| From: Daryn Voss | 5/07/99
15:59:36 |
| Subject: Life and DNA | post id:
21868 |
| I originally asked these
questions as part of another thread (may 2000 and
aliens started by third damn time), but I've
decided to reissue them as a separate thread, so that the responses would
not get mixed up with an argument about whether the music is
crap. 1/ Does anyone know of current theories about how DNA formed into a reliable genetic coding system? Here was what I originally said. Something that has bugged me for a while is DNA. Now, this is a digital code. If I am correct, it is believed that the same kind of DNA, (ie the same compatible & comparable coding system), is used in all known forms of metazoan life. Maybe I just lack imagination, but it is hard for me to see (i) how DNA could have formed suddenly, or alternatively (ii) how it could have formed gradually. 2/ Does any one have opinions (informed or otherwise) on the chances of finding life on Europa, in the atmosphere of Jupiter, or (as remains) on Mars? 3/ Would it be possible that life might restart from scratch on earth somewhere today, in much the same way that it initially started? Or are the conditions too different now? (I realise atmospheric oxygen would be an issue). Or have the established single-celled life forms filled the gaps too well, so that they would find it easy to kick the new life's arse? I'm not expecting authoritative answers to these questions, but I would be interested in hearing what people think. 8^) | |
| From: Darren | 5/07/99
18:05:51 |
| Subject: re: Life and DNA | post id:
21889 |
| You're right in finding it
difficult to understand how DNA could have "just happened". Specifically,
it requires an absolutely dazzling array of proteins to split the DNA and
make RNA which is then used to make proteins via inordinately complex
processes. So, you need a really well-designed set of proteins etc etc in order to use and maintain the DNA. If these don't exist, the DNA is useless. If the DNA is useless, you can't code for proteins. It's like the chicken and the egg, really. The more you look at the complexity of biochemical systems in living cells, the harder it gets to understand how any of it could have survived without the rest of the system already being in place. | |
| From: Terry Frankcombe | 5/07/99
18:15:43 |
| Subject: re: Life and DNA | post id:
21892 |
| 3/ Would it
be possible that life might restart from scratch on earth somewhere today,
in much the same way that it initially started? Or are the conditions too
different now? (I realise atmospheric oxygen would be an issue). Or have
the established single-celled life forms filled the gaps too well, so that
they would find it easy to kick the new life's arse? I gave my opinion on this one in a thread a while back, but I can't find it now. Someone asked if life appeared spontaneously, why doesn't life appearing spontaneously today? I replied: How do you know it doesn't? There are a couple of aspects to this. Say the odds of life appearing were such that you'd probably get some new single-celled organism every 100 thousand years or so, somewhere on the planet. Compare that to how long we've been looking! And if indeed this little bugger couldn't cut it in the cut-and-thrust of the modern environment, would anyone notice if on average once a year some little cell started reproducing in you garden pond, only to become extinct a few days later? | |
| From: James Richmond (Avatar) | 5/07/99
20:10:17 |
| Subject: re: Life and DNA | post id:
21905 |
| Daryn, As for your other questions, this isn't really my field, but here are a couple of brief ideas: 1. I suspect that there was no sudden leap from nothing to DNA. More likely, there were simpler replicators than DNA at the dawn of life. These replicators would have reproduced essentially by cloning themselves. Later, a more efficient way of storing a blueprint for an organism (apart from in the form of the organism itself) evolved. Eventually, the coding system of DNA developed. Then came sex as means of efficiently shuffling the genes, and so on. 2. The origin of life probably requires a reasonably stable environment with liquid water. I think there is a fair chance that life may have developed on Europa, perhaps near thermal lava vents on the ocean floor (assuming there is an ocean, which seems quite likely). I think life in Jupiter's atmosphere is less likely. Mars may have had life when there was a lot of liquid water around, but I have my doubts as to whether we'll find any life there now. On the other hand, we've barely scratched the surface of Mars, so who knows? There could be hidden deposits of liquid water somewhere underground. JR | |
| From: Daryn Voss | 5/07/99
20:56:21 |
| Subject: re: Life and DNA | post id:
21911 |
| Further to my second question: I
have read that in an anhydrous environment, at low temperatures, ammonia
would be a suitable life supporting fluid. It has many of the properties
that water possesses that make it good for this purpose: ionic and
low-mass covalent compounds are soluble in it. It auto ionizes, and is able
to support buffer solutions and so forth, but is basically chemically
stable. It is a liquid over a wide range, due to molecular polarity, and a
few other things I can't recall. This might be good news on colder planets. | |
| From: Dr Paul | 6/07/99
0:37:42 |
| Subject: re: Life and DNA | post id:
21933 |
