

Vitamin C is a bug that needs to be patched - sbierwagen
http://bbot.org/blog/archives/2012/02/24/the_pinnacle_of_evolution/

======
azakai
> The same hormone [vasopressin] that controls your blood pressure also
> determines if you can form a relationship. [..] Who the fuck designed this?
> The answer is, of course, "nobody". The blind idiot god of evolution cares
> not at all for separation of concerns, or design elegance

This is a very uncharitable interpretation of how the body works.

Vasopressin is being used as a _signal_ mechanism here. Saying that it being
involved with things from blood pressure to pair bonding is evidence of
inelegant design is like saying that the web is inelegant, because TCP is
involved in both code (transmitted JS) and data (transmitted JPEG images).
Yes, TCP is a mechanism used to deliver both of those (like vasopressin is a
mechanism used to cause pair bonding and change blood pressure), but that
doesn't mean there is a tangled web of dependencies here.

------
user2634
The best thing in this post was a link to <http://idlewords.com/> . Very
interesting blog.

------
joshu
guy brags about CSS and has a website that renders one word per line on an
iphone.

yeah.

~~~
sbierwagen
Shit, really? It rendered fine on Pre Webkit, which was the only mobile
platform I could test against.

Screenshot?

EDIT: Added some new rules to the 600px @media block that remove the 215 pixel
left margin, and the #links div. Which is a pretty dumb way to "fix" the
problem, but after all, I'm a dumb guy.

------
bjeanes
The author seems to confuse natural selection with evolution.

------
leoh
Interesting. I would like to point out, though, that The pathway for
L-ascorbate (Vitamin C) synthesis is not trivial <http://www.genome.jp/kegg-
bin/show_pathway?map00053>, but in first world countries, ingesting sufficient
amounts of the vitamin is trivial.

~~~
jbri
What's interesting is that the human body still does most of the synthesis -
it's only the enzymes for the last step that have been disabled.

------
jakeonthemove
Natural evolution is just super lazy - it does _just enough_ to get by, and
won't lift a finger for anything else...

------
hxa7241
> evolution cares not at all for separation of concerns

That is not really quite true. Look at human anatomy: it is structured into
various discrete organs. That is separation of concerns.

Evolution indeed appears to create, adjust, and maintain systems of
abstraction, somehow . . . and when you think about it, it seems central to
what evolution is doing.

You can start with the thought that there must be some coherent, discrete,
mapping from genome to body -- otherwise evolution, by selection, could not
work. It is not simple or clear, but there must be significant logical
structure.

Chaitin postulates hierarchy as a basic form
(<http://www.cs.auckland.ac.nz/~chaitin/jack.html>): it is a way to restrict
the effects of mutation, and is indeed evident in the body. Chaitin also
explains the genome/body separation
(<http://www.cs.auckland.ac.nz/~chaitin/ev.html>): it is a way of amplifying
mutation -- small changes in the genome make large effects in the body
(otherwise, large changes in the body would require comensurately large
mutation) -- thereby making evolution more powerful.

It seems there must be _some_ significant relationship to software yet to be
unravelled.

<http://www.hxa.name/notes/note-hxa7241-20090831T2006.html>

~~~
eru
> You can start with the thought that there must be some coherent, discrete,
> mapping from genome to body -- otherwise evolution, by selection, could not
> work. It is not simple or clear, but there must be significant logical
> structure.

Sorry, I can't follow that logic. Could you please elaborate?

------
akkartik
Very fun article.

Perhaps we'll be able to eliminate the bacteria one day, but it's a tall tall
order. Beyond a certain level of complexity paratisitism seems to
spontaneously emerge for reasons we don't fully understand. To avoid it you'd
have to either centrally design (micromanage) complex systems at least 4
orders of magnitude larger than anything attempted so far, or you'd have to
come up with a set of simple rules that causes complex behavior without
parasitism. I suspect the latter especially is an ill-posed meaningless
question.

Personally I think all our largest codebases today already have a parasitism
'problem'. They suffer from two kinds of parasites: dead code and crappy
programmers living off maintaining them.

I would bet on attaining immortality before eliminating parasites from the
human body. It's not a bug but a feature.

