tag:blogger.com,1999:blog-49488850595172091292024-03-13T11:54:07.458-07:00Quintessence of Dust<i>Quintessence of Dust</i> explores science, society, and human nature, focusing on genetics, development, evolution, neuroscience, systems biology, and topics related to scientific literacy. I occasionally discuss intelligent design, creationism, science denial, and other political/social influences on scientific literacy. Additional topics: philosophy, baseball, scientific culture, and Shakespeare. My main theme is <b><u>scientific explanation</u></b>.Stephen Mathesonhttp://www.blogger.com/profile/05057004085073574659noreply@blogger.comBlogger236125tag:blogger.com,1999:blog-4948885059517209129.post-46657567602901809072023-08-16T21:59:00.015-07:002023-08-16T22:24:17.272-07:00Science, intuition and the "strange inversion of reasoning"<p>A few days ago I wrote about <a href="https://sfmatheson.blogspot.com/2023/08/scientific-thinking-as-antidote-to.html" target="_blank">scientific thinking as an antidote to intuition</a>. Not just an alternative to it, but something like the opposite of intuition. The intentional, energy-consuming move to a systematic deliberative mode of thought is utterly different from the easy and instantaneous nature of intuition.</p><p>Some of our intuitions are clearly built-in. Many of the famous failings of our intuitive System 1, described by Daniel Kahneman in <i>Thinking, Fast and Slow</i>, seem to be hard-wired. Some are perhaps the unavoidable result of trade-offs that buy speed and decisiveness at the expense of accuracy and completeness. Others might be adaptive despite being occasionally delusional: I'm thinking here of <a href="https://hbr.org/2003/07/delusions-of-success-how-optimism-undermines-executives-decisions" target="_blank">optimism bias</a>. Some days we just need some good old optimism bias!</p><p>But some of our most famous intuitions are more complex and a bit harder to attribute to brain wiring or adaptive tricks. These are intuitions that seem to affect how we see the whole world, all of existence, all day. I think it's intuition (and nothing else) that makes us feel that something complex, that shows design, must have come from a designer. That a universe has to have a beginning, and therefore a "beginner." That a mind like ours must somehow come from a bigger mind somewhere else. That seemingly uncaused events must have had a cause. Which are all probably related to a sense that the universe is haunted.</p><p>I'm not sure that these intuitions are all universally human—some are likely to be deeply cultural. But the point is that well beyond our intution that the sun moves through the sky or that the earth can't be a spinning ball, there are intuitions about the very fabric of existence.<span></span></p><a name='more'></a><p></p><p>Evolution flies in the face of some of these, and Dan Dennett writes elegantly about the ways that evolution challenges ancient intuitions. His 2009 piece, <a href="https://doi.org/10.1073/pnas.0904433106" target="_blank">Darwin's “strange inversion of reasoning”</a>, is a great basic overview of those ideas. It's open access and not overly technical.</p><p>The phrase "strange inversion of reasoning" comes from an <a href="https://openlibrary.org/books/OL23430706M/The_Darwinian_Theory_of_the_Transmutation_of_Species" target="_blank">indignant religious opponent of evolution</a>, writing just a few years after publication of <i>The Origin of Species</i>. This critic described Darwin as someone...</p><p></p><blockquote><p>...who, by a strange inversion of reasoning, seems to think Absolute Ignorance fully qualified to take the place of Absolute Wisdom in all of the achievements of creative skill.</p><p>—<a href="https://archive.org/details/darwiniantheory00bevegoog/page/n151/mode/2up" target="_blank">The Darwinian Theory of the Transmutation of Species</a>, p. 295</p></blockquote><p></p><p>In the 2009 paper, Dennett describes two cataclysmic "inversions" that Darwin brought to us:</p><p></p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh1Kh9grOBW24BHrX-jAbmOVKuQB66Pj3jQXYduywTeoI9KWjHZZ9URd05F9g5DJthoRUXe3Qtn1wjWP40eGANviaqiMj7mxmDm05Np9f0WrkIMN8c4CDE-1BiPLlOIzu-5WckdPGlgUxKndOx7L_gZWUbBxCtv3jSTdiLJMckMPGqepfsnTWsn9D_d4Ew/s3303/s3___eu-west-1_dlcs-storage_2_8_V0034162.jpg" style="clear: right; float: right; margin-bottom: 1em; margin-left: 1em;"><img border="0" data-original-height="3303" data-original-width="2404" height="320" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh1Kh9grOBW24BHrX-jAbmOVKuQB66Pj3jQXYduywTeoI9KWjHZZ9URd05F9g5DJthoRUXe3Qtn1wjWP40eGANviaqiMj7mxmDm05Np9f0WrkIMN8c4CDE-1BiPLlOIzu-5WckdPGlgUxKndOx7L_gZWUbBxCtv3jSTdiLJMckMPGqepfsnTWsn9D_d4Ew/s320/s3___eu-west-1_dlcs-storage_2_8_V0034162.jpg" width="233" /></a></div>1. Darwin replaced the "trickle-down" theory of creation, in which life proceeds "down" from a god or other superbeing, with "bubble-up creation":<p></p><p></p><blockquote>When we turn to Darwin's bubble-up theory of creation, we can conceive of all of the creative design work metaphorically as lifting in Design Space. It has to start with the simplest replicators, and gradually ratchet up, by wave after wave of natural selection, to multicellular life in all its forms.</blockquote><p></p><p>2. Darwin opened our eyes to what Dennett elsewhere calls "<a href="https://www.theatlantic.com/technology/archive/2012/06/-a-perfect-and-beautiful-machine-what-darwins-theory-of-evolution-reveals-about-artificial-intelligence/258829/" target="_blank">competence without comprehension</a>," an inversion that Dennett links to the great Alan Turing:</p><p></p><blockquote>Before Turing there were computers, by the hundreds, working on scientific and engineering calculations. Many of them were women, and many had degrees in mathematics. They were human beings who knew what arithmetic was, but Turing had a great insight: they didn't need to know this! As he noted, “The behavior of the computer at any moment is determined by the symbols which he is observing, and his ‘state of mind’ at that moment …”. Turing showed that it was possible to design machines—Turing machines or their equivalents—that were Absolutely Ignorant, but could do arithmetic perfectly. And, he showed that, if they can do arithmetic, they can be given instructions in the impoverished terms that they do “understand” that permit them to do anything computational. [...] A huge Design Space of information-processing was made accessible by Turing, and he foresaw that there was a traversable path from Absolute Ignorance to Artificial Intelligence, a long series of lifting steps in that Design Space.