Intelligent Design

A Modest Proposal for Academic Freedom Bills

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One endless discussion that always happens with the proposal of academic freedom bills in state legislatures is that the Darwin camp always says that they are about introducing religion into science classrooms. Even if the bill says, “this does not permit anyone to introduce religion into the classrooms,” the pro-Darwin crowd somehow misses this clause, or thinks that judges interpret bills based on the “secret agenda” of those proposing them, rather than the actual language of the bill.

I think a better way of settling this, is to formally define what constitutes legitimate scientific discussion in a science class. I think that there is, at least for biology, a perfectly reasonable reposity of standard information – Pubmed.

Pubmed is run by the NIH, and its purpose is to help the dissemination of information for medicine. Rather than argue tirelessly about what constitutes the introduction of religion into the classroom, why not just punt the definition of science to the NIH, and simply say something like “any paper indexed by Pubmed within the last 20 years should be considered a valid topic of discussion in the sciences.” That way, if someone thinks that these papers are about religion, then someone needs to explain what the NIH is doing indexing papers on religion!

I think this would give the academic freedom movement a more objective means of determining scientific discourse, and would mean that our detractors would have to spell out why they think that the NIH is incapable of distinguishing science from non-science, and why they think that the NIH is indexing papers on religious topics.

I, frankly, would enjoy listening to that conversation.

95 Replies to “A Modest Proposal for Academic Freedom Bills

  1. 1
    Seversky says:

    Personally, I have no objection to religion or ID being discussed in the science classroom. The problems arise when teachers suggest or imply that ID or even the Book of Genesis have a scientific standing which is not the case or even proselytise their own faith to some extent. It may be inadvertent but, to avoid the risk, it is probably best to leave discussions of those topics to another class such as comparative religions or philosophy.

  2. 2
    johnnyb says:

    Seversky –

    I think you missed the point – academic freedom bills generally have NOTHING to do with ID theory. They usually are about being able to teach criticisms of Darwinism, which are replete throughout the scientific literature. Whether or not ID is science (I think it is) I don’t see how anyone can see how the criticisms of Darwinism _found in the scientific literature_ are not science.

  3. 3
    Seversky says:

    “Academic freedom” bills are most commonly associated with religious groups who object to the theory of evolution. Those objections are grounded in the threat that, rightly or wrongly, they believe evolution poses to their faith. The criticisms of the theory itself are either well-known already in biology or ill-founded. That said, science must be prepared to consider any and all scientific criticism from whatever source.

    Not just evolution but all theories in science today, however well-established, have their shortcomings and they are probably better understood by the scientists themselves than by their lay critics. By singling out evolution for special attention, critics undermine their claim to be interested only in academic freedom. They merely reinforces the suspicion that this is just another tactic in the campaign by elements on the religious right to bring science to heel and make it subservient to their beliefs.

    If campaigners for academic freedom are genuinely interested in promoting it then I would hope their bills would include measures to protect science teachers from harassment and intimidation by students, parents and even school administrators for even mentioning evolution in the classroom.

  4. 4
    johnnyb says:

    “Academic freedom” bills are most commonly associated with religious groups who object to the theory of evolution.

    You don’t think that this might be because this is the group being denied academic freedom most often?

    Those objections are grounded in the threat that, rightly or wrongly, they believe evolution poses to their faith.

    So what? The point of a secular state isn’t to exclude religious people from the public sphere, but rather have them give public, secular arguments for their position. If you base the discussion on the personal religious commitments of the adherents, rather than the text of their bills or their public arguments, it is you who are being sectarian.

    The criticisms of the theory itself are either well-known already in biology or ill-founded

    That’s the whole point of the bills! There are a number of criticisms of Darwinism that are well-known within the scientific community. Why is it problematic to give teachers and students the opportunity to discuss those that are well-founded and published in the scientific literature? What paper in pubmed are you afraid of being discussed, and, if so, why do you think that the NIH was mistaken in thinking it was scientific?

    By singling out evolution for special attention, critics undermine their claim to be interested only in academic freedom

    Why? Is the ACLU going after physics teachers who give evidence that a steady-state universe might also be a possibility to the big bang? Are principals firing Earth science teachers who give evidence for an abiotic origin of oil?

    None of these things are happening, at least to my knowledge. But what is happening is that teachers are being denied academic freedom for teaching the problems with Darwinism. That is why it is explicit in the language. Is that so hard to understand?

    If campaigners for academic freedom are genuinely interested in promoting it then I would hope their bills would include measures to protect science teachers from harassment and intimidation by students, parents and even school administrators for even mentioning evolution in the classroom.

    I agree about school administrators, but what do you propose doing about students and parents? Students and parents are always in conflict with teachers for any number of reasons, but as long as that doesn’t put a teacher’s career in jeopardy, I’m not sure how it is part of academic freedom as opposed to simple disagreement.

  5. 5
    Nakashima says:

    Mr JohnnyB,

    It is an interesting proposal. As expressed, it really only covers the biology class. PubMed is not going to help define science for Earth Science or Physics. But fundamentally I think you are erring by assuming that indexing is or has an editorial and quality control step. If PubMed indexes journal X, and journal X publishes an article on astrology, it will be indexed in PubMed. Has astrology thereby become science?

  6. 6
    scordova says:

    the Darwin camp always says that they [freedom proponents] are about introducing religion into science classrooms

    The pro-Darwin camp says that, but even if true that academic freedom fighters have ulterior motives, students still have the right to hear the truth. Whether the freedom fighters have ulterior motives or not is a separate issue.

    The issue is what is right.

    When there was a move to prohibit slavery, many of the freedom proponents were religiously motivated, does that fundamentally negate the fact that freedom was the right thing to have and that is independent of whether the motivation for freedom was religious or secular.

    The same applies here. Student have the right to know the truth. They have the right to know the difference between real science and Darwinism (which is not science, but story telling).

  7. 7
    scordova says:

    By singling out evolution for special attention, critics undermine their claim to be interested only in academic freedom

    I know of no one making that claim that they are ONLY interested in academic freedom.

    And even granting for the sake of argument that there are ulterior motives at work, the students still have the right to be told the truth.

    They have the right to know evolutionary theories are at the bottom of sciences pecking order, far closer to phrenology than to physics. That the ideas are speculative and possibly wrong and based more on storytelling than empirical facts. Students have the right to the truth.

  8. 8
    O'Leary says:

    SCordova at 7, and all: Students have the right to discuss what is on their minds, if education is the point of the exercise.

    You never get anywhere teaching if people are not allowed to voice genuine puzzles or questions or objections.

    For example, if the response to skepticism about Darwinian claims about butterfly evolution is “Most scientists think Darwin was right, and here ends the discussion” – well, so much the worse for most scientists, then.

    Obviously, something non-Darwinian is at work.

    It all comes from having a tax-funded salary, I guess.

  9. 9
    Heinrich says:

    Medical Hypotheses is in PubMed, so this definition would allow all sorts of silly stuff through. I do, though, like the idea of defining physics to not be ‘science’.

    The deeper point is over who gets to decide what counts as “science”. Why should it be an NIH body who’s remit certainly wasn’t to define science? Do you know what criteria they used to decide what to index in PubMed?

  10. 10
    Toronto says:

    O’Leary @8,

    You never get anywhere teaching if people are not allowed to voice genuine puzzles or questions or objections.

    If this is the case, would you be open to presenting evolution in Christian schools and allowing students to decide?

  11. 11
    johnnyb says:

    All –

    The point about Pubmed is that Pubmed is a government agency. Therefore, any establishment clause issue with regards to teaching biology would also be an establishment clause issue with Pubmed. I am assuming that most scientists don’t think that Pubmed is violating the establishment clause, though I could be wrong. If that is so, then maybe that’s the cause of the problem – people in education are reading pubmed on the erroneous assumption that it is science. I would love to see the NCSE argue that one in a legislative session or in court.

    Basically, my ulterior motive would be to get the NCSE to be real – why is it that they think it is wrong to address points that are being discussed in the scientific literature, using a government-developed standard of scientific literature?

  12. 12
    scordova says:

    johnnyb,

    Your proposal is comletely reasonable, but we aren’t dealing with reasonable people. We’re dealing with the likes of PZ Myers and Sam Harris.

    Had we been dealing with reasonable people, there would have been much more academic freedom by now.

    I think the fundamental problem is that the Darwinists will find any excuse to allow liberty and their political arms will resort to unethical means to maintain the status quo. The Darwinian paradigm takes precedence over students rights in their minds.

    They know free inquiry and academic freedom will erode their cultural advantage.

    Darwinian evolution cannot withstand being held to the same scientific standards which other theories (like Electro Dynamics and Quantum Mechanics) are held to.

    I think deep down the Darwinists know this, and even Coyne said as much. But they would rather perpetuate their ideas than let their ideas be subject to proper scientific scepticism.

    For the record, I’m ambivalent about teaching ID in public schools. I support the policy of “exploring evolution” as represented by the book of the same title.

  13. 13
    CannuckianYankee says:

    SCordova,

    “Had we been dealing with reasonable people, there would have been much more academic freedom by now.”

    Of course I agree. What has happened so far with academic freedom legislations, is that the writers of them have gone far out of their way to make the legislation reasonable. That some people object to this legislation, only shows that their motives come from something outside of scientific legitimacy and public interest. I’ve even found the odd atheist/darwinian who supports academic freedom legislation. Clearly some people in that camp can be reasonable, without interjecting the ‘right’ of Darwinism to never be questioned.

    I don’t think the PubMed approach is the right way to go. I think that we ought to stay the course as it stands now. We have made inroads in several states, and the momentum does not appear to be ending soon. People want the truth.

    What is good for science ought to be the prime motivator of anyone involved in this issue. Clearly what is good for science is that science becomes transparent. This means that no theory can withstand scrutiny – not Darwinism, not ID, not quantum mechanics, not global warming – nothing. Everything must be reasonably evaluated, and we teach our students good science by making it so.

  14. 14
    DATCG says:

    JohnnyB,

    You make an eloquent argument. So do others.

    The problem is agenda set by the zealots of Darwinian religion have innoculated their beliefs from any outside critical commentary.

    The ACLU and judicial decisions swung the establishment clause 180 degrees in direction of atheism, a religion today with one a theological pillar being Darwinism. High priest of Darwinism now schedule a special day of resurrection for Darwin celebrated in churches. This is in every sense a religion. No different than Easter or celebrating a Saint.

    The problem today for Darwinist, is how NOT to look like a religion.

    A good team of lawyers might make a case Darwinism has become a cult religion due to recent church events all across America. This according to precedent sets dangerous grounds violationg church and state.

    Therefore, Darwinsm should not be allowed in schools due to Judicial interpretations. They are establishing a religion in our schools daily.

    The only step to take, is open the door back up to all religions.