~~~
lukeschlather
Calling out bacteria as parasites is pretty silly. One might as well call out
the appendix (which is composed entirely of human cells) as parasitic.
Bacteria are much more like shared libraries. Libraries can of course have
malicious code embedded in them, and human systems are prepared for that
inevitability, but that doesn't mean the wholesale removal of shared libraries
is very desirable.

~~~
ars
Funny that you mention the appendix in a post about bacteria - because that is
the function of the appendix: To tend to and maintain bacteria during times of
intestinal illness.

------
LarryMade
My thought is we are built for our world, you try tinker with the natural
processes bad stuff will likely result. We know a lot about how we function,
but we don't really get the big picture of how everything here on earth works
with us and we with it.

~~~
bermanoid
We're actually pretty intelligent, though, and we don't need to know how
_everything_ works together in order to be able to tinker with natural
processes just enough to keep from dying, in a lot of cases.

Keep in mind that a healthy percentage of the people reading this discussion
would be dead right now if it weren't for modern medicine. I've personally had
several bacterial infections as a child that would have stood a reasonable
chance of killing me if it wasn't for antibiotics, and one nasty infected
wound as an adult that I was told would have had me at 50/50 if it wasn't for
the meddling that doctors were able to do to clean it up.

------
js2
See also the recurrent laryngeal nerve for more of nature's absurdity.

[http://whyevolutionistrue.wordpress.com/2011/05/28/the-
longe...](http://whyevolutionistrue.wordpress.com/2011/05/28/the-longest-cell-
in-the-history-of-life/)

~~~
nn2
and large parts of our genome is bit-rotted and non functional

Larry Moran has a lot of good material on this
[http://sandwalk.blogspot.com/2008/02/theme-genomes-junk-
dna....](http://sandwalk.blogspot.com/2008/02/theme-genomes-junk-dna.html)

~~~
colonel_panic
Bit rot is a feature. It allows genes that don't impact survival to attain
greater diversity within the population so that, if the environment changes
and the gene becomes relevant, some part of the population may be better able
to adapt.

~~~
nn2
Does your explanation for junk DNA pass the onion test?
<http://www.genomicron.evolverzone.com/2007/04/onion-test/>

------
josscrowcroft
I don't get it - do I keep taking these 1000mg Vitamin C supplements or not?

~~~
derleth
They almost certainly won't hurt, but, unless you're otherwise in danger of
Vitamin C deficiency, they likely aren't doing you a lot of good, either.

[http://www.quackwatch.org/01QuackeryRelatedTopics/DSH/colds....](http://www.quackwatch.org/01QuackeryRelatedTopics/DSH/colds.html)

~~~
adammichaelc
I would take anything from quackwatch with a huge grain of salt. It is very
biased against all non-synthetic, non-pharmaceutical medical treatments. The
author either willfully ignores the science published on herbal pharmacology
and nutritional medicine, or he isn't paying attention, or he has an agenda.
In any case, I'd rather get my info on medicine from a more balanced source.

Edit: here's a balanced source on the current research on vitamin C
supplements. Scroll down to disease treatment
(<http://lpi.oregonstate.edu/infocenter/vitamins/vitaminC/>)

------
emmelaich
The _benefit_ of a tangle of dependences or _lack_ of separation of concerns
is that you need less energy to drive the organism. Analogously, the benefit
of having thing look like a nail when all you've got is a hammer is that you
_only_ "need" the hammer.

I'm approaching the tautological thought that organisms are by definition
perfect for their ecological niche because if they weren't, they would be
something else (given enough stability and time in that niche)

Random fun trivia: dogs do synthesize vitamin C.

~~~
zvrba
> Random fun trivia: dogs do synthesize vitamin C.

And another random fun trivia: chocolate is poisonous to dogs. I'm happy to be
human! :D

~~~
bdunbar
It's more accurate to say that theobromine is poisonous to dogs: 100mg to 1kg
of body weight.

Which is why my shepherd can filch the occasional candy bar and not die. One
candy bar - annoying (to me) but not fatal. A pound of bakers chocolate and
she'd be in doggy heaven.

------
DrJokepu
I'm no biologist or evolutionist but it appears to me that welfare society and
mass healthcare greatly reduced the effects of natural selection. As long as
Vitamin C food supplements are easily accessible and people are educated to
take them, there's simply no evolutionary imperative to "fix this bug." Maybe
the author was referring to some sort of future artificial genetic
engineering-based solution?

