Abiogenesis

[Realitycheck]

How do you get a self-replicating molecule to form a cell wall around it or perfectly designed nucleic acid perfectly nestled in the right environment to develop into a self-replicating protocell?

 

How do you make this jump from what we know to what we expect?

 

What are you thoughts?

 

I'm starting to envision this primordial world of nano-bots, a world full of nothing but virus-like organisms and prions, before they developed further. Of course, their precursors are just an idea. How can you have a functioning cell without known components? How simple can you get it to where it can still be called life?

[Dak]

How do you get a self-replicating molecule to form a cell wall around it

 

phospho-lipids (the thingies that cell membranes are made out of) will spontaniously form vesicles in water due to hydro-phillic/-phobic interactions.

 

so, phospho-lipids + water + self-replicating molecule = self-replicating molecule in a vesicle just by chance.

 

actually, phosopho-lipid vesicles have some of the properties of life themselves: they can 'grow' (by absorbing new phospholipids that they bump into) and 'replicate' (too large and they become unstable, and can split in two)... if they've got a molecule inside them that self-replicates, then in theory you could have some inheritance going on as the 'daughter' vesicles will also contain said molecule... if the molecule somehow strengthens the vesicle or aids the formation of vesicles or something then you'd have the very begginnings of an evolution-capable system.

[Realitycheck]

I'm still not seeing how this nucleic acid starts doing its job of running a cell unless it just happens to have (.01^-1000 chance) all of the right instructions in the perfect startup environment, matching, making the chances of life under our scenario far less likelier.

 

Maybe a prion somehow acquired a nucleic acid to organize processes.

 

This scenario makes the chances of life more likelier.

Edited November 2, 2008 by agentchange
multiple post merged

[foodchain]

I don't know but I think "time" gets looked over here. I mean in all of the earth through history can we speculate that maybe some small chunk of mass with the right elements could not have "evolved" or differentiated in time that would lead to such? We are after all I think looking for a physical mechanism here of how it occurred in nature.

 

I mean what if just one of the steps in the reaction, or the entire reaction mechanism for just one part takes two years to complete under correct conditions?

 

Just to end we look for an answer to abiogenesis because evolution starts out with microbes, or that evolution occurred. If you accept the biochemical reality of life why is it so impossible for abiogenesis to have occurred then? I mean a biochemist like Behe who is against evolution from sort of a complexity perspective wont even accept genetics then, which if you want you can have serious empirical proof of evolution with chemistry right there. Giving selection is what it is, why is convergent evolution so withdrawn from the landscape of microbial evolution? They would have I think very similar biochemistry and evolution shows, yet in that the idea that convergent evolution could have operated on the flagellum is some remote impossibility even though it occurs with life which means it operates thusly at the cellular and molecular level of life, its not even this but if all of life was exactly similar in every regard molecularly speaking I think evolution would have not taken place because there would have been no change at all, man that guy is a bag, its amazing how something so wrong can get so far.

[MedGen]

Following on from Dak with the basic lipid membrane enclosed replicator; it also depends on what the replicator is. If it's RNA then it can form secondary structures that can catalyse reactions like an enzyme, called ribozymes.

 

So you've got replicating molecules that can catalyse reactions, including their own synthesis, et voila!

[Edtharan]

I ahve found this to be a good explanation: http://au.youtube.com/watch?v=U6QYDdgP9eg&feature=PlayList&p=0696457CAFD6D7C9&index=0

[Realitycheck]

Edtharan, you are THE MAN!!!!! Thank you.

[iNow]

Here's another really good one:

http://www.youtube.com/watch?v=ozbFerzjkz4

 

 

 

Also, for a longer course on the probability of it all, climbing mount improbable was very well done:

http://video.google.com/videoplay?docid=-690865967686494800&ei=ZQAOScKYJoruqAKevL2YCg&q=growing+up+in+the+universe+ep+3

[Realitycheck]

Founders

Jack Szostak, Ph. D.

http://ccib.mgh.harvard.edu/founders-szostak.htm

 

From what I have read over the past year or so, I really think that this guy has the best take on putting all of these missing pieces together.

 

Dr. Szostak is an Investigator of the Howard Hughes Medical Institute, Professor of Genetics at Harvard Medical School, and the Alex Rich Distinguished Investigator in the Department of Molecular Biology at the Massachusetts General Hospital.

