Legendary bacterial evolution experiment enters new era | Hacker News Reader

Legendary bacterial evolution experiment enters new era

nature.com

145 pointssohkamyung46 comments

This is an absolutely fantastic experiment and probably part of the reason I'm a biologist today. Keeping a single experiment going for so long is quite a feat, and it has payed off handsomely. Lots of great science came out of the Lenski lab in the last 30 years, not least because of the consistency and thoroughness of their work. Glad to see the LTEE moving on to a new chapter - many happy landings!

>Thirty years and 75,000 generations — it’s a drop in the evolutionary bucket. So I would guess that if we could come back — in one million years or whatever, the bacteria probably would have extremely reduced genomes. That’s a reason to keep it going.

Can't speed up nature, though I wonder if we could add something to the medium that increases the chance of deletions.

> I wonder if we could add something to the medium that increases the chance of deletions

The bacteria beat you to it: Several strains developed elevated mutation rates, already back in the 90s (https://doi.org/10.1038/42701).

>Can't speed up nature

If you are moving at the speed of light, then it would happen faster to you. So couldn't we just do the opposite of that?

Kinda? Taking the experiment outside of earth`s (and the sun`s, I guess) gravity well would have the effect you have in mind. But the impact would not be particularly pronounced considering the magnitude of the curvatures we are experiencing.

Just go a little faster than light and conduct the experiment in the past.

Can't speed up nature

We can, with computers. Well, maybe not today, not at the atomic level, but quite possible in a few decades.

> We can, with computers.

Lenski and his colleagues have been working on that too, with the Avida platform (https://doi.org/10.1038/nature01568). Although that was 20 years ago and I haven't heard much from it lately, so I don't know how active this still is.

So… we can’t?

People working in labs today must be speeding up nature significantly on a daily basis. Perform lots of concurrent experiments, apply different environmental stresses, provide different nutrition, cross different variants you find useful, automate all the processes and tests. I think the project referenced seems to be deliberately not doing that, to observe the natural speed of change.

We can't today, but maybe in the future.

So we can’t

That's pretty weird position.

Eg I can fly to Hong Kong. Not today, because I haven't booked a flight and it's getting late, but probably in the next few days, if I really wanted to. You'd say that I "can't"?

It is currently feasible for anyone, with the right resources, to fly to Hong Kong.

It is not currently feasible for anyone to speed up or simulate nature in silico.

These are quite different positions, the idea that you would equivocate them frankly is bizarre

You could just increase the population and thereby the overall number of mutations tried.

It is worth mentioning that Richard Lenski has a blog where he writes about the LTEE: https://telliamedrevisited.wordpress.com/

Jeez. I’m old enough to remember when this experiment was just getting started.

> Thirty thousand generations into the experiment, one of the 12 lines evolved the ability to consume citrate, instead of just glucose. And that garnered quite a lot of attention, and even some, shall we say, hostility from some people who are sceptical of the power of evolution.

In case you haven't heard of this, Dr. Lenski dealt with some science deniers who tried to smear the experiment:

https://www.conservapedia.com/Conservapedia:Lenski_dialog

Ah, Conservapedia. Here is their page which "disproves" the theory of relativity, which starts off by conflating the theory of relativity with moral relativism.

https://www.conservapedia.com/Counterexamples_to_Relativity

In addition to ignoring all the experiments which confirm relativistic predictions, there cite various open issues (eg, no general solution to the equations) as if that is disproof, and they also cite the bible in a few places.

So conservapedia is wishful thinking and plugging your ears to anything one doesn’t like?

Why do people do this to themselves?

> In the field of psychology, cognitive dissonance is the perception of contradictory information. Relevant items of information include a person's actions, feelings, ideas, beliefs, values, and things in the environment. Cognitive dissonance is typically experienced as psychological stress when persons participate in an action that goes against one or more of those things.[1] According to this theory, when two actions or ideas are not psychologically consistent with each other, people do all in their power to change them until they become consistent.[1][2] The discomfort is triggered by the person's belief clashing with new information perceived, wherein the individual tries to find a way to resolve the contradiction to reduce their discomfort.[1][2][3]

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

Self-soothing. It feels good. The world is confusing and difficult, so holding on to what is familiar, comfortable, and feels good is nice to do for your brain.

It's massively common, but I would argue that almost everyone who does it denies that's what they're doing. To them, they're just using the best sources they can find.

It's sad, and I'm sure it's a problem.

I have always been able to detach emotions from reasoning, but observing I notice not everyone has that skill. And maybe like you said, the ability to see that it is happening.

