Uncommon Descent Serving The Intelligent Design Community

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.

Comments
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.Nakashima
March 12, 2010
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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.bornagain77
March 12, 2010
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#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.rna
March 12, 2010
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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.Upright BiPed
March 12, 2010
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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.Nakashima
March 11, 2010
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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.Upright BiPed
March 11, 2010
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tgpeeler, thanks for the quotes, I shall store them away for future reference.bornagain77
March 11, 2010
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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. :-)tgpeeler
March 11, 2010
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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?bornagain77
March 11, 2010
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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/2009/07/leading_advocate_of_intelligen.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/releases/2009/10/091008142957.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/releases/2009/12/091215160649.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/2009/04/shoddy_engineering_or_intellig.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.bornagain77
March 11, 2010
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#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.rna
March 11, 2010
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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?bornagain77
March 11, 2010
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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.rna
March 11, 2010
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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?bornagain77
March 11, 2010
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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/shannon_comm_channel.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.)bornagain77
March 11, 2010
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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.Nakashima
March 11, 2010
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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=FtMQUFOwEFobornagain77
March 11, 2010
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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/4104651/stephen_c_meyer_the_scientific_basis_for_intelligent_design/ Stephen Meyer - Functional Proteins And Information For Body Plans - video http://www.metacafe.com/watch/4050681/stephen_meyer_functional_proteins_and_information_for_body_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/4018204/the_origin_of_life_and_god_henry_fritz_schaefer_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.bornagain77
March 11, 2010
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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.scordova
March 11, 2010
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# 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.rna
March 11, 2010
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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?Nakashima
March 11, 2010
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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.Nakashima
March 11, 2010
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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).scordova
March 11, 2010
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Nak, for you to insinuate I have never cited peer review to you is insulting. Please refrain from insulting me any more!bornagain77
March 11, 2010
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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.Nakashima
March 11, 2010
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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.Nakashima
March 11, 2010
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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.Seversky
March 10, 2010
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What does it matter Nak, whether I quote peer review or cite it directly? You never listen anyway.bornagain77
March 10, 2010
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Mr BA^77, Yes, now in your own words?Nakashima
March 10, 2010
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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.Nakashima
March 10, 2010
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