Minimum Genome

[Maddad]

When we consider how life came about, we need know how complex chemicals had to be before they could qualify as life. One qualification for life is that it be able to reproduce. Before you can talk about these chemicals evolving, something has to create a replication mechanism first.

It seems easy to get the amino acids by mixing basic ingredients in a bottle and zapping it with energy. However, it is a huge leap from there to life. You have to encase whatever you are doing in a sack of some kind. That sack has to let the good stuff in and get rid of the bad stuff. Then there is the issue of replication. DNA is ungodly complex, but you already had to have it for there to be life. Our DNA has 3.2 billion base pair on each of 46 chromosomes which works out to about 5 trillion [5,000,000,000,000] atoms. You can get by with a lot fewer base pair for a simple primitive replication mechanism.

http://www.virtuallaboratory.net/Biofundamentals/lectureNotes/Topic4-1_GeneExp.htm
Mycoplasma Genitalium is an organism with close to the minimum number of DNA base pair required to carry out minimum life functions. It has 580,074 base pair, but could probably do what it does with about 300,000. However, it is a parasite, so it depends on its host to provide some of its life functions. You would have to bump the base pair count back up to 500,000, possibly a bit more, to achieve minimum genome: the fewest number of DNA base pair to carry on life functions.

When each base pair needs about 100 atoms to construct the DNA molecule, the minimum genome requires somewhere around 50 million atoms properly arranged before life can exist. Raise any even modest number to the 50,000,000th power and you get an astoundingly large figure. Just pulling a wild number out of the air, if the average atom can combine with another in any of four ways, then you have to try 10<Sup>30,000,000</Sup> combinations before one of them works.

I will give you an idea how improbable this is to happen by accident. Suppose that in the experiment to create life you try a different combination every trillionth of a second. You never repeat a previous combination, so each attempt is a unique effort. For round numbers you try a new combination in every 30 molecules of water. You cannot use much fewer than this number because you have to suspend the chemicals that will be building the DNA. Since there are 10<Sup>9</Sup> cubic kilometers of ocean, there are 10<Sup>18</Sup> cubic meters and 10<Sup>24</Sup> cubic centimeters of ocean. In each cc of seawater there will be 10<Sup>21</Sup> groups of 30 water molecules, so you should have 10<Sup>45</Sup> combinations of chemicals tried each trillionth of a second to produce DNA. In one second you will try 10<Sup>57</Sup> combinations, and in a year you will try 10<Sup>65</Sup> combinations. After the age of our universe, 13 billion years, you will have tried 10<Sup>75</Sup> unique atomic combinations in search of a DNA molecule.

The problem is that you needed to try 10<Sup>30,000,000</Sup> unique combinations before chance happens to give you one. Actually, I rounded 30,000,000 down from 30,103,000. If a hundred thousand zeros is not significant, then certainly 75 zeros does not mean anything. You would have to continue trying unique combinations of atoms for 10<Sup>30,102,925</Sup> times the current age of the universe before chance will create the smallest DNA molecule needed to sustain life.

It ain’t gonna happen.

 

[Idle Mind]

Our DNA has 3.2 billion base pair on each of 46 chromosomes

Nope. We have about 3.2 billion base pairs if the 23 chromosomes are lined up end to end. That number is doubled to 6.4 billion due to each of our cells (except gametes) having 2 copies of each chromosome.

You can get by with a lot fewer base pair for a simple primitive replication mechanism.

True. Bacteria can get by with around 1,000,000 base pairs, and viruses with even fewer. However, viruses lack the enzymes to replicate and transcribe their genome.

Mycoplasma genitalium (<-- Note: scientific names are always written in the notation I have shown...genus capitalized, species not, and usually in italics) is an organism with close to the minimum number of DNA base pair required to carry out minimum life functions. It has 580,074 base pair, but could probably do what it does with about 300,000. However, it is a parasite, so it depends on its host to provide some of its life functions.

It is a parasite, but it's a parasitic baterium. As such, it does not get genetic information from it's host. It will obtain nutrients and things, but not mechanisms for replication.

Just pulling a wild number out of the air, if the average atom can combine with another in any of four ways, then you have to try 1030,000,000 combinations before one of them works.

This is just plain nonsense. It varies for each group of atom. Carbon happens to able to make 4 bonds, but that is not the standard, and simply cannot be applied to every other atom. Remember, there are Oxygen, Nitrogen, and Phosphorus in DNA as well (and hydrogen).

