Friday, April 24, 2009

Abiogenesis: Can The Game Start Without A Kickoff?

Listening to someone who has a different view is not a waste of time. Otherwise we'd be preaching to the choir of those who already convinced. When it comes to different views on science, theAgora forums have featured speakers from both theistic evolutionist AND YE creationist :D

Today, let's take a brief look at the topic of 'abiogenesis' - the idea that living organisms developed naturalistically from nonliving matter. If the game of natural selection that accounts for diverse life forms on earth is to begin without divine intervention, then somehow the first primitive living organisms must have developed from non-living matters.

If there is no kickoff, how can the game even get started? (Greg Koukl)

Here, scientists have tried for decades to find this 'holy grail' but the results seem to be rather disappointing not for the lack of trying or technological capability. Rather much creative research and advanced molecular biology had been invested through the years to unravel more dead-ends than possible pathways.

Let me begin with some quotes from a the panspermia website:
"The undreamt-of breakthrough of molecular biology has made the problem of the origin of life a greater riddle than it was before: we have acquired new and deeper problems." — Karl R. Popper

"Nobody understands the origin of life. If they say they do, they are probably trying to fool you." — Ken Nealson

But quite frequently, certain famous experiments were cited as if it had given confirming evidence that abiogenesis is not only possible/viable but also relatively easy. (It needs to be deceptively easy bcos the most primitive cell appeared relatively early in the earth's development so there is not much time for 'chance' to work its magic)

In the article THE ORIGIN OF LIFE ON THE EARTH, Leslie Orgel a scientist who has invested 30 years of his life researching the origins of life to give his review verdict on the state of research in this field in Scientific American. He is the kind of scholar who really knows his stuffs and therefore, more careful in his assertions. For example, you won’t find him citing Fox, Miller and Ferris as if they have already given experimental confirmation for abiogenesis when they are far from even close to doing so. A serious scientist would not say such a thing with how things are panning out these days.

The article is a tour de force of different theories proposed so far and it ends on a rather somber note below:

“Whether RNA arose spontaneously or replaced some earlier genetic system, its development was probably the watershed event in the development of life. It very likely led to the synthesis of proteins, the formation of DNA and the emergence of a cell that became life's last common ancestor. The precise events giving rise to the RNA world remain unclear. As we have seen, investigators have proposed many hypotheses, **but evidence in favor of each of them is fragmentary at best. The full details of how the RNA world, and life, emerged may not be revealed in the near future.** Nevertheless, as chemists, biochemists and molecular biologists cooperate on ever more ingenious experiments, they are sure to fill in many missing parts of the puzzle.”
(emphasis mine)

What James Ferris has done is interesting but modest. However with all due respect, we can’t simply flash his experiment and hope that it would self-evidently convince people. It may impress those already convinced, but a careful evaluation of what his experiment actually can or cannot prove will do much better. To be more accurate, Ferris finds that a common clay could catalyze the formation of oligonucleotides (short sequences of nucleotides) and it would do well to remember that these are short, random sequences. We have not even come close to explaining how self-replicating RNA was created from these constituents.

As an analogy, when we play Scrabble, it is easy to get alphabets like ‘ran’ or ‘cat’ or ‘police’ randomly but it is hardly evidence that such random processes can yield strings of words that form a Shakepeare play.

Let’s see what Orgel has to say about this research direction:
“Let us assume investigators could prove that ribonucleotides were able to emerge nonenzymatically. Workers who favor the simple scenario described above would still have to demonstrate that the nucleotides could assemble into polymers and that the polymers could replicate without assistance from proteins. Many researchers are now struggling with these challenges. Once again, minerals could conceivably have catalyzed the joining of reactive nucleotides into polymers. Indeed, James P. Ferris of the Rensselaer Polytechnic Institute finds that a common clay, montmorillonite, catalyzes the synthesis of RNA oligonucleotides.

It is harder to conceive of the steps by which RNA might have begun to replicate in the absence of proteins. Early work in my laboratory initially suggested that such replication was possible. In these experiments, we synthesized oligonucleotides and mixed them with free nucleotides. The nucleotides lined up on the oligonucleotides and combined with one another to form new oligonucleotides… (skip)

***After years of trying, however, we have been unable to achieve the second step of replication - copying of a complementary strand to yield a duplicate of the first template - without help from protein enzymes. Equally disappointing, we can induce copying of the original template only when we run our experiments with nucleotides having a right-handed configuration. All nucleotides synthesized biologically today are right-handed. Yet on the primitive earth, equal numbers of right- and left-handed nucleotides would have been present. When we put equal numbers of both kinds of nucleotides in our reaction mixtures, copying was inhibited.***

(emphasis mine)

Here is another relevant evaluation by Orgel:
“Formation of nucleotides by combining phosphate with nucleosides has been achieved by simple prebiotic reactions. But the kinds of nucleotides that occur in nature arose along with related molecules having incorrect structures. If such mixtures were produced on the young planet, the abnormal nucleotides would have interacted with the normal ones to interfere with catalysis and RNA replication. Hence, although each step of ribonucleotide synthesis can be achieved to some extent, it is not easy to see how prebiotic reactions could have led to the development of the ribonucleotides needed for producing self-replicating RNA.

