Truthquest defense of ID

The problem for Darwinists is actually, as bad as it is laid out to be by Dr. Durston in this paper, far worse. As if, the probability of finding a novel protein by neo-Darwinian processes were not already overwhelmingly difficult, it is now found that amino acid positions in a functional protein sequence are interdependent to other amino acid positions, thus exponentially exasperating the problem for neo-Darwinists:

(A Reply To PZ Myers) Estimating the Probability of Functional Biological Proteins? Kirk Durston , Ph.D. Biophysics - 2012 Excerpt (Page 4): The Probabilities Get Worse This measure of functional information (for the RecA protein) is good as a first pass estimate, but the situation is actually far worse for an evolutionary search. In the method described above and as noted in our paper, each site in an amino acid protein sequence is assumed to be independent of all other sites in the sequence. In reality, we know that this is not the case. There are numerous sites in the sequence that are mutually interdependent with other sites somewhere else in the sequence. A more recent paper shows how these interdependencies can be located within multiple sequence alignments.[6] These interdependencies greatly reduce the number of possible functional protein sequences by many orders of magnitude which, in turn, reduce the probabilities by many orders of magnitude as well. In other words, the numbers we obtained for RecA above are exceedingly generous; the actual situation is far worse for an evolutionary search. http://powertochange.com/wp-content/uploads/2012/11/Devious-Distortions-Durston-or-Myers_.pdf

And here is the paper from Durston and company:

Statistical discovery of site inter-dependencies in sub-molecular hierarchical protein structuring - Kirk K Durston, David KY Chiu, Andrew KC Wong and Gary CL Li - 2012 Results The k-modes site clustering algorithm we developed maximizes the intra-group interdependencies based on a normalized mutual information measure. The clusters formed correspond to sub-structural components or binding and interface locations. Applying this data-directed method to the ubiquitin and transthyretin protein family multiple sequence alignments as a test bed, we located numerous interesting associations of interdependent sites. These clusters were then arranged into cluster tree diagrams which revealed four structural sub-domains within the single domain structure of ubiquitin and a single large sub-domain within transthyretin associated with the interface among transthyretin monomers. In addition, several clusters of mutually interdependent sites were discovered for each protein family, each of which appear to play an important role in the molecular structure and/or function. Conclusions Our results demonstrate that the method we present here using a k-modes site clustering algorithm based on interdependency evaluation among sites obtained from a sequence alignment of homologous proteins can provide significant insights into the complex, hierarchical inter-residue structural relationships within the 3D structure of a protein family. http://bsb.eurasipjournals.com/content/2012/1/8 "Why Proteins Aren't Easily Recombined, Part 2" - Ann Gauger - May 2012 Excerpt: "So we have context-dependent effects on protein function at the level of primary sequence, secondary structure, and tertiary (domain-level) structure. This does not bode well for successful, random recombination of bits of sequence into functional, stable protein folds, or even for domain-level recombinations where significant interaction is required." http://www.biologicinstitute.org/post/23170843182/why-proteins-arent-easily-recombined-part-2

Related notes:

“Close to a miracle” - October 2013 Excerpt: Getting function in the first place is tough going. Szostak did an experiment with Anthony Keefe in 2001. They tested 6 trillion peptides, each with 80 randomly selected amino acids, for ATP binding. “We were able to select out small, single-domain proteins that did bind ATP. But they were rare, on the order of one in 10^11 sequences,” says Szostak. “Getting function from randomness is hard.” For selection to start happening to peptides, there has to be that spark of function. How that spark appears remains the big, elusive question in the field of protein origin.,,, ,, under normal circumstances, about one-third of a modern cell’s resources is devoted to protein quality control and turnover. “We’re not talking about a few proteases here and there. We’re talking about substantial resources of the cell just for this routine maintenance,” says Lupas. “You wouldn’t have to commit this amount of resources if protein folding was not problematic.”,, Over all, what the field of protein evolution needs are some plausible, solid hypotheses to explain how random sequences of amino acids turned into the sophisticated entities that we recognize today as proteins. Until that happens, the phenomenon of the rise of proteins will remain, as Tawfik says, “something like close to a miracle.” http://www.asbmb.org/asbmbtoday/asbmbtoday_article.aspx?id=48961 How Proteins Evolved - Cornelius Hunter - December 2010 Excerpt: Comparing ATP binding with the incredible feats of hemoglobin, for example, is like comparing a tricycle with a jet airplane. And even the one in 10^12 shot, though it pales in comparison to the odds of constructing a more useful protein machine, is no small barrier. If that is what is required to even achieve simple ATP binding, then evolution would need to be incessantly running unsuccessful trials. The machinery to construct, use and benefit from a potential protein product would have to be in place, while failure after failure results. Evolution would make Thomas Edison appear lazy, running millions of trials after millions of trials before finding even the tiniest of function. http://darwins-god.blogspot.com/2010/12/how-proteins-evolved.html Physicists Discover Quantum Law of Protein Folding – February 22, 2011 Quantum mechanics finally explains why protein folding depends on temperature in such a strange way. Excerpt: First, a little background on protein folding. Proteins are long chains of amino acids that become biologically active only when they fold into specific, highly complex shapes. The puzzle is how proteins do this so quickly when they have so many possible configurations to choose from. To put this in perspective, a relatively small protein of only 100 amino acids can take some 10^100 different configurations. If it tried these shapes at the rate of 100 billion a second, it would take longer than the age of the universe to find the correct one. Just how these molecules do the job in nanoseconds, nobody knows.,,, Their astonishing result is that this quantum transition model fits the folding curves of 15 different proteins and even explains the difference in folding and unfolding rates of the same proteins. That's a significant breakthrough. Luo and Lo's equations amount to the first universal laws of protein folding. That’s the equivalent in biology to something like the thermodynamic laws in physics. http://www.technologyreview.com/view/423087/physicists-discover-quantum-law-of-protein/

bornagain77

October 16, 2013

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