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	<title>Dear Science &#187; Dear Science Column</title>
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	<link>http://dearscience.org</link>
	<description>Seattle's Only Scientist</description>
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		<title>It&#8217;s Difficult to Say Nice Things About NDs</title>
		<link>http://dearscience.org/2009/05/27/its-difficult-to-say-nice-things-about-nds/</link>
		<comments>http://dearscience.org/2009/05/27/its-difficult-to-say-nice-things-about-nds/#comments</comments>
		<pubDate>Wed, 27 May 2009 19:32:29 +0000</pubDate>
		<dc:creator>Jonathan Golob</dc:creator>
				<category><![CDATA[Dear Science Column]]></category>
		<category><![CDATA[Response to Critique]]></category>

		<guid isPermaLink="false">http://dearscience.org/?p=848</guid>
		<description><![CDATA[A recent column of mine responded to a question/rant about naturopathic medicine: A dear friend of mine is about to enter a prestigious program of naturopathic medicine. There—in exchange for hundreds of thousands of dollars and five years of his life—he will study homeopathy, osteopathy, water therapy, etc. Apparently, after gaining his ND credential, he [...]]]></description>
			<content:encoded><![CDATA[<p>A recent column of mine <a href="http://www.thestranger.com/seattle/dear-science/Content?oid=1540601">responded to a question/rant about naturopathic medicine</a>:</p>
<blockquote><p><em>A dear friend of mine is about to enter a prestigious program of naturopathic medicine. There—in exchange for hundreds of thousands of dollars and five years of his life—he will study homeopathy, osteopathy, water therapy, etc. Apparently, after gaining his ND credential, he will not only be allowed to practice medicine in Washington, but also to prescribe drugs. Why does state law allow these practitioners to dole out the pills? Can this possibly be safe?</p>
<p>Incredulous Friend</p>
<p>P.S. <strong>Is there a polite way to tell someone that everything he passionately believes in is bunk and that he&#8217;s throwing his life away?</strong></em></p></blockquote>
<p>I <strong>disagreed with the questioner</strong>; a lot of alternative medicine is worthwhile, and increasingly demonstrated to be so by the scientific method. </p>
<blockquote><p>Fortunately, <strong>not all of naturopathic medicine is bunk</strong>&#8230;.The less a branch of naturopathic medicine defines itself as being in opposition to &#8220;allopathic medicine&#8221; (i.e., scientific medicine), the more useful it seems to be for patients. Most massage therapists or acupuncturists will gladly admit the limits of their techniques, and the benefits from receiving treatment from either can be scientifically demonstrated. For things like chronic back pain, arguably these practitioners will be of more use to a patient than a doctor armed with pills and surgery. Training in osteopathy is becoming ever closer to the curriculum one would find in a medical school; Science would trust an osteopath as a primary caregiver as much as an MD.</p>
<p><strong>Only when the naturopathic fields refuse to have their claims tested by experimentation does Science find them to be silly or even fraudulent.</strong></p></blockquote>
<p>This position&#8211;that an ND curriculum based upon science is as valid as one taught at a traditional medical school&#8211;is a bit out there, a more generous stance in favor than typical for naturopathic medicine. </p>
<p>The response from the local ND community? Emails like these:</p>
<blockquote><p>First problem:  it is an opinion dressed in an article called &#8216;Science.&#8217;  That is shitty science. It is also crappy journalism to advance opinion as fact.  Some simple searches on PubMed would have improved the entire article, or maybe call a few people with credentials like Dan Savage does. </p>
<p>Bigger problem:  <strong>Bastyr University pays the Stranger for ad space.</strong>  Obviously, you print what you think is important and everybody is better off because censorship creates fear and drones.  However, I think taking money from a University for ad space and bashing them in an opinion-laden article passed as Science is low.  It is one thing to take ads for cigarettes and then criticize, but Naturopathy is not cigarettes, <strong>it leads to health not health problems.</strong></p>
<p>You paper shapes peoples opinions.  Do you really want to suggest that current medical practices are ideal?  Do you want to discredit the ND&#8217;s who heal while <strong>not partaking in the fraud that is our current healthcare system</strong> and medical practice?  I would like you to publish articles on &#8216;iatrogenic&#8217; disease.  There is a story.</p></blockquote>
<p>Ugh. </p>
<p><img src="http://dearscience.org/wp-content/uploads/2009/05/ebpd.jpg" alt="ebpd" align='left' title="ebpd" width="200" height="323" class="alignleft size-full wp-image-853" />Modern medicine works because of a long legacy of scientific inquiry to human health&#8211;from peer-reviewed, double-blind, randomized and controlled trials to simple correlations of observations to disease states. After pulling out the horrors of our employer-based private insurance system, for-profit hospitals and other aggravations, this body of knowledge&#8211; continually expanded, pruned and refined&#8211;is the basis for the dramatic successes of a deeply flawed health care system. </p>
<p>Take <em>Evidenced-Based Physical Diagnosis</em>, written by a Seattle VA doctor Steven McGee, as an exemplar example. Any caregiver (MD, ND, DO, whatever) with this book, or similar, in their mind is skittering on top of a vast and precise body of knowledge that has taken centuries to accumulate. This collection of carefully curated information, that some of my ND readers are ready to call fraudulent, is beautiful and scientific in the deepest sense of the word. To the extent that alternative caregivers are contributing to it&#8211;using differing philosophies and point of view to open whole new areas to observation&#8211;they deserve a warm embrace. To the extent they are furiously, blindly and stupidly lashing out at it, they are the enemies of health.</p>
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		<title>Yet Another Reason to Dislike CFLs: Horrible Power Factors</title>
		<link>http://dearscience.org/2009/04/09/yet-another-reason-to-dislike-cfls-horrible-power-factors/</link>
		<comments>http://dearscience.org/2009/04/09/yet-another-reason-to-dislike-cfls-horrible-power-factors/#comments</comments>
		<pubDate>Thu, 09 Apr 2009 19:17:50 +0000</pubDate>
		<dc:creator>Jonathan Golob</dc:creator>
				<category><![CDATA[Dear Science Column]]></category>
		<category><![CDATA[Environmental]]></category>

