Uncommon Descent Serving The Intelligent Design Community

Evidence for irreducible complexity in proteins


Using, as an illustration, a toy familiar to those who have spent time with small infants:

Tim describes the chirality problem as evidence against creation by chance. Tim Barnett, “Evidence for Intelligent Design in Proteins (Video)” at Stand to Reason

Hat tip: Ken Francis, author, with Theodore Dalrymple of The Terror of Existence: From Ecclesiastes to Theatre of the Absurd

Follow UD News at Twitter!

See also: Determining irreducible complexity using power sets

Bob O'H:
I don’t know of any serious model of abiogenesis that says that long polypeptides spontaneously formed.
Is there any evidence that short polypeptides can form? Is there any evidence that long polypeptides can form into functional proteins starting from a short polypeptide and adding amino acids? ET
Bob (and weave) O' Hara states:
" I don’t myself have a proposal to get around chirality: it’s not my area of expertise. But a quick google reveals there are several articles for non-scientists on the problem, so you might want to research that."
Oh goody. Bob expects me to not only defend my position but to also do his research on a problem he apparently assumed was non-existent. You simply can't make the arguments that Atheists try to use up. Nobody would believe somebody could be so obtuse. bornagain77
L There’s nothing special about proteins. :) E3 Ubiquitin Ligase TRIM Proteins, Cell Cycle and Mitosis Santina Venuto and Giuseppe Merla Cells 2019, 8(5), 510; https://doi.org/10.3390/cells8050510 OLV
ba77 - I don't myself have a proposal to get around chirality: it's not my area of expertise. But a quick google reveals there are several articles for non-scientists on the problem, so you might want to research that. Bob O'H
Bob O'H,
ba77 – No, I wasn’t saying anything about abiogenesis, I was responding to Tim Barnett’s argument, which wasn’t about it either. I don’t know of any serious model of abiogenesis that says that long polypeptides spontaneously formed.
Well Bob O'H how you 'seriously' propose to get around the elephant in the living room problem of Chirality at the origin of life I have no idea. I guess denying it is a problem, as you, apparently, are doing right now, might be one way to go about it. :) But others not so enamored to deny that monumental problems exist, might not find your particular 'scientific' method of denialism so appealing. The problem of 'left handed' homochirality is certainly of no small concern to any realistic Origin Of Life scenario put forth by evolutionists:
Homochirality and Darwin: part 2 - Robert Sheldon - May 2010 Excerpt: With regard to the deniers who think homochirality is not much of a problem, I only ask whether a solution requiring multiple massive magnetized black-hole supernovae doesn't imply there is at least a small difficulty to overcome? A difficulty, perhaps, that points to the non-random nature of life in the cosmos? https://uncommondesc.wpengine.com/intelligent-design/homochirality-and-darwin-part-2/ Life's 'Left-Handed' Amino Acids Still A Puzzle - Jun 29, 2013 Excerpt: Benner says it’s unlikely we will ever know Earth’s real route to biological chirality. https://www.forbes.com/sites/brucedorminey/2013/06/29/lifes-left-handed-amino-acids-remain-astrobiological-head-scratcher/
Here are 7 other problems, besides Chirality, that ensure that life by chance is untenable.
