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Thread: Systemic Altruism and the Ecologically Driven Evolutionary Model

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    Persona Oblongata OrionzRevenge's Avatar
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    Systemic Altruism and the Ecologically Driven Evolutionary Model

    This is intended as a scrapbook for News Items, Observations, and Opinions as it relates to the idea: that our understanding of the fundamentals of evolutionary change require a paradigm shift.

    This snippet of a previous post briefly addresses the point via way of an example:

    Quote Originally Posted by OrionzRevenge View Post
    ...Yet I think that examples like CRE illustrate a needed paradigm shift towards a notion that the mindless (wildfire-like: simply exploiting every source of fuel in its path) replication of the progenitor to all life (DNA & pre-biotic forms), and not its tools (Genes) is what is being passed forward in time.

    Replicate, recycle parts, repeat.

    Thus nature isn't pushing the survival of the fittest but rather is selecting for fully integrated ecosystems that are fine-tuned to maximize the replication of DNA.
    Therefore if we shift our focus to looking for various examples of systemic altruism... I think we'll find them.

    Here with CRE we have evolution granting favor to a system where we start with one genetically gifted Enterobacter that, instead of putting all it's energy and resources into rapidly mitosing its entire genetic portfolio repeatedly, exerts a great effort to rattle off hundreds of plasmids containing the resistance gene(s) and casting them into the watery medium. There, far & wide, very genetically diverse organisms can uptake and incorporate the genes that convey resistance and thus are able to compete more effectively for the resources the benevolent cell could have used exclusively for self replication.

    Now, one could argue that the Gene(s) contained in the plasmid are being perfectly Dawkins-like and selfishly making sure they are passed forward. But the genes that build the machinery to rattle-off plasmids are doing so most decidedly at there own disadvantage and so you'd think they'd get a little selfish themselves. Yet, plasmid making was probably ancient 3 billion years ago and is obviously something nature wants bacteria to do for the entire community.
    ------------------------------------------------

    This thread is prompted here & now due to a recently published study:

    http://www.sciencedaily.com/releases...1008142620.htm

    Evidence for functional redundancy in nature
    Many species may play essentially the same role


    While it is clear that species fulfill many different roles in ecosystems, it has also been suggested that numerous species might actually share the same function in a near neutral way. So-far, however, it was unclear whether such functional redundancy really exists. The new study addresses this question using extensive data on the world's 4168 species of diving beetles. It shows that across the globe these animals have evolved towards a small number of regularly-spaced body sizes, and that locally co-existing species are either very similar in size or differ by at least 35%. Surprisingly, intermediate size differences (10-20%) are rare. As body-size reflects functional aspects such as the food that these generalist predators can eat, these beetles thus form relatively distinct groups of functional look-a-likes. The striking global regularity of these patterns support the idea that a self-organizing process drives such species-rich groups to self-organize evolutionary into clusters.

    "This finding has important implications for how we look at the risks of losing species," says Marten Scheffer of Wageningen University and lead author on the paper. "Our work suggests that evolution is a generator not only of functional complementarity but also of functional redundancy. However, such redundancy does not mean that these species are not needed for the functioning of nature." Scheffer stresses that while functional complementarity promotes the magnitude of ecosystem processes, redundancy promotes resilience of such ecosystem processes through the insurance effect of biodiversity. This insurance effect is due to the fact that species that are near-neutral when it comes to their functional role (e.g. their niche in terms of the food they eat), will typically still differ in their response to various stressors. Such response diversity may include sensitivity to specific parasites and diseases. As a result the resilience of a functional role should be expected to increase with the number of species in a near-neutral group.
    So instead of seeing nature favor the 'fittest' we repeatedly see evolution granting favor to ecosystems that can survive insults.

    Because ecosystems that couldn't survive mortal stress to one species...
    Or ecosystems that truly did experience a run-away 'Arms Race' between prey & predator...
    Or ecosystems driven by Selfies Genes...

    Have all long ago failed.
    Creativity is the residue of time wasted. ~ Albert Einstein

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    Persona Oblongata OrionzRevenge's Avatar
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    Certain Research Discoveries, that have unfolded over the past 3 months at UC San Diego, illustrate why I think we need to discard a Dawkins-esque approach to the mechanics of evolution.

