The secondary role of DNA

[pioneer]

If you look at basic observation, it appears to indicate that the DNA, although the template molecule of life, plays a support role. It is given the lead role based on an unproven assumption. That assumption is life began with some version of genetic replicators. This has never been proven but we treat it as true without any requirement of proof.

 

We need to look at what we can prove. Cells, like red blood cells can continue to be alive without DNA. But DNA is useless without a cell body, except in the above hypothetical scenario. Based on that the hierarchy is cell body then DNA. We could take a cell, remove the DNA, spread out all the cell material, add the DNA back, and it will never put the cell back together again. DNA is reactionary not proactive.

 

Another observation that suggests the same thing is cellular replication. When the DNA is duplicated it is taken off-line. After it is duplicated it is packed, off line and totally inert, yet the cell is alive. When the daughter cells divide the DNA is gradually brought back on-line. What this indicates are the cell bodies are restoring DNA functionality. The DNA can do nothing until the cell body provides it enzymes. Some mutations occur when the DNA is off-line, indicating a cell body role.

 

If you look at a maturing ovum, again the DNA is taken off-line, duplicated and then 3/4 of that is expel from the main cell body. That DNA is junk in terms of what the cell body has in mind. When the male and female DNA merge the cell body will shuffle the genes. When it starts to divide, the DNA is still off-line.

 

If you use a computer analogy the DNA is like the hard drive. It is the device with programs and data. We can add viruses, new programs or even bad data clusters; defects. The cell body is the rest of the computer with the user interface devices that allow input and output and access to the hard drive. Recently scientists added a new hard drive to a cell body and the cell body didn't seem to mind. However, it will need to go through the hard drive and figure out the programs available.

[MedGen]

If you look at basic observation, it appears to indicate that the DNA, although the template molecule of life, plays a support role. It is given the lead role based on an unproven assumption. That assumption is life began with some version of genetic replicators. This has never been proven but we treat it as true without any requirement of proof.

 

The point is that DNA is the replicator, life is a series of replications (a generation). At the end of the day the cells and organisms that carry the DNA are in fact just vehicles for the DNA. I would suggest reading Richard Dawkins The Selfish Gene if you have not already.

 

We need to look at what we can prove. Cells, like red blood cells can continue to be alive without DNA. But DNA is useless without a cell body, except in the above hypothetical scenario. Based on that the hierarchy is cell body then DNA. We could take a cell, remove the DNA, spread out all the cell material, add the DNA back, and it will never put the cell back together again. DNA is reactionary not proactive.

 

Firstly red blood cells do not replicate, therefore they have a finite lifetime (about 120 days max IIRC). They are differentiated from haematopoetic stem cells in the bone marrow. So the fact that they have no nuclear DNA is neither here nor there, they do not replicate. In fact their purpose does not require the presence of nuclear DNA, they are formed with the requisite cell components and sufficient proteins for their short lifetime. Even then if they become irrepairably damaged then they can undergo apoptosis.

 

Another observation that suggests the same thing is cellular replication. When the DNA is duplicated it is taken off-line. After it is duplicated it is packed, off line and totally inert, yet the cell is alive. When the daughter cells divide the DNA is gradually brought back on-line. What this indicates are the cell bodies are restoring DNA functionality. The DNA can do nothing until the cell body provides it enzymes. Some mutations occur when the DNA is off-line, indicating a cell body role.

Great, but what you fail to realise here is that prior to mitosis there are several complex checkpoint pathways that initiate cascades of gene expression for the regulatory proteins for before, during, and prior to replication. The fact that eukaryote DNA is tightly packaged into heterochromatin is because of its size. In every human cell there is around 2m of nuclear DNA split between the 23 pairs of chromosomes, to replicate that much takes a long time for a start. But also to avoid massive loss it is required to be tightly packaged so that it can be passed onto the daughter cell. This also falls apart when you consider this in the context of bacteria, they do not package their DNA, in fact they do have actively expressed genes during replication.

