Apr 04 2013

Vaccines are Gay

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54 responses so far

54 Responses to “Vaccines are Gay”

  1. MikeBon 04 Apr 2013 at 8:30 am

    How dare you sully peanut butter and chocolate! Maybe it’s more like flies and sh*t?

  2. SARAon 04 Apr 2013 at 9:18 am

    I had a friend who embraced all sorts of weirdness. And reading this article reminded me of him.

    He started off learning about vitamins. Which lead to all the predictable quackery associated with massive doses of vitamins. This led to CAM, acupuncture and far east alt meds. This led TM. Which led to an odd conglomeration of all far east philosophy and religions with special emphasis on supernatural miracles. At some point he jumped into conspiracy theories and I never did find the connector to that.

    He became obsessed with reading about all of it and soon he was making all sorts of interconnection between all of them. He would ramble on thinking he was making perfect sense and sounding just like this guy.

    My point is that his thirst for knowledge was profound. But because he had no critical thinking skills, he was ripe for all sorts of quackery. Once he was identified with it, there was no way to talk him out it. The confirmation bias was too strong.

  3. mmarinoon 04 Apr 2013 at 10:05 am

    Hi Steve,
    Actually the term “grillino” means someone who supports Beppe Grillo’s political party “Five stars movement” in Italy. It just happens to also mean “cricket”.
    So the title would be more like: The Grillo’s follower urotherapy proponent that has gone around the world.

  4. locutusbrgon 04 Apr 2013 at 10:49 am

    To follow this to it’s illogical conclusion.
    If I get the MMR booster do I, or my children, become more “Gay”?
    I can see it now, in the US the Gay to straight conversion camps, will have chelation therapy to get out the gay.
    Churches will outlaw mercury thermometers.

    This would be hysterical if he were kidding.

    I think we can use this to an advantage in the Anti-Vax Community. If you are anti-vax you are homophobic. That will short out a few brain circuits in the Hollywood anti-vaxers.

  5. Marshallon 04 Apr 2013 at 11:33 am

    Cell phone usage causes homosexuality!

  6. Murmuron 04 Apr 2013 at 11:51 am

    “You will see how many gays there will be in the next generation, it will be a disaster.”

    How can he claim to not be homophobic and then say more gays is a “disaster”? Is he implying the population will stop increasing at such a rapid rate? Even if this were a bad thing since when does gay mean barren or impotent and without parental desires?

    I know it is a drop in an ocean of idiocy, but that sentence really struck me as ludicrous.

  7. DOYLEon 04 Apr 2013 at 12:29 pm

    Calling this dude a douchebag is an insult to douchebags.

  8. Karl Withakayon 04 Apr 2013 at 12:41 pm

    As side side note about the flu vaccine, I believe at lest one state, Missouri, has a law against administering Thimerosal containing vaccines to children. I’m not sure if it applies only to the Flu vaccine or to vaccines in general. In MO, you have to use the single dose flu vaccine with children.

  9. DavidCTon 04 Apr 2013 at 1:23 pm

    If mercury is such a threat to normal childhood development, where if the outrage over tuna sandwiches? Oh I forgot. It is the magic mix of “toxins” that causes the problem. Unfortunately these cranks have managed to create doubt and that is all they need to cause significant damage.

  10. jreon 04 Apr 2013 at 7:41 pm

    DavidCT’s question got me thinking, so I looked it up.

    For purposes of comparison with the total ethylmercury in the vaccine schedule, one study (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1280342/) used a dosage by weight of 20 mcg/kg, which corresponds to a total dose of 100 mcg for a small infant, or 200 – 300 mcg for a toddler. That matches well with Price et al., (http://pediatrics.aappublications.org/content/early/2010/09/13/peds.2010-0309.full.pdf) who found a mean cumulative dose in their population of about 140 mcg and a max of about 260 mcg. Call it 200 mcg.

    Now, methylmercury levels in fish vary widely (http://www.fda.gov/food/foodsafety/product-specificinformation/seafood/foodbornepathogenscontaminants/methylmercury/ucm115644.htm), but a typical tuna comes in around 0.14 ppm to 0.69 ppm. Call it 0.4 ppm.

    One serving of tuna is 154g (trust me). That gives us about 60 mcg of methylmercury in your typical middle-of-the-road tuna sandwich. Setting aside the difference between ethylmercury and methylmercury, the total mercury load in the entire vaccine schedule appears to be about that of three to four tuna sandwiches.

