The Evolution of Cooperation

When and why individual organisms work together at the game of life, and what keeps cheaters in check
 

By | January 1, 2016

ANT LADDER: Nestmates will climb on top of their nest mates to achieve collective goals, such as reaching food.© VOLKER MOHRKE/CORBIS

Evolution by natural selection, Darwin wrote, mainly depends on “success in leaving progeny.”1 He also recognized that such success may be achieved by “dependence of one being on another.” When are individuals most successful living on their own, and when can they benefit from working with others?

It’s not always an easy question to answer. For parasites living in or on other organisms, for example, maximizing reproduction is a tricky proposition. Using more host resources lets parasites produce more offspring, but overexploitation shortens host life span, reducing the amount of time the parasites have to reproduce. So it may make sense for parasites to avoid harming their hosts, and parasites that increase host life span may fare even better. As British evolutionary biologist and  geneticist John Maynard Smith noted more than 100 years after Darwin’s musings on reproduction and cooperation, you shouldn’t kill the goose that lays the golden eggs.2

But Maynard Smith recognized that this strategy is based on a critical assumption: that if you do not kill the golden goose, no one else will either. In other words, limiting host exploitation will only benefit a parasite if the host isn’t also inhabited by other, more virulent strains or species. If another parasite is using so many resources that it kills the host anyway, why should any organisms on the same host limit their own reproduction by using fewer host resources? This “tragedy of the commons” type of dilemma, in which individuals benefit from activities that undermine shared benefits, is a major reason why cooperation is not universal.

 

Whenever there are different genotypes in the mix, cheaters can arise.

Nevertheless, cooperation is found throughout the living world—from the cellular to the societal level. Our cells are descended from single-celled organisms that once competed with or preyed on one another, but now work together to function as a cohesive unit. Within our cells, the mitochondria that provide energy are descended from free-living bacteria that gave up their autonomy for a cooperative existence. Lichens, corals, and many plants host beneficial bacteria or fungi within their bodies and depend on them for vital nutrients; and different species of microorganisms living within a host may be interdependent on one another. Ants defend trees that house and feed them. Animals, from bees to lions, cooperate with close relatives, and human civilization depends on cooperation even among unrelated individuals.

What drives the evolution of these relationships, and why are they not more widespread? And can humans harness cooperative biology for their own benefit, for example, to increase crop yields?

Cooperating with kin

An early example of different species coming together to work as a team—one that changed the course of the evolution of life on Earth—is the origin of the eukaryotic cell. The cells of animals, plants, and fungi all contain mitochondria, which generate energy via respiration. Mitochondria are distant descendants of symbiotic bacteria, surrounded by their own membranes and containing their own DNA. Mitochondria presumably passed through a cooperative-but-potentially-independent stage before becoming completely integrated with their host cells. Today, mitochondria have lost enough genes that they cannot survive and reproduce outside of host cells, solidifying the cooperative relationship.

Interestingly, similarities among all mitochondria suggest that animals, plants, and fungi evolved from a one-time origin of this ancestral symbiosis between two microbial species. This is in stark contrast to the repeated evolution of multicellularity, which has appeared more than 20 times across the eukaryotic kingdom. (See “From Simple To Complex,” The Scientist, January 2011.) This discrepancy highlights how it is easier for cooperation to evolve among genetically identical cells. Indeed, multicellular organisms serve as the ultimate example of cooperation on a cellular level, with millions, billions, or even trillions of cells working together to form the tissues and organs of a complex individual. Such organisms cannot exist without cooperation among their cells, and the cells cannot exist outside of the cooperative system. The surprising ease with which these systems arose may be attributed to the fact that all the cells of a multicellular individual carry an identical (or nearly identical) genome.

In theory, multicellular organisms could have formed as individual cells banding together. For example, single-celled Dictyostelium amoebas and Myxobacteria both form multicellular structures that produce starvation-resistant spores, and bacteria can aggregate into seemingly cooperative multispecies biofilms, which show enhanced resistance to antibiotics. Alternatively, today’s multicellular organisms may have descended from cells that failed to go their own ways following cell division. This process is recapitulated by most modern multicellular organisms, which develop from single-celled embryos that divide repeatedly but remain in contact. This ensures that the cells have a shared genotype.

