Tuesday, June 17, 2014

Here’s That Algae Study That Decouples Phylogeny and Competition

“We Were Completely Baffled”

In Charles Darwin’s theory of evolution the engine of progress is death. Nature is one big Malthusian battlefield as natural selection kills off the less-fit designs. As David Hume had put it a century before, “A perpetual war is kindled amongst all living creatures,” and nature is so arranged so as “to embitter the life of every living being.” In Darwin’s day Alfred, Lord Tennyson found that nature was “red in tooth and claw” and Herbert Spencer summarized Darwin’s new theory as the “Survival of the Fittest.” Or as Nietzsche lamented, it is the weak “who most undermine life.” But there’s only one problem: this is all the result of junk science. For every Serengeti Plain there are untold stories of mutualism and cooperation between species which contradict one of evolution’s most fundamental predictions. All of this came to light once again in a massive evolutionary study of algae.

In the algae study the researchers competed various pairs of freshwater green algae species against each other. Those species that are thought to be more closely related in the evolutionary tree should have competed against each other more intensely. On the other hand, species that are farther apart in the evolutionary tree should exhibit less competition.

But none of this was found in the experimental results. No such trends were found and once again the theory of evolution produced a false prediction and did not help to explain the scientific evidence. The team spent months trying to resolve the problem, but to no avail. As one of the researchers explained:

It was completely unexpected. When we saw the results, we said ‘this can’t be.’ We sat there banging our heads against the wall. Darwin’s hypothesis has been with us for so long, how can it not be right? … When we started coming up with numbers that showed he [Darwin] wasn’t right, we were completely baffled. … We should be able to look at the Tree of Life, and evolution should make it clear who will win in competition and who will lose. But the traits that regulate competition can’t be predicted from the Tree of Life.

Of course none of this has anyone doubting the truth of evolution. It just must be more complicated than was previously thought. Perhaps algae are “plastic” and diverging in ways unrelated to competition. Or perhaps nature’s species cooperate at greater levels than was thought. Perhaps there is more co-evolution between species, resulting in more cooperation.

You see there are always more epicycles for evolution. With each new absurdity another new complicated just-so story is woven into evolutionary theory. As Lakatos explained, some theories simply are not falsifiable. But as a result they sacrifice realism and parsimony.

Religion drives science, and it matters.

38 comments:

  1. Of related note, while learning, from Dr. Behe in the 'Edge Of Evolution', that HIV is a 'mutational powerhouse' which greatly outclasses the 'mutational firepower' of the entire spectrum of higher life-forms combined for millions of years, and about the devastating effect HIV has on humans with just one trivial binding site being generated by the Random Variation - Natural Selection process, I realized if evolution were actually the truth for how all life came to be on Earth then the only 'life' that would be around would be extremely small organisms with the highest replication rate, and with the most mutational firepower, since only they would be the fittest to survive in the dog eat dog world where blind pitiless evolution rules and only the 'fittest' are allowed to survive. The logic of this is nicely summed up here:

    Richard Dawkins interview with a 'Darwinian' physician goes off track - video
    Excerpt: "I am amazed, Richard, that what we call metazoans, multi-celled organisms, have actually been able to evolve, and the reason [for amazement] is that bacteria and viruses replicate so quickly -- a few hours sometimes, they can reproduce themselves -- that they can evolve very, very quickly. And we're stuck with twenty years at least between generations. How is it that we resist infection when they can evolve so quickly to find ways around our defenses?"
    http://www.evolutionnews.org/2012/07/video_to_dawkin062031.html

    i.e. Since successful reproduction is all that really matters on a neo-Darwinian view of things, how can anything but successful reproduction be realistically 'selected' for? Any other function besides reproduction, such as sight, hearing, thinking, etc.., would be highly superfluous to the primary criteria of successfully reproducing, and should, on a Darwinian view, be discarded as so much excess baggage since it would slow down successful reproduction. But, as the study Dr. Hunter highlighted clearly illustrates, that is not what we find:

    Indeed, instead of eating us, time after time we find these different types of microbial life to be helping us in essential ways that have nothing to do with their ability to successfully reproduce,,,

    NIH Human Microbiome Project defines normal bacterial makeup of the body – June 13, 2012
    Excerpt: Microbes inhabit just about every part of the human body, living on the skin, in the gut, and up the nose. Sometimes they cause sickness, but most of the time, microorganisms live in harmony with their human hosts, providing vital functions essential for human survival.
    http://www.nih.gov/news/health/jun2012/nhgri-13.htm

    We are living in a bacterial world, and it's impacting us more than previously thought - February 15, 2013
    Excerpt: We often associate bacteria with disease-causing "germs" or pathogens, and bacteria are responsible for many diseases, such as tuberculosis, bubonic plague, and MRSA infections. But bacteria do many good things, too, and the recent research underlines the fact that animal life would not be the same without them.,,,
    I am,, convinced that the number of beneficial microbes, even very necessary microbes, is much, much greater than the number of pathogens."
    http://phys.org/news/2013-02-bacterial-world-impacting-previously-thought.html#ajTabs

    The Microbial Engines That Drive Earth’s Biogeochemical Cycles - Falkowski 2008
    Excerpt: Microbial life can easily live without us; we, however, cannot survive without the global catalysis and environmental transformations it provides. -
    Paul G. Falkowski - Professor Geological Sciences - Rutgers
    http://www.genetics.iastate.edu/delong1.pdf

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    1. Music:

      Thrive – Casting Crowns
      lyric: “It’s time for us to more than just survive
      We were made to thrive”
      http://myktis.com/songs/thrive/

      Delete
    2. Jim Tour on "The Importance of the Scriptures" - video
      https://www.youtube.com/watch?v=1cZvpBe9QDg

      Delete
  2. Other ideas of Darwin have been found to be wrong as well. Nor does evolutionary theory as a whole stand or fall based on this one, indirect prediction. So what?

    Implicit in your post is the fallacy that ideas should be judged based on their source, not their contents. Also, that theories should be effectively prophecy, in that they should never change or should be able to account for all parallel, yet unrelated events via some inexplicable means, etc.

    IOW, you seem to think theories should not be incomplete and contain errors to some degree. So, exactly how would that work, in practice? And not just for evolutionary theory, but any theory?

    For example, give us a theory that isn't incomplete and doesn't contain errors to some degree. And, while you're at it, explain how we supposedly achieved it. Please be specific.

    This is yet another example of rampant bad philosophy displayed on this blog on a regular basis.

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  3. Thank you Scott, especially for the first sentence. So we can now be open to any and all of Darwin's ideas shown to be wrong in coming years. And we can be assured the educational establishment will be so open to Darwin being wrong, and teachers can teach the kids as much without fear. And the NCSE can now plan a new strategy, that of Darwin being wrong, and to promote the policy that no teacher should be fired for saying what you and I just wrote. BTW I can give you an example of an error-free theory from my own field and that example is linear system theory, which should clearly designate your last 4 paragraphs as bad philosophy.

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    1. First, thanks for pointing out how disingenuous your comment is by ignoring the rest of the paragraph and the preceding paragraph.

      Specifically, biological Darwinism doesn't hinge on the prediction in question. So, again, either this represents character assassination, which implies jugging theories based on their source, or ignorance about the explanation that actually underlines biological darwinism.

      Second, please provide your *exhaustively complete*, error free theory, and how you actually reached the conclusion that is exhibits either of those properties, in practice. Please be specific.

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    2. Scott: Linear system theory is not my theory to provide for you and don't expect me to teach it to you here unless you think you can magically absorb integral transforms, convolution, state space, linear differential equations and stochastic processes among scores of other subtopics. Meaning of course that your request is absurd. And I didn't say it was "*exhaustively complete*" , because man-made systems can be increasingly complex without bound, and new tools of analysis cannot be ruled out. You should be aware that mathematicians use terms like 'elegant' and 'beautiful' to describe objects of their study. I've never, ever seen anything described as 'beautiful but error riddled' or 'elegant but flawed' in my studies. But thinking I should leave something concrete for you, take a look at "Methods of Signal and System Analysis" by McGillam and Cooper and if you think there are theoretical errors let us know.

