10 ms·

Vitamin C is a bug that needs to be patched

143 points by sbierwagen 15y ago

Tichy 15y ago
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 15y ago
  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 15y ago
    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 15y ago
      I've looked around to find more about the N2 fixing bacteria, and found http://en.wikipedia.org/wiki/Rhizobia#Nodule_formation_and_functioning http://en.wikipedia.org/wiki/Rhizobia#Nodule_formation_and_f... - but no definitive treatment. If you have a chance, can you please point an interested reader to more info?
      - ars 15y ago
        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.
    - Daniel_Newby 15y ago
      Colon bacteria are all mixed together, so selectively rewarding symbiotes is hard. And anyway vitamin C is sufficiently energy-rich that if a bacterial species started making it in quantity, other species would rapidly evolve to eat vitamin C for energy.
      - ars 15y ago
        Here's one possible design: Currently the immune system prevents bacteria from living too close to the cells of the intestines (they have to stay in the mucus). Setup a signaling system where bacteria that make vitamin C are permitted to stay close, and are shielded from the actions of the immune system. This lets you selectively host those bacteria, and it puts the vitamin C right where it can be immediately absorbed before other bacteria can get to it. It also punished cheaters, since without the vitamin C the immune system would attack them and force them to stay farther from the food. It's not much father from there to a dedicated organelle (or cells) the specifically host desired bacteria and all others are killed by the immune system. And from there the host might incorporate the genes from the bacteria in the same way mitochondria are setup.
akkartik 15y ago
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 15y ago
  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 15y ago
    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.
  - bermanoid 15y ago
    Hell, we might as well call our mitochondria "parasites", if we're going all the way - those things have their own DNA, which evolves in tandem but separately from our own, in a rather different way from "normal" DNA.
mhurron 15y ago
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 15y ago
  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 15y ago
    Nearly every other mammal on the planet can make their own vitamin C. Aren't primates & guinea pigs the only exceptions?
    - pkulak 15y ago
      I would assume so, just because I've never seen a shark eating a lime.
      - ThaddeusQuay2 15y ago
        This doesn't mean that they don't tend secret lime farms on the ocean floor.
    - mrleinad 15y ago
      Is the process to convert glucose into Vitamin C understood? Would it require something that could be seen as a tradeoff in our case?
      - maxerickson 15y ago
        Probably not a tradeoff. Scurvy is devastating and Wikipedia says an animal like a 70 kg goat makes ~13 grams of Vitamin C a day (which isn't very much of anything).
leoh 15y ago
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 http://www.genome.jp/kegg-bin/show_pathway?map00053, but in first world countries, ingesting sufficient amounts of the vitamin is trivial.
- jbri 15y ago
  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.
js2 15y ago
See also the recurrent laryngeal nerve for more of nature's absurdity. http://whyevolutionistrue.wordpress.com/2011/05/28/the-longest-cell-in-the-history-of-life/ http://whyevolutionistrue.wordpress.com/2011/05/28/the-longe...
- nn2 15y ago
  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.html http://sandwalk.blogspot.com/2008/02/theme-genomes-junk-dna....
  - colonel_panic 15y ago
    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 15y ago
      Does your explanation for junk DNA pass the onion test? http://www.genomicron.evolverzone.com/2007/04/onion-test/ http://www.genomicron.evolverzone.com/2007/04/onion-test/
  - Gatsky 15y ago
    This is just hubris. A worm has the same number of protein coding genes as us. Obviously the 'non-functinal' DNA is doing something important, we just haven't worked it out yet. I would be very hesitant to criticize an evolutionary construct that has developed on a billion year timescale.
    - Tuna-Fish 15y ago
      Back in bio class, my professor said that in lab tests, replacing the non-protein-coding dna with something man-made hasn't been shown to have any effect. (Removing it does have an effect).
easp 15y ago
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 15y ago
  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 15y ago
    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 15y ago
      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.
DrJokepu 15y ago
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 15y ago
  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 15y ago
    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.
joshu 15y ago
guy brags about CSS and has a website that renders one word per line on an iphone. yeah.
- sbierwagen 15y ago
  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.
josscrowcroft 15y ago
I don't get it - do I keep taking these 1000mg Vitamin C supplements or not?
- derleth 15y ago
  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.html http://www.quackwatch.org/01QuackeryRelatedTopics/DSH/colds....
  - adammichaelc 15y ago
    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/ http://lpi.oregonstate.edu/infocenter/vitamins/vitaminC/)
emmelaich 15y ago
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.
- derleth 15y ago
  > 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 Meditate on what a simple hill-climbing algorithm does when it finds a tiny foothill right below a major peak. > Random fun trivia: dogs do synthesize vitamin C. From Wikipedia: "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)." That's one reason guinea pigs are used as, well, guinea pigs.
  - emmelaich 15y ago
    Late response, but yes, the article mentioned local maxima. But I think it's hubris to think we could do a LOT better. The human body is a gigantic "engineering" effort involving a vast number of trade-offs and compromises.
- zvrba 15y ago
  > 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
  - newman314 15y ago
    Yet another fun fact: if your dog eats something bad like a hotdog or chocolate, pour some hydrogen peroxide down its throat. It'll make the dog puke up the bad bits. Obviously, do this outside or in an area you can easily clean up.
UseofWeapons 15y ago
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]
- derleth 15y ago
  You're being downvoted because your arguments sound like post-hoc rationalizations and you're adopting a very combative, insulting tone. Mainly the second one, to be honest.
  - UseofWeapons 15y ago
    http://www.ncbi.nlm.nih.gov/pubmed/14962674 http://www.ncbi.nlm.nih.gov/pubmed/14962674 I can provide many more: this "bug" is a field of science that many, many papers have addressed: I'm being downvoted because few people here are mature enough to do their own research and instead prefer a "cool, wacky, zeitgeist" take on it. Trust me: about 100 years of biology has been done on this "bug". The OP piece is a joke.
    - 15y ago
wheels 15y ago
> 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 15y ago
  > 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 15y ago
    > 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.)
LarryMade 15y ago
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 15y ago
  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.
azakai 15y ago
> 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.
jakeonthemove 15y ago
Natural evolution is just super lazy - it does just enough to get by, and won't lift a finger for anything else...
hxa7241 15y ago
> 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 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 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 http://www.hxa.name/notes/note-hxa7241-20090831T2006.html
- eru 15y ago
  > 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?
bjeanes 15y ago
The author seems to confuse natural selection with evolution.
user2634 15y ago
The best thing in this post was a link to http://idlewords.com/ http://idlewords.com/ . Very interesting blog.

