This philosophy site's mutated vitamin C gene

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Steve3007
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This philosophy site's mutated vitamin C gene

Post by Steve3007 » December 5th, 2017, 7:40 am

As some people probably noticed, this website recently went offline for a few days because (according to the error reports) it was using a modifier in a PHP command that had become obsolete and was no longer supported. As a software engineer myself I know from experience that this kind of thing (constant updates to various pieces of technology on which your software/site depends) means that you often have to do a fair bit of work just to stand still; just to keep the software/site functioning as it did before. If you do no work on your software/website then it will eventually "break" of its own accord. If the software/site is not used then there will be no "selective pressure" to fix it. Use it or lose it.

Humans and many other primates are not capable of manufacturing vitamin C in our bodies. Many other mammals are. We all have the gene which "codes for" the manufacture of vitamin C, but ours is broken. So we need vitamin C in our diets. The evolutionary reason why that gene is broken is because we do have vitamin C in our diets. There is no selective pressure to keep it functioning, so it eventually an "update" in the environment breaks it. Use it or lose.

Are these two situations analogous?
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Steve3007
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Re: This philosophy site's mutated vitamin C gene

Post by Steve3007 » December 5th, 2017, 7:45 am

There was a slight grammatical error in this sentence:

"There is no selective pressure to keep it functioning, so it eventually an "update" in the environment breaks it."

It should have said something like this:

"There is no selective pressure to keep it functioning, so eventually an "update" in the environment breaks it."
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LuckyR
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Re: This philosophy site's mutated vitamin C gene

Post by LuckyR » December 6th, 2017, 3:11 am

My guess is since there is little evolutionary pressure to keep the gene, it is logical that the broken gene is not selected against. However this situation does not explain the vitamin C gene's absence, merely the presence of the broken one. To explain the functioning gene's absence there must either be a separate disadvantage of the gene itself (unlikly), or my guess it is located near a different gene that has been heavily selected against and it went along for the ride, as it were.
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Re: This philosophy site's mutated vitamin C gene

Post by Steve3007 » December 6th, 2017, 4:12 am

LuckyR:
My guess is since there is little evolutionary pressure to keep the gene, it is logical that the broken gene is not selected against. However this situation does not explain the vitamin C gene's absence, merely the presence of the broken one.
There is little evolutionary pressure to keep the gene creating vitamin C. In all mammals (I gather) it is not absent. It is always present in some form. But in humans and some other primates it doesn't cause the creation of vitamin C because there is a mutation in one particular part of the chain of events that does that. Interestingly, in some other mammals who also can't make vitamin C in their bodies and therefore need it in their diets, different parts of the gene are "broken". This lends weight to the idea that in the absence of selective pressure to keep them functioning, things break in essentially random ways. i.e. "use it or lose it".
To explain the functioning gene's absence there must either be a separate disadvantage of the gene itself (unlikly), or my guess it is located near a different gene that has been heavily selected against and it went along for the ride, as it were.
I don't see why possession of the non-functioning gene (i.e. the functioning gene's absence) needs to have a selective advantage in order to be the case. Mutations happen randomly. If the possession of a gene which does not result in the creation of vitamin C does not confer any selective disadvantage then it will inevitably eventually "break", or mutate. There does not need to be selective pressure for it to do that.

Relating this back to software: I know from personal experience that very similar things happen in that world. If you have a software project and you arrange things such that a section of code is never called (e.g. by commenting it out) then eventually that section of code often breaks and if you try to reinstate it you find that it causes compiler errors and no longer works. Obviously software doesn't mutate in the same way that genes do (well, not often!) but other equivalent things do happen. You sometimes accidentally change something in it and don't notice, because there are no consequences. More often what happens is that the rest of the code, or external libraries on which your code depends, change and render the code obsolete. The latter is what happened to this philosophy website. If there hadn't been any philosophers who wanted to use the website (i.e. there hadn't been any "selective pressure" to keep it functioning) then it would no doubt have stayed non-functioning and gradually got more and more obsolete as the external software environment changed around it. It would have become an increasingly obsolete and corrupted software fossil, perhaps to be re-discovered by future generations of software paleontologists.
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Re: This philosophy site's mutated vitamin C gene

Post by Eduk » December 6th, 2017, 12:33 pm

I think of Evolution as ultimately defined by shapes. Whatever shape exists, exists. Whichever shapes continue to exist, continue to exist. I don't see the evolution of life on earth as any different from the evolution of the earth from (whatever came before). In this regard it is to be expected that evolution is a term that can be applied analogously to many situations. For example the introduction of the word Meme into everyday use by (at first) Dawkins.
So in short, yes :)

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Re: This philosophy site's mutated vitamin C gene