		<guid isPermaLink="false">http://dearscience.org/?p=817</guid>
		<description><![CDATA[Many of you already know of my skepticism of compact fluorescent lightbulbs. Now utilities are joining in the hate: CFLs use about twice as much energy than previously claimed. Lightbulbs, TVs, ovens, baseboard heaters&#8211;whatever&#8211;draw energy from alternating current with varying degrees of efficiency, due to the funkiness of alternating current. Allow me to explain, by [...]]]></description>
			<content:encoded><![CDATA[<p>Many of you already know of my <a href="http://www.thestranger.com/seattle/Content?oid=279476">skepticism of compact fluorescent lightbulbs</a>. Now utilities are joining in the hate: CFLs use about <a href="http://www.edn.com/blog/1470000147/post/450043045.html">twice as much energy than previously claimed</a>. </p>
<p>Lightbulbs, TVs, ovens, baseboard heaters&#8211;whatever&#8211;draw energy from alternating current with <a href="http://en.wikipedia.org/wiki/Power_factor">varying degrees of efficiency</a>, due to the funkiness of alternating current. </p>
<p>Allow me to explain, by taking us all bowling. Kinda.</p>
<p>We want to pump up a tire with a foot bicycle pump down on the far end of the bowling lane. We screw the pump down on its side, and aim with our bowling ball. We hit it, and it shatters into pieces. No good. Marbles would be safe for the pump, but getting them all the way down the alley is next to impossible. They slow down and stop due to friction almost immediately, where the heavy bowling balls have enough momentum to make it all the way to the end. Now what? </p>
<p>We get a clever idea: Let&#8217;s line up a whole bunch of bowling balls in the gutter, placing the last one on the handle of the pump. On our side of the lane, we put a spring on the end of the line of bowling balls. We pull back our spring, a little bit, with the first ball and then let it go. The energy is transferred to the far end through each ball. The last ball at the end of the line presses down on the handle. Some of the energy transferred goes to pump up our tire; the rest goes to compress the pump&#8217;s spring. Eventually, the pump spring gives back most of this stored energy, sending the bowling balls back to our spring. Since some of the energy was used up, we pull our spring back a bit more, and release it again. We now have waves of energy successfully transmitting from our end of the lane to the pump&#8217;s end: Alternating current.</p>
<p>(If this doesn&#8217;t make sense to you, you should feel really thankful for <a href="http://en.wikipedia.org/wiki/Nikolai_Tesla">Nikola Tesla</a>. Without his genius, you would be cold and hungry right now.)</p>
<p>What the power company is doing is constantly adding energy back into the spring at their end of the chain of bowling balls (electrons, unpacking our metaphor). A/C devices with a perfect power factor of 1.0 act as perfect springs: all of the leftover energy delivered is returned in phase back to the power plant. Compact fluorescent lightbulbs mess up the line of bowling balls like an obnoxious kid. When the wave is outgoing, they push in on the chain a little bit; when incoming, they push outward. CFLs make a portion of the alternating current go out of phase. The bowling ball waves still work, but it takes the power company more effort to keep each wave going. </p>
<p>About <em>half</em> the energy used up by a CFL goes to this naughty out of phase game. While there are ways of designing well-behaved CFLs, most companies making them (typically in China, with factory workers twisting hot glass filled with mercury powder by hand) don&#8217;t exactly seem interested. As per <a href="http://www.sfgate.com/cgi-bin/article.cgi?f=/c/a/2009/03/18/DD6P16G9SJ.DTL">Better Off Ted</a>, the corporate motto is, &#8220;Money before people. It&#8217;s engraved right there in the lobby floor. It just looks more heroic in Latin.&#8221;</p>
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		<title>The Carbon Impact of Reading On Paper or Online</title>
		<link>http://dearscience.org/2009/02/13/the-carbon-impact-of-reading-on-paper-or-online/</link>
		<comments>http://dearscience.org/2009/02/13/the-carbon-impact-of-reading-on-paper-or-online/#comments</comments>
		<pubDate>Fri, 13 Feb 2009 21:18:39 +0000</pubDate>
		<dc:creator>Jonathan</dc:creator>
				<category><![CDATA[Dear Science Column]]></category>
		<category><![CDATA[Environmental]]></category>
		<category><![CDATA[Featured Articles]]></category>