</blockquote><p></p><p>That second inversion is about human consciousness, but I think the basic idea is simple and more broad than just the human mind: the behavior of seemingly dumb replicators can add ... and add and add and add ... up to complexity and design and even the shocking miracle of the human mind.</p><p>If that's too reductionist for your taste, I understand, but my main assertion is simply this: we know evolution has accomplished the creation of design, and we don't need magic to explain it. This is, to quote Dennett, deeply counterintuitive. Because our sense that design has to come from a mind is deep intuition. It's much more than a flighty theory tossed out by some influential dingbat and subsequently fossilized in dogma or recorded wisdom. It's an intuition.</p><p>And I firmly believe that even these big deep intuitions, some of which partially constitute the foundations of vast systems of thought and belief, should be disrespected. Science should ignore them. Scientific thinking should put the intuition of a god-designer right next to the intuition of a stationary earth. Because ultimately, in my view, evolution is not a strange inversion of reasoning (or at least of reason). It's just a death blow dealt to another crude human intuition.</p><hr /><p>Image credit: <a href="https://wellcomecollection.org/works/ufhcuemm/images?id=q94w6wdf" target="_blank">The hand of God spans out heaven with a compass while surrounded by angels. Line engraving by Robert Pranker, ca. 1761.</a> Wellcome Collection, public domain. </p>Stephen Mathesonhttp://www.blogger.com/profile/05057004085073574659noreply@blogger.com0tag:blogger.com,1999:blog-4948885059517209129.post-23129390473955028992023-08-12T23:56:00.005-07:002023-12-19T12:51:32.872-07:00Scientific thinking as the antidote to intuition<p></p><div class="separator" style="clear: both; text-align: center;"><a href="https://mpd-biblio-covers.imgix.net/9780374533557.jpg?w=900" style="clear: right; float: right; margin-bottom: 1em; margin-left: 1em;"><img border="0" data-original-height="800" data-original-width="535" height="200" src="https://mpd-biblio-covers.imgix.net/9780374533557.jpg?w=900" width="134" /></a></div>As I work on a book that will claim that evolution is easy, I have a parallel task of exploring the reasons we sense that it is hard or even impossible. Some of those influences are the result of efforts by religions to maintain dependence on supernaturalism or to defend ancient sacred writings. Some are the result of antipathy to science itself, framed in terms of culture war. But others are less clearly related—at least directly—to religions or tribes. Our brains are wondrous indeed but are known to be prone to various kinds of error. To be brutally frank: there are things that can seem obvious to us but that are false.<p></p><p>Daniel Kahneman's 2011 book <i><a href="https://www.google.com/books/edition/Thinking_Fast_and_Slow/ZuKTvERuPG8C?hl=en" target="_blank">Thinking, Fast and Slow</a></i> was a life-changer for me. As soon as I read it in 2013, I urged colleagues to read it, even convening a book club at work. (The job of a journal editor is fundamentally about making decisions and judgments, and that's what the book is about.) One of the key messages of the book is that our fast thinking system (Kahneman calls it System 1) is both speedy and utterly important for survival. It's not about reflexes—it's still a kind of thought. But it's quick and dirty, often making guesses or approximations, and is prone to error. "Intuition" is a function of System 1.<span></span></p><a name='more'></a><p></p><p>Now let's back up. Because it's not adequate to merely say that System 1 is prone to error. You might get the impression that it has a particular error rate (which is true) such that it sometimes misses threats or inaccurately identifies things. But the problem is bigger and more dangerous than that. The system is prone to specific <i>kinds</i> of error. It's prone to <i>systematic mistakes</i> that are built into how it works in the first place. <i>Thinking, Fast and Slow</i> explores these system-wide problems, and I found them very sobering. Look up "<a href="https://thedecisionlab.com/biases/framing-effect" target="_blank">framing</a>" for an interesting example.</p><p>Now consider "intuition" in the context of scientific questions. We know that intuition renders quick judgments, and we also know it is vulnerable to repeated and systematic error. We can run experiments on ourselves to see this. I suggest this one: revisit the time when you were learning that the Earth is a ball. I can remember this pretty clearly. What I remember was a struggle between "knowing" that it must be true that the Earth is a spinning ball, and simultaneously "knowing" that it was flat and didn't feel like it was moving at all. I "knew" that the people on the other side of the ball didn't fall off or feel like they were upside down, but I also knew what it was like to be upside down and my brain had no system to jump in and help me understand how people on the opposite side of the Earth didn't know they were upside down. To this day, I find it unintuitive to consider trees and water and people on the opposite side of our terrestrial ball. My intuition is a permanent hindrance.</p><p>What can we do about this? I would say this is an urgent question in a world awash in misinformation that is often crafted to exploit intuition or cognitive biases that characterize System 1. I suggest that science is the answer. That sounds trite but hear me out.</p><p>Here's my claim: <i><b>thinking scientifically is a discipline that seeks to intentionally negate intuition</b></i>.</p><p>Some things I'm not claiming:</p><p></p><ul style="text-align: left;"><li>That science and intuition always disagree;</li><li>That intuition never tracks with scientific reasoning;</li><li>That scientific thinking always works;</li><li>That scientific thinking is always the best approach to every problem.