Noyau (2)

…the noyau, an animal society held together by mutual animosity rather than co-operation

Robert Ardrey, The Territorial Imperative.

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2,941 thoughts on “Noyau (2)

  1. Adapa: So you don’t take your own advice. Got it.

    So you have no evidence at all that I have a long and sordid history of anti-gay bigotry. Got it. I’ve known that for a long time and so have you. It was a spurious slur that you’ve never had the guts to retract. So not only are you liar you’re also a coward. So now I’m scared.

    Make up some more lies about me and post them.

  2. Adapa:

    Mung
    I have a long and sordid history of anti-gay bigotry.

    Not something to boast about.

    Do you think this helps your case?

    You are truly pathetic. Can’t you find something more worthwhile to hate? Baby seals maybe? I hear they are pretty helpless.

  3. Mung,

    Is there a book then that is more fit than the Bible? I wonder what the mean rate of increase of the Bible is.

    This is, actually, a fair swing at the ball, better than the endless play-and-miss we’ve been getting so far. Now, are you going to argue with yourself that the Bible is not in fact a ‘replicat(ed/ing) thingy’? For sure, it does not self-replicate, but then neither do viruses. And, indeed a Bible that is copied turns out not to ‘increase’ at all. It just sits there, all passive like. And yet, somehow, you were able to grope your way in the general direction of the concept of fitness anyway.

    It’s a start.

  4. phoodoo,

    Copies? Are you a copy of your mom? Are you and your mom the same entity? And if you are different entities, how do I measure the mean rate of increase of each of you?

    I’m really not sure whether you are trying to make the most important issue my perceived inability to successfully encapsulate the concept of fitness in a brief sentence, or a fundamental problem with the concept I am trying to articulate. I know you’ll take either or both. But …

    You plant rice every year. Presumably you have a yield. That would be reducible to a mean number of grains harvested per grain planted. That would – surely – also be the rate of increase? The two are interchangeable.

    ‘But’, you object, ‘they are not exact copies’. OK, my formulation only works strictly for asexual species, good catch. There is still some degree of inheritance though, albeit diluted by partners. ‘And’, you object, the seed grains themselves don’t increase’. That’s weaker, don’t you agree? If you return more-from-fewer, I call that increase. YMMV.

    Here’s a further digression that will lose you, but I’ll give it anyway. There is an important distinction, emphasised by Orr: “Much confusion can be avoided by distinguishing between the fitness of particular individuals and fitness as a summary statistic. “. This is the kind of confusion on which you thrive, of course. But, while each single individual has a simple fitness – the number of offspring it rears to maturity – you can also sum and average those fitnesses for organisms sharing a chosen property, and establish relative performance. This is why people talk of ‘fit alleles’ – it’s shorthand for ‘alleles which raise the mean fitness of carriers vs non-carriers’.

    An allele can thus easily increase fitness itself, and be selected for. We can choose that as our ‘property’. So, if you wanted to increase the overall yield, and you felt that each plant’s yield might reasonably be heritable, wouldn’t you have a look at different-yielding plants and try and breed from those with the higher yield, splitting one year’s crop into percentiles – effectively, treating fitness as a phenotype, and trying to maximise it? Now, it’s true that the mean fitness of your entire crop has a different value from the mean fitnesses of each yield-range percentile – fitness is context dependent. So, you go into your tautologous field and tautologously plant your tautologous high-yield crop, then count your tautologous dollars.

  5. Mung: Losos defined fitness as survival in one of his experiments. Are there different definitions then of fitness when the term is applied to actual biological cases? Do they at all differ from the mathematical definition?

    In experimens and nature, t is easier to measure the individual fitness components than fitness as a whole. If you expect that survival is going to be the main contributor to fitness (e.g. you are studying developmental lethals), it is fair to use it as a proxy.

    Mung: Why don’t we start there. In the mathematical framework known as population genetics how many different definitions of fitness are there and what are they?

    In basic Haldane-Fisher models it is zygote-to-adult viability (of genotypes), but as you have guessed that is hardly inclusive of all instances of selection we may want to model. I am not going to deny that there are several definitions of fitness (I can’t be bothered to make a list). Yet all definitions somehow broadcast the same idea: that there is variation in the ability to transmit heritable information to the next generation.

