[Martin J Sallberg (OP)]

Martin, you're making me curious. Can you link your evidence so I can see what you're talking about?

Yes, there is "Amoebas Anticipate Climate Change" (on Physics News Update's archive), showing that something that can functionally only be described as learning to predict the future, actually "evolved" in a single generation, without cell divisions. Sorry I could not find an URL link, but it is googleable.

[damocles]

Facts:
(1) Models that attempt to simulate real ecosystems are unstable.
(2) 2-dimensional models (predator/prey) are quite stable and account well for observations.

Possible explanations:
(1) Additional factors are operating in the real systems (like the one that the OP suggested).
(2) Something is going wrong with the modelling when the number of dimensions is increased.

Against  explanation (1): it would appear to involve new science that would not be comfortable fitting into the body of existing knowledge.
In favour of explanation (2): although there is an implication of instability and chaos, there remains the possibility of the system finding a steady state:

https://en.wikipedia.org/wiki/Attractor

Similar things -- models of systems that are stable in a few dimensions becoming unstable when the number of dimensions is increased -- are found and recognised in other areas of science.

[Martin J Sallberg (OP)]

The fact that introduced species often do seriously upset ecosystems in ways that causes extinctions proves that "flaws in the computer simulations" are not an adequate explanation. And if the theory of flawed computer simulations is taken seriously, it is the same as supporting the Gaia hypothesis, and are you really willing to do that? I doubt so. Furthermore, the whole gene-centered theory of how life behaves predicts that there should be "intergenomic conflict" between the cellular nuclei and the mitochondria in our cells, and a three-side standoff with chloroplasts in plant cells (cellular nuclei, mitochondria and chloroplasts all have their own genomes and are not closely related at all). So why are there no such conflicts?

[yor_on]

Stupid of me. Don't know why I forgot that one Damocles? You're perfectly right, and that one needs to be included, although it somehow makes us (life) out as a expression of some possible constants, aka Feigenbaum. at least when it comes to population pressures. But I think there exist some formulas for describing it from chaos? Think I read about some Australian example, or if it was New Zealand? In where they had some population disappearing, and what was possible to do about it, or not possible would probably be the correcter, ahem, definition.

As for "the fact that introduced species often do seriously upset ecosystems in ways that causes extinctions proves that "flaws in the computer simulations" are not an adequate explanation." Martin. I would say that if you define it from chaos mathematics you will get effects not easily foreseen, but still explainable from it.

[yor_on]

But I will also need to look your link up Martin
And hopefully see what you're thinking of there.

[yor_on]

Not sure what it proves Martin? That amoebas are capable of learning? Isn't that what i would call adaption? And so a evolution? What it states may be that you can see simple organisms adapt at short time scales though?

" A new experiment demonstrated that amoebas slow their motion in synchronization with periodic hostile changes in their environment.  The amoebas even displayed anticipation to the periodically appearing unfavorable conditions. This meant that they even slowed down when the adverse condition was to be expected to appear even it did not occur.  A new experiment demonstrated that amoebas slow their motion in synchronization with periodic hostile changes in their environment. The amoebas even displayed anticipation to the periodically appearing unfavorable conditions. This meant that they even slowed down when the adverse condition was to be expected to appear even it did not occur.A team of scientists from Hokkaido University  and the ATR Wave Engineering Laboratories in Japan  cultured the single celled slime mold Physarum polycephalum (a member of the amoeba clan) in a bed of oat flakes on an agar media.

Every ten minutes the air was made slightly cooler and drier, which had the effect of slowing the movement of the amoebas.Then more favorable air would be restored and the motion continued as before. After several cycles, the amoebas slowed down their motion even when the hostile conditions were not applied. Later still, when the organisms have been tricked into anticipating impending climate change several times, they stop from slowing without an actual change in conditions. One of the researchers, Toshiyuki Nakagaki from Hokkaido (nakagaki@es.hokudai.ac.jp), cautions that amoebas do not have a brain and that this is not an example of classic “Pavlovian” conditioned response behavior. Nevertheless, it might represent more evidence for a primitive sensitivity or intelligence, based on the dynamic behavior of the tubular structures deployed by the amoeba.  (Saigusa et al., Physical Review Letters, 11 January 2008 ).  Source: American Institute of Physics."

