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Author Topic:   How is DNA even possible anyway?
Doofy
Inactive Member


Message 1 of 14 (144113)
09-23-2004 2:26 PM


Hi guys, I'm an undergraduate biology student at a north Texas university. Today in one of my classes we were talking about DNA replication, and part of it failed to make good sense to me.

What does current evolutionary theory say about a situation like the following: How DNA came into being in the first place, when it is made of bases, but in order to replicate new bases have to be constructed (from parts that we get from food, I guess), but the DNA contains the information that tells cells how to construct bases.

There are other kinds of paradoxical sounding questions I have seen in biology classes that I can understand. For example, I understand the concept of how a species can radiate to a habitat not taken by another species, then slowly change over time to take on features that make it more successful, then become so interwoven with other parts of the habitat (like a plant) so that in retrospect it appears neither could ever have existed without the other. But the thing with the DNA seems more circular. Could someone tell me what the cutting edge theory is? If anyone knows but doesn't want to explain it, but could give me a link to a good article, that would be awesome.


Replies to this message:
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AdminNosy
Administrator
Posts: 4754
From: Vancouver, BC, Canada
Joined: 11-11-2003


Message 2 of 14 (144116)
09-23-2004 2:37 PM


I've promoted this just to allow some answers to be posted.

I suggest that you should have read over the Origins Of Life topics. There has been some discussion of this in there.

I'm no expert but quick answer is that researchers don't figure that DNA came first. It is, perhaps, an evolutionary development by earlier evolving replicators.

Thread moved here from the Proposed New Topics forum.

This message has been edited by AdminNosy, 09-23-2004 01:39 PM


  
Rei
Member (Idle past 5149 days)
Posts: 1546
From: Iowa City, IA
Joined: 09-03-2003


Message 3 of 14 (144128)
09-23-2004 3:18 PM
Reply to: Message 1 by Doofy
09-23-2004 2:26 PM


A good question! Here's a way to help you picture it.

Imagine that you were exploring at the bottom of the ocean, and you saw an arrangement of shells that looked like this:

It would be hard to picture - even though all of the evidence says that there have been no other humans here - that some sort of intelligence didn't place these shells in an arch for some unknown purpose. Namely, because if any of the shells was missing, the structure would collapse. This type of argument is known as "irreducible complexity".

However, the structure - while irreducibly complex in its *current form*, doesn't mean that it was always so. For example, picture a situation in which soil was layed down over time, with mollusks living and then leaving their shells behind as this happens, and then some time later, the soil erodes away:

The reason that the shells can be built up is that the soil acted as a "scaffolding". Later, the scaffolding was eroded away without a trace, but the shells remained.

The same can hold true with life. Almost noone proposes that the earliest forms of proto-life life were themselves DNA-based. However, when DNA came into play as a helper molecule - initially likely just tiny strands that coded for a single piece of RNA - it proved very effective (with good reason) at coding for RNA, and spread throughout the population.

The standard theories for abiogenesis typically runs along the lines of (one example below):

1. The amino acids naturally form in the world (and in space!), fairly widely. This much is well known, and is little contested.

2. Amino acids randomly link up into proteins in some circumstances. With the scale of the earth, and ample sources of input energy, this is not unlikely. Again, this much is known.

3. Proteins can often catalyze reactions. This much, again, is well known. Randomly arranged proteins will randomly catalyze reactions.

4. If a certain type of catalysis tends to produce proteins that are more "like" the protein that caused it, proteins "like" the original protein will become more common in a given area.

5. The more "like" the original protein that results from a reaction, and the wider the possible range of input materials, the more common it will become. Soon, you effectively have an effective self replicator, or more likely, a group of molecules that work together to replicate each other. This is known as a "hypercycle".

6. Any hypercycle that can poison off its competitors without hurting itself will become dominant. Also, by keeping themselves more concentrated, they can react more frequently. This leads to the slow progression of "walling off" of hypercycles. This stage is usually known as an "ur-cell", "protocell", or other such terms.

7. The more efficient an ur-cell functions, and especially *adapts*, the more dominant it will become. DNA and RNA are both excellent for both of these functions, so they start to take over from self-replicating or group-replicating proteins. You end up with normal (albeit simple) cells that steadily increase in complexity as they compete with each other - more proteins being coded for in the DNA and/or RNA.

