Monday, May 25, 2015

Attempted Refutation of the Difficulty in Producing First Life

I've been looking at the various calculations regarding the random assembly of DNA, RNA, RNA-polymerase, and the necessary proteins and their component amino acids, in the context of first life emerging by abiogenesis. And I stumbled across the following "refutation" of the presumed difficulty due to the emergent self-assembly of RNA found in the Bartel/Zostak experiment:
"Now I will recall a classic experiment by David Bartel and Jack Szostak, published in Science in 1993. Their goal was to see if a completely random system of molecules could undergo selection in such a way that defined species of molecules emerged with specific properties. They began by synthesizing many trillions of different RNA molecules about 300 nucleotides long, but the nucleotides were all random nucleotide sequences. Nucleotides, by the way, are monomers of the nucleic acids DNA and RNA, just as amino acids are the monomers, or subunits, of proteins, and making random sequences is easy to do with modern methods of molecular biology.

They reasoned that buried in those trillions were a few catalytic RNA molecules called ribozymes that happened to catalyze a ligation reaction, in which one strand of RNA is linked to a second strand. The RNA strands to be ligated were attached to small beads on a column, then were exposed to the trillions of random sequences simply by flushing them through the column. This process could fish out any RNA molecules that happened to have even a weak ability to catalyze the reaction. They then amplified those molecules and put them back in for a second round, repeating the process for 10 rounds. By the way, this is the same basic logic that breeders use when they select for a property such as coat color in dogs.

The results were amazing. After only 4 rounds of selection and amplification they began to see an increase in catalytic activity, and after 10 rounds the rate was 7 million times faster than the uncatalyzed rate. It was even possible to watch the RNA evolve. Nucleic acids can be separated and visualized by a technique called gel electrophoresis. The mixture is put in at the top of a gel held between two glass plates and a voltage is applied. Small molecules travel fastest through the gel, and larger molecules move more slowly, so they are separated. In this case, RNA molecules having a specific length produce a visible band in a gel. At the start of the reaction, nothing could be seen, because all the molecules are different. But with each cycle new bands appeared. Some came to dominate the reaction, while others went extinct.

Bartel and Szostak’s results have been repeated and extended by other researchers, and they demonstrate a fundamental principle of evolution at the molecular level. At the start of the experiment, every molecule of RNA was different from all the rest because they were assembled by a chance process. There were no species, just a mixture of trillions of different molecules. But then a selective hurdle was imposed, a ligation reaction that allowed only certain molecules to survive and reproduce enzymatically.

In a few generations groups of molecules began to emerge that displayed ever-increasing catalytic function. In other words, species of molecules appeared out of this random mixture in an evolutionary process that closely reflects the natural selection that Darwin outlined for populations of higher animals. These RNA molecules were defined by the sequence of bases in their structures, which caused them to fold into specific conformations that had catalytic properties. The sequences were in essence analogous to genes, because the information they contained was passed between generations during the amplification process.

The Bartel and Szostak experiment directly refutes the argument that the odds are stacked against an origin of life by natural processes. The inescapable conclusion is that genetic information can in fact emerge from random mixtures of polymers, as long as the populations contain large numbers of polymeric molecules with variable monomer sequences, and a way to select and amplify a specific property."

[Emphasis added]
The conclusion of refutation is absurd, for the following reason: the information contained in the RNA replicators was random, not semantic. The information was gibberish and was being perpetuated chemically and randomly selected, not for informational quality or utility for life, but merely for the chemical ability of aggressive replication of one catalytic type over others. So the odds against the creation of meaningful, prescriptive, semantic information describing a living entity remain exactly as before: the information still must be randomly acquired, yet meet all the needs of life.

These experiments in no manner comes close to refuting the necessity of assembling a working cell which already contains the proper prescriptive semantic information which describes (a) the cell's semipermeable membrane, (b) the multi-featured mechanism for reproduction by mitosis, (c) the necessary DNA, and RNA polymerases and associated transcription molecules, and (d) the necessary proteins for the life processes of the cell - including metabolism, energy acquisition and waste elimination, (e) the necessary amino acids for creating the proteins and polymerases. Further, all of this MUST be present in the first cell, if the cell is to be "alive" in the sense of metabolically sound and functioal, properly enclosed, accurately mitotic reproductive, and thus qualify to be the ancestor of all life on earth.

The fact that RNA self-catalyzes is unremarkable when it is attempted to be factored into the actual necessary complexity of the sufficient requirements for first life. And the odds against the random generation of these necessary components in first life remain beyond astronomical.

There is no "emergence" theory that has any meaning without the ability to produce, simultaneously, not only the physical components of the first cell, but also the information which is necessary for life and reproduction of the first cell.

I'm looking at the minimum sized Archaea cell, attempting to discern just how large the set of necessary components might have been in the simplest abiogenetic first life proposed under Materialism. It might take a while, because Archaea cells are fiendishly tiny, and I've not found much information on their internal structures, beyond DNA length. But stay tuned, I might find something reliable, sometime. And any suggestion for source material would be appreciated.

3 comments:

Robert Coble said...

I'm faintly curious:

Surely the environment within which the experiment was conducted is NOT even a vague attempt at replication of the natural environment within which "evolution" supposedly occurred. Can anyone seriously imagine ANY natural setting in which TRILLIONS of anything so microscopic could be flushed through a column under tightly controlled conditions over an unspecified deep period of time - until "life" appeared "spontaneously"?

Actually, the experiment does NOT claim to have produced "life" but, instead, a "suggestion" of a process similar to that postulated via natural (macro?) evolution. By way of suggestion, perhaps we could simply spill out the solution containing our result and see how long it will remain viable, much less how long it will take for it to reproduce itself.

If this experiment actually were similar to the putative natural process of evolution (which it is NOT), is it also prima facie evidence of intelligent design at work?

If intelligent design is required to produce the results, then why the vociferous denial of an intelligent agent as a NECESSARY requirement of the natural process in question?

Never fear, brave Scientismists! Soon (perhaps in a few billion years or more), we shall ascend to the Olympian heights, driven there in a futuristic vehicle "designed" by totally random experiences.

Somehow, I don't think so.

We have barely begun to scamper around on the bottom of Mt. Improbable. Sideways motion does not move us up the mountain.

yonose said...

Hello everyone!!

My expertise here is close to nil, but, considering the experiment and the textual deduction from those scientists, it is still really hard to ponder, why the indoctrination on certain, useless paradigm, is still so pervasive??

Wouldn't those "other" theoretical approaches deserve some attention, would they?

Closed-minded science, because life is too short to admit it is.

This is an interesting result which is produced by a predetermined arrangement of components --while this configuration is quite similar, in a behavioral aspect, as a genetic circuit-- when is changing its properties. An approximate mathematical model may be done with the usage of non-linear Partial Differential Equations, when all the independent values are the new quantites of substances applied in continuous or discrete intervals in time.

Mind you, this is the farthest from natural selection, as natural selection can get. This is the farthest from macroevolution, as evolution may get. Sadly, there are some scientists who also fall flat regarding the actual, logical concept of statistical significance --something like, like Higgs Boson says or something--, and those types of conclusion arise, by mere personal bias. Nothing new in science, but needs to be pointed out every single time it happens.

Kind Regards.

Russell (106) said...

@Robert

"If this experiment actually were similar to the putative natural process of evolution (which it is NOT), is it also prima facie evidence of intelligent design at work?"

I had the same thought. If you are rigging the game, how is that random?