{"id":796,"date":"2007-06-14T12:00:34","date_gmt":"2007-06-14T17:00:34","guid":{"rendered":"http:\/\/brucegarrett.com\/brucelog\/796"},"modified":"2007-06-14T12:40:30","modified_gmt":"2007-06-14T17:40:30","slug":"natures-logic","status":"publish","type":"post","link":"https:\/\/brucegarrett.com\/brucelog\/796","title":{"rendered":"Nature&#8217;s Logic"},"content":{"rendered":"<p>There&#8217;s a kind of primitive variable that probably everyone who writes computer code knows and understands these days&#8230;the Boolean.&nbsp; Unlike other variables which can hold a range of values, be they numbers, or strings of ascii characters, the Boolean is a relentlessly either-or variable.&nbsp; And for that reason, it maps pretty well to the fundamental logic by which all digital computers operate, and to their smallest unit of data, the bit.&nbsp; But humans have been considering their world in Boolean logic ever since our minds first emerged from out of the biological background noise.<\/p>\n<p><em>Yes-No.&nbsp; True-False.&nbsp; Right-Wrong.&nbsp; Good-Bad.<\/em>&nbsp; Even as we admit to ourselves that there are often only shades of gray, we persist in reducing our experiences to these terms.&nbsp; It&#8217;s as basic an evaluation as can be.&nbsp; The second postulate of Aristotelian logic is that of &#8216;either-or&#8217;.&nbsp; A thing cannot both be, and at the same time not be.&nbsp; Either yes, or no.&nbsp; Either true, or false.&nbsp; Either right, or wrong.&nbsp; Either it is, or it is not.&nbsp; It must be one or the other.<\/p>\n<p>Well&#8230;tell it to Schrodinger&#8217;s cat.&nbsp; It&#8217;s probably no coincidence that our machines are made in our image, that they resemble the way our minds like to think.&nbsp; The canvas always speaks of the artist.&nbsp; But as it turns out, that&#8217;s not actually the way our brains operate.&nbsp; It may not even be the way nature, at its most elemental level, works.&nbsp; There&#8217;s this intriguing tri-position logic in the natural world that I keep seeing raise its hand and wave at us from time to time.&nbsp; But it seems to go unexamined most of the time, and I think that&#8217;s because like the extra space-time dimensions physicists keep telling us are there, it&#8217;s hard for our minds to wrap themselves around it.&nbsp;&nbsp; And that&#8217;s really interesting, because one place you really see this tri-position logic is in how our brains actually physically work.<\/p>\n<p>Consider the humble synapse.&nbsp; It is the gap between brain cells, across which two different kinds of chemical &quot;messages&quot; can cross.&nbsp; One kind of chemical causes the cell on the other side of the gap to fire.&nbsp; The other chemical inhibits the cell on the other side of the gap from firing.&nbsp; So far, so good.&nbsp; We&#8217;re still comfortably in the basic Boolean logic of things.&nbsp; Fire-Don&#8217;t fire.&nbsp; Yes-No.&nbsp; Off-On.&nbsp; Either-Or.&nbsp; But there&#8217;s a third thing that synapse can do: <em>Nothing<\/em>.<\/p>\n<p>So synapse logic has three states, not two.&nbsp; Fire, don&#8217;t fire, and&#8230;what?&nbsp; Here&#8217;s where it gets interesting for me.&nbsp; What is the word here.&nbsp; We don&rsquo;t really have one.&nbsp; And that I think, is because the concept is difficult for us.&nbsp; The state itself seems foreign enough to the way our minds naturally work, that as far as I know, humans don&#8217;t really have a good enough word for that third position.&nbsp; Neutral doesn&#8217;t quite do it.&nbsp; It isn&#8217;t that it isn&#8217;t engaged, like a gear shift you put into neutral, say.&nbsp; It&#8217;s connected, to the rest of the brain.&nbsp; &#8216;Off&#8217; isn&#8217;t quite it either.&nbsp; Each half of the synaptic gap has a current state that influences the state of the cells on either side of the synaptic gap depending on the direction of the message, or the absence of one.&nbsp; So there are really three states possible here:&nbsp; Fire, don&#8217;t fire, and a third, that is neither fire or don&#8217;t fire.&nbsp; Depending on the state of the synapses it&#8217;s connected to, a brain cell may or may not fire.&nbsp; So the cell itself may have just two states.&nbsp; But the synapses have three.<\/p>\n<p>Our minds just don&#8217;t seem to grasp that third logical state very well, and we fumble to describe it.&nbsp; <em>It&#8217;s a between state.&nbsp; No&#8230;it&#8217;s a middle state.&nbsp; Wait&#8230;a transitional state&#8230;&nbsp; Uhm&#8230;&nbsp; No&#8230;it&#8217;s&#8230;it&#8217;s&#8230;&nbsp;&nbsp; (shrug)&nbsp; I dunno&#8230;<\/em><\/p>\n<p>Maybe &#8216;zero&#8217; is the right way to think about it.&nbsp; But I can only say that because I write software code and I understand how zero is actually something distinct from a positive value, is distinct from a negative value.