Uncommon Descent Serving The Intelligent Design Community

“What is Intelligent Design?” Lecture by William Dembski


Purple bacteria's light-harvesting prowess lies in highly symmetrical molecules - May 15, 2013 Excerpt: Purple bacteria are among Earth's oldest organisms, and among its most efficient in turning sunlight into usable chemical energy. Now, a key to their light-harvesting prowess has been explained through a detailed structural analysis by scientists at MIT.,,, You would not expect a regular structure, almost a perfect structure," as is found in this primitive microbe, he says. In these regular round complexes, Cao says, "nature only used certain symmetry numbers: mostly ninefold, some eightfold, very few tenfold. It's very selective." His group's mathematical analysis shows there are good reasons for that, he says. These ring-shaped molecules, in turn, are arranged in a hexagonal pattern on the spherical photosynthetic membrane of purple bacteria, Cao says. "With these symmetry numbers, the interactions between all pairs of the symmetric rings are optimized at the same time. … We believe that nature found the most robust structures in terms of energy transfer," Cao says. Both eightfold and tenfold symmetries also work, though not as well: Only a lattice made up of ninefold symmetric complexes can tolerate an error in either direction. "You want consecutive numbers so it can tolerate such mistakes," Cao says. http://phys.org/news/2013-05-secret-efficient-photosynthesis-purple-bacteria.html bornagain77
JonathanM has a new article up on ATP Synthase: ATP Synthase, an Energy-Generating Rotary Motor Engine - Jonathan M. May 15, 2013 http://www.evolutionnews.org/2013/05/atp_synthase_an_1072101.html bornagain77
Eric, I thought it was sarcasm too!,, Something along the lines of,, I have a combination 2/4-Wheel drive truck that senses when the terrain is rough and automatically switches from 2 to 4 wheel drive accordingly. Thus it is an inescapable conclusion that my truck was not designed. :) bornagain77
As I posted elsewhere: The ATP Synthase is a system that consists of two subsystems-> one for the flow of protons down an electrochemical gradient from the exterior to the interior and the other (a rotary engine) that generates ATP from ADP using the energy liberated by proton flow. These two processes are totally unrelated from a purely physiochemical perspective*- meaning there isn't any general principle of physics nor chemistry by which these two processes have anything to do with each other. Yet here they are. How is this evidence for Intelligent Design? Cause and effect relationships as in designers often take two totally unrelated systems and intergrate them into one. The ordering of separate subsystems to produce a specific effect that neither can do alone. And those subsystems are composed of the ordering of separate components to achieve a specified function. ATP synthase is not reducible to chance and necessity and also meets the criteria of design. * Emergent collective properties, networks, and information in biology, page 23:
In the same vein, ATP synthesis in mitochondria can be conceived of and explained only because there is a coupling between ATP-synthase, the enzyme responsible for ATP synthesis, and the electrochemical potential. Hence ATP synthesis emerges out of this coupling. The activity of ATP-synthase alone could have in no way explained ATP synthesis. It is the merit of Mitchell, to have shown that it is precisely the interaction between two different physico-chemical events that generates this novel remarkable property. (italics in original)
Next we take a look inside ATP synthase- “Thermodynamic efficiency and mechanochemical coupling of F1-ATPase”:
Abstract: F1-ATPase is a nanosized biological energy transducer working as part of FoF1-ATP synthase. Its rotary machinery transduces energy between chemical free energy and mechanical work and plays a central role in the cellular energy transduction by synthesizing most ATP in virtually all organisms. However, information about its energetics is limited compared to that of the reaction scheme. Actually, fundamental questions such as how efficiently F1-ATPase transduces free energy remain unanswered. Here, we demonstrated reversible rotations of isolated F1-ATPase in discrete 120° steps by precisely controlling both the external torque and the chemical potential of ATP hydrolysis as a model system of FoF1-ATP synthase. We found that the maximum work performed by F1-ATPase per 120° step is nearly equal to the thermodynamical maximum work that can be extracted from a single ATP hydrolysis under a broad range of conditions. Our results suggested a 100% free-energy transduction efficiency and a tight mechanochemical coupling of F1-ATPase.
Highly effiecient, irreducibly complex, and no way- physiochemcially to get the two subunits to come together-> there's no attraction and no coupling. See also: Davies et al., “Macromolecular organization of ATP synthase and complex I in whole mitochondria,” Proceedings of the National Academy of Sciences Tamás Beke-Somfai, Per Lincoln, and Bengt Nordén, “Double-lock ratchet mechanism revealing the role of [alpha]SER-344 in F0F1 ATP synthase,” Proceedings of the National Academy of Sciences Joe
If it developed a beneficial mutation that was selected for then it stands to reason that the other “irreducible complex” parts were also mutated in a step wise fashion.