Chemistry by Chance: A Formula for Non-Life by Charles McCombs, Ph.D. Excerpt: The following eight obstacles in chemistry ensure that life by chance is untenable. 1. The Problem of Unreactivity 2. The Problem of Ionization 3. The Problem of Mass Action 4. The Problem of Reactivity 5. The Problem of Selectivity 6. The Problem of Solubility 7. The Problem of Sugar 8. The Problem of Chirality The chemical control needed for the formation of a specific sequence in a polymer chain is just not possible through random chance. The synthesis of proteins and DNA/RNA in the laboratory requires the chemist to control the reaction conditions, to thoroughly understand the reactivity and selectivity of each component, and to carefully control the order of addition of the components as the chain is building in size. http://www.icr.org/article/chemistry-by-chance-formula-for-non-life/
Moreover, even if I granted you all the molecules of life in whatever state of preparation you wanted the molecules to be in, and said to you. "here are the molecules of life, go and build a cell", you still would have no clue where to start:
Origin of Life: An Inside Story - Professor James Tour – May 1, 2016 Excerpt: “All right, now let’s assemble the Dream Team. We’ve got good professors here, so let’s assemble the Dream Team. Let’s further assume that the world’s top 100 synthetic chemists, top 100 biochemists and top 100 evolutionary biologists combined forces into a limitlessly funded Dream Team. The Dream Team has all the carbohydrates, lipids, amino acids and nucleic acids stored in freezers in their laboratories… All of them are in 100% enantiomer purity. [Let’s] even give the team all the reagents they wish, the most advanced laboratories, and the analytical facilities, and complete scientific literature, and synthetic and natural non-living coupling agents. Mobilize the Dream Team to assemble the building blocks into a living system – nothing complex, just a single cell. The members scratch their heads and walk away, frustrated… So let’s help the Dream Team out by providing the polymerized forms: polypeptides, all the enzymes they desire, the polysaccharides, DNA and RNA in any sequence they desire, cleanly assembled. The level of sophistication in even the simplest of possible living cells is so chemically complex that we are even more clueless now than with anything discussed regarding prebiotic chemistry or macroevolution. The Dream Team will not know where to start. Moving all this off Earth does not solve the problem, because our physical laws are universal. You see the problem for the chemists? Welcome to my world. This is what I’m confronted with, every day.“ James Tour – leading Chemist https://uncommondesc.wpengine.com/intelligent-design/origin-of-life-professor-james-tour-points-the-way-forward-for-intelligent-design/
Here is a recent scathing review of present day Origin of Life research:
James Tour: The Mystery of the Origin of Life – video – March 2019 https://www.youtube.com/watch?v=zU7Lww-sBPg James Tour defends his 2019 lecture here: http://www.jmtour.com/wp-content/uploads/John-West-on-Szostak-Article.pdf of note: James Tour is presently considered one the premiere Chemists in the world
ba77 - No, I wasn't saying anything about abiogenesis, I was responding to Tim Barnett's argument, which wasn't about it either. I don't know of any serious model of abiogenesis that says that long polypeptides spontaneously formed. Bob O'H
Bob @ 10,
it means his argument is utterly irrelevant to biology. Proteins do not form randomly from scratch.
Somebody needs a pee test! :) Besides it being central to the question of biological origins, are you saying, as ET pointed out, the proteins were therefore intelligently designed? bornagain77
Bob O'H:
Proteins do not form randomly from scratch.
They had to have. Or are you saying that living organisms were intelligently designed? ET
ba77 @ 4 -
And yet the speaker did not assume a living cell. He assumed building a protein from scratch.
Which is my point - it means his argument is utterly irrelevant to biology. Proteins do not form randomly from scratch. Bob O'H
Bob O'H:
Oh dear, what an awful argument.
