A voice for free speech, from the other side

_{Vincent Torley

March 18, 2014

Intelligent Design}

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I was very gratified to read Professor Larry Moran’s recent post, On teaching creationism in American public universities (17 March 2014). Professor Moran not only believes that Intelligent Design qualifies as science, but he also believes that it should be legal to teach science courses in Intelligent Design at university. To be sure, Moran thinks that ID is very bad science; nevertheless, he insists that “university students are mature enough to handle diverse points of view.” Good for him, I say. While Professor Moran and I have had our disagreements about evolution in the past, I salute him as a fair-minded man.

Professor Moran’s post concludes with a zinger aimed at Professor Jerry Coyne, who maintains that “although it’s illegal (as well as dereliction of duty) to teach intelligent design creationism in public schools and universities, it is okay to criticize it, for you can criticize ID on the grounds of bad science without bashing religion.” Moran comments:

It’s okay to criticize ID as bad science but it’s illegal and a dereliction of duty to allow any professors to defend ID and make the case that it’s actually good science. My head is spinning.

Professor Moran is also bemused at the antics of the lawyers and scientists who are agitating to keep Intelligent Design out of university science classrooms (highlighting mine – VJT):

It’s fun to watch while my American colleagues wiggle and squirm over this issue. The latest “problems” are whether you can categorically label intelligent design as religion and not science[2] and whether you can criticize it in a science class without seeming to criticize religion.[3]

Footnotes

2. I think that much of what Intelligent Design Creationists advocate qualifies as science by my definition of science. It’s just bad science.

3. There’s a fine line between banning all mention of religion and promoting atheism. It’s not clear whether promoting a solely materialist view of the world violates the US Constitution.

For anyone who would question Professor Moran’s commitment to free speech, the following passage from his post should lay all doubts to rest (highlighting mine – VJT):

It’s not a good idea to offer astronomy courses on an Earth-centered solar system or geology courses based on the idea that the Earth is only 6000 years old. Those ideas are just too far out on the fringe. You’re unlikely to find any university professors who want to teach such courses.

However, there are lots of other controversies that aren’t so easily dismissed. If some of the more enlightened Intelligent Design Creationists want to teach a science course at my university, I would not try to prevent them. Just as I didn’t try to prevent Michael Behe and Bill Dembski from speaking on my campus…

If Ken Miller, Francis Collins, or Simon Conway-Morris want to teach a course on theistic evolution, I’d be happy to support them. It would be fun to start a debate about the conflict between science and religion and let students see both sides of the issue…

There are … people who would use the legal system to prevent courses on Intelligent Design or Theistic Evolution at publicly-funded American universities. It seems incredible to me that they would resort to lawyers to block the teaching of certain subjects at a university but there you go.

Moran marvels at the fact that his American scientific colleagues “don’t see this as censorship.” Having attended two universities where lecturers were not afraid of discussing the “big issues” in front of their students, I have to say that I share his astonishment. It’s high time for the anti-free speech zealots seeking to bar Intelligent Design from American campuses to realize that university students are not children, and won’t tolerate being treated as such.