I thought you were being sarcastic, but upon closer inspection it looks like you are serious. You can't possibly think this is a logical conclusion can you? If so, please go back to the drawing board and think again. Eric Anderson
OT: Skeptiko interview with Dr. Eben Alexander about his book, Proof of Heaven. http://castroller.com/podcasts/Skeptiko/3062162 bornagain77
JLA: Minor variation of an existing functional complex integratedly functional system is not equal to the origin thereof. ENV is not merely spinning. Notice, "The number of c-ring subunits varies between species from 5 to 17. This kind of bacterium normally has 12, but the extremophile version has 13." KF kairosfocus
Sorry Guys It looks like ATP Synthase is a product of darwinian evolution after all. If it developed a beneficial mutation that was selected for then it stands to reason that the other "irreducible complex" parts were also mutated in a step wise fashion. Of course, ENV news is spin doctoring it to safe face. http://www.evolutionnews.org/2013/05/evolution_found071671.html JLAfan2001
ba77: Thanks for the videos @3. The glycolysis pathway is interesting. Let's see: There is a 10-step pathway to produce ATP. Yet the first 5 steps actually consume ATP in order to change the sugar molecule and set things up for a larger amount of ATP production in the last 5 steps. Further, we have enzymatic catalysts operating, as well as a couple of irreversible reaction results at some steps. Sure, we can imagine how this complex, highly integrated, and carefully controlled system could come about through mutations in a series of slight, successive changes. Yeah, that's the ticket. It is astounding what some people will believe. Eric Anderson
OT: fairly new animation upload: 10 Step Glycolysis Pathway In ATP Production: An Overview - video (2013) http://www.youtube.com/watch?v=8Kn6BVGqKd8 At the 6:00 minute mark of the following video, Chris Ashcraft, PhD - molecular biology, gives us an overview of the Citric Acid Cycle, which is, after the 10 step Glycolysis Pathway, also involved in ATP production: Evolution vs ATP Synthase - Molecular Machine - video http://www.metacafe.com/watch/4012706 bornagain77
Supplemental note: Encoded ‘classical’ information such as what Drs. Dembski and Marks have demonstrated the conservation of,,, http://www.evoinfo.org/index/ ,,and such as what we find encoded in computer programs, and yes, as we find encoded in DNA, is found to be a subset of ‘transcendent’ (beyond space and time) quantum entanglement/information by the following method:,,,
Quantum knowledge cools computers: New understanding of entropy – June 2011 Excerpt: No heat, even a cooling effect; In the case of perfect classical knowledge of a computer memory (zero entropy), deletion of the data requires in theory no energy at all. The researchers prove that “more than complete knowledge” from quantum entanglement with the memory (negative entropy) leads to deletion of the data being accompanied by removal of heat from the computer and its release as usable energy. This is the physical meaning of negative entropy. Renner emphasizes, however, “This doesn’t mean that we can develop a perpetual motion machine.” The data can only be deleted once, so there is no possibility to continue to generate energy. The process also destroys the entanglement, and it would take an input of energy to reset the system to its starting state. The equations are consistent with what’s known as the second law of thermodynamics: the idea that the entropy of the universe can never decrease. Vedral says “We’re working on the edge of the second law. If you go any further, you will break it.” http://www.sciencedaily.com/releases/2011/06/110601134300.htm Quantum no-hiding theorem experimentally confirmed for first time Excerpt: In the classical world, information can be copied and deleted at will. In the quantum world, however, the conservation of quantum information means that information cannot be created nor destroyed. This concept stems from two fundamental theorems of quantum mechanics: the no-cloning theorem and the no-deleting theorem. A third and related theorem, called the no-hiding theorem, addresses information loss in the quantum world. According to the no-hiding theorem, if information is missing from one system (which may happen when the system interacts with the environment), then the information is simply residing somewhere else in the Universe; in other words, the missing information cannot be hidden in the correlations between a system and its environment. http://www.physorg.com/news/2011-03-quantum-no-hiding-theorem-experimentally.html
The implications of finding non-local, beyond space-time, quantum entanglement/information in molecular biology, on a massive scale, are fairly deep and dramatic to contemplate:
Does Quantum Biology Support A Quantum Soul? – Stuart Hameroff - video (notes in description) http://vimeo.com/29895068
Verse and Music:
Acts 17:28 for “‘In him we live and move and have our being’; as even some of your own poets have said, “‘For we are indeed his offspring.’ High School Musical 2 - You are the music in me http://www.youtube.com/watch?v=IAXaQrh7m1o