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    3. MSEE: So we can now be open to any and all of Darwin's ideas shown to be wrong in coming years.

      Lots of Darwin's ideas have been shown to the wrong, such as his pangenesis theory of genetics.

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    4. MSEE: BTW I can give you an example of an error-free theory from my own field and that example is linear system theory

      You seem to be confusing the mathematical model with its application. The fit between model and application is often going to be imperfect.

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    5. Not confusing anything here. To quote " give us a theory that isn't incomplete and doesn't contain errors to some degree."

      I did exactly that, according to the second criterion. I said nothing about whether implementation conforms to analysis. It is not strictly the theoreticians problem if a resistor heats up, smokes, and becomes an open circuit. So if you want to be more specific about my example of a theory as error-free give it another shot.

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    6. MSEE: I did exactly that, according to the second criterion. I said nothing about whether implementation conforms to analysis.

      The request was clearly for a scientific theory, not a mathematical theory.

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    7. And in case a known non-conformity to lumped parameters or a non-linearity exists, then linear system theory may have limitations. So what. Like I said, this is an error-free theory just like what Scott says shouldn't exist.

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    8. MSEE: And in case a known non-conformity to lumped parameters or a non-linearity exists, then linear system theory may have limitations.

      So it's error-free as long as it has no errors.

      Delete
    9. Oh I get it. Nothing scientific about applying mathematics to physical systems. Hee hee. There goes orbital mechanics, nothing that a circus clown can't do there.

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    10. MSEE: Nothing scientific about applying mathematics to physical systems.

      Didn't say that. Rather, you said that the application only works unless it doesn't work.

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    11. MSEE: And in case a known non-conformity to lumped parameters or a non-linearity exists, then linear system theory may have limitations.

      zachSo it's error-free as long as it has no errors

      Silly girl. Where did I say that? Reread. Linear system theory has limitations when applied to systems for which it is not formulated such as one containing a NONLINEAR component. In such a case, modelling the component as linear or piecewise linear, results may be accurate enough for practice. Has nothing to do with error in theory get that? Has everything to do with possible misapplication of the theory, Get that? REREAD


      Look all you have to do is come up with an error for me in what I claim to be error- free. It's that simple. Point out for me an error in the below linked book. It's that simple. If you are unwilling to be specific and show me, you're blowing smoke. You really ready to claim theoretical errors in the book? Really? Whether or not you peruse it, REALLY? http://www.amazon.com/Signals-Systems-Edition-Alan-Oppenheim/dp/0138147574/ref=sr_sp-atf_title_1_1?ie=UTF8&qid=1403117045&sr=8-1&keywords=signals+and+systems

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    12. MSEE: Linear system theory has limitations when applied to systems for which it is not formulated such as one containing a NONLINEAR component.

      Which is most everything.

      MSEE: In such a case, modelling the component as linear or piecewise linear, results may be accurate enough for practice.

      So in some cases, the errors are negligible, other times within reason, and other times completely unworkable.

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    13. MSEE, you're confusing a theory for which we currently have no criticism of with a theory being error free.

      For example, do we not have classic and modern control theory? Did classic control theory contain "errors", while modern theory does not? Are you suggesting that we currently possess the end of all theories for linear systems, and no further progress can be made?

      Furthermore, linear systems theory is part of an incomplete theory: control theory. How do you know a system is actually linear, so it's application will always actually solve the problem at hand? You don't.

      And, as Zachriel pointed out, linear systems theory is an mathematical model. It's abstract, like a geometrically perfect circle. There are no perfect circles in the real world. To my point, LST allows us to solve problems despite these discrepancies with varying degrees of success.

