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    <title>Stephen Malina</title>
    <link>https://stephenmalina.com/</link>
    <description>Recent content on Stephen Malina</description>
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    <item>
      <title>Biologizing the stack</title>
      <link>https://stephenmalina.com/post/2023-11-04-biologizing-the-stack/</link>
      <pubDate>Sat, 04 Nov 2023 00:00:00 +0000</pubDate>
      
      <guid>https://stephenmalina.com/post/2023-11-04-biologizing-the-stack/</guid>
      <description>I&amp;rsquo;m experimenting with writing some shorter, less polished posts. These come with the disclaimer that I&amp;rsquo;m optimizing for getting thoughts out there while they&amp;rsquo;re still crystallizing rather than achieving maximum rigor. For this post in particular, I&amp;rsquo;m not arguing that this direction is definitely worth pursuing so much as exploring a frame/idea to see where it gets me.
A while ago, a friend asked me why I like the idea of working with cells better than cell-free systems and I gave some hand-wavy answer about cells being cool.</description>
    </item>
    
    <item>
      <title>Continuous glucose monitors (CGM) and beyond: A dialogue</title>
      <link>https://stephenmalina.com/post/2023-08-13-cgm-and-beyond/</link>
      <pubDate>Sun, 13 Aug 2023 00:00:00 +0000</pubDate>
      
      <guid>https://stephenmalina.com/post/2023-08-13-cgm-and-beyond/</guid>
      <description>What are continuous glucose monitors good for? More broadly, what are continuous measures of physiology (CxM) good for?
Similar to Elliot and I&amp;rsquo;s dialogue, this post has an unconventional format. It&amp;rsquo;s both a synthesis of Willy&amp;rsquo;s, Eryney&amp;rsquo;s, and my opinions on continuous monitoring combined with a debate in places where we disagree. To try and make it clear which views are coming from each person, we&amp;rsquo;ve annotated sections that come from a subset of us rather than all of us with e.</description>
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    <item>
      <title>What are the bottlenecks to safe, repeatable edits in humans? Part 1</title>
      <link>https://stephenmalina.com/post/2023-06-07-editing-part-i/</link>
      <pubDate>Wed, 07 Jun 2023 00:00:00 +0000</pubDate>
      
      <guid>https://stephenmalina.com/post/2023-06-07-editing-part-i/</guid>
      <description>Summary # Gene editing has made a lot of progress over the past few decades. CRISPR-Cas9 sparked the recent fervor and won some of its early pioneers a Nobel Prize, and more recently Prime Editing and Cytosine/Adenine Base Editors (CBEs/ABEs) have further expanded the range of editing targets and types of edits that are possible while increasing efficiency and reducing the rate of off-target effects.
From the perspective of safe, ubiquitous editing in humans using these systems, a few major challenges for editing remain towards translating novel target discovery into clinical application:</description>
    </item>
    
    <item>
      <title>Dialogue on Viriditas</title>
      <link>https://stephenmalina.com/post/2023-01-11-viriditas-dialogue/</link>
      <pubDate>Wed, 11 Jan 2023 00:00:00 +0000</pubDate>
      
      <guid>https://stephenmalina.com/post/2023-01-11-viriditas-dialogue/</guid>
      <description>Introduction # A few months ago, Elliot Hershberg, one of my favorite Substack writers, wrote a post laying out his personal mission. I really enjoyed his post and, as is customary in blogging, the best way I could think of to compliment it was to share some (hopefully constructively) critical thoughts on it.
After sending my post to Elliot, he proposed the great idea of us having a discussion of this over email, which we could then potentially publish.</description>
    </item>
    
    <item>
      <title>Reflections on 2022</title>
      <link>https://stephenmalina.com/post/2023-01-02-reflections-on-2022/</link>
      <pubDate>Sun, 01 Jan 2023 00:00:00 +0000</pubDate>
      
      <guid>https://stephenmalina.com/post/2023-01-02-reflections-on-2022/</guid>
      <description>2022 was another exciting, fun year. To round it out, I wrote up some scattered reflections. Enjoy, or if you aren&amp;rsquo;t a fan of this genre of post, don&amp;rsquo;t! Also, each section is mostly self-contained and they&amp;rsquo;re not organized in any special order, so don&amp;rsquo;t hesitate to skip a section if it sounds boring.
Writing # 2022 felt like a productive year for blogging even though my post count dropped down from 11 in 2021 to 6.</description>
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    <item>
      <title>Decentralization of Atoms is Underrated</title>
      <link>https://stephenmalina.com/post/2022-11-21-decentralization-of-atoms-is-underrated/</link>
      <pubDate>Mon, 21 Nov 2022 00:00:00 +0000</pubDate>
      
      <guid>https://stephenmalina.com/post/2022-11-21-decentralization-of-atoms-is-underrated/</guid>
      <description>This post was co-authored with Austin Vernon.
Summary # While the internet often focuses its furious debate energy on decentralization in the realm of bits, in the realm of atoms, decentralization is currently underrated in terms of its feasibility and desirability. New technologies in areas like aviation, freight, and life sciences can and are shifting the scales towards decentralized models being possible. This has the potential to broaden access, reduce costs, and increase individual empowerment.</description>
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    <item>
      <title>GPT4 Predictions</title>
      <link>https://stephenmalina.com/post/2022-11-16-gpt4-predictions/</link>
      <pubDate>Wed, 16 Nov 2022 00:00:00 +0000</pubDate>
      
      <guid>https://stephenmalina.com/post/2022-11-16-gpt4-predictions/</guid>
      <description>As a way to keep myself honest, I&amp;rsquo;m going to be recording GPT4 predictions here and archiving versions of the post so I can&amp;rsquo;t go back and change it without people knowing. Not that I would do this anyway, but it&amp;rsquo;s been a tough week for &amp;ldquo;trust me, I&amp;rsquo;m telling the truth&amp;rdquo; so I&amp;rsquo;m doing this in case readers want the receipts.
I predict GPT4 won&amp;rsquo;t be able to&amp;hellip; # Write a blog post about gene therapy that I consider to be of equivalent quality to my own Write a scientific paper about machine learning.</description>
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    <item>
      <title>AI Omens: Signs of AI acceleration</title>
      <link>https://stephenmalina.com/post/2022-09-17-ai-omens/</link>
      <pubDate>Sat, 17 Sep 2022 00:00:00 +0000</pubDate>
      
      <guid>https://stephenmalina.com/post/2022-09-17-ai-omens/</guid>
      <description>A friend recently asked me what my &amp;ldquo;AI timelines&amp;rdquo; were. Especially with recent progress in image generation, language modeling, code generation, robotics, protein folding, and other areas, this has become an increasingly popular question amongst those who are paying attention.
However, I find trying to answer this question pretty frustrating. There already exist long, thorough reports (another) which build quantitative models and carefully define terms to make sure there&amp;rsquo;s as little ambiguity as possible.</description>
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    <item>
      <title>Movie Review - Top Gun: Maverick</title>
      <link>https://stephenmalina.com/post/2022-06-07-top-gun-maverick-review/</link>
      <pubDate>Tue, 07 Jun 2022 00:00:00 +0000</pubDate>
      
      <guid>https://stephenmalina.com/post/2022-06-07-top-gun-maverick-review/</guid>
      <description>Since I&amp;rsquo;ve been going around telling everyone how Top Gun: Maverick (TG:M) is one of the best action movies of our generation, I&amp;rsquo;d figured I&amp;rsquo;d try and write down some of my thoughts while they&amp;rsquo;re still fresh.
The core reason I love TG:M is that it&amp;rsquo;s an unapologetic paean to excellence, Captain Pete &amp;ldquo;Maverick&amp;rdquo; Mitchell (Maverick) embodies excellence as a fighter pilot and teacher, pushing both himself and his students to exceed their perceived limits and their planes&amp;rsquo;.</description>
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    <item>
      <title>Book Review - Elmer Gates and the Art of Mind-using</title>
      <link>https://stephenmalina.com/post/2022-04-24-book-review-egamu/</link>
      <pubDate>Sun, 24 Apr 2022 00:00:00 +0000</pubDate>
      
      <guid>https://stephenmalina.com/post/2022-04-24-book-review-egamu/</guid>
      <description>Introduction # Generally when someone tells you they&amp;rsquo;ve invented an &amp;ldquo;art of mind-using&amp;rdquo; that involves lots of made-up words and comes packaged with a spiritual philosophy, you should tell them &amp;ldquo;no thanks&amp;rdquo; and walk away. But, what if that same would-be crackpot was also an incredibly successful inventor whose contemporaries considered a genius? Moreover, what if that would-be crackpot also ran careful, rigorous experiments to validate their theories? And so we have Elmer Gates.</description>
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    <item>
      <title>2050 Predictions</title>
      <link>https://stephenmalina.com/post/2022-01-01-2050-predictions/</link>
      <pubDate>Sat, 01 Jan 2022 00:00:00 +0000</pubDate>
      
      <guid>https://stephenmalina.com/post/2022-01-01-2050-predictions/</guid>
      <description>Introduction # Along with a few internet blogger friends, inspired by Erik Hoel&amp;rsquo;s post (parts of which I disagree with, including the headline), I&amp;rsquo;ve decided to make predictions for 2050. The rest of this post discusses some meta aspects of making these predictions and then lists out the predictions. In case you&amp;rsquo;re waiting for my (hopefully) less speculative 2022 annual predictions, fear not! Those will be coming in the next few weeks.</description>
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    <item>
      <title>Scoring my 2021 Predictions</title>
      <link>https://stephenmalina.com/post/2021-12-31-scoring-my-2021-predictions/</link>
      <pubDate>Fri, 31 Dec 2021 00:00:00 +0000</pubDate>
      
      <guid>https://stephenmalina.com/post/2021-12-31-scoring-my-2021-predictions/</guid>
      <description>At the beginning of last year, I made predictions for the year. Now it&amp;rsquo;s time to score them (before I make my 2022 predictions).
Data &amp;amp; code # Here is a spreadsheet containing my scored predictions. If you want to see my full analysis, you can look at my Jupyter notebook which contains Brier score calculations plus plotting.
High level analysis # The key metrics I looked at were my overall and by category Brier scores plus calibration.</description>
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    <item>
      <title>Beware silver bullets</title>
      <link>https://stephenmalina.com/post/2021-12-05-beware-silver-bullets/</link>
      <pubDate>Sat, 04 Dec 2021 00:00:00 +0000</pubDate>
      
      <guid>https://stephenmalina.com/post/2021-12-05-beware-silver-bullets/</guid>
      <description>Note: This post was co-written with Uri Bram of The Browser, who deserves all credit for the good parts and no blame for the bad parts and inevitable mistakes (which things fall into which category is at your, the reader’s, discretion).
A recurring problem I, and I think people similar to me, face is letting my excitement about something new transform from being based on curiosity and a sense of usefulness into viewing the thing as a Fully General Solution to All Problems.</description>
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    <item>
      <title>Crazy ideas for future synthetic biology &amp; bioengineering</title>
      <link>https://stephenmalina.com/post/2021-11-crazy-synthetic-bio-ideas/</link>
      <pubDate>Fri, 26 Nov 2021 00:00:00 +0000</pubDate>
      