Comments

Allen_MacNeill @29: Certainly sorry to hear about the challenges, but I'm sure you'll pull through. Our thoughts are with you and we appreciate your participation here at UD.Eric Anderson_{March 23, 2014
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Haven't had a chance to read it yet. When I have I will respond.Allen_MacNeill_{March 23, 2014
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Hi Allen MacNeill, Thanks for your response. I had no idea that the identification of genes (let alone orphan genes) in eukaryotes was such a complicated process. I was however very interested in your last sentence in #26 above:
An unambiguous signature of design, as compared with accident/natural law would be a surprisingly high rate of production of genuinely functional, genuinely unique coding sequences that could not be explained by the known mechanisms of producing novel sequences via retrotransposition and the insertion of active promoters in formerly inactive sequences.
That sounds reasonable enough to me. Sounds like we have a testable hypothesis, then. Another idea which I had was prompted by your remark that the identification of true "orphan" sequences in bacteria is relatively easy. I thought that if biologists sequenced a large enough number of genomes for a large enough number of species, then if orphan genes appear at a uniform rate over time, it should be possible for scientists to spot one emerging. But then I read an article on Wisegeek at http://www.wisegeek.org/how-many-species-of-bacteria-are-there.htm which states:
Estimating the exact number of species of bacteria is impossible with today's technology. To really move close to having an objective number, people would need a machine that could process soil, water, and rock in large amounts, isolate the bacteria from their habitat, then sequence the genomes of as many bacteria as possible within the sample. Today, given that sequencing a bacterial genome costs half a million US dollars and takes a few months, this is infeasible. Even if costs fall by a factor of a trillion, there are so many microbes in soil that categorizing them in this way would be prohibitively expensive.
It goes on to add that "[i]nstead of sequencing entire genomes, bacterial surveys use snippets to distinguish between different species," but I don't suppose a partial survey would be much use for identifying the appearance of new orphan genes in a population of bacteria. Incidentally, I noticed that you wrote in #24 above that orphan genes were pretty rare in bacteria. Dr. Branko Kozulic's 2011 paper, "Proteins and Genes, Singletons and Species" at http://vixra.org/pdf/1105.0025v1.pdf , seemed to suggest that each species of bacterium should have 200 or so chemically unique singleton genes. Are his estimates out of date? (Incidentally, what's your impression of his paper?)vjtorley_{March 19, 2014
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We are blessed you are still with us Allen. For the readers not familiar with Allen, he risked his reputation and standing to defend academic freedom of ID students at Cornell even though, as you can see, he disagrees with ID.scordova_{March 19, 2014
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Thanks, KF. It's been a tough year, but looking up now. I was diagnosed with pancreatic cancer last April, but after many tests, it turned out to be sclerosing autoimmune pancreatitis. Difficult but treatable. My third cancer "scare" in as many decades. Talk about memento mori.Allen_MacNeill_{March 19, 2014
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Mr MacNeill, good to see you back, I trust in good shape. KFkairosfocus_{March 19, 2014
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Allen MacNeill To knock the socks of evolution does not require such efforts. Evolution is not wearing socks of science. Evolutionary biology has no moral right to be proven wrong scientifically since its not based on biological scientific investigation and results. Many other claims of other subjects to back it up but NO science ala biology. If so name three or the best one!! betcha can't or your any of your students. I'm YEC and am pretty sure I'm right.Robert Byers_{March 19, 2014
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VJ: Thinking about your question further, it occurs to me that the concept of an "orphan" gene is inherently an evolutionary concept. How does one determine if a particular sequence is an "orphan?" If it is not homologous with a sequence in another organism. One of the peculiarities of DNA replication is that it does not have a mechanism that would produce genuinely non-homologous sequences longer than a few nucleotides. DNa polymerase can "skip-replicate" (this is what produces tandem repeats, among other things), but the product of such processes are not long non-homologous sequences. That said, the origin of genuinely non-homologous long sequences isn't difficult to explain using naturalistic assumptions. All that is necessary for this is to insert a non-homologous sequence of any arbitrary (but relatively long) length into an existing DNA molecule. This is what both transposons and reverse transcriptase do all the time. To insert a genuinely non-homologous sequence into an existing genome can be done by retrotransposition, either by a cell's own reverse transcriptase or that of an RNA retrovirous. We can infer that such retrotransposition events are common and ubiquitous by assaying how much of a given genome consists of "dead" (i.e. non-transcribed), non-polypeptide-binding sequences similar to those in active RNA retroviruses, but with non-functional promoter sequences. Most people who have studied the genomes of most eukaryotes have concluded that huge amounts of eukaryote non-coding sequences consist of such "dead" (i.e. non-transcribed and non-regulatory) retrotransposed sequences. If, as much of the evidence to date indicates, there is a large number of non-transcribed and non-regulatory sequences in the genomes of eukaryotes (again, bacteria don't have them), then converting them into transcribed, and therefore potentially "live" genes is also relatively straight-forward. All that would be necessary is to insert an active promoter "upstream" from a "dead" sequence, and if the cell has active regulators (especially activators) that will bind to that promoter, the sequence "downstream" from it will immediately become a coding sequence. Personally, I suspect that this happens a lot, but that most of the newly "live" sequences have little or no biological effect. We still tend to think of eukaryotes as functioning genetically like bacteria, since our models of how genes work were first figured out using bacteria. However, it is becoming increasingly likely that eukaryotes are genetically "noisy," producing surprisingly large amounts of relatively non-fiunctional mRNA and polypeptide sequences. Even if a fraction of the RNAs and polypeptides that a eukaryotic cell produces have little or no biological function, the cell can usually carry on with little or no deleterious effects. It's like a large social organization, compared with a small one. Unlike a small group with only a few members, a large organization with thousands of members can have a surprisingly large number of nearly non-functional members and still manage to function as a whole (believe me, Cornell is a perfect example of this). This is one of the huge advantages of multicellularity, compared with the unicellularity of bacteria. Consequently, determining if a subset of the coding sequences in a given genome are genuinely unique and genuinely functional, as compared with "pseudo-unique" (because of transposition from another genome) and Pseudofunctional" (because they are trasncribed and translated, but have no significant phenotypic effects) will be difficult. An unambiguous signature of design, as compared with accident/natural law would be surprisingly high rate of production of genuinely functional, genuinely unique coding sequences that could not be explained by the known mechanisms of producing novel sequences via retrotransposition and the insertion of active promoters in formerly inactive sequences.Allen_MacNeill_{March 19, 2014
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BTW, Vincent, I may not always agree with you, but I appreciate the way your mind works.Allen_MacNeill_{March 19, 2014