And yet it is much better than any argument for the blind watchmaker. Bob doesn't grasp the fact that there isn't any evidence nor any way to test the claim that blinbd and mindless processes can produce proteins. ET
uploaded yesterday and highly relevant:
DNA Is Code: Who Coded It? (Science Uprising 03) https://www.youtube.com/watch?v=qxhuxg3WRfg&list=PLR8eQzfCOiS1OmYcqv_yQSpje4p7rAE7-&index=4
Here’s one of the papers referenced (through an EN article) by BA77 in his informative comments above: The ribosome can discriminate the chirality of amino acids within its peptidyl-transferase center Michael T. Englander, Joshua L. Avins, Rachel C. Fleisher, Bo Liu, Philip R. Effraim, Jiangning Wang, Klaus Schulten, Thomas S. Leyh, Ruben L. Gonzalez Jr., and Virginia W. Cornish PNAS May 12, 2015 112 (19) 6038-6043; first published April 27, 2015 https://doi.org/10.1073/pnas.1424712112 Edited by Ignacio Tinoco, Jr., University of California, Berkeley, CA, and approved March 24, 2015 (received for review January 8, 2015) OLV
BA77, Thank you for those very informative (as usual) comments @2, 4, 5. Really appreciate it. OLV
Of related note:
Origin: Probability of a Single Protein Forming by Chance - video https://www.youtube.com/watch?v=W1_KEVaCyaA Mathematical Basis for Probability Calculations Used in Origin PROBABILITY The estimated probability for a 150-amino-acid protein comes from the work of Douglas Axe and Stephen Meyer. Axe published a paper in 2004 that calculated the fraction of useful proteins in random chains of amino acids.b A “useful” protein must be able to fold into a stable structure to perform any function. Compared to the huge number of random chains that would not fold, the number of proteins with this ability is miniscule. After carefully measuring the tolerance to change in particular enzymes, Axe estimated that only one in 10^74 chains of 150 amino acids would fold and be functional. This implies that you would have to search through 10^74 chains of that length to find a single useful protein. So we start by looking for one protein (any chain of 150 amino acids) that could be useful in a primitive cell by spontaneously folding into a stable shape. In his book, Signature in the Cell,c Stephen Meyer recognized two additional constraints for the chance origin of a protein. First, amino acids need to be “one-handed.” In nature, amino acids (except the simplest, glycine) come in two forms: left-handed and right-handed. All living things use only the left-handed form. This is what gives proteins the ability to fold. Experiments show that random chains using both hands become useless lumps of molecules. Indeed, living cells cannot tolerate wrong-handed amino acids, and employ quality controls to ensure their amino acids are left-handed. The earliest imaginable life form could have used either left-handed or right-handed building blocks, but would have to select one or the other--and stick with it. With that constraint, Meyer assumes an additional 1-out-of-2 chance the correct form would be selected at each point in the chain (after the positioning of the first building block). For 150 amino acids, that becomes 0.5-149 or one chance in 10^45. The second constraint concerns the type of bond that must form between amino acids. Proteins use peptide bonds in which the H atom on one end joins with the OH atoms on the other end, releasing H20—a water molecule. (This, incidentally, is why proteins cannot be expected to form spontaneously in water, because peptide bond formation would go against chemistry’s law of mass action; such bonds would be far more likely to break than join.) Other bonds between amino acids, however, are possible. They result in clumps of useless “tar” as biochemists call it. Meyer assumed another 1-out-of-2 chance that each bond would be a peptide bond (a generous assumption). That decreases the probability by another 1045. Putting the probabilities together means adding the exponents. The probability of getting a properly folded chain of one-handed amino acids, joined by peptide bonds, is one chance in 1074+45+45, or one in 10^164 (Meyer, p. 212). This means that, on average, you would need to construct 10^164 chains of amino acids 150 units long to expect to find one that is useful. How long would that take? THE TIME PROBLEM The amoeba illustration used in Origin is adapted from the book Evolution: Possible or Impossible? by James F. Coppedge (ch. 6-7).d He constructed a fictional scenario to give readers a way to visualize the powerlessness of chance. In his memorable illustration, he set up a race between a world filled with amino acids and an amoeba . To give protein formation (by chance) the best possible circumstances to succeed, Coppedge imagined the Earth stocked with sets of amino acids, using all the available atoms of nitrogen, carbon, and oxygen on the planet—for a total of 10^41 possible sets. Although no one knows the exact quantities of these atoms, the 10^41 