Posted on 06/17/2002 4:40:34 PM PDT by Nebullis
CHAMPAIGN, Ill. — Life did not begin with one primordial cell. Instead, there were initially at least three simple types of loosely constructed cellular organizations. They swam in a pool of genes, evolving in a communal way that aided one another in bootstrapping into the three distinct types of cells by sharing their evolutionary inventions.
The driving force in evolving cellular life on Earth, says Carl Woese, a microbiologist at the University of Illinois at Urbana-Champaign, has been horizontal gene transfer, in which the acquisition of alien cellular components, including genes and proteins, work to promote the evolution of recipient cellular entities.
Woese presents his theory of cellular evolution, which challenges long-held traditions and beliefs of biologists, in the June 18 issue of the Proceedings of the National Academy of Sciences.
Cellular evolution, he argues, began in a communal environment in which the loosely organized cells took shape through extensive horizontal gene transfer. Such a transfer previously had been recognized as having a minor role in evolution, but the arrival of microbial genomics, Woese says, is shedding a more accurate light. Horizontal gene transfer, he argues, has the capacity to rework entire genomes. With simple primitive entities this process can "completely erase an organismal genealogical trace."
His theory challenges the longstanding Darwinian assumption known as the Doctrine of Common Descent – that all life on Earth has descended from one original primordial form.
"We cannot expect to explain cellular evolution if we stay locked in the classical Darwinian mode of thinking," Woese said. "The time has come for biology to go beyond the Doctrine of Common Descent."
"Neither it nor any variation of it can capture the tenor, the dynamic, the essence of the evolutionary process that spawned cellular organization," Woese wrote in his paper.
Going against traditional thinking is not new to Woese, a recipient of the National Medal of Science (2000), and holder of the Stanley O. Ikenberry Endowed Chair at Illinois.
In the late 1970s Woese identified the Archaea, a group of microorganisms that thrive primarily in extremely harsh environments, as a separate life form from the planet’s two long-accepted lines – the typical bacteria and the eukaryotes (creatures like animals, plants, fungi and certain unicellular organisms, whose cells have a visible nucleus). His discovery eventually led to a revision of biology books around the world.
The three primary divisions of life now comprise the familiar bacteria and eukaryotes, along with the Archaea. Woese argues that these three life forms evolved separately but exchanged genes, which he refers to as inventions, along the way. He rejects the widely held notion that endosymbiosis (which led to chloroplasts and mitochondria) was the driving force in the evolution of the eukaryotic cell itself or that it was a determining factor in cellular evolution, because that approach assumes a beginning with fully evolved cells.
His theory follows years of analysis of the Archaea and a comparison with bacterial and eukaryote cell lines.
"The individual cell designs that evolved in this way are nevertheless fundamentally distinct, because the initial conditions in each case are somewhat different," Woese wrote in his introduction. "As a cell design becomes more complex and interconnected a critical point is reached where a more integrated cellular organization emerges, and vertically generated novelty can and does assume greater importance."
Woese calls this critical point in a cell’s evolutionary course the Darwinian Threshold, a time when a genealogical trail, or the origin of a species, begins. From this point forward, only relatively minor changes can occur in the evolution of the organization of a given type of cell.
To understand cellular evolution, one must go back beyond the Darwinian Threshold, Woese said.
His argument is built around evidence "from the three main cellular information processing systems" – translation, transcription and replication – and he suggests that cellular evolution progressed in that order, with translation leading the way.
The pivotal development in the evolution of modern protein-based cells, Woese said, was the invention of symbolic representation on the molecular level – that is, the capacity to "translate" nucleic acid sequence into amino acid sequence.
Human language is another example of the evolutionary potential of symbolic representation, he argues. "It has set Homo sapiens entirely apart from its (otherwise very close) primitive relatives, and it is bringing forth a new level of biological organization," Woese wrote.
The advent of translation, he said, caused various archaic nucleic-based entities to begin changing into proteinaceous ones, emerging as forerunners of modern cells as genes and other individual components were exchanged among them. The three modern types of cellular organization represent a mosaic of relationships: In some ways one pair of them will appear highly similar; in others a different pair will.
This, Woese said, is exactly what would be expected had they individually begun as distinct entities, but during their subsequent evolutions they had engaged in genetic cross-talk – they had indulged in a commerce of genes.
No, I don't think there is any best temperature for that to happen. But I'll let someone else say the same thing.