    Or, allow liberty given us from the Constitution to question the theory, expose faults and problems. And discuss potentials, for and against unguided vs guided evolution.

    It is the best way children learn.

    Koonin expressed in one of his papers that the concept of Darwin’s single TOL is failed as an overall heuristic tool. That the concept might be useful for teaching purposes to children. But I disagree. The truth is useful for teaching children. Not a failed idea no longer contributing to actual scientific education. If there are a forest of trees, then teach it.

    If there are problems and discoveries show them to be valid issues and flaws, then open them to discussion and debate. Dumbing down children until college is silly.
    It dulls minds, retards natural curiosity, especially for highly curious at a young age.

    Intrepidness is to be encouraged, not put off due to orthodoxy.

    The Darwinist are making the same mistakes Creationist made. By attempting to adhere to an untenable orthodoxy, they throw aspersions onto the whole field of study. They make it appear as a closed temple only to an elite and special few. They cloister themselves in pretentious ridicule of doubters to their own folly.

  15. 15
    DATCG says:

    School Choice is another answer.

    Allow tax dollars to follow children to schools chosen by the parents. It opens up competition, holds down cost and allows parents to protect and control how their children matures in a learning environment. One they agree with.

    Creeping centralized control has led to disaster across major cities and millions of children lost in decades of shame.

    Free our children, free their minds from centralized authority.

  16. 16
    DATCG says:

    “By singling out evolution for special attention, critics undermine their claim to be interested only in academic freedom.”

    Darwinian Evolution is the only field that disallows critical thought. Therefore, your claim is invalid.

    “They merely reinforces the suspicion that this is just another tactic in the campaign by elements on the religious right to bring science to heel and make it subservient to their beliefs.”

    No, you are projecting your worst fears into the valid argument made by JohnnyB. This way, you do not have to address the real issue and challenges facing Darwinism.

    This has nothing at all to do with religious beliefs. It has everything to do with academic freedom and the tyranny of a few against the many.

  17. 17
    Joseph says:

    Toronto:

    If this is the case, would you be open to presenting evolution in Christian schools and allowing students to decide?

    The theory of evolution is presented in Christian schools.

  18. 18
    Joseph says:

    Seversky:

    The problems arise when teachers suggest or imply that ID or even the Book of Genesis have a scientific standing…

    ID is based on observations and experiences. It can be objectively tested.

    Seversky’s position, OTOH, is based on nothing but the refusal to allow the design inference at all costs.

    As for Creation well it correctly predicted the universe had a beginning and it correctly predicted reproductive isolation.

    That is two more predictions than Seversky’s position has.

  19. 19
    Nakashima says:

    scordova,

    When there was a move to prohibit slavery, many of the freedom proponents were religiously motivated, does that fundamentally negate the fact that freedom was the right thing to have and that is independent of whether the motivation for freedom was religious or secular.

    Remembering of course that slavery’s proponents also had religious motivations, I am fascinated that someone who is a biblical literalist about creation is so cavalier about slavery. We know slavery is morally bad via something independent of the revealed Word of God?

    I don’t want to derail this thread’s discussion, so let’s just hold that thought until the next “There Exists An Objective Moral Code” thread.

  20. 20
    johnnyb says:

    Nakashima –

    Are you familiar with Biblical rules about slavery? It was basically used as an alternative to jails, was much more humane, and required that the slaves go free after a certain period.

    It wasn’t beautiful, but it wasn’t the same thing as 19th century slavery. 19th century slavery was condemned by Biblical literalists (such as Charles Hodge), who was not against the notion of slavery itself.

    In fact, under OT rules, if you permanently injure a slave (such as knocking out their tooth), they automatically go free. In addition, slaves were automatically freed after 6 years, and when they were freed, the owner had to give them food and clothing to start out with.

    In the NT, you were to treat all slaves as brothers.

    This is a common problem with Biblical interpretation – the word “slave” that we think of is not the same thing as “slave” in that time. It is certainly worthy of discussion whether the Hebrew system was good or bad, just or unjust, necessary or unnecessary, and the like, but it is a category error to make a simple equation of Hebrew slavery with 19th century Western slavery.

  21. 21
    Toronto says:

    johnnyb @20,

    You make a good point about category errors where we try to map our current definition of a term to the way it was defined in a different one.

    The way you describe the slavery of the OT is almost the way chain gangs operated in the early part of the 20th century.

  22. 22
    johnnyb says:

    Toronto –

    Yes, and not only was it used for punishment, it was also used for welfare. The interesting thing about the system is that it allowed for both welfare and punishment in a way that didn’t require the large overhead that ours do. In an entirely agrarian economy, there aren’t a lot of extra resources for jails and welfare checks, and instead, slavery is the way we dealt with it. We wouldn’t have Gitmo, we would have slaves. It is a perfectly legitimate question which way (or even another way) is more just, which is more efficient, and which is more effective. A good argument could be made that the Hebrew system was completely unjust. But it is good to approach the discussion without bringing in our modern categories and circumstances.

  23. 23
    scordova says:

    Remembering of course that slavery’s proponents also had religious motivations, I am fascinated that someone who is a biblical literalist about creation is so cavalier about slavery

    Nakashima-san,

    Are you referring to me as a “biblical literalist”. That’s presumptuous of you since I’ve publicly said I’m not, I’m undecided.

    I don’t think it appropriate to say I’m cavalier about slavery either.

    The issue is not me, my beliefs, or attitudes, but rather the modest proposal for academic freedom.

    I was merely pointing out the issue of students rights should not be derailed with irrelevancies such as the motivations of people involved in promoting bills.

    Even granting that freedom proponents might have ulterior motives, the existence of ulterior motives should not have bearing on whether we liberate students to learn the truth.

    The truth is Darwinian evolution can be critically compared to other theories in other scientific disciplines.

    I have an comparably modest proposal. We don’t need to let the students decide whether Darwinism is true or not. I would encourage them to look at other scientific theories (like say theories of electricity), compare the theoretical arguments and empirical evidences in support of such theories, and then compare them with the theoretical and evidential support (or lack thereof) for Darwinism. They don’t even need to decide if Darwinism is true, they merely are given the learn whether Darwinism is closer to operational science or story telling.

  24. 24
    Nakashima says:

    Mr JohnnyB,

    Yes, I am familiar with the Biblical rules for slavery. What you are referring to in the Hebrew Bible are the rules for how Jews should treat Jewish slaves. Non-Jewish slaves were slaves permanently, and Bible says nothing about the treatment of slaves in other nations. The NT is equally accepting of the institution. Wouldn’t it have been easier to treat fellow Christians as brothers if you freed them? And what of non-Christian slaves?

    I think your hypothesis that Biblical slavery was not like that experienced in pre-Civil War America is wishful thinking. The Mosaic Law might have laid out a relatively compassionate institution, but the Prophets show by their criticisms of Israelite societies that the reality was not like that.

    The last part of your comment is the attitude that I find most interesting when it occurs in one person (and scordova, if this person is not you, I apologize) yom is yom is 24 hours, but ‘ebed, well ‘ebed needs to be interpreted. We “know” slavery is wrong even though the Bible accepts the institution, but the creation story must be taken literally because the Bible is the ultimate authority.

  25. 25
    Nakashima says:

    scordova,

    My apologies for assuming you are a biblical literalist. Your message is a good attempt to recenter the conversation, thank you.

    To the points of your message, the leap from academic freedom in general to Darwinian evolution in particular is the agenda of these bills as clear as can be. And then the slide from Darwinian evolution to Darwinism – is this just casual writing when you know there is a difference but don’t care to be accurate, is it intentional equivocation, or do you think they are one and the same?

    Theories of electricitry would be great choices for comparison with evolution. (Yes, I am purposefully cutting back on your freighted Darwin centric language.) The movement of one electron doesn’t amount to much, add a lot of them up, you get lightning. Not that we have a perfect explanation of lightning in every detail. Similarly, individual genetic variations might not be much, but add them up across time, geography and populations and you get a world of diverse species.

  26. 26
    scordova says:

    Similarly, individual genetic variations might not be much, but add them up across time, geography and populations and you get a world of diverse species

    Individual genetic variation create a diversity of damage on average, not increase in integrated complexity. This has been empirically demonstrated in cobalt bomb labs that tried to accelerate muations. It will also be demonstrated, I predict, as we get more gene sequences.

    The presumption has been that natural selecton will filter out the bad. But there is plenty of empirical evidence to the contrary, and the cobalt bomb labs are a good example.

    Selection didn’t spontaneously arise to help the creatures in the cobalt bomb labs. There is little reason to expect it will spontaneously arise with sufficient efficacy in the wild either. It is a specualtion with no empirical grounding.

    Electrical theories have large amounts of empirical grounding, as evidenced by the fact we are communicating via computers and internet.

    Regarding the original point by johnnyb, I’d argue we don’t even need a special academic freedom bill. Showing the scientific method and contrasting it with Darwinism would be sufficient. Darwinism isn’t science, it is story telling, not empirically verified science like theories of electrodynamics and quantum mechanics.

  27. 27
    bornagain77 says:

    Similarly, individual genetic variations might not be much, but add them up across time, geography and populations and you get a world of diverse species

    A seemingly modest claim that is the basis for the entire Neo-Darwinian framework. Yet a modest claim that has zero empirical support to withstand scrutiny.

    Stephen Meyer – Functional Proteins And Information For Body Plans – video
    http://www.metacafe.com/watch/.....ody_plans/

    Waiting Longer for Two Mutations, Part 5 – Michael Behe
    Excerpt: the appearance of a particular (beneficial) double mutation in humans would have an expected time of appearance of 216 million years,
    http://behe.uncommondescent.co.....ns-part-5/

    The Paradox of the “Ancient” Bacterium Which Contains “Modern” Protein-Coding Genes:
    “Almost without exception, bacteria isolated from ancient material have proven to closely resemble modern bacteria at both morphological and molecular levels.” Heather Maughan*, C. William Birky Jr., Wayne L. Nicholson, William D. Rosenzweig§ and Russell H. Vreeland ;
    http://mbe.oxfordjournals.org/...../19/9/1637

    “Whatever we may try to do within a given species, we soon reach limits which we cannot break through. A wall exists on every side of each species. That wall is the DNA coding, which permits wide variety within it (within the gene pool, or the genotype of a species)-but no exit through that wall. Darwin’s gradualism is bounded by internal constraints, beyond which selection is useless.” R. Milner, Encyclopedia of Evolution (1990)

    “There is no known law of nature, no known process and no known sequence of events which can cause information to originate by itself in matter.” Werner Gitt, “In the Beginning was Information”, 1997, p. 106. (Dr. Gitt was the Director at the German Federal Institute of Physics and Technology) His challenge to scientifically falsify this statement has remained unanswered since first published.

