Origin of Life

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Origin of Life

Postby Majisha » Fri Jun 18, 2010 8:26 am UTC

I was over at another science board on another website and i was shown a video from youtube on the origin of life. it's beauty in how it explained the origin of life brought a tear to my eye. the original poster claimed that the video was debunked somehow but wasn't sure on the specifics. i told him/her that i'll come over here to see if there's any accuracy to it and here i am.

Since i'm not at my 5 post mark yet, as this is my first post, i was wondering if the scientific community could explain for all of us over at *censored website* the different theories of the origin of life.
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Re: Origin of Life

Postby You, sir, name? » Fri Jun 18, 2010 9:07 am UTC

My theory is that at some point, we invent a time machine, and use it to find out the origin of life, which contaminates the primordial soup with microbes from the future, which proceed to evolve into life as we know it.
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Re: Origin of Life

Postby Majisha » Fri Jun 18, 2010 9:14 am UTC

You, sir, name? wrote:My theory is that at some point, we invent a time machine, and use it to find out the origin of life, which contaminates the primordial soup with microbes from the future.


So... from one perspective, you are your own great great great... grandfather AND your own great great great... grandson. I love these kind of paradoxes.
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Re: Origin of Life

Postby You, sir, name? » Fri Jun 18, 2010 9:30 am UTC

Majisha wrote:
You, sir, name? wrote:My theory is that at some point, we invent a time machine, and use it to find out the origin of life, which contaminates the primordial soup with microbes from the future.


So... from one perspective, you are your own great great great... grandfather AND your own great great great... grandson. I love these kind of paradoxes.


That's a nice bonus. And it still requires a smaller a smaller assumption than that of intelligent design.
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Re: Origin of Life

Postby Majisha » Fri Jun 18, 2010 9:42 am UTC

You, sir, name? wrote:
Majisha wrote:
You, sir, name? wrote:My theory is that at some point, we invent a time machine, and use it to find out the origin of life, which contaminates the primordial soup with microbes from the future.


So... from one perspective, you are your own great great great... grandfather AND your own great great great... grandson. I love these kind of paradoxes.


That's a nice bonus. And it still requires a smaller a smaller assumption than that of intelligent design.


That it does... that it does... *new religion comes into play, with You, sir, name? as the creator of all*
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Re: Origin of Life

Postby Interactive Civilian » Fri Jun 18, 2010 10:58 am UTC

Majisha wrote:Since i'm not at my 5 post mark yet, as this is my first post, i was wondering if the scientific community could explain for all of us over at *censored website* the different theories of the origin of life.

Do you like scientific papers? I like scientific papers. Here are a few really interesting scientific papers which address modern hypotheses about the origin of life on Earth. Some are more difficult to read than others, but they are all definitely worth taking a look at, and even if some of the text is beyond you (sometimes the deep chemistry aspects are beyond me, and this is part of my profession), the diagrams do a great job at helping to convey the main points (all links have full text PDFs available for download, my commentary between the ~~):

  • Martin, W. & Russell, M.J., 2003. On the origins of cells: a hypothesis for the evolutionary transitions from abiotic geochemistry to chemoautotrophic prokaryotes, and from prokaryotes to nucleated cells. Philosophical transactions of the Royal Society of London. Series B, Biological sciences, 358(1429), 59-83; discussion 83-5. Available at: http://rstb.royalsocietypublishing.org/content/358/1429/59.abstract. ~~This is a good paper to start with for the hypothesis of abiogenesis at hydrothermal vents. It is thorough, logical, and has supporting evidence for many aspects.~~
  • Martin, W. & Russell, M.J., 2007. On the origin of biochemistry at an alkaline hydrothermal vent. Philosophical transactions of the Royal Society of London. Series B, Biological sciences, 362(1486), 1887-925. Available at: http://rstb.royalsocietypublishing.org/content/362/1486/1887.abstract. ~~This is a more in depth paper with a detailed look at how certain precursor biomolecules could have formed from geochemistry.~~
  • Russell, M.J., 2007. The alkaline solution to the emergence of life: energy, entropy and early evolution. Acta biotheoretica, 55(2), 133-79. Available at: http://www.gla.ac.uk/projects/originoflife/html/2001/pdf_files/Russell%20Acta%20Biotheoretica2.pdf. ~~this paper is also pretty in depth~~
  • Koonin, E.V. & Martin, W., 2005. On the origin of genomes and cells within inorganic compartments. Trends in genetics : TIG, 21(12), 647-54. Available at: http://www.molevol.de/publications/135.pdf. ~~Another look at this hypothesis, focusing on how genetic information could have spread in early life/pre-life.~~
  • Koonin, E.V., 2007. An RNA-making reactor for the origin of life. Proceedings of the National Academy of Sciences of the United States of America, 104(22), 9105-6. Available at: http://www.pnas.org/content/104/22/9105.extract.
  • Wolf, Y.I. & Koonin, E.V., 2007. On the origin of the translation system and the genetic code in the RNA world by means of natural selection, exaptation, and subfunctionalization. Biology direct, 2, 14. Available at: http://www.biology-direct.com/content/2/1/14/.~~a conceptual model, rather than formal hypothesis, to consider regarding the origin and evolution of the genetic code.~~