To determine how the first multicellular organisms may have arisen, my (R.F.D.’s) former student Will Ratcliff and colleague Mike Travisano used artificial selection in 2012 to evolve simple multicellular forms from single-celled yeast.3 Once a day, they separated liquid cultures based on how fast they settled to the bottom of the test tube. Cluster-forming mutants settled faster, and only these faster settlers were transferred to fresh media. Simple multicellularity evolved within a few weeks, and closer analysis of the faster-settling mutants revealed that clusters were formed by cells staying together after division, not by independent cells aggregating together. The same outcome occurred when selecting for clumps formed by yeast strains—such as the flocculating yeasts used for brewing beer, which are known to aggregate under certain conditions4—and when conducting the experiments with algae.5 Collectively, these studies suggest that multicellularity likely arose from incomplete separation following cell division, and support the idea that genetic similarity matters in the evolution of cooperation.

Genetic similarity among multicellular individuals also plays a major role in the evolution of cooperation on the macro level. The great evolutionary theorist William Hamilton noted that a gene for cooperation can spread if cooperation helps others with that same gene to survive and reproduce.6 Close relatives are more likely to share genes, including genes for cooperation, so “kin selection” can favor cooperation. Evolutionary biologist J.B.S. Haldane joked that he would die for “two brothers or eight cousins,” the number of relatives who, on average, would replace his own contribution to the gene pool. Many animals follow this basic philosophy. A worker bee, for example, will give up her own reproductive capabilities and even die defending the hive to help the queen keep laying eggs—which contain the worker’s sisters and brothers. Most of these siblings will have the same hive-defense genes as the dying worker.

Kin selection is also apparent in animals that don’t have such extreme eusocial societal structures. Squirrels, for example, will occasionally adopt orphans, but only when they are so closely related that this is likely to increase representation of the foster mother’s genes in the gene pool.7 Closely related female lions in a pride will cooperate to defend their territory against intruders.

Such systems are not immune to cheating, however.  In the mid-1990s, Robert Heinsohn of Australian National University and Craig Packer of the University of Minnesota found that some lions, while no less closely related, are less likely to fight an intruder, thus reducing their own risk of injury.8 Bolder lions apparently resent this, but they don’t seem to retaliate against the “cheaters.” However, punishment of cheaters is often needed to maintain cooperation among unrelated individuals or between species.

Keeping cheaters in check

KEEPING CONTROL: Rhizobia bacteria live inside root nodules of plants, fixing nitrogen in exchange for energy-rich organic molecules. But if the rhizobia fail to fix nitrogen, the plant will induce senescence of the nodules (blue, far right). ALEX MAYWhenever there are different genotypes in the mix, cheaters can arise. For example, when Dictyostelium cells aggregate to form a fruiting body with spores supported by a stalk, only spore cells produce progeny. When a fruiting body forms from a mixture of two strains, one strain may contribute less to the stalk and more to the spores. For cooperation to evolve in the face of such competition, a system of checks and balances must be in place to guard against cheaters—strains that enhance their own Darwinian fitness at the expense of the others. One way is simply to exclude dissimilar strains from the cooperative group, a practice of at least some Dictyostelium strains.9 Similarly, Pseudomonas aeruginosa bacteria tend to kill nearby strains to create single-strain biofilms.10

Cooperation can also evolve when organisms become mutually dependent on one another, especially if the same individuals interact repeatedly. Among free-living bacteria, if some bacteria unavoidably “leak” expensive nutrients, nearby cells that have lost the ability to make those nutrients might be able to gather them from their neighbors. Without the cost of making expensive nutrients, these mutants might have greater fitness than their nutrient-making ancestors. Researchers at Michigan State and the University of Tennessee have suggested that this could lead to cooperation among species, with each species evolving to make only a subset of the nutrients they all need and getting the rest from their neighbors.11 But such systems are also prone to cheating. Planktonic bacteria floating around in oceans or lakes, for example, have only loose associations with one another, and selection would seem to favor species or strains that use, but do not make, any of these public goods. Why help neighbors who will soon leave? When pairs of bacterial species were mixed in liquid culture, selection favored the less-productive, not the more-productive, species.12 But interactions may not always be random, even among free-living bacteria. Christian Kost of the Max Planck Institute for Chemical Ecology and colleagues have shown that some bacteria connect to other cells, of the same and different species, via nanotubes through which they exchange amino acids.13 (See “Live Wires,” The Scientist, May 2013.) If such connections are common, that would allow cooperation based on reciprocity—trade rather than piracy.

