New discoveries in genomics?

[azimuth]

A month or two ago I remember reading an article in a German newspaper (Die Zeit) about new discoveries which had been made about the human genome. I don't speak perfect German so I might have misunderstood some parts of it, but after going through it with a friend who does I'm pretty sure I've got at least the main ideas right.

The article talked about a 'paradigm shift' in genomics, saying that new discoveries had led people to discover that DNA was far more complex than previously thought. Instead of having a stable genetic make-up which is near enough identical in every cell, DNA mutations are far more common than scientists imagined - so common that even as embryos, identical twins are already beginning to develop genetic differences between one another. It also described each cell as being 'a genetic universe in itself', suggesting that there are vast differences between the DNA found in each cell of a single organism.

When I first read this article I was sceptical, thinking it was just the paper's way of being sensationalist and trying to make more out of the story than there really was. But after reading it through again and (I think) understanding it a bit better, it doesn't seem quite so implausible.

I don't know much about genetics, but my understanding is that if this were true it would be pretty big news for biologists. However, I haven't been able to find anything about it since, either in newspapers or on the internet.

Is anyone able to enlighten me a bit? Could this be true, or is it completely exaggerated? Or is it something which everyone has known for ages and is being made into more than it should be?

I appreciate your help, and any other information (preferably in English ) would be welcome. I hope my post made sense and that I'm not asking something completely stupid...

If anyone wants to read the original article it's here (be warned - it's very long and in German)

[BioSci]

This is not so much a new discovery but more of a realization that such changes are important in regulating how genes are expressed.
These differences are not changes in the gene sequences - they are changes in how genes are turned on and off.
That this occurs has been known a long time - for example each different tissue in one's body expresses a different set of genes but all the our genes are present in all cells.

This regulation of genes can even be followed into the progeny across several generations. This epigenetic control of gene expression is well known from plant genetics and more recently, examples have been identified in human genetics.

The important thing to remember is that biology is very complex, simple ideas of how things work may help one to recognize important steps but the more one looks at the details, the more convoluted and complex the regulatory processes become.

[slang]

I went over the first page, but it seems they like to put a bit of a sensationalistic spin on the story by setting up straw men. Like this:

Die Genetiker müssen sich von ihrem Bild eines stabilen Genoms verabschieden, in dem Veränderungen krankhafte Ausnahmen sind.

The geneticists must abandon their view of a stable genome, in which changes are sickly exceptions.

I very much doubt that that is a fair characterisation of the modern view of how the genome acts. To me it feels a bit exaggerated, but then again, I didn't go through the entire article, and I'm not a biologist.

[Ronald Brak]

The article may be referring to junk DNA which doesn't do anything and is free to mutate without causing any effect. (Note that if some junk DNA is found to do something, then it's not junk DNA. It's simply been but in the wrong category due to a lack of knowledge.)

[tdvance]

I wonder how much "junk DNA" is really pieces of a redundant system of bases not all located in the same place on the strand.

Say, you wipe out or randomize or whatever section A, B, C, D, ..., Z individually or in pairs or... and nothing happens, but if you hit all of them, suddenly the creature is born with extra fingers.

Evolution is funny in that it finds solutions, not necessarily simple, easy-to-understand solutions, to problems. It's like, remove one bolt from a car, car still runs (probably). Remove 100 bolts, there could be trouble. One cannot say that "bolt x"
is the bolt that makes the car run.

[azimuth]

This is not so much a new discovery but more of a realization that such changes are important in regulating how genes are expressed.
These differences are not changes in the gene sequences - they are changes in how genes are turned on and off.
That this occurs has been known a long time - for example each different tissue in one's body expresses a different set of genes but all the our genes are present in all cells.

(emphasis mine) I understand this, but I don't think it's what the newspaper is saying. The article is about how the occurence of mutations when DNA is replicated are so common that the DNA itself is completely different in each cell, rather than just which genes are expressed. As in, right from the point where the zygote begins to divide several mutations are already occuring in each new cell which is created, so that by the time a person is XYZ age the DNA in any one of their cells bears little resemblance to the DNA in any other cell. That was how I understood it, and that's why I was so surprised - because this theory seems to completely go against so much that scientists previously held to be true about the genome - and also why I was very sceptical when I heard nothing else about it.

The geneticists must abandon their view of a stable genome, in which changes are sickly exceptions.

I very much doubt that that is a fair characterisation of the modern view of how the genome acts. To me it feels a bit exaggerated

The part about all changes being sickly exceptions does sound quite exaggerated, but surely it is true to say that the genome is generally considered to be stable? As BioSci said, the same genes are (or were always thought to be) present in every cell. On the other hand, seeing as I really don't know much about this subject it's probably a lot more complicated than I think, so that could be a massive oversimplification.

tdvance, I like your junk DNA idea - that was something I hadn't considered, but it seems like it could make sense. Isn't there a possible problem with the fact that junk DNA varies so much between individuals though? I mean that even though some people have junk DNA that others don't, and everyone has different amounts of it in completely different patterns, very few people end up with twelve fingers (or whatever)?

Thanks for all your help

[BioSci]

..The article is about how the occurence of mutations when DNA is replicated are so common that the DNA itself is completely different in each cell, rather than just which genes are expressed. As in, right from the point where the zygote begins to divide several mutations are already occuring in each new cell which is created, so that by the time a person is XYZ age the DNA in any one of their cells bears little resemblance to the DNA in any other cell.

Then I think that your skepticism was correct and the paper got the facts mixed up. Somatic gene mutations do occur but they are not that prevalent. The interesting effects are seen in patterns of gene expression - such that if one looks at "identical twins" even though they do have the same genes, they are being expressed differently and the differences increase as they get older.

Search for epigenetics for more detailed information - also, Nova had a recent program discussing this.

[azimuth]

Epigenetics looks like it will be useful, but what is Nova? Is it something American, because I've never heard of it...?

[BioSci]

Epigenetics looks like it will be useful, but what is Nova? Is it something American, because I've never heard of it...?

It is a US, PBS science program. Here is a link to the one on epigenetics:
http://www.pbs.org/wgbh/nova/sciencenow/3411/02.html

[tdvance]

tdvance, I like your junk DNA idea - that was something I hadn't considered, but it seems like it could make sense. Isn't there a possible problem with the fact that junk DNA varies so much between individuals though? I mean that even though some people have junk DNA that others don't, and everyone has different amounts of it in completely different patterns, very few people end up with twelve fingers (or whatever)?

Thanks for all your help

it was of course just an idea, wild guess. But what I was thinking--if lots of pieces have to mutate at the same time to cause a change, that won't happen very often (I think the biologists call it "canalization"--lots of mutations before there's a significant effect, or everybody would be deformed in some way--fruit flies used for hereditary experiments, in particular, are bred to be sensitive to mutations--wild fruit flies wouldn't work so well).

[azimuth]

I can't get the video to work (I think it's my browser being a pain, it does this quite often) but the other links are great - thanks!

EDIT - you got your post in before I finished typing, tdvance, but that sounds like it could make sense. I wish I knew more about genetics in general, as it's something I find really interesting.

[HenrikOlsen]

The geneticists must abandon their view of a stable genome, in which changes are sickly exceptions.

I very much doubt that that is a fair characterisation of the modern view of how the genome acts. To me it feels a bit exaggerated, but then again, I didn't go through the entire article, and I'm not a biologist.

That idea is one of the strawmen commonly used by the ID'ers, it's not held by any modern geneticists.