Alright, that's probably enough for now. If you want more, feel free to poke around through my "Evolution and Abiogenesis" collection on my Menedeley. :)

Standard disclaimer: these are not the end-all-be-all of abiogenesis hypotheses, but they are definitely more complete and lacking fewer problems than most (such as the energy problems, the compartmentalization problem, the concentration problem, etc.). There are other competing hypotheses, but these are the ones that have impressed me the most. Cheers. :)
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Re: Origin of Life

Postby Majisha » Fri Jun 18, 2010 11:17 am UTC

Interactive Civilian wrote:
Majisha wrote:Since i'm not at my 5 post mark yet, as this is my first post, i was wondering if the scientific community could explain for all of us over at *censored website* the different theories of the origin of life.

Do you like scientific papers? I like scientific papers. Here are a few really interesting scientific papers which address modern hypotheses about the origin of life on Earth. Some are more difficult to read than others, but they are all definitely worth taking a look at, and even if some of the text is beyond you (sometimes the deep chemistry aspects are beyond me, and this is part of my profession), the diagrams do a great job at helping to convey the main points (all links have full text PDFs available for download, my commentary between the ~~):

  • Martin, W. & Russell, M.J., 2003. On the origins of cells: a hypothesis for the evolutionary transitions from abiotic geochemistry to chemoautotrophic prokaryotes, and from prokaryotes to nucleated cells. Philosophical transactions of the Royal Society of London. Series B, Biological sciences, 358(1429), 59-83; discussion 83-5. Available at: http://rstb.royalsocietypublishing.org/content/358/1429/59.abstract. ~~This is a good paper to start with for the hypothesis of abiogenesis at hydrothermal vents. It is thorough, logical, and has supporting evidence for many aspects.~~
  • Martin, W. & Russell, M.J., 2007. On the origin of biochemistry at an alkaline hydrothermal vent. Philosophical transactions of the Royal Society of London. Series B, Biological sciences, 362(1486), 1887-925. Available at: http://rstb.royalsocietypublishing.org/content/362/1486/1887.abstract. ~~This is a more in depth paper with a detailed look at how certain precursor biomolecules could have formed from geochemistry.~~
  • Russell, M.J., 2007. The alkaline solution to the emergence of life: energy, entropy and early evolution. Acta biotheoretica, 55(2), 133-79. Available at: http://www.gla.ac.uk/projects/originoflife/html/2001/pdf_files/Russell%20Acta%20Biotheoretica2.pdf. ~~this paper is also pretty in depth~~
  • Koonin, E.V. & Martin, W., 2005. On the origin of genomes and cells within inorganic compartments. Trends in genetics : TIG, 21(12), 647-54. Available at: http://www.molevol.de/publications/135.pdf. ~~Another look at this hypothesis, focusing on how genetic information could have spread in early life/pre-life.~~
  • Koonin, E.V., 2007. An RNA-making reactor for the origin of life. Proceedings of the National Academy of Sciences of the United States of America, 104(22), 9105-6. Available at: http://www.pnas.org/content/104/22/9105.extract.
  • Wolf, Y.I. & Koonin, E.V., 2007. On the origin of the translation system and the genetic code in the RNA world by means of natural selection, exaptation, and subfunctionalization. Biology direct, 2, 14. Available at: http://www.biology-direct.com/content/2/1/14/.~~a conceptual model, rather than formal hypothesis, to consider regarding the origin and evolution of the genetic code.~~

Alright, that's probably enough for now. If you want more, feel free to poke around through my "Evolution and Abiogenesis" collection on my Menedeley. :)

Standard disclaimer: these are not the end-all-be-all of abiogenesis hypotheses, but they are definitely more complete and lacking fewer problems than most (such as the energy problems, the compartmentalization problem, the concentration problem, etc.). There are other competing hypotheses, but these are the ones that have impressed me the most. Cheers. :)


wow, this was way more than what i was asking for! thanks! unfortunately i really can't read it right now as my reading abilities deteriorate immensely past the 2:00 am thing. (currently 4:32 am) So i'll just skim them tonight and read them tomorrow.
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Re: Origin of Life

Postby Interactive Civilian » Fri Jun 18, 2010 12:27 pm UTC

Majisha wrote:wow, this was way more than what i was asking for! thanks! unfortunately i really can't read it right now as my reading abilities deteriorate immensely past the 2:00 am thing. (currently 4:32 am) So i'll just skim them tonight and read them tomorrow.

No worries. This stuff fascinates me, so it is my pleasure to share. :)

Oh, and here's one more excellent resource to look at. It is full of citations backing up its every point, and it covers a broader range of information and hypotheses than the papers I linked to.

Stones and Bones: A Short Outline of the Origin of Life

It's a LOT of material, but definitely worth poking through. :)

[edit]
By the way, I don't want to seem like I'm ducking your question by linking to sources rather than outlining things here. The truth is, it's a HUGE topic and involves not only biology, but geology, chemistry, climatology, and cosmology, to name a few.

