[HN Gopher] Using paleogenomics to elucidate 10k years of immune...
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Using paleogenomics to elucidate 10k years of immune system
evolution
Author : gmays
Score : 29 points
Date : 2023-01-16 16:46 UTC (6 hours ago)
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| remote_phone wrote:
| The immune system is one of the reasons why I stopped believing
| in large scale evolution. I still believe small scale evolution
| exists, but I do not believe that our immune system came about
| randomly.
|
| There are two main factors to our immune system that protect us:
|
| 1) all our cells are marked uniquely and exactly the same across
| every cell in our body. Every human, and I think every animal,
| has this same feature where all cells are marked the same. But
| unless there was an immune system to enforce this, it has no
| value. If it were random you would expect every cell to be marked
| randomly but it's not.
|
| 2) our immune system is designed to attack anything that isn't
| marked with that unique identification. If we had random
| identification per cell, the immune system we have couldn't be
| created.
|
| This system couldn't be designed separately. It's essentially a
| single transaction two-step evolution that simply couldn't have
| been done randomly at different points in time. If you created an
| immune system that attacked things that weren't marked the cell
| across all cells, the organism would die because the immune
| system would attack itself the way transplant patients would. The
| immune system we have couldn't be created unless all the cells
| were marked the same.
|
| Both parts (unique identification are the same across all cells,
| and the immune system that attacks any other things that aren't
| marked the same) must have been created at the same time.
|
| If anyone has any counter arguments I would love to hear it
| because I've been thinking about this long and hard during Covid
| and couldn't think of anything else.
| pazimzadeh wrote:
| The fact that each of our cells has an identical unique marker
| (you must be referring to the MHC?) is not the basis of how the
| immune system functions. Instead, during development in the
| thymus, lymphocytes carrying a wide _variety_ of unique immune
| receptors are exposed to proteins from all over your body
| (heart protein, lung protein, etc..) and any lymphocyte that
| reacts with self is killed (negative selection), thus leaving
| you with remaining cells which which do not react to your body.
| https://en.wikipedia.org/wiki/Autoimmune_regulator
|
| The fact that the MHC regions is so diverse is just another
| layer of security which prevents major biases within the
| population in the presentation of chopped up bits of foreign
| and self antigens. However if we all had the same MHC, the
| function of the adaptive immune system would remain intact.
| Plus, we would be able to transplant organs between people much
| more easily.
|
| The basis for the existence of these varied adaptive immune
| receptors which perform the recognition of self vs non-self is
| under investigation and you might want to read up on the latest
| research before jumping to conclusions:
| https://europepmc.org/article/pmc/6084782
|
| If I remember correctly though, one of the major hypotheses is
| that an ancestor of the HIV or similar virus or transposon
| integrated itself within the gametes of some jawed fish without
| killing it, resulting in the ability to generate variation in
| immune receptors. https://pubmed.ncbi.nlm.nih.gov/7584143/
|
| Oh, and there is not just one way to have an adaptive immune
| system, as even jawless fish have a way of rearranging their
| receptors to generate diversity:
| https://pubmed.ncbi.nlm.nih.gov/15241406/
| https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3805090/
|
| In sum, the only GOD we have evidence for around in the
| Generation of Diversity.
| https://www.nature.com/articles/430157a
| [deleted]
| AdrianB1 wrote:
| "came about randomly" is a strange statement; natural
| selection, where you filter out weaker specimens of the species
| in favor of the stronger ones is not random, it is a long time
| process.
| the-printer wrote:
| I don't necessarily follow everything that the parent comment
| is covering, but I gather that he may be referring to the
| sheer existence of the immune system. How can natural
| selection account for that?
| pazimzadeh wrote:
| There is no "immune system." There is an innate immune
| system which reacts quickly but only to general threat
| patterns (kind of like racial profiling, to be crude). It
| is really easy to explain the evolution of this system.
|
| The adaptive immune system is the one that runs a mini-
| evolution within your own body as way to counter the
| extremely rapid rate of evolution in pathogens. There are a
| few explanations as to how this came about - see my last
| comment.
|
| Paradoxically, it may be the very success of our immune
| system which puts selective pressure on pathogens to evolve
| even faster.
|
| The acquired immune system: a vantage from beneath
| https://pubmed.ncbi.nlm.nih.gov/15539148/
| fernandopj wrote:
| You're making the same mistake as the OP: looking in
| isolation at the current, final step of a process that took
| millions of years. Also, you're gonna find a lot of
| different immune systems in nature, just as you can find
| many different eyes/vision in animals. There's a lot of
| middle ground in species that saw no advantage in evolving
| that particular system against their environment.
|
| You're also confusing the randomness of the steps with the
| somewhat previsible trend of an entire ecosystem which is
| evolving. If world is getting warmer and air more dense,
| you wouldn't be able to guess which mutation occurs but you
| can predict in time animals would be more adapt to that new
| ecosystem.
|
| Darwin famously looked at a unusual orchid with a long
| "tube" leading to nectar, and spoke that "there must be a
| bird with a long beak here somewhere". He didn't find it at
| first, but it was discovered later [1]. So you can apply
| some predictions at how evolution took place if you take a
| look at the environment. Just as one would guess there must
| be an immune system in animals if you discover diseases,
| virus, bacteria etc - or else how would large animals
| exist?
|
| [1]https://laidbackgardener.blog/2017/04/12/darwins-orchid
| mrkeen wrote:
| > I stopped believing in large scale evolution. I still believe
| small scale evolution exists
|
| It's always been small scale, the whole time.