sets of 20 different amino acids estimated for our experiment is a very generous total. e We then calculated the self–assembly rate of 150-amino-acid chains at one chain per second. In the assumed 4.6-billion-year age of the earth, we could expect the construction of at least 1.45 x 10^58 chains. That is far short of the 10^164 chains that would have to self-assemble (on average) to expect one useful protein. So, now we can ask, how long would you have to wait before the single lucky protein forms? The answer can be calculated by letting the experiment run as long as necessary to expect, on average, a successful chain to form.f Dividing the number of trials needed by the rate of formation yields a waiting time of 3.15 x 10^115 years. That’s far, far longer than the assumed age of the entire universe (13.7 x 10^9 years). In ORIGIN, we set out to visualize how much time would be involved. THE TRAVELING AMOEBA First, we construct a bridge across the universe and position an amoeba that will carry a single atom from one end to the other. Using 90 billion light years as the assumed diameter of the observable universe, it would take the amoeba (traveling one foot per year), 5.7 x 10^27 years to travel across the universe, drop the atom off, and return for more. Since there are approximately 10^80 atoms in the universe, g the amoeba could transport them all in 5.7 x 10^107 years at one atom per round trip. But that number is seven orders of magnitude smaller than the time required for the protein to form by chance. Dividing one by the other, we learn that in the time we could expect chance to build one protein, the amoeba would have plenty of time--traveling just one foot per year, one atom per round trip--to haul over 56 million universes! http://www.originthefilm.com/mathematics.php
Bob O'Hara states,
"Oh dear, what an awful argument. (1) the living cell isn’t a lab, so all (or almost all?) amino acids are left handed. If the probability that you select an amino acid is 1, the probability of selecting 150 is, um, 1. (2) the cellular machinery only works with left-handed amino acids, so even if the mix was 50/50, it would just reject any right-handed amino acids."
And yet the speaker did not assume a living cell. He assumed building a protein from scratch. Thus his assumption for handedness is correct. If you cook up a batch of amino acids, sugars or their precursor molecules in a laboratory, you’ll always get a 50-50 mixture of left and right. Moreover Bob, in the second part of your response you state that the cellular machinery "would just reject any right-handed amino acids." Yet, you did not tell us how the machinery of the cell gained this amazing ability to discriminate between the two types of amino acids.
How Cells Keep Right-Handed Amino Acids Out - April 29, 2015 Excerpt: One of the wonders of life at the molecular scale -- a fact that defies chance -- is the purity of left-handed amino acids in proteins. Without this "homochirality," as it is known, proteins would never fold properly into the functional structures that make life possible. Theoretically, life could be built backwards, using only right-handed amino acids -- as long as the mixture is pure. But the cell's translation machinery (TM) would have to be redesigned to accommodate the change. (Note: left-handed amino acids are prefixed by L- and right-handed ones by D-). Whenever amino acids form naturally, they occur in "racemic" mixtures of L- and D- "isoforms." It's been a long-standing mystery in the origin-of-life community how cells first discriminated between them. The physical and thermodynamic properties of L- and D- forms are identical; the only way they can be discriminated in the lab is by seeing which way they rotate polarized light. How could a primordial soup lead to a homochiral protocell? Unless the TM already existed to discriminate between the isoforms, the probability of getting a usable protein of any functional length is vanishingly small.,,, ,,,(it is found that) the ribosome itself participates in the rejection of D-amino acids.,,, "Collectively, these methods have allowed us to conclusively demonstrate that the ribosome itself discriminates the chirality of the amino acid",,, Natural selection could not have operated before the first accurately replicating system (i.e. ribosome) arose. But without this complex proofreading and error-correcting equipment (made up of proteins and RNA) already in operation, functional proteins would be impossible. So how did the first proteins (and nucleic acids, which are also homochiral) arise from a primordial soup of racemic ingredients? The short answer is, they didn't. The improbability of that occurring exceeds the Universal Probability Bound. An inference to intelligent causation is thus warranted. http://www.evolutionnews.org/2015/04/how_cells_keep095601.html
Perhaps you care to tell us (or better yet, care to tell George Church) where the amazing ribosome came from Bob?
