Retiring Ideas, or That One Concept You Think Should Just Die Already

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Discussion by: Zeuglodon

Over at Edge.org, there's the annual article on the subject of science, and several academics of various fields (including some names that are well-known here) have submitted essays based on a single question put forward. The article is entitled: "What Scientific Idea is Ready for Retirement?"

 

I bring this up for two reasons. Firstly, to bring the article to your attention in case you haven't seen it but might be interested. Secondly, as a lead-in to a broader question about the retirement of ideas.

 

Are there any ideas – chiefly scientific, but maybe philosophical too - that you think should just die, or at least be confined to history? Perhaps you are convinced, like Eric R. WeinsteinFrank Tipler, and Peter Woit (in his own fashion) from the article mentioned above that string theory has had its day? Maybe you think repression and other Freudian frameworks are just plain nonsense that need to be dropped, as David G. Myers does? Or maybe you agree with Lisa BarrettRichard Dawkins, and Peter Richerson, though they approach it from different angles, and think essentialism is a flawed conception of the world that needs to be replaced by something less ethereal and more grounded?

 

The issue is yours to choose. The question is: What big scientific idea (or not-so-scientific idea, if you prefer) do you think needs retirement?

100 COMMENTS

  1. Really cracking topic, Zeug, but don’t expect posts anytime soon. We’ll all be reading the background material… Having said that, I always found the idea of “emergence” as singularly unhelpful, also the promotion of “understanding” as the peak of scientific achievement.

  2. I think that the neo-Darwinian idea of mutation as the source of variety needs to be tossed with great haste.

    Natural selection with mutation as being the sole source of variety, to create something as complex as the eye, is not realistic (in Intelligent Design circles, this relates to irreducible complexity). In addition to the problem of irreducible complexity, there is the problem of entropy versus complexity and the logical fallacy of something as exquisitely complex as the eye to be a product of accumulated but lucky deformities (mutations) being selected by environmental pressures. The following web page of the Institute for Creation Research does an admirable job of enumerating the most salient points:

    http://www.icr.org/index.php?module=articles&action=view&ID=270

    While the website’s reasoning is sound, we have good reason to object to the website’s obvious creationist agenda, so I’ll summarize Byles’ observations in my own words (I am NOT a creationist, and I have NO belief in any kind of nobodaddy in the sky). And so, with reference to the work of GENETICIST R.H. Byles**… Byles covers the sorts of things that should be apparent to many of us, as far as macro (and perhaps also micro) mutations are concerned. For example, the conflicts between mutation rates (back-mutation, forward-mutation, etc). Byles’ analysis renders the whole notion of macro-evolution-by-mutation as simply impracticable. It would seem that the practical reality of dumb deformities in competition with lucky accidents has not been taken seriously enough. Indeed, Charles Darwin himself did not factor in mutations as the source of variety for natural selection.

    ** Byles, R. H. Limiting Conditions for the Operation of the Probable Mutation Effect. Social Biology, 19 (March 1972):29-34.

    • In reply to #2 by Jarold:

      I think that the neo-Darwinian idea of mutation as the source of variety needs to be tossed with great haste.

      Sadly Irreducible Complexity cannot be formed into a general scientific (refutable) hypothesis and is useless. All specific examples have failed to show any irreducible attributes. The idea is deeply flawed as much because it fails to note that the function served by the feature can change to meet different environmental challenges. This is typical of genetic feature re-use.

      The entropy/complexity thing comes from a failure to note that the planet is not at some point of thermodynamic equilibrium but bathed in a huge flux of energy from the sun.

      • In reply to #3 by phil rimmer:

        In reply to #2 by Jarold:

        I think that the neo-Darwinian idea of mutation as the source of variety needs to be tossed with great haste.

        Sadly Irreducible Complexity cannot be formed into a general scientific (refutable) hypothesis and is useless. All specific examples have failed to show any irred…

        You write that “… the idea is deeply flawed as much because it fails to note that the function served by the feature can change to meet different environmental challenges.” The topic of irreducible complexity has been well documented, so unless I’m misunderstanding you, how can you have “half” an eye? Pinhole camera eyes (such as those of the Nautilus) work because they fulfil a function, and so can be an intermediate step. But a pinhole without a retina is useless. A retina without a pinhole or a lens can fulfil an intermediate step because it detects light differences that are relevant to survival. But an iris without a retina or lens is useless. And so on. So of course some steps will definitely fulfil a need… but others will not. And those that do not become useless dead weights that impact negatively on survival efficiency.

        The problem with the “mutations as source of variety” school of thought is that it cannot appreciate how a pinhole camera eye is PERFECT in meeting the survival needs of Nautilus. Nautilus does not NEED anything other than a pinhole lens, because the rest of its body is capable of kicking in to accommodate its survival needs.

        Of course the “huge flux of energy from the sun” to which you refer is integral to the complexity of life on earth, I have no problems with that. But only plants are constructed to utilize it directly. Animals are not. But either way, both animals and plants operate at the bounds of efficiency (boundary of chaos). Mutational deformities masquerading as intermediate steps to something of utility, if they cannot fulfil any immediate purpose, are DEAD WEIGHTS that are detrimental to survival because they erode efficiency… efficiency of flight, pursuit, etc. Peacocks can afford to carry around dead weights because their bodies are built to efficiently utilize and carry said dead weight… their cumbersome tail feathers are an expression of the efficiency of the body designed to carry them.

        • In reply to #11 by Jarold:

          The topic of irreducible complexity has been well documented…

          …by creationists, and almost universally refuted by actual biologists. Notably Dawkins himself has refuted it many times and your post on this board strikes me as being completely ignorant of this refutation. It’s like arguing that the Earth isn’t flat with someone who is completely ignorant to the fact that human’s have been travelling to space since the 60′s.
          The fact that your best source is a creationist website speaks multitudes.

          That something seems far-fetched, especially by creationists, is nothing but a testament to the scope of the creationist’s ability to comprehend deep time and vast populations.

          Every documented stage of development of the human eye was useful. Our current complex eye is the product of billions of years of refinement, all the basic components evolved when they were far simpler and the mutations far less resource intensive. Also, nothing evolves independently from the rest of it’s hosts body, we did not evolve a fully working human eye minus an iris and then suddenly mutate an iris, or any other single part of the eye. This is a blatant straw-man and is far more far-fetched than the actual theory could possibly be.

          As for Lamarkism, you would first need to discover a mechanism for organisms to transfer learned adaptations genetically to their offspring, and then collect your Nobel prize. Without that you may as well be discussing Alchemy.

          • In reply to #13 by Seraphor:

            In reply to #11 by Jarold:

            The topic of irreducible complexity has been well documented…

            …by creationists, and almost universally refuted by actual biologists. Notably Dawkins himself has refuted it many times and your post on this board strikes me as being completely ignorant of this refutati…

            “The fact that your best source is a creationist website speaks multitudes.”

            The fact that you dismiss a compelling argument just because of the author’s agenda suggests that you are unable to think for yourself. Does the author’s argument, on its own merits, make sense to you or doesn’t it? We should put on our big-boy pants and think for ourselves, make up our own minds. One should not need to reference authority in order to make sense of a compelling argument. If we do this, then we become little better than the adherents of religious dogma.

            In order to justify mutation-theory in the context of natural selection, you would need to do complex laboratory work with data and mathematical and statistical analyses… and realistically, would the effort and expense required justify the pay-off? Especially given that these interpretations are being foisted on us in the absence of any kind of axiomatic framework.

            By means of comparison to understand what I’m getting at, Isaac Newton was a genius who combined an axiomatic framework (his three laws of motion) with mathematical analysis (calculus) to provide a rock-solid foundation that went on to change the world. Mutation theory, by contrast, is neither part of an axiomatic framework that hangs together, nor is it substantiated anywhere in any kind of rigorous anaytical context. It is a proffered, unproven mechanism, not a principle or axiom (compare this with Newton’s axioms of motion). Its only foundation is as an appeal to established authority… ie, it is dogma.

            “Notably Dawkins himself has refuted it many times”

            It has been some time since I’ve read The Blind Watchmaker, but my references to Nautilus’ pinhole eye were in relation to Dawkins’ writings.

            But the issue from my perspective is less with irreducible complexity than with the fact that mutation-variety theory has not been proven to any satisfactory standard. It is dogma masquerading as truth. I’ve got my big-boy pants on. I don’t care whether it’s an ID adherent, a christian, a physicist or a biologist… if they can present a compelling argument, I’ll listen… without feeling any obligation to have to buy into their agenda.

            “As for Lamarkism, you would first need to discover a mechanism for organisms to transfer learned adaptations genetically to their offspring”

            If you’ve been keeping up with developments, you would realize that epigenetics (phenotypic plasticity) and other mechanisms are constantly being explored and discovered even as we speak… eg, in reddit.com/science. It’s a dynamic and constantly evolving field.

        • In reply to #11 by Jarold:

          how can you have “half” an eye?

          Write me a list of twenty attributes (capabilities) of the human eye, or ten if you are struggling. Put a line through half at random (leave sensitivity to light as a minimum and to make sense of some of the attributes we need two sensitive regions as a minimum so two nerves in the optic nerve bundle).. Now I will describe a creature, one of our antecedents, a fish perhaps, and its environment such that it will make full use of half the chosen attributes.

          Your optical mouse works with a tiny fraction of the human eye but can detect any direction of movement on a huge variety of surfaces. A little bit of eye can achieve very clever and useful things.
          http://www.sciencedaily.com/releases/2009/01/090107134539.htm
          Eyes have been evolved on six separate occasions to differing levels of sophistication. This fish has a great trick all done with mirrors. As Neil Shubin explains in Your Inner Fish, evolution mostly proceeds by using pre-existing features in a novel way (two layer skin to make hair follicles, glands and nipples). These fish had a mutant silvery scale appear in the eyes of some great….great grand parents, that meant it could now explore untapped food at greater depth and still keep an eye on predators above. The mutation led to the ability to exploit other environmental niches. In the evolution of complex organs there will have been a parallel “evolution” (change) in the habitat, prey and food along the way. All sophistications of an organ are opportunistic and contingent.

          With a very few tiny exceptions all living things draw their energy ultimately from the nuclear fusion reactor of the sun, animals included. The tiny exceptions draw their energy from the nuclear fission reactor at the earth’s core. Eating your sun-kissed corn flakes of a morning is all part of the cascade of energy, one little rivulet, mouthful by mouthful…(Its concentrated too. One bowl full is 120Watt hours. If only your iPad would eat them.)

          • In reply to #25 by phil rimmer:

            In reply to #11 by Jarold:

            how can you have “half” an eye?

            Write me a list of twenty attributes (capabilities) of the human eye, or ten if you are struggling. Put a line through half at random (leave sensitivity to light as a minimum and to make sense of some of the attributes we need two sensitiv…

            All well and good phil, but where’s the axiomatic framework to explain how this happens? Natural selection is an important mechanism, but it doesn’t explain how this happens. And mutation as the source of variety most certainly does not explain any of this.

          • In reply to #26 by Jarold:

            In reply to #25 by phil rimmer:

            All well and good phil,

            I’m delighted you can see that half an eye is functional and can serve a variety of useful purposes that can suit the immediate requirements of our earlier (say) fishy (etc.) selves .

            If you want illustrations of how gradual changes can gradually both improve, and create new, visual functions, I’ll be glad to elucidate.

            And mutation as the source of variety most certainly does not explain any of this.

            Lets see if Zeuglodon’s excellent post and links work for you.

    • In reply to #2 by Jarold:

      I think that the neo-Darwinian idea of mutation as the source of variety needs to be tossed with great haste.

