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Does the human genome have “serious molecular shortcomings”?

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John Avise commences his paper with a quotation from Michael Behe affirming that research into the molecular workings of the cell leads unambiguously to the conclusion: “design!” To counter this, Avise presents the human genome as clear evidence for non-sentient design. He thinks that conventional evolutionary mechanisms are perfectly capable of explaining complexity, declaring: “it is not my intent here to repeat the voluminous evidence for how natural selection in conjunction with other nonsentient evolutionary forces can yield complex adaptations”. Instead, he suggests that the decision as to whether the design is intelligent or non-sentient can be made by looking at the imperfections and flaws evident in the cell’s molecular systems.

“Both a Creator God and natural selection are powerful shaping forces that might be expected to have engineered beautiful functionality and efficiency into complex biological features, such as the human genome. The much greater challenge – for proponents of ID and for scientists alike – is to explain complex biological traits that operate inefficiently or even malfunction overtly. On closer inspection, the human genome itself becomes a prime example of a highly complex trait with serious molecular shortcomings.”

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suckerspawn, It definitely is not in bacteria's best interest to kill its host. The most successful ones have a symbiotic/helpful relationship with its host rather than killing it. My hypothesis about viruses is that they once had (and maybe some still do) a useful function. Perhaps some viruses target and kill cancer cells. Who knows. I'd love to hear more of the research that that creation scientist is doing. Collin
Other research in the creationist camp. When did "good" bacteria turn "bad"? http://www.youtube.com/watch?v=a_CLIGJW6Ic suckerspawn
Biblical creationists who accept and insist on Genesis being a accurate witness know that the fall of man into sin changed everything. Its not true that God created and everything works from that point. there was a major disaster in biology. So this guys saying there are unlikely flaws in our bodies if a creator was involved is not dealing with historic creationism. Indeed everything in order to deal with a new blood and guts world had to change within and without everything of their bodies. likewise all biology was put into a new gear for maintaining life. The creator created great complexity but not death. Yet death and chasing it away is the main occupation of biology. Adam did not need or have anything in him to fight disease. There was no disease or possible injury to the body. So no defence mechanisms. So everything was a later change from the original creation. I know this is a I.D. place but biblical creationism can answer these things quite well. Robert Byers
I just loaded this video on the polyfunctionality of DNA: DNA - Evolution Vs. Polyfuctionality http://www.metacafe.com/w/4614519 This page gives a better example than Sodoku" DNA - Poly-Functional Complexity equals Poly-Constrained Complexity http://docs.google.com/Doc?docid=0AYmaSrBPNEmGZGM4ejY3d3pfMjdoZmd2emZncQ Further notes: As former president of the French Academy of Sciences Pierre P. Grasse has stated: “What is the use of their unceasing mutations, if they do not change? In sum, the mutations of bacteria and viruses are merely hereditary fluctuations around a median position; a swing to the right, a swing to the left, but no final evolutionary effect.” Random Mutations Destroy Information - Perry Marshall - video http://www.metacafe.com/watch/4023143 Needless to say, this limit to the variability of "simple" single cell organism, bacteria, and viruses, is extremely bad news for the materialist. Materialists simply do not have the "beneficial" mutations they need to make evolution work. The following site has numerous quotes, studies and videos which reveal the overwhelmingly negative mutation rate which has been found in life: Mutation Studies, Videos, And Quotes http://docs.google.com/Doc?docid=0AYmaSrBPNEmGZGM4ejY3d3pfMjZjZnM5M21mZg Evolution vs. Genetic Entropy - video http://www.metacafe.com/watch/4028086 bornagain77
David Tyler, My point and it is not really much different than yours is that there are 50 or more processes that somehow modify a genome (courtesy of Allan MacNeil) and these processes will indeed create some junk. So on that there is nothing we disagree on. The one thing I push occasionally and I do not know if this can be researched is that the process itself that produces these changes is great design. In other words micro evolution and all the mechanisms that produce change is great design and allows variation to happen and adaptation to proceed so that an organism can adapt to changing environments. If I were designing something to fit into an environment for hundreds of thousands if not millions of years then that would be mandatory. But I would also design into it limitations because without these limitations there would be a high probability that some change would overwhelm an environment and destroy the ecology and the organism in the process. We see both these things in life. The ability to change but definite limitations on the range of changes possible. The most obvious limitation we see is life expectancy. Somehow things do not live longer and Darwinian processes would definitely favor the longer living members of the population. To me this is the most damning finding for applicability of Darwinian processes to more than just minor adaptations. jerry
