Stephen E. Jones

Projects: Book (Outline): "Progressive Creation: A Scientific General Theory of Creation":
Chapter 9, Creation of Life

[Home] [Site map] [Updates] [Projects] [Contents, 1. Introduction, 2. What?, 3. History, 4. Objections, 5. Need, 6. Bible, 7. Universe, 8. Earth, 10. Plants, 11. Animals, 12. Man, 13. Conclusion, 14. Bibliography]

This is Chapter 9, Creation of life, of the outline of a book that I plan to write on Progressive Creation.

"Progressive Creation" (Outline): Chapter 9. Creation of life
Copyright (c) 2004-2005, Stephen E. Jones

1. Origin of Life
1. Failure to synthesise life
2. Miller-Urey experiment
3. Proteins
4. Oceanic soup
5. Little ponds
6. Hydrothermal vents
7. RNA first
1. My double-stranded RNA origin of life theory

2. Origin of the Cell
1. Information
3. Origin of Bacteria (Prokaryotes)
1. Complexity

1. Origin of Life
1. Failure to synthesise life

All attempts to synthesis life in a laboratory in the last half-century have failed (Bryson, 2003, p.253).
2. Miller-Urey experiment

Repeating the Miller-Urey experiment with gases representing the likely atmosphere of the early Earth, nitrogen and carbon dioxide, has produced only one primitive amino acid (Bryson, 2003, p.253)!
3. Proteins

Even if life's 20 amino acids were produced by a Miller-Urey experiment, the chance of the amino acids spontaneously forming even a small protein like haemoglobin, with 146 amino acids, is 20¹⁴⁶ or about 1 chance in 10¹⁹⁰, a number which is far, far greater than the estimated about 10⁸⁰ atoms in the universe." (Bryson, 2003, pp.253-254)
4. Oceanic soup

Oparin hypothesised that as the early Earth cooled, hydrocarbons in the atmosphere would have been washed down into the oceans forming a `primordial soup' within which further chemical reactions would have led to the origin of life (Oparin, 1938, pp.108-109). This was long assumed to be fact (Monod, 1971, p.143). However, geologists found no evidence of such an oceanic prebiotic `soup' (Brooks, 1985, p.118; Denton, 1985, pp.260-261). Eventually it was realised that an oceanic `primordial soup' would have been too dilute for direct formation of polymers (Thaxton, Bradley & Olsen, 1984, pp.61-62). Also, it was eventually realised that water severs the hydrogen bond links between amino acids necessary to build protein in a reaction called hydrolysis (literally "splitting with water") (Ball, 1999, p.210). Moreover, when two amino acids link they release a molecule of water, which means hydrolysis will predominate over amino acid link forging (Ball, 1999, p.210). The problem is even greater for nucleic acids where the sugar molecules in RNA and DNA are hydrolysed rapidly in water (Ball, 1999, p.210)
5. Little ponds

A "warm little pond, with all sorts of ammonia and phosphoric salts, light, heat, electricity, &c., present" was Darwin's 1871 proposal (Darwin, 1898, pp.II:202-203; Shapiro, 1986, p.185; Depew & Weber 1995, pp.399-400; Denton, 1985, p.53; de Beer, 1963, p.271; Orgel, 1982, p.149; Johnson, 1993, p.103). It regained favour when it was realised that an oceanic organic `soup' would have been too dilute for the formation of polymers led to a theory of "reactions in more limited zones" (Bernal, 1960), such as lakes, pools, and lagoons, and the like (Thaxton, Bradley & Olsen, 1984, pp.61-62). However these more limited local zones needed naturalistic mechanisms for concentrating the necessary chemicals, such as evaporation and freezing the body of water (Thaxton, Bradley & Olsen, 1984, pp.62-63). But like the oceanic primordial `soup, no geological evidence has been found for such organic pools, nor any mechanisms for concentrating chemicals in them. What was needed was a naturalistic sorting mechanism that selecting organic compounds and isolated them from other chemicals with which they would destructively cross-react, but no such naturalistic sorting mechanism has been found (Thaxton, Bradley & Olsen, 1984, pp.65-66). Moreover, the same problem of preferential hydrolysis in water that led to the abandonment of the oceanic soup theory (Ball, 1999, p.210), would also apply to small bodies of water. [top]
6. Hydrothermal vents

