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The Origin of Specious Nonsense. Twelve years on. Still going. Answer soon.

  • 14-02-2013 9:33pm
    #1
    nagirrac
    Closed Accounts Posts: 2,019 ✭✭✭nagirrac


    Original thread from 2005 here:

    http://www.boards.ie/vbulletin/showthread.php?p=2362555

    icon4.png
    Mod Note
    This is the tail end of the last discussion in "The Origin of Specious Nonsense" thread, which due to it's size now needs to be *retired*. This thread is now the new home for such talk as previously was restricted to the now closed thread above. The post below seemed a good a place as any to make the transition.
    Dades


    Although I came late to it, this is a fascinating thread. I would say every misconception about evolution is contained within its pages, along with lots of sensible and valid argument. I have not read the entire thread but have sampled extensively as it meandered back and forth from the extremes of the "evolution proves there's no God" strong atheist worldview to the "God made everything all at once" creationist position. Both positions are absurd given how little we really know and how much our knowledge evolves over time.

    If nothing else the thread is a caution to resist making too many claims for current science. Evolution as a theory is ongoing science, with complexity far beyond anything Darwin or Dawkins for that matter could have dreamed of. The complexity of evolutionary mechanisms is staggering and as we peel back the onion layers it gets virtually incomprehensible (sound like something familiar? the physical universe for example).

    A shout out to the much maligned Mick Rock who has been entirely consistent as far as I can see on this thread. He has stuck to one basic tenet, that evolution by natural selection of variations that arise from random mutation of genes is far too simplistic to explain evolution of life on earth. I suspect Mick has arrived at this position from logical reasoning and intuition as he has never tried to defend it on a scientific basis.

    Although it may be unpopular to say this, he is most likely correct as modern scientific research is suggesting. Anyone who is actually following the research would be aware of this rather than pandering to Darwinian and neo-Darwinian dogma.

    The most recent research suggests there are four mechanisms involved in evolution:

    1. Genetic or DNA based. This is reasonably well understood although we have a long way to go in terms of understanding how genes are regulated to build a complete organism from a zygote. Clearly any changes in DNA for whatever reason are passed on from generation to generation. However, random changes in DNA appear quite rare in nature, in fact what we are finding is that the genome has highly sophistocated protection mechanisms to protect from mutation.

    2. Epigenetics. Changes in the chemistry within the genome that does not change the DNA sequence but has an impact on how genes are expressed. This is a relatively new field but research is suggesting that these changes that occur during the organisms lifetime may be passed on for multiple generations. This helps to explain rapid evolution in species which has been widely reported in the scientific literature and simply cannot be attributed to chance mutations. Lamarckism arisen from the ashes.

    3. Behavioral (learning). Darwinian evolution does not address how organisms react to their environment, develop traits to respond to it and pass on these traits to their offspring. Anyone who looks at an ant hill will understand this point. The underlying mechanism here is not well understood yet, although it is clearly to do with neurological development.

    4. Language. Perhaps the most interesting of all. This is the basis for group evolution or societal evolution and is likely the primary driver for the rapid evolution of the human brain over the past 10,000 years. Not much idea yet what mechanisms are involved here.

    All four share one common trait, information transmission. It seems absolutely clear that organisms since the beginning of life on earth have adapted to their environments in ways that are inherited by future generations and there is nothing "undirected" or "purposeless" about the overall process. Nature contains complex creativity that we are just beginning to comprehend.


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Comments

  • #2
    expectationlost
    Registered Users Posts: 11,753 ✭✭✭✭expectationlost


    how did the wonders of life thread get mixed in this nonsense :/


  • #3
    robindch
    Moderators, Society & Culture Moderators Posts: 24,396 Mod ✭✭✭✭robindch


    nagirrac wrote: »
    He has stuck to one basic tenet, that evolution by natural selection of variations that arise from random mutation of genes is far too simplistic to explain evolution of life on earth. I suspect Mick has arrived at this position from logical reasoning and intuition as he has never tried to defend it on a scientific basis. Although it may be unpopular to say this, he is most likely correct as modern scientific research is suggesting.
    It's not "unpopular" to say it. It's wrong to say it, as his failure to response to the mountains of evidence presented to him suggests.

    Mick has almost certainly arrived at his position not from logic, but -- as you say -- from intuition: he's simply arguing from personal incredulity.