      <guid>https://stephenmalina.com/post/2021-11-crazy-synthetic-bio-ideas/</guid>
      <description>One thing I like about the synthetic biology community is that, from the early days, its participants have been willing to entertain &amp;ldquo;wild&amp;rdquo; ideas like building dragons. While this willingness comes with all of the risks associated with building a lot of hype around a nascent technology, against the backdrop of cultural indefinite pessimism, I still prefer it. In that vein, inspired by Milan Cwitkovic&amp;rsquo;s legendary listicles on Things you&amp;rsquo;re allowed to do and Market failures in science, I decided to make my own listicle of cool ideas for future synthetic biology &amp;amp; bioengineering projects.</description>
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    <item>
      <title>Energetic Aliens</title>
      <link>https://stephenmalina.com/post/2021-07-01-energetic-aliens-among-us/</link>
      <pubDate>Thu, 01 Jul 2021 00:00:00 +0000</pubDate>
      
      <guid>https://stephenmalina.com/post/2021-07-01-energetic-aliens-among-us/</guid>
      <description>Reading biographies and observing friends, family, and colleagues has led me to become interested in what factors drive the variance in cognitive stamina and observed levels of energy between individuals. Identifying the biological, environmental, or motivational factors which produce this difference seems important and neglected. Understanding this is a research agenda&amp;rsquo;s worth of work, so my contribution will be to draw a conceptual boundary around the idea of an &amp;ldquo;energetic alien&amp;rdquo; and explore some (not selected i.</description>
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    <item>
      <title>Book Review - A World Without Email</title>
      <link>https://stephenmalina.com/post/2021-04-01-world-without-email-review/</link>
      <pubDate>Thu, 01 Apr 2021 00:00:00 +0000</pubDate>
      
      <guid>https://stephenmalina.com/post/2021-04-01-world-without-email-review/</guid>
      <description>A World Without Email (AWWE) is Cal Newport&amp;rsquo;s new book arguing for an overhaul in our workplace communication and project management style. This topic is a natural follow up to Newport&amp;rsquo;s previous two books &amp;ndash; Deep Work and Digital Minimalism. These books focused on the individual benefits of hard focused effort and deliberate technology reduction respectively. This book applies a similar lens to the modern frenetic knowledge economy workplace. According to Newport, priortizing responsiveness and heavily relying on general purpose communication tools in the workplace is making us miserable and unproductive.</description>
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    <item>
      <title>A personal post-mortem on almost giving very misleading advice</title>
      <link>https://stephenmalina.com/post/2021-03-06-bad-advice-near-miss/</link>
      <pubDate>Sat, 06 Mar 2021 00:00:00 +0000</pubDate>
      
      <guid>https://stephenmalina.com/post/2021-03-06-bad-advice-near-miss/</guid>
      <description>I recently had someone ask me what I felt helped me grow the most in my first few years working as a software engineer. Upon them asking me this, I initially drafted an answer that looked something like the following:
A combination of building systems and seeing how they failed and then reading lots of code and books including: (list of programming books I&amp;rsquo;ve read).
However, upon writing this &amp;ndash; and before sending it thankfully &amp;ndash; I realized I was almost entirely misrepresenting the things that actually helped me grow.</description>
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    <item>
      <title>Ideas not mattering is a psyop</title>
      <link>https://stephenmalina.com/post/2021-02-21-ideas-not-mattering-is-a-psyop/</link>
      <pubDate>Sun, 21 Feb 2021 00:00:00 +0000</pubDate>
      
      <guid>https://stephenmalina.com/post/2021-02-21-ideas-not-mattering-is-a-psyop/</guid>
      <description>Originally posted on Alexey&amp;rsquo;s blog.
By Stephen Malina, Alexey Guzey, Leopold Aschenbrenner.
Introduction # Conventional startup and business wisdom has become “there are plenty of good ideas, all that matters is execution.” We don&amp;rsquo;t buy it. Empirically, all our aspiring founder friends are desperate for startup ideas, with few managing to land on something worthwhile, and all our scientist friends are desperate for research ideas. Good ideas are essential, even ones that seem obvious in retrospect were non-obvious ex ante, and in fact good execution itself depends critically on good ideas.</description>
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    <item>
      <title>Three observations from a surprisingly emotionally evocative winter walk</title>
      <link>https://stephenmalina.com/post/2021-02-01-emotional-winter-walk/</link>
      <pubDate>Mon, 01 Feb 2021 00:00:00 +0000</pubDate>
      
      <guid>https://stephenmalina.com/post/2021-02-01-emotional-winter-walk/</guid>
      <description>I just went on a short nighttime mid-snow storm walk and it unexpectedly provoked three separate observations along with a desire to capture them.
Reveling in the beauty of our creations # Everyone loves to hate on Ayn Rand but noone else can give me ASMR writing about skyscrapers.
I would give the greatest sunset in the world for one sight of New York&amp;rsquo;s skyline. Particularly when one can&amp;rsquo;t see the details.</description>
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    <item>
      <title>Book Review - The Art of Learning</title>
      <link>https://stephenmalina.com/post/2021-01-23-book-review-the-art-of-learning/</link>
      <pubDate>Wed, 20 Jan 2021 00:00:00 +0000</pubDate>
      
      <guid>https://stephenmalina.com/post/2021-01-23-book-review-the-art-of-learning/</guid>
      <description>This is a review of The Art of Learning: A Journey in the Pursuit of Excellence by Joshua Waitzkin.
I&amp;rsquo;m sort of surprised how much I liked this book. At times, it bordered on self-help, spiritual BS but Waitzkin&amp;rsquo;s undeniable competitive success and tempering of the more spiritually flavored advice with insightful musing on how to master a domain or understand one&amp;rsquo;s opponent elevated it far above the self-help morass.</description>
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      <title>My favorite random internet writing - A tier list</title>
      <link>https://stephenmalina.com/post/2021-01-20-internet-writing-tier-list/</link>
      <pubDate>Wed, 20 Jan 2021 00:00:00 +0000</pubDate>
      
      <guid>https://stephenmalina.com/post/2021-01-20-internet-writing-tier-list/</guid>
      <description>As someone who has and continues to derive tremendous value from writing on the internet, I&amp;rsquo;ve recently felt an urge to share some of my favorite semi-esoteric internet writing in part so that I have a post to refer back to instead of resending the same articles to friends over and over again. Since many of these articles resist easy categorization, I&amp;rsquo;m organizing this in the form of a tier list (inspirational examples: 1, 2).</description>
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    <item>
      <title>2021 Predictions</title>
      <link>https://stephenmalina.com/post/2021-01-09-2021-predictions/</link>
      <pubDate>Sat, 09 Jan 2021 00:00:00 +0000</pubDate>
      
      <guid>https://stephenmalina.com/post/2021-01-09-2021-predictions/</guid>
      <description>For the past two years, my friends have had a tradition of making predictions and scoring them at the end of the year. This year, I decided why not just post my predictions on my blog and score them publicly (with a few redacted)? This will hopefully incentivize me to be more thoughtful about them and also will help direct my endless desire for internet acclaim towards something that has a positive side effect.</description>
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    <item>
      <title>My Maniac Week - A Review</title>
      <link>https://stephenmalina.com/post/2020-10-20-maniac-week-review/</link>
      <pubDate>Tue, 20 Oct 2020 00:00:00 +0000</pubDate>
      
      <guid>https://stephenmalina.com/post/2020-10-20-maniac-week-review/</guid>
      <description>Previously: Upcoming Maniac Week.
Summary # Inspired by Nick Winter, Bethany Soule, Danny Reeves, Brent Yorgey, and Alex Strick, I undertook a &amp;ldquo;maniac week&amp;rdquo; from Friday, October 9th (9:00 AM) through Thursday, October 15th (12:00 PM). During my maniac week, I worked 11+ hours a day on schoolwork and my primary research project while avoiding social media and other internet distractions.
By my own assessment, my maniac week was a success.</description>
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    <item>
      <title>Upcoming Maniac Week</title>
      <link>https://stephenmalina.com/post/2020-09-25-upcoming-maniac-week/</link>
      <pubDate>Sat, 26 Sep 2020 00:00:00 +0000</pubDate>
      
      <guid>https://stephenmalina.com/post/2020-09-25-upcoming-maniac-week/</guid>
      <description>Abstract # Guy on internet decides to follow lead of other people on internet and pre-commits to working much more than usual . Plans to document whole thing under illusion people care about some guy on the internet working a more-than-average number of hours relative to his baseline.
Summary # From Friday, October 9th (9:00 AM) through Thursday, October 15th (2:00 PM), I&amp;rsquo;ll attempt to work 11+ hours a day on schoolwork and my primary research project.</description>
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    <item>
      <title>Becoming a more playful, deeper thinker</title>
      <link>https://stephenmalina.com/post/2020-07-11-learning-to-love-thinking/</link>
      <pubDate>Sat, 11 Jul 2020 00:00:00 +0000</pubDate>
      
      <guid>https://stephenmalina.com/post/2020-07-11-learning-to-love-thinking/</guid>
      <description>Note: Ignore the weird Markdown formatting, it’s because I copied this from the blog source code.
Inspiration: Understanding by Nabeel Qureshi, David Deutsch&amp;rsquo;s The Beginning of Infinity and Fun Criterion.
Meta: This is an experimental post in which I dissect something about myself rather than write about some technical topic. Feedback and criticism encouraged as always!
One commonality I&amp;rsquo;ve noticed amongst profiles of thinkers I respect&amp;ndash;Richard Feynman, John Von Neumann, David Deutsch, Donald Knuth, George Church&amp;ndash;is that these folks enjoy(ed) “thinking as play”.</description>
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      <title>Course Review - Causal Inference</title>
      <link>https://stephenmalina.com/post/2020-05-15-ci-course-review/</link>
      <pubDate>Fri, 15 May 2020 00:00:00 +0000</pubDate>
      
      <guid>https://stephenmalina.com/post/2020-05-15-ci-course-review/</guid>
      <description>This semester, I had the pleasure of taking a course on Causal Inference with Professor Elias Bareinboim, one of Judea Pearl&amp;rsquo;s former students and author of some seminal results in Causal Inference. I feel like this course highlighted not only the content Causal Inference researchers consider important but also the types of understanding they value. In this review, I&amp;rsquo;ll focus on the latter. I hope to write some blog posts in the future about the former but have learned from past experience not to promise future posts unless I have time during which I know I can write them.</description>
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      <title>Digital Reduction Experiment</title>
      <link>https://stephenmalina.com/post/2020-03-18-digital-minimalism-exp/</link>
      <pubDate>Wed, 18 Mar 2020 00:00:00 +0000</pubDate>
      
      <guid>https://stephenmalina.com/post/2020-03-18-digital-minimalism-exp/</guid>
      <description>Intro / Motivation # I know I&amp;rsquo;m a walking millenial trope, but I&amp;rsquo;m starting a deliberate experiment to dramatically reduce my internet engagement. Especially while I&amp;rsquo;m quarantined for who knows how long, I want to almost entirely stop:
checking Twitter; reading about the virus throughout the day; checking email; reading blogs frequently; and constantly texting with people (mostly about the virus). Instead, I want to focus on:
doing lots of (ML) research; schoolwork; spending time outside; exercising; video calls with friends; reading books; and writing more blog posts.</description>
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      <title>Deriving the front-door criterion with the do-calculus</title>
      <link>https://stephenmalina.com/post/2020-03-09-front-door-do-calc-derivation/</link>
      <pubDate>Mon, 09 Mar 2020 00:00:00 +0000</pubDate>
      
