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	<title>davinci’s notebook &#187; academic writings</title>
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		<title>Why Computer Scientists Should Adopt Open Notebook Science</title>
		<link>http://stargrads.net/blogs/davinci/2010/10/why-computer-scientists-should-adopt-open-notebook-science/</link>
		<comments>http://stargrads.net/blogs/davinci/2010/10/why-computer-scientists-should-adopt-open-notebook-science/#comments</comments>
		<pubDate>Sun, 24 Oct 2010 03:01:17 +0000</pubDate>
		<dc:creator>davinci</dc:creator>
				<category><![CDATA[★grads.net]]></category>
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		<category><![CDATA[open notebook science]]></category>

		<guid isPermaLink="false">http://stargrads.net/blogs/davinci/?p=2981</guid>
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I wrote this essay using MediaWiki (formerly at the address <a href="http://stargrads.net/wiki">http://stargrads.net/wiki</a>) as a proof-of-concept to see if I can write an essay or a paper online. Since I&#8217;m removing MediaWiki from this web site, I have copied its contents below. What is &#8220;Open Notebook Science&#8221;? The term &#8220;open notebook science&#8221; was first coined by Jean-Claude [...]
]]></description>
			<content:encoded><![CDATA[<p>I wrote this essay using MediaWiki (formerly at the address <a href="http://stargrads.net/wiki">http://stargrads.net/wiki</a>) as a proof-of-concept to see if I can write an essay or a paper online.  Since I&#8217;m removing MediaWiki from this web site, I have copied its contents below<span id="more-2981"></span>.</p>
<hr />
<h1>What is &ldquo;Open Notebook Science&rdquo;?</h1>
<p><!--adsensestart-->The term &ldquo;open notebook science&rdquo; was first coined by Jean-Claude Bradley in a blog post<sup><a class='footnote' id='note-2981-1' href='#footnote-2981-B06'>[1]</a></sup> to clarify and distinguish between several related concepts in the open access movement in science.  Bradley defines the term to mean that</p>
<blockquote><p>there is a URL to a laboratory notebook&hellip; that is freely available and indexed on common search engines. It does not necessarily have to look like a paper notebook but it is essential that all of the information available to the researchers to make their conclusions is equally available to the rest of the world. Basically, no insider information.</p></blockquote>
<p>Open notebook science is thus analogous to open source software, but applies to <em>all types of data</em> and not just <em>source code</em>.  It is also distinct from but related to open access <em>publication</em>, which denotes the public availability of preprints of journal articles.  Bradley coined the term in order to properly describe the philosophy behind the UsefulChem<sup><a class='footnote' id='note-2981-2' href='#footnote-2981-UsefulChem'>[2]</a></sup> project.  </p>
<p>The principle behind open notebook science is that <em>anyone</em> can access the primary research record of a project, including preliminary results of experiments, and even raw data as it is gathered.  By this definition, open source software projects in computer science, such as those found on SourceForge<sup><a class='footnote' id='note-2981-3' href='#footnote-2981-SourceForge'>[3]</a></sup>, are also open notebook science projects if the &ldquo;notebooks&rdquo; are taken to mean not just the source code but also the web pages, documentation, forums, and other materials associated with these projects.  </p>
<p>For the purposes of open notebook science, a &ldquo;notebook&rdquo; is thus quite broadly defined: it might be anything from scribbles which appear to be random gibberish to outsiders to somewhat polished half-baked thoughts.  However, it should be noted that traditional notebooks are probably similarly broad in their diversity.</p>
<p>For computer science theorists, an open notebook might consist of a research diary where one records one&rsquo;s thoughts on open problems and questions which one is working on. </p>
<p>I believe that computer scientists should lead the charge to adopt open notebook science, and in this essay I will explain why I hold this belief.</p>
<h1>Examples of Open Notebook Science Projects</h1>
<p>Perhaps the best way to illustrate the concept of open notebook science is by way of example.  Many of the large and well-known open notebook science projects are in chemistry (cheminformatics) and biology (bioinformatics), disciplines in which it is typical to generate and work with large amounts of data.  This data may be costly to produce in terms of money and/or time, and there may be a great deal of redundancy and reduplication between the efforts of different laboratories or research groups.  Two examples of large open notebook science projects are OpenWetWare<sup><a class='footnote' id='note-2981-4' href='#footnote-2981-OpenWetWare'>[4]</a></sup> and UsefulChem<sup><a class='footnote' id='note-2981-5' href='#footnote-2981-UsefulChem'>[5]</a></sup>.</p>
<p>The goals of the OpenWetWare project are to &ldquo;support open sharing of research, education, publication, and discussion in biological sciences and engineering&rdquo;, according to their mission statement<sup><a class='footnote' id='note-2981-6' href='#footnote-2981-OpenWetWare_mission_statement'>[6]</a></sup>.  To this end, their web site provides blogs and wikis to users and research groups.  The wikis are specialised for certain tasks, such as <a href="http://www.openwetware.org/wiki/Help:Notebook">lab notebooks</a> and <a href="http://www.openwetware.org/wiki/Help:Hosting_courses">hosted courses</a>. </p>
<p>The UsefulChem project is an open notebook science project in chemistry originated by the Bradley Laboratory at Drexel University.  It is hosted on <a href="http://www.wikispaces.com/">Wikispaces</a>, a web site that allows users to set up free wikis, and has an associated blog<sup><a class='footnote' id='note-2981-7' href='#footnote-2981-UsefulChem_blog'>[7]</a></sup> hosted on <a href="http://www.blogger.com/">Blogger.com</a>, another free service.  The UsefulChem project illustrates how researchers in fields outside of computer science are using readily available tools to create their open notebook science projects.</p>
<p>I was unable to locate any open notebook science projects of a similar focus and scope for physics and computer science.  As note above, projects to develop open source software, hosted on publicly accessible code repositories such as SourceForge<sup><a class='footnote' id='note-2981-8' href='#footnote-2981-SourceForge'>[8]</a></sup> or Google Code<sup><a class='footnote' id='note-2981-9' href='#footnote-2981-GoogleCode'>[9]</a></sup>, might be considered examples of open notebook science projects if all documentation and other materials related to the projects are also accessible to the public.  And the physics community is actually an early adopter of open access publishing, with its embrace of the arXiv<sup><a class='footnote' id='note-2981-10' href='#footnote-2981-arXiv'>[10]</a></sup> repository of electronic preprints (or e-prints) in 1991.  </p>
