General Observations on the ‘Reasons to Believe’ Website
I thought I would pick up the gauntlet Shayla threw down and tackle one of those articles on the Reasons to Believe website. The strategy used by its contributors is to make claims against evolution which sound good to the less-than-knowledgeable but do not stand up to scrutiny by anyone with a good working knowledge of biology. In other words, the strategy is about making the position to which they are opposed look like it falsifies itself to make it seem that their own position is consequently enhanced. Setting aside for the moment that every attack on evolution that I read on this website was disingenuous, this strategy is just another instance of the false dichotomy – show the other guy wrong to make me look right even though there may be another possibility. To impress me requires positive evidence in support for their position, not negative. Other tactics include the usual ‘God-of-the-gaps’ inanity that I’m sure we all tire of. This intellectual dishonesty is ubiquitous throughout the articles on this website.
I noticed in several articles ‘debunking’ evolution a common thread: take what Stephen Gould said about rewinding the tape of life a little too far. Gould presents the idea in his popular book on the 80 million year Cambrian so-called explosion, Wonderful Life, that if the tape of life is rewound and played back evolution would take a different path. This is because evolution is a chaotic system in the mathematical sense. Note that this does not mean randomness:
I am not speaking of randomness, but of the central principle of all history—contingency. A historical explanation does not rest on direct deductions from laws of nature, but on an unpredictable sequence of antecedent states, where any major change in any step of the sequence would have altered the final result. This final result is therefore dependent, or contingent, upon everything that came before—the unerasable and determining signature of history. ~ Stephen J. Gould
In other words, we would get a different set of species along the evolutionary tree each time the tape of evolutionary history was rewound. What the contributors to this website believe is that this means that evolution can not arrive at the same solutions to problems of survival. One article claims that the concept of historical contingency in evolution means that various genera of flightless birds is a problem for evolution because the same pathway in a gross sense has been reinvented.
The problem with this logic is that evolution can arrive at a solution to the survival problem in more than one way even if superficially it seems to be the same solution in the gross sense. In the case of birds, they became flightless. But did they become flightless in the same manner? This is highly unlikely and certainly different environments will create a variety of selection pressures. But there may be very different reasons why different genera of birds become flightless, thus arriving at similar solutions to different problems. Indeed, it may be as simple as a relaxation of selection pressures pushing for better flying skill.
In the ecological niches flightless birds occupy, becoming flightless is what Daniel Dennett describes as a ‘good trick’, the same solution arrived at from different angles. There are many such ‘good tricks’. I think the evolution of the eye is a prime example. Indeed, the selection pressures are so strong for development of the eye that it has evolved has arrived at about 35 different times in the history of life on this planet!
But wait! They’re still eyes, right? Sure they are, but they are structurally-speaking completely different. Once a light-sensitive cell evolves, development of the eye follows rapidly. But this is not at all a problem for evolution and I fail to see the relevance of the argument. Evolution is dependent on historical contingency. That is, it works on what has happened in the genome to this point. The misguided (the most gracious word I can use) claim that evolution can’t arrive at the same solution to survival problems is a totally artificial and arbitrary barrier. Every time this canard is used in the articles on the ‘Reasons to Believe’ website they make the same mistake: an eye is an eye is an eye. But this is just not so.
An Instance of Historical Contingency Observed in the Laboratory
I’ve written on my own blog (Shamelessly Atheist - perhaps I should change it to ‘Shameless Self-promoter’) on the observation of the ability of E. coli to suddenly utilize citrate as an energy source by Richard Lenski. Published in the Proceedings of the National Academy of Sciences, the work has received more attention from the anti-evolution crowd than I have ever witnessed outside of The Origin itself. The infamous creationist lawyer Andy Schlafly, creator of the somewhat less-than-objective version of Wikipedia, Conservapedia, objected strenuously to the conclusions of this experiment and in a comical farce has tried to obtain the original data for the experiment I will be describing presently. But you can read about that in my blog on the matter.
For the last 20 years Lenski and his students have been growing bacteria (starting from a single bacterium and creating 12 lines) and periodically freezing samples (every 500 generations or so) to see if these bacteria evolve in the lab. At the time this paper was published, over 44,000 generations had passed.
Periodically, the frozen ‘fossil’ bacteria can be thawed and DNA compared over time. Since the bacteria are cloned and reproduce asexually, only natural selection and genetic drift can act on the gene populations, the analysis is greatly simplified. Previous to this paper, changes in growth rates, reduced lag phases when the bacteria were transferred to a fresh culture medium, reduced peak population densities and larger cell sizes relative to their ancestors were reported. Most populations evolved increased DNA supercoiling.