      <guid>https://stephenmalina.com/post/2020-03-09-front-door-do-calc-derivation/</guid>
      <description>Attention conservation notice: Narrow target audience - will only make sense to people somewhat familiar with causal inference who don&amp;rsquo;t find the result entirely boring.
The Front-Door Criterion # Suppose we have a causal graphical model that looks like the following.
Assume $ U $ is unmeasured whereas $ X, M, Y $ can be measured. Notice that:
All directed paths from $ X $ to $ Y $ flow through $ M $.</description>
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      <title>Decaf vs. regular coffee blinded experiment</title>
      <link>https://stephenmalina.com/post/2020-03-01-coffee-rct/</link>
      <pubDate>Sun, 01 Mar 2020 00:00:00 +0000</pubDate>
      
      <guid>https://stephenmalina.com/post/2020-03-01-coffee-rct/</guid>
      <description>Abstract # I conducted a two-week blinded, randomized experiment to test whether drinking regular vs. decaf coffee had a detectable effect on my mood and alertness. Each day, I drank one cup of coffee in the morning and immediately took a Quantified Mind test. I also tracked hours of sleep each night and measured subjective factors such as mood and alertness a few times throughout the day. Overall, the experiment was a success in terms of being able to follow my original plan.</description>
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      <title>All of Statistics - Chapter 3</title>
      <link>https://stephenmalina.com/learning/2019-12-12-all-of-statistics-ch3-notes/</link>
      <pubDate>Thu, 12 Dec 2019 00:00:00 +0000</pubDate>
      
      <guid>https://stephenmalina.com/learning/2019-12-12-all-of-statistics-ch3-notes/</guid>
      <description>Selected Exercises # 1. Suppose we play a game where we start with $ c $ dollars. On each play of the game you either double or halve your money, with equal probability. What is your expected fortune after $ n $ trials?
I&amp;rsquo;m pretty sure we can use a trick that I&amp;rsquo;ve seen a lot in machine learning to solve this using plain old expectations. If I&amp;rsquo;m right, we let $ X \sim \text{Binomial}(n, \frac{1}{2}) $ and can create a new random variable, $ Z $, where</description>
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      <title>Paper Review - Network Mendelian Randomization</title>
      <link>https://stephenmalina.com/post/2019-11-16-network-mendelian-randomization/</link>
      <pubDate>Sat, 16 Nov 2019 00:00:00 +0000</pubDate>
      
      <guid>https://stephenmalina.com/post/2019-11-16-network-mendelian-randomization/</guid>
      <description>In which I record my thoughts on Network Mendelian Randomization by Burgess et al.
What is this paper about? # This paper describes a method for doing Mendelian Randomization (MR) in the presence of a potential mediating variable. In the typical MR setting, we have an instrumental variable which &amp;ldquo;instruments&amp;rdquo; an exposure that we believe causally influences the outcome we care about. True mediators &amp;ldquo;mediate&amp;rdquo; the causal influence of exposures on outcomes.</description>
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      <title>Causal Inference Notes</title>
      <link>https://stephenmalina.com/learning/2019-11-08-causal-inference/</link>
      <pubDate>Fri, 15 Nov 2019 00:00:00 +0000</pubDate>
      
      <guid>https://stephenmalina.com/learning/2019-11-08-causal-inference/</guid>
      <description>Causal Inference in Statistics # Questions # Why is the causal effect identifiable in an IV DAG when the dependencies are linear (from an SCM perspective)? I think this may relate to factor models. Advanced Data Analysis from an Elementary Point of View (Ch. 18-23) # Chapter 18 # Exercises # 18.2. Proof that every path must go through a collider:
Observe that every path between two exogenous variables starts with variables going in the opposite direction.</description>
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      <title>Paper Review - IVs and Mendelian Randomization</title>
      <link>https://stephenmalina.com/learning/2019-11-02-ivs-mendelian-randomization/</link>
      <pubDate>Sun, 03 Nov 2019 00:00:00 +0000</pubDate>
      
      <guid>https://stephenmalina.com/learning/2019-11-02-ivs-mendelian-randomization/</guid>
      <description>Summary # Detailed Notes # 3 IV Requirements # IV must have a direct influence on the treatment IV must not covary with the unmeasured confounding that impacts the outcome IV must not have a direct influence on the outcome Relevant considerations for deciding whether to do an IV analysis # Is there any unmeasured confounding?
If not, is the answer that we can just use a normal regression? When is unmeasured confounding especially likely?</description>
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      <title>Matrix Potpourri</title>
      <link>https://stephenmalina.com/post/2019-09-07-matrix-potpourri/</link>
      <pubDate>Tue, 13 Aug 2019 00:00:00 +0000</pubDate>
      
      <guid>https://stephenmalina.com/post/2019-09-07-matrix-potpourri/</guid>
      <description>Matrix Potpourri # As part of reviewing Linear Algebra for my Machine Learning class, I&amp;rsquo;ve noticed there&amp;rsquo;s a bunch of matrix terminology that I didn&amp;rsquo;t encounter during my proof-based self-study of LA from Linear Algebra Done Right. This post is mostly intended to consolidate my own understanding and to act as a reference to future me, but if it also helps others in a similar position, that&amp;rsquo;s even better!</description>
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      <title>Paper Review - DeepSEA</title>
      <link>https://stephenmalina.com/post/2019-08-08-deepsea/</link>
      <pubDate>Thu, 08 Aug 2019 00:00:00 +0000</pubDate>
      
      <guid>https://stephenmalina.com/post/2019-08-08-deepsea/</guid>
      <description>In which I record my thoughts on DeepSEA.
Terminology # ChIP-seq (Chromatin Immunoprecipitation Sequencing): Expression Quantitative Trait Locis (eQTLs) Cofactor Binding Sequences Histone Marks: modifications to histone proteins in the nucleosome that impact the shape of chromatin. gkm-SVMs: The gkm-SVM is the previous SOTA model for predicting transcription factor binding based on ChIP-seq data. Allele: variants of a gene at the same position on a chromosome. What is this paper about?</description>
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      <title>Paper Review - Basset</title>
      <link>https://stephenmalina.com/post/2019-08-05-basset/</link>
      <pubDate>Mon, 05 Aug 2019 00:00:00 +0000</pubDate>
      
      <guid>https://stephenmalina.com/post/2019-08-05-basset/</guid>
      <description>In which I record my thoughts on Basset.
Bio Background # The genome consists of (broadly) two types of genes, coding genes and noncoding genes. Coding genes get translated into proteins (as laid down by the Central Dogma) and are what most of us learned about in bio class. Non-coding genes&amp;hellip; don&amp;rsquo;t. As I understand it, noncoding genes can do a bunch of different things, but part of their function is to regulate coding gene activity through a number of mechanisms.</description>
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      <title>Paper Review - DeepBind</title>
      <link>https://stephenmalina.com/post/2019-07-26-deepbind/</link>
      <pubDate>Fri, 26 Jul 2019 00:00:00 +0000</pubDate>
      
      <guid>https://stephenmalina.com/post/2019-07-26-deepbind/</guid>
      <description>In which I record my thoughts on DeepBind.
What is this paper about? # The authors of this paper designed a conv net model to predict how well different proteins will bind to sequences of DNA or RNA. They train one model per protein for many different sequences and show that these models can predict binding affinities for sequences well enough to produce insights regarding the impact of single nucleotide mutations.</description>
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      <title>Linear Algebra Done Right - Chapter 6</title>
      <link>https://stephenmalina.com/learning/2019-05-20-linear-algebra-done-right-ch6-notes/</link>
      <pubDate>Mon, 20 May 2019 00:00:00 +0000</pubDate>
      
      <guid>https://stephenmalina.com/learning/2019-05-20-linear-algebra-done-right-ch6-notes/</guid>
      <description>Selected Exercises # 6.B # 1. (a) Suppose \( \theta \in \mathbf{R} \). Show that $ (\cos \theta, \sin \theta), (-\sin \theta, \cos \theta) $ and $ (\cos \theta, \sin \theta), (\sin \theta, -\cos \theta) $ are orthonormal bases of $ \mathbf{R}^2 $.
(b) Show that each orthonormal basis of $ \mathbf{R}^2 $ is of the form given by one of the two possibilities of part (a).
(a) First, we show that both lists of vectors are orthonormal (using the Euclidean inner product), i.</description>
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      <title>Current Thoughts on Stoicism</title>
      <link>https://stephenmalina.com/post/2019-05-18-thoughts-on-stoicism/</link>
      <pubDate>Sat, 18 May 2019 00:00:00 +0000</pubDate>
      
      <guid>https://stephenmalina.com/post/2019-05-18-thoughts-on-stoicism/</guid>
      <description>Meta: While I originally set out to write this essay about why I no longer &amp;ldquo;endorse&amp;rdquo; Stoicism as an operating framework, re-reading a bunch of Stoic stuff led me to realize that I still agree with ~90% of Stoic principles.
Peter Thiel recently talked about (in German) why he&amp;rsquo;s not a Stoic,
Stoics, for example, are obsessed with death. However, I am the opposite of a stoic, I loathe the peace and have no sense in the countryside to live and meditate on the environment.</description>
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      <title>Linear Algebra Done Right - Chapter 5</title>
      <link>https://stephenmalina.com/learning/2019-04-01-linear-algebra-done-right-ch5-notes/</link>
      <pubDate>Mon, 01 Apr 2019 00:00:00 +0000</pubDate>
      
      <guid>https://stephenmalina.com/learning/2019-04-01-linear-algebra-done-right-ch5-notes/</guid>
      <description>Selected Exercises # 5.A # 12. Define $ T \in \mathcal L(\mathcal P_4(\mathbf{R})) $ by
$$ (Tp)(x) = xp&amp;rsquo;(x) $$
for all $ x \in \mathbf{R} $. Find all eigenvalues and eigenvectors of $ T $.
Observe that, if $ p = a_0 + a_1 x + a_2 x^2 + a_3 x^3 + a_4 x^4 $, then $$ x p&amp;rsquo;(x) = a_1 x + 2 a_2 x^2 + 3 a_3 x^3 + 4 a_4 x^4.</description>
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      <title>Linear Algebra Done Right - Chapter 4</title>
      <link>https://stephenmalina.com/learning/2019-03-31-linear-algebra-done-right-ch4-notes/</link>
      <pubDate>Sun, 31 Mar 2019 00:00:00 +0000</pubDate>
      
      <guid>https://stephenmalina.com/learning/2019-03-31-linear-algebra-done-right-ch4-notes/</guid>
      <description>Selected Exercises # 4. Suppose $m$ and $n$ are positive integers with $ m \leq n $, and suppose $ \lambda_1, \dots, \lambda_m \in F $. Prove that there exists a polynomial $ p \in \mathcal P(\mathbf{F}) $ with $ \deg p = n $ such that $ 0 = p(\lambda_1) = \cdots = p(\lambda_m) $ and such that $ p $ has no other zeros.
First, we can show that the polynomial $p&amp;rsquo;(z) = (z - \lambda_1) \cdots (z-\lambda_m) $ with $ \deg p&amp;rsquo; = m $ has $ 0 = p&amp;rsquo;(\lambda_1) = \cdots = p&amp;rsquo;(\lambda_m) $ and no other zeros.</description>
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      <title>Linear Algebra Done Right - Chapter 3</title>
      <link>https://stephenmalina.com/learning/2019-03-30-linear-algebra-done-right-ch3-notes/</link>
      <pubDate>Sat, 30 Mar 2019 00:00:00 +0000</pubDate>
      