In deep sea hydrothermal vents, most of which are at the edge of tectonic plates, sea water percolates down through fissures in the ocean floor, is heated by an underlying body of magma, and erupts out through mineralised chimneys, carrying a rich load of inorganic minerals and gases, including hydrogen sulfide (H₂S), methane (CH₄), and ammonia (CH₃), from which carbon compounds can be built and nutrients and energy provided (Shapiro, 1986, p.115; Ball, 1999, p.207; Overman, 1997, p.80; Horgan, 1991, p.105; Lemonick, 1995, pp.54-55; Zimmer, 1996, pp.63-64). Archaean bacteria obtain their source of energy not from light but from sulfur compounds flowing from these vents and in turn support surrounding colonies of polychaete tube worms, and clams (Horgan, 1991, p.105; Overman, 1997, p.79; Shapiro, 1986, p.115; Wills & Bada, 2000, pp.96-98, 166). However, the water in such vents under the pressure at that depth may exceed 300°C (Shapiro, 1986, p.115) and so any organic compounds would be destroyed (Bradley & Thaxton, 1994, p.194; Henahan, 1996; Overman, 1997, p.80; Horgan, 1991, p.106). The bacteria around the vents can survive temperatures only as high as 120°C (Horgan, 1991, p.106; Overman, 1997, p.80). And since the entire ocean is recycled through those vents every 10 million years, this places a constraint on how much organic material could ever build up in the ocean (Horgan, 1991, p.106; Bradley & Thaxton, 1994, p.194; Henahan, 1996; Wills & Bada, 2000, p.258). Proponents of the hydrothermal vent origin of life hypothesis admit that current life at the vents migrated there (Horgan, 1991, p.105; Bradley & Thaxton, 1994, p.194; Overman, 1997, p.80; Wills & Bada, 2000, pp.166- 167). Also, the bacteria still require oxygen that has been produced by photosynthetic bacteria on the surface (Wills & Bada, 2000, pp.167). Modern hydrothermal vents are short-lived, lasting only for a few decades (Horgan, 1991, p.106). The hypothesis is very speculative and vague (Bradley & Thaxton, 1994, p.194; Overman, 1997, p.80). Like the oceanic prebiotic soup hypothesis, it requires an optimistic chain of serendipitous events to overcome the problem of hydrolysis (Ball, 1999, pp.210-211; Shapiro, 1986, p.198). [top]
7. RNA first
1. double-stranded RNA origin of life theory

"My Progressive Mediate Creation theory on this in my book "Progressive Creation" (http://members.iinet.net.au/~sejones/pc09life.html) will be that: 1) this change did happen, but it was a complete, irreducibly complex self-replicating *system* of *double-stranded RNA* (there is such a thing)" (My CED message #12760)
:

"RNA is very similar to DNA. Instead of the sugar deoxyribose, it has just plain ribose (hence the name RiboNucleic Acid), which has an -OH group whose deoxyribose has an -H one. Three of the four bases (A, G and C) are identical to those in DNA. The fourth, Uracil (U), is a close relative of Thymine (T), since thymine is just uracil with a -CH3 group replacing an -H group. This has little effect on the base-pairing. U can pair with A, just as, in DNA, T pairs with A. RNA might be described as using the same language as DNA but with a different accent. RNA can form a double helix, similar but not quite identical to the DNA double helix. It is also possible to form a hybrid double helix which has one chain of RNA and one of DNA. By and large, long RNA double helices are rare, RNA molecules being typically single-stranded, though often folded back on themselves to form short stretches of double helix. In modern organisms we find RNA used for three purposes. For a few small viruses, such as the polio virus, it is used instead of DNA as the genetic material. Some viruses employ single-stranded RNA; a few use it double-stranded. RNA is also used for structural purposes. The ribosomes, the complex assembly of macromolecules which are the actual site of protein synthesis, are made of several structural RNA molecules, assisted by several tens of distinct protein molecules. The molecules which act as the interface between the amino acid and the triplet of bases associated with it are also made of RNA. This family of RNA molecules, called tRNA (for transfer RNA), are used to carry each amino acid to a ribosome, where it will be added to a growing polypeptide chain which will, when complete, become a folded protein. The third and perhaps the most important use the cell makes of RNA is as messenger RNA. The cell does not use the DNA itself for everyday work but instead keeps it as the file copy. For working purposes it makes many RNA copies of selected parts of the DNA. It is these tapes of messenger RNA which direct the process of protein synthesis on the ribosomes, using the genetic code outlined in the Appendix." (Crick F.H.C, "Life Itself: Its Origin and Nature", Simon & Schuster: New York, 1981, pp.174-175)