|
| Otherwise you'd have the bizarre discontinuities that people
| like to straw-man evolution with. Like a fish that just decides
| to walk out of the ocean and breathe air one day.
| pvg wrote:
| This argument is 'irreducible complexity' from Intelligent
| Design, a pseudoscientific attempt to shoehorn creationism back
| into science education.
|
| https://en.wikipedia.org/wiki/Irreducible_complexity
|
| is a good starting point, of course you can also just google
| 'intelligent design' and go from there.
| 1auralynn wrote:
| You're not understanding the timescale or the context of the
| immune system's evolution. Imagine a cluster of unicellular
| organisms forming a multicellular organism for the first time.
| A multicellular organism stands a much better chance of
| survival than a single cell. Imagine a mutation that resulted
| in a cell surface protein that indicated cells were "friendly"
| and maybe even allowed them to glom together.
|
| Later on, a billion or so years later after the system of cell
| surface proteins have grown in complexity, imagine a
| multicellular organism like a sponge, where the ocean flows
| freely through the inner compartment, helped along by simple
| differentiated cells containing primitive cilia/flagella. Some
| of the cells that line the wall of the inner compartment become
| proto-macrophages, capable of "eating" foreign objects that
| flow through. The context here is that the immune system has
| deep ties with the digestive system evolutionarily. So, a ton
| of the functionality of the immune system has an overlap with
| the digestive system... "self vs not self" goes way back.
| meindnoch wrote:
| The cells of an organism can have attributes that are:
|
| 1. unique to each individual cell
|
| 2. unique to the organism, but identical among its cells (i.e.
| cells descending from the same egg cell)
|
| 3. identical among all members of the species, or even across
| species
|
| Any immune system will _necessarily_ evolve to use the
| attributes from group #2. If it were to use #1, the organism
| dies. If it were to use #3, then rogue cells from other
| compatible organisms can infiltrate and steal the organism's
| resources, which is evolutionarily disadvantageous (unless it's
| a beneficial relationship, c.f. gut microbiome).
| Drakim wrote:
| Usually when there is a two-step process needed for something
| to evolve, then there is often an advantage to one of the steps
| in isolation that isn't easily apparent, or the advantage it
| gave might have been lost to time.
| stevenhuang wrote:
| I think you need to learn more about the immune system.
|
| But to continue your analogy, it doesn't need to be a two-step
| process. You can start with an immune system and "randomly
| marked" cells (they're not random, but say they are). Millions
| of cells are created by your body every second. The cells that
| are marked "incorrectly" will die off, leaving those the immune
| system recognizes to continue reproducing. Overtime the
| remaining cells DNA will only contain instructions to create
| new cells "marked" to not provoke an immune response.
|
| Why is one such counterexample so unthinkable a process to you?
| flobosg wrote:
| Note that there are two different types of immune systems:
| innate and adaptive, which work together to protect against
| pathogens. It seems that you are conflating both.
| DoreenMichele wrote:
| This is just a press release, so a general overview. It's not
| that deep.
|
| It's sort of a pet peeve of mine that _the immune system_ doesn
| 't mean what most people seem to think it means.* However, it's
| already been established that certain mutations -- even deadly
| mutations -- are more common due to improving odds of survival
| against specific infections that swept specific regions
| historically.
|
| So, "survival of the fittest" doesn't mean what a lot of people
| think it means. It's rooted in a _winnowing_ process where those
| who don 't die get to pass on their genes. That's all it means.
|
| Cystic fibrosis is a predominantly Caucasian genetic disorder.
| Studies suggest this is so because, like Sickle Cell protects
| against malaria, it protects against tuberculosis and I think one
| other disease but I'm not remembering which one nor readily
| finding a reference.
|
| _Cystic fibrosis carriership and tuberculosis: hints toward an
| evolutionary selective advantage based on data from the Brazilian
| territory_
|
| https://pubmed.ncbi.nlm.nih.gov/28499359/
|
| _Cystic fibrosis gene protects against tuberculosis_
|
| https://www.newscientist.com/article/dn10013-cystic-fibrosis...
|
| So this is already fairly well established. Cystic fibrosis is an
| inflammatory condition, which fits with their observations.
|
| ----
|
| * ..."the immune system" doesn't really mean a specific set of
| organs like "the circulatory system" or "the digestive system"
| means a specific set of organs. It's just kind of a catch phrase
| for "how the body protects itself" and it's not really that well
| understood or explained exactly that happens.
|
| https://news.ycombinator.com/item?id=25167263
| flobosg wrote:
| > it protects against tuberculosis and I think one other
| disease but I'm not remembering which one
|
| Cholera and typhoid fever are other candidates:
| https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2358959/
| jyscao wrote:
| >it protects against tuberculosis and I think one other disease
| but I'm not remembering which one
|
| I recall reading long time ago that carriers of CF are
| hypothesized to be more resistant against cholera.
| pazimzadeh wrote:
| I'm kind of disappointed that there's no mention of cancer in the
| article. The rise of cancer (presumably due to increased nutrient
| availability following agriculture?) could be a reason why the
| immune system may have started skewing towards autoimmunity.
|
| In fact, several microbes have been found to have anti-cancer
| properties - either directly of by stimulating the immune system.
| So maybe success in tackling pathogens led to a deficit in
| combatting the enemy within.
|
| Otherwise, it's not exactly clear why the ability to fight off
| pathogens (foreign bodies) would necessarily lead to an increase
| in autoimmunity (attacking your own cells).
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(page generated 2023-01-16 23:01 UTC)