<?xml version="1.0" encoding="utf-8"?><feed xmlns="http://www.w3.org/2005/Atom" ><generator uri="https://jekyllrb.com/" version="3.10.0">Jekyll</generator><link href="https://abhixphys.github.io/feed.xml" rel="self" type="application/atom+xml" /><link href="https://abhixphys.github.io/" rel="alternate" type="text/html" /><updated>2025-09-28T12:35:43+00:00</updated><id>https://abhixphys.github.io/feed.xml</id><title type="html">Abhishek</title><subtitle>Personal webiste to record some of the events worth sharing.</subtitle><author><name>Abhishek Singh</name><email>abhishek.singh21@niser.ac.in</email></author><entry><title type="html">Perspective on ‘Why Sex’?</title><link href="https://abhixphys.github.io/posts/2025/blog-post-2/" rel="alternate" type="text/html" title="Perspective on ‘Why Sex’?" /><published>2025-08-11T00:00:00+00:00</published><updated>2025-08-11T00:00:00+00:00</updated><id>https://abhixphys.github.io/posts/2025/Why-Sex</id><content type="html" xml:base="https://abhixphys.github.io/posts/2025/blog-post-2/"><![CDATA[<p>Multiplicative Updates and Sexual Reproduction</p>

<p><em>This blog is primarily derived from <a href="https://arxiv.org/pdf/1208.3160">Multiplicative Updates in Coordination Games and the Theory of Evolution (2012) (arXiv:1208.3160)</a> authored by E. Chastain, A. Livnat, C. Papadimitriou &amp; U. Vazirani. The paper takes a crack on the famous enigma in evolutionary biology.</em></p>

<hr />

<p>The longstanding puzzle of <strong>‘Why sex?’</strong> remains one of the widely debated upon questions in evolutionary biology. Sexual reproduction is everywhere in nature — yet, from a cost–benefit point of view, it looks almost irrational.</p>

<p>Consider the drawbacks:</p>
<ul>
  <li>It’s complex, risky, and energy-hungry.</li>
  <li>It breaks apart well-adapted gene combinations.</li>
  <li>It halves/dilutes a parent’s genetic contribution to offspring.</li>
</ul>

<p>Classic explanations — like faster adaptation, removal of deleterious mutations, or Red Queen–style arms races — have been insightful, but none have perfectly nailed down why sex consistently wins out despite these costs.</p>

<h2 id="a-different-angle-mixability">A Different Angle: Mixability</h2>

<p>The authors propose reframing the problem. Under sexual reproduction, natural selection doesn’t chase the single “fittest” combination of alleles. Instead, it rewards <strong>alleles that play well with others</strong>.</p>

<blockquote>
  <p>Mixability of an Allele: An allele’s ability to work reasonably well with a wide range of genetic partners.</p>
</blockquote>

<p>From this angle, what used to be called sex’s biggest flaw — constantly breaking apart “lucky” genetic combinations — becomes its central feature. 
The shuffling keeps the focus on robustness and flexibility, not on a brittle, perfect match.</p>

<p>The central result is proved in the <em>weak selection regime</em>, where fitness differences are small (think fitness values in \([1-s,\, 1+s]\) with small \(s\)).</p>

<p>Key points:</p>

<ol>
  <li>
    <p>Quick drift to the Wright manifold<br />
The system rapidly settles into a state with no linkage disequilibrium — meaning genes behave as if inherited independently. Genotype distributions can then be     written as products of allele frequencies, which simplifies the analysis.</p>
  </li>
  <li>
    <p>Evolution ≡ Multiplicative Updates<br />
In weak selection, the population genetics dynamics are <em>exactly</em> the same as the multiplicative update rule from online learning (classes of learning algorithm that Netflix might be using  for optimizing the recommendations) and game theory.</p>

    <ul>
      <li><em>Genes</em> are the players.</li>
      <li><em>Alleles</em> are strategies.</li>
      <li><em>Allele frequencies</em> are strategy probabilities.</li>
      <li>The payoff is <em>mixability</em>.</li>
    </ul>

    <p>The paper is very emphatic:</p>
    <blockquote>
      <p>“We are not saying the equilibrium <em>can</em> be found through multiplicative updates — 
we are saying something stronger: <strong>Evolution <em>is</em> multiplicative updates</strong>.”</p>
    </blockquote>
  </li>
  <li>
    <p>Robust convergence<br />
This process converges to an equilibrium and remains stable even under small random perturbations to fitness values.</p>
  </li>
</ol>

<h2 id="the-diversity-question">The Diversity Question</h2>

<p>But simply convergence to equilibrium is not good enough for a population. One of the most appealing outcomes of this framework is that it ensures that <strong>diversity can persist</strong> at equilibrium (opposed to the case where a population of a bacterium would become uniform eventually).
It’s not obvious — multiplicative updates often converge to narrow supports in other contexts — so the authors go further:</p>

<ul>
  <li>They show that for <em>two genes</em>, there are <strong>exponentially many equilibria</strong> where the support (the set of alleles with nonzero frequency) contains a significant fraction of the alleles for <em>each</em> gene.</li>
  <li>This “exponential support” result means the loss of diversity is <em>not</em> inevitable — the dynamics can sustain large, mixed populations.</li>
</ul>