    These discoveries offer the potential for innovative approaches in both Brain Health and Environmental concerns, but the researchers seem to have stumbled upon the mechanics behind the observed behavior due to making a connection to esoteric knowledge as to how neurons make use of Glutamate to signal.

    If you read the explanation for the hypothesized mechanics, when they first made the discovery of the behavior 3 months ago, they dismiss the notion that this is non-Dawkins-like Altruism and were trying to find a solution that jived with the current paradigm. They were looking for a mechanism that is the result of members in a community, that are being put under stress by other members some distance way, temporarily inhibiting the growth of these other members in order to relieve said stress:

    Resolving Social Conflict Is Key to Survival of Bacterial Communities

    Far from being selfish organisms whose sole purpose is to maximize their own reproduction, bacteria in large communities work for the greater good by resolving a social conflict among individuals to enhance the survival of their entire community.


    It turns out that, much like human societies, bacterial communities benefit when they can balance opposing needs within the group.


    The discovery of this unusual behavior among bacteria in large communities, detailed in a paper in the July 22 advance online publication of Nature, comes not from any inherent altruism among the bacteria. Instead, it “emerges” spontaneously from the community in which the bacteria grow.


    “It’s an example of what we call ‘emergent phenomena’,” explained GŁrol SŁel, an associate professor of molecular biology at UC San Diego who headed the research effort. “Emergent phenomena are processes that you cannot observe or understand if you are studying individuals. You can only understand the process if you look at the collective.”


    SŁel and his colleagues observed this unusual phenomenon while carefully measuring the growth of a microbial community called a “biofilm.” Such communities of bacteria and other microorganisms form thin structures on surfaces—such as the tartar that develops on teeth—that are highly resistant to chemicals and antibiotics.


    The UC San Diego biologists discovered that when the biofilm community reached a certain size, it suddenly began to oscillate in its growth. By complementing their experiments with mathematical modeling, the researchers discovered that these oscillations resolved a social conflict between individual cells that were cooperating, but also had to compete for food. The reason these biofilms are so hardy is that individuals within the community manage to resolve this internal conflict through coordinating their activities in space and time.

    ....


    The conflict is essentially this: Bacteria at the outer edges of the biofilm are the most vulnerable within their community to chemical and antibiotic attacks. At the same time, they also provide protection to the interior cells. But the bacteria at the outer edge are the closest to nutrients necessary for growth. So if they grow unchecked, they can consume all the food and starve the sheltered interior cells.

    But that doesn’t happen, because the biofilm develops an ingenious solution to this problem that the scientists call “metabolic codependence.” Essentially, the interior cells produce a metabolite necessary for the growth of the bacteria on the outside. This provides the inner cells with the ability to periodically put the brakes on the growth of outer cells, which otherwise would consume all the food and starve the cells they are protecting from attack. By periodically preventing the growth on the periphery, inner cells ensure that they have sufficient access to nutrients. By keeping the protected inner cells alive, the biofilm has a much higher chance of surviving antibiotic treatment.


    Ok, so this explanation for the mechanism of colony growth oscillations Jives with a the notion of looking out for number one. But dose it really make any sense????

    The inner bacteria assume a division of labor where they expend a lot capital to over-produce a certain "metabolite" so that the outer bacteria reproduce at full throttle and threaten to starve the inner bacteria... because they expend a lot capital to over-produce a certain "metabolite".


    This week the group published again in Nature the surprising results of their search for Metabolite X:

    Biologists Discover Bacteria Communicate Like Neurons in the Brain


    In a study published in this week’s advance online publication of Nature, the scientists detail the manner by which bacteria living in communities communicate with one another electrically through proteins called “ion channels.”


    “Our discovery not only changes the way we think about bacteria, but also how we think about our brain,” said GŁrol SŁel, an associate professor of molecular biology at UC San Diego who headed the research project. “All of our senses, behavior and intelligence emerge from electrical communications among neurons in the brain mediated by ion channels. Now we find that bacteria use similar ion channels to communicate and resolve metabolic stress. Our discovery suggests that neurological disorders that are triggered by metabolic stress may have ancient bacterial origins, and could thus provide a new perspective on how to treat such conditions.”


