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Quizzing the Anonymous
Ignoramus et ignorabimus
On the Enlightenment 
2nd-Oct-2008 12:32 pm
related http://shkrobius.livejournal.com/134936.html (On Sacrifice and Common Good)
http://shkrobius.livejournal.com/121758.html (Leaders and followers)

...For many pathogens, the outcome of the interaction between host and bacterium is strongly affected by the bacterial population size. Coupling the production of virulence factors with cell population density ensures that the host lacks sufficient time to mount an effective defence against consolidated attack. Such a strategy depends on the ability of an individual bacterial cell to sense other members of the same species and in response, differentially express specific sets of genes. Such cell-cell communication is called "quorum sensing" and involves the activation of a response regulator. http://www.ncbi.nlm.nih.gov/pubmed/11437336?dopt=Abstract&holding=npg

...Bacteria which use quorum sensing produce and secrete signaling compounds called autoinducers. When the inducer binds to it’s receptor, it activates transcription of certain genes, including those for inducer synthesis. When only a few other bacteria of the same kind are in the vicinity, diffusion reduces the concentration of the inducer in the surrounding medium, so the bacteria produce little inducer. With high concentrations of bacteria, the concentration of the inducer passes a threshold, so more inducer is synthesised. This forms a positive feedback loop, and the receptor becomes fully activated. http://microbiologybytes.wordpress.com/2006/09/25/quorum-sensing-in-bacteria-we-two-are-one

...Quorum sensing was first observed in V. fischeri, a bioluminiscent bacterium that lives as a symbiont in the photophore of a squid. When V. fischeri cells are free-living (or planktonic), the autoinducer is at low concentration and thus cells do not luminesce. However, when they are highly concentrated in the photophore transcription of luciferase is induced, leading to bioluminescence. The bioluminescence would not be visible if it were produced by a single cell. By using quorum sensing to limit the production of luciferase to situations when cell populations are large, V. fischeri cells are able to avoid wasting energy on the production of useless products. (Wiki)

The herding mechanism invented by the pathogens for coordinated destruction of their Universe and their immediate gain can also be used to produce light for the sake of the Great Friendly Squid on the High Seas seeking its mate. It's astonishing how little is the difference between people and bacteria...

The bacteria living in the photophore of the squid and cooperatively producing light when there is enough of them have no idea why do they cooperate to produce this light.

When we cooperate, for whom do we cooperate?
2nd-Oct-2008 08:39 pm (UTC)
We cooperate for each other (for the sake of the population in general, in result). It is nothing to do with a special plan or a conscious wish.
But we also have many symbiotic bacteria in our guts, on the skin, on mucosa etc. Actually there are much more bacteria cells than our own cells in our body. Considering bacteria are much older, we can conclude that we are just reservoirs for growing those myriads of bacteria (smart enough to struggle all environmental severities).
Even more: our own eukaryotic cells are just symbiotic cooperation of ancient bacteria (mitochondria f.e. have 2 membranes and their own DNA which means once they were independent bacteria incorporated into another primitive bacterial cell, result - huge aromorphosis!).
1. Nowadays, in our bodies, many bacteria species live intracellularly as pathogens (chlamidias, rickettsias etc), but they tent to loose their pathogenicy to become mutualists - universal evolutional law).
Evolution is evolution! No metaphysic supernatural mind to rule. It goes on itself by the path of natural selection. And the symbiosis is a very significant tool here.
2nd-Oct-2008 09:01 pm (UTC)
So we cooperate for each other, like the cholera bacteria in the first example, in order to infect our planet with humans, correct? Observe that in the second example the bacteria also cooperate and acquire indirect benefit from this cooperation (the host provides them with food), but they do not cooperate for their own sake. The goal for which they cooperate and tolerated by their host (giving bright light that the host uses to its own ends) is totally obscure to the bacteria. Why cannot I relate that to people? Are not we in a symbiotic relation with the rest of the biosphere? Is not, for example, agriculture an example of mutualistic symbiosys? Why are you so sure that we cooperate for our own sake rather than the sake of our floral symbiont? Conversely, you can consider our entire planet as our host. Maybe we cooperate for the sake of this host and are given our daily bread for our good service? I do not see how natural selection excludes such possibilities. The bacteria are as much a subject to this natural selection as the rest of us and yet the goal of their cooperation can be both internally and externally imposed. Is not the rise of civilization typically explained by the needs of farming? So here you have the clear-cut example of collective behavior, cooperation, and complex social structure imposed by grassy plants on their human symbiont. "No metaphysic supernatural mind to rule," as you say. And this is just one example of interspecies interaction involving H. sapiens. Are you still absolutely sure that we are in charge of our own cooperative behavior?
2nd-Oct-2008 09:58 pm (UTC)
You can widen symbiotic relationships to biosphere, Solar system etc, but it is not quite correct. Symbiotic (parasitic, mutualistic or commensalistic) relationships should be considered only between individuals of 2 species to make sense.