    Clearly the problem is too much tuna, too soon.

  11. eiskrystalon 05 Apr 2013 at 4:50 am

    “You will see how many gays there will be in the next generation, it will be a disaster.”
    How can he claim to not be homophobic and then say more gays is a “disaster”?

    Probably the same way he can claim that homosexuality is a sign of poor brain development and a disease.

    It’s merely another sign of the crank. The inability to see the huge inconsistencies across the spectrum of their thinking.

  12. Steven Novellaon 05 Apr 2013 at 7:32 am

    Actually infants who are breast fed get more mercury from the breast milk than all the vaccines they will ever get.
    http://www.ncbi.nlm.nih.gov/pubmed/8687245

  13. Murmuron 05 Apr 2013 at 7:43 am

    And that Steven, is proof that God wants us to all be gay.

  14. PharmD28on 05 Apr 2013 at 10:56 am

    “And that Steven, is proof that God wants us to all be gay.”

    LMAO!!

    Oh, Im skeptical about this not having “homophobia” as a motivation.

    The term itself is in part defined by “an irrational aversion to homosexuality”…if there were rational grounds that massive spikes in homosexuality would lead to extinction of the population, then I suppose we could call that perhaps rational…but there is no grounds for such a concern….therefore the whole premise is irrational.

    Therefore, I am having a hard time seeing how the “disaster” as the guy talks about it is anything but irrational…and therefore homophobic by definition.

  15. tmac57on 05 Apr 2013 at 11:36 am

    jre-

    Clearly the problem is too much tuna, too soon.

    Funny,but in reality,there is something to this. The EPA’s 2004 guidelines suggest limiting canned ‘light’ tuna to 12 oz’s per week,and albacore tuna to 6 oz’s per week. A typical small can of tuna is about 4.5 oz’s ,which for me,makes about 2 sandwiches. So I guess you really could get “too much tuna too soon”.

  16. ConspicuousCarlon 05 Apr 2013 at 2:05 pm

    In this post we have both the title and plot for a new South Park episode. Imagine the bikini-man reporter reading the quotes above (“Well Tom, what happens is the vaccine is introduced into the child… “). Also, Stan’s dad is drunk and running around with no pants on while demanding that everyone look at his rubella lesions to confirm that he totally can’t be gay.

  17. daedalus2uon 05 Apr 2013 at 3:26 pm

    There may be physiology behind the idea of urine therapy where it originated, in Tibet. Tibet is at high altitude where it is cold and dry and things don’t grow well. An important nutrient in green leafy vegetables is nitrate. A lack of green leafy vegetables in Tibet may have led them to substitute urine, which also contains nitrate (the terminal metabolite of nitric oxide).

  18. Jake in LAon 07 Apr 2013 at 2:51 pm

    He’s just another wacko. I suppose that if you believe in Lamarckism, it is reasonable to think that “gayness” is an acquired characteristic that can be inherited.

    I just found out about someone else who believes in Lamarckism. This is Dr. Mark Hyman, who seems to have a lot of good ideas about preventing/treating diabetes (he is one of the Dr. Oz supporters).

    In Hyman’s latest book he gives an example where if your grandmother ate too much sugar (and consequently developed diabetes), her DNA would then be modified (apparently by her diabetic condition) and passed down to her children and grandchildren.

    Where do they come from?

  19. BillyJoe7on 07 Apr 2013 at 4:39 pm

    Jake,

    It’s usually from often quite clever people giving opinions which require kowledge outside their area of expertise. Check out James Shapiro, a first rate microbiologist who has presumed to tell evolutionary biologists why they are wrong about “darwinism”, but who simply exposes his lack of knowledge about the subject. He’s been banging on for about two decades now and still wonders why he is not taken seriously by actual evolutionary biologists. He needs to study evolution from the ground up but he is too proud to do so. Meanwhile he is spreading his misunderstandings to the general public via articles at the Huffington Post and has found quite a following. He has got to the stage now where he is not ever going to admit he is wrong.

  20. Davdoodleson 07 Apr 2013 at 10:11 pm

    “homosexuality is a disease, even though the WHO has decided that it is not. Who cares!”

    Who’s on first?
    .