		<guid isPermaLink="false">http://dearscience.org/?p=696</guid>
		<description><![CDATA[Is reading The Stranger online actually any greener than reading the printed-in-Yakima hard copy? It was time to roll up my sleeves and do some real, primary, research on the question. Allow me to show my work.]]></description>
			<content:encoded><![CDATA[<p>For my most recent <a href="http://www.thestranger.com/seattle/Author?oid=224756&amp;category=223715">Dear Science column</a>, a reader asked:</p>
<blockquote><p><em>Dear Science,</em></p>
<p><em>I<a href="http://www.thestranger.com/seattle/dear-science/Content?oid=1061697">s reading</a></em><a href="http://www.thestranger.com/seattle/dear-science/Content?oid=1061697"> The Stranger </a><em><a href="http://www.thestranger.com/seattle/dear-science/Content?oid=1061697">online actually any greener than reading the printed-in-Yakima hard copy</a>? Doesn&#8217;t it take a shitload of electricity to run the servers and keep them cool? How would one even figure out how to compare the carbon footprint of, say, going to the coffee shop once a week and reading the print version versus reading it online, as well as checking in with Slog on a regular basis? Folks talk about the internet as being green, but part of me suspects that all it does is put its pollution somewhere out of sight.</em></p></blockquote>
<p>Usually, when I get a question like this, I do a search to see if anyone else&#8211;particularly in the scientific literature&#8211;has done an analysis. All I could find was a high-on-sensation, low-on-content article from a Harvard professor touting his company.</p>
<p>It was time to roll up my sleeves and do some real, primary, research on the question. (If you just want the answer, go <a href="http://www.thestranger.com/seattle/dear-science/Content?oid=1061697">read the column for the condensed answer</a>.) Allow me to show my work.</p>
<p>For print on paper, I assumed the two major carbon impacts would be the manufacturing of the paper itself, and the physical distribution of the printed copies.</p>
<p>The EPA maintains <a href="http://www.epa.gov/climatechange/wycd/waste/calculators/ReCon_Online.html">a fantastic online calculator</a> intended to help manufactures figure out ways of reducing their carbon impact by using recycled materials. Newsprint is one of the categories. Kevin (at <em>The Stranger</em>) was kind enough to tell me the amount of recycled paper (pre- and post-) consumer: 40% pre-consumer, 40% post-consumer recycled and 20% pulp from freshly cut down trees. As my column notes, only the use of post-consumer recycled paper reduces the carbon impact. Both pre-consumer recycled paper and pulp require the cutting down of trees. As I noted in another column, <a href="http://www.thestranger.com/seattle/dear-science/Content?oid=309823">trees actively sequester carbon</a>. Cutting them down, if you&#8217;re accounting properly, has a really nastly net impact on the atmosphere.</p>
<p>I independently calculated the tons of paper needed each week by weighing a single copy (150 grams) and multiplying by the total circulation. The total weekly weight was about 13,500 kg (about 30,000 pounds) of paper. Kevin confirmed this was about right. For the mix of recycled paper used, that worked out to 5.2 metric tons of carbon equivalent (MTCE) released into the atmosphere each week for just the paper. If <em>The Stranger</em> used (much more expensive) 100% post-consumer recycled paper, this would drop to a mere 0.30 MTCE per week&#8211;17.5 fold less than currently emitted.</p>
<p>For the distribution, I first started with the semi-truck from Yakima to Seattle&#8211;140 miles at about 5 miles per gallon, or about 28 gallons of diesel fuel consumed per trip. Burning a gallon of diesel fuel releases about 2.8 kg of carbon into the atmosphere, so 28 gallons is about 0.08 MTCE emitted.</p>
<p>The in-town distribution consumes another 76 gallons of gasoline per week. Burning gasoline releases about 2.4 kg of carbon per gallon, making the total emissions from the in-town distribution 0.19 MTCE per week.</p>
<p>The total for the physical delivery of the paper? 0.26 MTCE per week. The overall total (paper + distribution) carbon impact for the paper each week worked out to about 5.5 MTCE per week, almost all of which coming from the newsprint itself. Divide by the current circulation of The Stranger, and that works out to about 71g of carbon equivalent per printed paper: 67.4 g for the paper itself, 3.4g for distribution.</p>
<p>Were my assumptions valid? I&#8217;m ignoring the energy costs of running the printing presses, figuring they are probably predominantly powered by non-carbon emitting hydroelectric and wind power. I&#8217;m also ignoring the carbon impact of manufacturing the soy-based ink, assuming it&#8217;s a small contributor. That might be dangerous, as farms are massive contributors to atmospheric carbon emissions. I couldn&#8217;t find a good source for the MTCE per gallon of soy-based ink. If anyone knows, I&#8217;ll be glad to incorporate it into my analysis.</p>
<p>For online, we have a few things to consider: how much energy does it take to serve, deliver and read the content.</p>
<p>A <a href="http://imc2.com/Documents/CarbonEmissions.pdf">nicely done study</a> figured it takes about 12.5kWh per gigabyte of data served and delivered on the internet. On average in the US, generating one kWh of electricity emits 0.00012 MTCE into the atmosphere.</p>
<p>Anthony was kind enough to provide me with hard numbers for the number of visitors and views on <em>The Stranger</em>&#8216;s website in a week. I measured a bunch of pages to calculate the average pageview on <em>The Stranger</em>&#8216;s website weighs in at about one megabyte. The total weekly carbon imact of serving and delivering the content on <em>The Stranger</em>&#8216;s website is about 1.7 MTCE; interestingly, that&#8217;s more than the weekly carbon impact of distributing the physical paper. Per unique visitor, that works out to 9.4 grams of carbon equivalent each just on the delivery.</p>
<p>The carbon impact of reading things on the internet really is dependent upon which computer you are using&#8211;and how many watts the computer uses. A relatively modern laptop, consuming 45 watts, emits 5.4 grams of carbon equivalent per hour to operate. A big honking desktop PC, weighing in at 250 watts, emits 30g per hour.</p>
<p>I have no clue how many hours a week people spend reading and commenting on <em>The Stranger</em>&#8216;s website, nor the mixture of computers. So, I cannot make an honest estimate of the total carbon impact of the online presence of the paper. I can tell you about 11.4 hours of online reading on a laptop, per week, has about the same carbon impact as a single paper copy. Reading on a desktop PC? Only two hours equals the carbon impact of the paper.</p>
<p><img class="aligncenter size-full wp-image-715" title="per-reader-impact" src="http://dearscience.org/wp-content/uploads/2009/02/per-reader-impact.png" alt="per-reader-impact" width="434" height="261" /></p>
<p>Want to calculate for your own PC? Here&#8217;s the formula:</p>
<p>(Watts of your PC) * 0.00012 * 1000 = your grams of carbon emitted per hour.</p>
<p>For the number of hours until reading online on your PC equals the carbon impact of a single paper:</p>
<p>61.6 / (grams of carbon per hour from your PC) = number of hours.</p>
<p>How are my assumptions here? I&#8217;m not considering the carbon impact of manufacturing the laptops and computers. But, I&#8217;m not considering the carbon impact of manufacturing the roads, trucks either.</p>
<p>And, as I end my column noting, reading isn&#8217;t even close to your biggest carbon impact. A <a href="http://openthefuture.com/cheeseburger_CF.html">single cheeseburger emits the equivalent of a kilogram of carbon</a>. Driving the average car on the road today one mile emits more carbon equivalent into the atmosphere than a single paper.</p>
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		<title>Special Bonus Dear Science: Why is My Car Shit in Snow?</title>
		<link>http://dearscience.org/2008/12/21/special-bonus-dear-science-why-is-my-car-shit-in-snow/</link>
		<comments>http://dearscience.org/2008/12/21/special-bonus-dear-science-why-is-my-car-shit-in-snow/#comments</comments>
		<pubDate>Mon, 22 Dec 2008 00:44:17 +0000</pubDate>
		<dc:creator>Jonathan Golob</dc:creator>
				<category><![CDATA[Dear Science Column]]></category>