      IOW, that theories are always incomplete and contain errors to some degree is expected, due to our epistemological explanation of how knowledge grows. Nor does it prevent us from making progress.

      On the other hand, Cornelius seems to think errors and incompleteness is somehow not the norm and prevent us from making progress. It's unclear how this assumption is reasonable or even something we should expect. Apparently, this is the result of some other epistemological explanation, which he has yet to disclose or argue for.

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    14. Look it's you guys who have to point out theoretical errors equivalent to the gross errors of Darwin. I can point to errors IN PRINT all over the place in neo-Darwinian formulations. Even as noted by Darwinians such as you. This discussion shows you guys cannot wrap your mind around a beautiful theory and an INHERENTLY highly flawed one with gross conceptual errors obvious from Scott's first comeback at me. The fact that Zach got to the point of "The request was clearly for a scientific theory, not a mathematical theory." kind of indicates a broadside caused mind slip. Really what we have here is squishy squishy stuff promulgated by you guys as a "theory as well established as the theory of gravity". Really now. So the last post by Scott doesn't take into account the every day promotion of Darwin to the public and especially to students as being as concrete as any abstract mathematically based theory. You guys can't even admit this as a major problem, this squishy stuff so promoted. Now an easy out for you: Either Darwinism is as well proven as LTI systems theory, or it is "just a theory" as the laypersons say. Otherwise show me an error in the following, just on one page: http://en.wikibooks.org/wiki/Control_Systems/State-Space_Equations

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    15. MSEE what exactly is your point in comparing Evolutionary theory to LST?

      The comparative "mathy-ness" of two theories, and the robustness of that math to scrutiny by non-mathemeticians, says absolutely nothing about the utility of EITHER theory.

      What a silly objection!

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    16. Scott: IOW, you [Cornelius] seem to think theories should not be incomplete and contain errors to some degree. So, exactly how would that work, in practice? And not just for evolutionary theory, but any theory?

      Scott: For example, give us a theory that isn't incomplete and doesn't contain errors to some degree. And, while you're at it, explain how we supposedly achieved it. Please be specific.

      I asked two questions above.

      The first was for an explanation for how it would be possible to end up with a theory that isn't incomplete and contains errors to some degree. How would it work, in practice?

      I then asked for a concrete example of an actual, specific theory to allow them to work backwards and explain how we supposedly achieved that theory being error free, in practice.

      MSEE: BTW I can give you an example of an error-free theory from my own field and that example is linear system theory, which should clearly designate your last 4 paragraphs as bad philosophy.

      Here, MSEE hints that he might be willing to provide such a theory. So, I repeat the challenge again...

      Scott: please provide your *exhaustively complete*, error free theory, and how you actually reached the conclusion that is exhibits either of those properties, in practice. Please be specific.

      IOW, my entire point is that one's expectations of whether all theories should be incomplete and contain errors to some degree is a function of one's theory about how knowledge grows. it's a problem of epistemology. Furthermore, if a theory is not exhaustively complete then, well, it's incomplete, right? And incompleteness is a supposedly an insurmountable problem for evolutionary theory. For example evolution cannot explain the evolution of protein because it does not explain how the first protein evolved.

      MSEE: Linear system theory is not my theory to provide for you and don't expect me to teach it to you here unless you think you can magically absorb integral transforms, convolution, state space, linear differential equations and stochastic processes among scores of other subtopics. Meaning of course that your request is absurd.

      Apparently, MSEE thinks that LST is such a concrete theory. However, it seems the entire point of the exercise goes right over his head as he gives a laundry list of disclaimers that suggests, at a minimum, he thinks it is incomplete.

      More importantly, he does not explain how we reached the conclusion that it does not contain errors to some degree, beyond claiming it's based on complex, beautiful mathematics, so he can't explain it to us, and mathematics that is beautiful doesn't contain errors.

      But what's odd is that MSEE seems to have a firm grasp of what it means for a theory to contain errors to some degree, while at the same time exerting extreme effort to avoid actually acknowledging it. For example....