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Re 23/vjtorley: An interesting idea. Two difficulties with such a test of hypothesis would be: 1) determining reliably whether a gene is genuinely functional, and 2) determining reliably whether a gene is genuinely unique. Indeed, an even more fundamental problem would be determining exactly what criteria one would use to determine what qualifies as a gene, and how something that qualifies as a gene according to those criteria is related to a corresponding phenotypic trait. Sorting these out is not too difficult when one is dealing with bacteria, but they become difficult when applied to multicellular eukaryotes. To identify functional genes in bacteria it is usually necessary to simply locate active promoter sequences in the DNA. A bacterial gene is a sequence of DNA nucleotides beginning with a promoter sequence and ending with a terminator sequence and which is therefore consistently transcribed into an mRNA molecule which can then be translated into a corresponding polypeptide sequence by a ribosome. To qualify as a gene that would participate in natural selection, the polypeptide coded for by a bacterial gene would also have to have a significant effect on the phenotype of the bacterium (e.g. allowing it to metabolize something, such as citrate or nylon, which it could not metabolize without that polypeptide). A "significant" phenotypic effect would be one that consistently affected the longevity and ability to reproduce by binary fission in the environment in which the bacterium were located. In eukaryotes the situation is immensely more complex and difficult to sort out. All eukaryotic genes require polypeptides that bind to regulatory sequences in the DNA that are located outside the promoter—template—terminator sequence that corresponds to a given polypeptide. In many cases, other polypeptides (and in many cases, small RNA molecules) are necessary for the full transcription of the promoter—template—terminator sequence into a primary mRNA molecule. Even after a primary mRNA transcript is encoded, it is almost always edited by spliceosomes prior to translation by ribosomes. Even after translation, many polypeptides are modified prior to their eventual function in cells. Even after they are modified, the function of many polypeptides depends on when and where they are made, transported, and ultimately located, including functional modification by other polypeptides, changes in substrate and/or product concentrations, presence or absence of activators and/or inhibitors, etc. And finally, even after they are modified, polypeptides may have no significant effect on the survival and reproduction of the organism of which it is a part. If not, it is "invisible" to natural selection. This analysis is further complicated by how one determines if a gene is a genuine "orphan." Again, in bacteria this is relatively easy. If a DNA sequence located in the same part of the genome of two different bacteria are sufficiently similar, they can be assumed to have descended from a similar sequence in a common ancestor to both bacteria. Since it is often the case that bacteria have only one copy of each functional gene (as defined in the second paragraph, above) and almost no sequences that are not transcribed or part of a gene (i.e. part of a promoter—template—terminator sequence), this makes identifying true "orphan" sequences relatively easy. BTW, bacteria seem to have very few of them. Again, eukaryotes are very different in this respect. Only if one has shown that a particular promoter—template—terminator sequence and all of its regulatory correlates produce a functioning polypeptide that has a significant effect on the organism's phenotype would it even be relevant to consider if it is a genuine orphan. If it is, it would fulfill all of the criteria noted above and have both a coding sequence and a set of regulatory modifiers that were sufficiently non-homologous with a similar sequence in another eukaryote as to indicate that it did not derive from a common ancestral sequence. This criterion is further complicated by the fact that the same polypeptide can have vastly different phenotypic effects in different organisms, and that different polypeptides can have very similar phenotypic effects in different organisms. Personally, I think that it is far too early to determine if many eukaryotic coding sequences are genuinely functional genes, or even to isolate their functions. We have been able to do this with a few genes, such as the hemoglobin gene. We have also been able to show evolutionary homologies between subunits of the hemoglobin gene and similar genes, such as the gene for myoglobin. However, there are at least 20,000 other coding sequences (and an unknown number of modifications of those coding sequences) in a typical multicellular eukaryote, so doing the kind of analysis you suggest would be very difficult. Not impossible, but difficult. That said, it is an intriguing idea. Your suggestion is conceptually similar to the idea of the molecular mutation "clock," originally proposed in 1962 by Emile Zuckerkandl and Linus Pauling. The hinge of the test would be determining how different two sequences from two different organisms would have to be for one of them to be considered to be a genuine "orphan" sequence, and then to determine if the "orphan" sequence had any significant effect on the organism's phenotype. If the number of genuine "orphans" that had significant phenotypic effects were above some agreed-upon threshold frequency, then the appearance of such sequences would be unlikely to be the result of chance, and therefore the result of either law-like "natural" processes or magic.Allen_MacNeill_{March 19, 2014
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Hi Allen MacNeill, Glad to hear you're back. I hope your treatment is going well for you. I fixed the link problem in #5 above. While reading it, I was struck by your comment regarding Uncommon Descent posts:
Virtually none of them present positive empirical evidence in support of ID, nor do they propose methods of empirical validation/falsification of ID hypotheses.
In my latest post, "Does Professor Larry Moran (or anyone else) understand macroevolution?" (see https://uncommondescent.com/intelligent-design/does-professor-larry-moran-or-anyone-else-understand-macroevolution/ ) I discussed orphan genes, focusing in particular on those which are chemically unique and do not belong in any existing family. These were the ones discussed in Dr. Branko Kozulic's article, "Proteins and Genes, Singletons and Species" at http://vixra.org/pdf/1105.0025v1.pdf , which highlighted the fact that each species has hundreds of these new genes which distinguish it from other species. I mentioned in passing that if it turned out that these new functional proteins and genes all appear simultaneously in an evolutionary lineage, it would lend support to an Intelligent Design hypothesis, whereas if they appear sequentially (one at a time) at a uniform rate, that would tend to support a naturalistic explanation for their origins. The average lifespan of a species is about 5 million years. If each species can be characterized by 100 unique, functional genes which have no analogue in other species - Kozulic thinks the true figure is more like 1,000 - then if these new genes are appearing at a uniform rate in Nature, we should see one cropping up every 50,000 years. If biologists were to keep close tabs on the genomes of (say) 10,000 species, then they should witness the appearance of a new functional gene every 5 years. That's a test which could support or discredit ID. What do you think? Fair test?vjtorley_{March 19, 2014
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As an aside, as in Intro to Intelligent Design I would teach from (a minimum) 3 books- 1- "Nature, Design and Science" by Del Ratzsch 2- "The Design Matrix" by Mike Gene 3- "Not By Chance" by Dr. Lee Spetner These books address the fundamentals- what is design, assessing the evidence, and perhaps the watchmaker isn't blind after all. Included in the course would be time spent with forensic science and other design-centric venues, ie how to we determine design from not, what techniques do we use. Then onto "The Privileged Planet" to demonstrate that the design inference extends beyond biology and how we can apply the methodology there. All along the students will be asked to think about and discuss the options, as in what are the alternatives that can explain the evidence and is sheer dumb luck really a valid option?Joe_{March 19, 2014