      <guid>https://stephenmalina.com/learning/2019-03-30-linear-algebra-done-right-ch3-notes/</guid>
      <description>Selected Exercises # 3.D # 7. Suppose $ V $ &amp;amp; $ W $ are finite-dimensional. Let $ v \in V $. Let $$ E = \{ T \in \mathcal L(V, W): T(v) = 0 \}. $$
(a) Show that $ E $ is a subspace of $ \mathcal L(V, W) $.
(b) Suppose $ v \neq 0 $. What is $\dim E$?
For (a), to show $ E $ is a subspace of $ \mathcal L(V, W) $, we need to show that $ E $ contains zero and is closed under both addition and multiplication.</description>
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      <title>Better Project Planning With Prediction Markets</title>
      <link>https://stephenmalina.com/post/2019-03-22-internal-prediction-markets-for-better-institutions/</link>
      <pubDate>Fri, 22 Mar 2019 00:00:00 +0000</pubDate>
      
      <guid>https://stephenmalina.com/post/2019-03-22-internal-prediction-markets-for-better-institutions/</guid>
      <description>As I understand it, much of Coase&amp;rsquo;s work focuses on why companies&amp;rsquo; internal structures don&amp;rsquo;t resemble markets all that much. Instead, most firms have feudal-ish structures. The CEO has, at the discretion of the board, final decision making power on nearly all decisions, and then their power trickles down recursively to their subordinates for decisions in which they&amp;rsquo;re not involved.
While I&amp;rsquo;m willing to swallow the bitter pill that feudal-ish structures are actually more efficient for many company functions than democratic ones would be, in my own experience, I&amp;rsquo;ve observed a few places where I think market-based decision making systems could improve both company efficiency and employee satisfaction.</description>
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      <title>Linear Algebra Done Right - Chapter 2</title>
      <link>https://stephenmalina.com/learning/2018-12-24-linear-algebra-done-right-ch2-notes/</link>
      <pubDate>Mon, 24 Dec 2018 00:00:00 +0000</pubDate>
      
      <guid>https://stephenmalina.com/learning/2018-12-24-linear-algebra-done-right-ch2-notes/</guid>
      <description>Intro # I&amp;rsquo;ve recently been making my way through Axler&amp;rsquo;s Linear Algebra Done Right and, as a way to motivate myself to continue, have decided to blog my notes and solutions for exercises as I go.
Insights # Section 2.A # You can convert any linearly dependent list to a linearly independent list with the same span. # By the linear dependence lemma, if you have a list that&amp;rsquo;s linearly dependenty, then you can remove one item without changing the list&amp;rsquo;s span.</description>
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      <title>Babble, Learning, and the Typical Mind Fallacy</title>
      <link>https://stephenmalina.com/post/2018-12-16-babble-learning/</link>
      <pubDate>Sun, 16 Dec 2018 00:00:00 +0000</pubDate>
      
      <guid>https://stephenmalina.com/post/2018-12-16-babble-learning/</guid>
      <description>Babbling About Babble # In a series of posts on his blog (or LessWrong if you prefer), alkjash writes about &amp;ldquo;babble&amp;rdquo; and &amp;ldquo;prune&amp;rdquo;, the two components of an adversarial model of knowledge production in humans. Alkjash describes babble and prune like this:
Here’s a simplistic model of how this works. I try to build a coherent sentence. At each step, to pick the next word, I randomly generate words in the category (correct part of speech, relevance) and sound them out one by one to see which continues the sentence most coherently.</description>
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      <title>My Interpretation of Movember</title>
      <link>https://stephenmalina.com/post/2018-12-02-movember/</link>
      <pubDate>Sun, 02 Dec 2018 00:00:00 +0000</pubDate>
      
      <guid>https://stephenmalina.com/post/2018-12-02-movember/</guid>
      <description>(Cross-posted from Facebook.)
This is the first time I&amp;rsquo;ve posted on Facebook in &amp;hellip; long. However, at the encouragement of a few friends, I&amp;rsquo;ve decided to leverage my no-shave November stunt as an opportunity to urge people to donate to one of the many worthwhile causes out there. Technically, my friends said I should do &amp;ldquo;the Movember thing&amp;rdquo; but this long-winded post is my characteristically difficult, verbose interpretation of that.</description>
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      <title>State of my Mind</title>
      <link>https://stephenmalina.com/progress/</link>
      <pubDate>Fri, 12 Oct 2018 00:00:00 +0000</pubDate>
      
      <guid>https://stephenmalina.com/progress/</guid>
      <description>This page tracks things about which I&amp;rsquo;ve changed my mind over time and things about which I&amp;rsquo;m still confused. For some things, there was one moment or event that caused me to revise my view. For others, it was just a slow process of evidence accumulating and then me retroactively realizing I no longer believed what I once did. Interestingly enough, none of the mind shifts listed here came about through me setting out to change my view.</description>
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      <title>Statistical Models - Theory and Practice</title>
      <link>https://stephenmalina.com/post/2018-06-12-statistical-models-ch-2/</link>
      <pubDate>Tue, 12 Jun 2018 00:00:00 +0000</pubDate>
      
      <guid>https://stephenmalina.com/post/2018-06-12-statistical-models-ch-2/</guid>
      <description>Questions # What does the regression equation mean? Is the idea that we get bigger $ r $ values when $ x $ and $ y $ deviate together? What does it mean for a function to be convex beyond $ f((x + y) / 2)) \leq (f(x) + f(y)) / 2 $? Put another way, why is this the proof of convexity? $$ h\{son} = slope * h\{father} + yint = 70.</description>
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      <title>Statistical Models - Theory and Practice</title>
      <link>https://stephenmalina.com/post/2018-06-09-statistical-models-ch-1/</link>
      <pubDate>Sat, 09 Jun 2018 00:00:00 +0000</pubDate>
      
      <guid>https://stephenmalina.com/post/2018-06-09-statistical-models-ch-1/</guid>
      <description>Summary # This chapter introduces basic terminology and describes three separate experiments to introduce us to statistical methods in action.
We learn about the difference between randomized controlled experiments and observational experiments. A randomized controlled experiment is an experiment in which subjects are randomly assigned to two groups: experiment and control. Members of the experimental group receive the &amp;ldquo;treatment&amp;rdquo;, whereas members of the control do not. We expect that randomized controlled experiments minimize confounding &amp;ndash; other factors seeping in to impact our results without us knowing &amp;ndash; because we expect members of the experimental and control group to be on average the same outside of whatever difference the treatment produces.</description>
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      <title>JIT Reading</title>
      <link>https://stephenmalina.com/post/2018-02-24-jit-reading/</link>
      <pubDate>Sat, 24 Feb 2018 00:00:00 +0000</pubDate>
      
      <guid>https://stephenmalina.com/post/2018-02-24-jit-reading/</guid>
      <description>Seibel, James Hague and others have all tried to justify why code reading is so uncommon, and they make good points. But perhaps the conversation is led astray by use of the word read. I wonder if Abelson and the others would have had more examples if Seibel had asked them what code they had learned about for fun. Perhaps the word &amp;ldquo;read&amp;rdquo; put them in a passive frame of mind, caused them to filter out programs they&amp;rsquo;d hacked on?</description>
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      <title>Weekly Newsletter</title>
      <link>https://stephenmalina.com/post/2015-12-06-nl12062016/</link>
      <pubDate>Sun, 06 Dec 2015 00:00:00 +0000</pubDate>
      
      <guid>https://stephenmalina.com/post/2015-12-06-nl12062016/</guid>
      <description>Links # Physics # What is Spacetime, Really?
Stephen Wolfram talks about the difficulty inherent to coming up with a universal theory about spacetime. In the same way Einstein&amp;rsquo;s theories brought Wolfram to awe, Wolfram&amp;rsquo;s ideas consistently bring me to awe. After reading Rudy Rucker&amp;rsquo;s The Lifebox, The Seashell, and The Soul, I&amp;rsquo;m increasingly drawn to computationalist theories of the universe, but reading this article has solidified my decision to read A New Kind of Science.</description>
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      <title>Weekly Newsletter</title>
      <link>https://stephenmalina.com/post/2015-11-29-nl1/</link>
      <pubDate>Sun, 29 Nov 2015 00:00:00 +0000</pubDate>
      
      <guid>https://stephenmalina.com/post/2015-11-29-nl1/</guid>
      <description>This week, I&amp;rsquo;m going to try something a little different with the newsletter. I&amp;rsquo;m going to add 3 new categories to the newsletter: Books I&amp;rsquo;m Reading, Quotes I&amp;rsquo;ve Enjoyed, and People I&amp;rsquo;m Following. In case you&amp;rsquo;re worried about these polluting your newsletter experience, don&amp;rsquo;t worry. I&amp;rsquo;m putting these sections at the bottom after the normal newsletter content.
Links # Climate Change # What Can A Technologist Do About Climate Change?</description>
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      <title>Weekly Newsletter</title>
      <link>https://stephenmalina.com/post/2015-11-22-nl/</link>
      <pubDate>Sun, 22 Nov 2015 00:00:00 +0000</pubDate>
      
      <guid>https://stephenmalina.com/post/2015-11-22-nl/</guid>
      <description>Education # A Radical Way of Unleashing a Generation of Geniuses
Phenomenal piece that profiles an unconventional teacher in a poor Mexican border town. Uses this to broadly discuss the changing role and viewpoint on education. I&amp;rsquo;m a total convert to the idea that children need to be allowed to explore rather than have information forced down their throats.
Business # When Software Eats Bio
The leader of Andreessen Horowitz new bio arm gives a Q&amp;amp;A about the motivations and direction they will take.</description>
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      <title>Weekly Newsletter</title>
      <link>https://stephenmalina.com/post/2015-11-15-nl/</link>
      <pubDate>Sun, 15 Nov 2015 00:00:00 +0000</pubDate>
      
      <guid>https://stephenmalina.com/post/2015-11-15-nl/</guid>
      <description>Brain Computer Interfaces # Meet the Neuroscientist Who Installed an Implant in His Own Brain Profiles the risk-taking neuroscientist Phil Kennedy. Kennedy researches enabling locked-in patients to communicate using implanted electrodes. Kennedy took his research into his own hands after the FDA prevented him from continuing his work. Kennedy had a surgeon from Belize implant a set of electrodes in his head so that he could continue studying neuronal correlates of speech.</description>
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      <title>SICP 1.1</title>
      <link>https://stephenmalina.com/post/2015-11-14-sicp-1-1/</link>
      <pubDate>Sat, 14 Nov 2015 00:00:00 +0000</pubDate>
      
      <guid>https://stephenmalina.com/post/2015-11-14-sicp-1-1/</guid>
      <description>Key Concepts # Environments, Syntax, Programming Languages v. Natural Languages, Applicative Order of Operations Environments # Understanding meaning is a matter of combining primitives with context. Syntax # Lisp programmers tend to eschew syntactic sugar in favor of building their own syntax. Procedures are noticeably more composable than other languages I&amp;rsquo;ve used previously. There&amp;rsquo;s little difference between user-defined and language-defined procedures Comparison between programming and natural languages # We can define procedures (verbs) and use variables (pronouns) to build higher-level abstractions.</description>
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      <title>Weekly Newsletter</title>
      <link>https://stephenmalina.com/post/2015-11-08-nl11082015/</link>
      <pubDate>Sun, 08 Nov 2015 00:00:00 +0000</pubDate>
      