    Random Mutations Destroy Information – Perry Marshall – video
    http://www.metacafe.com/watch/....._marshall/

    Estimation of spontaneous genome-wide mutation rate parameters: whither beneficial mutations? (Thomas Bataillon)
    Abstract……It is argued that, although most if not all mutations detected in mutation accumulation experiments are deleterious, the question of the rate of favourable mutations (and their effects) is still a matter for debate.

    A review of The Edge of Evolution: The Search for the Limits of Darwinism
    The numbers of Plasmodium and HIV in the last 50 years greatly exceeds the total number of mammals since their supposed evolutionary origin (several hundred million years ago), yet little has been achieved by evolution. This suggests that mammals could have “invented” little in their time frame. Behe: ‘Our experience with HIV gives good reason to think that Darwinism doesn’t do much—even with billions of years and all the cells in that world at its disposal’ (p. 155). http://creation.com/review-mic.....-evolution

    etc..etc..etc..

    http://lettherebelight-77.blogspot.com/

  28. 28
    Nakashima says:

    scordova,

    Again, let’s be careful about language sliding from ‘variation’ to ‘mutation’.

    Even so, the point of bringing up a forcing of high levels of mutation is what, exactly? What hypothesis do you think has been falsified? They couldn’t turn an ordinary bacteria into D. radiodurans in a week? You’re not poking evolution with a very sharp stick, here.

    Selection is just differential survival, it doesn’t ‘arise’ or have to be invented. I’d love ot see the scientific description of this cobalt bomb lab experiment, do you have a reference? I’d like to compare it to

    Adaptation of Drosophila melanogaster populations to high mutation pressure: evolutionary adjustment of mutation rates.
    Nöthel H.

    Evolutionary aspects of high mutation pressure were studied in laboratory populations of Drosophila melanogaster that have irradiation histories up to 600 generations. Dose-response regressions for the x-ray induction of various types of mutation were obtained from six of these populations. The sensitivity of these irradiated populations relative to an unirradiated control population was characterized by dose reduction factors. Sensitivity decreased stepwise with the stepwise increase in irradiation levels to which the populations had been exposed every generation (0 R, 2 kR, 4 kR, 8 kR; 1 R = 0.258 mC/kg) but remained the same over hundreds of generations when the irradiation levels were constant. Resistance is controlled by single genetic factors. Additional factors evolved in subpopulations exposed to increased irradiation levels, and different factors evolved in populations that were kept separate from the beginning of their irradiation histories. Two of three factors persisted in subpopulations no longer irradiated, but one factor disappeared; this last one behaved like a transposon. Factors of relative radio-resistance are stage specific (immature oocytes) and some of them are assumed to modify or control mutation-rate genes. The resistance factors enable populations to achieve an equilibrium between the amounts of environmental mutagens and intrinsic mutation rates.

    How should we summarize that experiment? Genetic Entropy was demonstrated when small populations of fruit flies went extinct under high levels of radiation. No, that doesn’t quite capture it, does it? How about – Genetic Entropy went extinct as fruit flies demonstrated evolution under high levels of radiation. I think that is about right.

  29. 29
    Nakashima says:

    Mr BA^77,

    If a random mutation turns AAAAA into AABAA, has information been created or destroyed? If a gene duplication turns ABCDE into ABCDECDE, has information been created or destroyed? If a retrovirus changes ABCDE into ABCDXYZE, has information been created or destroyed?

    Try to answer in your own words. The relevant definition of information is …?

  30. 30
    scordova says:

    Selection is just differential survival, it doesn’t ‘arise’ or have to be invented.

    Diffrential reproductive success exists, but it does not imply it will lead to complexity. It has been shown selection actually works agains the formation of complexity and rube-goldberg type systems (and life is full of such systems)…..

    What doesn’t arise spontaneously are selective pressures that lead to integrated complexity. The only places where it does are in the stories of evolutionists, not in empirical reality.

    I’ve posed the question before: what rate are new protein protein binding sites in all species being created and at what rate are they being lost (exinction events like those int he Amazon rain forest count as binding sites being lost). There are two reasonable answers:

    1. we don’t really know
    2. given the exinction rate, the total number of protein binding sites in existence are being reduced

    Ergo, Darwinism is story telling, not empirical science. I don’t think we even need an academic freedom bill to tell the students the truth. It’s unethical and possibly illegal that the truth is being withheld from students.

  31. 31
    scordova says:

    a perfectly reasonable reposity of standard information – Pubmed.

    One addendum: include also publications of the IEEE, and Chaos Solitons and Fractals (wink, wink).

  32. 32
    scordova says:

    How should we summarize that experiment? Genetic Entropy was demonstrated when small populations of fruit flies went extinct under high levels of radiation. No, that doesn’t quite capture it, does it? How about – Genetic Entropy went extinct as fruit flies demonstrated evolution under high levels of radiation. I think that is about right.

    That would be highly unethical since you are ignoring cases where irradation or outright exinction from even less extreme causes occur. These are invalid generalizations from limited data.

    The data you presented is cherry picked and prejudicial, that’s not science…

    Furthermore, it does not address the fundamental issue of whether things will evolve more complexity, at best they just survive.

  33. 33
    bornagain77 says:

    How to Play the Gene Evolution Game – Casey Luskin – Feb. 2010
    http://www.evolutionnews.org/2.....ution.html

    Jonathan Wells Hits an Evolutionary Nerve:
    “duplicating a gene doesn’t increase information content any more than photocopying a paper increases its information content.”
    http://www.evolutionnews.org/2.....oluti.html

    The Evolution-Lobby’s Useless Definition of Biological Information – Feb. 2010
    Excerpt: By wrongly implying that Shannon information is the only “sense used by information theorists,” the NCSE avoids answering more difficult questions like how the information in biological systems becomes functional, or in its own words, “useful.”,,,Since biology is based upon functional information, Darwin-skeptics are interested in the far more important question of, Does neo-Darwinism explain how new functional biological information arises?
    http://www.evolutionnews.org/2.....ss_de.html

    Mathematically Defining Functional Information In Molecular Biology – Kirk Durston – short video
    http://www.metacafe.com/watch/.....k_durston/

    Functional information and the emergence of bio-complexity:
    Robert M. Hazen, Patrick L. Griffin, James M. Carothers, and Jack W. Szostak:
    Abstract: Complex emergent systems of many interacting components, including complex biological systems, have the potential to perform quantifiable functions. Accordingly, we define ‘functional information,’ I(Ex), as a measure of system complexity. For a given system and function, x (e.g., a folded RNA sequence that binds to GTP), and degree of function, Ex (e.g., the RNA-GTP binding energy), I(Ex)= -log2 [F(Ex)], where F(Ex) is the fraction of all possible configurations of the system that possess a degree of function > Ex. Functional information, which we illustrate with letter sequences, artificial life, and biopolymers, thus represents the probability that an arbitrary configuration of a system will achieve a specific function to a specified degree. In each case we observe evidence for several distinct solutions with different maximum degrees of function, features that lead to steps in plots of information versus degree of functions.

    Could Chance Arrange the Code for (Just) One Gene?
    “our minds cannot grasp such an extremely small probability as that involved in the accidental arranging of even one gene (10^-236).”
    http://www.creationsafaris.com/epoi_c10.htm

    Evolution vs. Functional Proteins – Doug Axe – Video
    http://www.metacafe.com/watch/.....hen_meyer/

  34. 34
    bornagain77 says:

    Severe Limits to Darwinian Evolution: – Michael Behe – Oct. 2009
    Excerpt: The immediate, obvious implication is that the 2009 results render problematic even pretty small changes in structure/function for all proteins — not just the ones he worked on.,,,Thanks to Thornton’s impressive work, we can now see that the limits to Darwinian evolution are more severe than even I had supposed. http://www.evolutionnews.org/2......html#more

    The Capabilities of Chaos and Complexity – David L. Abel – 2009
    Excerpt: “A monstrous ravine runs through presumed objective reality. It is the great divide between physicality and formalism. On the one side of this Grand Canyon lies everything that can be explained by the chance and necessity of physicodynamics. On the other side lies those phenomena than can only be explained by formal choice contingency and decision theory—the ability to choose with intent what aspects of ontological being will be preferred, pursued, selected, rearranged, integrated, organized, preserved, and used. Physical dynamics includes spontaneous non linear phenomena, but not our formal applied-science called “non linear dynamics”(i.e. language,information).
    http://www.mdpi.com/1422-0067/10/1/247/pdf

    i.e. There are no physical or chemical forces between the nucleotides along the linear axis of DNA (where the information is) that causes the sequence of nucleotides to exist as they do. In fact as far as the foundational laws of the universe are concerned the DNA molecule doesn’t even have to exist at all.

    Stephen Meyer is interviewed about the “information problem” in DNA, Signature in the Cell – video
    http://downloads.cbn.com/cbnne.....f?aid=8497

    The DNA Enigma – Where Did The Information Come Frome? – Stephen C. Meyer – video
    http://www.metacafe.com/watch/.....n_c_meyer/

    Stephen C. Meyer – Signature In The Cell:
    “DNA functions like a software program,” “We know from experience that software comes from programmers. Information–whether inscribed in hieroglyphics, written in a book or encoded in a radio signal–always arises from an intelligent source. So the discovery of digital code in DNA provides evidence that the information in DNA also had an intelligent source.”
    http://www.evolutionnews.org/2.....ligen.html

  35. 35
    bornagain77 says:

    The Origin of Biological Information and the Higher Taxonomic Categories – Stephen Meyer”Neo-Darwinism seeks to explain the origin of new information, form, and structure as a result of selection acting on randomly arising variation at a very low level within the biological hierarchy, mainly, within the genetic text. Yet the major morphological innovations depend on a specificity of arrangement at a much higher level of the organizational hierarchy, a level that DNA alone does not determine. Yet if DNA is not wholly responsible for body plan morphogenesis, then DNA sequences can mutate indefinitely, without regard to realistic probabilistic limits, and still not produce a new body plan. Thus, the mechanism of natural selection acting on random mutations in DNA cannot in principle generate novel body plans, including those that first arose in the Cambrian explosion.”
    http://eyedesignbook.com/ch6/eyech6-append-d.html

    Stephen Meyer – Functional Proteins And Information For Body Plans – video
    http://www.metacafe.com/watch/.....ody_plans/

    Fearfully and Wonderfully Made – Glimpses At Human Development In The Womb – video
    http://www.metacafe.com/watch/....._the_womb/

    Darwin’s Theory – Fruit Flies and Morphology – video
    http://www.youtube.com/watch?v=hZJTIwRY0bs

    etc.. etc.. etc…

  36. 36
    Nakashima says:

    scordova,

    These are invalid generalizations from limited data.

    Sez the man who has yet to produce a scientific paper about results from a “cobalt bomb lab” experiment. I gave you a published paper on the exact subject you were blowing smoke about.

  37. 37
    Nakashima says:

    Mr BA^77,

    Yes, now in your own words?