From Primordial Soup to the Prebiotic Beach
| What about submarine vents as a source of prebiotic compounds? I have a very simple response to that . Submarine vents don't make organic compounds, they decompose them. Indeed, these vents are one of the limiting factors on what organic compounds you are going to have in the primitive oceans. At the present time, the entire ocean goes through those vents in 10 million years. So all of the organic compounds get zapped every ten million years. That places a constraint on how much organic material you can get. Furthermore, it gives you a time scale for the origin of life. If all the polymers and other goodies that you make get destroyed, it means life has to start early and rapidly. If you look at the process in detail, it seems that long periods of time are detrimental, rather than helpful.
A number of people tried prebiotic experiments. But they used CO2F, nitrogen and water. When you use those chemicals, nothing happens. It's only when you use a reducing atmosphere that things start to happen.
Temperature seems to be a talking point regarding prebiotic hypotheses. We know we can't have a very high temperature, because the organic materials would simply decompose. For example, ribose degrades in 73 minutes at high temperatures, so it doesn't seem likely. Then people talk about temperature gradients in the submarine vent. I don't know what these gradients are supposed to do. My thinking is that a temperature between 0 and 10 degrees C would be feasible. The minute you get above 25 degrees C there are problems of stability. |
Go to the Devil's Paint Pot at Yellowstone National park and sit for a while observing the clumps of bubbles that form up and persist for amazingly long times in mud that's hot enough to scold you. Individual bubbles, as you and the author have noted, do not persist, but the clumps do.
This is because these hot mineral vents contain what it takes to build polymers with hydrophobic and hydrophilic heads, which a) reinforce the bubbles to make them persist, and b) when one bubble bursts, the neighboring bubbles inherit the burst bubble's load of re-enforcing polymers.
This is a very broad hint as to how a complex chemical cycle can take on an enduring life in a medium, any one of whose compontents are evanescent due to high temperature. A crystalline rock face containing enzymatic organics embedded in it's structure could take on the same role. Unless the temperatures are high enough to melt rock, there are plenty of opportunities for persistent structure at temperatures far higher than are comfortable for us. Like most modern cavils, this author's are predicated on the unconscious assumption that RNA-world entities want a nice, comfortable, unambiguous, though flexible, skin to be in--discard this notion and you can observe that there are plenty of potential structuring elements at higher temps.
...
ribose degrades in 73 minutes at high temperatures
...And mRNA, the basic translation tool of modern DNA life, decays even faster.
By my lights, almost nothing persists in RNA world. In RNA world, you are one giant step closer to life (or whatever) being just a naked chemical cycle. RNA world, under my proposal, does not have fixed structures to decay, it is a chain of temporary chemical plants that produce other RNA, which is shipped to yet another temporary chemical plant to build yet another RNA, to be shipped to yet another chemical plant...and, finally, the end product ends up at the chemical factory floor that's just like the one we started with.
What has to persist, is that usable energy is obtained by this cycle--nothing else is required to persist.
Yes and they are called bubbles. This is a very nice just so story but adds nothing against the arguments presented by Stan the man Miller. He has evidence in a particular situation that the reagents of life can be formed without life. The experiment he helped perform provided that evidence. However, it has since been learned that some of the assumptions used in that experiment are not valid for the early earth. As a consequence it appears that his attitude towards the formation of life on this planet has acquired a distinctive extraterrestrial flavor. His observations have not been refuted by your claims.
What you note at bubbling pots are bubbles, not cyclic exchanges of energy. Heat goes one way from the heat source to the mud to the environment. It does not go the other way. Bubbles are not formed by the mere presence of polymers, nor are polymers even required for bubbles. Bubbles form in pure boiling water. Now you may claim that water is a polymer, but that claim was made and debunked in the 60's. So the final claim you make is that epibubbles are suggestive of a cyclic chemical process which could lead to life. I'll believe that when you present a persistant chemical cycle which could lead to life not involving life, in execution or planning.(and I don't mean like the Belousov-Zhabotinsky Reaction)
However, I did like your dim view of the scolding mud. :^)
Nor confirmed by anything terribly convincing. Pasteur also demonstrated the impossibility of spontaneous generation when he showed it couldn't happen in a pig pen in France in a few months. Yet I remain unconvinced, for some strange reason, that all the possibilities have now been exhausted. Just stubborn, I guess.
What you note at bubbling pots are bubbles, not cyclic exchanges of energy.
Not true. When a bubble in a cluster bursts, it gives it's all, literally, to the bubbles around it, including any additional potential energy opposed to dissolution embodied in chemical entities that are hydrophilic/phobic. What isn't demonstrated is a cycle that manages to increase it's energy store, and maintain itself over long periods of time. Although, as I think about it, I would argue that, from the point of view of gaining potential energy in the re-enforcement of bubble structure, there has, indeed, been an increase in potential energy in the surviving surrounding bubbles.
