Doubting Didymus

Thank you, rufus.

Pz, I did not mean any offense by comparing you to behe, in fact that was not what I was even doing. You argued that genes could not accomplish anything without the cytoplasm, and that simply struch me as sounding like an argument that behe might use, that's all. Stop being so sensitive.

This subject may very well be dear to you, but I think the problem is that you have not gone to much effort to actually explain your position. The inheritance of epigenetic patterns sounds extremely interesting, so how about you go to the small trouble of actually explaining them a bit? I am both a full-time biology student and working full time, and I do not have the time to read what sound like fairly advanced articles in developmental biology journals as well as textbooks the size of phone books and all the supplemental ecology journal articles I have on my plate. Sorry if this puts you out, but if you are not willing to actually try to explain anything, like rufus is for example, then your hunch to simply post your references and leave may have been correct.

Yes, I grant that I know sod all about this topic compared to you, but you're a lecturer in biology, aren't you? Teach us something for crying out loud. Do your students get nothing but directions to the library? I have actually asked you directly to explain your position on a couple of occasions in this thread, and I will do so again: What do you mean, exactly?

pz

And that should be obviously true...do you mean you disagree with that statement?
That says both that you know nothing about Behe and nothing about me. It is nothing like what he would say, and I've been pretty forceful in my criticism of Behe.

You could at least acknowledge that it was a pretty stupid comparison to make, especially if you are asking me to explain something.
What, and get complaints that I'm being condescending?

Imagine a multicellular organism with a very simple genome that contains only two genes, A and B. You look in the adult, and you find a complex pattern: some cells express only A, some express only B, some express both. Can you explain that pattern in terms of the genome? Of course not. All the cells have exactly the same genes; where they differ is in their ontogenetic history, which represents a significant additional pool of information beyond that in the genome.

Now consider an egg cell produced by this organism. Let's say it has A turned on, and B turned off -- this is a necessary precondition for development. There is nothing in the genome that says what the starting state for ontogeny is, just as a CD does not contain a description of a CD player, or even the format of the information on the disc. This starting state is also a very important piece of information, and it is obviously inherited and transmitted to the next generation, which must reconstitute it epigenetically.

Now multiply the complexity of this non-genetic information a few thousand fold, to get it into the range more appropriate for real organisms.

Development was left out of the neo-Darwinian synthesis (for good reason...db wasn't ready for prime time 70 years ago), and it shows. The message of developmental biology since Driesch, if not longer, has been epigenesis, epigenesis, epigenesis. Genes are obviously central, and the field has really taken off with the addition of molecular genetics to the toolbox, but there's still this huge, complex aspect of the problem of development that has not been incorporated into evolutionary thinking by most people, yet. Many biologists are still closet preformationists, who consider the genome to be a blueprint for the organism, when it clearly is not. Oyama has called this the fallacy of the homonculoid genome, and it is amazingly common.

So yes, there are more factors that affect evolution than genetics. There is more to evolution than changes in allele frequency.

And no, this is not a creationist or IDiot position, OK?

Coragyps

Won't happen with me! I thought that was an excellent explanation that'll hold me until I get the gumption to read up on it!

Doubting Didymus

Of course I agree with that. The genes will generally also not accomplish anything without a breathable atmosphere either, but that does not mean that the atmosphere evolves. The argument is a strawman and you know it.

All I meant was that saying 'you take this part away, and it all stops working' is exactly what behe bases IC on. Am I wrong?

Fine, it was a stupid comparison


Now, to buisiness. If you have read my conversations with Rufus, you will see that I put a lot of emphasis on heritability. For something to evolve over the generations in a way that makes cumulative mutation possible, it must be fairly precise in its copying. Anything that is not directly copied, such as a nose, must have the information that makes that nose encoded somewhere, agreed? wherever that information is, it must be able to be copied with a degree of precision that can survive for many generations without fading to noise. Dawkins thinks that the only, or at least the most important place that nose information is encoded in the genome, but you suggest that information for epigenesis is encoded elsewhere. I can easily accept this, but where is the epigenesis pattern information encoded? How does a nose cell obtain from a gamete the information to specialise into nose tissue, if that information is not encoded in the genes? I do not mean these questions as knock down argumants against you, but I genuinely want to know, how do cells know what to develop into?

Concerning the heritability of epigenetics, the first question that comes into my mind is; if my mother has a mutation in her epigenetic patterns, do I have the same mutation? If so, how did I get it?

pz

No, it is not a strawman argument...unless you want to concede that all the arguments about significance of the genome are also strawmen. I'm not willing to do that.
You're looking at all of this the wrong way. You're trying to map the concept into something with which you are familiar, the genome, and it doesn't fit. It's completely different. There is no central repository of hard coded information.