      Natural selection with mutation as being the sole source of variety, to create something as complex as the eye, is not realistic (in Intelligent Design circles, this relates to irreducible…

      Your post shows an abject failure to understand the 2nd law. We are not a closed system. We exist as an eddy in the flow of entropy. As do stars.

      As for the irreducible complexity of an eye, I can’t really see how it is any more, or less, irreducibly complex than an arse?

      Or even a creator.

      Anvil.

      • In reply to #10 by Anvil:

        In reply to #2 by Jarold:

        I think that the neo-Darwinian idea of mutation as the source of variety needs to be tossed with great haste.

        Natural selection with mutation as being the sole source of variety, to create something as complex as the eye, is not realistic (in Intelligent Design circles, t…

        Ultimately the topic is complex, because if we are to take the idea of evolution by mutation seriously, then these ideas would need to be tested in the laboratory, and we would need to examine in earnest the mathematics and stochastics that might conclusively test the reality of dumb deformities in competition with lucky accidents. But I think my own basic outline (with reference to Byles) provides some idea of why evolution by mutational deformity should be at least highly suspect indeed.

        Of course some mutations might indeed turn out to be “lucky”. A moth’s wing colouring, or a predator’s larger size or it’s prey’s smaller size enabling it to disappear into smaller nooks and crannies… and so on. But the idea of complex forms, like eyes, wings or legs, relying on mutations, is rather more far-fetched.

        What alternative might we put in place to account for natural selection’s source of variety? Why shouldn’t Jean Baptiste Lamarck provide a reasonable starting point? Factor in systems/complexity theory and the idea that collectives of cells are predisposed to swarm-like behaviour, and that should not be too alien a concept to incorporate into natural selection. Charles Darwin himself, knowing nothing of the work of Gregor Mendel or mutation-theory, was on occasion inclined to Lamarckian adaption as the source of variety.

    • Natural selection with mutation as being the sole source of variety, to create something as complex as the eye, is not realistic (in Intelligent Design circles, this relates to irreducible complexity). In addition to the problem of irreducible complexity, there is the problem of entropy versus complexity and the logical fallacy of something as exquisitely complex as the eye to be a product of accumulated but lucky deformities (mutations) being selected by environmental pressures.<

      I’m surprised that any long term viewer/user would have any doubt about the logical failure of the ‘Second Law of Thermodynamics’ argument- which applies to CLOSED SYSTEMS only.
      “exquisitely complex” is too close to Creationist talk, the appeal to personal incredulity. Dawkins wrote extensively on evolution of eyes, and also about loss of vision in life existing in dark environments; he also mentioned the flaws in the human eye’s “design”.
      ‘Lucky’ is not the correct term for natural selection- as above, do you consider loss of sight ‘lucky’? It’s neither lucky or unlucky, just a process of optimisation.

      Natural selection is not accepted as the only driver of evolution- there’s also Genetic Drift, and Gene Flow, plus sexual selection (hope I got that right). You contradict yourself, I think.

      • In reply to #16 by Fritz:

        Natural selection with mutation as being the sole source of variety, to create something as complex as the eye, is not realistic (in Intelligent Design circles, this relates to irreducible complexity). In addition to the problem of irreducible complexity, there is the problem of entropy versus compl…

        Regarding your reference to thermodynamics, you misinterpret the context of my reference. Complexity doesn’t just happen solely through bathing in energy.

        “”exquisitely complex” is too close to Creationist talk, the appeal to personal incredulity.”

        Oh pahlease… mining for the most irrelevant comments is a sign of desperation.

        “Dawkins wrote extensively on evolution of eyes, and also about loss of vision in life existing in dark environments; he also mentioned the flaws in the human eye’s “design”.”

        I don’t care how much detail an explanation covers… what I want is an axiomatic framework that hangs together. I want claims to be substantiated, and if it is difficult or expensive to substantiate a claim, as it would be for mutation-variety theory, then I want the explanation to be compelling, and in compliance with an axiomatic framework. Mutation-variety theory does neither. Heck, even creationists are able to identify its flaws.

        Christians have been explaining god for centuries, and no amount of their explanation will succeed in converting me. Again, just because it is Richard Dawkins doing the explaining, on what basis should I regard it as anything other than dogma? I want something that hangs together within the context of an axiomatic framework… eg, Isaac Newton.

        “Natural selection is not accepted as the only driver of evolution- there’s also Genetic Drift, and Gene Flow, plus sexual selection (hope I got that right). You contradict yourself, I think.”

        Yay! I’m glad we agree on something… but let’s dump mutation as the source of variety theory first. It’s misleading, and it reflects poorly on natural selection theory… heck if creationists are able to so compellingly refute “mutation fixation” theory (as per the link I provided earlier) but neo-Darwinists cannot, then what hope can there be for Neo-Darwinism/evo-psych?

        • In reply to #23 by Jarold:

          Welcome to the site, and thank you for joining the discussion! It’s nice to see a new name every once in a while on the comments. I hope you enjoy your time here.

          From what I can tell, your posts thus far on the subject of mutations producing variation basically centre around the argument that sizeable-enough beneficial mutations can’t and therefore don’t exist, which would explain both your objection to mutation as a source of variety in a species and your objection to the evolution of the eye by natural selection on the grounds that no variety could get started in that direction. The assumption in the latter in particular is that a complex organ had to be exactly as complex and intricate as it is each generation, and could not have arisen from functional and simpler antecedents without destroying its host’s survival and reproductive chances. Furthermore, it seems to me that the point can be broken down into two: that beneficial mutations are simply too rare to have been a basis for natural selection; and that a beneficial mutation would be insufficient, even over the long run, for shaping complex and functional organs.

          In which case, I think your objection is incorrect, but incorrect for interesting reasons. If you are interested, I think a good starting point would be to look into the subject of mutations in genetics, specifically mutations that follow the “deleterious-neutral-advantageous” category. Wikipedia’s article on mutations would make a suitable starting point, especially the subsections 3.3. (Classification of mutation types by effect on fitness) and 6. (On beneficial mutations). Long story short, beneficial mutations do have some empirical basis in reality, and it’s actually quite interesting to compare their rates with those of neutral and deleterious mutations.

          Beneficial mutations are rare, to be sure, compared with neutral and deleterious mutations and compared with the mutation rates in a particular lineage. Certainly, they’re rare in everyday human life. If you look at the Wikipedia article on mutation rates, specifically subsection 3 (Variation in mutation rates), it’s easy to see why beneficial mutations would be difficult to observe over a human lifespan without referral to short-lived creatures like mice, yeast, bacteria, and fruit-flies, which is where most of the genetic studies are carried out.

          On a time-scale of one million years, however, what would be “luck” to us would become a regular occurrence, and that’s the key. For example, a mutation rate of three mutations per thousand genomes per generation – if you limited the population to one thousand per generation, and make a generation reproduce every twenty five years, for simplification – could produce 120,000 mutations in one million years. If only one percent of these were beneficial, that would still leave 1,200 beneficial mutations, making for 1.2 million in a billion years. This is just for one lineage. Note also that these limits are extremely conservative, and in practice the number of beneficial mutations would most likely be much higher.

          While I’m pointing you at Wikipedia, I would also note that they have an article on the evolution of the eye. You might be interested in the subsection “Stages of eye evolution”, which describes how simpler eyes potentially gave rise to more complex eyes.

          The general principle is that each modification of the eye design in the lineage is a gradual enhancement morphologically, but functionally is improvement enough to bias the birth/reproduction and death rates of the members possessing it in their favour, relative to other members (i.e. give them a greater share in the former, and a lower share in the latter, compared with fellow species members). To put it crudely, metaphorically, and with some considerable exaggeration; among blind people, a one-eyed man is king.

          As for how “big” a mutation’s phenotype can be, well, that’s an interesting debate in evolutionary biology, but the most dramatic I know being observed are antennapedia in fruit flies and polycephaly. On a scale from biggest to smallest, you can get from there, through duplicated body parts – like extra ribs and vertebrae – down to different metabolic systems in cells, all the way down to neutral mutations that might as well not have occurred. In general, it’s a bit like mutation at the genetic level: you can have loss of function or change of function, and sometimes duplication or even addition (whether indirectly via duplication and modification, or directly, by straight-up addition of a protein to a system that alters how it’s built and/or how it works). The general trend, though, is towards gradualism.

          I think this will suffice for now, and I hope this explanation is helpful to you.

    • In reply to #2 by Jarold:

      I think that the neo-Darwinian idea of mutation as the source of variety needs to be tossed with great haste.

      why? What’s your alternative (some form of creationism I suppose). You do know mutation and selection can be shown to produce better fitted life forms (eg. bacteria and antibiotic resistance)

      Natural selection with mutation as being the sole source of variety,

      I suppose there could be viral transmission of genetic information.

      to create something as complex as the eye, is not realistic

      evidence? reasoning?

      (in Intelligent Design circles, this relates to irreducible complexity).

      ID is just Creationism in a frock.

      [...] there is the problem of entropy versus complexity

      there is no problem. Most creationists’ understanding of the TLoT precludes the existence of fridges and snow flakes.

      and the logical fallacy of something as exquisitely complex as the eye to be a product of accumulated but lucky deformities (mutations) being selected by environmental pressures.

      there is no logical fallacy

      The following web page of the Institute for Creation Research does an admirable job of enumerating the most salient points:

      http://www.icr.org/index.php?module=articles&action=view&ID=270

      you know who these people are, right?

      While the website’s reasoning is sound, we have good reason to object to the website’s obvious creationist agenda, so I’ll summarize Byles’ observations in my own words (I am NOT a creationist, and I have NO belief in any kind of nobodaddy in the sky).

      yeah, right.

      And so, with reference to the work of GENETICIST R.H. Byles**… Byles covers the sorts of things that should be apparent to many of us, as far as macro (and perhaps also micro) mutations are concerned. For example, the conflicts between mutation rates (back-mutation, forward-mutation, etc). Byles’ analysis renders the whole notion of macro-evolution-by-mutation as simply impracticable. It would seem that the practical reality of dumb deformities in competition with lucky accidents has not been taken seriously enough. Indeed, Charles Darwin himself did not factor in mutations as the source of variety for natural selection.

      Darwin didn’t know about genetics

      ** Byles, R. H. Limiting Conditions for the Operation of the Probable Mutation Effect. Social Biology, 19 (March 1972):29-34.

      • In reply to #42 by nick keighley:

        “you know who these people are, right?”

        If an idea is logical and stands on its own merits, then what difference does it make who the author is?

        Taking my example to the extreme… if a complete idiot can understand a simple concept but an expert cannot, what does that say about the credentials of said expert?

        ‘Nuff said.

        • In reply to #46 by Jarold:

          In reply to #42 by nick keighley:

          “you know who these people are, right?”

          a known creationist lobbying site

          If an idea is logical and stands on its own merits, then what difference does it make who the author is?

          oh quite true. There’s even a name for the fallacy of rejecting an argument because it was posted by a particular person, ad hominem. But I think it’s quite reasonable to be skeptical of certain views expressed by certain people (“well, he would say that wouldn’t he?” Mandy Rice-Davis).

          The point is the arguments put forward by the site don’t stand on their merit. They are not logical.

          Taking my example to the extreme… if a complete idiot can understand a simple concept but an expert cannot, what does that say about the credentials of said expert?

          I see no sign for the phenomenon you describe

          ‘Nuff said.

          no attempt to address any of the substantive points I made?

  3. How about the concept of God or gods, and all the other concepts — religious and cultural — which are linked to it?? That would eliminate most of the superstitious beliefs and behaviors around the world.