  38. 38
    bornagain77 says:

    What does it matter Nak, whether I quote peer review or cite it directly? You never listen anyway.

  39. 39
    Seversky says:

    johnnyb @ 4
    My apologies about the delay in replying but there are a few quick comments I would like to add.

    “Academic freedom” bills are most commonly associated with religious groups who object to the theory of evolution.

    You don’t think that this might be because this is the group being denied academic freedom most often?

    I might if there was any reason to think it.

    What I see are a lot of outraged claims that academic freedom is being violated. What I don’t see is any evidence. What I see is that concern limited to creationist critics of evolution. When biology teachers are intimidated into not even mentioning evolution in class, we hear not a whimper from all these gallant “academic freedom fighters”.

    The criticisms of the theory itself are either well-known already in biology or ill-founded

    That’s the whole point of the bills! There are a number of criticisms of Darwinism that are well-known within the scientific community. Why is it problematic to give teachers and students the opportunity to discuss those that are well-founded and published in the scientific literature?

    Who says it is problematic? Oh, that’s right, the same “academic freedom fighters” who are choosy about whose freedom to defend. You need to do better then that.

    But what is happening is that teachers are being denied academic freedom for teaching the problems with Darwinism. That is why it is explicit in the language. Is that so hard to understand?

    What is so hard to understand about burden of proof? Just making the same claim over and over again doesn’t cut it. I don’t see any evidence of teachers being denied academic freedom to teach the problems of Darwinism. What I see is at least one prominent case where the teacher in question was disciplined for refusing to teach the subject he was being paid to teach.

    I agree about school administrators, but what do you propose doing about students and parents?

    What I would do is seek the removal of school administrators who fail in their duty to stand by teachers who are just trying to do their job. What I would expect is that school principals will tell parents and students that school premises are not places of immunity from the law. If staff are threatened then the offenders should be told in no uncertain terms that the police will be called and, if warranted, charges brought. It shouldn’t matter what church they go to.

    As for academic freedom, let’s be quite clear, it does not mean unrestricted freedom for teachers and students to say and do whatever they like in class.

    For students, it does not mean they can hold a Bible class in a biology period. They are there to learn the science. They don’t have to believe it but they do have to understand it.

    As for teachers, have no more freedom of action, perhaps less. They required to teach what they are being paid to teach. They are bound by their contract of employment to teach the curriculum prescribed by the appropriate educational authorities. If the fail to do that,regardless of whether it is conflict with their personal religious beliefs, they could be in breach of the terms of their contract.

  40. 40
    Nakashima says:

    scordova,

    The data you presented is cherry picked and prejudicial, that’s not science…

    Strange, published in PNAS, indexed by PubMed, looks like a science paper to me! According to Mr Johnnyb’s operational definition of science good enough for the classrooms of public school America, it’s science.

    Furthermore, it does not address the fundamental issue of whether things will evolve more complexity, at best they just survive.

    AKA, moving the goal posts. You brought up high mutation rates under strong radiation (in what scientific paper was that?) to say something about Genetic Entropy, which would predict a quick death. Fruit flies don’t have to evolve how to foxtrot in order to disprove your point. They just have to survive, survive by the spread of beneficial (What’s that you say, Bunky? Beneficial mutations?) mutations.

  41. 41
    Nakashima says:

    Mr BA^77,

    What does it matter Nak, whether I quote peer review or cite it directly? You never listen anyway.

    Start citing the peer reviewed scientific literature, I might start paying attention.

    What I asked for in your own words was whether information was created in different common scenarios, and what definition of information you used to answer the question. Links to YouTube videos and creationist web sites don’t cut it.

  42. 42
    bornagain77 says:

    Nak, for you to insinuate I have never cited peer review to you is insulting. Please refrain from insulting me any more!

  43. 43
    scordova says:

    Sez the man who has yet to produce a scientific paper about results from a “cobalt bomb lab” experiment. I gave you a published paper on the exact subject you were blowing smoke about.

    So you think I need to cite peer-reviewed papers on the harm that radiation creates on living organisms?

    The research I referred to was in the 1950’s etc. such as this:

    FSHS on Cobalt Bomb Lab

    and this discussion:

    Cobalt and Cesium Irradiation of Plants

    The reasons there aren’t a lot of peer-reviewed articles on the beneficial mutations is that there aren’t practically any (except maybe beneficial to humans who like freak plants!)

    Most modern mutation of plants is done via genetic engineering (aka intelligent design) not random mutation. Genetic engineering methods were developed by the likes of John Sanford.

    Funny isn’t it that in the 1950’s we thought we could accelerate Darwinims by creating more mutations!!!! Then suddenly the sheer absence of excitement of using radiation to improve species. What should be noticeable is the LACK of peer-reviewed articles praising the benefits of random mutation after the era of Cobalt bomb labs!

    By the way, your citation of Drosophilla is totally irrelevant to the question of the evoltution of complexity. This sort of literature puffing isn’t science, it’s equivocation.

    Your citation:

    Factors of relative radio-resistance are stage specific (immature oocytes) and some of them are assumed to modify or control mutation-rate genes

    Has nothting to do with the evolution of integrated complexity. The reason cobalt-bomb labs are not in the forefront of genetic engineering is that intelligent design (genetic engineering) is a superior mechanism to random mutation followed by selection (even intelligent selection).

  44. 44
    Nakashima says:

    Mr BA^77,

    Look back over the links you have posted on this discussion. I’m not insulting you, but you’re not participating very effectively. I asked you a direct question and you are not answering it by linking to videos.

  45. 45
    Nakashima says:

    scordova,

    I’m glad you’re reading the current literature. Googling “cobalt bomb lab” I find the only references are your posts here on UD.

    Be that as it may, have you read this paper? It contains a citation that 1 in 800 mutations is beneficial. This is how you support Genetic Entropy?

    By the way, your citation of Drosophilla is totally irrelevant to the question of the evoltution of complexity.

    But not to the question of whether artifically high mutation rates from radiation is supportive or non-supportive of Genetic Entropy – the issue you raised and would now like to forget.

    This sort of literature puffing isn’t science, it’s equivocation.

    Really? What two terms have I equivocated on? Whose language has slid from Darwinian evolution to Darwinism, from variation to mutation?

  46. 46
    rna says:

    # bornagain @ 34

    ” …i.e. There are no physical or chemical forces between the nucleotides along the linear axis of DNA (where the information is) that causes the sequence of nucleotides to exist as they do. …”

    This is simply wrong. The aromatic bases of the nucleotides stack on top of each other mediated by interactions between the aromatic ring electrons of the bases and the distribution of partial charges around the base. The different chemical nature of the four nucleotides making up DNA leads to differences in the stacking interactions. Stacking between two adenine bases along the horizontal axis of a dna is more favourable then stacking between two C’s. This is very basic biochemistry and I do not understand why you use the above argument so often in discussions.

  47. 47
    scordova says:

    Be that as it may, have you read this paper? It contains a citation that 1 in 800 mutations is beneficial

    “Beneficial” in the Darwinian sense does not mean beneficial in the functional sense. Sickle cell anemia, cystic fybrosis, tay-sachs, etc. etc. are “beneficial”.

    Saying such “benficials” lead to integrated complexity is equivocation, not science. Passing off evolutionary equivocations as science unethical to students wanting to learn science.

    Really? What two terms have I equivocated on?

    I just pointed out the notion of “beneficial” being one of equivocation.

  48. 48
    bornagain77 says:

    rna, since you seem to think there actually is a overriding chemical force/law which determines the specific sequences of nucleotides in DNA, or even a chemical force/law which accounts for the origination of the DNA molecule itself, (A molecule which is a fairly spectacular violation of the second law), and as such can thus be fully brought to bear on the “origin of life” issue, I suggest you write a detailed explanation to Stephen Meyer, as to this natural information generating power you have found for chemistry, and have him make a full public retraction of his argument in “Signature In The Cell” that intelligence is the only known casually adequate explanation for the origination of such digital information we find in the DNA.

    Stephen Meyer describes the intelligent design argument as follows:

    “Premise One: Despite a thorough search, no material causes have been discovered that demonstrate the power to produce large amounts of specified information.
    “Premise Two: Intelligent causes have demonstrated the power to produce large amounts of specified information.
    “Conclusion: Intelligent design constitutes the best, most causally adequate, explanation for the information in the cell.”

    Stephen C. Meyer – The Scientific Basis For The Intelligent Design Argument – video
    http://www.metacafe.com/watch/.....nt_design/

    Stephen Meyer – Functional Proteins And Information For Body Plans – video
    http://www.metacafe.com/watch/.....ody_plans/

    But if you can’t convince Meyer of your profound insight into the information generating power of raw chemistry, which apparently has eluded thousands of chemist/scientists before you, You may be able to convince Dean Kenyon, author of Biological Predestination, to reconvert back to his materialistic ways and retract this statement:

    “We have not the slightest chance for the chemical evolutionary origin of even the simplest of cells”.

    Origin Of Life? – Probability Of Protein And The Information Of DNA – Dean Kenyon – video
    http://www.youtube.com/watch?v=9VhR2BHhxeo

    or maybe if you can’t convince him you can convince Henry Schaefer, who is certainly no slouch as a chemist himself, to retract his position:

    On The Origin Of Life And God – Henry F. Schaefer, III PhD. – video
    http://www.metacafe.com/watch/.....aefer_phd/

    FURTHER NOTE:

    “The problem of the origin of life is clearly basically equivalent to the problem of the origin of biological information.”
    Origin of life theorist Bernd-Olaf Kuppers in his book “Information and the Origin of Life”.

    Biophysicist Hubert Yockey determined that natural selection would have to explore 1.40 x 10^70 different genetic codes to discover the optimal universal genetic code that is found in nature. The maximum amount of time available for it to originate is 6.3 x 10^15 seconds. Natural selection would have to evaluate roughly 10^55 codes per second to find the one that is optimal. Put simply, natural selection lacks the time necessary to find the optimal universal genetic code we find in nature. (Fazale Rana, -The Cell’s Design – 2008 – page 177)

    Ode to the Code – Brian Hayes
    The few variant codes known in protozoa and organelles are thought to be offshoots of the standard code, but there is no evidence that the changes to the codon table offer any adaptive advantage. In fact, Freeland, Knight, Landweber and Hurst found that the variants are inferior or at best equal to the standard code. It seems hard to account for these facts without retreating at least part of the way back to the frozen-accident theory, conceding that the code was subject to change only in a former age of miracles, which we’ll never see again in the modern world.
    https://www.americanscientist.org/issues/pub/ode-to-the-code/4

    Deciphering Design in the Genetic Code
    Excerpt: When researchers calculated the error-minimization capacity of one million randomly generated genetic codes, they discovered that the error-minimization values formed a distribution where the naturally occurring genetic code’s capacity occurred outside the distribution. Researchers estimate the existence of 10 possible genetic codes possessing the same type and degree of redundancy as the universal genetic code. All of these codes fall within the error-minimization distribution. This finding means that of the 10 possible genetic codes, few, if any, have an error-minimization capacity that approaches the code found universally in nature.