&nbsp; But that seems to be a non-intuitive concept for us humans.&nbsp; Consider that the Arabic invention of the zero as a form of notation actually came well after a lot of other very basic mathematical concepts.&nbsp; Well of course everyone knew that you can have a zero quantity.&nbsp; But expressing it abstractly seemed to be a difficulty.&nbsp; And in many programming languages, 0 evaluates to false anyway, and any other value is true (except in Basic, where&nbsp; &ndash;1 is (was) true, which I think is right from a bitwise NOT sense&#8230;but don&#8217;t get me started&#8230;).&nbsp; And&#8230;this third position isn&#8217;t really a &#8216;nothing&#8217;.&nbsp; It&#8217;s more of a &#8216;neither&#8217;.&nbsp;&nbsp;<\/p>\n<p>Another place you see this tri-position logic is natural selection.&nbsp; In the grand scheme of things, the winners are those organisms that are best adapted to their environment.&nbsp; Variation then, that gives an organism an advantage tends to be passed on, and variation that puts an organism at a disadvantage tends not to be passed on.&nbsp; Over time the advantages accumulate, and the disadvantages get culled out.&nbsp; Either-Or.&nbsp; But there is a third thing that can happen.&nbsp; <em>Nothing.<\/em>&nbsp; A variation can simply be neither an advantage nor a disadvantage.&nbsp; Those variations it seems, get placed in the genetic portfolio right along with the advantages too&#8230;\n<\/p>\n<blockquote><p><a href=\"http:\/\/rawstory.com\/news\/afp\/Landmark_study_prompts_rethink_of_g_06142007.html\"><strong>Landmark study prompts rethink of genetic code<\/strong><\/a>\n<\/p><\/blockquote>\n<blockquote><p>The most detailed probe yet into the workings of the human genome has led scientists to conclude that a cornerstone concept about the chemical code for life is badly flawed.<\/p><\/blockquote>\n<blockquote><p>The ground-breaking study, published in more than two dozen papers in journals on both sides of the Atlantic, takes a small percentage of the genome to pieces to draw up a &quot;parts list,&quot; identifying the biological role of every component.<\/p><\/blockquote>\n<blockquote><p>For the international team of investigators, the four-year project was the computer-equivalent of passing a fine-toothed comb through a mountain of raw data.<\/p><\/blockquote>\n<blockquote><p>Reporting in the British journal Nature and the US journal Genome Research on Thursday, they suggest that an established theory about the genome should be consigned to history.<\/p><\/blockquote>\n<blockquote><p>Under this view, the genome is rather like a ribbon studded with some 22,000 &quot;nuggets&quot; in the form of genes, which make proteins, the essential stuff of life.<\/p><\/blockquote>\n<blockquote><p>Genes &#8212; deemed so valuable that some discoverers of them have been prompted to file patents over them for commercial gain &#8212; amount to only around a twentieth, or even less, of the genetic code.<\/p><\/blockquote>\n<blockquote><p>In between the genes and the sequences known to regulate their activity are long, tedious stretches that appear to do nothing. The term for them is &quot;junk&quot; DNA, reflecting the presumption that they are merely driftwood from our evolutionary past and have no biological function.<\/p><\/blockquote>\n<blockquote><p>But the work by the ENCODE (ENCyclopaedia of DNA Elements) consortium implies that this nuggets-and-dross concept of DNA should be, well, junked.<\/p><\/blockquote>\n<blockquote><p>The genome turns out to a highly complex, interwoven machine with very few inactive stretches, the researchers report.<\/p><\/blockquote>\n<blockquote><p>Genes, it transpires, are just one of many types of DNA sequences that have a functional role.<\/p><\/blockquote>\n<blockquote><p>And &quot;junk&quot; DNA turns out to have an essential role in regulating the protein-making business.<\/p><\/blockquote>\n<blockquote><p>Previously written off as silent, it emerges as a singer with its own discreet voice, part of a vast, interacting molecular choir.<\/p><\/blockquote>\n<blockquote><p>&quot;The majority of the genome is copied, or transcribed, into RNA, which is the active molecule in our cells, relaying information from the archival DNA to the cellular machinery,&quot; said Tim Hubbard of the Wellcome Trust Sanger Institute, a British research group that was part of the team.<\/p><\/blockquote>\n<blockquote><p>&quot;This is a remarkable finding, since most prior research suggested only a fraction of the genome was transcribed.&quot;<\/p><\/blockquote>\n<blockquote><p>Francis Collins, director of the US National Human Genome Research Institute (NHGRI), which coralled 35 scientific groups from around the world into the ENCODE project, said the scientific community &quot;will need to rethink some long-held views about what genes are and what they do.