No one is saying that we go from atoms to DNA all in one step. That obviously is not probable. However, there are different parts to DNA. There is a sugar; ribose as a furan ring, which is it's most stable form: a nitrogenous base; nitrogenous rings which are stable and found in nature: and a phosphate; very common. These three things can combine and form a single molecule, and will thermodynamically, else DNA wouldn't exist.

Also, no one is saying we went from a molecule of DNA to a fully formed 500,000 base pair organism with fully functional proteins and membrane all in one step either. Over billions of years, and trillions of interactions we got a single small piece of replicable material.

It's not impossible if it happened.

 

[Maddad]

No one is saying that we go from atoms to DNA all in one step.

I am saying it. You have to, because before you do, you have no way to replicate. Without replication, you do not have life. Therefore you must go all the way from non-life to a functioning string of 300,000 base pair of DNA or life doesn't work. If you miss by even one step in 300,000, then you do not get life.

Over billions of years, and trillions of interactions we got a single small piece of replicable material.

Won't happen. 4.5 billion years is only 130 x 10<Sup>15</Sup> seconds. The oceans have 1.4 x 10<Sup>9</Sup> cubic kilometers of water, or 1.4 x 10<Sup>18</Sup> cubic meters, or 1.4 x 10<Sup>24</Sup> cubic centimeters, or 1.4 x 10<Sup>27</Sup> microliters. If you try a new 300,000 strand DNA combination at random each microsecond in each cubic microliter of the ocean, then you can randomly try 180 x 10<Sup>42</Sup> combinations since the beginning of the world. However, there are 10<Sup>180,000</Sup> combinations to try before you hit pay dirt. You would have to keep trying random combinations for 10<Sup>179,957</Sup> times as long as the world has existed before you have a 50-50 chance of getting your small piece of replicable material.

And that's assuming you can randomly assembled large, complex molecules into a 300,000 step chain, accidentally, in each microliter of ocean for ever microsecond the world has existed.

It ain’t gonna happen.

It's not impossible if it happened.

I do not argue that life never happened. Since we are talking about it, it did. Howsomever, I am arguing that the way we explain how it happened leaves something to be desired.

 

[guthrie]

I dont know much about this subject, buts lets have a go....

I am saying it. You have to, because before you do, you have no way to replicate. Without replication, you do not have life. Therefore you must go all the way from non-life to a functioning string of 300,000 base pair of DNA or life doesn't work. If you miss by even one step in 300,000, then you do not get life.

No you dont. You can go to some kind of intermediate, it neednt even be DNA, RNA is a contender, even if there are holes in the RNA world hypothesis. Why are you defining 300,000 base pairs as teh minimum for replicable life?

">Sol Spegelman in the 60s experimented with a supply of virus which he
>placed in a test tube, enriched a supply of the replicase enzyme that was
>required by the virus in order to replicate its RNA and an ample supply of
>free nucleotides. After he mixed these, and arranged a flow of materials
>into the system, he waited to see what happened. In the beginning the
>RNA copied itself rather faithfully. However, mutations quickly started
>cutting the RNA strands in half. These strands became increasingly
>shorter until after about 70 generations the RNA lengths stabilized at
>the shortest possible length capable of replicating itself. This strand
>contained about 220 nucleotides, little more than the recognition sight
>for the replicase enzyme."
http://www.talkorigins.org/origins/postmonth/apr98.html

Won't happen. 4.5 billion years is only 130 x 10<Sup>15</Sup> seconds. The oceans have 1.4 x 10<Sup>9</Sup> cubic kilometers of water, or 1.4 x 10<Sup>18</Sup> cubic meters, or 1.4 x 10<Sup>24</Sup> cubic centimeters, or 1.4 x 10<Sup>27</Sup> microliters.

Thats todays oceans. How do you know how much was in oceans billions of years ago?

And that's assuming you can randomly assembled large, complex molecules into a 300,000 step chain, accidentally, in each microliter of ocean for ever microsecond the world has existed.
It ain’t gonna happen.
I do not argue that life never happened. Since we are talking about it, it did. Howsomever, I am arguing that the way we explain how it happened leaves something to be desired.

Nobody is suggesting that large com[plex molecules were assmebled, they are suggesting small ones were first. Stop setting up a straw man and actually look at what is being said.

http://www.talkorigins.org/faqs/abioprob/abioprob.html
http://www.evowiki.org/index.php/Abiogenesis

 

[Maddad]

guthrie
If you say that RNA is an alternative contender to DNA, you are not decreasing the number of base pair needed. RNA can be thought of as a mirror copy of DNA, organized with the same base pair arrangement (even though one pair involves a different second chemical - uracil in place of thymine. The other differences are so minor, like the 2 prime carbon of the ribose sugar having an -OH group instead of a -H group. Even being single stranded as opposed to DNA's double stranding does not play role since it is the sequence of either one strand or the other that codes for information.