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Where is this alleged "abundant confirmative evidence for" blind watchmaker, ie unguided and unplanned, evolution? Why is it being kept a super top-secret? What is the testable model for unguided and unplanned evolution? Come on Allen, don't leave us hangin'...Joe_{March 19, 2014
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I wonder if Moran thinks that blind watchmaker evolution is science. Or if materialism is science. I bet neither Moran nor McNeil can produce a testable hypothesis wrt blind watchmaker evolution that would supports its claim as being a designer mimic.Joe_{March 19, 2014
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Allen McNeil:
Figure out a convincing empirical test that unambiguously distinguishes between evolution and ID by falsifying the former and verifying the latter.
We have, Allen. We used Darwin's criteria and blind watchmaker evolution has been falsified. As for Intelligent Design it can be tested and potentially falsified. And we have said exactly how to do so. However no one has said how we can test blind watchmaker evolution, as in how can we test to see if it can actually produce something beyond disease and deformaties. As far as anyone can tell BWE can't even get beyond prokaryotes given a starting point of prokaryotes.Joe_{March 19, 2014
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corrected link: Darwin's Doubt - Chapter 12 - Complex Adaptations and the Neo-Darwinian Math - Dr. Paul Giem - video http://www.youtube.com/watch?v=ZFY7oKc34qs&list=SPHDSWJBW3DNUaMy2xdaup5ROw3u0_mK8t&index=7bornagain77_{March 19, 2014
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The reason why a ‘higher 4-Dimensional’ structure, such as the ‘horrendously complex metabolic pathway, would be, for all intents and purposes, completely invisible to a 3-Dimensional process, such as Natural Selection, is best illustrated by ‘flatland’:
Flatland – 3D to 4D shift – Carl Sagan – video http://www.youtube.com/watch?v=UnURElCzGc0
I personally hold that the reason why internal physiology and anatomy operate as if they were four-dimensional instead of three-dimensional is because of exactly what Darwinian evolution has consistently failed to explain the origination of. i.e. functional information. ‘Higher dimensional’ information, which is bursting at the seams in life, simply cannot be reduced to any 3-dimensional energy-matter basis:
John Lennox – Is There Evidence of Something Beyond Nature? (Semiotic Information) – video http://www.youtube.com/watch?v=F6rd4HEdffw “One of the things I do in my classes, to get this idea across to students, is I hold up two computer disks. One is loaded with software, and the other one is blank. And I ask them, ‘what is the difference in mass between these two computer disks, as a result of the difference in the information content that they posses’? And of course the answer is, ‘Zero! None! There is no difference as a result of the information. And that’s because information is a mass-less quantity. Now, if information is not a material entity, then how can any materialistic explanation account for its origin? How can any material cause explain it’s origin? And this is the real and fundamental problem that the presence of information in biology has posed. It creates a fundamental challenge to the materialistic, evolutionary scenarios because information is a different kind of entity that matter and energy cannot produce. In the nineteenth century we thought that there were two fundamental entities in science; matter, and energy. At the beginning of the twenty first century, we now recognize that there’s a third fundamental entity; and its ‘information’. It’s not reducible to matter. It’s not reducible to energy. But it’s still a very important thing that is real; we buy it, we sell it, we send it down wires. Now, what do we make of the fact, that information is present at the very root of all biological function? In biology, we have matter, we have energy, but we also have this third, very important entity; information. I think the biology of the information age, poses a fundamental challenge to any materialistic approach to the origin of life.” -Dr. Stephen C. Meyer earned his Ph.D. in the History and Philosophy of science from Cambridge University for a dissertation on the history of origin-of-life biology and the methodology of the historical sciences. Information and entropy – top-down or bottom-up development in living systems? Excerpt: This paper highlights the distinctive and non-material nature of information and its relationship with matter, energy and natural forces. It is proposed in conclusion that it is the non-material information (transcendent to the matter and energy) that is actually itself constraining the local thermodynamics to be in ordered disequilibrium and with specified raised free energy levels necessary for the molecular and cellular machinery to operate. A.C. McINTOSH - Dr Andy C. McIntosh is the Professor of Thermodynamics Combustion Theory at the University of Leeds. (the highest teaching/research rank in U.K. university hierarchy) - per witpress Storing information in DNA – Test-tube data – Jan 26th 2013 Excerpt: Dr Goldman’s new scheme is significant in several ways. He and his team have managed to set a record (739.3 kilobytes) for the amount of unique information encoded. But it has been designed to do far more than that. It should, think the researchers, be easily capable of swallowing the roughly 3 zettabytes (a zettabyte is one billion trillion or 10^21 bytes) of digital data thought presently to exist in the world and still have room for plenty more. http://www.economist.com/news/science-and-technology/21570671-archives-could-last-thousands-years-when-stored-dna-instead-magnetic
Moreover, matter and energy are now both shown to reduce to ‘quantum information’. In fact, an entire human can now, theoretically, be reduced to quantum information and teleported to another location in the universe:
Quantum Teleportation Of A Human? – video https://vimeo.com/75163272
Thus not only is Information not reducible to a 3-Dimensional energy-matter basis, as is presupposed in Darwinism, but in actuality energy and matter both reduce to a information basis as is presupposed in Christian Theism:
Why the Quantum? It from Bit? A Participatory Universe? Excerpt: In conclusion, it may very well be said that information is the irreducible kernel from which everything else flows. Thence the question why nature appears quantized is simply a consequence of the fact that information itself is quantized by necessity. It might even be fair to observe that the concept that information is fundamental is very old knowledge of humanity, witness for example the beginning of gospel according to John: “In the beginning was the Word.” Anton Zeilinger – a leading expert in quantum teleportation:
Whereas evolution has no mathematical basis, no empirical support, nor does it even have a plausible mechanism, Intelligent Design does not suffer from such embarrassment. ID has a mathematical basis:
Conservation of Information Made Simple - William A. Dembski - August, 2012 Excerpt: Biological configuration spaces of possible genes and proteins, for instance, are immense, and finding a functional gene or protein in such spaces via blind search can be vastly more improbable than finding an arbitrary electron in the known physical universe. ,,, ,,,Given this background discussion and motivation, we are now in a position to give a reasonably precise formulation of conservation of information, namely: raising the probability of success of a search does nothing to make attaining the target easier, and may in fact make it more difficult, once the informational costs involved in raising the probability of success are taken into account. Search is costly, and the cost must be paid in terms of information. Searches achieve success not by creating information but by taking advantage of existing information. The information that leads to successful search admits no bargains, only apparent bargains that must be paid in full elsewhere. http://www.evolutionnews.org/2012/08/conservation_of063671.html