~~~
darkandbrooding
As far as I can tell, the term "evolutionist" is not used within the
scientific community. It does, however, seem to have found a home in the
vocabulary of anti-evolution, creationist communities. This makes me suspect
something of your political/spiritual philosophy.

Your use of the phrases "welfare society" and "mass healthcare" strengthen the
above suspicion. You next suggest that the "welfare society" (which has been
practiced by a small fraction of the global population for - what, four
generations now?) might already have reduced the effects of natural selection.

First, let me opine that welfare societies and mass healthcare would not
"reduce the effects" of natural selection, they would simply re-order the
traits that were being selected for.

Second, let me respectfully suggest that you would benefit from a more
detailed study on the topic of natural selection.

Lastly, I would encourage you to consider the evocative power of the words you
use in your arguments. Because of your choice of words a lazy reader, or one
who arrived at this thread with conflicting opinions, might write you off as a
politically conservative creationist who does not understand some (or several)
of the terms you are using. You would be well served by avoiding shorthand
terms like "evolutionist."

~~~
DrJokepu
You seem to have misunderstood my comment which is probably my fault due to
unclear wording. Evolutionist was indeed a bad choice of word but in my
defence over here in Europe the word "evolution" is really not that
emotionally charged. I should have written "evolution researcher" or something
similar.

Welfare society is a common expression to describe the model of post-1960
Western and North European societies. America is rather different but my
understanding is that in many states there have are at least some measures in
place to help people in need.

About "mass healthcare": here in Europe we have universal healthcare. That's
not the case in America, however, regardless of its problems, healthcare is
accessible to large portions of the American society, as opposed to other
countries or historical times where only a very small percentage of the
society has or had access to any form of healthcare. I don't think that this
expression is a very bad way to describe that.

It's really nobody's business but to put things in context, I do believe that
"welfare society", "universal healthcare" are very good things, and I would
describe myself as a "non-believer" and a "European conservative".

I agree that with your opinion that these phenomena "re-order the traits that
are being selected for" but I stand by my assertion that being able to compose
Vitamin C is not one of those traits. In general, my understanding is that
many genetic features in the past that put individuals at disadvantage are
considerably less relevant today. Even in extreme cases where these traits
make reproduction impossible these effects mean that individuals affected by
them will be able to stay around and increase the survival chances of others
in the family. Once again, I would like to mention that this is only my
understanding and I am not qualified enough in these areas to make
authoritative statements. However, I would consider myself to be as well-
informed about these subjects as anyone in the general population cat get,
having read numerous books on the subject aimed at the general population
authored by scientists who are considered to be experts in the area. One of
them is a well-known advocate of atheism these days which I personally think
is a shame, I much preferred when he was "only" a very good writer of books
about evolution.

In addition, I appreciate your constructive intentions but this kind of
patronising tone is really not necessary.

------
Tichy
Couldn't some of those stomach bacteria be patched to produce Vitamin C? I
suppose some humans already have such bacteria in their gut, without knowing
it?

~~~
Daniel_Newby
Yes, but what's in it for them? Vitamin C synthesis uses a lot of energy.
Patched microbes that mutated to stop making vitamin C would rapidly
outcompete their ancestors.

~~~
ars
That can be dealt with, just like nitrogen fixing bacteria in legumes are
punished if they try to cheat. All you need is some method of signaling who
cheats and who doesn't.

~~~
sounds
I've looked around to find more about the N2 fixing bacteria, and found
[http://en.wikipedia.org/wiki/Rhizobia#Nodule_formation_and_f...](http://en.wikipedia.org/wiki/Rhizobia#Nodule_formation_and_functioning)
\- but no definitive treatment.

If you have a chance, can you please point an interested reader to more info?

~~~
ars
The second paragraph in the section you linked to discusses how the plant
punishes cheaters.

I don't think there is a definitive treatment. There are lots of experiments
and many possible mechanisms that have been discovered or proposed, and
probably all are used by the plant.

------
easp
Fun post, but I don't think it supports its own conclusion. Given the tangle
of dependancies involved in a properly functioning human, why put focused
effort into patching something as easily remediated as the inability to
synthesize Vitamin C, given the opportunity for unforeseen side effects?

I think he just doesn't want to eat his applesauce like a good wittle man.

