benefit of (the) evolution (model)

A while back, I posted a query regarding the usefulness of the evolution model. While much of the discussion was off topic, I did get some leads out of it which I subsequently investigated, so here is a followup. The post is long, so if all you care about is the arguments, skip down to them.

What I care about: This is an argument on why the evolutionary model of life is practically useful as compared to an ID model. In other words, how the following model of the tree of life:

EV:      A
        / \
       B   C
      / \   \
     /  D    \
    E         F
   / \       /
  G   H     I 

has been useful in ways that the following model is incapable of:

ID:  A     B      C
     |     |     / \
    / \    |    /\  \
   |   |   |   /  \  \
   A' A''  B  C' C'' C''' 

Please avoid arguing about the scientific merits of these models - I am interested in the practical merit. I am also not interested in arguing against other variations of ID such as guided evolution or artificial abiogenesis or creation of the universe. Those are largely irrelevant to the public controversy for the time being.

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The arguments here are intended for the layman, because to those outside scientific professions, much of the public controversy is opaque in the scientific sense. People don't care about models, or what is science, etc. However, people do care about what works, and here, I try to go into that direction of argument in the hope that this could prove useful to others when speaking to ID proponents.

Inadmissible arguments: There are various applications I discarded. Almost everything to do with single-celled organisms was unacceptable because proponents of ID generally agree that microevolution happens (the distinction between micro and macro evolution is not something most scientists agree with, but this is not meant to be targeted at scientists). Second, areas for which evolution was a motivator, but not necessary (such as understanding the genetic code), did not fit my criteria, because that research could have been motivated by ID theory.

In essence, I was looking for research which depends on the model of common descent (beyond that within a species) and for which there have been real world applications. I was also particularly interested in applications which were not already commonly discussed.

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Arguments:

So, here are real world applications of the theory of common descent.

1) Treating long-term genetic defects:

Given the EV model above, a genetic defect can be introduced at some point and propagate to its children. Then, if we notice a defect among several modern animals (e.g. G and H), it is possible to do a search across species to localize when this problem was introduced (if it occurs in G, H and D, it could have originated at B), identify where in the genetic code it is (by comparative genetic analysis), and how to circumvent it.

This was used in the investigation of an absence of an enzyme that produces ascorbic acid. This lack is the underlying cause of scurvy. The (previously thought to be human-only) disease was found in a guinea pig around 1907, which caused a search which found the defect to also occur in some monkeys, but not other mammals. Further searches narrowed down the boundary, which led to an estimate of where and when the defect originated in evolutionary history. This helped explain why the disease exists. Examining the lifestyle of the species affected by it changed the accepted ideal doses of vitamin C. Further: knowing which species are similar but do not have the defect can allow it to be removed from human genetic code in the future. (Just think - our progeny may no longer need to eat those healthy fruits and vegetables.)

This area of research is nonsensical if you do not believe in common descent. A design would either have the defect or not - so either all the animals would be affected or they would not be. A subsequent mutation could cause some of the animals to have the defect, but it would not be grouped within evolutionary history by a common ancestor. Therefore, the line of inquiry would not have been pursued, and the medically helpful information would not have been discovered.


2) Understanding and modeling protein folds:

Currently, one of the most difficult problems in biology is mapping genetic function, typically by finding out how a gene maps to a protein. Understanding this is key to figuring out solutions to genetic problems. This has been extremely challenging because of the complexity of the models involved, and there has been no way to simulate protein structure based solely on the genetic string.

Recently, however, there has been some success in identifying key genetic elements by comparative genetic analysis. The genetic strings that represent similarly functioning proteins within various animals are compared. Based on the evolutionary distance between the animals, it is possible to analyze which parts of the genes change quickly, and which change more slowly. (If you compare G, H, and D above, then there is more 'distance' between G and D than between G and H, and knowing the common ancestor allows the estimation of rate of change.) The genes that change more slowly are the ones that are more key to the way the corresponding protein folds and functions. Using this method, it has been possible to isolate gene sequences commonly responsible for folding, which resulted in some success in predicting via simulation what a protein looks like based on the gene sequence. (Jonathan A. Eisen and Martin Wu, 2002. "Phylogenetic Analysis and Gene Functional Predictions: Phylogenomics in Action", Theoretical Population Biology 61)

Again, this is an area of research that is nonsensical with the ID model. There, the genetic distance between species is absolute - based on the original design plus mutation since then, so there is no way to get a sequence of gradually diverging gene sequences and no reason to pursue this line of inquiry.

3) Finding functional genes / Filtering out 'noise'

An extension of the above is that beyond just understanding protein folds, it is possible to gain a lot of understanding of the functionality of genetic segments by seeing how much and how quickly they tend to change. DNA segments which change rapidly and randomly tend to be non-coding or noncritical. Segments which change very slowly typically represent important functionality. Moreover, genes which are selected for more rapidly than chance would suggest (the mutation rate does not change, but the gene's shift in a population can and does) may be ones which represent functionality that is being selected for. An example of this is the FOXP2 gene, which was discovered to have changed very rapidly in humans in recent (in terms of evolution) history. The gene turns out to be critical to the development of part of the brain, and it is believed that its rapid change is what helped humans develop language. (Anyone have examples of noise being filtered out / or genes thought to be noise found out to be functional after such comparison?)

4) Assessing vestigial structures:

If the common descent model is accepted, organs whose function is unknown can be assessed through comparative anatomy, and we can decide whether or not it is harmful to mess with certain parts of our bodies. In humans, the appendix, wisdom teeth and coccyx are fairly commonly removed when they cause problems. It is understood that it is safe to do so because we understand the origins of the organs, and thus their lack of functionality. If the common descent model is not accepted, we do not have that rationale for removing these organs, so would not so lightly be able to proceed with such surgeries. In that way, the evolution model is medically useful. (The converse is true: we can understand functional organs through comparative anatomy, but this meshes with template reuse in ID theory, so is not a good argument.)

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Discarded arguments: These are some examples I discarded as not being sufficiently strong. If there is a way to strengthen any of them, that would be great, but for now, I think they will be easily taken apart by a someone prepped for them or someone of reasonable intelligence.

• Genetic algorithms: The idea of evolution has been used extensively in programming. This shows that evolution is a powerful and effective model, and demonstrates its plausibility, but just because something can work does not mean it happened, so it is not a good argument for biological evolution.
  
• Evolutionary psychology: Evolutionary psychology has been a highly hyped notion, and may go a long way to explain certain aspects of human behavior, but I have not found any studies that show it being immediately useful, other than possibly subjectively to individual patients (which is a weak argument).
  
• Genetics: Modern genetics was largely prompted by evolution. Trying to understand how traits are passed on and change is what prompted Gregor Mendel's research, but this work would still have been done at some point even with the ID model, since traits still get passed down. On the other hand, there would have been no case for the assumption that all organisms share the same or similar genetic structure, so the work may have been adversely affected/delayed.
  
• Ecology: You can use the idea of evolution to understand and aid response to things like invasive species. However, this can generally be done via observation/common sense, so the degree to which the idea of evolution is helpful is unclear.
  
• Interpolation: Given some set of organisms with desired traits, we can estimate where in the evolutionary tree the trait originated, and then be able to identify other organisms which would likely share the same trait. I have not found any actual uses for this, however.
  
• Diseases/Pathology: Practically every aspect of modern disease research, including things like forensics using genetic comparison, requires an understanding of evolution. However, as stated above, ID proponents reject this being evolution... annoying, but true.

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Discuss:

For those who actually made it through all that, a few questions. Do you think these arguments are/would be effective, particularly when talking to a layman? Could they be made better, and how do they compare to the typical arguments from the nature of science? Given the examples, can you think of other ways the model has been used?

For those who favor ID theory, do you have counter arguments to these points? Are there weaknesses here that were not listed?

Thanks to those who made suggestions in the aforementioned thread, and below, particularly lowk for a sequence of references, tom_kbel for various suggestions below, and scorpy1 for the ascorbic acid article.