In a nutshell, you have to think of what would be necessary to get life started. Here's a brief outline:
- an abiotic source of precursor molecules that may react to form fundamental biomolecules. (in the case of the posted hypotheses, the geochemistry of a hydrothermal vent)
- A source of energy to fuel reactions to form biomolecules (thermal, pH, and electrochemical gradients at the vent/ocean interface)
- reaction surfaces that can help catalyze the reactions (for example Iron/Nickel Sulfide in the rocks of the vent)
- Semipermeable compartments to hold and concentrate the molecules so they will react (the microscopic compartments that form in the rocks of these vent systems. Concentration is facilitated by water flow through the vent, as well as the thermal gradient. Compartments are important so that any newly formed molecules aren't just diluted into the surrounding ocean)
- time (a good estimate is about 300 million years from a cool enough Earth covered with ocean for this to start until the first fossil evidence of free living microbial life about 3.8 billion years ago)

After you have all that, things start to react, resources build up, and the fundamental building block of life emerges: the replicator. The first replicators were probably RNA based (self-replicating RNA has been created in the lab). Once you have replicators, there will be a competition for resources. Imperfect replication leads to variation, and viola! Natural selection begins and we have chemical evolution. Chemical evolution "goes nuts" and expands to fill every possible "niche" in that environment: replicators that "feed" off of new geochemically created molecules, replicators which cooperate and form the beginnings of biochemical pathways to make their own building blocks for further replication, replicators which get their resources from breaking down the other replicators and using their blocks for further replication, etc. Competition, mutation, and natural selection lead to an arms race of offense and defense out of which finally (after developing the biochemical pathways to create membrane phospholipids) emerges free living cellular life. 3.8 billion years later, here we are talking about it. ;)

So, that's basically it in a nutshell.
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Re: Origin of Life

Postby Coffee » Fri Jun 18, 2010 6:17 pm UTC

One of the most difficult (for me anyway) concepts is that, if we go far enough into the ancient past, we find we're descended from abiotic molecules.

If I could build a time machine that would be near the top of the list of events I would like to witness.
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Re: Origin of Life

Postby BlackSails » Fri Jun 18, 2010 6:53 pm UTC

Coffee wrote:If I could build a time machine that would be near the top of the list of events I would like to witness.


It would not be very exciting.
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Re: Origin of Life

Postby Majisha » Fri Jun 18, 2010 8:34 pm UTC

Welp, i made it to 5 posts (and hopefully many more to come) so i feel as if it's appropriate to link the video.

http://www.youtube.com/watch?v=U6QYDdgP ... re=related

Thoughts? Concerns? Any feedback is good feedback.
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Re: Origin of Life

Postby Interactive Civilian » Sat Jun 19, 2010 11:20 am UTC

Majisha wrote:Welp, i made it to 5 posts (and hopefully many more to come) so i feel as if it's appropriate to link the video.

http://www.youtube.com/watch?v=U6QYDdgP ... re=related

Thoughts? Concerns? Any feedback is good feedback.

While I don't have time to do a point by point right now, it seems over-simplified and over-assumptive. I certainly don't agree with their ideas on how cells started, because such a thing in the way they described it seems highly unlikely. It glosses over too many details and doesn't answer a lot of problems. It ignores a lot of important aspects of biochemistry. It seems overly focused on debunking creationists and not focused enough on the actual science, especially the actual chemistry involved, as well as energy sources, sources of raw materials, etc.

Overall, I do not find the ideas presented in the video as a plausible or convincing presentation of the origin of life.

Perhaps if I have time later, I'll do a point-by-point, but for now, it's time to watch some World Cup. ;)
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Re: Origin of Life

Postby Majisha » Sun Jun 20, 2010 12:01 am UTC

Hey no problem. I'll just link the board to here so my people can see whats going on. VERY interesting stuff happening here :D A point by point would be pretty fucking cool if you could do that.

Or if anyone else has any ideas feel free to talk! I'm going into computer sciences so i really have no idea what most of these things are :P
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Re: Origin of Life

Postby nash1429 » Sun Jun 20, 2010 11:46 pm UTC

4:26 "Surface area grows faster than volume." :?

It's still a somewhat entertaining video, if factually lacking. And I don't see a problem with focusing on arguing against creationism. The music was pretty epic, too.
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Re: Origin of Life

Postby Majisha » Mon Jun 21, 2010 12:28 am UTC

nash1429 wrote:4:26 "Surface area grows faster than volume." :?

It's still a somewhat entertaining video, if factually lacking. And I don't see a problem with focusing on arguing against creationism. The music was pretty epic, too.


Well, understand that they tried to fit it all into a 10:00 video meant for people who knows very little of actual biology. Like me! :wink:
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Re: Origin of Life

Postby Interactive Civilian » Mon Jun 21, 2010 4:10 am UTC

Majisha wrote:
nash1429 wrote:4:26 "Surface area grows faster than volume." :?

It's still a somewhat entertaining video, if factually lacking. And I don't see a problem with focusing on arguing against creationism. The music was pretty epic, too.


