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Introduction to Biology - The Secret of Life

edX · Massachusetts Institute of Technology · 5 HN comments

HN Academy has aggregated all Hacker News stories and comments that mention edX's "Introduction to Biology - The Secret of Life" from Massachusetts Institute of Technology.
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Explore the secret of life through the basics of biochemistry, genetics, molecular biology, recombinant DNA, genomics and rational medicine.

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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.




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.
To me, the main controversy is that evolution seems to work too well. Almost as if some "intelligent designer" guided it.
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.

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.

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.
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...

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.
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.

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...
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.
> 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.

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 ( 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?

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.
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.

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.
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.
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.
Do a review of literature mr silver platter.
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.)

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.

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?

> 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")

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:

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.

What's strange about asking a clarifying question about the contents of an interview being discussed, which is all the parent has done?
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.

please stop deleting and recreating comments. If you believe the parent is using sockpuppets, contact the mods at [email protected]
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, 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.
Invaluable for understanding the Central Dogma of molecular biochemistry:

Followed by a daily diet of Nature, Cell, & Science

Much obliged.
This is not the end of the arms race.

At some point we will have AI designing and AI delivering ads, and while we may have AI designed to prevent us from having to watch ads we don't want we will also have AI that watches everything, gathering and filtering information that is too much for us to handle but tuned to our needs since it's "our AI". Then the race will be that one AI wants to trick the consumer AI into giving their information more weight and attention.

So instead of the race humans against humans we'll have a race humans => AI ("sellers" of anything, from goods to news) => AI (consumers) => human (us).

It's going to be a lot more complex: Right now all that people on both sides have to know is human psychology. In that future they'll have to understand the potentially far more varied world of possible AIs - and if that isn't enough the complex interactions between them and also between the AIs and the humans.

Are we creating the diversity and complexity that we remove from the biosphere (the ongoing mass extinction and/or reduction of many species) anew but in a completely different space? In addition to technical systems we are also getting much better (and better faster!) in controlling biological systems, creating our own ideas. At least some programmers of the future will write their code in DNA - or possibly even something more complex, something that can encode completely new proteins that the current code can't represent. And then there's combining biology and technology... an explosion of complexity and diversity?

I studied CS more than two decades ago. I kept up to date and continue to do the odd course in my field, but what I consider an amazing experience (for an IT guy) was when I spent the last few years taking hundreds of hours of courses in biology and medicine. Looking for new ideas? Take an introduction to biology and genetics course instead of learning an only very mildly different programming language, for example (free):

Yeah, "end of the arms race", are you kidding me Vice?

I see 13 year olds watching their favorite youtube stars showing off the new products they're being sponsored with this week. How exactly would you block this?

Assuming vice is right and this is the end of it and people use it, how do you expect youtube to stay online once google lose its advertising revenue ? This product placement problem just solved itself.

Streaming video on the scale of youtube or facebook is not sustainable due to bandwidth cost.

That's just a return to how video advertising worked initially on TV, where Boston Blackie would light up a Lucky Strike and casually comment on how great it was in the middle of the action.
That's a very good point. But maybe it's a theoretical end of the arms race when it comes to predatory ads. I will take ads spoken by the host of a YouTube channel over autoplaying videos, adult dating banners, scrolljacking, and annoying modals any day. If all those things get replaced by advertising that is essentially voluntary and not deceptive or wasteful of computing power, then the ad blocking war may be won. We'll see.

Also, your username. lol

This is an asymmetrical game because most ads are meant to be recognized as such (product placement and sponsored content are subtler than that). So the anti ad AI has an advantage over the ad publishing one. If an ad gets through because the adblocker doesn't recognizes it AI probably the reader won't notice it too.
You assume ads will be recognizable as such, but even today we have ads that few people recognize. From waves of reddit /r/funny posts about certain sitcoms or sugary beverages to product placements in articles, shows, films to magazine and news articles, not always recognizable as ads because often they are not actually ads but actual articles that only happen to mention some products. Very nice for publishers who get whole articles that they don't have to do much to produce.