Post by LuckyR » December 7th, 2017, 2:16 am

Steve3007 wrote:
December 6th, 2017, 4:12 am
LuckyR:
My guess is since there is little evolutionary pressure to keep the gene, it is logical that the broken gene is not selected against. However this situation does not explain the vitamin C gene's absence, merely the presence of the broken one.
There is little evolutionary pressure to keep the gene creating vitamin C. In all mammals (I gather) it is not absent. It is always present in some form. But in humans and some other primates it doesn't cause the creation of vitamin C because there is a mutation in one particular part of the chain of events that does that. Interestingly, in some other mammals who also can't make vitamin C in their bodies and therefore need it in their diets, different parts of the gene are "broken". This lends weight to the idea that in the absence of selective pressure to keep them functioning, things break in essentially random ways. i.e. "use it or lose it".
To explain the functioning gene's absence there must either be a separate disadvantage of the gene itself (unlikly), or my guess it is located near a different gene that has been heavily selected against and it went along for the ride, as it were.
I don't see why possession of the non-functioning gene (i.e. the functioning gene's absence) needs to have a selective advantage in order to be the case. Mutations happen randomly. If the possession of a gene which does not result in the creation of vitamin C does not confer any selective disadvantage then it will inevitably eventually "break", or mutate. There does not need to be selective pressure for it to do that.

Relating this back to software: I know from personal experience that very similar things happen in that world. If you have a software project and you arrange things such that a section of code is never called (e.g. by commenting it out) then eventually that section of code often breaks and if you try to reinstate it you find that it causes compiler errors and no longer works. Obviously software doesn't mutate in the same way that genes do (well, not often!) but other equivalent things do happen. You sometimes accidentally change something in it and don't notice, because there are no consequences. More often what happens is that the rest of the code, or external libraries on which your code depends, change and render the code obsolete. The latter is what happened to this philosophy website. If there hadn't been any philosophers who wanted to use the website (i.e. there hadn't been any "selective pressure" to keep it functioning) then it would no doubt have stayed non-functioning and gradually got more and more obsolete as the external software environment changed around it. It would have become an increasingly obsolete and corrupted software fossil, perhaps to be re-discovered by future generations of software paleontologists.
Sorry for confusing you. If the previously ubiquitous functional gene is now essentially absent, random mutations over time do not explain this change. It explains the presence of the mutation, even it's persistence over long periods of time. But if both genes are in a population without an advantage or disadvantage, both will continue in the population.

Moving from complete function to complete dysfunction can happen in computers because their code is either connected or at least runs on the same operating system. One screw up and the system goes down. People have indépendant and separate codes and only update through the incredibly inefficient technique of having kids (one at a time). Not exactly a system-wide update.
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Re: This philosophy site's mutated vitamin C gene

Post by Steve3007 » December 7th, 2017, 10:39 am

LuckyR:
Sorry for confusing you. If the previously ubiquitous functional gene is now essentially absent, random mutations over time do not explain this change.
I don't understand what you mean by this. The functional gene does not become absent. A single random mutation stops it from performing the function that it previously performed. In the case of the gene which previously coded for the production of vitamin C, in humans it is a single mutation which stops a single function near the end of the chain of events leading to the production of vitamin C.

Why do you say that a random mutation cannot explain this?
It explains the presence of the mutation, even it's persistence over long periods of time.
Yes. The presence of the mutation which stops the production of vitamin C in the body.
But if both genes are in a population without an advantage or disadvantage, both will continue in the population.
I don't get what you're trying to say.
Moving from complete function to complete dysfunction can happen in computers because their code is either connected or at least runs on the same operating system.
What do you mean by conncted? The same operating system as what?

Moving from complete function to complete dysfunction can happen in software due the change of a single byte of computer code for the same reason that it can happen due to a single mutation of a gene.
People have indépendant and separate codes and only update through the incredibly inefficient technique of having kids (one at a time). Not exactly a system-wide update.
I don't understand your point here.
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LuckyR
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Re: This philosophy site's mutated vitamin C gene

Post by LuckyR » December 8th, 2017, 2:56 am

Steve3007 wrote:
December 7th, 2017, 10:39 am
LuckyR:
Sorry for confusing you. If the previously ubiquitous functional gene is now essentially absent, random mutations over time do not explain this change.
I don't understand what you mean by this. The functional gene does not become absent. A single random mutation stops it from performing the function that it previously performed. In the case of the gene which previously coded for the production of vitamin C, in humans it is a single mutation which stops a single function near the end of the chain of events leading to the production of vitamin C.