Why are you defining 300,000 base pairs as teh minimum for replicable life?

That is the point of the biofundamental page that I referenced in the original post. You must have at least a number of base pair comparable to this number in order to code for all the functions to carry out independent life. Although Mycoplasma genitalium has 580,000 base pair, it may not have the very smallest genome possible necessary to support life. I very arbitrarily picked 300,000 out of the air as a mid point between the smallest known genome and nothing at all.

The '60's experiments with viruses are interesting. I notice that you cut the quote off prior to the statement that "This molecule, labeled the Spiegelman Monster was able to reproduce itself at a fantastic rate in this protected test tube environment. But could not survive in the unprotected world, to say nothing of its survival in the primordial ocean." When you add this last quote in, the 220 base pair are no longer enough for replication. We do not know what the minimum number would be, but the author curiously then claims that while 220 would not be enough, 100 would be. I would want independent cohoberation before accepting that statement, as well as a reason why it should be so. The .org source does not give us high confidence in the information, and the information quoted looks like it's been passed around in emails.

Another troubling aspect is that the article references 40 year old work, even though Spiegelman lived another 20 years. A quick check of the net though does indicate that a number of respectable institutions reference his work, so we are unable to pass his contribution off as that of a kook. I note though that his work speaks to the opposite direction that we've been talking about. His experiments shown the catabolism of an existing viral RNA fragment. It showed that RNA tends to shed nucleotides that are unnecesary for rapid replication. It does not explain how that viral fragment came into being in the first place, and that is the subject of this thead.

Still though, you have provided a fascinating insight into primitive evolution.

Those 220 nucleotides involve 10<Sup>132</Sup> possible combinations. That's a lot smaller than 10<Sup>180,000</Sup> of course, but it still needs something like 10<Sup>90</Sup> times as much time as the age of the world. That would still be a million trillion trillion trillion trillion trillion trillion trillion times as long as the world has been around.







<Strong><Em></Em></Strong>

 

[zyncod]

First of all, for a complex, functioning cell with membranes and proteins to spontaneously form would be even less likely than the 10^30,000,000 number that you gave. The way that life probably initiated was as a single molecule of RNA (DNA with only one strand and with an extra hydroxyl group on the sugar molecule). There are autocatalytic ribozymes in life right now, that is, molecules of RNA that can carry on chemical reactions in much the way that protein does. Some of the introns in your genes (useless genetic information that must be spliced out of the RNA before it can serve as a template for making protein) splice themselves out - they don't need proteins or anything else. And these are very small pieces of RNA, less than 300 bases long.

So, we will assume that the first life was a piece of RNA that could replicate itself (something that does not exist on the planet right now because RNA is less stable than DNA and all free-living RNA organisms were probably made extinct by the more evolutionarily fit DNA organisms). This piece of RNA did not have to be very long - most proteins are only a few hundred amino acids long and we will further assume that this RNA-life was similarly made up of only 500 nucleic acid building blocks. To use your math, this would be 50 atoms per base (as RNA has only one strand) or 25000 atoms total. And I'm going to further downgrade this because the nucleic acids that make this up are (almost by definition) very stable molecules and would not need to be reformed every time you wanted to try to make life. If you have 5 possible nucleic acids and you want to make a string of 500 nucleic acids, that's 3X10^350 possible combinations. Which is not a trivial difference from the 10^75 combinations you will try throughout the age of the universe when you consider:
1) That was only the combinations tried in our own ocean
2) That the rate that these combinations were being tried was probably much higher because organic molecules stuck to clay and other surfaces and were thus in much closer proximity and the resulting equilibrium constant would tend to make them form combinations much more rapidly
3) That these nucleic acid molecules probably formed the more stable substrands that would eventually lead to the RNA-life first. Life is not a fragile thing and the first life would probably be made up of a fairly stable molecule
4) And most important... it only had to happen once. I am a realist and do believe that life is fairly improbable. But, just like mineral crystals, the initial microscopic seed leads over and over again to huge crystals. As long as you have that seed, you can have very complex crystals that seem to defy the natural order of randomness. Like humans (the apex of life - HA!) from tiny pieces of RNA. If you find that you feel inadequate because you came from an essentially random process, I'd suggest you get in touch with that feeling. You were not made by a God that loves you - you came from tepid pond scum and monkeys.

 

[guthrie]

Its nice to see someone actually reads the links.