~~~
gwern
Why would we expect patching vitamin C to be hard or come with consequences?
As pointed out, it's trivial enough that almost all animals do it.

~~~
Scriptor
We don't know whether any other genes have adapted in the last 10 million
years to the lack of the pathway needed to synthesize vitamin C. Reintroducing
the proteins for this pathway may cause unintended interactions with existing
proteins.

Imagine a large software system that had a small mobile website. New changes
to the code must be compatible with this mobile website and can't break it.
Now imagine that one day this mobile website was taken out. Development
continues but since there's no need to worry about the mobile site numerous
incompatible changes creep in over time.

Now suddenly new management comes in and decides that the mobile site should
be brought back. Clearly, as soon as they try to put it back in they run into
every incompatible change ever made to the code and the whole thing becomes
highly unstable.

So that's what (might) have happened in the body. With no worrying about
whether a new mutation might negatively interact with the vitamin C pathway
that new mutation can proliferate freely, especially if it is beneficial. All
reverse-compatibility is lost.

~~~
simcop2387
In theory it might be possible to test this experimentally. Rather than
genetically modify them from the start, synthesize the protein in question and
try to get it into cell cultures. This should make it possible to get an idea
of what will happen in that situation, e.g. will it kill the cells or cause
anything obviously wrong. After that test it on some animals with similar
Vitamin C problems. Shouldn't be impossible to test this, after the animals
test it in adults to find out. etc.

------
UseofWeapons
This is my first response, so I'll try and make it information>noise.

This is a typically non-biological / ecological dunce post for Ycomb, n/and an
ignorant post that I see commonly espoused by the bottom layers of the 2.0 /
transitional ideological parties.

The lack of a genetic ability to produce Vitamin C is neither a bug nor an
issue for the mammals that do not possess it. In all cases, either the mammal
in question gains from the lack [i.e. the lack has driven forward other
behaviours that have proved more beneficial whilst searching out sources of
Vit C, e.g. dextral abilities to harvest fruit from trees in the case of some
early primates] or is neutrally aligned to it [i.e. Vit C is already a
mainstay of their diet, so there is never a lack of it, e.g. fruitivores].

The proof? They. Fucking. Survived. For. Millions / 100' Thousand Years.

This is only a "bug" when you add in a modern [last 3000 years] lifestyle
where fruit / veg is a "limited resource".

>> The "bug" is not the inability to produce Vit C, the real bug is living in
a system that doesn't allow easy access to Vit C. Living on a ship off worm-
riddled meat for a year? That's an environmental problem. Same goes for inner
city "food deserts" where Walmart has stomped on any and all local garden
produce.

Category error. Sheesh, I'd have hoped you people were more intelligent than
this.

[and for the record: producing Vit C chemically is a hella lot easier than
genotyping in a fix, you fucking moron]

~~~
UseofWeapons
-2?

This Angel is getting a good 'vibe' for the average user already ~ and here we
were thinking this was different from Reddit or Zero Hedge.

>Here's a tip: if you downvote, add a response to the why, otherwise, we
ignore your input<

~~~
enko
> Sheesh, I'd have hoped you people were more intelligent than this.

"You people"? Really? I wonder who you are imagining "you people" to be?

> and here we were thinking this was different from Reddit or Zero Hedge

Well, you're wrong. Still humans, I'm afraid, a lot of them, in a wide range
of shades and dispositions.

"Use of Weapons" is one of my favourite books, if you're going to assume its
name as your HN identity then please do it justice.

------
mhurron
I don't see how the requirement to ingest $SPECIFIC_CHEMICAL_A is any
different than the need to ingest any other chemical i.e. food.

~~~
SeveredCross
Because the chemical in this case is something we have all the necessary
things to produce.

I can't _make_ energy (ie. food) from no input, but with some energy
expenditure, my body could carry out the set of reactions to convert glucose
(which is readily available in the diet) to Vitamin C.

~~~
pja
Nearly every other mammal on the planet can make their own vitamin C. Aren't
primates & guinea pigs the only exceptions?

~~~
skoob
Quoting <http://en.wikipedia.org/wiki/Vitamin_C> :

 _It is made internally by almost all organisms although notable mammalian
group exceptions are most or all of the order chiroptera (bats), guinea pigs,
capybaras, and one of the two major primate suborders, the Anthropoidea
(Haplorrhini) (tarsiers, monkeys and apes, including human beings)._

So not all primates.