A similar example of interspecies trade can be found in just about every soil ecosystem, where most plant species depend on symbiotic fungi that help them acquire soil phosphorus, and a smaller number of plant species (including legumes) depend on symbiotic bacteria such as rhizobia to convert atmospheric nitrogen into compounds that plants use to make essential proteins. Legumes are unlikely to cheat their bacterial symbionts because the rhizobia bacteria can’t fix nitrogen without the energy-rich organic molecules provided by plants. The nitrogen the rhizobia provide can allow greater host-plant photosynthesis, potentially generating more organic molecules for the rhizobia.

That said, each plant typically hosts several different strains of rhizobia. And just like multiple parasites inhabiting a single host, strains that divert resources to their own reproduction would tend to outcompete strains that put all their energy into the “public good” of host-plant health. One widespread form of rhizobial cheating is hoarding more plant resources for future reproduction, rather than using those resources only to power nitrogen fixation. Even if cheaters supply some nitrogen, they reduce a host plant’s overall health by occupying root nodules that would otherwise be occupied by more-beneficial strains.

But plants have evolved ways to prevent a two-way trade from degenerating into a one-way resource grab. If the bacteria inside one root nodule stop fixing nitrogen, the plant can shut off the oxygen supply to that nodule, limiting rhizobial reproduction. The best evidence that plants respond to rhizobial behavior comes from experiments by my (R.F.D.’s) group, led by former students Toby Kiers and Ryoko Oono. Comparing soybean and alfalfa root nodules in normal air to nodules on the same plant in an atmosphere with only traces of nitrogen, we found that rhizobia reproduced less frequently when they could only fix enough nitrogen for their own needs, with no surplus for the plant.14 Soybean plants reduced oxygen supply to rhizobia that didn’t supply them with nitrogen. This presumably limits rhizobial metabolism so they waste fewer plant resources and may also explain their decreased reproduction. Similarly, plants supplied less energy to mycorrhizal fungi that provided them with less phosphorus.15  Without such sanctions by the plant host, strains that diverted resources to their own reproduction would displace more-cooperative strains over the course of evolution.

Some hosts manipulate their partners in ways that enhance current cooperation. Alfalfa and some other legume species cause rhizobia in their root nodules to swell to two or more times their usual size. Swollen rhizobia can no longer reproduce, but we (Oono and R.F.D.) found that they fix more nitrogen, relative to their cost to the plant.16 Similarly, researchers in Mexico and Germany found that Acacia cornigera trees protected by Pseudomyrmex ferrugineus ants manipulate the ants to keep them loyal. The nectar they give the ants contains chemicals that prevent the ants from digesting nectar from other plants. Individual ants apparently learn to stay on their host plant.17 This sort of manipulation can ensure that partners continue to cooperate with their current hosts. But cooperation based on manipulation may lapse whenever manipulation does, and thus does not necessarily favor the evolution of cooperation over generations. Sanctions that reduce the frequency of cheaters in future generations may have longer-lasting benefits.

Obligatory cooperation

MAINTAINING COOPERATION: For cooperation between species to withstand the inherently selfish nature of evolution, individuals that fail to cooperate must have fewer descendants than cooperators, on average. This could result from fitness-reducing sanctions against cheaters or strict dependence of each partner on the other for survival. Partners may also manipulate each other in ways that enhance cooperation in the short term, without necessarily favoring evolution of cooperation over generations. Among related individuals, kin selection favors cooperation with related individuals that are likely to also carry the same genes for cooperation. These mechanisms for enhancing cooperation are not always foolproof, however.
See full infographic: WEB | PDF
© LUCY CONKLIN
Another way to reduce cheating in interspecies relationships is to increase mutual dependence. When symbionts lose genes needed for survival outside their host, they cannot escape and may evolve to be even more beneficial, especially if their next host is their current host’s offspring.

Aphids, for example, rely on symbiotic bacteria contained in specialized cells for essential amino acids lacking in their diet of sugary plant sap. In return, bacteria gain access to their host’s offspring by entering aphid egg cells, being ingested by the offspring, or other mechanisms of transmission. Such symbiont inheritance, known as vertical transmission, means that bacterial strains benefit from helping their host lay as many eggs as possible. Thus, the most beneficial symbionts become the most frequent in the host population.  

