Science doesn’t need a consensus, it forms a consensus based on the evidence. A consensus is what happened when the the majority of scientists who research and study a phenomenon agree with the conclusions drawn from the evidence. The introduction of new evidence can in some cases overturn a current consensus. Students entering into science as a vocation need to know and understand the current consensus views so they can do productive work. In that way they can be ready to challenge the consensus if and when it becomes necessary.
This is one of the basic things I’ve been trying to get across to Bill for years. Basic organic chemistry would dispel many of Bill’s misconceptions about protein sequence space. High school level organic chemistry would go a substantial way towards giving Bill a different picture of protein biochemistry.
In basic organic chemistry you are taught concepts like inter -and intramolecular binding and molecular charges. This provides the basis for understanding concepts like polarity, solvents, affinity and so on. Even a cursory glance at a modern period table will show there’s something called electronegativity, which explains some of the basic properties of attraction and repulsion of individual atoms. With these concepts understood, one can proceed to look at the chemical attributes of individual amino acids.
These first principles of chemistry, once understood, COMPLETELY undermines Bill’s view of how likely it is for proteins to fold, and bind substrates. Binding is UNAVOIDABLE at the molecular level.
I still remember being taught the concepts of protein sequences and structures. Primary structure, which is the sequence of amino acids, secondary structure like sheets, helices, turns and so on. The sizes, affinities, solubility, polarity and so on of the individual amino acids. One can’t take basic organic chemistry and fail to see how all this stuff about proteins folding and binding is utterly, utterly trivial.
The ironic thing is I was taught these concepts completely divorced of any evolutionary considerations, merely to understand what proteins are and how they function. And it was immediately apparent to me that any conceivable amino acid sequence will always have some non-zero level of affinity to any imaginable substrate, and that any substitution in that sequence will either increase or decrease that affinity by altering the surface of the total structure, and either producing an increase or decrease in exposure of parts of the structure with different binding attributes.
So does evolution. Which is why basically the total scientific community, following Darwin’s publication of The Origin of Species, eventually came to the consensus that evolution is true.
Generations of bible-believing geologists and paleontologists were convinced by the evidence from artificial breeding, comparative anatomy, and the fossil record, that evolution was a fact. Theoretical predictions about relative timings of fossils, and the stratigraphic and geographical distributions of species and fossils, consistently aligned. This all before the age of genetics. Eventually, over a century after the publication of The Origin, did scientists come to understand the mechanism of inheritance, and a new prediction was immediately born. The phylogenies inferred from comparative anatomy and paleontology must statistically significantly align with the phylogenies that will be able to be inferred from protein and nucleic acid sequences. There are famous, much-cited publications detailing these predictions before they were even tested. Before it was actually known whether they would.
Theobald cites one of these papers in his 29+ Evidences article:
“It will be determined to what extent the phylogenetic tree, as derived from molecular data in complete independence from the results of organismal biology, coincides with the phylogenetic tree constructed on the basis of organismal biology. If the two phylogenetic trees are mostly in agreement with respect to the topology of branching, the best available single proof of the reality of macro-evolution would be furnished. Indeed, only the theory of evolution, combined with the realization that events at any supramolecular level are consistent with molecular events, could reasonably account for such a congruence between lines of evidence obtained independently, namely amino acid sequences of homologous polypeptide chains on the one hand, and the finds of organismal taxonomy and paleontology on the other hand. Besides offering an intellectual satisfaction to some, the advertising of such evidence would of course amount to beating a dead horse. Some beating of dead horses may be ethical, when here and there they display unexpected twitches that look like life.”
Emile Zuckerkandl and Linus Pauling, discussing the possibility of the twin nested hierarchy before the first molecular phylogenies had been made.
(1965) “Evolutionary Divergence and Convergence in Proteins.” in Evolving Genes and Proteins , p. 101.
Just like general relativity predicts the behavior in the orbits of certain celestial bodies, and the gravitation affects on light passing those objects, which can be observationally verified. So does common descent predict the existence of certain observable patterns in the gene sequences of different organisms, which can then be observationally verified. It can even be modeled mathematically,
simulated in computers and shown to really do produce such patterns, and on shorter timescales observed in experimental populations.
How do you think it dispels my misconceptions? I know you have pitched that Axe was several orders of magnitude off in his experiments yet you never repeated his experiments. You used different proteins to support your claim.
Do you still believe that Axe was off his estimates by 60 orders of magnitude?
Can you describe his experiment precisely?
Do you think all proteins have the same requirements for sequence precision?