 

The cell only provides the enzymes as a result of direct transcription, followed by RNA modification and transport from the nucleus, then translation by ribosomes, finishing with any post-translational modifications. So lets see where this starts, oh that's right with the genes that code for the various enzyme subunits.

 

 

If you look at a maturing ovum, again the DNA is taken off-line, duplicated and then 3/4 of that is expel from the main cell body. That DNA is junk in terms of what the cell body has in mind. When the male and female DNA merge the cell body will shuffle the genes. When it starts to divide, the DNA is still off-line.

 

So you mean when the cells are dividing? See above. The cell has nothing in mind, it is not sentient, it follows certain pathways depending on stimuli and signals from its environment, then reacts accordingly.

 

If you use a computer analogy the DNA is like the hard drive. It is the device with programs and data. We can add viruses, new programs or even bad data clusters; defects. The cell body is the rest of the computer with the user interface devices that allow input and output and access to the hard drive. Recently scientists added a new hard drive to a cell body and the cell body didn't seem to mind. However, it will need to go through the hard drive and figure out the programs available.

 

Bad analogy, why? A cell is not a computer and DNA is not a hard drive, nor is it a blueprint. What it is however is more like a recipe, it gives a list of the requisite ingredients, but does not provide them directly. It can indirectly provide some of the tools and certainly provided the control points and regulatory elements in the shape of proteins via transcription then translation, but also microRNA's are a major regulatory element in a cellular environment.

 

When it comes to adding genes to a cell it has to be beneficial else the cell will reject and degrade it. This is one of the basic tenets of cloning in a lab, if you want to add a new gene to a bacterial or yeast culture then it has to give it an advantage in some manner.

 

Overall you fail to understand what DNA actually is, it is the prime replicator. It does not care for your feelings or how you interpret its functions with bad analogy, it simply is what it is. It provides the information for synthesising proteins, which keep the cell running. For a cell to divide/replicate/reproduce then it needs its prime replicator. A cell without DNA is doomed to die in a natural environment.

[iNow]

Overall you fail to understand what DNA actually is, it is the prime replicator. It does not care for your feelings or how you interpret its functions with bad analogy, it simply is what it is.

Great point, MedGen. Pioneer has missed this in nearly every post regarding DNA he has ever made on this site and others.

 

Thanks for clearing up some of the misconceptions for other readers not as well versed on the topic as you.

[jimmydasaint]

Interesting points made in the OP, most of which have been already addressed. Suffice to say the DNA is actually active, not inert, during the main part of the cell cycle in Interphase. It is making and providing regulation for enzymes that speed up the chemical reactions of the cell. Enzymes are crucial to the functioning of the cell at the correct time and in the correct number.

 

I like the way you are trying to think independently. However, you would have more luck with debating the origins of and functions of RNA. Good luck.

[MedGen]

Great point, MedGen. Pioneer has missed this in nearly every post regarding DNA he has ever made on this site and others.

 

Thanks for clearing up some of the misconceptions for other readers not as well versed on the topic as you.

 

Thankyou, I aim to learn always and educate where I can, glad to be of help.

[pioneer]

The DNA and the cell are intimately connected. The fact remains the DNA apart from a cell has no life nor can it replicate either. The other way around has some features of life. If we separate the two, cell body on the left and DNA on the right, which is alive and which just sits there?

 

The best observation that suggests the DNA plays a very important secondary role is the molecular stability of the DNA. It is not designed to be reactive unless acted upon. If the DNA was semi-stable able to break and reform spontaneously within water it would more make sense.

[ecoli]

The DNA and the cell are intimately connected. The fact remains the DNA apart from a cell has no life nor can it replicate either.

This is false. We can replicate DNA in the lab, outside of a cell with just a couple of different enzymes.

 

The best observation that suggests the DNA plays a very important secondary role is the molecular stability of the DNA. It is not designed to be reactive unless acted upon. If the DNA was semi-stable able to break and reform spontaneously within water it would more make sense.