    Mung: If you ask me this is part of the problem. People switch back and forth between different definitions without making it clear which one they are talking about and applying the wrong definition to the wrong scenario. As if every use of the term has the exact same meaning.

    Well yes, and another part of the problem is that people immediately declare the whole concept meaningless whenever this happens, although it is crystal clear that there exist examples we can all agree on.

  6. phoodoo: Its meaningless, there is no rate of increase of two distinct entities. Then three distinct entities. Then four…

    Because they are entities. Which is what I have been telling you all along.

    That is so dumb it is unfathomable. An apple is an entity. A cell is an entity. A rock is an entity. A soap bubble is an entity.

    Entities can increase in number in many ways. An apple can become an apple-tree, which can yield many apples. All of those apples are distinct entities.

    A cell can divide into two, and those two can divide into four and so on. All of those cells are distinct entities.

    A rock can be split into two smaller rocks, and split again into three or four smaller rocks still. And all of the rocks are distinct entities.

    A soap bubble can split into two or more smaller soap bubbles. And they are all distinct entities.

    Why, WHY can’t you figure this out? Why is this so hard for you? What the hell is wrong with you?

  7. phoodoo: Ok, I don’t understand why you don’t understand that alleles don’t have offspring, entities do. And then they become OTHER entities.

    Alleles are entities.

    http://www.dictionary.com/browse/entity
    “entity
    [en-ti-tee]
    noun, plural entities.
    1.
    something that has a real existence; thing:
    corporeal entities.”

    https://en.wikipedia.org/wiki/Entity
    “Entity
    An entity is something that exists as itself, as a subject or as an object, actually or potentially, concretely or abstractly, physically or not. It need not be of material existence. In particular, abstractions and legal fictions are usually regarded as entities. In general, there is also no presumption that an entity is animate, or present.

    The word is abstract in intention. It may refer, for example, to Bucephalus, the horse of Alexander; to a stone; to a cardinal number; to a language; or to ghosts or other spirits.

    The word entitative is the adjective form of the noun entity. Something that is entitative is considered in its own right.”

    Please help me to understand why you struggle to understand.

    But it is not me that is struggling to understand. I undertand the concept of fitness very well. And I understand why you don’t understand it.

    By even implying that it is me who doesn’t understand, you reveal it is you who is having issues of comprehension.

    I think the reason you don’t understand is because you’ve got into a hostile mindset where you have decided it’s all crap. The whole subject has been polluted in your mind to the extend that you are literally incapbable of reason if you suspect the subject is even tangentially related to evolution or the grand skeptical conspiracy against your worldview.

    And it appears to be subconscious, because I also believe you wouldn’t deliberately be obtuse. Call me naive. But you’ve fallen into the classic epistemological trap of all conspiracy nutters. You have failed to notice that you have corrupted your own method such that you have made it impossible for you to discover when you are wrong. Your go-to rationalization in all circumstances seems to be something like, “if the evidence is against me, the evidence is fake”.

    When you operate under such a mindset, then you literally cannot discover a way out of your current position, because all evidence that potentially contradicts it, you subconsciously render as “probably the result of fraud”.

  8. Mung: Do you think this helps your case?

    You are truly pathetic. Can’t you find something more worthwhile to hate? Baby seals maybe? I hear they are pretty helpless.

    You have to admit it is pretty ironic that you, of all people, is being quotemined.

  9. Rumraket,

    What does an allele weigh?

    Not only are they not entities, but more important, they don’t have offspring.

    And even more important, if they DID have offspring, it would then be a different entity, and thus would have no rate of increase.

    Spectacularly wrong Rummy.

  10. phoodoo: And even more important, if they DID have offspring, it would then be a different entity, and thus would have no rate of increase.

    These valuable insights I’m sure would be of use to a wider community then the people who happen to read this site. Have you ever considered writing an article for EN&V?

  11. phoodoo: What does an allele weigh?

    It depends on the allele. What does an apple weigh? What does a stone weigh? Depends on the individual case. They are still entities. And the number of such entities can increase or decrease.