Here are the two seminal papers on conservation of information that William Dembski has written with Robert Marks:
"The Search for a Search: Measuring the Information Cost of Higher-Level Search," Journal of Advanced Computational Intelligence and Intelligent Informatics 14(5) (2010): 475-486 "Conservation of Information in Search: Measuring the Cost of Success," IEEE Transactions on Systems, Man and Cybernetics A, Systems & Humans, 5(5) (September 2009): 1051-1061 For other papers that Dembski, Marks, and his students have done to extend the results in these papers, visit the publications page at http://www.evoinfo.org
And, unlike evolution which has no rigid falsification criteria, ID can easily be falsified:
The Law of Physicodynamic Insufficiency - Dr David L. Abel - November 2010 Excerpt: “If decision-node programming selections are made randomly or by law rather than with purposeful intent, no non-trivial (sophisticated) function will spontaneously arise.”,,, After ten years of continual republication of the null hypothesis with appeals for falsification, no falsification has been provided. The time has come to extend this null hypothesis into a formal scientific prediction: “No non trivial algorithmic/computational utility will ever arise from chance and/or necessity alone.” http://www-qa.scitopics.com/The_Law_of_Physicodynamic_Insufficiency.html Orr maintains that the theory of intelligent design is not falsifiable. He’s wrong. To falsify design theory a scientist need only experimentally demonstrate that a bacterial flagellum, or any other comparably complex system, could arise by natural selection. If that happened I would conclude that neither flagella nor any system of similar or lesser complexity had to have been designed. In short, biochemical design would be neatly disproved.- Dr Behe in 1997 Michael Behe on Falsifying Intelligent Design - video http://www.youtube.com/watch?v=N8jXXJN4o_A
Verse and Music:
John 1:1-4 In the beginning was the Word, and the Word was with God, and the Word was God. He was in the beginning with God. All things were made through Him, and without Him nothing was made that was made. In Him was life, and the life was the light of men. Redeemed – Big Daddy Weave http://myktis.com/songs/redeemed/
bornagain77_{March 18, 2014
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Another reason why Darwinian evolution is more realistically thought of as a pseudo-science rather than a proper physical science is that the two foundational pillars of Darwinian evolution, Random Mutation/Variation and Natural Selection, are both now shown to be severely compromised as to having the causal adequacy that Darwinists have presupposed for them. For instance, although Darwinian evolution appeals to unguided ‘random mutations/variations’ to DNA as the main creative source for all evolutionary novelty, there are now known to be extensive layers of error correction in the cell to protect against any unguided “random” changes happening to DNA in the first place:
The Evolutionary Dynamics of Digital and Nucleotide Codes: A Mutation Protection Perspective – February 2011 Excerpt: “Unbounded random change of nucleotide codes through the accumulation of irreparable, advantageous, code-expanding, inheritable mutations at the level of individual nucleotides, as proposed by evolutionary theory, requires the mutation protection at the level of the individual nucleotides and at the higher levels of the code to be switched off or at least to dysfunction. Dysfunctioning mutation protection, however, is the origin of cancer and hereditary diseases, which reduce the capacity to live and to reproduce. Our mutation protection perspective of the evolutionary dynamics of digital and nucleotide codes thus reveals the presence of a paradox in evolutionary theory between the necessity and the disadvantage of dysfunctioning mutation protection. This mutation protection paradox, which is closely related with the paradox between evolvability and mutational robustness, needs further investigation.” http://www.arn.org/blogs/index.php/literature/2011/04/26/dna_repair_mechanisms_reveal_a_contradic
Moreover, for the vast majority of times that changes do happen to DNA, they are now known to be ‘directed changes’ by sophisticated molecular machines, not unguided ‘random changes’ from a cosmic ray, chemical imbalance, or some such entropy driven event as that:
How life changes itself: the Read-Write (RW) genome. – 2013 Excerpt: Research dating back to the 1930s has shown that genetic change is the result of cell-mediated processes, not simply accidents or damage to the DNA. This cell-active view of genome change applies to all scales of DNA sequence variation, from point mutations to large-scale genome rearrangements and whole genome duplications (WGDs). This conceptual change to active cell inscriptions controlling RW genome functions has profound implications for all areas of the life sciences. http://www.ncbi.nlm.nih.gov/pubmed/23876611 Shapiro on Random Mutation: “What I ask others interested in evolution to give up is the notion of random accidental mutation.” http://www.huffingtonpost.com/james-a-shapiro/jerry-coyne-fails-to-unde_b_1411144.html of note: Shapiro's 'natural genetic engineering' also fails to account for the origination of functional information
What should be needless to say, having ‘cell-mediated processes’ direct changes to DNA is in direct contradiction to the ‘undirected randomness’ which is widely held to be foundational to neo-Darwinian thought. Moreover, Natural Selection, that other great pillar upon which Darwinian evolution rests, has also been undermined as having the causal adequacy that neo-Darwinists have attributed to it. i.e. Natural Selection is grossly inadequate to do the work required of it because of what is termed ‘the princess and the pea’ paradox. The devastating ‘princess and the pea’ paradox is clearly elucidated by Dr. John Sanford, at the 8:14 minute mark, of this following video,,,
Genetic Entropy – Dr. John Sanford – Evolution vs. Reality – video http://vimeo.com/35088933
Dr. Sanford points out, in the preceding video, that Natural Selection acts at the coarse level of the entire organism (phenotype) and yet the vast majority of mutations have effects that are only ‘slightly detrimental’, and have no noticeable effect on phenotypes, and are thus far below the power of Natural Selection to remove from genomes before they spread throughout the population. Here are a few more notes on this insurmountable ‘princess and the pea’ problem for natural selection:
Evolution Vs Genetic Entropy (Kimura’s Distribution)– Andy McIntosh – video http://www.metacafe.com/watch/4028086/ The GS Principle (The Genetic Selection Principle) – Abel – 2009 Excerpt: The GS Principle, sometimes called “The 2nd Law of Biology,” states that selection must occur at the molecular/genetic level, not just at the fittest phenotypic/organismic level, to produce and explain life.,,, Natural selection cannot operate at the genetic level. http://www.bioscience.org/2009/v14/af/3426/fulltext.htm
Moreover, as if that were not devastating enough as to undermining any credibility Natural Selection might have had as to having the causal adequacy to explain the highly integrated levels of overlapping functional information found in organisms, dimensionally speaking, Natural Selection is now known to not even be on the right playing field in the first place:
The predominance of quarter-power (4-D) scaling in biology Excerpt: Many fundamental characteristics of organisms scale with body size as power laws of the form: Y = Yo M^b, where Y is some characteristic such as metabolic rate, stride length or life span, Yo is a normalization constant, M is body mass and b is the allometric scaling exponent. A longstanding puzzle in biology is why the exponent b is usually some simple multiple of 1/4 (4-Dimensional scaling) rather than a multiple of 1/3, as would be expected from Euclidean (3-Dimensional) scaling. http://www.nceas.ucsb.edu/~drewa/pubs/savage_v_2004_f18_257.pdf “Although living things occupy a three-dimensional space, their internal physiology and anatomy operate as if they were four-dimensional. Quarter-power scaling laws are perhaps as universal and as uniquely biological as the biochemical pathways of metabolism, the structure and function of the genetic code and the process of natural selection.,,, The conclusion here is inescapable, that the driving force for these invariant scaling laws cannot have been natural selection.” Jerry Fodor and Massimo Piatelli-Palmarini, What Darwin Got Wrong (London: Profile Books, 2010), p. 78-79