      <guid>https://stephenmalina.com/post/2015-11-08-nl11082015/</guid>
      <description>I&amp;rsquo;ve been reading more technical neuroscience / psychology papers recently, so the newsletter reflects that. I&amp;rsquo;m trying to better understand the variety and universality of mental imagery, and the only way to do that is to dive into the literature.
Mental Imagery # Representing Exact Numbers Visually
This journal article discusses mental abacus representations. Be forewarned, the paper is fairly technical and a bit dry. If you just want to get the take-aways of the paper, I recommend reading the Introduction until you feel like you&amp;rsquo;re in over your head and then skipping to page 13.</description>
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      <title>Weekly Newsletter</title>
      <link>https://stephenmalina.com/post/2015-11-01-nl11012015/</link>
      <pubDate>Sun, 01 Nov 2015 00:00:00 +0000</pubDate>
      
      <guid>https://stephenmalina.com/post/2015-11-01-nl11012015/</guid>
      <description>Journalism # The Future of News is not an Article
A NY Times Labs writer argues that the future of news lies in smaller, contextually-aware primitives called particles. If you&amp;rsquo;ve never explored the NYT Labs website before, I highly recommend it. I particularly enjoy this infographic.
Biography # Genghis John
Paints a portrait of John Boyd, military theorist and legendary aircraft designer. Boyd&amp;rsquo;s devotion to his ideals and unconventional thinking resonates with me and I definitely intend to read his papers and books.</description>
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      <title>Weekly Newsletter</title>
      <link>https://stephenmalina.com/post/2015-10-25-nl10252015/</link>
      <pubDate>Sun, 25 Oct 2015 00:00:00 +0000</pubDate>
      
      <guid>https://stephenmalina.com/post/2015-10-25-nl10252015/</guid>
      <description>The Blockchain # Blockchains in Context
An easy to understand article about blockchains by a core contributor to Ethereum. Ethereum aims to create an understandable, general-purpose system for creating and enforcing contracts on the web. Potential applications of this system are more varied than you might initially expect. This picture breaks down areas in which Ethereum could prove an effective tool.
Medicine and Biology # Can we end the war on Cancer?</description>
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      <title>Weekly Newsletter</title>
      <link>https://stephenmalina.com/post/2015-10-18-nl10182015/</link>
      <pubDate>Sun, 18 Oct 2015 00:00:00 +0000</pubDate>
      
      <guid>https://stephenmalina.com/post/2015-10-18-nl10182015/</guid>
      <description>Design # UX and the Civilizing Process
Another piece from the author of last week&amp;rsquo;s 4-part series that took us through the theories of Julian Jaynes. This piece focuses on similarities between User Experience design, which aims to create seamless interactions between humans and products, and etiquette. My super-secret goal for the newsletter has always been to find at least one article my sister will genuinely enjoy and I may actually have a winner with this one.</description>
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      <title>Weekly Newsletter</title>
      <link>https://stephenmalina.com/post/2015-10-11-nl10112015/</link>
      <pubDate>Sun, 11 Oct 2015 00:00:00 +0000</pubDate>
      
      <guid>https://stephenmalina.com/post/2015-10-11-nl10112015/</guid>
      <description>Mind and Brain # Below is a series of 4 articles that explore Julian Jaynes&amp;rsquo; theory of consciousness and its relationship to unusual minds. I found this series incredibly fascinating. It reminds me of Blindsight, a creepy sci-fi novel by Peter Watts that explores the relationship between self-awareness and intelligence. If you&amp;rsquo;ve ever questioned the nature of consciousness, you&amp;rsquo;ll enjoy this series. After reading this, I&amp;rsquo;m committing to reading Julian Jaynes&amp;rsquo; Origin of Consciousness in the Breakdown of the Bicaemral Mind.</description>
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      <title>Weekly Newsletter</title>
      <link>https://stephenmalina.com/post/2015-10-04-nl10042015/</link>
      <pubDate>Sun, 04 Oct 2015 00:00:00 +0000</pubDate>
      
      <guid>https://stephenmalina.com/post/2015-10-04-nl10042015/</guid>
      <description>Biology and Computation # Better Living Through Quantum Mechanics
Seth Lloyd, the first and only self-proclaimed quantum mechanical engineer from MIT, discusses new discoveries of quantum mechanical phenomena in plants and animals. I included this for the understandable metaphors used to explain quantum processes.
Linguistics # The Whistled Language of Northern Turkey
Profiles a language that conveys meaning through whistling and clicks. I loved this article. You&amp;rsquo;ll get twice as much out of it if you listen to the samples of the language.</description>
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      <title>Weekly Newsletter</title>
      <link>https://stephenmalina.com/post/2015-09-27-nl09272015/</link>
      <pubDate>Sun, 27 Sep 2015 00:00:00 +0000</pubDate>
      
      <guid>https://stephenmalina.com/post/2015-09-27-nl09272015/</guid>
      <description>Neuroscience and Neurotech # Hypnosis reaches the parts brain scans and neurosurgery cannot
A good, succint article about the use of hypnosis in real neuroscience. Makes me hope I&amp;rsquo;m in the 10% of people who are highly suggestible.
Playing 20 Questions with the Mind
Summarizes a new study in which two individuals in isolation played 20 questions using a brain-to-brain interface. This is a big first step towards more usable brain-to-brain interfaces.</description>
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      <title>Weekly Newsletter</title>
      <link>https://stephenmalina.com/post/2015-09-20-nl09202015/</link>
      <pubDate>Sun, 20 Sep 2015 00:00:00 +0000</pubDate>
      
      <guid>https://stephenmalina.com/post/2015-09-20-nl09202015/</guid>
      <description>Cryonics # A Dying Young Woman’s Hope in Cryonics and a Future
Cancer claimed Kim Suozzi at age 23, but she chose to have her brain preserved with the dream that neuroscience might one day revive her mind. I really enjoyed this article. Unlike many of the readers, I&amp;rsquo;ve considered signing up for cryonics and went so far as to ask for it for my birthday (a request which my mother politely denied).</description>
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      <title>Weekly Newsletter</title>
      <link>https://stephenmalina.com/post/2015-09-13-nl09132015/</link>
      <pubDate>Sun, 13 Sep 2015 00:00:00 +0000</pubDate>
      
      <guid>https://stephenmalina.com/post/2015-09-13-nl09132015/</guid>
      <description>Ethics # The Philosopher Who Says We Should Play God
The following quote sums up the article well:
So the idea that we could play god and tamper with the laws of nature, creating things that wouldn’t otherwise exist, is a red herring?
We’re playing god every day. As the English philosopher Thomas Hobbes said, the natural state for human beings is a life that’s nasty, brutish, and short. We play god when we vaccinate.</description>
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      <title>Weekly Newsletter</title>
      <link>https://stephenmalina.com/post/2015-09-06-nl09062015/</link>
      <pubDate>Sun, 06 Sep 2015 00:00:00 +0000</pubDate>
      
      <guid>https://stephenmalina.com/post/2015-09-06-nl09062015/</guid>
      <description>Nutrition and Health # Starving Your Way to Vigor (see attached)
A writer discusses his experience fasting for over a week. He cites scientific and historical sources showing the effectiveness of fasting in treating several ailments. My own understanding of nutrition supports this author’s claims. For a more scientific take on fasting, make your way through some of there (https://scholar.google.com/scholar?q=valter+longo+fasting&amp;amp;hl=en&amp;amp;as_sdt=0&amp;amp;as_vis=1&amp;amp;oi=scholart&amp;amp;sa=X&amp;amp;ved=0CBsQgQMwAGoVChMI1s3smvTjxwIVgZMeCh1FLQ6r) articles. If you&amp;rsquo;re interested in trying out fasting but don&amp;rsquo;t want to commit to a longer fast, I recommend Eat Stop Eat by Brad Pilon.</description>
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      <title>Weekly Newsletter</title>
      <link>https://stephenmalina.com/post/2015-08-30-nl08302015/</link>
      <pubDate>Sun, 30 Aug 2015 00:00:00 +0000</pubDate>
      
      <guid>https://stephenmalina.com/post/2015-08-30-nl08302015/</guid>
      <description>Ambition and Achievement # Sources of Power
Argues that college applicants should seek out &amp;ldquo;sources of power&amp;rdquo; which improve their chances of acceptance by orders of magnitude. This article fits with my observations about the college process.
Alternative Businesses # The Cheese Board Collective
Profiles a cooperative cheese shop where all employees are owners. I&amp;rsquo;ve expressed my enthusiasm for business model experimentation and co-ops in particular before so I&amp;rsquo;ll refrain from doing so again now.</description>
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      <title>Weekly Newsletter</title>
      <link>https://stephenmalina.com/post/2015-08-09-nl08092015/</link>
      <pubDate>Sun, 09 Aug 2015 00:00:00 +0000</pubDate>
      
      <guid>https://stephenmalina.com/post/2015-08-09-nl08092015/</guid>
      <description>Future of Food # The $200 Hydroponic Greenhouse You Control With a Smartphone
Reports on a new product that promises to automate the process of hydroponic gardening such that individuals will be able to grow vegetables in their home with minimal effort and maximal control. This type of product, while different from Soylent, illustrates another viable direction for the future of food that focuses more on the decentralization and automation of food production.</description>
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      <title>Weekly Newsletter</title>
      <link>https://stephenmalina.com/post/2015-08-02-nl08022015/</link>
      <pubDate>Sun, 02 Aug 2015 00:00:00 +0000</pubDate>
      
      <guid>https://stephenmalina.com/post/2015-08-02-nl08022015/</guid>
      <description>Plant Genetics # How Driscoll’s Is Hacking the Strawberry of the Future
Profiles Phil Stewart, Driscoll&amp;rsquo;s chief strawberry geneticist. I enjoyed learning about the challenge of breeding an optimal set of characteristics into Driscoll&amp;rsquo;s strawberries.
Education # A College Without Classes
Explores the recent phenomenon of online, competence-based university programs, which, rather than holding lectures, test their students periodically on competency in course topics. I view competence-based metrics for education as an important alternative to traditional grades.</description>
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      <title>Weekly Newsletter</title>
      <link>https://stephenmalina.com/post/2015-07-26-nl07262015/</link>
      <pubDate>Sun, 26 Jul 2015 00:00:00 +0000</pubDate>
      
      <guid>https://stephenmalina.com/post/2015-07-26-nl07262015/</guid>
      <description>Linguistics # How to Say (Almost) Everything in a Hundred-Word Language
Explores Toki Pona, the world&amp;rsquo;s smallest language. Describes the linguistic idiosyncrasies that arise from the severely limited vocabulary of the language.
Nature&amp;rsquo;s Algorithms # Decoding the Remarkable Algorithms of Ants
Interviews a scientist studying the swarm behavior of ants in an attempt to translate ant colony behavior into computer algorithms.
Education # A New Look at Apprenticeships as a Path to the Middle Class</description>
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      <title>Weekly Newsletter</title>
      <link>https://stephenmalina.com/post/2015-07-19-nl07192015/</link>
      <pubDate>Sun, 19 Jul 2015 00:00:00 +0000</pubDate>
      