&quot;<\/p><\/blockquote>\n<blockquote><p>&quot;This could have significant implications for efforts to identify the DNA sequences involved in many human diseases,&quot; he said.<\/p><\/blockquote>\n<blockquote><p>Another rethink is in offing about how the genome has evolved, said Collins.<\/p><\/blockquote>\n<blockquote><p>Until now, researchers had thought that the pressure to survive would relentlessly sculpt the human genome, leaving it with a slim, efficient core of genes that are essential for biological function.<\/p><\/blockquote>\n<blockquote><p>But the ENCODE consortium were surprised to find that the genome appears to be stuffed with functional elements that offer no identifiable benefits in terms of survival or reproduction.<\/p><\/blockquote>\n<blockquote><p>The researchers speculate that there is a point behind this survival of the evolutionary cull. Humans could share with other animals a large pool of functional elements &#8212; a &quot;warehouse&quot; stuffed with a variety of tools on which each species can draw, enabling it to adapt according to its environmental niche.\n<\/p><\/blockquote>\n<p>IMO, there&#8217;s that third logical position at work again.&nbsp; The variation is neither good, nor bad, it&#8217;s just there.&nbsp; At some future point, say a rapid change in the organism&#8217;s environment, and that gene might be a handy thing to have all of a sudden.&nbsp; Or, conversely, it might turn into a complete disaster for the organism.&nbsp; But for the moment, it&#8217;s just there, evaluated to position three.&nbsp; Zero, let&#8217;s say.&nbsp; Neither positive nor negative.&nbsp; It has the potential to be either one, given a chance to express itself.<\/p>\n<p>From somewhere deep in the physical fabric of the universe, Schrodinger&#8217;s cat licks its chops and smiles.&nbsp; Or doesn&#8217;t.&nbsp; Or both.&nbsp; Just don&#8217;t open the box.<\/p>\n<p>The science fiction writer Larry Niven once averred that giving gay people what we want would be the quickest way of breeding us out of the population.&nbsp; But then, he didn&#8217;t get the fact that his Ringworld needed attitude jets until some real engineers pointed that fact out to him.&nbsp; I happen to think that having a gay minority does in fact provide a survival advantage to the human line.&nbsp; But as it turns out, homosexuality can fit comfortably into our gene pool just fine, along with a bazillion other random variations on a theme that simply are, and do no harm.&nbsp;<\/p>\n<p>I don&#8217;t need to pass on my gay genes.&nbsp; My heterosexual brethren probably have them too&#8230;they just aren&#8217;t expressing them.&nbsp; For some reason, I expressed mine.&nbsp; But I&#8217;m fine with that, and so is nature.&nbsp; I happen to think it&#8217;s a plus.&nbsp; But the point is that a variation only gets culled out if it&#8217;s a minus.&nbsp; A really big minus.&nbsp; And this one isn&#8217;t.<\/p>\n<p><em>[Edited a tad&#8230;]<\/em>&nbsp;<\/p>\n","protected":false},"excerpt":{"rendered":"<p>There&#8217;s a kind of primitive variable that probably everyone who writes computer code knows and understands these days&#8230;the Boolean.&nbsp; Unlike other variables which can hold a range of values, be they numbers, or strings of ascii characters, the Boolean is a relentlessly either-or variable.&nbsp; And for that reason, it maps pretty well to the fundamental [&hellip;]<\/p>\n","protected":false},"author":3,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[1],"tags":[64,29,55],"class_list":["post-796","post","type-post","status-publish","format-standard","hentry","category-uncategorized","tag-cosmos","tag-science","tag-this-and-that"],"_links":{"self":[{"href":"https:\/\/brucegarrett.com\/brucelog\/wp-json\/wp\/v2\/posts\/796","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/brucegarrett.com\/brucelog\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/brucegarrett.com\/brucelog\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/brucegarrett.com\/brucelog\/wp-json\/wp\/v2\/users\/3"}],"replies":[{"embeddable":true,"href":"https:\/\/brucegarrett.com\/brucelog\/wp-json\/wp\/v2\/comments?post=796"}],"version-history":[{"count":0,"href":"https:\/\/brucegarrett.com\/brucelog\/wp-json\/wp\/v2\/posts\/796\/revisions"}],"wp:attachment":[{"href":"https:\/\/brucegarrett.com\/brucelog\/wp-json\/wp\/v2\/media?parent=796"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/brucegarrett.com\/brucelog\/wp-json\/wp\/v2\/categories?post=796"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/brucegarrett.com\/brucelog\/wp-json\/wp\/v2\/tags?post=796"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}