<p>The proof uses a neat trick:</p>

<ul>
  <li>Represent the differential fitness between allele combinations as a <em>random matrix</em>.</li>
  <li>Show (via a <em>potential function argument</em>) that, with high probability, the inverse of this matrix has <em>non-negative row and column sums</em>.</li>
  <li>This property guarantees the existence of large-support equilibria.</li>
</ul>

<p>The potential function argument is simple but clever: 
Flip the sign of any row or column whose sum is negative, track a global measure or potential (here the sum of all the elements of the matrix), and observe that it always increases. Eventually, one end up in a state where all row/column sums are non-negative.</p>

<h2 id="limitations--open-questions">Limitations &amp; Open Questions</h2>

<p>The framework is elegant but comes with boundaries:</p>

<ul>
  <li>
    <p>The proof relies on small fitness differences (weak-selection). It’s unclear which other fitness landscapes would yield the same multiplicative-update dynamics.</p>
  </li>
  <li>
    <p>The results assume that linkage disequilibrium disappears quickly (Wright manifold assumption). A characterization of landscapes that stay on or return to this manifold still remains open.</p>
  </li>
  <li>
    <p>Once an allele is lost, it’s gone (unless mutation reintroduces it). Real evolution, of course, never stabilizes — mutations are a slow but constant background force.</p>
  </li>
  <li>
    <p>The equilibrium reached may not be a Nash equilibrium of the <em>full</em> game, but of a smaller ‘subgame’ containing only the alleles that survived.</p>
  </li>
  <li>
    <p>The formal diversity result is proved for the two-gene case. Extending it to three or more genes is mathematically tough beacuse it would involve tensors of higher order, though simulations hint that large-support equilibria still exist.</p>
  </li>
</ul>

<h2 id="a-computational-detour-the-pls-question">A Computational Detour: The PLS Question</h2>

<p>Here’s where things get unexpectedly fun for anyone who likes computational complexity theory. The row/column-flipping step above isn’t just a neat trick — it’s also a <strong>search problem</strong> in disguise:</p>

<blockquote>
  <p>Given a nonsingular square matrix, can one flip rows and columns so that its inverse has non-negative row and column sums?</p>
</blockquote>

<p>The authors point out that this problem lives in the complexity class PLS — <em>Polynomial Local Search</em>. PLS problems have three key traits:</p>
<ol>
  <li>A solution always exists.</li>
  <li>One can check the quality of a solution efficiently (in polynomial time).</li>
  <li>One can move to a better solution by a small local change.</li>
</ol>

<p>The authors ask:</p>
<blockquote>
  <p>Is this matrix-flipping problem <em>PLS-complete</em>?</p>
</blockquote>

<ul>
  <li>PLS-complete problems are the ‘hardest’ in PLS. If one can solve a single such problem efficiently, one solve <em>all</em> of them.</li>
  <li>But if this matrix problem were PLS-complete, it would mean the computational challenge of predicting diversity-maintaining equilibria is as hard as any local search problem we know.</li>
</ul>

<p>In other words: <em>If this is PLS-complete, the challenge of predicting/determining evolution’s equilibrium won’t be just due to messy biology and bad data— it’d be a fundamentally (or more aptly computationally) hard.</em>.</p>

<h2 id="closing-thoughts">Closing Thoughts</h2>

<p>This work reframes sexual mode of reproduction as a <em>coordination game between genes</em>, where multiplicative updates naturally push the system toward alleles with strong mixability. 
It’s a clean, learning-theoretic way to capture the <em>why</em> of sex — at least in the weak selection regime — and it opens the window into other questions.</p>

<hr />

<p><em>Me and my friend <a href="https://pritipriya-dasbehera.github.io/">Pritipriya</a> redid the calculations of the paper as a part of project in our ‘Theoretical ML’ coursework. The blog was one of the attempts at commentary on the article. For technical details on calculations/proof one can take a look at the preliminary <a href="/assets/report_adv_ml.pdf">project report</a> we wrote.</em></p>]]></content><author><name>Abhishek Singh</name><email>abhishek.singh21@niser.ac.in</email></author><category term="evolution" /><category term="theo bio" /><category term="theo cs" /><summary type="html"><![CDATA[Multiplicative Updates and Sexual Reproduction]]></summary></entry><entry><title type="html">First Blog</title><link href="https://abhixphys.github.io/posts/2025/blog-post-1/" rel="alternate" type="text/html" title="First Blog" /><published>2025-05-24T00:00:00+00:00</published><updated>2025-05-24T00:00:00+00:00</updated><id>https://abhixphys.github.io/posts/2025/First-Blog</id><content type="html" xml:base="https://abhixphys.github.io/posts/2025/blog-post-1/"><![CDATA[<p>This is to try out blog features in jekyll.</p>

<h1 id="headings-are-cool">Headings are cool</h1>

<h1 id="you-can-have-many-headings">You can have many headings</h1>

<h2 id="arent-headings-cool">Aren’t headings cool?</h2>]]></content><author><name>Abhishek Singh</name><email>abhishek.singh21@niser.ac.in</email></author><category term="cool posts" /><category term="category1" /><category term="category2" /><summary type="html"><![CDATA[This is to try out blog features in jekyll.]]></summary></entry></feed>