bornagain77 @ 2 and 3 Thanks for answering your own question! Yes, we have every reason to be wary of mutations and examples of benefits always seem to be linked to some other threatening affliction. Regarding your lactase example, I have blogged on it here: http://www.arn.org/blogs/index.php/literature/2006/12/26/do_you_take_milk_with_your_muesli jerry @ 4 "But to say that none is junk is also nonsense based on what we know today." I don't think anyone is claiming that none is junk - if we recognise mutations at all, then there will be junk. Examples of degradation are present. However, design perspectives have never, to my knowledge, swallowed the claim that 98% of the human genome is junk. The driver for that has been theory (Darwinism) and ignorance. The design approach is not to infer that because we do not know what non-coding DNA does, it has no function, but rather to infer that it must have a function (thereby stimulating reasearch to find out what that functionality is!). bornagain77 @ 10 Yes, a good excerpt. My blog on this topic is here: http://www.arn.org/blogs/index.php/literature/2010/04/11/the_molecular_revolution_s_unfulfilled_p David Tyler
and this beaut that just came out: Human Genome “Infinitely More Complex” Than Expected - April 2010 Excerpt: Hayden acknowledged that the “junk DNA” paradigm has been blown to smithereens. “Just one decade of post-genome biology has exploded that view,” she said, speaking of the gene regulation was a straightforward, linear process of gene coding for regulator protein that controls transcription. “Biology’s new glimpse at a universe of non-coding DNA – what used to be called ‘junk’ DNA – has been fascinating and befuddling.” If it’s junk, why would the human body decode 74% to 93& of it? The plethora of small RNAs produced by these non-coding regions, and how they interact with each other and with DNA, was completely unexpected when the project began.,,, In the heady post-genome years, systems biologists started a long list of projects built on this strategy, attempting to model pieces of biology such as the yeast cell, E. coli, the liver and even the ‘virtual human’. So far, all these attempts have run up against the same roadblock: there is no way to gather all the relevant data about each interaction included in the model.,,, The p53 network she spoke of is a good example of unexpected complexity. Discovered in 1979, the p53 protein was first thought to be a cancer promoter, then a cancer suppressor. “Few proteins have been studied more than p53,” she said. “...Yet the p53 story has turned out to be immensely more complex than it seemed at first.” She gave some details: "Researchers now know that p53 binds to thousands of sites in DNA, and some of these sites are thousands of base pairs away from any genes. It influences cell growth, death and structure and DNA repair. It also binds to numerous other proteins, which can modify its activity, and these protein–protein interactions can be tuned by the addition of chemical modifiers, such as phosphates and methyl groups. Through a process known as alternative splicing, p53 can take nine different forms, each of which has its own activities and chemical modifiers. Biologists are now realizing that p53 is also involved in processes beyond cancer, such as fertility and very early embryonic development. In fact, it seems willfully ignorant to try to understand p53 on its own. Instead, biologists have shifted to studying the p53 network, as depicted in cartoons containing boxes, circles and arrows meant to symbolize its maze of interactions. Network theory is now a new paradigm that has replaced the one-way linear diagram of gene to RNA to protein. That used to be called the “Central Dogma” of genetics. Now, everything is seen to be dynamic, with promoters and blockers and interactomes, feedback loops, feed-forward processes, and “bafflingly complex signal-transduction pathways.” http://www.creationsafaris.com/crev201004.htm#20100405a bornagain77
Does the human genome have “serious molecular shortcomings”? well let's see what the evidence says, 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 Moreover the first DNA code in life had to be at least as complex as the current DNA code found universally in life: “Because of Shannon channel capacity that previous (first) codon alphabet had to be at least as complex as the current codon alphabet (DNA code), otherwise transferring the information from the simpler alphabet into the current alphabet would have been mathematically impossible” Donald E. Johnson – Bioinformatics: The Information in Life 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. DNA - The Genetic Code - Optimal Error Minimization & Parallel Codes - Dr. Fazale Rana - video http://www.metacafe.com/watch/4491422 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. Here, we show that the universal genetic code can efficiently