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Jonnnyyyzzz
Trad climber
San Diego,CA
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Feb 23, 2012 - 01:01am PT
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This is from a link that healyje posted earlier.
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The RNA World And Other Origin-of-Life Theories** |
What's NEW
Virtually all biologists now agree that bacterial cells cannot form from nonliving chemicals in one step. If life arises from nonliving chemicals, there must be intermediate forms, "precellular life." Of the various theories of precellular life, the most popular contender today is "the RNA world."
RNA has the ability to act as both genes and enzymes. This property could offer a way around the "chicken-and-egg" problem. (Genes require enzymes; enzymes require genes.) Furthermore, RNA can be transcribed into DNA, in reverse of the normal process of transcription. These facts are reasons to consider that the RNA world could be the original pathway to cells. James Watson enthusiastically praises Sir Francis Crick for having suggested this possibility :
" The time had come to ask how the DNA→ RNA→ protein flow of information had ever got started. Here, Francis was again far ahead of his time. In 1968 he argued that RNA must have been the first genetic molecule, further suggesting that RNA, besides acting as a template, might also act as an enzyme and, in so doing, catalyze its own self-replication."
It was prescient of Crick to guess that RNA could act as an enzyme, because that was not known for sure until it was proven in the 1980s by Nobel Prize-winning researcher Thomas R. Cech and others. The discovery of RNA enzymes launched a round of new theorizing that is still under way. The term "RNA world" was first used in a 1986 article by Harvard molecular biologist Walter Gilbert:
"The first stage of evolution proceeds, then, by RNA molecules performing the catalytic activities necessary to assemble themselves from a nucleotide soup. The RNA molecules evolve in self-replicating patterns, using recombination and mutation to explore new niches. ... they then develop an entire range of enzymic activities. At the next stage, RNA molecules began to synthesize proteins, first by developing RNA adaptor molecules that can bind activated amino acids and then by arranging them according to an RNA template using other RNA molecules such as the RNA core of the ribosome. This process would make the first proteins, which would simply be better enzymes than their RNA counterparts. ... These protein enzymes are ... built up of mini-elements of structure."
"Finally, DNA appeared on the scene, the ultimate holder of information copied from the genetic RNA molecules by reverse transcription. ... RNA is then relegated to the intermediate role it has today—no longer the center of the stage, displaced by DNA and the more effective protein enzymes."
Today, research in the RNA world is a medium-sized industry. Scientists in this field are able to demonstrate that random sequences of RNA sometimes exhibit useful properties. For example, in 1995, a trio at the Whitehead Institute for Biomedical Research reported "Structurally Complex and Highly Active RNA Ligases Derived from Random RNA Sequences" . (Ligases are enzymes that splice together other molecules such as DNA or RNA.) The results are interesting—they suggest that randomness can produce functionality. The authors interpret the results to mean that "the number of distinct complex functional RNA structures is very large indeed."
There is a lot to learn about RNA, and research like this is how we learn it. But these and other similar findings arrived at in highly orchestrated experiments that start with biologically produced RNA are very far from proving that the RNA world is the pathway between nonlife and life. In nature, far from the sterilized laboratory, uncontaminated RNA strands of any size would be unlikely to form in the first place. "... The direct synthesis of ... nucleotides from prebiotic precursors in reasonable yield and unaccompanied by larger amounts of unrelated molecules could not be achieved by presently known chemical reactions" .
Francis Crick himself has become much less enthusiastic about the RNA world than Watson. In 1973, he and another eminent researcher into the origin of life, Leslie E. Orgel, published a paper advocating the theory called "Directed Panspermia" . In 1981, Crick published Life Itself, a whole book about that theory . And by 1993 he says, "It may turn out that we will eventually be able to see how this RNA world got started. At present, the gap from the primal 'soup' to the first RNA system capable of natural selection looks forbiddingly wide" .
At the Salk Institute for Biological Studies, in 1994, Leslie Orgel observes, "Because synthesizing nucleotides and achieving replication of RNA under plausible prebiotic conditions have proved so challenging, chemists are increasingly considering the possibility that RNA was not the first self replicating molecule..." .