  21. sonicon 08 Apr 2013 at 11:42 am

    Jake in LA-
    You might not have seen these findings–

    http://www.cam.ac.uk/research/news/scientists-discover-how-epigenetic-information-could-be-inherited
    “Scientists have witnessed epigenetic inheritance, the observation that offspring may inherit altered traits due to their parents’ past experiences.”

    http://www.sciencedaily.com/releases/2009/05/090518111723.htm
    “An article forthcoming in the July issue of The Quarterly Review of Biology lists over 100 well-documented cases of epigenetic inheritance between generations of organisms, and suggests that non-DNA inheritance happens much more often than scientists previously thought.”

    I believe ‘gestational diabeties’ can be passed from mother to child as well.
    (Just google the term…)

    Does that answer where they come from?

    BillyJoe7-
    Perhaps I misunderstand Shapiro. It seems he is suggesting that mutations are not random, but occur in rather predictable ways given various stressors.

    As I understand it, the code for the most basic life functions almost never mutates. This implies that mutations are not random with respect to survival. Also, under different conditions the code mutates differently- different parts of the code respond to different stressors.
    Am I right about that?–
    Because if I’m right about that, then I don’t think it makes sense to say mutations are random at all.

    Note: This is a different topic than if mutations are ‘directed’ or not. :-)

    Help me out– I’m not sure why this guy gets so much upset going– I’ve read Coyne- he makes no sense. Even Moran- a guy I can often relate to– I don’t understand what he is saying about this.
    What’s the big deal?

    Perhaps I’m just confused. ;-)

  22. BillyJoe7on 08 Apr 2013 at 4:01 pm

    sonic,

    We’ve had this conversation many times before. If you are still confused I’m not sure there’s much more I can do to help you. For example, you continue to say that mutations are not random despite all the explanations that I and others have given you of why mutations are random and what is actually meant by the word “random”. If you continue to think that “non-random” does not mean “directed”, then you still do not understand what is meant when an evolutionary biologists uses the word “random”. Worse still, you still do not understand what Shapiro means by that word and why he continues to be marginalised when he wanders outside his field of microbiology and presumes to give evolutionary biologist a lesson in their own area of expertise.

  23. sonicon 08 Apr 2013 at 7:31 pm

    BillyJoe7-
    I believe that evolutionary biologists mean ‘random with respect to survival’ when that term is used.
    Can you give me a reference that indicates otherwise?

  24. BillyJoe7on 09 Apr 2013 at 6:14 pm

    I’m going to leave you to explore the numerous old threads where this has been discussed before. But I’ll do you a favour (which I hope you won’t abuse), by leaving you with very short summary to guide your re-exploration of your misunderstanding regarding random mutation…

    Within the constraints that, themselves, have been built up over evolutionary time by random mutation and non-random natural selection, mutation is random in the sense that no particular outcomes are favoured over any other.

    If you disagree with the above statement, then you are necessarily saying, as James Shapiro does, that mutation is directed towards outcomes that favour the organisms survival. There is both no evidence for this and no mechanism by which this could possibly occur. It is pseudoscience, pure and simple.

  25. sonicon 10 Apr 2013 at 11:47 am

    BillyJoe7-
    Thanks for helping me understand this better.

    Perhaps an article like this makes sense to you–
    http://www.nature.com/nature/journal/v485/n7396/full/nature10995.html

    When you say “no outcomes are favored”, or when they say “mutations occur randomly with respect to their value to an organism,” the terms used have no measurable metric associated with it. I don’t know what the organism values- what does an amoeba value? How would I know that the mutation isn’t exactly what the ameba wanted and valued– an interview? :-)

    If I claim that every mutation that has ever occurred in my body was exactly what I desired and brought great value to me, does that statement disprove the theory? Why not? Now I’m being a bit silly, but … :-)

    I think the usual metrics used to measure value are survival and reproduction.

    I believe that mutations are not random with respect to either of those.

    How are we doing so far?

  26. BillyJoe7on 10 Apr 2013 at 3:44 pm

    Sonic,

    Sifting out the jokes from your post, we are left with the following misstatements:

    “I think the usual metrics used to measure value are survival and reproduction.
    I believe that mutations are not random with respect to either of those.”

    Well, let’s just say that it doesn’t matter what you think or believe.
    You also link to an article where the authors – also microbiologist I assume – make the same mistake that James Shapiro makes. I will highlight the part of my statement that they don’t seem to understand and then I will get off your merry-go-round and leave you to it…

    Within the constraints that, themselves, have been built up over evolutionary time by random mutation and non-random natural selection, mutation is random in the sense that no particular outcomes are favoured over any other”

  27. steve12on 10 Apr 2013 at 5:04 pm

    Sonic, what do you think is driving non-random mutation – what mechanism? Don’t feel as though you need to have something definitive – what’s your best guess given what you’ve read?