Here is, what a Darwinist termed, a ‘horrendously complex’ metabolic pathway (which operates as if it were ’4-Dimensional):
ExPASy - Biochemical Pathways - interactive schematic http://web.expasy.org/cgi-bin/pathways/show_thumbnails.pl
And remember, Darwinian evolution has yet to explain how a single gene of those ‘horrendously complex’ metabolic pathways came about.
"Charles Darwin said (paraphrase), 'If anyone could find anything that could not be had through a number of slight, successive, modifications, my theory would absolutely break down.' Well that condition has been met time and time again. Basically every gene, every protein fold. There is nothing of significance that we can show that can be had in a gradualist way. It's a mirage. None of it happens that way. - Doug Axe PhD. - Nothing In Molecular Biology Is Gradual - video http://www.metacafe.com/watch/5347797/
bornagain77_{March 18, 2014
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Allen_MacNeill, not to be petty towards you in any way considering our past relationship, but you are sadly mistaken if you think ID is 'bad science' and that evolution is good science. The fact of the matter, which you may not like one bit since you make your living from trying to convince people that evolution is good science, is that Darwinian evolution is a pseudo-science. What the vast majority of Darwinists fail to realize (or ever honestly admit to) is that Darwinian evolution is not even a 'real' physical science in any proper sense in the first place but that Darwinian evolution is more realistically thought of as a pseudo-science. Even Jerry Coyne himself, the self-appointed Grand Inquisitor of Darwinian evolution, admits that Darwinian evolution lacks the rigor of a proper physical science:
“In science’s pecking order, evolutionary biology lurks somewhere near the bottom, far closer to phrenology than to physics. For evolutionary biology is a historical science, laden with history’s inevitable imponderables. We evolutionary biologists cannot generate a Cretaceous Park to observe exactly what killed the dinosaurs; and, unlike “harder” scientists, we usually cannot resolve issues with a simple experiment, such as adding tube A to tube B and noting the color of the mixture.” - Jerry A. Coyne – Of Vice and Men, The New Republic April 3, 2000 p.27 - professor of Darwinian evolution at the University of Chicago
The main reason why Darwinian evolution is more properly thought of as a pseudo-science instead of a proper science is because Darwinian evolution lacks a rigid mathematical basis, like other overarching physical theories of science have. A rigid mathematical basis in order to potentially falsify it (in fact math, in so far as math can be applied to Darwinian claims, constantly shows us the Darwinian evolution is astronomically unlikely),,
“On the other hand, I disagree that Darwin’s theory is as `solid as any explanation in science.; Disagree? I regard the claim as preposterous. Quantum electrodynamics is accurate to thirteen or so decimal places; so, too, general relativity. A leaf trembling in the wrong way would suffice to shatter either theory. What can Darwinian theory offer in comparison?” (Berlinski, D., “A Scientific Scandal?: David Berlinski & Critics,” Commentary, July 8, 2003) Oxford University Seeks Mathemagician — May 5th, 2011 by Douglas Axe Excerpt: “Grand theories in physics are usually expressed in mathematics. Newton’s mechanics and Einstein’s theory of special relativity are essentially equations. Words are needed only to interpret the terms. Darwin’s theory of evolution by natural selection has obstinately remained in words since 1859.”… http://biologicinstitute.org/2011/05/05/oxford-university-seeks-mathemagician/ Active Information in Metabiology – Winston Ewert, William A. Dembski, Robert J. Marks II – 2013 Except page 9: Chaitin states [3], “For many years I have thought that it is a mathematical scandal that we do not have proof that Darwinian evolution works.” In fact, mathematics has consistently demonstrated that undirected Darwinian evolution does not work. http://bio-complexity.org/ojs/index.php/main/article/view/BIO-C.2013.4/BIO-C.2013.4 “It is our contention that if ‘random’ is given a serious and crucial interpretation from a probabilistic point of view, the randomness postulate is highly implausible and that an adequate scientific theory of evolution must await the discovery and elucidation of new natural laws—physical, physico-chemical, and biological.” Murray Eden, “Inadequacies of Neo-Darwinian Evolution as a Scientific Theory,” Mathematical Challenges to the Neo-Darwinian Interpretation of Evolution, editors Paul S. Moorhead and Martin M. Kaplan, June 1967, p. 109. HISTORY OF EVOLUTIONARY THEORY – WISTAR DESTROYS EVOLUTION Excerpt: A number of mathematicians, familiar with the biological problems, spoke at that 1966 Wistar Institute,, For example, Murray Eden showed that it would be impossible for even a single ordered pair of genes to be produced by DNA mutations in the bacteria, E. coli,—with 5 billion years in which to produce it! His estimate was based on 5 trillion tons of the bacteria covering the planet to a depth of nearly an inch during that 5 billion years. He then explained that the genes of E. coli contain over a trillion (10^12) bits of data. That is the number 10 followed by 12 zeros. *Eden then showed the mathematical impossibility of protein forming by chance. http://www.pathlights.com/ce_encyclopedia/Encyclopedia/20hist12.htm Darwin’s Doubt – Chapter 12 – Complex Adaptations and the Neo-Darwinian Math – Dr. Paul Giem – video http://behe.uncommondescent.com/2010/12/the-first-rule-of-adaptive-evolution/ Using Numerical Simulation to Test the Validity of Neo-Darwinian Theory - 2008 Abstract: Evolutionary genetic theory has a series of apparent “fatal flaws” which are well known to population geneticists, but which have not been effectively communicated to other scientists or the public. These fatal flaws have been recognized by leaders in the field for many decades—based upon logic and mathematical formulations. However population geneticists have generally been very reluctant to openly acknowledge these theoretical problems, and a cloud of confusion has come to surround each issue. Numerical simulation provides a definitive tool for empirically testing the reality of these fatal flaws and can resolve the confusion. The program Mendel’s Accountant (Mendel) was developed for this purpose, and it is the first biologically-realistic forward-time population genetics numerical simulation program. This new program is a powerful research and teaching tool. When any reasonable set of biological parameters are used, Mendel provides overwhelming empirical evidence that all of the “fatal flaws” inherent in evolutionary genetic theory are real. This leaves evolutionary genetic theory effectively falsified—with a degree of certainty which should satisfy any reasonable and open-minded person. http://www.icr.org/i/pdf/technical/Using-Numerical-Simulation-to-Test-the-Validity-of-Neo-Darwinian-Theory.pdf Using Numerical Simulation to Better Understand Fixation Rates, and Establishment of a New Principle - "Haldane's Ratchet" - Christopher L. Rupe and John C. Sanford - 2013 Excerpt: We then perform large-scale experiments to examine the feasibility of the ape-to-man scenario over a six million year period. We analyze neutral and beneficial fixations separately (realistic rates of deleterious mutations could not be studied in deep time due to extinction). Using realistic parameter settings we only observe a few hundred selection-induced beneficial fixations after 300,000 generations (6 million years). Even when using highly optimal parameter settings (i.e., favorable for fixation of beneficials), we only see a few thousand selection-induced fixations. This is significant because the ape-to-man scenario requires tens of millions of selective nucleotide substitutions in the human lineage. Our empirically-determined rates of beneficial fixation are in general agreement with the fixation rate estimates derived by Haldane and ReMine using their mathematical analyses. We have therefore independently demonstrated that the findings of Haldane and ReMine are for the most part correct, and that the fundamental evolutionary problem historically known as "Haldane's Dilemma" is very real. Previous analyses have focused exclusively on beneficial mutations. When deleterious mutations were included in our simulations, using a realistic ratio of beneficial to deleterious mutation rate, deleterious fixations vastly outnumbered beneficial fixations. Because of this, the net effect of mutation fixation should clearly create a ratchet-type mechanism which should cause continuous loss of information and decline in the size of the functional genome. We name this phenomenon "Haldane's Ratchet". http://media.wix.com/ugd/a704d4_47bcf08eda0e4926a44a8ac9cbfa9c20.pdf