    “Much of our understanding of electrical signaling in our brains is based on structural studies of bacterial ion channels” said SŁel. But how bacteria use those ion channels remained a mystery until SŁel and his colleagues embarked on an effort to examine long-range communication within biofilms—organized communities containing millions of densely packed bacterial cells. These communities of bacteria can form thin structures on surfaces—such as the tartar that develops on teeth—that are highly resistant to chemicals and antibiotics.


    The scientists’ interest in studying long-range signals grew out of a previous study, published in July in Nature, which found that biofilms are able to resolve social conflicts within their community of bacterial cells just like human societies. When a biofilm composed of hundreds of thousands of Bacillus subtilis bacterial cells grows to a certain size, the researchers discovered, the protective outer edge of cells, with unrestricted access to nutrients, periodically stopped growing to allow nutrients—specifically glutamate, to flow to the sheltered center of the biofilm.
    ...


    The scientists noted that glutamate is also known to drive about half of all human brain activity. So they designed an experiment to test their hypothesis. The object was to carefully measure changes in bacterial cell membrane potential during metabolic oscillations.


    The researchers observed oscillations in membrane potential that matched the oscillations in biofilm growth and found that ion channels were responsible for these changes in membrane potential. Further experiments revealed that oscillations conducted long-range electrical signals within the biofilms through spatially propagating waves of potassium, a charged ion.




    As these waves of charged ions propagate through the biofilm, they coordinated the metabolic activity of bacteria in the inner and outer regions of the biofilm. When the ion channel that allows potassium to flow in and out of cells was deleted from the bacteria, the biofilm was no longer able to conduct these electrical signals.


    “Just like the neurons in our brain, we found that bacteria use ion channels to communicate with each other through electrical signals,” said SŁel. “In this way, the community of bacteria within biofilms appears to function much like a ‘microbial brain’.”


    SŁel added that the specific mechanism by which the bacteria communicate with one another is surprisingly similar to a process in the human brain known as “cortical spreading depression,” which is thought to be involved in migraines and seizures.


    “What’s interesting is that both migraines and the electrical signaling in bacteria we discovered are triggered by metabolic stress,” he said. “This suggests that many drugs originally developed for epilepsy and migraines may also be effective in attacking bacterial biofilms, which have become a growing health problem around the world because of their resistance to antibiotics.”
    So the actual mechanism relies on the Ion Channels, found in the surface membranes of all bacteria, and ubiquitous Potassium Ions.

    Unlike sterile labs growing mono-cultures of Bacillus subtilis, natural biofilms would be a thriving community of a multitude of prokaryotic cells of various strains and even species.

    Evolution has granted favor to a signalling system that mandates that completely self-sufficient single-celled critters should THINK the whole community is what must survive, and dose so using the same mechanism a single Neuron in our Brain would use to tell our feet not to run off a cliff.
    Creativity is the residue of time wasted. ~ Albert Einstein

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    Senior Member Starjots's Avatar
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    Q: Are these biofilms made up of the same type of bacteria or an assortment?

    This thread topic reminds me of congestion control algorithms built into TCP to combat congestion collapse in the network where most of the data packets get thrown away due to buffer overflow in the routers, triggering retransmissions which in turn clog the buffers etc. and the flow of information across the net slows to a crawl.

    For the first few years after TCP/IP went live on the Arpanet (1983) everything was fine. More computers were added to the network, network traffic increased and the information was getting through. Then in 1986 the amount of information getting through started nose-diving by orders of magnitude. The early internet was, for the first time, a victim of its success. The percentage of packets lost to buffer overflow crossed a threshold where the retransmissions caused the congestion to get even worse. A crude/imprecise analogy being, if there was a traffic jam and you heard about it on the radio, you immediately drove to the where the traffic jam was.

    The answer was to modify the TCP protocol used in all networked computers to behave altruistically. If packet loss is detected (by not receiving an acknowledgement from receiver in time), the sending computer cuts its transmission window size multiplicatively (in half for example) and waits a while before slowing adding to the window size. If more packets are lost it cuts the window again etc.

    The point isn't to get the computers information through faster, the point is to keep the network from collapsing and becoming useless to all computers.