So even today even 100% human "ad blockers" are unable to block a lot of ads because they are unaware they are looking at one.

I am fine with ads that are subtle enough to pass by an AI guardian. What I want to kill is stuff that dominates the page space, can't be ignored, follows you down the page as you scroll, autoplays video, runs so many scripts that my cooling fan spins up to full speed...

I don't object to the existence of advertising. I object to advertising that is intrusive and/or resource-intensive enough to impair site usability. (And malware served over ad networks, of course, but that's a bit different as a problem.)

I'm more concerned about ads that subtly and insidously impair my life, than ads that overtly impair a website.
My issue with advertisements is that they are designed to be manipulative, esp. emotionally. "Smart, young, beautiful people" buy this product - don't you want to be like them? The ads that are strictly informational ("This product exists, here is why!") typically don't make good advertisements or are so poorly done that they become a form of comedy.

Ads subtle enough to get past an "AI Guardian" mean they are meant to influence your behavior. That is my issue with advertisements and why I actively refuse to purchase products I'm introduced to through advertising.


I'd like to clarify that by "make good advertisements" I mean as in the goal of advertisements (get people to buy) and not "good" as in "acceptable".

You could train an AI to rewrite manipulative psychology out of all content.

Has the added bonus of fixing a lot of news in the process.

(Okay, so it's slightly more complicated in practice -- you would have to reduce the manipulative content there, and then add back a certain chosen bias so the reduced manipulation is overpowered by the chosen one.)

Even mentioning /r/HailCorporate in a Reddit thread generates hostility and defensiveness from people angry at the thought that they upvoted what amounts to an ad, even if it wasn't overtly one.

Ads as content works really well, so well that people refuse to believe it. Huh? It's just a funny picture of a tall, frosty bottle of Coca-Cola!

Soon Adsense will offer server-side content placement instead of just 3rd-party-served banner ads. People act like the arms race is over because they added some entries into a hosts file. Not even close.

No you won't because that's ilegal. An advertisement must be clearly understood as such (at least in EU) and in fact (for instance) now the channels in here are actually having to tell you that you are about to see advertisements.

So, no, we won't have AI tuning the advertisements so that they can't be catch by software like this one because that means it also wouldn't be catch by humans and that a very big no.

I can see this as a paradigm change in the internet it's true, and it's hard to see the full reprecursions of this all.

Then again, I think that if we get back to sane advertisements in web pages, that are just a couple of lines of text clearly marked as such (like Google ads used to be), then people would be ok not using an ad blocker in those cases. The thing is, the marketing companies just pushed it too far...

I'm not sure what to make of your comment, it's a little.. "weltfremd" (unworldly says the dictionary, not sure if that conveys the same meaning as in German though). There are MANY ways around it. It is like lobbying: Bribes are clearly not allowed, and yet politicians can easily be bought without actually breaking any laws.

The problem with that attitude is that when you are looking for bad things you are looking for intent, which is really not necessary for bad things to happen. This is like looking at individual neurons and not finding psychopathy (or whatever else actually is a system outcome of the network's actions, not of individuals).

I think it's myopic to dismiss this based on legality; companies of all sizes frequently flout laws and regulations. I agree that it's difficult to see the big picture (we didn't even see the paradigm shift of smartphones coming - there's no way anyone can be expected to predict how the advertising landscape will look in 15 years) but I certainly don't envisage a return to vintage era Google Ads. We tend to forget that (mostly due to this echo chamber in which we're participating) that regular people don't think like us and without the momentum of a large group, a reversion is unlikely to be affected.

That said, WRT GP's post, I don't think it's a million miles off. AI will undoubtedly become a cornerstone of modern life and I don't think the scenario they outline is entirely unlikely. Siri is objectively pretty hopeless, particularly when compared to its counterparts but it's been a nice clue as to what we can expect from modern innovation.