</li></ul><p></p><p>But I think that when we consider the depth and reach of science denialism and its bases in human cognitive structure/habits, one major influence we confront is something that is often explicitly described as "intuition." It travels under other names, most notably common sense and often "instinct." We see it when we hear earnest talk about "other ways of knowing" and we are in its mystical presence when someone hears from gods or spirits.</p><p>But intuition is a crappy tool for understanding the world. System 1 wasn't built for that purpose. It was built for speed. Intuition can't understand a terrestrial ball. It doesn't expect a caterpillar to turn into a butterfly. It can't help you understand how ice can fall from the sky an hour after the temperature peaked (in Tucson) at 105 F (40 C). It has never seen continents move.</p><p>In parallel, Kahneman explains the second system, System 2:</p><p></p><blockquote><p>System 2 allocates attention to the effortful mental activities that demand it, including complex computations. The operations of System 2 are often associated with the subjective experience of agency, choice, and concentration.</p>—<i>Thinking, Fast and Slow,</i> p. 21</blockquote><p></p><p>System 2 kicks in when it's time to stop and think. When it's time to <i>deliberate</i>. But something has to throw the switch. We have to realize that it's <u>time</u> to stop and think. We have to recognize a problem or situation that System 1 can't resolve. More crucially, we sometimes have to exert effort to switch to System 2. The prompts might come from someone else ("Wait, let's think about this") or from our hard-earned wisdom that installs a tracker looking for the kinds of hasty judgments and errors that System 1 cranks out all day long.</p><p></p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi6G7zFT9wYlNKBbXzFNPMeLmn0JNcmZZvhMNRqOBKvtMbFeYkR6y5aucZY1nbQ9Df_BsGJ5EMf_IR6BqiE2DNIjyUNmX52tx775KAV69Nm0PPgztUwbid7ZvNbFEaCstCufoPp3aLlArvaCruFe_3hu4PbP-PdhEydTPDHkHtVYg0K36tAEh8yPks2S3E/s4032/thinking%20fast%20and%20slow.jpg" style="clear: right; float: right; margin-bottom: 1em; margin-left: 1em;"><img border="0" data-original-height="4032" data-original-width="2268" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi6G7zFT9wYlNKBbXzFNPMeLmn0JNcmZZvhMNRqOBKvtMbFeYkR6y5aucZY1nbQ9Df_BsGJ5EMf_IR6BqiE2DNIjyUNmX52tx775KAV69Nm0PPgztUwbid7ZvNbFEaCstCufoPp3aLlArvaCruFe_3hu4PbP-PdhEydTPDHkHtVYg0K36tAEh8yPks2S3E/w113-h200/thinking%20fast%20and%20slow.jpg" width="113" /></a></div>And that's where I think scientific thinking, as a discipline, often enters the chat. Scientific thinking is the work of System 2. It is systematic, deliberative, and intolerant of bullshit. (<a href="https://en.wikipedia.org/wiki/On_Bullshit" target="_blank">I'm using this term in its technical sense</a>.) <u>At its best, it is intentionally and explicitly opposed to intuition</u>. In scientific thought, intuition is barely better than background noise. It can generate hypotheses galore, and it does this regularly in science, but those hypotheses are just fodder for the deliberative work of System 2. My favorite coffee mug says "Science Doesn't Give a F*** What You Believe," and the message is not about faith or believers but about beliefs and intuitions that scientific thought seeks to ignore.<p></p><p>Scientific thinking feels that way to me. I can <i>feel</i> the move in my mind from the constant important work of System 1 to the deliberative work of System 2. Knowing how often my intuition has been a hindrance to my understanding of the world, I welcome the feeling of going to the place where the adult is in charge. Sometimes my intuitions are vindicated. Sometimes they're just irrelevant chaff. Sometimes they are exposed as errors: slapdash guesses, biases, outright prejudice.</p><p>Evolution is a great place to observe the folly of human intuition. The next post will use Dan Dennett's 2009 piece <a href="https://www.pnas.org/doi/10.1073/pnas.0904433106" target="_blank">Darwin's “strange inversion of reasoning”</a> to explore how evolution challenges some big ancient human intuitions about our world.</p>Stephen Mathesonhttp://www.blogger.com/profile/05057004085073574659noreply@blogger.com0tag:blogger.com,1999:blog-4948885059517209129.post-71295339610921865952023-08-10T21:01:00.003-07:002023-08-10T21:07:15.411-07:00What I learned about me when I started reading novels again<div class="separator" style="clear: both; text-align: center;"><a href="https://mpd-biblio-covers.imgix.net/9781250313225.jpg?w=900" style="clear: right; float: right; margin-bottom: 1em; margin-left: 1em;"><img border="0" data-original-height="800" data-original-width="518" height="200" src="https://mpd-biblio-covers.imgix.net/9781250313225.jpg?w=900" width="130" /></a></div>A few years ago, I somehow realized that I wanted to read more stories.<div><br /></div><div>My work as a journal editor involved hours of intense scientific reading every day, and my insatiable interest in biology meant that my recreational reading was almost exclusively about science. But I could remember how much I loved stories as a kid: <i>Tom Sawyer</i>, <i>The Black Stallion</i>, all the Roald Dahl things. I read almost no fiction at all as a high schooler, then as a young Christian adult I read <i>The Lord of the Rings</i> trilogy and (urp) the <i>Chronicles of Narnia</i>. As a dad, I read (aloud with the family) all of the Harry Potter books, and that was great memorable fun. Somehow about 15 years ago I decided to read <i>The Poisonwood Bible</i>. (Unforgettable.) But my extensive reading habits were largely focused on science and Shakespeare.</div><div><br /></div><div>To be sure, I derive both enjoyment and inspiration from science and from Shakespeare, but in retrospect it seems I needed to feed a part of me that finds inspiration in stories. In novels. And so I started collecting novels, specifically from female authors. I put a few on my Christmas list, and my loved ones obliged, and there they were on my shelves. Unread.</div><div><br /></div><div>Then for some reason, not even two years ago, I decided to do it. I had a trip coming up: my annual journey to New York to co-lead the <a href="https://meetings.cshl.edu/courses.aspx?course=c-write&year=23" target="_blank">Scientific Writing Retreat</a> at Cold Spring Harbor Laboratory. We had moved to Arizona, so the journey had evolved from a 4-hour ride on Amtrak to an all-day trip across the continent. I don't remember why, but I picked <i><a href="https://www.hachettebookgroup.com/titles/alix-e-harrow/the-ten-thousand-doors-of-january/9780316421980/" target="_blank">The Ten Thousand Doors of January</a></i> by <a href="https://alixeharrow.wixsite.com/author/books" target="_blank">Alix Harrow</a>, and started reading on the plane.