So, as expected, things changed over time. But something new happened that surprised the researchers. Under normal circumstances, E. coli does not take up citrate and use it as an energy source (rare cases have been reported where populations of E. coli have acquired a plasmid from other citrate-using bacteria allowing them to do so, but this could not have happened in this experiment), but they do secrete it into the medium. Thus, one would expect that bacterial populations which could take up citrate would have an advantage over the wild type variant which can not. Lo-and-behold, after 31,500 generations one of the populations suddenly developed the ability to uptake citrate and the gene which allowed this very rapidly spread throughout the population. But this Cit+ variant did not make the Cit- one extinct within the population, but coexisted with it.
The Cit+ variant could not be the result of a single mutation. Why not? Because the number of generations passed, coupled with the rate of DNA copying errors, would result in more mutations than the number of base pairs in the entire genome (4.6 million bp’s) of this strain of E. coli. Thus, if a single mutation imparted this kind of advantage, it would have manifested itself long since.
Two competing hypotheses were tested: the first - that Cit+ arose through a rare mutation, one that does not scale with typical mutation rates; the second - the mutation is ordinary, but the expression is contingent on prior mutations in the population. It is tempting to speculate that this is exactly what occurred with the development of a nylon-eating strain of Flavobacteria. In this case it was a duplicated gene coupled with a frameshift mutation.
The long-term evolution experiment design allowed the researchers to attempt something that Stephen Gould suggested couldn’t happen - to rewind the tape of life and watch the same course of evolution happen. Thawing out samples of the ‘fossil’ bacteria, they repeated the same experiment with that bacterial line. Samples from the 20,000 generation mark became Cit+, whereas samples from before 20,000 generations had passed did not repeat this fete! Thus, some mutation happened that prepared the way for a particular line to become a Cit+ variant. It did not in and of itself cause the bacteria to become Cit+, but was a necessary condition for it to happen and greatly increased the chances that the bacteria in that line would go on to become Cit+.
The results of their experiments suggest that it was not one, not two, but three mutations which occurred to produce the Cit+ variant. The first, as noted, occurred around 20,000 generations. The second at around 31,000 generations (which, in fact, slowed citrate uptake). The final one was at 33,000 generations. Finding the mutations themselves an active area of research in Lenski’s laboratory.
’Reasons to Believe’ Critique
According to the author of the article on ‘Reasons to Believe’ entitled Inability to Repeat the Past Dooms Evolution,
The experimental demonstration of historical contingency in E. coli raises significant questions about the validity of evolutionary explanations for life’s origin and history. Even though evolution shouldn’t repeat, it appears as if it has numerous times at a biochemical level and an organismal level.
I’ve already gone over why this is not true, and it certainly doesn’t bother Lenski one bit. There is nothing to say that after the tape of evolutionary history has been rewound, as was ingeniously done by Lenski and his minions, that evolution can’t produce the same result, particularly in the short run. It is simply unlikely to do so. But even this has to be qualified since the likelihood of history repeating itself is going to also be determined by the strength of the evolutionary pressure causing the genetic changes. The stronger the selection force (and it would be very strong in this case), the more likely the ability to utilize citrate as an energy source will recur.
In fact, it was only those bacterial populations where the first of the three mutations occurred that repeated the ‘good trick’. This indicates a genetic drift phenomenon, where a benign mutation can propagate through a population in the absence of natural selection. In fact, a benign mutation can only do that or disappear altogether and is a very important mechanism of gene propagation.
Contrary to the author’s assertion that
Biological convergence not only questions the validity of biological evolution, it points to the work of a Creator,
biological convergence is predicted by evolution, particularly when there are strong selection pressures and many examples this phenomenon are known. What is also predicted is that the species which show convergence will be the same every time the tape is run. This is what Gould was driving at, not that instead of eyes there would be some other light-sensing organ. Eyes are just too good at what they do to not have evolved numerous times independently. But just because H. sapiens has eyes does not mean that we would evolve again (let alone specific instances of H. sapiens like you and I) if the tape is replayed. The idea that convergence (a well-known phenomenon in evolutionary biology) falsifies evolution is as bizarre as it is wrong.
At the end the author of this nonsense pulls out the poster child for ID – the bacterium flagellum – and the microevolution-isn’t-macroevolution canards. The distinction between micro- and macroevolution is again semantic and arbitrary. A lot of microevolution will produce new species. But I’ll save those for other entries. However, if you can’t wait to find out exactly how the flagellum evolved, you can view the spoiler here.
Sorry. Another shameless plug, wasn’t it?