Well, understand that they tried to fit it all into a 10:00 video meant for people who knows very little of actual biology. Like me! :wink:

There's nothing wrong with simplifying and breaking things down into easy to understand terms for the layman who doesn't know a lot of biology, but that's no reason to be inaccurate. Of course, I probably shouldn't criticize too much unless I've tried it myself, so here's an attempt to summarize the papers I cited in more layman's terms (please excuse anthropomorphic terms -- I'm pretty sure we all accept that molecules don't "want", "need", "invent", "figure out", etc... but these are useful metaphors for getting the idea across, especially when contracting hundreds of millions of years of chemical reactions into a few minutes of brief history):

-----

1.) A few hundred million years after the Earth first formed, the surface had cooled enough to support being covered with water. Evidence suggests that early Earth at this time was completely covered in water. It had an atmosphere high in carbon dioxide, which in turn made the oceans very acidic (remember: the difference between acid and alkaline is how much hydrogen (as protons) there is in the solution; acid = a lot of hydrogen, alkaline = a very little hydrogen).

2.) Ocean water can circulate through the crust, entering in some areas and flowing slowly through the rock, heating up, and reacting with chemicals in the rocks. This removes the acid from the water as it flows through, and allows a number of simple molecules like carbon monoxide, ammonia, methane, phosphates, sulfates, etc. to form. This water circulates back into the ocean at "hydrothermal vents". Some of these vents are extremely hot, and while life may have found a way to live there now, were probably too hot for life to form. Others are much milder with temperatures not so different from what modern life is most comfortable at.

3.) The rocks at these vents can be rather porous (full of small holes and compartments). The rocks are rich in iron, nickel, and sulfur, which are important elements in life for helping life reactions happen. Warm alkaline vent water flows through these tiny (even the size of cells in modern life) compartments, mixing with the cold acid sea water. This sets up some important conditions. Warm tends to rise and cold tends to sink, so the temperature difference sets up small circular currents through the compartments in these rocks. As this "convection current" flows, it serves to concentrate larger molecules in the compartments (if there were no compartments, molecules from the vents would just dilute into the sea and never react with each other). Also, difference between warm and cold can act as a source of energy. More importantly, the difference between acid sea water and alkaline vent water means that the hydrogen will flow from high concentration to low concentration, which also can act as a source of energy. There is also an electrical gradient in the rocks due to the difference in sea water and vent water when they mix. This is also a source of energy.

4.) This sets the stage for the reactions that lead to life to begin. The simple carbon, nitrogen, and sulfur molecules in the vent water will start reacting with each other using the energy in the vent system. They will start to form simple versions of the important molecules to life, a.k.a. biomolecules: simple sugars, amino acids, nitrogenous bases (which will later become the nucleic acids), etc. These larger molecules get concentrated by the flow through the compartments, and continue to react with each other. Some may build up into larger complex molecules while others are broken down and re-formed into different molecules. New molecules are always being added from the constant flow of the vent water, and there is always energy available from the differences between the vent water and the sea water. Sugars may get together and form chains, or larger sugars. A few amino acids may get together and form simple proteins, which may or may not have some functions as they float around the compartments or stick to the compartment walls. A sugar, phosphate, and nitrogenous base get together to form the first nucleic acid: RNA. Single RNA units get linked together and form chains. And so on, always building up from the constant supply of energy and raw materials. However, this is just very complex geochemistry, not life.

5.) After millions of year of this, one of the most world-changing things in the history of the Earth happens. A molecule in these compartments, probably an RNA chain, starts to copy itself, using the materials available. RNA has been known to do this, and self-copying RNA has been made in the laboratory. If humans can do it in the lab after only a few decades of study, imagine what nature can do with perhaps a hundred million years and a practically unending supply of raw material. This RNA making copies of itself is the "replicator". It is not perfect, and it makes mistakes. Not all of its copies are exact. Some of them are better at copying themselves. Some of them are worse. The only constant is that all of them need materials to copy themselves.

6.) This is the beginning of evolution by natural selection. Imperfect copies passing on their traits to their copies all competing for resources in the environment. May the best copies win. Nothing breeds invention like necessity and competition for survival. If you have the better copying strategy, then your copies will expand and spread out. If you have a worse strategy, you may be too slow to get the resources you need to make copies, and eventually you disappear (become extinct). If you can figure out a way of making use of the hard work of other replicators, say by breaking them down and using their parts, then you may have an advantage. If, instead, you cooperate with other replicators so that all of your copying gets better, you may have a different advantage. Some replicators may continue building from raw materials, others may act like predators breaking others down, and still others make cooperate and become bigger, better, and stronger than their rivals. This is the nature of pre-life in the "RNA world".

7.) After millions of years of this kind of competition, a lot of things can happen. These RNA replicators may develop many strategies for offense and defense as they flow through their microscopic compartments in the rocks of the vent. Some may start working with amino acids to help make their copying reactions faster. As certain amino acids associate with certain bits of RNA, the beginnings of the genetic code are born. Other RNAs which are good at attaching amino acids to each other may start working with those to build new useful molecules which help them accomplish their copying better than others: these new molecules are proteins. Some may simply form repeating structures of sheets which RNAs may use for protection from other RNAs that would break them down (this is similar to how modern viruses are). Some may find certain proteins can help make the RNA more stable and aid directly in replicating it. If RNA can delegate replicating from itself to a protein, this may be more efficient and therefore be an advantage. We are now in a microscopic chemical world of RNA and Protein together in the competition for best RNA replicators. Cooperation between units of RNA (genes, in a sense) make bigger replicators, but all aspects of offense and defense, breaking down food or building up from resources, etc. are now on a single large molecule, so this may be a big advantage. Scientists sometimes call this stage the "RNP world" for RNA and Proteins working together.

