Maggots--disgusting as they may be--are highly organized forms of life with anatomic structures, highly specialized cells, and that develop by developmental differentiation through sequential patterns of gene expression. The idea of spontaneous generation referred to such complex creatures, and by extension to all organisms, not just bubbling primal soup.
Even if such soup were to exist today in little cauldrons in the rocks or sea, it would not produce such organisms. That is the key difference between life as a chemical phenomenon--which it most clearly is--and life as a complex ecology of different organisms, each of which is itself an internal ecology of different organs, which are ecologies of different cell types, and cells have their own internal ecology of subregions, specialized functions, and the like. This is true even of bacteria, singly and in aggregates, fossils of which have been found from as early as 3.8 billion years ago. Those don't arise spontaneously! And that is the very central key to why life is not like crystal formation, volcanoes, and solar systems. And, of course, it's the deeply insightful awareness of this, by Charles Darwin and at the same time by Alfred Wallace, that we call 'evolution', that was one of the most transforming insights a human being ever had.
Life is about continuation of a reaction--that's, after all, what you are relative to your parents, and their parents, and theirs, and......so on back to the initial lively cauldron. And more importantly, centrally, life is about the accumulation of divergence of subsets of this reaction. Divergence requires isolation (we called it partial sequestration in Mermaid's Tale), and transmission with memory (largely resident in DNA) that preserves divergence. And the way that such divergence with memory accumulates in the kind of life we have here on earth, at least, is brought about by the fact that the basic processes of life are combinatorial and polymeric (see our prior series on this topic).
Genes and the proteins they code for are polymers, long molecules of sequences of a few possible subunits, whose behavior depends on, resides in, and is all about the number, location, and arrangement of particular substrings along the polymer. That is what accumulates 'information' over time and produces functional subdivision like tissues and organs.
No matter what you may think of maggots (some people actually eat them!), they are marvelously organized, complex forms of life. New flies are not spontaneously generated; instead, they are just cellular continuations of parent flies.
Any spontaneous generation of new 'living' (biochemical) reactions would simply be simple. Organization of sequestered substructures and the DNA and protein polymers that make that possible, took hundreds of millions of years, if we can trust the earliest fossil evidence, found by our friend Bill Schopf at UCLA and others. What we don't allow in modern biological thinking is spontaneous generation of highly organized life. It must be possible in principle: after all, you and we are just chemical reactions that were generated by the chemical reactions in the eggs that founded us and all the way back to the first soup. But the probability that a bunch of molecules randomly bouncing around in some puddle in your back yard would generate a bacterial cell, much less a bunny rabbit, is astronomically small (if the universe is truly infinite, however, that must be occurring infinitely many times at this very instant and at every instant--think about that for a while!).
In boring mundane terms, at least, it's not happening here. Nor are organized structures like, say, bunny ears, being generated out of a tadpole pond. No, these things are products of very long histories, not short-term instances.
We need to carry the point forward, because it has fundamental lesson for our view of how evolution works and, generally, is strong support for and reflection of a key point in Darwin's founding theory of evolution. It's that complex structures arise gradually. If bunny ears or even just maggots could arise spontaneously, Darwin rightly thought, religious Creationist arguments would be more plausible than historical evolutionary ones. But the facts show that the evolutionary arguments are the only plausible ones of those that have been offered so far.
Even when complex traits do seem to arise out of nowhere, such as extra vertebrae in the backs of children that were not present in their parents, this is not spontaneous generation in the usual sense, because these are just anomalous repetitions of processes--like the one that generates vertebrae--that stutter more than usual.
This is why we never find, say, an organ from some dead organism that is totally unlike anything ever seen before. Nowhere on the tree of the major life-forms that we know of (image grabbed from the Smithsonian Museum's webpage: http://www.mnh.si.edu/exhibits/darwin/treeoflife.html). Or, less fantastical, we would never unearth a long DNA sequence that was totally unrelated to that of any known type of organism--that could not be shown to fit somewhere in the 'tree' of DNA sequences from plants, animals, and microbes for which we do have sequence. DNA sequences carry the information for organisms, coding for their traits, and must reflect their history.
If we really found a long DNA sequence with no similarity to those we know of, and no structure (such as protein coding elements) that are universal to the life we do know of, we would be in a real quandry: it would be some trick, some product of a DNA sequencing machine rather than a remnant of actual life, or we would have to rethink our entire theory of the history of life. It would be very exciting and upsetting--a lot of fun to live through--but there's no sign of it happening.
So this is the deeper sense in which biologists can seriously say that, yes, spontaneous generation did occur once, but no, it is not an explanation for subsequent life. We're not having our cake and eating it too: we're saying that a cake takes time to bake!
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