Stephen Meyer - Proteins by Design - Doing The Math

Evolution vs. Functional Proteins - Doug Axe - Video
http://www.metacafe.com/watch/4018222

Stephen Meyer - Functional Proteins And Information For Body Plans - video
http://www.metacafe.com/watch/4050681

Nothing In Molecular Biology Is Gradual - Doug Axe PhD. - video
http://www.metacafe.com/watch/5347797/

"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.

Estimating the prevalence of protein sequences adopting functional enzyme folds: Doug Axe:
Excerpt: Starting with a weakly functional sequence carrying this signature, clusters of ten side-chains within the fold are replaced randomly, within the boundaries of the signature, and tested for function. The prevalence of low-level function in four such experiments indicates that roughly one in 10^64 signature-consistent sequences forms a working domain. Combined with the estimated prevalence of plausible hydropathic patterns (for any fold) and of relevant folds for particular functions, this implies the overall prevalence of sequences performing a specific function by any domain-sized fold may be as low as 1 in 10^77, adding to the body of evidence that functional folds require highly extraordinary sequences.
http://www.ncbi.nlm.nih.gov/pubmed/15321723

Minimal Complexity Relegates Life Origin Models To Fanciful Speculation - Nov. 2009
Excerpt: Based on the structural requirements of enzyme activity Axe emphatically argued against a global-ascent model of the function landscape in which incremental improvements of an arbitrary starting sequence "lead to a globally optimal final sequence with reasonably high probability". For a protein made from scratch in a prebiotic soup, the odds of finding such globally optimal solutions are infinitesimally small- somewhere between 1 in 10exp140 and 1 in 10exp164 for a 150 amino acid long sequence if we factor in the probabilities of forming peptide bonds and of incorporating only left handed amino acids.
http://www.arn.org/blogs/index.php/2/2009/11/10/minimal_complexity_relegates_life_origin

The Case Against a Darwinian Origin of Protein Folds - Douglas Axe - 2010
Excerpt Pg. 11: "Based on analysis of the genomes of 447 bacterial species, the projected number of different domain structures per species averages 991. Comparing this to the number of pathways by which metabolic processes are carried out, which is around 263 for E. coli, provides a rough figure of three or four new domain folds being needed, on average, for every new metabolic pathway. In order to accomplish this successfully, an evolutionary search would need to be capable of locating sequences that amount to anything from one in 10^159 to one in 10^308 possibilities, something the neo-Darwinian model falls short of by a very wide margin."
http://bio-complexity.org/ojs/index.php/main/article/view/BIO-C.2010.1

Shortcuts to new protein folds - October 2010
Excerpt: Axe concludes that all of these putative shortcuts are dead ends. The Darwinian search mechanism is not capable of finding new protein folds by random sampling and all the shortcuts to new folds are dead ends.
http://idintheuk.blogspot.com/2010/10/shortcuts-to-new-protein-folds.html

The probabilities against life 'spontaneously' originating are simply overwhelming:

In fact Dean Kenyon, who was a leading Origin Of Life researcher as well as a college textbook author on the subject, admitted after years of extensive research:

"We have not the slightest chance for the chemical evolutionary origin of even the simplest of cells".

Origin Of Life? - Probability Of Protein And The Information Of DNA - Dean Kenyon - video
http://www.youtube.com/watch?v=9VhR2BHhxeo

Signature in the Cell - Book Review - Ken Peterson
Excerpt: If we assume some minimally complex cell requires 250 different proteins then the probability of this arrangement happening purely by chance is one in 10 to the 164th multiplied by itself 250 times or one in 10 to the 41,000th power.
http://www.spectrummagazine.org/reviews/book_reviews/2009/10/06/signature_cell

In fact years ago Fred Hoyle arrived at approximately the same number, one chance in 10^40,000, for life spontaneously arising. From this number, Fred Hoyle compared the random emergence of the simplest bacterium on earth to the likelihood “a tornado sweeping through a junkyard might assemble a Boeing 747 therein”. Fred Hoyle also compared the chance of obtaining just one single functioning protein molecule, by chance combination of amino acids, to a solar system packed full of blind men solving Rubik’s Cube simultaneously.

