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	<title>Embracing Chaos &#187; Chemistry</title>
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	<link>http://www.embracingchaos.com</link>
	<description>Leo Parker Dirac on Business and Technology Trends</description>
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		<title>Two Big Questions Physics Isn&#8217;t Addressing</title>
		<link>http://www.embracingchaos.com/2008/01/two-big-questio.html</link>
		<comments>http://www.embracingchaos.com/2008/01/two-big-questio.html#comments</comments>
		<pubDate>Thu, 03 Jan 2008 13:41:26 +0000</pubDate>
		<dc:creator>leodirac</dc:creator>
				<category><![CDATA[Chemistry]]></category>
		<category><![CDATA[Philosophy]]></category>
		<category><![CDATA[Physics]]></category>
		<category><![CDATA[Science]]></category>

		<guid isPermaLink="false">http://wp.embracingchaos.com/2008/01/two-big-questio.html</guid>
		<description><![CDATA[One of the reasons I chose not to pursue a career in science was a feeling that all the interesting problems of physics have been solved. In a sense I still believe this -- I don't see the current line of pursuit bearing much fruit. But I do see two really important questions that physics hasn't answered. What makes them especially interesting is that most of the scientific establishment doesn't even recognize them as valid questions. Ever since Maxwell unified the theories of electricity and magnetism in 1864, physicists have been working towards a single model that can explain all...
]]></description>
			<content:encoded><![CDATA[<p><a href="http://www.flickr.com/photos/leodirac/2150295001/"><img class="top" src="http://farm3.static.flickr.com/2225/2150295001_dfa6158ea9_t.jpg" alt="" width="100" height="80" /></a>One of the reasons I chose not to pursue a career in science was a feeling that all the interesting problems of physics have been solved.  In a sense I still believe this &#8212; I don&#8217;t see the current line of pursuit bearing much fruit.  But I do see <strong>two really important questions</strong> that physics hasn&#8217;t answered.  What makes them especially interesting is that most of <strong>the scientific establishment doesn&#8217;t even recognize them as valid questions</strong>.</p>
<p>Ever since Maxwell unified the theories of electricity and magnetism in<br />
1864, physicists have been working towards a single model that can explain all observed forces.  It took another hundred years or so for<br />
us to understand how the electromagnetic and weak nuclear forces are really the same thing, and a grand unified theory is close to merging in quantum chromodynamics (QCD) and the strong nuclear force.  The only thing left now is to merge in gravity.  String theory is a popular contender for a so-called &#8220;theory of everything&#8221; which explains quantum gravity. Progress here is slow, but <strong>finding a theory which combines general relativity and quantum mechanics is widely regarded as one of the big unanswered questions in physics</strong>.  Personally, I&#8217;m not all that excited by it.  I think we have bigger fish to fry.</p>
<p>Let&#8217;s say we find a Theory of Everything that explains quantum gravity in addition to merging electricity, magnetism and the strong and weak nuclear forces.  What changes when we figure this out?  Of course, we<br />
can&#8217;t really know until we have the answer.  But consider the merging<br />
of the electromagnetic force and the weak magnetic force into the<br />
electro-weak force.  They look different under just about every condition we will ever encounter.  It&#8217;s only when the temperature exceeds about 10^15 Kelvin that they start to look the same.  For comparison, the middle of the sun is relatively frigid at 10^7 degrees.  So my guess is that <strong>when we figure this out, it isn&#8217;t going to lead to any new<br />
practical understandings about the world around us</strong>.</p>
<p><strong><br />