  4. I believe ethnic nationalism or self-determination should be retired. If a people united by ties of ethnicity, religion, language, culture or other unifying factor form a nation those within that nation who not share the defining paradigm are liable to become second-class citizens. That idea should be replaced with the idea that the government of every nation should not discriminate among its citizens on the basis of ethnicity, religion, language, culture, sex or sexual preferences.

    • In reply to #5 by dovidl:

      I believe ethnic nationalism or self-determination should be retired. If a people united by ties of ethnicity, religion, language, culture or other unifying factor form a nation those within that nation who not share the defining paradigm are liable to become second-class citizens. That idea should…

      Nationalism, like religion, is responsible for a lot of the bad things that have happened in recorded history. WW1 and 2. I don’t mind cheering for my countries sporting team, but I try to see myself, and behave as a citizen of the world first. The decisions we make as nationalist countries impact the citizens of the rest of the world. USA’s psychopathic fixation with capitalism and free market forces hurts the rest of the planet. The theory of capitalism requires unlimited exponential growth forever. You can’t have unlimited exponential growth forever in a closed system. One planet. One set of resources. You can’t burn fossil fuel like the USA does, in a culture of scientific denialism, without it hurting the people of Tuvalu who are up to their shins in sea water.

      So nationalism is an idea that has had its day. Take out citizenship of planet earth and make your decisions based on evidence as to what is good for the planet as a whole. To kick this off, the UN should be able to issue passports to World Citizens.

      • In reply to #6 by David R Allen:

        To kick this off, the UN should be able to issue passports to World Citizens.

        A novel idea, but it doesn’t accomplish anything.

        Who would qualify as a ‘world citizen’? Either everyone, in which case it would be pointless and ridiculous resource intensive. Or some people wouldn’t qualify, which would make it yet another divisive issue.

        • In reply to #8 by Seraphor:

          In reply to #6 by David R Allen:

          To kick this off, the UN should be able to issue passports to World Citizens.

          A novel idea, but it doesn’t accomplish anything.

          Who would qualify as a ‘world citizen’? Either everyone, in which case it would be pointless and ridiculous resource intensive. Or some…

          I know it wouldn’t work. Nationalism is an expression of tribalism which is a millions of years old evolutionary survival advantage hard wired in our brains that makes us want to belong to tribes. In the modern world, it explains sports fans and nationalism. This desperate need to belong. I’d like to change the thinking of human beings to think of the world as our tribe. Nationalism is a force for bad. I can find few redeeming features in nationalism.

      • In reply to #6 by David R Allen:

        In reply to #5 by dovidl:

        I believe ethnic nationalism or self-determination should be retired. If a people united by ties of ethnicity, religion, language, culture or other unifying factor form a nation those within that nation who not share the defining paradigm are liable to become second-class…

        How are you going to abolish nationalism, reign in capitalism and implement your UN World Citizen program without creating a global dictatorship? This is where I find a lot of “progressives” go off the rails, just as they did in the 1930s when they thought International Communism under Joe Stalin was the most rational future for mankind. Once you implement your globalist program, what will prevent the emergence of a global Stalin? Only with many power centers and societal models can you prevent that, while ensuring real diversity and freedom. Do you really want a culturally uniform planet united under some kind of grey techno-totalitarian world government, because that’s most likely what you would get.

        The idea I would like to see retired is the notion that there is One True Progress that is true for all cultures, nations and peoples, who must all get with the program or be left in the dustbin of history. This kind of thinking may be necessary for science, but not for the rest of human civilization.

        • In reply to #20 by Imperius:

          In reply to #6 by David R Allen:

          In reply to #5 by dovidl:

          I believe ethnic nationalism or self-determination should be retired. If a people united by ties of ethnicity, religion, language, culture or other unifying factor form a nation those within that nation who not share the defining paradigm…

          The old left wing conspiracy theories ride again.

          Consider this for 5 minutes.. An ideology in the an argument in the absence of evidence. I cab prove to you why communism / socialism will always fail. That is why I will go to the barricades to oppose socialism. But there is also proof that capitalism, another ideology is just as bad and will always fail. I will opposed it with the same vigour as I oppose socialism. I do not advocate changing any country borders. Any democracy. Any forms of government that people want to live under. Go your hardest. Knock yourselves out.

          I suggest nationalism, the reason why you Imperius would take up arms and go to war against another nationalist state, is a failed ideology as well. Hence, under this topic, my proposal is that people should think of themselves as citizens of the world first, before they think of themselves as citizens of America, the UK, Russia or China. If the decisions you make are not good for the world, they WILL not be good for your nationalist state. That is my very simple proposition.

          Not your OMG, David R Allen is Joe Stalin trying to impose world government with the help of the UN and the Jewish and Catholic conspiracies in support. Or any other crazy right wing survivalist rubbish that comes out of America.

          Here are your exam questions Imperius.
          1. Why will communism always fail.
          2. Why will capitalism always fail.
          3. Name five communist countries.
          200 words on each. You’ve got a half an hour.

          • In reply to #21 by David R Allen:

            In reply to #20 by Imperius:

            In reply to #6 by David R Allen:

            In reply to #5 by dovidl:

            I believe ethnic nationalism or self-determination should be retired. If a people united by ties of ethnicity, religion, language, culture or other unifying factor form a nation those within that nation who no…

            How does the Edit Function work in these blogs??. The first line should read:-

            An ideology is an argument in the absence of evidence.

          • In reply to #22 by David R Allen:

            How does the Edit Function work in these blogs??. The first line should read:-
            An ideology is an argument in the absence of evidence.

            Right after posting a comment, the option should crop up in the bottom right, called “More”. There’s a drop-down menu that enables you to edit or delete the post. However, the edit option is on a time limit (I think about one hour), after which the post becomes untouchable and your only option is to post another comment.

  5. Any scientific that could be proved false or replaced by a simpler solution would be (and have been) automatically retired as a general rule of science so I cannot offer any current scientific ideas that should be retired. But there is plenty of popular beliefs that we would better of without. My personal least favorite common beliefs are “Science cannot offer anything on the big questions of life and morality”, “Humans are in some way above the rest of the biosphere (i.e Human Exceptionalism)”, “Religion is a force for good”, “America is the home of the free”, “Nationalism in general”, “Anybody can get rich if they work hard enough”, “Television generally provides accurate information”, “If it written in a book it must be true”,

  6. Great question. First, in general, and I haven’t read the article yet, but I’m not keen on the notion that theories need to be “retired”. I think the history of science shows us that it often happens that theories we realized were wrong actually come back in one form or another. The concept of the ether for example. When Newton defined the theory of gravity it was considered scandalous, an example of “occult” and “mystic” reasoning that the theory posited action at a distance. For gravity to have an effect on something there must be some medium that it travels through and so people postulated the ether, something that existed everywhere in space. Things like gravity were conceived as waves in the ether.

    We no longer need that concept at all and I think you could say it’s been effectively retired but IMO it also keeps coming back. So the Higgs Boson for example, and this may be just because of my amateur understanding of the concepts, but in some ways it seems similar to the ether.

    Which actually segues nicely into my candidate for retirement and that is the mind body problem. Chomsky has some insightful talks on the topic such as this:

    Noam Chomsky: The machine, the ghost, and the limits of understanding. Newton’s contribution to the theory of Mind

    Note: for those who get the vapors over Chomsky’s politics don’t worry, this video has no political discussion, just philosophy.

    Chomsky’s point in this lecture is that the mind-body problem is obsolete, not because he thinks dualism is flawed (i.e., the mind part of the theory is incoherent) but because the notion of a material world required to make the distinction in the first place, the foundation that Descartes was using when he first defined the theory, has been obsolete for a long time. That once people started accepting concepts like action at a distance (and later and even less materialistic quantum entanglement) the notion that physics was just about the material world consisting of smaller and smaller billiard balls bouncing off each other was gone. The material world isn’t really material in any meaningful sense so it’s pointless to worry about the distinction at all.

  7. Dear Jarold,

    Please go and learn some basic science. It will do you no harm, and might in fact, improve your quality of life.

    You mention the evolution of the eye as some sort of problem for Darwinian theory. Clearly you are unaware that “eyes” have evolved and unevolved many times since the 3.5 billion odd years that life has existed on Earth.

    As for that Great All Seeing Eye in the cosmos that worries about your sex life, and who will punish you in the fiery lake if you don’t believe in Him, how did that evolve ?

    (Oh dear, of course that particular eye always existed, – so silly of me ! )

  8. With regards to the notion of “retiring” ideas, I cannot think of many that need to be tossed out completely. Information, even if it is false or archaic, has historic value. It helps us understand precisely how much we have grown as a species and aids in preventing further mistakes. However, if I had to select one idea that I think needs to be completely eradicated, it would be faith. The idea that you can “know” something without demonstrating that it is true or providing sufficient evidence to justify it is not only silly and absurd, it is positively harmful. I think we would all be better off if we valued truth, sought earnestly to find it, and didn’t make excuses for believing something when we didn’t have answers.

    • In reply to #18 by petermead1:

      With regards to the notion of “retiring” ideas, I cannot think of many that need to be tossed out completely. Information, even if it is false or archaic, has historic value. It helps us understand precisely how much we have grown as a species and aids in preventing further mistakes. However, if I h…

      Wouldn’t faith be a concept of considerable historical value? Not only does the debate over faith and reason have a long philosophical history of thought, but it also underscores a lot of historical movements, which were the outcomes of some of the ideologies that people held. I suppose, however, you could take it that “retire” or “die” in context both mean “confined to history”.

  9. Jarold, what do you think is the other explanation for a source of variety in evolution? Apparently, your claim is that you believe “the neo-Darwinian idea of mutation as the source of variety needs to be tossed with great haste. Natural selection with mutation as being the sole source of variety… is not realistic”

    But you also claim that you are “NOT a creationist, and I have NO belief in any kind of nobodaddy in the sky.”

    So at this point in the discussion you are very long overdue to tell us what you DO think is the agent of evolution. How, for example, DO you believe the eye evolved? Obviously, I don’t need to remind you that you need to come up with something good in order to completely dismiss the previous idea. On the other hand, obviously I need to remind you that you need to come up with something god in order to dismiss the previous idea.

    • In reply to #19 by Marler:

      Jarold, what do you think is the other explanation for a source of variety in evolution? Apparently, your claim is that you believe “the neo-Darwinian idea of mutation as the source of variety needs to be tossed with great haste. Natural selection with mutation as being the sole source of variety……

      Thank you Marler, for the challenge that shows that you are thinking for yourself.

      Can I explain how the eye evolved? Of course I can’t… nobody can… if, by explanation, you mean knowing the precise conditions required to replicate said eye. However… Just as Isaac Newton was able to deliver on a compelling axiomatic framework for the physical sciences, so too, I believe that an analogous framework, as yet not identified, exists for the life sciences. In the absence of said axiomatic framework, no-one can explain how the eye works. We never will until we nail what the axioms of that framework are. Might natural selection constitute one of its axioms? Or is natural selection a mechanism, one aspect of a broader principle (axiom)? Might we need to understand the very nature of matter itself (eg, quantum physics) in order to identify axioms that make life possible? Maybe. Irrespective of any of this, what we do not yet have is an axiomatic framework for the life sciences.

      “Obviously, I don’t need to remind you that you need to come up with something good in order to completely dismiss the previous idea.”

      No, not at all. It is better to leave things undefined than to pretend that you have an answer and construct an edifice built on a fiction as its foundation. At least if you leave things undefined, you will keep your eyes open for clues. Why is this important? Heck, if even creationists are able to refute mutation-fixation theory with a simple, compelling argument but neo-Darwinists cannot, what does that imply for neoDarwinism as just another form of dogma?