Another incorrect statement, unpackaged DNA molecules can be quite brittle, and can even be broken apart just by stirring DNA in solution.

 

Packed DNA is much more dense and stable. Prokaryotic DNA accomplishes this in the cell by supercoiling (it's circular). Eukaryotic DNA is linear, but is packed with histone proteins and a bunch of other good stuff to add tremendous stability.

 

I suggest you take a biochemistry course before speculating on subjects you clearly have no idea about.

 

Moved to speculations.

[MedGen]

The DNA and the cell are intimately connected. The fact remains the DNA apart from a cell has no life nor can it replicate either. The other way around has some features of life. If we separate the two, cell body on the left and DNA on the right, which is alive and which just sits there?

 

Well as E.coli has already said; we can replicate DNA in an in vitro environment using DNA polymerases, the largest application of which is that old workhorse of molecular biology, the polymerase chain reaction. Without the ability to amplify (replicate) DNA outside of cells we would not have the wonders of genomic sequencing, DNA paternity testing, DNA based forensic science. So yes it can be replicated outside of the lab, but now what's this I hear you say; "but I meant without the aid of cellular material like proteins. Ah, now this is the crux of the argument. On its own a genome is quite rightly nothing more than some DNA, but it is the potential that is contained within that makes it so important. Yours, his, mine and everyone else's genome contain all of the information require to synthesise all of the proteins we need. Further to that it also codes for all of the regulatory, metabolic and housekeeping proteins and enzyme, which themselves catalyse the wonderful metabolic reactions that keep us all alive. But it is not just proteins that are coded for, RNA does not just come in the form of messenger RNA. There are also the transfer RNA's vital to translation, the small nuclear and small nucelolar RNA's that help to form the splicesome, the ribosomal RNA that catalyses the process of translation, and finally to one of my favourites, the microRNA's that can regulate and influence various stages in the synthesis of proteins right from the start at chromatin decondensation, all the way through to translation. Wonderful thing RNA, and strangely incredibly close to DNA, if wasn't for that pesky oxygen atom missing our genomes would be an RNA based one.

 

So how does this even relate to you speculations on the secondary importance of DNA. Well the clue is in its similarity to RNA for a start. RNA has been show to a) self polymerise under certain conditions, b) catalyse reactions that we would now consider only to be under the realm of proteins catalysed reactions and c) the ability of RNA to catalyse its own replication. Further to this we also have to consider the conditions under which RNA and DNA first arose as the prime replicators on this planet, they certainly weren't the same as today. In fact you can get a wee taster by looking for the Miller-Urey experiment (although this does not deal with DNA or RNA specifically) they show that the organic building blocks of life can be formed in a prebiotic-like environment, outside of a cellular context. See a pattern emerging here.

 

So your supposition that DNA cannot replicate itself outside of the cell meets its final stumbling block in the shape of fidelity. Fidelity is how well something replicates itself, or is replicated, without changing. In DNA these changes are referred to as mutations. Now we can expect that when the first prime replicators arose there were many numbers of different molecules that could self replicate, however it was the ability of DNA (or RNA as is thought among many biological circles, I'm undecided personally as the verdict is still out on that one) to replicate itself with a high fidelity.

In a cell there are many mechanisms that have evolved to deal with any problems in copying fidelity, that is why such a large amount of energy is devoted to DNA repair mechanisms and the proofreading during and immediately after to prevent detrimental mutations. When there were no cells I imagine that this wasn't exactly a necessity, something that arose as a later adaptation when the vehicles started to become more than just micelles and simple lipid bilayers.

 

 

The best observation that suggests the DNA plays a very important secondary role is the molecular stability of the DNA. It is not designed to be reactive unless acted upon. If the DNA was semi-stable able to break and reform spontaneously within water it would more make sense.

