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Author Topic:   Manipulation of DNA by cells?
Solstice
Junior Member (Idle past 2120 days)
Posts: 3
Joined: 07-20-2012


Message 1 of 36 (668333)
07-20-2012 1:34 AM


I was having a discussion with a creationist recently, and an argument which caught my attention was raised.

quote:
Thus the new genomic foundations of biology were no longer as convenient. So much DNA rearrangement within normal cellular processes proved that they are not fixed structures and cells can manipulate their own DNA. That means there are no genomic units to life. Thus the cell is no longer a Cartesian duality, meaning separate molecules as information carriers, and a separate set up for carrying out that information. Or the whole cell participates in the cellular process.

Now, the main thing about this that confounded me was the claim that cells can manipulate their own DNA. It's not a concept that I am familiar with. The only example I can think of in which cells come remotely close to manipulating their own genetic code is the process of crossing over in meiosis, but that scenario doesn't fit the description given.

I scoured google for some scientific literature on the issue, but I came up empty handed. (It's possible that my search terms are inadequate)

My question is : Does a cellular process exist which deliberately alters the structure of the genome? I'd like to know what you guys think. My personal suspicion is that this creationist is either fabricating the claim, or misrepresenting data as they are prone to do. I also fail to see how this claim---even if it was true---could be used as evidence against evolution, but that's a bit of a side thought. I am very curious about the possible existence of such a process.

Edited by Solstice, : No reason given.

Edited by Solstice, : No reason given.

Edited by Solstice, : No reason given.

Edited by Solstice, : No reason given.


Replies to this message:
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 Message 5 by Dr Adequate, posted 07-20-2012 3:40 AM Solstice has not yet responded
 Message 8 by Wounded King, posted 07-20-2012 5:06 AM Solstice has not yet responded
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Adminnemooseus
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Message 2 of 36 (668335)
07-20-2012 1:41 AM


Thread Copied from Proposed New Topics Forum
Thread copied here from the Manipulation of DNA by cells? thread in the Proposed New Topics forum.
    
Jon
Inactive Member


Message 3 of 36 (668336)
07-20-2012 2:06 AM
Reply to: Message 1 by Solstice
07-20-2012 1:34 AM


I was having a discussion with a discussion

How'd that work out for ya?

I'd like to know what you guys think.

I think any discussion attempting to relate cellular division and Cartesian philosophy is a great way to break the needle on a bullshit meter.

I am very curious about the possible existence of such a process.

What process? No process has been describedonly a potential philosophical connection between two purely physical, nonsentient entities.

And that's just nonsense.

Edited by Jon, : No reason given.

Edited by Jon, : who divides their cellar?


Love your enemies!

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Solstice
Junior Member (Idle past 2120 days)
Posts: 3
Joined: 07-20-2012


(1)
Message 4 of 36 (668337)
07-20-2012 2:10 AM
Reply to: Message 3 by Jon
07-20-2012 2:06 AM


Discussion with a creationist is what I meant.
It's late here. Give me a break will ya?
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Dr Adequate
Member
Posts: 16052
Joined: 07-20-2006
Member Rating: 3.4


Message 5 of 36 (668344)
07-20-2012 3:40 AM
Reply to: Message 1 by Solstice
07-20-2012 1:34 AM


Whether or not cells can manipulate their DNA, what follows from this assertion is vague rambling bullshit. Nor would it seem to assist creationists in any way, since it would suit them better to have the genome be immutable.
This message is a reply to:
 Message 1 by Solstice, posted 07-20-2012 1:34 AM Solstice has not yet responded

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foreveryoung
Member (Idle past 35 days)
Posts: 901
Joined: 12-26-2011


Message 6 of 36 (668347)
07-20-2012 4:22 AM
Reply to: Message 5 by Dr Adequate
07-20-2012 3:40 AM


No, it wouldn't. The genome of the creationist would be pliable and controlled by the environment to go in predetermined paths. What the OP describes, fits the bill perfectly.

Edited by foreveryoung, : No reason given.