  • #4
    nagirrac
    Closed Accounts Posts: 2,019 ✭✭✭nagirrac


    robindch wrote: »
    It's not "unpopular" to say it. It's wrong to say it, as his failure to response to the mountains of evidence presented to him suggests.

    Mick has almost certainly arrived at his position not from logic, but -- as you say -- from intuition: he's simply arguing from personal incredulity.

    How do you know he is wrong?

    You are suggesting his is an argument from ignorance. An argument form ignorance is accepting something as truth because it has not been proven false. It is ignoring the fact that there may be other explanations.

    To my knowledge, but maybe I missed it, Mick has not proposed anything explaining evolution. What he has said is he does not accept that Darwin's theory explains evolution.

    Darwin's theory is an wonderful scientific theory and has withstood 1.5 centuries of effort to falsify it. That does not make it truth.


  • #5
    Ziphius
    Registered Users Posts: 714 ✭✭✭Ziphius


    You said "[mickrock] is most likely correct as modern scientific research is suggesting".

    What research suggests that the modern synthesis is incorrect?

    No one has provided any.

    Moreover, no one has given an alternative to the modern synthesis.

    Just vague statements about how complex evolution is and how we really need to include "intelligence".

    It's not necessary, none of your "four mechanisms" contradict the modern darwinism.


  • #6
    Zombrex
    Closed Accounts Posts: 25,848 ✭✭✭✭Zombrex


    nagirrac wrote: »
    How do you know he is wrong?

    Two things

    Firstly Mickrock is not presenting the actual issues with neo-darwinian evolution that all biologists are aware of and are working on. He is not presenting the actual problems with evolution. He is presenting a whole host of non-issues, based on his own ignorance, things that scientists long ago sorted out.

    It would be like someone coming up to you and saying "Well clearly there are a lot of issues with space flight that have to be sorted out before it can be successfully commercialized". You might go "Oh yes, that is very true" and think this person is bringing a good point to the table. But I imagine if the next sentence from this person was "I mean it is ridiculous, the idea that humans might fly in the sky like birds, I just can't see how that would work, God placed humans on the ground and we are not meant to fly", you would probably reconsider.

    Secondly, even if Mickrock was pointing out the actual problems with neo-Darwinian evolution, none of these issues are a reason to abandon evolution as a theory. The evidence for evolution is so over whelming that any holes or mistakes in our idea of how it works at a detailed level must be viewed in that context, the same way that if you find a mistake in your GPS while driving through North Dublin you don't then conclude that Ireland must not exist.


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  • #7
    nagirrac
    Closed Accounts Posts: 2,019 ✭✭✭nagirrac


    Ziphius wrote: »
    You said "[mickrock] is most likely correct as modern scientific research is suggesting".

    What research suggests that the modern synthesis is incorrect?

    No one has provided any.

    Moreover, no one has given an alternative to the modern synthesis.

    Just vague statements about how complex evolution is and how we really need to include "intelligence".

    It's not necessary, none of your "four mechanisms" contradict the modern darwinism.

    The modern synthesis continues to evolve and there are many evolutionary biologists today who would not describe theselves as Darwinists. For example there are many who believe random genetic drift and not natural selection is the primary mechanism of evolution (Larry Moran for example).

    What I am saying is that Darwin's theory tells part of the story of evolution.

    The modern synthesis only considers random mutation of genes over time leading to changes driven by natural selection, and recently has accepted random genetic drift. It does not yet incorporate epigenetics, behavior or language contributions.


  • #8
    nagirrac
    Closed Accounts Posts: 2,019 ✭✭✭nagirrac


    Zombrex wrote: »
    Secondly, even if Mickrock was pointing out the actual problems with neo-Darwinian evolution, none of these issues are a reason to abandon evolution as a theory. The evidence for evolution is so over whelming that any holes or mistakes in our idea of how it works at a detailed level must be viewed in that context, the same way that if you find a mistake in your GPS while driving through North Dublin you don't then conclude that Ireland must not exist.

    You are confusing evolution as a fact with the theory of evolution. Nobody should abandon evolution as a fact.


  • #9
    Ziphius
    Registered Users Posts: 714 ✭✭✭Ziphius


    nagirrac wrote: »
    The modern synthesis continues to evolve and there are many evolutionary biologists today who would not describe theselves as Darwinists. For example there are many who believe random genetic drift and not natural selection is the primary mechanism of evolution (Larry Moran for example).

    What I am saying is that Darwin's theory tells part of the story of evolution.

