Perplexed about DNA - Help please?

[espritch]

Now here is where it gets foggy for me, when we introduce the theory of evolution via random mutation. If it is indeed true that the first organisms had very little or no junk DNA and that only miniscule amounts of damage to the strand would cause the organism to be destroyed then the idea of random mutation seems to break down. By definition, random means there is a 50/50 chance of a positive mutation occuring that will be beneficial to the overall structure of the DNA or the organism and 50/50 chance of a negative mutation happening.

Practically speaking, it is impossible to have a half-million positive mutations occur consecutively, even if we give room for say 1000 negative mutations that won't damage the DNA. This is basically your 1,000,000 monkey/ typewriter for 1,000,000 years idea. Realistically speaking, you would probably need several trillion monkeys and typewriters typing over eons to have this happen and even then it seems very bleak unless the monkeys are somehow more inclined to press certain keys more than others at different times, based on a set of ordered influences.

What do you guys think about that?

Evolution doesn't involve a single strand of DNA (or RNA) evolving. It involves thousands or millions of strands of DNA replicating and evolving. If a particular organism (or replicating molecule) has a bad mutation and dies, it is out of the game and the bad mutation dies with it. If a particular organism has a good mutation, it tends to produce more offspring and the good mutation spreads rapidly. This is what is meant by natural selection.

Random mutation by itself will not produce evolution. But random mutation in the context of self replicating populations in a competitive enviroment, filtered by natural selection, inevitably will.

One person said it may take about 100 base pairs of RNA compounds (sorry if my terminology is wrong here) - basically, 100 'instructions' to build the most basic organism.

Not an organism, a self replicating molecule (just for clarification).

 

[Kevin_Lowe]

Wow, thanks for all the information and thank you for the links you guys.

One person said it may take about 100 base pairs of RNA compounds (sorry if my terminology is wrong here) - basically, 100 'instructions' to build the most basic organism. Since I have not read or heard of anything like this in genetics I take it with a grain of salt; however, I have seen a lot evidence that it takes far more than that to form a living cell. The half-million guestimate sounds more in line with what I've heard on nature shows and read in science mags. Still, I appreciate everybody's input.

The source of your confusion is that a living cell is not the most basic organism, it is in fact very complex. The most basic organisms running around now are viruses, or arguably prions, and they are very much simpler than cells. They are much more like self-replicating molecules. The one hundred base pair creature would be a very simple virus-like organism.

(If you aren't up to speed on what cells, prions, viruses and molecules are you should do some googling since these are the kind of concepts you need a handle on to grasp this stuff).

Now here is where it gets foggy for me, when we introduce the theory of evolution via random mutation. If it is indeed true that the first organisms had very little or no junk DNA and that only miniscule amounts of damage to the strand would cause the organism to be destroyed then the idea of random mutation seems to break down. By definition, random means there is a 50/50 chance of a positive mutation occuring that will be beneficial to the overall structure of the DNA or the organism and 50/50 chance of a negative mutation happening.

Remember that this hypothetical hundred base pair thing is self-replicating. So if it makes a million copies of itself, and one hundred thousand have a negative mutation and die, there are still plenty left to carry on the game.

Practically speaking, it is impossible to have a half-million positive mutations occur consecutively, even if we give room for say 1000 negative mutations that won't damage the DNA. This is basically your 1,000,000 monkey/ typewriter for 1,000,000 years idea. Realistically speaking, you would probably need several trillion monkeys and typewriters typing over eons to have this happen and even then it seems very bleak unless the monkeys are somehow more inclined to press certain keys more than others at different times, based on a set of ordered influences.

It does not have to be consecutive. It could happen that there are one million primitive self-replicating molecules, and one hundred thousand mutate badly and die out, and only one develops a positive mutation.

Since that one with the positive mutation has a competitive advantage, its descendants will tend to outnumber or even wipe out the ones without the advantageous mutation. So then we have one million mutants, and maybe one of those mutants develops the next advantageous mutation and so on and on. The typewriting monkeys don't press certain keys more than others, but it might look like they do because we throw out all the pages where they hit the wrong keys.

The real question is not how we got from very simple life forms to humans, but how we got from organic chemicals just lying around to very simple life forms. Nobody has much of a clue about that question.