<span><a name='more'></a></span></div><div><br /></div><div>Now, I think I got lucky because that's a great novel and Alix Harrow is now one of my favorite authors. I loved the book, yay, but that's not the whole story. Because I noticed that I particularly liked the fantastical and supernatural in the story. I wondered if that was just because it's a good book, so I decided to mix things up and read other female novelists. Over the following several months, I read:</div><div><br /></div><blockquote style="border: none; margin: 0px 0px 0px 40px; padding: 0px; text-align: left;"><div><i><a href="https://us.macmillan.com/books/9780374117948/thecactusleague" target="_blank">The Cactus League</a></i></div><div><i><a href="https://www.penguinrandomhouse.com/books/671891/velvet-was-the-night-by-silvia-moreno-garcia/" target="_blank">Velvet Was the Night</a></i></div><div><i><a href="https://jenniferegan.com/books/a-visit-from-the-goon-squad/" target="_blank">A Visit From the Goon Squad</a></i></div><div><i><a href="https://www.hachettebookgroup.com/titles/alix-e-harrow/the-once-and-future-witches/9780316422048/" target="_blank">The Once and Future Witches</a></i></div><div><i><a href="https://www.emilymdanforth.com/pbh" target="_blank">Plain Bad Heroines</a></i></div></blockquote><div><br /></div><div>Those are all excellent novels, and I recommend all of them. They have little in common other than the fact that they are all novels written by women. But I discovered I have a strong preference. The last two made a much stronger impression than the first three. In fact, I re-read the last chapter of <i>Plain Bad Heroines</i> three times.</div><div><br /></div><div>What those last two novels have in common is fantasy. They both contain supernatural stuff.</div><div><br /></div><div>This actually surprised me, being a scientist and an atheist and all. At first I thought it meant that because I deconverted from Christianity several years ago, I had some kind of vacuum I needed to fill with supernatural stuff. But I think that's probably wrong, or at least woefully incomplete. I think it's simpler than that: I like stories of inspiration that are willing to break the rules, to use magic or mystery or whatever to go places that we're not usually allowed to go. I'm <a href="https://sfmatheson.blogspot.com/2023/08/rebel-scum.html" target="_blank">rebel scum</a>, always have been, and after all, I loved Harry Potter long before I <a href="https://sfmatheson.blogspot.com/2023/03/on-jane-anger-shakespeare-apostasy-and.html" target="_blank">woke up from Christianity</a>.</div><div><br /></div><div>Knowing this about myself, I'm now steering myself toward the fantasy/sci-fi genre, something I would have found surprising just a few years ago. I recently finished the first three books in the Locked Tomb series and count <i><a href="https://us.macmillan.com/books/9781250313225/harrowtheninth" target="_blank">Harrow The Ninth</a></i> among my all-time favorites. I'm currently reading <i><a href="https://us.macmillan.com/books/9781250278555/hester" target="_blank">Hester</a></i>, which has some nice fantasy seasoning, and I have <i><a href="https://www.otherscribbles.com/thelongway" target="_blank">The Long Way to a Small, Angry Planet</a></i> waiting next.</div><div><br /></div><div>It took a few decades, but now I know. See more about my reading in my <a href="https://sfmatheson.blogspot.com/search/label/What%20I%27m%20reading" target="_blank">What I'm Reading series</a> or at my <a href="https://bookwyrm.social/user/sfmatheson/books" target="_blank">Bookwyrm profile</a>.</div>Stephen Mathesonhttp://www.blogger.com/profile/05057004085073574659noreply@blogger.com0tag:blogger.com,1999:blog-4948885059517209129.post-60095251039832908222023-08-09T21:54:00.011-07:002023-08-10T11:22:03.874-07:00The known unknowns of biology: welcome to the unknome<p></p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi2NNG3bMAsweSTvVy_cMjRH__-SdZTcnwW71sydrz99eVPmmkZtVZYcua9Uj91_HJLwZ6WYRFcVBpYutSfLJH71BRjmpcuDne7m_bJGdLS8jHgm443EMEzxjwvS5ADMfLxLCw_ngQefxwAdNYlS-IiYbQij5AY2GMesiFIIqmIO1L6OflYMdenDtgxAnQ/s1088/Key%20to%20unknowne%20knowledge%20Wellcome.jpg" style="clear: right; float: right; margin-bottom: 1em; margin-left: 1em;"><img border="0" data-original-height="1088" data-original-width="760" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi2NNG3bMAsweSTvVy_cMjRH__-SdZTcnwW71sydrz99eVPmmkZtVZYcua9Uj91_HJLwZ6WYRFcVBpYutSfLJH71BRjmpcuDne7m_bJGdLS8jHgm443EMEzxjwvS5ADMfLxLCw_ngQefxwAdNYlS-IiYbQij5AY2GMesiFIIqmIO1L6OflYMdenDtgxAnQ/w140-h200/Key%20to%20unknowne%20knowledge%20Wellcome.jpg" width="140" /></a></div>'Genome' is now a pretty standard word in our social vocabulary. We have to put up with overloaded metaphors like "blueprint" and reverent talk like "language of god" but it does seem to me that the word is reasonably well understood by laypeople—not as jargony as "gene expression" or as inscrutable as "chromatin." The word was <a href="https://www.npr.org/2010/07/09/128410577/where-the-word-genome-came-from" target="_blank">born in 1920</a> when someone blended 'gene' with 'chromosome'. (The <nobr>-some</nobr> in 'chromosome' is from a root that means 'body' as in 'somatic' or 'psychosomatic'.)<p></p><p>So, a genome is a "body" of genetic material, and specifically the whole body of genetic material in an organism (or a cell or a species). For decades now, science has been regularly adding more <nobr>-omes</nobr>. The proteome is the full body of proteins. The transcriptome the full body of transcripts. It gets a bit weirder: the phenome is the full body of phenotypes. There's even the spliceome, the full body of splice variants. Many of those are pretty jargony; the point is that <nobr>-ome</nobr> is a suffix that's being used a lot like <nobr>-gate</nobr> is used in political news (to indicate a kind of scandal, as in Watergate or Gamergate). Among the <nobr>-omes</nobr> (let's call it the omeome, ha ha!), the best by far is the unknome: the set of all genes of unknown function.