Now Evolution Must Have Evolved Different Functions Simultaneously in the Same Protein

_{Cornelius Hunter

December 1, 2012

Intelligent Design}

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Proteins consist of a long sequence of amino acids and those amino acids are supplied by the so-called transfer RNA, or tRNA, molecules. The tRNA molecules, in turn, are loaded with the right amino acid by the so-called aminoacyl-transfer RNA synthetases, or aaRS, proteins. There are several different versions of aaRS proteins, which load the different tRNA molecules with the different kinds of amino acids. These aaRS proteins hang around the ribosome where proteins are constructed. But as I discussed in the previous post, the lysine aaRS, also known as LysRS, has an interesting dual role. Normally it hangs around the ribosome where it binds to another LysRS to form what is known as a dimer. In this dimer configuration, there is a weak binding between (i) the 207th amino acid (a serine) of one of the LysRS proteins and (ii) the 540th and 541st amino acids (a glycine and a leucine, respectively) of the other LysRS protein. The serine side chain consists of a hydroxyl group attached to a methyl group and when the 207th amino acid’s hydroxyl group is phosphorylated (the hydrogen is replaced by a phosphate group), its binding to the opposing 540th and 541st amino acids is broken. Not surprisingly this allows the serine dimer to loosen. But this is only the beginning of a series of events caused by the phosphorylation of that serine. The serine molecules move away from the ribosome, enter the cell’s nucleus, interact with a DNA transcription factor causing (i) the production of a signaling molecule, diadenosine tetraphosphate, (ii) release of one of the transcription factor’s proteins and (iii) expression of the transcription factor’s target genes. Simply put, depending on the phosphorylation state of its 207th amino acid, LysRS has two different structural and functional states. When not phosphorylated LysRS is a crucial part of the translation process, supplying lysine amino acids to tRNA molecules. When phosphorylated it regulates gene expression. This is a major problem for evolutionary theory. Read more

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By the way, I would appreciate a comment on my own blog at www.billmaz.com. Thanks. billmaz

Thank you, Upright BiPed. billmaz

BillMaz, welcome to UD. Upright BiPed

billmaz, Actually 'tinkering' is not what the evidence is indicating: A. L. Hughes's New Non-Darwinian Mechanism of Adaption Was Discovered and Published in Detail by an ID Geneticist 25 Years Ago - Wolf-Ekkehard Lönnig - December 2011 Excerpt: The original species had a greater genetic potential to adapt to all possible environments. In the course of time this broad capacity for adaptation has been steadily reduced in the respective habitats by the accumulation of slightly deleterious alleles (as well as total losses of genetic functions redundant for a habitat), with the exception, of course, of that part which was necessary for coping with a species' particular environment....By mutative reduction of the genetic potential, modifications became "heritable". -- As strange as it may at first sound, however, this has nothing to do with the inheritance of acquired characteristics. For the characteristics were not acquired evolutionarily, but existed from the very beginning due to the greater adaptability. In many species only the genetic functions necessary for coping with the corresponding environment have been preserved from this adaptability potential. The "remainder" has been lost by mutations (accumulation of slightly disadvantageous alleles) -- in the formation of secondary species. http://www.evolutionnews.org/2011/12/a_l_hughess_new053881.html Genetic Entropy and The Mystery Of the Genome - Dr. John Sanford - video http://www.youtube.com/watch?v=GwCu4rh7kUk bornagain77

Dear bornagain77, sorry not to respond earlier. I want to make it clear that I am not an atheist. In fact, even if one takes those physicists who claim that, by using quantum theory, one can explain the "birth" of the universe from nothing, the question still remains, "Where did those mathematical equations of quantum physics come from?" If your case is that God created them, I have no way of quarreling with you. However, ID people like Behe doesn't say that. He claims a direct role for God or some other Intelligent Designer in the design of the form and function of organisms, not "just" in the mathematical laws that govern the universe. That is a very different proposition. It says that God is constantly involved in our physical world, tinkering with our DNA and with the process of evolution, creating organisms for some ultimate goal. Maybe the goal is embedded in the math, which is actually becoming more and more probable. If IDers stuck with that, I would not disagree. The problem is that there is no way of proving it. Science can only deal with what it can prove. ID doesn't have any way of using experimental evidence to prove its claims of direct design by an Intelligent Designer. It only uses deus ex machina as a fallback for things that evolution seems inadequate to as yet, in its present form, prove. As the ENCODE studies have recently shown, the genome is vastly more complex than previously imagined. Not only does the theory of evolution have to explain how the protein-coding genes evolved, but how the thousands of inter-connected mechanisms of gene expression evolved simultaneously. A tall order which will require a more robust theory of evolution, even a revolutionary one. Which doesn't mean that the laws of evolution, whatever they may turn out to be, were not pre-written into the mathematics of the universe by a god. billmaz