LIFE: WHAT A CONCEPT! Excerpt: The ribosome,,,, it's the most complicated thing that is present in all organisms.,,, you find that almost the only thing that's in common across all organisms is the ribosome.,,, So the question is, how did that thing come to be? And if I were to be an intelligent design defender, that's what I would focus on; how did the ribosome come to be? George Church http://www.edge.org/documents/life/church_index.html Paper Finds Functional Reasons For "Redundant" Codons, Fulfilling a Prediction from Intelligent Design - Casey Luskin - August 25, 2014 Excerpt: Redundancy of the genetic code enables translational pausing - Abel - 2014 Abstract: They write that the ribosome's ability to undergo translational pausing "reveal[s] the ribosome, among other things, to be not only a machine, but an independent computer-mediated manufacturing system." The paper even suggests, "Cause-and-effect physical determinism...cannot account for the programming of sequence-dependent biofunction." http://www.evolutionnews.org/2014/08/paper_finds_fun089301.html
Oh dear, what an awful argument. (1) the living cell isn't a lab, so all (or almost all?) amino acids are left handed. If the probability that you select an amino acid is 1, the probability of selecting 150 is, um, 1. (2) the cellular machinery only works with left-handed amino acids, so even if the mix was 50/50, it would just reject any right-handed amino acids. Bob O'H
Actually demonstrating the irreducible complexity of proteins is a bit more nuanced than that. To demonstrate that proteins are irreducibly complex you must demonstrate that the amino acids of the proteins are necessary for the protein to be functional and that removing or replacing the amino acids within the proteins will result in a loss of functionality for the protein.
“Mutations are rare phenomena, and a simultaneous change of even two amino acid residues in one protein is totally unlikely. One could think, for instance, that by constantly changing amino acids one by one, it will eventually be possible to change the entire sequence substantially… These minor changes, however, are bound to eventually result in a situation in which the enzyme has ceased to perform its previous function but has not yet begun its ‘new duties’. It is at this point it will be destroyed” Maxim D. Frank-Kamenetski, Unraveling DNA, 1997, p. 72. (Professor at Brown U. Center for Advanced Biotechnology and Biomedical Engineering) "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: per uncedu Stability effects of mutations and protein evolvability. October 2009 Excerpt: The accepted paradigm that proteins can tolerate nearly any amino acid substitution has been replaced by the view that the deleterious effects of mutations, and especially their tendency to undermine the thermodynamic and kinetic stability of protein, is a major constraint on protein evolvability,, - ncbi Darwin's God: Post Synaptic Proteins Intolerant of Change - December 2010 Excerpt: Not only is there scant evidence of intermediate designs leading to the known proteins, but the evidence we do have is that these proteins do not tolerate change. - darwin'sgod Extreme functional sensitivity to conservative amino acid changes on enzyme exteriors - Doug Axe Excerpt: Contrary to the prevalent view, then, enzyme function places severe constraints on residue identities at positions showing evolutionary variability, and at exterior non-active-site positions, in particular. http://nsmserver2.fullerton.edu/departments/chemistry/evolution_creation/web/AxeProteinEvolution.pdf Corticosteroid Receptors in Vertebrates: Luck or Design? - Ann Gauger - October 11, 2011 Excerpt: Based on a realistic population genetics model, we calculate that the waiting time for a bacterial population to acquire seven specific mutations in a duplicated gene, none of which provide any functional benefit until all seven are present, is something like 10^27 years. That’s a ten with 27 zeros after it. To put this in perspective, the age of the universe is believed to be on the order of 10^10 years. In response to our work, one critique was that we didn’t start with the right ancestral protein.,,, ,,, if merely changing binding preferences is hard, even when you start with the right ancestral form, then converting an enzyme to a new function is completely beyond the reach of unguided evolution, no matter where you start. http://www.evolutionnews.org/2011/10/luck_or_design051801.html Following the Evidence Where It Leads: Observations on Dembski's Exchange with Shapiro - Ann Gauger - January 2012 Excerpt: So far, our research indicates that genuine innovation, a change to a function not already pre-existent in a