  28. BillyJoe7on 10 Apr 2013 at 6:13 pm

    Steve,

    I think it’s some sort of cosmic consciousness created somehow via intracellular microtubules to the indeterminacy of quantum physics or something like that. :)

  29. steve12on 10 Apr 2013 at 6:14 pm

    I know…consider morbidly curious!

  30. Aardwarkon 11 Apr 2013 at 5:39 am

    With an apology to Dr Novella for joining a discussion thread that has already gone far off-topic, let me once again try (as I had tried before) to isolate the crucial point of confusion in the above discussion about randomness of mutations.

    When we look whether the mutations are random, do we mean:

    1) That certain mutations have greater probability TO OCCUR, depending on their value (ehm, survival/reproductive fitness value, of course, not the value of being particularly fancied ones in, say, an Amoeban society);

    or

    2) That there is a greater probability TO FIND certain mutations than TO FIND other mutations when we compare an organism’s genome to the genome(s) of its ancestral organism(s).

    Now, Sonic, please do not tell me that you do not see the difference between 1) and 2). It is this difference that accounts for most of your disagreement with BillyJoe7 and others (myself included). You see, proposition 2) is, as you correctly stated, well known and documented to be true. The interpretation is that between the appearance of mutations and the time when we look for them, something filters out some of the mutations and leaves others. That ‘something’ is the process of natural selection – mutations that are too harmful to their host usually do not remain present in the population over generations, as the carriers of such mutations are likely to produce little or no offspring. That is the explanation why you rarely find mutations in essential genes, and very often do in genes whose functions are somewhat redundant. So, it is NOT NECESSARY that the letter be favored AT THE LEVEL OF OCCURRENCE RATE in order to find more of them at some later time. In evolutionary biologists’ jargon, harmful mutations simply get ‘selected out’ in the interval between their appearance and the time we do the genome analysis.

    But can 1) somehow also be true? Well, it is an interesting question. There is a general consensus in evolutionary biology, ever since the early Modern Synthesis, that the answer is no. This does not mean, of course, that every possible mutation has an absolutely equal chance to happen. It merely states that there is no evidence for any mechanism that would select mutations AT OCCURRENCE – i.e. make ‘favorable’ ones happen (or happen more often) and ‘unfavorable’ ones not happen (or happen less often). Long and deep observation of how Nature works, to say the least, failed to find any candidate for such a mechanism or principle. It really appears that all mutations can and do occur – with some probability, admittedly not a constant one, and not necessarily an equal probability among all mutations. But the PROBABILITY OF OCCURRENCE of a mutation does NOT appear to be INFLUENCED by whether it would LATER TURN OUT TO BE ‘good’ or ‘bad’ for its carrier (in the survival/reproduction sense, of course).

    I also wish to emphasize that the above discussion does not apply to epigenetic inheritance. But that is another story (or another part of the ‘big story’), so better left for another time. Apologies to everyone for speaking too long.

  31. ccbowerson 11 Apr 2013 at 10:55 am

    Aardwark-

    The distinction you make is really the crux of the problem here, but unfortunately this issue has been raised many times in the past with apparently no progress. Perhaps there is a problem with some in the conceptual understanding of this distinction, or perhaps it is a strategy to conflate the 2 meanings.

    I don’t think I need to point this out, but example #2 in your comment is not an example of a nonrandom mutation, but is actually result of selection on random mutations. Of course that is very basic and necessary for evolution to work.

    Those who want to say there are nonrandom mutations (in terms of occurrence, which is what is meant by the term) have not shown evidence for, nor proposed a mechanism for such a thing.

  32. sonicon 12 Apr 2013 at 12:02 pm

    Aarwark-
    I understand the difference. But what you bring up is almost completely unrelated to what I’m trying to say—

    Oh my!

    Here is a link to an excellent article about this subject.
    http://quod.lib.umich.edu/p/ptb/6959004.0002.003?rgn=main;view=fulltext
    Evolutionary Chance Mutation: A Defense of the Modern Synthesis’ Consensus View

    After reading this the subject can be discussed properly-
    For example, he tells us why the term ‘random’ is incorrect and attempts to explain what the consensus view is and has been about what is meant by that term.