This message has been edited by Rei, 09-23-2004 03:18 PM


"Illuminant light,
illuminate me."
This message is a reply to:
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Replies to this message:
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Loudmouth
Inactive Member


Message 4 of 14 (144130)
09-23-2004 3:21 PM
Reply to: Message 1 by Doofy
09-23-2004 2:26 PM


quote:
What does current evolutionary theory say about a situation like the following: How DNA came into being in the first place, when it is made of bases, but in order to replicate new bases have to be constructed (from parts that we get from food, I guess), but the DNA contains the information that tells cells how to construct bases.

Current thought is that DNA may not have been the first molecule to carry the information required for replication. Catalytic RNA may have been the first molecule to carry out both replication and information storage. Normal RNA found in the cell carries the information from the DNA to protein translation. However, there are certain RNA molecules that are able to carry out reactions just like proteins are. In fact, these catalytic or enzymatic RNA's are able to construct other RNA molecules. The implication is that both proteins and DNA may have been an offshoot of RNA activity. This makes sense since DNA is more stable than RNA and proteins are more dynamic in the number of conformations they are able to assume. In other words, DNA and proteins do a better job than RNA.

A good site for an overall idea of what I am talking about:
http://www.panspermia.org/rnaworld.htm

A google search can turn up more. If you want, I could do a more in depth search if you have questions on specifics.


This message is a reply to:
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Doofy
Inactive Member


Message 5 of 14 (144139)
09-23-2004 3:42 PM
Reply to: Message 3 by Rei
09-23-2004 3:18 PM


Thanks, both of you. I already knew a (small) part of this. I knew that the very prototype self replicating molecules were a lot simpler. I don't know how to do the quote yet, I will figure it out later.

Rei wrote:
5. The more "like" the original protein that results from a reaction, and the wider the possible range of input materials, the more common it will become. Soon, you effectively have an effective self replicator, or more likely, a group of molecules that work together to replicate each other. This is known as a "hypercycle".

I've never heard of a "hypercycle" before. I know proteins commonly function as enzymes that catalyze reactions. So you're saying that according to this theory, a protein that formed, essentially, randomly, and then catalyzes a reaction, and the result of the reaction is to make more proteins of its "kind"--that is a hypercycle? And that would be the very very first self-replicating molecule, a protein that causes more of its "kind" to be formed? Then several of these enzymes..get together somehow? In something like a symbiotic relationship. That really does make a lot of sense. What is this theory called? Who thought it up?

I think I will check out that link and see what it says. By the way, in an astronomy class I took I did learn about the amino acids which have been found in outer space--I thought that was very cool!


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Doofy
Inactive Member


Message 6 of 14 (144148)
09-23-2004 4:02 PM
Reply to: Message 4 by Loudmouth
09-23-2004 3:21 PM


Loudmouth said:
A google search can turn up more. If you want, I could do a more in depth search if you have questions on specifics.

Thank you, but that's okay. That link you gave was very good. I can find stuff on the internet, I just didn't know where to start. I have biology books, but their mention of those theories is very very uninformative. I guess one studies that stuff in molecular. I am more into organism/ecology. I have not studied molecular biology at all in college yet.


This message is a reply to:
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Rei
Member (Idle past 5149 days)
Posts: 1546
From: Iowa City, IA
Joined: 09-03-2003


Message 7 of 14 (144152)
09-23-2004 4:17 PM
Reply to: Message 5 by Doofy
09-23-2004 3:42 PM


quote:
Who thought it up?

M. Eigen and P. Schuster. You can read more about it here. The initial hypercycle proposal involved RNA, although we don't know for sure that the first stable cycle involved RNA (that very well could have occured at the protocell stage, after the hypercycles are walled off), but we really don't know. Unfortunately, hypercycles and protocells don't fossilize ( *darn!!* )


"Illuminant light,
illuminate me."
This message is a reply to:
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Loudmouth
Inactive Member


Message 8 of 14 (144178)
09-23-2004 5:27 PM
Reply to: Message 6 by Doofy
09-23-2004 4:02 PM


quote:
I have biology books, but their mention of those theories is very very uninformative. I guess one studies that stuff in molecular. I am more into organism/ecology. I have not studied molecular biology at all in college yet.

My guess is that you probably won't here much about it at all throughout your college career. Most scientific academic programs focus on applicable aspects of biology and chemistry. Abiogenesis really doesn't have any commercial application and probably won't in the near future. At best, it might be brought up in a seminar type class where current research is discussed.

And I almost forgot, welcome to EvC. If you want to make those fancy quote boxes follow this syntax:

{quote} text being quoted {/quote}
and instead of using "{" use the same key without the shift key. You can find other formatting suggestions by clicking on the faq option at the top of the page.

Added in edit:

An easier way to figure it out is to click on the "raw text" button at the bottom of each post. Try mine out if you want.