    I will posit that for the internet to work best (best being defined as highest throughput of all users), altruism or at least cooperation is required from all users. Congestion control, for example, relies on other computers 'playing by the rules' or implementing protocols as specified. ISPs who insist on the capitalist concept of ownership of the internet, implying they can do what they want to extract maximum revenue, are working at cross purposes against the network itself. Also, clearly host computers can cheat by not fully implementing the protocols...

    Blog post on Google & Microsoft Slow Start

    Slides on TCP Congestion Control

    Video on Early History of TCP Congestion Control


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    Persona Oblongata OrionzRevenge's Avatar
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    Quote Originally Posted by Starjots View Post
    Q: Are these biofilms made up of the same type of bacteria or an assortment?

    This thread topic reminds me of congestion control algorithms built into TCP to combat congestion collapse in the network where most of the data packets get thrown away due to buffer overflow in the routers, triggering retransmissions which in turn clog the buffers etc. and the flow of information across the net slows to a crawl.
    ...
    The answer was to modify the TCP protocol used in all networked computers to behave altruistically. If packet loss is detected (by not receiving an acknowledgement from receiver in time), the sending computer cuts its transmission window size multiplicatively (in half for example) and waits a while before slowing adding to the window size. If more packets are lost it cuts the window again etc.

    The point isn't to get the computers information through faster, the point is to keep the network from collapsing and becoming useless to all computers.
    ...
    It's a mono-culture of Bacillus subtilis. (Your classic textbook Gram Positive long Rod shaped bacteria used in every Microbiology Intro course) B. subtilis, like its Gram Negative short rod shaped classroom co-star: E. coli, has been used in research for ages and is well understood.

    Microbiologist have long noted oscillations in the growth rate of bacterial colonies both single and mixed. But the thing is that there is nothing specific to B. subtils as to what they discovered.

    Potassium Ion Channels have a very specific function (only allow the passage of K+ ions due to the Potassium Atom's specific size ~ like coin vending machines: Nickles, not Dimes or Quarters) and so no species-specific variation is applicable.

    Too, until this research unfolded, over the past few months, no one knew why bacteria even had K+ Channels. It was like some weird appendix. However, Bacterial K+ Channels have been the subject of a lot of research over the decades. Because K+ Ion Channels are fundamental as to how higher lifeforms passed information to the various cells of their being. And all our other Ion Channels are based on the Bacterial K+ design.



    Yet, it has taken all this time for someone to have a problem that made them think that these single-celled critters, filled with their selfish genes and a manifest destiny for numero uno, might be communicating with each other. Even then, the K+ Ion Channel wasn't the obvious route. After all, what could you signal a bacteria to do? Become dormant??? Why???

    So there is nothing here that suggest it is specific to B. subtilis. The example of the CRE plasmid in the OP is a good example as to why multiple species of bacteria would receive evolution's favor to coexist in the same film or infection. One E. coli-like bacterial species had a genetic gadget in its toolbox that allowed it to mutate into something that could resist Carbapenem Antibiotics. It then expended a lot of metabolic capital to spit out little DNA rings with its discovery so that any E. coli-like bacteria in the vicinity could uptake and incorporate its discovery into it's DNA

    Your analogy of TCP protocol evolution is an excellent one. Not only because it illustrates the dead-end of not incorporating systemic altruism, but because it also illustrates that SA allows you to reach maximum network capacity.

    DNA replication is just a mindless Wildfire chemical reaction seeking more fuel to maximize the burn. The genes are just tools, and they only gain favor if they allow for diverse and very productive ecosystems that have the genetic agility to rapidly adapt to a potential threat to production. IMO

    Replicate, Recycle parts, Repeat.
    Creativity is the residue of time wasted. ~ Albert Einstein

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    Quote Originally Posted by Starjots View Post
    ...
    that guy looks a bob odenkirk clone defect.

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    Persona Oblongata OrionzRevenge's Avatar
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    Quote Originally Posted by MarkovChain View Post
    ...Off topic, this video is a great example of game theory in nature, and explains why trees are so tall.
    Derek Muller is a Sexy little Geek but this whole thread is about seeing these sorts of situations in terms other than a Survival-of-the-Fittest Arm's Race. And Derek is doing it wrong this time.