      • In reply to #24 by Jarold:

        Jarold, that pompous creationist site is complete and utter shite. Anyone who has even written a genetic algorithm on a computer knows it, and anyone who does so in the future will soon discover it for themselves.
        I suggest you stop pretending black is white and write some computer code.

  10. There’s a lot of interesting articles in the link provided by the OP. One in particular of interest to this thread is by Athena Vouloumanos. She puts forth the idea that intergenerational transmission of acquired traits (or Lamarckism) is making a bit of a comeback. It has to do with study in which mice conditioned against an odor could pass this trait to their off-spring by a mechanism called methylation. I don’t have the technical expertise to substantiate or refute her claim. I’d be interested to learn a little more. Has this been peer reviewed? Does this line of thinking have merit?

    To be clear, Athena says “Natural Selection is still the primary shaper of evolutionary change…”. Also, I see nothing in her article that supports irreducible complexity or intelligent design. To say otherwise misrepresents the work being done, IMO.

    I’m also confused by the need for an “axiomatic framework”. My understanding of the definition of axiomatic as “pertaining to a to a self-evident truth that requires no evidence.” I don’t think anyone claims that Natural Selection (with mutations) is self evident nor that it requires no evidence. Natural Selection is supported by a wealth of evidence. In what way could a framework that appears true with no evidence be superior?

  11. Thank you Zeuglodon for your carefully explained and referenced post, which I enjoyed mulling over. It’s tempting to be drawn to this perspective of the argument, but the references provided are not conclusive… hard to distinguish objective truths from the authors’ agendae (assumptions). There is also the question of whether or not unexpected changes are, in fact, always mutations – I recall reading an article (New Scientist?) some time ago, discussing the ability of bacteria to rapidly adapt to a new toxin introduced to their environment that defied the odds… it did not appear to be random (as in, mutational). Ultimately I remain dissatisfied as to the absence of an axiomatic framework in the life-sciences, and therefore sceptical of the mechanisms that are often proffered as solutions.

    • In reply to #33 by Jarold:

      Thank you Zeuglodon for your carefully explained and referenced post, which I enjoyed mulling over. It’s tempting to be drawn to this perspective of the argument, but the references provided are not conclusive… hard to distinguish objective truths from the authors’ agendae (assumptions). There is…

      Nothing will convince you Jarold. Zeuglodon evidence was conclusive. Statements like “References provided are not conclusive” AND “hard to distinguish objective truths from the author’s agendae (Assumptions) etc. indicate a predetermined position, that is not open to evidentiary persuasion, the mark of a scientific skeptic.

      This is the New Scientist article you refer to and contrary to your recollection “it did not appear to be random (as in, mutational).” it was pure random mutation. A seminal experiment that proved evolution. I commend the article to the readers.

      http://www.newscientist.com/article/dn14094-bacteria-make-major-evolutionary-shift-in-the-lab.html#.UvbDWft0b_I

      • In reply to #34 by David R Allen:

        In reply to #33 by Jarold:

        Thank you Zeuglodon for your carefully explained and referenced post, which I enjoyed mulling over. It’s tempting to be drawn to this perspective of the argument, but the references provided are not conclusive… hard to distinguish objective truths from the authors’ agen…

        A quote from the New Scientist article.

        Lenski’s experiment is also yet another poke in the eye for anti-evolutionists, notes Jerry Coyne, an evolutionary biologist at the University of Chicago. “The thing I like most is it says you can get these complex traits evolving by a combination of unlikely events,” he says. “That’s just what creationists say can’t happen.”

      • In reply to #34 by David R Allen:

        “This is the New Scientist article you refer to and contrary to your recollection “it did not appear to be random (as in, mutational).” it was pure random mutation. A seminal experiment that proved evolution. I commend the article to the readers.”

        No, it wasn’t the article I was referring to… The study I was referring to related to a deadly toxin introduced into a population of bacteria and the researchers were unable to fathom how it was that the bacteria were able to adapt so quickly to it. Still, the article you reference is interesting, so responding to the last three paragraphs of it to clarify my position with respect to this discussion:

        “Lenski and his colleagues are now working to identify just what that earlier change was, and how it made the Cit+ mutation possible more than 10,000 generations later.”

        Here Lenski is making reference to an “earlier change” that “made the Cit+ mutation possible”. Therefore we should infer that this Cit+ mutation was not random (not to mention that not all changes in the DNA should necessarily be assumed to be due to mutations). What was this precondition to which Lenski is referring? Furthermore, in subsequent reruns, the Cit+ mutation did not repeat in any of the other populations… it only repeated in the same population that it appeared in the first time, according to the article.

        “In the meantime, the experiment stands as proof that evolution does not always lead to the best possible outcome. Instead, a chance event can sometimes open evolutionary doors for one population that remain forever closed to other populations with different histories.”

        “Different histories”? “Chance event”? This does not suggest randomness. It suggests some kind of predisposition attributable to history.

        “Lenski’s experiment is also yet another poke in the eye for anti-evolutionists, notes Jerry Coyne, an evolutionary biologist at the University of Chicago. “The thing I like most is it says you can get these complex traits evolving by a combination of unlikely events,” he says. “That’s just what creationists say can’t happen.””

        I am not an anti-evolutionist (just as Darwin, who had never factored in mutations, was not an anti-evolutionist). And the matter is not yet settled as to whether said “combination of unlikely events” relates to random mutations or to other predisposing factors.

        • In reply to #36 by Jarold:

          In reply to #34 by David R Allen:

          “This is the New Scientist article you refer to and contrary to your recollection “it did not appear to be random (as in, mutational).” it was pure random mutation. A seminal experiment that proved evolution. I commend the article to the readers.”

          No, it wasn’t th…

          Jarold reading of the same material I have read, is a classic case of looking for diamonds with your eyes closed. Jarold, somehow, finds support for his claim in an article that debunks it. This is a similar psychological profile to a religious fundamentalist, who can find gold at the end of every refraction induced rainbow. Rose coloured glassed.

          Lenski didn’t stop his research at the time the New Scientist article was published. It has continued and continues to pull the rug out from under the Jarold of this world.

          In the early years of the experiment, several common evolutionary developments were shared by the populations. The mean fitness of each population, as measured against the ancestor strain, increased, rapidly at first, but leveled off after close to 20,000 generations (at which point they grew about 70% faster than the ancestor strain). All populations evolved larger cell volumes and lower maximum population densities, and all became specialized for living on glucose (with declines in fitness relative to the ancestor strain when grown in dissimilar nutrients). Of the 12 populations, four developed defects in their ability to repair DNA, greatly increasing the rate of additional mutations in those strains. Although the bacteria in each population are thought to have generated hundreds of millions of mutations over the first 20,000 generations, Lenski has estimated that within this time frame, only 10 to 20 beneficial mutations achieved fixation in each population, with fewer than 100 total point mutations (including neutral mutations) reaching fixation in each population.[3]

          Full Wikipedia found here.

          http://en.wikipedia.org/wiki/E._coli_long-term_evolution_experiment

          In summary. Evolution happens. God didn’t do it.

          • In reply to #37 by David R Allen:

            “Jarold reading of the same material I have read, is a classic case of looking for diamonds with your eyes closed. Jarold, somehow, finds support for his claim in an article that debunks it.”

            lol No, it’s just that you don’t understand where I’m coming from.

            So how does your quoted reference… the quoted passage that you made available to read… establish that random mutation is the way to go? It does not.

            Back mutations, forward mutations happen, we all agree on that. And, like at the macro level, some simple mutations might turn out to be fortuitous, we all agree on that. At issue here is the role of mutation fixation to account for higher-level complexities especially in the context of irreducible complexity. How do your referenced studies address the question of irreducible complexity? There is also the question as to whether some changes in the bacterial cultures might actually be ADAPTATIONS to enviornmental pressures, and not random mutations at all.

            Apart from which, I have never been made aware of any bacteria that possess irreducibly complex structures such as eyes or knees.

            So no, that matter of random mutations especially in higher level organisms in relation to irreducible complexity has not been settled… and I assume that the wikipedia link you provide will similarly not settle the matter…

            If we are going to be serious, the question needs to be tested on higher level organisms with eyes and knees and wings in ecosystems where the evolving patterns can be observed over time, not on bacteria where irreducible complexity is unlikely to apply, and where it is not clear which changes are random-mutational and which changes are directed adaptations to environmental pressure. In this context, the work of Eshel Ben Jakob might be relevant (intelligent bacterial colonies adapting to change).

          • In reply to #45 by Jarold:

            irreducibly complex structures such as eyes

            No. Youv’e been offered the chance for this to be explained and not taken it. A better (more challenging) example of irreducible complexity is the flagellum.

            Read Ken Miller’s account of it here. Come back with an assessment of it and detail why you may think his account fails. Do some work for once rather than dropping items and moving to new areas then swing around back hoping that we haven’t noticed you have not engaged in any detail.

            Give proper detailed feedback. Don’t change the subject, and we can make progress.

            Whilst your at it report back on this

          • In reply to #47 by phil rimmer:

            In reply to #45 by Jarold:
            “example of irreducible complexity is the flagellum.”

            flagellum… point taken

          • In reply to #47 by phil rimmer:

            I am unable to explain the flagellum, so that disqualifies me as a creationist.

            I have my unsubstantiated hunches that might account for the flagellum, relating to the nature of physical entities (atoms, molecules) as you get down to smaller and smaller scales. The smaller you go, the more disproportionate the mass/volume relationship (mass varying with length to the power of three), the more volatile become the possibilities. But is it random mutation? Or is it something more directed? Does quantum physics have some part to play? I have no idea.

            But can you be so sure that random mutation is, in and of itself, sufficient to account for the flagellum?

          • In reply to #47 by phil rimmer:

            Whilst your at it report back on this [videoclip - Irreducible complexity cut down to size]

            There is nothing in this videoclip that I disagree with. But then, no reference appears to have been made to random mutation as the source of variety. This is consistent with Charles Darwin, who was not aware of the work in genetics of his contemporary, Gregor Mendel.

          • In reply to #53 by Jarold:

            In reply to #47 by phil rimmer:

            There is nothing in this videoclip that I disagree with. But then, no reference appears to have been made to random mutation as the source of variety.

            Delighted you now have no problem whatsoever with the contentless concept of Irreducible Complexity. You do jump about though. There is entirely zero need to engage with mutation to dispatch this first concept.

            Lets see what the others have said on this jumpiness…

          • In reply to #43 by Red Dog:

            I accept what you say in principle, but sadly, only the Internet can accommodate every possible position (and even then, technically not), and if you accept that some ideas have more weight behind them than others, then for practical purposes, the ones that had their chance and failed belong in the archives. That means, for every idea that has been vindicated, there must be countless others that had to be retired. Ideas are tools just as much as they are truths, and old tools wear out their welcome.

            In saying this, I appreciate that we should keep an open mind in case future results make it necessary to revise our ideas. To take your example, group selection, for a moment; group selection has been refuted and criticized, which is sufficient to discard it, if not for ever, at least for the time being. By all means, Wilson has a right to make a case, and by all means is he entitled to less patronizing responses than to be told his ideas are dead. To prevent established ideas from becoming dogma, counter ideas have to have their fair shots, since you never know if Wilson’s successors – or Wilson himself – will find a way to make group selection work.