Even in these systems, however, cheating can arise. When a host carries different strains or species of vertically transmitted bacteria, they may compete with each other to reach the host’s offspring. The winners in such within-host competitions will not necessarily be those that are most beneficial to the host, unless the host has specific mechanisms for favoring more-beneficial strains. The problem of competition between symbionts is somewhat alleviated by the fact that a very small fraction of symbiotic bacteria reaches the next generation of hosts. This bottleneck means that a hypothetical mutation that allows a strain to gain a slight advantage over a competitor by exploiting the host does not greatly improve its chances in reaching the next generation. To accomplish this advantage, a strain would have to exploit its host enough to reduce total egg production—with negative consequences that could outweigh the benefits of occupying a larger fraction of those eggs.

Harnessing cooperation

Our own research focuses on the problem of mediocre rhizobia strains that provide soybeans or alfalfa with some nitrogen, but much less than the best strains. While host sanctions keep root symbionts that provide little or no nitrogen or phosphorus in check, rhizobia may not trigger sanctions until they reduce their nitrogen fixation rate by more than 50 percent of their potential.18 Breeding soybeans and other legume crops for stricter sanctions could increase yields significantly, while still relying on symbiosis rather than fertilizer. Within a few years, we should have enough data to tell whether this approach will work.

Whenever there are different genotypes in the mix, cheaters can arise.

In other systems, it may be beneficial to reduce cooperation. While research into the interspecies relationships of the bacteria, fungi, and protozoans living in and on the human body is still in its infancy, recent theoretical work has suggested that microbial cooperation causes instability of species networks, and that competition reduces cooperation and promotes network stability.19

The key to harnessing such cooperative relationships is to understand them at the most basic biological levels. Continued research on within- and between-species cooperation will be necessary to make the most of our social world. 

R. Ford Denison is an adjunct professor at the University of Minnesota. Katherine Muller is a PhD student in his lab.

References

  1. C.R. Darwin, On the origin of species by means of natural selection, or the preservation of favoured races in the struggle for life, 1st ed., London: John Murray, 1859, page 62.
  2. J. Maynard Smith, “Generating novelty by symbiosis,” Nature, 341:284-85, 1989.
  3. W.C. Ratcliff et al., “Experimental evolution of multicellularity,” PNAS, 109:1595-1600, 2012.
  4. J.T. Pentz et al., “Clonal development is evolutionarily superior to aggregation in wild-collected Saccharomyces cerevisiae,” in H. Sayama et al., eds., Artificial Life 14: Proceedings of the Fourteenth International Conference on the Simulation and Synthesis of Living Systems, (Cambridge, MA: The MIT Press, 2014), 550549-554, 2014.
  5. W.C. Ratcliff et al., “Experimental evolution of an alternating uni- and multicellular life cycle in Chlamydomonas reinhardtii, ” Nat Commun, 4:2742, 2013.
  6. W.D. Hamilton, “The evolution of altruistic behavior,” Am Nat, 97:354-56, 1963.
  7. J.C. Gorrell et al., “Adopting kin enhances inclusive fitness in asocial red squirrels,”  Nat Commun, 1:22, 2010.
  8. R. Heinsohn, C. Packer, “Complex cooperative strategies in group-territorial African lions,” Science, 269:1260-62, 1995.
  9. E.A. Ostrowski et al., “Kin discrimination increases with genetic distance
  10. in a social amoeba,” PLOS Biol, 6:e287, 2008.
  11. N.M. Oliveira et al., “Biofilm formation as a response to ecological competition,” PLOS Biol, 13:e1002191, 2015.
  12. J.J. Morris et al., “The black queen hypothesis: Evolution of dependencies through adaptive gene loss,” mBio, 3:e00036-12, 2012.
  13. K.R. Foster, T. Bell, “Competition, not cooperation, dominates interactions among culturable microbial species,” Curr Biol, 22:1845-50, 2012.
  14. S. Pande et al., “Metabolic cross-feeding via intercellular nanotubes among bacteria,” Nat Commun, 6:6238, 2015.
  15. E.T. Kiers et al., “Host sanctions and the legume-rhizobium mutualism,” Nature, 425:78-81, 2003.
  16. E.T. Kiers et al., “Reciprocal rewards stabilize cooperation in the mycorrhizal symbiosis,” Science, 333:880-82, 2011.
  17. R. Oono, R.F. Denison, “Comparing symbiotic efficiency between swollen versus nonswollen rhizobial bacteroids,” Plant Physiol, 154:1541-48, 2010.
  18. M. Heil et al., “Partner manipulation stabilises a horizontally transmitted mutualism,” Ecol Lett, 17:185-92, 2014.
  19. E.T. Kiers et al., “Measured sanctions: Legume hosts detect quantitative variation in rhizobium cooperation and punish accordingly,” Evol Ecol Res, 8:1077-86. 2006.
  20. 19.    K.Z. Coyte et al., “The ecology of the microbiome: Networks, competition, and stability,” Science, 350:663-66, 2015.
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Avatar of: Cognosium