 

His current research interests are in the laboratory synthesis of self-replicating systems and the origin of life. He and his colleagues have developed in vitro selection as a tool for the isolation of rare functional RNA, DNA and protein molecules from large pools of random sequences. His laboratory has used in vitro selection and directed evolution to isolate and characterize numerous nucleic acid sequences with specific ligand binding and catalytic properties.

 

For this work, Dr. Szostak was awarded, along with Dr. Gerald Joyce, the 1994 National Academy of Sciences Award in Molecular Biology and the 1997 Sigrist Prize from the University of Bern. Dr. Szostak is a member of the National Academy of Sciences, and a Fellow of the New York Academy of Sciences and the American Academy of Arts and Sciences. In 2000, Dr. Szostak was awarded the Medal of the Genetics Society of America.

 

Interesting that much of his studies were done this far back and I am just now getting to them. Shows you what I know. All of these steps already performed in a lab!

[foodchain]

Interesting that much of his studies were done this far back and I am just now getting to them. Shows you what I know. All of these steps already performed in a lab!

 

I would have to agree. I mean what does it all take to understand chemically life as is? I think having understanding of it to the point of being able to recreate how it came to be in the first place would be a serious advance in understanding. I question if we really are at that point in regards to such an endeavor, I mean it would require I think the use of all the natural sciences in some capacity if not more.

 

I have some serious issues with what that study would mean.

 

-Can we actually try to empirically study dynamic chemical processes that may have occurred naturally over an extended period of time. I mean if the reality of how life came to be involved a series of steps that takes say 2 years or more for example, can we empirically conduct such a study? It may seem a simple point but I think many times the study of such gets shrugged off not simply because of the topic, but that instant results I think is what is expected. Such as some series of reactions in some glassware that is done in eight hours or a day.

[pioneer]

One definition for life involves growth, reproduction and metabolism. Virus can reproduce, but since they don't metabolize, they are not considered alive. They really can't grow either, except in numbers. Cells show all three aspects, as do higher life forms.

 

Relative to abiogenesis, the easiest of these three steps, in a passive way, is growth in a loose sense. All that requires, before life, is a simple snow ball affect where things stick together to form bigger states all connected with simple chemical attraction. It is not alive, because it can't metabolize, but the blob can get bigger. The blob can also passively reproduce with simple shear, with each daughter blob then able to grow using the simple snowball affect or an extraction.

 

Simple things, like the polymerization of animo acids, by any means, including clays, is growth in a loose sense. Many such proteins chains can then stick together, with weak bonding forces, Of the three requirements of life, growth, in a loose sense, should be easiest to achieve first since it doesn't require anything beyond intermolecular bonding forces.

 

How things will grow in this very passive way, depends on the type of intermolecular bonding forces available. I will step forward for this example. Growing a simple membrane blob from lipids, can happen quite fast using the combination of the lipid van der Waals forces and aqueous surface tension. It is not alive but can grow further due to absorption/extraction from water. It can even replicate, in a loose sense, by breaking into two, with each daughter blob able to absorb independently.

 

The simple membrane blob can also diversify and evolve by including hydrophobic proteins into its structure. This is totally passive and based on extraction and availability. While depending on the forces between the proteins, these protein can island or try to repel each other and distribute more evenly. The next shear division can form two of the same or one with an island of protein.

 

We can also grow blobs the other way around. We can start with growing protein blobs, with some lipids or oils getting encompassed into the protein blob. These can also loose replicate, using simple shear to form two of the same or two with a slanted lipid distribution. Again is not life but it brings things together in a passive way using whatever stuff just so happens to be available at the time. The blob distributes based on secondary forces.

 

Passive metabolism is another thing that can happen in a simple way. The earth originally did not have oxygen in the atmosphere. This means no ozone layer and therefore higher UV. This type of passive metabolism is not life eating food, but the sun degrading blobs, at the same time they are snowballing and/pr breaking up due to shear. It is all passive but is giving a variety of blob states from which active steps will begin to emerge. The first active growth might be simply absorbing small things and trapping them into bigger things so there is net growth. It doesn't have to be pretty or even specific. That comes with practice.

[Edtharan]

One definition for life involves growth, reproduction and metabolism. Virus can reproduce, but since they don't metabolize, they are not considered alive. They really can't grow either, except in numbers. Cells show all three aspects, as do higher life forms.