<p>The quantum computing community in particular has <em>two</em> wikis, Quantiki<sup><a class='footnote' id='note-2981-11' href='#footnote-2981-Quantiki'>[11]</a></sup> and Qwiki<sup><a class='footnote' id='note-2981-12' href='#footnote-2981-Qwiki'>[12]</a></sup>.  However, these wikis are intended to be references for researchers rather than notebooks for recording ongoing research.</p>
<p>Many individual researchers keep openly accessible notebooks, or have blogs on which they discuss their research semi-regularly.  These are far too numerous to list, but there are a number of portals such as BlogScholar<sup><a class='footnote' id='note-2981-13' href='#footnote-2981-BlogScholar'>[13]</a></sup> in which research-related blogs are organised by category.  </p>
<p>For researchers outside of computer science, technologies such as blogs and wikis are only tools to assist in their research.  For computer scientists, however, these technologies and their impact on society are in and of themselves objects of study.  It is therefore a little disappointing that open notebook science is not more widely practised in the computer science community.  </p>
<h1>Advantages of Open Notebook Science</h1>
<p>The movement towards openness in science is based on the belief that sharing and cooperation leads to swifter progress than hoarding and competition.  </p>
<p>Even leaving aside for the moment the advantages of openness, there are many benefits to using the latest note and record keeping technologies, such as wikis and blogs, whether or not they are made public.  These include advantages common to all derivatives of digital text formats, such as the legibility of typed text as opposed to handwriting, the ability to copy, share, search, and archive notes, and the portability and extensibility of the notes unconstrained by the limitations of physical notebooks (or loose sheets of paper), which may be difficult to carry around and may be misplaced.  </p>
<p>Technologies such as blogs and wikis also perform the role of versioning software, keeping a timestamped history of all edits, arbitrating between conflicting ones, and maintaining a record of all contributions and their contributors.  Furthermore, these technologies also offer advanced search and organisational capabilities, such as the labeling of notes with tags, the arrangement of notes into a hierarchy of categories, and the inclusion of semantics through metadata.  These search and record keeping capabilities would be very useful to scientists when the time comes to write grants and progress reports.  </p>
<p>The use of digital media also means that notes may be dynamic and interactive.  For example, instead of writing a mathematical formula, a digital notebook might contain a form for evaluating that formula with different inputs.  A more trivial example of interactivity is that digital notebooks allow the reader to go back and forth between the main body of a text and a footnote<sup><a class='footnote' id='note-2981-14' href='#footnote-2981-footnote'>[14]</a></sup>, or between different pages or even different documents, very quickly, by clicking with a mouse or using keyboard shortcuts instead of fumbling with physical sheets of paper.</p>
<p>Making a notebook public brings several benefits in addition to the above.  The sharing of notes is made much easier if one can simply pass around a URL (or DOI) instead of copies.  An open notebook is available &ldquo;everywhere&rdquo; (limited by Internet access, which is ubiquitous at all research institutions anyway), and the notebook cannot be misplaced.  </p>
<p>Many of the advantages of open source software also apply, mutatis mutandis, to open notebook science as well.  An open notebook potentially has &ldquo;many eyeballs&rdquo; on it, allowing researchers other than the main investigators to submit &ldquo;patches&rdquo;, i.e., contribute slight tweaks or even major suggestions.  This facilitates scientific discovery and creates more opportunities for better scientific conversations.</p>
<p>Considering the large number of open scientific problems and the diverse backgrounds of scientists, there are bound to be many instances in which the solutions to problems are known to or can be easily produced by researchers other than those who are actively examining them.  Conversely, there may be discoveries which do not appear important in one field but which can bring about significant progress in another.  Open notebooks allow minor questions or serendipitous discoveries to be made publicly known without having to attach them to a paper primarily about another more major (and possibly not very related) result.  This is, in fact, what is already happening in several blogs maintained by scientists<sup><a class='footnote' id='note-2981-15' href='#footnote-2981-annoying_questions'>[15]</a></sup>.  </p>
<p>The open availability of &ldquo;insider information&rdquo; such as data, ideas, and detailed experimental procedures or proofs of theorems which have been condensed in published journal papers for brevity, allow these to be verified and increases the accountability of scientists and the transparency of science.</p>
<p>By performing their work in the open, it becomes possible for scientists to more efficiently allocate their resources, contributing their expertise where it is needed and summoning the expertise of others when that is required.  The scientific community as a whole benefits from this openness.  Keeping an open notebook also helps the individual scientist, because it increases his or her visibility in the major search engines.</p>
<p>There are benefits to the general public as well.  The public accessibility of notebooks which are research diaries serves as a kind of real-time science journalism.  This gives the public a closer look at the actual lives of scientists (which one hopes would dispel negative stereotypes), and helps to acquaint new researchers with what the life of scientists are actually like.  The low cost of entry of starting a blog or a wiki might also serve to get young scientists, such as ambitious high school students, involved in the research process early.</p>
<h1>Credit, Plagiarism, and Other Issues</h1>
<p>The concept of open notebook science is not without its problems.  The primary concern seems to be the issue of priority, or, in the common parlance, &ldquo;getting scooped&rdquo;.  </p>
<p>Science has changed considerably since the days when scientists such as Galileo Galilei or Robert Hooke would encrypt their findings as Latin anagrams to establish their claim while concealing the actual contents of their discovery to give them a head start on research over their rivals.  The history of science is filled with rancorous debates over who first came up with certain ideas, or whether an idea should be attributed to an originator who subsequently did very little with it or to someone who later developed and expanded on it.  </p>