    The modern synthesis only considers random mutation of genes over time leading to changes driven by natural selection, and recently has accepted random genetic drift. It does not yet incorporate epigenetics, behavior or language contributions.

    No, the modern synthesis states that evolution is explained by selection between competing alleles. Genetic drift is not excluded, though perhaps its role was initially understated. As you said: scientific theories are open to constant revision.

    Epigenetic, behavioural, and linguistic factors can all be considered as aspects of the either the external environment or the phenotypic expression of genes.

    Until there are some major revolutionary discoveries in these fields that indicate an independent evolutionary mechanism (i.e. not selection on genes) there is no need to incorporate it into evolutionary theory. It merely unnecessarily complexifies (and I mean this in the vernacular sense) an elegant and very simple idea.


  • #10
    nagirrac
    Closed Accounts Posts: 2,019 ✭✭✭nagirrac


    Ziphius wrote: »
    No, the modern synthesis states that evolution is explained by selection between competing alleles. Genetic drift is not excluded, though perhaps its role was initially understated. As you said: scientific theories are open to constant revision.

    Epigenetic, behavioural, and linguistic factors can all be considered as aspects of the either the external environment or the phenotypic expression of genes.

    Until there are some major revolutionary discoveries in these fields that indicate an independent evolutionary mechanism (i.e. not selection on genes) there is no need to incorporate it into evolutionary theory. It merely unnecessarily complexifies (and I mean this in the vernacular sense) an elegant and very simple idea.

    I agree (and you clearly know your stuff).

    However, there is a lot of data supporting these other fields and they are making rapid progress. I don't think in terms of independent mechanisms (although I know I suggested that), I think they are all connected and all relate to the genome ultimately.


  • #11
    Zombrex
    Closed Accounts Posts: 25,848 ✭✭✭✭Zombrex


    nagirrac wrote: »
    You are confusing evolution as a fact with the theory of evolution. Nobody should abandon evolution as a fact.

    That is the kind of nonsense Mickrock would say.

    Neo-Darwinian evolution is the only theory of biological evolution that hasn't been dis-proven. We only know biological evolution takes place because we have neo-Darwinian evolution explaining it


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  • #12
    nagirrac
    Closed Accounts Posts: 2,019 ✭✭✭nagirrac


    Zombrex wrote: »
    Neo-Darwinian evolution is the only theory of biological evolution that hasn't been dis-proven. We only know biological evolution takes place because we have neo-Darwinian evolution explaining it

    Sorry if this sounds offensive zombrex but you truly appear to have no idea what the distinction is between a fact and a scientific theory. Facts are a collection of data that lead to firm conclusions, or in the words of Steven J. Gould "confirmed to such an extent that it would be perverse to withhold provisional consent". Scientific theories attempt to explain facts.

    Biological evolution is a fact. If you personally spent enough time observing nature as Darwin did you will be convinced of this fact. The Greeks were aware of evolution 2,000 years before Darwin and there were theories of evolution long before Darwin. The evidence for biological evolution is overwhelming and comes from a wide range of fields of science. Biologists are certain about the fact of evolution, they are less certain about the mechanisms of evolution. No honest biologist would say otherwise.

    A scientific theory tries to explain a fact. As an example gravity is a fact, but we have no consensus scientific theory for gravity as Newton's classical universe, Einsteins theory of relativity, and quantium mechanics have no agreed mechanism for gravity. No scientist has as yet isolated a gravitron to explain the force of gravity.

    The theory of evolution is ongoing science. We do not have a complete picture of the mechanisms involved in evolution because we still do not understand how the genome operates in detail. This data is now just becoming available. When we understand how the genome actually functions in detail we will then likely understand how evolution progressed. Don't be too surprised when this happens if Darwin's mechanism is found to be a minor contributor in the evolution of species.

    There is nothing simple about the genome or how evolution works, it is very elegant but not simple.


  • #13
    BizzyC
    Registered Users Posts: 3,010 ✭✭✭BizzyC


    nagirrac wrote: »
    The theory of evolution is ongoing science. We do not have a complete picture of the mechanisms involved in evolution because we still do not understand how the genome operates in detail. This data is now just becoming available. When we understand how the genome actually functions in detail we will then likely understand how evolution progressed. Don't be too surprised when this happens if Darwin's mechanism is found to be a minor contributor in the evolution of species.