 

[Paul C. Anagnostopoulos]

Filip, get The Cartoon Guide to Genetics, by Gonnick and Wheelis. You'll love it.

~~ Paul

 

[epepke]

One person said it may take about 100 base pairs of RNA compounds (sorry if my terminology is wrong here) - basically, 100 'instructions' to build the most basic organism. Since I have not read or heard of anything like this in genetics I take it with a grain of salt; however, I have seen a lot evidence that it takes far more than that to form a living cell. The half-million guestimate sounds more in line with what I've heard on nature shows and read in science mags. Still, I appreciate everybody's input.

That was I. 100 base pairs is certainly not enough to make a cell. However, it is enough to make something that can undergo evolution. This has been shown in vitro.

DNA probably came much, much later.

Practically speaking, it is impossible to have a half-million positive mutations occur consecutively, even if we give room for say 1000 negative mutations that won't damage the DNA. This is basically your 1,000,000 monkey/ typewriter for 1,000,000 years idea. Realistically speaking, you would probably need several trillion monkeys and typewriters typing over eons to have this happen and even then it seems very bleak unless the monkeys are somehow more inclined to press certain keys more than others at different times, based on a set of ordered influences.

Several trillion is not so far off. My body contains about two hundred trillion cells, which means many quadrillion loops of DNA and many more strands of RNA. I'm a pretty big guy, but I'm much smaller than the ocean. And it did take eons, approximately 2 1/2 eons before there was anything more complex than a bacterium.

 

[clarsct]

Eos:
I did not say impossible. An electron could be knocked out of a strand of DNA, and we have protiens that can repair such damage. It is possible for a cancer to start this way, though.

However, reaction with a peroxide or superoxide changes the DNA signifigantly, mainly by the addition of an -OH group to the ribose ring. If this occurs with the right(or wrong..whichever) timing, then you have a miscoded protein, and perhaps a broken/damaged DNA strand. Many of these are not viable, but those that are form tumors. If the breaks are happening in the correct spots, then the tumor becomes malignant.

The 'burn' from a sunburn is caused by the damage done to the proteins and lipids of your cells through an excess of peroxides and superoxides. In short, your cells are eaten away from within.

BTW: Cancers can also be caused by the action of these oxygen species on RNA and proteins, depending on if the cell is dividing at the time, what proteins are affected and how. I would be more worried about the electron being knocked off a strand of RNA, as it is a single-strand variety. An electron knocked off the correct protein is also a concern, as the protein will fold in unsual ways which could be very harmful.
Cancers can also be caused by viral action, as with Cervical cancer.

In short, protect yourself from excess radiation. (ok, don't be paranoid, but some sunblock isn't a bad idea....)

As you can see, this is a fairly complex issue, and there are some good books out there, Filip. It isn't a 'snap answer' type of issue. I think Dawkins had something to say about this somewhere, as well, but I may be wrong....

 

[hammegk]

That was I. 100 base pairs is certainly not enough to make a cell. However, it is enough to make something that can undergo evolution. This has been shown in vitro.

Sounds interesting; would you give a bit more detail on that? Perhaps a cite, too?

 

[Dymanic]

100 base pairs is certainly not enough to make a cell. However, it is enough to make something that can undergo evolution. This has been shown in vitro.

I'm also curious as to what you have in mind here. I think the smallest plasmids are around 1300 base pairs... but 100?

 

[Filip Sandor]

The source of your confusion is that a living cell is not the most basic organism, it is in fact very complex. The most basic organisms running around now are viruses, or arguably prions, and they are very much simpler than cells. They are much more like self-replicating molecules. The one hundred base pair creature would be a very simple virus-like organism.

I guess that solves the evolution of the virus or prion, but what about a cell?

It does not have to be consecutive. It could happen that there are one million primitive self-replicating molecules, and one hundred thousand mutate badly and die out, and only one develops a positive mutation.

Since that one with the positive mutation has a competitive advantage, its descendants will tend to outnumber or even wipe out the ones without the advantageous mutation. So then we have one million mutants, and maybe one of those mutants develops the next advantageous mutation and so on and on. The typewriting monkeys don't press certain keys more than others, but it might look like they do because we throw out all the pages where they hit the wrong keys.