carry arbitrary parallel codes much better than the vast majority of other possible genetic codes.... the present findings support the view that protein-coding regions can carry abundant parallel codes. http://genome.cshlp.org/content/17/4/405.full The data compression of some stretches of human DNA is estimated to be up to 12 codes thick (12 different ways of DNA transcription) (Trifonov, 1989). (This is well beyond the complexity of any computer code ever written by man). John Sanford - Genetic Entropy The multiple codes of nucleotide sequences. Trifonov EN. - 1989 Excerpt: Nucleotide sequences carry genetic information of many different kinds, not just instructions for protein synthesis (triplet code). http://www.ncbi.nlm.nih.gov/pubmed/2673451 As well as coding optimization, DNA is also optimized to prevent damage from light: DNA Optimized for Photostability Excerpt: These nucleobases maximally absorb UV-radiation at the same wavelengths that are most effectively shielded by ozone. Moreover, the chemical structures of the nucleobases of DNA allow the UV-radiation to be efficiently radiated away after it has been absorbed, restricting the opportunity for damage. The materialist must also account for the overriding complex architectural organization of DNA: DNA Packaging: Nucleosomes and Chromatin each of us has enough DNA to go from here to the Sun and back more than 300 times, or around Earth's equator 2.5 million times! How is this possible? Dr. Jerry Bergman, "Divine Engineering: Unraveling DNA's Design": The DNA packing process is both complex and elegant and is so efficient that it achieves a reduction in length of DNA by a factor of 1 million. DNA Wrapping (Histone Protein Wrapping to Cell Division)- video http://www.youtube.com/watch?v=gbSIBhFwQ4s Human DNA is like a computer program but far, far more advanced than any software we've ever created. Bill Gates, The Road Ahead, 1996, p. 188 The Coding Found In DNA Surpasses Man's Ability To Code - Stephen Meyer - video http://www.metacafe.com/watch/4050638 Bill Gates, in recognizing the superiority found in Genetic Coding, compared to the best computer coding we now have, has now funded research into this area: Welcome to CoSBi - (Computational and Systems Biology) Excerpt: Biological systems are the most parallel systems ever studied and we hope to use our better understanding of how living systems handle information to design new computational paradigms, programming languages and software development environments. The net result would be the design and implementation of better applications firmly grounded on new computational, massively parallel paradigms in many different areas. http://www.cosbi.eu/index.php/component/content/article/171 Yet the DNA code is not even reducible to the laws of physics or chemistry: Life’s Irreducible Structure Excerpt: “Mechanisms, whether man-made or morphological, are boundary conditions harnessing the laws of inanimate nature, being themselves irreducible to those laws. The pattern of organic bases in DNA which functions as a genetic code is a boundary condition irreducible to physics and chemistry." Michael Polanyi - Hungarian polymath - 1968 - Science (Vol. 160. no. 3834, pp. 1308 – 1312) “an attempt to explain the formation of the genetic code from the chemical components of DNA… is comparable to the assumption that the text of a book originates from the paper molecules on which the sentences appear, and not from any external source of information.” Dr. Wilder-Smith The Capabilities of Chaos and Complexity - David L. Abel - 2009 Excerpt: "A monstrous ravine runs through presumed objective reality. It is the great divide between physicality and formalism. On the one side of this Grand Canyon lies everything that can be explained by the chance and necessity of physicodynamics. On the other side lies those phenomena than can only be explained by formal choice contingency and decision theory—the ability to choose with intent what aspects of ontological being will be preferred, pursued, selected, rearranged, integrated, organized, preserved, and used. Physical dynamics includes spontaneous non linear phenomena, but not our formal applied-science called “non linear dynamics”(i.e. language,information). http://www.mdpi.com/1422-0067/10/1/247/pdf etc.. etc.. bornagain77
"it is not my intent here to repeat the voluminous evidence for how natural selection in conjunction with other nonsentient evolutionary forces can yield complex adaptations" Aside from various appeals to sequence homologies (such as chromosome #2), does such evidence actually exist??? Well, here goes another argument from evil. Just goes to show that as design becomes more apparent, less choose to challenge that conclusion. Why bother explaining something in light of whatever theory you propose when you can just "psychoanalyze" the proposed intelligence in question and claim to know ahead of time what it ought to produce? F2XL
"... as clear evidence for non-sentient design ..." You mean 'sapient' (relating to wisdom), not 'sentient' (relating to sensation/perception) ... even slugs are sentient. Ilion
John Avise:
“it is not my intent here to repeat the voluminous evidence for how natural selection in conjunction with other nonsentient evolutionary forces can yield complex adaptations”.