 

Actually this supports its role as a molecule for holding genetic information, even then it may stable as in not highly reactive, but as E.coli has already pointed out DNA can be sheared and nicked simply by stiring it (has its pro's and cons depending on what you're doing with the DNA). Even when DNA is "acted upon" (whatever that is supposed to mean) it remains stable, yes you do not want a molecule that stores information to be highly reactive. Blimey if the primary composite of our genetic material was made of caesium I doubt we'd exactly be around long to post on forums about it.

 

Well it's a shame that you view DNA in this way, once again to ape E.coli's sentiments; go and read about biochemistry, molecular biology and genetics, you never know you might learn something.

[ecoli]

Hey MedGen, you're lengthy explanation was great, and I hope you stay at SFN... you really know your stuff. I recommend, however, not spending so much time explaining things to pioneer. Judging from some of his other posts, he's not really interested in being told the truth. He's just a troll.

 

Also, to avoid confusion in the future, just refer to me as "ecoli" (all lower case, 1 word), it can get confusing otherwise, in threads where the topic of discussion happens to be E. coli.

 

Anyway, great post, hope to see more of you around here.

[Mr Skeptic]

[pioneer]'s just a troll.

 

I'm not so sure about that. He mentioned once how he liked to play with large amounts of mercury. This seems a likelier explanation. If he is a troll, he is not a very successful one.

[iNow]

I'm not so sure about that. He mentioned once how he liked to play with large amounts of mercury. This seems a likelier explanation. If he is a troll, he is not a very successful one.

 

When I read your comment about his experience with mercury it's like I had an epiphany. Suddendly I could understand why his posts are the way they are. Thank you for pointing this out. It makes total sense.

[Mr Skeptic]

When I read your comment about his experience with mercury it's like I had an epiphany. Suddendly I could understand why his posts are the way they are. Thank you for pointing this out. It makes total sense.

Thank you. I dug up the post I mentioned earlier, it is right here:

Fluoroantimonic acid is the king of acids. It is called super acid. It is formed from from one of the former champs antimony pentafluoride.

 

Aqua regia or the queen's bath is still up there. The queen's bath or nitric and hydrochloric is one of the few acids that can dissolve the king of metals, which is often seen as gold due to its color and resistance. Aqua Regia was an alchemist concoction during their research of trying to turn lead into gold. They needed to know the limits of gold before they could figure out how to turn lead into gold. It didn't happen but they did come up with many of the basic chemistry lab supplies of today.

 

What is interesting, the alchemist discovered a non-acid liquid that could dissolve gold. It was the liquid metal mercury. It will form an amalgon and then begin to dissolve the gold if the mercury is the bulk phase. They would then boil the mercury and make the gold reappear. Call EPA. After a few of those experients, dementia would often set in. They took the hit for the gipper and thanks to their personal sacrifice at the alter of early science, they set the stage for the conversion to modern chemistry.

 

Additional Info

 

When I was a development engineer in Oak Ridge, one of my final projects ,before setting out on my own, was to develop the technology needed to decommision the Li isotope separation facility. It used Mercury as the solvent or the continuous phase in the isotope separation. After the system was drained there was still 100,000 pounds to account for. Being a hands-on guy, I would put on the coveralls and explore the historical facility even climbing on top of some of the large equipment. It was sort of dimlly lit and quiet. But during explorations, I could imagine the sound of all the excitement, sort of flashbacks to the busy activity of its hayday. I was fortunate enough to be able to talk to many of the old timers. Their stories fueled my imagination and allowed to see former glory.

 

I considered myself an old time engineer, i.e., fast ideas and experiments, then move on to the next stage. I wished I had been a part of that early development effort. It was a unique time and circumstance, within science, where the scientists led the rapid pace and the beaucrats would play the role of support. One could get the impossible done in record time, since the bearocrats were doing what they did best which was organize and expedite. Even they did the impossible. When beaurocrats play chef the whole process gets drawn out and bogged down, since the mission becomes secondary to political power games. This may be due to less skilled personel leading, and this is their best effort.