The interesting thing about viruses is that they had to have evolved from something that is alive.

 

They share many DNA traits with other living organisms, and so are very likely to share some common ancestor. Also, they would have had to develop after other organisms as they can not reproduce without their host.

 

This means that even if virus are not "alive" according to some criteria, they did indeed come from something that would have once passed those criteria.

 

Personally, because there is no "Elan Vital" that causes something to be Alive, and that all organisms are really just complex chemical reactions, I believe that the definition of something as being "Alive" is necessarily blurry. Viruses are a case in point.

[pioneer]

Say we started with with beaker of virus parts, where the DNA or RNA is separated from proteins in sort of a mishmash virus part soup. Given time, chemical attractions will result in some of the virus assembling. This is not done with consciousness but with chemical attractions. In early evolution, even random parts will try to lower energy. If composites can lower the energy, this will happen. These may not be minimum energy. But the potential that remains means a potential for further change.

 

Let me give a hypothetical abiogenesis example, the evolution of proof reading enzymes, using only energy considerations. Say we have a DNA double helix that is full of defects due to sloppy base pairing all over the place. At this hypothetical time in early evolution, the DNA fabrication skill is new and the process writes like a preschooler with a lot of typos. Everywhere where the base pairing is wrong the hydrogen bonding is messed up due to the wrong pairing. These are all at slightly higher energy states than where the base pairing is perfect. These are the zones that need to lower energy. They have potential energy build into imperfection, with perfection at a lower energy.

 

The goal is to lower this energy, but it is all over the DNA. One passive way to do this to stick other stuff everywhere, on the DNA, where there is a defect, so the composite is at lower overall energy. The imperfection potential energy is like the teacher with the red pen circling everywhere. The energy areas stand out with long stretches of defects standing out even more, with a lot of red ink. What is useful about this is we may need hundreds of prototype proteins all loosely associated with the DNA like ants to help structurally lower the potential energy in the imperfections. The one that does the best, sort of has its own selective advantage.

 

A modern proof reading enzyme would not leave a base pairing, after fixing the defect, unless the change into perfection was not at a lower energy state than perfection plus attachment. The attachment lowers the energy of a defect even before it does anything. But this attachment becomes an energy problem, after it fixes the defect into perfection. This is why it avoids perfection in the first place and seeks imperfection. There is a small but significant energy difference between these two states. The energy given off due to attachment becomes available. In preschool, this energy can have a tweaking affect on the attacher.

 

If we go back to DNA pre-school, although adding something physically can lower energy, this is still no match for perfection. There is this linger energy difference. Even if the teacher circles the mistakes and the child tries to correct it, it may still not be perfect like the final goal. So you keep practicing until one day perfection. The better the attachment, the more energy given off to tweak itself and finally the DNA.

 

There is a degree of random but all is trying for this energy goal. In the early days, it is possible a long stretch of DNA could have thousands of little students, all very similar, all seeing some nagging residual potential energy, even in attachment. They are using this potential for attachment to self tweak, trying to the lower the overall energy all the way to perfection. Once they finally do that, they become the energy problem, and have leave for a new defect. There is a nebulous line toward the final energy goal but is not coincidence the energy goal was finally achieved. It was always the goal, from the beginning.

 

Based on this, an interesting research project is to make defective DNA, with the maximum defects possible before it come apart. This is high energy DNA. It is not good for genetic use. It may offer insight into pre-school. For one thing, it should be possible to duplicate high energy DNA without unzipping enzymes since the silly thing is ready to come apart all by itself.

Edited November 6, 2008 by pioneer

[foodchain]

In nanotechnology I think one of the most dominating factors faced with engineering on that scale is thermal stuff, like random motion or something if I remember. I also know that fear exists with nanotech over the possibility of building something can can self sustain or replicate and have “mutations” or what not occur during this.

 

I think it dwells on what can be applied to try and study such a system that could lead to tests. I mean what kind of apparatus and chemical mixtures do you need, how do they have to be treated in experiment and for how long. I mean can you use some kind of computer program to model that?