The theoretical basis for most everything that we experience on a daily basis was figured out</strong> in the early 20th century <strong>with quantum mechanics</strong>.  It provides a theoretical foundation which reduces essentially all of chemistry to solving mathematical equations.  Admittedly these are horrendously difficult equations that even modern computers can only approximate for relatively small molecules.  But the theory is there.  And with chemistry solved, we have a theoretical basis for all of biology, and everything to do with life.  Not to say there aren&#8217;t interesting problems to solve there and plenty we don&#8217;t understand, but on some level, it&#8217;s all applications of an understood theory.</p>
<p>I completely realize this is a simplification of the state of science,<br />
but this is what I thought when I was an undergrad.  This realization<br />
and disillusionment drove me away from science towards my career in<br />
software, which I love because of its ability to directly improve people&#8217;s lives on a massive scale.</p>
<p>But now as I write about things like <a href="http://www.embracingchaos.com/2007/04/why_not_star_tr.html">the fate of humanity</a>, the <a href="http://www.embracingchaos.com/2007/08/do-we-live-in-a.html">nature of consciousness</a> and <a href="http://www.embracingchaos.com/2007/02/why_only_geeks_.html">how to save the world</a>, <strong>I see two huge gaps in what science can explain</strong>.  For context, here&#8217;s a quote that I love:</p>
<p style="margin-left: 40px;"><em>The most exciting phrase to hear in science, the one that heralds new discoveries, is not &#8216;Eureka!&#8217; (I found it!) but &#8216;That&#8217;s funny &#8230;&#8217;</em></p>
<div style="margin-left: 40px;">-Isaac Asimov</div>
<p>Whoever finds the Higgs Boson, or explains quantum gravity will yell &#8220;Eureka!&#8221; at the top of their lungs.  Two things that make me say &#8220;that&#8217;s funny&#8221; about about how physics explains the world today are:<strong> </strong></p>
<ul>
<li><strong>quantum randomness</strong></li>
<li><strong>the big bang</strong></li>
</ul>
<p>I&#8217;ll spare the details for now and write more on each of these later.  (I&#8217;ve written some about <a href="http://www.embracingchaos.com/2007/02/turing_complete.html">quantum randomness and the nature of free will</a> before.)  But for now I&#8217;ll summarize by saying these are a couple of areas where the standard explanation really doesn&#8217;t sit well with me.  Moreover, I think <strong>a better understanding of these issues would do a lot to answer questions that have troubled humanity since the birth of consciousness.</strong></p>
<p><strong> </strong></p>
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		<title>Free Will and Turing-completeness of the Brain</title>
		<link>http://www.embracingchaos.com/2007/02/turing_complete.html</link>
		<comments>http://www.embracingchaos.com/2007/02/turing_complete.html#comments</comments>
		<pubDate>Thu, 22 Feb 2007 23:20:00 +0000</pubDate>
		<dc:creator>leodirac</dc:creator>
				<category><![CDATA[Chemistry]]></category>
		<category><![CDATA[Computer Science]]></category>
		<category><![CDATA[Philosophy]]></category>
		<category><![CDATA[Physics]]></category>
		<category><![CDATA[Science]]></category>
		<category><![CDATA[Technology]]></category>
		<category><![CDATA[Transhumanism]]></category>
		<category><![CDATA[Uploading]]></category>

		<guid isPermaLink="false">http://wp.embracingchaos.com/2007/02/turing_complete.html</guid>
		<description><![CDATA[In this essay, I'm going to explore the question "If the human brain is Turing complete, what does that imply about the existence of free will?" And moreover, what does that mean about the ability to upload our consciousness into computers? First, a little computer science background. Turing completeness is the idea that a computing system has the same capabilities as a universal Turing machine. This theoretical machine moves along a long tape which has various symbols on it that the machine can read and write. The machine itself is always in one internal state, but will change to different...
