This post is not a breakdown of a paper, but purely an opinion piece based on my own views. I'd love to hear any different opinions people have, feel free to leave them in the comments box.
Definitions of scientific theory can vary slightly (usually depending on the theory the person currently making the definition has in mind) but they tend to boil down to a few basic elements. Explaining observational data, creating a model, falsifiability and predictive power are some of the most usual phrases used. The idea of the predictive power of a theory is an important one, both because it's a good way to make a distinction between a theory and an observation and because it imparts some kind of real-world use to the science.
One of the criticisms of the Theory of Evolution is that at first glance it appears not to contain any appreciative predictive power. You can trace the evolutionary lineage of a horse, or a whale (or a staphylococcus bacteria if you are so inclined) but you can't make any predictions about what they're going to turn into next. What strange creatures will be walking the earth in five thousand years time is occasionally brought up on random TV shows but there's hardly a way to test the accuracy, and it's not exactly science.
However this criticism seems to be conflating 'prediction' with 'predicting the future'. Very few scientific theories can predict the future. Mendelian theory can predict the likelihood of future outcomes, and I'm lead to believe that Newtonian physics can predict planet orbitals to a certain extent (provided you nudge mercury sideways occasionally) but generally the predictive power of a theory can be used to provide explanations for observations without needing to try and head into the future at all.
To use an example from my current revision: chloroplast gene movement. Chloroplasts are little organelles in plants that carry out photosynthesis and contain the green-coloured pigment that makes plants look mostly green. They are thought to have arisen (and there is by now lots of substantive evidence for this) when a free-living cell engulfed a little photosynthesising bacteria (image below taken from George Washington University page explaining eukaryote evolution):
As the little photosynthesising bacteria contained its own DNA the new chloroplast containing cell now has two genomes, the one in the nucleus and the one in the newly-made chloroplast (ignoring mitochondria for the minute to make things simpler). However when you look at modern plants and compare the chloroplast genome to any bacteria genome you can see that the chloroplast genome is massively reduced. Most of the genes have been lost. Further research will identify several of these chloroplast genes inside the nucleus. The genes have migrated out of the chloroplast, and into the nucleus, where they are being expressed by the nucleus.
There's plenty of reasons why the genes would want to be in the nucleus. It provides centralised control, it keeps the DNA safe from all the reactive oxygen species in the chloroplast, and it means that the chloroplast genes can experience sexual selection. However not all of the genes have left. Some have remained inside the chloroplast, and the question is, why? If the nucleus is such a good place to be, why do some genes get left behind?
In answering this (in fact in answering many question here, including why the genes left as well as why some remain) the theory of evolution can be used to provide a predictive framework in which to suggest an answer. These predictions can then be tested with the data to see which ones fit. In the case of why genes remain in the chloroplast, for example, our theory tells us that if there is a reason (they might just have remained through chance if it was one event that transferred the genes, or they might still be moving) it will be to give the cell an evolutionary advantage. These are genes, and there is a lot of selective pressure on what happens to genes, especially in bacteria, which have a limited supply. The genes that stay behind must provide a selective advantage, there must be a reason why these genes help the chloroplast, and the cell to survive, better than they would if the genes moved to the nucleus.
Once in the nucleus, the genes are used to make the corresponding protein, and this protein is then transported back into the chloroplast. In view of this, one of the first suggestions made was that the genes left behind coded for big bulky proteins that were hard to transport through the chloroplast membrane. Chloroplasts that lost these genes would loose valuable proteins, leaving them at a disadvantage. It's a nice prediction, but unfortunately it got shot down after a close examination of the genes that had actually moved revealed that some of them did code for quite big bulky proteins. And artificially moving some of the bigger and bulkier protein-coding genes into the nucleus showed they could get back into the chloroplasts quite happily, although not quite as efficiently.
Another prediction made (which is looking far more likely) is that the genes left behind very specifically control the redox potential (the balance of positive and negative ions) inside the chloroplast. Due to the photosynthesis the chloroplast is carrying out, the redox potential can change quite dramatically (and regularly) and it needs to be sorted out quickly if it does, as it has the potential to cause a lot of problems within the chloroplast. Having the genes that need to respond to redox change in the nucleus means that a) it takes a lot longer for the signal to get to the nucleus and get the proteins made and b) once the proteins are made they will be sent to all the chloroplasts, despite the face that different chloroplasts will be in different redox states. So far the evidence supports this prediction.
Without the theory of evolution behind this, there's almost no reason to look for a reason. Why the genes moved, and why some stayed behind can be answered by 'they just did'. The framework of an answer that requires an increase in the 'fitness' of the resulting organism helps to give suggestions, and predictions, that can be looked into with further study and gives a focus for directed research.
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