Cognosium

Posts: 1

January 1, 2016

An excellent article that reflects the sentiments expressed in my own writings, particularly my latest work   "The Intricacy Generator: Pushing Chemistry and Geometry Uphill".   The ubiquity of cooperation within the biosphere was, of course, noted by Marguilis and Lovelock as a component of the "Gaia Hypothesis".  A notion flawed by the specious attribution of sentience.

One aspect which is often overlooked is that predation, for instance,  or cheating, when viewed from a sufficiently wide perspective can be interpreted in terms of cooperation.

In general, biology should be treated as a network phenomenon and nowhere is this so important  as in evolution, where it must be firmly borne in mind that the true evolving entity is the entire interactive network. 

A network that actually extends beyond the biological phase. An evolutionary continuum that can be traced from at least as far back as the formation of chemical elements in the first stars right through to the currently most active manifestation, the evolution of technology. 

 

 

Avatar of: Alexandru

Alexandru

Posts: 85

January 2, 2016

1. „Interestingly, similarities among all mitochondria suggest that animals, plants, and fungi evolved from a one-time origin of this ancestral symbiosis between two microbial species.”(from article)

Yes, similarities in the maternal mitochondria Evolution.

Only the human paternal mitochondria is different: it looks like a „quantum cascade lasser”.

 

2. „As British evolutionary biologist and geneticist John Maynard Smith noted more than 100 years after Darwin’s musings on reproduction and cooperation, you shouldn’t kill the goose that lays the golden eggs.2” (from article)

 

Because John Maynard Smith speaks about „golden eggs” of the Evolution, do not forget that the known Romanian sculptor Constantin Brancusi „speaks” in his artistic language about „The Newborn” egg, where the human genome builders eliminate a very, very small and very, very important part: the paternal mitochondria = Adam mtDNA.

That means to struggle and harness the Creation and NOT “means of natural selection, or the preservation of favoured races in the struggle for life” (Reference 1).

http://www.moma.org/collection/works/81655

Constantin Brancusi - The Newborn - version I, 1920 (close to the marble of 1915)

Please, read with the open mind the short Evolution description in the world: Daniel 7.

January 5, 2016

Thanks for your useful article and work. I believe that the issue of competition mentioned at the end of the article is greatly under-examined and one which will be very fruitful. In my opinion, if we are to understand the evolution of cooperation and symbiotic relationships fully we will need to examine competition between species sharing a host. 

Avatar of: Heeseasun

Heeseasun

Posts: 2

January 5, 2016

What an amazing article! Speaking out of the biology field, cooperation is very crucial for the development of society because it is sustainable throughout the history of evolution, which creates this world. The human society is no exception and cooperation is more valuable than I've thought only after I read this article. This biological concept helps me more aware of the issue which is  available as always in the daily life, but sometimes I do not realize it or take it for granted or even neglect it.

 
Avatar of: C Goodnight

C Goodnight

Posts: 1

January 7, 2016

I appreciate the citations to Ratcliff and Travisano, but please be aware that there is much more out there.]

"And can humans harness cooperative biology for their own benefit, for example, to increase crop yields?"