 

Because of previous mercury techology, which I had invented in 3 weeks, I was given lead development engineer in this project. I was playfully called the mercury man. This could have been my life's project. The facility was huge. It would have taken decades to recycle, all the way to my retirement, i.e.., assumes beaurocrats chefs leading the charge.

 

Because of my early enthusiasm and cavalier attitude about mercury, such as stories of people walking on pools of mercury with hip boots, it was very likely, I have become over-exposed to the mercury. I began to become more and more off the wall. In retropsect, it was the early stages of dementia. I remember writing a technical report that used alchemy considerations. I am sure it is on file. That went over like a brick ballon. Rather than test me for possible mercury over-exposure, I was treated like I was a rebel and was stripped of my authority to make decisions. I regained some of my equilibrium ,,during a probation period, but was never quite the same. I soon left to pursue an illusion, that I was going to evolve science to another level. What began was an esculation into the deep dark places of the mind. The need for self healing became how I developed my prolific creativity. Where once the unconscious would become spontaneously active, now it is a faithful dog that fetches from the deep layers of the mind. Too much time trying to break the bucking bronco has atropied my social skills. That is why I hide, anonomously.

 

I am not bragging, maybe I am, but I have more direct experience with the workings of the human mind than anyone out there. I did not sit on the sidelines watching others so I could develop my theories. I had to put on the coveralls and get in the trenches and wrestle the beast. If I had to depend on most of the " acceptable stuff" I would gone over the edge. I tried it at first, the stuff was useless under those conditions. I needed to develop things from scratch, while collecting real time, data.

 

I used to go by the screen name "sunspot". I was banished from this forum for being too militant. That was good for me. Maybe I needed to burn out the last of the mercury. I feel more rational now. In retropsect, I began way outside the box trying to get back in. I could not figure how to get past the sentries, so I decided to lay seige. So I surrounded the six sides of the box ,with my armarda of ideas, and started to pound the walls to see if I could make a breech. I had plenty of ammo and I was able to manufacture ammo ideas as fast as I needed to. What I didn't count on, was the box had nukes. They nuked me by pulling the plug. It was actually good for me, because I was having too much fun making war. The last of the dementia was really cranking out the weapons. They weren't all weapons, I was also lofting food and drinks at the same time.

 

After that, I went to the other science forum and the physics forum, with a little more caution, because I thought they might also nuke me. Although I was initially thinking strategy, a seige was not necessary since their wall seemed a more permeable to ideas. This is a teaching forum, so teachers need to limit the scope to help the students build background. They need to keep the walls of the box tighter for the needs of students. The other forums were not as involved in teaching, so the walls of the box were more permeable. This semi-permeable access allowed me to get closer and enter the box. It gave me an opportunity to inspect the walls. I was also able to gain some important recon. Many of those inside the wall would often argued the differences of acceptable opinions. I was able to see points of vulnerabilies much better. At first I figured, rather than barrage the box with saturation bombing, pin-point is better. But it still lead to the problem of the box having nukes to my conventional weapons.

 

As I went further into the box, all miltary strategy became moot. I realized, I not wish to harm what was inside the box, since it seemed good. I was really trying to make the wall more organic. The walls of the box is the like the bark of a tree. This is where the tree grows. If the bark is surrounded by a heart of stone, this will stunt the growth. Maybe my seige had really been directed to the heart of stone.

 

With things inside looking better than expected, I wandered deeper into the box to see if maybe the heartwood was rotten. Maybe there was a type of disease that was eating the heart that required the stone wall. What I came upon was the inner santuary of the box. It was a box inside the box, that had it own fortifications. Its walls weren't defended. The strength of its structure, is the test of time. Being near the walls of the inner santurary brought back memories of the past when I was once allowed to moves freely inside the santuary. It suddenly dawned on me, what I had been trying to do. I had been trying to return home.

 

I too found it quite enlightening.

Edited July 29, 2008 by Mr Skeptic
Replaced link with quote