		<guid isPermaLink="false">http://dearscience.org/?p=621</guid>
		<description><![CDATA[This just in to the Dear Science SNOWPOCALYPSE 2008 &#8482; (Hannukah eve again, bitches) crisis center war room control: Dear Science, Do AWD or 4WD help me STOP my vehicle faster in inclement weather? I&#8217;ve always assumed that even with my extra weight and wider tires this was true&#8230; hence my absent mindedness when tailgating [...]]]></description>
			<content:encoded><![CDATA[<p>This just in to the Dear Science SNOWPOCALYPSE 2008 &#8482; (Hannukah eve again, bitches) crisis center war room control:</p>
<blockquote><p><em>Dear Science,<br />
     Do AWD or 4WD help me STOP my vehicle faster in inclement weather?  I&#8217;ve always assumed that even with my extra weight and wider tires this was true&#8230; hence my absent mindedness when tailgating other drivers and driving 5mph above the posted speed limit (cops are too busy dealing with traffic accidents to be shooting a radar gun anyway) when it snows.</p>
<p>Thanks Dear Science!</em></p></blockquote>
<p>Your all-wheel or four-wheel drive <strong>does not help you stop or steer</strong>; such devices only help you get your vehicle more readily achieve a speed at which you will be unable to control it. So, stop tailgating. Stop now. Stop. Park your car and stop. Stop. Do not drive. Stop. Stop. Go home and eat soup. Stop.</p>
<p>Why? The frictional force generated by your vehicle&#8217;s tires keeps your car in place, allows you to steer, stop and start. It&#8217;s your tires, and the weight of the vehicle, that really determine how well you can steer and stop&#8211;not how many wheels the motor turns.</p>
<p>This is what your car looks like where it touches the ground, four little patches of rubber. <center><img src="http://dearscience.org/wp-content/uploads/2008/12/patches.png" alt="patches" title="patches" width="75" height="129" class="alignright size-full wp-image-630"  /></center></p>
<p>When the tires are rolling down the road, these little patches should <em>not</em> move. The moment the other forces you&#8217;re applying to these patches exceed the frictional force, the patches start to move relative to the ground. When they do, you&#8217;re skidding, i.e. fucked. </p>
<p>What kind of forces do you apply to tires, when driving? Well, when you try to stop, you apply a force going backwards to to your tires:<br />
<center><img src="http://dearscience.org/wp-content/uploads/2008/12/stop.png" alt="stop" title="stop" width="75" height="140" class="aligncenter size-full wp-image-631" align="center" /></center></p>
<p>When turning, you apply a force perpendicular to the motion of the car:<br />
<center><img src="http://dearscience.org/wp-content/uploads/2008/12/turning.png" alt="turning" title="turning" width="85" height="130" class="aligncenter size-full wp-image-632" align="center" /></center></p>
<p>When accelerating, you&#8217;re applying a forward force to your tires. (This is where four-wheel or all-wheel drive helps. This forward force is spread over all four tires, rather than just two. So you can apply, roughly, twice as much accelerating force to the ground before breaking above the frictional force.)<br />
<center><img src="http://dearscience.org/wp-content/uploads/2008/12/accelerate.png" alt="accelerate" title="accelerate" width="75" height="129" class="aligncenter size-full wp-image-633" align="center" /></center></p>
<p>If this reads as gibberish to you, here&#8217;s what you need to know: The amount of frictional force generated by your tires determines how fast you can change the speed of your car (speeding up or down) and how fast you can turn. <strong>The less friction, the slower you can make your car change speed or direction.</strong></p>
<p>Friction is a nifty little force, with a fantastically simple formula, filled with eeevil, to calculate it:</p>
<p><center><code>F = μ*N</code></center></p>
<p>Let&#8217;s talk about N first. N is equal to normal force&#8211;the force shoving your car into the pavement, generally gravity. The bigger your car, the mass gravity has to grab and pull to the center of the earth. On flat ground, that means more normal force, and thus more frictional force.</p>
<p>μ is a bit trickier. μ is how sticky the meeting between the tire and the road is. The wider your tires are and the stickier the rubber they&#8217;re made of, the higher your μ. The snowier and icier the road is, the lower your μ becomes, regardless of your tires.</p>
<p>μ comes in two flavors, static (when stuck) and kinetic (when slipping.) When the tires are still stuck to the road&#8211;when the sum of the forces applied to the tire is less than the frictional force, it&#8217;s static μ that counts. Once things start slipping, kinetic μ takes charge. Here&#8217;s the evil: kinetic μ is always less than static.</p>
<p>Let&#8217;s play this out. You&#8217;re attempting to go up Denny Way, despite the road closed sign. Your (idiotic) strategy? Floor it, fuckers! </p>
<p>Just before you start, your tires are still stuck to the road&#8211;static friction is in charge. You press the gas all the way down, causing the tires to apply a <em>huge</em> force to the road, speeding you up a bit. Pretty quickly, this force exceeds the modest static frictional force your tires are producing. They start to spin. Now it&#8217;s kinetic friction&#8217;s turn! Not only is your car not going forward, now you cannot steer or stop as you slowly drift into a pole. You panic and slam on the brakes, figuring you should at least be able to stop since the brakes <em>just</em> worked a few seconds ago. But they don&#8217;t. Because the kinetic friction generated by your tires is so much less than the static friction you had to work with before, even the modest force generated by braking exceeds it. </p>
<p>So, once your tires start slipping, it&#8217;s really difficult to get them stuck to the road again.<br />
The solution? Do things slowly. Accelerate slowly. Turn slowly. Brake slowly. Go unbearably slow, slow enough that the forces you&#8217;re applying to turn, accelerate or brake are less than static friction.</p>
<p>If you do start to skid, the best thing to do is get your tires moving at about the speed your car is moving relative to the road. Take you feet off the gas and brakes. Turn into the skid. Wait, and you&#8217;ll soon feel the shift from kinetic friction to static. Then, you&#8217;re back in charge, and can start steering.</p>
<p>And this is why tailgating is such a profoundly bad idea. You simply cannot stop quickly. If you try to stop too quickly, you&#8217;ll totally lose control and fuck over someone more responsible than you. Stop. </p>
<p>Double Bonus Time: Why are hill such a pain in the ass in the snow?</p>
<p>Normal force is always perpendicular to the surface. When you&#8217;re on a flat, all of gravity goes to make normal force. When going up a hill, it&#8217;s split, part stays as normal force, part becomes a new pull-you-down-the-hill-force. This force is not your friend:<br />
<center><img src="http://dearscience.org/wp-content/uploads/2008/12/hill.png" alt="hill" title="hill" width="177" height="169" class="aligncenter size-full wp-image-640" /></center></p>
<p>The steeper the hill, the more you shift from normal force to this evil force. If the hill is steep enough, this force can all by itself exceed the dwindling static friction generated by your tires&#8211;dwindling because the normal force is declining.  Hence the &#8220;road closed&#8221; signs on Seattle&#8217;s steepest hills, that you should heed. </p>
<p>Bonus bonus bonus: Why do chains work? By dramatically increasing μ. Put &#8216;em on your front tires to help you stop and steer. </p>
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		<title>New Milk Knowledge</title>
		<link>http://dearscience.org/2008/12/04/new-milk-knowledge/</link>
		<comments>http://dearscience.org/2008/12/04/new-milk-knowledge/#comments</comments>
		<pubDate>Thu, 04 Dec 2008 23:33:17 +0000</pubDate>
		<dc:creator>Jonathan Golob</dc:creator>
				<category><![CDATA[Dear Science Column]]></category>