This message has been edited by Loudmouth, 09-23-2004 04:29 PM

This message has been edited by Loudmouth, 09-23-2004 04:30 PM


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AdminAsgara
Administrator (Idle past 438 days)
Posts: 2073
From: The Universe
Joined: 10-11-2003


Message 9 of 14 (144283)
09-23-2004 9:31 PM
Reply to: Message 6 by Doofy
09-23-2004 4:02 PM


Welcome to EvC Doofy,

Here is some formating help for the forum.


AdminAsgara
Queen of the Universe


http://asgarasworld.bravepages.com
http://perditionsgate.bravepages.com
This message is a reply to:
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extremophile
Member (Idle past 3731 days)
Posts: 53
Joined: 08-23-2003


Message 10 of 14 (145500)
09-28-2004 9:32 PM


I'm interested in that too, I'll check the links. Some time ago I found this on nature news:

Evolved DNA stitches itself up
Philip Ball

Could DNA have kick-started life on Earth instead of RNA?

Researchers have managed to create bits of DNA that can stitch themselves together without a helping hand from other molecules. By contrast, natural DNA needs enzymes to stitch itself up, correct mutations, or make copies of itself.

The creation of this super-capable DNA suggests that rare bits of natural DNA might have evolved the same capability in the past. That could alter our thinking about how life began.

http://www.nature.com/news/2004/040329/full/040329-7.html

The site requires a free registration to see the news.

If i understood it right, abiogenesis this way would be the same hipercycle thing, but with DNA. Then later RNA would assume some functions of this DNA I guess, dividing the task of replication.
I don't understand much of that to have an opinion in whether would be more likely, DNA or RNA... I guess that RNA is more common, but in the other hand DNA is more stable...


  
Mission for Truth
Inactive Member


Message 11 of 14 (155254)
11-02-2004 4:01 PM


I've read in some science magazine that DNA could have also evolved from a more simple type of DNA.
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NosyNed
Member
Posts: 8842
From: Canada
Joined: 04-04-2003
Member Rating: 4.8


Message 12 of 14 (155257)
11-02-2004 4:39 PM
Reply to: Message 11 by Mission for Truth
11-02-2004 4:01 PM


RNA life
I've read in some science magazine that DNA could have also evolved from a more simple type of DNA.

I think you are referring to the idea that the immediate precursor to DNA based life was RNA based. RNA has been shown to be able to self-catalyze. That is, it can promote it's own chemical formation. DN A cannnot and would require a reproduction mechanism which is taken as too complex to be the first life form that could arise.

I'm pretty sure that many would suggest that RNA would not be the first imperfect replicator either.


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judhajeetray
Inactive Member


Message 13 of 14 (164643)
12-02-2004 11:00 AM
Reply to: Message 1 by Doofy
09-23-2004 2:26 PM


You are curious about the fact that how DNA could be the first genetic material which should itself require information to be formed.
Actually many theories have been proposed to explain this,but I think that the first genetic material first came to exist in viruses.You know that virus is a non living nucleoprotein particle, but it contains a genetic material which follows the universal genetic code.This genetic material seems to be formed by the organic reactions and alignment of nitogenous bases (which is even possible in-vitro conditions).Probably this genetic material was an RNA molecule,because you will see according to evolution the single stranded genetic material evolved first than the double standed one.
This may be explained by the theory of chemical polymerisation as well as by thermodynamics that the entropically most favourable condition for a polymer to remain in an aquous condition (specially to protect its hydrophobic bases) should be in the form of random coil.When this virus infected a living cell (devoid of genetic material) the RNA utilised the host enzymes or itself catalytically (catalytic RNA) produced a DNA which replicated and was transferred to the next generations.(you can also check my article on "first genetic material" in the 'Origin of Life').
This message is a reply to:
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Brad McFall
Member (Idle past 3169 days)
Posts: 3428
From: Ithaca,NY, USA
Joined: 12-20-2001


Message 14 of 14 (164644)
12-02-2004 11:06 AM
Reply to: Message 13 by judhajeetray
12-02-2004 11:00 AM


There may indeed be something consequential here as well but what I said was perhaps more fringish"" than your comments.

See as to which came first, the virus or the information:
www.evcforum.net/cgi-bin/dm.cgi?action=msg&f=13&t=53&m=15#15 -->www.evcforum.net/cgi-bin/dm.cgi?action=msg&f=13&t=53&m=15#15">http://www.evcforum.net/cgi-bin/dm.cgi?action=msg&f=13&t=53&m=15#15

This message has been edited by Brad McFall, 12-02-2004 11:07 AM


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