8.) Over the course of RNP world, something interesting and important starts happening. Proteins coded by the RNA take over more and more of the functions of replicating, protecting, maintaining, and providing energy for the RNA, and the RNA replicators become more like information storage molecules than being active in their own replication. However, RNA tends to be less stable and more vulnerable to attack than another up and coming nucleic acid: DNA. DNA has mostly the same bases and structure as RNA (to be specific, each unit of DNA has one less oxygen than the corresponding RNA, hence the name "DeoxyriboNucleicAcid"). DNA, however, has a tendency to form a very stable double-stranded molecule. At first, RNA only keeps some parts of it copied into DNA, but over time DNA becomes the master copy of all of the information necessary to replicate the molecule. DNA by itself is not a replicator, but all of the machinery is in place for it to take over. RNA gets "demoted" into being a messenger molecule between the master copy and the machinery to build proteins for the sake of the master copy.

9.) Is this life? Well, it is at least getting very close. The reactions taking place in these compartments at this stage may seem very similar to the life reactions going on inside a modern bacterium. The key difference is that the bacterium is a free-living lifeform, while back in our vent system of long ago, all of this biochemistry is trapped inside of compartments in the rock. Any compartments closer to the ocean side which erode away lose all of their contents to the surrounding ocean, so whatever "life" may have been occurring in them dies. :(

Clearly something needs to change to give an advantage. There would be a strong advantage in not dying when your compartment wears away. If only you could have a compartment of your own.

10.) Which brings us to the next big step in the early evolution of life, which leads us to free-living cells. To this point, everything happening in the compartments is serving the replicators. It is likely that replicators are sharing their genes among the entire system, as bits move between compartments (just like they do in modern bacteria, transferring things like antibiotic resistance between each other). However, other types of reactions are happening in the compartments. Some molecules are being broken down for energy for replicating or maintainance. Other molecules are being built up for storing energy and providing structure. Among these are lipids (fats, waxes, cholesterol, oils, etc.), and at one point a very important kind of lipid is formed: the phospholipid. If you could see a phosopholipid, it might resemble a head area with two tails. The "head" likes water, and the "tails" do not, so when they are in a solution, in interesting thing happens. The tails will face away from the water (and in the case of our ancient compartments, towards the rock walls of the compartments), while the heads will face towards the water. So, as phospholipids start to form, they quickly line the walls of the compartment, forming the first membranes. Any proteins attached to the wall, perhaps as an anchor, or perhaps as a tunnel to the next compartment, will get stuck in the membrane. As life goes on and that compartment starts to wear down and be exposed to the ocean, any phospholipids will now form another layer on the outside as their "tails" try to get away from the water. Viola! Cells with membranes, free to live and grow in the sea on the rocky surface of the vent.

11.) There was probably a lot of trial and error and a lot of false starts for this early life, but while it was near the vent, it had abundant resources with which to grow and spread (and die). After hundreds of millions of years of this kind of thing, life was able to spread through the darkness of the sea and eventually up to the light, where a new, very abundant energy source awaited any who could evolve to take advantage of it.

And, 3.8 billion years later (after #10), here we are talking about it. :)

-----

Hmmmm... So, I guess it is hard to over-simplify AND be accurate. I feel this explanation is still pretty complex. :? But, well, life is a complex thing, and even the best hypotheses for its formation don't lend themselves to the most simple explanations. ;)

Comment and critique on this are very welcome. :)

[edit]
If anyone finds this to be a reasonable explanation and has some mad animating skills, making it into an animation to explain it would be awesome (and probably much clearer than trying to convey it in words alone). Feel free. ;)
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Re: Origin of Life

Postby Majisha » Mon Jun 21, 2010 11:11 am UTC

Holy crap! i'm positive that the people over yonder will be pleased with this! This went WAY beyond what i was expecting! Thank you sir! And thank all of the scientific community! I agree, seeing this in a video format would be pretty epic.
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Re: Origin of Life

Postby Interactive Civilian » Mon Jun 21, 2010 2:46 pm UTC

Majisha wrote:Holy crap! i'm positive that the people over yonder will be pleased with this! This went WAY beyond what i was expecting! Thank you sir! And thank all of the scientific community! I agree, seeing this in a video format would be pretty epic.

You're very welcome. It was interesting to try to break it down to basic but still reasonably accurate terms. I'm not sure how well I succeeded in that.