| Hi guys, What a great thread. The meaning of life, the distribution of life,.. Viruses do not have a DNA sequence for storage of information for protein replication. They rely on RNA (I think specifically messenger RNA) This means that their "genetic " code is always primed to generate proteins when it reaches a suitable environment. Life does therefore NOT need DNA. It is a nice storage device but not required just yet. Transcription RNA can bind amino acids and interact with mRNA in a process which will allow the chains of amino acids to form polypeptides. At this point for protein replication, mRNA and tRNA are desirable. OK now to get to tRNA and mRNA. These two are formed from chains of ribose (a sugar, 5 carbons) linked to phosphate and bases , two purine type bases (adenine and guanidine) and two pyrimidine bases (cytosine and thymines and uracil) These are the ATGCU bases. Each of these components should be able to develop in a complex chemical soup over time. This is essentially chemistry and Boltzmann probability. The linking to form chains is likely to be chance until some binding of amino acids and polypeptide chain formation starts generating somewhat useable catalysts. It is whence these are generated that life may begin to organise as cellular structures. This would involve usurping the RNA's and the proteins associated. It could be likely that this usurping may have already started, with the successful usurper having picked the right RNA sequences to carry on. (Am I allowed to say now variation and selection criteria?) Time and chemistry and Boltzmann probablility and a low (much required) oxygen atmosphere. The importance of a lack of oxygen in the formative processes must not be understated. Most of the above may be acheived by reductive chemistry, oxygen would be a strong poison for most of this. I think the main requirement is time. Can anyone get their head around the patience of 1 billion years of chemical evolution before cellular life may be observed in a nature that may leave fossils. If Europa has had the conditions of liquid water and volcanic vents (smokers) then my 20 bucks goes into the pot for a bet that life will exist. I keep saying that life is tough and will look towards generation under any condition that may organise it. As for Mars, the consideration of fossils in rocks may be complete shash, but would be a consideration if water had existed in liquid form, then either dried up, blew into space by some disaster, or absorbed into the soil system on Mars. This may be why the only (unlikely) signs of life have been microcellular (possibly at the RNA usurping stage??). Interesting side point from the Cobalt bomb thread. If the Cobalt nuclear device was discharged across the surface of our wonderful blue green planet, this would not necessarily be the end of life and evolution, It will change the selection criteria for survival a great deal, but many invertebrates would likely survive. Maybe some smaller vertebrates survive as well. But whole classes of bacteria and algae and invertebrates should be able to withstand the radiation pressure to continue life and evolution as we would probably not know it. This may be the equivalent of a 1 billion year jump backwards in evolution. Another big number of years. Fossils of what may be considered life have been dated to about 3 to 3.5 billion years old. That places the start of life about 1 to 1.5 billion years after the coalescence of this rocky structure we call home. These are BIG time numbers , but we have likely four or so billion years of evolution behind us to help in comprehension. Paul Hope this helps somewhat, {:~)] | |
| From: Daryn Voss | 6/07/99
1:15:38 |
| Subject: re: Life and DNA | post id:
21938 |
| Thanks a heap, Dr Paul. I'm beginning to understand why people talk about life forming in "pools", to allow the mRNA and tRNA to build up to a workable concentration so that suitable collisions would happen more often. On the Mars thing, I've seen nice clear photographs of the Martian surface of what look very much like large, dry river beds, implying that maybe there once was liquid water (I assume water) on the surface. 8^) | |
| From: Dr. Ed G (Avatar) | 6/07/99
3:30:56 |
| Subject: re: Life and DNA | post id:
21951 |
| Paul, nice one man! Are there any
good pop-science books that you know of with this sort of stuff at this
sort of level in them? Soupie twist, Ed G.  | |
| From: Spun | 6/07/99
10:59:22 |
| Subject: re: Life and DNA | post id:
21970 |
| Just to follow on from what Dr
Paul was saying, I have read that RNA might have developed on the surface
of clays (montmorillonite I think) which act as a catalyst. If this is
correct then the creation of life would be far more likely than with a
random mixture of chemicals. Another idea is that the necessary organic
chemicals were concentrated in oil
vesicles. | |
| From: Darren | 6/07/99
18:29:26 |
| Subject: re: Life and DNA | post id:
22109 |
| One small point for Dr. Paul to
think about.... Viruses only replicate in cells. They are absolutely dependent on the proteins and other cellular machinery which is already in place to do so. The RNA (many actually have DNA or some other configurations of nucleic acid) only serves to blueprint what needs to be made. It can't replicate itself and it can't make what it needs to replicate itself. Therefore it's not really reasonable to assume that RNA could have replicated in any way in an external environment (ie. without all the ridiculously complicated machinery already in place). Keep looking at it, the questions just get bigger. There is one answer to it all, but it's not evolution. It just doesn't add up, does it? | |