Also of related note is how precise, and mysterious, the 'roundness' of the Cosmic Microwave Background Radiation is:
The Cosmic Background Radiation Excerpt: These fluctuations are extremely small, representing deviations from the average of only about 1/100,000 of the average temperature of the observed background radiation. The highly isotropic nature of the cosmic background radiation indicates that the early stages of the Universe were almost completely uniform. This raises two problems for (a naturalistic understanding of) the big bang theory. First, when we look at the microwave background coming from widely separated parts of the sky it can be shown that these regions are too separated to have been able to communicate with each other even with signals traveling at light velocity. Thus, how did they know to have almost exactly the same temperature? This general problem is called the horizon problem. Second, the present Universe is homogenous and isotropic, but only on very large scales. For scales the size of superclusters and smaller the luminous matter in the universe is quite lumpy, as illustrated in the following figure. ,,, Thus, the discovery of small deviations from smoothness (anisotopies) in the cosmic microwave background is welcome, for it provides at least the possibility for the seeds around which structure formed in the later Universe. However, as we shall see, we are still far from a quantitative understanding of how this came to be. http://csep10.phys.utk.edu/astr162/lect/cosmology/cbr.html Wilkinson Microwave Anisotropy Probe - Main result Excerpt: The microwave background is very homogeneous in temperature (the relative variations from the mean, which presently is still 2.7 kelvins, are only of the order of 5x10?5.) http://en.wikipedia.org/wiki/Wilkinson_Microwave_Anisotropy_Probe#Main_result
From initial entropic considerations, the precision of the initial isotropic (uniform) condition of the 'sphere of the universe' really stands out:
The Physics of the Small and Large: What is the Bridge Between Them? Roger Penrose Excerpt: "The time-asymmetry is fundamentally connected to with the Second Law of Thermodynamics: indeed, the extraordinarily special nature (to a greater precision than about 1 in 10^10^123, in terms of phase-space volume) can be identified as the "source" of the Second Law (Entropy)." How special was the big bang? - Roger Penrose Excerpt: This now tells us how precise the Creator's aim must have been: namely to an accuracy of one part in 10^10^123. (from the Emperor’s New Mind, Penrose, pp 339-345 - 1989)
Also of interest is two other places in the universe where 'unexpected roundness' is found:
Sun's Almost Perfectly Round Shape Baffles Scientists - (Aug. 16, 2012) — Excerpt: The sun is nearly the roundest object ever measured. If scaled to the size of a beach ball, it would be so round that the difference between the widest and narrow diameters would be much less than the width of a human hair.,,, They also found that the solar flattening is remarkably constant over time and too small to agree with that predicted from its surface rotation. http://www.sciencedaily.com/releases/2012/08/120816150801.htm
and this 'unexpected roundness':
Bucky Balls - Andy Gion Excerpt: Buckyballs (C60; Carbon 60) are the roundest and most symmetrical large molecule known to man. Buckministerfullerine continues to astonish with one amazing property after another. C60 is the third major form of pure carbon; graphite and diamond are the other two. Buckyballs were discovered in 1985,,, http://www.3rd1000.com/bucky/bucky.htm
It should be noted that Sir Fred Hoyle converted from atheism to Deism/Theism after he discovered the stunning precision from which carbon is synthesized in stars: The flatness of the ‘entire’ universe, which 'coincidentally' corresponds to the diameter of pi in Euler’s identity, is found on this following site; (of note this flatness of the universe is an extremely finely tuned condition for the universe that could have, in reality, been a multitude of different values than 'flat'):