If fits right in with the complicated behavior we had in those bacterias to me though, seems we have different mechanisms for evolution, don't know how to check for chemical and genes differing in the population after the experiment though? Because if you could prove a change there then I would call it a 'mutation' through a changing environment I think. But there is one thing more, and that is what information they already have inscribed. Because if 'nature' meet such occasions before, then I think it should become easier for them to adapt, than if there was nothing similar ever happening to amoebas before, all as I see it?

[yor_on]

This might throw some light on possible relations.

"Biologists have been estimating the size of genomes for decades. In 1971, for example, researchers reported that a species of Italian bat, Miniopterus, has a genome half the size of the human genome. Similarly, the genome of Muntiacus, a species of Asian barking deer, was estimated at about 70 percent of that of humans. As reported this week, the human genome contains about 3 billion chemical units of DNA, or base pairs.

In the animal kingdom, the relationship between genome size and evolutionary status is not clear. One of the largest genomes belongs to a very small creature, Amoeba dubia. This protozoan genome has 670 billion units of DNA, or base pairs. The genome of a cousin, Amoeba proteus, has a mere 290 billion base pairs, making it 100 times larger than the human genome. " http://www.genomenewsnetwork.org/articles/02_01/Sizing_genomes.shtml

You might think of it this way. We have a evolution through simple small organisms to complex large ones. but the amount of genes they have may be a result of different climates and ways of life, amoebas have been here for a very long time as I understands it, and maybe the idea of dormant genes awakening may play a part in it? Or you could see the genes that are active as a 'synthesis' of all those dormant ones too, meaning that they already were 'ready' for a change, and so able to react on it?
==

what i mean is that it might be possible to see the amount of genes as 'information' defining 'rules'. Those rules will behave 'intelligently'  to us, but they are not the same as us humans using our mind consciously. We could all decide today to throw our car keys away, amoebas can not, We can also decide to limit our population today, through freely deciding one kid per person, ameobas might do the same due to environment, but not before it was there.

Thinking about it, the worst thing I might say about us then would be that we are closer to amoebas than previously thought That is, if we don't start doing something positive about our environment inside the closest decades. Because, every year will count for more, as it accelerates, as I think.

But it's still nice news, as it mean that Nature will be able to adapt, given time. The problem there is just how much time complex organisms will need, migrating etc. We have a accelerating global warming, combined with a increasing CO2 man made, each year. I don't mean that it is 'the end' of anything, but we will see species disappear, due to our ignorance, and greed.

[damocles]

I am absolutely not a biologist. I thought I was seeing a pattern that I recognised from similar cases in the physical sciences -- smog simulations, and weather/climate models.

The fact that introduced species often do seriously upset ecosystems in ways that causes extinctions proves that "flaws in the computer simulations" are not an adequate explanation.

I do not see how or why this is the case. "flaws in the computer simulations" are not intended as a catch all explanation, especially not if the ecosystem undergoes some basic change.

And if the theory of flawed computer simulations is taken seriously, it is the same as supporting the Gaia hypothesis, and are you really willing to do that? I doubt so.

You will need to lead me by the hand here. What does all this have to do with the Gaia hypothesis?

Furthermore, the whole gene-centered theory of how life behaves predicts that there should be "intergenomic conflict" between the cellular nuclei and the mitochondria in our cells, and a three-side standoff with chloroplasts in plant cells (cellular nuclei, mitochondria and chloroplasts all have their own genomes and are not closely related at all). So why are there no such conflicts?

How are the cellular nuclei and the mitochondria and the chloroplasts supposed to attack one another?
Is there perhaps a symbiotic arrangement that benefits all parties?
Are not the mitochondria essentially "hitching a ride" on the operations of the cellular nuclei, which should not matter as long as they do not interfere?
Is there not a model for the interaction of parasites, which have an interest in weakening but not killing the host animal?