		<guid isPermaLink="false">http://dearscience.org/?p=615</guid>
		<description><![CDATA[First, Science Magazine is both impressed and disgusted by the clever chemistry behind melamine finding its way into infant formula: A weeks-long investigation into China&#8217;s tainted milk scandal has left scientists astonished by the technical sophistication of those who used melamine to adulterate food products. Chinese investigators, meanwhile, are puzzling over the precise mechanisms of [...]]]></description>
			<content:encoded><![CDATA[<p>First, <a href="http://www.sciencemag.org/cgi/content/full/322/5906/1310">Science Magazine is both impressed and disgusted</a> by the clever chemistry behind melamine finding its way into infant formula:</p>
<blockquote><p>A weeks-long investigation into China&#8217;s tainted milk scandal has left scientists astonished by the technical sophistication of those who used melamine to adulterate food products. Chinese investigators, meanwhile, are puzzling over the precise mechanisms of exposure and toxicity in infants who developed kidney damage&#8230;</p>
<p>Researchers say the adulteration was<a href="http://www.sciencemag.org/cgi/content/full/322/5906/1310"> nothing short of a wholesale re-engineering of milk</a>. Weeks ago, investigators established that workers at Sanlu and at a number of milk-collection depots were diluting milk with water; they added melamine to dupe a test for determining crude protein content. &#8220;Adulteration used to be simple. What they did was very high-tech,&#8221; says Chen. Researchers have since learned that the emulsifier used to suspend melamine—a compound that resists going into solution—also boosted apparent milk-fat content.
</p></blockquote>
<p>When the first melamine scandal broke in the United States,<a href="http://www.thestranger.com/seattle/Content?oid=242809"> I was similarly impressed and distressed</a>:</p>
<blockquote><p>The killer pet food used &#8220;human-grade protein&#8221; from China which had melamine—a slightly toxic coal byproduct—mixed in to make a crappy product mimic a high-quality one. It was crafty chemistry. Melamine is a six-member ring of alternating carbons and nitrogens. The three NH2s—the amino groups—hanging off the ring chemically behave like the amino groups that hang off every amino acid in proteins. The chemical reaction that determines protein amounts in food works by detecting these amino-to-carbon bonds. The test doesn&#8217;t care if the amino groups are in melamine or protein, so it gets duped&#8230;.</p>
<p><a href="http://www.thestranger.com/seattle/Content?oid=242809">These schemes are brilliant, employing clever chemistry and marketing</a>—everything but manufacturing a quality product. Imagine what China&#8217;s emerging businessmen and scientists could accomplish in a system that punishes cheating your customers, demands quality products, and protects intellectual property.</p></blockquote>
<p>Next, <a href="http://www.pnas.org/content/105/48/18964.full">a pleasant symbiotic relationship between breast milk, bacteria and babies</a> in the Proceedings of the National Academy of Sciences. </p>
<p>In order to develop properly—to grow the brain and nervous system in particular—babies need specific nutrients like foliate. Mothers cannot directly provide these nutrients, because humans lack the enzymes to generate them. Some bacteria can make these nutrients, but need a food source to do so. </p>
<p>Mothers make a particular collection of food molecules in breast milk, that the baby cannot directly use, to be consumed by a friendly family of bacteria. These bacteria, in turn, produce foliate and other crucial nutrients for the baby. How impressive and heartening.</p>
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		<title>Mutating: The Results</title>
		<link>http://dearscience.org/2008/12/02/mutating-the-results/</link>
		<comments>http://dearscience.org/2008/12/02/mutating-the-results/#comments</comments>
		<pubDate>Tue, 02 Dec 2008 23:44:35 +0000</pubDate>
		<dc:creator>Jonathan Golob</dc:creator>
				<category><![CDATA[Dear Science Column]]></category>