    Tall tress lock-up Carbon for decades on end and slowly release it back into the ecosystem when they fall.
    Tall Tress allow for vertical ecosystems and leave the surface tier for a totally different ecosystem.
    Tress are not all extremely tall. Research using a field guide will reveal that deciduous trees come in low, medium, high, and super high canopy varieties and very often share the same forest.

    The canopy as a whole buffers the impact of heavy rain of the creatures and soil underneath, and look how tress cold-cock the typical gale-force oceanic winds when they come ashore.
    Creativity is the residue of time wasted. ~ Albert Einstein

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    Senior Member Spartan26's Avatar
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    Are you meaning biological or cycles or trends in human nature or behavior?

    Because time for us is linear, I don't know if it's possible to not view or label change as being evolutionary. We'll always view things happening in succession as advancing. It seems impossible to devolve. Also, what causes the change? Is it within, freewill, the environment, thereby adaptation, or do the changes happen to the thing evolving and then the species incorporates it into daily living? I'd kinda like to apply these to the nature of the world and the sort of paradigm shifts man/civilizations have gone through. Like political systems, fundamental laws, mores, cultural expectations. Not really looking for incinerary topics either. I could think of changes over the past century with marketing practices, movies, Las Vegas, sports...

    If merely biological, what are the types of things to look for? I'm assuming beyond does it exist or doesn't it (not because that's concrete) but what would make us think of evolution different? If any of that makes sense...

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    Persona Oblongata OrionzRevenge's Avatar
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    Quote Originally Posted by Spartan26 View Post
    Are you meaning biological or cycles or trends in human nature or behavior?

    Because time for us is linear, I don't know if it's possible to not view or label change as being evolutionary. We'll always view things happening in succession as advancing. It seems impossible to devolve. Also, what causes the change? Is it within, freewill, the environment, thereby adaptation, or do the changes happen to the thing evolving and then the species incorporates it into daily living? I'd kinda like to apply these to the nature of the world and the sort of paradigm shifts man/civilizations have gone through. Like political systems, fundamental laws, mores, cultural expectations. Not really looking for incinerary topics either. I could think of changes over the past century with marketing practices, movies, Las Vegas, sports...

    If merely biological, what are the types of things to look for? I'm assuming beyond does it exist or doesn't it (not because that's concrete) but what would make us think of evolution different? If any of that makes sense...
    Upfront admission: I'm fresh home from a drunk after finishing the night with some tunes featuring the smoky & sultry voice of a member hereof. (Guess) ~ newer members would be blown away by the revelation.

    Anyways, no, this is strictly about the boring science of evolution and and what I see as a needed change in the way we describe & think about the force that drives it.

    I quoted MarkovChain above because (something you might understand from the Biz) He, like Hitler Marx and Rockefeller has commandeered Darwin's ideas to justify his social behavior.

    And I'm saying not only isn't it applicable, but that reality is proving to be contrary from the initial thumbnail understanding of it as: Survival of the Fittest.
    Creativity is the residue of time wasted. ~ Albert Einstein

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    Senior Member Starjots's Avatar
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    This also seems applicable to that threshold crossing from single celled to multi-celled organisms. Given your examples are in bacteria, are similar mechanism and behaviors present in Eukaryote single celled species?

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    Senior Member Spartan26's Avatar
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    Quote Originally Posted by OrionzRevenge View Post
    Upfront admission: I'm fresh home from a drunk after finishing the night with some tunes featuring the smoky & sultry voice of a member hereof. (Guess) ~ newer members would be blown away by the revelation.
    Does @Madrigal sing? Listening to her speak Spanish would be my kryptonite. If I ever get to meet her, I'll make her speak Spanish exclusively. Won't be able to understand what she's saying but damn, I'll feel good!

    Doesn't @kitsune have a performing arts background? She'd be my first guess. @Sappho writes and plays music. I picture her with more of a crisp soprano singing voice. Seeing @attila_the_hunny, dressed like Jessica Rabbit, belting out some old jazz in front of a piano bar would be my adult Disneyland but I somehow doubt she can, as they say, really sang, or else she'd already be famous. But, in case she can, please start to take it seriously now. Please!!

    I'm sure i'm forgetting people.

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