Apparently NASA has lost enthusiasm for the RNA world as well. In the Final Report issued after the "Astrobiology Workshop" held September 9-11, 1996 at Ames Research Center, California, we read ,
"It has been postulated that there was a time in protobiological evolution when RNA played a dual role as both genetic material and a catalytic molecule ("the RNA world"). However, this appealing concept encounters significant difficulties. RNA is chemically fragile and difficult to synthesize abiotically. The known range of its catalytic activities is rather narrow, and the origin of an RNA synthetic apparatus is unclear"
The Time Problem
To go from a bacterium to people is less of a step than to go from a mixture of amino acids to a bacterium. — Lynn Margulis
The only premise that all of the precellular theories share is that it would be an extremely long time before the first bacterial cells evolved. If precellular life somehow got going, it could then conceivably begin to crank out, by some precellular process, random strings of nucleotides and amino acids, trying to luck into a gene or a protein with advantages which would lead to bacterial life. There is no evidence in life today of anything that produces huge quantities of new, random strings of nucleotides or amino acids, some of which are advantageous. But if precellular life did that, it would need lots of time to create any useful genes or proteins. How long would it need? After making some helpful assumptions we can get the ratio of actual, useful proteins to all possible random proteins up to something like one in 10^500 (ten to the 500th power). So it would take, barring incredible luck, something like 10^500 trials to probably find one. Imagine that every cubic quarter-inch of ocean in the world contains ten billion precellular ribosomes. Imagine that each ribosome produces proteins at ten trials per minute (about the speed that a working ribosome in a bacterial cell manufactures proteins). Even then, it would take about 10^450 years to probably make one useful protein. But Earth was formed only about 4.6 x 10^9 years ago. The amount of time available for this hypothetical protein creation process was maybe a few hundred million or ~10^8 years. And now, to make a cell, we need not just one protein, but a minimum of several hundred.
So even if we allow precellular life, there is a problem getting from there to proteins, genes and cells. The random production of proteins does not succeed as an explanation. Other intermediate, unspecified stages must be imagined. We could call these stages post-precellular life. By whatever means, life's evolution through these stages would have to be time-consuming.
One advocate of the RNA world, Gerald Joyce, allows 400 million years for "The Rise and Fall of the RNA World" :
// "...At some point RNA organisms began to dabble in the use of short peptides, leading eventually to the development of protein synthesis. Other "experiments" led to the discovery of DNA, which provided a more stable repository for genetic information. By 3.6 to 3.8 billion years ago all of these events had come to pass; the RNA world had fallen and the DNA/protein world had risen in its place."//
But other researchers see evidence for prokaryotic cells in the first 100 million years, maybe even immediately. "...Actual cells have been found in the earth's oldest unmetamorphosed sediments...," says Gould in Wonderful Life. Bada says that cyanobacteria may have emerged only ten million years after the first precellular life. In November, 1996, S. J. Mojzsis of the Scripps institution of Oceanography and others reported isotopic evidence that cellular metabolism was under way before 3.8 billion years ago. Even before the research by Mojzsis et al., Francis Crick was worried by the time problem. "...The real fossil record suggests that our present form of protein based life was already in existence 3.6 billion years ago.... This leaves an astonishingly short time to get life started". Another researcher, Peter B. Moore, says this about the time problem :
"Of one thing we can be certain: The RNA world—if it ever existed—was short-lived. The earth came into existence about 4.5 x 10^9 years ago, and fossil evidence suggests that cellular organisms resembling modern bacteria existed by 3.6 x 10^9 years before the present.... There are even hints that those early organisms engaged in photosynthesis, which is likely to have been a protein-dependent process then, as now. Thus it appears likely that organisms with sophisticated, protein based metabolisms existed only 0.9 x 10^9 years after the planet's birth."
//
" The "window of opportunity" for the RNA world was much shorter than 0.9 x 10^9 years. The earth's surface was uninhabitable at the beginning due to heat generated by meteoric bombardment and its geological differentiation. ...Thus, the interval in which the biosphere could have been dominated by RNA-based life forms may be less than 100 million years. Incidentally, when one starts thinking along these lines, one must consider the unthinkable, i.e., that the length of time that RNA-based proteins actually bestrode the earth might be zero."//
Summary
It goes without saying that the emergence of this RNA world and the transition to a DNA world imply an impressive number of stages, each more improbable than the previous one — François Jacob, 1997
There is no remnant or trace evidence of precellular life anywhere today. That it ever existed is entirely conjectural.