| From: Dr. Ed G (Avatar) | 6/07/99
20:17:12 |
| Subject: re: Life and DNA | post id:
22137 |
| Yes, but a lot of that is simply
due to the fact that the environment today is a hell of a lot different to
the environment of the primordial Earth. Oxygen for one, as Dr. Paul
points out is a real killer. This is why for any RNA or DNA to be
replicated they must be surrounded by a cell wall that keeps out and
controls the levels of oxygen around. Now, to say, for example, that
obviously RNA could not have spontaneously formed and hung around long
enough to replicate because it would have oxidised outside a cell's walls
ignores the fact that there weren't no significant amounts of molecular
oxygen around, at least not until those bothersome photosynthetic
organisms started making it! Now, I'm not saying this is your specific argument, but it is the sort of argument that misses the point that the environment is now completely different to what it was 100's of millions of years ago, so to say the forms of TODAY could not have arisen in TODAY's environment is missing the point, and misrepresenting the whole issue. Soupie twist, Ed G. | |
| From: Dr Paul | 7/07/99
10:54:58 |
| Subject: re: Life and DNA | post id:
22178 |
| Hi all, I wrote that speil based on what I would consider good logic and knowledge of Physics, chemistry and physiology. Maybe something by Richard Dawkins or Stephen Jones may have something similar to this. What I have read of them, they more tend to cellular evolution. The point about the virus requiring the generation of DNA for replication is a good point. Viruses are great piggy backers. They will use very complicated tricks to get the DNA synthesis sytem inside an infected cell to create a DNA strand based on the RNA, then replicate the RNA from this DNA, then output huge amounts of varying proteins from the RNA, then self organise to generate new viruses and then escape the cell. This last bit has been subject to news recently as Prof Peter Gage of JCSMR (John Curtin School of Medical Research at ANU) has found that to escape cells, the viruses generate a pore or channel forming protein which inserts into the cell membrane. The virus then escapes via the channel. Brilliant stuff by such an apparently simple organism. Prof Gage (Hi Prof Gage if you ever read this, I was an undergraduate while you were at UNSW many years ago) has found a system to block these channel proteins, preventing the virus from exiting the cells. Even better. What smart things living organisms are. What a war is waged. My guess would be that the Deoxyribose nucleic acids (RNA missing an hydoxyl group on one of the ring carbons, (read an OH is replaced by an H on the ring carbon) developed as a more stable from of the RNA somehow. Somewhere along the line, the cells stored the DNA as a way of generating the knowledge for RNA and protein replication. We may have just picked up another important step in generating cellular life as we know it. We still have the billion or billion and a half years to play with. If this technology of forming RNA or DNA from replicating strands of RNA was slowly developed, back up a bit, question, is DNA MORE stable in long strands (multiprotein data storage strands) compared to RNA? I will look for this and get back. Any others have ideas. Wow, we are putting thoughts for early life, and hopefully considering the patience of evolution. Back soon (hopefully on a human time scale rather than evolutionary time scale) Considering the importance of life for the development of the universe whilst doing ESR Paul | |
| From: Dr Paul | 7/07/99
11:03:22 |
| Subject: re: Life and DNA | post id:
22179 |
| Hi all, just something I have found whilst searching one of my books In "Organic and Biological Chemistry" by Mundy, Armold and Amend, Chapter 13 has a picture (fig 13.1) of cute little babies and kittens detailing individual differences between species and within species. On the NEXT page, it has an Exercise Example 13.1 "Name the kittens in Figure 13.1" and the n the solution "Solution:(just kidding, but the fourth one from the left in the top row should be named Igor)" It is lazing over on its side with its front paws together looking very intently at whoever is taking the photo. (Maybe rubbing hands together saying "yes master, I will test the serum on the rest of these kittens in a little while" Still looking, but having a laugh at some humour whilst so Paul | |
| From: Terry Frankcombe | 7/07/99
11:08:09 |
| Subject: re: Life and DNA | post id:
22180 |
| That sounds like the 'Are koalas
social creatures'? review question in "Theory of unimolecular and
Recombination Reactions" by Smith and
Gilbert. | |
| From: Dr Paul | 7/07/99
11:51:04 |
| Subject: re: Life and DNA | post id:
22185 |
