# X-Men Constructive Neutral Evolution

**URL:** <https://discourse.peacefulscience.org/t/x-men-constructive-neutral-evolution/4950>\
**Category:** Conversation\
**Tags:** Science, Pedagogy\
**Created:** [February 20, 2019, 5:43pm UTC](https://discourse.peacefulscience.org/t/x-men-constructive-neutral-evolution/4950 "2019-02-20T17:43:14Z")\
**Posts on this page:** 14\
**Page:** 2

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**Author:** ![AndyWalsh](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/andywalsh/32/506_2.png) [@AndyWalsh](https://discourse.peacefulscience.org/u/AndyWalsh)\
**Post date:** [March 6, 2019, 9:32pm UTC](https://discourse.peacefulscience.org/t/x-men-constructive-neutral-evolution/4950/21 "2019-03-06T21:32:54Z")

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> [@swamidass](#):
>
> You haven’t explained much about the population parameters. How many individuals per generation? What types of mutation do you allow? Recombination?

The population size is 1. I’m using the same _(1+1)EA_ evolutionary algorithm used in chapter 5 of _Compositional Evolution_, because I thought this was also a good excuse to play with some of the concepts in that book as well. I didn’t expect to be able to stick with that algorithm this long, but so far it has been fruitful.

Only point mutations are allowed right now, no inserts or deletes or larger scale changes. I ultimately intend to include more variety here. Also, the genome is represented as a character string using the ACGT alphabet, and the probability of mutation varies with the type of mutation, e.g. “transitions” are more likely than “transverions.”

I have not yet implemented recombination, but intend to.

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**Author:** ![swamidass](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/swamidass/32/3_2.png) [@swamidass](https://discourse.peacefulscience.org/u/swamidass)\
**Post date:** [March 6, 2019, 9:37pm UTC](https://discourse.peacefulscience.org/t/x-men-constructive-neutral-evolution/4950/22 "2019-03-06T21:37:26Z")

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You are on to something here. It needs to be more efficient, and make sure it is modular. But this is really interesting.

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**Author:** ![NLENTS](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/nlents/32/1158_2.png) [@NLENTS](https://discourse.peacefulscience.org/u/NLENTS)\
**Post date:** [March 6, 2019, 10:23pm UTC](https://discourse.peacefulscience.org/t/x-men-constructive-neutral-evolution/4950/23 "2019-03-06T22:23:18Z")

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Okay so this discussion makes my article look really low brow!

> **[Are the X-men Mutants “the Next Step in Evolution?” (RIP Stan Lee)](https://thehumanevolutionblog.com/2018/11/19/x-men-mutants-next-step/)**
>
> Stan Lee was definitely on to something when he posited that mutations were the way to deliver new abilities to an otherwise run-of-the-mill human being.

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**Author:** ![Mung](https://avatars.discourse-cdn.com/v4/letter/m/a5b964/32.png) [@Mung](https://discourse.peacefulscience.org/u/Mung)\
**Post date:** [March 6, 2019, 10:28pm UTC](https://discourse.peacefulscience.org/t/x-men-constructive-neutral-evolution/4950/24 "2019-03-06T22:28:43Z")

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> [@swamidass](#):
>
> @mung see this.

Well, I saw the bit about hill climbing. Perhaps @AndyWalsh could explain that. Why have that at all?

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**Author:** ![Djordje](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/djordje/32/3673_2.png) [@Djordje](https://discourse.peacefulscience.org/u/Djordje)\
**Post date:** [March 6, 2019, 10:32pm UTC](https://discourse.peacefulscience.org/t/x-men-constructive-neutral-evolution/4950/25 "2019-03-06T22:32:11Z")

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> [@NLENTS](#):
>
> Okay so this discussion makes my article look really low brow!

So I’m never gonna get my regenerative healing factor? 😞

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**Author:** ![AndyWalsh](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/andywalsh/32/506_2.png) [@AndyWalsh](https://discourse.peacefulscience.org/u/AndyWalsh)\
**Post date:** [March 7, 2019, 3:05am UTC](https://discourse.peacefulscience.org/t/x-men-constructive-neutral-evolution/4950/26 "2019-03-07T03:05:55Z")

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> [@Mung](#):
>
> Well, I saw the bit about hill climbing. Perhaps @AndyWalsh could explain that. Why have that at all?

The first set of experiments I posted today were not about constructive neutral evolution. They were exploring what kinds of adaptive solutions are possible in this space, mainly just to understand the domain a little better. I used a particular evolutionary algorithm that is comparable to hill-climbing optimization.

The second set of experiments were about constructive evolution. While the same evolutionary algorithm was employed, the starting population already had an optimal solution and so no “hill climbing” occurred. Instead, the evolutionary algorithm provides negative selection, preventing loss-of-function mutations from persisting. Here, loss-of-function means inability to achieve a perfect score as a team. This selection does not favor any particular way of achieving that score. So the distributed solutions that emerge are not adaptive.

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**Author:** ![AndyWalsh](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/andywalsh/32/506_2.png) [@AndyWalsh](https://discourse.peacefulscience.org/u/AndyWalsh)\
**Post date:** [March 7, 2019, 4:15am UTC](https://discourse.peacefulscience.org/t/x-men-constructive-neutral-evolution/4950/27 "2019-03-07T04:15:13Z")

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> [@swamidass](#):
>
> If you start then all with the same genome in the Sam location, you can simulate duplication then divergence. You should see different copies specializing in different sentinels.