[yor_on]

There is one thing more, RNA (micro RNA) and DNA seems to have a very complex relationship as I gather. A lot of new 'patents' in genetics are no more that copying natural designs, and then restricting a description of how it is thought to work. I'm very tired of the American way of 'patenting' nature myself. All a question of unbridled greed. I suspect one could say that most of our inventions are no more than copying, although we present it as if we 'invented' it instead. That behavior goes very well with the way we mishandled our resources naturally, the sort of hubris typical for human greed I would say. Yeah, I know, I'm not very nice in my outlook of us all here, feel free to prove me wrong. And I don't think that hubris to be isolated to industrialized countries, it exist everywhere, in different disguises.

http://www.vetmeduni.ac.at/en/infoservice/current-issues/presseinformation/presseinfo2013/press-release-04-19-2013-a-surprising-new-function-for-small-rnas-in-evolution/

[Martin J Sallberg (OP)]

The "Amoebas Anticipate Climate Change" link can be googled. Relevance is achieved by googling with quotation marks for the exact phrase.

The point about the amoebas is that they learned to adapt to the cycle within their lifetime, without cell divisions and thus without the conventional form of evolution. They learned a specific cycle. Have you ever heard of 10 minute cycles being predominant in "nature"? They sure have faced lots of different kinds of cycles in "nature", so specific adaptation to certain types of cycles theough natural selection cannot explain it.

The point about mitochondria, chloroplasts and cellular nuclei is that they are not closely related, but yet cooperate without "intergenomic conflict". Yes, they depend on each other, but so do organisms in an ecosystem. So "selfish replicators" cannot be the reason for destruction of ecosystems. This shows that anti-ecological selfishness is all a faliure of communication, sometimes combined with justification poisoning.

And the reason why I mentioned the Gaia hypothesis is because the computer simulations about collapsing ecosystems is what is considered to have falsified Gaia.

[yor_on]

Are you telling me that this quote is incorrect Martin?
Then present me the paper involved instead.

I will read it with interest.

[damocles]

OK Martin, I can see now that you have used sloppy logic regarding Gaia.

The original proposition can be expressed
If A then B
not B
therefore not A
(A perfectly valid syllogism)

However when you reverse it:
If A then B
B
therefore A
the logic becomes invalid.

[damocles]

The whole point about symbiotic arrangements is that there has to be "something in it" for each party. Dismissing it by saying that an ecosystem is dependent on similar arrangements is a bit of a cop out:
• Regarding an ecosystem as an organism is a little like taking a gestalt view of the situation (reminiscent of Gaia?).
• There is no advantage for any "prey" organism to co-operate with its predator, as can readily be seen in the enormous variety of mechanisms that prey organisms use to hide from/confuse/distract their predators.

[CliffordK]

A model is only as good as the design and the input to the model.

One of the important parts of our environment are niches.

Each species has become optimized for a particular niche.  Some plants like dry soil, some plants like moist soil.  Some tolerate dry summers, some don't.  Cold winters?  Lack of freezing? 

Then you have the herbivores.  If they eat all their food supply, they die off.  If there is excess food, they flourish. 

And, the carnivores.  Some are good at hunting large game.  Some hunt small game.  Some in forests, some in meadows and plains. 

Perhaps one important part of an ecological niche is a way to preserve oneself at times of stress.  Some desert plants can survive as dormant seeds for decades, waiting for the next big rainfall. 

Now, the models may be absolutely correct.  If two species share the exact same niche, then it may be common for the one to become slightly favored over the other and out compete the other.  In this case, the lesser species will have to either find its own niche, or be driven to extinction.

There likely are a couple of forms of evolution.  In some cases, all members of a species or subspecies will interbreed, and the species as a whole will drift towards the strongest and fittest. 

If, however, there is a mutation such as chromosomes splitting or merging, then there may be no interbreeding, and a new species would originate.  If the new species out competes the old species, then all members of the old may eventually die off.

I.E.  we have horses, but no 3-toed-horses.

Due to predator/prey feedback, some predators, in particular severely limit their offspring, often to one viable baby per year, or perhaps even less. 