| Hi all, Hi Terry, How is Qld?. It freezing down here in Canberra at the moment. Some basic differences and possible advantages disadvantages, remember input from a better source is urged and aids in the understanding, including by me. Ribose, DeoxyRibose, one hydroxyl group difference on a ring position is the only difference here. From a small understanding of carbohydrate organic chem, the lack of the hydroxyl group may make the DNA less likely to be esterified or methylated or acetylated (Or some attack by another organic compound realising Rib-OH + HO-X Rib-O-X or Rib-X, removing the OH group in a dehydroxylation reaction. Could be understood similarly to acetic acid and the combination of two acetic acids to form acetic anhydride and water as products CH3-COOH vs CH3-(OC)-O-(CO)-CH3 +H2O). This may stabilise the ribose phosphate chain system from attack and allow generation of long chains. ALSO allows tighter control over the actual generation of the chains if there is less points for chain polymerisation or base attachment. The RNA does not have Thymine as a base, but uses Uracil. Difference is a methyl group on one of the thymine pyrimidine ring positions. (apologies for the chemo techo talk, but if you can get a book with pictures of these, you will understand). The thymine HAS the methyl group. The Uracil lacks this methyl group. This will add a level of steric structure to the ring of the thymine and hence DNA that is not present on the RNA. From pictures of DNA strands, this methyl group (this is my view, it may not be supported by DNA structuralists, if any are out there, please correct me) appears to stabilise the planar nature of the thymine relative to the normal orientation to the (poly) deoxyribose-phosphate chain backbone. In RNA, the chains can turn at odd angles, transcription RNA is a beaut of a twister. THis is getting to a point where I could put in the further hypothesis (read: guess) that some time along the path, some deoxyribose nucleic acid polymerised with itself, rather than possibly mixing with ribose nucleic acid. This would have a stable conformer and hydrogen bonding and hydrophobicity would lead to the pairing of the bases leading to chains ( I did say physics as well as chem and biology) This would get us to the stage of forming relatively stable DNA chains. now we need to get to the unwinding and RNA replication off such chains. Maybe at the early points, RNA was the matching pair for small chains, while at a later time DNA happened along to pair leading the twisted chains of DNA as storage devices. Are we getting there yet?? 250 million years of chemical evolution, 750 to 1250 million years to get to reasonable life. (Maybe longer for the chem evolution time path.) Patience is definitely a virtue Paul | |
| From: Darren | 7/07/99
14:33:41 |
| Subject: re: Life and DNA | post id:
22230 |
| Hi again, Sounds like you've got a good theoretical argument going for achieving stability in the molecule. For my purposes, I'm going to assume that somehow the molecule is stable in whatever environment it's in. How does the DNA make it's very first protein (i.e. this is the first protein ever manufactured in all of pre-historic time up to this point - it's a big moment) without the presence of the proteins that are required to split the DNA and then read the code and make the new protein. I still can't see how one could have come about without the other. | |
| From: Spun | 7/07/99
15:48:36 |
| Subject: re: Life and DNA | post id:
22257 |
| In a very simplified
explanation, DNA produce RNA which produce Proteins. If some form of self
replicating RNA existed in the primordal soup, then it could make proteins
without DNA. DNA developed because it is more stable and has error
correction abilities. The big questions are could a self replicating RNA
exist and how can RNA be made without proteins. Don't know about the first
bit but I like the theory that an inorganic catalyst such as clay was
involved for the second bit (this is probably because I studied a bit of
pedology at Uni and like the idea of clay being important in the creation
of life). | |
| From: Dr Paul | 7/07/99
17:12:34 |
| Subject: re: Life and DNA | post id:
22277 |
| Hi Spun, Hi Daryn you have placed a modern component of evolution onto the DNA. Early RNA and DNA would have been subject to many replication errors. Only when the combinations of RNA's has been tried and a polypeptide was found to bind to DNA and allow replication with some accuracy would DNA be said to be "error free" This would have been much later down the track. RNA and DNA should be synthesisable in the primordial soup, but their effectiveness would require much much variation and interaction of results with whatever was in the primordial soup. Someone mentioned an ammonia atmosphere somewhere either in this thread or in another thread. I was thinking about this, the ammonia when mixed with methane CO2 and water would be an ideal environment for forming the primidines and purines that are the bases Good one. . Give the soup a million years of volcanic chemical and heat input, lots of atmospheric lightening and (remember, no dioxygen yet, so no ozone) a strong UV component in the incoming EM radiation. All serve to expand the range of compounds and bits floating around in the soup. We still need the definitipon of what would describe the first "life". With the mix of proteins (polypeptides) lipids (did we mention them) RNA, DNA, sugars, amino acids, we should be able to put together all the combinations of lipophilic proteins into the lipids and put some other components into the micelle. When do we get life? Paul | |
| From: Spun | 7/07/99
17:32:29 |
| Subject: re: Life and DNA | post id:
22284 |
| I reckon it's when the first
molecule (RNA, DNA or something else entirely) starts replicating itself.