 

I like the idea myself of using thermodynamics or entropy if I understand such. Now giving that microbes inhabit places that are freezing to burning hot and everything in between really says something. Mutation seems to be able to grant access, or the ability to change allows for life to radiate to all kinds of differing ecosystems. With microbes you find the same thing pretty much as metabolism is supported by something physical such as with a chemotroph. So could entropy provide some mechanism for some reaction to eat at and change to better do that? I think its interesting, simply because you might find some physical mechanism to support such variance or just straight up metabolism. I think its easy to see with photosynthetic microbes that an energy source can be an important thing.

[Realitycheck]

I'm looking for the first situation where you have interaction between the nucleic acid, the lipid, and the outside world. I guess that has already been addressed. Then, I am looking for cell division, not mechanical breakage, but where the cell has outgrown its limits and must divide and the daughter cell is mostly identical to the parent. I am thinking that at some point the nucleic acid develops a greater role of interaction and, just by chance, a fluke of evolution, it does something to signal cell division. The nucleic acid somehow creates a copy of itself, which then splits off.

 

think having understanding of it to the point of being able to recreate how it came to be in the first place would be a serious advance in understanding. I question if we really are at that point in regards to such an endeavor, I mean it would require I think the use of all the natural sciences in some capacity if not more.

 

I have some serious issues with what that study would mean.

 

-Can we actually try to empirically study dynamic chemical processes that may have occurred naturally over an extended period of time. I mean if the reality of how life came to be involved a series of steps that takes say 2 years or more for example, can we empirically conduct such a study? It may seem a simple point but I think many times the study of such gets shrugged off not simply because of the topic, but that instant results I think is what is expected. Such as some series of reactions in some glassware that is done in eight hours or a day.

 

You did know that people are already working on that, right? Craig Venter, mapper of the genome, has now set his sights on making a man-made Mycoplasma laboratorium, to possibly help fight pollution or produce fuel, etc. If I remember right, he was working on a man-made copy of a known cell, but it seems that he has set his sights higher. MIT has also done extensive work on modelling man-made cells.

Edited November 7, 2008 by agentchange
multiple post merged

[pioneer]

I am of the belief that simple energy considerations and logic can be used to deduce the steps of abiogenesis. There is chance involved in the middle, but the general goals of each step can be deduced from energy considerations.

 

Let us go back to high energy DNA. It is only called high energy because it contains a lot of defects and therefore a lower proportion of the lowest energy perfect base pairing. This state of DNA is what one would expect, during the earliest days of pre-school, since imperfection is easier and doesn't require too much skill. This also applies to RNA, but is easier to see with DNA, which is why I use DNA for the analysis.

 

If you look at a modern gene, it has start and stop points, so the enzymes know where to begin and where to end. If we compare mRNA with rRNA, the ribosomal RNA are much longer in length compared to the mRNA. In terms of high energy DNA and base pairing imperfection, the rRNA prototypes should have been favored first, since it requires less perfection in terms of the amount of perfection in a greater number of starts and stops.

 

In other words, the more perfection we add, the more perfect starts and stops we can add. This level of perfect is not only base pairing perfection but all long strings of perfect base pairing. If we add a few defects they sort of lose the start or stop distinction. The highest level of imperfection in the starts and stops favors duplicating the DNA since, it may never see a good stop.

 

The logical implication is pre-school pseudo ribosomal size RNA was the first genetic type RNA to form since it requires less DNA perfection in terms of the number of perfect starts and stops. These pseudo-rRNA, in turn, would have passively stuck together with proteins, before the DNA develops the lower energy perfection needed for mRNA. When the DNA reaches that level of perfection the ribosomes have a head start. They will evolve further by the potential created by the mRNA association.

 

If we look in terms of imperfect DNA, with a high ratio of defects, consider the energy difference between perfect starts and stops, and defective starts and stops. The starts are rich in A-T, which form two hydrogen bonds and stops are high in G-C which have three hydrogen bonds. Imperfection always has 2 hydrogen bonds. Imperfection is closer to starts in terms of the number of hydrogen bonds or energy. While stops have the highest potential with their own imperfection. The stops have the most potential to form in terms in the push toward perfection. While a high ratio of imperfection is not too much different from a pseudo- start.

 

As such, before there was enough perfection to make good starts or stops, imperfection almost looks like start. But at the same time, stop has the highest potential for change, so these form perfection before the real starts. This happens with the number of stops first small to favor rRNA, with more stops shifting toward the mRNA.