]]></description>
			<content:encoded><![CDATA[<p>In this essay, I&#8217;m going to explore the question &quot;<strong>If the human brain is Turing complete, what does that imply about the existence of free will?</strong>&quot;&nbsp; And moreover, what does that mean about the ability to upload our consciousness into computers?</p>
<p>First, a little computer science background.&nbsp; Turing completeness is the idea that a computing system has the same capabilities as a universal Turing machine.&nbsp; This theoretical machine moves along a long tape which has various symbols on it that the machine can read and write.&nbsp; The machine itself is always in one internal state, but will change to different states based on its programming and input.&nbsp; It is programmed by a huge state transition table which says &quot;if you&#8217;re in state <em>X</em>, and you&#8217;re reading symbol <em>Y</em>, then write symbol <em>Z</em>, move <em>left n</em> spaces, and switch to state <em>W</em>&quot; for all possible states and symbols.&nbsp; It turns out that with a long enough tape and enough states this device can do just about anything you think of a computer being able to do.&nbsp; In fact, computer scientists have shown that every modern computer system is functionally equivalent to a Turing machine.&nbsp; That is to say <strong>all modern computers are Turing complete</strong>.&nbsp; It&#8217;s useful because it&#8217;s simple enough to prove theorems about.&nbsp; Some important things we know about Turing machines and anything which is functionally equivalent to one: </p>
<ul>
<li><strong>Turing machines are deterministic</strong> &#8212; given a set of inputs they&#8217;ll always reach the same output.</li>
<li>It&#8217;s impossible to reliably predict whether or not a program on a Turing machine will ever finish.</li>
</ul>
<p>I see two ways to interpret the question of whether or not a human brain is Turing complete.&nbsp; The first one is &quot;<strong>Can a human brain perform the same functions as a Turing machine?</strong>&quot;&nbsp; I think that given a pen, paper, and enough patience the answer is <strong>clearly yes</strong>.&nbsp; But that&#8217;s not the question that interests me.</p>
<p>As a transhumanist, the interesting question for me is &quot;<strong>Can a Turing-complete computer perform the same functions as a human brain?</strong>&quot;&nbsp; This question is important to me because if the answer is yes, then it is possible for a computer to simulate a human personality.&nbsp; That is to say uploading of a human consciousness into a computer is possible.&nbsp; I&#8217;m going to dodge the detailed analysis of this question today, and get back to it in a later article.&nbsp; For now, let&#8217;s <strong>assume</strong> the answer is <strong>&quot;Yes&quot;</strong> and see what that implies about free will.</p>
<p>Remember that theorem that says Turing machines are deterministic?&nbsp; That is, once you start it going with a given set of inputs, that it&#8217;s always going to reach the same answer?&nbsp; If this were true for us as humans, then we would have no free will &#8212; our actions would be entirely determined by our current state and our surroundings.&nbsp; We might think we are making choices, but in fact a fast computer could run the same calculation and tell us what our answer would be before we thought we had decided.&nbsp; So by this logic <strong>if uploading is possible, then humans have no free will</strong>.&nbsp; Troubling, eh?</p>
<p>Fortunately, I think the above analysis has a flaw.&nbsp; Let&#8217;s dive down a little deeper into neurochemistry.&nbsp; Neurons fire as a result of electro-chemical processes.&nbsp; Basic chemistry tells us that the rates of chemical reactions are deterministic based on concentrations of the relevant input chemicals.&nbsp; But if you took stat-mech then you learned that these predicted rates are actually just statistical averages and that they&#8217;re only accurate if the brazillions of molecules involved happen to collide with each other at a constant frequency as they randomly bounce around in solution.&nbsp; And quantum mechanics tells us that this apparently random bouncing around is in fact, to Einstein&#8217;s chagrin, truly random &#8212; god does play dice with the universe.&nbsp; (I&#8217;m not sure I completely buy this, but I&#8217;ll have to save that for another article too.&nbsp; Yes, I know that the Bell inequalities were experimentally observed in the 1980&#8217;s but it still sits funny with me.&nbsp; Sorry <a href="http://en.wikipedia.org/wiki/Paul_Dirac">grandpa</a>.&nbsp; More on this later.)&nbsp; Because of this randomness, <strong>the instantaneous rate of any chemical reaction will vary randomly</strong>, while still averaging around the classically predicted rate.&nbsp; So the upshot is that neurons don&#8217;t behave completely deterministically, but that <strong>the exact timing of neurons firing has a truly (quantum) random component to it</strong>.</p>