"Are you still absolutely sure that we are in charge of our own cooperative behavior?" - Humans are the only animals who MAY make a conscious choice here or at least understand why we cooperate to each other, that is why many comparisons with other species and especially with questions WHY could be irrelevant.

"Why are you so sure that we cooperate for our own sake rather than the sake of our floral symbiont?" - This is exactly what I mean: it is mutual profit here!

P.S.: Goal - is human word. Nature is goalless, but there are just natural laws for the entropy to evolve. We should not confuse too terms.
3rd-Oct-2008 12:57 am (UTC)
What you suggest here is... how to put it - debatable.

For starters, bacteria are not individuals and quite a few microbiologists deny that "species" even applies to prokaryotes. Rather, what is called species are ecotypes and so by being in symbiosis with a bacterium a eukaryot (which is a species) enters in a relationship with the entire Prokarya. Furthermore, there is a popular school of thought that the latter cannot be considered separately from the Earth itself, due to the manifold feedbacks between microbial activity and the atmospheric and geo- chemistry. So it is not only correct to consider symbiosys on the planetary scale, that is what quite a few biologists, starting from Margulis, have been arguing for over the last 35 years.

Furthermore, you begin from the assumption that cooperation is your conscious choice. I do not know any proof of that. The majority of evolutionary theories of cooperation and altruism make the opposite assumption: the cooperation is genetically wired. What happens at the conscious level is the rationalization of this hardwired program.

The profit of the early agriculture was famine, disease, chronic vitamin deficiency, shortening of life span, of size, etc. I do not know any publication on the origin of agriculture in the last 40 years that found any benefit for fitness in the transition from hunting/gathering to agriculture. You can read this summary of the standard view
The symbiosis was not mutualistic. So it is entirely to a point asking for whose sake it was.

As for the Nature not having a goal, tell this the squid that lights up his bacteria to find a mate. It has a well-defined goal and it achieves it by releasing nutrients into its photophore. On a broader note, one the most widely held definitions of life is that of an autopoietic system, which actively and exclusively maintains the whole regardless of external influences. This very property then is the goal of a living system. Observe also that I can say, too, with the same degree of confidence, that you do not have a goal - any goal. There is no way you can prove it to me that you have it. Only an organism itself has this realization. We deduce that the others have goals only by extrapolation. The more dissimilar is the system, the more strained is this extrapolation. Only "Nature" itself, whatever you mean by that, can be aware of its goal.

BTW, entropy does not evolve, it is a number.

3rd-Oct-2008 05:27 pm (UTC)
Here we should avoid demagogy. Species criteria are not ideal even in higher eukaryotes due to evolution is continuous and not discrete, but it doesn't mean we should not use the term. Bacterial species and their strains are quite well identified in microbiology and this is just a question of how far you need to tell between them to call a species (or a strain, or serovar etc).

The cooperation among humans is genetically PREDISPOSED, but still we have a conscious choice. The more developed is intellect the more varieties in such choice is seen in primates. Some behave quite unpredictably.

We use the word "goal" in different ways. I meant a conscious purpose (sorry for bad English). Of coarse there is a mutual goal in mutualistic relationships, but I call it �profit�. Due to the relationships are not realized by mindless creatures, they do not know about each other as individual creatures. The squid�s body is just an environment for the luminescent bacteria, while the bacteria are just the useful �organ� or tool for the squid.