All the cell membranes and other stuff are just enhancements to the
process. | |
| From: Darren | 8/07/99
14:45:45 |
| Subject: re: Life and DNA | post id:
22540 |
| Spun wrote: "If some form of self
replicating RNA existed in the primordal soup, then it could make proteins
without DNA." I think you've over-simplified the process. RNA requires special protein "machine" to interpret it and build the new protein. It does not just magically produce the protein by itself. We still need to show a way of having the DNA/RNA make a new protein in the absence of the necessary translating proteins. Without that, it doesn't matter whether the DNA is stable or whether the RNA is self-replicating. They still can't make anything. And, yes, I am continually amazed by the level of complexity and organisation that goes into every part of our world. Something as simple as an ant walking around requires more design brilliance than I can even imagine. | |
| From: Dr Paul | 9/07/99
15:28:57 |
| Subject: re: Life and DNA | post id:
22867 |
| Hi all, with time and a lack of O2 in the atmosphere, random RNA strands could aggregate through the energy influence of clays, metals, uv light. It takes time, but without O2, a measure of stability is offered. transcriptional RNA can bind amino acids at their 3' end (one end of the strand). This is well away from the site for reading off the messenger RNA. In the early soup, is there any chemistry stopping an RNA chain with more than say 5 nucleotide bases as a chain binding an amino acid? If this was the case, then polypeptides would have been thick on the ground. Protein structuralists are observing that sets of amino acids within a protein tend towards similar structures between differing proteins containing that amino acid set. The rules for hydrophobic folding, hydrogen bonding, metal ligation , membrane insertion must have been written in the early primordial mud. Given enough different types or polypeptides (20+ different amino acids, unlimited chain length initially so (>)20^n different combinations of amino acids for a polypeptide chain length of n amino acids) random patterns may be able to generate the combinations to form proteins to bind to DNA twisted strands, untwisting them then allowing transcription. This is very deep (possibly even voodoo at this stage, but I can see the physics in the protein foldings and the chemistry to form the complexes in the soup) and again the time frame is immense. For life, initial life, my guess would have to be to find the urge for self sustenance. When something wakes up to realise that the soup would be nice for dinner, then life starts. Self replication would be long after this, as a guess again. Paul | |
| From: Dr Paul | 12/07/99
12:03:15 |
| Subject: re: Life and DNA | post id:
23266 |
| Hi all, well, I have tried to logic through why a grouping of varied chemicals would gain the "self awareness" for self sustenance. Unfortunately I can not find it. I am in a position where I must invoke a divine intervention (here we go) with the one word command to the DNA, EVOLVE. Given this, life would be self sustaining and seek out ways to improve itself, through getting bigger, eventually dividing, eventually realising a sharing of genetic material may enhance a survival, initially looking for an expansion of DNA and RNA variants, maybe later for reducing the self copies that the next (should I note for those of the fairer gender) Daughter generations so that variability and advance may be continued. At this point, unless someone can show me otherwise, the gift of life must be by initial divine intervention. Evolve. Paul | |
| From: Terry Frankcombe (Avatar) | 12/07/99
12:30:58 |
| Subject: re: Life and DNA | post id:
23273 |
| Your missing the point about
evolution, Paul. There is no one way street, no sign pointing 'this way to
prosperity'. Things get more prosperous (smarter, bigger and uglier,
reproducing more) because if they didn't, then those things that did get
more prosperous would whip their
arses. | |