I think it's myopic to dismiss this based on legality; companies of all sizes frequently flout laws and regulations. I agree that it's difficult to see the big picture (we didn't even see the paradigm shift of smartphones coming - there's no way anyone can be expected to predict how the advertising landscape will look in 15 years) but I certainly don't envisage a return to vintage era Google Ads. We tend to forget that (mostly due to this echo chamber in which we're participating) that regular people don't think like us and without the momentum of a large group, a reversion is unlikely to be affected.

That said, WRT GP's post, I don't think it's a million miles off. AI will undoubtedly become a cornerstone of modern life and I don't think the scenario they outline is entirely unlikely. Siri is objectively pretty hopeless, particularly when compared to its counterparts but it's been a nice clue as to what we can expect from modern innovation.

I don't think people will understand the point you're making here, so let me recommend the absolutely fabulous analogous exploration of your point in David Brin's Existence.
Native ads will always evade this tool.

Also the end composition of the page can reveal to javascript what is or is not removed

Check out "General Adversarial Networks". It's basically training a two-part AI via an arms race; one part is trying to fake out the other, the other is trying to detect the fake.
> Check out "General Adversarial Networks"

Another way to describe GANs is that the loss function, which used to be hand-made, now is a whole separate neural net and can be learned bottom-up instead of dictated top-down.

There was a time when features were hand-made. Now we have deep learning and finding good features is automatic. GANs automate another part of the process.

So you start a company to produce two networks with GAN techniques, then sell them as separate products, to the opposing sides...
Essentially how AdBlock operates, without the GAN/ML (yet)
Small fix, I believe it's "Generative" Adversarial Networks.
You are correct sir.
Usually yes - but it depends. Anything programming related I rarely like as a lecture and completely agree with you, unlike it's general concepts and then it depends, see below. I'm an avid reader, so historically I always favored reading and only the last few years did I get a more nuanced opinion with exposure to new subjects and lecturers.

On the other hand, when I took "Medical Neuroscience" [0], a pretty heavy course with 16 hrs/week ~25 hours (or was it 35?) lectures total (the 1st edition of that course - I have not checked if they made any changes to the edition online now, Coursera switched to a different course format), at least for the duration of the course I ignored the textbook [1] even though I had it. The lecturer was mesmerizing, I just started the videos and listened for hours - and actually learned. The fact that most of the time you do want to take that textbook (even for this exact same subject) is that it's exceedingly rare to find such a specimen of a teacher.

Similarly with basic physiology lectures, even though they were done cheaply and he has stopped making new ones Aaron Mullally's lectures are of the same kind, I could just listen and listen and learn stuff. I tried many different ones, all of them prepared more "professionally" (I don't like that word because the dirtiest and cheapest solution can still be more professional than the one with the best packaging, but you know what I mean, I hope).

Math, physics, chemistry, biology: It depends (so the same), I found lectures - I guess that actually means I found lecturers - that at least for me are better than learning the same from a book. Another example where given the choice between book and lecture I would take the lecture any time: [3] (and that is 100% because of the person giving the lecture).





> (I don't like that word because the dirtiest and cheapest solution can still be more professional than the one with the best packaging, but you know what I mean, I hope).

I had to take a math class while getting my AAS. The class didn't teach me anything with its sleek book, poor explanations, and ineffective teacher. I only passed because of this YouTube channel:

It's professional quality now in this era of professional YouTubers, but not back in the 2000s. Still better than a $100+ textbook.

Eric Lander's incredible 'Introduction to Biology - The Secret of Life' was my first step away from data analysis for online marketing clients (which I didn't love) to bioinformatics (which I do very much love)

A Fantastic course from a legendary educator.

I'd like to second this. I had only slight interest in Biology but got completely hooked into the course because the teacher makes things so plausible and exciting. I wish one could do bioinformatics remotely, I'd seriously change careers ;)
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