Why do you say that a random mutation cannot explain this?
It explains the presence of the mutation, even it's persistence over long periods of time.
Yes. The presence of the mutation which stops the production of vitamin C in the body.
But if both genes are in a population without an advantage or disadvantage, both will continue in the population.
I don't get what you're trying to say.
Moving from complete function to complete dysfunction can happen in computers because their code is either connected or at least runs on the same operating system.
What do you mean by conncted? The same operating system as what?

Moving from complete function to complete dysfunction can happen in software due the change of a single byte of computer code for the same reason that it can happen due to a single mutation of a gene.
People have indépendant and separate codes and only update through the incredibly inefficient technique of having kids (one at a time). Not exactly a system-wide update.
I don't understand your point here.
Okay. Lets say a gene C is ubiquitous within the population of humans, ie 100% of the genes in the population. At a future time one kid is born with a spontaneous mutation, C prime. If it is a lethal mutation, the kid dies and the mutation dies with it, the population is still 100% C. Later another mutation happens, C prime 2. This is neither selected for or against. The kid grows up and passes it to half of his kids, and so on. Of course, greater than 99% of the population is C type. If C prime 2, has no advantage over C type, it will exist in the population at some nominal level, but the original C type will dominate. For the mutation to replace the original within the population as a whole it either has to have a huge advantage itself (less likely) or be located near a gene that does (more likely, in my opinion).

In computers, if a program has an unused line of code that silently becomes incompatible with an update to the Operating system, that program can crash on every machine that has updated the OS, ie it can hit the whole system since updates are practically systemwide. People as everyone knows only update their genetic material (for the purposes of the population) when they have kids, much slower, inefficient and fun than getting a message that OS 10 is ready for download.
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Re: This philosophy site's mutated vitamin C gene

Post by Steve3007 » December 8th, 2017, 3:51 am

LuckyR:

Ah, ok. I see what you mean now. Good point. As you say, if the mutation has no selective advantage but is merely neutral then you wouldn't expect it to spread to the whole population.

Thinking about it, I suppose if a functioning vitamin C gene confers neither an advantage nor a disadvantage in a given species then, over a long period of time, one might expect various different mutations to be present in that gene in various different sections of the population. And the distributions of those different mutations might give us useful information about our genetic origins. But if (as I've read) the entire human population has the same single mutation in that gene then either that mutation must actually confer a selective advantage after all or it must reflect the fact that the mutation happened before there was an extreme "bottleneck" in the total human population of the world. I've read that there was a point in the past when the human population shrank almost out of existence. So maybe that's it?

It'd be interesting to do some more reading on the subject and see whether the evidence suggests if either of those things (or both) is the answer.
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Re: This philosophy site's mutated vitamin C gene

Post by Eduk » December 8th, 2017, 4:36 am

But if (as I've read) the entire human population has the same single mutation in that gene then either that mutation must actually confer a selective advantage after all or it must reflect the fact that the mutation happened before there was an extreme "bottleneck" in the total human population of the world.
I believe there is a third option. The 'faulty' gene is just along for the ride with other 'successful' genes. It comes as part of the package, so to speak.

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Re: This philosophy site's mutated vitamin C gene

Post by Steve3007 » December 8th, 2017, 5:20 am

Eduk:

Yes, sounds reasonable. Possibly the same as what LuckyR meant by:
...or be located near a gene that does (more likely, in my opinion).
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Re: This philosophy site's mutated vitamin C gene

Post by Ecurb » December 8th, 2017, 1:10 pm

It is a logical mistake to assume the antecedent. Evolutionary theory states that if a gene promotes descendant-leaving success it will tend to spread (I'm over simplifying). It is a mistake to assume that because a gene is widespread, it must have promoted descendant leaving success. (There are many examples, like genes which promote the existence of tailbones in humans.)

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Re: This philosophy site's mutated vitamin C gene

Post by LuckyR » December 9th, 2017, 2:26 am

Steve3007 wrote:
December 8th, 2017, 5:20 am
Eduk:

Yes, sounds reasonable. Possibly the same as what LuckyR meant by:
...or be located near a gene that does (more likely, in my opinion).
Exactly correct
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Re: This philosophy site's mutated vitamin C gene

Post by JamesOfSeattle » Yesterday, 10:22 pm

Um, to answer the original question ("Are these two situations analogous"), I would say they are, but there is a better analogy. The situation that happened with the software is not that the code broke but instead that the environment changed. The code was perfectly fine until that happened.

So a better gene analogy might look like this: say gene x is useful for making red apples edible. As it turns out, gene x also turns green apples into a deadly poison. So gene x spreads in the population where red apples are abundant and green apples don't exist. But when a group moves from Redappleland to Greenapple Island, things go south, or, um, pear shaped? If green apples are an important food source on the island, then a point mutation in x making it non-functional might spread pretty fast.

*

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