You have to think of it more practically than that. Even if the monkey's avoided bashing the key board with their palms or several fingers at once and were trained to only press a single key at a time (thereby reducing the chances of errors) it would be impossible for a monkey to create on of Shakespears fat books, in fact, they wouldn't even come close. Think of how many billions of key strokes it would take to create something even remotely resembling a paragraph, riddled with spelling errors, but close enough to be legible. Now let's say that by some miracle, one monkey manages to make it to his third or fourth, perfectly written paragraph... then he makes a couple errors and all his work is whiped out.

There are two main problems here that aren't likely to be overcome without some sort of a discriminating mechanism between the 'good' and 'bad' mutations.

First, a 'good' mutation may be good in the context of hundreds of thousands of other good mutations, but on it's own it can't provide any advantage in the early stage of developement of DNA. An example of this would be an eagle who's DNA is altered by solar debris let's say, it get's sliced at some point and reconnects. Let's say this section of the DNA controls the size of the eagle's talons, which could very likely give the eagle an advantage at this point, but don't forget, there are likely hundreds of thousands of instructions that make the talon itself already in place.

Before DNA made up any useful aspects of an organism it required hundreds of thousands of positive mutations to get there. A few positive mutations, or even hundreds wouldn't have made enough of a change to do anything at all at this point because there was no 'functioning' sections of the strand that could be modified yet.

Second problem is this, it only takes a few negative mutations to destroy the whole thing apparently and chances are the negative are 50/50 with the positive. This in essence would disable the positive mutations in an 'original blend' of DNA to reach any useful number before it was basically destroyed due to a number of negative mutations. To better illustrate what I mean, imagine you had a coin and a chart of about 500,000 different states listed, each being either heads or tails. If you were to flip a coin enough times, discarding the negative flips, you would eventually match all the states or 'choices' written on the chart, but what if I introduced a new rule, make 10 or more errors and you have to start all over again.

Mathematically speaking yes, it's "possible" for you to flip a coin 500,000 times and match each random state depicted on the chart perfectly, but realistically speaking it's more than a long shot, it's basically impossible because of the rule that nearly all your flips must be consecutively correct in order to avoid making any errors. Sure, you might produce 50-60 or maybe even by some miracle, over 200-300 consecutive flips after several billion years that are truly random and matching each state on the chart, but you make a few errors and you'll have to start all over!!

Now let's say there are trillions of you, flipping for trillions of years and one of you make it to 500 flips (to give you an idea how unlikely this is, it's basically the same thing as flipping heads or tails 500 times in a row)... but wait, we are talking about half a million flips needing to be right and the chances of breaking the code long before you even get close to making it are simply too high. There would have to be some discriminating mechanism that improves your chances of flipping the right state and lessening your chances of flipping the wrong state if you are to reach that high of a number.

 

[PatKelley]

Okay, I'll have to say at this point that you are mistaken about the magnitude of mutations. Some mutations that are deleterious or advantageous are the matter of a few base pairs, or in the extreme case, a single base pair. For instance, in those with a mutation in elastin production (a very basic molecule that controls the elasticity of skin and tissue, and is present in most land creatures) the symptoms are large stature, a particular look to the face and head, nonacromegalic enlargement, and eventually thinned aortic walls (something like a balloon.) This is a simple mutation. Very simple.

The mistaken impression I'm seeing is that there are always hundreds of genes for each part of an organism. This is not so. There might be one gene for a chemical in the body, like elastin or collagen, that has major effects on many stages of development. It is not always hundreds of mutations that result in a change; sometimes it is just one. One kink in how hormones are timed, one kink in how pigmentation is expressed.

This idea that an entire batch needs to be built up before going forward is fallacious, as genetic diversity is a continuum, not a set of discrete plateaus and predefined niches. Reaching a particular exact set of mutations twice in a row is, in fact, quite improbable. However, simply accruing mutations and having them weeded is, well, nearly certain. It's the specific outcome that is in question, and evolution does not predict a specific outcome. Evolution has no end-goal. But the crux of this comes back to the flawed "half a wing isn't a wing" argument.