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Dr Adequate
Member
Posts: 16052
Joined: 07-20-2006
Member Rating: 3.4


Message 7 of 36 (668348)
07-20-2012 4:45 AM
Reply to: Message 6 by foreveryoung
07-20-2012 4:22 AM


No, it wouldn't. The genome of the creationist would be pliable and controlled by the environment to go in predetermined paths.

Unless "the creationist" is the same creationist who swears blind that there are no beneficial mutations, rather than the creationist who has gotten so turned round in his head that he thinks he can argue against evolution by postulating mechanisms that would make it more efficient.


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Wounded King
Member (Idle past 2046 days)
Posts: 4149
From: Edinburgh, Scotland
Joined: 04-09-2003


(2)
Message 8 of 36 (668349)
07-20-2012 5:06 AM
Reply to: Message 1 by Solstice
07-20-2012 1:34 AM


Does a cellular process exist which deliberately alters the structure of the genome?

The simple answer is yes, such processes do exist. The most obvious example would be in the B and T cells of the immune system where the genome of individual cells are rearranged to form novel genetic combinations coding for antibodies. This process, V(D)J recombination, both selects a random combination of pre-existing genes coding for sections of the antibody, deleting those it doesn't use from the cell's genome, and also adds additional random sequences which vastly increase the variability of the resulting antibodies.

Of course this particular mechanism is only found in the immune system of vertebrates and is limited to somatic tissues, so none of these changes will be inherited by the organism's offspring.

There are other more problematic mechanisms which are sometimes suggested to be forms of this, we have had a couple of previous threads which have brought up several examples, Wright et al. on the Process of Mutation, Message 643, Message 776. Most of these are confined to unicellular organisms however.

TTFN,

WK


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NoNukes
Inactive Member


Message 9 of 36 (668400)
07-20-2012 5:40 PM
Reply to: Message 8 by Wounded King
07-20-2012 5:06 AM


Of course this particular mechanism is only found in the immune system of vertebrates and is limited to somatic tissues, so none of these changes will be inherited by the organism's offspring.

Not inherited genetically, but couldn't the changes in immune system be passed from mom to offspring in the womb?


Under a government which imprisons any unjustly, the true place for a just man is also in prison. Thoreau: Civil Disobedience (1846)

The apathy of the people is enough to make every statue leap from its pedestal and hasten the resurrection of the dead. William Lloyd Garrison


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Wounded King
Member (Idle past 2046 days)
Posts: 4149
From: Edinburgh, Scotland
Joined: 04-09-2003


Message 10 of 36 (668402)
07-20-2012 5:55 PM
Reply to: Message 9 by NoNukes
07-20-2012 5:40 PM


couldn't the changes in immune system be passed from mom to offspring in the womb?

Not really, antibodies can pass across the placenta and provide protection to the fetus but cells with the genetic sequence corresponding to those antibodies will not pass to the fetus. As with the antibodies in colostrum this is a temporary immunity which will be lost over time as the child's own immune system develops.

TTFN,

WK


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greentwiga
Member (Idle past 1379 days)
Posts: 213
From: Santa
Joined: 06-05-2009


Message 11 of 36 (668682)
07-23-2012 6:20 PM


There are many facets to evolution. One is when new genes are created. Another is the timing of genes. The body turns genes on and off at different times. Though there are about 2% genetic differences between humans and Chimps, there are many unstated differences in timing. The changes in timing allow a much faster mechanism of evolution than gene changes. For example, most mammals leg bones are similar. The main difference is the time the genes are active. The Body has the ability to turn on and off the genes. True, most of this is controlled by non-gene parts of DNA, but it is the body that adds and removes the methyl and other groups that turn on and off the genes.

Another example of environmental influences changing the DNA is cancer. Whether bad sunburns or chemical causes, mutations arise in genes. In a sense, the body causes the changes in DNA. When enough accumulate (often about 5-10) the cancer takes off. Both these might be what the creationist was referring to, but neither makes his point.