<p>Now this implies quite firmly that our brains cannot be simulated by a Turing machine since Turing machines can&#8217;t act randomly, and thus wouldn&#8217;t be able to properly simulate the randomness of neurons firing.&nbsp; But if we modify a Turing machine slightly so that a spot on its tape read a different random symbol each time you check, I think we&#8217;re good.&nbsp; Given this, it seems reasonable that <strong>a modern computer that has a source of truly random data could simulate a brain</strong>.&nbsp; Some have argued that we need quantum computers to simulate consciousness, but I don&#8217;t think so.&nbsp; (Again, more on this later.)</p>
<p>Computers are pretty good at generating psuedo-random data internally, and by listening to the outside world (hard drive vibration, microphones, etc) can generate what is probably actually random data.&nbsp; If true randomness is really important, we can build small accessory cards that sample thermal noise on<br />
a resistor and produce large volumes of truly (quantum) random data.&nbsp; Some advanced cryptographic systems do this today.&nbsp; So it&#8217;s totally possible today to build this modified Turing machine that also incorporates random input.</p>
<p>Now our transhuman dilemma is solved.&nbsp; The <strong>essence of free will lies in the quantum randomness of electro-chemical processes in our brain</strong>.&nbsp; Moreover, it will be possible to upload our personalities into computers, complete with our free wills in tact, by incorporating random processes into the hardware that simulates our brains.&nbsp; If the computers we upload into are only psuedo-random (as almost all software is today), we will appear to have free will, in fact we will believe that we have it, but we will in fact be total robots.&nbsp; Now, who can come up with <strong>a Turing test for free will?</strong></p>
<p><em>[[Thanks to Barry Brummit.&nbsp; This article is a rehash of a couple good conversations we had over New Year's and this morning after yoga practice.]]</em></p>
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		<title>100% Chance of Rain in Seattle</title>
		<link>http://www.embracingchaos.com/2006/12/100_chance_of_r.html</link>
		<comments>http://www.embracingchaos.com/2006/12/100_chance_of_r.html#comments</comments>
		<pubDate>Fri, 15 Dec 2006 17:04:08 +0000</pubDate>
		<dc:creator>leodirac</dc:creator>
				<category><![CDATA[Chemistry]]></category>
		<category><![CDATA[Geography]]></category>
		<category><![CDATA[Humor]]></category>
		<category><![CDATA[Science]]></category>
		<category><![CDATA[Seattle]]></category>

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		<description><![CDATA[I've had my own system for interpreting that "chance of rain" numbers that meteorologists use to predict weather. Along the lines of how people say eskimos have 137 different words for snow, here in Seattle, rain isn't a simple yes/no thing. I wrote about it here a little while ago. The basic idea is that the % chance of rain is actually the % chance that a random person on the street would consider the current weather to be "rain." I've also long believed that in Seattle it's impossible to get over about 98% chance of rain because some die-hard...
]]></description>
			<content:encoded><![CDATA[<p>I&#8217;ve had my own system for interpreting that &quot;chance of rain&quot; numbers that meteorologists use to predict weather.&nbsp; Along the lines of how people say eskimos have 137 different words for snow, here in Seattle, rain isn&#8217;t a simple yes/no thing.&nbsp; I wrote about it <a href="http://www.embracingchaos.com/2006/09/30_chance_of_ra.html">here</a> a little while ago.&nbsp; The basic idea is that the % chance of rain is actually the % chance that a random person on the street would consider the current weather to be &quot;rain.&quot;</p>