At any note, combine that description with the very nice diagram on the second page of the Koonin & Martin (2005) paper in my first response above, and you can get a decent visual to go along with the description. :)

Again, I feel I should disclaim that this is not the end-all-be-all of abiogenesis hypotheses, and I'm sure other plausible explanations exist in competition with this one. I like this one because it seems to fit the current evidence fairly well, and it neatly solves several of the biggest problems of earlier hypotheses. But, there is a lot of research still to be done, and I'm sure many parts of this hypothesis will end up being revised and clarified, so take it with as much salt as you feel necessary. ;)
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Re: Origin of Life

Postby nash1429 » Tue Jun 22, 2010 5:05 am UTC

Majisha wrote:I was over at another science board on another website


What website?
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Re: Origin of Life

Postby Eebster the Great » Tue Jun 22, 2010 8:05 am UTC

Interactive Civilian wrote:Again, I feel I should disclaim that this is not the end-all-be-all of abiogenesis hypotheses, and I'm sure other plausible explanations exist in competition with this one. I like this one because it seems to fit the current evidence fairly well, and it neatly solves several of the biggest problems of earlier hypotheses. But, there is a lot of research still to be done, and I'm sure many parts of this hypothesis will end up being revised and clarified, so take it with as much salt as you feel necessary. ;)


Wikipedia tells me that the Iron-Sulfur World Hypothesis is still a major contender.
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Re: Origin of Life

Postby Interactive Civilian » Tue Jun 22, 2010 8:43 am UTC

Eebster the Great wrote:
Interactive Civilian wrote:Again, I feel I should disclaim that this is not the end-all-be-all of abiogenesis hypotheses, and I'm sure other plausible explanations exist in competition with this one. I like this one because it seems to fit the current evidence fairly well, and it neatly solves several of the biggest problems of earlier hypotheses. But, there is a lot of research still to be done, and I'm sure many parts of this hypothesis will end up being revised and clarified, so take it with as much salt as you feel necessary. ;)


Wikipedia tells me that the Iron-Sulfur World Hypothesis is still a major contender.

That hypothesis is not mutually exclusive from the one I've presented. In fact, the alkaline vent hypothesis draws a lot from that, suggesting that the rocks with the compartments were rich in Fe/Ni S clusters.

I've read some of Wächtershäuser's work on that (though not recent... perhaps I'll have something different to say after I read the 2006 paper I downloaded yesterday), and the main place I take issue with it is the concentration problem. From what I have read, he contends that new-formed molecules will stick to the Fe/S surfaces and react together, but he didn't make a good case for why the molecules wouldn't just drift away and dilute into the surrounding ocean. Also, he contended that lipid membranes then formed over these surfaces and cells essentially "bubbled" off of them.

Technically these things may be plausible, but I find the cell-like compartments solution to be more compelling. It sets the stage for 3D spacial orientation inside a cell (including chemical gradients and "polarity" in the sense of a cell having a front and back end), it sets up membrane proteins already in good positions in the membrane, and it solves the problem of getting molecules to stick around in enough concentration to react together.

Essentially, the Alkaline Vent hypothesis extends and clarifies the Fe/S World hypothesis while taking it in a slightly different direction.

There is further contention between the two in the formation and evolution of phospholipids. The Alkaline Vent hypothesis suggests that life experienced its first major split into the ancestral Archaea and Eubacteria BEFORE membrane phospholipids evolved (and therefore before free-living cells), and each line therefore evolved its own way of making phospholipids, which explains the fundamental differences in the membranes between the two domains. Wächtershäuser's Fe/S World hypothesis suggests that both types of phospholipids formed readily enough, and the first cells may have had mixed membranes. The two branches emerged from that, perhaps due to disruptive selection (i.e. making one membrane or the other turned out to be advantageous, but making both was enough of a disadvantage to be selected out). I don't know enough about this to suggest one way or the other, and there is yet a third hypothesis regarding membranes, by Thomas Cavalier-Smith, that suggested that it all started with eubacterial membranes and that the archaea were a relatively late split, evolving their unique membrane chemistry in response to living in extreme conditions (most extremophiles are archaea).

So, yeah, there are a lot of ideas going around. A lot of the generalities seemed to be agreed upon, but there is still a good amount of contention among even major details. Time will tell which hypotheses survive. ;)

(will edit and clarify this if the 2006 Wächtershäuser paper says anything different than what I've posted... when I get a chance to read it)
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Re: Origin of Life

Postby Majisha » Tue Jun 22, 2010 9:05 am UTC

nash1429 wrote:
Majisha wrote:I was over at another science board on another website


What website?


Oh, uh, 99chan. slow as fuck, but if you get used to it it's really nice. i especially like the /gent/ board. I believe many users on this site would feel right at home somewhere on 99.
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Re: Origin of Life

Postby Interactive Civilian » Tue Jun 29, 2010 1:48 am UTC

Sorry to bump, but...
Majisha wrote:Welp, i made it to 5 posts (and hopefully many more to come) so i feel as if it's appropriate to link the video.

http://www.youtube.com/watch?v=U6QYDdgP ... re=related

Thoughts? Concerns? Any feedback is good feedback.

We've already said that this video is over-simplified and meant for the layman. I still don't think that justifies its inaccuracies, but my attention has been brought to the research that it is based on (with some GORGEOUS 3D videos):

Szostak Lab

I've only just begun to scratch the surface there (downloading the videos now, and grabbing a few of his publications to read), so I don't really have any comment on the research. However, it will be interesting to see what it all says and if and how it addresses certain big questions in abiogenesis hypotheses.