<p>Given the principle of &ldquo;no insider information&rdquo;, a scientist might be understandably concerned about intellectual property theft.  There are, essentially, two ways to address the issue: social and legal.</p>
<p>As some commentators<sup><a class='footnote' id='note-2981-16' href='#footnote-2981-French_chef'>[16]</a></sup> have observed, there are already social norms in place which heavily discourage plagiarism and lack of proper attribution by scientists and scholars.  This may be called the &ldquo;French chef&rdquo; approach to protecting intellectual property, after a study by Fauchart and von Hippel<sup><a class='footnote' id='note-2981-17' href='#footnote-2981-FH06'>[17]</a></sup> who showed that the contents of recipes among accomplished French chefs are protected by a system of implicit social norms, rather than by law.  Such a &ldquo;norms-based&rdquo; intellectual property system may deter would-be plagiarists and people who do not give proper credit.  More public information about when each scientist came up with or worked on a particular idea should in theory decrease disputes about priority rather than increase them.  When scientific conversations are timestamped, viewable to the public, and indexed and cached by multiple search engines and crawlers, it would be extraordinarily difficult to have honest disputes over the history of events related to a claim of priority.  Social norms among scientists should encourage offers of collaboration and discourage &ldquo;scooping&rdquo;.</p>
<p>When norms-based deterrents against intellectual property theft are insufficient, there is always recourse to law-based systems.  Creative Commons<sup><a class='footnote' id='note-2981-18' href='#footnote-2981-CreativeCommons'>[18]</a></sup>, for example, provides a number of legal tools for sharing intellectual property, including various free licenses with different stipulations<sup><a class='footnote' id='note-2981-19' href='#footnote-2981-CreativeCommons_license'>[19]</a></sup> which may be attached to creative works.  </p>
<p>An open notebook science web site or project may choose a license based on its specific needs and legal requirements.  Most open notebook science web sites have licenses that allow sharing and distribution conditioned only on <a href="http://creativecommons.org/licenses/by/3.0/">attribution</a>.  Others add a <a href="http://creativecommons.org/licenses/by-sa/3.0/">&ldquo;share alike&rdquo; clause</a>, which allows derivative works conditioned on these being under the same, similar, or compatible license.  There are also licenses which <a href="http://creativecommons.org/licenses/by-nd/3.0/">forbid derivative works</a>, <a href="http://creativecommons.org/licenses/by-nc/3.0/">commercial usage</a>, or <a href="http://creativecommons.org/licenses/by-nc-nd/3.0/">both</a>.</p>
<p>Some proposed solutions to the problem of intellectual property theft with open notebooks are technical rather than social or legal in nature, such as <a href="http://scienceblogs.com/pontiff/2008/06/pseudo_open_notebook_science.php">restricting information to registered users or introducing a delay in the notebook</a>.  However, such solutions violate the spirit of &ldquo;no insider information&rdquo;, and the result could not be properly called open notebook science.</p>
<p>There are several other intellectual property issues related to open notebook science, such as what constitutes prior publication for peer-reviewed journals, and premature disclosure for the purposes of obtaining patents.  Many journals, however, already accept papers which have previously appeared as preprints in repositories such as the arXiv<sup><a class='footnote' id='note-2981-20' href='#footnote-2981-arXiv'>[20]</a></sup>.  However, patent law has yet to catch up to many recent developments in technology.</p>
<p>The release of large amounts of data which have not undergone careful review raises a number of problems in trust and credibility.  If a set of data is posted publicly before it is thoroughly checked, it may contain errors which may be propagated.  However, as the open source movement shows, for active projects, bugs are usually caught and fixed quickly.  Furthermore, it is not clear that reviewers of published papers necessarily check the data used to support the arguments of the papers they review very thoroughly (although, in principle, they should).</p>
<p>The use of data from open notebooks, then, imposes a duty upon the user to be vigilant and to take on some aspects of the role of reviewer.  This, however, should be the case anyway, even with peer-reviewed published data.  The recent Merck/Elsevier fake journals scandal<sup><a class='footnote' id='note-2981-21' href='#footnote-2981-Merck_scandal'>[21]</a></sup> amply illustrates the point that even an established publisher of scientific journals should not be naïvely trusted. </p>
<p>Other criticisms of open notebook science deal with the user experience, whether from the point of view of a producer or a consumer of open notebooks.  On the one hand, a scientist&rsquo;s notekeeping style may consist of what may appear to others to be random scribbles, and keeping an open notebook would force him to clean up his spontaneous output and restrain his creativity.  On the other hand, most of a scientist&rsquo;s notes may not be very meaningful to others.  But not all open notebooks are meant to be read as research diaries.  Rather, search and organisational tools should allow relevant information to be found even in a sea of irrelevancies.</p>
<p>Finally, another criticism of open notebooks is their stability, or the ability to reference their data.  But this is a problem that is not unique to open notebooks, and applies to all electronically published information.  Solutions include stable URLs or DOIs, or the use of an archival service such as WebCite<sup><a class='footnote' id='note-2981-22' href='#footnote-2981-WebCite'>[22]</a></sup>.</p>
<h1>Proposed Process</h1>
<p>I believe that computer scientists should adopt open notebook science not only for the benefits discussed above, but because it is a subject that is <em>inherently</em> a part of computer science.  Computer scientists, <em>as computer scientists</em>, have a duty to explore technologies for archiving and communicating information as well as their social and legal implications.  </p>
<p>I can&#8217;t very well advocate computer scientists to make their notebooks publicly accessible without doing so myself.  This is why I created the <a href="http://stargrads.net/">&#9733;grads.net</a> web site (read as &ldquo;star grads dot net&rdquo;), as a platform in which to experiment with various aspects of open notebook science.</p>
<p>Currently, the web site consists of four software packages:</p>
<ul>
<li><a href="http://www.mediawiki.org/">MediaWiki</a> for taking notes and writing papers,
</li>
<li><a href="http://wordpress.org/">WordPress</a> for keeping a research diary,
</li>
<li><a href="http://bbpress.org/">bbPress</a> for collaborative discussions, and
</li>
<li><a href="http://http//wikindx.sourceforge.net/">Wikindx</a> for bibliography management.
</li>
</ul>
<p>The software packages are integrated with one another, to the extent that this is possible to my knowledge at the moment.  For example, it is possible to generate citations using the bibliography management system in both the wikis and the blogs.  Furthermore, through the use of the <a href="http://www.math.union.edu/~dpvc/jsMath/">jsMath</a> package, it is possible to typeset mathematical equations using the widely known TeX syntax throughout the web site.  </p>
<p>The intention is to use the blog to keep a diary of research activities, such as meetings or talks that I attend, or ideas that I have.  These ideas may then be discussed in the blog comments, or if there is serious interest, in the forums.  When an idea gets developed enough, a wiki page will be started for it.  Some of these wiki pages may then evolve into papers, such as <a href="http://stargrads.net/blogs/davinci/2010/10/why-computer-scientists-should-adopt-open-notebook-science">the one you are currently reading</a>.  Since this is an experiment, the roles of these tools may change over time.</p>
<p>One of the goals of the web site is to experiment with collaborative paper-writing.  Currently, papers are written by passing around the document source through e-mail along with an indication of who is in possession of a virtual &ldquo;token&rdquo;.  When a paper is sufficiently mature, a draft may be passed around to other researchers for comments.  There is in principle no reason why the draft should not be publicly available at every stage for outside comments or suggestions.  Wikipedia<sup><a class='footnote' id='note-2981-23' href='#footnote-2981-Wikipedia'>[23]</a></sup> has shown that this sort of collaborative process can result in documents of reasonably good quality.  </p>
<p>As the history<sup><a class='footnote' id='note-2981-24' href='#footnote-2981-history'>[24]</a></sup> of this paper shows, it began with a list of headings for the sections that I planned to write.  The sections were then filled with rough notes, which were subsequently expanded into this paper.</p>
<p>Papers written in this fashion have not passed peer review, and thus should be treated like preprints on the arXiv or blog posts.  Ideally, however, if enough experts participate in the commenting process, such a paper should have been reviewed quite thoroughly.  This distributed evaluation process may be called &#8220;soft&#8221; peer review, as opposed to the traditional &#8220;hard&#8221; peer review.</p>
<p>At the moment, I am the only user on this web site capable of editing wiki pages, and hence of authoring papers.  But the idea is that multiple authors can work on a paper, and contributors may be elevated to the status of co-author if they make significant contributions.</p>
<p>The contents of the &#9733;grads.net wiki are under a Creative Commons <a href="http://creativecommons.org/licenses/by-nc-nd/3.0/">Attribution-Noncommercial-No Derivative Works</a> license.  The &ldquo;No Derivative Works&rdquo; clause may seem a little restrictive, but as the license notes, any of its conditions &ldquo;can be waived if you get permission from the copyright holder&rdquo;.  The purpose of this clause is to protect the contents of paper drafts until they are finished.  Drafts should have the same <em>social</em> protection and status as if they had been written using more traditional means, that is, they should not be cited or used without the authors&#8217; explicit permission.</p>
<p>(I will write out a more comprehensive <a href="http://stargrads.net/wiki/%E2%98%85grads.net:Copyrights">copyright policy</a> for each section of the web site when I get around to it.)</p>
<p>This paper is still a draft<sup><a class='footnote' id='note-2981-25' href='#footnote-2981-draft'>[25]</a></sup>, and I invite your comments and suggestions, which I will take into consideration in revising it.  There is an acknowledgements section at the end of this paper for listing contributors.  The goal is to submit this paper somewhere for &ldquo;official&rdquo; publication after it is sufficiently polished<sup><a class='footnote' id='note-2981-26' href='#footnote-2981-again'>[26]</a></sup>.</p>
<h1>For Further Reading</h1>
<p>The Wikipedia <a href="http://en.wikipedia.org/wiki/Open_notebook_science">article on Open Notebook Science</a> actually isn&#8217;t bad and discusses many of the same points.</p>
<h1>Acknowledgements</h1>
<p>The author would like to thank <a href="http://www.razaghpour.org/">Mina Razaghpour</a> for her suggestions.<!--adsensestop--></p>
<h1>Bibliography</h1>
<p><references /></p>
<img src="http://stargrads.net/blogs/davinci/?ak_action=api_record_view&id=2981&type=feed" alt="" /><p>Related posts:<ol>
<li><a href='http://stargrads.net/blogs/davinci/2008/09/open-notebook-science/' rel='bookmark' title='Open notebook science'>Open notebook science</a></li>
<li><a href='http://stargrads.net/blogs/davinci/2009/06/an-essay-on-open-notebook-science/' rel='bookmark' title='An essay on open notebook science'>An essay on open notebook science</a></li>
<li><a href='http://stargrads.net/blogs/davinci/2009/04/overcoming-my-writers-block-part-5-writing-about-open-notebook-science-in-high-school/' rel='bookmark' title='Overcoming my writer&#8217;s block, part 5: writing about open notebook science in high school'>Overcoming my writer&#8217;s block, part 5: writing about open notebook science in high school</a></li>
</ol></p>]]></content:encoded>
			<wfw:commentRss>http://stargrads.net/blogs/davinci/2010/10/why-computer-scientists-should-adopt-open-notebook-science/feed/</wfw:commentRss>
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		<title>Adversary lower bounds in the Hamiltonian oracle model</title>
		<link>http://stargrads.net/blogs/davinci/2009/08/adversary-lower-bounds-in-the-hamiltonian-oracle-model/</link>
		<comments>http://stargrads.net/blogs/davinci/2009/08/adversary-lower-bounds-in-the-hamiltonian-oracle-model/#comments</comments>
		<pubDate>Sun, 09 Aug 2009 06:43:19 +0000</pubDate>
		<dc:creator>davinci</dc:creator>
				<category><![CDATA[academic writings]]></category>
		<category><![CDATA[open notebook science]]></category>
		<category><![CDATA[adversary method]]></category>
		<category><![CDATA[adversary theorem]]></category>
		<category><![CDATA[Hamiltonian oracle model]]></category>
		<category><![CDATA[lower bound technique]]></category>
		<category><![CDATA[lower bounds]]></category>
		<category><![CDATA[Richard Cleve]]></category>

		<guid isPermaLink="false">http://stargrads.net/blogs/davinci/?p=1241</guid>
		<description><![CDATA[
In this series of posts, I write about my experiences as a Ph.D. researcher, and transfer my research notes from my private wiki to my public one.
]]></description>
			<content:encoded><![CDATA[<p>When I switched into quantum computing for my Ph.D. topic, one of the the first research questions that my (former) supervisor, Dr. Richard Cleve, had asked me was whether the adversary method for quantum lower bounds applied in the Hamiltonian oracle model.</p>
<p>The answer is &#8220;yes&#8221;<span id="more-1241"></span>.</p>
<p>It took me a while to figure this out, and in retrospect the answer is (maybe) obvious.  </p>
<p>I think this question is a very nice example of a research question for a beginning Ph.D. student, in that it&#8217;s not too difficult, and at the same time could potentially lead to a body of research culminating in a Ph.D.  (Although this didn&#8217;t happen for me.)</p>
<p>I had been meaning to put my research notes online for a while, but had put it off because they&#8217;re not as useful to as many people as they could be, in the form that they&#8217;re in.  </p>
<p>(I had actually wanted to put all of my research notes online from the very beginning, but refrained from doing so because I didn&#8217;t want my parents to find out that I was studying quantum computing, since <a href="http://stargrads.net/blogs/davinci/2009/04/overcoming-my-writers-block-part-3-science-writing-in-high-school/">they had threatened to disown me</a> if I did so.  But now that <a href="http://stargrads.net/blogs/davinci/2009/06/my-depression-in-waterloo-part-10-disowned/">they <em>have</em> disowned me</a>, I no longer have a reason <em>not</em> to write about quantum computing in public.)</p>
<p>In this next series of posts (which might be interspersed between posts about other things), I&#8217;m going to write about the experiences I went through, and the topics that I learned, while trying to answer the above question.  I&#8217;m also going to clean up the relevant sections of my research notes, and post them online, along the way.  I hope that my posts and research notes will be useful not only to other quantum computing researchers, but also to potential graduate students in any theoretical field who might have to undergo similar experiences when they begin their research.</p>
<p>I&#8217;ve created <a href="http://stargrads.net/wiki/Notes_on_Adversary_Lower_Bounds_in_the_Hamiltonian_Oracle_Model">a page on my wiki</a> where my notes on this research question will eventually go.</p>
<p>Interestingly, I&#8217;ll be inadvertently implementing the Quantum Pontiff&#8217;s idea of a <a href="http://scienceblogs.com/pontiff/2008/06/pseudo_open_notebook_science.php">delayed open notebook</a>, since the research I&#8217;ll be writing about took place about three years ago.</p>
<p>&#8211; davinci 11744</p>
<img src="http://stargrads.net/blogs/davinci/?ak_action=api_record_view&id=1241&type=feed" alt="" /><p>No related posts.</p>]]></content:encoded>
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		<title>The causes of my depression, part 3: &#8220;stop wasting money on worthless books&#8221;</title>
		<link>http://stargrads.net/blogs/davinci/2009/04/the-causes-of-my-depression-part-3-stop-wasting-money-on-worthless-books/</link>
		<comments>http://stargrads.net/blogs/davinci/2009/04/the-causes-of-my-depression-part-3-stop-wasting-money-on-worthless-books/#comments</comments>
		<pubDate>Fri, 24 Apr 2009 05:00:45 +0000</pubDate>
		<dc:creator>davinci</dc:creator>
				<category><![CDATA[academic meetings]]></category>
		<category><![CDATA[academic writings]]></category>
		<category><![CDATA[autobiography]]></category>
		<category><![CDATA[personal]]></category>
		<category><![CDATA[abusive parents]]></category>
		<category><![CDATA[books]]></category>
		<category><![CDATA[child abuse]]></category>

		<guid isPermaLink="false">http://stargrads.net/blogs/davinci/?p=77</guid>
		<description><![CDATA[
One of the main criticisms that my parents made against me was that I "wasted" a lot of money on "worthless" books.  In this post, I explain why this criticism is so stupid.
]]></description>
			<content:encoded><![CDATA[<p>Of course, I cannot speak of anyone else&#8217;s experience, but my sense is that other students of Chinese background were, like me, also pressured by their parents <em>not</em> to read any books outside of school.  The ones I knew always seemed surprised that I was reading books all the time which were not required for school.  But more importantly, their parents <em>lead by counterexample</em>: whenever I have visited the homes of my Chinese classmates, I have noticed that by far the majority of books on their parents&#8217; bookshelves were of a serious technical nature.  In contrast, whenever I have visited the homes of my university professors, their shelves were filled with books which, by my parents&#8217; criteria, &#8220;had nothing to do&#8221; with their research.  Similarly, the bookshelves in my non-Asian classmates&#8217; homes were filled with fiction or books on subjects which were clearly unrelated to their parents&#8217; work.  </p>
<p>In my parents&#8217; house, it was apparent which shelves belonged to my father and which belonged to me: <span id="more-77"></span>his were filled only with technical books, while mine had popular books on various scientific and mathematical subjects, as well as history, literature, arts, and religion.  I was continually criticised for &#8220;wasting money&#8221; on books which I &#8220;didn&#8217;t need&#8221;.  Now, in a sense, this was true: I didn&#8217;t <em>need</em> to own any of the books I bought, because I <em>could</em> have read them at the library or in a bookstore.  For that matter, I didn&#8217;t actually <em>need</em> to own <em>any</em> books at all.  </p>
<p>The criticism that buying books is a &#8220;waste of money&#8221; is extraordinarily shortsighted.  The fact is that reading the books my parents didn&#8217;t want me to read put me at an enormous advantage in school, and would later make career opportunities and scholarships available to me which would have been unattainable had I obeyed them.  The books would have <em>far more than</em> paid for themselves.  (I wrote &#8220;would have&#8221; only because when those opportunities <em>did</em> arise, my parents acted to prevent me from taking them.)  I had friends who spent thousands of dollars on clothes or music CDs, and not only did their parents not criticise them for wasting their money, they would actually give them more of the same as gifts on their birthdays or other special occasions.  I suspect that their parents would have been overjoyed if only my friends had spent their money instead on books.</p>
<p>There is also an aspect to buying books which cannot be quantified economically, and that is that the books you buy make you a member of a community.  There have been numerous instances in my life where I have connected with someone because we have read the same books.  In certain circles, being able to converse knowledgeably about certain authors marks you as a serious member and places you in a sort of inner circle.  Based on my conversations with various people, researchers in a field seem much more likely to have read popular science books related to their field, especially as children, than people outside the field; I suppose this is also simply commonsensical.  Repeatedly telling a child that certain books are &#8220;worthless&#8221; is therefore a pretty good way to ensure that he would not succeed as a researcher in the areas touched upon by those books.  Besides depriving him of the necessary early exposure to certain subjects which is needed to develop a deep understanding of them, it also removes him from the <em>cultural sphere</em> of other researchers in the field and makes it more difficult for him to socialise with his colleagues (some of whom may even be the authors of those books).</p>
<p>Anyhow, I was simply <em>incapable</em> of not buying books.  First, my teachers and friends would recommend books to me, and I treated each recommendation as an <em>expectation</em> that I would go read the book and come back to discuss it with them.  Second, having popular books on science lying around allowed me to understand the subjects much more effectively.  While you cannot learn a scientific subject just by reading popular books, what you <em>can</em> learn is how various ideas are related to one another, both in terms of their content and in their historical development.  I noticed that, for whatever bizarre reason, the ideas covered in each of my high school science classes were presented more or less by the chronological order of their discovery.  I could not understand why things should have been arranged in this way, other than a lack of imagination on the part of the people who designed the curriculum.  Pedagogically, it was a <em>terrible</em> way of organising things.  My classmates were forever confused about having to <em>unlearn</em> incorrect ideas they had previously accepted as facts, and I had to be careful not to be penalised for knowing too much (for example, I had to go along with the <em>lie</em> that protons were elementary particles despite already knowing about quarks and quantum mechanics).  Reading a lot of books on the <em>history</em> of science clarified matters greatly for me.  And finally, because these books gave me a very accurate intuition for what was coming up in the actual science classes themselves, I could study ahead.  (I&#8217;ve always wondered about those students who seemed to spend <em>all</em> of their time studying but <em>only</em> from their textbooks.  What do they do once they&#8217;ve understood the material &#8212; study it over and over again?)  I <em>had</em> to buy a lot of books, because the textbooks assigned by the school were confusing; and, I would have been bored out of my mind otherwise, because I didn&#8217;t have the patience to wait for my teachers to tell me what I should learn next.</p>
<p>&#8211; davinci</p>
<img src="http://stargrads.net/blogs/davinci/?ak_action=api_record_view&id=77&type=feed" alt="" /><p>Related posts:<ol>
<li><a href='http://stargrads.net/blogs/davinci/2009/04/the-causes-of-my-depression-part-5-the-stephen-hawking-incident/' rel='bookmark' title='The causes of my depression, part 5: the Stephen Hawking incident'>The causes of my depression, part 5: the Stephen Hawking incident</a></li>
<li><a href='http://stargrads.net/blogs/davinci/2009/04/the-causes-of-my-depression-part-6-how-mrs-mallo-saved-my-academic-career/' rel='bookmark' title='The causes of my depression, part 6: how Mrs. Mallo saved my academic career'>The causes of my depression, part 6: how Mrs. Mallo saved my academic career</a></li>
<li><a href='http://stargrads.net/blogs/davinci/2009/04/the-causes-of-my-depression-part-9-rolling-with-the-punches/' rel='bookmark' title='The causes of my depression, part 9: rolling with the punches'>The causes of my depression, part 9: rolling with the punches</a></li>
</ol></p>]]></content:encoded>
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		<title>Overcoming my writer&#8217;s block, part 3: science writing in high school</title>
		<link>http://stargrads.net/blogs/davinci/2009/04/overcoming-my-writers-block-part-3-science-writing-in-high-school/</link>
		<comments>http://stargrads.net/blogs/davinci/2009/04/overcoming-my-writers-block-part-3-science-writing-in-high-school/#comments</comments>
		<pubDate>Fri, 10 Apr 2009 03:00:13 +0000</pubDate>
		<dc:creator>davinci</dc:creator>
				<category><![CDATA[academic writings]]></category>
		<category><![CDATA[autobiography]]></category>
		<category><![CDATA[personal]]></category>
		<category><![CDATA[abusive parents]]></category>
		<category><![CDATA[authoritarian parenting]]></category>
		<category><![CDATA[gifted children]]></category>
		<category><![CDATA[Ph.D.]]></category>
		<category><![CDATA[physics of computation]]></category>
		<category><![CDATA[quantum computing]]></category>
		<category><![CDATA[research proposal]]></category>
		<category><![CDATA[science]]></category>
		<category><![CDATA[thesis]]></category>
		<category><![CDATA[writing]]></category>

		<guid isPermaLink="false">http://stargrads.net/blogs/davinci/?p=24</guid>
		<description><![CDATA[
My father prevented me from writing about science, and in particular about the physics of computation, when I was in high school.  This is the cause of my current inability to write my research proposal in quantum computing.
]]></description>
			<content:encoded><![CDATA[<p>I have already written previously about how counterproductive authoritarian parenting is, but this is a fact that I simply <em>cannot emphasise enough</em>.  Educators are always talking about the importance of encouraging children to read and write, but my parents have always <em>discouraged</em> me from both.  Maybe this sounds unbelievable, but I think it is quite common among parents from certain cultural backgrounds.  My parents dismissed anything that I read or wrote outside of what was required for school or a job or some other official purpose as &#8220;frivolous&#8221; and a &#8220;waste of time&#8221;.</p>
<p>My parents had mostly ignored my writings in elementary school, but I think this was because they had assumed that everything I wrote was &#8220;for school&#8221;.  My father would occasionally pick up something I had written; he would frown or glare at me, or make some negative remarks, but at <em>that time</em> he did not order or pressure me to stop.  I think his comments at the time were mostly directed at the school system for what he perceived to be a waste of my time for requiring me to write essays on topics he considered unimportant &#8212; or, even <em>worse</em>, fictional stories<span id="more-24"></span>.  I have never witnessed my father reading anything but newspapers and technical books, nor my mother anything but recipes, and to my knowledge neither has ever read any novels or other forms of fiction outside of what they were required to study when they were in school.  </p>
<p>I wrote whatever was &#8220;in demand&#8221; &#8212; I received requests from friends, classmates, and teachers for my thoughts and opinions on various subjects, and if some topic or idea was especially popular, I wrote about it.  Homework assignments I treated as a kind of &#8220;top priority&#8221; request, because they had externally imposed hard deadlines.  But I was so far ahead in my writing assignments that many were near completion by the time they were assigned, ready to be handed in after putting in some finishing touches.  A large part of the reason for that was because I had a lot of friends who were one or two years older than I was.  When we got together, they would occasionally discuss their homework assignments, and so I got a glimpse into what was required of me in school a year or two ahead.  The open secret with high school homework assignments is that they don&#8217;t change very much from year to year.</p>
<p>So I used to write a lot &#8212; and I mean <em>a lot</em> &#8212; about everything, most of which had absolutely nothing &#8220;to do with school&#8221;.  I wrote poems, short stories, <em>long</em> stories, book reviews, essays on science and technology and politics and religion &#8212; I wrote down my thoughts on pretty much everything and anything.  I think this was the one aspect of the gifted program in elementary school that had <em>really</em> stuck with me through high school.  </p>
<p>In high school, my parents began to <em>really</em> attack me for my writings.  Actually, they attacked me for a lot of things, including <em>reading</em>, holding tutorials and organising study sessions for my classmates, founding the school&#8217;s literary magazine, being the captain of the school&#8217;s mathematics and computer science teams, and going out and socialising.  But since I am writing now about my writer&#8217;s block, I will restrict myself to their attacks on my writings.</p>
<p>There were two topics that I wrote about in particular which especially earned my parents&#8217; ire, namely, science and religion.  My science teachers recognised how far ahead I was of my classmates, and so they encouraged me to begin studying at a level more appropriate to university students.  They recommended books (both popular books and textbooks), magazines, journals, and articles to me, which I would read and discuss with them.  I also started visiting the University of Toronto&#8217;s Erindale (Mississauga) campus and spending a lot of them there, meeting with and talking to people.  So I had a pretty good idea at the time of what sorts of ideas were being discussed at the university level when it came to computer science and physics, which were my primary scientific interests.</p>
<p>My interest in science, and the actions that I undertook to learn about various scientific topics and to promote interest in them (as well as in science in general), eventually led to my parents locking me out of the house and threatening to disown me if I continued with my studies.  I will tell the full story of how my parents persecuted me for my interest in science later.  But I think that the main cause of my writer&#8217;s block, as it pertains to my current inability to write anything related to science, and <em>especially</em> to quantum computing, is the fact that my father did everything he could to prevent me from writing my first scientific papers when I was in high school &#8212; papers on the <em>very same topics</em> that I am now required to write about to complete a Ph.D. degree.</p>
<p><em>My father insisted when I was in high school that I cease to write about the physics of computation, on the grounds that I was wasting my time and diminishing my chances of getting into university and graduate school.  When I refused to stop despite his harassment, he first began to scream at me whenever he caught me writing scientific papers at home, and then he began to hit me.  I continued writing, but elsewhere &#8212; at the high school, at the university, at a friend&#8217;s home.  He then forbid me from visiting the university or my friends, so I just snuck out at night or when I knew he would not be home.  This culminated in my being locked out of the house after going to the university library late one night &#8212; I came home to find the door locked and the handle of the screen door tied to the door frame with twine.  But even </em>this<em> did not deter me &#8212; I only made sure not to get caught again.  I only </em>finally<em> conceded defeat after my parents threatened not only to disown me, but to disallow my younger brother from attending university, if I did not do as they demanded.</em></p>
<p>Because of the punishments and threats from my parents, I stopped writing about the physics of computation at the end of high school.  And now that I am in the Ph.D. program in computer science &#8212; which my father insisted I would never get into if I continued to write about the physics of computation &#8212; I am supposed to write a research proposal <em>on the physics of computation</em>.  </p>
<p>I just couldn&#8217;t do it.  All I could think about, every time I sat down to write, was how I could have completed this <em>more than a decade ago</em>, if only I had run away from home as a teenager.  To make things worse, after I entered the Ph.D. program, my father kept nagging me for being too &#8220;slow&#8221; in starting to write my thesis &#8212; <em>the very same thesis that I would have been working on over a decade ago if he hadn&#8217;t beaten me, locked me out of the house, and threatened to disown me for writing</em>.  The way I see it is this: he can either beat me and lock me out of the house for writing what would have been my Ph.D. thesis, or he can pressure me to finish it faster &#8212; but he cannot do both.  <em>He is the very cause of the problem for which he placed the blame on me.</em></p>