Allow me to demonstrate - falling is bad. But being on the ground is bad, especially if you are small. So we have a selection pressure that will favor small animals that can be off of the ground, contrasted with a selection pressure against falling damage. Heavier means harder to climb, but also sturdier and more able to survive falls. We have a conundrum. Now, no one is suggesting that a single pressure built up and BAM suddenly, flight. This, however, is often how evolutionary theory is misstated in creationist arguments. If you look at the spectrum of arboreal species closely, you will see many who have developed protective coloration (if they can't be seen, they don't have to move quickly to escape arboreal predators and risk falling). There are many slow arboreal animals that move in a cryptic fashion (walking sticks, many types of spiders that resembe bird droppings, katydids and mantises, sloths) or are active at night (slow lorises, Aye Aye, and the like). Why? Because being seen is bad, and independantly many of these animals were put under pressures that, if their coloration even marginally more resembled the background or their movement gave them an advantage, it stuck. And it was continually refined.

This spectrum, however, of continuous improvement is not the only model, and so we get to the wing fallacy. Many creatures have developed bodies to allow them to sustain a controlled fall, as the largest danger in falling is landing where you don't want to. There are many creatures that have mutations that allow them to flatten part of their bodies, or extend them, or in some way ameliorate the damage from an uncontrolled fall. The extension of this is those who had better mutations could not only control their fall, but avoid the ground altogether. While not hitting the ground hard is good, not hitting it at all is better. From there it is an extension to powered flight- so a half-formed wing is actually, after all, quite useful. And immediately so, not "in the future."

 

[Dymanic]

...chances are the negative are 50/50 with the positive.

If we're talking about the monkey/typewriter/Shakespeare metaphor, such a statement may be defended on the basis that there is a specific 'target' state -- an exact copy of the original work. Within this fixed context, "good" or "bad", "negative" or "positive" may be regarded as binary properties. But (as PatKelly has just illustrated) in biology (or proto-biological chemistry), environmental context is never fixed; what works at one place and time may, in a different situation, either fail utterly or simply not work well enough to justify whatever costs it incurs (and everything incurs a cost).

It might be argued that there is a target state, that being the minimum requirement for sustained replication. But there isn't any reason why this requirement would have to be self-contained; it could just as easily be a property distributed among (say) molecules which somehow replicated each other (this needn't be as long a walk as it might seem if you consider the reciprocal relationship between a living cell and the DNA it contains; neither is capable of autonomous replication without the other).

 

[Filip Sandor]

Okay, I'll have to say at this point that you are mistaken about the magnitude of mutations. Some mutations that are deleterious or advantageous are the matter of a few base pairs, or in the extreme case, a single base pair. For instance, in those with a mutation in elastin production (a very basic molecule that controls the elasticity of skin and tissue, and is present in most land creatures) the symptoms are large stature, a particular look to the face and head, nonacromegalic enlargement, and eventually thinned aortic walls (something like a balloon.) This is a simple mutation. Very simple.

The mistaken impression I'm seeing is that there are always hundreds of genes for each part of an organism. This is not so. There might be one gene for a chemical in the body, like elastin or collagen, that has major effects on many stages of development. It is not always hundreds of mutations that result in a change; sometimes it is just one. One kink in how hormones are timed, one kink in how pigmentation is expressed.

Ok PatKelley, I get what you are saying, but aside from allowing different parts of a cell to be generated it doesn't actually generate them. Elasticity may be fairly simple and highly advantageous to a cell, but I thought the actual cell structure, all the parts and functions thereof require far more, properly formed base pairs than those which control chemical elasticity. Don't get me wrong, this problem can be off-set if most of the DNA is harmless 'junk' DNA in a basic, single celled organism and the number of base pairs required to form the more complex parts of a cell is in fact far less than half a million, in which case I have no arguement.

This idea that an entire batch needs to be built up before going forward is fallacious, as genetic diversity is a continuum, not a set of discrete plateaus and predefined niches. Reaching a particular exact set of mutations twice in a row is, in fact, quite improbable. However, simply accruing mutations and having them weeded is, well, nearly certain. It's the specific outcome that is in question, and evolution does not predict a specific outcome. Evolution has no end-goal. But the crux of this comes back to the flawed "half a wing isn't a wing" argument.