Thought people might be interested in seeing it straight from the source to form their own opinions. :)
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Re: Origin of Life

Postby Coffee » Tue Jun 29, 2010 4:09 am UTC

We can form hypotheses about how life formed but would we ever be able to sufficiently test them? Of the plausible solutions how can we definitively disprove any of the possible ones?
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Re: Origin of Life

Postby Interactive Civilian » Tue Jun 29, 2010 4:29 am UTC

Coffee wrote:We can form hypotheses about how life formed but would we ever be able to sufficiently test them? Of the plausible solutions how can we definitively disprove any of the possible ones?

By testing aspects of them and seeing if the hold up in the lab and fit situations that are plausible for life to have formed in. If they don't, then they are disproved.

Beyond that, we can't prove which of the possible ones actually did happen either. We can go with the ones that match the evidence best as most plausible, but we can never definitively say "This IS how it happened."

However, in addition to providing possible explanations, it gives us good indications of what to look for in the search for life elsewhere. Understanding well the conditions by which it may have formed here can tell us something about what kinds of conditions to look for elsewhere in the future. Also, there is the (possibly slim) possibility that certain aspects of how things happened with the formation of life on Earth are the way it has to happen with organic life given a few assumptions. For example, there may be the possibility that given the formation of a genetic code, the code assignments of the genetic code on Earth were a thermodynamic inevitability rather than a fixed accident. Mind you, I'm not saying this is so, but speculating that it is, it would mean that if other organic life with similar chemistry exists in the universe, it may have the same or similar genetic code. Highly unlikely, sure. But something that these studies may eventually be able to tell us one way or the other.
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Re: Origin of Life

Postby nash1429 » Fri Jul 09, 2010 1:37 am UTC

This uncertainty is essentially true of anything that happened in the past.
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Re: Origin of Life

Postby Cobramaster » Fri Jul 09, 2010 2:05 am UTC

It is possible to test aspects of the theory, such as RNA and Protein formation from a primordial soup of sorts, and even the membrane formation. But to test the entire theory start to finish it would take a very short few hundred years to the more reasonable, but long few hundred million years. That simply makes it impractical to test and it would be easier and faster to just build a time machine, if we can find enough energy to do so.
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Re: Origin of Life

Postby Interactive Civilian » Fri Jul 09, 2010 4:54 am UTC

nash1429 wrote:This uncertainty is essentially true of anything that happened in the past.

Yup. Exactly. This is pretty much my point, and is meant to waylay any "But you'll never have a definite answer!" types. ;)

Science never provides definite answers. What it provides are descriptive and useful answers with an innate degree of uncertainty. When it claims absolute certainty, it stops being science. :)
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Re: Origin of Life

Postby Eebster the Great » Fri Jul 09, 2010 2:55 pm UTC

Interactive Civilian wrote:
nash1429 wrote:This uncertainty is essentially true of anything that happened in the past.

Yup. Exactly. This is pretty much my point, and is meant to waylay any "But you'll never have a definite answer!" types. ;)

Science never provides definite answers. What it provides are descriptive and useful answers with an innate degree of uncertainty. When it claims absolute certainty, it stops being science. :)


The difference is that science can determine many historic events with very high degrees of accuracy, whereas it is likely to never determine by which mechanism abiogenesis occurred on Earth as long as there is more than one viable possibility. It is just impossibly difficult to obtain real evidence about the first protolife.
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Re: Origin of Life

Postby Thesh » Sat Jul 10, 2010 10:57 am UTC

Eebster the Great wrote:
Interactive Civilian wrote:
nash1429 wrote:This uncertainty is essentially true of anything that happened in the past.

Yup. Exactly. This is pretty much my point, and is meant to waylay any "But you'll never have a definite answer!" types. ;)

Science never provides definite answers. What it provides are descriptive and useful answers with an innate degree of uncertainty. When it claims absolute certainty, it stops being science. :)


The difference is that science can determine many historic events with very high degrees of accuracy, whereas it is likely to never determine by which mechanism abiogenesis occurred on Earth as long as there is more than one viable possibility. It is just impossibly difficult to obtain real evidence about the first protolife.


Unfortunately people will take that and say "Science doesn't have an answer... They have no way to prove any of this and are just making guesses. This is why we should teach intelligent design in schools!"
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Re: Origin of Life

Postby qetzal » Sat Jul 10, 2010 6:54 pm UTC

Thesh wrote:Unfortunately people will take that and say "Science doesn't have an answer... They have no way to prove any of this and are just making guesses. This is why we should teach intelligent design in schools!"


Yes, some people will say that, but they'll be (mostly) wrong. Science does have possible answers to the OOL, and could well converge on a single answer in the future. It's true that there's no way to prove beyond doubt that the answer is correct, but it's not true that science is "just making guesses." And even if it were, that doesn't justify teaching ID, because ID is demonstrably wrong (at least for the most common incarnations of ID).

Unfortunately, most of the people who will say that aren't really interested in being rational about this question. Their religion already tells them the "right" answer. The inherent uncertainty of science is just a convenient excuse to reject science's answer whenever it conflicts with their beliefs, and no amount of logic or rational discussion is likely to convince them otherwise. We can only hope to convince the ones who haven't yet closed their minds.