</p><p>How big is the unknome? In other words, how many of the 20,000 or so genes in the human genome are unknown (in function)? Is there a gradient of unknown-ness? <a href="https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3002222" target="_blank">A new paper in <i>PLOS Biology</i></a> by Rocha and colleagues introduces us to the unknome and then adds some good stuff, which is the least the authors can do after telling us how little we know about human gene function. <a name='more'></a>(They created a <a href="https://unknome.mrc-lmb.cam.ac.uk/" target="_blank">database</a> where you can surf the unknome and explore our ignorance.) The title and abstract:<p></p><p></p><p></p><blockquote><p>Functional unknomics: Systematic screening of conserved genes of unknown function</p><p>The human genome encodes approximately 20,000 proteins, many still uncharacterised. It has become clear that scientific research tends to focus on well-studied proteins, leading to a concern that poorly understood genes are unjustifiably neglected. To address this, we have developed a publicly available and customisable “Unknome database” that ranks proteins based on how little is known about them. We applied RNA interference (RNAi) in Drosophila to 260 unknown genes that are conserved between flies and humans. Knockdown of some genes resulted in loss of viability, and functional screening of the rest revealed hits for fertility, development, locomotion, protein quality control, and resilience to stress. CRISPR/Cas9 gene disruption validated a component of Notch signalling and 2 genes contributing to male fertility. Our work illustrates the importance of poorly understood genes, provides a resource to accelerate future research, and highlights a need to support database curation to ensure that misannotation does not erode our awareness of our own ignorance.</p></blockquote><p></p><p>One nice feature of the database is an index of known-ness. (The authors call it 'knowness' which just looks wrong to me.) So you can browse/search by knowness and by family of genes and so on. I like that, but then the authors took a big cool step: they generated a list of 260 unknown genes (in human) that seem to be represented in the fruit fly. Using a method called RNA interference that lends itself to large-scale experiments, they interfered with the function of those genes in flies and found a range of effects that are listed in the abstract.</p><p>Their conclusion (from the <a href="https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3002222#sec019" target="_blank">Discussion</a> of the paper):</p><p></p><blockquote>We have developed an approach to tackle directly the huge but under-discussed issue of the large number of well-conserved genes that have no reliably known function, despite the likelihood that they participate in major and even possibly completely new areas of biological function. We hope that our work will inspire others to define and characterise further the unknome and also to seek to ensure that gene annotation has the support and technology to preserve and recognise true ignorance.</blockquote><p></p><p>"Recognise true ignorance" is, I think, their way of pointing to the importance of knowing what we don't know.</p><p>There's another theme here, about how we sometimes seem to prefer to talk about what we don't know and to reach conclusions about that—the origin of life and the so-called Cambrian Explosion are two examples of topics that highlight how much we don't know, and this ignorance can tempt us to think that we can't know how these things work, even in principle. Let's pay attention to the difference between that kind of ignorance and the "true ignorance" that Rocha et al. point to.</p><hr /><p></p><p>Image credit: "<a href="https://wellcomecollection.org/works/vh22ytdj/images?id=d885eq95" target="_blank">The Key to unknowne knowledge. Or, a shop of five windowes ...</a>" 1599. From Wellcome Images, CC-BY 4.0 license.</p><p><br /></p><p><br /></p><p></p>Stephen Mathesonhttp://www.blogger.com/profile/05057004085073574659noreply@blogger.com0tag:blogger.com,1999:blog-4948885059517209129.post-9401531667691273052023-08-08T19:59:00.003-07:002023-09-11T10:46:56.177-07:00Rebel scum<p>This week in the <a href="https://aggronaut.com/2023/07/12/blaugust-2023-is-coming/" target="_blank">Blaugust 2023 blogging festival</a>, the broad theme is "Introduce yourself." Yesterday I <a href="https://sfmatheson.blogspot.com/2023/08/thoughts-on-quintessence-mutation-and.html" target="_blank">alluded to my bardolatry and its place in the cornerstone of <i>Quintessence of Dust</i></a>, but that's not really an introduction. So here is a bit more about me: I love the <i>Star Wars</i> universe and I'm into evolution, and both of those things are deeply connected to my main tendency—I'm a rebel.</p><p></p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjE0tc75Yar_LfhIkoQScYcOb50nY1aUiIgd4hq5bo_QsycEUyPXmY8V1CJs3sxlSdIVSkERAnx44pvDi0J7GaQqfjxtXcWG_AwvtOPCPwUt4YQZacDtXmEnVgQQXsKS8Gyjaup7ALI1crz2ky0QdVMqXX0CUl4PfkNHnCHPowpvN16zzkVgyyj24udP-k/s2500/Rogue%20One%20poster%20from%20StarWars%20dot%20com.jpg" style="clear: right; float: right; margin-bottom: 1em; margin-left: 1em;"><img border="0" data-original-height="2500" data-original-width="1688" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjE0tc75Yar_LfhIkoQScYcOb50nY1aUiIgd4hq5bo_QsycEUyPXmY8V1CJs3sxlSdIVSkERAnx44pvDi0J7GaQqfjxtXcWG_AwvtOPCPwUt4YQZacDtXmEnVgQQXsKS8Gyjaup7ALI1crz2ky0QdVMqXX0CUl4PfkNHnCHPowpvN16zzkVgyyj24udP-k/w135-h200/Rogue%20One%20poster%20from%20StarWars%20dot%20com.jpg" width="135" /></a></div>That might sound romantic and all, but I'm actually being somewhat precise and referring to some useful counsel I got in the past few years as I considered <a href="https://gretchenrubin.com/four-tendencies/" target="_blank">Gretchen Rubin's Four Tendencies</a>. The <a href="https://gretchenrubin.com/quiz/the-four-tendencies-quiz/rebel/" target="_blank">Rebel tendency</a> describes me all too well. I hate being told what to do. I hate being controlled. I hate even <i>suspecting </i>that I'm being controlled. Here's how Rubin captures much of my life: "Telling a Rebel what to do makes them less likely to do it, even if it’s something they <i>want </i>to do."