Another primary reason why Darwinian evolution is more realistically thought of as a pseudo-science rather than a proper physical science is that Darwinian evolution does not have a demonstrated empirical basis to support its grand claims (in fact, like math, empirical evidence also consistently shows us that Darwinian evolution is astronomically unlikely),,
“The First Rule of Adaptive Evolution”: Break or blunt any functional coded element whose loss would yield a net fitness gain – Michael Behe – December 2010 Excerpt: In its most recent issue The Quarterly Review of Biology has published a review by myself of laboratory evolution experiments of microbes going back four decades.,,, The gist of the paper is that so far the overwhelming number of adaptive (that is, helpful) mutations seen in laboratory evolution experiments are either loss or modification of function. Of course we had already known that the great majority of mutations that have a visible effect on an organism are deleterious. Now, surprisingly, it seems that even the great majority of helpful mutations degrade the genome to a greater or lesser extent.,,, I dub it “The First Rule of Adaptive Evolution”: Break or blunt any functional coded element whose loss would yield a net fitness gain. per Behe - Uncommon Descent Where’s the substantiating evidence for neo-Darwinism? https://docs.google.com/document/d/1q-PBeQELzT4pkgxB2ZOxGxwv6ynOixfzqzsFlCJ9jrw/edit Waiting Longer for Two Mutations – Michael J. Behe Excerpt: Citing malaria literature sources (White 2004) I had noted that the de novo appearance of chloroquine resistance in Plasmodium falciparum was an event of probability of 1 in 10^20. I then wrote that ‘for humans to achieve a mutation like this by chance, we would have to wait 100 million times 10 million years’ (1 quadrillion years)(Behe 2007) (because that is the extrapolated time that it would take to produce 10^20 humans). Durrett and Schmidt (2008, p. 1507) retort that my number ‘is 5 million times larger than the calculation we have just given’ using their model (which nonetheless “using their model” gives a prohibitively long waiting time of 216 million years). Their criticism compares apples to oranges. My figure of 10^20 is an empirical statistic from the literature; it is not, as their calculation is, a theoretical estimate from a population genetics model. http://www.discovery.org/a/9461 Don’t Mess With ID (Overview of Behe’s ‘Edge of Evolution’ and Durrett and Schmidt’s paper at the 20:00 minute mark) – Paul Giem – video http://www.youtube.com/watch?v=5JeYJ29-I7o
bornagain77_{March 18, 2014
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Sal:
Few individuals are qualified to teach ID and creation [science].
Those are two different things. Intelligent design is very simple at its core. There are many people, including commenters on this site, who are perfectly qualified to teach what ID is, and could provide at least a decent introduction and understanding to students of average intelligence in the course of an hour. There are, to be sure, lots of related issues and numerous interesting biological science examples that could easily fill a several credit course for an entire year or more. But the basic concepts of ID are extremely simple and straight forward. This simple, straight-forward, well-defined approach to intelligent design of course differs significantly from all the myriad ideas that sometimes crop up under "creation science," everything from Big Bang to solar physics to moon dust to Adam and Eve to radiometric dating and on and on. I think you are quite right that no-one is, personally, qualified to talk about all those topics.Eric Anderson_{March 18, 2014
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@ 9/Mapou: Agreed! Want to knock the socks off the scientific community, make yourself famous, and probably win a MacArthur Prize? Figure out a convincing empirical test that unambiguously distinguishes between evolution and ID by falsifying the former and verifying the latter. If you can do that, the scientific community will begin to pay attention to you. Until you do, you're just blowing smoke. And you are, of course, completely correct: merely criticizing something does nothing whatsoever to validate a competing explanation.Allen_MacNeill_{March 18, 2014
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One more thing, Sal: I would enjoy corresponding with you on the concepts of design and purpose (as I have enjoyed corresponding with Hannah Maxson). If you would like to do so, please "friend" me on FaceBook (be sure to search for me using the correct spelling of my name: Allen MacNeill). I will accept your friend request and send you a private message with my contact information via that channel. This one is far too open...Allen_MacNeill_{March 18, 2014
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Hi, Sal. Unfortunately, the weblog of our evolution/design class disappeared from the web without any notice of its passing being communicated to me. This is very unfortunate, as I had been maintaining it as an archive of our seminar course. As far as ID being accepted as "science," if one means empirical science, that is no closer than it was back in 2006. Indeed, I see little or no attempt to verify/falsify ID empirically, only the same tired old criticisms of evolutionary biology. All of that aside, my offer to you still stands: if you are ever in Ithaca, please stop by our rambling farmhouse (we now live on the west shore of Cayuga's waters, overlooking the lake and Cornell). I will show you around Ithaca/Utopia and let you sample the finest wines the Finger Lakes have to offer (including the finest Rieslings in the world).Allen_MacNeill_{March 18, 2014
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Nice to see you Allen. You're a far better individual than I and an example for all of us. I learned a lot tracking the public blogs on your class. Some of the criticism of ID from your class I've actually agreed with and developed alternate approaches to ID as a result: Fundamental Law of ID Nice to see you again, it has been too long. I had a bottle of Michigan Cherry wine on my shelf waiting to give to you in case I ever visit John Sanford in Livonia near Ithaca. Salscordova_{March 18, 2014
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ID and creation science will not be accepted in the schools any time soon. However, when they do, they will not be taught alongside Darwinism and materialism. They will replace them. It will be a Kuhnian revolution. And for that to happen, the ID side will have to come up with something amazing that blows everybody's socks off. This is not something that will come about by debating the pros and cons of ID and creation with Darwinists and atheists.Mapou_{March 18, 2014
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By the way, I am now working on a monograph with the title On purpose: The evolution of design by means of natural selection, or the proliferation of intentional agents in the struggle for existence and another entitled The metaphysical foundations of biological science. I thought last year that I would be unable to finish them, as I had been diagnosed with pancreatic cancer. However, it turned out to be sclerosing autoimmune pancreatitis (a treatable condition), and so I am hopeful that I will be able to finish them. No matter what happens, these projects have made my life more interesting!Allen_MacNeill_{March 18, 2014