Entropy is just a result. The universe and matter it consists of evolve to the entropy. That's what I mean. Technically speaking "entropy" is a function that changes (=evolves). The process is described by formulas you can find on Web. The word τρoπή means "changing"="transformation".
Entropy has a result of homogenous equation with 0 temperature and energy in the end.
3rd-Oct-2008 06:25 pm (UTC)
It is not demagoguery, as it goes to the very definition of a species, which requires genetic isolation. Any bacterium can swap genes with any other bacterium. "Telling" them apart is neither here nor there. What I told you is the standard view, eg http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=PubMed&list_uids=12142474
and you will do yourself great service learning from it.

You live in society and you have no other choice than interacting with a society. You can reject it, but you are still a social animal.

The goal is not mutual. The goal of producing light is squid's. The goal of the bacteria is getting food to multiply.

Functions do not evolve either.

3rd-Oct-2008 08:06 pm (UTC)
I know what you are talking about. But their are several criteria of species and genetic isolation is not relevant to bacteria actually. Bacteria are genetically classified by difference in a part of their DNA (coding citrase enzime - the less changible through evolution). For different kingdoms of nature different genes are compared to define their genetical similarity and to draw cladas.

I am not talking about ignoring SOCIETY. I am talking about cooperation of level individual-individual.

So why it is not mutual is both in profit???

If parts of function (T and Q) change why the function does not change?
3rd-Oct-2008 09:44 pm (UTC)
If you do understand that the concept of species does not apply to bacteria and the latter have a single common gene pool, then you have to admit that humans are a symbiont of the entire prokaryote kingdom, which is a single species. You told me that you object the notion that we may have a planet-wide host symbiont (that plays the role of a squid in my example). I do not see any reason why I cannot consider the Prokarya as such a host. You are very willing to consider bacteria living in your gut as your endosymbiont and that you as a host can facilitate cooperation between these bacteria on your behalf. Do you realize that you are just such an endosymbiont with regard to the Prokarya and that it can, as your host, also be selectively breeding cooperation in human population? The simplest example would be socialization -> easier spread of infectious disease, but I can invent hundreds of other scenarios. You should realize that the evolution of social animals is an enigma; nobody quite knows why animals become social. There all kinds of theories for, say, apes, eg that social grooming was one of the factors. Then the socialization is driven by parasites. There is a whole theory, by O'Donnell that eusociality is induced by castrating parasites, etc. etc. Asking whether our sociality is caused by intrinsic factors or extrinsic factors (symbionts, parasites) and who is the beneficiary are perfectly legitimate concerns.

Because bacteria do not "profit" from producing light. They just happen to use luciferase pathway for shunting electrons to oxygen. It is like you making a trumpeting sound when blowing your nose (the purpose is not making sound, it is something else). The bacteria have no clue that they make light and they do not use this light in any way. It just happens that one of the reactions yilds chemiluminescence, it is completely accidental. It the squid that needs light. Only the squid knows why this light is needed, he needs it. The bacterium only knows that only when there is a lot of signalling molecule (AHL) in solution it should switch electron transport pathway to luciferase pathway. It does not realize that it is cooperating. Why it has to be this way, it has no clue. If it fires at will, food is not coming. It is the squid that in the course of evolution made these bacteria to light up in cooperative fashion for its own needs, by selective breeding. Well, maybe our crops are doing the same...
4th-Oct-2008 12:51 am (UTC)
�If you do understand that the concept of species does not apply to bacteria and the latter have a single common gene pool, then you have to admit that humans are a symbiont of the entire prokaryote kingdom, which is a single species�
- Not at all. I very well differ between bacteroids, salmonellas, e. coli, clostridias, b. bifidum and many other species of my flora :) Some of them have not significantly changed since billions years ago.

Evolution of symbiotic species is not a big enigma for me. It seems to be very evident per se. Lichen can survive in environment where neither algi nor fungi, it consists of, cannot. The mutual profit is a clue to the evolution here. Not more, not less.

Yes, the luminescence is just a "side effect" of bacteria' metabolism and the squid only needs it, so what? Due to this "side effect" the bacteria could only survive in the bodies of squids and maybe in nature in general. Squids with such bacteria (especially those strains which make a brighter light, and only when the squid needs it) have more chances to mate and give the offspring. Bacteria receives perfect environment in return. So, the cooperation is mutually profitable in your example. And evolution of this cooperation is very clear.
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