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Basic Worldview:
102 Atheism vs. Theism


Not Theories, Unsubstantiated Hypotheses 3

Prelude: "Atheism/Theism" vs. "Science, the Bible, & Creation"
Atheism: Introduction and Charges
Charge 1, Deduction and Induction
Charge 2, Question 1
Charge 2, Questions 2 and 3
Charge 2, Summary and Question 4
Charges 3 and 4, Definitions
Empirical Evidence
Scientists Acting as Mechanisms, Article 1
Scientists Acting as Mechanisms, Article 2
Scientists Acting as Mechanisms, Article 3
Occam's Razor and Conclusions
Footnote 1
Footnote 2 and 3
Proof of Life
Not Theories, Unsubstantiated Hypotheses 1
Not Theories, Unsubstantiated Hypotheses 2
Not Theories, Unsubstantiated Hypotheses 3
Not Theories, Unsubstantiated Hypotheses 4
Scientists: Life on Earth Imported from Outer Space
Atheisms Circle of Reasons
Is God a White Crow?



(Continued...)

In the following series of paragraphs continue in the same manner as the above series of paragraphs. The author continues with this same line of unsubstantiated assumptions about early RNA development.

12) In all likelihood, the four bases arose together with a number of other substances similarly constructed of one or more rings containing carbon and nitrogen.

The first nucleic acid-like molecules probably contained an assortment of these compounds. Molecules rich in A, U, G and C then were progressively selected and amplified, once some rudimentary template-dependent synthetic mechanism allowing base pairing arose. RNA, as it exists today, may thus have been the first product of molecular selection.

A third stage in the evolution of the RNA world was the development of RNA-dependent protein synthesis. Most likely, the chemical machinery appeared first, as yet uninformed by genetic messages, as a result of interactions among certain RNA molecules, the precursors of future transfer, ribosomal and messenger RNAs, and amino acids. Selection of the RNA molecules involved could conceivably be explained on the basis of molecular advantages, as just outlined. But for further evolution to take place, something more was needed. RNA molecules no longer had to be selected solely on the basis of what they were, but of what they did; that is, exerting some catalytic activity, most prominently making proteins. This implies that RNA molecules capable of participating in protein synthesis enjoyed a selective advantage, not because they were themselves easier to replicate or more stable, but because the proteins they were making favored their replication by some kind of indirect feedback loop.

This stage signals the limit of what could have happened in an unstructured soup. To evolve further, the system had to be partitioned into a large number of competing primitive cells, or protocells, capable of growing and of multiplying by division. This partitioning could have happened earlier. Nobody knows. But it could not have happened later. This condition implies that protometabolism also produced the materials needed for the assembly of the membranes surrounding the protocells. In today's world, these materials are complex proteins and fatty lipid molecules. They were probably simpler in the RNA world, though more elaborate than the undifferentiated "goo" or "scum" that is sometimes suggested.

Once the chemical machinery for protein synthesis was installed, information could enter the system, via interactions among certain RNA components of the machinery--the future messenger RNAs--and other, amino acid-carrying RNA molecules--the future transfer RNAs. Translation and the genetic code progressively developed concurrently during this stage, which presumably was driven by Darwinian competition among protocells endowed with different variants of the RNA molecules involved. Any RNA mutation that made the structures of useful proteins more closely dependent on the structures of replicatable RNAs, thereby increasing the replicatability of the useful proteins themselves, conferred some evolutionary advantage on the protocell concerned, which was allowed to compete more effectively for available resources and to grow and multiply faster than the others.

The RNA world entered the last stage in its evolution when translation had become sufficiently accurate to unambiguously link the sequences of individual proteins with the sequences of individual RNA genes. This is the situation that exists today (with DNA carrying the primary genetic information), except that present-day systems are enormously more accurate and elaborate than the first systems must have been. Most likely, the first RNA genes were very short, no longer than 70 to 100 nucleotides (the modern gene runs several thousand nucleotides), with the corresponding proteins (more like protein fragments, called peptides) containing no more than 20 to 30 amino acids.