<p>And this was a very common occurrence throughout my life &#8212; my parents would blame me, or people associated with me, for the <em>very things</em> for which <em>they themselves were entirely and exclusively responsible.</em>  This will become very apparent as I continue my story.</p>
<p>It might seem like the above would be the main source of my writer&#8217;s block and my depression, but that is only a small part of it.  Despite being unable to write about science, I continued to write about other subjects &#8212; and my parents continued to punish me for writing.  </p>
<p>&#8211; davinci</p>
<img src="http://stargrads.net/blogs/davinci/?ak_action=api_record_view&id=24&type=feed" alt="" /><p>Related posts:<ol>
<li><a href='http://stargrads.net/blogs/davinci/2009/04/overcoming-my-writers-block-part-5-writing-about-open-notebook-science-in-high-school/' rel='bookmark' title='Overcoming my writer&#8217;s block, part 5: writing about open notebook science in high school'>Overcoming my writer&#8217;s block, part 5: writing about open notebook science in high school</a></li>
<li><a href='http://stargrads.net/blogs/davinci/2009/04/overcoming-my-writers-block-part-4-high-school-and-being-editor-in-chief/' rel='bookmark' title='Overcoming my writer&#8217;s block, part 4: high school and being editor-in-chief'>Overcoming my writer&#8217;s block, part 4: high school and being editor-in-chief</a></li>
<li><a href='http://stargrads.net/blogs/davinci/2009/04/overcoming-my-writers-block-part-2-elementary-school-esl-and-fiction/' rel='bookmark' title='Overcoming my writer&#8217;s block, part 2: elementary school, ESL, and fiction'>Overcoming my writer&#8217;s block, part 2: elementary school, ESL, and fiction</a></li>
</ol></p>]]></content:encoded>
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		<title>Writing my Ph.D. Research Proposal live</title>
		<link>http://stargrads.net/blogs/davinci/2008/10/writing-my-phd-research-proposal-live/</link>
		<comments>http://stargrads.net/blogs/davinci/2008/10/writing-my-phd-research-proposal-live/#comments</comments>
		<pubDate>Wed, 15 Oct 2008 23:51:40 +0000</pubDate>
		<dc:creator>davinci</dc:creator>
				<category><![CDATA[academic writings]]></category>
		<category><![CDATA[personal]]></category>
		<category><![CDATA[comprehensive requirement]]></category>
		<category><![CDATA[electronic publishing]]></category>
		<category><![CDATA[MediaWiki]]></category>
		<category><![CDATA[Ph.D.]]></category>
		<category><![CDATA[Ph.D. program]]></category>
		<category><![CDATA[research proposal]]></category>
		<category><![CDATA[University of Waterloo]]></category>
		<category><![CDATA[WIKINDX]]></category>

		<guid isPermaLink="false">http://stargrads.net/blogs/davinci/?p=7</guid>
		<description><![CDATA[
In this post, I describe an experiment in open notebook science: writing my Ph.D. Research Proposal live and online.
]]></description>
			<content:encoded><![CDATA[<p>One of the requirements of the Ph.D. program in Computer Science at the University of Waterloo is the <a href="http://www.cs.uwaterloo.ca/grad/programs/#phd_compII">Comprehensive-II (Depth)</a> requirement, which consists of a written research proposal and an accompanying oral presentation.</p>
<p>I have decided to write my research proposal <a href="http://stargrads.net/wiki/Research_Proposal_%28D._L._Yonge-Mallo%29">live and online</a>.  Besides being a way to test out theories about electronic publishing as well as an excuse to experiment with the relevant technologies, I have a more personal reason for doing this.</p>
<p>Over the years, I have acquired a number of absolutely horrendous academic habits due to the necessity of <a href="http://stargrads.net/blogs/davinci/2008/10/my-academic-and-personal-background/">hiding my studies from my parents</a>, such as keeping a low profile and limiting my publishing.  I would usually not even begin a project unless I believed that there was a chance I could complete it without being discovered, and would reveal it only after it was already a fait accompli<span id="more-7"></span> which my parents could do nothing about.  Often I would destroy my own work.  These are of course habits which are impossible to maintain at the postgraduate level, and I have to break them.</p>
<p>The task of writing online immediately raises a number of questions.  For example, what about copyright and other legal issues?  Which tools would I need or should I use?  </p>
<p>I have set up a <a href="http://stargrads.net/wiki/">wiki</a> for the purpose of writing the proposal, with the goal of using it for future academic writings also.  The <a href="http://www.mediawiki.org/">MediaWiki</a> software (the wiki engine originally created for <a href="http://en.wikipedia.org/wiki/Wikipedia">Wikipedia</a>) keeps a history of edits, which dissuades me from continually deleting the contents of the document and restarting from scratch.  The <a href="http://www.mediawiki.org/wiki/Extension:JsMath">jsMath extension</a> allows me to render LaTeX formulas in the wiki.  I have also been keeping a <a href="http://stargrads.net/bibliography/">bibliography</a> using <a href="http://http://wikindx.sourceforge.net/">WIKINDX</a>, from which I can insert citations into the wiki.  I haven&#8217;t yet figured out what to use for figures and diagrams, but most of the major tools necessary for writing a scientific paper seem to be covered.</p>
<p>I don&#8217;t want to dwell on the legal issues, except that the proposal should have the same legal status as if I had written it using more traditional means and submitted it on paper.  I have put the entire wiki under a Creative Commons <a href="http://creativecommons.org/licenses/by-nc-nd/3.0/">Attribution-Noncommercial-No Derivative Works</a> license.</p>
<p>The research proposal is <a href="http://stargrads.net/wiki/Research_Proposal_%28D._L._Yonge-Mallo%29">here</a>.  It&#8217;s far from complete, but that&#8217;s exactly the point.</p>
<p>&#8211; davinci</p>
<img src="http://stargrads.net/blogs/davinci/?ak_action=api_record_view&id=7&type=feed" alt="" /><p>Related posts:<ol>
<li><a href='http://stargrads.net/blogs/davinci/2009/04/overcoming-my-writers-block-part-3-science-writing-in-high-school/' rel='bookmark' title='Overcoming my writer&#8217;s block, part 3: science writing in high school'>Overcoming my writer&#8217;s block, part 3: science writing in high school</a></li>
<li><a href='http://stargrads.net/blogs/davinci/2008/11/why-and-for-whom-am-i-writing-this/' rel='bookmark' title='Why and for whom am I writing this?'>Why and for whom am I writing this?</a></li>
<li><a href='http://stargrads.net/blogs/davinci/2009/06/my-depression-in-waterloo-part-8-disguising-my-research/' rel='bookmark' title='My depression in Waterloo, part 8: disguising my research'>My depression in Waterloo, part 8: disguising my research</a></li>
</ol></p>]]></content:encoded>
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