I’m looking for evidence that’s not just anecdotal, but substantive that can be used to confirm, not just “be consistent with.” When you can provide something that shows clearly macro-evolution is occurring without having to be imaginative, I’ll read it. Give me something to read that will clearly distinguish between something that results from “mutation/natural selection” and something that is the result of epigenetic adaptation. How would you or anyone else (since you’re leaving) decide that?
Hi Ray,
All of the papers and articles deal with changes in nucleotide sequences. None of them deal with changes in expression due to methylation.
Chris
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Ceteris Paribus?
No methylation at all.
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It’s good to see that even after a conversation is obviously dead, there can still be talk about methylation. It’s truly transgenerational! 
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They have done the same thing when Darwin Devolves and the science review
NOTHING in that post supports any of those claims. Also, Wells butchers paleontology. I have seriously cried from laughing so hard at some things he has said. If you want to talk whales come to someone who has worked or works on them (me. I have literally held some of the fossils in my hand)
A lot of cetacean evolution happened through the formation of pseudogenes:
https://www.sciencedirect.com/science/article/pii/S0169534714000846
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Thanks. I’ll look at the reference, and get back to you. I look forward to digging into this as it seems to be an important issue with regard to our discussion on evidence.
If you have any particular notes on the Wells article especially where you think he’s wrong, I would find that helpful as examine both sides. I give them as hard a time as you guys. I’m learning a lot, and I really appreciate the contributions of all of you.
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I think I could have used the Latin phrase “quid erat demonstrandum” after post #414. On further reflection, I am not even sure what “ceteris” you had in mind that would be “paribus.”
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Just means “all other things being equal.” I got sick of hearing it in my Economics classes. But it’s an important concept. In complex systems where there’s lots of interdependency, all other things are usually not equal. So when you said “None of them deal with changes in expression due to methylation.” I wondered if methylation was the only way gene expression is modulated. Not being a biologist, I don’t know that much. I’ve read a little about gene regulatory networks and recall the following form Meyer’s book “Darwin’s Doubt” Here’s the quote:
When they proposed their theory in 1969, Britten and Davidson acknowledged that “little is known . . . of the molecular mechanisms by which gene expression is controlled in differentiated cells.”24 (Britten and Davidson, "Gene Regulation for Higher Cells, " 57.) Nevertheless, they deduced that such a system must be at work. Given: (1) that tens or hundreds of specialized cell types arise during the development of animals, and (2) that each cell contains the same genome, they reasoned (3) that some control system must determine which genes are expressed in different cells at different times to ensure the differentiation of different cell types from each other—some system-wide regulatory logic must oversee and coordinate the expression of the genome. Note - 25 (Britten and Davidson, "Gene Regulation for Higher Cells, " 353.)
Sounds like the GRN’s also change gene expression. Thus, my question, “All other things being equal.” What I was really driving at is the question, "Is methylation the only way to change gene expression? If not, then all other things may not be equal. Isn’t that what epigenetics is about, viz. changes in gene expression from outside influence? Is methylation the only cause?
How cells take on different functions during development (and express a certain subset of the genes within the genome) is not epigenetics - it’s developmental biology (though epigenetics adds some minor variation to the process). A major mechanism is asymmetric cell division that divides regulatory proteins into different cells, giving them different subsets of proteins that then go on to regulate other genes (i.e. express them), which are then asymmetrically divided, and so on.
This all runs backwards to the asymmetry found in a fertilized oocyte - and a major determinant of the first asymmetry there is the point of sperm entry.
So, we know a lot about how gene regulatory networks work.
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@Raymond_Isbell Meyer is using a paper from 1969 in a book written in 2014? A 45 year old paper in a field that is rapidly changing. Not having the book myself, do you think maybe Meyer was just looking for a good quote for his book with no regard to what may currently be known?
To elaborate a bit on Dennis’ excellent explanation, the substantial changes in gene regulatory networks identified in the papers were all changes in nucleotide sequence. Methylation of gene regulatory networks can yield short-term changes in gene expression and are referred to as epigenetic changes. But the peer-reviewed research identified non-epigenetic changes–i.e., changes in nucleotide sequence.
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Indeed. GRNs are robust to single nucleotide changes over time within a lineage, and to mixing and matching of different alleles through sexual recombination.
I’m puzzled at why you challenge this unless you know it’s wrong. Is it wrong? Remember that the goal we have (or at least me) is to determine which is the better explanation of the data, evolution or design. Why would you challenge a book that you haven’t read? Is it possible that he may have had a good reason to have included that reference? Getting to the truth on an issue requires that one examine both sides with an open mind and withholding conclusions until the data is in, analysis is completed, and both sides are heard. Am I wrong? When one side adopts your style of argument, it arouses suspicion.