<p>I&#8217;ve also long believed that in Seattle it&#8217;s impossible to get over about 98% chance of rain because some die-hard hold out would always say &quot;This ain&#8217;t rain.&nbsp; Back where I come from we have real rain and this ain&#8217;t it.&quot;&nbsp; Well last night I feel confident there was a 100% chance of rain.&nbsp; It was a full on&nbsp; storm.&nbsp; Things broke.</p>
<p>
<a href="http://www.flickr.com/photos/leodirac/323174223/" title="Broken tree branch"><img width="240" height="180" src="http://static.flickr.com/128/323174223_1a2ed4adf3_m.jpg" alt="broken branch" /></a><br />
<a href="http://www.flickr.com/photos/leodirac/323176761/" title="Fallen Tree"><img width="240" height="180" src="http://static.flickr.com/140/323176761_a6dd85a581_m.jpg" alt="Fallen tree lays on car" /></a><br />
<a href="http://www.flickr.com/photos/leodirac/323174913/" title="Destroyed fence"><img width="180" height="240" src="http://static.flickr.com/124/323174913_e7ff35bff5_m.jpg" alt="siding down" /> </a>
</p>
<p>In one night we got a <strong>record 2.2&quot; of rain with winds gusting to 74 mph</strong>.&nbsp; Roads were closed everywhere.&nbsp; Power flickered all night.&nbsp; Things banged loudly.&nbsp; My neighbor&#8217;s basement flooded because water was coming up through the drain!&nbsp; By work I saw a manhole cover that looked like a beautiful fountain with jets of water squirting up through the holes.&nbsp; My rug in my basement got fairly wet, as far as I can tell because of <strong>water coming down the chimney</strong>!!&nbsp; It was a bad time to realize that the last time I pulled my fileserver out to work on it I didn&#8217;t plug it into a UPS.&nbsp; Oops.</p>
<p>A couple friends and I wanted to experience the weather so we put on full snowboarding / mountaineering outfits and wandered out.&nbsp; We ended up spending a good chunk of the evening standing on a rooftop patio with a great view of the city, watching the city be destroyed.&nbsp; Explosions filled the night from lightning and transformers blowing.&nbsp; We could always tell which ones were lightning because the flashes were white and brief.&nbsp; Whenever a transformer would blow, there would be a pulsing glow that would linger for a second or two.&nbsp; They were also typically bright green, although we did see one or two redding purple ones.&nbsp; I&#8217;m pretty sure the <strong>green blasts were from large amounts of copper wire burning very quickly</strong> in a&nbsp; giant short-circuit.&nbsp; I&#8217;m not sure what metal they&#8217;d use in transformers that burns reddish purple.&nbsp; Occasionally we saw what must have been a whole substation go because the glow would last 3 or 4 seconds.&nbsp; For some reason we were cheering.&nbsp; After one such explosion, we saw all of Bellevue go dark, only to light up again half a second later.</p>
<p>It was amazing.</p>
<p>At some point we realized that the street&#8217;s own transformer was at eye level less than 20&#8242; from where we were standing.&nbsp; When we finally connected the large explosions in the distance to the utility pole mounted bomb next to us, we decided to go inside.&nbsp; Show&#8217;s over.&nbsp; Don&#8217;t wanna die tonight.</p>
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		<title>New York bans Trans-fats</title>
		<link>http://www.embracingchaos.com/2006/12/new_york_bans_t.html</link>
		<comments>http://www.embracingchaos.com/2006/12/new_york_bans_t.html#comments</comments>
		<pubDate>Sun, 10 Dec 2006 16:18:51 +0000</pubDate>
		<dc:creator>leodirac</dc:creator>
				<category><![CDATA[Chemistry]]></category>
		<category><![CDATA[Cooking]]></category>
		<category><![CDATA[Science]]></category>
		<category><![CDATA[Societal Values]]></category>

		<guid isPermaLink="false">http://wp.embracingchaos.com/2006/12/new_york_bans_t.html</guid>
		<description><![CDATA[I'm a little slow to re-report this, but but I find it fascinating so I want to share it in case you missed it. New York City has banned the use of trans-fats in restaurants. They've done this almost completely (a few exceptions for things like donut shops) and very quickly (by middle of next year) and extremely decisively. I find this amazing for a couple of reasons. First, it drives home the artificial nature of trans-fats. I've thought of them as similar to saturated fats in a lot of ways -- things that are everywhere but should be avoided....