    The coding system used for living beings is optimal from an engineering standpoint.
    Werner Gitt, – In The Beginning Was Information – p. 95

    Collective evolution and the genetic code – 2006:
    Excerpt: The genetic code could well be optimized to a greater extent than anything else in biology and yet is generally regarded as the biological element least capable of evolving.

    The Digital Code of DNA – 2003 – Leroy Hood & David Galas
    Excerpt: The discovery of the structure of DNA transformed biology profoundly, catalysing the sequencing of the human genome and engendering a new view of biology as an information science.

  49. 49
    bornagain77 says:

    Nak, as Sal has pointed out, you are disingenuous,

    I directly linked Szostak’s paper for defining functional information and Abel’s paper for the null hypothesis for “functional” information generation. I believe you want to play head games with Shannon’s definition of information:

    yet, when looked at soberly, Shannon’s work actually fully supports the ID position as Perry Marshall clearly points out in this following video:

    DNA and The Genetic Code Pt 3
    http://www.youtube.com/watch?v=FtMQUFOwEFo

  50. 50
    Nakashima says:

    scordova,

    Please stick to the subject. Genetic Entropy, mutation, radiation elevated rates of mutation.

    “Beneficial” in the Darwinian sense does not mean beneficial in the functional sense. Sickle cell anemia, cystic fybrosis, tay-sachs, etc. etc. are “beneficial”.

    Yes, now which sense of beneficial did you just use, Darwinian or functional? What is the distinction?

    Saying such “benficials” lead to integrated complexity is equivocation, not science. Passing off evolutionary equivocations as science unethical to students wanting to learn science.

    Wow, good thing I didn’t say that! You are constantly trying to drag the conversation away from the failure of Genetic Entropy to be demonstrated in an experiment which should have highlighted it clearly. Genetic Entropy is a failed hypothesis for sexual organisms. It fails to explain even a bacteria such as D. radiodurans. Genetic entropy cannot be demonstrated, even Sanford’s own software, beyond small populations of asexual reporduction with no strong signal from the environment for fitness. It just isn’t relevant to explaining the history of a species.

  51. 51
    bornagain77 says:

    further note:
    This following site has a more detailed defense of Marshall’s argument:

    Skeptic’s Objection to Information Theory #1:
    “DNA is Not a Code”
    http://cosmicfingerprints.com/dnanotcode.htm

    of note:

    http://cosmicfingerprints.com/.....hannel.JPG

    Above: Claude Shannon’s communication model (From The Mathematical Theory of Communication, University of Illinois Press, 1998).

    http://cosmicfingerprints.com/dna_isomorphic.JPG

    Above: Hubert Yockey’s DNA communication channel model. Notice that it contains the exact same components as Shannon’s – the two systems are isomorphic. My thesis is that communication systems of this type are always, without exception, products of design. (From Hubert Yockey, Information Theory, Evolution, and the Origin of Life, Cambridge University Press, 2005.)

  52. 52
    bornagain77 says:

    Nak, it really is a shame for you to accuse Sal of obfuscating the issue when in reality it is you. For you to claim Genetic Entropy is refuted would demand a fairly concise methodology! Do you care to know exactly what you must do?

  53. 53
    rna says:

    bornagain @48

    I simply pointed out that the statement “There are no physical or chemical forces between the nucleotides along the linear axis of DNA (where the information is)” is chemically totally wrong.
    Base stacking is a physically and chemically well characterized interaction in many functional nucleic acids structures. It is also experimentally known that stacking forces between different types of nucleotides are different.
    Maybe have a look into Wolfram Saengers ‘principles of nucleic acid structures’ or similar textbooks. These experimental facts have not eluded ‘thousands of chemists’ apart from Dr. Meyer. Instead they have experimentally characterized these forces. If Dr. meyer doesn’t know about these basic facts or even choose to ignore them I am not sure if I can trust his further statements.
    All other links you posted are rather irrelevant to the above.

  54. 54
    bornagain77 says:

    rna, I believe you are being purposely misleading in the fact that I, and the statement, mean the particular sequences of DNA and you mean the basic chemical makeup of the DNA molecule.

    Here is the part of the statement you so “innocently” left out:

    “that causes the sequence of nucleotides to exist as they do”

    Do you want to extrapolate the basic chemical forces that allow single nucleotide bases to exist as they do, along the spine, to a more general theory of “information generation” of sequences? If so then the rest of my references are directly relevant to what you would like to be able to say. As I said before I believe you are being purposely misleading. Why is this rna?

  55. 55
    rna says:

    #54 bornagain

    “Do you want to extrapolate the basic chemical forces that allow single nucleotide bases to exist as they do, along the spine, …”

    stacking forces have nothing to do with the chemical forces, that allow single nucleotide bases to exist as they do. they are interactions between neighbouring nucleotides along the spine. And they differ beween different sequences.

  56. 56
    bornagain77 says:

    rna, are you saying that chemistry is what is driving the information formation of the sequences? If so take it up with Meyer, Kenyon and Schaefer, write up a paper, create life in a test tube, and collect your Nobel prize:

    Stephen C. Meyer – Signature In The Cell:
    “DNA functions like a software program,” “We know from experience that software comes from programmers. Information–whether inscribed in hieroglyphics, written in a book or encoded in a radio signal–always arises from an intelligent source. So the discovery of digital code in DNA provides evidence that the information in DNA also had an intelligent source.”
    http://www.evolutionnews.org/2.....ligen.html

    ; but to dumb ole me, whom you feel so much smarter than, (or do you think your smarter than everybody?) if what you say is true, and I have no reason to doubt you, then it just sounds like another level of “higher order” information, that was purposely encoded onto the DNA in order for the DNA to achieve such dense packing:

    3-D Structure Of Human Genome: Fractal Globule Architecture Packs Two Meters Of DNA Into Each Cell – Oct. 2009
    Excerpt: the information density in the nucleus is trillions of times higher than on a computer chip — while avoiding the knots and tangles that might interfere with the cell’s ability to read its own genome. Moreover, the DNA can easily unfold and refold during gene activation, gene repression, and cell replication. http://www.sciencedaily.com/re.....142957.htm

    and choreography:

    Scientists’ 3-D View of Genes-at-Work Is Paradigm Shift in Genetics – Dec. 2009
    Excerpt: Highly coordinated chromosomal choreography leads genes and the sequences controlling them, which are often positioned huge distances apart on chromosomes, to these ‘hot spots’. Once close together within the same transcription factory, genes get switched on (a process called transcription) at an appropriate level at the right time in a specific cell type. This is the first demonstration that genes encoding proteins with related physiological role visit the same factory.
    http://www.sciencedaily.com/re.....160649.htm

    and to achieve such as this very interesting refutation of so called “junk” dna:

    Shoddy Engineering or Intelligent Design? Case of the Mouse’s Eye – April 2009
    Excerpt: — The (entire) nuclear genome is thus transformed into an optical device that is designed to assist in the capturing of photons. This chromatin-based convex (focusing) lens is so well constructed that it still works when lattices of rod cells are made to be disordered. Normal cell nuclei actually scatter light. — So the next time someone tells you that it “strains credulity” to think that more than a few pieces of “junk DNA” could be functional in the cell – remind them of the rod cell nuclei of the humble mouse.
    http://www.evolutionnews.org/2......html#more

    You know rna, I don’t have any PhD. in chemistry, molecular biology, or whatever, and would probably blow myself up in a lab if left unsupervised, but one thing I do have a PhD in is common sense, and my common sense is telling me that this is fantastically complex and is very easily worthy to be inferred to the Creator of this universe.

  57. 57
    bornagain77 says:

    as a side note rna:

    Did you know that transcendent information is know known to be its own entity separate from matter and energy. Whats more, transcendent information is shown to exercise dominion of matter and energy in quantum teleportation experiments.

    On top of all that the “quantum information wave” will not collapse to its “uncertain” 3-D particle state until a conscious observer is present. So please tell me how is it possible for a 3 dimensional material reality to give rise to the consciousness upon which it is dependent on for its own reality in the first place?

  58. 58
    tgpeeler says:

    bornagain77 – not that rna will believe Yockey (2005) either but your post reminded me of a couple of things he said:

    “The reason that there are principles of biology that cannot be derived from the laws of physics and chemistry lies simply in the fact that the genetic information content of the genome for constructing even the simplest organisms is much larger than the information content of these laws.” Information Theory, Evolution, and the Origin of Life. page 2.

    “One of the properties of the genetic program is that it can supervise its own precise replication and that of other living systems such as organelles, cells, and whole organisms. There is nothing exactly equivalent in nature.” page 5.

    “The belief of mechanist-reductionists that the chemical processes in living matter do not differ in principle from those in dead matter is incorrect. There is no trace of messages determining the results of chemical reactions in inanimate matter. If genetical processes were just complicated biochemistry, the laws of mass action and thermodynamics would govern the placement of amino acids in the protein sequences.” page 5.

    “The genetic information system is the software of life and, like the symbols in a computer, it is purely symbolic and independent of its environment. Of course, the genetic message, when expressed as a sequence of symbols, is nonmaterial but must be recorded in matter or energy.” page 7.

    “The paradox is seldom mentioned that enzymes are required to define or generate the reaction network, and the network is required to synthesize the enzymes and their component amino acids. There is no trace in physics or chemistry of the control of chemical reactions by a sequence of any sort of a code between sequences. Thus, when we make the distinction between the origins of the genetic code and its evolution we find the origin of the genetic code is unknowable.” page 93.

    Well, actually it isn’t unknowable, but the rest of his points are good. 🙂

  59. 59
    bornagain77 says:

    tgpeeler,
    thanks for the quotes, I shall store them away for future reference.

  60. 60
    Upright BiPed says:

    rna,

    “…along the horizontal axis of a dna…”

    It’s the vertical axis of DNA which is in question. There are no physico-chemical forced along the vertical axis of DNA (where the information is) that determines the sequencing of nucleotides.

    If you think there is, then I suggest publishing your data and collecting your Nobel prize.

    BTW, if nucleotide X was determined by chemical regularity to always follow nucleotide Y, then the molecule would be physically unable to hold the amount of data it contains.

    The opposite is observationally evident.

  61. 61
    Nakashima says:

    Mr BiPed,

    BTW, if nucleotide X was determined by chemical regularity to always follow nucleotide Y, then the molecule would be physically unable to hold the amount of data it contains.

    Mr rna was not saying “always follow”, he was saying there was a non-uniform probability distribution based on chemistry. A non-uniform distribution is still quite capable of carrying information. For example, the letters of English have a non-uniform distribution, and q is always followed by u, but English can still carry information quite well.