If you're applying this analogy to something that's already there and hence, can be modified then I agree, but in the case of the first living organisms, the "half wing" was missing... not even the "skeletal structure" was there yet and indeed, it needed to be built up from scratch, so this analogy wouldn't apply in this case.

Allow me to demonstrate - falling is bad. But being on the ground is bad, especially if you are small. So we have a selection pressure that will favor small animals that can be off of the ground, contrasted with a selection pressure against falling damage. Heavier means harder to climb, but also sturdier and more able to survive falls. We have a conundrum. Now, no one is suggesting that a single pressure built up and BAM suddenly, flight. This, however, is often how evolutionary theory is misstated in creationist arguments. If you look at the spectrum of arboreal species closely, you will see many who have developed protective coloration (if they can't be seen, they don't have to move quickly to escape arboreal predators and risk falling). There are many slow arboreal animals that move in a cryptic fashion (walking sticks, many types of spiders that resembe bird droppings, katydids and mantises, sloths) or are active at night (slow lorises, Aye Aye, and the like). Why? Because being seen is bad, and independantly many of these animals were put under pressures that, if their coloration even marginally more resembled the background or their movement gave them an advantage, it stuck. And it was continually refined.

This spectrum, however, of continuous improvement is not the only model, and so we get to the wing fallacy. Many creatures have developed bodies to allow them to sustain a controlled fall, as the largest danger in falling is landing where you don't want to. There are many creatures that have mutations that allow them to flatten part of their bodies, or extend them, or in some way ameliorate the damage from an uncontrolled fall. The extension of this is those who had better mutations could not only control their fall, but avoid the ground altogether. While not hitting the ground hard is good, not hitting it at all is better. From there it is an extension to powered flight- so a half-formed wing is actually, after all, quite useful. And immediately so, not "in the future."

I like the way you describe all this and I agree for the most part, but I don't see how it applies to an organism with no parts (an organism which doesn't actually exist yet). All I am saying is that there must have been some discriminating factor there. Environmental changes don't affect the random nature of these "early mutations". Forgive me for not knowing more on this subject, I'm sure there is a lot that we haven't covered here, stuff geneticists know much better. I find that a lot of people simplify their explinations for different phenomenon by using terms that refer to very complicated processes which they don't actually understand. I just thought I would throw out the idea and see what others think of the numbers. I'm not saying I'm right, but since we're not all experts it's food for thought nonetheless!

Edited to add: I don't think attributing the things you don't understand to God is the intelligent thing to do, but I also don't believe that using simplistic, blanket arguements to explain things you don't understand is wise either.

 

[Kevin_Lowe]

I guess that solves the evolution of the virus or prion, but what about a cell?

An excellent question which no one has a detailed answer to. Presumably primordial organisms that worked well together stumbled on a way of sticking together and eventually accreted into something that is to a virus what a human is to a single-celled organism, but nobody knows exactly how it happened.

Which isn't surprising. It happened a very long time ago, possibly over a very long period of time, under conditions we do not fully know. As I said before the most reasonable theory based on our current knowledge of the universe is that it probably involved perfectly ordinary chemical processes going about their business and there is no evidence supernatural agencies participated in the process.

You have to think of it more practically than that. Even if the monkey's avoided bashing the key board with their palms or several fingers at once and were trained to only press a single key at a time (thereby reducing the chances of errors) it would be impossible for a monkey to create on of Shakespears fat books, in fact, they wouldn't even come close.

Actually if you immediately throw out every wrong keystroke, and immediately distribute copies of every correct keystroke to millions of other monkeys, you can get there very quickly.

Evolution is guided by the environment, it is not a process of random flailing about.

There are two main problems here that aren't likely to be overcome without some sort of a discriminating mechanism between the 'good' and 'bad' mutations.

First, a 'good' mutation may be good in the context of hundreds of thousands of other good mutations, but on it's own it can't provide any advantage in the early stage of developement of DNA.

If it provides no advantage it simply is not a good mutation, end of story.

Before DNA made up any useful aspects of an organism it required hundreds of thousands of positive mutations to get there. A few positive mutations, or even hundreds wouldn't have made enough of a change to do anything at all at this point because there was no 'functioning' sections of the strand that could be modified yet.

There was a critical path that had to be followed, certainly. A single celled organism has no use for genes for hands. That is why you can see the process of evolution over time building up more and more complex and specialised organs and organisms.