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Dr Jack
Member (Idle past 57 days)
Posts: 3507
From: Leicester, England
Joined: 07-14-2003


Message 12 of 36 (668764)
07-24-2012 4:43 AM
Reply to: Message 1 by Solstice
07-20-2012 1:34 AM


My question is : Does a cellular process exist which deliberately alters the structure of the genome?

Depending on what exactly structure of DNA means in this sentence, yes, definitely - as an absolute fundamental part of Eukaryotic biology.

Simplifying a little: DNA is a long thin molecule, in normal cells it is wrapped and coiled up with proteins into chromatin. How loosely or tightly this chromatin is packaged is a fundamental part of gene regulation. In fact, it's coming to be seen as the major unsolved part of how gene regulation works, probably as important as transcription factor regulation.

What's more a significant part of the control of how chromatin is arranged is through DNA modification via methylation (a semi-heritable form of epigenetic control).

So, yeah, cells modify the structure of their DNA both chemically and physically.

In any case, this:

quote:
Thus the cell is no longer a Cartesian duality, meaning separate molecules as information carriers, and a separate set up for carrying out that information. Or the whole cell participates in the cellular process.

is wrong anyway. Early work on DNA may have thought that, but it's well understood that the idea of passive DNA is wrong although unfortunately widely spread through poor analogies such as "DNA is the blueprint for life". DNA has a key role to play in the ongoing control of biological activity, it is not a passive molecule that simply make things that then go do their stuff.

edit

Oh, and - of course - transposons. There are parasitic* elements called transposons that exist within the genome that code for proteins that will cut them out of the gene and re-insert them elsewhere or make copies of themselves. These can occasionally also move other bits of DNA around.

* - some thing that transposons have an adaptive purpose, I think they're merely parasites. I think my view is probably more common.

Edited by Mr Jack, : Added transposons


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Taq
Member
Posts: 7594
Joined: 03-06-2009
Member Rating: 3.4


Message 13 of 36 (668780)
07-24-2012 12:27 PM
Reply to: Message 11 by greentwiga
07-23-2012 6:20 PM


Though there are about 2% genetic differences between humans and Chimps, there are many unstated differences in timing.

Those differences in gene regulation are due to differences in DNA sequence. One is strongly related to the other.

Also, humans do not give birth to chimpanzees. Obviously, this is not about the human genome being plastic enough to produce a wide array of variation. So we can not explain the differences between species solely on epigenetic factors. The differences are due to sequence differences that manifest themselves as differences in gene regulation.


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greentwiga
Member (Idle past 1379 days)
Posts: 213
From: Santa
Joined: 06-05-2009


Message 14 of 36 (668868)
07-25-2012 9:49 AM
Reply to: Message 13 by Taq
07-24-2012 12:27 PM


Yes, I realize that non gene portions control the gene portions. I was just trying to figure out how someone misreading a scientific article might think that the cell changes the DNA. This was one method, where if you just focused on the part of the chain of events where the cell puts the deactivation groups on the DNA, one could come to the (wrong) conclusion. I have seen them cherry pick points out of scientific papers that support their point, though the sentence in the context of the paper might say the opposite.
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shadow71
Member (Idle past 885 days)
Posts: 706
From: Joliet, il, USA
Joined: 08-31-2010


Message 15 of 36 (669416)
07-29-2012 9:05 PM
Reply to: Message 8 by Wounded King
07-20-2012 5:06 AM


Wounded King writes:


The simple answer is yes, such processes do exist. The most obvious example would be in the B and T cells of the immune system where the genome of individual cells are rearranged to form novel genetic combinations coding for antibodies. This process, V(D)J recombination, both selects a random combination of pre-existing genes coding for sections of the antibody, deleting those it doesn't use from the cell's genome, and also adds additional random sequences which vastly increase the variability of the resulting antibodies.

Do these processes, that deliberately alter the structure of the genome, indicate in some way a purposeful process?


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Replies to this message:
 Message 16 by Dr Jack, posted 07-30-2012 6:57 AM shadow71 has responded
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