    Yes, but it is also accepted that the theory that provides explanation for observable facts, while making the fewest assumptions, is the most likely explanation.

    The problem with mickrock's argument was that it was solely based on an un-supported personal opinion.
    You've been able to provide some reasoning for other possible theories, which is great, that can be discussed.
    His reasoning was more along the line of "I don't like the idea, so it must be wrong and I have no interest in discussing why"....


  • #14
    nagirrac
    Closed Accounts Posts: 2,019 ✭✭✭nagirrac


    kiffer wrote: »
    While there may be differing hypothesis with regard to what causes variations in genetics it still comes down to natuallly inheritable characteristics, natural selection and time.
    Mickrock's guided/theistic evolution position is not supported at all.
    The idea that mutations are deliberate changes towards some outsider's goal is unsupported... for all intents and purposes, and in every way we can measure, as far as I am aware*, the changes a statistically random.
    *Please if you have data that show otherwise please provide it. Something meaty, not "I read on a website that 5% of biologists think that it's deliberately controlled by some sort of external meddler"...

    It does all come down to inheritance, there's no doubt about that, otherwise we wouldn't be here to talk about it. The question is not related to some outsider's goal, the question is whether evolution is due to random, unguided process or whether evolution is an ongoing creative process that adapts intelligently to its environmemnt. You don't even have to think about God.


  • #15
    Doctor Strange
    Closed Accounts Posts: 965 ✭✭✭Doctor Strange


    nagirrac wrote: »
    It does all come down to inheritance, there's no doubt about that, otherwise we wouldn't be here to talk about it. The question is not related to some outsider's goal, the question is whether evolution is due to random, unguided process or whether evolution is an ongoing creative process that adapts intelligently to its environmemnt. You don't even have to think about God.

    You're right AND wrong here. Evolution is the non-random survival of random mutations/variants. So it doesn't specifically adapt to the environment, but those species that adapt best survive. However, as implied, the mutations/variations are what make it an "unguided" process, as they are spontaneous and random, often useless or harmful, mutations on a single chromosome.


  • #16
    robindch
    Moderators, Society & Culture Moderators Posts: 24,396 Mod ✭✭✭✭robindch


    nagirrac wrote: »
    How do you know he is wrong?
    Because he says that the modern evolutionary synthesis doesn't explain the diversity of life. Now, as above, mickrock certainly doesn't understand how it does and -- from personal incredulity -- he concludes that it can't. But his own lack of understanding of the modern synthesis doesn't mean that it's wrong.
    nagirrac wrote: »
    You are suggesting his is an argument from ignorance. [...] It is ignoring the fact that there may be other explanations.
    Mickrock has been asked time and again for alternate explanations to the modern synthesis and he's provided nothing. In this embarassing-for-him absence, I think it's quite reasonable to assume that the modern synthesis is the best current explanation.


  • #17
    swampgas
    Registered Users Posts: 3,535 ✭✭✭swampgas


    nagirrac wrote: »
    How do you know he is wrong?

    Isn't that a bit like proving a negative?

    Surely it's up to MickRock to prove that he's right?


  • #18
    Zombrex
    Closed Accounts Posts: 25,848 ✭✭✭✭Zombrex


    nagirrac wrote: »
    Sorry if this sounds offensive zombrex but you truly appear to have no idea what the distinction is between a fact and a scientific theory. Facts are a collection of data that lead to firm conclusions, or in the words of Steven J. Gould "confirmed to such an extent that it would be perverse to withhold provisional consent". Scientific theories attempt to explain facts.

    You are confusing "change" with "evolution".

    For centuries humans observed that animals changed from one generation to the next. And for centuries humans supposed that this change might be of an evolutionary variety, ie that this change was not hap hazard or random, that the change followed a slow direction and order imposed on it by some unknown process. Without a process of evolution you cannot say evolution is taking place, only that you have observed change. You cannot comment on the structure of said change without a process that structures it in the evolutionary variety of change.

    It was not until Darwinian evolution that this supposed process behind evolutionary change was identified properly, ie the method was discovered and we could actually say that yes life not only changed, but it evolved.

    Others suggested other methods of evolutionary change, which would also have provided the "fact" that life evolved, but which were proven wrong when examined (Lamarkian evolution for example).

    The fact that animals change is well observed, but we have no evidence that evolution takes place other than Darwinian evolution. It is nonsensical to claim that evolution is a fact but Darwinian evolution is merely the theory to explain that fact. Change is a fact, and Darwinian evolution is both the theory that explains the method of change and the only way we can tell evolution is actually taking place at all.