Second problem is this, it only takes a few negative mutations to destroy the whole thing apparently and chances are the negative are 50/50 with the positive.

Actually negative mutations far outnumber the positive, but as long as you make enough copies of the positive mutation it doesn't matter.

Mathematically speaking yes, it's "possible" for you to flip a coin 500,000 times and match each random state depicted on the chart perfectly, but realistically speaking it's more than a long shot, it's basically impossible because of the rule that nearly all your flips must be consecutively correct in order to avoid making any errors.

A much better analogy would be starting at the beginning of the chart, and flipping the coin as often as you need to, to get the first entry right. Then you move on to the second entry and flip your coin as often as you need to in order to get that one right, and so on. You should get there in a million flips or so.

 

[PatKelley]

Ok PatKelley, I get what you are saying, but aside from allowing different parts of a cell to be generated it doesn't actually generate them. Elasticity may be fairly simple and highly advantageous to a cell, but I thought the actual cell structure, all the parts and functions thereof require far more, properly formed base pairs than those which control chemical elasticity. Don't get me wrong, this problem can be off-set if most of the DNA is harmless 'junk' DNA in a basic, single celled organism and the number of base pairs required to form the more complex parts of a cell is in fact far less than half a million, in which case I have no arguement.

This is where we start talking about ribozymes. These are folded bits of RNA that act like enzymes. That's right, it might have been that originally, the first start was a bit of chemistry that allowed a molecule (a particular kind of sugar and substrate) to link together, perhaps a more stable configuration than surrounding molecules. At this point, everything is both food and consumer. Stability, however, is not enough, and the particular molecule only makes headway for a while, but it is reactive and produces more of itself. Eventually, each is colliding with the other, some with oxidizing groups to break up other molecules, until two link up. The two, though now joined, have fewer reactive surfaces and are less susceptible to reaction with other molecules. The beginnings of RNA. Each still makes copies, but the copies are bigger and less reactive per unit surface area. More resources go into this new molecule and are taken from the environment, increasing competetive advantage. With three or four, it is multiplied still further. Now the daily cycle of hot and cold becomes a factor, as during cold periods the new RNA folds into a new shape, maybe just tens of base pairs, but still less reactive when the seas are cold. Eventually, though most molecules are inactive at night, this folded RNA begins colliding with other RNA creatures, and if the shape is right- *snip* food in the morning. The first ribozyme (or enzymatic activity RNA).

Now, for cells. There were naturally occuring lipid bilayers, made out of early chemicals and the action of the surf. (These are reproducable) These made for tiny pools of food; they reduced competition, but limited the food supply. An RNA able to get in and out would have an advantage; any trapped become food for invaders, any locked out are potentially left without food. Better still if one can open or repair such a lipid bilayer, as then one could open it to let in new food, but close it to keep out competing RNA creatures.

We've gone from a few base pairs to primitive cells, still nothing impossible.

If you're applying this analogy to something that's already there and hence, can be modified then I agree, but in the case of the first living organisms, the "half wing" was missing... not even the "skeletal structure" was there yet and indeed, it needed to be built up from scratch, so this analogy wouldn't apply in this case.

Turns out all that might be needed for the initial structure is a bunch of carbon, nitrogen, oxygen and hydrogen. Early earth had methane(CH4), ammonia(NH3), and water(OH2 or more commonly written H2O). The most basic of backbones.

I like the way you describe all this and I agree for the most part, but I don't see how it applies to an organism with no parts (an organism which doesn't actually exist yet). All I am saying is that there must have been some discriminating factor there.

The nature of chemical reactions in an ionic solvent over time.

Environmental changes don't affect the random nature of these "early mutations". Forgive me for not knowing more on this subject, I'm sure there is a lot that we haven't covered here, stuff geneticists know much better. I find that a lot of people simplify their explinations for different phenomenon by using terms that refer to very complicated processes which they don't actually understand. I just thought I would throw out the idea and see what others think of the numbers. I'm not saying I'm right, but since we're not all experts it's food for thought nonetheless!

Edited to add: I don't think attributing the things you don't understand to God is the intelligent thing to do, but I also don't believe that using simplistic, blanket arguements to explain things you don't understand is wise either.