It is during this stage that protein enzymes must have made their first appearance, emerging one by one as a result of some RNA gene mutation and endowing the mutant protocell with the ability to carry out a new chemical reaction or to improve an existing reaction. The improvements would enable the protocell to grow and multiply more efficiently than other protocells in which the mutations had not appeared. This type of Darwinian selection must have taken place a great many times in succession to allow enzyme-dependent metabolism to progressively replace protometabolism.

The appearance of DNA signaled a further refinement in the cell's information-processing system, although the date of this development cannot be fixed precisely. It is not even clear whether DNA appeared during the RNA world or later. Certainly, as the genetic systems became more complex, there were greater advantages to storing the genetic information in a separate molecule. The chemical mutations required to derive DNA from RNA are fairly trivial. And it is conceivable that an RNA-replicating enzyme could have been co-opted to transfer information from RNA to DNA. If this happened during the RNA world, it probably did so near the end, after most of the RNA-dependent machineries had been installed.

What can we conclude from this scenario, which, though purely hypothetical, depicts in logical succession the events that must have taken place if we accept the RNA-world hypothesis? And what, if anything, can we infer about the protometabolism that must have preceded it? I can see three properties.

First, protometabolism involved a stable set of reactions capable not only of generating the RNA world, but also of sustaining it for the obviously long time it took for the development of RNA replication, protein synthesis and translation, as well as the inauguration of enzymes and metabolism.

Second, protometabolism involved a complex set of reactions capable of building RNA molecules and their constituents, proteins, membrane components and possibly a variety of coenzymes, often mentioned as parts of the catalytic armamentarium of the RNA world.

Finally, protometabolism must have been congruent with present-day metabolism; that is, it must have followed pathways similar to those of present-day metabolism, even if it did not use exactly the same materials or reactions. Many abiotic-chemistry experts disagree with this view, which, however, I see as enforced by the sequential manner in which the enzyme catalysts of metabolism must have arisen and been adopted. In order to be useful and confer a selective advantage to the mutant protocell involved, each new enzyme must have found one or more substances on which to act and an outlet for its product or products. In other words, the reaction it catalyzed must have fitted into the protometabolic network. To be sure, as more enzymes were added and started to build their own network, new pathways could have developed, but only as extensions of what was initially a congruent network.

It may well be, then, that clues to the nature of that early protometabolism exist within modern metabolism. Several proposals of this kind have been made. Mine centers around the bond between sulfur and a carbon-containing entity called an acyl group, which yields a compound called a thioester. I view the thioester bond as primeval in the development of life.
- American Scientist article

NOTE: It is worth noting in this long series of paragraphs the repeated use of phrases such as "likelihood," "probable," and "may have," to describe speculative events. Near the middle of the above section, the author even admits that his proposed scenario is "purely hypothetical." It is significant that this unsubstantiated, purely hypothetical scenario includes the development of nucleotides, diversified forms of RNA, DNA, proteins, and a whole host of new enzymes, and finally proto-cells themselves. In other words, the explanation of how these very critical molecules came about is purely a matter of speculation with no empirical evidence to substantiate those hypothetical explanations.

13) I have tried here to review some of the facts and ideas that are being considered to account for the early stages in the spontaneous emergence of life on earth. How much of the hypothetical mechanisms considered will stand the test of time is not known. But one affirmation can safely be made, regardless of the actual nature of the processes that generated life. These processes must have been highly deterministic. In other words, these processes were inevitable under the conditions that existed on the prebiotic earth. Furthermore, these processes are bound to occur similarly wherever and whenever similar conditions obtain. - American Scientist article

NOTE: Here again at the end the author simultaneously refers to this series of speculative events as both "facts and ideas" as well as "hypothetical machinery." He is not even confident this speculation "will stand the test of time."

14) All of which leads me to conclude that life is an obligatory manifestation of matter, bound to arise where conditions are appropriate. - American Scientist article

15) Life is a cosmic imperative. The universe is awash with life. - American Scientist article

NOTE: The author has already admitted that this scenario is "purely hypothetical." And now he admits that his conclusion that "life is an obligatory manifestation of matter" is based entirely on these unsubstantiated speculations. His conclusion is based upon pure speculation, not evidence.


Sources

http://www.americanscientist.org/articles/95articles/cdeduve.html
September-October 1995
The Beginnings of Life on Earth
by Christian de Duve

http://www.discover.com/archive/index.html
First Cell
By Carl Zimmer