Did the Universe Hyperinflate? – Hugh Ross – April 2010 Excerpt: Perfect geometric flatness is where the space-time surface of the universe exhibits zero curvature (see figure 3). Two meaningful measurements of the universe’s curvature parameter, ½k, exist. Analysis of the 5-year database from WMAP establishes that -0.0170 < ½k < 0.0068.4 Weak gravitational lensing of distant quasars by intervening galaxies places -0.031 < ½k < 0.009.5 Both measurements confirm the universe indeed manifests zero or very close to zero geometric curvature,,, http://www.reasons.org/did-universe-hyperinflate
This following video shows that the universe also has a primary characteristic of expanding/growing equally in all places, which 'coincidentally' strongly corresponds to the 'e' in Euler's identity. 'e' is the constant that is used in equations of math for finding what the true rates of growth and decay are for any given mathematical problem trying to find as such in this universe:
Centrality of Earth Within The 4-Dimensional Space-Time of General Relativity - video http://www.metacafe.com/w/8421879
This following video shows how finely tuned the '4-Dimensional' expansion of the universe is (1 in 10^120);
Fine Tuning Of Dark Energy and Mass of the Universe - Hugh Ross - video http://www.metacafe.com/watch/4007682
Here are the verses in the Bible, which were written over 2000 years before the discovery of the finely tuned expansion of the universe by 'Dark Energy', that speak of God 'Stretching out the Heavens'; Job 9:8; Isaiah 40:22; Isaiah 40:24; Isaiah 48:13; Zechariah 12:1; Psalm 104:2; Isaiah 42:5; Isaiah 45:12; Isaiah 51:13; Jeremiah 51:15; Jeremiah 10:12. The following verse is one of my favorites out of the group of verses:
Job 9:8 He alone stretches out the heavens and treads on the waves of the sea.
Towards the end of the following video, Michael Denton speaks of the square root of negative 1 being necessary to understand the foundational quantum behavior of this universe. The square root of -1 is also 'coincidentally' found in Euler's identity:
Michael Denton – Mathematical Truths Are Transcendent And Beautiful – Square root of -1 is built into the fabric of reality – video http://www.metacafe.com/watch/4003918
I find it extremely strange that the enigmatic Euler's identity, which was deduced centuries ago, would find such striking correlation to how reality is actually found to be structured by modern science. In pi we have correlation to the 'sphere of the universe' as revealed by the Cosmic Background radiation, as well pi correlates to the finely-tuned 'geometric flatness' within the 'sphere of the universe' that has now been found. In 'e' we have the fundamental constant that is used for ascertaining exponential growth in math that strongly correlates to the fact that space-time is 'expanding/growing equally' in all places of the universe. In the square root of -1 we have what is termed a 'imaginary number', which was first proposed to help solve equations like x2+ 1 = 0 back in the 17th century, yet now, as Michael Denton pointed out in the preceding video, it is found that the square root of -1 is required to explain the behavior of quantum mechanics in this universe. The correlation of Euler's identity, to the foundational characteristics of how this universe is constructed and operates, points overwhelmingly to a transcendent Intelligence, with a capital I, which created this universe! It should also be noted that these universal constants, pi,e, and square root -1, were at first thought by many to be completely transcendent of any material basis, to find that these transcendent constants of Euler's identity in fact 'govern' material reality, in such a foundational way, should be enough to send shivers down any mathematicians spine. Myself, I'm more partial to the Fibonacci Number, rather than to fractals, for showing God's fingerprint on nature:
Nature by Numbers – The Fingerprint of God - video https://vimeo.com/9953368
bornagain77