Although its emergence from nonliving matter is hard to conceive, precellular life must have appeared almost immediately.
There was almost no time for precellular life to evolve into the simplest bacterial cells.
Precellular life has never been created in a lab.
In spite of the RNA world, there is no consensus on the model for precellular life.
We said that research in the RNA world is a medium-sized industry. This research has demonstrated how exceedingly difficult it would be for living cells to originate by chance from nonliving matter in the time available on Earth. That demonstration is a valuable contribution to science. Additional research will be valuable as well. But to keep insisting that life can spontaneously emerge from nonliving chemicals in the face of the newly comprehended difficulties is puzzling. It is reminiscent of the persistent efforts of medieval alchemists to turn lead into gold.
There is another scientific explanation for the origin of life on Earth. It is that whole cells arrived here from space.
What's NEW
If life pops up readily in Earth-like conditions, surely it should have started many times right here on Earth — Professor Paul Davies, 2011
The Origin of Handheld Calculators:
Let's put the current paradigm of how life on Earth might have begun in terms of the computer analogy. (See CA's A Cell is Like a Computer). The fossil record indicates that there were handheld calculators with 240 kilobytes of stored programs — prokaryotic cells — in existence almost as soon as the earth cooled. Here's how the story might go:
Handheld calculators originated when special conditions allowed the formation of silicon chips and circuit boards (primitive genes). Heat, possibly generated by radioactivity, volcanoes or meteor impacts, melted some sand to form a silicon flake. Random splashing of molten metal caused metal filaments to form a circuit board on the flake. Oily film on ponds dried into the hard plastic material needed for the shell.
Lightning provided the first source of electrical power. Prototypes in seawater, at just the right distance from the strike, received sufficient voltage without being destroyed. Batteries (allowing independent metabolism) came later. The first batteries were iron acid batteries, formed in mud pockets. Lithium batteries were a very late development.
This primitive protocalculator somehow acquired ten to 25 bytes of stored programs (40 to 100 nucleotides) that enabled it to have some function that made it useful. Now we find evidence for only the fully evolved handheld calculators similar to the ones used today, with function keys and lengthy built-in programs, because the fossil record is incomplete.
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Ed Hartouni
Trad climber
Livermore, CA
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Feb 23, 2012 - 01:33am PT
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Jonnnyyyzzz
you can find the more quantitative argument filled out in this Wikipedia article:
http://en.wikipedia.org/wiki/Rare_Earth_hypothesis
let's avoid the bits of the "Rare Earth equation" that have to do with life, and just calculate the likelihood using the unsupported probabilities given in the video... we have the product of 10^-5 which represents the probability that if we look at a star in the sky it would be "Earth like" enough to support life.
Currently there are many extrasolar planet surveys being conducted by the astronomical community. This research, relatively new, has already completely changed our view of what a "solar system" is, in fact, the type of planetary system to which we belong seems atypical from what we have observed so far. Theories of planetary system development are now undergoing radical revision.
You can check this out yourself at this site: http://exoplanets.org/
Given our calculation above, we can calculate the success of a star survey, for instance, The Palomar/MSU Nearby Star Spectroscopic Survey which you can read about here: http://www.stsci.edu/~inr/nstarsres/pmsu4.pdf their survey included 558 main sequence stars as "nearby."
