Weighed and Found Wanting
A critical analysis of The Origin of Life - Five Questions Worth Asking and Was Life Created?
Vivid and pragmatic examples of evolution innovating and creating “well designed" biological structures can be found in the constantly changing worlds of viruses and bacteria. Viruses are relatively simple, they are just pieces of DNA or RNA with a protein coat. Viruses latch onto cells, inject their genetic code, and utilize the machinery of the cell to replicate themselves. Viruses are constantly mutating and thereby stumbling upon new ways to infect other cells. This is the reason that a new flu vaccine is required every season; the virus has changed so significantly that the old antibodies cannot recognize it. Similarly, the rapid evolution of HIV has biological systems are very well “designed" by evolution to evade immune systems and multiply themselves.
2.8 Different Perspectives
Some object that these examples are merely 'microevolution' and are hardly comparable to the 'macroevolution' that leads to new species. However, this is a false distinction. Mutation and natural selection only work at one scale, the scale of the genome. To a strand of DNA, the only difference between gaining resistance to a drug and developing some other novel trait is a pattern of nucleotides. Humans are able to view the resulting changes on difference scales, micro and macro, but the distinction is arbitrary. Just as someone is able to walk across a room, using the same method they could walk down the street or even across town. The scale of the observation is different, but the salient action, putting one foot in front of the other, is identical. There is no magical point where walking ceases to become effective for movement. There is similarly no mysterious barrier that mutation and natural selection cannot pass. Whether evolution is shaping a novel virus or a new species, the process is exactly the same.
Though not obvious, it can be understood how a slow, undirected process can create complex and well adapted biological structures. “Creativity" comes from the random mutations. These changes are selected based upon their ability to confer a reproductive advantage to the genome of which they are a part. Over long periods of time, this natural process “feels" out the figurative 'landscape' of survival, snaking around and discovering new genetic patterns that lead to increased survival rates. Complex biology does not just pop into existence by chance, but slowly builds through generations of natural selection. The various parts of a cell work well together because they have developed side by side over billions of years. No scientist claims that these systems appeared out of nowhere by "accident." There is a demonstrable natural process creating these biological synergies. Pages 13, 14 and 15.
Something very different takes in the real world. We have degree regarding complexity. Viruses are wildly mutational. However, that is not true of more complex species. The more complex the species, the more static the genome. Things we learn, about the genetic variability of viruses in reality aren't valid for more complex species. The empirical evidence speaks for itself.
Popular evidence for evolution in a complex species:
http://www.pbs.org/wgbh/evolution/library/05/2/l_052_05.html
Ring Species: Salamanders:
Some critics of the theory of evolution argue that it doesn't convincingly explain the origin of new species. They say that members of one species couldn't become so different from other individuals through natural variation that they would become two separate non-interbreeding species.
One of the most powerful counters to that argument is the rare but fascinating phenomenon known as "ring species." This occurs when a single species becomes geographically distributed in a circular pattern over a large area. Immediately adjacent or neighboring populations of the species vary slightly but can interbreed. But at the extremes of the distribution -- the opposite ends of the pattern that link to form a circle -- natural variation has produced so much difference between the populations that they function as though they were two separate, non-interbreeding species.
A well-studied example of a ring species is the salamander Ensatina escholtzii of the Pacific Coast region of the United States. In Southern California, naturalists have found what look like two distinct species scrabbling across the ground. One is marked with strong, dark blotches in a cryptic pattern that camouflages it well. The other is more uniform and brighter, with bright yellow eyes, apparently in mimicry of the deadly poisonous western newt. These two populations coexist in some areas but do not interbreed -- and evidently cannot do so.
By the time the salamanders reached the southernmost part of California, the separation had caused the two groups to evolve enough differences that they had become reproductively isolated. In some areas the two populations coexist, closing the "ring," but do not interbreed. They are as distinct as though they were two separate species. Yet the entire complex of populations belongs to a single taxonomic species, Ensatina escholtzii.
http://godlessliberal.xanga.com/693669753/the-fallacy-of-the-discontinuous-mindset-and-ring-species/
The Fallacy of the Discontinuous Mindset and Ring Species
These ring species are easy to explain through evolution, but difficult to explain via ID (unless we're assuming the designer wanted to design evidence of evolution).
The ring species is excellent evidence for evolution. It's the kind of thing we expect to find if we think species are evolving. However, assuming a static history of life (as we'd see if life was designed to not evolve), this is completely illogical and antithetical to the concept (unless we counter for some sort of whimsy and mischief on the part of the designer). Of course, if someone has an explanation for this, I'd be more than willing to hear it.
Ring species are easy to explain explain via ID using a substitution model. DNA replication, for biological inheritance, is a process occurring in all living organisms to copy their DNA. This process is "replication" in that each strand of the original double-stranded DNA molecule serves as a template for the reproduction of the complementary strand. Hence, following DNA replication, two identical DNA molecules have been produced from a single double-stranded DNA molecule. Cellular proofreading and error toe-checking mechanisms ensure near perfect fidelity for DNA replication. In phylogenetics, sequences are often obtained by firstly obtaining a nucleotide or protein sequence alignment, and then taking the bases or amino acids at corresponding positions in the alignment as the characters. Sequences achieved by this might look like AGCGGAGCTTA and GCCGTAGACGC.
Assuming AGCGGAGCTTA is a DNA code necessary for reproduction (the complete substitution model would be much longer). If environmental adaptation has impacted the species at the DNA level and the DNA sequence AGCGGAGCTTA has mutated to ATCGGAACTTA, making the Ensatina escholtzii incapable of interbreeding with its common ancestor at the other end of the ring (genetically unidentical), the mutation for all practical purposes was destructive as macroevolution never progresses beyond this point. It would evidently take an intelligent designer to complete the process.
Basically, we are still looking for an adequate demonstration of evolution in terms of being able to produce some sort of novel complex phenotype structure with function based on changes at the cellular level (genetic or epigenetic) from simpler lifeforms. Any test would have to show that the genetic structure wasn't the result of a minor genetic mutation. There are several challenges of degree regarding complexity.
We have degree regarding adaptation. Creationists expect species to adapt to their environments just as evolutionists do. Are there limits to the degree of adaptation? Is the salamander going to develop new structures based on complex cellular changes so that we will no longer recognize it as a salamander (showing progressive complexity)? Or is this example of a ring species the limit of adaptation and genetic drift? If you answer the questions you will have no empirical evidence.
The theory of common ancestry has to show a mechanism to derive complexity from simpler organisms. The superficial explanation in the pdf document is in no way sufficient. Vertebrates are extraordinarily complex at all levels of organization. How did they achieve this? What are the cellular mechanisms?
A whole sequence of mutations would have to be identified and determined along these lines. You can apply any and all scientific methods to this salamander outside its natural habitat and it will still remain a salamander. Species are static and they stay that way.