143 points by sbierwagen 15y ago

Tichy 15y ago

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 15y ago
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 15y ago
  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 15y ago
    I've looked around to find more about the N2 fixing bacteria, and found http://en.wikipedia.org/wiki/Rhizobia#Nodule_formation_and_functioning http://en.wikipedia.org/wiki/Rhizobia#Nodule_formation_and_f... - but no definitive treatment. If you have a chance, can you please point an interested reader to more info?
    - ars 15y ago
      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.
  - Daniel_Newby 15y ago
    Colon bacteria are all mixed together, so selectively rewarding symbiotes is hard. And anyway vitamin C is sufficiently energy-rich that if a bacterial species started making it in quantity, other species would rapidly evolve to eat vitamin C for energy.
    - ars 15y ago
      Here's one possible design: Currently the immune system prevents bacteria from living too close to the cells of the intestines (they have to stay in the mucus). Setup a signaling system where bacteria that make vitamin C are permitted to stay close, and are shielded from the actions of the immune system. This lets you selectively host those bacteria, and it puts the vitamin C right where it can be immediately absorbed before other bacteria can get to it. It also punished cheaters, since without the vitamin C the immune system would attack them and force them to stay farther from the food. It's not much father from there to a dedicated organelle (or cells) the specifically host desired bacteria and all others are killed by the immune system. And from there the host might incorporate the genes from the bacteria in the same way mitochondria are setup.

akkartik 15y ago

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 15y ago
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 15y ago
  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.
- bermanoid 15y ago
  Hell, we might as well call our mitochondria "parasites", if we're going all the way - those things have their own DNA, which evolves in tandem but separately from our own, in a rather different way from "normal" DNA.