~~~
UseofWeapons
Ok, look back at the wiki.

Do you know <i>why</i> you can't internally produce Vit C?

~~~
jbri
Because a mutation turned off our precursor's ability to do so, and (due to
the abundance of vitamin C in their diet), wasn't immediately deleterous but
instead managed to spread throughout the entire population.

------
wheels
> _For evolution, the person who died at the age of 29, with six children, and
> the person who lived for two hundred years and won six dozen Nobel prizes,
> but never had children, it considers the latter person to have failed._

That's not necessarily true. Since our genetic programming can also dictate
social behaviors, the fundamental genetic unit isn't always the individual:
there are a lot of organisms where they've evolved to have a large percentage
of the population not reproduce, yet are absolutely vital to the species. For
example, worker bees aren't a "failure". Whether or to what extent such things
influence human evolution is hard to speculate on.

I don't get the point that the author is trying to make about gut flora
either, but it also seems misguided. Humans have evolved in symbiosis with our
gut flora. Why would we want to eliminate them? There seems to be a built in
assumption that having foreign cells in our body must be inherently bad, but
that has no basis in science. If a foreign, symbiotic organism can perform a
task efficiently inside of the human body, what is the advantage of having it
instead done by that person's cells?

~~~
derleth
> there are a lot of organisms where they've evolved to have a large
> percentage of the population not reproduce, yet are absolutely vital to the
> species

It sounds like post-hoc rationalizing to apply this logic to humans.

> Humans have evolved in symbiosis with our gut flora. Why would we want to
> eliminate them?

It complicates the system to have to maintain a balanced internal ecology;
look at the probiotic yogurts out there to see how often it gets out of whack
in the real world.

~~~
wheels
> _It sounds like post-hoc rationalizing to apply this logic to humans._

With the complexity of human social interactions, it would bewildering were it
_not_ the case that there are at least some small instances of genetic
advantage being conferred to population groups based on the existence of non-
reproductive members.

The concrete case where I've heard this considered is (strict) homosexuality.
Logically, in so far as there's a genetic component to such, one would expect
homosexuality to be eliminated from the gene-pool over time. One of the
guesses as to why that has not happened is that homosexuality may confer some
social benefit which increases the overall survival and reproductive capacity
of the genetic group to which the homosexual members belong. (There are other
plausible explanations as well, but it's not incredibly far fetched to believe
that such _could_ be the case.)

~~~
bermanoid
While that's certainly a conceivable explanation (the "gay uncle" theory, that
the gay members of a family help raise their family's offspring), I've always
found it really tough to swallow the numbers there. More or less, it would
require that each gay uncle increases the fitness of the family [see note 1
below, "family" is very important here, as opposed to "group"!] by enough to
make sure that on average, more than 1 additional child is produced per gay
uncle. Put another way, with a 10% rate of homosexuality in the population at
large, that would mean that at least 10% of our total reproductive success
should be due to the helping hand that gays provide for family members'
children. That's a lot, probably more than I'd realistically believe.

More likely, the gene that predisposes us to homosexuality (it doesn't cause
it, as MZ vs DZ twin studies have shown that homosexuality has well below 50%
genetic cause, with a much higher component based on individual environment,
both pre and post-natal) is either beneficial in some other way (for instance,
a recent study showed that female relatives of homosexuals tend to have more
children, which could mean that the heritable bits behind homosexuality
actually increase female reproductive rates enough to overwhelm the negatives
on the male end), or live close on the chromosome to another gene that's more
important, so the gene tends to stick around because of linkage even if it's
harmful in some cases.

[1] The "gay uncle" theory relies on the fact that it's family members, i.e.
people that are causally likely to share the gene in question, that are helped
by the behavior. Google "kin selection" and "group selection" to understand
the difference - briefly, kin selection is a totally legitimate effect because
a gene helps itself through its prevalence in a family (and specifically, due
to the fact that the gene will appear in the offspring that the gene helps
make possible, even if it comes from other individuals), but group selection
is completely bogus, because Prisoner's Dilemma-style defection is always the
right strategy for a gene there.

~~~
moonchrome
>both pre and post-natal

Wait - if twin studies showed bellow 50% correlation, how can it be pre-natal
environment ?

But you make a stronger point in the footnote, his initial argument relies on
group selection and can be dismissed on those grounds, no need to debate how
that relates to homosexuality.