No doubt you know all this, but I thought I'd make it explicit for the benefit of any open-minded lurkers. :wink:
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Re: Origin of Life

Postby Eebster the Great » Sat Jul 10, 2010 9:25 pm UTC

qetzal wrote:
Thesh wrote:Unfortunately people will take that and say "Science doesn't have an answer... They have no way to prove any of this and are just making guesses. This is why we should teach intelligent design in schools!"


Yes, some people will say that, but they'll be (mostly) wrong. Science does have possible answers to the OOL, and could well converge on a single answer in the future. It's true that there's no way to prove beyond doubt that the answer is correct, but it's not true that science is "just making guesses." And even if it were, that doesn't justify teaching ID, because ID is demonstrably wrong (at least for the most common incarnations of ID).

Unfortunately, most of the people who will say that aren't really interested in being rational about this question. Their religion already tells them the "right" answer. The inherent uncertainty of science is just a convenient excuse to reject science's answer whenever it conflicts with their beliefs, and no amount of logic or rational discussion is likely to convince them otherwise. We can only hope to convince the ones who haven't yet closed their minds.

No doubt you know all this, but I thought I'd make it explicit for the benefit of any open-minded lurkers. :wink:


What bothers me the most is when such people have the nerve to tell me I am just being close-minded when I reject their views.
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Re: Origin of Life

Postby nash1429 » Mon Jul 12, 2010 5:23 am UTC

Thesh wrote:Unfortunately people will take that and say "Science doesn't have an answer... They have no way to prove any of this and are just making guesses. This is why we should teach intelligent design in schools!"


My favorite counter to this argument is to point out that we have more empirical, scientific evidence for evolution than we do for gravity. But in truth what annoys me more than the uncertainty arguments are the people who use scientific principles to attempt to show that evolution is fallacious, i.e. thermodynamics, missing link, etc. American culture at least needs to get out of the mindset that all viewpoints in all areas must be given equal opportunity.

EDIT: I also love when people argue for intelligent design on the grounds that evolution is not falsifiable.
Last edited by nash1429 on Wed Jul 14, 2010 4:52 am UTC, edited 1 time in total.
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Re: Origin of Life

Postby Coffee » Mon Jul 12, 2010 3:46 pm UTC

Eebster the Great wrote:What bothers me the most is when such people have the nerve to tell me I am just being close-minded when I reject their views.


A nice counter to that would be to point out the difference between a closed mind, an open mind, and a mind that's simply not empty.
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Re: Origin of Life

Postby samk » Thu Aug 05, 2010 2:44 am UTC

Late night crank suggestion - life originated in ammonia, explaining the nitrogen rich structures of the dna bases and arginine. Someone with actual knowledge of biochemistry is welcome to explain why this is utterly wrong, adjusting to a much more acidic environment doesn't seem very likely.
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Re: Origin of Life

Postby Eebster the Great » Thu Aug 05, 2010 8:11 am UTC

samk wrote:Late night crank suggestion - life originated in ammonia, explaining the nitrogen rich structures of the dna bases and arginine. Someone with actual knowledge of biochemistry is welcome to explain why this is utterly wrong, adjusting to a much more acidic environment doesn't seem very likely.


This is wrong because life actually originated in the water from Uranus's severed testies.
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Re: Origin of Life

Postby Gary_Hurd » Tue Jun 21, 2011 3:22 am UTC

I backtracked a URL from my blog to your discussion of the origin of life. Delighted to meet you. I see a very interesting set of ideas, happily free of creationists.

A problem we all face when attempting to understand the origin of life here on Earth is that the planet is so very dynamic. There is very little of the original material still around for analysis. So, lacking such direct evidence we are left with showing plausible mechanisms.

The genetics people have taken the approach of backtracking the metabolism of the cells using the notion that the most widely shared is the most ancient. An number of recent results of this approach are now on-line at NASA's "Program for Molecular Paleontology and Resurrection: Rewinding the Tape of Life"

{Usual URL stuff} astrobiology.nasa.gov/nai/ool-www/program
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Re: Origin of Life

Postby Gary_Hurd » Tue Jun 21, 2011 3:50 am UTC

Majisha wrote:Welp, i made it to 5 posts (and hopefully many more to come) so i feel as if it's appropriate to link the video.

http://www.youtube.com/watch?v=U6QYDdgP9eg&feature=related

Thoughts? Concerns? Any feedback is good feedback.


I liked the video generally. The last few minutes had a few problems. I'll bookmark this discussion and try to make a better reply in the morning.
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Re: Origin of Life

Postby Tass » Tue Jun 21, 2011 6:50 pm UTC

Eebster the Great wrote:What bothers me the most is when such people have the nerve to tell me I am just being close-minded when I reject their views.


Here's a nice present:

http://www.youtube.com/watch?v=T69TOuqaqXI
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Re: Origin of Life

Postby Gary_Hurd » Tue Jun 21, 2011 7:40 pm UTC

Heh, I just noticed the date stamps on the posts.

Interesting that someone hit my blog yesterday from a year old discussion. The cyber is ageless </joke>.

@ Tass, Thanks for the link.
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