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Fred Sanger, Protein Sequences and Evolution Versus Science


The passing of the great biochemist Frederick Sanger this week reminds us of another one of evolution’s many scientific failures, namely the view that protein sequences are random. Here is how one obituaryexplains it:  Read more

A note on insulin:
Let us consider insulin, one of the simplest proteins. It has fifty-one possible locations for an L-amino acid to occupy. If we theoretically try every possible combination of putting the twenty different L-amino acids in the fifty-one places possible, and we filled a basket (large) with just one electron from all the combinations, the basket would weigh one-hundred billion times the weight of the earth!! More amazing yet.... The possibilities of making a specific one-hundred L-amino acid sequence into a desired protein by pure chance are even more astronomical, EVEN IF every atomic particle in the entire universe were dedicated to being L-amino acids. A universe full of L-amino acids trying totally new and unique combinations for groups of one-hundred, at the rate of a trillion times a second for thirty billion years, would have only a one in a trillion, trillion possibility of having made a specific one-hundred L-amino acid protein during that thirty billion years. In other words, only one trillion, trillionth of all the total combinations possible for a simple one-hundred L-amino acid protein would have been made during that thirty billion years!! The simplest life form on earth requires millions of proteins molecules which are divided into hundreds (or thousands) of different and distinctly shaped types. When considering the interwoven complexity required for these millions of precisely shaped protein molecules, it becomes apparent life originating, or evolving, by natural means is clearly impossible. (disclaimer: I am not a mathematician and the preceding calculations were 'back of the envelope' calculations from me)
Supplemental notes:
The Humpty-Dumpty Effect: A Revolutionary Paper with Far-Reaching Implications - Paul Nelson - October 23, 2012 Excerpt: Put simply, the Levinthal paradox states that when one calculates the number of possible topological (rotational) configurations for the amino acids in even a small (say, 100 residue) unfolded protein, random search could never find the final folded conformation of that same protein during the lifetime of the physical universe. http://www.evolutionnews.org/2012/10/a_revolutionary065521.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/ Francis Collins on Making Life Excerpt: 'We are so woefully ignorant about how biology really works. We still don't understand how a particular DNA sequence—when we just stare at it—codes for a protein that has a particular function. We can't even figure out how that protein would fold—into what kind of three-dimensional shape. And I would defy anybody who is going to tell me that they could, from first principles, predict not only the shape of the protein but also what it does.' - Francis Collins - Former Director of the Human Genome Project http://www.pbs.org/wgbh/nova/tech/collins-genome.html
Of note as to how far our simplistic thinking about the 'simple' cell has changed in the last few decades:
We have always underestimated cells. Undoubtedly we still do today. But at least we are no longer as naïve as we were when I was a graduate student in the 1960s. Then, most of us viewed cells as containing a giant set of second-order reactions: molecules A and B were thought to diffuse freely, randomly colliding with each other to produce molecule AB -- and likewise for the many other molecules that interact with each other inside a cell. This seemed reasonable because, as we had learned from studying physical chemistry, motions at the scale of molecules are incredibly rapid. Consider an enzyme, for example. If its substrate molecule is present at a concentration of 0.5mM,which is only one substrate molecule for every 105 water molecules, the enzyme's active site will randomly collide with about 500,000 molecules of substrate per second. And a typical globular protein will be spinning to and fro, turning about various axes at rates corresponding to a million rotations per second. But, as it turns out, we can walk and we can talk because the chemistry that makes life possible is much more elaborate and sophisticated than anything we students had ever considered. Proteins make up most of the dry mass of a cell. But instead of a cell dominated by randomly colliding individual protein molecules, we now know that nearly every major process in a cell is carried out by assemblies of 10 or more protein molecules. And, as it carries out its biological functions, each of these protein assemblies interacts with several other large complexes of proteins. Indeed, the entire cell can be viewed as a factory that contains an elaborate network of interlocking assembly lines, each of which is composed of a set of large protein machines." (Bruce Alberts, "The Cell as a Collection of Protein Machines: Preparing the Next Generation of Molecular Biologists," Cell, 92 (February 6, 1998): 291-294 (emphases added).) http://www.evolutionnews.org/2013/06/did_scientists_072871.html
Verse and music:
Deuteronomy 31:6 Be strong and courageous. Do not fear or be in dread of them, for it is the Lord your God who goes with you. He will not leave you or forsake you.” You Are I Am - Mercyme http://myktis.com/songs/you-are-i-am/

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