		<guid isPermaLink="false">http://dearscience.org/?p=600</guid>
		<description><![CDATA[I asked you to help me with an experiment as a follow up to a recent column on mutation. Here are the results: (Click on the image for a full-sized version.) Ultimately, I decided to not filter out all of the noise comments (including my own) that weren&#8217;t attempts to copy the original. Almost all [...]]]></description>
			<content:encoded><![CDATA[<p>I asked you to <a href="http://slog.thestranger.com/slog/archives/2008/11/25/mutating">help me with an experiment</a> as a follow up to <a href="http://www.thestranger.com/seattle/Content?oid=770464&#038;hp">a recent column on mutation</a>.</p>
<p>Here are the results:</p>
<p><a href="http://dearscience.org/wp-content/uploads/2008/12/plot.png"><img src="http://dearscience.org/wp-content/uploads/2008/12/plot-254x191.png" alt="" title="plot" width="254" height="191" class="aligncenter size-medium wp-image-601" /></a><br />
(Click on the image for a full-sized version.)</p>
<p>Ultimately, I decided to not filter out all of the noise comments (including <a href="http://slog.thestranger.com/slog/archives/2008/11/25/mutating#BlogComments-comment-787292">my own</a>) that weren&#8217;t attempts to copy the original. Almost all of these clustered together in the green block.</p>
<p>The attempts that riffed off the original&#8211;like <a href="http://slog.thestranger.com/slog/archives/2008/11/25/mutating#BlogComments-comment-787312">Fnarf</a>&#8216;s and <a href="http://slog.thestranger.com/slog/archives/2008/11/25/mutating#BlogComments-comment-787571">Urgutha Forka</a>&#8216;s&#8211;clustered together as well in the blue blocks. </p>
<p>My original paragraph was slotted in as comment zero, located in the <a href="http://en.wikipedia.org/wiki/Dendrogram">dendrogram</a> as the left-most leaf in the red block. All of the legitimate attempts to copy the paragraph ended up clustered together in the red block. </p>
<p>A few cool mutations emerged. My original:</p>
<blockquote><p>CCR is short for chemokine receptor. Chemokines and chemokine receptors allow the cells in your immune system to speak to one another; their epic fight against invaders is like a game of Marco Polo. CCR5 is the chemokine receptor found on macrophages—the gobbling-up cells at the front line of your immune system.</p></blockquote>
<p><a href="http://slog.thestranger.com/slog/archives/2008/11/25/mutating#BlogComments-comment-785341">Luckier&#8217;s Comment #10</a>:</p>
<blockquote><p>CCR is short for chemokine receptor. Chemokines and chemokine receptors allow the cells in your immune system to speak to one another; their epic fight against invaders is like a game of Marco Polo. CCR5 is <strong>a the</strong> chemokine receptor found on macrphages&#8211;the gobbling-up cells at the front line of your immune system.</p></blockquote>
<p>Like most mutations during the copying of DNA, the differences in the copies didn&#8217;t really change the meaning, just a few little details of how it was written or punctuated. </p>
<p>See any others?</p>
<p><span id="more-600"></span><br />
Here&#8217;s the python code it took to make this output:</p>
<blockquote><p><code>
<pre>
from HTMLParser import HTMLParser
import string
import sys
import os.path
import copy
import matplotlib
matplotlib.use('Agg')
import matplotlib.pyplot as plt
from hcluster import pdist, linkage, dendrogram, totree
import numpy

class Spider(HTMLParser):
    def __init__(self, file, inlist):
        HTMLParser.__init__(self)
        self.inComment = False
        self.tempComment = []
        self.commentList = inlist
        self.feed(file.read())

    def handle_starttag(self, tag, attrs):
        if tag == 'div' and attrs:
            for att in attrs:
                if att[0] == "class" and att[1] == "commentText clearfix":
                    self.inComment = True

    def handle_data(self,data):
        if self.inComment:
                self.tempComment.append(data)

    def handle_endtag(self, tag):
        if tag == 'div' and self.inComment:
            self.commentList.append(copy.deepcopy(self.tempComment))
            self.tempComment = []
            self.inComment = False

    def getCommentList(self):
        return self.commentList

filename = sys.argv[1]

if os.path.isfile(filename):
    myfile = open(filename,'r')
    rawCommentList = []
    # Let's initialize the CommentList with my original seed text
    CommentList = [{'text': "								CCR is short for chemokine receptor. Chemokines and chemokine receptors allow the cells in your immune system to speak to one another; their epic fight against invaders is like a game of Marco Polo. CCR5 is the chemokine receptor found on macrophages--the gobbling-up cells at the front line of your immune system.", 'num': '0'}]
    tempVector = []
    for c in CommentList[0]['text']:
        if not c == '\t':
           tempVector.append(ord(c))