billmaz as to:
It is becoming clear that evolution itself uses fractals to develop new functions for all manner of biological entities by reusing already existing structures to form slightly new versions with different uses.
How exactly is it, billmaz, that you know for a fact that 'evolution' uses fractals and that it is not an Intelligent Designer that uses fractals (if they so be used as you claim)?? The phrase 'evolution uses', as you have used it to signify implementing a mathematical structure onto a material substrate, denotes a personification of possessiveness that belongs solely to the realm of conscious Intelligent Designers. Moreover mathematical equations themselves are shown to be incomplete and do not stand on their own as to their existence but are contingent on a external cause, i.e. God, for their validity:
Kurt Gödel - Incompleteness Theorem - video http://www.metacafe.com/w/8462821 THE GOD OF THE MATHEMATICIANS - DAVID P. GOLDMAN - August 2010 Excerpt: we cannot construct an ontology that makes God dispensable. Secularists can dismiss this as a mere exercise within predefined rules of the game of mathematical logic, but that is sour grapes, for it was the secular side that hoped to substitute logic for God in the first place. Gödel's critique of the continuum hypothesis has the same implication as his incompleteness theorems: Mathematics never will create the sort of closed system that sorts reality into neat boxes. http://www.firstthings.com/article/2010/07/the-god-of-the-mathematicians
Notes: Sometimes atheists will appeal to chaos theory to explain how complexity can arise from simplicity in this universe. A vivid example of what they are proposing is here:
Mandelbrot Set Zoom - video http://www.youtube.com/watch?v=gEw8xpb1aRA
Yet in criticism to complexity 'naturally' arising from simplicity, as is assumed in chaos/fractal theory, it should be noted that, at the very least, two very different equations, rather than chaos/fractal equations, govern the foundational structure of the universe. One equation governs micro actions of the universe, and the other equation governs the macro shape of the universe: The following is the equation that governs 'micro' actions:
Finely Tuned Big Bang, Elvis In The Multiverse, and the Schroedinger Equation - Granville Sewell - audio http://www.metacafe.com/watch/4233012
At the 4:00 minute mark of the preceding audio, Dr. Sewell comments on the ‘transcendent’ and ‘constant’ Schroedinger’s Equation;
‘In chapter 2, I talk at some length on the Schroedinger Equation which is called the fundamental equation of chemistry. It’s the equation that governs the behavior of the basic atomic particles subject to the basic forces of physics. This equation is a partial differential equation with a complex valued solution. By complex valued I don’t mean complicated, I mean involving solutions that are complex numbers, a+bi, which is extraordinary that the governing equation, basic equation, of physics, of chemistry, is a partial differential equation with complex valued solutions. There is absolutely no reason why the basic particles should obey such a equation that I can think of except that it results in elements and chemical compounds with extremely rich and useful chemical properties. In fact I don’t think anyone familiar with quantum mechanics would believe that we’re ever going to find a reason why it should obey such an equation, they just do! So we have this basic, really elegant mathematical equation, partial differential equation, which is my field of expertise, that governs the most basic particles of nature and there is absolutely no reason why, anyone knows of, why it does, it just does. British physicist Sir James Jeans said “From the intrinsic evidence of His creation, the great architect of the universe begins to appear as a pure mathematician”, so God is a mathematician to’.
i.e. the Materialist/Atheist is at a complete loss to explain why this should be so, whereas the Christian Theist presupposes such ‘transcendent’ control of our temporal, material, reality,,,
John 1:1 In the beginning was the Word, and the Word was with God, and the Word was God. of note; 'the Word' is translated from the Greek word ‘Logos’. Logos happens to be the word from which we derive our modern word ‘Logic’.
The following is a very 'different' equation that is found to govern the 'macro' structure of the universe:
0 = 1 + e ^(i*pi) — Euler
Believe it or not, the five most important numbers in mathematics are tied together, through the complex domain in Euler's number, And that points, ever so subtly but strongly, to a world of reality beyond the immediately physical. Many people resist the implications, but there the compass needle points to a transcendent reality that governs our 3D 'physical' reality.
God by the Numbers - Connecting the constants Excerpt: The final number comes from theoretical mathematics. It is Euler's (pronounced "Oiler's") number: e^pi*i. This number is equal to -1, so when the formula is written e^pi*i+1 = 0, it connects the five most important constants in mathematics (e, pi, i, 0, and 1) along with three of the most important mathematical operations (addition, multiplication, and exponentiation). These five constants symbolize the four major branches of classical mathematics: arithmetic, represented by 1 and 0; algebra, by i; geometry, by pi; and analysis, by e, the base of the natural log. e^pi*i+1 = 0 has been called "the most famous of all formulas," because, as one textbook says, "It appeals equally to the mystic, the scientist, the philosopher, and the mathematician.",,, The discovery of this number gave mathematicians the same sense of delight and wonder that would come from the discovery that three broken pieces of pottery, each made in different countries, could be fitted together to make a perfect sphere. It seemed to argue that there was a plan where no plan should be.,,, Today, numbers from astronomy, biology, and theoretical mathematics point to a rational mind behind the universe.,,, The apostle John prepared the way for this conclusion when he used the word for logic, reason, and rationality—logos—to describe Christ at the beginning of his Gospel: "In the beginning was the logos, and the logos was with God, and the logos was God." When we think logically, which is the goal of mathematics, we are led to think of God. http://www.christianitytoday.com/ct/2006/march/26.44.html?start=3
(of note; Euler's Number (equation) is more properly called Euler's Identity in math circles.) Moreover Euler’s Identity, rather than just being the most enigmatic equation in math, finds striking correlation to how our 3D reality of this universe is actually structured,,, The following picture, Bible verse, article, and videos are very interesting since, with the discovery of the Cosmic Microwave Background Radiation (CMBR), the universe is found to actually be a circular sphere which 'coincidentally' corresponds to the circle of pi within Euler's identity:
Picture of CMBR https://webspace.utexas.edu/reyesr/SolarSystem/cmbr.jpg Proverbs 8:26-27 While as yet He had not made the earth or the fields, or the primeval dust of the world. When He prepared the heavens, I was there, when He drew a circle on the face of the deep, The Known Universe by AMNH – video - (please note the 'centrality' of the Earth in the universe in the video) http://www.youtube.com/watch?v=17jymDn0W6U Planck satellite unveils the Universe -- now and then (w/ Video showing the mapping of the 'sphere' of the Cosmic Microwave Background Radiation with the satellite) - 2010 http://phys.org/news197534140.html#nRlv
bornagain77