    He covers and defines the notion of ‘directed’ mutations rigorously- and points out that the current experiments do not show mutations being ‘directed’…

    So much good in this paper– perhaps it is what can be used to further the discussion…

  33. steve12on 12 Apr 2013 at 4:02 pm

    Hi Sonic,

    Read the paper, still a bit confused. Can you summarize? Sometimes that’s helpful before re-reading. Don’t sweat the details – I can get those from the paper.

  34. BillyJoe7on 13 Apr 2013 at 3:00 am

    Sonic,

    Jumping back onto your merry-go-round….

    I’m pretty sure that evolutionary biologists are not going to change their nomenclature just because some fringe dwellers in the microbiological community don’t understand evolution and, as a result, have deluded themselves into thinking that they are spearheading a paradigm shift in an area of expertise outside their own.

    But are you saying that you agree with the referenced article?
    If so, you have either misunderstood what is written there, or misunderstood what has been written on this subject on this blog over the past couple of years, because there is essentially no difference between the two, and you’ve been disagreeing with us from the word go.
    If you do not agree with the article, what exactly do you not agree with?

    And, please, no play on words.
    If you throw a six sided die, not any random number will come up, a random number between one and six will come up. The result is constrained by the characteristics of the system (six sided die), and all systems have constraints built into them, especially biological ones. But it’s still random within those constraints. If we didn’t allow that, the word “random” would lose all meaning. Random doesn’t mean, and never did mean, non-constrained. Random means non-directed (the author’s third definition). It is possible to throw a coin in such a way as to make it come up heads more often. Evolution does not work like that. Mutations are random. Don’t let those confused fringe dwelling microbiologists confuse you.

    …now I’m off the merry-go-round again.

  35. BillyJoe7on 14 Apr 2013 at 9:54 am

    sonic,

    Totally off topic…

    I came across an old friend this afternoon. She has degrees in mathematics and astronomy but has chosen to be an organic gardener. She grows wildflowers and designs and prepares flower arrangements for weddings, funerals, and special occasions. Apparently she has a problem with hydrophobic soil and is looking for an “organic” solution. Do you have any ideas or links to pass on to her.

  36. sonicon 14 Apr 2013 at 10:05 am

    BillyJoe7-
    First the OT-
    I’ve heard that ‘Happy Frog’ is very good bagged soil-
    (I’ll respond to the other in a bit).

  37. sonicon 15 Apr 2013 at 12:22 am

    Steve12-
    This paper covers a number of issues– I will mention one and see if an agreement can be reached.

    One point that is made in the paper is that mutations are not random- at least not in any mathematical or usual sense. The author changes the terminology to ‘evolutionary chance’ mutations to account for the fact that mutations are not random.
    That is what the author does (and why he does it)– right?

    Two issues- 1) is he justified to make the attempt to improve the terminology
    2) is his attempt any good?

    I think he is justified in the attempt-

    BillyJoe7-
    It seems you have some very basic disagreements with the article I linked to.
    Perhaps you should tell me what they are.

  38. Aardwarkon 15 Apr 2013 at 5:03 am

    Sonic,

    I find the article that you linked to very interesting (I admit I have not read it before). I also completely agree with its conclusion.

    Now, in the conclusion, it is clearly stated that the Extended Synthesis fully appreciates the possibility of variable mutation rates across a genome, depending on the ‘mutator’ mechanism(s). Indeed, a ‘loosening’ of DNA repair (resulting in an increased mutation rate) is shown to be, in certain cases at least, an evolutionary strategy (that, as such, itself had to evolve previously, of course) deployed by some microorganisms when resources become scarce. So, the term ‘random mutations’ (at least in the Extended Synthesis) clearly does not imply constant mutation rates. It does not even imply that mutation rates of particular genes must necessarily depend solely on ‘chance’, without a degree of complex input, or even a sort of feedback (though not in a ‘strong’ Lamarckian sense) from many internal and external factors. ‘Random’ means just ‘not determined’ and ‘not directed’.

    However, are you sure that we really need to get rid of the term ‘randomness’ in favor of ‘evolutionary chance’, as the authors of the article propose? After all, under Extended Synthesis, it is already fully appreciated that the term ‘randomness’ of mutations means simply ‘absence of a directional (or intentional) mechanism’ and by no means points to an uniform distribution of probabilities of particular mutations across the genome (or of the consequent phenotypic changes across the morphological space). This ‘less than randomness’ (the formulation I personally prefer) is nowadays usually discussed under the important subfield of ‘evolutionary constraints’ (as BillyJoe7 correctly points out). This is where war currently between ‘contingentists’ and ‘convergentists’ (with a lot of promising and largely unexplored middle ground).