            On the other hand, his argument for his scientific idea should go through the same channels as any other scientific idea. From the same argument that points out we can’t explore all the ideas possible and have to narrow them down to the most likely, he would also do well not to waste other people’s time when they are trying to get at correct answers that could be difficult to find. To date, I believe Wilson has departed in recent years from listening to his critics on the subject, up to and including going directly to the public with ideas that don’t serve his otherwise bright reputation. In such a scenario of repeating the old arguments and ignoring counters, can we not say that the idea is retired, at least to the historian’s archives?

            In reply to #44 by Red Dog:

            My knowledge of the aether’s history seems to be incomplete. I just remember aether being a big thing in the early 20th century. Wasn’t there a famous experiment – I forget its name – performed that disproved its existence?

            In reply to #45 by Jarold:

            I’m not entirely convinced you understand the role mutations play in evolution, nor how natural selection works. The selection occurs on variety irrespective of whether or not that variety was produced randomly or with bias. Once variety exists, however, natural selection removes the deleterious varieties and preserves the advantageous ones, enabling them to reach fixation and provide the default for the next round of selection. It is selection that builds the complex organs, not the mutations on their own.

            The key point is that it is both accumulative and biased in favour of functional benefit. Dawkins provides an analogy of getting the combination to a safe when the safe clicks each time you get a digit right and keeps it, as opposed to getting the entire combination in one go, as one way of conceiving of the difference, since it reduces a colossal improbability to an easy series of bite-sized possibilities. Putting it simply, natural selection preserves a series of wins and destroys the losses acquired at any point, which makes a big difference over a timescale of millions of years, as my example of beneficial mutation rates from earlier would show (1200 beneficial mutations per million years could be enough to redesign an organ, add modifications to it, and/or enable a modification to grow and evolve into an organ of its own).

            By accumulating the beneficial mutations, it can quickly build up a body design that gets more and more complex and more and more efficient at its function or functions, even switching between functions (for instance, when arms evolve into flippers, or feathers for flight evolve to become sexual displays) and building on previous work. In such a way does it direct bodies, in the long run, towards complex body designs, made from the elements freely available, such as carbon, hydrogen, nitrogen, and oxygen, and their compounds in the forms of proteins and acids.

          • In reply to #45 by Jarold:

            In reply to #37 by David R Allen:

            Back mutations, forward mutations happen, we all agree on that. And, like at the macro level, some simple mutations might turn out to be fortuitous, we all agree on that. At issue here is the role of mutation fixation to account for higher-level complexities especially in the context of irreducible complexity.

            Just what do you suppose happens when a quantum fluctuation trips a chemical reaction which results in a change to the chemical structure of a bond within DNA? Not random? Not rational? And if it happens to be beneficial, (refer Zeuglodon’s excellent post) the bulldozer of natural selection will grab this random mutation and run with it.

            Some quotes from Jarold

            create something as complex as the eye, is not realistic (in Intelligent Design circles, this relates to irreducible complexity).

            And

            Mutational deformities masquerading as intermediate steps to something of utility, if they cannot fulfil any immediate purpose, are DEAD WEIGHTS that are detrimental to survival because they erode efficiency..

            And

            Or is natural selection a mechanism, one aspect of a broader principle (axiom)?

            And yet more

            my objection is not with natural selection but with the unquestioning acceptance of mutation fixation as the source of variety. Assuming said mutation to be a given blinds us to other possibilities that might be taking place.

            What else “Might be taking place”.

            If it walks like a duck. If it quacks like a duck. Its a intelligent design advocate in a pseudo-scientific lab coat.

            I don’t care. I enjoy debating on the fringes of rationality. But don’t hide. Have the courage of your convictions and declare your true position. God is going to reward you with an upgrade in heaven. None of those standard rooms. You hint, and reference, and subtlely drift ID references into your argument. State truly, what you think is directing evolution, if not random mutation.

          • In reply to #60 by David R Allen:

            My true position? Relates to my axiomatic framework. For example, where one respondent might be of the view that it’s an accidental universe (in accordance with the strong/weak anthropic principle), I am of the view that it’s not “accidental”. This changes the approach and how you look at cause-effect. And no, there is no need to factor any kind of god into the equation, for then you need to follow up with who created god, and god-god, and god-god-god after him, and you would need to factor in why a god made in man’s image, inhabiting a formless void, should have the form of a human (man created in god’s image), with legs with which to walk and mouth with which to speak… itt’s nonsense. There is something else going on, and it MUST make sense, and it MUST be inevitable (not accidental), for we are here to witness our own inevitability extended across time.

          • In reply to #64 by Jarold:

            In reply to #60 by David R Allen:

            My true position? Relates to my axiomatic framework. For example, where one respondent might be of the view that it’s an accidental universe (in accordance with the strong/weak anthropic principle), I am of the view that it’s not “accidental”. This changes the appr…

            Now we are getting somewhere. This is your key sentence.

            There is something else going on, and it MUST make sense, and it MUST be inevitable (not accidental), for we are here to witness our own inevitability extended across time.

            While you profess not to be religious, you are submitting to a very primitive evolutionary trait possessed by all humans. We have an excessive compulsive need to assign CAUSE, to EFFECT. From the very first time in our evolutionary history when your ancestor ask
            Why?” we have undergone cognitive behavioural therapy to reinforce this in our brains. If I hear a rustle in the grass, it could be a predator. Etc.

            The impulse that infects you, is exactly the same impulse that has created and sustained all of the religions and gods that have ever existed since we became sentient. It was the only explanation to the “Why” question, or it was, until we started to find out the scientific “Why” to many daily events.

            In your concluding sentence quoted above you have capitalized the word “MUST” twice. The compelling evolutionary trait that is strong in your brain, as evidenced by the capitalized “MUST” will not let you imagine a world where stuff just happens. It doesn’t need a reason. It just happens. While in denial, you are seeking a god to give your psyche some calm and order, some solid ground to enable your next inhalation to be relaxed.

          • In reply to #66 by David R Allen:

            Don’t read more into it than is justified, you are over-interpreting. How do you get this out of the requirement that something must make sense and that existence is inevitable? Without even enquiring into the many nuances that are possible? Think Copernicus… Newton’s laws are not just local, but MUST extend the length and breadth of the universe… nothing mystical about that, just commonsense.

          • In reply to #67 by Jarold:

            In reply to #66 by David R Allen:

            Don’t read more into it than is justified, you are over-interpreting. How do you get this out of the requirement that something must make sense and that existence is inevitable? Without even enquiring into the many nuances that are possible? Think Copernicus… .Newton’s laws are not just local, but MUST extend the length and breadth of the universe…

            Newtons laws do extend the lengh and the breadth of the universe, but that is a very different “MUST” from the context you used the word “MUST” in the revealing sentence. In that sentence repeated here for the readers:-

            There is something else going on, and it MUST make sense, and it MUST be inevitable (not accidental), for we are here to witness our own inevitability extended across time.

            Your contention is that “There is something else going on” Something else that is not explained by science? And that “Something Else” must make sense. That is, it must explain the “Why” to your satisfaction. And there is a compulsion that this will be the outcome, by the second use of the word “MUST” in conjunction with the word “inevitable” . To paraphrase, you seek an explanation, external to the universe, unexplained by science, that gives your existence meaning.

            How is that any different from a god, which I contend, is what you are in self denial about, that you won’t or can’t believe your brain wants a “guiding hand” explanation for something that may have no explanation at all, except chance.

        • In reply to #36 by Jarold:

          “Lenski and his colleagues are now working to identify just what that earlier change was, and how it made the Cit+ mutation possible more than 10,000 generations later.”

          Here Lenski is making reference to an “earlier change” that “made the Cit+ mutation possible”. Therefore we should infer that this Cit+ mutation was not random (not to mention that not all changes in the DNA should necessarily be assumed to be due to mutations). What was this precondition to which Lenski is referring? Furthermore, in subsequent reruns, the Cit+ mutation did not repeat in any of the other populations… it only repeated in the same population that it appeared in the first time, according to the article.

          Here is your confirmation bias at it’s finest.

          This scenario of mutation working on mutation, that was unable to be reproduced in strains that did not make the first mutation, is actually more indicative of random mutation than anything else.

          The organisms did not pre-empt the second mutation and so make a “choice” to make the first mutation, otherwise the experiment would have been reproduced in the other strains almost immediately. The fact that it was a rare occurrence rather than a reliable and reproducible process shows it was a random mutation.

          This experiment is a perfect demonstration of two chance events coming together to produce an unexpected beneficial mutation, this is a perfect refutation to irreducible complexity, yet you only see what you want to see.

          .

          Back to Lamarkism. Any theory that takes Lamarkism into account has to explain how an autonomic process can make conscious decisions, because that’s what is required for our bodies to edit their own genetic code for practical purposes.

          DNA is not a blueprint for building organisms that can be edited in retrospect. It is a set of step-by-step instructions that when followed by the proteins results in a complex organism, it cannot be read and understood by the organism in question. Building a body is a bottom-up process, not a top-down process. Those instructions can be altered by other factors such as hormones or toxins in the womb, and genes can be switched on and off, that’s epigentics. Epigentics however cannot take external input (say a Giraffe stretching to reach higher branches) translate that into a biological change (grow a longer neck) translate that into a certain genetic code (the genes for growing a longer neck) and then insert that code into the right place in the right chromosome into every gamete in it’s sexual organs. This sort of process would require an external, intelligent force orchestrating it. Not only that, but if this was the case we would expect to see much more rapid genetic changes in populations and far less genetic abnormalities. Giraffe’s wouldn’t have needed millions of years to grow longer necks, they could have done it in a couple hundred years. Bodybuilders would have heavily muscled children, ballet dancers would have ballet dancing children, professors would have super-intelligent children. The whole proposal is ridiculous.

          .

          You say you need an axiomatic explanation that explains how life in it’s current form is inevitable instead of accidental. First off, I would suggest why you would think there would be a simple axiomatic explanation for something as complex as life. Other axioms in the realms of mathematics, physics and chemistry will go into the explanation but there isn’t going to be one axiom purely for life. Secondly, why do you think ‘accidental’ and ‘inevitable’ are mutually exclusive properties?

          If I were to roll a ball down an uneven hill, it would be impeded by the imperfections n the slope and it’s course would be altered, it would end up at a “random” place at the bottom of the slope and it would be accidental. At the same time, the precise imperfections in the slope and the force and direction of which the ball struck them would have made the result inevitable.

          Genetic mutations are the same. Each gene can only react in so many ways according to certain factors, and those factors rely on certain other external factors, and so from a cause and effect perspective every genetic mutation is inevitable. However every genetic mutation is also accidental, because they have no purpose, there is no logical connection between the factors influencing a genetic mutation, and the phenopytical result of said mutation.

          • In reply to #73 by Seraphor:

            DNA is not a blueprint for building organisms that can be edited in retrospect. It is a set of step-by-step instructions that when followed by the proteins results in a complex organism,

            Most of the rest of the paragraph these sentences occur in are correct, but there are a couple of errors in these. Firstly, there are occasions in which DNA can be edited by reverse transcriptase enzymes, which is effectively conversion of RNA into DNA strands. A similar principle could potentially underlay a mechanism by which the immune system can update the gametes using variable genes in the immune system, as a potential means of combating fast-evolving diseases, though Steele’s theory is not entirely accepted as a strongly supported one. There have also been cases of horizontal gene transfer, which could technically count as editing the genome, if only by adding to the sum of the genes in the cells, occasionally infecting a gamete (which would most likely count as a mutation). The Weisman barrier between somatic genes and gametic ones (basically body cells and reproductive ones) is permeable, but only in a few specific circumstances, and only via chemical conversion, not from physical characteristics.