      <guid>https://stephenmalina.com/post/2015-07-19-nl07192015/</guid>
      <description>Human Potential # The Science of Mental Fitness
Aggregates recent research findings regarding the effect of visualization on skill learning and physical development.
Biotech # Your body, the battery: Powering gadgets from human &amp;ldquo;biofuel&amp;rdquo;
Discusses the various ways in which the human body could be used to power electronics.
Letters # Why Explore Space?
In this letter, Dr. Ernst Stuhlinger, the past director of science at a NASA facility, responded to a Zambia-based nun&amp;rsquo;s letter questioning the allocation of billions of dollars towards the space program with this letter.</description>
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      <title>The Myth of the Arc of Justice by Will Baird</title>
      <link>https://stephenmalina.com/post/2015-07-12-themythofthearchofjustice/</link>
      <pubDate>Sun, 12 Jul 2015 00:00:00 +0000</pubDate>
      
      <guid>https://stephenmalina.com/post/2015-07-12-themythofthearchofjustice/</guid>
      <description>The past few weeks have seen major shifts in two important areas of American society: race and sexual orientation. Following the Charleston shooting, an increasing number of leaders such as South Carolina Governor Nikki Haley have called for the removal of the Confederate flag from state grounds due to its symbolic association with racism and support for slavery. And on June 26, the Supreme Court ruled in favor of a constitutional right for same-sex marriage.</description>
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      <title>Weekly Newsletter</title>
      <link>https://stephenmalina.com/post/2015-07-12-nl07122015/</link>
      <pubDate>Sun, 12 Jul 2015 00:00:00 +0000</pubDate>
      
      <guid>https://stephenmalina.com/post/2015-07-12-nl07122015/</guid>
      <description>Evolutionary Biology and Health # To Stop Mosquito Bites, Silence Your Skin&amp;rsquo;s Bacteria
Discusses a technique which could prevent mosquitoes bites by silencing the communication between bacteria on human skin. Mosquitoes detect this communication on human skin and bite people after detecting it.
Cognitive Science # What&amp;rsquo;s the evidence on using rational arguments to change people&amp;rsquo;s minds?
Argues that reason is more powerful than recent cognitive science research might lead us to believe.</description>
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      <title>Weekly Newsletter</title>
      <link>https://stephenmalina.com/post/2015-06-14-nl06142015/</link>
      <pubDate>Sun, 14 Jun 2015 00:00:00 +0000</pubDate>
      
      <guid>https://stephenmalina.com/post/2015-06-14-nl06142015/</guid>
      <description>I apologize for the short newsletter this week. Graduation has limited the amount of time I&amp;rsquo;ve been able to spend on it, and I &amp;rsquo;d rather shorten it than include lower quality articles.
Biology and Physiology # Lost Posture: Why Some Indigenous Cultures May Not Have Back Pain
Discusses a hypothesis for widespread back pain and profiles Esther Gokhale, a woman who has studied indigenous cultures in an attempt to gain insight into why they don&amp;rsquo;t suffer from back pain.</description>
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      <title>Weekly Newsletter</title>
      <link>https://stephenmalina.com/post/2015-06-07-nl06072015/</link>
      <pubDate>Sun, 07 Jun 2015 00:00:00 +0000</pubDate>
      
      <guid>https://stephenmalina.com/post/2015-06-07-nl06072015/</guid>
      <description>Neuroscience # Researchers Find Missing Link Between Brain and Immune System
Discusses a recently discovered vessel that connects the brain and the lymphatic system. Although this article&amp;rsquo;s not great, the discovery itself is a huge deal.
Better not look down&amp;hellip;
A neurosurgeon reflects on his career and the mistakes he made. An introspective piece.
Droughts and Water Shortage # To Save California, Read &amp;ldquo;Dune&amp;rdquo;
Argues that Frank Herbert&amp;rsquo;s ideas from Dune are becoming a reality in California.</description>
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      <title>Weekly Newsletter</title>
      <link>https://stephenmalina.com/post/2015-05-31-2015-nl05312015/</link>
      <pubDate>Sun, 31 May 2015 00:00:00 +0000</pubDate>
      
      <guid>https://stephenmalina.com/post/2015-05-31-2015-nl05312015/</guid>
      <description>Learning and Education # How I Rewired My Brain to Become Fluent in Math
An engineering professor recounts how she went from being a language person without a college degree to an engineer with a doctorate. The author provides a unique perspective on the process of learning technical subjects and supplements her own experience with knowledge taken from her subsequent study of learning processes.
How to learn 30 languages</description>
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      <title>Weekly Newsletter</title>
      <link>https://stephenmalina.com/post/2015-05-24-nl05242015/</link>
      <pubDate>Sun, 24 May 2015 00:00:00 +0000</pubDate>
      
      <guid>https://stephenmalina.com/post/2015-05-24-nl05242015/</guid>
      <description>Psychology and Brain Science # Is LSD about to return to polite society?
Profiles the matriarch of the Beckley Foundation, an organization which aims to popularize scientific research focused on psychedelic therapies for addiction. Does a good job of presenting both sides of the issue.
The meanings of life
Famous psychologist and author of Willpower, Roy Baumeister, discusses the relationship between feelings of meaningfulness and happiness. Baumeister uses these topics as a jumping off point for a discussion of what factors contribute to individuals&amp;rsquo; feelings of meaning.</description>
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      <title>Weekly Newsletter</title>
      <link>https://stephenmalina.com/post/2015-05-17-nl05172015/</link>
      <pubDate>Sun, 17 May 2015 00:00:00 +0000</pubDate>
      
      <guid>https://stephenmalina.com/post/2015-05-17-nl05172015/</guid>
      <description>Public Health # Why an iron fish can make you stronger
Presents a simple but ingenious way to combat anaemia in Cambodia by giving villagers iron fish to put in their cooking pots.
Osama Bin Laden Raid Questions # I&amp;rsquo;m trying to cover this issue in depth since I think it sits at the intersection of a few key issues: balancing transparency and national security concerns, the efficacy of torture, and the treatment of journalists in the United States.</description>
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      <title>Weekly Newsletter</title>
      <link>https://stephenmalina.com/post/2015-05-10-nl05102015/</link>
      <pubDate>Sun, 10 May 2015 00:00:00 +0000</pubDate>
      
      <guid>https://stephenmalina.com/post/2015-05-10-nl05102015/</guid>
      <description>Police Brutality # Why Cops Like Me Are Quiet
A former NYPD officer discusses police brutality from an officer&amp;rsquo;s perspective.
Neuroscience # The Science of Craving
Profiles Dr. Kent Berridge&amp;rsquo;s research into the science of craving. Presents an interesting perspective on the difference between desire and pleasure and discusses meditation, a favorite topic of mine.
Medicine # Overkill
Argues that the American health system encourages careless overtreatment of illness. I&amp;rsquo;m sympathetic to this view but wish the author had delved more into alternative payment models since it seems these models contribute to the problem.</description>
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      <title>Weekly Newsletter</title>
      <link>https://stephenmalina.com/post/2015-05-03-nl05032015/</link>
      <pubDate>Sun, 03 May 2015 00:00:00 +0000</pubDate>
      
      <guid>https://stephenmalina.com/post/2015-05-03-nl05032015/</guid>
      <description>Warning: These next few paragraphs are about the origins and goals of the newsletter. If you don&amp;rsquo;t care about these things skip to here.
As I mentioned last week, I&amp;rsquo;ve decided to mark this week as the 6 month anniversary of this newsletter. To honor this, I&amp;rsquo;m going to quickly describe why I circulate this newsletter and what criteria I use to determine which articles I include in it. The circulation of the newsletter began on a whim.</description>
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      <title>Weekly Newsletter</title>
      <link>https://stephenmalina.com/post/2015-04-26-nl04262015/</link>
      <pubDate>Sun, 26 Apr 2015 00:00:00 +0000</pubDate>
      
      <guid>https://stephenmalina.com/post/2015-04-26-nl04262015/</guid>
      <description>Note: Next week will be the arbitrarily but mostly correctly determined 6th month anniversary of my newsletter. If you have any ideas for interesting things I could do for this, I&amp;rsquo;d love to hear them. So far, I&amp;rsquo;ve considered a &amp;ldquo;Best Of&amp;rdquo; week or piece written by me reflecting on the newsletter and explaining in detail why I put so much time into this.
Languages # Utopian for Beginners
Tells the story of one man&amp;rsquo;s created language and its journey into the world.</description>
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      <title>Weekly Newsletter</title>
      <link>https://stephenmalina.com/post/2015-04-19-nl04192015/</link>
      <pubDate>Sun, 19 Apr 2015 00:00:00 +0000</pubDate>
      
      <guid>https://stephenmalina.com/post/2015-04-19-nl04192015/</guid>
      <description>Politics # Clinton Begins the 2016 Campaign, And It&amp;rsquo;s a Toss-Up
Nate Silver, renowned election results predictor and sports statistician, speculates on the likelihood of a Hilary Clinton victory in 2016, taking into account different scenarios and opposing candidates. I really enjoy Nate Silver&amp;rsquo;s logical, data-driven approach to prediction.
Dolphins # Dolphin Intelligence
The author of Moonwalking with Einstein, Joshua Foer, explores the fascinating world of dolphin intelligence. Foer takes a cautiously optimistic approach to the field, speaking with multiple scientists about the prospects and obstacles of communicating with dolphins.</description>
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      <title>Weekly Newsletter</title>
      <link>https://stephenmalina.com/post/2015-04-12-nl04122015/</link>
      <pubDate>Sun, 12 Apr 2015 00:00:00 +0000</pubDate>
      
      <guid>https://stephenmalina.com/post/2015-04-12-nl04122015/</guid>
      <description>Mystery # The Mystery of the Millionaire Metaphysician
A republishing of an old story, this piece recounts a writer&amp;rsquo;s search for the author of a mysterious metaphysics manuscript. I don&amp;rsquo;t want to spoil the story so you&amp;rsquo;ll have to read it to learn more.
Psychological Warfare and Foreign Policy # Inside the Kremlin&amp;rsquo;s hall of mirrors
Investigates the Kremlin&amp;rsquo;s disinformation campaign and questions its reach. I thought this article did a phenomenal job of explaining the theory that led to the Kremlin&amp;rsquo;s employment of these tactics.</description>
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      <title>Weekly Newsletter</title>
      <link>https://stephenmalina.com/post/2015-04-05-nl04052015/</link>
      <pubDate>Sun, 05 Apr 2015 00:00:00 +0000</pubDate>
      
      <guid>https://stephenmalina.com/post/2015-04-05-nl04052015/</guid>
      <description>Mind and Brain # Electrified
Investigates the promises and perils of tDCS, the electrical stimulation of the brain proponents claim will help treat depression and other neurological disorders.
Evolution # Defending Darwin
A biology professor at the University of Kentucky discusses his experiencing teaching evolution to a group largely composed of Creationists. This article interests me on two levels: 1) I come from an area where evolution is largely unchallenged.</description>
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      <title>Weekly Newsletter</title>
      <link>https://stephenmalina.com/post/2015-03-29-nl03292015/</link>
      <pubDate>Sun, 29 Mar 2015 00:00:00 +0000</pubDate>
      
      <guid>https://stephenmalina.com/post/2015-03-29-nl03292015/</guid>
      <description>Books # Rapt
Reviews H is for Hawk, a non-fiction book about grief, hawking, and T.H. White. Discusses grief and the quirkiness of hawks and hawking.
Memory # Memory in the Flesh
Explores research on the radical idea that memory can exist outside the brain in other parts of the body. This article&amp;rsquo;s interesting because it shows how political science can be. I&amp;rsquo;m always drawn to articles which challenge scientific dogma as I think innovation often arises from these challenges.</description>
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      <title>Weekly Newsletter</title>
      <link>https://stephenmalina.com/post/2015-03-22-nl03222015/</link>
      <pubDate>Sun, 22 Mar 2015 00:00:00 +0000</pubDate>
      
