We look at these things in a laboratory environment because it allows us to disregard all of the confounders that one finds outside of a lab. But yes, for the adaptation experiment allmendream described, what happens in the lab would be what we would expect to happen outside of the lab.
Are you using bacteria — microscopic, single-celled organisms which do not have either a membrane-enclosed nucleus or other membrane-enclosed organelles like mitochondria — as a proxy for all biological systems in nature, in particular of the most highly complex one we know about, human beings?
It is often very insightful to examine processes in simpler organisms before we look at the process in a more complex organism. We can disrupt processes in simpler organisms that we simply cannot do in higher organisms; we do this because often, the purpose of a metabolic function does not become apparent until we can see what happens when it is absent.
It is not the case that humans are the most complex organism we know about. The respiratory system of birds, for example, is far more complex and efficient than the mammalian system. Plant reproduction is far more complex than animal reproduction.
It appears from what you wrote that the "marching order" signals are all triggered locally. I.e., they are the effects of local causes. For a bacterium, this may be good enuf.
I recall discussing this some time back. All organisms respond to signals. Those signals can be anything, from any source--environmental, from within the organism, or from other organisms of the same or different species. The signals cause a response. The signals should not, in any way, be interpreted as indicative of intelligent involvement. The sun doesn't decide to irradiate you with UV rays; you don't decide to tan or burn or make vitamin D in response. Those processes all happen spontaneously and without thought.
But what happens with the astronomically more complex higher life forms? Do you believe that the behavior of bacteria really sheds light on the organization of these higher life forms? It seems clear to me that such organization can only be accomplished by a non-local cause, one that coordinates and governs the entire system, not just the behavior of the system's components.
Yes, the functions of bacteria behavior do shed light on human functions. In some cases, the functions are the same (respiration of aerobic organisms, for example). In the case of some organelles, studying bacteria is superior to studying eukaryotes: both mitochondria and chloroplasts are bacteria that took up residence inside eukaryotic cells many millions of years ago. They have their own DNA, arranged in a chromosome that still looks more like a bacterial chromosome than a eukaryotic chromosome. Their proteins resemble bacterial proteins.
As for the control of a multicellular system, it occurs at all levels, from the single cell up to the entire body. If a cell needs more energy, it acts to acquire more energy without involving other cells. If an organism perceives danger, the entire organism reacts.
In short, assuming you can do as you claim in the above italics — and I really don't doubt this — what relevance does it have for the understanding of complex biological systems in nature? All the bacteria studies can do is to demonstrate local-cause behavior. It sheds no light on the complexities involved in the organization and governance of higher-order biological systems in nature.
Bacterial studies do far more than that. Metabolic pathways that are similar between bacteria and multicellular organisms can be studied without complicating factors. Bacteria talk to each other and coordinate with each other. Bacteria can be used to produce proteins of higher organisms for in vitro studies that wouldn't be possible otherwise. And so on. When I was doing my PhD research, I was interested in the function of a human metabolic pathway, but I used bacteria, yeast, human, mouse, monkey, and hamster cells, as well as protein extracts from a variety of organs from different species. That is because many approaches are needed to find answers.
Actually it was careless of me to say that "humans are the most complex organism we know about." What I should have said is: the human brain — an astronomically complex, non-locally ordered, distributed information processing "machine" which undergirds all processes of the human mind and its perceptions and thoughts — is the single most complex system in Nature.
"Bird-brains" need not apply for this distinction!
BTW, I did not "make this up." I've been reading the mathematicians engaged in theoretical biology these days. It seems to me that some of Darwin's worst critics are mathematicians. Most of the rest are physicists.
Also I do not know why people think there is any such thing as "junk" DNA.
My reason for wondering is not "scientific," rather "philosophical."
Philosophers of Natural Law theory have long propounded the idea that "Nature is parsimonious," or relentlessly economical. The entire logic of "Occam's Razor" arguably rests on this presupposition.
In short, Nature doesn't "do junk."
What we think of as "junk" may simply indicate something about which we are presently ignorant.
At least, I wouldn't rule that out as a possibility.
Thank you so very much for your series of thoughtful essay/posts (all three!) exDemMom, which I found highly instructive/constructive!