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Will Provine and I have repeatedly invited Michael Behe and Phillip Johnson to present with us at Cornell. Will has now retired to "emeritus" status, but I continue teaching evolutionary biology to Cornell students, and continue to try to present both sides of this issue to them. Let a hundred flowers bloom and a hundred schools of thought contend!Allen_MacNeill_{March 18, 2014
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Sorry about the open link. This site seriously needs an "edit" and/or "preview" option before posting.Allen_MacNeill_{March 18, 2014
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I agree with Larry (and disagree with Jerry Coyne). That's why I offered a seminar in evolutionary biology at Cornell in 2006 in which we read books by Behe, Dembski, Johnson, Mayr, Provine, and Ruse. Like Larry, we concluded that intelligent design is bad science (i.e. not religion). You can read about it here. Admittedly, our seminar was unlike the ID course at Ball State, in which the professor offering the course was advocating for ID, rather than critically examining it. In our seminar course we critically examined both sides of the issue as fairly as we could. As part of my effort to do so, I invited the president of the Cornell IDEA club (Hannah Maxson) to be a co-presenter, along with Will Provine (Cornell historian of science) and Warren Allmon, director of Ithaca's Museum of the Earth. As far as possible, I tried to act as a moderator between the two positions, with some success. By the end of the summer all of the participants agreed on this summary:
"Currently, there is abundant confirmative evidence for most of evolutionary theory (with the exception of the origin of life, the [origin of the] genetic code, and selected biochemical pathways) and virtually no empirical confirmative evidence for ID theory. Unless ID “theorists” take steps to become ID “scientists,” this situation is unlikely to change." [emphasis added] In my opinion, a perusal of the posts at this website continues to support this conclusion. Virtually none of them present positive empirical evidence in support of ID, nor do they propose methods of empirical validation/falsification of ID hypotheses. Rather, they merely criticize current evolutionary theory in much the same way that postmodernists criticize literature, movies, etc. And, like postmodernist criticism, they do not produce anything new or useful. Until this changes (if it ever does, which I personally doubt), ID will remain what we concluded it is now: "...a footnote to the progress of empirical science, of interest only to those interested in failed pseudo-scientific 'theories.'"
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A relatively safe place (at least in terms of legal barriers) is teaching it in the philosophy and religion departments, but then who would be qualified to teach it? Some years ago, I gave ID DVD's to a religion professor and he started showing them in class for years. So ID got taught that way at university. :-) Maybe it reached a few thousand students, but that's a drop in the bucket.... Another complication is we have formal ID literature, but it's not quite in the form that is usable in classrooms. In addition to free-speech problems, there are logistical problems. Few individuals are qualified to teach ID and creation. At the discovery institute, ID is taught by several scientists in their own specialization. So even there, they don't put the burden on one individual. Creation science would even be harder to teach as one would need to add more physics and geology to the mix, not to mention, the models are not quite as defensible as ID models. It's relatively easy to criticize Darwin, but several orders of magnitude to deal with the distant starlight problem. Few creationists will fare well on the distant starlight problem unless they are an OEC or YLC (young life creationists, old unviverse). The problem is that even if evidence is against mindless OOL and Darwinian evolution, a full-up creationist model is not even agreed upon by creationists. One of the problems is religion and philosophy departments are notoriously anti-Christian, anti-design. That may slowly be changing, but it is a problem. I tried to sell a department chair on the idea that he'd be over run with students wanting to take classes if ID and creation were offered. I conducted a poll (the results were even mentioned in the journal Nature) that 75% of students would be glad to get some of the Gen Ed requirements statisfied by taking such courses. At a campus of 20,000 students, that would be 15,000 students, and even if my poll was off by a factor of 10, that would still be 1,500 students! He'd have to hire some full-time faculty just to deal with the deluge of interest! I have to mention, I finally had to discontinue ID student clubs in part because biology faculty were dropping in and identifying the students who were part of the club! It would be logistically sensible for that reason not to have it taught in science departments. Some of the students in my club were persecuted and screamed at and otherwise intimidated by their professors. The way they behave on the internet is sometimes indicative of their behavior in the classroom and university. UD has been a vetting ground for some of the ideas of how to teach ID and creation science in simple, accessible, and unassailable ways. Some of the pioneering ID literature is still too technical to get through the general college audience. The Illustra Media DVD's, the programming of life are good pedagogical tools. Creation Science stuff however is overtly theological, too much discussion of theology and evangelism and world views, not enough circumspect, falsifiable and tentative science for university consumption. Much harder to get the same quality in creationist materials suitable for university classes since most of the material is more suitable for churches. It's good church stuff, not necessarily for secular universities! I asked a respected professor of Chemistry if he'd ever teach an ID course. He replied, "and commit career suicide?" It's more than just legal barriers, there are institutional barriers as well. One very shocking thing is Darwinist students giving pro-ID professors bad ratings! One biology professor who admitted to his students he believe in creation got bi-polar student ratings -- they were either very very good or awful -- nothing in between. He was well aware of the hostility of Darwinists students not wanting to hear the truth, even though he never taught ID in class. So again, free speech though legal is stymied by factors we may not even see. The institutional barriers are quite formidable. How can this be remedied? Don't know. The DI's summer seminar series is a small step in the right direction. We could start with churches and Christian schools and campus ministries. I've been utterly shocked at the chilly reception ID and creation science has received from churches and church related organizations. How many Catholic schools would feel comfortable teaching ID? Even evangelical protestant groups have given ID their fair share of the cold shoulder, It was a somewhat liberal professor of religion at a secular university who was even eager to show his students Privileged Planet. I've been horrified at how some seminaries treat the topic. I managed a few times to get students homework credits for attending my ID presentations, but I had to pull a lot of strings. The ID and creationist community might want to think about creative strategies to get college students credit for spending time studying these subjects. Some will say, "they can study it on their own." To which I say, "why not get credit and recognition for the time invested in learning?" Finally, it would be good that the classes are listed under stealth titles. Seeing "ID and Creation Science" on a school transcript my prejudice prospective employers and graduate schools from accepting that student. So there is yet another barrier. It is better to advertise the class as "Special Topics in Religion". The problem of free speech in the university isn't purely legal, that's only the first barrier!scordova_{March 18, 2014
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