    I agree that we should work on improving our understanding of ‘randomness’ – in my view, one of the most important and least understood concepts in science and human thought. For an exploration of how the concept of ‘randomness’ evolved over time, I sincerely recommend the highly inspired (and very useful) book ‘Drunkard’s Walk’ by Leonard Mlodinow

  39. BillyJoe7on 15 Apr 2013 at 7:01 am

    And so the merry-go-round keeps turning…

    sonic: “It seems you have some very basic disagreements with the article I linked to”

    And yet, in my previous post, I stated quite clearly that the views expressed in that article are identical to those that have been expressed on this blog over the past couple of years – and, in case you misunderstood, that includes my view.
    (As you can see, Aardwark is in agreement with my assessment here)

    As I said, the only part I disagree with is changing the nomenclature (“random” to “evolutionary chance”) – just because a few fringe microbiologists don’t understand evolution. I don’t even see how it would make any difference to them. And “random” is the correct word. You just need to understand “random”. “Random” means “non-directed”. Always has. If it doesn’t mean that, it means nothing.
    (As you can see Aardwark is also in agreement here)

    sonic: “Perhaps you should tell me what they [your disagreements with the article] are”

    Okay, so I have answered this question yet again.
    Round and round the mulberry bush.
    Now, please, do me the courtesy of answering my questions:
    “[A]re you saying that you agree with the referenced article?”
    “If you do not agree with the article, what exactly do you not agree with?”
    No jokes, no flippant remarks, no dismissive one-liners. Just a concise and honest answer. Please.

  40. BillyJoe7on 15 Apr 2013 at 7:04 am

    sonic: “I’ve heard that ‘Happy Frog’ is very good bagged soil”

    Thanks for that, but we don’t seem to have that product down here.
    …and I’m not sure I’m going to win her over with a frog :)

  41. BillyJoe7on 15 Apr 2013 at 6:13 pm

    sonic,

    Let me put it in a nutshell for you…

    Mutations are random
    ….within the constraints built into the system.
    These constraints are built into the system
    …by random mutation and natural selection.

    That’s it!

    No argument about the meaning of “random” is going to change that fact of evolution.
    And that is what this argument is all about – a paradigm shift which ain’t happinin’.

  42. sonicon 15 Apr 2013 at 11:57 pm

    Aardwark-
    Before we get to the conclusion let’s agree on how we get there– OK?

    I suggest the author does not claim mutations are random because
    1) They are not (as exemplified by the Simpson quote)
    and
    2) The formulations that use the word are ‘improper’.

    Examples of point 2) (from the article)

    “Random from the point of view of adaptation and functional integration” (Simpson 1984 [1944], 55-56); “Random with respect to the direction of adaptation” (Stebbins 1966, 35); “A random process with respect to the adaptive needs of the species” (Dobzhansky 1970, 65).

    But the paper is about a situation where the mutations are not random with respect to functional integration or adaptation or the ‘needs’ of the species.
    In other words, every formulation of the theory presented using the word ‘random’ is incorrect in terms of the actual observation- or at least open to improper interpretation. :-)

    Now you claim that “it is fully appreciated that the term ‘randomness’ of mutations means simply ‘absence of a directional (or intentional) mechanism.’”

    Where did you get that? What is the objective measure being used? Doesn’t the experiment show a situation where the mutations are directed to a location on the genome by a mechanism? Is it then the absence of ‘intention’ that makes these ‘random’?
    How does one determine the intention of the genome?

    BillyJoe7-
    Everything is random within the constraints of the system.
    The outcome of a two-headed coin flip is ‘random’ within the constraints– isn’t it?
    The earth’s motion is ‘random’.
    Let’s find other uses of this term that are misleading– shall we?
    And you really should look up ‘begging the question’.

  43. BillyJoe7on 16 Apr 2013 at 12:52 am

    sonic,

    “Everything is random within the constraints of the system”

    Correct.
    Just one more step and you’re there.

    “The outcome of a two-headed coin flip is ‘random’ within the constraints”

    Nope.
    You can make heads come up more often by manipulating the throw.
    We would call that a directed outcome.

    “Let’s find other uses of this term that are misleading”

    Let’s not.
    That’s what the fringe dwellers in the microbiological world are doing – misleading with arguments about the meaning of “random”

    “And you really should look up ‘begging the question’”

    And you should look up step two:
    These constraints are built into the system
    …by random mutation and natural selection.