Professor Harold Morowitz shows the Origin of Life 'problem' escalates dramatically over the 1 in 10^40,000 figure when working from a thermodynamic perspective,:

"The probability for the chance of formation of the smallest, simplest form of living organism known is 1 in 10^340,000,000. This number is 10 to the 340 millionth power! The size of this figure is truly staggering since there is only supposed to be approximately 10^80 (10 to the 80th power) electrons in the whole universe!"
(Professor Harold Morowitz, Energy Flow In Biology pg. 99, Biophysicist of George Mason University)

Dr. Don Johnson lays out some of the probabilities for life in this following video:

Probabilities Of Life - Don Johnson PhD. - 38 minute mark of video
a typical functional protein - 1 part in 10^175
the required enzymes for life - 1 part in 10^40,000
a living self replicating cell - 1 part in 10^340,000,000
http://www.vimeo.com/11706014

Dr. Morowitz did another probability calculation working from the thermodynamic perspective with a already existing cell and came up with this number:

DID LIFE START BY CHANCE?
Excerpt: Molecular biophysicist, Horold Morowitz (Yale University), calculated the odds of life beginning under natural conditions (spontaneous generation). He calculated, if one were to take the simplest living cell and break every chemical bond within it, the odds that the cell would reassemble under ideal natural conditions (the best possible chemical environment) would be one chance in 10^100,000,000,000. You will have probably have trouble imagining a number so large, so Hugh Ross provides us with the following example. If all the matter in the Universe was converted into building blocks of life, and if assembly of these building blocks were attempted once a microsecond for the entire age of the universe. Then instead of the odds being 1 in 10^100,000,000,000, they would be 1 in 10^99,999,999,916 (also of note: 1 with 100 billion zeros following would fill approx. 20,000 encyclopedias)
http://members.tripod.com/~Black_J/chance.html

The Theist holds the Intellectual High-Ground - March 2011
Excerpt: To get a range on the enormous challenges involved in bridging the gaping chasm between non-life and life, consider the following: “The difference between a mixture of simple chemicals and a bacterium, is much more profound than the gulf between a bacterium and an elephant.” (Dr. Robert Shapiro, Professor Emeritus of Chemistry, NYU)
http://www.faithfulnews.com/contents/view_content2/49631/rabbi-moshe-averick-the-theist-holds-the-intellectual-high-ground-apologetics-christian-apologetics-defending-gospel

Ilya Prigogine was an eminent chemist and physicist who received two Nobel Prizes in chemistry. Regarding the probability of life originating by accident, he said:

“The statistical probability that organic structures and the most precisely harmonized reactions that typify living organisms would be generated by accident, is zero.”
Ilya Prigogine, Gregoire Nicolis, and Agnes Babloyantz, Physics Today 25, pp. 23-28.

Book Review - Meyer, Stephen C. Signature in the Cell. New York: HarperCollins, 2009.
Excerpt: As early as the 1960s, those who approached the problem of the origin of life from the standpoint of information theory and combinatorics observed that something was terribly amiss. Even if you grant the most generous assumptions: that every elementary particle in the observable universe is a chemical laboratory randomly splicing amino acids into proteins every Planck time for the entire history of the universe, there is a vanishingly small probability that even a single functionally folded protein of 150 amino acids would have been created. Now of course, elementary particles aren't chemical laboratories, nor does peptide synthesis take place where most of the baryonic mass of the universe resides: in stars or interstellar and intergalactic clouds. If you look at the chemistry, it gets even worse—almost indescribably so: the precursor molecules of many of these macromolecular structures cannot form under the same prebiotic conditions—they must be catalysed by enzymes created only by preexisting living cells, and the reactions required to assemble them into the molecules of biology will only go when mediated by other enzymes, assembled in the cell by precisely specified information in the genome.
So, it comes down to this: Where did that information come from? The simplest known free living organism (although you may quibble about this, given that it's a parasite) has a genome of 582,970 base pairs, or about one megabit (assuming two bits of information for each nucleotide, of which there are four possibilities). Now, if you go back to the universe of elementary particle Planck time chemical labs and work the numbers, you find that in the finite time our universe has existed, you could have produced about 500 bits of structured, functional information by random search. Yet here we have a minimal information string which is (if you understand combinatorics) so indescribably improbable to have originated by chance that adjectives fail.
http://www.fourmilab.ch/documents/reading_list/indices/book_726.html