  62. 62
    Upright BiPed says:

    Hello Nakashima,

    …and then, of course, you agree that a non-uniform probability distribution does not determine DNA sequencing. And then you must also agree that neither chemical affinity nor regularity offers a mechanism to create aperiodic sequencing (which also just happens to specifiy the functional coordination of discreet chemical ensembles).

    And by the way, the u only follows the q because its is a semiotic rule that we’ve placed upon the coding of the English language.

    The chemistry in neither the ink nor the paper requires it.

  63. 63
    rna says:

    #60 Upright BiPed

    sorry, my misspelling: the original quote was about the “linear axis of the dna (where the information is)” which is indeed the vertical axis:

    along this axis there are stacking forces between nucleotide bases next to each other in the sequence. these stacking forces are different between different neighbouring nucleotides and this has been measured.

    Along the horizontal axis, there are hydrogen bonds between nucleotides that hold the two strands of the dna together as you all know. these are also of different strength between different pairs of nucleotides – the reason for the Watson-crick base pairing rules.
    The first data describing the presence and strengths of these forces are maybe 50 years old and have been confirmed many times over since then. so no need for me to publish them again and no nobel prze in waiting.

  64. 64
    bornagain77 says:

    rna,
    thanks for your insight and think there may be something worth learning as to why “subtle” stacking forces exist along the linear axis (i.e. does it tie directly into the dense packing we find in DNA?), but still I feel you are far from solidly making your case as to why the sequences exist as they do chemically, and as such I believe the overall intent of the quote, which you felt was wrong, is none-the-less correct in its meaning.

  65. 65
    Nakashima says:

    Mr BiPed,

    Yes, I think it would be relatively easy for Dr Meyer to update his speaking materials to reflect the reality of DNA connection probabilities. I also agree that these don’t have any serious bearing on the issue of DNA sequences that we se in nature, or that might have first formed during some OOL phase.

    More relevant are the non-uniformly distributed bindings of amino acids to RNA triplets. It seems that some part of the genetic code is driven by pure chemistry.

  66. 66
    Nakashima says:

    Mr BA^77,

    For you to claim Genetic Entropy is refuted would demand a fairly concise methodology! Do you care to know exactly what you must do?

    I would be fascinated to hear what you think such a concise methodology might be. In your own words. Without YouTube links.

    Here’s what I came up with:

    1 – A claim about ALL cases can be disproved with a single counter-example.
    2 – Genetic Entropy is a claim about ALL populations – that they must inevitable go extinct under the burden of accumulating mutations.
    3 – Mutations can be expected to accumulate faster in small populations in a high radiation environment.
    4 – An actual experiment with a small population under high radiation did NOT see the population go extinct or accumulate mutations (except ones that helped the flies cope with high radiation).
    5 – This single counter-example disproves Genetic Entropy. (See 1 and 2 above.)

  67. 67
    bornagain77 says:

    Nak,
    I don’t know where you got your definition of Genetic Entropy from but it is way off base.

    The foundational rule of Genetic Entropy for biology, which can draw its foundation in science from the twin pillars of the Second Law of Thermodynamics and from the Law of Conservation of Information (Dembski, Marks), can be stated something like this:

    “All beneficial adaptations away from a parent species for a sub-species, which increase fitness to a particular environment, will always come at a loss of the optimal functional information that was originally created in the parent species genome.”

    The primary tenet of Genetic Entropy holds that functional information will never increase over what was originally created in the parent species “optimal” genome: i.e. all subspeciation events will come at a loss of the optimal information from the parent species genome.

    “…but Natural Selection reduces genetic information and we know this from all the Genetic Population studies that we have…”
    Maciej Marian Giertych – Population Geneticist – member of the European Parliament – EXPELLED

    It seems you have somehow distorted the second phase of Genetic Entropy, which Dr. Sanford elucidated in his book Genetic Entropy, in that the accumulation of slightly deleterious mutations will eventually lead to genetic meltdown. But as you well know there are highly intricate compensatory mechanisms, error correction mechanisms, and such, which permeate the genome, to guard against “random” mutations. Yet these mechanisms, as far as we can tell are experimentally, are incapable of generating novel functional information and can never reach the optimal information found in the genome of the original parent species.

    as far as falsifying Genetic Entropy, it goes somewhat like this:

    For a broad outline of the “Fitness test”, required to be passed to show a violation of the principle of Genetic Entropy, please see the following video and articles:

    Is Antibiotic Resistance evidence for evolution? – “The Fitness Test” – video
    http://www.metacafe.com/watch/.....ness_test/

    Testing the Biological Fitness of Antibiotic Resistant Bacteria – 2008
    http://www.answersingenesis.or.....-drugstore

    Thank Goodness the NCSE Is Wrong: Fitness Costs Are Important to Evolutionary Microbiology
    Excerpt: it (an antibiotic resistant bacterium) reproduces slower than it did before it was changed. This effect is widely recognized, and is called the fitness cost of antibiotic resistance. It is the existence of these costs and other examples of the limits of evolution that call into question the neo-Darwinian story of macroevolution.
    http://www.evolutionnews.org/2.....s_wro.html

    This “fitness test” fairly conclusively demonstrates “optimal information” was originally encoded within a “parent” bacteria/bacterium by God, and has not been added to by any “teleological” methods in the beneficial adaptations of the sub-species of bacteria. Thus the inference to Genetic Entropy, i.e. that God has not specifically moved within nature in a teleological manner, to gradually increase the functional information of a genome, still holds as true for the principle of Genetic Entropy.

    It seems readily apparent that to conclusively demonstrate God has moved within nature, in a teleological manner, to provide the sub-species bacteria with additional functional information over the “optimal” genome of its parent species, the “fitness test” must be passed by the sub-species against the parent species. If the fitness test is shown to be passed then the new molecular function, which provides the more robust survivability for the sub-species, must be calculated to its additional Functional Information Bits (Fits) it gained in the beneficial adaptation, and then be found to be greater than 140 Fits. 140 Fits is what has now been generously set by Kirk Durston as the maximum limit of Functional Information which can reasonably be expected to be generated by the natural processes of the universe over the entire age of the universe (The actual limit is most likely to be around 40 Fits)(Of note: I have not seen any evidence to suggest that purely material processes can exceed the much more constrained “2 protein-protein binding site” limit, for functional information generation, found by Michael Behe in his book “The Edge Of Evolution”). This fitness test, and calculation, must be done to rigorously establish materialistic processes did not generate the functional information (Fits), and to rigorously establish teleological, within nature, processes were indeed involved in the increase of Functional Complexity of the beneficially adapted sub-species.

    The Universal Plausibility Metric (UPM) & Principle (UPP) – Abel – Dec. 2009
    Excerpt: Mere possibility is not an adequate basis for asserting scientific plausibility. A precisely defined universal bound is needed beyond which the assertion of plausibility, particularly in life-origin models, can be considered operationally falsified. But can something so seemingly relative and subjective as plausibility ever be quantified? Amazingly, the answer is, “Yes.”,,,

    c?u = Universe = 10^13 reactions/sec X 10^17 secs X 10^78 atoms = 10^108

    c?g = Galaxy = 10^13 X 10^17 X 10^66 atoms = 10^96

    c?s = Solar System = 10^13 X 10^17 X 10^55 atoms = 10^85

    c?e = Earth = 10^13 X 10^17 X 10^40 atoms = 10^70

    http://www.tbiomed.com/content/6/1/27

    Mathematically Defining Functional Information In Molecular Biology – Kirk Durston – short video
    http://www.metacafe.com/watch/.....k_durston/

    Evolution vs. Genetic Entropy – video
    http://www.metacafe.com/watch/.....c_entropy/

    more references here:
    http://lettherebelight-77.blogspot.com/

  68. 68
    Toronto says:

    “All beneficial adaptations away from a parent species for a sub-species, which increase fitness to a particular environment, will always come at a loss of the optimal functional information that was originally created in the parent species genome.”

    1)Could you point me to any studies that support this?

    2)I don’t see how you can use the term Genetic Entropy in a ID/Evo debate if that definition includes the assertion that Intelligent Design was responsible for the parent species genome.

    …information that was originally created in the parent species genome.”

  69. 69
    Upright BiPed says:

    Nak,

    Yes, I think it would be relatively easy for Dr Meyer to update his speaking materials to reflect the reality of DNA connection probabilities.

    My reading of Dr Meyer’s book is that he has nothing to update. I thought it was abundantly clear that there are no determining factors among the bonds.

    More relevant are the non-uniformly distributed bindings of amino acids to RNA triplets. It seems that some part of the genetic code is driven by pure chemistry.

    The aa-rna interaction tell us that the parts of the system actually work to their purpose. Returning to your earlier analogy, if the ink did not stick to the paper and was not visible for reading, then we wouldn’t use it.

    But just because it does, doesn’t explain why the u follows the q.

  70. 70
    Upright BiPed says:

    Hello rna,

    My reading of your comments was that you were simply ignoring that the fact that the discussion was specifically about the determining factors in sequencing (ie. “…causes the sequence of nucleotides to exist as they do”).

    That is the part of the comment (you were reacting to) which you simply ignored in #46 and and completely left out of the quote in #53.

    This would of course, give you the opportunity to say something like:

    “If Dr. meyer doesn’t know about these basic facts or even choose to ignore them I am not sure if I can trust his further statements.”

    Regular visitors to UD find that there are many commentors who come here to willfully attack ID and it proponents over the weakest reading of their work. They will ignore context, split hairs, demand clarifications for the obvious, and generally flop about.

    It is therefore up to the proponents of design to correct them.

  71. 71
    rna says:

    #69 upright biped

    Again, I simply pointed out that there are stacking forces between bases along the linear axis of a DNA. These stacking forces are different for different pairs of nucleotides following along the sequence due to the difference in their chemical nature. Thus, some sequences are energetically more favourable then others or (more prone to adopt functional structures). If these energy differences matter in determining or at least biasing the distribution of sequences occuring in nature is then a question one can discuss. However, for a meaningful discussion about this one would need first to know or to admit that these forces exist. My personal opinion is that in the large genomes we see in modern organisms these forces do not matter in general. basically all sequences can occur since e.g. genomic dna is stabilized by a huge number of accessory proteins but there are many other reasons.
    But there are at least two examples where the occurence of certain sequences where the differences in the chemical properties between different nucleotides ‘determine’ (some variation allowed) the sequence. One example are the ends of chromosomes – the telomeres – where G-containing sequences dominate since G is the only nucleotide due to its special chemical properties that can form so called quadruplexes which are thought to be involved in telomere stabilization.
    The second example are GC-rich sequences that can form Z-DNA – a special helical geometry which is involved in regulation of gene expression and recognized by certain proteins. Again this has to do only with the special chemical properties of GC-rich sequences.