Um, yes.  Your breakfast depends on it.  Bill Muir and colleagues used group selection to increase egg yeild in caged chickens, and Piter Bijma and colleagues use it to increase production in hogs.  Grain yield has typically been increased by "strain selection" (Griffing).  So, without group selection and the evolution of cooperation, no eggs, no bacon, no toast.  These are not just theoretical, by the way.  virtually all caged chickens in the EU are bred using multi level selection approaches. 

And, yes, it is about using cooperation.  In Muir's chickens the increased yield occurred because the chickens spent less energy fighting and pecking each other.  Bird mortality went down (dead chickens don't lay eggs), and debeaking was no longer necessary.  The reliance on using group selection approaches in the EU is due to the recent rulings declaring debeaking to be animal cruelty, and outlawing its use.

Avatar of: Roy Niles

Roy Niles

Posts: 88

January 7, 2016

Bacteria make choices, yet they follow orders to make those choices.   And orders that they've made for themselves as a group.  Group choices in other words based on strategies, instinctive and newly learned, that all have ordered themselves to follow.  Except not all of the individual choices needed to carry out those orders are group choices.   And in one way or another, we all order ourselves to choose, as if we stop choosing, we die. So bacteria that disobey or disregard, or slack off a bit on their orders, or are perhaps too innovative, are called by us as cheaters.  Cheaters are deceptive by definition.  But are there deceptive bacteria that are in fact disloyal?  Are there not rebellious groups that form that are in that sense cheating groups, except that cheating is too simple a term for their purposes?  And are the less competent bacteria cheating by necessity rather than intent? Because simply referring to deception as cheating doesn't recognize that bacteria are intelligent enough to intentionally deceive.  Yet they certainly intentionally plan to cleverly deceive their prey and do the same with competing groups of different bacterial strains.
Avatar of: naturalist

naturalist

Posts: 5

January 7, 2016

I've been teaching this for a while.

Here are a few links you might enjoy:

'Policing' stops cheaters from dominating groups of cooperative bacteria

http://www.sciencedaily.com/releases/2011/05/110526103002.htm

 

The Portuguese man-of-war is a siphonophore, an animal made up of a colony of organisms working together.

http://animals.nationalgeographic.com/animals/invertebrates/portuguese-man-of-war

 

Why prisoners join gangs

http://www.economist.com/blogs/economist-explains/2014/11/economist-explains-7

More available on request.

January 7, 2016

Very thought provoking.

We accept that diversity is the best measure for a system's health. Is not diversity related to cooperation? But cooperation is countered by stability enhancing maneuvers of the individual members--maneuvers gained by natural selection. Therefore diversity is not found in cooperative environments.

We see survival and diversity as the two poles of evolution; both are necessary. Survival is stimulted by threats--bacteria increase their mutation rate, tabletop corals use epigenetic means to adapt faster. Diversity seems stimulated on a human scale by cooperative efforts in a community. How do you stimulate a healthy diverse biome in your gut that is at the same time stable and resilient? Must be how you feed it.  

Avatar of: James V. Kohl

James V. Kohl

Posts: 349

Replied to a comment from Roy Niles made on January 7, 2016

January 9, 2016

All "choices" among all microbial species occur in the context of chemical gradients and nutrient-dependent receptor-mediated behaviors that must be linked to the pheromone-controlled physiology of reproduction in mammals.

Everything known about cell type differentiation in all species has been linked from nutrient-dependent microRNAs to adhesion proteins and supercoiled DNA, which protects the organized genomes of all living genera from virus-driven entropy.

That fact was recently placed into an interesting context by the Zechiedrich lab in this parody: Theorists may not recognize what they are joking about. They attempt to support their claim that anyone who claims that bacteria re-evolved their flagellum over-the-weekend is biologically uninformed. See also: Evolutionary Rewiring.

Avatar of: James V. Kohl

James V. Kohl

Posts: 349

Replied to a comment from Dr. J at Common Sense Medicine made on January 7, 2016

January 9, 2016

Feedback loops are the key to the stability of all organized genomes. For example, Feedback loops link odor and pheromone signaling with reproduction

That fact links microbes to humans by what is currently known about octopuses in the context of links from molecular epigenetics compared to virus-driven pathology in humans.