 

Consider the intermediate state, of moderate stops, where the forming RNA is too long to be called modern mRNA. One practical use for this is ribosome school. Being too long means we have more flexibility for positioning the pseudo-protein template. We can slide it left or right and still make a whole protein since we have extra. It is like we only need 2 inches of tape, but we have four inches. If we calibrate the tape into 1/8 inch increments, there are 32 possible ways to place it, and still use 2 inches of tape.

Edited November 7, 2008 by pioneer

[iNow]

http://www.sciencedaily.com/releases/2008/12/081218213634.htm

With the aid of a straightforward experiment, researchers have provided some clues to one of biology's most complex questions: how ancient organic molecules came together to form the basis of life.

 

Specifically, this study demonstrated how ancient RNA joined together to reach a biologically relevant length.

[granpa]

How simple can you get it to where it can still be called life?

 

a single molecule.

[frankcox]

It seems you are all talking around the real question. Where did the first cell come from . This story about phospho-lipids spontaneously forming cell membranes is beside the point.

A cell is more specifically complex than anything man can dream of making so whether the story you tell is correct or not is irrelevant, finding a clay pit does not mean somewhere a brick wall has built itself. How can you seriously believe that something that the combined intelligence of all mankind can not even totally grasp much less dream of recreating just happened by a trillion trillion trillion trillion trillion lucky accidents?

Even then you need infinately more to end up with a living creature.

 

We have never found any evidence that there was a precursor to D.N.A. and the only reason that so many present these ideas that evolutionists themselves refute such as magical R.N.A. worlds is not because of the evidence but because they don't want to consider the obvious, that we were created by a being with intelligence beyond our ability to comprehend. That is where the observable evidence leads.

 

Man can not create a single grain of sand from nothing therefore someone else did. These stories about RNA worlds and phospho-lipids are red herrings, they do not address the question of origins at all, where did they come from, "Just There" is a fairy tale .

 

Once upon a time there was hydrogen, no one knows why , it was just there.

Hydrogen is a colorless , odorless gas.

Hydrogen turned into all the other elements

These elements turned into plants , pets ,and people

Hydrogen is a colorless , odorless gas, that left alone long enough, turns into plants , pets ,and people.

 

Ain't science cool!

[Sayonara]

Man can not create a single grain of sand from nothing therefore someone else did.

Faulty logic.

[ecoli]

A cell is more specifically complex than anything man can dream of making

 

Yet...

 

http://en.wikipedia.org/wiki/Synthetic_biology

[mooeypoo]

Once upon a time there was hydrogen, no one knows why , it was just there.

Hydrogen is a colorless , odorless gas.

Hydrogen turned into all the other elements

These elements turned into plants , pets ,and people

Hydrogen is a colorless , odorless gas, that left alone long enough, turns into plants , pets ,and people.

 

Ain't science cool!

... WOW.

 

Okay, let me give you a piece of advice. If you're going to summarize a scientific theory that evolved (oh yes, theories evolve too! ain't science cool) for a hundred years, and combine it with a mixture of theories from other disciplines (evolution is not abiogenesis), I think you should - first - read a bit what it *ACTUALLY* says.

 

That would save you the trouble of writing such blatant misrepresentation of it, and us the misfortune of reading it.

 

~moo

[frankcox]

Faulty logic.

 

 

Faulty logic? That is a statement, not an argument. Why is it faulty? What logic says that matter pre-existed intelligence? If that was true then matter created intelligence and you have no reason to believe any of your thoughts .

 

Nothing can create itself as it would have to pre-exist itself. Logic dictates matter was created by intelligence.

[mooeypoo]

I think my post explained why your logic was faulty, you just ignored it.

 

Let me make it simpler: Your statement of what evoultion is *DOES NOT FIT* with what evolution *ACTUALLY IS*.

What you've done is TWIST evolution in your statement so it will be easier for you to "destroy" it. Nice trick, but it is absolutely faulty logic.

 

 

Ignoring posts you can't answer is another form of faulty logic, too.

 

~moo

[Sayonara]

Faulty logic? That is a statement, not an argument. Why is it faulty? What logic says that matter pre-existed intelligence? If that was true then matter created intelligence and you have no reason to believe any of your thoughts .

It is faulty because your premise does not lead to your conclusion.

 

QED.

 

Logic dictates matter was created by intelligence.

No it doesn't.