One way around this problem is to assume that inorganic catalysts were available to ensure that only the correct nucleotides formed. For instance, when the components of nucleotides became adsorbed on the surface of some mineral, that mineral might have caused them to combine only in specific orientations. The possibility that minerals served as useful catalysts remains real, ***but none of the minerals tested so far has been shown to have the specificity needed to yield only nucleotides having the correct architecture.***

While the experiment is promising but it has also yielded deep and worrisome problems which need to be overcome. I’m not saying these are insurmountable problems but it would not be exaggerating to say that with the advance of science, we’ve found more gaps than answers to abiogenesis.

What about the famous Miller experiment? His experiments are based on a reducing
atmosphere condition he assumed actually existed on the early earth but independent geochemical evidence now strongly suggests that chemically hostile conditions prevailed. So if those conditions are not of early earth, all you are simulating is how amino acids could form frm inorganic materials in an alternate universe setting. (hardly relevant to our topic here). It is a serious objection and explains
why scholars need to come up with other unconfirmed theories to fill in the gaps. ('science of the gap' strategy?)

But lets for the **sake of discussion** assume that the conditions on early earth are accurately simulated in spite of evidence to the contrary.

Would Miller's experiment show that “it can be done”? Again, not so. These experiments produce amino acids along with non biological stuffs which will react with each other to produce useless sludge or tar. Without the experimenter’s intelligent intervention to prevent this chemical reaction, they have to artificially removed these other stuffs and use short wavelength UV light (which is unrealistic on this planet) otherwise these amino acids would quickly degrade. If it shows anything, it accidentally proves that an intelligent designer (Miller
himself!) is required to get those amino acids...

In summary, we find the words of Francis Crick revealing: "An honest man, armed with all the knowledge available to us now, could only state that in some sense, the origin of life appears at the moment to be almost a miracle, so many are the conditions which would have had to have been satisfied to get it going."

And that brings us to the notion of Intelligent Design, I have recently heard some pretty weird arguments being brought against the movement:
1. You can't measure God's intelligence
2. Harmful, imperfect, less than ideal biological structures or mosquitoes or diseases disprove an intelligent designer
3. Pro evolution websites are more readily available on the google search and
scientific journal/literature.

There are much better arguments against ID but these are the ones I have been hearing from friends so maybe they deserve some discussions here. Btw I am not against Darwinism on theological grounds but do have reservations on its scientific basis. I'm also not 100% sold on ID either, but would like to see it being given a chance in public dialogue.

Well, to be fair, ID never claimed that we can measure God's intelligence or that every biological structure is ideal in the best in all possible worlds. So that appears to be a strawman argument here.

What ID folks do claim though is that design can be scientifically detected through certain mathematical models (see Dembski's Design Inference). And such designs can be found in biological organisms/information content in DNA etc. And just because a watch is 'poorly designed' doesn't prove that it is not designed at all. Argument 2 is a theological/philosophical argument rather than a scientific one, so one may respond by saying that the good creation is now a fallen world so it's not surprising to see entrophy and harmful mutations and diseases to occur.

On the last argument, I wish evolutionists would do better than the fallacy that just because a position was more abundant in literature and Google search, therefore it is true. The burden of proof is on the person who asserts. So if A asserts evolution is true, he has the burden of proof. And if B asserts ID is true, he also has the burden.

Science is familiar with new kids on the block who were ignored and persecuted at first but eventually took over the throne. Why not give ID a chance to do what they claim they can? All we need to do is patiently wait and see. If it not of science (or God) it will wither away...

Some people also say ID is not testable/falsifiable, but the same people then produce materials that try to refute irreducible complexity. For example, Kenneth Miller cited Barry Hall’s experiment to disprove Michael Behe! (for details see here and here) So the evolutionist has got to get their act together and be consistent. If you say ID is not science, then don’t try to use experiments to falsify it. If you say it is already falsified, then don’t claim that ID is not by definition a scientific enterprise. You can’t have it both ways!

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