See:

Role of olfaction in Octopus vulgaris reproduction

The octopus genome and the evolution of cephalopod neural and morphological novelties

Distinct E-cadherin-based complexes regulate cell behaviour through miRNA processing or Src and p120 catenin activity

Avatar of: James V. Kohl

James V. Kohl

Posts: 349

Replied to a comment from Cognosium made on January 1, 2016

January 9, 2016

Re: "...the true evolving entity is the entire interactive network."

No experimental evidence of biologically-based cause and effect suggest that the interactions between metabolic and genetic networks have "evolved."

Re: A network that actually extends beyond the biological phase.

That networks cannot be linked from atoms to ecosystems, which means that your conceptualization of the network is irrelevant to serious scientists.

Re: An evolutionary continuum that can be traced from at least as far back as the formation of chemical elements..."

There is no such evolutionary continuum known to anyone I know who is capable of linking atoms to ecosystems via what is known about physics, chemistry, and the conserved molecular mechanisms of biologically-based cause and effect that Dobzhansky detailed in 1973.

Avatar of: Roy Niles

Roy Niles

Posts: 88

January 9, 2016

That response to my comment is as far off the mark as pseudoscoence theorizing can get. Bacteria are intelligent and make choices for intelligent purposes.  Kohl apparently believes that these microbial beings have no purposes and operate by predetermined means, mechanically, and through the use of thoughtless chemicals..  James A Shapiro has written a paper entitled Bacteria Are Small but Not Stupid, http://shapiro.bsd.uchicago.edu/2006.ExeterMeeting.pdfKohl has written elsewhere that he is a "weasel worded" failure as a scientist.

Kohl's "pheromone-controlled physiology of reproduction in mammals" is senseless, since pheromones carry messages and have no way of controlling what the message were being sent to say, or of understanding what they mean when being sent.. A good article that rebuts Kohls unscientific proclamations in that and many other respects is here:  http://www.uphs.upenn.edu/news/publications/PENNMedicine/files/PennMedicine-2011-01-winter-2-ednote.pdf

Also see where has shot himself in the foot here:

http://jonlieffmd.com/blog/human-brain/how-does-diet-influence-immunity#comment-2447892052

 

Avatar of: James V. Kohl

James V. Kohl

Posts: 349

Replied to a comment from Roy Niles made on January 9, 2016

January 9, 2016

See also: Virome-associated antibiotic-resistance genes in an experimental aquaculture facility

It seems likely that everything any neo-Darwinist or other evolutionary theorist was taught to believe about mutations and evolution has been eliminated from consideration by what has been learned about viruses during the past 30+ years.

For example, the links from viruses to antibiotic resistance involve aspects of quantum and classical physics linked to the biophysically constrained chemistry of RNA-mediated nutrient-dependent protein folding by fixation of amino acid substitutions. The substitutions differentiate all cell types in all individuals of all living genera. Fixation occurs in the context of the physiology of reproduction, which links atoms to ecosystems.

So far as I know, my invited review of nutritional epigenetics is the only review that links metabolic networks to genetic networks in the context of the "Precision Medicine Initiative."  Testing is currently available for the amino acid substitutions that link life history transitions in human behavior to the honeybee model organism of human immunity, disease resistance, allergic reaction, circadian rhythms, antibiotic resistance, the development of the brain and behavior, mental health, longevity, diseases of the X chromosome, learning and memory, as well as conditioned responses to sensory stimuli.

Unfortunately, many medical practitioners are being faced with the possibility of malpractice suits if they fail to implement testing. As always, a few heads will roll before managed practices allow their practitioners to add any time to patient visits for non-invasive testing and the interpretation of results that could be spent making more money for the practice.

But, as the psychopath, Roy Niles suggests, I could be wrong.

Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems. 

Avatar of: Roy Niles

Roy Niles

Posts: 88

Replied to a comment from James V. Kohl made on January 9, 2016

January 9, 2016

The usual "argument by insult" from Kohl, rambling away about how viruses are linked to this and that and those and are therefor the cause of biological evolution, not considering at all that there would have had to be an evolutionary cause of viruses to have allowed them to, in his pseudoscientific world, exist at all.  Or did they just emerge mechanically from the big nothing.

Avatar of: JM_1234321

JM_1234321

Posts: 7

Replied to a comment from Roy Niles made on January 9, 2016

January 15, 2016

The only "big nothing" is between your ears.

 

And you deserve to be insulted. You are not intellectually or EMOTIONALLY equipped enough to understand and accept the `domino-effect reality you are looking at.

