Tuesday, January 22, 2008

Abiogenesis For Creationists Part 1

This was written at an online forum in order to counter creationists' constant attacks on abiogenesis. There is an excellent video on the origin of life which does a great job explaining the basics. And of course, due to creationist attacks, the creator of that video had to address some erronous claims.

First of all, there has been an accusation that there's no evidence for the primordial soup. That's simply not true. The primordial soup is just the ocean, with a small amount of chemicals and amino acids. Experimental evidence shows that amino acids can be synthesized under plausible prebiotic conditions.

And even if amino acids could not form on earth, we know that they are carried on meteorites. We know meteorites hit the early earth.

Amino Acids:

Meteors striking the early earth (This link also discusses evidence for the primordial earth being covered in water)

Now, Amino Acids don't automatically mean life. We need a way to get from the soup to life. And here's the most likely way to do that: Form a replicator. A replicator is something that reproduces itself, just like living things. Its copies are mostly like it, displaying true heredity, yet some of them differ in small ways due to copy errors (mutations). If we have replicator, it can make copies slightly different from itself, and they can do the same, and so on. Eventually, this descent with modification should produce something like primitive cells (We know, by the way, that membrane like barriers can form from simple lipids and fatty acids, see Finding Darwin's God, page 276).

And yes, we have observed replicators forming. A famous example is Spiegelman's monster:

"The Qb virus doesn't need anything as complicated as a cell in order to
replicate: a test tube full of suitable chemicals is enough. The
experiment, conducted by Sol Spiegelman of the University of Illinois,
consisted of introducing the viral RNA into a medium containing the RNA's
own replication enzyme, plus a supply of raw materials and some salts, and
incubating the mixture. When Spiegelman did this, the system obligingly
replicated the strands of naked RNA. Spiegelman then extracted some of the
freshly synthesized RNA, put it in a separate nutrient solution, and let it
multiply. He then decanted some of that RNA into yet another solution, and
so on, in a series of steps.
"The effect of allowing unrestricted replication was that the RNA that
multiplied fastest won out, and got passed on to the 'next generation' in
the series. The decanting operation therefore replaced, in a highly
accelerated way, the basic competition process of Darwinian evolution,
acting directly on the RNA. In this respect it resembled an RNA world.
"Spiegelman's results were spectacular. As anticipated, copying errors
occurred during replication. Relieved of the responsibility of working for
a living and the need to manufacture protein coats, the spoon-fed RNA
strands began to slim down, shedding parts of the genome that were no
longer required and merely proved to be an encumbrance. The RNA molecules
that could replicate the fastest simply out-multiplied the competition.
After seventy-four generations, what started out as an RNA strand with
4,500 nucleotide bases ended up as a dwarf genome with only 220 bases. This
raw replicator with no frills attached could replicate very fast. It was
dubbed Spiegelman's monster.
"Incredible though Spiegelman's results were, an even bigger surprise lay
in store. In 1974, Manfred Eigen and his colleagues also experimented with
a chemical broth containing Qb replication enzyme and salts, and an
energized form of the four bases that make up the building blocks of RNA.
They tried varying the quantity of viral RNA initially added to the
mixture. As the amount of input RNA was progressively reduced, the
experimenters found that, with little competition, it enjoyed untrammeled
exponential growth. Even a single RNA molecule added to the broth was
enough to trigger a population explosion. But then something truly amazing
was discovered. Replicating strands of RNA were still produced even when
not a single molecule of viral RNA was added! To return to my architectural
analogy, it was rather like throwing a pile of bricks into a giant mixer
and producing, if not a house, then at least a garage. At first Eigen found
the results hard to believe, and checked to see whether accidental
contamination had occurred. Soon the experimenters convinced themselves
that they were witnessing for the first time the spontaneous synthesis of
RNA strands form their basic building blocks. Analysis revealed that under
some experimental conditions the created RNA resembled Spiegelman's
monster." Paul Davies, The Fifth Miracle, (New York: Simon and Schuster,
1999), p.127-128

(This was copied from the following:

For the peer reviewed paper on the monster, see:

We also know that protein fragments can replicate. Mad Cow Disease is caused by replicating protein fragments:

And of course, there are self replicating peptides (a peptide is the most likely thing to have formed in the primordial soup):

And, finally, what are the odds of a scenario like this happening? I'm going to quote from 2 NCSE articles:

These investigators observe that the building blocks of life (amino acids and other compounds known to form spontaneously) can link together, and some of the compounds formed are "autocatalytic": they cause other amino acids to link up. Something like a primitive metabolism emerges in these models -- and scientists are testing these models in laboratories. Exciting developments in the production of something very close to RNA, a major chemical of life, have recently been announced. If life is capable of self-organization, the criticisms raised by Meyer against "primal soup" biochemistry are irrelevant.

Scientists do not agree on how life began - yet. And "yet" is a very important word in science. One should not assume that just because something is not currently understood that it never will be understood. Meyer suggests that because some models of the natural origin of life have been disproved, we must give up our search and seek a supernatural explanation.