protein, is beyond the reach of natural processes, even when the starting proteins are very similar in structure. http://www.evolutionnews.org/2012/01/observations_re055171.html "Enzyme Families -- Shared Evolutionary History or Shared Design?" - Ann Gauger - December 4, 2014 Excerpt: If enzymes can't be recruited to genuinely new functions by unguided means, no matter how similar they are, the evolutionary story is false.,,, Taken together, since we found no enzyme that was within one mutation of cooption, the total number of mutations needed is at least four: one for duplication, one for over-production, and two or more single base changes. The waiting time required to achieve four mutations is 10^15 years. That's longer than the age of the universe. The real waiting time is likely to be much greater, since the two most likely candidate enzymes failed to be coopted by double mutations. We have now addressed two objections raised by our critics: that we didn't test the right mutation(s), and that we didn't use the right starting point. We tested all possible single base changes in nine different enzymes, Those nine enzymes are the most structurally similar of BioF's entire family We also tested 70 percent of double mutations in the two closest enzymes of those nine. Finally, some have said we should have used the ancestral enzyme as our starting point, because they believe modern enzymes are somehow different from ancient ones. Why do they think that? It's because modern enzymes can't be coopted to anything except trivial changes in function. In other words, they don't evolve! That is precisely the point we are making. http://www.evolutionnews.org/2014/12/a_new_paper_fro091701.html "Shared Evolutionary History or Shared Design?" - Ann Gauger - January 1, 2015 Excerpt: The waiting time required to achieve four mutations is 10^15 years. That's longer than the age of the universe. The real waiting time is likely to be much greater, since the two most likely candidate enzymes failed to be coopted by double mutations. http://www.evolutionnews.org/2015/01/happy_new_year092291.html
Simply put, the irreducible complexity of proteins is demonstrated by showing that amino acids are interdependent and/or 'context dependent' in regards to producing a functional protein, Moreover, Dr Gauger states that context dependent effects are found "at the level of primary sequence, secondary structure, and tertiary (domain-level) structure' of proteins.
"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
She is basically saying that there are three interlocking levels of irreducible complexity within proteins. That ‘contextual’ information resides along the entire 'irreducibly complex' protein structure is also established here
Proteins with cruise control provide new perspective: “A mathematical analysis of the experiments showed that the proteins themselves acted to correct any imbalance imposed on them through artificial mutations and restored the chain to working order.” http://www.princeton.edu/main/news/archive/S22/60/95O56/
Kirk Durston states that the context dependency and/or irreducible complexity of the amino acids of a protein "reduce the number of possible functional protein sequences by many orders of magnitude"
(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, (i.e. context dependent), 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
How many of orders of magnitude are the chances reduced by the interdependency and/or irreducible complexity of a protein? The following paper on quantum criticality gives us a glimpse,,,
Quantum criticality in a wide range of important biomolecules Excerpt: The permutations of possible energy levels of biomolecules is huge so the possibility of finding even one that is in the quantum critical state by accident is mind-bogglingly small and, to all intents and purposes, impossible.,, of the order of 10^-50 of possible small biomolecules and even less for proteins,”,,, “what exactly is the advantage that criticality confers?” https://medium.com/the-physics-arxiv-blog/the-origin-of-life-and-the-hidden-role-of-quantum-criticality-ca4707924552
In fact, since quantum entanglement/information falsified local realism in the first place, then the probability is zero. i.e. There is NO chance! Simply put, materialism has no beyond space and time cause to appeal to so as to explain 'non-local' quantum coherence in proteins. i.e. No possible cause equals no possible chance! bornagain77
If the premise is sound and the logic likewise, they should be told the argument is over. They lost. To get over it, because otherwise they are are continuing to dig the hole that will define them to all future generations. Axel

Leave a Reply