Fair enough. But the picture of a ZFP “bumping around”, fomented solely by collisions with solvent or solute, still doesn’t make sense, as it is going to be moving about in a cell much as do ions, sugar molecules, and other small molecules.
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For the reader’s benefit regarding Brownian motion and Zinc Fingers:
https://aip.scitation.org/doi/10.1063/1.4810915
The predictable engineering of well-behaved transcriptional circuits is a central goal of synthetic biology. The artificial attachment of promoters to transcription factor genes usually results in noisy or chaotic behaviors, and such systems are unlikely to be useful in practical applications. Natural transcriptional regulation relies extensively on protein-protein interactions to insure tightly controlled behavior, but such tight control has been elusive in engineered systems. To help engineer protein-protein interactions, we have developed a molecular dynamics simulation framework that simplifies features of proteins moving by constrained Brownian motion, with the goal of performing long simulations.
…
For example, in constructing artificial DNA-binding proteins to bind to arbitrarily chosen sequences, it is straightforward to fuse zinc-finger proteins to match a given DNA target, but binding to non-target sequences needs to be minimized by quantitative tuning. In addition, actual binding to DNA may involve bending around the DNA helix, which may require either flexible attachment points to be introduced into the protein or use of multiple subunits that non-covalently assemble onto DNA. The simulation tools we propose here could also be used for designing novel DNA-binding complexes, or artificial proteins acting at any other step in signal transduction.
A good vizualization of microstate vs. macrostate from:
http://universe-review.ca/R01-02-z1-information04.htm
Since there are cells, this doesn’t seem to be a hurdle for evolution.
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A post was merged into an existing topic: Is Evolutionary Biology a “Soft” Science?
I don’t know those people. Are they scientists? Are they at all familiar with evolutionary biology? Most importantly, do they agree with you that only experimental science is real science?
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If you say that in class, you’ll be teaching falsehoods.
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I suppose so. The number of possible permutations in the example is 2.37 x 10^150, so those are pretty long odds. You’d have to have a lot of trials before you could reasonably expect them to come up all heads.
OTOH, if we were only tossing two coins, the odds are 1/4. Pretty good chance you would get it on your first try, and a near certainty you’d get it in at most a matter of minutes.
So if I said the odds of functional protein arising thru evolution it similar to that of two coins coming up heads, would you buy that argument? If not, why should we buy the argument you similarly just pulled out of thin air?
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Agreed.
So if I said the odds of functional protein arising thru evolution it similar to that of two coins coming up heads, would you buy that argument? If not, why should we buy the argument you similarly just pulled out of thin air?
Some proteins,such as TopoIsomerase and Helicase I consider highly improbable as a matter of principle. There is a thread that is discussion those issue now.
Maybe you should take some classes before pulling slides out of context and telling people who work in the field that you understand it better than they do?
Just a thought…
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As I thought, it’s the Texas sharpshooter argument. A particular sequence is highly unlikely, and the specification is a posteriori. No thought as to whether a different sequence could perform the same function, or a similar function, or another function that would result in a viable substitute for the observed function.
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@stcordova This may have occurred to you already, but you should note the sort of objections made here, and make these objections known to your students. Your students will most certainly encounter these same objections themselves.
For example, if the “Texas Sharpshooter” might be a criticism, then it would help your students to know how that criticism does and does not apply (or at very least that a criticism exists). If you don’t present this to them, someone else certainly will.
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I plan to provide mechanisms for criticism to be aired. I intend to link to some comments at peaceful science.
Also, a 1-on-1 forum where I engage select critics on select topics is also in the making. I don’t have time to engage every possible critic under the sun. I will encourage students to post objections they here as well.
And if I’m convinced mistake was made, retractions will be made. I’ve made retractions in the past. That’s the responsible thing to do.
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I think you get it - I was aiming at responsibility too. I did not mean for you to address every criticism, only that students should have some idea what the most likely criticisms will be.