      <guid>https://stephenmalina.com/post/2015-03-22-nl03222015/</guid>
      <description>Evolution # Possible Creatures
A professor of Evolutionary Biology discusses his work mapping &amp;ldquo;nature&amp;rsquo;s library&amp;rdquo; of proteins. He makes tenuous parallels to Platonism, but the work stands on its own whether you take those into account or not.
Mind and Brain # The Science of Near Death Experiences
Explores the debate about the mechanism of near-death experiences between scientific materialists and spiritual believers. I surprisingly fall somewhere in the middle on this and other similar issues.</description>
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      <title>Weekly Newsletter</title>
      <link>https://stephenmalina.com/post/2015-03-15-nl03152015/</link>
      <pubDate>Sun, 15 Mar 2015 00:00:00 +0000</pubDate>
      
      <guid>https://stephenmalina.com/post/2015-03-15-nl03152015/</guid>
      <description>Genocide # Interview with a Torturer
An author and survivor of the Khmer Rouge genocide in Cambodia attempts to come to terms with his experience. At times, this piece was hard to read at times, but I think that quality adds to its power. This quote really resonated with me:
&amp;ldquo;There’s a contemporary notion that we’re all potential torturers. This fatalism tinged with smugness exercises literature, film, and certain intellectuals.</description>
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      <title>Weekly Newsletter</title>
      <link>https://stephenmalina.com/post/2015-03-08-nl03082015/</link>
      <pubDate>Sun, 08 Mar 2015 00:00:00 +0000</pubDate>
      
      <guid>https://stephenmalina.com/post/2015-03-08-nl03082015/</guid>
      <description>Mental Health # The voices in my head: Eleanor Longden&amp;rsquo;s &amp;lsquo;psychic civil war&amp;rsquo;
The Guardian interviews Elanor Longden, a woman who started hearing voices while in college. Longden discusses her ordeal and subsequent recovery, shedding light on the nature of her disease. One of the commenters on this article wrote a thoughtful comment, which I&amp;rsquo;ve included
&amp;ldquo;It makes me wonder that we all have these voices to some degree, but that it&amp;rsquo;s rarer to have them be so articulate, so able to enunciate distinct aspects of our personalities.</description>
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      <title>Weekly Newsletter</title>
      <link>https://stephenmalina.com/post/2015-03-01-nl03012015/</link>
      <pubDate>Sun, 01 Mar 2015 00:00:00 +0000</pubDate>
      
      <guid>https://stephenmalina.com/post/2015-03-01-nl03012015/</guid>
      <description>Science and Technology # Futures of Text
A survey of all the current innovation in text as a medium. Argues for the superiority of text-based communication and interaction over app-based communication and interaction.
First human head transplant could happen in two years
Discusses the prospects for transplanting a human head onto another body. Neglects to discuss from where the second body would come, but, otherwise does a good job of explaining the idea and the issues surrounding it.</description>
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      <title>Weekly Newsletter</title>
      <link>https://stephenmalina.com/post/2015-02-22-nl02222015/</link>
      <pubDate>Sun, 22 Feb 2015 00:00:00 +0000</pubDate>
      
      <guid>https://stephenmalina.com/post/2015-02-22-nl02222015/</guid>
      <description>Technology # How I Taught my Computer to Write its Own Music
Discusses a successful endeavor to create a computer-based entity that writes music. Mindblowing.
Digital Reality
Edge interviews Neil Gershenfeld, head of MIT&amp;rsquo;s Center for Bits and Atoms. He discusses the future of manufacturing and fabrication and its impact on the world economy. This is a long one, but I really enjoyed it.
Hand of a Superhero
Profiles E-nable and other groups focused on improving upon the process of creating and distributing prosthetic hands for children.</description>
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      <title>Weekly Newsletter</title>
      <link>https://stephenmalina.com/post/2015-02-15-nl02152015/</link>
      <pubDate>Sun, 15 Feb 2015 00:00:00 +0000</pubDate>
      
      <guid>https://stephenmalina.com/post/2015-02-15-nl02152015/</guid>
      <description>Philosophy # Do Easy
The film and source essay (linked to at the bottom of the page) both convey a philosophy rooted in Taoism, but understandable for the modern American. It&amp;rsquo;s important to note that William S. Burroughs (the essay&amp;rsquo;s author and the author of Naked Lunch) struggled with a debilitating heroine addiction for much of his life. Looking at this essay in light of that, I found that many of the ideas took on a dual meaning.</description>
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      <title>Weekly Newsletter</title>
      <link>https://stephenmalina.com/post/2015-02-08-nl02082015/</link>
      <pubDate>Sun, 08 Feb 2015 00:00:00 +0000</pubDate>
      
      <guid>https://stephenmalina.com/post/2015-02-08-nl02082015/</guid>
      <description>Mind and Brain # The Trip Treatment
Reviews new research on psychedelics and their gradual integration into mainstream psychiatry. Recounts the effects of psychedelic treatment on patients suffering from addiction or nearing the end of their lives.
Biographical # Meet Walter Pitts, The Man Who Tried to Redeem the World With Logic
Profiles Walter Pitts, a mathematician who worked alongside the founders of modern information theory but eventually suffered a crippling breakdown.</description>
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      <title>Weekly Newsletter</title>
      <link>https://stephenmalina.com/post/2015-02-01-nl02012015/</link>
      <pubDate>Sun, 01 Feb 2015 00:00:00 +0000</pubDate>
      
      <guid>https://stephenmalina.com/post/2015-02-01-nl02012015/</guid>
      <description>Corporations # Are We Ready For Companies That Run Themselves?
Covers the rise of autonomous corporations and discusses its underlying forces and technologies. Questions whether these corporations will liberate us from scarcity or further enslave us to it.
Farming # An Ex-Industrial Fisherman Rethinks His Job
Reviews Bren Smith, an ocean farmer working to use sustainable farming methods on the sea to make a living and produce food and fuel.</description>
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      <title>Weekly Newsletter</title>
      <link>https://stephenmalina.com/post/2015-01-25-nl01252015/</link>
      <pubDate>Sun, 25 Jan 2015 00:00:00 +0000</pubDate>
      
      <guid>https://stephenmalina.com/post/2015-01-25-nl01252015/</guid>
      <description>Human Potential # Natural Born Heroes
Sometimes, when I read an article, I think it would be great for the newsletter because it calls into question a widely-held belief or delves deep into an esoteric topic in a profound way. This isn&amp;rsquo;t one of those articles &amp;ndash; this is an article that you read and think &amp;ldquo;this is awesome.&amp;rdquo; The article covers a few different groups reviving or creating new uses of the human form.</description>
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      <title>Weekly Newsletter</title>
      <link>https://stephenmalina.com/post/2015-01-18-nl01182015/</link>
      <pubDate>Sun, 18 Jan 2015 00:00:00 +0000</pubDate>
      
      <guid>https://stephenmalina.com/post/2015-01-18-nl01182015/</guid>
      <description>Education # The Unappreciated Success of Charter Schools
Convincingly argues for charter schools&amp;rsquo; effectiveness at educating underpriviliged students.
Mind and Brain # Postcards from the Edge of Consciousness
Describes the experience of sensory deprivation and the biological mechanisms it activates.
Muscle Strength is in the Mind
Summarizes a recent study with results indicating that imagining muscular contractions affects the strength of the muscles involved. I&amp;rsquo;ve skimmed through the original study paper, and the methodology seems sound.</description>
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      <title>Weekly Newsletter</title>
      <link>https://stephenmalina.com/post/2015-01-11-nl01112015/</link>
      <pubDate>Sun, 11 Jan 2015 00:00:00 +0000</pubDate>
      
      <guid>https://stephenmalina.com/post/2015-01-11-nl01112015/</guid>
      <description>Foreign Policy # Paris attacks: Millions rally for unity in France
Covers massive French rallies meant to demonstrate unity after the attacks on Charlie Hebdo.
Je Suis Charlie (Until Je Get Scared)
Asserts that many Westerners hold inconsistent views on free speech. Illustrates this with examples of newspapers blurring out the Charlie Hebdo comics and journalists subtly blaming Hebdo authors for publishing &amp;ldquo;inflammatory&amp;rdquo; content.
Is Saudi Arabia trying to cripple American fracking?</description>
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      <title>Weekly Newsletter</title>
      <link>https://stephenmalina.com/post/2015-01-04-nl01042015/</link>
      <pubDate>Sun, 04 Jan 2015 00:00:00 +0000</pubDate>
      
      <guid>https://stephenmalina.com/post/2015-01-04-nl01042015/</guid>
      <description>Power of the Mind # Secrets of a Mind Gamer
Narrates how a journalist won the U.S. Memory Championship. Summarizes the techniques used by memory athletes &amp;ndash; individuals who competitively memorize card sequences, digit strings, and poems. I&amp;rsquo;ve been discussing memory with a few newsletter readers, so I thought I&amp;rsquo;d include this piece. If you enjoy this piece, I highly recommend the author&amp;rsquo;s book on this topic, Moonwalking with Einstein: The Art and Science of Remembering Everything.</description>
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      <title>Weekly Newsletter</title>
      <link>https://stephenmalina.com/post/2014-12-28-nl12282014/</link>
      <pubDate>Sun, 28 Dec 2014 00:00:00 +0000</pubDate>
      
      <guid>https://stephenmalina.com/post/2014-12-28-nl12282014/</guid>
      <description>Stoicism # Stoicism has been at the forefront of my thoughts this break. I&amp;rsquo;m most of the way through Seneca&amp;rsquo;s Letters from a Stoic: Epistulae Morales AD Lucilium, a primary source for Stoic philosophy and recently finished Ryan Holiday&amp;rsquo;s The Obstacle Is the Way, which presents a simplified version of Stoicism that caters to modern audiences.
The first article about Stoicism in this newsletter, Indifference is a power, reveals Stoicism&amp;rsquo;s tenets and discusses its application both by its founders during Roman times and in modern cognitive behavioral therapy (the creator of Cognitive Behavioral Therapy struggled as a psychoanalyst until he remembered the teachings of ancient Stoicism, citation.</description>
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      <title>Weekly Newsletter</title>
      <link>https://stephenmalina.com/post/2014-12-21-nl12212014/</link>
      <pubDate>Sun, 21 Dec 2014 00:00:00 +0000</pubDate>
      
      <guid>https://stephenmalina.com/post/2014-12-21-nl12212014/</guid>
      <description>Psychology and Neuroscience # A Meditation on the Art of Not Trying
Introduces wu wei, the art of effortless grace. Taoists use wu wei to express the Tao (translates to &amp;ldquo;The Way&amp;rdquo;), while Confucians use it to express the grace that results from intense study and practice. Moreover, wu wei also resembles a state of mind which modern psychologists label &amp;ldquo;flow&amp;rdquo;. In addition to defining wu wei, the article offers a compelling hypothesis for why alcohol frequently accompanies business deal dinners, a phenomenon which I had never thought to explain.</description>
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      <title>Weekly Newsletter</title>
      <link>https://stephenmalina.com/post/2014-12-14-nl12072014/</link>
      <pubDate>Sun, 14 Dec 2014 00:00:00 +0000</pubDate>
      