    It’s actually pretty easy to figure out the exact atomic weight of an allele of a genetic locus. DNA (and RNA, and protein) is made of atoms, and individual genes have a sequence of ribonucleic acids, which are molecules with a known structure and weight. You simply add them up according to how frequently they appear in the sequence.

    You know basic addition right?

    Not only are they not entities, but more important, they don’t have offspring.

    Not only ARE they entities, they sit inside enties which have offspring. Such entities can also be copied, so individual carriers of alleles can carry multiple such alleles simultaneously.

    And even more important, if they DID have offspring, it would then be a different entity, and thus would have no rate of increase.

    When alleles are copied, there would be a rate of increase in the number of such distinct entities pr. unit time.

    Spectacularly wrong Rummy.
    Look, you are just plain clueless about this, and your anti-evolutionary psychosis is literally making you incapable of reason. You have a disease of the mind on this subject and you need some sort of help.

  12. phoodoo, if alleles are not entities, neither are mules.

    Your objection to Allan’s definition doesn’t even rise to the level of a quibble. It’s just a misunderstanding hollered out a high volume.

  13. walto:
    phoodoo, if alleles are not entities, neither are mules.

    Your objection to Allan’s definition doesn’t even rise to the level of a quibble.It’s just a misunderstanding hollered out a high volume.

    And if they are entities, they don’t have a rate of increase, because each one is one.

  14. phoodoo: And if they are entities, they don’t have a rate of increase, because each one is one.

    And mules are infertile of course, so their fitness is zero.

  15. Corneel: And mules are infertile of course, so their fitness is zero.

    Not according to Allan’s definition. According to Allan’s definition, since they don’t replicate, there is no measure of their fitness. Fitness could only measure things that replicate.

  16. phoodoo: Not according to Allan’s definition. According to Allan’s definition, since they don’t replicate, there is no measure of their fitness. Fitness could only measure things that replicate.

    When replicators fail to replicate, they are no longer replicators?

    Like, whenever a xerox breaks down, it ceases to be a copy machine?

    Deeper into the rabbit hole we go!

  17. Corneel: And mules are infertile of course, so their fitness is zero.

    I mean, its pretty laughable really, the definition of an entity makes it the very anti-thesis of something that can increase or decrease. An entity is an entity because it means one.

    Now this may seem like a semantic quibble, that is poking fun of Allan’s definition, but there is more to it than that. The whole reason I quarrel with Allan’s concept of fitness, is because of the very notion that every individual is a separate individual-an entity! That has been my argument all along. And since every living thing is a separate entity, there is no justification for grouping them as the same thing.

    Let me try to put it this way. Every new birth is a new branch on the tree of life. But Allan’s idea is to count some births as new branches, and some as the same branch. Let’s take any sexual reproduction. Once you have a sexual reproduction, it creates an entirely new being. Why would you ever count that as having the same ability to reproduce as its parents? Its a totally different thing from its parents, so it has totally different potential for reproducing. Just like any child it would have, also would have another new potential.

    To count that all as one is just unsupportable logic.

  18. phoodoo: And if they are entities, they don’t have a rate of increase, because each one is one.

    I’m sorry, phoodoo, but that’s the silly quibble part of your remark. (The “they’re not entities” is the misunderstanding part.)

  19. phoodoo: Not according to Allan’s definition.According to Allan’s definition, since they don’t replicate, there is no measure of their fitness.Fitness could only measure things that replicate.

    That’s wrong too.

  20. phoodoo: I mean, its pretty laughable really, the definition of an entity makes it the very anti-thesis of something that can increase or decrease. An entity is an entity because it means one.

    OMG

  21. phoodoo: I mean, its pretty laughable really, the definition of an entity makes it the very anti-thesis of something that can increase or decrease.An entity is an entity because it means one.

    Now this may seem like a semantic quibble, that is poking fun of Allan’s definition, but there is more to it than that.The whole reason I quarrel with Allan’s concept of fitness, is because of the very notion that every individual is a separate individual-an entity!That has been my argument all along.And since every living thing is a separate entity, there is no justification for grouping them as the same thing.

