<p>This is an interesting question that has plagued me for some time.</p>
<p>We know that all objects aren’t really fundamentally different from one another, as they are all made of up quarks, down quarks, and electron-leptons. Nor are they fundamentally different from energy - as they can be annihilated with antimatter to form gamma rays.</p>
<p>So then comes the problem - what is a “fundamental difference?” Thales held that there were 4 elements - fire, air, earth, and water, each of which were fundamentally different from one another.</p>
<p>The word “fundamental difference” seems to imply an aura of importability. If something works in conjunction with one but not with the other - then a fundamental difference would exist if it was impossible to tweak the other system such that the “something” could actually work. But if we abide by this definition strictly - there isn’t really a fundamental difference in play unless we say that “the other system” MUST have fundamental properties in which case we cannot tweak properties without violating the fundamentals.</p>
<p>Which brings us to the issue that “fundamental differences” seem to be rooted in societal constructs. Yet can you tweak an up quark into a down quark? Maybe it’s theoretically possible, not within the boundaries of our current theories perhaps. But to do so is to violate one of the fundamental assumptions of quarks.</p>
<p>Of course, back in the days of creationism, there were fundamental differences between each and every organism. Why is that? Because ordinary mortals could not tweak one organism into another. </p>
<p>And what of biological systems? Are they fundamentally different from non-biological ones? Is my brain fundamentally different from your brain? Is a conscious brain fundamentally different from one that has been replaced by electrodes? Are Linux computers fundamentally different from MACs?</p>
<p>A “fundamental difference” is nothing more than a difference that someone defines as “fundamental.” “Fundamental” is a word that reflects the perspective of its user – just as “good” or “evil” do…and given we haven’t agreed on what “good” or “evil” mean, we probably won’t agree on what “fundamental” means either…</p>
<p>(of course, that made no sense whatsoever, because i’m sick and can’t even think well enough to play nethack effectively.)</p>
<p>Not to get into the academic ****ing contest that I’m sure IK wants, but there are many things that are fundamentally different. The first thing that comes to my mind are theories. The philosophical foundations upon which theories are built are often different. To fully grasp theoretical differences and evolutions you need to be able to grasp the ontological and epistemological differences between them.</p>
<p>this is a local vs. global question. undoubtedly, things take on different properties on a global scale. the fundamental difference is in the interactions as systems. Linux and Macs have the same structures (Unix based), however the interaction of the “local” parts make the “global” system different.</p>
<p>Almost all real differences between materials arise from the interactions of electrons, I think (I’m not much of a physicist, so people correct me if I’m wrong). The interactions between photons and electrons, based on probability, and, at a more basic level, both the amount of protons and the electron configuration, determine the properties of an element.</p>
<p>A question similar to that about biological and non-biological systems, mentioned by the OP, is, “What incentive does a virus or prion have to be infectious?” This is a question that has plagued me for some time. By the way, The Origins of Life by John Maynard Smith and Eors Szathmary (or The Major Transitions in Evolution, same authors) may help to answer your question.</p>