tag:blogger.com,1999:blog-1812431336777691886.post3836118683929280708..comments2024-02-29T03:57:00.088-05:00Comments on The Mermaid's Tale: Making a genomic Skype callAnne Buchananhttp://www.blogger.com/profile/09212151396672651221noreply@blogger.comBlogger1125tag:blogger.com,1999:blog-1812431336777691886.post-50867166998922234702015-06-08T13:11:27.083-04:002015-06-08T13:11:27.083-04:00A friend (Anonymous) has commented on this post by...A friend (Anonymous) has commented on this post by email, and Ken has replied. Copied and pasted below (with Anonymous's permission):<br /><br />Anonymous: Your blog Friday lays out the challenge that I have been arguing is the most important question in genetics. I.e. what is the molasses that controls the balance between the order and disorder that defines life in general and the behavior of the genome in particular? Is it material that we know and have measurements in hand, but we don’t yet know how to model its role? Or is it something like the dark energy/dark matter that we have yet to measure? Is it the same molasses for the genome, metabolism and cognition? How do you suggest that we go about finding it and measuring it? How would we know if there is really no molasses? <br />Just how much more evidence do we need to convince the molecular reductionists among us that the behavior of the whole cannot be explained by the sum of the behaviors of the individual parts? Even if one accepts that it is the interaction between parts that is causal, what controls the interactions? And, what can we offer as an alternative research strategy that acknowledges the whole is more than the sum of the parts? But first, what tools are needed to test the hypothesis that there is dark matter/dark energy that coordinates the order and disorder that characterizes function of the genome?<br />It seems to that most research in genetics is expanding the number of unanswered questions and making understanding more distant. This is one reason why I have my doubts as to whether we have the capability as humans to fully understand the etiology of life.<br /><br />Ken: Of course I agree with what you say. I think we're not asking the right question in some sense. For example, what is an 'interaction'? We all talk about it, and we may explain how we document it (e.g., non-additive effects in samples, molecules binding with each other....). But is an interaction a thing or a phenomenon, and if the latter, of what kind? To me, it is useful (conceptually at least) to think of particles and fields in physics. A 'field' is in a sense an 'interaction' when you have particles. It has properties in itself, not just that are identified by samples. So are there such things in biology that can usefully be conceived, and that are not just physics envy?<br /><br />A: Our good friend Brian Goodwin imposed field thinking (the growing points in plants for eg.) in his explanations of development (see How the Leopard Changed its Spots and many of his other scholarly pieces long before the molecular revolution took priority over how we think about in science).<br /><br />K: Yes, I know that work and his book Form and Transformation. But I'd go back to Bateson and then Turing, and it was these concepts that led to my working on developmental mechanisms in tooth formation (a nested modular trait). Reaction-diffusion types of models, and some recent experimental data, use waveform analysis. That's among cells. Population ecologists use models like Lotka-Volterra, which also are similar in spirit. But can this be extended much farther, to encompass other sorts of interaction (like, for example, the formation of Hi-C associations)?Anne Buchananhttps://www.blogger.com/profile/09212151396672651221noreply@blogger.com