This stuff is complex and difficult to understand. Coming to a conclusion on which side is correct requires patience, discipline and a willingness to be open minded. Condemning an argument because it’s citing an old source may be correct if that old source has been replaced and shown to be wrong. However, if the old source is still correct, I would read that argument carefully and completely to see if there was a good reason for including it. Perhaps he is stressing the point that not only is it true, but it has been known to be true for a long time? Thoughts?
@Raymond_Isbell The problem is when an ID author quotes a paper simply to cast doubt on the theory of evolution. It is a consistent pattern that I have seen. And when a very old paper is used when much more is now known about GRN, just do a Google Scholar search, the reality is the author is being dishonest.
The quote is
Yes it was true that “little is known” but that was in 1969. It isn’t true today as Dennis and Chris point out. Do you still think the quote is a good use of the content of that particular paper?
And one more point, when I see the ellipses in a quote I suspect something important might have been left out. In this case that didn’t happen. I found the quote is on the page you can see here Read it and see what you think of Meyer’s use.
Hi Bill, the quote is from a section of the book (Darwin’s Doubt) in which Meyer is introducing the whole concept of GRNs. In that section he is highlighting Davidson’s ideas. The book is pretty worthless overall, but this section is rather nice and the historical reference to the Britten-Davidson model is fine. You are justified in suspecting quote mining, but in this case Meyer is not doing that, and is instead noting that Britten & Davidson were proposing a model of gene expression regulation before much was known about the topic in animals. Of course, a Nobel had already been awarded, 4 years before, for work on the lac operon, so the notion of DNA-based control switches was already established. But the quote from Meyer is not inherently misleading or problematic, IMO.
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Casting doubt on the theory of evolution (macro that is) is exactly what he’s doing. He believes it is wrong, and is making an honest attempt to present his reasoning. Are you saying that he should not challenge evolution? If evolution is wrong, then his action is justified, maybe even noble. Would it be a good thing to talk someone down from jumping off a tall building? For our discussion, Meyer’s motives are not the issue. His hypothesis and reasoning are.
I would think that the issue before us is the explanatory power of design vs. evolution. That’s certainly my goal. I’m listening to both sides, and I won’t condemn either side until I have looked at their reasoning carefully. Meyer is presenting an argument that shows the evolution argument requires embracing things that are highly unlikely. Is it wrong to point that out? Meyer is trying to convey the notion that random changes to the whole network of interactive signaling molecules is more likely to be destructive than beneficial. Since you haven’t read the book, here’s a quote from pg 264-5 in “Darwin’s Doubt” that shows his point: (emphasis is mine)
Another line of research in developmental biology has revealed a related challenge to the creative power of the neo-Darwinian mechanism. Developmental biologists have discovered that many gene products (proteins and RNAs) needed for the development of specific animal body plans transmit signals that influence the way individual cells develop and differentiate themselves. Additionally, these signals affect how cells are organized and interact with each other during embryological development. These signaling molecules influence each other to form circuits or networks of coordinated interaction, much like integrated circuits on a circuit board. For example, exactly when a signaling molecule gets transmitted often depends upon when a signal from another molecule is received, which in turn affects the transmission of still others—all of which are coordinated and integrated to perform specific time-critical functions. The coordination and integration of these signaling molecules in cells ensures the proper differentiation and organization of distinct cell types during the development of an animal body plan. Consequently, just as mutating an individual regulatory gene early in the development of an animal will inevitably shut down development, so too will mutations or alterations in the whole network of interacting signaling molecules destroy a developing embryo.
Meyer, Stephen C… Darwin’s Doubt (pp. 264-265). HarperOne. Kindle Edition.
The reason I find Meyer’s argument appealing is that it’s consistent with my assertions about Systems Engineering principles. INCOSE calls it “rich interdependence.” If a random change to a nucleotide happens which affects the protein specified by it, and there are many other proteins that depend on the one that changed for their correct function, they may fail unless the change is non-critical or all the other dependent proteins are insensitive to random changes to others. You claim that the cell is robust enough so that that change is tolerated, and you claim that testing has demonstrated it. How many proteins are there, and how many have been tested? Has the testing included all possible nucleotide changes and determined that all proteins are robust to all changes? Or are there certain nucleotide positions that are more critical and thus cause the corresponding protein function to be more sensitive? If the latter, does Meyer have a point? Have all protein coding genes been tested? If not, is it reasonable to generalize the results of those you have tested to conclude that all proteins are robust and insensitive to random nucleotide changes?
I think Meyer has some good points that are not being answered by evolutionists like yourself. Instead of giving carefully reasoned responses, you just dismiss them as Meyer’s deceitful attempts to trash evolution.
You claim this recent example regarding Davidson’s work is an example of bad tactics from the ID folks. I read your excerpt from Davidson’s paper and see nothing wrong with Meyer’s quote of it. Maybe I’m missing something. You’ll have to explain it if I did.
Apparently Evolution News just published this article this morning. Seems relevant to our current discussion.
Enjoy.