 ![JubileeTeamPerPlayerFitnessOverTimeSameStart](https://us1.discourse-cdn.com/flex016/uploads/peacefulscience/original/2X/6/6df588eefb860ec5e1369a07fdf5fe6d1d91b964.png)

Here’s what the scores look like if the four identical players start in the same location with the same genome that encodes a full solution. The fact that all of them tend toward a score of 3 suggests specialization on a single enemy each. I wanted to try to visualize that more explicitly using the player location over time, but so far the aggregate data seems to noisy to make anything clear.

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**Author:** ![swamidass](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/swamidass/32/3_2.png) [@swamidass](https://discourse.peacefulscience.org/u/swamidass)\
**Post date:** [March 7, 2019, 2:16pm UTC](https://discourse.peacefulscience.org/t/x-men-constructive-neutral-evolution/4950/28 "2019-03-07T14:16:23Z")

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@Joe_Felsenstein, good to see you here. What do you think of this?

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**Author:** ![Joe\_Felsenstein](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/joe_felsenstein/32/8176_2.png) [@Joe\_Felsenstein](https://discourse.peacefulscience.org/u/Joe_Felsenstein)\
**Post date:** [March 7, 2019, 6:09pm UTC](https://discourse.peacefulscience.org/t/x-men-constructive-neutral-evolution/4950/29 "2019-03-07T18:09:51Z")

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Haven’t read the right comics. Do I really have to go see some superhero movie? I hope not.  
At The Skeptical Zone in February, 2016 ([http://theskepticalzone.com/wp/wright-fisher-and-the-weasel](http://theskepticalzone.com/wp/wright-fisher-and-the-weasel)) I explored the connection between Dawkins’s Weasel and the Wright-Fisher model of theoretical population genetics. In the Weasel one always moves uphill on the fitness surface. In effect, selection is infinitely strong. In a Wright-Fisher that comes close to being a Weasel, one sometimes moves downhill.

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**Author:** ![swamidass](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/swamidass/32/3_2.png) [@swamidass](https://discourse.peacefulscience.org/u/swamidass)\
**Post date:** [March 8, 2019, 3:25am UTC](https://discourse.peacefulscience.org/t/x-men-constructive-neutral-evolution/4950/30 "2019-03-08T03:25:34Z")

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> [@Joe\_Felsenstein](#):
>
> Haven’t read the right comics. Do I really have to go see some superhero movie? I hope not.

No need to understand the comics. Think of it like a video game with characters that move and shoot based on their DNA “genome.”

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**Author:** ![AndyWalsh](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/andywalsh/32/506_2.png) [@AndyWalsh](https://discourse.peacefulscience.org/u/AndyWalsh)\
**Post date:** [March 8, 2019, 7:53pm UTC](https://discourse.peacefulscience.org/t/x-men-constructive-neutral-evolution/4950/31 "2019-03-08T19:53:46Z")

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> [@swamidass](#):
>
> No need to understand the comics. Think of it like a video game with characters that move and shoot based on their DNA “genome.”

To that end, here’s an example session without the X-Men trappings. The 4 blue players/agents have to take out the purple ones, using their ‘genome’ encoded action sequences. All 4 players contribute partially to the overall success. They evolved via neutral (with respect to overall success) mutations from a ‘genome’ that allowed one player to succeed alone while the other 3 contributed nothing to the score.

![AllAbstractCyclops](https://us1.discourse-cdn.com/flex016/uploads/peacefulscience/original/2X/0/0b9b94e66efba537cddda569dcd86f4733c126fc.gif)

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<div class="post-metadata">

**Author:** ![swamidass](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/swamidass/32/3_2.png) [@swamidass](https://discourse.peacefulscience.org/u/swamidass)\
**Post date:** [February 21, 2020, 9:51pm UTC](https://discourse.peacefulscience.org/t/x-men-constructive-neutral-evolution/4950/32 "2020-02-21T21:51:50Z")

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I see @AndyWalsh has made major updates to the [Danger Room](http://www.faithacrossthemultiverse.com/DangerRoom.html) described, here: [X-Men Constructive Neutral Evolution](https://discourse.peacefulscience.org/t/x-men-constructive-neutral-evolution/4950).

Check it out!

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**Author:** ![AndyWalsh](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/andywalsh/32/506_2.png) [@AndyWalsh](https://discourse.peacefulscience.org/u/AndyWalsh)\
**Post date:** [February 22, 2020, 4:04am UTC](https://discourse.peacefulscience.org/t/x-men-constructive-neutral-evolution/4950/33 "2020-02-22T04:04:09Z")

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After my sabbatical ended I didn’t have as much time to work with this as I had wanted. But I’ve been noodling around more recently, trying to get a better sense of how it behaves and what it might or might not be useful for.

It is possible to set up challenges which are very difficult/practically impossible to solve because there is no adaptive pathway. So in addition to illustrating constructive neutral evolution, it can also illustrate some of the limitations of RM + NS (or really just RM). Obviously there are other options in that regard (such as the problems discussed in Watson’s [Compositional Evolution](https://discourse.peacefulscience.org/t/richard-a-watson-compositional-evolution/2104). But I like that this has a concrete and visually dynamic phenotype.

Happy to discuss possible applications & modifications if anyone thinks they might have a need.

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**Author:** ![Dan\_Eastwood](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/dan_eastwood/32/2368_2.png) [@Dan\_Eastwood](https://discourse.peacefulscience.org/u/Dan_Eastwood)\
**Post date:** [March 3, 2021, 4:13pm UTC](https://discourse.peacefulscience.org/t/x-men-constructive-neutral-evolution/4950/34 "2021-03-03T16:13:34Z")

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How is it I am only now seeing this great thread! 🙂

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