Some of the blanket arguments are based on, well, a century or more of research,but it is still good to demand specifics, to question, to prod and poke. Scientists rip at each other's work on a regular basis; it's part of the process. A poor argument won't stand up to scrutiny or questioning.

 

[Jon_in_london]

Ummm...

I rather think that there were self-replicating molecules that pre-dated RNA. What they were nobody knows, but to speculate on RNA mutation rates blagh blagh seems a tad simplistic when dicussing the possibility of the spontaneous emergence of elementary "life"

 

[Filip Sandor]

An educated opinion..

I found this article which might shed some light on the subject. A good read for those who don't understand why I made the suggestion that the hundreds of thousands of 'instructions' in the DNA of a living cell couldn't have come to exist through random mutation. The article basically provides some in depth information about the structural dynamics of DNA with the conclusion that we don't know how the base pairs in the DNA strand aquired their orderly formation. Plenty of references included!

 

[stup_id]

Also something that contributes to lower the rate of problems in mutations, specifically in the more complex organisms' cells, is the fact that there are 64 different combinations of 3 bases, (codons) 4 X 4 X 4 =64, that codify for 20 different aminoacids (taking the human as our sample animal, some plants and other organisms codify some other extra ones), this happening there can be single point mutations that are completely silent for instant, let's assume AGA (adenine-guanine-adenine) is changed into ACA (adenine-citosine-adenine) AGA and ACA may codify both for let's us say... Valine so the change is silent and won't change the structure of the possible protein that gene is coding for.

Furthermore, even if a substitution of aminoacid takes place, some of this aominoacids fall into one of the same subcategories (basic aminoacids, alifatic aminoacids, sulphur bearing aminoacids, acidic aminoacids...) and neither the subsitution makes a big change in the structure or function of the protein (as for instance if is an structure protein and the region that involves the change doesn't have to be sterometrically specific)

 

[PatKelley]

Biggest problem is stop codons included in a region where previously there was a protein.

 

[epepke]

Sounds interesting; would you give a bit more detail on that? Perhaps a cite, too?

The first time I read about this was quite a long time ago. I did a Google search and found this: http://rnaworld.bio.ku.edu/class/RNA/RNA00/RNA_World_4.html

This is not the research I was referring to, which was much older (early 1980s). But at least is supports the idea that RNA strands as short as 100 base pairs can meaningfully undergo evolution by, in this case, artificial selection.

I haven't had a chance to look up the Ellington and Szostak paper; perhaps this has some more references.

 

[Elind]

I have some questions about DNA and was wondering if someone could help me.

Apparently DNA is a highly comlex, ordered structure composed of several compounds. Does anyone know approximately how many lines or 'segments' of code exist for something like the most basic, single celled organisms which first inhabited our planet? Also, in conjunction with the previous question, does anyone know approximately how much alteration such a strand of DNA requires before the organism would most likely not live or be able to reproduce. In other words, how much damage would you have to do to the DNA to essentially destroy the organism?

I mean no offense, but I suggest going to graduate school and getting a PHD on that thesis.

I'm not a geneticist, but I know that of the billions of sections in genes it doesn't take but a few tiny screwups to be born without a brain, or perhaps one of the slower deaths, like accelerated aging perhaps. It's not a matter of quantity, it's a matter of quality of defect.

 

[Dymanic]

I made the suggestion that the hundreds of thousands of 'instructions' in the DNA of a living cell couldn't have come to exist through random mutation.

Hence the reason so much emphasis is placed upon the importance of selection.

...we don't know how the base pairs in the DNA strand aquired their orderly formation.

I assume that by "orderly formation" you are referring to the way the nucleotides map to amino acid sequences, rather than to the chemical structure of the molecule itself (which is no more difficult to explain than the chemical structure of other molecules). You're right, we don't know. In science, things often eventually boil down to the amount of confidence we place in our guesses. Abiogenesis is one area in which a lot of the guesses are made without a lot of confidence, but one reason RNA is the subject of so much attention regarding the origins of the system is that unlike DNA, RNA comes in a single strand. This means that since the nucleotide bases aren't all paired up with complementary bases on the other strand, they are free to pair up with each other, so the molecule can assume a wide variety of shapes, much like a protein.