If you say that RNA is an alternative contender to DNA, you are not decreasing the number of base pair needed. RNA can be thought of as a mirror copy of DNA, organized with the same base pair arrangement (even though one pair involves a different second chemical - uracil in place of thymine. The other differences are so minor, like the 2 prime carbon of the ribose sugar having an -OH group instead of a -H group. Even being single stranded as opposed to DNA's double stranding does not play role since it is the sequence of either one strand or the other that codes for information.

OK, so youve been reading up on chemistry textbooks. I think that part of the point is that if you go back to using RNA, your cutting out some complexity such as the need for mechanisms to break up and reform the DNA helix. Therefore that makes it both more likely and easier to do.

That is the point of the biofundamental page that I referenced in the original post. You must have at least a number of base pair comparable to this number in order to code for all the functions to carry out independent life. Although Mycoplasma genitalium has 580,000 base pair, it may not have the very smallest genome possible necessary to support life. I very arbitrarily picked 300,000 out of the air as a mid point between the smallest known genome and nothing at all.

The 300,000 base pair point though is that it is approximately that necessary for a functioning, modern DNA based cell. There is nothing in that that says some kind of lipid membrane like structure with RNA or anything else cannot either multiply or be formed in the first place. Thats what I mean by setting up a straw man, your trying to compare something in the present that is, although evolved from, probably not that close to the possible first replicating chemicals.



The '60's experiments with viruses are interesting. I notice that you cut the quote off prior to the statement that "This molecule, labeled the Spiegelman Monster was able to reproduce itself at a fantastic rate in this protected test tube environment. But could not survive in the unprotected world, to say nothing of its survival in the primordial ocean." When you add this last quote in, the 220 base pair are no longer enough for replication. We do not know what the minimum number would be, but the author curiously then claims that while 220 would not be enough, 100 would be. I would want independent cohoberation before accepting that statement, as well as a reason why it should be so. The .org source does not give us high confidence in the information, and the information quoted looks like it's been passed around in emails. [/QUOTE]
Yup, thats right. A test tube is a protected environment. You'll also note that the person annotating the e-mail pointed out that there werent necessarily any other competing life forms/ replicators around then, so that doesnt necessarily mean it couldnt survive out there. All that it shows is that some form of RNA replication is possible, exactly how much in what circumstances I do not know, though there are no doubt various groups looking into it.
I'd like ot know what you mean by the .org source doesnt inspire confidence, given that that .org is part of talkorigins, a scientific website combatting creationist claims, therefore part of an actual databse set up by people knowledgeable in their field. Of course the argument in the e-mail may have been superseded by newer research.

Another troubling aspect is that the article references 40 year old work, even though Spiegelman lived another 20 years. A quick check of the net though does indicate that a number of respectable institutions reference his work, so we are unable to pass his contribution off as that of a kook. I note though that his work speaks to the opposite direction that we've been talking about. His experiments shown the catabolism of an existing viral RNA fragment. It showed that RNA tends to shed nucleotides that are unnecesary for rapid replication. It does not explain how that viral fragment came into being in the first place, and that is the subject of this thead.

I am interested in why you say "we are unable to.." Are you a borg?

As for how the viral fragment came into being, well, we shall never know for certain. All we can do is try and replicate experiments and possible and known environmental conditions. Or we could say its due to an intelligent designer, but that leaves us with the obvious question, where does the designer come from?

 

[Idle Mind]

And we aren't going from atoms to DNA, we are going from a sugar (again, ribose and deoxyribose as a furan ring) and a nitrogenous base mixing together, and a phosphate being added to that. Then, nucleotides interacting to form chains. There are very small sequences that can copy themselves, such as Variable Number Tandem Repeats, and transposons. You can't read a site that breaks complex mechanisms down to the fundamentals in order to explain them to broad audiences, and have a full understanding of all that's involved.

 

[zyncod]

Actually VNTRs and transposons can't copy themselves without protein intermediaries. VNTRs and other repetitious sequences, such as those that cause Huntington's Disease "take advantage" of the cellular homologous recombination machinery to "replicate." And transposons either encode for a transposase protein or take advantage of other transposases encoded elsewhere in order to replicate. However, the "RNA world" hypothesis of a self-replicating RNA requiring no exogenous proteins is definitely a real possibility given the almost omnipresence of ribozymes in organisms' genomes.
But I will wholeheartedly agree that atoms will spontaneously form the more stable phosphates, sugars, and nitrogenous bases and therefore the argument that maddad puts forth is more than a little specious.

 

[Idle Mind]

Yes, I suppose I didn't fully explain myself. Of course VNTRs and transposons requite protein "machinery", but my point was that you don't need a 300,000 base pair long sequence before you obtain the ability to replicate.