  44. sonicon 16 Apr 2013 at 1:31 am

    Aardwark-
    Oops– perhaps a bit carried away–

    Anyway—
    What would be better terminology?

    ‘less than random’ isn’t too bad– but why use a word that fits so poorly?
    If one describes what the actual mutations are, then one could try to summarize what those findings are. ‘Random’ would apply to a certain number of mutations– stuff happens :-) — but other mutations are not random, but rather they occur depending on situation and circumstance–

    It does seem there is always some ‘trial and error’ involved in the search for better survival.
    Yes– we can describe mutations as more or less random or more or less directed–

    Trial and error. Yes, the observation is that when the life forms survival is threatened it goes into a mode of ‘trial and error’ in order to survive (the trials more or less stop when the solution is found– or they stop if no solution is found.)
    One can see even the most random of mutations (a point mutation in an area of ‘junk’, perhaps?) as ‘trial and error’ as well.

    Something is very good about that- trial and error- it does fit with each kind of mutation I’m aware of…

    But I think something is very wrong about that too– I’m not sure what at this moment, however.
    Perhaps you can help me out with that– I’m having some difficulty getting a firm grasp on what it is I don’t like about that formulation…

  45. sonicon 16 Apr 2013 at 1:38 am

    BillyJoe7-
    Exactly how do you get more heads to come up on a two-headed coin? :-)

    So the outcome of a two-headed coin is ‘directed’, because it is ‘random’ within the constraints of the system?

    I am aware that everything evolved to be just like it is.

    I’m guessing you are thinking the terminology shouldn’t be changed because you think it is clear and everyone understands it well. :-)

    Or do you have some other reason for not wanting to change it? ;-)

  46. Aardwarkon 16 Apr 2013 at 3:16 am

    Sonic,

    I see your point. It is true that the term ‘random’ may be somewhat misleading, whether we use it to describe the outcome of a die roll or the occurrence of an accidental nucleotide switch in a gene. In both cases it is crucial to have an understanding of what exactly a ‘random’ outcome of a process is – and when we think hard about it, it is a difficult concept, especially when divorced from the ninetieth century Laplacian determinism and wedded to twentieth century concepts, like chaos and non-linear dynamics.

    However, all words, notions and concepts, in science and anywhere, may be misleading, especially if we do not have a consensus about their exact meanings. So, the same risk applies equally to the term ‘non-random’ – it misleads some (much to the dismay of people like BillyJoe7, Ccbowers and myself) to think that saying that an evolutionary process includes ‘non-random’ elements means that it works toward a goal – that it is ‘directed’ in teleological sense.

    But let’s discard for the moment our respective misgivings about the use of words ‘random’ and ‘non-random’ and return to the core of the problem, where, I think, we find ourselves close to being in agreement: how do we perceive evolutionary ‘trial and error’? That is what (in a really nice play of words) the evolutionary theory is itself evolving toward a better understanding of. Evolving, from embryonic concepts of some classical philosophers (Anaxagoras) and the core principles outlined by Darwin and Wallace, through early and late Modern Synthesis, right on to the Extended Modern Synthesis of today and toward a horizon promising perhaps an even more inclusive evolutionary biology of days to come.

    It is only natural that our understanding of evolution also evolves, for the story of evolution is nothing less than the story of life itself.

    Sorry for succumbing to the poetic urge. Back to the core of the discussion: if it is not ‘quite right’ to say that mutations are ‘random’ and (I plea) no more ‘quite right’ to call them simply ‘non-random’, then how best to define the role of chance in the inner workings of the evolutionary process? Just how much ‘random’ (or how little ‘non-random’) is the ‘trial’ part in ‘trial and error’? Is there anything systematic about how Nature performs its ‘trials’? Or (the classical view) the ‘trials’ of Nature are constrained only by the properties of the system and their outcome judged only later – by natural selection?

  47. Aardwarkon 16 Apr 2013 at 3:22 am

    Oops, an erratum in line 4: nineteenth century, of course. Sorry, I’ve been typing in a hurry. Who knows how the Ultra-Extended-Even-More-Modern-Than-Modern-Synthesis of evolutionary theory in 90th century is going to look like… :)

  48. BillyJoe7on 16 Apr 2013 at 6:46 am

    I suggest we go with “The Modern Theory of Evolution”.
    That way the name need never change.

  49. sonicon 16 Apr 2013 at 10:57 am

    Aardwark-
    Yes,the history of evolutionary theory demonstrates the ‘trial and error’ as you so poetically state– and the questions about how nature preforms the trials is of interest.

