger systems it all fell apart (communism - in which I grew up).

No single entity can manage the complexity, unless that entity is the universe ("it models itself") - at which point we have a useless tautology.

p1esk
No design in economy? Are you serious? Do you really think that US (or any other developed country) does not plan or regulate its economy and just lets things happen?

Also, it's funny you mention communism, because no "design" was planned there originally, and the economy was supposed to just "emerge" from fundamental principles and real life conditions.

My understanding of biological evolution is that seemingly random mutations take place. This is like having a bunch of monkeys with typewriters, and hoping they produce a Shakespeare's sonnet. Yes, it's possible, but highly unlikely.

I see several explanations of why biological evolution is successful:

1. trillions of trillions of planets launched evolutionary processes during the last 14B years, and ours just happened to be extremely lucky one, where intelligent life has appeared (through random mutations) against all odds.

2. intelligent life has emerged through random mutations on some other lucky planet, and those intelligent beings planted some kinds of seeds capable of developing into intelligent life eventually on other planets.

3. life on Earth was not planted like in the second scenario, but the random mutations are not really random, and are guided by something we don't understand (yet). Living in a simulation, all-mighty God, or some not yet developed branch of complexity theory, would belong here.

Note that the second scenario is extremely more likely than the first one, and the third one imo is more likely than the second one. In any case, it's not just "controversy". It's a serious lack of understanding of biological evolution (either on my part, or in general), similar to how there's a serious lack of understanding of how a brain works.

heurist
No, that's just how existence works. Systems that perpetuate themselves are more likely to continue existing. Systems that don't perpetuate themselves stop existing. No intelligence required.
p1esk
Perpetuate themselves by making random changes? Or the changes are not quite random? Software simulations of the former do not lead to much intelligence, and the latter hints at some higher order.

I'm not an evolutionary biologist, so this is just a layman's pondering...

ithkuil
Higher order doesn't imply design by an intelligent agent. Higher order can be an emergent property of a system under the pressure of raw, inanimated, constraints.
p1esk
That's hand-waving. Again, how does it "emerge"? Through random mutations? Perhaps so, but it is statistically highly unlikely. Clearly there's a significant gap in our understanding of evolution, because otherwise we would have modeled it by now.

Theory of evolution is like theory of how brain works: incomplete.

heurist
Yes, random mutations. Random mutations that cause cancer kill an organism and random mutations that make them more attractive to mates make them more likely to pass that mutations to offspring, who pass it to their offspring, and so on. This is all basic evolutionary theory...
p1esk
Yes, I'm questioning the "basic evolutionary theory" (and it appears that Dyson does too), because all efforts to test it in software have failed so far. Which is especially troubling given that processing power has been increasing exponentially for decades since people started experimenting with genetic algorithms and artificial life simulations.
heurist
> all efforts to test it in software have failed so far

What does "failed" mean? Evolution is a universal concept with infinite potential implementations. Trying to measure "success" means nothing unless you have some particular goal in mind, and as soon as you add a goal you severely restrict the pool of potential "successful" implementations, which makes success harder to find. Even then, you can look to processes like stochastic gradient descent as a "successful" use. It goes a lot deeper than that but as someone who has spent many years studying evolutionary biology, computer science, information theory, cognitive science, socioeconomics, and complex adaptive systems I have no idea where your comment is coming from so I won't elaborate here.

ithkuil
I didn't intend to start an argument in favour of proving or disproving one point or the other. Just wanted to mention that the existence of an "higher order" is not a proof in itself in the existence of a purposeful creator of that higher order.

Consider for example the game of Go board game (https://en.wikipedia.org/wiki/Go_(game)). It has an extremely small set of rules, yet it produces astounding patterns in the way games develop. The Go board game obviously has a creator; humans invented it. But that doesn't mean that whover thought up the rules of Go knew upfront the intricate complexity that we explored throughout the centuries (by playing games).

We gain no further insight in the higher order that emerges by following the rules of Go by knowing the precise circumstances that led to its creation.

When thinking about the universe and life itself, I think this aspect is more important than the unknowable answer about whether there was a creator or not: would knowing the creator necessarily explain most of the complex behaviour we see?

p1esk
Not only we don't know if there is/was a "creator", we don't even know the "rules". Using your Go analogy, we are watching the game and assume the moves are random.
ithkuil
sure we know the rules: laws of physics on which chemistry is based.

if a random mutation produces a protein that cannot act as a catalyst for a given chemical reaction that reaction won't happen and that can make a hell of a difference to the the organism that had everything else setup depending on that thing to happen, decreasing the odds of survival (which often simply means not even survive for long enough to develop).

There are so many constrains at so many levels, many we know of, many are in plain sight, many are hidden, some we know since long time, some we have yet to discover. There are so many things we don't know, but pretending we are completely oblivious about the rules of the game is a stretch.

The sheer complexity of it all is mind-boggling, but that doesn't mean the only reasonable approach is just to give up. So far every time humanity has thought that we've reached our limit in understanding and that only the existence of a deity can explain the next step, we unveiled the next layer of the puzzle.