"DNA replication is central to all extant cellular organisms. There are substantial functional similarities between the bacterial and the archaeal/eukaryotic replication machineries, including but not limited to defined origins, replication bidirectionality, RNA primers and leading and lagging strand synthesis. However, several core components of the bacterial replication machinery are unrelated or only distantly related to the functionally equivalent components of the archaeal/eukaryotic replication apparatus. This is in sharp contrast to the principal proteins involved in transcription and translation, which are highly conserved in all divisions of life. We performed detailed sequence comparisons of the proteins that fulfill indispensable functions in DNA replication and classified them into four main categories with respect to the conservation in bacteria and archaea/eukaryotes: (i) non-homologous, such as replicative polymerases and primases; (ii) containing homologous domains but apparently non-orthologous and conceivably independently recruited to function in replication, such as the principal replicative helicases or proofreading exonucleases; (iii) apparently orthologous but poorly conserved, such as the sliding clamp proteins or DNA ligases; (iv) orthologous and highly conserved, such as clamp-loader ATPases or 5'-->3' exonucleases (FLAP nucleases). The universal conservation of some components of the DNA replication machinery and enzymes for DNA precursor biosynthesis but not the principal DNA polymerases suggests that the last common ancestor (LCA) of all modern cellular life forms possessed DNA but did not replicate it the way extant cells do. We propose that the LCA had a genetic system that contained both RNA and DNA, with the latter being produced by reverse transcription. Consequently, the modern-type system for double-stranded DNA replication likely evolved independently in the bacterial and archaeal/eukaryotic lineages." (Leipe D.D., Aravind L., and Koonin E.V., "Did DNA replication evolve twice independently?" Nucleic Acids Res, September 1, 1999; 27(17): 3389-3401)

The Economist ... Nanotechnology cures cancer! May 5th 2005 Well, it might... DRUG molecules not only have to be effective at treating disease, they also have to be robust enough to get from the place where they enter the body to the place where they are designed to act. Given that bodies devote a lot of effort to hunting down and destroying things that are in the wrong place-whether those things be molecules, viruses, bacteria or even errant body cells-designing drugs that can do this is no mean feat. That is doubly true when the drug in question actually acts by stimulating one of these "thing-in-the-wrong-place" mechanisms-which is precisely how drugs that provoke a phenomenon called RNA interference work. RNAi, as it is known for short, is an approach to pharmacology that might revolutionise the field if it could be made to work routinely. It uses a natural anti-virus mechanism to block the activity of disease-causing genes, so any illness caused by the activity (as opposed to the inactivity) of a particular gene might, in principle, be treated by it. ... RNAi works by mugging one of the cell's molecular messengers. The information needed to make proteins-the molecules that do most of the work in a cell-is stored as genes in the double-stranded DNA of a cell's nucleus. When a particular protein is needed, this information is copied into a single-stranded molecule called RNA. The RNA then carries the message to the places where proteins are made, and the message is translated into protein. Many viruses work by subverting this mechanism-injecting their own RNA into a cell in order to make that cell produce viral proteins instead. But viral RNA is often double-stranded when it enters a cell, so a nifty way for a cell to deal with viral invasions is to recognise and destroy double- stranded RNA. Which is exactly what happens. Double-stranded RNA of any variety is rapidly chopped up by most cells. ...

with RNA enzymes to carry out all the above *minimum* functions; 2) but such a change could only *plausibly* happen either wholly or partly "supernaturalistically* by an Intelligent Designer/God. [...]

2. Origin of the Cell
1. Information

The cell is the equivalent of a digital information processor, so the problem for all naturalistic origin of life theories is how the molecular equivalent of computer hardware wrote its own software (Davies, 2002). [top]

3. Origin of Bacteria (Prokaryotes)
1. Complexity
A `simple' bacterium is enormously complex, and is in fact a miniaturised chemical factory. For example, Geobacter sulfurreducens, a proteobacterium, plays an important role in the global cycling of metals and carbon, and its sequenced genome reveals it has potential to be used in the bioremediation of radioactive metals and also in the generation of electricity (Methé, 2003) [top]