            Secondly, the instructions in DNA are technically “followed” (via transcription and translation) by the various kinds of RNA molecule, which read the DNA strands and then convert them into polypeptide chains, which ultimately become the proteins used in the cells. However, in both cases one could argue that the RNA and the DNA both constitute “genes”, and no evidence has been found that proteins can convert their structures into RNA or DNA, as shown in this diagram of the Central “Dogma” of Molecular Biology.

          • In reply to #75 by Zeuglodon:

            In reply to #73 by Seraphor:

            DNA is not a blueprint for building organisms that can be edited in retrospect. It is a set of step-by-step instructions that when followed by the proteins results in a complex organism,

            Most of the rest of the paragraph these sentences occur in are correct, but there…

            Thank you for the clarification and elaboration, I apologize for over simplifying it. However my point is (and I’m sure I don’t even need to ask if you agree) that in neither case is the RNA or DNA aware of the outcome of the processes they’re tied into. By ‘reading’ I of course meant ‘comprehending’ in some way, and by ‘retrospect’ I meant taking into account the ultimate results of the genetic code. It is not a blueprint in that it is not a ‘design’, it’s simply the inevitable outcome of the processes involved in converting the DNA into the proteins that make up a body. Bottom-up.

            Sorry, you edited your post after I replied.

            A similar principle could potentially underlay a mechanism by which the immune system can update the gametes using variable genes in the immune system, as a potential means of combating fast-evolving diseases, though Steele’s theory is not entirely accepted as a strongly supported one.

            This part seems unlikely to me but I’m completely ignorant of it, I will have to look into it when I have more time.

          • In reply to #76 by Seraphor:

            Thank you for the clarification and elaboration, I apologize for over simplifying it.

            You’re welcome. I’m actually glad you brought it up because it reminded me of the concept of the Weismann barrier, which I recall reading about in The Extended Phenotype. I was aware of horizontal gene transfer, but had almost completely forgotten about the immune system business and the RNA. Even if it was indirect and inadvertent, I have to thank you in turn for that.

            However my point is (and I’m sure I don’t even need to ask if you agree) that in neither case is the RNA or DNA aware of the outcome of the processes they’re tied into. By ‘reading’ I of course meant ‘comprehending’ in some way, and by ‘retrospect’ I meant taking into account the ultimate results of the genetic code. It is not a blueprint in that it is not a ‘design’, it’s simply the inevitable outcome of the processes involved in converting the DNA into the proteins that make up a body. Bottom-up.

            Naturally; it’s automatic molecular processes. Lamarkism is nowhere near as plausible a mechanism for adaptative evolution as natural selection is, both because of lack of evidence and because it demands the existence of more mechanisms that themselves have to be adaptive evolutionary traits and that lack evidence in their turn.

          • In reply to #73 by Seraphor:

            In reply to #36 by Jarold:

            “Lenski and his colleagues are now working to identify just what that earlier change was, and how it made the Cit+ mutation possible more than 10,000 generations later.”

            Here Lenski is making reference to an “earlier change” that “made the Cit+ mutation possible”. Theref…

            as per my reply to Frankmill, Zeuglodon. Why do you think that Larckian adaption cannot be another source of variety? I am, after all, of the view that giraffes are making conscious decisions just as humans do… and that sort of assumption is a part of my axiomatic framework. Are you assuming that nonhumans are just instinct-programmed automatons? If you are , then we are back to the “humans are special” school, which I do not subscribe to. Hence the relevance of axioms right there [apologies, skimming quckly here I'm under other time constraints]

          • In reply to #84 by Jarold:

            I don’t know where you’re coming from here… natural selection is the filter that selects for the fittest… mutation is one of the sources of the variety that gets filtered for fitness (transmission/rejection). Other sources of variety include sexual selection, etc.

            Care you explain how sexual selection provides variety without mutation?

            Here I was thinking that sexual selection was another form of selection. Silly me.

            I don’t understand where the confusion lies.

            I think you’re the one who’s confused.

            In reply to #85 by Jarold:

            as per my reply to Frankmill, Zeuglodon. Why do you think that Larckian adaption cannot be another source of variety? I am, after all, of the view that giraffes are making conscious decisions just as humans do… and that sort of assumption is a part of my axiomatic framework. Are you assuming that nonhumans are just instinct-programmed automatons? If you are , then we are back to the “humans are special” school, which I do not subscribe to. Hence the relevance of axioms right there [apologies, skimming quckly here I'm under other time constraints]

            My god man! I overestimated your intelligence by a mile, and that was already pretty narrow margin. Please re-read the post of mine that you replied to, I can’t even dignify this with a response, it would be cruel. I can only hope you misread my post because this misses the mark completely.

  12. In reply to #9 by Red Dog:

    Great question. First, in general, and I haven’t read the article yet, but I’m not keen on the notion that theories need to be “retired”. I think the history of science shows us that it often happens that theories we realized were wrong actually come back in one form or another.

    My reply to petermead1 earlier provides my own stance on what “retired” could be taken to mean, but that aside, I disagree strongly with your claim here. There’s a potentially limitless quantity of ideas that are bound to be incorrect, and only a finite amount of time and space to keep them in. Since science is ultimately about sorting the wheat from the chaff, at some point you have to admit that any empirical claims that haven’t been tested – or that have been tested and have fallen short – are disposable compared with the ones that graduated.

    When Newton defined the theory of gravity it was considered scandalous, an example of “occult” and “mystic” reasoning that the theory posited action at a distance. For gravity to have an effect on something there must be some medium that it travels through and so people postulated the ether, something that existed everywhere in space. Things like gravity were conceived as waves in the ether.

    We no longer need that concept at all and I think you could say it’s been effectively retired but IMO it also keeps coming back. So the Higgs Boson for example, and this may be just because of my amateur understanding of the concepts, but in some ways it seems similar to the ether.

    As far as I’m aware, the aether was invoked to explain how the waves of light reached Earth from the Sun. I think, though my memory might be at fault here, that it was invoked as a reaction to Maxwell’s equations, which showed that light waves could travel independently of a medium, so to “action at a distance” of a sort. However, the Higgs Boson isn’t similar to aether.

    Admittedly, I’m no expert either, but the Higgs boson, as far as I can tell, is an elementary particle invoked as a force-carrier in order to explain how massless particles have mass, with its own suite of properties and interactions. It is not a reactionary explanation for how gravity’s action at a distance was possible, which is still the province of the theories of relativity, as far as I know. Moreover, suggesting that aether was a precursor is as tenuous as saying the first chapter in Genesis is a stunningly precise account of the history of the universe as science understands it; they were arrived at independently, and outright contradict each other at times, so preserving the former would have had no effect on the vindication of the latter.

    Chomsky’s point in this lecture is that the mind-body problem is obsolete, not because he thinks dualism is flawed (i.e., the mind part of the theory is incoherent) but because the notion of a material world required to make the distinction in the first place, the foundation that Descartes was using when he first defined the theory, has been obsolete for a long time. That once people started accepting concepts like action at a distance (and later and even less materialistic quantum entanglement) the notion that physics was just about the material world consisting of smaller and smaller billiard balls bouncing off each other was gone. The material world isn’t really material in any meaningful sense so it’s pointless to worry about the distinction at all.

    Thank you for the link. I have watched the first twenty nine minutes, and at the risk of presumption, I think I’ve seen what he’s getting at.

    Unfortunately, at present I don’t agree with, or perhaps misunderstand, the points he makes or the points you raise, and I’ll explain why. A large part of it rests on the word “material”, which I think is being used in at least two different senses that are being mixed indiscriminately. Certainly, the notion that the universe runs like clockwork (i.e. is deterministic) has been cast into doubt, if not confined to history, by the indeterminacy of quantum mechanics. This was a pretty big discovery in the 20s, given the general attitude of physics nearing completion back then.

    Yet, this has nothing to do with the distinction between mind and body, or between consciousness dualism and monism, since quantum mechanics on that discussion is still technically materialistic. A failure to appreciate this point means Chomsky is, however unwittingly, suggesting that pseudoscientific “quantum consciousness” is vindicated by the history of quantum physics.

    Moreover, Chomsky seems to be treating what is at least a trichotomy (mysticism, classical science, and quantum science) as if it were a dichotomy, as evidenced by his argument that evolution implies “mysterianism”. It would be like treating pessimistic incompatibilism as if it vindicated free will. I agree that the mind-body problem is obsolete, but the argument to get there would involve pointing out that one can manipulate through physical tampering (i.e. with the brain) the experiences of the recipient, and in highly specific ways, which would render the boundary between “subjective” and “objective” events as practically meaningless.

    • In reply to #39 by Zeuglodon:

      There’s a potentially limitless quantity of ideas that are bound to be incorrect, and only a finite amount of time and space to keep them in. Since science is ultimately about sorting the wheat from the chaff, at some point you have to admit that any empirical claims that haven’t been tested – or that have been tested and have fallen short – are disposable compared with the ones that graduated.

      I’m not sure we are really disagreeing, just stating things differently. I just don’t see much of a need to officially “retire” any idea. Let’s forget about the Higgs because my knowledge of physics is so pathetically low. Consider group selection. Most people that I respect in biology don’t like the idea and for excellent reasons. BTW, I recently found a great little paper by Ridley and Dawkins called The Natural Selection of Altruism that really gives a nice overview of why group selection as commonly considered doesn’t work. It’s a question that even smart people still get wrong on comments here and I think this paper is a nice one to point them to. It’s nothing new but it’s really a nice concise summary of both why people thought group selection made sense and why it really doesn’t.

      But there are still people I think are worth reading like Wilson who want to bring group selection back in some form. My point, I’m finally getting to it, gee now who needs an editor, is that we shouldn’t dismiss Wilson by just saying “Sorry EO go back to your termites we’ve retired the idea of group selection” Instead, we listen to their arguments and we dismiss based on that, not because we’ve just ruled group selection to be a retired idea.

  13. In reply to #39 by Zeuglodon:

    As far as I’m aware, the aether was invoked to explain how the waves of light reached Earth from the Sun. I think, though my memory might be at fault here, that it was invoked as a reaction to Maxwell’s equations, which showed that light waves could travel independently of a medium, so to “action at a distance” of a sort. However, the Higgs Boson isn’t similar to aether.

    I don’t think that is correct. Actually, I think this is a very interesting example of how memes, conepts whatever evolve even in our life times. I remember when I was a kid reading one of Asmov’s non fiction books an essay about the aether and it was all about “action at a distance” and how that was such a mysterious concept. I remember for once I was just scratching my head, I couldn’t see what the fuss was. Having been interested since a kid in space and science I just had the idea of gravity already so hard coded into my brain that action at a distance just seemed quite natural.

    But according to Chomsky it wasn’t natural at all to Newton and his contemporaries and that was really the problem the aether was trying to solve — at least originally. It evolved no doubt because if you have a wave (people thought) there has to be a wave of something so aether. But I think originally it was even more basic than needing some medium to carry the wave it was that things don’t just arbitrarily change in the material world. It’s all clocks and billiard balls, things need to physically touch in order to interact and the aether was what enabled that.

    The aether carried light waves but that is because light is one form of EM radiation. The idea was the aether carried all those waves. At least that is my understanding.

  14. Jarold :

    At issue here is the role of mutation fixation to account for higher-level complexities especially in the context of irreducible complexity. How do your referenced studies address the question of irreducible complexity?

    My sense of smell is not too bad. Evolution can explain that, but can Jarold ? Whilst Jarold dodges and weaves, I smell a YEC.

    • In reply to #54 by Mr DArcy:

      Ducking and weaving? Some people seem to be misreading my posts and inferring things that I had never said or implied. So for clarity I’ll state this just once… my objection is not with natural selection but with the unquestioning acceptance of mutation fixation as the source of variety. Assuming said mutation to be a given blinds us to other possibilities that might be taking place at the micro level.