One of the most significant discoveries in genomics is that the genome as well as the cytoplasm have chaotic properties. Fractal geometry (an elemnt of chaos theory) is characterized by self-similarity (the bifurcating branches of a tree, the circulatory and neural systems of the body) and self-similarity at various levels of magnification (main arteries go to smaller arteries to arterioles to capillaries). Fractals also occur in time (heart rhythm, brain activity). We also know that protein surfaces are fractal, as well as mass, hydrophobicity, and polarization distribution of protein interiors. Many other protein properties are also fractal, as described in the good review by Banerji below. It is becoming clear that evolution itself uses fractals to develop new functions for all manner of biological entities by reusing already existing structures to form slightly new versions with different uses. For a fuler discussion of chaos theory and evolution visit http://www.billmaz.com. 1) Banerji A, Ghosh I (2011) Fractal symmetry of protein interior: what have we learned? Cell. Mol. Life Sci. DOI 10.1007/s00018-011-0722-6 billmaz

OT: Waikele Christmas Light Display 2012 - video http://www.youtube.com/watch?v=PEDMErtIhIU bornagain77

Here is a good condensed comment on the 'non-evidence' for protein evolution:
Now Evolution Must Have Evolved Different Functions Simultaneously in the Same Protein - Cornelius Hunter - Dec. 1, 2012 Excerpt comment section: In one study evolutionists estimated the number of attempts that evolution could possibly have to construct a new protein. Their upper limit was 10^43. The lower limit was 10^21. http://rsif.royalsocietypublishing.org/content/5/25/953.long These estimates are optimistic for several reasons, but in any case they fall short of the various estimates of how many attempts would be required to find a small protein. One study concluded that 10^63 attempts would be required for a relatively short protein. http://www.ncbi.nlm.nih.gov/pubmed/2199970 And a similar result (10^65 attempts required) was obtained by comparing protein sequences. http://www.sciencedirect.com/science/article/pii/0022519377900443 Another study found that 10^64 to 10^77 attempts are required. http://www.ncbi.nlm.nih.gov/pubmed/15321723 And another study concluded that 10^70 attempts would be required. In that case the protein was only a part of a larger protein which otherwise was intact, thus making the search easier. http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0000096 These estimates are roughly in the same ballpark, and compared to the first study giving the number of attempts possible, you have a deficit ranging from 20 to 56 orders of magnitude. Of course it gets much worse for longer proteins. http://darwins-god.blogspot.com/2012/12/now-evolution-must-have-evolved.html?showComment=1354423575480#c6691708341503051454
bornagain77

The serine molecules move away from the ribosome, enter the cell’s nucleus, interact with a DNA transcription factor causing (i) the production of a signaling molecule...
Dr. Hunter. Do they perform the same function in non-eukaryotes? How do they pass through the nuclear membrane? Mung

Allostery and cooperativity revisited Mung

The comments section of the posting in the OP has some interesting links. Mung

In fact, evolutionists have accepted so many contradictions and false predictions that new contradictions have little impact. Evolutionists simply make vague speculations and move on.
Evolutionary theory rots the mind. Mung

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