Logical atomism is an understandable development, given the intellectual history of the 19th century. I am even in sympathy with it to some extent. When I teach my course Imagining Science, I begin the discussion of scientific reductionism by talking about what a powerful tool it is & how much it has affected the shape of modern life. Only then do I begin to suggest the problems that arise when taking an exclusively reductionist view of the lived world. Your distinction, that logical atomism is not science but a "philosophical reflection" upon science is well-taken; at the same time, many scientists have adopted exactly this "philosophical reflection" when attempting to explain what it is that they do. Therein lies one of the internal problems of contemporary scientific thought.

I have spent a good deal of intellectual energy over the course of thirty years trying to figure out for myself the underlying relations between things & words. I should have come to philosophy sooner. What I arrived at all on my own, before ever reading a word of Wittgenstein, was the realization that the relationship was complex, not simple; that it defied reductionism. If there has been one theme to my own thinking since I was 20, it would be, things are always more complicated than we think. Two terms need to be foregrounded here: appearance & Russell's notion of acquaintance. To take the second term first, Russell claims that the subjects of true propositions must be objects with which we can be acquainted, but this really does not get us very far unless we can rigorously define what it means to be acquainted with an object. Certainly, I am acquainted with the computer mouse with which I navigate the page I am currently writing: it is black plastic, has two buttons & a little wheel . . . I could go on. But I am also acquainted with William Blake's Urizon:



What's the dif? The point being, that acquaintance is just not a rigorous notion. Can we perform the same critique of appearance? I think Blake has already done it for us: Everything that can be imagined is an image of the truth. Morally speaking, appearance is where the action is. It's where we live. Reductionism & generalization tend (in opposite directions) away from the world that appears before us & in which we must act. You have previously used the example of racism: It is possible to reduce an individual to the characteristics of his or her race & it is equally possible to generalize the characteristics of an individual to an entire "race." [Note: scare quotes added because there is only a human race.] Both these moves are moral mistakes--applying useful intellectual tools in the wrong domain.