    • In reply to #54 by Mr DArcy:

      My sense of smell is not too bad. Evolution can explain that, but can Jarold ? Whilst Jarold dodges and weaves, I smell a YEC.

      Dodging and weaving? Some people seem to be misreading my posts and inferring things that I had never said or implied. So for clarity I’ll state this just once… my objection is not with natural selection but with the unquestioning acceptance of mutation fixation as the source of variety. Assuming said mutation to be a given blinds us to other possibilities that might be taking place.

      • In reply to #56 by Jarold:

        In reply to #54 by Mr DArcy:

        My sense of smell is not too bad. Evolution can explain that, but can Jarold ? Whilst Jarold dodges and weaves, I smell a YEC.

        Dodging and weaving? Some people seem to be misreading my posts and inferring things that I had never said or implied. So for clarity I’ll sta…

        Then why do you keep bringing in the evolution of the eye, the flagellum, and irreducible complexity? Those are objections to natural selection, not random mutation. Also, “mutation fixation” (it’s called gene fixation or just fixation), which comes about by natural selection or genetic drift, is entirely different from the question of how mutations arise in the first place.

        In fact, the major causes of mutation are pretty well understood, such as copying errors, exposure to radiation, toxins (basically mutagenic chemicals), and even other genes affecting the mutation rates of other genes. They are not blindly assumed, but discoveries from the field of genetics which has set out to answer such questions. Again, Wikipedia is a good starting point.

        • In reply to #58 by Zeuglodon:

          “In fact, the major causes of mutation are pretty well understood, such as copying errors, exposure to radiation, toxins (basically mutagenic chemicals), and even other genes affecting the mutation rates of other genes.”

          I don’t buy it. For the most part, these are assumptions based on the sorts of techniques that are predisposed to self-fulling conclusions… i.e., you find what you are looking for. Glancing down the list just now, I notice that Juju expresses the phenomenon admirably… confirmation bias. The question is… whose confirmation bias wins the day? To settle this, we need to address axioms. Have you established your axiomatic framework? If so, how do you justify your assumptions?

          • In reply to #62 by Jarold:

            I don’t buy it.

            What’s with the unwillingness to looking at links I bring to you? That’s twice now you’ve rejected my offerings out of hand, as if I was presenting a fishy political manifesto rather than just pointing you to basic science.

            For the most part, these are assumptions based on the sorts of techniques that are predisposed to self-fulling conclusions… i.e., you find what you are looking for. Glancing down the list just now, I notice that Juju expresses the phenomenon admirably… confirmation bias. The question is… whose confirmation bias wins the day?

            Far be it from me to think ill of a skeptic, but frankly I’m surprised you apparently know so much about the techniques used in biochemistry to make such a statement, especially considering that it’s been a sitting target for decades, yet no scientists apparently sought to challenge it. How exactly do you get confirmation bias from testing how mutations are caused? What assumptions do you claim to have spotted that means you refuse to accept the findings of genetics?

            To settle this, we need to address axioms. Have you established your axiomatic framework? If so, how do you justify your assumptions?

            I’m frankly puzzled as to your obsession with axioms, which quite frankly are of limited use outside of mathematics and logic (and even then, are subject to scrutiny). Unless they have practical applications in real life (i.e. there is evidence that they work), you’re basically looking for air. It doesn’t matter if you have axioms: the history of science has not been kind to empty assumptions or assumptions that fell to countermanding evidence, so evidence – or the experts who work with it – are what you need to look for and seek out.

            Newton’s “framework”, as you so often refer to it, (if by that you mean classical physics), is as good an example as any. Since its assumptions have long since been disproved, that makes it a compelling example of why hunting for axioms before you believe anything – irrespective of evidence – is a bad idea. Even Newton had to show that his framework matched what was really happening in the solar system, rather than just asserting the axiom and sticking to it regardless. If you’re that interested in mutations, look at the evidence for it and its mechanisms.

            Also, I notice you haven’t responded to a point I made in 58:

            Then why do you keep bringing in the evolution of the eye, the flagellum, and irreducible complexity? Those are objections to natural selection, not random mutation. Also, “mutation fixation” (it’s called gene fixation or just fixation), which comes about by natural selection or genetic drift, is entirely different from the question of how mutations arise in the first place.

            Would you please respond to this? I would be particularly interested in seeing an answer.

            In reply to #71 by The Jersey Devil:

            Kevin Kelly’s contribution to the linked article in the OP is interesting. It’s easy to find, just scroll all the way to the bottom. He suggests retiring “fully random mutations”. He does add a caveat regarding creationists ‘misunderstanding and twisting’ the idea which seams particularly salient.

            True, but this has not gone unnoticed; Jerry Coyne on his blog wrote a criticism of Kelly’s submission, which he states has missed the mark regarding what “random mutations” means and the “motivation” behind it. The summarized version is that Kelly misinterpreted the phrase’s usual meaning in biology, rendering some of his essay unnecessary and casting doubt on the rest.

            In anycase, i want to thank zeuglodon for brining the article to my attention and also for the contributions on this thread. I’m afraid some of the finer technical aspects are out of my reach as i cant make the necessary time commitment to fully study evolution but i do enjoy picking up bits and pieces.

            You’re welcome. Glad to see you’re enjoying the thread, either way.

          • In reply to #74 by Zeuglodon:

            Since its assumptions have long since been disproved

            Where do you get this from? The assumptions of Newtonian physics do not transfer to relativity theory or to quantum theory or within the context of non-Euclidian geometry, that is true. But within the context of the 3D world that we inhabit, with the physics of buildings and cars and so on, Newtonian physics serves us flawlessly.

            Having said this, Newtonian physics need not be abandoned in the context of relativity theory at all. It needs to be refined and relativity theory needs to be factored in.

          • In reply to #74 by Zeuglodon:

            What’s with the unwillingness to looking at links I bring to you? That’s twice now you’ve rejected my offerings out of hand, as if I was presenting a fishy political manifesto rather than just pointing you to basic science.

            For the most part, these are a…

            My reply to FrankMill might clarify more where I’m coming from.

          • In reply to #74 by Zeuglodon:

            “How exactly do you get confirmation bias from testing how mutations are caused?”

            By presuming that the differences you observe are due to mutations and not some other phenomena… e.g., as per the broader context in Kevin Kelly’s contribution that The Jersey Devil pointed us to. When you presume that the differences are due to mutations, you see the differences and you yell out “Eureka! There we have it, evidence of mutation!” Maybe Kelly’s interpretation has been criticized as you suggest, but the issue is much more complex than random mutations as the source of variety, so in that sense, I take Kelly’s side. But I’d suggest that the issue is even deeper than that when you factor in the work of complexity theorists like Eshel Ben Jacob. There is every reason in the world to regard the idea of random mutation fixation as highly suspect.

            “Would you please respond to this? I would be particularly interested in seeing an answer.”
            “Then why do you keep bringing in the evolution of the eye, the flagellum, and irreducible complexity? Those are objections to natural selection, not random mutation.”

            I don’t know where you’re coming from here… natural selection is the filter that selects for the fittest… mutation is one of the sources of the variety that gets filtered for fitness (transmission/rejection). Other sources of variety include sexual selection, etc. I don’t understand where the confusion lies.

          • In reply to #84 by Jarold:

            In reply to #74 by Zeuglodon:
            By presuming that the differences you observe are due to mutations and not some other phenomena… e.g., as per the broader context in Kevin Kelly’s contribution that The Jersey Devil po…

            You even managed to misrepresent Kevin Kelley’s position. Did you even read it?

          • In reply to #86 by The Jersey Devil:

            In reply to #84 by Jarold:

            In reply to #74 by Zeuglodon:
            By presuming that the differences you observe are due to mutations and not some other phenomena… e.g., as per the broader context in Kevin Kelly’s contribution that The Jersey Devil po…

            You even managed to misrepresent Kevin Kelley’s pos…

            What part of “…as per the broader context in Kevin Kelly’s contribution…” do you not understand?

          • In reply to #87 by Jarold:

            What part of “…as per the broader context in Kevin Kelly’s contribution…” do you not understand?

            You quote mined your own self.

            By presuming that the differences you observe are due to mutations and not some other phenomena… e.g., as per the broader >context in Kevin Kelly’s contribution that The Jersey Devil pointed us to.

            There, that’s better. Funny how you left of the part that demonstrated you hadn’t even read Kelley’s article.

            I take Kelly’s side.

            As per the broader context of Jarold’s contribution, you’ve exposed yourself as intellectually dishonest.

            Good day, sir.

          • In reply to #88 by The Jersey Devil:

            In reply to #87 by Jarold:

            What part of “…as per the broader context in Kevin Kelly’s contribution…” do you not understand?

            You quote mined your own self.

            By presuming that the differences you observe are due to mutations and not some other phenomena… e.g., as per the broader >context in Ke…

            What the hell are you going on about? I like your imagination, but you are inferring much from a few lines of casual conversation. What are you smoking? I want some :)

  15. Jarold :

    So for clarity I’ll state this just once… my objection is not with natural selection but with the unquestioning acceptance of mutation fixation as the source of variety. Assuming said mutation to be a given blinds us to other possibilities that might be taking place

    If you have a problem with mutations, how else do you explain how life evolves ? Yes there are environmental and other pressures on a population, but basically those with the “right” genes go on to multiply, whilst those who fail to reproduce die along with their genes. Nature doesn’t care either way. We are the lucky ones.

    • In reply to #57 by Mr DArcy:

      “but basically those with the “right” genes go on to multiply, whilst those who fail to reproduce die along with their genes. Nature doesn’t care either way. We are the lucky ones.”

      THIS is the crux of the problem… the presumption that we are all here as the end point of a progression of happy accidents.

      I mentioned earlier on about the need for axioms… for example, Isaac Newton’s contributions to the physics that rightfully bears his name. What are the axioms that you operate from?

  16. @ Jarold #56

    Assuming said mutation to be a given blinds us to other possibilities that might be taking place.

    What do you mean by “assuming”?, does accepting decades of research and experiments confirming mutations as the driver of natural selection count as “assuming”. What do you mean by “blind”? A lot of other ideas have been looked at and evolution by natural selection acting upon random mutations is the only idea still standing at this point.

    “Other possibilities”

    I’ve seen something like this before and I think its has to do with confirmation bias. The lamarckian view that acquired characteristics of an organism can be passed on to its offspring, and that the environment some how permeates the body and alters the DNA purposely in order for the organism to fit into its environment better all sounds appealing. It almost feels logical, so much so that a confirmation bias is formed.

    Once this bias has taken hold its hard to break from it, kind of like the proponents of the Aquatic Ape Hypotheses. They only see the information which seems to support their view and flat out ignore all the evidence that contradicts it.

    Jarold, have you considered yourself as being in the predicament? It seems like you are ignoring what science already knows.

    Maybe the Dunning Kruger effect, You don’t know enough about it to realize you don’t know enough about it.

    • In reply to #59 by JuJu:

      Thank you JuJu I was looking for the very phrase… see above, my response to Zeuglodon. I repeat the same question to you… have you established your axiomatic framework (to understand what I’m getting at, refer Isaac Newton). What is the equivalent in your biology, to Newton’s three laws of motion and the calculus that verifies its rock-solid foundation? Other than natural selection, there is nothing in your biology that resembles any kind of axiomatic framework or approach.