Throw humans in the mix, and we stir up the niches.  Take the best for ourselves.  We over-hunt, so that species that were adapted to slow reproductive cycles suffer.   Some species adapt.  There are many suburban deer that may consider flower gardens a delicacy.  Other species fare poorly.

[CliffordK]

• There is no advantage for any "prey" organism to co-operate with its predator, as can readily be seen in the enormous variety of mechanisms that prey organisms use to hide from/confuse/distract their predators.

Perhaps no overt cooperation between predators and prey.  But they do function together.  The predators may help remove the diseased animals from a herd, and in that way help protect the whole herd.  And, of course, also pushing constant evolution towards the "fittest", or at least pushing evolution away from the unfit.

The predators are also an important part to keep the prey from overpopulation, and thus destroying their own survival niche, with more prey bringing better predator survival, and less prey bringing less predator survival, neither destroying their whole niche.

[Martin J Sallberg (OP)]

Adding predators to "manage the herbivore population" does not solve the problem, it just moves it. Predators are just as likely to overkill their prey as herbivores are to overkill plants. This is an example as good as any showing that it takes something absolutely qualitatively different from anything explainable by "genetic self-interest" to avert very rapid mass extinction, humans or no humans.

And even considered that it is possible for herbivores to provide carnivores with nutrition without dying themselves? I think of eggs, milk, blood, etc. The carnivore could then fertilize the herbivore's food with dung. Arrangements where plants provide for herbivores without being killed is also concievable. Those would, if they were common, have been macroscopic equivalents of the cellular nuclei/mitochondria/chloroplast arrangement. The point is that what causes ecosystems to conflict is faliure of communication and not "fundamental interest". Communication over short distances is easier. Did you know that dying from new diseases "immunological naivity" is generally due to immunological overreaction and not the germ itself?

[yor_on]

I like the idea of genes meaning rules myself. That transforms it into something that you can treat mathematically. And the type of mathematics you will need for treating it (life and competition) is non linear, which makes it chaos mathematics. And there you will find a lot of surprises, as 'mystical attractors', as well as hidden constants (Feigenbaum for example). It's one of the main things we believe in, that each time you get a amount of something interacting, it should be possible to find a mathematical description of it. The problem is that you have a lot of interactions, too many to treat distinctly, also making small initial differences into major as the complexity builds up. But there are constants existing in those chaotic behaviors too, and if there are you can be assured that the pattern evolving is treatable and logical. But I wish you could simplify what you mean Martin, because I lose myself reading you, not being sure what ideas you argue for?

That we can't explain how life co-exist?
Or that we can't explain what leads to species extinction?
Or is it something more to it? Intelligent design?

[yor_on]

I don't know if selfish genes are the right description either, if it is solely that you are disputing? I would say it is a game of probability, related to what environment presented, genes becoming 'rules' adapting to it. More like emerging patterns than 'one to one' relations, even though those too must be present. All as a guess..

[Martin J Sallberg (OP)]

I am arguing that since organisms would have time to eat their food stocks to extinction before starving to death themselves, some form of learning from mistakes qualitatively different from hardwiring by natural selection is necessary to explain why it does not lead to incessant mass extinction that wipes all life out. The learning from mistakes and the emergent foresight that follows from it does only involve emergent processes based on conventional chemical reactions, not anything like "souls", "deities" or anything like that.

[yor_on]

Don't know if it always can be assumed to have been a competition myself? We had very simple organisms in the beginning getting their nutrition from nature itself, what did they 'compete' with? Then climate change, as well as the organisms mutates, creating different (sub? New?) species. And suddenly you have upped the complexity to one where they might need to compete for some food source. And that's where kismet and genetics starts to play a role for the balance. Also one need to remember that mutations won't stop in either case, so if one species are more prepared than the other it should force the other to adapt in some other way, meaning that those that won't adapt will die out. It should fast become very complicated, the more species you introduce. As for all organisms coming from the same start I agree, and neither do I think that humans have some special place reserved in nature. Not from geological time processes and from the view of a earth 'creating' or at least allowing emergent life forms.