The volume here must be in reference to the amount of hot air, not the amount of solid evidence. SCheesman
Concerning the explanation of the genesis of 'molecular workings of the cell'.... Mr. Avise responds that, "the voluminous evidence for how natural selection in conjunction with other nonsentient evolutionary forces can yield complex adaptations." Wow. I did not know that scientists like Mr. Avise already have access to the 'voluminous evidence' which finally demonstrates how molecular motors developed in piecemeal fashion via naturally selective processes. Can anyone show me what this evidence consists of? I may have had my head sunk deep inside a sand-hole for too long. JPCollado
I believe there is useless stuff in the human genome. I have no hard data for that and would have no problem if I was proven wrong. But I have a theory that the genome does get modified over time by various processes that are well understood and this process was built in or designed. This is a process that allows genomes to adapt to changing environments. And it is possible that some of these changes are not productive nor harmful and thus junk. That does not say that most is junk or even a large proportion only that there is good reason to believe that some is. Can some of this junk become useful in the long run. Probably some small percentage can and it appears that the percentage is indeed very small. The only rational way to deal with this is based on percentages and right now the positive benefits are so small that to say they account for much is nonsense based on today's understanding. But to say that none is junk is also nonsense based on what we know today. jerry
David Tyler I found his reference: Inside the Human Genome: A Case for Non-Intelligent Design - Pg. 57 By John C. Avise Excerpt: "Another compilation of gene lesions responsible for inherited diseases is the web-based Human Gene Mutation Database (HGMD). Recent versions of HGMD describe more than 75,000 different disease causing mutations identified to date in Homo-sapiens." http://books.google.com/books?id=M1PRvkPBKfQC&pg=PA57&lpg=PA57&dq=human+75,000+different+disease-causing+mutations&source=bl&ots=gkjosjq030&sig=gAU5AfzMehArJYinSxb2EMaDL94&hl=en&ei=kbDqS_SQLYS8lQfLpJ2cBA&sa=X&oi=book_result&ct=result&resnum=6&ved=0CCMQ6AEwBQ#v=onepage&q=human%2075%2C000%20different%20disease-causing%20mutations&f=false I went to the mutation database website and found: HGMD®: Now celebrating our 100,000 mutation milestone! http://www.biobase-international.com/pages/index.php?id=hgmddatabase I really question their use of the word "celebrating". here is their main site: HGMD® http://www.hgmd.cf.ac.uk/ac/index.php But as you pointed out David, the burning question is where in the world are all the hypothetical beneficial mutations??? The two most popular examples given Sickle cell and Lactase persistence, Sickle Cell is only beneficial in a limited sense and clearly detrimental in a molecular sense. Whereas Lactase persistence is the same in that it confers an advantage but it loses information in the genome for turning the lactase enzyme off. thus both of the most popular examples cited by evolutionists lose functional information. bornagain77
David Tyler, This caught my attention, "75,000 different disease-causing mutations," I would love to have a reference for that. Do you happen to know if there is one? bornagain77
In other words, "I wouldn't have done that if I were God. Therefore there is no God." Didn't know he was an authority on the behavior of omniscient beings... EvilSnack

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