In the Paris EvoDevo meeting that we attended a couple of weeks back, one speaker was the developmental biologist Scott Gilbert. Scott spends his time between Swarthmore and the University of Helsinki, and is the author of the world's foremost text on developmental biology but is also author of a long list of books and articles that put the subject in its historical context.
One point he's been making recently, as in his Paris talk, is that there has been too narrow a focus recently on genes as essentially the only cause of development or its evolution -- genes are not all that's inherited in life. Environmental effects of various kinds can be inherited in different ways, too. Some developmental biologists criticize this message for being 'anti-genetic', but Scott does his own genetics work, and certainly doesn't dismiss its importance. His examples certainly do not undermine genetics, but simply show, convincingly, that other factors contribute to development and evolution.
We pointed this out in our book Mermaid's Tale as well, and in fact plasticity -- varying responses to environmental factors during development -- was a major theme of the EED meetings. Our gut bacteria (E coli) are vital for survival, and newborns are 'infected' from their mothers or their environment. Gilbert provided numerous other examples. Some fly eggs receive bacteria (Wolbachia) that are needed for their proper gene expression and development (as in the image to the left; Credit -- without that, the egg dies. Maternal uterine conditions can cause fetal gene expression that affects the baby for its whole future life, in terms of things like obesity and blood pressure.
In this sense, laboratory organisms may be in such artificial environments that we don't really get a good picture from them, of how things are out there in the real world.
Since these various kinds of commensalism involve the genomes of more than just the species in question (and other non-genetic environmental factors are also transmitted to or needed by an organism's genome), understanding development requires a broader perspective. Information from the environment can be transmitted 'horizontally' in the sense that it is not transmitted 'vertically' from parent to offspring.
As Gilbert cleverly put it, the environment is not just the sieve of natural selection, deciding who shall live and who shall die. It is a source of information to an organism. And, because response to that information potentially affects survival and evolutionary success, the environment is like a professor: It gives information.....and then gives the recipient a test!
And these tests, like university final exams, determine whether the organism shall graduate!