This claim appears to be correct however you now show differential binding based on sequence.
If sequence is not important how do we see preserved sequences over deep evolutionary time in some cases and not in others? How can proteins function if they cannot differentiate themselves? How do they differentiate themselves?
There is a very big difference here. General relativity can predict what the orbits will look like in the future evolution cannot. Evolution does not make future predictions of what the diversity of life will look like 2000 years from now. There is no general testable model here.
i think that is very matter. say that we want to change a watch into a cell-phone. it cant be done by small steps.
Science depends on teamwork.
I suggest you read some history. There was a lot of teamwork involved. The expression “Lorentz-Fitzgerald contraction” was not concocted out of thin air. It comes from the names of some of the other thinkers who influenced Einstein. Even then, relativity was at first quite controversial. It was the teamwork of scientists testing out its ideas that made it accepted science. And that cooperation is what builds the consensus. And, of course, the Michelson-Morley experiment was an important part of why relativity was accepted. And that’s more teamwork.
Yes, history tends to describe science as if it were the work of a few brilliant individuals. But it was never thus.
Valid points. Even more relevant with the current access to information via the internet.
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That’s a classic logic fallacy. (The Negative Association or Genetic Fallacy.) It makes good sense that the NCSE, founded to foster evolution education, would cooperate with other organizations which support evolution education. The fact that one of those groups happened to be atheist does not thereby automatically “taint” the educational objective of NCSE.
Did that atheist organization undertake the project as part of its own ideological agenda? Probably. But that doesn’t somehow transform the NCSE from an educationally-oriented organization to mere “political advocacy.”
Perhaps the NCSE has changed in some ways since the retirement of Dr. Scott. I don’t know. I for one always appreciated Dr. Scott’s insistence that the NCSE maintained its original educational purposes of fostering evolution education without getting distracted by secondary partisan agendas.
I will repeat my question for @colewd:
so what is your prediction? what finding we should not find if common descent is true?
Hi Allen
It has to do with teaching critical thinking vs indoctrination. The NCSE is about indoctrination as its two subjects are evolution and global warming which are two theories who’s grand claims lack a tested model and in the cased of evolution any predictive model of its grand claim. If a theory has weaknesses those should be discussed. If you do not discuss a theories weaknesses you are just selling ideology.
If any of these other subjects have controversial claims the unresolved issue should be discussed.
Evolutionary biology is taught in the public schools because evolutionary processes have been observed since before you and I were born. That is reality.
Likewise, climate change (or “global warming” in your post) is observed and is an undeniable reality. It is a fact. The “warmest years on record” statistics continue to astound and alarm us. Do you really think it likely that public school students are sufficiently trained in “critical thinking skills” to second guess climate scientists and reach better conclusions than the world’s most experienced climatologists? Yours is a view of education which sounds like ideology replacing learning real science. People all over the world are already suffering very real hardships (and threats to public health) due to the warming of the planet. Many Christ-followers are concerned about this. I certainly do.
Bill, what is your evidence that (1) “the kids are smart” and (2) are qualified to contradict the conclusions of climatologists?
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Allan
Have you read scientific papers on global warming? They are very different then what is sold to the public.
Can you show conclusively that it is driven by increased C02 levels. Are you claiming the models are tested and accurate at this point?
I hadn’t previously known that Bill is a global warming denier too. MAGA!
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Evolution denier, anthropogenic climate change denier, probably an anti-vaxxer and 911 conspiracy nutter too. Bill and science just don’t get along at all. 
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Bill, why do you keep dodging my questions? Your CO2 question was in response to my questions challenging your surprising claims. Here’s what I posted:
You also continue to dodge my question about your previous claim about public school pedagogy:
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They might not be. They may be simply dodging the political spin that Tim and John and show good command of. The spin term denier came from the NCSE.
This was the answer I gave.
If no two computer codes are the same out of 7 billion computers, how is that precise?
I am pointing out that your theory is based on the non-existence of any other system, and you need to evidence this premise.
That is a bare assertion. You need to evidence it.
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Whats precise is executing the code just like the cells ability to divide.
As you would say a bare assertion. 
Just picture in your mind evolving a spliceosome. Is the protein the works with PRPF8 completely independent of how PRPF8 is structured?
Please show us this precise operation in cells.
You have already claimed that the evolution of these systems is highly improbable. This necessitates the premise that these proteins are the only ones that could evolve. Your argument is based on this premise, and you need to evidence it.
You need to show the complete history of how PRPF8 emerged in eukaryotes, and the proteins that interacted with it as soon as it emerged.
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