    CommentList[0]['vector'] = copy.deepcopy(tempVector)
    Spider(myfile, rawCommentList)

    for rawComment in rawCommentList:
        tempCommentDict = {}
        tempCommentDict['num'] = rawComment[2]
        tempCommentDict['text'] = rawComment[6]
        tempVector = []
        for c in rawComment[6]:
            if not c == '\t':
                tempVector.append(ord(c))

        tempCommentDict['vector'] = copy.deepcopy(tempVector)

        CommentList.append(copy.deepcopy(tempCommentDict))

    vectorList = []
    maxVectorLen = 0
    for Comment in CommentList:
        vectorList.append(Comment['vector'])
        if len(Comment['vector']) > maxVectorLen:
            maxVectorLen = len(Comment['vector'])

    for index, v in enumerate(vectorList):
        if len(v) < maxVectorLen:
            paddingLen = maxVectorLen - len(v)
            vectorList[index] = v+ [0]*paddingLen

    dm = pdist(vectorList)
    lm = linkage(dm)
    dendrogram(lm)

    plt.savefig('plot.png', dpi=(200))
</pre>
<p></code>
</p></blockquote>
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		<title>Why Do I Have to Poop When Browsing, Redux</title>
		<link>http://dearscience.org/2008/09/18/why-do-i-have-to-poop-when-browsing-redux/</link>
		<comments>http://dearscience.org/2008/09/18/why-do-i-have-to-poop-when-browsing-redux/#comments</comments>
		<pubDate>Thu, 18 Sep 2008 21:06:22 +0000</pubDate>
		<dc:creator>Jonathan Golob</dc:creator>
				<category><![CDATA[Response to Critique]]></category>

		<guid isPermaLink="false">http://dearscience.org/?p=401</guid>
		<description><![CDATA[This just in to the Dear Science mailbag: Dear Science, I recently read your response to Bothered Bowels&#8217; inquiry from 2/13/2008. Sadly, BB is not alone. I actually know several people who experience this same issue, most with #2, but others with #1. Indeed, it particularly occurs at Value Village, libraries, bookstores, and also when [...]]]></description>
			<content:encoded><![CDATA[<p>This just in to the Dear Science mailbag:</p>
<blockquote><p>Dear Science,</p>
<p>I recently read your <a href="http://www.thestranger.com/seattle/Content?oid=511078">response to Bothered Bowels&#8217; inquiry</a> from 2/13/2008.    Sadly, BB is not alone.  I actually know several people who experience this same issue, most with #2, but others with #1.  Indeed, it particularly occurs at Value Village, libraries, bookstores, and also when shopping to CD&#8217;s.  I find your Pavlovian theory rather interesting and plausible, but I would like to be so bold as to add a comment. </p>
<p>The common theme for BB and others like him/her seems to be situations that involve the act of browsing.  Is there something relaxing about the process of roaming through large spaces while searching for non-specific items of marginal necessity that activates the parasympathetic nervous symptom and its associated &#8220;urges&#8221;? </p>
<p>Or, could it be that people are more likely to have downed a cup of coffee shortly before entering one of these establishments?</p>
<p>Thanks for your excellent column,<br />
Laurie</p></blockquote>
<p>Laurie,</p>
<p>I like your theories as well. I almost always have to pee after public speaking&#8211;I figure from the loss of sympathetic tone from the relief of it finally being over allows my bladder to reassert itself. </p>
<p>Coffee is a <a href="http://en.wikipedia.org/wiki/Sympathomimetic">sympathomimetic</a>, forcing the activation of the wrong side of the autonomic nervous system. But it&#8217;s also a diuretic, causing you to have to pee. More research is warranted. </p>
<p>Thanks for reading and writing!</p>
<p>- Jonathan (aka Science)</p>
<p>(Don&#8217;t forget to check out <a href="http://podcasts.thestranger.com/2008/02/dear_science_behavior_modifica">the podcast for this column</a>, one of my all-time favorites!)</p>
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		<title>Science, Trashed</title>
		<link>http://dearscience.org/2008/07/17/science-trashed/</link>
		<comments>http://dearscience.org/2008/07/17/science-trashed/#comments</comments>
		<pubDate>Thu, 17 Jul 2008 20:18:02 +0000</pubDate>
		<dc:creator>Jonathan Golob</dc:creator>
				<category><![CDATA[Dear Science Column]]></category>

