New revelations on gene expression

_{Mark

March 8, 2008

Intelligent Design}

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Research led by Prof Frank Gannon has uncovered new revelations on possible ways to switch genes on and off and how cells interpret their DNA.

Only some genes are expressed in any given tissue. Proteins active in nerve cells are not expressed in the liver. How this is controlled is complex. One fundamental factor is whether the DNA is tagged or modified (methylated) in the region of a gene. This is important in gene expression and balancing the level proteins in different cell lines.

Although gene methylation (when a gene is turned on or turned off) was thought to be stable and unchangeable, this is not the case. Things are even more complicated than previously thought. Transient, cyclical and dynamic methylation is a general phenomenon occurring at many different genes and in many different cell types.

Yet another unexpected level of complexity needing a “just so story” from Darwinian devotees. The obvious Design is only an illusion!

Comments

jerry, It's good to talk about it. My main area is pathogens, so I fully admit from the start that this is outside my range, though I know a little about it and these papers seem really interesting. As far as my understanding goes, epigenetics refers to modifications to the DNA (like methylation) and chromatin structure that is (at least it was thought to be, perhaps no longer as these papers point out) stable through cell division. Meaning differences at the chromosome level as opposed to the sequence level. That being said, I don't think that maternal enzymes would qualify unless they are involved directly in modifying the genome, i.e. methylases. I can talk a little bit about imprinting, as this is something that I worked on. Back then (2001), no one was quite sure what caused imprinting, just that it occurred and it was an important force in development (though most thought methylation was the key). Briefly, an imprinted gene is one in which either the maternal or the paternal copy is expressed while the other copy of the exact same gene is not (this can occur spatially (only in certain tissues), temporally (only during certain stages of development), or totally). Turns out that the copy that is not expressed is methylated somewhere in the promoter which stop it from being turned on, or there are histone modifications which do not allow the chromosome to uncoil and hence leave the gene inaccessible. The problem being, in the germline, the imprint is lost and then must be reformed according to the sex of the individual. Meaning, if the father passes on his maternal copy of a chromosome to a child, it has to have a paternal imprint. Thus, the modifications are not genetic, but epigenetic. - they occur above the sequence. Now, is the ultimate cause genetic? Likely, but the action occurs on the chromosome or DNA level as opposed to the sequence level and that is why the term epigenetic is applied. It refers to the site of action as opposed to the cause (at least in my understanding). And, of course, there are evolutionary hypotheses as to why/how this occurred. If these papers say that methylation can cycle on/off a promoter, that has far reaching consequences. I am very interested to read them.leo_{March 9, 2008
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leo Design is not a "just so story". We already know that intelligent engineers often design systems with feedback and control systems. We have no demonstrated mechanism for natural law creating complex systems.idnet.com.au_{March 9, 2008
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@ Leo (Note: I hope my words don't come as hostile! Sometimes in these dialogs it seems that way, but I'm really not!) I hope you understand my comment was not intended to go in depth on the inadequacy of environmental pressure to produce such changes. I think that is an unfair task, esp. on a blog where you can simply post to cheer on your side right? For instance, I really like the Shaq trade to Phoenix, can't I just come on a blog and say "GO SHAQ" without explaining myself? You want me to tell you how this is designed? Well I'll try, but I don't think you will like the answer- God designed the genome that way. That's why its called intelligent design, b/c no natural function known to man can create such complex order. The intricacy of the genome, screams out that it was programmed that way, not through happenstance become so complex. If you want a more satisfying answer (this prb doesn't but I'm gonna try anyway): epigenetic control of the genome was part of the initial design of the cell and did not come about after successive environmental pressure. Things like hair color, body habitus, and natural ranges of intellectual ability may have, but from a design perspective (dare say logical), epigenetics is not something that came about via natural selection, much like the genome itself, it was in place with the design of the first organism. The example you gave, you a priori started out with a complex organism that already can control itself epigenetically, so of course if you have a fully programed/designed genome with the epigenetics already in place, slight changes in it will cause different methylation patterns. My question was more along the lines of, without intelligence, from the primitive soup, how did nucleic acids naturally come about in such a way that they not only reproduced, but were environmentally pressured to control itself in an intricate way of self checking and organizing it self via methylation. You mentioned histones, like it so obvious how that much supercoiling could evolve in the first place. The question I'm asking is not "how can mutations in a designed genome react to environmental pressures through existing epigenetic phenomenon" rather how did epigenetics arise without design. Currently, the tools we know that must have been at disposal for evolution, BEFORE the era of epigenetics are highly inadequate to create such a phenomenon. With Respect, jpark320jpark320_{March 9, 2008
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leo, Glad to see you discussing biology. From what little I understand the egg contains mucho enzymes that are accessed at conception to affect gestation. It is only till much later that transcripted proteins start playing a major role. Is that your understanding? So do such enzymes present in the egg qualify at epigenesis? They were created by the genome of the mother. Also the genome of the mother created the egg cell and any spatial configurations that might affect cell division and lead to different genes being expressed at different times and different places in the development. Is this epigenesis or genetic? Are there any other factors besides these that affect cell division and cell differentiation that are known? I find this a fascinating topic, just why are certain genes expressed and others not as cells differentiate. This seems to be the origin of cell types but what causes it will be interesting. Methylation has been called epigenesis but is it really? Suppose it is found that the cause of it is due to some genetic component. While it does not change the DNA sequence it does put a layer on top of it. Is any of this inherited? These are just questions since much of this is new and interesting. I do not think this will affect the ID vs naturalism debate very much because I personally think the complexity is so immense to defy any naturalistic method of happening and this is just another layer of complexity so it will add little to the debate which already seems one sided. I am sure you will disagree but that is not the issue now which is trying to understand this phenomena.jerry_{March 9, 2008
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I've always thought that the mechanism for cell differentiation will be irreducibly complex. If you aren't a materialist, it wouldn't have taken a rocket scientist to figure that out.geoffrobinson_{March 9, 2008
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jpark320, Why not? There is certainly a phenotype result to such actions. Aside from you reasoned argument of: "Crazy talk!" why don't you think epigenetic changes can about through evolutionary forces. To my mind, imprinting, histone modifications, etc. actually lend themselves quite nicely to an evolutionary perspective. Fairly basic changes at the genetic level lead to vast changes in chromatin formation, histone deposition, methylation, acetylation. A change in CpG motifs (through repeats, transposons, or simple mutations) changes methylation patterns and therefore changes gene expression. It is also an excellent defense mechanism, as bacterial and viral species have a much higher GC content, which would select for some of these phenomenon. I did some undergrad work on imprinted genes, we looked for them by manual sequencing and SNP screening. Not exactly high tech stuff, but simple changes can cause far reaching effects. Now, I cannot comment on these two papers at this time, as I have yet to read them. I clearly don't have the money that you do to afford a Nature subscription. I'll have to look at work tomorrow. However, apart from any of that, seeing as you are so sure that this phenomenon did not form through evolution and you abhor the 'just so story', please, let me know how this was designed? And no 'just so stories' please.leo_{March 9, 2008
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Epigenetics... what a wonderful thing. Seriously, I really want to hear how Darwinist will explain this. Environmental pressures selecting for epigenetic phenomenon? Crazy talk!jpark320_{March 8, 2008
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