Creationists seem to be proud of their calculations that supposedly show how thermodynamics and probability prevent the chance formation of biologically useful macromolecules such as enzymes. Their "evidence" usually consists of quotations from such authors as Hubert P. Yockey, who agrees that catalytically active proteins cannot occur by chance. Yockey (1977a and b), looking at fully evolved proteins, says that their information content is too high for their chance formation.

Creationists do their own calculations to show that the chance formation of biologically useful proteins is impossible. These calculations almost always involve the erroneous assumption that each of the many amino acid positions in a protein must be filled by the one particular amino acid suitable for that position. Since there are twenty different amino acids available for each position, the chance of randomly getting a string of 200 amino acids all in the right order is (1/20)200. If you plug this expression into a calculator, it will tell you that it equals essentially zero. Thus, the creationists say, you can't get such a protein by a chance ordering of amino acids. As Duane Gish of the Institute for Creation Research (ICR) put it (1976), "The time required for a single catalytically active protein molecule to arise by pure chance would be billions of times the assumed age of the earth."

But proteins, even modern highly evolved specialized proteins, are not built with that degree of specificity. What's more, many proteins show in their structure that they were built of smaller subunit sequences of amino acids (Doolittle, 1981) or they have a simple metalo-organic core that could have functioned alone as a primitive precursor of today's complex enzyme. So the creationist calculations give an answer of zero probability because the creationists make at least two major errors in their assumptions: they assume a degree of specificity that has not been shown to exist in real proteins, and they insist that newly formed proteins must be as efficient as their older and highly evolved counterparts.

We've been trying to explain all this to the protein "experts" at ICR for the last seven years. We have told them that new proteins could indeed form from the random ordering of amino acids. We have warned them that their calculations were based on faulty assumptions and soon someone would document the natural formation of a new protein from the random association of amino acids.

Now it has happened! Not one, but two, new proteins have been discovered. In all probability new proteins are forming by this process all the time, but this seems to be the first documentation of this phenomenon. The newly discovered proteins are enzymes that break down some of the byproducts produced during nylon manufacture. Since nylon first came into commercial production in 1940, we know that the new enzymes have formed since that time.

When the enzymes were first discovered about 1975 (Kino****a, et al, 1981), it was at first thought the new enzymes arose through the modification of preexisting enzymes that had similar functions. To test this notion, the discoverers looked to see if the other enzymes in the same organism would react to antibodies made against the new enzymes. But by this criterion the new enzymes were unique. Antibodies against them found nothing similar with which to react among the array of other enzymes in the organism.

Again it was reasoned that if the new enzymes were just old enzymes with minor changes to allow digestion of nylon byproducts, they should retain at least a slight amount of activity with their original substrates. But the new enzymes had no activity on biologically derived molecules having similar chemical structures. So, by this attribute as well, the new enzymes were seen to be unique.

It seemed that if the new enzymes were indeed derived from randomly ordered amino acids, they would be very inefficient compared to the usual highly evolved enzyme, since the new enzymes would not have had billions of years of natural selection to reach a pinnacle of biological perfection. It has been shown that one of the new enzymes (the linear oligomer hydrolase) has about 2% of the efficiency demonstrated by three other enzymes that perform similar reactions with biologically derived substrates (Kino****a, et al). Thus, by this criterion, as well as the others, the enzyme appears to be newly formed.

More recently, another analysis (Ohno, 1984) added further evidence that at least one of the proteins was formed from an essentially random sequence of amino acids. This evidence is a little bit more difficult to understand since its comprehension involves some understanding of how the genetic code works. I'll just have to refer readers who do not have this background to an explanation such as Suzuki, et. al, 1976. It appears that the DNA that formed the gene was somewhat unusual since it could be "read" without finding a "stop" word in any of the three "reading frames." It can be shown that such DNA sequences could easily occur through the well-known process of duplication. The DNA sequence suggests that a simple "frame-shift" mutation could have brought about the chance formation of at least this one enzyme. "Frame-shift" mutations are known for forming totally new and essentially random arrays of amino acids since the code is "read" in a new reading frame. Usually the proteins that are formed by frame-shift mutations are totally useless sequences of amino acids that have no structural, antigenic, or enzymatic relationship to the original protein. This time, however, the new protein was useful. Being useful, it was retained by natural selection and was finally discovered by biochemists who noticed a bacterium that could live on industrial waste.

All of this demonstrates that Yockey (1977a and b), Hoyle and Wickramasinghe (1981), the creationists (Gish, 1976), and others who should know better are dead wrong about the near-zero probability of new enzyme formation. Biologically useful macromolecules are not so information-rich that they could not form spontaneously without God's help. Nor is help from extraterrestrial cultures required for their formation either. With this information in hand, we can wonder how creationists can so dogmatically insist that life could not have started by natural processes right here on earth.


For more on the odds, please read "Lies, Damned Lies, Statistics and Probability of Abiogenesis"

Keep in mind that there are billions of planets, and out of all the billions of years they orbit their star, and out of all the billions of chemical reactions that take place on them, abiogenesis need only happen once.

Something Irrelevant: Even though cells have not been created in the lab, viruses have!


No comments: