tag:blogger.com,1999:blog-29617918050487062932024-03-12T18:20:55.461-07:00Parsing Science: Understanding the scientific methodThis blog will explain some of the mysteries of the research world and also give you some insights into the the way scientists think. I hope to tell you how scientific research works so that you can better understand the scientific results you encounter in your daily life.Nicolehttp://www.blogger.com/profile/10056174002046814636noreply@blogger.comBlogger28125tag:blogger.com,1999:blog-2961791805048706293.post-24586509501885667852015-09-23T10:00:00.000-07:002015-09-23T10:00:01.045-07:00Adventures in Data Science: Labeling DataNow that my environment is set up, I can finally start doing some coding.<br />
<br />
My current project is creating a spam filter for okcupid messages. I have a dataset of about 700 messages as well as the profile of the woman that the messages were sent to.<br />
<br />
Setup: The profile is of a straight cis-woman. The messages are from straight men writing first messages to her.<br />
<br />
As I mentioned in my last post, I initially had a csv of these messages that I loaded into a MYSQL table.<br />
<br />
I have also started thinking about what features I should use to analyze this data and what the end goal is.<br />
<br />
Some of the initial features I thought of were:<br />
- length of messages (number of characters or number of words)<br />
- match percentage<br />
- enemy percentage<br />
- keywords<br />
<br />
I also started thinking about what type of learning algorithm to use. I decided that I should do some form of supervised learning. <br />
<br />
I was initially planning on just labeling the messages as spam or not. However, I quickly realized that I needed another category of messages. This new category I am calling "terrible".<br />
<br />
Here are the definitions I am using so far.<br />
Spam: A message that has no reference to the profile of the woman they are messaging. This type of message is often really short, focuses on the woman's looks , or asks lame arbitrary questions ("How are you", "how's your weekend")<br />
<br />
Terrible: This message does reference the woman's profile in some way, but typically in a shallow way. This message may focus on the woman's looks, doesn't ask any questions, or is otherwise terrible in some way.<br />
<br />
I realize this is all arbitrary labeling, but I have to start somewhere.<br />
<br />
You can check out the <a href="https://github.com/parsing-science/Message_Filter/blob/master/scripts/tag_messages.py" target="_blank">code</a> for the labeling on my github.Nicolehttp://www.blogger.com/profile/10056174002046814636noreply@blogger.com0tag:blogger.com,1999:blog-2961791805048706293.post-59505063740351480392015-09-16T10:00:00.000-07:002015-09-16T10:00:00.119-07:00Adventures in Data Science: MYSQL on a ChromebookAfter a thousand million years, I was finally able to put data into a MYSQL table. <br />
<br />
I first tried to follow this <a href="http://zetcode.com/db/mysqlpython/" target="_blank">tutorial</a> to learn how to use MYSQL with python.<br />
<br />
However, I quickly got stuck at the step of:<br />
<span style="color: #666666;">$ mysql -u root -p</span><br />
This brought me the first error message:<br />
<span style="color: blue;">- "ERROR 2002 (HY000): Can't connect to local MySQL server through socket '/var/run/mysqld/mysqld.sock' (2)""</span><br />
<br />
I followed this down a rabbit hole of other commands and error messages, some of which are listed below.<br />
<br />
<span style="color: #666666;"><span style="background-color: white;">$ /etc/init.d/mysql</span></span><br />
<span style="color: blue;">- "Rather than invoking init scripts through /etc/init.d, use the service(8)<br />utility, e.g. service mysql start<br />/etc/init.d/mysql: 54: /etc/init.d/mysql: initctl: not found<br /><br />Since the script you are attempting to invoke has been converted to an<br />Upstart job, you may also use the start(8) utility, e.g. start mysql<br />/etc/init.d/mysql: 82: /etc/init.d/mysql: start: not found/usr/bin/service: 123: exec: start: not found"</span><br />
<br />
<span style="color: #666666;">$ service mysql start</span><br />
<span style="color: blue;">- "start : Unknown job: mysql"</span><br />
<br />
Many hours of research brought me to this page after I searched for "initctl not found crouton": <a href="https://github.com/dnschneid/crouton/wiki/Running-servers-in-croutonO" target="_blank">https://github.com/dnschneid/crouton/wiki/Running-servers-in-croutonO </a><br />
<br />
Thr problem apparently transpired because I was running Crouton on a chromebook. Turns out the MYSQL server doesn't start automatically when the chroot boots up. Never would have guessed that.<br />
<br />
Once I applied the solution listed on the github site, the MYQL server started running when I start my chroot. Fingers crossed that it will stay like that! <br />
<br />
I went back and finished the python tutorial mentioned above. I found it to be really useful for getting me started with mysqldb in python.<br />
<br />
I finally got to read in my csv of data, and put it into a mysql table.<br />
<br />
I'm very happy that I don't have to deal directly with the csv anymore. I'm hoping the MYSQL database will be easier to handle.<br />
<br />
Next time: labeling data.Nicolehttp://www.blogger.com/profile/10056174002046814636noreply@blogger.com0tag:blogger.com,1999:blog-2961791805048706293.post-22036287607139601552015-09-09T10:00:00.000-07:002015-09-14T15:34:48.683-07:00Adventures in Data Science: Setting up a ChromebookAfter a year and a half of no posts, I'm back with a new blog series about doing data science on a chromebook.<br />
<br />
Recently, I decided to up my coding skills by working on some programming side projects. Unfortunately, my personal computer is a Windows laptop, which is terrible for programming.<br />
<br />
During Amazon Prime Days, I purchased a Chromebook with the intention of putting Linux on it. <br />
<br />
The model I purchased was the Acer C720-3871 (<a href="http://www.amazon.com/Acer-C720-3871-11-6-Inch-Chromebook-Granite/dp/B00KOUIZ9E/ref=sr_1_1?s=pc&ie=UTF8&qid=1441555428&sr=1-1&keywords=acer+c720-3871" target="_blank">Amazon</a>).This one has 2GB of RAM, an Intel processor, and 32 Gb of solid state storage.<br />
<br />
<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiKPIg65Hn4E7YA89vSRunFf9R1QHF8HLFiFwcbokId2gjvK9jZ1eK655G6qTapiU2N0-gwUd8-1z9AmBNdd6I8hlV35LGgAi0ttcfO50jwPfhsqDqQgq2ERbT3NOVyTrkkma1L-I3cd6fG/s1600/acer_closed.jpg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="320" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiKPIg65Hn4E7YA89vSRunFf9R1QHF8HLFiFwcbokId2gjvK9jZ1eK655G6qTapiU2N0-gwUd8-1z9AmBNdd6I8hlV35LGgAi0ttcfO50jwPfhsqDqQgq2ERbT3NOVyTrkkma1L-I3cd6fG/s320/acer_closed.jpg" width="320" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Stickers so you know I'm a real programmer.</td></tr>
</tbody></table>
<br />
<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgH7AdX60Ocxujt1q9wXUZL0lOWj2zykEx9hA2HLQmFmcdIzhqIRuZ8NHzWU5lKBhrsqyLE0Py0zffEwmx4TkRjRTAtheJ3rRSY-h2O6w9FNw2Ju4j6zOcvsAqTPfsq36FNgJrhApaw3UbC/s1600/acer_open.jpg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="320" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgH7AdX60Ocxujt1q9wXUZL0lOWj2zykEx9hA2HLQmFmcdIzhqIRuZ8NHzWU5lKBhrsqyLE0Py0zffEwmx4TkRjRTAtheJ3rRSY-h2O6w9FNw2Ju4j6zOcvsAqTPfsq36FNgJrhApaw3UbC/s320/acer_open.jpg" width="320" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">The open chromebook.</td></tr>
</tbody></table>
<br />
For loading Linux, I followed this tutorial from <a href="http://lifehacker.com/how-to-install-linux-on-a-chromebook-and-unlock-its-ful-509039343?disableinsets=on&utm_expid=66866090-49.VYy4WCNHSyuP6EmjnM93MQ.2" target="_blank">LifeHacker</a> and used Crouton. I chose to load xfce4 on top of ubuntu.<br />
<br />
This version is pretty light weight so it might not work for everyone. I'm only planning on using the chromebook for programming so I didn't care about having a pretty interface or graphics.<br />
<br />
Once I installed Linux, I set up my environment with:<br />
- git<br />
- ipython<br />
- sublime text<br />
- and more!<br />
<br />
Since I'm a scientist, I'm sticking with Python 2.7 right now.<br />
<br />
So far, the chromebook has been good enough for me. There are times when the laptop feels slow to respond, but I'm not sure yet whether that's a result of only having 2 GB of RAM or me not remembering how to use Linux.<br />
<br />
More on installation issues next time.Nicolehttp://www.blogger.com/profile/10056174002046814636noreply@blogger.com0tag:blogger.com,1999:blog-2961791805048706293.post-84225165758279461972014-02-09T18:57:00.002-08:002014-02-09T18:57:29.405-08:00Camera, Camera on the wall, who's the hottest of them all?<div dir="ltr" style="line-height: 1.15; margin-bottom: 0pt; margin-top: 0pt; text-indent: 36pt;">
<span style="font-family: Arial; font-size: 15px; line-height: 1.15; text-indent: 36pt; white-space: pre-wrap;">If you have ever stood next to another human being, then you probably felt some body heat radiating from her. What you might not realize is that everything emits radiation: you, your dog, your chair. Everything! (see this article: </span><a href="http://discovermagazine.com/2007/jun/life-is-rad" style="font-family: Arial; font-size: 15px; line-height: 1.15; text-indent: 36pt; white-space: pre-wrap;">http://discovermagazine.com/2007/jun/life-is-rad</a><span style="font-family: Arial; font-size: 15px; line-height: 1.15; text-indent: 36pt; white-space: pre-wrap;">). </span><br />
<span style="font-family: Arial; font-size: 15px; line-height: 1.15; text-indent: 36pt; white-space: pre-wrap;"><br /></span></div>
<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><img height="339px;" src="https://lh4.googleusercontent.com/sUE7P0lEIurGlhg-pG12l3XLbIxulblDta0sWnXbKlgILDjFfJoCf5r5qoe1NX28-z3_eAGz5nTHyEqZG9y12V5KUegIb9hxJ1tGxhPQPmZjkxxqxoUz6xxjwQ" style="border: 0px solid transparent; margin-left: auto; margin-right: auto;" width="452px;" /></td></tr>
<tr><td class="tr-caption" style="text-align: center;"><span style="font-family: Arial; font-size: 15px; line-height: 17.25px; text-align: start; white-space: pre-wrap;">Explainers play in the infrared camera with ice and hot water. Photo courtesy of Sylvia Algire* </span></td></tr>
</tbody></table>
<br /><a name='more'></a><div dir="ltr" style="line-height: 1.15; margin-bottom: 0pt; margin-top: 0pt; text-indent: 36pt;">
<span style="background-color: transparent; color: black; font-family: Arial; font-size: 15px; font-style: normal; font-variant: normal; font-weight: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><span style="line-height: 1.15; text-indent: 36pt;">Now you are probably asking yourself “Am I the same as a chair?”. While only you can truly answer that question, for the purposes of this blog post, the answer is “no”. The key difference is that you and your chair radiate different amounts of energy.</span></span><br />
<span style="background-color: transparent; color: black; font-family: Arial; font-size: 15px; font-style: normal; font-variant: normal; font-weight: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><span style="line-height: 1.15; text-indent: 36pt;"><br /></span></span></div>
<b style="font-weight: normal;">
<span style="background-color: transparent; color: black; font-family: Arial; font-size: 15px; font-style: normal; font-variant: normal; font-weight: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"></span></b> <br />
<div dir="ltr" style="line-height: 1.15; margin-bottom: 0pt; margin-top: 0pt; text-indent: 36pt;">
<span style="background-color: transparent; color: black; font-family: Arial; font-size: 15px; font-style: normal; font-variant: normal; font-weight: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Physicists model objects that radiate heat as <a href="http://en.wikipedia.org/wiki/Black_body">black bodies</a></span><span style="background-color: transparent; color: black; font-family: Arial; font-size: 15px; font-style: normal; font-variant: normal; font-weight: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">. A black body is an idealized object that absorbs all energy (specifically, <a href="http://en.wikipedia.org/wiki/Electromagnetic_radiation">electromagnetic radiation</a></span><span style="background-color: transparent; color: black; font-family: Arial; font-size: 15px; font-style: normal; font-variant: normal; font-weight: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">) that hits it. A black body will emit radiation in a way that is solely determined by its temperature. The emitted radiation is described by <a href="http://en.wikipedia.org/wiki/Planck%27s_law">Planck’s Law</a>. </span><span style="background-color: transparent; color: black; font-family: Arial; font-size: 15px; font-style: normal; font-variant: normal; font-weight: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Note: only click on the link if you can handle lots of maths. </span><br />
<span style="background-color: transparent; color: black; font-family: Arial; font-size: 15px; font-style: normal; font-variant: normal; font-weight: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><br /></span></div>
<b style="font-weight: normal;">
<span style="background-color: transparent; color: black; font-family: Arial; font-size: 15px; font-style: normal; font-variant: normal; font-weight: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"></span></b> <br />
<div dir="ltr" style="line-height: 1.15; margin-bottom: 0pt; margin-top: 0pt; text-indent: 36pt;">
<span style="background-color: transparent; color: black; font-family: Arial; font-size: 15px; font-style: normal; font-variant: normal; font-weight: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Thus, if we could measure the radiation emitted by a black body, we could determine the object’s temperature. Luckily, the world we live in has such measuring devices: infrared cameras!</span><br />
<span style="background-color: transparent; color: black; font-family: Arial; font-size: 15px; font-style: normal; font-variant: normal; font-weight: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><br /></span></div>
<b style="font-weight: normal;">
<span style="background-color: transparent; color: black; font-family: Arial; font-size: 15px; font-style: normal; font-variant: normal; font-weight: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"></span></b> <br />
<div dir="ltr" style="line-height: 1.15; margin-bottom: 0pt; margin-top: 0pt; text-indent: 36pt;">
<span style="background-color: transparent; color: black; font-family: Arial; font-size: 15px; font-style: normal; font-variant: normal; font-weight: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">An infrared camera measures the infrared radiation emitted by objects and then calculates the apparent temperature of each object. The objects are then colored based on their temperatures (see attached photos for some examples).</span><br />
<span style="background-color: transparent; color: black; font-family: Arial; font-size: 15px; font-style: normal; font-variant: normal; font-weight: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><br /></span></div>
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<span style="font-family: Arial; font-size: 15px; line-height: 1.15; text-indent: 36pt; white-space: pre-wrap;">However, real objects are not black bodies because they only absorb part of the energy that hits them while the rest of the energy is reflected. The percentage of energy that an object emits back is defined as the object’s </span><a href="http://en.wikipedia.org/wiki/Emissivity" style="font-family: Arial; font-size: 15px; line-height: 1.15; text-indent: 36pt; white-space: pre-wrap;">emissivity</a><span style="font-family: Arial; font-size: 15px; line-height: 1.15; text-indent: 36pt; white-space: pre-wrap;">. Therefore, if the emissivity of an object is known, the camera can correctly estimate the temperature of the object and produce an amazing picture.</span><br />
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<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><img height="359px;" src="https://lh5.googleusercontent.com/Ua_cHNKxhZwDyiZMn2T-qPVXSo1lrgclT9LTAKuXr3MbcP7mSrbH7rob71NRcz9lTfvF4pr83sYkhrvGpZbYuZQMDl_5WXmI01NRNiUqROyr1vG89A-uiXLxqQ" style="border: 0px solid transparent; margin-left: auto; margin-right: auto;" width="479px;" /></td></tr>
<tr><td class="tr-caption" style="text-align: center;"><span style="font-family: Arial; font-size: 15px; line-height: 17.25px; text-align: start; white-space: pre-wrap;">Photo courtesy of Sylvia Algire* </span></td></tr>
</tbody></table>
<div class="separator" style="clear: both; text-align: center;">
<b style="font-weight: normal; margin-left: 1em; margin-right: 1em;"></b></div>
<div dir="ltr" style="line-height: 1.15; margin-bottom: 0pt; margin-top: 0pt;">
<span style="background-color: transparent; color: black; font-family: Arial; font-size: 15px; font-style: normal; font-variant: normal; font-weight: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"> In short, infrared cameras give us an opportunity to see into a completely different world. Now that you're done reading, go play in front of an infrared camera with hot water, dry ice, and your own body.</span></div>
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<span style="font-family: Arial; font-size: 15px; line-height: 1.15; text-indent: 36pt; white-space: pre-wrap;"> To learn more about the nitty gritty details of infrared cameras, look up Thermography. Thermography is the field dedicated to infrared imaging including measuring radiation and estimating/measuring emissivities. Thermographers (I totally made up this word) develop fancy algorithms and methods for calibrating infrared cameras. If you are interested in reading more about thermography, check out these links: </span></div>
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<ul>
<li><a href="http://www.testosites.de/export/sites/default/thermalimaging/es_AR/local_downloads/testo_thermalimager_pocketguide.pdf" style="color: #1155cc; font-family: Arial; font-size: 15px; line-height: 1.15; text-decoration: none; text-indent: 36pt; white-space: pre-wrap;">http://www.testosites.de/export/sites/default/thermalimaging/es_AR/local_downloads/testo_thermalimager_pocketguide.pdf</a></li>
<li><span style="color: #1155cc; font-family: Arial; font-size: 15px; line-height: 1.15; text-decoration: underline; text-indent: 36pt; vertical-align: baseline; white-space: pre-wrap;"><a href="http://oce.jpl.nasa.gov/practices/at9.pdf" style="line-height: 1.15; text-decoration: none; text-indent: 36pt;">http://oce.jpl.nasa.gov/practices/at9.pdf</a></span><span style="font-family: Arial; font-size: 15px; line-height: 1.15; white-space: pre;"> </span></li>
</ul>
<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><img height="395px;" src="https://lh5.googleusercontent.com/ye244J_9EBkkA2q_5MCA_XO7nter_K6BXuTDz9r6WPulbYloopwXJDVsMYuzs6iG7FyIz0rhX53K_RbAwDchR1Q4bf7pxiy7iS3NbEX_JxXVbQ2kqOXH9fyMqA" style="border: 0px solid transparent; margin-left: auto; margin-right: auto;" width="527px;" /></td></tr>
<tr><td class="tr-caption" style="text-align: center;"><span style="font-family: Arial; font-size: 15px; line-height: 17.25px; text-align: start; white-space: pre-wrap;">Short-wave infrared camera picture of mock-dead Explainers. Photo courtesy of Jenny Situ* </span></td></tr>
</tbody></table>
<span style="font-family: Arial; font-size: 15px; vertical-align: baseline; white-space: pre-wrap;"></span> <br />
<div dir="ltr" style="line-height: 1.15; margin-bottom: 0pt; margin-top: 0pt;">
<span style="background-color: transparent; color: black; font-family: Arial; font-size: 15px; font-style: normal; font-variant: normal; font-weight: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">*All pictures were taken with the infrared camera or short-wave infrared camera at the Exploratorium (</span><a href="http://www.exploratorium.edu/" style="text-decoration: none;"><span style="background-color: transparent; color: #1155cc; font-family: Arial; font-size: 15px; font-style: normal; font-variant: normal; font-weight: normal; text-decoration: underline; vertical-align: baseline; white-space: pre-wrap;">www.exploratorium.edu</span></a><span style="background-color: transparent; color: black; font-family: Arial; font-size: 15px; font-style: normal; font-variant: normal; font-weight: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">) during a Field Trip Explainer training session.</span></div>
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<span style="background-color: transparent; color: black; font-family: Arial; font-size: 15px; font-style: normal; font-variant: normal; font-weight: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">
</span></div>
<div dir="ltr" style="line-height: 1.15; margin-bottom: 0pt; margin-top: 0pt;">
<span style="background-color: transparent; color: black; font-family: Arial; font-size: 15px; font-style: normal; font-variant: normal; font-weight: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">** Apologies to any physicists reading this post if I simplified things too much!</span></div>
Nicolehttp://www.blogger.com/profile/10056174002046814636noreply@blogger.com0tag:blogger.com,1999:blog-2961791805048706293.post-62968201325409073942013-11-20T19:10:00.001-08:002013-11-20T19:10:45.633-08:00Unnecessary Superpowers: Seeing Polarized Light<div class="separator" style="clear: both; text-align: center;">
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<span style="line-height: 1.15; white-space: pre-wrap;"><span style="font-family: Arial, Helvetica, sans-serif;">“Once you see it, you can’t unsee it”*</span></span></div>
<b id="docs-internal-guid-606749c6-7899-5e70-8999-0a22415969e4" style="font-weight: normal;"><span style="font-family: Arial, Helvetica, sans-serif;"><br /><span style="background-color: transparent; color: black; font-style: normal; font-variant: normal; font-weight: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"></span></span></b>
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<span style="background-color: transparent; color: black; font-style: normal; font-variant: normal; font-weight: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><span style="font-family: Arial, Helvetica, sans-serif;">Earlier this fall, I conversed with my coworker, Julie, about what superpower we would choose. She mentioned that she and another coworker, Rob, were interested in learning how to see different types of light. I immediately grew excited because this seemed like an attainable superpower. I decided to focus on seeing polarized light.</span></span></div>
<b style="font-weight: normal;"><span style="font-family: Arial, Helvetica, sans-serif;"><br /><span style="background-color: transparent; color: black; font-style: normal; font-variant: normal; font-weight: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"></span></span></b>
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<span style="font-family: Arial, Helvetica, sans-serif;"><span style="background-color: transparent; color: black; font-style: normal; font-variant: normal; font-weight: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">During my search, I even found a <a href="http://io9.com/5601591/developing-useless-superpowers-101-how-to-detect-polarized-light">website </a>that listed seeing polarized light as a useless superpower</span><span style="background-color: transparent; color: black; font-style: normal; font-variant: normal; font-weight: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">. My search ended with <a href="http://en.wikipedia.org/wiki/Haidinger%27s_brush">Haidinger’s Brush</a></span><span style="background-color: transparent; color: black; font-style: normal; font-variant: normal; font-weight: bold; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">, </span><span style="background-color: transparent; color: black; font-style: normal; font-variant: normal; font-weight: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">the manifestation of how humans see polarized light. </span></span></div>
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<a href="https://lh4.googleusercontent.com/TrkhPYMxwq6gr5QXrFSr8dOdYN8W012VQq0qaypHiJMMnYNAKuJq8B7OJwEFUhzzU5-7oH_XZk0T8BdRvmKuO8UIABZx-8f-hjNBRb86jkSDAm1IZLUSx8Zndw" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="190px;" src="https://lh4.googleusercontent.com/TrkhPYMxwq6gr5QXrFSr8dOdYN8W012VQq0qaypHiJMMnYNAKuJq8B7OJwEFUhzzU5-7oH_XZk0T8BdRvmKuO8UIABZx-8f-hjNBRb86jkSDAm1IZLUSx8Zndw" width="186px;" /></a></div>
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<span style="font-family: Arial, Helvetica, sans-serif;"><span style="vertical-align: baseline;">Figure 1: Open source image of Haidinger’s brush from Wikipedia</span></span></div>
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<span style="background-color: transparent; color: black; font-style: normal; font-variant: normal; font-weight: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><span style="font-family: Arial, Helvetica, sans-serif;">Haidinger’s brush is a visual phenomenon seen in polarized light that looks like a yellow bowtie with a blue bowtie perpendicular to it (see Figure 1). People do not usually see it naturally, but most can train themselves to detect it. The easiest way to see the brush is on the white screen of an LCD monitor (for example, you could use the computer that you reading this blog post on). Be warned though, once you train yourself to see it, you will probably see it on every future computer that you look at. </span></span></div>
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<span style="background-color: transparent; color: black; font-style: normal; font-variant: normal; font-weight: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><span style="font-family: Arial, Helvetica, sans-serif;">After this initial research, I quickly coerced my study group (Raquel and Hartley) into investigating this phenomenon. We initially tried staring at blank Safari tabs on iPads. Hartley was the first to reach success, but Raquel and I needed some extra help. We decided to go on a search for polarizing filters in the museum.</span></span></div>
<b style="font-weight: normal;"><span style="font-family: Arial, Helvetica, sans-serif;"><br /><span style="background-color: transparent; color: black; font-style: normal; font-variant: normal; font-weight: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"></span></span></b>
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<span style="background-color: transparent; color: black; font-style: normal; font-variant: normal; font-weight: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><span style="font-family: Arial, Helvetica, sans-serif;">During our trip to the shop with senior Explainer, Kate, we fortuitously ran into the museum’s neuroscientist, Richard Brown. He immediately knew what we were talking about and agreed to help us out. He gave us some tips on ways to train our eyes, and he also mentioned that some light-eyed people might never be able to see the brush (take that recessive genes).</span></span></div>
<b style="font-weight: normal;"><span style="font-family: Arial, Helvetica, sans-serif;"><br /><span style="background-color: transparent; color: black; font-style: normal; font-variant: normal; font-weight: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"></span></span></b>
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<span style="background-color: transparent; color: black; font-style: normal; font-variant: normal; font-weight: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><span style="font-family: Arial, Helvetica, sans-serif;">Richard’s main tip was to try rotating the iPad smoothly while looking at it from a distance. We achieved this by using a turntable provided by Kate and standing on the Explainer Hub table. Soon Raquel, Kate, and I were able to see a rotating yellow brush. Hartley claimed that he could also see the blue bowtie as well, but this claim has yet to be verified. </span></span></div>
<b style="font-weight: normal;"><span style="font-family: Arial, Helvetica, sans-serif;"><br /><span style="background-color: transparent; color: black; font-style: normal; font-variant: normal; font-weight: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"></span></span></b>
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<span style="background-color: transparent; color: black; font-style: normal; font-variant: normal; font-weight: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><span style="font-family: Arial, Helvetica, sans-serif;">We decided to share our new-found powers with the other Explainers during our Friday meeting. Although I had to miss that training, Raquel and Hartley reported back that some Explainers were able to see the brush. Unfortunately, Julie was not one of them; she’ll have to find her own superpower. </span></span></div>
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<span style="background-color: transparent; color: black; font-style: normal; font-variant: normal; font-weight: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><span style="font-family: Arial, Helvetica, sans-serif;"><br /></span></span></div>
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<span style="background-color: transparent; color: black; font-style: normal; font-variant: normal; font-weight: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><span style="font-family: Arial, Helvetica, sans-serif; line-height: normal; text-indent: 0px;">Overall, I am ecstatic that I have succeeded in turning myself into a superhero. The next challenge is training myself to see Haidinger’s brush in the sky. And like every superhero, I've already obtained a supervillian: the rain in San Francisco is deliberately thwarting my attempts to see the brush in the sky.</span></span></div>
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<span style="font-family: Arial, Helvetica, sans-serif;"><span style="vertical-align: baseline; white-space: pre-wrap;">*</span><span style="vertical-align: baseline; white-space: pre-wrap;">This post was originally posted at </span><a href="http://explainers.wordpress.com/" style="line-height: 1.15;">http://explainers.wordpress.com/</a><span style="line-height: 1.15;">. It's based on a study group that I was part of at the <a href="http://www.exploratorium.edu/">Exploratorium</a>.</span></span><br />
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Nicolehttp://www.blogger.com/profile/10056174002046814636noreply@blogger.com1tag:blogger.com,1999:blog-2961791805048706293.post-33137899778571028602013-01-29T18:17:00.003-08:002013-01-29T18:18:23.834-08:00Science Theories in Practice:<br />
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As the evolution/creationism debate continues in
the US, one argument that creationists repeatedly use is that evolution
is just a theory, not something that is actually proven (Creationist arguments:
<a href="http://www.talkorigins.org/faqs/faq-misconceptions.html">http://www.talkorigins.org/faqs/faq-misconceptions.html</a>).<o:p></o:p></div>
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Unfortunately, people
who make this argument don’t understand evolution (topic for another post) or
scientific theory (http://en.wikipedia.org/wiki/Theory#Scientific_theories).</div>
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First, what is a scientific theory?<o:p></o:p></div>
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A theory is a set of statements that explains a
group of observations; usually the statements have been widely tested and
accepted. (In physics, either the theory or observations
can come first.)</div>
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<o:p></o:p></div>
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However, a theory is not taken to be the gospel
truth (Bible reference used intentionally). Scientists understand that theories are not necessarily the final answer to everything in the universe.</div>
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For example, in my experience, most candy that is
blue tastes like blue raspberry (http://www.candywarehouse.com/colors/blue-candy/). Thus, my theory is that all blue candy will taste like blue raspberry (as it should).<o:p></o:p></div>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhKbzCpMwBmsSIFtLZEuMXCV8cS9keCyaIjY89F_W7FsorqQYCTe0mbNMQCbVsyApY7z9Pcbv4OBSODU8qODJATI9-ZqZHfidCY31ZEXHpNY-jsuqLpWcILzT0-QyicLK-ZgFdrgllSMokY/s1600/candy.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="320" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhKbzCpMwBmsSIFtLZEuMXCV8cS9keCyaIjY89F_W7FsorqQYCTe0mbNMQCbVsyApY7z9Pcbv4OBSODU8qODJATI9-ZqZHfidCY31ZEXHpNY-jsuqLpWcILzT0-QyicLK-ZgFdrgllSMokY/s320/candy.png" width="256" /></a></div>
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Figure 1: Young woman about to eat what appears to be a
tasty blue raspberry lollipop (based on my theory).<o:p></o:p></div>
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However, if I come across a blue M&M that is
disgustingly chocolate flavored, then I need to revise my theory that all blue
candies are flavored like blue raspberry. This new piece of data has proven that my theory is either incorrect or incomplete.<o:p></o:p></div>
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<o:p>I can either get rid of my theory entirely or adjust it.</o:p></div>
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My new theory might be that most blue candies
are blue raspberry (not all), or all good blue candies taste like blue
raspberry, etc.<o:p></o:p></div>
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So, when a scientist says that a theory is
true, this is short-hand for “this is the theory that makes the most sense of
the data we have so far. If more data comes along that disproves this theory,
then we will revise our theory.”<o:p></o:p></div>
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This subtext is what many non-scientists neglect: Theories can and must be altered if the data requires
them to be changed.<o:p></o:p></div>
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A theory is not immutable, but instead our
understanding of a theory can change in response to new data.<o:p></o:p></div>
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So if a person argues that evolution is just a
theory, and it’s not proven, he or she has misunderstand scientific theory entirely (and proven how bad science education in this country can be).<o:p></o:p></div>
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Nicolehttp://www.blogger.com/profile/10056174002046814636noreply@blogger.com0tag:blogger.com,1999:blog-2961791805048706293.post-26423589114476407662013-01-02T19:43:00.000-08:002013-01-02T19:44:10.482-08:00Best in Show!<br />
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Scientists often discuss (or bicker) about the
order of authorship on papers. “I got a first-author paper published!” or “I
was only second author on the paper.”<o:p></o:p></div>
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What do such phrases mean?<o:p></o:p></div>
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The first author on a paper is supposed to be the
person who worked the most on the paper. Usually, the researcher who did the
research of the paper, not necessarily the person who did the most writing.
(See Lead Author, <a href="http://en.wikipedia.org/wiki/Lead_author">http://en.wikipedia.org/wiki/Lead_author</a>).
Often, this is the graduate student who worked on the project.<o:p></o:p></div>
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The last author*
is usually the professor, the one who had the vision of the project (and the
money). This author is the researcher who was overseeing the project.<o:p></o:p></div>
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The other authors (second, third, etc) are other
people who have worked on the project. This can include other graduate
students, undergraduates, post-docs, lab techs, etc.<o:p></o:p></div>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEib2EDAeHDJaT64SC0gbUadfbFFR8LL2fEaRnnyCCAHIcjxndAq324gWCV67a1HA5b_38va1OPPyQF0aP0qew7uyLttvgvyWNl2z-SYKlGTFQ3CuMLTeI9KQLlWuhwIUv8s4qi47fT00b4m/s1600/first_place.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="232" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEib2EDAeHDJaT64SC0gbUadfbFFR8LL2fEaRnnyCCAHIcjxndAq324gWCV67a1HA5b_38va1OPPyQF0aP0qew7uyLttvgvyWNl2z-SYKlGTFQ3CuMLTeI9KQLlWuhwIUv8s4qi47fT00b4m/s320/first_place.png" width="320" /></a></div>
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Figure 1: First Author: The happy grad student
who is now closer to graduation.<o:p></o:p></div>
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Second Author: The fuming grad student who
wishes they were first author.<o:p></o:p></div>
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Third author: The happy professor who is closer
to getting tenure.<o:p></o:p></div>
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While you’re in grad school or your post-doc,
you try to accumulate as many first author papers as possible. These papers
prove that you can finish a research project AND write up the results.<o:p></o:p></div>
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However, once you’ve become a professor, then
you want as many last author papers as possible. You’re showing the academic world
that you can manage students and get them to produce results.<o:p></o:p></div>
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<u>Issues</u>:<o:p></o:p></div>
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1) Who do you include as another author: <o:p></o:p></div>
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It’s more impressive to be the first author on
a 2 person paper than on a 3 person paper so sometimes people will try to not
include people who deserve to be on the paper. Ultimately, the professor is
usually the one who gets the final say.<o:p></o:p></div>
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Conversely, sometimes you are forced to include
someone as an author as an honorary gesture.<o:p></o:p></div>
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2) What if two people contributed to a project
equally: <o:p></o:p></div>
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In this case, more than one person might
deserve to be a first author. Sometimes, the journal will allow you to list the
first two names with asterisks near them saying that these two authors
contributed equally. <o:p></o:p></div>
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Unfortunately, many people don’t read the
asterisk so if you’re the second author, you are SOL. <o:p></o:p></div>
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To solve some of these issues, journals require
researchers to list author contributions.<o:p></o:p></div>
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Ex: Author 3 developed the project, Author 1 performed
the experiments, Authors 2 and 3 wrote the paper.<o:p></o:p></div>
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If you’re hanging out with a scientist and she
has just published a first author paper, congratulate her on the great
accomplishment.<o:p></o:p></div>
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And if the scientist has been relegated to
second or third author, buy her drink and help her drown her sorrows in
alcohol.<o:p></o:p></div>
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<u>Links</u>:<o:p></o:p></div>
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Survey of Perceived Authorship (the importance
of being first, second, or last): http://www.nature.com/embor/journal/v8/n11/full/7401095.html<o:p></o:p></div>
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Fun fact:
Even cats have authored papers<o:p></o:p></div>
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(Cats and Publishing Physics Research, <a href="http://www.chem.ucla.edu/harding/cats.html">http://www.chem.ucla.edu/harding/cats.html</a>)<o:p></o:p></div>
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A Paper with 2900 Authors: http://www.nature.com/nature/journal/v412/n6846/extref/412565aa.html<o:p></o:p></div>
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*There are very few single author papers nowadays
(http://www.nature.com/nature/history/full/nature06243.html).<o:p></o:p></div>
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Nicolehttp://www.blogger.com/profile/10056174002046814636noreply@blogger.com0tag:blogger.com,1999:blog-2961791805048706293.post-12862229854218289272012-12-24T17:33:00.001-08:002012-12-24T17:33:43.416-08:00Three C’s in Science: Correlation, Confound, and Causation<br />
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If you want to irritate a
scientist, start a loud conversation about how two things are connected and therefore, you know that one causes the other. </div>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgnSMCttTx4fg2pvWj0z7do0YqrSyXqE8s5l-UwP161CuajWphN1zNNqVeboGNp8tj6Vep_ZMK6TDAloJ8wydvffaPoVqiQXq1mjz6Yu6eCsQPqTZZc7Io98_KB2MIJTvvO5lAruflmpWdN/s1600/Ice_Cream_003_Girl_and_Boy.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em; text-align: center;"><img border="0" height="320" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgnSMCttTx4fg2pvWj0z7do0YqrSyXqE8s5l-UwP161CuajWphN1zNNqVeboGNp8tj6Vep_ZMK6TDAloJ8wydvffaPoVqiQXq1mjz6Yu6eCsQPqTZZc7Io98_KB2MIJTvvO5lAruflmpWdN/s320/Ice_Cream_003_Girl_and_Boy.png" width="286" /></a></div>
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Two ice cream friends!</div>
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For example, below I show a fake
chart of the number of clothing items worn against the number of ice cream
scoops consumed.</div>
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<br /></div>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjEB_ICWajc2iXqCNvsyVvyi-VeQqjzWDgq-9tt7ytkK725t1aiRDyRuQ8kUxTQdKrW3-g0r5e91bPCw7icjDv5ooM0vBnS4PBMfuTMhLhOahlorNUyP2w5vssgkCDUlId3gv_lfP2o3zbY/s1600/ice_cream_clothes.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="270" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjEB_ICWajc2iXqCNvsyVvyi-VeQqjzWDgq-9tt7ytkK725t1aiRDyRuQ8kUxTQdKrW3-g0r5e91bPCw7icjDv5ooM0vBnS4PBMfuTMhLhOahlorNUyP2w5vssgkCDUlId3gv_lfP2o3zbY/s400/ice_cream_clothes.png" width="400" /></a></div>
<div style="text-align: center;">
<span style="text-align: center;">Graph of the number of clothing items worn vs. number of ice cream scoops consumed. Does this mean that not wearing clothing makes you more likely to eat ice cream?</span></div>
<span style="text-align: center;"><br /></span>
As you can see, there is an apparent trend of eating more ice cream and wearing less clothing.<br />
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</div>
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And as is famously said, “Correlation
does not imply causation”.<o:p></o:p></div>
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<a href="http://en.wikipedia.org/wiki/Correlation_does_not_imply_causation">http://en.wikipedia.org/wiki/Correlation_does_not_imply_causation</a><o:p></o:p></div>
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<br /></div>
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Correlation occurs when two
things occur together more often than chance. For example, ice cream and
clothing or little kids and sticky hands.<o:p></o:p></div>
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<br /></div>
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In fact, it is pretty easy to find correlations between all sorts of random pairs of variables. For one famous example, check out pirates and global warming (http://en.wikipedia.org/wiki/Flying_Spaghetti_Monster#Pirates_and_global_warming). The claim is that diminishing numbers of pirates cause global warming.</div>
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However, two things can occur together for no reason or there can be a third variable.<o:p></o:p></div>
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<br /></div>
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This third variable is known as a hidden variable or confound
(<a href="http://en.wikipedia.org/wiki/Confounding">http://en.wikipedia.org/wiki/Confounding</a><span class="MsoHyperlink">)</span>. <o:p></o:p></div>
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<br /></div>
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A confound is another variable that is actually the cause of the
two variables. The confound is often a cause that you wouldn't have otherwise connected with the data.</div>
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<br /></div>
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In this case, the hot temperatures are most likely causing people to
eat more ice cream and be more naked (both good things).<o:p></o:p></div>
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<br /></div>
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Confounds are a big deal for scientists because a confound can
ruin all of your data if you don’t discover it before you publish your paper.<o:p></o:p></div>
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<br /></div>
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Many people do not think about confounds when talking about correlations. This does not mean that correlations are not useful, but rather that there is often some underlying cause connecting the variables. </div>
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<br />So when you hear reports about connections between two variables, keep in mind that the two variables might not cause one another. However, feel free to feign ignorance and piss off any annoying scientists near you.</div>
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<br /></div>
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Links:<o:p></o:p></div>
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10 Weird Correlations: <a href="http://www.businessinsider.com/crazy-correlations-2011-6?op=1">http://www.businessinsider.com/crazy-correlations-2011-6?op=1</a><o:p></o:p></div>
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<br /></div>
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Cautionary Article: <a href="http://www.slate.com/articles/health_and_science/science/2012/10/correlation_does_not_imply_causation_how_the_internet_fell_in_love_with_a_stats_class_clich_.html">http://www.slate.com/articles/health_and_science/science/2012/10/correlation_does_not_imply_causation_how_the_internet_fell_in_love_with_a_stats_class_clich_.html</a><o:p></o:p></div>
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Nicolehttp://www.blogger.com/profile/10056174002046814636noreply@blogger.com0tag:blogger.com,1999:blog-2961791805048706293.post-61136327965927327852012-12-11T18:29:00.001-08:002012-12-11T18:29:53.343-08:00Fight Night: Tenure vs. Adjunct Professors<br />
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Normal Job: you are
offered a contract with a salary and benefits. Usually, you can get fired at
almost any time, but you have some legal protections to prevent you being treated terribly.<o:p></o:p></div>
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<br /></div>
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In academia, things are not so normal. The two
extremes are tenure and adjunct. This post is a short explanation of the two types along with links.</div>
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<o:p></o:p></div>
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In a tenure job (<a href="http://en.wikipedia.org/wiki/Tenure_(academic)">http://en.wikipedia.org/wiki/Tenure_(academic)</a>),
the position is guaranteed for life along with your salary, benefits, and other
perks of university life. <o:p></o:p></div>
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<br /></div>
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The main idea
behind this type of position is that the professor can do research without
having to worry about outcomes and receiving grants. He or she can do new
research to explore new science without deadlines and practicality. While this
may sound silly, some of the best research can come out of this type of work. (The pros and cons of tenure could be their own blog post.)<o:p></o:p></div>
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<br /></div>
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Tenure track professors
are basically the royalty of the university world.<o:p></o:p></div>
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<br /></div>
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The opposite end of
this spectrum is an adjunct position. <a href="http://en.wikipedia.org/wiki/Tenure_(academic)">http://en.wikipedia.org/wiki/Tenure_(academic)</a><o:p></o:p></div>
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<br /></div>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgUnStaPwvkejceL_qANFnLOuZBYolvmEIWz-ieLTAtXcb1Aoaq9LVU2CzQFYbbY9sMZnLSqbew4jstLWU7B405fwD1L1DI3toVVgmE3G6VcG0fw9nM8CXkFUYLMSd5IrP-wqC3Jt6WJShm/s1600/professor_comic.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="320" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgUnStaPwvkejceL_qANFnLOuZBYolvmEIWz-ieLTAtXcb1Aoaq9LVU2CzQFYbbY9sMZnLSqbew4jstLWU7B405fwD1L1DI3toVVgmE3G6VcG0fw9nM8CXkFUYLMSd5IrP-wqC3Jt6WJShm/s320/professor_comic.png" width="320" /></a></div>
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<span style="font-family: Times New Roman, serif; font-size: small;">Figure 1: Adjunct Professor. Look at this poor
adjunct professor; he </span><span style="font-family: Times New Roman, serif;">doesn't</span><span style="font-family: Times New Roman, serif; font-size: small;"> even get a white board as part of his job, only
the pen.</span></div>
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<span style="font-family: "Times New Roman","serif"; font-size: 12.0pt; mso-ansi-language: EN-US; mso-bidi-font-size: 11.0pt; mso-bidi-language: AR-SA; mso-bidi-theme-font: minor-bidi; mso-fareast-font-family: Calibri; mso-fareast-language: EN-US; mso-fareast-theme-font: minor-latin;"><br /></span></div>
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</div>
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Adjunct professors
are people without permanent positions at universities; they are hired part-time to teach classes. Adjuncts teach more than half the courses
at public universities. Sounds like a regular job, you say?<o:p></o:p></div>
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<br /></div>
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Not quite:
adjuncts are often paid poorly and have very few benefits. Most adjunct
professors don’t even have access to copying, office space, or curriculum guidelines. Teaching a
class at a university isn't even enough to guarantee library access!<o:p></o:p></div>
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<br /></div>
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Adjunct positions
almost never lead to full time positions so they are not even a good stepping
stone to a career. <o:p></o:p></div>
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<br /></div>
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Adjuncts are just another fun example of the problems rampant in academia. Luckily, adjuncts are starting to unite together (<a href="http://www.adjunctproject.com/">http://www.adjunctproject.com/</a>) to fight for their rights. Hopefully, in the future, adjuncts will be better protected since they are responsible for teaching a great fraction of the classes at universities.</div>
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If this type of
terribleness sounds familiar, that’s because they are remarkably similar to
post-doc positions (<a href="http://www.parsingscience.com/2012/10/so-you-want-to-be-indentured-servant.html">http://www.parsingscience.com/2012/10/so-you-want-to-be-indentured-servant.html</a>)<o:p></o:p></div>
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<br /></div>
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<u>Additional
Links:<o:p></o:p></u></div>
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A list of 25 facts about adjunct profs: <a href="http://www.bestcollegesonline.com/blog/2012/09/17/25-telling-facts-about-adjunct-faculty-today/">http://www.bestcollegesonline.com/blog/2012/09/17/25-telling-facts-about-adjunct-faculty-today/</a><o:p></o:p></div>
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Compare and Contrast Tenure and Adjunct: <a href="http://sciencecareers.sciencemag.org/career_magazine/previous_issues/articles/2006_02_24/science.opms.r0600003">http://sciencecareers.sciencemag.org/career_magazine/previous_issues/articles/2006_02_24/science.opms.r0600003</a><o:p></o:p></div>
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<br /></div>
Nicolehttp://www.blogger.com/profile/10056174002046814636noreply@blogger.com0tag:blogger.com,1999:blog-2961791805048706293.post-30829721294187750212012-11-28T20:08:00.002-08:002012-11-28T20:09:10.635-08:00First place-Physics!<br />
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For the average high school student, the science requirements
consist of one of the following sequences:<o:p></o:p></div>
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9<sup>th</sup> grade- Biology; 10<sup>th</sup> grade-
Chemistry; 11<sup>th</sup> grade-Physics</div>
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or</div>
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9<sup>th</sup> grade-Earth Science; 10<sup>th</sup> grade-
Biology; 11<sup>th</sup> grade- Chemistry; 12<sup>th</sup> grade- Physics<o:p></o:p></div>
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<br /></div>
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The original order was developed because educators thought
it was the easiest way to teach science. Each course requires successively more
difficult mathematics. Students could learn Biology more easily than Chemistry or Physics.<o:p></o:p></div>
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This has been the science sequence for decades, but recently
some educators have questioned the wisdom of this order. <o:p></o:p></div>
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The new version that people recommend is Physics First (<a href="http://en.wikipedia.org/wiki/Physics_First">http://en.wikipedia.org/wiki/Physics_First</a>,
<a href="http://www.physicsfirstmo.org/">http://www.physicsfirstmo.org/</a>). <o:p></o:p>The big leader of Physics First is Nobel Prize Winner Leon Lederman (<a href="http://en.wikipedia.org/wiki/Leon_Lederman">http://en.wikipedia.org/wiki/Leon_Lederman</a>).</div>
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The main issue with the traditional order is that Biology, Chemistry, and Physics all share many concepts.You often need ideas from Chemistry to explain parts of Biology, and ideas from Physics to explain parts of Chemistry and Biology.</div>
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Any student who has taken the traditional order probably remembers discussions where the teacher has to say “well, I can’t explain this to you until you get to chemistry and then to physics.”</div>
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Here is a quote from an AAPT pamphlet on Physics First (http://www.aapt.org/upload/phys_first.pdf):<o:p></o:p></div>
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“The wisdom of placing physics last is being reconsidered by educators because 1) in order to understand modern molecular biology and the biochemical processes in cells, students need a solid background in bothphysics and chemistry, and 2) mastery of the basic physics concept of electrostatic and nuclear forces and the concept of energy storage and transfer are crucial to the understanding of chemical structures, atomic binding, gas laws, and the periodic table of the elements”</div>
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Proponents of Physics First advocate teaching the courses in this order:<o:p></o:p></div>
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9<sup>th</sup>-grade Introductory Physics; 10<sup>th</sup>
grade- Chemistry; 11<sup>th</sup> grade-Biology; 12<sup>th</sup> grade-Advanced
Physics<o:p></o:p></div>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgHh-N_CwsHoNRys9CInDjVkdPCFr1aSY7q9f_hpdXzj0yzBnNJoTcODEW70xmxsfsGzSDtX47uKEiDeDuC0jO0S7Hqii5AEtTqdBSn5shWv5H2k_zWdXGF0kGc0plRvJVLqIUnUy-LalIm/s1600/physics_first.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="400" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgHh-N_CwsHoNRys9CInDjVkdPCFr1aSY7q9f_hpdXzj0yzBnNJoTcODEW70xmxsfsGzSDtX47uKEiDeDuC0jO0S7Hqii5AEtTqdBSn5shWv5H2k_zWdXGF0kGc0plRvJVLqIUnUy-LalIm/s400/physics_first.png" width="286" /></a></div>
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<span style="font-family: 'Times New Roman', serif; font-size: 12pt;">Figure 1: Bookshelf with books representing the different science sequences. Shelf 1 is Physics First, Shelves
2 and 3 are the traditional science sequences.</span></div>
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<span style="font-family: 'Times New Roman', serif; font-size: 12pt;"><br /></span></div>
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<span style="font-family: 'Times New Roman', serif; font-size: 12pt;">The introductory physics class is focused on conceptual physics and lends itself to inquiry-based learning (See previous post: </span><span style="text-align: left;">http://www.parsingscience.com/2012/08/the-science-inquisition.html). With a foundation in physics, students can then learn biology and chemistry more easily. The advanced physics class can be more mathematically rigorous.</span></div>
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<span style="text-align: left;"><br /></span></div>
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<span style="text-align: left;">The hope with Physics First is that students will be more likely to take Physics classes and that learning Biology and Chemistry will be more natural and easy.</span></div>
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<span style="text-align: left;"><br /></span></div>
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Of course, Physics First is not without its critics. Some people believe that many high schools will not have the personnel to teach these new physics classes or that it will be too difficult to implement. Others question whether all students actually need to learn Physics.</div>
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Results are still being gathered on whether this type of program is beneficial or not.</div>
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In my opinion, Physics First is a great idea, and I look forward to seeing how progress unfolds.</div>
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If you want to learn more about Physics First, here are some links:<o:p></o:p></div>
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APS: <a href="http://www.aps.org/publications/apsnews/200907/physicsfirst.cfm">http://www.aps.org/publications/apsnews/200907/physicsfirst.cfm</a><o:p></o:p></div>
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AAPT: <a href="https://www.aapt.org/Resources/policy/physicsfirst.cfm">https://www.aapt.org/Resources/policy/physicsfirst.cfm</a><o:p></o:p></div>
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Nicolehttp://www.blogger.com/profile/10056174002046814636noreply@blogger.com0tag:blogger.com,1999:blog-2961791805048706293.post-63545289582619894382012-11-17T11:48:00.000-08:002012-11-17T11:48:19.054-08:00Jury of Your Peers<br />
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If you ever read a popular science article that
references papers, you’ll often see the phrase “peer-reviewed” (<a href="http://en.wikipedia.org/wiki/Peer_review">http://en.wikipedia.org/wiki/Peer_review</a><span class="MsoHyperlink">)</span> Scientists typically only trust peer-reviewed
papers, but sometimes the public will accept papers that haven’t been
peer-reviewed. With the internet, any yahoo can post an article online. So what does this phrase mean?<o:p></o:p></div>
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<br /></div>
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Peer Review is the process by which scientific
papers get accepted and how the scientific community works in general. Basically, your
work isn't accepted until your peers agree with you. <o:p></o:p></div>
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Steps to Publishing your Article<o:p></o:p></div>
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Step 1: Send article to a journal.<o:p></o:p></div>
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Step 2: Article is read by an editor.<o:p></o:p></div>
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Step 3: Either the article is rejected or it
gets assigned reviewers.<o:p></o:p></div>
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Step 4: Paper is sent to 2-3 reviewers
carefully chosen by the editor.<o:p></o:p></div>
<div class="MsoNoSpacingCxSpMiddle">
Step 5: The reviewers anonymously send back
comments and recommend the article to be accepted or rejected.<o:p></o:p></div>
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Step 6: Author makes revisions if needed.<o:p></o:p></div>
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Step 7: Article is published!<o:p></o:p></div>
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<br /></div>
<div class="MsoNoSpacingCxSpLast">
Cartoon of the process: <a href="http://undsci.berkeley.edu/article/howscienceworks_16">http://undsci.berkeley.edu/article/howscienceworks_16</a><span class="MsoHyperlink"><o:p></o:p></span></div>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhU8x6nvEuwG8BrAns5vgYJfL6RWo1Z1ef8tOGHK6_ydnVKPWyk71LYo73HQ1zbUitlMmQlecfO4WhDSM301R00rhxs-rzvxxf_RlTv3mmh2SxI9WKmQH3_glaBzisyx8uSxBQdbrnpt2_A/s1600/scientist.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="320" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhU8x6nvEuwG8BrAns5vgYJfL6RWo1Z1ef8tOGHK6_ydnVKPWyk71LYo73HQ1zbUitlMmQlecfO4WhDSM301R00rhxs-rzvxxf_RlTv3mmh2SxI9WKmQH3_glaBzisyx8uSxBQdbrnpt2_A/s320/scientist.png" width="264" /></a></div>
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</div>
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Figure 1: An example reviewer. Would you like to be reviewed by this man?<o:p></o:p></div>
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<br /></div>
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</div>
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Let’s take a closer look at Step 4: Choosing
editors: a complicated process. The reviewers are other professors or
scientists in the field.<o:p></o:p></div>
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<br /></div>
<div class="MsoNoSpacingCxSpMiddle">
Factors in the Process:<o:p></o:p></div>
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<!--[if !supportLists]-->1)<span style="font-size: 7pt;">
</span><!--[endif]-->Rivals of the author: People who will trash the paper<o:p></o:p></div>
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<!--[if !supportLists]-->2)<span style="font-size: 7pt;">
</span><!--[endif]-->Friends of the author: People who will only praise the paper<o:p></o:p></div>
<div class="MsoNoSpacingCxSpMiddle" style="margin-left: .5in; mso-add-space: auto; mso-list: l0 level1 lfo1; text-indent: -.25in;">
<!--[if !supportLists]-->3)<span style="font-size: 7pt;"> </span>G<span style="text-indent: -0.25in;">rading scale of the individual reviewer: Some people are
negative about everything and some are positive about everything.</span></div>
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<o:p></o:p></div>
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Overall, the editor tries to make a fair review
committee.Occasionally, there are
some issues because reviewers are anonymous and people often have personal
biases against certain people or types of research. <o:p></o:p></div>
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One example of this issue is the case of Jo Baeler. Baeler is a math
education researcher whose research has been shut down by two other professors who have done shady things to discredit her. Read about it here: <a href="http://www.stanford.edu/~joboaler/">http://www.stanford.edu/~joboaler/</a></div>
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So what’s the solution? <o:p></o:p></div>
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Some people have recommended open review where
both authors and reviewers identities are revealed. Here is a Nature paper
about the pros and cons of open peer review <a href="http://www.nature.com/nature/peerreview/debate/nature04991.html">http://www.nature.com/nature/peerreview/debate/nature04991.html</a><o:p></o:p></div>
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Personally, I’m
holding out for robots that can read papers.<o:p></o:p></div>
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Until then, the peer review process will stay in place.</div>
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Nicolehttp://www.blogger.com/profile/10056174002046814636noreply@blogger.com0tag:blogger.com,1999:blog-2961791805048706293.post-4931435727173991782012-11-06T18:51:00.001-08:002012-11-06T18:51:10.036-08:00Scribbling on paper<script type="text/x-mathjax-config"> MathJax.Hub.Config({tex2jax: {inlineMath: [['$','$'], ['\\(','\\)']]}}); </script> <script src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML" type="text/javascript"> </script><br />
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Quote from a reader: “<i>I've learned that if you ask a physicist a hypothetical question, they will most likely try to give you a real answer. As a result, never ask a physicist a hypothetical unless you're ready for a real explanation and potentially hand-drawn diagrams on napkins. I love you guys.</i>”<o:p></o:p></div>
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A back of the envelope calculation is a rough estimate performed on a random scrap of paper (like the back of an envelope). They are synonymous with physicists. <a href="http://en.wikipedia.org/wiki/Back-of-the-envelope_calculation">http://en.wikipedia.org/wiki/Back-of-the-envelope_calculation</a><o:p></o:p></div>
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Let's go through an example of one of these calculations:<br />
Estimate the number of pizzas consumed by all the students at the Northwestern University during one quarter. (Adapted from University of Maryland)</div>
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<o:p></o:p></div>
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Step 1: Estimate known information.<br />
Let’s say that there ~10,000 students at NU.</div>
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<o:p></o:p></div>
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And that one quarter is about 10 weeks. <o:p></o:p><br />
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Now, obviously, we could look up the exact numbers online, but the point of these types of calculations is to be quick so we estimate.</div>
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<br />
Step 2: Make an educated guess about the other information in the problem.<br />
For this question, we need to estimate how much pizza each student eats on average. As far as I know, there's no easy way to look up this information so we have to come up with an answer ourselves.<br />
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Based on being at college, I'll say that each pizza-eating student eats pizza once or twice a week averaging 1 pizza a week.<br />
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But not every student eats pizza. Again, I'll make a guess that approximately a quarter of students eat pizza.<o:p></o:p><br />
<br />
Note: we're trying to make this problem as simple as possible so I'm not worrying about things like some people eating pizza all the time and some every once in awhile. Just try to guess an average value.<br />
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Step 3: Calculate your answer.</div>
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$10000$ students $\cdot \frac{1}{4} \cdot 1 \frac{pizza}{week \:student} \cdot 10$ weeks <o:p></o:p></div>
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$= 25,000$ pizzas <br />
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Now we've done a back of the envelope calculation!<br />
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgW10LhMWzWKUjUsg7HhEP9YhEGXW9Tu3Nujje7VL0o_uUET-ii1EBrPB7swVaPNBtwVy0lgpiQ5_e67xvLbgWVkEAkV8U9yYU6nKYO4JVCxUYy6KxpndrAYT2nBPYjWMTpTk51eh6oPg_K/s1600/pizzacalc.JPG" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="240" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgW10LhMWzWKUjUsg7HhEP9YhEGXW9Tu3Nujje7VL0o_uUET-ii1EBrPB7swVaPNBtwVy0lgpiQ5_e67xvLbgWVkEAkV8U9yYU6nKYO4JVCxUYy6KxpndrAYT2nBPYjWMTpTk51eh6oPg_K/s320/pizzacalc.JPG" width="320" /></a></div>
Figure 1: The calculation done on an actual envelope that used to contain a Halloween card.<br />
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If you're worried about facts, we can try to check our answer.<br />
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Let’s use some pizza facts from this website.<a href="http://www.statisticbrain.com/pizza-statistics/">http://www.statisticbrain.com/pizza-statistics/</a><o:p></o:p></div>
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There are ~3 billion pizzas sold every year in the US. <o:p></o:p><br />
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The population of the US is ~300 million. <o:p></o:p><br />
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So now we can find the proportion of the 300 billion pizzas that should be eaten by NU students during a quarter.<o:p></o:p></div>
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$3$ billion $\frac{pizzas}{year}$ $\cdot$ $\frac{10,000 NU students}{300 million Americans} \cdot \frac{10 weeks (quarter)}{52 weeks (year)}$<br />
<o:p></o:p></div>
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$= \sim 20, 000 pizzas$<o:p></o:p></div>
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<br />
As you can see, the back of the envelope estimate is the same order of magnitude as this slightly more factual answer. (<a href="http://en.wikipedia.org/wiki/Order_of_magnitude">http://en.wikipedia.org/wiki/Order_of_magnitude</a>)</div>
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<o:p></o:p></div>
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Our back of the envelope calculation worked! (If this was a more scientific calculation, you'd have more precise answers available after performing the actual experiment.)<o:p></o:p></div>
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Why do physicists perform back of the envelope calculations?<o:p></o:p></div>
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<!--[if !supportLists]-->1)<span style="font-size: 7pt;"> </span><!--[endif]-->To check if you’re correct. If you have a rough idea of the answer, it’ll be easier to catch mistakes<o:p></o:p></div>
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<!--[if !supportLists]-->2)<span style="font-size: 7pt;"> </span><!--[endif]-->To find the order of magnitude of an answer (like our pizza example).<o:p></o:p></div>
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<!--[if !supportLists]-->3)<span style="font-size: 7pt;"> </span><!--[endif]-->A fun party trick.<o:p></o:p></div>
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<!--[if !supportLists]--> 4)<span style="font-size: 7pt;"> </span><!--[endif]-->To help a friend estimate the answer to a question (see quote at the beginning of this post).<o:p></o:p></div>
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I encourage you to do some back of the envelope calculations yourself or find your local physicist and have him/her do it for you (provide your own envelope).<o:p></o:p></div>
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And if you need further convincing of the merits of this type of calcuation, here’s a video of Charles Townes (inventor of the laser) talking about inventing the laser and using a back of the envelope calculation: <a href="http://laserfest.org/lasers/video-history.cfm">http://laserfest.org/lasers/video-history.cfm</a><o:p></o:p></div>
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Some Resources:<o:p></o:p></div>
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Books: <a href="http://www.amazon.com/Back-Envelope-Physics-Hopkins-Paperback/dp/0801872634">http://www.amazon.com/Back-Envelope-Physics-Hopkins-Paperback/dp/0801872634</a><o:p></o:p></div>
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Fermi Problem (similar to back of the envelope calcualtions) : <a href="http://en.wikipedia.org/wiki/Fermi_problem">http://en.wikipedia.org/wiki/Fermi_problem</a><br />
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Example Fermi problems: <a href="http://www.physics.umd.edu/perg/fermi/fermi.htm">http://www.physics.umd.edu/perg/fermi/fermi.htm</a><o:p></o:p></div>
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* This blog post was inspired by this SMBC comic. “Pi=3, g=10, and anything we don’t like=0.”<o:p></o:p></div>
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http://www.smbc-comics.com/index.php?db=comics&id=2783<o:p></o:p></div>
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Nicolehttp://www.blogger.com/profile/10056174002046814636noreply@blogger.com0tag:blogger.com,1999:blog-2961791805048706293.post-53217506205675075892012-10-24T15:29:00.000-07:002012-10-24T15:54:45.536-07:00Significant Other<br />
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What’s significant in your life?<o:p></o:p></div>
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Regular person: my partner, my job, my friends,
etc. <o:p></o:p></div>
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Scientist: hopefully my data<o:p></o:p></div>
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In everyday use, significance means that something
is important and meaningful.<o:p></o:p></div>
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For scientists, significance has a very
specific definition, which is referred to as statistical significance (<a href="http://en.wikipedia.org/wiki/Statistical_significance">http://en.wikipedia.org/wiki/Statistical_significance</a>).<o:p></o:p></div>
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Basically, if I have a result, what are the odds my result occurred from some specific factor versus the odds that my result just occurred by chance. If I'm confident
my result came from some effect, then the result is considered significant.<o:p></o:p></div>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgHJA0IB4jCF3hmJEVYuU1IzEO7T3JBDGt1EXAWrAxetXE1xNUMeIoY5yo0t7Iy00dkeK_M0Y9RWJAYXxNQT6siojDAfeJTiyYaJjDWi5E_pwe083b_wbM_49Ut3uCRCXzpocwMqpYM2B9b/s1600/signficant_heart.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="294" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgHJA0IB4jCF3hmJEVYuU1IzEO7T3JBDGt1EXAWrAxetXE1xNUMeIoY5yo0t7Iy00dkeK_M0Y9RWJAYXxNQT6siojDAfeJTiyYaJjDWi5E_pwe083b_wbM_49Ut3uCRCXzpocwMqpYM2B9b/s320/signficant_heart.png" width="320" /></a></div>
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Sympathy Card for a Scientist<o:p></o:p></div>
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For this post, our
example is going to be the lovely topic of food poisoning.<o:p></o:p></div>
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If I go to a restaurant
and get food poisoning once, is this significant? Maybe, but it could
be due to one bad apple or piece of produce or something else.<o:p></o:p></div>
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If five people eat there and get sick, this is
probably significant.</div>
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The food poisoning is probably not happening randomly. Maybe the kitchen is buying rotten food
because it’s cheaper, etc. <o:p></o:p></div>
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So the question is: how confident does the
health inspector have to be about the food poisoning in order for this to be a
significant result?<o:p></o:p></div>
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(Un)Fortunately, there is an entire field
called significance testing dedicated to this very question (<a href="http://en.wikipedia.org/wiki/Statistical_hypothesis_testing">http://en.wikipedia.org/wiki/Statistical_hypothesis_testing</a>).<o:p></o:p></div>
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The idea is that you set some arbitrary significance
level before you run your tests. In this case, the health inspector might say: “I
want to be 95% sure that these 5 people did get food poisoning
from this restaurant.”<o:p></o:p></div>
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Then the health inspector runs his tests and
one of two things happen:<o:p></o:p></div>
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<!--[if !supportLists]-->1)<span style="font-size: 7pt;">
</span><!--[endif]-->He’s above 95% confident so the result is
significant, and thus the restaurant is shut down<o:p></o:p></div>
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<!--[if !supportLists]-->2)<span style="font-size: 7pt;">
</span><!--[endif]-->He’s below 95% confident so the restaurant stays
open. <o:p></o:p></div>
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Now, if you are reasonably intelligent as I
assume most of my readers are, then you will have noticed a couple of problems
with this procedure. <o:p></o:p></div>
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<b>Issue 1:</b>
First of all, where did this number 95% come from? Who decided on that?<o:p></o:p></div>
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For this blog post, I made it up, but common levels
in the scientific world are 90%, 95%, and 99%. <o:p></o:p></div>
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If the health inspector tells me the food
poisoning isn't significant because he’s only 94% sure the restaurant gave me
food poisoning, I’m probably still not going to eat there. <o:p></o:p></div>
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So where do we draw the line?<o:p></o:p></div>
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Unfortunately, there is no easy solution to
this problem. Journals and the science community have come up with their own
standards, but these numbers are still widely debated.<o:p></o:p></div>
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Personally, I would prefer if I was given the
actual number and the significance level so that I could judge for myself.<o:p></o:p></div>
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However, many articles only report whether a
result is significant or not, leaving the actual number hidden away in the Methods
section. <o:p></o:p></div>
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<b>Issue 2:
</b>We can never be 100% sure about a result. <o:p></o:p></div>
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With our food poisoning restaurant, even if the
health inspector is 95% sure the restaurant did cause the food poisoning; there
is still a 5% chance that the restaurant isn't poisoning everyone!<o:p></o:p></div>
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But if your result is not significant, it’s
extremely difficult to get published.<o:p></o:p></div>
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Journals have
a strong bias towards publishing significant results (as they should in most
cases), but maybe non-significant results deserve a place to go to?<o:p></o:p></div>
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One such home for these articles is the Journal
for Articles in Support of the Null Hypothesis, <a href="http://www.jasnh.com/">http://www.jasnh.com/</a>.
This journal only publishes results that are not considered significant.<o:p></o:p></div>
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<o:p><br /></o:p></div>
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So is significance testing inherently bad?<o:p></o:p></div>
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No. The problems occur when people just rely on
what the tests tell them and forget that significance levels come with a number
of assumptions and caveats.<o:p></o:p></div>
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To avoid this fate, keep your skepticism handy
and draw your own conclusions from the data. <o:p></o:p></div>
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<br />Nicolehttp://www.blogger.com/profile/10056174002046814636noreply@blogger.com0tag:blogger.com,1999:blog-2961791805048706293.post-22286502974558682772012-10-14T21:03:00.002-07:002012-10-14T21:12:51.487-07:00I like free stuff!<br />
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Imagine your favorite ice cream shoppe gives
away all of their ice cream for free! <o:p></o:p></div>
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They even include the ice cream recipes and
their favorite sundae recipes. <o:p></o:p></div>
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But wait, there’s more!<o:p></o:p></div>
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Anyone can add in their favorite sundae recipes
or make their own ice cream.<o:p></o:p></div>
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Sound awesome? Yes.<o:p></o:p></div>
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Well guess what, the free ice cream sundae of software is open source software (tasty analogy, eh?).</div>
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<o:p></o:p></div>
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What is open source software (<a href="http://en.wikipedia.org/wiki/Open-source_software">http://en.wikipedia.org/wiki/Open-source_software</a>)?</div>
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<o:p></o:p></div>
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Software that is completely free (yea!),
including the source code. Anyone can use it and modify it.<o:p></o:p></div>
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You may have even used open
source software yourself.<o:p></o:p></div>
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Notably, Android phones run open source software (<a href="http://en.wikipedia.org/wiki/Android_(operating_system)">http://en.wikipedia.org/wiki/Android_(operating_system)</a>,
<a href="http://www.android.com/">http://www.android.com/</a>).</div>
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<o:p></o:p></div>
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Here are some other common open source software products: <a href="http://www.tripwiremagazine.com/2010/03/20-most-popular-open-source-software-ever-2.html">http://www.tripwiremagazine.com/2010/03/20-most-popular-open-source-software-ever-2.html</a><span class="MsoHyperlink"><o:p></o:p></span></div>
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Things I’ve personally used and recommend:<o:p></o:p></div>
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-Calibre (e-books)<o:p></o:p></div>
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-Firefox (web browser) <o:p></o:p></div>
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-Audacity (audio manipulation)<o:p></o:p></div>
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- GIMP (Image manipulation) <o:p></o:p></div>
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-Open Office (analogous to Microsoft Office)<o:p></o:p></div>
<div class="MsoNoSpacingCxSpMiddle">
-VLC Media Player (analogous to Windows Media
Player)<o:p></o:p></div>
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<br /></div>
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The aforementioned software are the ice cream toppings of an open source sundae.</div>
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<br /></div>
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You can also have an operating system (OS, <a href="http://computer.howstuffworks.com/operating-system.htm">http://computer.howstuffworks.com/operating-system.htm</a>) that
is open source. The OS is the ice cream base of the open source sundae.</div>
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<o:p></o:p></div>
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<br /></div>
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The two most common OS’s are Windows and Apple.
Most people will go their whole lives using one of these two without ever realizing other options exist. My personal favorite is Ubuntu (<a href="http://www.ubuntu.com/">http://www.ubuntu.com/</a>).</div>
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<o:p></o:p></div>
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<br /></div>
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Should you use an Open Source OS? Here’s a
handy flow chart.<o:p></o:p></div>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEixS_WDrD91GoYnCUStEcXO3Yb4AJ33m6hxSVtGTrlYl5SewnBRgabR8kwxsP4EdleUkPLEJDscJ9W_Le5fcT832z_fH2Q9R2t3kV5gMCD8DfRRJZm5Fv1sUT55WLIrpqw3xR05JnsVeCBF/s1600/opensource2.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="478" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEixS_WDrD91GoYnCUStEcXO3Yb4AJ33m6hxSVtGTrlYl5SewnBRgabR8kwxsP4EdleUkPLEJDscJ9W_Le5fcT832z_fH2Q9R2t3kV5gMCD8DfRRJZm5Fv1sUT55WLIrpqw3xR05JnsVeCBF/s640/opensource2.png" width="640" /></a></div>
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Pros and Cons of open source software<o:p></o:p></div>
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Pros:<o:p></o:p></div>
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<!--[if !supportLists]-->1.<span style="font-size: 7pt;">
</span><!--[endif]-->Free!<o:p></o:p></div>
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<!--[if !supportLists]-->2.<span style="font-size: 7pt;">
</span><!--[endif]-->Strong community of online users.</div>
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3.<span style="font-size: 7pt;"> </span><o:p></o:p> Innovative software is released immediately instead of lingering in testing for months.</div>
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4. Nerds will think you're cool.</div>
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Cons:<o:p></o:p></div>
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<!--[if !supportLists]-->1.<span style="font-size: 7pt;">
</span><!--[endif]-->No user hotline to call if something goes wrong.<o:p></o:p></div>
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<!--[if !supportLists]-->2.<span style="font-size: 7pt;">
</span><!--[endif]-->Not always the easiest to set-up.</div>
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3.<span style="font-size: 7pt;"> </span>Can be difficult to fix if there’s a bug.</div>
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<o:p></o:p></div>
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The delicious world of open source sundaes awaits! Go out there and test some products out. </div>
<br />Nicolehttp://www.blogger.com/profile/10056174002046814636noreply@blogger.com0tag:blogger.com,1999:blog-2961791805048706293.post-21646181032908862052012-10-09T18:46:00.002-07:002012-10-09T18:46:44.708-07:00So you want to be an indentured servant?<br />
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Question: How do I become an indentured servant in this day and age?<o:p></o:p></div>
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Answer: Become a postdoctoral researcher! (post-doc, <a href="http://en.wikipedia.org/wiki/Postdoctoral_research)*">http://en.wikipedia.org/wiki/Postdoctoral_research)</a><o:p></o:p></div>
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<o:p>See also: National Postdoctoral Association (</o:p><a href="http://www.nationalpostdoc.org/policy/what-is-a-postdoc">http://www.nationalpostdoc.org/policy/what-is-a-postdoc</a>)</div>
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Why do postdocs exist?<o:p></o:p></div>
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Graduate schools started
graduating more PhDs than there were professor positions available. (Note: this is true for the sciences, but not necessarily for other disciplines.)</div>
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<o:p></o:p></div>
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</div>
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Rational Solution: 1) accept fewer grad students or 2) encourage PhDs
to explore alternate career plans. <o:p></o:p></div>
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What actually happened: The postdoc system was created.</div>
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PhDs are forced to take “temporary” research
positions with professors after they complete grad school. These positions last anywhere from 1 to a million years. <o:p></o:p></div>
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Stated reasons for taking a postdoc:</div>
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<span style="text-indent: -0.25in;">- Gain more experience in a lab</span></div>
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<span style="text-indent: -0.25in;">- </span><span style="font-size: 7pt; text-indent: -0.25in;"> </span><span style="text-indent: -0.25in;">Learn a new experimental technique</span></div>
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<span style="text-indent: -0.25in;">- Acquire more publications before applying to professorships</span></div>
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<o:p></o:p></div>
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Real reason(s):</div>
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<span style="text-indent: -0.25in;">- You can’t get a professor job right away.</span></div>
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<o:p></o:p></div>
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<br /></div>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh4PBwoJhK4k6N8QoypG9XoN6t8WP93a8UsGgLTr0bHGcruXmqBHSXATpN4bcXxeXTcmGx2Kl3vqG5_aLsRwpUcc8UpP7LQBhVQceRf5tpv15PKd68TRIRTS1slSscHTD61Dbd_xAmh9HN-/s1600/route_to_tenure.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="246" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh4PBwoJhK4k6N8QoypG9XoN6t8WP93a8UsGgLTr0bHGcruXmqBHSXATpN4bcXxeXTcmGx2Kl3vqG5_aLsRwpUcc8UpP7LQBhVQceRf5tpv15PKd68TRIRTS1slSscHTD61Dbd_xAmh9HN-/s320/route_to_tenure.png" width="320" /></a></div>
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Here's a handy flowchart to learn how to get tenure</div>
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See this post from my friend Jess for more on why PhDs take post-docs:<o:p></o:p></div>
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<a href="http://womeninastronomy.blogspot.com/2012/09/permanent-jobs-elusive-for-recent-phds.html">http://womeninastronomy.blogspot.com/2012/09/permanent-jobs-elusive-for-recent-phds.html</a><span class="MsoHyperlink"><o:p></o:p></span></div>
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Cons of being a postdoc:</div>
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<span style="text-indent: -0.25in;">- </span><span style="font-size: 7pt; text-indent: -0.25in;"> </span><span style="text-indent: -0.25in;">Your job can be canceled at any time if your
professor runs out of money.</span></div>
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<span style="text-indent: -0.25in;">- </span><span style="text-indent: -0.25in;">You’re rarely protected by a union so you can be
denied benefits. (California is a rare exception and
this union only formed in 2010! </span><a href="http://news.sciencemag.org/scienceinsider/2010/08/california-postdocs-embrace-union.html" style="text-indent: -0.25in;">http://news.sciencemag.org/scienceinsider/2010/08/california-postdocs-embrace-union.html</a><span style="text-indent: -0.25in;">)</span></div>
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<span style="text-indent: -0.25in;">- </span><span style="font-size: 7pt; text-indent: -0.25in;"> </span><span style="text-indent: -0.25in;">You need your professor as a reference (especially
if they’re prominent in your field) so you’re basically powerless. Example: A friend’s
professor forced all his lab members to work full-time for 70% of their
salaries because he ran out of money.</span></div>
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<span style="text-indent: -0.25in;">- You might need more than one postdoc.</span></div>
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<span style="text-indent: -0.25in;">-</span><span style="font-size: 7pt; text-indent: -0.25in;"> </span><span style="text-indent: -0.25in;">Even if you stay in a postdoc forever, you
might never get a professor job.</span></div>
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<span style="text-indent: -0.25in;">- </span><span style="font-size: 7pt; text-indent: -0.25in;"> </span><span style="text-indent: -0.25in;">Even getting a good postdoc is competitive nowadays!</span></div>
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<o:p></o:p></div>
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So if you routinely hang out with postdocs or your grad student friends are becoming them, please be compassionate
towards them and buy them a drink.<o:p></o:p></div>
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<o:p><br /></o:p></div>
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Additional blog posts about postdocs:<o:p></o:p></div>
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<a href="http://dr-becca.blogspot.com/2010/02/on-being-post-doc-generally-speaking.html">http://dr-becca.blogspot.com/2010/02/on-being-post-doc-generally-speaking.html</a><o:p></o:p></div>
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<a href="http://sciencecareers.sciencemag.org/career_magazine/previous_issues/articles/2012_08_24/science.opms.r1200121">http://sciencecareers.sciencemag.org/career_magazine/previous_issues/articles/2012_08_24/science.opms.r1200121</a><o:p></o:p></div>
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*Caveat: I've never actually been a postdoc, but I think grad schools should do a better job preparing PhDs for alternative careers.<o:p></o:p></div>
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Nicolehttp://www.blogger.com/profile/10056174002046814636noreply@blogger.com0tag:blogger.com,1999:blog-2961791805048706293.post-74718666813539967142012-10-01T12:16:00.001-07:002012-10-01T12:16:58.875-07:00Proportionality and Disproportionality: Not just words with too many syllables!<div class="separator" style="clear: both; text-align: center;">
This dog’s legs are disproportionately short for his body!</div>
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<o:p></o:p></div>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhV-f6069Qb345cwUy34PUZuErYF8e35H3k3B-QDxaNMeg_1HGQOdIU3Vy6yg51PGbj_e4RYguO8ECIri6PXN0IfzZ5K98WRbCJ8TbKDsdP2bNUx6CkYW1R-5oOqFA8xIpOlF0TMHk4tmAn/s1600/daschund.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="240" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhV-f6069Qb345cwUy34PUZuErYF8e35H3k3B-QDxaNMeg_1HGQOdIU3Vy6yg51PGbj_e4RYguO8ECIri6PXN0IfzZ5K98WRbCJ8TbKDsdP2bNUx6CkYW1R-5oOqFA8xIpOlF0TMHk4tmAn/s320/daschund.jpg" width="320" /></a></div>
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A proportion relates two different objects via size or some other
characteristic.</div>
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</div>
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<o:p></o:p></div>
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To evaluate a proportion, establish three factors:<o:p></o:p></div>
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<!--[if !supportLists]-->1)<span style="font-size: 7pt;"> </span><!--[endif]-->The
original object/group<o:p></o:p></div>
<div class="MsoListParagraphCxSpMiddle" style="text-align: center; text-indent: -0.25in;">
<!--[if !supportLists]-->2)<span style="font-size: 7pt;"> </span><!--[endif]-->The
object/group of comparison<o:p></o:p></div>
<div class="MsoListParagraphCxSpLast" style="text-align: center; text-indent: -0.25in;">
<!--[if !supportLists]-->3)<span style="font-size: 7pt;"> </span><!--[endif]-->The
underlying cause/relationship (if any)<o:p></o:p></div>
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<br /></div>
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Proportions go awry when someone tries to draw
an incorrect conclusion from the data. <o:p></o:p></div>
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Let’s go through some goofy examples:<o:p></o:p></div>
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Example #1: A disproportionate number of physicists die from
rock climbing.<o:p></o:p></div>
</div>
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<div style="text-align: center;">
(<a href="http://www.nytimes.com/2001/02/20/science/a-passion-for-physical-realms-minute-and-massive.html?pagewanted=all&src=pm">http://www.nytimes.com/2001/02/20/science/a-passion-for-physical-realms-minute-and-massive.html?pagewanted=all&src=pm</a>)<o:p></o:p></div>
</div>
<div style="text-align: center;">
<br /></div>
<div style="text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh_DbXXkDmrXhnQ4gz_MEw0Lso5UAjCZwih_JPkupYtkGtozUj7LQfIxai9dFyDlb3Ng_cR3bTTBuppJwgl0wKXBaDq4fb6_5nRCAtT6MdcUkj_O-z2KYXQoTlP20V4HajuOCqNUERVwEe6/s1600/Rockclimb_book.JPG" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="320" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh_DbXXkDmrXhnQ4gz_MEw0Lso5UAjCZwih_JPkupYtkGtozUj7LQfIxai9dFyDlb3Ng_cR3bTTBuppJwgl0wKXBaDq4fb6_5nRCAtT6MdcUkj_O-z2KYXQoTlP20V4HajuOCqNUERVwEe6/s320/Rockclimb_book.JPG" width="240" /></a></div>
<div style="text-align: center;">
Rock shoes and "Quantum Mechanics" textbook</div>
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We’re comparing:<o:p></o:p></div>
</div>
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<div style="text-align: center;">
<!--[if !supportLists]-->1)<span style="font-size: 7pt;"> </span><!--[endif]-->the
percentage of physicists who die from rock climbing<o:p></o:p></div>
</div>
<div class="MsoListParagraphCxSpMiddle" style="mso-list: l0 level1 lfo2; text-indent: -.25in;">
<div style="text-align: center;">
<!--[if !supportLists]-->2)<span style="font-size: 7pt;"> </span><!--[endif]--> the percentage of the general population who
die from rock climbing <o:p></o:p></div>
</div>
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<div style="text-align: center;">
<!--[if !supportLists]-->3)<span style="font-size: 7pt;"> </span><!--[endif]-->Both
physics and rock-climbing are types of problem-solving so I’m not surprised
that physicists are drawn to rock-climbing (or vice-versa).</div>
<div style="text-align: center;">
<br /></div>
</div>
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Example #2 (based on my experience): A disproportionate number
of (male) particle physicists have ponytails so growing a ponytail will make you better at particle physics.<o:p></o:p></div>
</div>
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<div style="text-align: center;">
<!--[if !supportLists]-->1)<span style="font-size: 7pt;"> </span><!--[endif]-->Percentage
of particle physicists with ponytails.<o:p></o:p></div>
</div>
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<div style="text-align: center;">
<!--[if !supportLists]-->2)<span style="font-size: 7pt;"> </span><!--[endif]-->Percentage
of the general male population with ponytails.<o:p></o:p></div>
</div>
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<div style="text-align: center;">
<!--[if !supportLists]-->3)<span style="font-size: 7pt;"> </span><!--[endif]-->Guys
with ponytails are usually jerks; particle physicists are often jerks.
Hence, ponytails and particle physics are correlated, but one does not cause the
other so growing a ponytail will probably just make people think you’re an
jerk.<o:p></o:p></div>
</div>
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<br /></div>
</div>
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Example #3: There are a disproportionate number of women in
physics so women are worse at physics.<o:p></o:p></div>
</div>
<div class="MsoListParagraphCxSpFirst" style="mso-list: l1 level1 lfo1; text-indent: -.25in;">
<div style="text-align: center;">
<!--[if !supportLists]-->1)<span style="font-size: 7pt;"> </span><!--[endif]-->The
percentage of women in science (almost none)<o:p></o:p></div>
</div>
<div class="MsoListParagraphCxSpMiddle" style="mso-list: l1 level1 lfo1; text-indent: -.25in;">
<div style="text-align: center;">
<!--[if !supportLists]-->2)<span style="font-size: 7pt;"> </span><!--[endif]-->The
percentage of women in the general public (50%!)<o:p></o:p></div>
</div>
<div class="MsoListParagraphCxSpLast" style="mso-list: l1 level1 lfo1; text-indent: -.25in;">
<div style="text-align: center;">
<!--[if !supportLists]-->3)<span style="font-size: 7pt;"> </span><!--[endif]-->The
reasons behind this could probably be an entire blog by itself. Sexism is
probably one cause (<a href="http://www.pnas.org/content/early/2012/09/14/1211286109">http://www.pnas.org/content/early/2012/09/14/1211286109</a>),
and I think there's no way that it's because women are worse at physics.<o:p></o:p></div>
</div>
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<div style="text-align: center;">
<br /></div>
</div>
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<div style="text-align: center;">
Proportionality affects everyone when it comes to clothing
because clothes are sized according to some mythical “average person”. Because
of this, everyone is forced to measure their bodies and proportions against
this average person so we end up making statements like: <o:p></o:p></div>
</div>
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<div style="text-align: center;">
<br /></div>
</div>
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<div style="text-align: center;">
Example #4: My legs are disproportionately long for my body.</div>
</div>
<div style="text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjOJyV7DCXSp_DP85JPpN-r7VaQhq6xk9vbiRZCg6punOU1P6Gp4WNzGA0g9XGj1cuSrHRuuRiUqM3hkNeMx8ilx1cnTmTnuPBI5hTc-dmW1KovfizOQZa3bBReGfo10u_aIU0FmSWnGgle/s1600/short_pants.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjOJyV7DCXSp_DP85JPpN-r7VaQhq6xk9vbiRZCg6punOU1P6Gp4WNzGA0g9XGj1cuSrHRuuRiUqM3hkNeMx8ilx1cnTmTnuPBI5hTc-dmW1KovfizOQZa3bBReGfo10u_aIU0FmSWnGgle/s1600/short_pants.png" /></a></div>
<div style="text-align: center;">
My awesome paint drawing of legs with short pants.</div>
<div class="separator" style="clear: both; text-align: center;">
<br /></div>
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</div>
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<div style="text-align: center;">
<!--[if !supportLists]-->1)<span style="font-size: 7pt;"> </span><!--[endif]-->The
length of my legs<o:p></o:p></div>
</div>
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<div style="text-align: center;">
<!--[if !supportLists]-->2)<span style="font-size: 7pt;"> </span><!--[endif]-->The
leg length of the average person<o:p></o:p></div>
</div>
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<div style="text-align: center;">
<!--[if !supportLists]-->3)<span style="font-size: 7pt;"> </span><!--[endif]-->The
underlying cause here is the clothing industry in America. If we use
this criterion, everyone is disproportionate to their own bodies. This
criterion renders the statement meaningless, but I still use it because almost
everyone has the framework of the average person in their minds. <o:p></o:p></div>
</div>
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<div style="text-align: center;">
</div>
</div>
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<div style="text-align: center;">
Example #5 (completely made-up): 10% of baseball players die
of cancer so baseball causes cancer!<o:p></o:p></div>
</div>
<div class="MsoListParagraphCxSpFirst" style="mso-list: l0 level1 lfo2; text-indent: -.25in;">
<div style="text-align: center;">
<!--[if !supportLists]-->1)<span style="font-size: 7pt;"> </span><!--[endif]-->The
percent of baseball players that die of cancer (10%).<o:p></o:p></div>
</div>
<div class="MsoListParagraphCxSpMiddle" style="mso-list: l0 level1 lfo2; text-indent: -.25in;">
<div style="text-align: center;">
<!--[if !supportLists]-->2)<span style="font-size: 7pt;"> </span><!--[endif]-->The
percent of the general public that dies of cancer (unknown in this headline).<o:p></o:p></div>
</div>
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<div style="text-align: center;">
<!--[if !supportLists]-->3)<span style="font-size: 7pt;"> </span><!--[endif]-->In
this case, this fact is presented as a disproportionality. However, without
knowing the cancer rate in the general public, you can’t actually conclude that
baseball causes cancer. <o:p></o:p></div>
</div>
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<br /></div>
</div>
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<br /></div>
</div>
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As long as you keep the comparison parameters straight in
your head, you can’t get fooled!<o:p></o:p></div>
</div>
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<div style="text-align: center;">
<br /></div>
</div>
<div class="MsoNormal">
<div style="text-align: center;">
If you want some more examples, check out this cool photo
collection: <a href="http://formyhour.com/photo-project-disproportionate">http://formyhour.com/photo-project-disproportionate</a><o:p></o:p></div>
</div>
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<br /></div>
</div>
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<div style="text-align: center;">
<br /></div>
</div>
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<div style="text-align: center;">
PS: Some of you may have noticed that much of this post
deals with correlation and causation without directly mentioning those two
words. Don’t worry, it’s a topic for another blog post!<o:p></o:p></div>
</div>
<div style="text-align: center;">
<br /></div>
<div style="text-align: center;">
<br /></div>
<div style="text-align: center;">
<br /></div>
Nicolehttp://www.blogger.com/profile/10056174002046814636noreply@blogger.com0tag:blogger.com,1999:blog-2961791805048706293.post-69401526546423177792012-09-16T19:24:00.000-07:002012-09-16T19:24:07.964-07:00I hate cats: a mock scientific presentation<br />
<div class="MsoNormal">
If you continually interact with scientists, you will someday
end up in the fighting arena of the scientific world, the presentation.<o:p></o:p></div>
<div class="MsoNormal">
<br /></div>
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I have heard that non-scientific presentations are completely
different. Apparently, in business presentations, the audience actually listens
to the whole talk and waits till the end to ask questions.<o:p></o:p></div>
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<br /></div>
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Scientific presentations are nothing like that. <o:p></o:p></div>
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<br /></div>
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Below is a fake transcript of a talk including interruptions entitled “I hate cats”. (Many of the fake audience members (AM) are based on real incidents.)</div>
<div class="MsoNormal">
</div>
<a name='more'></a><br /><br />
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjy29UWw-_c8Qu3r35E0b-LBJBoolfOf4t6JV6TFAbn5mCoZAA3lQjZEWDDt7IqsEKp9J5jCgZBMdfmm9diT0V6su_6QRF2-X_Lqz6hcQ5Jo7INo58OKcpIWJBsulSCM_QTBg-ktAZhnxzy/s1600/Slide1.JPG" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="240" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjy29UWw-_c8Qu3r35E0b-LBJBoolfOf4t6JV6TFAbn5mCoZAA3lQjZEWDDt7IqsEKp9J5jCgZBMdfmm9diT0V6su_6QRF2-X_Lqz6hcQ5Jo7INo58OKcpIWJBsulSCM_QTBg-ktAZhnxzy/s320/Slide1.JPG" width="320" /></a></div>
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Me: Welcome to my talk entitled “I hate cats.”<o:p></o:p></div>
<div class="MsoNormal" style="margin-top: 12pt; text-align: left;">
AM1 (old jaded
grad student determined to spread his/her bitterness): How do you know you hate
cats?<o:p></o:p></div>
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<br /></div>
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Me: Uh, that’s the subject of this talk.<o:p></o:p></div>
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<br /></div>
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AM2 (upstart grad student convinced he knows everything
after his first semester of grad school): I don’t believe you. How can you hate
all cats? What about tigers?<o:p></o:p></div>
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<br /></div>
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Me: Well, I do like tigers. I mostly mean pet cats.<o:p></o:p></div>
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<br /></div>
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AM2: So the talk should really be titled “I hate
domesticated cats.”<o:p></o:p></div>
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<br /></div>
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Me: Yes, fine, let’s move past the title slide. <o:p></o:p></div>
<br />
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEijri7l2LYUONclEqb4W9HUtwflW-3lA_FAh83EEsYnRYHOh3yonMn1VRAs-C-7Qn2o9JbulR-9BFuUroQQgceZPfljagFQtU26GyUu4yi6bcuhl9H-79XTrxhzzaXLM_UeogPiulFoHXr1/s1600/Slide2.JPG" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="240" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEijri7l2LYUONclEqb4W9HUtwflW-3lA_FAh83EEsYnRYHOh3yonMn1VRAs-C-7Qn2o9JbulR-9BFuUroQQgceZPfljagFQtU26GyUu4yi6bcuhl9H-79XTrxhzzaXLM_UeogPiulFoHXr1/s320/Slide2.JPG" width="320" /></a></div>
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Me: Cats are evil. They will attack you for no reason.<o:p></o:p></div>
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<br /></div>
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AM3 (young professor trying to get tenure): What’s your
evidence for this?<o:p></o:p></div>
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<br /></div>
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Me: A cat came up and scratched me when I was sitting on a
couch at a friend’s house once.<o:p></o:p></div>
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<br /></div>
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AM3: Has every cat you’ve encountered attacked you? <o:p></o:p></div>
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<br /></div>
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Me: No. <o:p></o:p></div>
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<br /></div>
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AM3 (disgruntled look):
I think your sample size is too small. Not all cats are like that. <o:p></o:p></div>
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<br /></div>
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Me: Well, I don’t like cats so it’s not like I seek them
out. <o:p></o:p></div>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhjBXdqAnUz8Hy_JzqhzRR07C4wepLeEvbfxSEkmg7k6bC8pg2JSYlh3pY1YWkmdCUToqRT6T-K0sR1PcYSER_dhkD3OYdw2SwRx4IBtDFWxqU4LY5oKo8MbDNr5wuUugLEZdbuWTX7oLt9/s1600/Slide3.JPG" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="240" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhjBXdqAnUz8Hy_JzqhzRR07C4wepLeEvbfxSEkmg7k6bC8pg2JSYlh3pY1YWkmdCUToqRT6T-K0sR1PcYSER_dhkD3OYdw2SwRx4IBtDFWxqU4LY5oKo8MbDNr5wuUugLEZdbuWTX7oLt9/s320/Slide3.JPG" width="320" /></a></div>
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Me: Reason #2. I get all sneezy when I’m around them. They
cause horrible allergies. <o:p></o:p></div>
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<br /></div>
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AM4: Not everyone is allergic to cats. <o:p></o:p></div>
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<br /></div>
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Me: I never claimed that everyone was. <o:p></o:p></div>
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<br /></div>
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AM5: That does not seem like a reason to hate cats. It’s not
the cat’s fault. <o:p></o:p></div>
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<br /></div>
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Me: I don’t care. They’re evil. <o:p></o:p></div>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiUurQarYJ5RIGuRmNtEKZ3svtR88W8xtE3SKf3NbzqtFsTH1IwkPRcSpKNWAw8I37ugMDAwSI4TJ-dEvXz83uuJ3Ts0aYVgrULBmWTMl0W11fcMUjoXKU09Yu71NTJISL2fW3YWIiaNHWn/s1600/Slide4.JPG" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="240" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiUurQarYJ5RIGuRmNtEKZ3svtR88W8xtE3SKf3NbzqtFsTH1IwkPRcSpKNWAw8I37ugMDAwSI4TJ-dEvXz83uuJ3Ts0aYVgrULBmWTMl0W11fcMUjoXKU09Yu71NTJISL2fW3YWIiaNHWn/s320/Slide4.JPG" width="320" /></a></div>
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Me: Finally, cats, unlike dogs, are the worst because they
don’t like to cuddle. They might be content to sit with you for a minute, but
then suddenly they leave. <o:p></o:p></div>
<div class="MsoNormal" style="text-align: left;">
<br /></div>
<div class="MsoNormal" style="text-align: left;">
AM6: I have a cat, he loves to cuddle. <o:p></o:p></div>
<div class="MsoNormal" style="text-align: left;">
<br /></div>
<div class="MsoNormal" style="text-align: left;">
AM7: Yeah, my cat loves cuddling too. <o:p></o:p></div>
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<br /></div>
<div class="MsoNormal" style="text-align: left;">
AM8: Kittens like to cuddle.<o:p></o:p></div>
<div class="MsoNormal" style="text-align: left;">
<br /></div>
<div class="MsoNormal" style="text-align: left;">
Me: Well, I’ve never been able to find a cat that likes to
cuddle. <o:p></o:p></div>
<br />
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhySmyfzr6DlRl_HE_1k5ICQ1S8dJ_v8T8eQFQ5xXw4Pey-y0fFtrX46FNnFBm_LsjR5fQ2UPoZBFxIfmWzThf3ubTEwIHKFbui8mt-erB89a7fBvY7kYz6QQpHxsdlZq4M_6uRJvppLxZ6/s1600/Slide5.JPG" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="240" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhySmyfzr6DlRl_HE_1k5ICQ1S8dJ_v8T8eQFQ5xXw4Pey-y0fFtrX46FNnFBm_LsjR5fQ2UPoZBFxIfmWzThf3ubTEwIHKFbui8mt-erB89a7fBvY7kYz6QQpHxsdlZq4M_6uRJvppLxZ6/s320/Slide5.JPG" width="320" /></a></div>
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<div class="MsoNormal" style="text-align: left;">
Me: So for the three reasons outlined here, cats are
horrible and I hate them very much. I will now take any questions. <o:p></o:p></div>
<div class="MsoNormal" style="text-align: left;">
<br /></div>
<div class="MsoNormal" style="text-align: left;">
Polite applause. <o:p></o:p></div>
<div class="MsoNormal" style="text-align: left;">
<br /></div>
<div class="MsoNormal" style="text-align: left;">
AM2: Have you polled any other people about this topic?<o:p></o:p></div>
<div class="MsoNormal" style="text-align: left;">
<br /></div>
<div class="MsoNormal" style="text-align: left;">
Me: Yes, I’ve met many other cat haters. <o:p></o:p></div>
<div class="MsoNormal" style="text-align: left;">
<br /></div>
<div class="MsoNormal" style="text-align: left;">
AM1: I have grown up with cats my whole life, and I’ve never
had any problems with them. I disagree with your entire talk.<o:p></o:p></div>
<div class="MsoNormal" style="text-align: left;">
<br /></div>
<div class="MsoNormal" style="text-align: left;">
Me: Thank you for your feedback. <o:p></o:p></div>
<div class="MsoNormal" style="text-align: left;">
<br /></div>
<div class="MsoNormal" style="text-align: left;">
AM4 (professor with rival beliefs):
I have an alternate theory. I believe that in reality, cats hate you, not the
other way around. This hatred manifests itself in the ways you listed in your
talk. Your hatred is simply a reaction to their more intense hatred.</div>
<div class="MsoNormal" style="text-align: left;">
<br /></div>
<div class="MsoNormal" style="text-align: left;">
AM5: Dogs are the real menace to society. They bark, slobber,
and poop everywhere. In short, they are terrible. <o:p></o:p></div>
<div class="MsoNormal" style="text-align: left;">
<br /></div>
<div class="MsoNormal" style="text-align: left;">
Me: Do you have a question?<o:p></o:p></div>
<div class="MsoNormal" style="text-align: left;">
<br /></div>
<div class="MsoNormal" style="text-align: left;">
AM5: Yes, do you agree with this statement?<o:p></o:p></div>
<div class="MsoNormal" style="text-align: left;">
<br /></div>
<div class="MsoNormal" style="text-align: left;">
Me: No. Ok, next question. <o:p></o:p></div>
<div class="MsoNormal" style="text-align: left;">
<br /></div>
<div class="MsoNormal" style="text-align: left;">
AM9 (crotchety old professor): Back in my day, cats lived in
barns. None of this new-fangled nonsense about having cats indoors. <o:p></o:p></div>
<div class="MsoNormal" style="text-align: left;">
<br /></div>
<div class="MsoNormal" style="text-align: left;">
Me: Great, thanks for your input. Thank you everyone for
listening. We don’t have time for any more questions.<o:p></o:p></div>
<div class="MsoNormal" style="text-align: left;">
-- End script--<o:p></o:p></div>
<div class="MsoNormal" style="text-align: left;">
<br /></div>
<div class="MsoNormal" style="text-align: left;">
<br /></div>
<div class="MsoNormal" style="text-align: left;">
For a real talk, replace everything about cats with
scientific experiments and theories. This enactment of a scientific talk should prepare you
for the cast of characters you’ll encounter at a scientific talk. <o:p></o:p></div>
<div class="MsoNormal" style="text-align: left;">
<br /></div>
<div class="MsoNormal" style="text-align: left;">
PS: Don’t worry, only a small percentage of the animosity in
the room will actually be real. <o:p></o:p></div>
<br />
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Nicolehttp://www.blogger.com/profile/10056174002046814636noreply@blogger.com1tag:blogger.com,1999:blog-2961791805048706293.post-43859785991506394982012-09-11T18:08:00.001-07:002012-09-11T18:12:10.267-07:00Science is (Sometimes) Subjective!<br />
<div class="MsoNormal">
Imagine eavesdropping on students in a science class, working
on a problem set: “Do you know what the right answer is?” “Am I doing this
right?” “How do I know if this is working?”<o:p></o:p></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
One of the main misconceptions about science is the
existence of some mythical “right answer.” In fact, science is very similar to the issues you find in your day-to-day life. Two different groups reach the opposite conclusion with the same information (for examples, see everything the Republican or Democrat parties have ever said). </div>
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This is how people picture science working. <span style="font-family: 'Times New Roman', serif; font-size: 12pt;"> </span><span style="font-family: 'Times New Roman', serif; font-size: 12pt;">What it’s actually like: confusion at every turn.</span></div>
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All conclusions are categorically “right” or “wrong”.</div>
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People who practice science know that there is almost
never a right answer. There are many ways to be wrong, and it’s almost impossible 100% prove that you're right.</div>
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Most results are open to interpretation; two people with
the exact same set of data can reach the opposite conclusion. The most famous example of this is the glass half-empty or half-full
problem (<a href="http://en.wikipedia.org/wiki/Is_the_glass_half_empty_or_half_full%3F">http://en.wikipedia.org/wiki/Is_the_glass_half_empty_or_half_full%3F</a>). Most people will agree that those are both correct interpretations of the situation*.</div>
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The first picture I found when searching for glass
half-empty or half-full.</div>
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Science is like that glass problem, except even worse: you’re not really sure how much water is in the glass or even the true
volume of the glass.<o:p></o:p></div>
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For example, we take one of these nebulous glasses, and our measurements find that there amount of liquid is somewhere between 0.95 and 1.05. </div>
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My theory is that the glass has a volume of 2.1 cups so
I proclaim: “This cup is probably half-empty!” Your theory suggests that the glass has a volume of 1.9 cups
so the measurements tell you that the glass is half-full.</div>
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We end up in a screaming fight about who is correct (such shouting matches do actually occur in science).</div>
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This simple example illustrates how basically all of science works. There are very
few occasions where everyone unequivocally agrees on what the data implies**. Usually, you need multiple measurements and experiments before consensus is reached.</div>
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So does this mean that you shouldn't trust scientific results? Absolutely not! My point is that you should look at the data and reach your own conclusions; treat every piece of evidence with a healthy bit of skepticism. Since you are loyal readers of this blog, you are becoming more and more equipped to do this!</div>
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And if you're just feeling too lazy, ask your favorite scientist to do your thinking for you. </div>
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*This is not a philosophy blog so no nattering on about whether optimism or pessimism is the correct choice. </div>
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**I have never understand why people commonly mix up "imply" and "infer". If someone can explain this to me, leave a comment.</div>
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Nicolehttp://www.blogger.com/profile/10056174002046814636noreply@blogger.com0tag:blogger.com,1999:blog-2961791805048706293.post-30129422798507179492012-08-27T20:20:00.003-07:002012-08-27T20:20:36.077-07:00Paint, Tom Sawyer, and Errors<script type="text/x-mathjax-config"> MathJax.Hub.Config({tex2jax: {inlineMath: [['$','$'], ['\\(','\\)']]}}); </script> <script src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML" type="text/javascript"> </script><br />
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Today’s post is about the difference between random error (<a href="http://en.wikipedia.org/wiki/Random_error">http://en.wikipedia.org/wiki/Random_error</a>) and systematic error (<a href="http://en.wikipedia.org/wiki/Systematic_error">http://en.wikipedia.org/wiki/Systematic_error</a>). Another analogy awaits you. (This blog could probably be entirely about errors.)<o:p></o:p></div>
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Imagine painting a wall. You finish your first coat of paint. Before passing out from the paint fumes, you notice that there are spots missing paint. Furthermore, you notice there seem to be two types of areas without paint.<o:p></o:p></div>
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Random spots: the spots you can’t control. The spots have no pattern. They arise from chance when your brush sticks, the paint clumps up, etc. <o:p></o:p></div>
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Solution: To fully cover the wall, you paint more than one coat. With multiple coats, the random spots will average out because it’s unlikely that the brush will stick in the exact same spots the second or third time around.<o:p></o:p></div>
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Systematic spots: The right or left side of the wall has spots because of your handedness (unless you’re some mutant who’s ambidextrous). When you’re in the corner, your hand hits the other wall so you can’t paint fully into the corner.<o:p></o:p></div>
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Solution: More coats will not help in this case. Fortunately, you know the source of the error! Two options: 1) You can switch hands and awkwardly paint with the off-hand. 2) Pull a Tom Sawyer and get a friend with the opposite handedness to paint for you. <o:p></o:p></div>
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So how does this relate to science? (See this website for a nice description, <a href="http://www.physics.umd.edu/courses/Phys276/Hill/Information/Notes/ErrorAnalysis.html">http://www.physics.umd.edu/courses/Phys276/Hill/Information/Notes/ErrorAnalysis.html</a>.)<o:p></o:p></div>
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Well, taking scientific measurements is like painting a wall, but painting it blindly or painting with invisible paint. You have no idea how much of the wall you’ve actually covered after you’re done.<o:p></o:p></div>
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To account for random error: scientists take repeated measurements (just like adding more coats of paint). In fact, for every $n$ measurements, the error usually goes down by $\sqrt{n}$. <o:p></o:p></div>
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The sources of random errors are often related to precision (see <a href="http://parsingscience.blogspot.com/2012/07/five-hidden-facets-of-numbers.html">http://parsingscience.blogspot.com/2012/07/five-hidden-facets-of-numbers.html</a>). <o:p></o:p></div>
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To account for systematic error: If you’re lucky, the systematic error will be something simple like your handedness.<o:p></o:p></div>
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Unfortunately, systematic errors are often harder to identify and you may never determine the true source of the error. <o:p></o:p><br />
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Takeaway message: if you ever want to picture how difficult science is, imagine painting a wall with invisible paint. Have some sympathy for the scientists in your life and buy them a drink or a new paintbrush.<br />
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Funny example of systematic error: I knew a research team who was taking measurements in the basement of a physics building. They kept having errors in their measurements and discovered that it was correlated with the toilets being flushed!<o:p></o:p></div>
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Nicolehttp://www.blogger.com/profile/10056174002046814636noreply@blogger.com0tag:blogger.com,1999:blog-2961791805048706293.post-74018287745675860752012-08-22T19:15:00.000-07:002012-08-23T21:21:58.694-07:00The Science Inquisition<br />
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Memory of your time in K-12 classrooms probably conjures up
visions of memorizing facts and regurgitating them for exams. <o:p></o:p></div>
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In particular, science labs often consisted of a box of
equipment, a set of instructions, and the correct conclusion. Wrong answers
resulted in error analyses and feelings of shame. <o:p></o:p></div>
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Upon venturing into the science education world, I’ve repeatedly
heard the words “inquiry” and “inquiry-based learning” (<a href="http://en.wikipedia.org/wiki/Inquiry-based_learning">http://en.wikipedia.org/wiki/Inquiry-based_learning</a>).
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Inquiry-based learning is very opposite to traditional
learning, and science is the subject most conducive to inquiry-based inquiry or
open learning. In this type of classroom, there are no right or wrong answers.
Students are given the box of equipment with no instructions. They spend class
time exploring and then develop questions and theories based on their observations.<o:p></o:p><br />
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One awesome source is the Institute for Inquiry at the
Exploratorium (IFI, <a href="http://www.exploratorium.edu/ifi/">http://www.exploratorium.edu/ifi/</a>).
They describe the inquiry process as beginning with an observation, followed by
action: a question arises, a theory is created or more observations are taken.
This process yo-yos back and forth as the learner develops a framework for the
world around them. <o:p></o:p></div>
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Pros of Open Learning: <o:p></o:p></div>
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1. Students develop analytical and creative skills.<o:p></o:p></div>
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2. Learning proceeds based on the students’ interests rather
than a prescribed curriculum.<o:p></o:p></div>
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3. Students are more engaged and often find the process more
fun.<o:p></o:p></div>
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4. This provides excellent training for future scientists. <o:p></o:p></div>
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Cons of Open Learning:<o:p></o:p></div>
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1. Evaluation of students is extremely difficult.<o:p></o:p></div>
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2. Inquiry-based learning is really difficult to teach and
most teachers have no training in it.<o:p></o:p></div>
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3. Open learning requires a great deal of planning; you can’t
just turn your classroom into an open learning classroom in one day.<o:p></o:p></div>
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4. If students need to know certain facts or reach a certain
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Open learning has received a lot of hype in recent years,
and I think it’s amazing that people are thinking about pedagogy. One future
question is whether this type of learning is scalable for public school systems
or if open learning is only feasible in private or charter schools.<o:p></o:p></div>
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I personally think this is a great teaching method, and I
think it provides an excellent way for students to learn about how science
actually works. Feeling inquisitive, yet?<o:p></o:p></div>
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Try inquiry-based learning at home: One example from IFI is
called ice balloons (balloons filled with water that are subsequently frozen,
see <a href="http://www.exploratorium.edu/IFI/activities/iceballoons/iceballoons.html">http://www.exploratorium.edu/IFI/activities/iceballoons/iceballoons.html</a>).