Heat goes one way from the heat source to the mud to the environment. It does not go the other way.
Presently, heat goes one way from the sun to the organic entities, it does not go back to the sun.
Bubbles are not formed by the mere presence of polymers, nor are polymers even required for bubbles. Bubbles form in pure boiling water. Now you may claim that water is a polymer, but that claim was made and debunked in the 60's.
Water is a very weakly bonded polymer, which is why life can exist at all--I know of no sense in which this claim has ever been refuted, save maybe by tightening down on the definition of polymer above a certain bonding strength. At any rate, this seems truistic and irrelevant, but perhaps I'm missing something?
So the final claim you make is that epibubbles are suggestive of a cyclic chemical process which could lead to life. I'll believe that when you present a persistant chemical cycle which could lead to life not involving life, in execution or planning.(and I don't mean like the Belousov-Zhabotinsky Reaction)
Hey, it's just a theory. I'm not even claiming it's a scientific theory, since I can't think of a practical falsifying test.
That is a class answer and is indicative to me of the creative fire within you. I agree with your doubt that all possibilities have been exhausted. So all I can say to you is keep at it.
Your lack of awe at the genetic code may be more a function of your incomplete knowledge of its wonders rather than weakness in the code itself.
DNA does not need a 3-redundant hemming code, and it would on average be more wasteful of space to build triple redundnacy in a code that is so sublime it seldom needs such measures.
Don't take my word for it. Look at Journal of Molecular Evolution #47 of 1998. An article by Freeland and Hurst (pp238-248). They calculated the error-minimizing capacity of one million randomly generated codes and found that the actual genetic code fell outside the distribution. Further research used estimates of 1018 possible codes possing the same degree of redundancy of the universal genetic code and found all of them were inside the distribution. This was a follow-up by Freeland in Molecular Biology and Evolution #17 of 2000, pp 511-518.
The code we have is the best possible code given the amount of redundancy it has. And it has all it needs to produce an astounding array of life. I have serious doubts about your boast that you could do better. There is an intellegent designer, and His name isn't Don!!!
Neglecting your duty or moving the goal posts? You guys complain over and over again that there are no tests for ID. I give some, and this is not the first time I've done it, and you respond by adding wholly subjective requirements. How do you define "better explanation"? To one who is locked into closed-minded doctriniare naturalism ANY naturalistic explanation, no matter how absurd, will always seem better than ANY creationist explanation, no matter how rational. I think you have neglected your duty as well. You guys have a problem. I am not sure if it is a heart or a head problem, because I don't know enough about you, but you seem smart enough, in an 'inside the box' sort of way.
I think that you will post the same junk on the next trhead about 'there are no testable predictions for ID'. If you do, expect me to call you on it. Not because I am out to get you, though, I just want you to see the truth. It is so easy to see when the mind is free.
You think you have neglected your duty? So do I, you have neglected your duty to follow the facts wherever they takes you, even if it is Jesus Christ.
does not have instantaneous abiogenesis moments. The RNA world is acting like a long-lived, slow evolving common ancestor in Woese's scenario, and there was some shadowy something-else evolving before that. You're doing the creationist hand-wave on Woese's RNA world, while retaining Woese's idea that archea, bacteria, and eukaryotes are siblings
You accuse me of doing the hand wave? You are the one appealing to an unproven RNA world and then a 'shadowy something before that". Great is your faith, o preist of Naturalism!
I am doing a hand wave on his conjecture while accepting the FACTS that he has discovered. Among the reasons I reject this conjecture is that the RNA world has been a flop in the lab and not observed in the field even though the evidence indicates that the types of cells show up very quickly after the last total-extinction event. So quickly that one would expect us to have been able to replicate much of the RNA world if such ever existed.
You might check my replies to donh just above this one, should have included you in on them.
You ask if Woese is credible, the facts are credible, but the conjecture is no better than anyone else's, actually worse sense other facts are known where argue against his conjecture.
Again, you simply throw away the first half of Woese's story, then announce that the second half came out of nowhere. Instant creation! Tah-dah!
There is no proof you existed before you logged onto FR. Instant creation! Tah-dah!
The Freeland and Hurst article deals with one aspect of redundant coding along a single dimension of concern. It is painfully obvious that there are elements of our basic DNA design that that are far from optimal--I already named several:
1) There is so little orthogonal reuse of genome fragments that any present-day database packer would between double and triple the data-per-volume if allowed to run for a few hours looking for like fragments it could optimize to one fragment. Fragmenting and Offset routing of triplets, which I referred to is far from the only way to do this. Furthermore, nature does, in fact, do this, but only in a very sparse and haphazard way.