Given your video's calculation, we'd expect that the likelihood of one of those stars meeting their condition is something like 10^-3 to 10^-2, (one in a thousand to one in a hundred) so it is surprising that the planet candidate Gliese 581d has the interesting properties described in http://arxiv.org/pdf/1105.1031.pdf making it possibly habitable.
the abstract of which is:
It has been suggested that the recently discovered exoplanet GJ581d might be able to support liquid water due to its relatively low mass and orbital distance. However, GJ581d receives 35% less stellar energy than Mars and is probably locked in tidal resonance, with extremely low insolation at the poles and possibly a permanent night side. Under such conditions, it is unknown whether any habitable climate on the planet would be able to withstand global glaciation and/or atmospheric collapse. Here we present three-dimensional climate simulations that demonstrate GJ581d will have a stable atmosphere and surface liquid water for a wide range of plausible cases, making it the first confi rmed super-Earth (exoplanet of 2-10 Earth masses) in the habitable zone. We find that atmospheres with over 10 bar CO2 and varying amounts of background gas (e.g., N2) yield global mean temperatures above 0 C for both land and ocean-covered surfaces. Based on the emitted IR radiation calculated by the model, we propose observational tests that will allow these cases to be distinguished from other possible scenarios in the future.
My point is twofold: first) it is apparently not so rare to find candidate planets... we have observed one
and second) we can actually imagine studying that planet candidate for signs of biological activity.
This second point has been anticipated for a very long time, James Lovelock wrote the article "A physical basis of life detection experiments" in 1965 as a result of work he was doing for NASA, the Nature article is reproduced here: http://www.jameslovelock.org/page6.html he suggests that the atmospheres of planets with life are very different in character than those which are lifeless. It is quite possible that we would be able to directly observe these planets and even get spectroscopic information which would reveal their character.
It appears that the probabilities calculated in your video may be understated, which would be understandable as they are not based on very rigorous statistics in the first place.
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healyje
Trad climber
Portland, Oregon
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Feb 23, 2012 - 01:54am PT
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Jonnnyyyzzz - that's from the panspermia website where they desperately want to believe in life was transported to the earth whole, intact, and alive. I find it a stretch at best - and be it here or 'there' - life had to originate somewhere. Being familiar with the resilience of both mycological and bacterial spores I don't discount the panspermia theory out of hand, but I do find it unconvincing in cases like enodlithic life under many kilometers of rock.
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Jonnnyyyzzz
Trad climber
San Diego,CA
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Feb 23, 2012 - 03:40am PT
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Thanks Ed, I'll check out the links and I thank you for sharing your insight with everyone. As you can tell this stuff is not my profession but I have always loved science and try to keep up with it. We are living in such a cool time of discovery that it makes these questions really interesting. I hope that I'm keeping an open mind. I think I do mostly. I do worry the science community may be forcing the theory of evolution to account for everything without having enough evidence to take ID off the table completely the way it seems to have done. Probably because ID may give religious fundamentalists who are seen as being at odds with science something to hang there hat on or maybe they them self's tend to be atheist and are looking to have that validated by science I think both sides have a hard time staying objective because being human in that way but without ID (less any specific religion) being accepted as a valid theory potential in the education system it seems like were leaving out a important discussion that should be part of any balanced education. So I'm not part of any religious denomination and I try to live as a truth seeker as best I can and that has me playing the devil's advocate sometimes when exploring questions like the origins of Life.
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Ed Hartouni
Trad climber
Livermore, CA
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Feb 23, 2012 - 10:54am PT
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calculating the probability of abiogenesis is dicey given a single observation of life, and depends on how you interpret the history of life on Earth as input to the calculation
You can read a recent article about it here: http://arxiv.org/pdf/1107.3835.pdf which was published in PNAS... it identifies an important assumption made in the statistical analysis of a paper (see below) that argues life is highly likely...
basically, the argument that life is common in the universe stems from the observation that life started on Earth within a few hundred-million years after conditions on the Earth would allow it... look at this article: http://arxiv.org/pdf/astro-ph/0205014v2.pdf (which discusses many of the issues raised in the video in a more open, quantitative manner)
the point here is that this calculation is not yet possible given the information we have regarding abiogenesis and the example of one case, our own, is insufficient for making either claim, that life is rare or life is abundant out in the universe.
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Ed Hartouni
Trad climber
Livermore, CA
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Feb 26, 2012 - 12:56pm PT
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the reason why a theory of life is important is simply because we will probably never be able to show the direct "causal" link between the state of the early Earth and our existence... science doesn't work that way, it does not work on proof but on falsification.
While thinkers like Largo and WBraun have trouble imagining that natural process alone could result in life, science would be happy to conclude that what can be inferred from our observations is consistent with a physical theory of life. As far as I know, no one is satisfied with that theory, one indication being the lack of a strong definition of what life is...