Study properties of ice through questions such as “What happens if I submerge
it in water?” or “What happens if I shine a flashlight on it?”<o:p></o:p></div>
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Fun-fact: In Great Britain, they spell “inquiry” as “enquiry”!<o:p></o:p></div>
Nicolehttp://www.blogger.com/profile/10056174002046814636noreply@blogger.com0tag:blogger.com,1999:blog-2961791805048706293.post-36613197252487288462012-08-17T16:08:00.001-07:002012-08-17T16:08:19.179-07:00Cross Posting!Hey all,<br />
<br />
The Berkeley Science Review posted my original post on numbers as a guest blog post:<br />
<a href="http://sciencereview.berkeley.edu/five-hidden-facets-of-numbers/">http://sciencereview.berkeley.edu/five-hidden-facets-of-numbers/</a><br />
<br />If you're into repetition, feel free to read it again! There's some other really cool posts on there as well so check them out!Nicolehttp://www.blogger.com/profile/10056174002046814636noreply@blogger.com0tag:blogger.com,1999:blog-2961791805048706293.post-50487008671103060192012-08-11T15:02:00.002-07:002012-08-11T15:02:26.144-07:00Error Bars, Average Heights, and Pizza<script type="text/x-mathjax-config"> MathJax.Hub.Config({tex2jax: {inlineMath: [['$','$'], ['\\(','\\)']]}}); </script> <script src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML" type="text/javascript"> </script> <br />
Loyal reader, have you read your <a href="http://parsingscience.blogspot.com/2012/07/breaking-down-research-article.html">research article</a> yet? Perhaps, you've noticed little lines on all the figures and wondered what they are. Those are error bars.<br />
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In the first post, I talked about the type of error that arises due to our <a href="http://parsingscience.blogspot.com/2012/07/five-hidden-facets-of-numbers.html">finite measurements</a>.This post is about another type of error called standard deviation, which basically relates to the spread of a data set.<br />
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Group 1 Heights: 5’7”, 5’8”, 5’9”, 5’10”, and 5’11”<o:p></o:p></div>
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Group 2 Heights: 5’3”, 5’6”, 5’9”, 6’0”, and 6’3”<o:p></o:p><br />
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The average height of each of these groups is 5’9”. However, the variability in these two groups is quite different.<o:p></o:p><br />
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You make a graph without error bars and publish your findings on the <a href="http://parsingscience.blogspot.com/2012/07/archiving-not-just-for-librarians.html">arXiv</a>. Your readers conclude that the two groups are quite similar. </div>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgsOqizGZG5zgtdaYZm4ixTWO22YkAtBFb3JBGlrhGsY90C9MNPh1tjnJLdR46CkdJep48FzOgWDFROhI3eLLE_60-LprV3RE9YBEkAgKWMlwjTUgv17dB1YZB5PEn-Y44j4CTVC0tXPukA/s1600/AverageHeight.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="288" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgsOqizGZG5zgtdaYZm4ixTWO22YkAtBFb3JBGlrhGsY90C9MNPh1tjnJLdR46CkdJep48FzOgWDFROhI3eLLE_60-LprV3RE9YBEkAgKWMlwjTUgv17dB1YZB5PEn-Y44j4CTVC0tXPukA/s400/AverageHeight.png" width="400" /></a></div>
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Figure 1: Average Height Graph without error bars</div>
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If you make a graph with error bars, now your readers will realize that the two groups are actually pretty different from one another.<br />
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgwtzigKeVSIBr3fdrau4oEMYPw9A32MtbTJPZDBBFU5V9mpT1HCL9VLlAPcKIfDFXGQO10MYDSQF51mq-opXWnki4hXtjZud_k13RGc9Mc-9bCke5mXjAEp9lcP0JVekGBDuKxyHcV8mvw/s1600/AverageHeight_withErrorbars.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="288" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgwtzigKeVSIBr3fdrau4oEMYPw9A32MtbTJPZDBBFU5V9mpT1HCL9VLlAPcKIfDFXGQO10MYDSQF51mq-opXWnki4hXtjZud_k13RGc9Mc-9bCke5mXjAEp9lcP0JVekGBDuKxyHcV8mvw/s400/AverageHeight_withErrorbars.png" width="400" /></a></div>
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Figure 2: Average Height Graph with Error Bars</div>
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From Figure 2, you can see that Group 1 has a smaller bar (1.58 inches on each side) because the heights are similar to one another. Group two has a larger bar (4.74 inches on each side) showing that at least one person was very tall and at least one was quite short (Yes, I consider 5'3" to be short, deal with it.).<br />
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For those who are interested in the math,<o:p></o:p> the standard deviation tells you the average spread of all data points from the mean of the group.<br />
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$<br />
standard deviation=\sqrt{\frac{1}{N}\displaystyle\sum\limits_{i=1}^N(x_i-\overline{x})^2}<br />
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where $\overline{x}$ represents the average.<br />
(Check out a worked example here: <a href="http://en.wikipedia.org/wiki/Standard_deviation">http://en.wikipedia.org/wiki/Standard_deviation</a>)</div>
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You're probably thinking "This is all well and good, but how does this relate to my life?"<br />
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So let's use another important life example: sharing pizza with a group of people. (If you don't eat pizza, pretend I'm talking about something else that comes in slices like pie or quiche*).</div>
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You want to compare the pizza eating habits of two groups of friends. Group 1 eats on average 2.1 slices of pizza per person, and Group 2 averages 3.6 slices of pizza per person. (Somehow, you have created a controlled experiment that accounts for deep dish versus thin slices and the different toppings people like.)<o:p></o:p></div>
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“Aha!” you say, “I’m never inviting someone from Group 2 over, they’ll eat me out of house and home.”<o:p></o:p></div>
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Luckily, you remember that the mean isn't enough to characterize a data set so you look at the standard deviations of the groups as well. <o:p></o:p></div>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjLd7pheZo6tXJQ027z6Ncp_IiRRCABhM23vsdYuA1bMsrdF0_awLmHE0Et3OskApNUr35tIg3n2hRpiRvsy8NR5Cpf4wtA1vac3GXQV_CLC3bDHuBnhHxphxUX3adYZA6R8MaUun3h84qv/s1600/PizzaSlices_errorbars.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="272" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjLd7pheZo6tXJQ027z6Ncp_IiRRCABhM23vsdYuA1bMsrdF0_awLmHE0Et3OskApNUr35tIg3n2hRpiRvsy8NR5Cpf4wtA1vac3GXQV_CLC3bDHuBnhHxphxUX3adYZA6R8MaUun3h84qv/s400/PizzaSlices_errorbars.png" width="400" /></a></div>
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Figure 3: Graph of Pizza Eating Habits</div>
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Group 2 has a much larger standard deviation than Group 1. In the context of pizza, this means that some people in Group 2 ate way more than 3.6 slices (and probably made themselves sick), and some people ate fewer than 3.6 slices.<br />
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Additionally, the standard deviation of Group 1 demonstrates that there were some people in Group 1 who also ate at least 3.6 slices of pizza.<o:p></o:p></div>
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Thus, just excluding people from Group 2 will not guarantee guests who eat sparingly.<br />
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You conclude that although the means are different, this difference between the two groups may not actually be that important (in science, this relates to something called statistical significance which I’ll explore in a later post). You resign yourself to just inviting everyone over and ordering lots of pizza**.<br />
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*Note: I do not recommend eating this much pie or quiche in one sitting.<br />
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** Law of Pizza: No matter how much pizza you order for a group, it will get eaten even if people aren't that hungry.</div>Nicolehttp://www.blogger.com/profile/10056174002046814636noreply@blogger.com0tag:blogger.com,1999:blog-2961791805048706293.post-63483862422104722462012-08-07T09:50:00.000-07:002012-08-07T09:50:32.840-07:00How to survive an encounter with a physicist<br />
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If you’re reading this blog, there is a high probability
that you will encounter a physicist at some point in your life. <o:p></o:p></div>
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Here’s a roadmap to surviving this conversation.<o:p></o:p></div>
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<b>Introduction:</b> If
you’re like 99% of the population, you’ll have one of the following two reactions
upon meeting a physicist: “Oh, I loved physics in high school!” or “Oh, I hated
physics in high school!”<o:p></o:p></div>
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Guess what? We don’t care. Feel free to keep this thought
inside your own head. <o:p></o:p></div>
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Note: If you choose to exit at this point, please try to
leave politely. Wrong strategy: just walking away (it’s happened).We already
have enough rejection in our lives (grants, papers, dating, etc). <o:p></o:p></div>
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<b>Research: </b>Your
next question will probably be about our research. If you don’t care, just
follow the “don’t ask, don’t tell” policy. Many of us are quite happy to never
talk about our research. <o:p></o:p></div>
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Should you decide to ask, be prepared to ask for clarification.
Please don’t just stand there with a blank look on your face. It’s difficult to
determine whether it’s because you’re bored or you don’t understand us. <o:p></o:p></div>
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<b>Oh, can you explain…</b>:
the LHC or neutrinos or whatever new scientific discovery was on the Daily Show
last night. <o:p></o:p></div>
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The chances are that the answer is no. Just because we’re
physicists doesn’t mean that we know everything about physics. We can (and
often will) offer our opinions, but these are still just opinions. <o:p></o:p></div>
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This is akin to asking your dentist to diagnose you for
cancer. Yes, your dentist is a doctor, but focuses on a completely different body
part than an oncologist.<o:p></o:p></div>
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<b>Story-time</b>:
Somehow, you’ve survived the beginning of the conversation and are now telling
a story. <o:p></o:p></div>
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Here’s an example of a story told to me by a friend after I
got doored by a car on my bike:<o:p></o:p></div>
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P: I had a friend who was hit by a car last year.<o:p></o:p></div>
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Me: Was she biking?<o:p></o:p></div>
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P: No, walking, I think.<o:p></o:p></div>
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Me: How did the car end up hitting her?<o:p></o:p></div>
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P: She was in the cross-walk, and the car ran through.<o:p></o:p></div>
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Me: How fast was the car going?<o:p></o:p></div>
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P: I don’t know.<o:p></o:p></div>
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Me: Did the car stop?<o:p></o:p></div>
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P: I don’t know.<o:p></o:p></div>
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Me: Well, what happened to your friend, where was she hurt?<o:p></o:p></div>
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P: I don’t know.<o:p></o:p></div>
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Me: Is she recovered?<o:p></o:p></div>
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P: I don’t know! Why are you asking me all these questions!?<o:p></o:p></div>
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Because I’m a scientist! We’re extremely inquisitive and
want all the details before forming opinions. We’re not trying to be jerks
(most of the time). We’re taught to question everything in research, and this
curiosity spills into our daily lives*. <o:p></o:p></div>
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So you have two choices: 1) Don’t tell any stories or 2) Be
prepared for lots of questions. Forewarned is forearmed.<o:p></o:p></div>
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<b>Final warning</b>:
Most physicists are extremely arrogant. It’s both our best and worst quality.
Best because it makes us believe we can solve any problem in the world. Worst because
we think we know everything. Try not to play into that arrogance or you could
be in for a very long night.<o:p></o:p></div>
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If your conversation seems really awkward, don’t worry. The
physicist is used to awkward social situations. Good luck!<o:p></o:p></div>
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*Side note: To be fair, this is a chicken and egg problem:
Are we curious because we’re physicists? Or are we physicists because we’re
curious?<o:p></o:p></div>
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<br /></div>Nicolehttp://www.blogger.com/profile/10056174002046814636noreply@blogger.com2tag:blogger.com,1999:blog-2961791805048706293.post-10095351189823214012012-07-29T15:20:00.000-07:002012-07-29T15:20:01.762-07:00Archiving: Not just for Librarians anymore<br />
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Scenario 1: You’re 12 years old, and you’ve just discovered
a juicy new piece of gossip. You want to be the first to share it with your
friends. Unfortunately, you’re stuck in the 1960s so all you can do is try to
be the first one at school. Alas, a classmate has beaten you to it!<o:p></o:p></div>
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Flash forward to now. Instead of running to school, you can post
the news on Twitter or Facebook. It’s even time-stamped so nobody can dispute
that you were the first to know the news.<o:p></o:p></div>
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Scenario 2: You’re a poor struggling graduate student doing
research. You have an amazing new discovery that would allow you to graduate once
published. You rush to submit your article to a journal. <o:p></o:p></div>
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Disaster strikes! You’ve been scooped! (Someone has
published the same result before you.) Three years of your life wasted. If only
you could have published your research first. (<a href="http://www.phdcomics.com/comics/archive.php?comicid=794">http://www.phdcomics.com/comics/archive.php?comicid=794</a>)<o:p></o:p></div>
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Solution: The arXiv (<a href="http://arxiv.org/">http://arxiv.org/</a>)
<o:p></o:p></div>
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Pronunciation: arXiv is pronounced like the word “archive”
(The X is like the Greek letter “chi”). <o:p></o:p></div>
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On the arXiv, anyone can post a research article. Even
drafts can be posted to ensure that nobody scoops you. <o:p></o:p></div>
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The arXiv exists for the following fields: Physics,
Mathematics, Computer Science, Quantitative Biology, Quantitative Finance, and
Statistics. <o:p></o:p></div>
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An article on the arXiv can be cited just like a journal
article. In addition to setting precedent, posting on the arXiv allows you to
get feedback on your work before you publish it. <o:p></o:p></div>
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History: this project was first hosted by Los Alamos
National Laboratory (<a href="http://www.lanl.gov/">http://www.lanl.gov/</a>)
in 1991 and is now hosted by Cornell University.<o:p></o:p></div>
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The arXiv was at the forefront of open access publishing. Nowadays,
some papers are only printed on the arXiv and never even submitted to journals.
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So the next time you see a group of physicists sitting in a
group, checking their iphones and ipads, and not speaking, realize that they’re
probably all nerding out over the latest articles on the arXiv.</div>Nicolehttp://www.blogger.com/profile/10056174002046814636noreply@blogger.com0tag:blogger.com,1999:blog-2961791805048706293.post-74253668840862705802012-07-24T18:28:00.001-07:002012-07-24T18:28:48.759-07:00Erdős, the Kevin Bacon of the Math world<br />
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If you hang out with math nerds for an extended period of
time, they will inevitably bring up Erdős numbers. <o:p></o:p></div>
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So what is an Erdős number? And what does this have to do
with Kevin Bacon?<o:p></o:p></div>
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Most of us are familiar with “Six Degrees of Kevin Bacon”.
In this game, you try to connect any actor or actress with Kevin Bacon in the fewest
number of steps. <o:p></o:p></div>
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For example, Tilda Swinton was in “Constantine” with Pruitt
Taylor Vince who was in “Trapped” with Kevin Bacon. Thus, Tilda Swinton is
separated from Bacon by two degrees.<o:p></o:p></div>
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(To play this game online, go to <a href="http://oracleofbacon.org/">http://oracleofbacon.org</a>. It’s actually
quite hard to get a high number). <o:p></o:p></div>
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Back to our friend, Paul Erdős (<a href="http://en.wikipedia.org/wiki/Paul_Erd%C5%91s">http://en.wikipedia.org/wiki/Paul_Erd%C5%91s</a>).
He was a famous Hungarian mathematician known for publishing the most papers
(~1525) of any mathematician (among other things). <o:p></o:p></div>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEijXD2QcbTiAHo2hIRqBgRuW1AMkRtUl_BzQt6jjHY65D7s-_GRiUW3bBzF5NhMye2QYebNiuG6LqGoM6kmBFB5PYivaMF5ScZVov_JqhAzUGXPUIQUCGd-awmAYmVlWJqLLdTZbh1NGUs8/s1600/erdos.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="320" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEijXD2QcbTiAHo2hIRqBgRuW1AMkRtUl_BzQt6jjHY65D7s-_GRiUW3bBzF5NhMye2QYebNiuG6LqGoM6kmBFB5PYivaMF5ScZVov_JqhAzUGXPUIQUCGd-awmAYmVlWJqLLdTZbh1NGUs8/s320/erdos.jpg" width="130" /></a> A photo of Paul <span style="background-color: white;">Erdős</span><span style="background-color: white;"> (from Wikipedia)</span></div>
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An Erdős numbers is the degree of separation a mathematician
has from Erdős based on co-authorship of publications. <o:p></o:p></div>
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Say Person A published a paper with Person B who published a
paper with Erdős. Person A’s Erdős number would be two, and Person B’s would be
one. (Erdős’ Erdős number is zero). (For
a list of small Erdős numbers, see: <a href="http://en.wikipedia.org/wiki/List_of_people_by_Erd%C5%91s_number/">http://en.wikipedia.org/wiki/List_of_people_by_Erd%C5%91s_number/</a>)<o:p></o:p></div>
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Just like with actors and Kevin Bacon, it’s astonishingly
hard to find mathematicians with really high Erdős numbers (say over 10). <o:p></o:p></div>
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Side note: Interestingly, this will not be true in a few
hundred years. Because Erdős is dead, nobody new will ever have an Erdős number
of 1. In time, nobody will have an <o:p></o:p><span style="background-color: white;">Erdős</span><span style="background-color: white;"> number smaller than 10!</span></div>
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This phenomenon of small degrees of separation is called the
“small-world effect”, named after encounters in real life when you meet a
friend of a friend and exclaim “what a small world”.<o:p></o:p></div>
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The small world effect isn’t just a series of coincidences. As
long as there are some random connections in a network, it becomes relatively easy
to connect any two people in the network. <o:p></o:p></div>
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An example of an un-random network would be if you could
only be friends with someone if they lived within ten houses of you. In this
case, it would be really hard to pass a message via friends between two people who lived on
opposite sides of the country. <o:p></o:p></div>
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In the real world, we can become friends with people who
live anywhere. Thus, you are connected to almost everyone in the world by a
surprisingly small number of steps. <o:p></o:p></div>
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To read more about network theory, I highly recommend Duncan
Watt’s pop-sci book “Six Degrees: The Science of a Connected Age” (<a href="http://www.amazon.com/Six-Degrees-The-Science-Connected/dp/0393041425">http://www.amazon.com/Six-Degrees-The-Science-Connected/dp/0393041425</a>).
<o:p></o:p></div>
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He’s also a good author to practice reading research
articles, particularly the ones he co-wrote with Steven Strogatz (<a href="http://www.stevenstrogatz.com/">http://www.stevenstrogatz.com/</a>).
(Full disclosure: Duncan Watts is one of my science crushes.)<o:p></o:p></div>
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So now you are fully armed if this subject comes up with a
group of mathematicians. And if they get too uppity, remind them that they will
never be able to have Erdős numbers smaller than two. <o:p></o:p></div>
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Bonus fact: Erdős referred to children as “epsilons”. <o:p></o:p></div>Nicolehttp://www.blogger.com/profile/10056174002046814636noreply@blogger.com0