		<guid isPermaLink="false">http://dearscience.org/?p=178</guid>
		<description><![CDATA[What happens to biodegradable trash in a landfill? Entombed deeply in a landfill, your biodegradable trash is forced to degrade without oxygen, creating copious amounts of methane gas. Methane is a potent greenhouse gas, far worse than carbon dioxide. If you&#8217;re sending something to a landfill, it&#8217;s better for the planet if it never degrades. [...]]]></description>
			<content:encoded><![CDATA[<p><img class="alignnone size-full wp-image-185" title="landfill" src="http://dearscience.org/wp-content/uploads/2008/07/landfill.jpg" alt="" width="500" height="338" /></p>
<p>What happens to biodegradable trash in a landfill?</p>
<blockquote><p>Entombed deeply in a landfill, <a href=" http://www.thestranger.com/seattle/Content?oid=621774&amp;hp">your biodegradable trash is forced to degrade without oxygen, creating copious amounts of methane gas</a>. Methane is a potent greenhouse gas, far worse than carbon dioxide. If you&#8217;re sending something to a landfill, it&#8217;s better for the planet if it never degrades.</p>
<p>A landfill is intended to be a place without time, where trash is meant to stay isolated from the surrounding air, water, and soil—somewhat like the Republican plan for America, through immigration reform (a completely sealed USA). Degrading isn&#8217;t in the plan; it happens anyway, just in a different way.</p></blockquote>
<p>When shopping, I&#8217;m always astonished to find packaging or products loudly proclaiming their biodegradability. For some products, like anything that goes down the drain, this can really matter. Take detergents and soaps, for example. The better they biodegrade, the happier you make your sewage treatment plant.</p>
<p>But non-recyclable packaging boasting it&#8217;s biodegradability? Not so hot. About the only circumstance this really helps is with litter.</p>
<p>In the triad, it&#8217;s reduce, reuse and then recycle. Buy less crap. For every bag of garbage you put on the curb, several bags of industrial waste have already been landfilled making the crap you&#8217;re now throwing out.</p>
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		<title>Dear Science: Lightning Round!</title>
		<link>http://dearscience.org/2007/09/01/dear-science-lightning-round/</link>
		<comments>http://dearscience.org/2007/09/01/dear-science-lightning-round/#comments</comments>
		<pubDate>Sat, 01 Sep 2007 22:10:43 +0000</pubDate>
		<dc:creator>Jonathan Golob</dc:creator>
				<category><![CDATA[Dear Science Column]]></category>

		<guid isPermaLink="false">http://dearscience.org/2007/09/01/dear-science-lightning-round/</guid>
		<description><![CDATA[Vegetarians: outsource your meat eating. Venus fly traps can go vegan, if with a shortened and miserable life. Hybrid drivers: stop duping yourselves and others. Hybrids are no more environmentally friendly than a small regular car, and maybe even a bit worse. Want to be sanctimonious? Ride a bike. Bus riders: time does slow down [...]]]></description>
			<content:encoded><![CDATA[<p>Vegetarians: outsource your meat eating. <a href="http://www.thestranger.com/seattle/Content?oid=303627">Venus fly traps can go vegan</a>, if with a shortened and miserable life.</p>
<p>Hybrid drivers: stop duping yourselves and others. <a href="http://www.thestranger.com/seattle/Content?oid=298817">Hybrids are no more environmentally friendly than a small regular car</a>, and maybe even a bit worse. Want to be sanctimonious? Ride a bike.</p>
<p>Bus riders: <a href="http://www.thestranger.com/seattle/Content?oid=291133">time does slow down when you&#8217;re on the bus</a> &#8212; provided you&#8217;re traveling above about a tenth of the speed of light. Thanks Hendrik!</p>
<p><img src="http://dearscience.org/wp-content/uploads/2007/09/hendrik_lorentz.jpg" title="hendrik_lorentz.jpg" alt="hendrik_lorentz.jpg" align="middle" /></p>
<p>Pot smokers: yes, you might have &#8220;<a href="http://www.thestranger.com/seattle/Content?oid=284853">psychotic symptoms</a>&#8220;, like hallucination, disorganized thoughts, agitation, or aggression. Pot might make you crazy, or you might just be high. Science isn&#8217;t overly concerned.</p>
<p>Have a question on stem cells, yeast, epigenetics, transplant biology or gene therapy? Put it in the comments and I&#8217;ll answer it within a day, or your money back. Or send your questions to <a href="mailto:dearscience@thestranger.com">DearScience@thestranger.com</a>.</p>
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		<title>Incubator Space</title>
		<link>http://dearscience.org/2007/08/12/incubator-space/</link>
		<comments>http://dearscience.org/2007/08/12/incubator-space/#comments</comments>
		<pubDate>Mon, 13 Aug 2007 00:37:57 +0000</pubDate>
		<dc:creator>Jonathan Golob</dc:creator>
				<category><![CDATA[Response to Critique]]></category>
		<category><![CDATA[South Lake Union]]></category>

		<guid isPermaLink="false">http://dearscience.org/2007/08/12/incubator-space/</guid>
		<description><![CDATA[So, let&#8217;s say I woke up this morning with a great idea to deal with three critical problems in embryonic stem cell therapies with one tidy little trick. Could I found a company in Lake Union? In Seattle? In the region? Finding a vacant warehouse, sweeping out the rats and installing some desks won’t cut [...]]]></description>
			<content:encoded><![CDATA[<p>So, let&#8217;s say I woke up this morning with a great idea to deal with three critical problems in embryonic stem cell therapies with one tidy little trick.</p>
<p>Could I found a company in Lake Union? In Seattle? In the region? Finding a vacant warehouse, sweeping out the rats and installing some desks won’t cut it. Like any biotech start-up, I’ll need lab space, with specialized equipment, air handling and utility support. Some fee-for-service cores, for things like DNA sequencing or animal handling, are essential. So is access to a proper academic library—remember, most journal articles are subscription only.</p>
<p>Very little of the built <i>or planned</i> lab space in Lake Union is set up like this. The “biotech incubator” facilities on Eastlake—not technically in SLU—are woefully inadequate. Nor are the support services in the pipeline. Without some far better developed incubator space for start-ups, the neighborhood will fail as a biotech hub. Period.</p>
<p>UW is already the largest single employer in the city. Do you honestly think the most talented faculty will stick around without the ability to start companies and fully develop ideas? This isn’t a matter of real-estate or making a lovely neighborhood of near-downtown housing. This should be about economic development.</p>
<p>Think I’m just being a whiner? Check out <a href="http://www.nycbiotech.org/realestate.html">New York City’s biotech plan</a>. That is serious, and likely to succeed despite serious disadvantages relative to Seattle. Ours is a joke in comparison.</p>
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