Replies

https://uncommondescent.com/intelligent-design/evidence-for-irreducible-complexity-in-proteins/

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Excerpt: The accepted paradigm that proteins can tolerate nearly any amino acid substitution has been replaced by the view that the deleterious effects of mutations, and especially their tendency to undermine the thermodynamic and kinetic stability of protein, is a major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.ed.....lution.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/2.....51801.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/2.....55171.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/2.....91701.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/2.....92291.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.o.....ned-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/...../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-co.....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!