Abiogenic Origin of Life: A Theory in Crisis - Arthur V. Chadwick, Ph.D.
Excerpt: The synthesis of proteins and nucleic acids from small molecule precursors represents one of the most difficult challenges to the model of prebiological evolution. There are many different problems confronted by any proposal. Polymerization is a reaction in which water is a product. Thus it will only be favored in the absence of water. The presence of precursors in an ocean of water favors depolymerization of any molecules that might be formed. Careful experiments done in an aqueous solution with very high concentrations of amino acids demonstrate the impossibility of significant polymerization in this environment. A thermodynamic analysis of a mixture of protein and amino acids in an ocean containing a 1 molar solution of each amino acid (100,000,000 times higher concentration than we inferred to be present in the prebiological ocean) indicates the concentration of a protein containing just 100 peptide bonds (101 amino acids) at equilibrium would be 10^-338 molar. Just to make this number meaningful, our universe may have a volume somewhere in the neighborhood of 10^85 liters. At 10^-338 molar, we would need an ocean with a volume equal to 10^229 universes (100, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000) just to find a single molecule of any protein with 100 peptide bonds. So we must look elsewhere for a mechanism to produce polymers. It will not happen in the ocean.
http://origins.swau.edu/papers/life/chadwick/default.html

Moreover changing one functional protein to another functional protein is also found to be extremely constrained:

When Theory and Experiment Collide — April 16th, 2011 by Douglas Axe
Excerpt: Based on our experimental observations and on calculations we made using a published population model [3], we estimated that Darwin’s mechanism would need a truly staggering amount of time—a trillion trillion years or more—to accomplish the seemingly subtle change in enzyme function that we studied.
http://biologicinstitute.org/2011/04/16/when-theory-and-experiment-collide/

Dollo’s law, the symmetry of time, and the edge of evolution - Michael Behe - Oct 2009
Excerpt: Nature has recently published an interesting paper which places severe limits on Darwinian evolution.,,,
A time-symmetric Dollo’s law turns the notion of “pre-adaptation” on its head. The law instead predicts something like “pre-sequestration”, where proteins that are currently being used for one complex purpose are very unlikely to be available for either reversion to past functions or future alternative uses.
http://www.evolutionnews.org/2009/10/dollos_law_the_symmetry_of_tim.html

Severe Limits to Darwinian Evolution: - Michael Behe - Oct. 2009
Excerpt: The immediate, obvious implication is that the 2009 results render problematic even pretty small changes in structure/function for all proteins — not just the ones he worked on.,,,Thanks to Thornton’s impressive work, we can now see that the limits to Darwinian evolution are more severe than even I had supposed.
http://www.evolutionnews.org/2009/10/severe_limits_to_darwinian_evo.html#more

"A problem with the evolution of proteins having new shapes is that proteins are highly constrained, and producing a functional protein from a functional protein having a significantly different shape would typically require many mutations of the gene producing the protein. All the proteins produced during this transition would not be functional, that is, they would not be beneficial to the organism, or possibly they would still have their original function but not confer any advantage to the organism. It turns out that this scenario has severe mathematical problems that call the theory of evolution into question. Unless these problems can be overcome, the theory of evolution is in trouble."
Problems in Protein Evolution:
http://www.cs.unc.edu/~plaisted/ce/blocked.html

Intelligent Design - The Anthropic Hypothesis
http://lettherebelight-77.blogspot.com/2009/10/intelligent-design-anthropic-hypothesis_19.html

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