Stephen BERNATH[1]

Four billion years of evolution gradually added thousands of genes to a primordial single-celled organism to produce the wide variety of life today. This article presents evidence that, along with mutation, natural selection, genetic drift, and lateral gene transfer, design was also involved. Although previous design arguments are flawed, by studying these flaws we are led to a valid one. This article is a summary of a long technical one, which is available on request.

Some bacteria swim with the help of an intricate motor and propeller made of more than 60 different kinds of proteins. The motor plus propeller is called a flagellum. Torque is generated when systematic movements of the stator proteins MotA/B push against cams of the rotor protein FliG (Blair, 2006; Yakushi et al, 2006; Braun et al, 1999).

Bacteria have thousands of other proteins, some of which are very similar to flagellar proteins. In particular, the «Type III export system» for injecting molecules into other cells is strikingly similar to the flagellum. In fact, not more than four mutations may be all that’s needed to transform it into the flagellum: one to make its needle long enough to function as a propeller (Macnab, 1996); one to make this needle helical since a straight needle provides no thrust (Macnab, 1999; Mimori-Kiyosue et al, 1997; Macnab, 1996); one to create a cam similar to that of FliG (Braun et al, 1999); and one to create MotA/B. Since MotA/B are similar to ExbB/D of the outer-membrane-transport TonB organelle and TolQ/R of the outer-membrane-stability Tol-Pal organelle (Kojima and Blair, 2001), either of these organelles could have been a source for MotA/B.

Note that, except for MotA/B, all proteins needed for the first flagellum could have been obtained from the Type III injection system. Although the flagellum predates the extant Type III injection system, the possibility that this system and the flagellum both evolved from an earlier Type III system can not be excluded (Macnab, 1999).

What is the probability of these four mutations? Many studies have explored the effects of deleting various combinations of the genes responsible for DNA proof-reading and repair. These studies found that the maximum mutation rate per generation per gene for extant bacteria is 10^-3 (Marcobal et al, 2008). This is the rate in bacteria undergoing extreme hardship, such as starvation; when released from such duress they return to their normal mutation rate of 10^-6 per generation per gene. Mutation rates for animals and plants (whether normal or under duress) are never greater than those for bacteria. This will be useful later when describing human evolution; by using bacterial rates we will be giving the benefit of doubt to the chance hypothesis. The probability that these four mutations occur simultaneously is 10^-3 multiplied by itself four times, which equals 10^-12. This is the probability of the appearance of the first flagellum. Since 10³⁰ bacteria fit into a global ocean 10 kilometers deep, and a billion years allows 10¹³ generations of a bacterium that divides every 20 minutes, the number of genetic trials available for flagellar evolution on earth could have been as high as 10⁴³. When the number of trials is equal to or greater than the reciprocal of the probability, the event is expected to have occurred simply by chance, without design being involved.

Design proponents often declare that the modern version of a system is the simplest possible form of that system that works. Often we hear that the modern flagellum is «irreducibly complex,» but the references cited in this article indicate that major portions of the modern flagellum can be removed and the remainder still has some selection advantage. For example, even if the entire motor is deleted, the remaining structure is useful for injecting molecules into other cells, as demonstrated by the fact that bacteria have such structures. Some modern flagellar proteins are redundant, such as three of the four rod proteins. The protein that breaches the peptidoglycan layer, FlgJ, is not absolutely required because, due to the porous nature of this layer, the rod sometimes penetrates it without FlgJ (Nambu et al, 1999). The L and P rings are expendable since bacteria lacking these rings are still mobile (Ohnishi et al, 1987). The hook may be expendable for a bacterium with a single flagellum in a viscous medium where shear forces would not destroy a hook-less flagellum. If dozens of proteins involved in motor control are deleted, the resulting uncontrolled motor and propeller might still be an advantage for bacteria in a narrow channel with a glucose gradient if they are swimming towards a greater concentration of glucose.

Other organs have been made the basis of design arguments but, in every case I have seen in my 25 years in this field, they have the same defects.

Further research may reveal a lower probability for the appearance of the flagellum. For example, it may turn out that more mutations are required to create MotA/B and FliG. Since the nucleotide sequences of the genes encoding MotA/B and ExbB/D are known, one could figure out the minimum number of mutations required to transform ExbB/D into MotA/B. The same can be done with FliG. Another area for research is that more mutations may have been required to enable MotA/B and FliG to recognize each other in such a way that other proteins in the cell could not bind to either MotA/B or FliG since this binding would abolish motor function. These two considerations raise the possibility that I used a mutation rate that is too high. The value of 10^-3 means that the mutation could have occurred anywhere in the gene, but it may be that the mutation needs to be more precisely targeted to create minimal function. A typical gene has over 1000 nucleotides, and the value of 10^-3 allows the mutation to strike anywhere in these 1000 nucleotides. Needed interactions between proteins often require that they have a particular orientation. Creating this orientation usually requires mutations that target specific regions within a gene. If a mutation must target a ten-nucleotide region within a gene having 1000 nucleotides, then the probability of that mutation is 100 times smaller than the 10^-3 value I used above. Thus, some of the mutations required to create the flagellum are likely to have occurred at a rate of 10^-5. Another area for research is the evolution of the first type III export system.