    Let me try to put it this way.Every new birth is a new branch on the tree of life.But Allan’s idea is to count some births as new branches, and some as the same branch.Let’s take any sexual reproduction.Once you have a sexual reproduction, it creates an entirely new being.Why would you ever count that as having the same ability to reproduce as its parents?Its a totally different thing from its parents, so it has totally different potential for reproducing.Just like any child it would have, also would have another new potential.

    To count that all as one is just unsupportable logic.

    There it is. Turns out there’s no such thing as a species. Never mind mules, there aren’t even any donkeys!

  22. phoodoo: That has been my argument all along. And since every living thing is a separate entity, there is no justification for grouping them as the same thing.

    Recognizing organisms are individuals with their own unique mix does not prohibit grouping them on the basis of any shared characteristics. And notwithstanding the fact that everybody is a unique individual, you are not totally different, but also come to resemble your parents in many respects.

    Is that not OK?

  23. Corneel,

    Well, who knows. Maybe sometimes you are kind of like your mom, a little like your dad, more like your Uncle Harry, and even more like your great grandmother Reba.

    There is no categorizing of that, and how those different characteristics compliment or contradict. Its a whole new formula. Lye can both burn a hole through you, or it can clean off make-up, or you can use it for baking pretzels, it just depends on the combination with other things.

  24. phoodoo: I mean, its pretty laughable really, the definition of an entity makes it the very anti-thesis of something that can increase or decrease. An entity is an entity because it means one.

    You tell em Ray! You tell em!

  25. Rumraket,

    You have to admit it is pretty ironic that you, of all people, is being quotemined.

    Yuk yuk. Irony overdose. It certainly made my day to be accused both of word-gaming by Mung, and a pathological fear of admitting error by phoodoo. 😀

  26. phoodoo,

    Not according to Allan’s definition. According to Allan’s definition, since they don’t replicate, there is no measure of their fitness. Fitness could only measure things that replicate.

    You are incorrect phoodoo. According to ‘my definition’ (when the fuck did I become spokeman for biological fitness? 😀 ), the fitness of a mule would be zero (usually – in rare cases, I believe they are fertile).

    The whole of evolution comes crashing down because Bloke On Internet (that would be me) says ‘replicating entity’ when he could have said something else. CAN’T BE A REPLICATING ENTITY IF IT DOESN’T REPLICATE!!! ENTITIES DON’T REPLICATE ANYWAY!!!

    Hey, watch out for falling debris everyone.

  27. Shame phoodoo appears not to have read my ‘rice’ post, which anticipates several later objections. I thought it quite good, modesty aside.

    If an ‘entity’ cannot have a similar rate of increase to its parent – if fitness cannot have a heritable component – how and why could one select on yield?

  28. phoodoo: Well, who knows. Maybe sometimes you are kind of like your mom, a little like your dad, more like your Uncle Harry, and even more like your great grandmother Reba.

    There is no categorizing of that, and how those different characteristics compliment or contradict.

    You are talking to a geneticist. Let me assure you that you can categorize and quantify that. Predisposition to many diseases is heritable, length is heritable, blood type is heritable, in fact most traits have a heritable component.

  29. Corneel: Let me assure you that you can categorize and quantify that.

    No you can’t. I don’t think you are getting it.

    When every trait is combined as a whole, it doesn’t become a trait, a trait, and a trait, it becomes the ONE entity. Is dumb and tall and furry skin, and flat feet and having a cancer gene and a long tongue better than smart and medium height, and white skin and no cancer gene, and arched feet and gayness and a longer nose? Which one wins if both are pitted against each other in the reproduction race?

    You can’t say, well, the long tongue obviously, because long tongues win a lot.

    That is why you guys like to play the allele game, because then you can ignore same factors and just count the ones you like. Then once the long tongue becomes the more common trait, it must have been beneficial. But if the trait is something like high blood pressure or near-nearsightedness, you wildly throw out the crazy notion that , well, ok fine, some times detrimental alleles win, but that’s just an anomaly.

    Its not an anomaly if you are calling what is beneficial, that which becomes numerous.

    It is this which has lead to this tortuous destroying of what words actually mean, in order to overcome this crazy contradiction.

  30. Corneel,

    We made you Grand Predictor last week, remember?