  • #19
    Zombrex
    Closed Accounts Posts: 25,848 ✭✭✭✭Zombrex


    nagirrac wrote: »
    The question is not related to some outsider's goal, the question is whether evolution is due to random, unguided process or whether evolution is an ongoing creative process that adapts intelligently to its environmemnt.

    WTF are you talking about. Who is that the question for? :mad:

    Define "creative process"

    Define and detail how it "adapts intelligently" to its environment.

    You seem to be just throwing **** at a wall hoping some of sticks. You appreciate I hope that simply saying words that sound vaguely interesting is not science.


  • #20
    Sarky
    Closed Accounts Posts: 31,967 ✭✭✭✭Sarky


    Natural selection and random* genetic mutation covers most of evolution pretty damn well. Anything else is little details, things like figuring out that genes often have promoter regions before the start codon that help transcription enzymes bind to the strand to begin their work, making the start and end of genes a little blurry. There aren't exactly any huge mysteries waiting to be solved by some other mechanism.

    *Not strictly random, subject to several factors including the structure of DNA, the probability of dangerous mutations eliminating themselves, and the tendency of environmental pressures to skew chemistry and physics towards certain directions via heat, pressure, light, presence of solvents etc.


  • #21
    nagirrac
    Closed Accounts Posts: 2,019 ✭✭✭nagirrac


    Zombrex wrote: »
    You are confusing "change" with "evolution".

    It is nonsensical to claim that evolution is a fact but Darwinian evolution is merely the theory to explain that fact. Change is a fact, and Darwinian evolution is both the theory that explains the method of change and the only way we can tell evolution is actually taking place at all.

    Evolution is change, and in the consensus view of evolutionists is due to small random changes in allenes leading to natural selection and speciation over long periods of time.

    Darwin made two huge contributions to science, 1) confirming evolution as a fact (from observing nature to a degree no scientist had done before him), and 2) proposing a broad general mechanism to explain evolution (natural selection).

    "Evolutionists have been very clear about this distinction between fact and theory from the very beginning, if only because we have always acknowleded how far we are from understanding the mechanisms (the theory) by which evolution (the fact) occurred. Darwin continually emphasizied the distinction between his two great and separate acheievements, establishing the fact of evolution and proposing a theory - natural selection - to explain the mechanism of evolution."

    Stephen Jay Gould, "Evolution as fact and theory", 1981.


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  • #22
    nagirrac
    Closed Accounts Posts: 2,019 ✭✭✭nagirrac


    Sarky wrote: »
    Natural selection and random* genetic mutation covers most of evolution pretty damn well.

    There aren't exactly any huge mysteries waiting to be solved by some other mechanism.

    *Not strictly random, subject to several factors including the structure of DNA, the probability of dangerous mutations eliminating themselves, and the tendency of environmental pressures to skew chemistry and physics towards certain directions via heat, pressure, light, presence of solvents etc.


    One of the biggest controversies in evolutionary biology today is the relative importance of natural selection and random genetic drift. Go on Larry Moran's blog "Sandwalk" and read his essay "Evolution by Accident" which argues that evolution is random and makes a strong argument against mutation. While you are there read his essay "Why I am not a Darwinist". As an aside Larry is one of the most vocal critics of ID.

    Why do you think there is a controversy? Its because random mutation leading to natural selection does not explain many aspects of evolution and the more data we uncover the more conclusive this is. I am not saying Darwin's mechanism does not exist, I am saying it is one of several mechanisms.


  • #23
    nagirrac
    Closed Accounts Posts: 2,019 ✭✭✭nagirrac


    swampgas wrote: »
    Isn't that a bit like proving a negative?

    Surely it's up to MickRock to prove that he's right?

    No, the question is whether the theory of evolution is correct. There are four possible answers.

    1. It is true, the mechanism proposed by Darwin completely explains evolution
    2. It is false, other mechanisms are more important and natural selection is a minor mechanism
    3. It is both true and false, there are other mechanisms that are not yet understood but will eventually be understood to complement Darwin's mechanism (this is already the case, random genetic drift).
    4. It is unknowable as we will never understand the mechanisms fully.

    My position is #3. I suspect Mick's position is #4 but will let him speak for himself.