    I’d suggest that ‘trial and error’ is a good description of how life operates at many levels– and this is why I think it is a good description– because it seems to work all the way from a single celled life form to man’s attempts at animal husbandry.
    We could get rid of the whole ‘artificial vs. natural selection’ mumbo-jumbo that implies man’s activities are not part of nature.

    I agree that ‘trial and error’ seems to have a direction– in this case I think we might agree that it appears that ‘survival’ is the goal of the ‘trial and error search’ for a solution to the problem presented. (As I understand it, the hypermutational state is ended when the survival of the organism is secured).

    So if someone wants to think that because humans operate similarly to amoeba when solving problems is proof of god– or a teleological direction to evolution (other than survival as I suggested)– well, what you gonna do?

    BillyJoe7-
    How about “The New Revised Most Modern Theory of Evolution Ever” ?? :-)

  50. BillyJoe7on 16 Apr 2013 at 3:56 pm

    “I’d suggest that ‘trial and error’ is a good description of how life operates at many levels”.

    Trial and error is a good description.
    But random trial and natural elimination of error is a better description.
    And random mutation and natural selection is the best description.

    “I agree that ‘trial and error’ seems to have a direction”

    And that is exactly the problem.
    Random mutation and natural selection is just about the most beautiful idea ever to come out of science.
    You are not going to kill it with semantics.

  51. sonicon 17 Apr 2013 at 12:46 pm

    Aardwark-
    I’ve considered your questions more throughly-
    I have more questions than answers– perhaps you can help me out with this–

    It seems the trials all have some ‘random’ aspect to them– of course so does ‘natural selection’, by which I mean to say which genome replicates is not completely determined by the make-up of the genome. Correct?

    But we wouldn’t say ‘random selection’ because this would not really represent the whole of selection — all though it would represent any single case. Right?

    It seems that the recent findings indicate that mutations are not random with respect to the ‘needs’ of the organism in general– all though it appears that any one does have a random aspect to it. Right?

    But it seems each replication event could be similarly analyzed.

    How we doing so far?

  52. Aardwarkon 18 Apr 2013 at 8:06 am

    Sonic,

    Well, I’d say we are not doing so bad, actually. We seem to have cleared away much or all of the confusion and pinpointed the issue where we no longer as much disagree as differ in preferences regarding the best terminology and most promising avenues for further analysis.

    Yes, I also feel that there is more to understand about how evolution works – not necessarily contradicting the already known. This is why, in our first discussion, some months ago, I was eager to mention S.J. Gould – not as much because he understood evolution better than others (though he did, at least better than most at the time when he proposed the (r)evolutionary view of ‘punctuated equilibrium’) but because he accepted from the beginning that there may be more to Nature than we have fully grasped so far.

    But I am also aware that the latter may rightly be said for any successful scientific theory or concept and that BillyJoe7 is certainly quite right to point out that the formulation ‘random mutation and natural selection’ still – after a quite turbulent century and a half – stands the test of time. Whatever the future may offer to add to it or to complement it with, I very much doubt that it will ever be subtracted from how we see the world through the eyes of science.

    Sorry, getting poetic again – I’d better go now. We will, time and circumstances permitting, return to the discussion of ‘randomness’/'evolutionary chance’ when specific issues related to this fundamental problem pop up. And they are certain to.

  53. sonicon 18 Apr 2013 at 10:51 am

    Aardwark-
    I agree- we are not doing so badly.
    May any future meetings be so productive.
    Thank-you for your input (and I agree about Gould- he did seem to be wanting to continue to learn more– a trait that is enviable.)

  54. BillyJoe7on 19 Apr 2013 at 8:19 am

    sonic,

    I think that there has been progress.

    On this occasion, you have:
    1) Not linked to articles by microbiologists who see themselves as leaders in a paradigm shift in thinking about evolution.
    2) Not quoted a creationist as an example of your own thinking about evolution.
    3) Linked to an article by an actual “Darwinist”.
    4) Felt your interaction with Aardwark, whose opinions match my own, have been productive.

    But there is a way to go.

    There is no doubt that “random mutation and natural selection” is the algorithm by which complexity evolves from simplicity. The fact that the complexity that evolves via this algorithm acts to constrain “random mutation” that, together with “natural selection”, define the algorithm, in no way serves to negate this fact.

    Compared with this, the argument about the meaning of “random” is mere distraction.

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