mhurron 15y ago

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 15y ago
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 15y ago
  Nearly every other mammal on the planet can make their own vitamin C. Aren't primates & guinea pigs the only exceptions?
  - pkulak 15y ago
    I would assume so, just because I've never seen a shark eating a lime.
    - ThaddeusQuay2 15y ago
      This doesn't mean that they don't tend secret lime farms on the ocean floor.
  - mrleinad 15y ago
    Is the process to convert glucose into Vitamin C understood? Would it require something that could be seen as a tradeoff in our case?
    - maxerickson 15y ago
      Probably not a tradeoff. Scurvy is devastating and Wikipedia says an animal like a 70 kg goat makes ~13 grams of Vitamin C a day (which isn't very much of anything).

leoh 15y ago

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 http://www.genome.jp/kegg-bin/show_pathway?map00053, but in first world countries, ingesting sufficient amounts of the vitamin is trivial.

jbri 15y ago
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.

js2 15y ago

See also the recurrent laryngeal nerve for more of nature's absurdity. http://whyevolutionistrue.wordpress.com/2011/05/28/the-longest-cell-in-the-history-of-life/ http://whyevolutionistrue.wordpress.com/2011/05/28/the-longe...

nn2 15y ago
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.html http://sandwalk.blogspot.com/2008/02/theme-genomes-junk-dna....
- colonel_panic 15y ago
  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 15y ago
    Does your explanation for junk DNA pass the onion test? http://www.genomicron.evolverzone.com/2007/04/onion-test/ http://www.genomicron.evolverzone.com/2007/04/onion-test/
- Gatsky 15y ago
  This is just hubris. A worm has the same number of protein coding genes as us. Obviously the 'non-functinal' DNA is doing something important, we just haven't worked it out yet. I would be very hesitant to criticize an evolutionary construct that has developed on a billion year timescale.
  - Tuna-Fish 15y ago
    Back in bio class, my professor said that in lab tests, replacing the non-protein-coding dna with something man-made hasn't been shown to have any effect. (Removing it does have an effect).

easp 15y ago

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 15y ago
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 15y ago
  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 15y ago
    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.

DrJokepu 15y ago

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 15y ago
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 15y ago
  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.

joshu 15y ago

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

sbierwagen 15y ago
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.

josscrowcroft 15y ago

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

derleth 15y ago
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.html http://www.quackwatch.org/01QuackeryRelatedTopics/DSH/colds....
- adammichaelc 15y ago
  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/ http://lpi.oregonstate.edu/infocenter/vitamins/vitaminC/)

emmelaich 15y ago

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.

derleth 15y ago
> 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 Meditate on what a simple hill-climbing algorithm does when it finds a tiny foothill right below a major peak. > Random fun trivia: dogs do synthesize vitamin C. From Wikipedia: "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)." That's one reason guinea pigs are used as, well, guinea pigs.
- emmelaich 15y ago
  Late response, but yes, the article mentioned local maxima. But I think it's hubris to think we could do a LOT better. The human body is a gigantic "engineering" effort involving a vast number of trade-offs and compromises.
zvrba 15y ago
> 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
- newman314 15y ago
  Yet another fun fact: if your dog eats something bad like a hotdog or chocolate, pour some hydrogen peroxide down its throat. It'll make the dog puke up the bad bits. Obviously, do this outside or in an area you can easily clean up.

UseofWeapons 15y ago

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]

derleth 15y ago
You're being downvoted because your arguments sound like post-hoc rationalizations and you're adopting a very combative, insulting tone. Mainly the second one, to be honest.
- UseofWeapons 15y ago
  http://www.ncbi.nlm.nih.gov/pubmed/14962674 http://www.ncbi.nlm.nih.gov/pubmed/14962674 I can provide many more: this "bug" is a field of science that many, many papers have addressed: I'm being downvoted because few people here are mature enough to do their own research and instead prefer a "cool, wacky, zeitgeist" take on it. Trust me: about 100 years of biology has been done on this "bug". The OP piece is a joke.
  - 15y ago

wheels 15y ago

> 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 15y ago
> 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 15y ago
  > 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.)

LarryMade 15y ago

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 15y ago
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.

azakai 15y ago

> 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.

jakeonthemove 15y ago

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

hxa7241 15y ago

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

eru 15y ago
> 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?

bjeanes 15y ago

The author seems to confuse natural selection with evolution.

user2634 15y ago

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