]]></description>
			<content:encoded><![CDATA[<p>I&#8217;m a little slow to re-report this, but but I find it fascinating so I want to share it in case you missed it.&nbsp; <a href="http://www.nytimes.com/2006/12/06/nyregion/06fat.html?hp&amp;ex=1165467600&amp;en=d40223614d12957e&amp;ei=5094&amp;partner=homepage">New York City has banned the use of trans-fats in restaurants.</a>&nbsp; They&#8217;ve done this almost completely (a few exceptions for things like donut shops) and very quickly (by middle of next year) and extremely decisively.</p>
<p>I find this amazing for a couple of reasons.&nbsp; First, it drives home the artificial nature of trans-fats.&nbsp; I&#8217;ve thought of them as similar to saturated fats in a lot of ways &#8212; things that are everywhere but should be avoided.&nbsp; But thinking about what it would mean to not use them in a restaurant makes clear that they&#8217;re not so omnipresent.&nbsp; No crisco vegetable shortening, and no margarine.&nbsp; Other than that, what <em>ingredients</em> have trans fats in them?&nbsp; Partially hydrogenated vegetable oil &#8212; I&#8217;ve never used that.&nbsp; Have you?</p>
<p>I do want to mention olive oil a bit.&nbsp; Olive oil is primarily a monounsaturated fat, which is a very healthy kind of oil.&nbsp; Heating a monounsaturated oil like can turn it into a trans-fat.&nbsp; Some have concluded from this that cooking with olive oil is unhealthy, and I admit I&#8217;ve spread this rumor too.&nbsp; But from the little research I&#8217;ve managed to dig up (<a href="http://www.oliveoilsource.com/cooking_olive_oil.htm">1</a>, <a href="http://en.wikipedia.org/wiki/Cooking_oil#Health_and_nutrition">2</a>) this process doesn&#8217;t occur enough to be a real issue in traditional cooking settings.&nbsp; I will say this research is thin and minds may change.</p>
<p>I&#8217;d like to say a bit about the chemistry involved here.&nbsp; Trans-fats refers to the configuration of carbons on either side of a double-bond, or a place where the fat is unsaturated &#8212; it&#8217;s a <em>trans</em> rather than a <em>cis</em> configuration.&nbsp; Cis fats have marked bends, while trans fats have kinks in otherwise straight chains. I&#8217;m guessing the reduced mobility of the unsaturated fats caused by<br />
their bends are related to their health benefits, but I&#8217;m not sure.&nbsp; Here are two monounsaturated fats, in <em>cis</em> and <em>trans</em> forms: </p>
<table border="1">
<tbody>
<tr>
<td><center><em>Cis</em> fatty acid: <a href="http://en.wikipedia.org/wiki/Oleic_acid">oleic acid</a><br />
<img src="http://upload.wikimedia.org/wikipedia/commons/thumb/2/27/Oleic-acid-3D-vdW.png/300px-Oleic-acid-3D-vdW.png" /><br />
<br />
<img src="http://upload.wikimedia.org/wikipedia/commons/thumb/7/79/Oleic-acid-skeletal.svg/300px-Oleic-acid-skeletal.svg.png" /><br />
</center>
</td>
</tr>
<tr>
<td><center><em>Trans</em> fatty acid: <a href="http://en.wikipedia.org/wiki/Elaidic_acid">elaidic acid</a></p>
<p>
<img src="http://upload.wikimedia.org/wikipedia/commons/thumb/b/bc/Elaidic-acid-3D-vdW.png/300px-Elaidic-acid-3D-vdW.png" /><br />
<br />
<img src="http://upload.wikimedia.org/wikipedia/commons/thumb/0/02/Elaidic-acid-2D-skeletal.png/300px-Elaidic-acid-2D-skeletal.png" /><br />
</center>
</td>
</tr>
</tbody>
</table>
<p>Also, most of what I&#8217;ve been reading assumes that hydrogenation is the only way that trans fats can occur, which is wrong.&nbsp; Industrial hydrogenation converts unsaturated double-bonds to single bonds, preferentially in the trans configuration.&nbsp; But other chemical processes can do this too.&nbsp; Cows naturally produce small quantities of trans fats.</p>
<p>This law is a great example the government taking a broader interest in society values than any individual constituent would.&nbsp; The government pays for health care, so in this case they do have a direct interest in improving public health, and will likely see a benefit from this, so it&#8217;s not a perfect example of the principal I&#8217;m expounding.&nbsp; In general, I think it&#8217;s the government&#8217;s responsibility to legislate things that are for the &quot;long-term good of society&quot; (in quotes because I recognize that it&#8217;s hard to define or agree upon).&nbsp; This burden falls uniquely on the government when there&#8217;s nobody else who clearly benefits from this kind of legislation.&nbsp; Environmental protection is a classic example of this &#8212; do things that won&#8217;t directly help us or our kids but rather our great grand-kids.&nbsp; The Lorax spoke for the trees for the trees had tongues.&nbsp; Today, NGOs tend to do that speaking, and sometimes the government listens.&nbsp; I&#8217;m surprised, impressed and proud of New York for this bold move!</p>
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