Creating life?

reply to post by Phagette


You know what really bums me out? Having access to all kinds of very good scientific literature (on all kinds of subjects) but it is all copyrighted. I can download the pdfs because I am affiliated with a university that has that various subscriptions, but I can't just link to the articles because they are for-pay for everyone else (frowny emoticon here that I will someday learn how to embed). Someday I'll write a thread on the topic because it really bothers me, but for now I'll cheat a little:

A newer paper on the subject by Iris Fry, published in 2011 in Origins of Life and Evolution of Biospeheres (an actual peer-reviewed journal that has been around since the 60s - Origins of Life and Evolution of Biospheres) is actually quite good. Here's the abstract to her paper, which I think is freely available:

It is commonly accepted among origin-of-life scientists that the emergence of life was an evolutionary process involving at one stage or other the working of natural selection. Researchers disagree, however, on the nature of the chemical infrastructure that could have formed prebiotically, enabling the evolutionary process. The division of the origin-of-life research community into ‘geneticists’ and ‘metabolists’ usually revolves around the issue whether the first to arise prebiotically was a genetic polymer or a primitive metabolic system. In this paper I offer an alternative classification based on the attitude to the onset of natural selection. From this perspective I add to the conventional division between gene-first and metabolism-first groups a position I call “preparatory metabolism”. By this line of thought, an RNA or an RNA-like polymer could not have emerged prebiotically. Nevertheless, the onset of natural selection had to wait until such a polymer had arised. This paper examines the RNA-first, RNA-later, metabolism-first and preparatory-metabolism scenarios, assessing the weaknesses and strengths of each. I conclude that despite the recent theoretical advances in all these lines of research, and despite experimental breakthroughs, especially in overcoming several RNA-first hurdles, none of the examined paradigms has yet attained decisive experimental support. Demonstrating the evolvability of a potentially prebiotic infrastructure, whether genetic or metabolic, is a most serious challenge. So is the experimental demonstration of the emergence of such an infrastructure under prebiotic conditions. The current agenda before origin-of-life researchers of all stripes and colors is the search for the experimental means to tackle all these difficulties.

reply to post by Phagette


Okay. I've read that like 3xs, and I still can't really grasp what she's, the author, is trying to say that her paper will show. Is it me,(???) the holiday weekend, or did an eagle just fly into the room, because something just went way over my head.

reply to post by windword


I may be even more biased since I make my living working with and studying viruses. They ARE insanely interesting!

But yes, I think viruses do represent this weird in-between almost-life kind of organism. And it seems kind of unfair that an organism like chlamydia that needs to steal its biosynthetic precursors from its host and therefore cannot live outside its host is classified as alive, but viruses are not!

There was a great paper by Patrick Forterre published back in 2010 called Defining Life: The Virus Viewpoint. It might be Open-access (I can never tell) - try it. Here's the abstract:

Are viruses alive? Until very recently, answering this question was often negative and viruses were not considered in discussions on the origin and definition of life. This situation is rapidly changing, following several discoveries that have modified our vision of viruses. It has been recognized that viruses have played (and still play) a major innovative role in the evolution of cellular organisms. New definitions of viruses have been proposed and their position in the universal tree of life is actively discussed. Viruses are no more confused with their virions, but can be viewed as complex living entities that transform the infected cell into a novel organism—the virus—producing virions. I suggest here to define life (an historical process) as the mode of existence of ribosome encoding organisms (cells) and capsid encoding organisms (viruses) and their ancestors.I propose to define an organism as an ensemble of integrated organs (molecular or cellular) producing individuals evolving through natural selection. The origin of life on our planet would correspond to the establishment of the first organism corresponding to this definition.

And I love it when he says:

In fact, there is no life without living organisms and all presently known living organisms are thriving on planet Earth. If one day we hopefully meet friends from another world, it will then be possible to define “life” in term of the common properties shared by organisms from both planets.

because it reminds me that our definition of life CAN change and perhaps MUST change as we learn more about the inter-depedence of organisms like bacteria and viruses to their human hosts. And it represents what I think is so cool about science - when we find new reasons to break dogma!

reply to post by windword


Yeah, sorry, that is science-speak. I'll try to interpret. She's saying there are basically two camps as to what came first in the evolution of life:

(1) heritable information (genes that would be either RNA, which is more likely to have been in the pre-life soup since it is simpler than DNA)

or

(2) the ability to copy that heritable information - an enzyme that copies RNA

In this paper, she reviews all the possible theories and combinations of what could have come first and concludes that none really works if evolution were required to help life begin.