    Furthermore, differences in stacking forces along nucleic acid sequences matters if you start thinking about functional RNAs and DNAs (that not only store information but also act as enzymes) in general or in terms of an RNA-world scenario where differences in chemical stability could bias a random sequence pool towards more stable sequences.
    (And I do not want to start a dsicussion about the validity of an RNA-world scenario because there is still such a huge amount to learn about the possibilites of RNA that it would be really premature to already dismiss this just yet.)

  72. 72
    rna says:

    #69 upright biped

    Again, I simply pointed out that there are stacking forces between bases along the linear axis of a DNA. These stacking forces are different for different pairs of nucleotides following along the sequence due to the difference in their chemical nature. Thus, some sequences are energetically more favourable then others or (more prone to adopt functional structures). If these energy differences matter in determining or at least biasing the distribution of sequences occuring in nature is then a question one can discuss. However, for a meaningful discussion about this one would need first to know or to admit that these forces exist. My personal opinion is that in the large genomes we see in modern organisms these forces do not matter in general. basically all sequences can occur since e.g. genomic dna is stabilized by a huge number of accessory proteins but there are many other reasons.
    But there are at least two examples for the occurence of certain sequences where the differences in the chemical properties between different nucleotides alone ‘determine’ (some variation allowed) the sequence. One example are the ends of chromosomes – the telomeres – where G-containing sequences dominate since G is the only nucleotide due to its special chemical properties that can form so called quadruplexes which are thought to be involved in telomere stabilization.
    The second example are GC-rich sequences that can form Z-DNA – a special helical geometry which is involved in regulation of gene expression and recognized by certain proteins. Again this has to do only with the special chemical properties of GC-rich sequences.

    Furthermore, differences in stacking forces along nucleic acid sequences matters if you start thinking about functional RNAs and DNAs (that not only store information but also act as enzymes) in general or in terms of an RNA-world scenario where differences in chemical stability could bias a random sequence pool towards more stable sequences.
    (And I do not want to start a dsicussion about the validity of an RNA-world scenario because there is still such a huge amount to learn about the possibilites of RNA that it would be really premature to already dismiss this just yet.)

  73. 73
    rna says:

    #69 upright biped

    Again, I simply pointed out that there are stacking forces between bases along the linear axis of a DNA. These stacking forces are different for different pairs of nucleotides following along the sequence due to the difference in their chemical nature. Thus, some sequences are energetically more favourable then others or (more prone to adopt functional structures). If these energy differences matter in determining or at least biasing the distribution of sequences occuring in nature is then a question one can discuss. However, for a meaningful discussion about this one would need first to know or to admit that these forces exist. My personal opinion is that in the large genomes we see in modern organisms these forces do not matter in general. basically all sequences can occur since e.g. genomic dna is stabilized by a huge number of accessory proteins but there are many other reasons.
    But there are at least two examples for the occurence of certain sequences where the differences in the chemical properties between different nucleotides alone ‘determine’ (some variation allowed) the sequence. One example are the ends of chromosomes – the telomeres – where G-containing sequences dominate since G is the only nucleotide due to its special chemical properties that can form so called quadruplexes which are thought to be involved in telomere stabilization.
    The second example are GC-rich sequences that can form Z-DNA – a special helical geometry which is involved in regulation of gene expression and recognized by certain proteins. Again this has to do only with the special chemical properties of GC-rich sequences.

  74. 74
    bornagain77 says:

    rna, but all your examples beg the question as to if the information was first or the chemistry first in the sequence; i.e. was the information purposely sequenced in that way by God so as to achieve those advantageous chemical properties you cited (most likely explanation), or did the need for those chemical properties arise and then ever so luckily the properties of these sequences just so happened to fill the bill that had to be met.
    Should we just add this fortuitous “coincidence” to the encyclopedial long list we already have?

  75. 75
    scordova says:

    Nakashima-san insists:

    scordova,

    Please stick to the subject. Genetic Entropy, mutation, radiation elevated rates of mutation

    That isn’t the subject of this thread.

    But since this thread is several days old I’ll address somehting you said:

    Genetic entropy has a far better chance of being true that Darwin’s claim that we’ll be much more perfect than we are now in the future.

    You are constantly trying to drag the conversation away from the failure of Genetic Entropy to be demonstrated in an experiment which should have highlighted it clearly.

    Not so fast. See:
    Mutational Meltdown in Laboratory Yeast Populations

    But that is just the start.

    However, what is in question for school curricula is not John Sanford work but rather the illogical and illegitimate exptrapolations of Darwinism from zero data, circular reasoning and abundant story-telling.

    Evolution of deeply integrated structures has never been demonstrated. At least the claim of genetic entropy has been demonstrated in the lab and in the wild (aka extinction).

    It never ceases to amaze me that Darwinist interpret the extinction of novelty as proof that complexity increases. This is like going to a computer store, smashing a few computers and then proclaiming, “see Darwinism creates integrated novelty”. This isn’t science, this is double-speak!

    Demanding lab evidence isn’t exactly helpful to Darwinism, but rather an embarassment, just like the supposed acceleration of evolution attempted in Cobalt bomb labs: pipe dreams inspired by Darwinian story-telling. The real outcomes were more like nightmares. Natural selection acting on random mutation has yet to create deeply integrated structures in lab.

    So at least Sandford’s theories have better real-time empirical backing than Darwinism.

    By the way Nak, recombination won’t prevail if the mutation rates are sufficently high relative to the excess reproduction rate. I gave reasons to infer that we get at least 100 new mutations per individual. Nachman put the limit at about 3. We’re way beyond 3!

  76. 76
    scordova says:

    If these energy differences matter in determining or at least biasing the distribution of sequences occuring in nature is then a question one can discuss. However, for a meaningful discussion about this one would need first to know or to admit that these forces exist.

    Such forces were hypothesized, acknowledged, and studied by people like Kenyon for amino-acids and others for DNA. The conclusion was that there is insufficient biasing to create much of the novelty in existence. If the biasing forces are strong, you’d get many long repeats not useful for coding proteins.

    The quadraplex DNA that reapeats is developed through specialized cellular machinery, not through inherent chemical biasing. The biasing make the quadraplex possible and stable, but it is not the ultimate reason for the repeats.

  77. 77
    rna says:

    #76 scordova

    “The quadraplex DNA that reapeats is developed through specialized cellular machinery, not through inherent chemical biasing …”

    the quadruplexes form spontaneously in solution solely due to chemical interactions in isolated dna molecules (and even if you mix isolated guanine nucleotides with sodium ions) – no cellular machinery required

  78. 78
    bornagain77 says:

    rna, I feel you need to really evaluate the foundational basis of your argument. Your foundational basis presupposes materialism to be true. Yet quantum mechanics, as well as the transcendent origin of the universe, has shown materialism to be completely false. Thus, as a overriding matter of principle, even if you could demonstrate the ability of matter and energy to generate the massive amounts of highly organized complex functional information that we find in life, which, in spectacular fashion, you can’t, save for the very trivial uninteresting examples you cite, you would still just be left with Theistic Evolution. This is because matter and energy are ultimately resolvable/reducible to the “information waves” of quantum mechanics. That’s right rna, reality at its foundational basis is transcendent information, and here you are trying to prove, for whatever motive, that matter and energy have the ability to produce information!! Do you see how ironic it is?

    Yet even though reality itself is reducible to “transcendent information”, indeed even the most solid, indestructible, things in a atom are the unchanging, universal, transcendent, information, constants which, as far as we can tell, have not varied one iota from the creation of the universe, here you are operating from a presupposition that materialism is true;

    The Thermodynamic Argument Against Materialism and Evolution – Thomas Kindell
    http://www.metacafe.com/watch/.....s_kindell/

    Yet God

  79. 79
    bornagain77 says:

    further note rna:

    The Physics of the Small and Large: What is the Bridge Between Them? Roger Penrose
    Excerpt: “The time-asymmetry is fundamentally connected to with the Second Law of Thermodynamics: indeed, the extraordinarily special nature (to a greater precision than about 1 in 10^10^123, in terms of phase-space volume) can be identified as the “source” of the Second Law (Entropy).” http://www.pul.it/irafs/CD%20I.....enrose.pdf

    “Gain in entropy always means loss of information, and nothing more.”
    Gilbert Newton Lewis

    Why Quantum Theory Does Not Support Materialism – By Bruce L Gordon:
    Excerpt: Because quantum theory is thought to provide the bedrock for our scientific understanding of physical reality, it is to this theory that the materialist inevitably appeals in support of his worldview. But having fled to science in search of a safe haven for his doctrines, the materialist instead finds that quantum theory in fact dissolves and defeats his materialist understanding of the world.
    http://www.4truth.net/site/c.h.....ialism.htm

    Testing Creation Using the Proton to Electron Mass Ratio
    Excerpt: The bottom line is that the electron to proton mass ratio unquestionably joins the growing list of fundamental constants in physics demonstrated to be constant over the history of the universe.,,,
    http://www.reasons.org/Testing.....nMassRatio

  80. 80
    rna says:

    #78 bornagain

    until now I have only commented on results of measurements and actual experiments. These quadruplexes can actually be observed to form spontaneously in solution etc. …

    What this has to do with any foundational beliefs I might or might not hold is not clear to me.
    And the chemical properties of nucleotides that lead to stacking interactions and quadruplex formation are in total agreement with quantum mechanics as applied to atoms and molecules.

  81. 81
    bornagain77 says:

    rna,

    “These quadruplexes can actually be observed to form spontaneously in solution etc.”

    Really? and just how spontaneous was it?

    “chemical interactions in isolated dna molecules”

    And Did the DNA molecules form “spontaneously’?

    Methinks you take way too much for granted with the second law.

  82. 82
    scordova says:

    the quadruplexes form spontaneously in solution solely due to chemical interactions in isolated dna molecules (and even if you mix isolated guanine nucleotides with sodium ions) – no cellular machinery required

    Hang on, the sequence that create quadraplex DNA are generated in a specified sequence in the cell, the sequence pattern is not haphazard.

    The issue of whether it knots into quadraplex topographiies spontaneously in an isolated solution is a separate issue.

    But I hope this clarifies the sense that I was using for the formation of quadruplex DNA. I was referring to the origination of the sequence for the quadruplexes not the topography.

    I use it in the way Sternberg describes:

    the DNA sequences that are found at these genomic tips are tandem repetitions of TTAGGG. That’s right…TTAGGGTTAGGGTTAGGG…over and over and over again. A notable exception to this rule is the fruit fly, an organism that in this regard has provided the junk DNA notion no succor, since its telomeres have complex combinations of three different retrotransposons instead of those six-basepair units. What is important to note, though, is that telomeric sequences are essential to the cell, and it seems that hardly a week does not pass without some new role being discovered for these elements.