  17. Okay, let me see. From where I sit right now the earth appears to be flat. So I’m going to build my axiom framework off of that. Now just because you guys have a ton of evidence showing that I’m wrong and that the earth is actually round, well that doesn’t mean I have to acknowledge said evidence. I can just say that I’m coming from a different axiom and my way of thinking is perfectly valid from where I sit. I mean heck, there MUST be a reason it looks flat. Right?

  18. Jarold’s first sentence on this website is a real doozie:

    I think that the neo-Darwinian idea of mutation as the source of variety needs to be tossed with great haste.

    Its just so wrong in so many ways.

    Its like saying:

    The idea of water erosion as the primary reason for seaside cliff formation needs to be tossed out with great haste

    or

    The idea of plate tectonics as the reason for earthquakes and mountain range formation needs to be tossed out.

    I could probably make a long list of similar foolish sentences.

  19. Kevin Kelly’s contribution to the linked article in the OP is interesting. It’s easy to find, just scroll all the way to the bottom. He suggests retiring “fully random mutations”. He does add a caveat regarding creationists ‘misunderstanding and twisting’ the idea which seams particularly salient.

    In anycase, i want to thank zeuglodon for brining the article to my attention and also for the contributions on this thread. I’m afraid some of the finer technical aspects are out of my reach as i cant make the necessary time commitment to fully study evolution but i do enjoy picking up bits and pieces.

  20. Small comment to Jarold (and possibly others) based on things I’ve learned myself from posters on this website. For years I’d read “mutation” as shorthand for “point mutation” (shame on me, as a biologist!). In fact the term technically refers to any changes in DNA sequence, including massive alterations like gene deletion, chromosomal loss and duplication. The scope for phenotypic alterations resulting from all possible types of “mutation” is immense. I mention this in case y9ou too equate “mutation” with “point mutation”.

    Evolution by natural selection over immense periods of time (achieving the same types of changes humans wreak on nature in much shorter time windows) is the axiomatic framework you keep banging on about. It can’t be formulated as the kind of “law” you like in physics; like general and specific relativity it fits the proper definition of a “theory” that perfectly explains the observations. Mutation (in all its forms) really is the mechanism underpinning the phenotypic alterations seen in natural selection, as has been demonstrated experimentally many times over. Now we can easily sequence whole genomes the nature of the mutations associated with phenotypic changes becomes ever clearer. If you don’t buy this stuff you may benefit from broader education in biology, as many others have already pointed out.

    • In reply to #72 by FrankMill:

      It can’t be formulated as the kind of “law” you like in physics

      I say it can.

      Some kind of axiomatic framework is required whenever ideas are to be synthesized into a discipline. Without an axiomatic framework, you finish up with a mishmash of pieces from several jigsaw puzzles that don’t hang together… within the context of each piece, they might make sense, but you finish up with a narrow perspective, and you will be unable to link them all together into a single picture. With an axiomatic framework, however, you finish up with a clearer perspective where all the pieces of the jigsaw mesh into a single picture.

      Humans are a species of animal, yet we have been muddling along for centuries in the misguided belief that humans are “special”. Hence evolved religion, and a very anthropocentric form of psychology. Ah but humans have CULTURE, they used to tell us, so of course humans are special… and then we find more recently that animals also have culture. Ah but humans have LANGUAGE they used to tell us… but as is also being born out, so do many animals (eg, whales, dolphins). And so on (Reddit/Science is always posting the latest trends and publications in science).

      If many animals have culture and language, then what is it that distinguishes humans from animals? Is there room for a single axiomatic framework that addresses common properties? And if there is, then maybe we can begin to work with HOW it is that humans might be different from animals from a more realistic perspective.

      There are many categories of life processes, and without an axiomatic framework, it is only possible to see the categories from within their own levels, instead of seeing how they actually all mesh together… i.e., as specialists. Charles Darwin, at least partially, accomplished the first step of an axiomatic approach when his fellow Englishmen had to grapple with the novel idea that humans were not made in God’s divine image, but rather, descended from apes. Darwin’s partial synthesis removed humans from the sanctified, purified pedestal of wonderfulness that had persisted for centuries.

      Richard Dawkins accomplished a step towards an axiomatic approach in his memetic theory. He was able to step outside the box hamstrung by the genes-as-the-answer-to-everything approach to realize that there is actually a top-down dynamic coming from culture, and he did this by regarding memes as the cultural equivalent of genes. And extending on that approach, today we have the idea of neural plasticity, where these cultural influences actually wire the brain (e.g., Norman Doidge). And now they are even discovering that at least some categories of experience (that wire the brain) can be inherited! For example, the transmission of fear in mice to their offspring:

      http://www.washingtonpost.com/national/health-science/study-finds-that-fear-can-travel-quickly-through-generations-of-mice-dna/2013/12/07/94dc97f2-5e8e-11e3-bc56-c6ca94801fac_story.html

      And so on.

      Can all these disparate ideas be further synthesized into a single axiomatic framework? I would suggest that they can.

      I won’t bore everyone further, but the bottom line is that there is a way of connecting what appears at first to be disparate disciplines, into a single framework that connects biology with culture with mind with genes. Without an axiomatic framework, you finish up with a whole bunch of specialists who are experts on their piece of the jigsaw, and no-one with any sense of how all the different pieces of the jigsaw come together into the big picture.

      Acceptance of the idea that humans are just another form of animal is axiomatic thinking… regarding humans as “divine” is contrary to axiomatic thinking and results in pockets of narrow, bigoted thinking with specialists everywhere peddling the drivel that their view is THE correct view. Start there, and carry it through to all our other subcategories and specializations. An axiomatic approach would serve the life sciences splendidly… just as it has in physics. Of that I have no doubt.

      • In reply to #80 by Jarold:

        In reply to #72 by FrankMill:

        It can’t be formulated as the kind of “law” you like in physics

        I say it can.

        Some kind of axiomatic framework is required whenever ideas are to be synthesized into a discipline. Without an axiomatic framework, you finish up with a mishmash of pieces from several ji…

        The definition of AXIOM

        1. A self-evident or universally recognized truth; a maxim: “It is an economic axiom as old as the hills that goods and services can be paid for only with goods and services” (Albert Jay Nock).
        2. An established rule, principle, or law.
        3. A self-evident principle or one that is accepted as true without proof as the basis for argument; a postulate.

        Jarold. I think you may be searching for a “Truth” that cannot be revealed by the scientific method. You are looking for something you constantly refer to as an “Axiom” or “Axiomatic”. The science has been explained ad infinitum by knowledgeable persons in this blog. You seek something that science can’t deliver. While you won’t admit this to even yourself, you are seeking an universal entity, the golden blueprint, that you think supplies the missing axiom.

        • In reply to #89 by David R Allen:

          In reply to #80 by Jarold:

          In reply to #72 by FrankMill:

          It can’t be formulated as the kind of “law” you like in physics

          I say it can.

          Some kind of axiomatic framework is required whenever ideas are to be synthesized into a discipline. Without an axiomatic framework, you finish up with a mishma…

          Refer to my post in the freshly minted topic The moral issue on religion by Vitor Frota. As you can see, my axiomatic framework provides for a very different perspective, and I don’t expect that we’ll be seeing eye-to-eye anytime soon :)

          • In reply to #91 by Jarold:

            In reply to #89 by David R Allen:

            In reply to #80 by Jarold:

            In reply to #72 by FrankMill:

            It can’t be formulated as the kind of “law” you like in physics

            I say it can.

            Some kind of axiomatic framework is required whenever ideas are to be synthesized into a discipline. Without an axiomatic fra…

            I went over to the new topic and read your article. Try as I might, I find your ideas incomprehensible. Although I clearly understood, and was disturbed by this comment you wrote.

            So… if I live in culture best described as a lumbering, heaving miasma of stoopid (such as what the world has become under feminism and liberalism), I should rightfully be concerned.

          • In reply to #92 by David R Allen:

            In reply to #91 by Jarold:
            I went over to the new topic and read your article. Try as I might, I find your ideas incomprehensible. Although I clearly understood, and was disturbed by this comment you wrote.

            And there you have a clear example of the implications of one’s axiomatic framework on solving problems… when you base your ideas on a different axiomatic framework, you see the world from a different perspective, and you are in a position to provide solutions that were not evident before. Some people can find that disturbing, it can rock their world.

            The axiomatic framework that I operate from is based on the assumption that personality and identity are established not in the genes/DNA at the lower level, but rather, by the culture (or the ecosystem in the case of animals) coming from the upper level – genes/DNA provide for the predispositions, not the blueprint.

            [Removed by moderator - inflammatory and off-topic, and therefore likely to derail the thread.]

            The axiomatic framework that I operate from does not regard culture as merely incidental, but absolutely central to the development of human psychology. That’s why I’d like to see the field of memetics receive more attention than it’s been given.

          • In reply to #94 by Jarold:

            The axiomatic framework that I operate from is based on the assumption that personality and identity are established not in the genes/DNA at the lower level, but rather, by the culture (or the ecosystem in the case of animals) coming from the upper level – genes/DNA provide for the predispositions, not the blueprint.

            The axiomatic framework that I operate from does not regard culture as merely incidental, but absolutely central to the development of human psychology. That’s why I’d like to see the field of memetics receive more attention than it’s been given.

            Is this supposed to be profound? Because I don’t know that anyone would disagree.

          • In reply to #95 by Seraphor:

            In reply to #94 by Jarold:

            Is this supposed to be profound? Because I don’t know that anyone would disagree.

            hahahah you really are desperate to try to catch me out aren’t you?

            The significance of my comment might be better understood had the moderator allowed my real-life example to go through. But I respect the moderator’s decision, so perhaps if we leave it at that.

          • In reply to #96 by Jarold:

            Fair enough, however, are you going to reply to my previous post or are you happy for us to assume you either lack reading comprehension skills or just intelligence in general?

  21. Where is the Axiomatic framework! Axiomatic framework! Axiomatic framework! Axiomatic framework! Axiomatic framework!???

    What is the axiomatic framework for plate tectonics? Germ theory of disease?

    Stop feeding this troll.

    • In reply to #78 by BriRey:

      Where is the Axiomatic framework! Axiomatic framework! Axiomatic framework! Axiomatic framework! Axiomatic framework!???

      What is the axiomatic framework for plate tectonics? Germ theory of disease?

      Stop feeding this troll.

      hahahah! How about you outline your axiomatic framework instead of trying to create a diversion with irrelevent plate techtonics and such. It only shows that you haven’t a clue what you are talking about.

  22. I think Jarod is confused about “axiom.” Poking around I found that another term for axiom is principle or rule of nature. It seems to me this is what Newtons Laws are (he called them axioms). They were not just assumed, but found to be true upon examining evidence. You can’t just make an assumption (about culture vs genes, etc) and go from there (although it may be correct). You have to do experiments, examine evidence, etc to see if your axioms are really the way it is in the world. This is not quite the same as an axiom in mathematics or logic. Science is not deductive but rather inductive. Someone correct me if I’m wrong.

  23. In reply to #96 by Jarold,

    The axiomatic framework that you operate from seems to be further away from the ‘known’ then the frameworks any of the other contributors to this discussion seem to operate from. Maybe you are operating from a axiomatic framework based more around faith rather then fact or have just come to the battle poorly armed.

  24. Economic Growth

    As #6 puts it:

    The theory of capitalism requires unlimited exponential growth forever. You can’t have unlimited exponential growth forever in a closed system. One planet. One set of resources.

  25. One idea, not exactly scientific but espoused by many scientists, that should die is that religion and science do not conflict. If religion and science did not conflict, we would have a science that included gods, demons, angels and the like, and which explored such questions as, under what circumstances is prayer most likely to be effective? That we do not have such a science shows that science and religion do indeed conflict.

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