<p></p><p>There are advantages to being a Rebel but big weaknesses as well. Another tagline of the Rebel tendency is this LOLsob-inducing truism: "You can’t make me, and neither can I." So, the perhaps obvious disadvantage is that it can be extra difficult to get tasks done whenever there is a sense that someone or something is ordering it to be done. I'm not lazy; in fact, I work too much. But whenever I sense that someone is telling me what to do, I have to work around my natural instinct to resist their brazen attempt to control me. (Heh.) Otherwise, I'll find ways to not do the task (or meet the obligation, or whatever).</p><p>What are the advantages of that tendency? Are there any? <span></span></p><a name='more'></a>There are two that I see. First, I might be hard to shepherd but that also means I'm hard to manipulate. It's not cynicism so much, it's just my natural aversion to being controlled or feeling like someone else is pulling the strings. Second, I am inherently focused on mission. This is the only way to manage the Rebel tendency: you don't <i>control</i> the Rebel, you <i>unleash</i> her or him in pursuit of a mission. This is how I work and how I lead. I really can't do it any other way.<p></p><p>I think this probably explains in part why I'm a lifelong lover of <i>Star Wars</i>. My two favorite films in the collection are <i>The Empire Strikes Back</i> and <i>Rogue One</i>, both of which are intensely focused on outright rebellion. One of my favorite lines in the whole library belongs to Finn, who answers the taunt "You've always been scum" with an epic callback: "<i>Rebel </i>scum." To me, the heart of the whole <i>Star Wars</i> universe is rebellion and resistance, with a mission. "<a href="https://youtu.be/zVJtP2qYMQ0" target="_blank">Rebellions are built on hope</a>."</p><p><a href="https://media.tenor.com/oyQTHGibGa4AAAAC/finn-rebel-scum.gif" style="clear: right; float: right; margin-bottom: 1em; margin-left: 1em; text-align: center;"><img border="0" data-original-height="202" data-original-width="498" height="130" src="https://media.tenor.com/oyQTHGibGa4AAAAC/finn-rebel-scum.gif" width="320" /></a></p><p>What does this have to do with evolution? Well, evolution breaks the rules. It obliterates crusty old boundaries (between species and every other biological level of separation). It laughs in the face of the Intelligent Designer. It eschews the simple rules and "laws" that so many people believe are the basis of science and the universe. Evolution is rebellion, against the rules, against the status quo, against the past.</p><p><br /></p>Stephen Mathesonhttp://www.blogger.com/profile/05057004085073574659noreply@blogger.com0tag:blogger.com,1999:blog-4948885059517209129.post-60908448521721767982023-08-07T21:58:00.004-07:002023-08-07T21:58:21.396-07:00Thoughts on quintessence, mutation, and evolution<p><a href="https://sfmatheson.blogspot.com/2007/08/why-quintessence-of-dust.html" target="_blank">This blog's name</a> captures my longstanding <a href="https://sfmatheson.blogspot.com/p/about.html" target="_blank">interest in human nature</a>: humans are apes, and animals, and yet somehow able to create music and gods, and sometimes plays like <i>Hamlet</i>. But what's that strange word at the beginning, 'quintessence'? Here's the context from <i>Hamlet</i>:</p><p></p><blockquote><p>What a piece of work is a man, how noble in reason, how infinite in faculties, in form and moving how express and admirable, in action how like an angel, in apprehension how like a god: the beauty of the world, the paragon of animals — and yet, to me, what is this quintessence of dust?</p><p>—Hamlet, Act II, Scene II (Arden Shakespeare)</p></blockquote><p></p><p>The word's history suggests that Shakespeare was (as usual) playing games with words and his audience (all quotes from the <a href="https://www.oed.com/dictionary/quintessence_n?tab=meaning_and_use#27161776" target="_blank">OED</a>):</p><p></p><blockquote><p>a quintessence can be a pure or perfect example of something and/or "The most essential part or feature of some non-material thing" as in "This seems to us the very quintessence of penny wisdom and pound folly in management"</p><p>and quintessence used to refer to a "In classical and medieval philosophy: a fifth essence existing in addition to the four elements, supposed to be the substance of which the celestial bodies were composed and to be latent in all things."</p></blockquote><p></p><p></p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgJd_Iz-nyu6V3GtxvMcE_p9ifdfy2gvqELnEgKIrDdOogMGKpp6iqg6lla28VUSnocyBhxSZu9mxXKzIgqjhxkzGl6jNZdwe6-ki4tiCps32Ys8_BLGVh00YpN4nm98Fh72nI4UGx3KdzmRVtQBXH_McGkn0bx3qEwfiXRRXmWOCetWRRALtyT7M92uKU/s3647/Hamlet%20and%20Guildenstern%20(Smithsonian%20Cooper%20Hewitt).jpg" style="clear: right; float: right; margin-bottom: 1em; margin-left: 1em;"><img border="0" data-original-height="3647" data-original-width="2875" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgJd_Iz-nyu6V3GtxvMcE_p9ifdfy2gvqELnEgKIrDdOogMGKpp6iqg6lla28VUSnocyBhxSZu9mxXKzIgqjhxkzGl6jNZdwe6-ki4tiCps32Ys8_BLGVh00YpN4nm98Fh72nI4UGx3KdzmRVtQBXH_McGkn0bx3qEwfiXRRXmWOCetWRRALtyT7M92uKU/w158-h200/Hamlet%20and%20Guildenstern%20(Smithsonian%20Cooper%20Hewitt).jpg" width="158" /></a></div>So, it seems Hamlet is saying that a human is a pure example of a blob of dust, but perhaps stardust. Either way (or both), he is commenting on what a human is at their core. Not just essence, but <i>quintessence</i>.<p></p><p>I don't know if this is a Western thing (I suspect it is), but essentialism like Hamlet's, in which we assume that a thing (a person, a gender, a gene, a protein, a species) has a definable essence, is a big hindrance to thinking about evolution. <span></span></p><a name='more'></a>Such essences are usually immutable, sometimes by definition.<p></p><p>Now look at that word: immutable. It's about mutation, which is simply change. But that word (mutation) is caught up in ideas and feelings like 'normal' and 'good'. We often (and sometimes explicitly) define a mutation as a harmful change, but even when we're not doing that, we are prone to thinking of mutation as a departure from normal, from "wild type," from a status quo or standard.</p><p>I think that makes it harder for us to think about mutation, and it famously hinders thought about evolution. To a person who thinks that a species (or genus or whatever, it doesn't matter) is a thing, with an essence—the kind of thing about which the ancients wrote "<a href="https://www.biblegateway.com/passage/?search=Genesis%201:23-25&version=NIV" target="_blank">each according to its kind</a>"—evolution is a freakish departure from the way things should work.</p><p>What is the "essence" of a barn owl? Can it change? What is the "essence" of <a href="https://doi.org/10.1073/pnas.1302413110" target="_blank">Nerve Growth Factor</a>? Can it change? Just asking these questions is, to me, flirting with madness. Or at least confusion.</p><p></p><hr /><p>Image credit: "<a href="https://www.si.edu/object/illustration-hamlet-hamlet-and-guildenstern-iii2:chndm_1896-31-103" target="_blank">Illustration for Hamlet: Hamlet and Guildenstern (III,2)</a>," Cooper Hewitt, Smithsonian Design Museum, public domain</p>Stephen Mathesonhttp://www.blogger.com/profile/05057004085073574659noreply@blogger.com0tag:blogger.com,1999:blog-4948885059517209129.post-46071585076763540172023-08-06T17:09:00.006-07:002023-08-06T23:23:20.805-07:00Sky Islands: one of Earth's great evolution laboratoriesLet's think of places on Earth where scientists have done great big natural "experiments" on evolution.<table cellpadding="0" cellspacing="0" class="tr-caption-container" style="float: right;"><tbody><tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhDfXjm0TSAXU70lnd0YqlQW23PB0GyQg_y7ZMGn0BVf0sdO_4CblZtHjkfh0NV9DTvGvOwNVQ4lw424Tb6VkwdbtL5PsFySLRaMODdiMPF1l1dvvDF6m_dOhs8SFO_ZOfK_3Uhd71uHsZ0cjkfQyKyhDaapkYB7OeH56PGz2zA8oQXUOyrISvEPEPOLZo/s4160/IMG_20210202_130423644_HDR.jpg" style="clear: right; margin-bottom: 1em; margin-left: auto; margin-right: auto;"><img border="0" data-original-height="3120" data-original-width="4160" height="150" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhDfXjm0TSAXU70lnd0YqlQW23PB0GyQg_y7ZMGn0BVf0sdO_4CblZtHjkfh0NV9DTvGvOwNVQ4lw424Tb6VkwdbtL5PsFySLRaMODdiMPF1l1dvvDF6m_dOhs8SFO_ZOfK_3Uhd71uHsZ0cjkfQyKyhDaapkYB7OeH56PGz2zA8oQXUOyrISvEPEPOLZo/w200-h150/IMG_20210202_130423644_HDR.jpg" width="200" /></a></td></tr><tr><td class="tr-caption" style="text-align: center;">Looking east from near the top<br />of Mount Lemmon, January 2021</td></tr></tbody></table> Here are some that ought to come to mind (in no particular order other than the first):<div><br /><div>1. The Galapagos Islands, with their famous <a href="https://www.pbs.org/wgbh/evolution/library/01/6/l_016_02.html" target="_blank">finches</a> and their <a href="https://sfmatheson.blogspot.com/2008/05/finches-bah-what-about-darwins-tomatoes.html" target="_blank">less-famous tomatoes</a> and all their <a href="https://en.wikipedia.org/wiki/Marine_iguana" target="_blank">otherworldly animals</a>, probably belong at the top of the list. Mr. Darwin found inspiration there, but the greatest experiments began more than a century later. I can think of few more inspiring stories of great science done by great people than the lifetime-long work of <a href="https://paw.princeton.edu/article/people-who-saw-evolution" target="_blank">Rosemary and Peter Grant</a>. If you haven't yet read <i><a href="https://www.google.com/books/edition/_/hAqW3hA9qBAC?hl=en&sa=X&ved=2ahUKEwi5_szX5ciAAxXmJkQIHfjNA88Qre8FegQIAxAi" target="_blank">The Beak of the Finch</a></i>, get thee to a library or a bookstore.</div><div><br /></div><div>2. The Caribbean islands, and especially the Bahamas, are a fruitful laboratory for the study of the (rapid) evolution of lizards called anoles. <a href="https://www.science.org/content/article/meet-lizard-man-reptile-loving-biologist-tackling-some-biggest-questions-evolution" target="_blank">Jonathan Losos</a> was a major figure in launching and leading that subfield, and his 2017 book <i><a href="https://www.google.com/books/edition/Improbable_Destinies/HJkrDwAAQBAJ?hl=en" target="_blank">Improbable Destinies</a></i> is a great lay-level exploration of evolution and a resounding rebuttal to the random/luck/contingency views associated with Stephen Jay Gould.</div><div><br /></div><div>3. The Hawaiian Islands are home to hundreds of species of fruit fly (many of them are biology's adored <i>Drosophila</i>) and zero species of ant. These hundreds of species have all evolved in the last 25 million years! Check out the <a href="https://www.extavourlab.com/" target="_blank">laboratory of Cassandra Extavour at Harvard</a> for a glimpse into the latest research on the evolution of Hawaiian fruit flies.</div><div><br /></div><div>4. The <a href="https://en.wikipedia.org/wiki/African_Great_Lakes" target="_blank">Great Lakes of East Africa</a> (including Victoria and Tanganyika) hosted one of the most rapid and spectacular adaptive radiations known to humans. <a href="https://www.cell.com/current-biology/fulltext/S0960-9822(07)01704-6" target="_blank">Hundreds (likely thousands) of species of cichlid fish</a> live in these lakes, and all of them were "born" in a blink of evolutionary time.</div><div><br /></div><div>5. The streams of Trinidad are home to guppies, an unremarkable fact until you learn about one of the best-known <a href="https://evolution.berkeley.edu/lines-of-evidence/experiments/" target="_blank">experiments</a> in the history of evolutionary biology. Over many years, research teams led by John Endler and <a href="https://theguppyproject.weebly.com/natural-history-of-trinidadian-fish.html#:~:text=Guppies,that%20can%20be%20easily%20manipulated" target="_blank">David Reznick</a> used this natural laboratory to study natural selection (and other topics) in the wild.</div><div><br /></div><div>There are surely more. But I'm here to tell you about the one that literally surrounds us here in Tucson.