I would like to hear an in-depth update about this research. How does the standard evolutionary paradigm approach this subject matter and, if epigenetics is dismissed, how?
https://evolutionnews.org/2017/11/blindness-in-cave-fish-is-due-to-epigenetics/
You can start by searching Google Scholar and reading for yourself some of the research results. That way you may actually learn something instead of demanding to be spoon fed.
Did you read this from the NewScientist article cited?
It was assumed that these fish became blind because mutations disabled key genes involved in eye development. This has been shown to be the case for some other underground species that have lost their eyes.
What do the words in bold say?
What a pity, then, that the article didn’t actually provide a citation or link to that research. Perhaps you could find the original paper, read it, and get back to us.
In my experience, general misunderstanding of epigenetics is nearly as common as misunderstandings of quantum mechanics.
The hurdle you need to get over is how epigenetic patterns are inherited. If epigenetic patterns aren’t inherited then it can’t be the explanation for how these inherited characteristics came about. Remember, these patterns have to occur in gametes in order to be heritable. We already know that epigenetic patterns change in somatic cells which is a mechanism for many developmental pathways, but somatic cells are not used in reproduction. Those patterns can’t be inherited. Also, if you think about it, a gamete that already has the epigenetic pattern for producing an eye socket without an eye can only produce an eye socket without an eye. It can’t produce a stomach, lungs, or heart.
The link you are missing is HOW epigenetic patterns are produced in the first place. These are done by enzymes and other molecules in the cell. The DNA sequences that code for those enzymes and molecules are ultimately responsible for the epigenetic pattern that emerges. In addition, mutations to CpG islands and histone binding sites can also affect the results of epigenetic mechanisms. It still boils down to DNA sequence, which is part and parcel of the modern theory of evolution.
Well, I am surprised. I thought you would recall this from memory since it militates against your paradigm.
From your article:
What you would need to show is that the epigenetic pattern is present in both gametes and in the single celled zygote. If it isn’t, then these patterns emerge after fertilization and are a product of the DNA encoded enzymes and molecules in the cell, making it a product of DNA sequence.
Nope, that isn’t the original article. You need to try the primary literature. But your new reference is better. At least it reports what the article says and gives you Futuyma’s comments. And it also gives a citation to an unpublished version of the real article. The published version is unfortunately paywalled, but perhaps you can find a copy.
Something to consider: what makes those genes highly methylated is increased expression of another gene. What causes that gene to have increased expression in those tissues? If I were you, I’d look for a genetic cause.
You sound unsure. Is epigenetics a viable part of your paradigm? Is the jury still out? Do you personally accept it?
This seems to be a possible experiment for the DI to pursue. If they really think blind cavefish is an example of epigenetic inheritance and not DNA mutations then it would be really simple to keep some sighted fish in dark rooms and see if their offspring are born without eyes. These epigenetic changes should be immediate and shouldn’t take more than 1 or 2 generations. It should also happen in parallel populations at the same rate.
I wonder if the DI will actually do these experiments (he says rhetorically)?
You sound like you are projecting.
Depends on the species. There are known examples of epigenetic inheritance, most notably in some plant species and in nematodes (if memory serves). However, I have yet to hear of an example of transgenerational epigenetic inheritance of large morphological changes in vertebrates. There is tons of evidence for the development of epigenetic patterns AFTER fertilization which would not be inherited and be under the control of standard genetics.
Simply citing epigenetics as a mechanism for developmental pathways is not enough. You also need evidence that these epigenetic patterns are present in gametes and are inherited across generations.
From that paper:
The authors are saying that DNA mutations elsewhere in the genome are causing the changes in epigenetic patterns.
That one is still pay walled. Here’s an open access version from the author’s school.
From the DI article in the opening post:
Sometimes I wish I had gone into psychology so I could write studies on creationists. The amount of projection and cognitive dissonance is just amazing.
What Cornelius Hunter is really saying here is that he is afraid of the specter of DNA mutations resulting in changing patterns of DNA methylation which would support the standard evolutionary explanation for these morphological changes. It’s rather dishonest to know there are obvious mechanisms in the theory of evolution that explain these results and yet pretend these results somehow disprove the theory.
Have you ever read any of Cornelius Hunter’s blog? His projection of Creationism’s many flaws onto evolutionary theory are bright enough to be seen from low Earth orbit. 
Ha! I watched it for a few months back when he had comments! That was the Wild West of comment sections. To put it in perspective, JoeG was not (BY FAR) the most poorly-behaved of frequent commenters.
Edit: Sorry, I’m digressing… back to cavefish, please.
Fine. That is what they are saying. Is the epigenetic proposal then absolutely founded on genomic mutations? Has that been well established? Or are they still musing and guessing?
Did you look at the actual paper under discussion? I provided an open access version above so you can’t complain about not being able to see it.