      MSEE: Linear system theory has limitations when applied to systems for which it is not formulated such as one containing a NONLINEAR component. In such a case, modelling the component as linear or piecewise linear, results may be accurate enough for practice. Has nothing to do with error in theory get that? Has everything to do with possible misapplication of the theory, Get that? REREAD

      LST can be used to solve problems, despite containing being an incomplete model of a real world system. It allows control without being reductionist in nature. That's my very point.

      If you want to compare purely abstract model that doesn't need to reflect real world systems, then treat evolutionary theory as an abstract model as well. For example, compare it to an evolutionary algorithm applied to some problem, like antenna design.

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  4. Scott:

    Isn't Darwin's theory based entirely on natural selection, survival of the fittest? If that is shown to be incorrect, then Darwin's theory has no basis.

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    1. No, it's not, Nat.

      Darwin didn't know about genes. As such he was mistaken about that particular aspect of evolutionary theory. But all theories are incomplete and contain errors to some degree. So, this is just hand waving.

      Nat: If that is shown to be incorrect, then Darwin's theory has no basis.

      That's a non-sequitur, Nat. Darwin's theory doesn't hinge on that particular aspect because it was based on the underlying explanation of variation and selection from the start. And, as I pointed out in my original comment, its a fallacy to judge ideas by their source, rather than their content. For example, just as people now know more about general relatively that Einstein did, we now know more about Darwin's theory than he did.

      So, no, we're not "stuck" with exactly Darwin's predictions from 150 years ago. To assume that we are is unreasonable and an example of bad philosophy.

      Rather, the central idea of neo-Darwinism is that evolution favors genes that spread best though the population.

      But I've already given an example of this, previously, so I don't know why you keep bringing up this misconception. Even then, as someone who supposedly teaches biology at the college level, Cornelius would be quite aware of this. So, it's unclear why would imply otherwise. And if he not aware, this would represent a gross incompetence on his part.

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    2. From a comment on an earlier thread...

      Take a hypothetical island with a hypothetical species of bird. Currently this species nests in May, which is optimal for the islands climate and food supply. However, due to the islands geography, not all nesting areas are equal in that some are significantly farther from food, more exposed to predators, etc.

      Now, hypothetically, one of these birds is born with a mutation that causes it to nest in April, which is a month earlier. As such, it gets the best nesting location. It also finds a suitable mate and has offspring, which also inherit this same mutation. While being born a month early is a sub optimal for the island's climate and food supply, this is outweighed by the fact that they have the best nesting location. Next season, their offspring also nest earlier, obtain the best nesting locations, etc. This continues until eventually the early nesting mutation has spread throughout the entire population, which has made it less fit as a whole.

      If a bird is born with a mutation to nest a month later, which would again represent the optimal time, all of the best nesting locations would already be taken. The mutation would not spread thought the population. However, if a bird is born with a mutation to nest yet another month earlier, the process would repeat itself. This would results in the entire population is even less fit.

      At some point, mutations to nest earlier would eventually prove lethal to offspring. As such, if all things remain equal, there is a minimum level of fitness the entire species would maintain. But, this could still be far from the original fitness the species first exhibited. However, if the climate suddenly changes, such as cold weather last significantly longer in a season, the entire species could go extinct.

      So, rather than merely being "the survival of the fittest", we say that genes are biological replicators, in that they play a causal role in their own replication by their environment. Furthermore, we include the organism itself as part of the gene's environment. As such, it's the genome itself that becomes better adapted to be replicated by it's environment - even potentially at the expense of the the species becoming less fit as a whole.

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  5. Cornelius Hunter: In Charles Darwin’s theory of evolution the engine of progress is death.

    That's a bit of an overstatement. Darwin recognized that it was reproduction that determined evolutionary success, such as the struggle between the males for possession of the females, or the death of eusocial insects for the benefit of the colony. Darwin was also aware of mutualism, though that is often in unrelated organisms. While the algae experiment showed that there can be mutualism between closely related species, that doesn't undermine evolution generally. So while Homo sapiens and Homo neanderthalensis may have competed for the same resources, they may also have sometimes cooperated.