  • #24
    dlofnep
    Closed Accounts Posts: 20,759 ✭✭✭✭dlofnep


    nagirrac wrote: »
    I suspect Mick's position is #4 but will let him speak for himself.

    No, Mick's position is the invisible sky fairy did it. You're giving him too much credit. As for Larry Moran, I figured you were reading his blog as you were pretty much paraphrasing his entire arguments.

    Mick doesn't actually understand what the theory of evolution by natural selection states. He is the type of person who categories groups of animals by 'kind', rather than species and does not understand the implications of doing so. He does not understand what we mean when we use the word species, and as such is in no position to even begin to argue against the merits of evolution by natural selection. He is not arguing against it from a position of knowledge, but rather from a position of ignorance and personal incredulity.


  • #25
    nagirrac
    Closed Accounts Posts: 2,019 ✭✭✭nagirrac


    robindch wrote: »
    Because he says that the modern evolutionary synthesis doesn't explain the diversity of life.

    The modern synthesis represents the best established theory of evolution we have at present. There are many unanswered questions in evolution, genome function, the development of the human brain, etc, that are not yet explained by the modern synthesis. That's what makes science exciting.

    I would say the correct statement is that the modern synthesis partially explains the diversity of life, better than neo-Darwinism did, and better again than Darwin did. It is like peeling the layers of an onion, and each layer is more fascinating in terms of the mechanisms involved.


  • #26
    nagirrac
    Closed Accounts Posts: 2,019 ✭✭✭nagirrac


    dlofnep wrote: »
    No, Mick's position is the invisible sky fairy did it. You're giving him too much credit. As for Larry Moran, I figured you were reading his blog as you were pretty much paraphrasing his entire arguments.

    I read lots of blogs. Although he is an excellent scientist, I am not a fan of Larry Moran as he is very pompous and I am actually enjoying seeing him having his ass handed to him by the ENCODE project results. If random genetic drift were the primary mechanism for evolution, and admittedly there is a great scientific argument to be made that it is, then you would expect DNA to be full of junk. The fact that the data is suggesting that so much of DNA is functional is giving him fits.


  • #27
    darjeeling
    Registered Users Posts: 962 ✭✭✭darjeeling


    nagirrac wrote: »
    I read lots of blogs. Although he is an excellent scientist, I am not a fan of Larry Moran as he is very pompous and I am actually enjoying seeing him having his ass handed to him by the ENCODE project results. If random genetic drift were the primary mechanism for evolution, and admittedly there is a great scientific argument to be made that it is, then you would expect DNA to be full of junk. The fact that the data is suggesting that so much of DNA is functional is giving him fits.

    You keep pushing this line, and it is not true.

    The idea that the human genome contains 'junk' DNA was established in the 1970s, based both on discoveries from early investigations into genomes and on theoretical population genetic modelling. The reasons for thinking that the genome contained DNA that had no role in the functioning of the organism remain valid, and additional reasons and lines of evidence now also support the existence of superfluous DNA. However, it was never the opinion of most (any?) scientists that 'junk' DNA accounted for >98% of the human genome. Media claims that evidence has overturned the idea that almost all of the genome is junk are in fact describing a position that no-one seriously held.

    Evidence for junk DNA - some known in the 1970s, some discovered more recently:
    • 'C-value enigma' - massive variation in genome size observed between animals of similar complexity - even including closely related species. This makes no sense if all of the DNA in every genome is functional.
    • 'Mutational load' - tolerable No. of deleterious mutations / generation. As No. of functional sites increases, so the mutational load increases for a given (and observable) mutation rate. As load levels become high, so the proportion of unviable offspring escalates rapidly, meaning that massive reproduction rates are needed to avoid extinction of the species.
    • 'Selfish genetic elements' - replicating pieces of 'selfish DNA' that (transposons especially) have been found to proliferate throughout the genomes of animals to varying degrees. They provide a mechanism for generating large amounts of non-coding DNA, accounting for the C-value enigma.
    • Conservation of sequence between and within species - gives an indication of selective constraint, and is a proxy for functionality. Around 5% of the human genome is found to be highly conserved when compared with other mammalian species. A further 4% or so is well conserved between humans (1000 genome project data - link).
    • Deletion of large sections of junk has no apparent effect on phenotype - deletion of a 1Mb section of 'junk' DNA in mice led to no observed difference between the deletion mutant and wild-type mice (link). The authors of this work reported larger deletions of 3Mb also having no effect.