The original college course I envisioned in 2005 was for a secular university, not an online un-accredited course. But some elements of that original course I’m planning to retain. One of the elements is that the material the student is tested on is framed not as a profession of faith, but rather the students understanding of the claims and who made them. That is, an atheist should be able to get a score of 100% on the objective exams without stating things that go against his conscience. The test questions would be carefully framed in that way so as to avoid criticisms of indoctrination where by indoctrination I mean, “a student does get a good grade unless he believes what he is taught.” It is perfectly fine to say, “this is what Christians believe” in a secular context. The course will NOT be run like a Sunday school.
That said, as I pointed out the course will be run also as a buffet-style where people can select topics appropriate to their knowledge level. However, a comprehensive objective (multiple choice-type exam modeled after the FAA Knowledge Exam for pilots) proficiency exam will be offered if student wishes to certify himself in terms of knowledge. Otherwise the student can just go through the course material for amusement, entertainment and gaining of knowledge.
There might be a several levels of proficiency. At a basal level here are some really basic question like (subject to much revision until I get the exams written):
Who wrote the Origin of Species by Means of Natural Selection?
What is the generally accepted age of the Earth?
What is the generally accepted age of the Universe?
Who is Linnaeus?
Who is Paley?
Who is Bishop Usher?
Advanced topics would be something like:
What is Obler’s paradox?
State the evidences of the Big Bang.
Compare the total thermodynamic entropy of a live human to a frozen dead rat.
Use the law of large numbers to estimate the probability of macrostates in terms of the count of microstates.
What is the motivation for Modified Newtonian Dynamcis?
What is fine tuning?
What are multiverses and many worlds theories?
What are the features of Eukaryotes?
What are the elements James Tour, Change Tan, Rob Stadler describe as barriers to the Stairway of Life?
List the problems in evolving Eukaryotes.
Describe the Nested Hierarchy of life.
Use MEGA software to create an unrooted phylogenetic tree of ZNF136.
Describe the action of the HOTAIR lncRNA
What are promiscuous domains?
Estimate the likelihood a random-frameshift mutation will create a zinc-finger protein.
Identify key residues of a metal binding protein using sequence alignments
Why did variable speed of light theories emerge in secular quarters?
What is the nested-hierarchy?
Use MEGA software to compare select proteins between chimps, humans, and plants.
There will be modules on theological/philosophical issues, but for right now they won’t be graded except for things like “what scripture passage was cited” what were the claims and who made them. For example, there is an excellent article by Michael Ruse that criticizes ID. I could write a counter/rebuttal. The student would be responsible for at least identifying who is who (duh), and what the claims were and what the basic arguments were.
The “bad design” argument weighs heavily for example in the Creation/Evolution controversy.
The hiddeness of God is also a big one. But these are outside science, yet play a central role in debate.
The bad design argument, in my view, is poorly conceived.
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I see it used a lot implicitly whether a good or bad argument. I don’t have Jerry Coyne’s book, but I got the impression he used it.
Darwin used it:
I cannot persuade myself that a beneficent and omnipotent God would have designedly created parasitic wasps with the express intention of their feeding within the living bodies of Caterpillars. – Charles Darwin
Darwin amazingly uses the word “designedly” and “created.” They are actually slightly different concepts, and Darwin used both concepts. For example:
One cannot look at this Universe with all living productions & man without believing that all has been intelligently designed…Yet when I look to each individual organism, I can see no evidence of this.
This highlights the difference between Cosmological ID and Biological ID.
But in any case, here is an ancient bad design argument by Lucretius (translated by CS Lewis):
Had God designed the world, it would not be
A world so frail and faulty as we see.
Don’t confuse bad design with malicious design. Two different things.
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I agree. The quality of design is very subjective, and it takes away from more objective arguments that could foster better dialog. “It’s bad design” is just as shaky as “it looks designed”. We should be striving to find pieces of evidence that don’t rely on our personal opinions.
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