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  6. The original title of the reporting piece was "Doubting Darwin: Algae Findings Surprise Scientists," but the evolutionists forced it to be dumbed-down to the polictically-correct: "Old Idea About Ecology Questioned by New Findings." It was just an old idea about ecology, move along.

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    1. You don't say...

      So then why didn't the Richard Dawkins foundation change the title when they posted it? Isn't Dawkins and "evolutionist"?

      http://richarddawkins.net/2014/04/doubting-darwin-algae-findings-surprise-scientists/

      Since your prediction has been found false, you're going to abandon your "theory" and give up your blog, right?

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    2. Scott: Since your prediction has been found false, you're going to abandon your "theory" and give up your blog, right?

      CH: [No response]

      If I attempt to take your own objections seriously, doesn't your lack of a response indicate your prediction failing means nothing to you? Or are you suggesting that Dawkins, of all people, isn't an evolutionists? If not, then exactly who are these evolutionist anyway?

      If so, doesn't your lack of a response represent theory protectionism on your part? What gives?

      Or perhaps you don't really expect anyone to take your objections seriously. As such, It should come as no surprise when they do not. Why should we?

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    3. No Scott. Stop being rabid. He didn't make a prediction. He claimed what Nastika already admitted to in the comments of the LINK YOU POSTED.

      Do you, "really expect anyone to take your objections seriously" ??

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    4. John, Cornelius presented a theory for the change of the title of the article. Evolutionists didn't like it so they exerted force to change it. As opposed to say, the author pointing out it was misleading or ambiguous and the publication / author agreeing with him.

      Now, let's take his theory seriously, in that it's true in realty, then all observations should conform to it. Namely, that we should observe the same change for other reproductions of the article on other evolutionist's sites. This would be a testable prediction based on his explanation.

      But we do not. Dawkins, who is also an evolutionist, didn't change the title of the article.

      IOW, you should have no problem pointing out [1] where in that comment this supposed force by "the evolutionists" (plural) was exerted and [2] why that same supposed force wasn't observed on Dawkins' own site, where no force would have even been necessary.

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    5. Clarification: As opposed to say, the author *of the paper* pointing out it was misleading or ambiguous and the publication / author *of the article* agreeing with him

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  7. The whole OP rather overstates the novelty of the actual data, too. The fact that relatedness fails to predict competition in many cases has been known for some time (e.g., Cahill et al 2008). The attention paid by CH to the "surprise" element probably reflects a simple ignorance of the literature however. But as someone has pointed out, the whole post is based on a straw man.


    "there are untold stories of mutualism and cooperation between species which contradict one of evolution’s most fundamental predictions"

    Cornelius, did you just learn about mutualisms? They are indeed ubiquitous. You may wish to read the books Darwin wrote about pollination biology...

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    1. Stuart, In this study, did they test a prediction of evolution? (And yes folks, I know what the answer is: Yes, but not really, maybe and kind of, but under strict caveats which we'll tell you about sometime)

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    2. Cornelius Hunter: In this study, did they test a prediction of evolution?

      In evolutionary theory, there are usually countervailing influences, in this case, between competition and cooperation. Generally, it is expected that competition will be more important for closely related organisms utilizing the same resources, but it's not a hard and fast rule. Otherwise, colonial life would never have evolved. Sorry biology is so complicated, but that's the nature of bottom-up organization.

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  8. "In this study, did they test a prediction of evolution?"

    How is this related to my point?


    In any case, the difficulty in making a prediction like this does not arise because of opposing influences of competition and cooperation - the difficulty of making the prediction arises because one does not expect a pattern like this to hold if competition is actually important (and would thereby lead eventually to divergence in resource use among related species in sympatry).

    I hope you have enlightened yourself on Darwin and mutualisms!

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  9. I think you're missing the "D" in your QED.

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