Oh wow, didn’t know this was a thing. Reminds me of growing up in Christian school where they gave us all these crazy reasons why evolution was impossible and the world was 6000 years old

Yup, they have you covered there too:

https://www.conservapedia.com/Counterexamples_to_Evolution

It is full of "checkmate" logic like this: "Limestone and fossils exist at the highest peaks of altitude." The implication being that the earth has been inundated for long periods of time to a depth of many thousands of meters of water. What geology really says is that those limestone fossils were formed near sea level and subsequent uplift is why those fossils of sea life ended up at the tops of mountains. But because one of the presuppositions of conservapedia is a young earth, that explanation isn't accepted.

ah yes I am well versed in this argument :)

What an awesomely scaling rebuttal by Dr. Lenski

> In case you haven't heard of this, Dr. Lenski dealt with some science deniers who tried to smear the experiment:

Reading it, it seems like the first request was silly, but the second was very straightforward and not rude. The second response was an extreme overreaction to the second request, which did little more than say, "Actually the paper doesn't contain all the data; please may we have the data?"

It demonstrated that the requestor had not put in even the minimum amount of effort to identify the data present in the paper and lacked an understanding of how the entire domain and process worked. It is similar to going into a restaurant, ordering something that is not on the menu, and then being outraged that there's no wonton soup at the hotdog stand. The second response was also very rude. If someone is screaming at you that their taxes paid for your work, it is never polite.

Your analogies fall down in that they in no way relate to the tone of what's written there. Unless you mean the second response is analogous to screaming.

Judging by a 3 minute browse of some of the articles of conservapedia, Schlafy seems to be a dimwitted crank. So I'm actually amazed at what must either be his intellectual honesty or delusion that made him post this humiliating and deserved smackdown by Lenski apparently more or less unedited and without gloss. May he be model to others of his ilk, regardless of their persuasions.

That is one interesting web site

Conservapedia is interestingly stupid, in that it attracted the ire of many communities back in the day who, in addition to raiding it, stuck around and Poe's Law'd their way in.

There was a point where some of the more ridiculous claims were primarily from communities like /b/, seeing how insane they could be before they were called out. But the Conservapedia administration actually took it seriously.

Keep in mind that much of the content of Conservapedia might as well be written by trolls. It's sometimes hard to say.

My view on it has always been that the admins are dead serious, but the users may not completely be.

It would be far scarier if it was the other way around.

I did this same experiment to make my sourdough starter. Would recommend

> During their 75,000 generations of growth, the bacteria have made huge gains in their fitness — how fast they grow relative to other bacteria — and evolved some surprising traits. I am probably misunderstanding something, but this whole thing seems like a bad idea given the past couple years

I can't imagine the rate of mutation is higher for these colonies than, eg. those that are in your own gastro-intestinal tract. The difference is with the lab colonies they don't have the same selection pressure as bacteria in the wild. So my naive understanding is that they would actually be less fit in most environments outside the lab. For example, how fast they grow - the mutated growth strategy is probably optimised to the lab conditions and could result in an unviable lineage outside of the lab.

Even accounting for the generation of dangerous (to humans) mutations, the benefits gained from our increased understanding of bacterial lineages and genetics almost certainly outweighs the danger.

> I can't imagine the rate of mutation is higher for these colonies than, eg. those that are in your own gastro-intestinal tract.

What? Why not? Rate of mutation is an evolutionary parameter just like everything else.

Compare this other sidethread comment: https://news.ycombinator.com/item?id=31775592

I think bacteria are already doing this kind of thing in nature. Just here we get to document the results.

Yeah but in nature these organisms are forced to adapt more as generalists to the large variety of environments they're exposed to

One of the most invasive species in the world is the argentine ant. Which evolved over many many years under a very specific set of conditions until one day they were exported by colonists and have basically taken over the world. It turns out that that intense Amazonian environment, one which is very rare to find anywhere else, just happened to be an amazing training ground to evolve certain traits that gave them the ability to take over the rest of the world

When you leave organisms in such specific conditions, there's always the chance that you're selecting for incredible fitness for a specific ability. A specific ability that might not evolve in a more diverse set of conditions because perhaps it doesn't pay off until it's sufficiently developed.

With argentine ants this might be how well adapted they are at having multiple queens and quickly reproducing to recover from any sort of damage

Argentine ants are fascinating! And also a pain in the neck because they’re so hard to get rid of.

but this is difficult to get sample

If the colonies were fed human cells, I’d agree.

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