Even if a deity does exists, it doesn't appear reasonable to expect that we've finally exhausted all there was to learn and we finally found the truly unexplainable. We no longer have to posit the existence of a deity to explain our diurnal cycle and other everyday miracles, because we now know; we convinced ourselves that what seemed utterly incomprehensible to our ancestors (who we have no reason to assume less intelligent individually than us) is to be attributed to simple celestial mechanics governed that rules that no longer seem that incomprehensible. We moved our questions to the next layer, to the why those rules exist: what did set planets in motion etc; if you want, we never really "answered" the question, we just pushed it one layer further, and in the process we uncovered so many new beautiful layers of our reality.

p1esk
I agree with you. My previous comments were directed at those who believe that there's nothing controversial about evolution. The example I gave was we don't understand enough to explain why it works so well.
pokemongoaway
So much controversy in theories of evolution. All thinkers can benefit from this feeling that "we're over these solved problems." Get to the root of the problems by looking at the various paradigms before one went mainstream and trampled the rest - and stop trying to jump to the same conclusions the mainstream did.
ItsMe000001
Given that I was at least somewhat specific, I have no idea what you are trying to convey, and/or what your point is, unfortunately...? Yeah, I noticed that the article isn't (specific) either.
pokemongoaway
Do a review of literature mr silver platter.
mnl
He's been a very accomplished theoretical physicist* (a mathematician actually) and an inquisitive mind. He also has met literally everybody, he's living History of 20th century Physics and more. You just can't ignore this kind of figures if you're interested in Science.

When Freeman talks I always listen, even when he's wrong he still has a point: don't underestimate him, even at 94.

(*We're still using quite a bit of his QFT formalism... laid down almost 70 years ago now.)

ItsMe000001
Let me quote from my own very first paragraph:

> My comment is not about the person... only about one specific section in the linked article.

I don't see why anything you say should influence my opinion about what I wrote, when that is all I comment on? Do all his accomplishments mean he can say whatever he wants and I can't say anything? I admit I don't understand your response, given that I already limited the scope of my comment myself right from the start.

mnl
It's just strange for me reading something like "I don't know anything about Dyson, but -proceeds to talk about Science-". I think you should know him, he's been around. Science is made by people, it's a good idea to get to know who they are and where they're coming from before judging what they're trying to say. Most of the outsiders of a field spout nonsense, but there are really smart people out there as well.

Yeah, in my book Freeman Dyson can say whatever he wants, he's earned it. Of course I'm not saying he's right, but I'll double check.

But he's a physicist!... well, at some point Biology has to be Physics, what else could it be?

ItsMe000001
> It's just strange for me reading something like "I don't know anything about Dyson, but -proceeds to talk about Science-

Would you please read? I did not say anything about the guy, only about the article in front of me! And I DO know my biology well enough to know that what was written in that article did not make sense! (Because it's actually taught at beginner level already so how can he claim to have said something "controversial")

mnl
So you think you know your Biology well enough after some edX courses... OK. Maybe if you had an actual degree you'd get the gist of Dyson's argument and your contribution would be more interesting.

He's arguing that maybe genetic drift is more dominant than selection for small populations, and that small populations are not a bug, but a feature. A 30 second google search would have gotten you a Wikipedia page for the Kimura theory: https://en.wikipedia.org/wiki/Neutral_theory_of_molecular_ev...

And yes, it's strange to me that some people dismiss very important scientists, don't have a problem with not even being familiar with their name, on top of being unable to find any relevant information by themselves, at the same time they feel entitled to make objections because they've watched some lectures on the internet. And can't even read themselves because that interview wasn't about no one considering drift before, just what's dominant in evolution.

This uncalled redditization of HN is a waste of everybody's time. BTW, you should think twice before accusing people of using another accounts for I don't know what, because you're just making it up and being extremely unpleasant for no reason. Don't do this here.

detaro
What's strange about asking a clarifying question about the contents of an interview being discussed, which is all the parent has done?
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ItsMe000001
More revenge downvotes from you?

I suggest you flag yourself - I don't think your self-voting using several accounts is acceptable here, or at least I would hope that it isn't.

detaro
please stop deleting and recreating comments. If you believe the parent is using sockpuppets, contact the mods at [email protected]
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mistermann
I think OP's question was more along the lines of, if there is a controversy, it doesn't seemed to be contained within the article....so, is there actually a legitimate controversy on the topic and might it be found elsewhere? I don't think he could have possibly gone further out of his way to project politeness.
I recommend the MOOC and book for Nature in Code - evolutionary dynamics in Javascript

https://www.edx.org/course/nature-code-biology-javascript-ep...

Since we are talking about learning Javascript, there is a very interesting approach in this edX course: Teach biology and Javascript!

"Nature, in Code: Biology in JavaScript" -- Learn JavaScript programming by implementing key biology concepts in code, including natural selection, genetics and epidemics.

  Instead of just learning programming principles outside of
  any context, you will learn JavaScript programming by
  implementing key biological concepts in code so they can
  run in your browser.
https://www.edx.org/course/nature-code-biology-javascript-ep...
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