Very informative talk. It is amazing how articulate and focused Dr. Dembski was just speaking off the cuff like that. I think some of his best talks have been like that, where he, without prepared notes, just gives an overview of the situation. I would slightly disagree with Dr. Dembski on one point though. Whereas Dr. Demski holds that the empirical evidence from biology will only get us pointed in the right direction towards inferring a transcendent intelligence (i.e. God) for life, with evidence from cosmology and a beginning of the universe having to be brought in on top of the empirical evidence from biology, to make the inference towards God complete, I find that advances in science have brought forth empirical evidence from biology that directly implicates the a transcendent cause must be responsible for biological life. ,,, I commented on one such finding yesterday where they substantiated that a certain class of problems (traveling salesmen problems) are able to be accomplished very quickly by quantum computation,,
Speed Test of Quantum Versus Conventional Computing: Quantum Computer Wins - May 8, 2013 Excerpt: quantum computing is, "in some cases, really, really fast." McGeoch says the calculations the D-Wave excels at involve a specific combinatorial optimization problem, comparable in difficulty to the more famous "travelling salesperson" problem that's been a foundation of theoretical computing for decades.,,, "This type of computer is not intended for surfing the internet, but it does solve this narrow but important type of problem really, really fast," McGeoch says. "There are degrees of what it can do. If you want it to solve the exact problem it's built to solve, at the problem sizes I tested, it's thousands of times faster than anything I'm aware of. If you want it to solve more general problems of that size, I would say it competes -- it does as well as some of the best things I've looked at. At this point it's merely above average but shows a promising scaling trajectory." http://www.sciencedaily.com/releases/2013/05/130508122828.htm
The preceding finding goes a long way towards explaining how the following is even possible in biology:
Quantum Dots Spotlight DNA-Repair Proteins in Motion – March 2010 Excerpt: “How this system works is an important unanswered question in this field,” he said. “It has to be able to identify very small mistakes in a 3-dimensional morass of gene strands. It’s akin to spotting potholes on every street all over the country and getting them fixed before the next rush hour.” Dr. Bennett Van Houten – of note: A bacterium has about 40 team members on its pothole crew. That allows its entire genome to be scanned for errors in 20 minutes, the typical doubling time.,, These smart machines can apparently also interact with other damage control teams if they cannot fix the problem on the spot. http://www.sciencedaily.com/releases/2010/03/100311123522.htm
Of note: DNA repair machines ‘Fixing every pothole in America before the next rush hour’ is very similar to the traveling salesman problem. The traveling salesman problem is a NP-hard (read: very hard) problem in computer science; The problem involves finding the shortest possible route between cities, visiting each city only once. ‘Traveling salesman problems’ are notorious for keeping supercomputers busy for days.
NP-hard – examples http://en.wikipedia.org/wiki/NP-hard#Examples
and yes, the mechanism for quantum computation in DNA is now found to be present:
Quantum Information/Entanglement In DNA – Elisabeth Rieper – short video http://www.metacafe.com/watch/5936605/ Quantum entanglement between the electron clouds of nucleic acids in DNA – Elisabeth Rieper, Janet Anders and Vlatko Vedral – February 2011 http://arxiv.org/PS_cache/arxiv/pdf/1006/1006.4053v2.pdf Is DNA a quantum computer? Stuart Hameroff Excerpt: DNA could function as a quantum computers with superpositions of base pair dipoles acting as qubits. Entanglement among the qubits, necessary in quantum computation is accounted for through quantum coherence in the pi stack where the quantum information is shared,,, http://www.quantumconsciousness.org/dnaquantumcomputer1.htm
But what makes this evidence far more direct towards establishing a inference to a transcendent intelligence (i.e. God) for biology is that quantum entanglement requires a transcendent, beyond space-time, cause to explain its existence within biology (or within the universe for that matter).
Looking Beyond Space and Time to Cope With Quantum Theory – (Oct. 28, 2012) Excerpt: To derive their inequality, which sets up a measurement of entanglement between four particles, the researchers considered what behaviours are possible for four particles that are connected by influences that stay hidden and that travel at some arbitrary finite speed. Mathematically (and mind-bogglingly), these constraints define an 80-dimensional object. The testable hidden influence inequality is the boundary of the shadow this 80-dimensional shape casts in 44 dimensions. The researchers showed that quantum predictions can lie outside this boundary, which means they are going against one of the assumptions. Outside the boundary, either the influences can’t stay hidden, or they must have infinite speed.,,, The remaining option is to accept that (quantum) influences must be infinitely fast,,, “Our result gives weight to the idea that quantum correlations somehow arise from outside spacetime, in the sense that no story in space and time can describe them,” says Nicolas Gisin, Professor at the University of Geneva, Switzerland,,, http://www.sciencedaily.com/releases/2012/10/121028142217.htm The quantum (wave) state cannot be interpreted statistically - November 2011 http://lanl.arxiv.org/abs/1111.3328

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