James Linzel's List: Evolution: Transitions, Genetics, Evidence

• • It is very important to understand the difference between these terms to understand the main purpose of the article.
    a [perhaps not 100% accurate meaning] monophyletic refers to a trait shared within a single phylum with a common ancestor. Suggests a single evolutionary event.
    polyphyletic refers to a trait which is found between multiple phyla. Suggests multiple evolutionary events.
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• evolution is about populations, so many changes go on in parallel; selectable traits are usually the product of networks of genes, so there are rarely single alleles that can be categorized as the effector of change; and genes and gene networks are plastic or responsive to the environment. All of these complications make the actual story more complicated and interesting, and also, perhaps to your surprise, make evolutionary change faster and more powerful.
• Mutations are usually negligible changes that get tossed into the stewpot of the gene pool, where they simmer mostly unnoticed and invisible to selection
• Waddington noted that fruit flies expressed the odd trait of developing four wings (the bithorax phenotype) instead of two if they were exposed to ether early in development. This is not a mutation! This is called a phenocopy, where an environmental factor induces an effect similar to a genetic mutation
• The curious thing is, though, that the more elaborate the network, the more pieces tangled into the pathway, the smaller the effect of any individual component (in general, of course)
• The system is buffered to produce a reliable yield.
• Combine this with population effects. The population can accumulate many of these sneaky variants that have no significant effect on most individuals, but under conditions of strong selection, combinations of these variants, that together can have detectable effects, can be exposed to selection
• Everything is fluid. Biology isn't about fixed and rigidly invariant processes — it's about squishy, dynamic, and interactive stuff making do

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• In mammals, they help break down complex polysaccharides which we can then absorb through the wall of the digestive tract — these are compounds that would be simply lost without bacterial assistance. Even more dramatically, termite guts contain colonies of bacteria that produce enzymes to break down cellulose. Another insect, aphids, live in plant saps which have negligible protein components, and they rely on gut bacteria that can synthesize nine essential amino acids. One cool feature is that the bacteria can't complete the synthesis of leucine; the last step is carried out by aphid enzymes. The synthetic pathway is split acros two different species!
• it appears that the bacteria are actually regulating the growth of the gut lining.
• The intestinal lining arrests its development and fails to fully differentiate; the lining also grows much more slowly. They also have difficulty absorbing some nutrients. Add bacteria, though, and growth and differentiation resume
• . This is a case where the developmental program and the bacterial influences are interdependent, and it makes sense — they've co-evolved.
• The very best example of a developmental dependence on bacteria, though, is in squid. The bobtail squid has a light-emitting organ that relies on colonization by a luminescent bacterium, Vibrio fischeri. The animal gleans the bacteria from the water with a special ciliated epithelium and secreted mucus that seems to be just the right flavor for Vibrio, and the bacteria migrate deep into the light-emitting organ. Once colonized, the squid dismantles the harvesting cilia and downregulates the secretion of mucus. If no bacteria of the right species are present, it maintains the cilia. If the bacteria in the organ die, resumes mucus production.
• there are regulatory interactions between genes in a single cell that establish cell-type specific patterns of gene activity; all express a common core of genes, but different cell types, such as a neuron vs. a cell of the digestive epithelia, will also have their own unique special-purpose genes switched on
• cells are in constant negotiations with their neighbors, mainting a common pattern of expression within a tissue, and defining interacting edges with other tissues. Cells are continually sending out messages about their state into the system and responding to local and global signals
• we have to think in terms of networks of species that cooperate in the development and physiology of individual multi-cellular organisms

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