Since previous design arguments have failed, consider a new argument: A modern bacterium has around 3,000 protein-coding genes, and man has at least 18,000 protein-coding genes (Segal et al, 2008). We share 50% of these genes with bananas, over 80% with mice, and 99% with chimpanzees. Thus, at least 15,000 protein-coding genes must have been added during the course of evolution from a primordial single-celled organism to man. A new gene appears by modifying an existing gene. The bare minimum number of mutations required to create a new gene is 1. From now on we will assume that one mutation was sufficient to create a new gene useful for evolution to man. After a new gene appears in an individual, the rate at which this gene spreads throughout the population depends on how beneficial it is to this individual, as well as how beneficial other genes in that individual are relative to the rest of the population. Even a very beneficial gene will spread very slowly or not at all if it is in an individual whose overall genetic makeup is much less fit than the average. Conversely, an inferior gene can become prominent in the population if it is in an individual whose overall genetic makeup is far superior to the norm. The phenomenon in which an inferior gene rises to prominence by virtue of its association with other genes that happen to confer a fitness advantage is called «hitchhiking» in the science known as population genetics. The probability that a new gene was created by a mutation and subsequently spread throughout a population is obviously less than the simple probability of its creation by a mutation. Hence, by simply using the probability of its creation by a mutation (which is 10^-3 or 10^-5 as discussed earlier) in the following discussion, I will be giving the benefit of doubt to the chance hypothesis. So, in the highest-probability scenario, the probability of the evolution of man is 10^-3 multiplied by itself 15,000 times, which equals 10^-45,000. Using 10^-5 yields a probability of 10^-75,000 for the evolution of man.

Would these probabilities be significantly greater if, during the course of evolution, extensive lateral gene transfer between dissimilar organisms had occurred? Although such gene transfer was involved in prokaryotic (bacterial) and single-celled eukaryotic (more advanced) evolution, it does not appear to have played a significant role in the evolution of the multicellular eukaryotes leading to man, such as amphibians, reptiles, mammals and primates (Andersson, 2005; Kurland et al, 2003; Salzberg et al, 2001; Kurland, 2000). Even if it had played a significant role, it is not clear it would have increased the probability of the appearance of man, since the donated genes must have undergone an evolutionary process in the donor organism, and the probability is very small that the donor organism just happened to encounter, and then successfully transfer, the needed genes into a suitable receiving organism. Keep in mind that genetic exchange between dissimilar vertebrates is not as simple as it is between bacteria, which have a special organelle for this, namely the pilus. Even if special environmental conditions led to the rapid appearance of genes useful for making human beings within, for example, different mammals, the probability is very small that these mammals (who are from different species and so can not mate with each other) happened to be in the right place at the right time to exchange genetic material. Keep in mind that organisms do not maintain for long periods of time functional versions of genes that are not useful for them. It appears that suitable donors and receivers need to meet at the right time, which requires events of very low probability.

To avoid design, 10^45,000 evolution-supporting planets must exist, which requires: (A) a single large universe with that many planets, each of which exhibits some stage of evolution from the primordial soup up to man, or (B) nearly that many small universes, each of which has a few such planets, or (C) a small universe with a few such planets undergoing nearly that many Big Crunches and subsequent Big Bangs. Regarding (A), only a few hundred extra-solar planets have been detected so far. Since it becomes more difficult to detect a planet the further from the earth it is, we can safely conclude that there is no way that even an insignificant fraction of 10^45,000 evolution-supporting planets will be detected within the next few decades. The speed at which light reaches us and the speed at which electrons move through semiconductors in our computers impose fundamental limits on the speed at which even the best equipment can operate. Suppose this equipment can identify a new planet every pico-second (10^-12 seconds), which is an outrageous rate far beyond present or conceivable technology. This still means that we must wait 10^44,980 years to identify the number of planets needed for the chance hypothesis. Regarding (B), the unambiguous detection of a few other universes is presently considered difficult work, if it can be done at all, not to mention observing life on planets within those universes (Aguirre et al, 2007). Even if we had equipment capable of identifying a suitable planet in another universe every pico-second, we would still have to wait 10^44,980 years to verify the existence of the number of evolution-supporting planets required for the chance hypothesis. Regarding (C), even if each pico-second we could verify that our universe had, in the past, undergone a cycle of Big Crunch and subsequent Big Bang, we would still have to wait 10^44,980 years to verify the existence of the number of cycles required for the chance hypothesis. This means that the chance hypothesis is effectively unverifiable. Unverifiable hypotheses are scorned in science and quickly discarded when a verifiable hypothesis arrives. Hence, if there is a verifiable way to contact the designer, then the design hypothesis is superior to the chance hypothesis. Such a way, known as bhakti-yoga, is described in great detail in Bhagavad-gita and Srimad-Bhagavatam. I recommend the translations of these books by Bhaktivedanta Swami Prabhupada for clarity.

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