A few thoughts on TEs

1) Perhaps ecological risk assessment could be performed by looking at the transcriptome or the proteome of a population / sample. If the tscriptome has many non-coding RNAs that resemble TE, perhaps the organism is under stress. Similarly, if an organism is intensively expressing enzymes specific to retrotransposition, that may be an indicator of stress.

Side note: I believe the human body is highly resilient; it is a very intelligent machine. Yes, I am anthropomorphizing, and even though it was made through "tinkering" as Dr. King Jordan would say, I still believe that we live in the "best of all possible worlds."

2) Perhaps (and I know that i have suggested this before), the natural history of an organism could be reconstructed by looking at the type I TE to see how many of each kind exist, and how long each of the TEs have been a part of the genome. This approximate age could be determined by looking at the number of mutations away from a function TE it is in present form. However, it must be taken into account that mutations are almost certainly NOT random. Which brings me to a third idea...

3) Investigating why and how mutations are not random. Does it have to do with the 3-dimensional structure of the DNA (folds and everything)? Does the organism (cell) control if, when, and/or where mutagens can act?

4) Investigate the relative importance of the different means by which organisms deal with stress.

Excerpt from Madlung and Comai, 2004:

Stress, in any form, exerts strong evolutionary pressure on
all organisms. To survive, any organism must develop tolerance,
resistance or avoidance mechanisms. Tolerance
allows the organism to withstand the assault unharmed.
Resistance involves active countermeasures, while avoidance
prevents exposure to the stress.

I believe that it is easy to understand that plants would probably rely much more heavily upon tolerance and resistance whereas motile organisms like animals can take much greater advantage of avoidance. However, if people (humans) engage in behavior that causes the constant and continuous stress, tolerance might have to work overtime. Furthermore, if tolerance (namely the detoxifying mechanisms in the body e.g. the liver) can no longer prevent the degradation of the integrity of the (genomic) individual, then resistance (or other forms of tolerance) might be induced. As a side note, I think that is it very comical that humans consider themselves the smartest of all creation, and yet we are one of the only organisms that (across the board) find the most harmful chemicals, toxicants, etc. and make them habits and lifestyle choices. Most other organisms would "listen" to their bodies and realize that the action that they are taking is harmful and should be discontinued. With that being said, of course the people who put their bodies under greater stress will have the greater amounts of Transpositional events occurring in their DNA.

4b) With this in mind, I note that twins can be identical, even in their DNA, but have vastly different expression patterns for certain (very important) genes. (As a side note for myself, I have found it helpful to think of identical twins when thinking about gene expression and TE and stressors and DNA's 3-D structure.) Even if a scientist had the economic resources to perform a complete sequencing of the two genomes, it may be found that not a single mutation occurs in a gene-coding region. And still, the gene expression would be vastly different; perhaps because of DNA's 3-D structure; epigenetic control.

5) Furthermore, I feel as though I have just had an epiphany! Oh happy day! I have just synthesized a postulate that flies in the face of modern genetics. Genetics 101 claims that inheritance of acquired traits is utter non-sense and only happens in the rarest of cases. But what if inheritance of acquired traits is essential and very beneficial. I have an idea of how it could happen, but suffice it to say that expression of most (if not all) genes is affected by the structural formation taken by the DNA. The DNA takes it 3-D, tightly packaged shape from many smaller structures whose location and structure is intimately associated with the precise base pair sequence that the DNA has. What if stressful events modified the DNA (a mutation occurs); as a side note, the mutation could be exogenously (biotic or abiotic) induced or there may be some internal controls within the cell that 'cause,' 'select for,' or 'allow for' mutations to occur in a very specific place. The said mutation occurs not within any coded gene, rather, the change in nucleotide leads to conformational changes of the 3-d structure of the DNA, leading to epigenetic up- (or down-) regulation of specified genes.

Just a rant - there needs to be a faster and cheaper way to extract the entire transcriptome from a cell. Why don't you work on that, Kevin?