Here's an analogy: I presume you are familiar with the Mandelbrot set? There are lots of viewers available that let you visualize these elaborate, pretty pictures that can be made by plugging a set of coordinates into a simple iterated algorithm. Think of the algorithm as sort of like the genome (although I do not think the genome is an algorithm); you can change the algorithm in different ways and get different images, for instance the Mandelbrot vs. the Julia set. You can also change the coordinates and get very different images -- if I want to share a picture, I have to tell someone to use the Mandelbrot algorithm and to use a particular set of initial conditions and ranges.

To use a more biological example, here's what determines anterior/posterior polarity in Drosophila:



The red stuff in the diagram is the bicoid gene product, which is obviously essential. However, what is just as important is the pattern of packaging, which is determined by the spatial arrangement of nurse and follicle cells around the maturing oocyte. Genes affect all of that, but there is no set of genes that directly says "put all the nurse cells at the anterior pole of the egg". Instead, there is a long cascade of cellular interactions that are essential in forming the Drosophila ovary, and they impose cytoplasmic information in the egg that will in turn generate an organism epigenetically.
Well, obviously, you shouldn't use the term "mutation" here.

One common example of an epigenetic change is fetal alcohol syndrome. If your mother had soaked you in liquor as an embryo, you'd have a characteristic phenotype, which would probably include mild mental retardation, prominent philtrum, wide set eyes, small ears, etc. You'd be messed up. Your children would also be messed up...after all, they've got a mother/father like you! Can this be considered an evolutionary change? Of course -- if it is a change in the properties of a population across generations, why shouldn't we regard it that way?

We also don't know how much or how epigenetic factors influence subtle things, like the shape of your nose. We don't know how much genetics affect those things, but I think we tend to make the mistake of assuming it is determined by the genome, in the absence of evidence otherwise. Think about the Grants' study of beak sizes in Darwin's finches. They observed a change in response to selection pressures, but look closely -- they do not, anywhere, show a shift in an allele that is causal to the changes in beak size. Would their work be disqualified as an example of microevolution if it were found that the differences were a consequence of differences in diet or nest location or brood temperature?

Peez

I did not claim that you were the only one who's posts might have seemed abrasive, nor was it me who compared you to those people. I only pointed out that your point of view was likely not the sole reason that people have become upset with you. It is not necessary to become sarcastic. With all due respect, that is a condescending statement. For one thing, if we do not understand your position there are at least two posible reasons: we don't know enough to understand, or you have not explained it well. You seem to be assuming the former. I should also note that I find it frustrating when people seem to be having trouble understanding my position, while seeming to think that they do understand it. For example, when you posted: You implied that I had somehow taken the position that there might be some "examples of genetic inheritance that are entirely gene-autonomous",, but I have taken no such position. I am doing my best to understand your point of view, and I hope that you are doing the same, but let's not get into a pissing contest, please. Thank you. I will try to find time to look these up. It appears that we are using "inherited" differently, at least. Let me ask this, how is beta-catenin produced? That is, where does an oocyte get its beta-catenin?

Peez

Doubting Didymus

Why not? Mutation is not a term that is specific to genes. All I mean is 'small change'.

[/QUOTE]One common example of an epigenetic change is fetal alcohol syndrome. If your mother had soaked you in liquor as an embryo,... You'd be messed up.[/QUOTE]

Sure, okay, but the immediate suspicion in my mind is that this phenotypic change would be comparable to scarring. Please set me straight if I am wrong.

My children may be messed up, but have they inherited my wide set eyes or my mental retardation? Will my phenotypic features be present in the population ten generations down the track? Twenty? A thousand?

I don't quite see yet that fetal alcohol syndrome or anything like it is capable of producing traits that may become fixed in the population. You might consider that a purely semantic distinction, but without some boundaries you will end up with a definition that grows to encompass my hypothetical blue sheep. Speaking of which, do you consider that extreme example (I think it is on page 3) to be evolution?

pz

Never mind, I give up. I concede that I am not competent to communicate this issue here, and will just have to let the citations I've given stand on their own.

Doubting Didymus

Come on, pz, I thought we were getting somewhere? I am very interested in exactly how organisms pass on their epigenetic patterns. Is there a distinction here between 'the same as' and 'a copy of'?

lpetrich

I fail to see what's the big deal about non-genetic inheritance. Whatever it is, there does not seem to be very much of it.