    Not sure I’m up to it. Can’t even proofread my own posts. Spokeman indeed! Superhero on a bike.

  31. phoodoo: When every trait is combined as a whole, it doesn’t become a trait, a trait, and a trait, it becomes the ONE entity.

    You are saying that it is wrong to atomize organisms into an assembly of traits. I see your point, and somewhat agree (though not completely, because in many cases that is a fruitful approach). The important thing is that this is a very different lament from your assertion that fitness is a meaningless concept. If you carry an allele that predisposes you to Duchenne’s muscle dystrophy, this will have a marked effect on your prospect of having children, regardless of height, skin or tongue length. It’s not pretty or fair, but that is the way of things.

    phoodoo: Its not an anomaly if you are calling what is beneficial, that which becomes numerous.

    As Allan has desperately been trying to tell you, fitness is not defined by “what happens to become numerous”, because that would indeed mean we’d have a lot of ad hoc explaining to do. Biological plausibility always plays into it; a benefical allele needs to positively affect viabilty or reproductive success. As a mirror image, severe disease alleles negatively impact both, hence they confer low fitness on their bearers.

    We could have interesting discussions on the supernatural origin of beneficial alleles, the need for guidance in fixing them in a population, and whether atomizing organisms into traits is appropriate, but let’s dispense with the silly notion that fitness is a meaningless concept.

  32. Alan Fox:
    phoodoo,

    The niche, phoodoo. Remember the niche.

    That is such a stupid, meaningless defense Alan. Its not saying anything. You still have a new combination, an entirely novel combination, each time you create a new offspring. What does a niche have to do with that problem?

    Its like saying the word catfish, to explain away the problem. Its meaningless.

  33. Corneel,

    No Cornell what I am suggesting is fitness is a meaningless concept, when it is defined as Allan (and others) has often tried to define it. There are actual characteristics that may well help survival. Like being smart for example. But that is quite different that counting based on offspring numbers, instead it is counting based on intuition. Our intuition of what is fit, and the traits that actually do get passed on the most do not have to be the same at all.

    So, we know that high blood pressure it inherited to some degree, and yet we also know that this is likely to decrease you actual fitness, not increase it. But if we just use the method of counting offspring, than we must declare high blood pressure as a fitness component. Likewise for tongue rolling. And astigmatisms.

    And how about a symmetrical face, science tells us this is a a sign of attractiveness, and thus is a sign of good reproductive success, and yet MOST people DON’T have a symmetrical face, and thus we must conclude that being asymmetrical is a sign of fitness, using your typical definitions.

    Likewise for cancers, or any other host of things that we know are unhealthy, and yet are numerous throughout the population.

    So we either abandon common sense, or we abandon biologys silly definitions.

  34. phoodoo: So, we know that high blood pressure it inherited to some degree, and yet we also know that this is likely to decrease you actual fitness, not increase it. But if we just use the method of counting offspring, than we must declare high blood pressure as a fitness component. Likewise for tongue rolling. And astigmatisms.

    I strongly doubt that people able to roll their tongue or that have astigmatism have on average more (or less) children than people without those traits. My guess is that there are no differences to speak of (if you have numbers on that, you can prove me wrong). No fitness differences, no problem, right?

    phoodoo: And how about a symmetrical face, science tells us this is a a sign of attractiveness, and thus is a sign of good reproductive success

    Wrong person. Like you, I don’t buy that story 🙂

    Hypertension and cancer are better examples, because they clearly are bad news. For now, I am guessing that moderate hypertension has negligible effects on survival or offspring numbers. IOW, it is a disease, but without large fitness consequences. “Cancer” is more complex, as that is not a single disease. I am pretty sure that alleles that predispose to severe forms of cancer i.e. does with early onset and bad prognosis are not numerous, but actually very rare. I will try to look into that, if I have time.

  35. Corneel: I strongly doubt that people able to roll their tongue or that have astigmatism have on average more (or less) children than people without those traits.

    More people can roll than tongues than can’t by a large number. By the definitions given by biologists, then it must be a beneficial mutation which increases your chances of reproduction.

    Of course, if we don’t use the biologists definition of fitness, and instead use common sense, then we say its nonsense. Likewise with astigmatisms, or near-sightedness.