 

To keep it relevant...

Insane retarded humans like you are either parasites OR dumb hosts for all the "wrong" types of parasites.

 

"wrong" = types I simply don't like. ...That's right: along with _domino effect reality_ the other thing you don't understand is that perception is relative. Too bad, huh?

Avatar of: Roy Niles

Roy Niles

Posts: 88

January 17, 2016

Another mechanistic evolutionist has arisen.  Too much of a troll to use his real name.

And by the way evolution does NOT work by domino effects.  But apparently you're not able to explain why you believe it does.

To other readers:  Dominos do not cause other dominos to evolve, or at least have never been known to, and a domino seemingly cannot be made to have an evolutionary effect on other dominos by the domino player that has caused the 'reactive" process to start - one where we have each domino affecting the next one according to the order that none of these dominos has been responsible for setting itself up to be an effective part of.  

In other words, dominos serve a gamer's purpose, but have no purposes of their own.  While evolution on the other hand both has a purpose and serves a myriad of other purposes. (If there were room here to exxplain that, I would try my best to do service to that purpose.)

 

Avatar of: Dr. Chui

Dr. Chui

Posts: 1

January 18, 2016

I find it INCREDIBLE how the Autors are capable of self-cheating !

They write an excellent article, CONFIRMING the superiority of cooperation over competition in the governing dynamics of evolution, yet they are still victims of the neo-darwinian fraud pretending evolution to be "inherently selfish"...

As a 65 years doctor having successfully resisted the attempts of my teachers to indoctrinate me with the neo-darwinian doctrine still pervading every corner of our stuffy culture, may I encourage the Autors to free themselves from those biased prejudices and then re-read their own article with a more openly minded attitude?

Probably they will re-write the conclusion of their article somehow like that "...the key to make the most of our social world... is to understand... how Nature is harnessing such cooperative relationships...".

Thanks anyway.

Avatar of: typicalanimal

typicalanimal

Posts: 7

January 20, 2016

 

 

 

 

 

 

Quote Dr. Chui

 

 

 

 

 

I find it INCREDIBLE how the Autors are capable of self-cheating !

 

 

 

 

 

 

 

They write an excellent article, CONFIRMING the superiority of cooperation over competition in the governing dynamics of evolution, yet they are still victims of the neo-darwinian fraud pretending evolution to be "inherently selfish"...

 

 

 

As a 65 years doctor having successfully resisted the attempts of my teachers to indoctrinate me with the neo-darwinian doctrine still pervading every corner of our stuffy culture, may I encourage the Autors to free themselves from those biased prejudices and then re-read their own article with a more openly minded attitude?

 

 

 

Probably they will re-write the conclusion of their article somehow like that "...the key to make the most of our social world... is to understand... how Nature is harnessing such cooperative relationships...".

 

 

 

Thanks anyway.

 

 

 

 

 

 

 

 

 

Well said Dr. Chui. There is nothing "selfish" about evolution, not with any of the usual meaning of the word selfish. All Richard Dawkins did in his book The Selfish Gene was just frame evolution in a sinister way, using words like "selfish" and language such as that evolution is cold, ruthless, mathematically calculating, and rather vicious... just to freak out some people by his flowery use of language. That's really just rhetoric and appealing to human views and values, it's not objective like how science should be done.  

 

 

 

There is nothing that scientific circles like more than a supposed "revolution" or "breakthrough" - It creates work and excitement and gives the illusion of progress. I suspect this is what happened with the "group selection" idea being demonized and strawmanned and then replaced by the selfish gene idea which supposedly made much more sense. When you allow for a looser definition of the idea of "group selection" than a particular group living/dying together, then it turns into the exact same thing as "selfish gene selection". It's not really "incorrect" to call it a competition of selfish genes, it's just that it's not particularly useful or revealing anything to frame it that way, not to me and evidently not to ordinary people.  

 

 

 

Often writing on this subject tends to be more narrative, having said that this particular one has a reasonable amount real science. Unfortunately the science can be a bit boring and inconclusive, then something just seems to take hold of human imagination sometimes and comes up with that nature is inherently harsh, brutal and nasty, and us living in "civilized society" have it great by comparison when often nothing could be further from the truth. 

 

 

 

 

 

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