    For a good, accessible current view of the arguments, see Sean Eddy's paper from Cell responding to the ENCODE results - link.

    When the idea of junk DNA was first posited in the 1970s, estimates of the proportion of the human genome that was actively required were made. Douglas Comings (one of the people responsible for the concept of 'junk' DNA) in 1972 estimated the active percentage of the genome at 20%, based on arguments such as mutational load and C value paradox (link). Fast forward 40 years, and ENCODE's Ewan Birney says that - guess what - perhaps 20% of the human genome will turn out to be biologically active.

    The 20% activity is clearly larger than the 1.5% of the human genome known to code directly for proteins. Biologists have known for decades that gene activity is regulated by DNA sequences outside the protein coding sequences. This understanding was informed by such work as that of Jacob and Monod in establishing the mechanism of regulation of the lac operon by cis-acting DNA elements outside the protein-coding regions.

    The evolutionary importance of the non-coding but biologically active portion of the genome was noted early on when chimpanzee and human protein sequences were found to be near identical. Scientists reasoned that this meant that many of the differences between chimps and humans had to have their basis outside of protein-coding sequence. Recent sophisticated comparisons of whole genome sequences have borne this out. Comparing the marsupial opossum genome with a spread of placental mammal genomes shows that 95% of the conserved (hence likely functional) differences common to all placentals and arising since the placental/marsupial split are outside of protein-coding sequence. (link). Some can be seen to overlap with known transposons, which is unsurprising given that these represent a major source of mutations. However, at the same time, most transposons are not constrained in this way, hence functional transposons appear to be a small minority, with the rest being essentially 'junk'.

    The ENCODE data, incidentally, do not give us a firm idea of function as none of the experiments assayed directly for functionality, and the definition of funciton (as I have said previously) was one of mere biochemical activity, and not of biological function, let alone necessity.

    Anyone who is familiar with the primary literature on this, and with the history of genetics and genomics should be well aware of the true picture. Unfortunately, the popular media has not done such a good job of informing people.


  • #28
    nagirrac
    Closed Accounts Posts: 2,019 ✭✭✭nagirrac


    Zombrex wrote: »
    WTF are you talking about. Who is that the question for? :mad:

    Define "creative process"

    Define and detail how it "adapts intelligently" to its environment.

    You seem to be just throwing **** at a wall hoping some of sticks. You appreciate I hope that simply saying words that sound vaguely interesting is not science.


    http://www0.cs.ucl.ac.uk/staff/P.Bentley/BEC6.pdf

    The position you take on creativity in nature depends on your worldview. I would describe myself, based on this paper's summary, as a blend of an artist and a scientist.


  • #29
    PopePalpatine
    Registered Users Posts: 11,841 ✭✭✭✭PopePalpatine


    Forgive me for interrupting this fascinating conversation, but I remember when a creationist was interviewed on Moncrieff, who used to be a physicist (before something heavy hit his head, I'd presume) and all he could say in response to various forms of isotope dating was "God speeded up the process". Talk about God of the gaps! :rolleyes:


  • #30
    The Mad Hatter
    Registered Users Posts: 4,718 ✭✭✭The Mad Hatter


    dlofnep wrote: »
    No, Mick's position is the invisible sky fairy did it. You're giving him too much credit.

    In fairness, I don't think it is. Mickrock has, in point of fact, refused to state any position at all, preferring instead to say "but it's obviously not Darwinism, that doesn't make any sense." He has neither stated why he thinks it doesn't make sense, nor what alternative mechanism he thinks is causing evolution. This is why I think he's trolling.


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  • #31
    kiffer
    Registered Users Posts: 2,097 ✭✭✭kiffer


    PopePalpatine wrote: »
    Forgive me for interrupting this fascinating conversation, but I remember when a creationist was interviewed on Moncrieff, who used to be a physicist (before something heavy hit his head, I'd presume) and all he could say in response to various forms of isotope dating was "God speeded up the process". Talk about God of the gaps! :rolleyes:

    Don't get me started on that rapid decay bull... I don't recall if it was in this thread or the one in the other forum but the level of derp around it lead to nosebleed level fruatration. No matter how much you explain why it is the least possible situation and what else it means and why no geologist or physicist would ever think it makes sense... they just go "yeah well Guy-Who-Agrees-With-Me wouldn't lie."
    Then why would he not address the issues that are immediately obvious to anyone with any training in the field?
    "He does... he must..."


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