...the statistical nature of the physical theory, or the likely physical theory, is much more subtle than what Largo quipped above... but perhaps that is the essence of it, that in the early conditions of Earth there was time enough for everything to happen such that life was a result. The meaning of "life" here is essentially the approximate-self-replication required for evolution to take over the refining of those processes.
There is a lot of stuff that has to happen to get to the "first cell" and considerable uncertainty of what that was. Given the early history of Earth, it is entirely possible that many instantiations of life occurred and were extinguished during the period of Earth history referred to as "The Great Bombardment" where all nature of stuff rained down on the planet, stuff big enough to vaporize the oceans and raise the temperatures to the point of sterilization. Then the whole starting over again.
The fact that the physical evidence from the fossil record indicates that life was abundant and diverse 1 billion years after the Earth was formed, with much of that time truly hostile to life, must be consistent with any theory that we formulate. That seems to require that life will form quickly where the physical conditions for it are met.
That first cell has to have a set of attributes, quoting from R. Ege's essay, "Primal Eukaryogenesis: On the Communal Nature of Precellular States, Ancestral to Modern Life" Life 2012, 2, 170-212 (http://www.mdpi.com/2075-1729/2/1/170/);
"(i) to couple energy from the environment into usable chemical forms;
(ii) to carry out specific catalytic functions;
(iii) to make and/or copy macromolecules;
(iv) to give some of these informational significance."
where the attributes are not meant to be taken as independent, the italics indicating system-wide context.
This example is given to indicate the process of abstraction (or as Largo would point out, "reductive reasoning") which is a part of defining a physical theory. This abstraction for the "first cell" is already far advanced, many of the requirements for abiogenesis form an important foundation to get to this point. Further, this process of abstraction is necessarily generalizing the problem, the number of processes likely to satisfy these attributes is likely larger than the cases we know about. This is a good thing about theory, and the thing that allows it to be checked. It also frees the theory from the narrowness of explaining one observation only.
We aren't there yet, but you can see the process happening. Riley asks above "do we really need more than we have" to explain life? I responded "yes" (I think, and if not, here I do) since we don't have strong quantitative arguments to give regarding the observation of life on Earth.
While this scientific approach is unsatisfying to those who would like to see "life" squirming on the lab bench as the result of some recipe, perhaps the result of some biological "philospher's stone," we are likely only to have a theory that provides an understanding of life, and lays out the basis for a search for life in the universe that recognizes a larger diversity than what we know on Earth. Prepare yourselves for the realization that we are not special even there...
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Psilocyborg
climber
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Feb 26, 2012 - 01:36pm PT
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We are star dust. We are self aware. That in itself is mind boggling. Forget crystals and bacteria, the stardust has become self aware.
I like to think consciousness is part of an evolutionary system much bigger than the earth itself.
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SCseagoat
Trad climber
Santa Cruz
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Feb 26, 2012 - 01:49pm PT
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Sunday morn...shouldn't we be at church?
Susan
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cowpoke
climber
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Feb 26, 2012 - 02:13pm PT
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Prepare yourselves for the realization that we are not special even there... The underlying point that Ed is making in this comment notwithstanding, I think we are special. Given the story of life on earth -- as science, and specifically evolutionary theory, tells it -- everyone contributing to this thread, everyone reading it, and all others presently existing on this planet are pretty darn special.
David Buss, the evolutionary psychologist, makes this point much better than I could in the opening paragraph to his book The Dangerous Passion:
Every human alive is an evolutionary success story. If any of our ancestors had failed to survive an ice age, a drought, a predator, or a plague, they would not be our ancestors. If any had failed to cooperate with at least some others in the group or dropped below a minimal position in the social hierarchy, they would have met certain death by being cast out from the group. If even one had failed to succeed in choosing, courting, and keeping a mate, the previously inviolate chain of descent would have been irreparably broken, and we would not be alive to tell the tale.