  36. phoodoo: More people can roll than tongues than can’t by a large number. By the definitions given by biologists, then it must be a beneficial mutation which increases your chances of reproduction

    Not according to any definition I’d choose. But let’s revisit Allan’s definition, shall we:

    Biological fitness is the mean rate of increase of a replicating entity.

    Not the best definition to work with in this case, but it tells us that if the allele for tongue rolling is more fit than the non-rolling allele its numbers still have to be increasing since it can multiply at a faster rate than the allele it is competing with. I am willing to bet a considerable sum of money that it isn’t. Hence Allans definition is perfectly compatible with our intuition in this example.

    The current prevalence of tongue rolling is most likely coincidence (genetic drift). Allan will agree, and I don’t think you disagree either.

  37. Alan Fox,

    Can you in any possible way try to tie that into this discussion.

    “The niche is the designer…” Not only is it just a out of the blue assertion, it also has nothing whatsoever to do with fitness.

  38. phoodoo: So like having a brain is not an example of a fit trait, because there really is no increase in the number of organisms that have brains.

    As far as I know there is no variation for “having a brain” in humans or any other organism I know of. I am pretty sure that, if this were the case, heritable factors causing that trait would increase.

    phoodoo: But near-sightedness IS beneficial, because it is on the rise. Likewise for obesity.

    The increase in obesity is not a genetic change, but caused by changes in diet and life style. I am not familiar with the near-sightedness example, but the article you linked suggests a similar explanation (“excessive amounts of near work, the kind of tasks that require peering at written words or small objects”).

    Cue corny jokes about “not having a brain” in humans.

  39. Corneel: As far as I know there is no variation for “having a brain” in humans

    As I submitted this, I thought about anencephaly. Nothing about genetic disposition in the Wikipedia lemma though. Supposing there are predisposing variants, I hope everybody agrees there will be strong purifying selection against them

    ETA: … meaning they have low fitness

  40. Corneel,

    Not the best definition to work with in this case

    Aye, just a humble attempt to encapsulate related concepts in a sound bite – individual, absolute and relative fitnesses.

    A curious world we visit, though, where phoodoo insists an allele can neither increase nor decrease in a population – nor, I guess, stay the same – contingent upon any effect it has upon the fate of its bearers. I don’t know how it manages to do none of those things.

  41. phoodoo,

    Risking your tendency to misread and laziness to even try, here it goes. I think you’re misreading things here by focusing on but one aspect of a challenging issue.

    Suppose you’re honestly trying to figure out how to find which traits, if any, might be under positive selection. You study a population, and you see lots of variation in all sorts of traits. You measure those variations, and follow the population for some generations, you keep measuring, etc. How do you distinguish random changes in trait frequencies from one generation to the next from positively selected ones? The task is very hard, but you go for the most abundant ones as a first approximation! You even work the statistics, and you find the ones that have the lowest probability of being randomly increased.

    Well, guess what? If we left it there, no journal would accept that in a publication, except, as a resource for later mining of “real deals.” You have to then check for confounding factors. You have to check, very importantly, for inheritability (if you started with phenotypes, that is). If you started with genes, you’d have to check for linkages, for phenotypic effects.

    For any of it, you have to check for potential relationship with the environment. Is there really some advantage to this trait, this gene, this phenotype? What kind of advantage? Is there some experiment we could set up for testing this potential advantage? Other kinds of data to collect?

    You have to wait for the next generation to see if the same traits, or alleles, come out as increasing above random expectations. You have to do lots of stuff before other scientists will agree with your conclusion that maybe, of all of these things that seem to have increased beyond expectation, these few are actually showing good signs of being under positive selection, the ones that might be increasing the fitness of the population.

    So, forgetting that scientists go on after a first approach doesn’t make the science faulty, it makes your points into mere stubbornness to finding fault, for the sole reason that you don’t like the overall enterprise. Instead, I suggest that you should think that maybe that’s not all they do. You then check, and lo and behold, effectively, that’s not all they do. It’s but a step in a series.

    Just a suggestion. If you prefer to be perceived as some lunatic with no intention, or not capacity, for understanding, whose visions are held by mere stubbornness. Well. So be it.

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