    How, precisely, are miles and miles of TTAGGG of significance? From the standpoint of chromosome architecture, the repetitive elements en masse have the propensity to form complicated topologies such as quadruplex DNA. These sequences or, rather, topographies are also bound by a host of chromatin proteins and particular RNAs to generate a unique “suborganelle” — for the lack of better term — at each end. As a matter of fact, the chromatin organization of telomeres can silence genes and has been linked to epigenetic modes of inheritance in yeast and fruit flies. …
    “How, then, do you account for such ITSs in the first place…everyone knows they are out-of-place junk.” I tell him that I do have an answer but that first I must be excused for a moment. While making my way back to the bar, I mentally rehearse so as to be as succinct as possible. My rejoinders are, simply, that ITSs reflect sites where TTAGGG repeats have been added to chromosomes by telomerases, that these repeats are moreover engineered — literally synthesized by the telomerase machinery, that ITSs have a telomere-like chromatin organization and are associated with distinct sets of proteins, and that many have been linked to roles such a recombination hotspots.

  83. 83
    bornagain77 says:

    Thanks sal,

    This video adds to the “engineering” you pointed out:

    Telomere Replication
    http://www.youtube.com/watch?v=AJNoTmWsE0s

  84. 84
    bornagain77 says:

    rna,
    here is a video I loaded for you, that gives an overview of the scenario, anyone in your position, must give an adequate explanation for:

    How DNA Compares To Human Language – Perry Marshall
    http://www.metacafe.com/watch/....._marshall/

    further note:

    The Coding Found In DNA surpasses man’s ability to code – Stephen Meyer – video
    http://www.metacafe.com/watch/.....hen_meyer/

    DNA: The Alphabet of Life – David Klinghoffer
    Excerpt: But all this is trivial compared to the largely unheralded insight gained from the Human Genome Project, completed in 2003. The insight is disturbing. It is that while DNA codes for the cell’s building blocks, the information needed to build the rest of the creature is seemingly, in large measure, absent. ,,,The physically encoded information to form that mouse, as opposed to that fly, isn’t there. Instead, “It is as if the ‘idea’ of the fly (or any other organism) must somehow permeate the genome that gives rise to it.”
    http://www.evolutionnews.org/2....._life.html

    i.e. rna please tell me how the ink and paper, of physics and chemistry, writes book after book of breath-taking elegance.

  85. 85
    rna says:

    #81 bornagain

    “Really? and just how spontaneous was it?”

    As spontaneous as in mix with sodium ions and wait. And you don’t even need a defined sequence for it but only isolated G nucleotide or guanine base (which actually can form spontaneously from simple precursor molecules).
    Thus, quadruplex formation is an inherent consequence of the chemical properties of guanine. These properties are the reason why telomere sequences are guanine rich and contain some guanines in a row. the other nucleotides differ between different organisms and further stabilize the quadruplexes by stacking interactions and hydrogen bonds.
    Quadruplex formation is also nicely in agreement with the second law of thermodynamics since it reduces the solvent accessible surface of the guanines which in turn releases a lot of water molecules which form the hydration shell of the guanines. thus, the conformational entropy of the system is increasing despite the formation of a well ordered structure.

  86. 86
    rna says:

    #82 scordova

    The telomeres are of course synthesized by the telomerase enzyme. My point was that the reason for the occurence of multiple guanines in a row in the sequence has to do with the specific chemical properties of guanines and their resulting ability to form stabilizing quadruplexes. The sequences are not haphazard for this reason.

  87. 87
    bornagain77 says:

    rna,
    please tell me if the DNA molecule occurred “spontaneously”?.

    Elsewise you are artificial creating a “thermodynamically uphill” environment. As you well know this is cheating in origin of life research.

    As far as your remark to sal, my first reaction was to think you are completely agreeing that it is an engineered sequence, and that you are joining the ID camp. If not, which I am fairly sure is as it is, please explain the telomere machinery that lays down the sequences from your desired chemistry first standpoint. Shoot I would even be happy if you would do that for the far less complicated machinery of ATP synthase:

    Evolution Vs ATP Synthase – Molecular Machine – video
    http://www.metacafe.com/watch/.....r_machine/

  88. 88
    rna says:

    Where do i create artificially an ‘thermodynamically uphill’ environment? Solvation entropy effects are very important in biology and chemistry as you well know since you argue so frequently with the second law.

  89. 89
    bornagain77 says:

    rna,
    and how did you arrive at that DNA molecule? Did you fabricate the DNA molecule by purely chemical means? Is it even possible to have a DNA molecule without extensive labwork?
    As well, rna, did you look at that video I loaded for you? Can’t you see the absolute necessity for information to be implemented from a top down approach instead of from the bottom up approach you are trying to use? I would think that fact would be as clear as day. Surely you can’t be this blind. There must be some motive for you to be so stubborn as to acknowledging what is blatantly obvious. You must get paid money for holding your unreasonable position. Am I wrong?

  90. 90
    bornagain77 says:

    rna,
    If you are interested in, in what I consider, a very good, well written, book clearly highlighting the necessity for top down implementation of such highly ordered information as we find in life. I recommend:

    A Meaningful World by Benjamin Wiker & Jonathan Witt
    http://www.ameaningfulworld.com/

    you may taste of their style, and read chapter 1 here:

    http://www.ameaningfulworld.co.....lworld.pdf

    I especially liked how they took Dawkin’s famous “Methinks it is like a weasel” phrase and point out that the phrase has no meaning until the entirety of the book is taken into context. Yet when the entirety of the context is taken into account, it is very humerous to learn that the phrase in reality highlights the wishy washy thinking of a spineless character in the play who has not enough dignity within himself to stand up for the truth: Much like what we see in quite a few people here on UD:

    Hamlet: Do you see that cloud, that’s almost in shape like a camel?

    Polonius: By the mass, and ‘t is like a camel, indeed.

    Hamlet: Methinks, it is like a weasel.

    Polonius: It is backed like a weasel.

    Hamlet: Or, like a whale?

    Polonius: Very like a whale.

    Here is a synopsis of the book:

    In this groundbreaking book, Wiker and Witt show that nature offers all of the challenges and surprises, all of the mystery and elegance, we associate with design and, further, with artistic genius. They begin in Shakespeare and range through the fine-tuning of the laws of physics, the Periodic Table of Elements, the artistry of ordinary substances like carbon and water, the intricacy of biological organisms, and the drama of scientific exploration itself. In contrast to contemporary claims that the world is ultimately meaningless, Wiker and Witt reveal a cosmos charged with both meaning and purpose.

  91. 91
    scordova says:

    My point was that the reason for the occurence of multiple guanines in a row in the sequence has to do with the specific chemical properties of guanines and their resulting ability to form stabilizing quadruplexes. The sequences are not haphazard for this reason.

    There is something potentially unwholesome in this line of reasoning, namely the idea: “Something is not haphazard because it would fail to be functional.”

    But there is no a priori reason that it needs to be functional in the first place. Functionality is a privilege not an inevitable guarantee by nature! The fact that something is exists to make something else functional in the natural world does not mean mindless forces will necessarily assemble the functionality.

    If we used such reasoning to say fuel injectors make fuel injected cars functional, therefore mindless forces made cars, it would be obvious a non-sequitur has been put forward. The same issue applies here regarding the sequencing of DNA to allow quadruplex topographies!

  92. 92
    Nakashima says:

    scordova,

    Sorry for the delay in replying.

    Please stick to the subject. Genetic Entropy, mutation, radiation elevated rates of mutation

    That isn’t the subject of this thread.

    No, but somehow “cobalt bomb lab” experiments aren’t either.

    By the way Nak, recombination won’t prevail if the mutation rates are sufficently high relative to the excess reproduction rate. I gave reasons to infer that we get at least 100 new mutations per individual. Nachman put the limit at about 3. We’re way beyond 3!

    You gave? This is a back of the envelope calculation you did or are you citing research? Nachman’s own number for total mutations was about 175, and for deleterious mutations about 3. If you think you have evidence that the whole neutral theory of mutation is wrong, bring it on.

  93. 93
    bornagain77 says:

    High Frequency of Cryptic Deleterious Mutations in Caenorhabditis elegans ( Esther K. Davies, Andrew D. Peters, Peter D. Keightley)
    “In fitness assays, only about 4 percent of the deleterious mutations fixed in each line were detectable. The remaining 96 percent, though cryptic, are significant for mutation load…the presence of a large class of mildly deleterious mutations can never be ruled out.”
    http://www.sciencemag.org/cgi/...../5434/1748

    Contamination of the genome by very slightly deleterious mutations: why have we not died 100 times over? Kondrashov A.S.
    http://www.ingentaconnect.com/.....4/art00167

    The Frailty of the Darwinian Hypothesis
    “The net effect of genetic drift in such (vertebrate) populations is “to encourage the fixation of mildly deleterious mutations and discourage the promotion of beneficial mutations,” http://www.evolutionnews.org/2......html#more

    High genomic deleterious mutation rates in hominids
    Excerpt: Furthermore, the level of selective constraint in hominid protein-coding sequences is atypically (unusually) low. A large number of slightly deleterious mutations may therefore have become fixed in hominid lineages.
    http://www.nature.com/nature/j.....344a0.html

  94. 94
    rna says:

    #89 bornagain

    “You must get paid money for holding your unreasonable position.”

    So now we are at ad hominems. Very nice.
    It might well be that I hold unreasonable positions but if so I haven’t talked about any position I personally hold in this thread. I talked about things that have been measured and experimentally characterized over and over. e. g. that g-quadruplexes form spontaneously due to the inherent chemistry of the guanine nucleotide in solution is an observation not a position I happen to hold. That the formation of this complex structure is favored by the second law is also an experimental finding since the entropy change connected with g-quadruplex formation has been measured. and so on …

  95. 95
    bornagain77 says:

    rna, I’m sorry if you take it personally, but do you or do you not get paid for money for work related to the belief that the chemical evolutionary origin of life is possible?

    As well, try to look at what you have presented un-biasedly, just how much of a violation of the second law did you have to “tolerate” in order to have the DNA molecule in the first place so as to have the “limited reaction” to a thermodynamic equilibrium state with it? As well rna, as pointed out previously, there is a molecular machine that lays down the specific sequences in question:

    Telomere Replication
    http://www.youtube.com/watch?v=AJNoTmWsE0s

    Please tell me why this machine even exists if your position is correct.

    So apparently rna, from the existance of the machine, there is a very desirable reason for having these particular sequences in very specific places in the DNA molecule that they are at, so as to help achieve the stunning levels of information packing we witness in the DNA molecule, which is trillions of level higher that what we have been able to accomplish with our most advanced computer chips:

    rna, You stated you felt insulted that I would question if you got money for holding your unreasonable position, yet when looking at the evidence once again, I feel intellectually insulted that you hold your position in the first place, surely you can’t be this stubborn as to deny the obvious.

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