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Ed Hartouni
Trad climber
Livermore, CA
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Feb 26, 2012 - 02:38pm PT
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perhaps I should have said we will learn that the conceit that our life does not extend to the universe
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High Fructose Corn Spirit
Gym climber
-A race of corn eaters
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Feb 26, 2012 - 02:46pm PT
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Are we not "special" because we are above the (natural) law?
We are "above the law" - that is the unspoken, unwritten claim.
Paramecium and amoeba are NOT above the law. Honey bees and honey badgers are Not above the law.
But Man is above the law.
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High Fructose Corn Spirit
Gym climber
-A race of corn eaters
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Feb 26, 2012 - 03:12pm PT
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Prepare yourselves for the realization that we are not special even there...
A great Star Trek TNG episode, "First Contact" touches upon this. In the episode it was decided in the end - after First Contact - that the malcorians should live in ignorance ("sweet innocence") instead of knowledge (of space, warp, federation of planets, a chorus of life, etc.) - where they could continue to indulge their (archaic) conceits, ideologies.
Of course the lead in the episode (a scientist) in the end opts to leave the planet (her luddite home, culture and species) to venture out into the cosmic frontier with Picard and crew. Good for her.
Is it better to live with our inherited, hand me down conceits (having grown up with them, they're so ego-satisfying afterall) or to move past them (in the hope of better practices, but armed with anti-depressants, perhaps)? Seems we're divided on the issue. Just like in the ST TNG episode.
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Psilocyborg
climber
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Feb 26, 2012 - 03:34pm PT
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I think damming religion as ignorance is ignoring what it does for people on a personal level. It is a motivator for good and evil. It gives some "mo pow". Yes slaughter and control, a true opium of the masses, but thats on a societal level. On a personal level, the effect it has on ones personal perspective can be profound, which in turn affects evolution and natural selection. So religious belief is measurable in science. If science can measure it, does it exist? :-)
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Ed Hartouni
Trad climber
Livermore, CA
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Feb 26, 2012 - 04:52pm PT
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On a personal level, the effect it has on ones personal perspective can be profound, which in turn affects evolution and natural selection. So religious belief is measurable in science. If science can measure it, does it exist? :-)
this is an interesting vein we've mined in other threads, the possibility that religious belief is an evolved behavior that conveys a survival benefit... sort of the physical universe's own little joke..
HFCS you have a sketch of a theory, but not a theory... but if you think you have one, start with your theory's definition of life...
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Largo
Sport climber
The Big Wide Open Face
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Feb 26, 2012 - 05:57pm PT
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. . . start with your theory's definition of life...
----
What makes this challenging is that reductionism implies that something or any and all things are no more than a combination of their physical parts. Ergo we should be able to concoct a definition of "life" in strictly physical terms that satisfies Ed's question. But any physical definition can only be about objective, biological functioning, and at least some of us suspect there might be more, that matter does not so much "create" life as organize itself in a way to host or sustain it.
As I said many times earlier, the only way to be satisfied with a strictly physical explanation is to say that "life" and physical processing are the same thing, and that life is created or transmitted by matter. If so, then a physical description would exhaust the subject. As we all know, it doesn't, and it's easy to see why. Remember that bit from The Bride of Frankenstein: She's alive. Alive!
I suspect the essence of Ed's question is not quantifiable in our normal ways. At least the definition we come up with will always feel a little lacking - like a topo compared to the actual route, in starlight and storm.
But one thing is for sure - our life, however we might describe it, is what we have right now, right here, and the agency that experiences and chooses, while not a thing, is the greatest mystery of all.
JL
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Norton
Social climber
the Wastelands
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Feb 26, 2012 - 06:14pm PT
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nice contribution, Gobee
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WBraun
climber
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Feb 26, 2012 - 07:37pm PT
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While thinkers like Largo and WBraun have trouble imagining
Hilarious, Ed is telling us we should become be mental speculators ....
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cintune
climber
Midvale School for the Gifted
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Feb 26, 2012 - 07:49pm PT
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...like a topo compared to the actual route, in starlight and storm.
Like Gaston said, the game is to voluntarily commit yourself to this prison, and then to escape from it. (The nordwand of the Matterhorn in his context, but broadly applicable.)
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SuperTopo on the Web
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atoms to molecules to crude replicators to fancy replicators...
Let us know!