2) As I said, there is simple and quite useless redundancy in the fundamental coding: quite a few triplets map to the same amino acid. If you really wanted jet-age DNA, you would have used the redundant triplets to map some amino acids we don't currently have any use for, and thereby open up the protein space to more possibly useful codings.
3) There are actually two ways that you could be using the same genome fragment to generate different usable mRNA strings. You could be re-entering the DNA string at count-of-three offsets, which is what we observe, and you could be re-entering at less-than-count of three, thereby re-defining the start points of the triplet codons. We have examples of the former, which I was just talking about, but no examples of the latter, of which I am aware. If we could recode this densely, I'd predict that a database packer would probably produce a 5 to 1 compression or better.
Insofar as information density is concerned, I could do better--and if you gave me unlimited funds and modern computers and universal polymer generators (machines which currently exist), I could do so today. Would my constructs survive out in the real world? I don't know, and neither do you.
Ok. For the sake of argument, let's say this new wrinkle is true, and the previous theories are wrong. What then do the Darwinists say to all the public school children who have been lied to for the last 40 years?
The next time the "scientists" proclaim something as the undebatable truth, will we be able to throw the original, now discredited Darwin theories in their faces, or, as usual, are we suppose to conventiently forget how often scientists are wrong, and arrogantly wrong at that?
How generous. My mind is, indeed shackled to the ordinary rules of science. I ploddingly accept the current story until it is overthrown, just like the rest of the scientific sheep. Had my mind the soaring freedom to accept UFOs, Little Green Men, Big Boojum's In the Sky, or any of the rest of the tin foil brigades arsenal, as if it was just as credible as the explanations that are currently on the scientific table, however limited they may be, I guess I'd be where you are at, but, sadly, I'm not. I continue to insist on seeing tangible, unimpeachable, contradicting evidence before I give up the current, admittedly imperfect, scientific paradigm.
I'm sorry science can explain so little--however, I don't think that suddenly makes every crackbrained idea in the universe suddenly viable. Show me a little green man with a land patent claim on the earth, or an example of God whupping up a single celled Prokariote from spit of beach tar, and I'm ready to convert.
The three types of cells have a lot in common, which suggests common ancestor, but they also have a lot different, which suggest independent origin. Both ID and Woese's hypothesis explain those facts better than the current evolutionary paradigm do. What I did in the earlier posts was show that the timescale in which Woese's idea had to work was much narrower than earlier thought. So narrow that we should be able to get the nuts and bolts of a soup world and an RNA world in the lab. The fact that these experiments have hit one dead end after another helps tilt the scales away from the RNA world.
I, and donh for that matter, are attempting civil debate on the bases of FACTS. OTOH you, at this point, are just being cranky.
Could you give us a pointer to an example of this? What does it say on the marqee?
The Theory of Gravity
The Theory of Continental Drift
The Theory of Evolution
Can you not even read the titles of the books for understanding? What's the point of criticizing something you don't even grasp the first principals of?
There is a big difference between a lab, and a primordal world you are attempting to emulate from inferential evidence 4 billion years removed from the scene of the crime. Pasteur did not close the books on abiogenesis, and neither do the current failures of labs to produce life at the snap of a finger. It is painfully obvious that we don't have enough data to write closure to any options at this point.
Actually, I'd like an example of the "first time" science has proclaimed anything "undebatable" or "truth."
It's not that evolution is undebatable, it is that Creationism and its latest flavor, ID, is not even serious fiction. Work on your own case -- you seem to interesting in proving a negative. Prove creationism.
Heck, what about all the Christians who've been lied to for 2000 years. Science can be wrong for decades, the Bible is wrong forever.
As far as point number one goes, it is my understanding that a LOT of reuse of code occurs. This is why they found out that human beings only had about a third as many genes as expected on the Human Genome Project. There were more protiens made than genes to make them! The reason is that code is reused. This is how donh, intelligent designer, said it should be done and it is. Funny how things are really done the way an intellignet designer says they should be, eh?
As far as point two goes, the articles I cited earlier show that the rendundancy is a feature of the error-minimization properties of the code. The substitution errors most likely to occur are the ones where different codons code for the same amino acid!!!! I think God has found a way to minimize error that donh did not think of first. He did not have triple redundnacy tags on each codon, but He does have it so that the errors most often made are not really errors.
I have been amazed by what I know about the code often enough to where it is reasonable to assume that I have not been amazed for the last time. It is a safe bet that there are other discoveries out there that will address your #3.
I just cannot get over how blithely you assume you could write better code than DNA, the instructions for every part of your body are in every cell. How can you compress than much info in such a space?
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