Let me back up and explain that in life as we know it, enzymes (proteins with function) are encoded for by RNA (actually in DNA but then in RNA). And yet enzymes are responsible for copying AND interpreting that RNA- based code!

It is a chicken-egg kind of scenario. Iris is also saying that as life developed, it likely required evolution. Evolution meaning a system (infrastructure) that can adapt to its surroundings and the better adaptation survives and is therefore selected in future "generations." So, evolution requires some heritable information to be copied and passed on as well as enzymes to do the copying and passing on...chicken-egg.

So Iris is saying in the (2) scenario, how could an enzyme evolve to copy RNA if there was no RNA to copy to begin with? And, how could "evolution" (natural selection) have selected for an enzyme to function at all if there was no RNA to code for that enzyme?

She goes on to assert that RNA (a polymer of a simpler monomer form of RNA) is not likely to have existed in that pre-life soup of molecules, the (1) scenario.

She actually represents a dissenting viewpoint in early life origin. What's interesting is that she proposes that it is not likely RNA could have existed in this early soup but MANY RESEARCHERS DISAGREE - many researchers think based upon the most current data, that the monomers for RNA could have existed in that pre-life soul. And similarly, researchers think enzymes could have existed at the same time. But RNA is supposed to encode for enzymes! WTF?!

Many researchers think these copying/elongating enzymes could have existed completely independently of RNA monomers and were randomly copying and "playing" with these RNA monomers, threading them into polymers, just by random chemical interactions, until, amongst the trillions and trillions of resulting newly created RNA polymers lead to the creation of enzymes with function (the same function or different).

Another camp of researchers that she didn't even discuss think, well, we know that now there are RNAs that have function like enzymes, called ribozymes. Maybe these ribozymes were the first functioning enzymes that played with their RNA monomer-cousins to create a polymer-RNA. They can move RNA around, cut it into pieces and even have been shown to re-assemble RNA! So maybe (1) and (2) co-existed as RNA...

And remember, some kind of enclosure still had to develop - like a micelle or lipid bilayer - to eventually encase these RNAs and enzymes, which would have evolved into the "cells" we know today. She doesn't even talk about that at all either.

Nevertheless, I think her viewpoint is interesting and she makes the point that it is important to explore and match all possible theories with the most current data available. The question is, did SHE include all of the most current data?

Originally posted by SplitInfinity
reply to post by jiggerj

 

Some have raised the argument that LIFE cannot be created. This is not true. All one has to do is look at a VIRUS. A Virus has DNA but is NOT ALIVE!

I did not know that. Thank you!

"Viruses straddle the definition of life. They lie somewhere between supra molecular complexes and very simple biological entities. Viruses contain some of the structures and exhibit some of the activities that are common to organic life, but they are missing many of the others. In general, viruses are entirely composed of a single strand of genetic information encased within a protein capsule. Viruses lack most of the internal structure and machinery which characterize 'life', including the biosynthetic machinery that is necessary for reproduction. In order for a virus to replicate it must infect a suitable host cell".

Are Viruses Alive?

reply to post by jiggerj


Yeah, very cool! I suppose my problem is that I spend so much time reading boring science papers, I have forgotten that the internet has actual websites with great, comprehensive information. Love that T4 phage image:
I may use it as my avatar one day. Although, I suppose it might creep people out.

Too much napping? You'll be up all night ;-)

reply to post by Phagette


Fascinating stuff. Isn't evolution a process of successful, but random mutations? It kind of boggles my mind to think that life itself requires evolution. I guess I like to believe that at some point, life was a static reality at a given point in time. It's hard to grasp that life, and all that it encompasses required and depended on elements that weren't yet in existence, and required time as one of it's ingredients.

So metaphysically fascinating!

reply to post by jiggerj


as far as ive heard theyve done this up until ammino acids formed then killed the expiriment before any life formed

Originally posted by Phagette

You know what really bums me out? Having access to all kinds of very good scientific literature (on all kinds of subjects) but it is all copyrighted. I can download the pdfs because I am affiliated with a university that has that various subscriptions, but I can't just link to the articles because they are for-pay for everyone else (frowny emoticon here that I will someday learn how to embed). Someday I'll write a thread on the topic because it really bothers me, but for now I'll cheat a little:

Hear! Hear!

We've got subscriptions to the bigger archives at work, but most ATSers can only read abstracts, because who in their right minds are going to pay $35 for the article?

I vote that ATS subscribe to maybe JSTOR and Science Direct (could probably think of others but those two have a lot of stuff) as an "online university" and add us all on as users. Well, not me, but you know, the normal guys here.