      <guid>https://stephenmalina.com/post/2014-12-14-nl12072014/</guid>
      <description>On Writing # Writing with the Master
Profiles John McPhee, a staff writer for the New Yorker and professor at Princeton. Uses accounts from McPhee&amp;rsquo;s students to illustrate his erudition.
The Patch by John McPhee
As a companion to the profile of John McPhee, I&amp;rsquo;ve included this piece of his. In an attempt to understand better the reverence with which his students speak of him, I read three of his past New Yorker articles.</description>
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      <title>Weekly Newsletter (12-07-2014)</title>
      <link>https://stephenmalina.com/post/2014-12-07-nl12072014/</link>
      <pubDate>Sun, 07 Dec 2014 00:00:00 +0000</pubDate>
      
      <guid>https://stephenmalina.com/post/2014-12-07-nl12072014/</guid>
      <description>This week, I&amp;rsquo;m experimenting with something new. I&amp;rsquo;ve annotated certain articles I read and shared links to them, in addition to their original versions. Please let me know what you think of this. I don&amp;rsquo;t want to share the annotations if you aren&amp;rsquo;t interested in seeing them. On the other hand, if you like the annotated articles enough, I may start only sending annotated versions of certain articles. Finally, if you are someone who contributes articles (or wish to) and you want to annotate your articles too, I can help you get up and annotating within 10 minutes.</description>
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      <title>Weekly Newsletter (11-30-2014)</title>
      <link>https://stephenmalina.com/post/2014-11-30-nl11302014/</link>
      <pubDate>Sun, 30 Nov 2014 00:00:00 +0000</pubDate>
      
      <guid>https://stephenmalina.com/post/2014-11-30-nl11302014/</guid>
      <description>This week, I chose to focus exclusively on Ferguson, and only include Other Contributions outside of articles about Ferguson. I did this because I felt I could not give sufficient attention to Ferguson without including more than 2-3 articles about the topic.
On an unrelated note, I&amp;rsquo;ve been documenting my Winter Break Reading. While this is mostly for myself, I&amp;rsquo;ve reviewed two of the books I&amp;rsquo;ve read and intend to document my thoughts on the others subsequently.</description>
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      <title>Book Review - Regenesis by George Church</title>
      <link>https://stephenmalina.com/post/2014-11-26-regenesis-book-review/</link>
      <pubDate>Wed, 26 Nov 2014 00:00:00 +0000</pubDate>
      
      <guid>https://stephenmalina.com/post/2014-11-26-regenesis-book-review/</guid>
      <description>Synthetic biology is a burgeoning discipline that stems from a long lineage of genetic meddling. Synthetic biology&amp;rsquo;s ancestral legacy began when man first selected which seeds to plant based on the traits of the plants that birthed them. In Regenesis by George Church, Church takes the reader through this lineage, canvassing the past thousands of years and then focusing in on the past 30.
Church does a good job of balancing technical explanations with interesting anecdotes in the book.</description>
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      <title>Winter Break Reading Plans</title>
      <link>https://stephenmalina.com/post/2014-11-25-winter-break-reading/</link>
      <pubDate>Tue, 25 Nov 2014 00:00:00 +0000</pubDate>
      
      <guid>https://stephenmalina.com/post/2014-11-25-winter-break-reading/</guid>
      <description>To keep myself accountable, I&amp;rsquo;ve decided to post the books I plan to read over Winter Break (Nov. 25th, 2014 to Jan. 3rd, 2015) with a rough estimation of the time it will take to read them. My goal is to post short reviews for most or all of these books as I go through them. I expect reviewing these books will allow me to better reflect and remember my thoughts on them and the key messages that they impart.</description>
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      <title>Weekly Newsletter (11-23-2014)</title>
      <link>https://stephenmalina.com/post/2014-11-23-nl11232014/</link>
      <pubDate>Sun, 23 Nov 2014 00:00:00 +0000</pubDate>
      
      <guid>https://stephenmalina.com/post/2014-11-23-nl11232014/</guid>
      <description>Philosophy / History # Response to &amp;ldquo;Did Zen create the Kamikaze?&amp;rdquo;
A regular reader of the newsletter, Will Baird, responds to one of the articles I included in last week&amp;rsquo;s newsletter. If I could pick one article in this newsletter for you to read, it would be this one. Will worked hard on this response, bringing an expert&amp;rsquo;s mind to his critique and pulling knowledge from a wellspring of related sources and scholarly work.</description>
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      <title>Book Review - Existence by David Brin</title>
      <link>https://stephenmalina.com/post/2014-11-18-existence-david-brin-review/</link>
      <pubDate>Tue, 18 Nov 2014 00:00:00 +0000</pubDate>
      
      <guid>https://stephenmalina.com/post/2014-11-18-existence-david-brin-review/</guid>
      <description>Mind-blowing, challenging, and disturbing at times, David Brin&amp;rsquo;s view of the future is more comprehensive and more diverse than any other writer&amp;rsquo;s. The thing I love about this book is that it doesn&amp;rsquo;t shy away from discussing hard truths, like the myriad failure-modes humanity can enter. However, it accompanies this discussion with a constant sense that, if it&amp;rsquo;s possible, humanity will find a way.
Existence is a sci-fi novel for the Internet Age.</description>
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      <title>Response to &#34;Did Zen philosophy create the Kamikaze?&#34;</title>
      <link>https://stephenmalina.com/post/2014-11-17-response-to-nl11162014/</link>
      <pubDate>Mon, 17 Nov 2014 00:00:00 +0000</pubDate>
      
      <guid>https://stephenmalina.com/post/2014-11-17-response-to-nl11162014/</guid>
      <description>One of my readers, Will Baird, read the &amp;ldquo;Did Zen philosophy create the Kamikaze?&amp;rdquo; article in this past week&amp;rsquo;s newsletter, and, being a History buff, had a strong reaction to the article. Thus, he asked that I make his well though-out and well informed response available for my readers, as I have done below.
History as Clickbait # In his article “Into nothingness” Christopher Harding asks, “Did Zen ideas create the kamikaze?</description>
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      <title>Weekly Newsletter (11-16-2014)</title>
      <link>https://stephenmalina.com/post/2014-11-16-nl11162014/</link>
      <pubDate>Sun, 16 Nov 2014 00:00:00 +0000</pubDate>
      
      <guid>https://stephenmalina.com/post/2014-11-16-nl11162014/</guid>
      <description>Philosophy # Did Zen philosophy create the Kamikaze?
Pontificates on the relationship between WWII-era Zen philosophers and Japanese Jingoism.
A murderer&amp;rsquo;s warped idealism
Contrasts previous portrayals of Adolf Eichmann as &amp;ldquo;terrifyingly normal&amp;rdquo; and &amp;ldquo;banal&amp;rdquo; with stories of his devotion to &amp;ldquo;the Final Solution.&amp;rdquo;
Our Miraculous Biosphere # The Termite and the Architect
Begins by talking about an architect&amp;rsquo;s attempt to mimic the way termites&amp;rsquo; mounds manage air flow, and then uses this example as an example of biomimicry.</description>
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      <title>Weekly Newsletter (11-09-2014)</title>
      <link>https://stephenmalina.com/post/2014-11-09-nl11092014/</link>
      <pubDate>Sun, 09 Nov 2014 00:00:00 +0000</pubDate>
      
      <guid>https://stephenmalina.com/post/2014-11-09-nl11092014/</guid>
      <description>Questions or Comments? Contact me at [stephenmalina@gmail.com](mailto: stephenmalina@gmail.com) or on Twitter.
Philosophy # Marathon Monks of Mt. Hiei
Disclaimer: There is New-Agey-ness within this article. For a more accurate depiction of the Marathon Monks, I recommend this documentary or this book (I intend to consume both over winter break)
Despite the above disclaimer, I included this because I mentioned the Marathon Monks to a friend yesterday. Upon doing so, I decided that their story is worthwhile to share.</description>
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      <title>Weekly Newsletter (11-02-2014)</title>
      <link>https://stephenmalina.com/post/2014-11-02-nl11022014/</link>
      <pubDate>Sun, 02 Nov 2014 00:00:00 +0000</pubDate>
      
      <guid>https://stephenmalina.com/post/2014-11-02-nl11022014/</guid>
      <description>This is a weekly newsletter I publish each week that contains content I enjoyed and hope that you will enjoy. If you have questions or comments, you can find me at [stephenmalina@gmail.com](mailto: stephenmalina@gmail.com) or on Twitter.
Technology and Human Augmentation # A Spreadsheet Way of Knowledge
A long, in-depth piece on the history of spreadsheet modeling. The two points that stick with me from this piece are the dismissive attitude people initially had towards the spreadsheet and the obsession with modeling people displayed (and continue to display).</description>
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      <title></title>
      <link>https://stephenmalina.com/home/</link>
      <pubDate>Mon, 01 Jan 0001 00:00:00 +0000</pubDate>
      
      <guid>https://stephenmalina.com/home/</guid>
      <description>test</description>
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      <title></title>
      <link>https://stephenmalina.com/post/2023-08-05-protein-language-models-part-4/</link>
      <pubDate>Mon, 01 Jan 0001 00:00:00 +0000</pubDate>
      
      <guid>https://stephenmalina.com/post/2023-08-05-protein-language-models-part-4/</guid>
      <description>Scaling # Some of the earliest evidence for PLM scaling behaving similar to LLM scaling came from ESM-1b. The following plot shows model performance as a function of (log10) number of parameters. As seen there, they also trained LSTM models at two different sizes as baselines.
⊕ ESM-1b perplexity vs. log10(# of parameters) by model type on a held-out subset of UniRef50. RITA provided even stronger evidence for PLMs following scaling laws.</description>
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      <title></title>
      <link>https://stephenmalina.com/subscribe/</link>
      <pubDate>Mon, 01 Jan 0001 00:00:00 +0000</pubDate>
      
      <guid>https://stephenmalina.com/subscribe/</guid>
      <description>Thank you for reading my blog!
Sign up for my email newsletter or use this RSS feed to get notified of new blog posts.</description>
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    <item>
      <title>About me</title>
      <link>https://stephenmalina.com/about/</link>
      <pubDate>Mon, 01 Jan 0001 00:00:00 +0000</pubDate>
      
      <guid>https://stephenmalina.com/about/</guid>
      <description>Hi! I&amp;rsquo;m Stephen Malina. I&amp;rsquo;m currently the Head of Engineering at Dyno Therapeutics working on applying machine learning to engineer better gene therapy vectors. More broadly, I&amp;rsquo;m interested in the intersection of Machine Learning and engineering biology. Even more broadly, I like to think and talk about how we can make the future better and happen faster through better science, technology, and institutional mechanisms.
Before joining Dyno, I was a CS MS student at Columbia doing research at the intersection of ML, causal inference, and epigenomics in the Knowles Lab.</description>
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      <title>Bets</title>
      <link>https://stephenmalina.com/bets/</link>
      <pubDate>Mon, 01 Jan 0001 00:00:00 +0000</pubDate>
      
      <guid>https://stephenmalina.com/bets/</guid>
      <description>Inspired by Jose, Bryan Caplan, and others, this is a page where I track my ongoing and resolved bets publicly. Remember, bets are not endorsements!
Format # Bet: What is/was the bet? # For: Who is/was for in favor of the claim?
Against: Who is/was against the claim?
Amount: How much money (and in what currency) do/did the for/against person get paid by the other person if they won?
Implied probabilities: What are the bettor&amp;rsquo;s (implied) probabilities in the direction of their &amp;ldquo;preferred&amp;rdquo; outcomes?</description>
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