<span><a name='more'></a></span></div><div><br /></div><div><br /></div><table cellpadding="0" cellspacing="0" class="tr-caption-container" style="float: right;"><tbody><tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgQvafddwqOONHm3LiG9Lozpll8706svj_V8_xVMGBaV3-KAuan2ozm54bj0xRaa8zr5a-J_CpGYodakXPuiptm4F3RPrpnWsDOoDI7XVMY1DSzg4xEjDtXF0A7M6Jgge8im75jO8zs5Psgc0GoEr-DVDQZ4TsoPRIb8QE9UcLldp5KjOFMuzg7JWV8zYs/s4032/Rincon%20from%20plane.jpg" style="clear: right; margin-bottom: 1em; margin-left: auto; margin-right: auto;"><img border="0" data-original-height="3024" data-original-width="4032" height="150" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgQvafddwqOONHm3LiG9Lozpll8706svj_V8_xVMGBaV3-KAuan2ozm54bj0xRaa8zr5a-J_CpGYodakXPuiptm4F3RPrpnWsDOoDI7XVMY1DSzg4xEjDtXF0A7M6Jgge8im75jO8zs5Psgc0GoEr-DVDQZ4TsoPRIb8QE9UcLldp5KjOFMuzg7JWV8zYs/w200-h150/Rincon%20from%20plane.jpg" width="200" /></a></td></tr><tr><td class="tr-caption" style="text-align: center;">Rincon Mountains,<br />another Sky Island near Tucson</td></tr></tbody></table><div>The 55 <a href="https://skyislandalliance.org/the-sky-islands/" target="_blank">Sky Islands</a> of southern Arizona and northern Sonora are also called the Madrean Archipelago. Note first the emphasis on islands: these are patches of forest ecology perched on top of mountains that rise from deserts. To earn the title of "Sky Island", a mountain must be at least 3000 feet (915 m) tall and host a forest biome (an oak woodland, to be precise). Very near to where I live in Tucson, one of the most impressive Sky Islands rises to 9160 feet (2800 m) from a desert starting point of about 2600 feet (800 m). This is Mount Lemmon, the tallest peak in the Santa Catalina Mountains and the backdrop of Tucson itself.</div><div><br />It's a 45-minute drive from our home to the top of this mountain. That journey traverses eight biomes, beginning with desert scrub and ending at mixed conifer forest. It typically involves a drop of 30 degrees F (from, say 100 to 70) or 17 C (38 to 21 C). Rainfall differs by almost threefold.</div><div><br /></div><table cellpadding="0" cellspacing="0" class="tr-caption-container" style="float: right;"><tbody><tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh-Ky1uZ_iLbmclfmoASpYVZCHLFx18nxHrNMw-_6__LEDH5NZ_faN9Txt6vvSIPBZTT4ixCbg-_fzBg52B5VKHlIKXisxvPMQ9uXiQ3plCUDI6XzTtTV16q3TucLXPj_-kTGWPwidi0JpPtXZP4apU7CGKPxWlqYy23c3k7egeZZHgbqoQWpA6FG7cHMQ/s4032/snow%20catalinas.jpg" style="clear: right; margin-bottom: 1em; margin-left: auto; margin-right: auto;"><img border="0" data-original-height="4032" data-original-width="3024" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh-Ky1uZ_iLbmclfmoASpYVZCHLFx18nxHrNMw-_6__LEDH5NZ_faN9Txt6vvSIPBZTT4ixCbg-_fzBg52B5VKHlIKXisxvPMQ9uXiQ3plCUDI6XzTtTV16q3TucLXPj_-kTGWPwidi0JpPtXZP4apU7CGKPxWlqYy23c3k7egeZZHgbqoQWpA6FG7cHMQ/w150-h200/snow%20catalinas.jpg" width="150" /></a></td></tr><tr><td class="tr-caption" style="text-align: center;">The Santa Catalina Mountains<br />seen from east Tucson</td></tr></tbody></table><div>The Sky Islands are beautiful and interesting, so much so that <a href="https://www.youtube.com/watch?v=ybR8q7o8xWQ&list=PLhu6W2AJYR0zrbvwMHRNgUJ9AmHGGEvUh" target="_blank">I recorded a set of little videos about a journey to Mount Lemmon</a> last fall. But I want to focus on two other little things here.</div><div><br /></div><div>First, the Sky Islands are... islands. That means that populations on these islands are relatively close to each other but isolated from each other by the "ocean" of desert that separates islands. Populations of pine trees, burrowing mammals, or flightless insects are almost completely isolated and are therefore developing and evolving separately. This is what makes any set of islands (like some of those mentioned above) a laboratory to study rapid evolution. So, there are ongoing research programs (like the <a href="https://www.moorearthropods.com/" target="_blank">Moore Lab</a> at the University of Arizona, headed by Prof Wendy Moore) looking at evolution of populations on the various Sky Islands.</div><div><br /></div><div>Second, the Sky Islands can help us see a simple error we might make when we think about natural history, and this error is relevant in my <a href="https://sfmatheson.blogspot.com/search/label/Evolution%20is%20easy" target="_blank">ongoing discussion of how we tend to think that evolution is a lot harder than it is</a>. To reveal this potential error, just consider this question: how did the forests, with their plants and animals (and fungi and bacteria) get to the top of those mountains? We've established that the islands are isolated by desert. It's not hard to understand why a pine forest is happy at 9000 feet/3000 m but that's not the question. <i><b>How did it get there?</b></i></div><div><br /></div><div>The phrasing of the question contributes to its apparent mystery, because by asking it that way I have directed our attention to an active process, maybe some kind of improbable migration between one founder mountain and the others, or maybe the gradual accumulation of quasi-miracles like a pine cone being dropped by an eagle or something like that. The question tempts you to assume that the mountain rose up in the middle of a desert, and somehow a forest then grew there.</div><div><br /></div><div>That's not what happened. The real story is great but it's much less extraordinary: the whole region was previously forested. Then the climate changed, and the region got hotter and drier, and the forests were "trapped" on top of mountains, where they'd always been, but now surrounded by deserts that weren't there before. It's just like the way <a href="https://www.nhm.ac.uk/discover/the-making-of-an-island.html" target="_blank">Great Britain became an island</a>.</div><div><br /></div><div>Maybe the Sky Islands can help us avoid that error when we consider things like <a href="https://sfmatheson.blogspot.com/2023/08/the-library-of-possible-proteins-is.html" target="_blank">proteins in a vast library of possibility</a>. Asking "how did it get there" is potentially misleading.</div><div><br /></div><div>But mostly I hope to write more about the Sky Islands, to visit them more often, and perhaps to get involved in a research project. They're very inspiring!</div><div><br /></div><div><br /></div></div>Stephen Mathesonhttp://www.blogger.com/profile/05057004085073574659noreply@blogger.com0tag:blogger.com,1999:blog-4948885059517209129.post-3223005016650981502023-08-05T16:27:00.004-07:002024-01-27T20:43:42.439-07:00Contemplating libraries in biology. Not that kind. Not that one either.What is a library? If you ask a biologist (especially a molecular biologist) this question, they are likely to ask for clarification. In their work, they are likely to make regular use of two very different kinds of libraries.<div><br /><div></div><div><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjFLMconrRLe8XNuSbBh8cLIR1LNfTqRWKxdGAinkQZ1Lb1X63ToXlkXe0ynOB42yG987b4mjgo2eFHcRbzJyh0xJ3S2jtcqMBsp6h9ip9SXfwchqLlHKExpYONQTl3Dsx3AXJKl5rOFvjwJnZ_63yuo3Xk-Ly4A8W22DjygZS0Bs9DHaN6dIVf72anqJQ/s3332/Bodleian%20library%20public%20domain%20Wellcome.jpg" style="clear: right; float: right; margin-bottom: 1em; margin-left: 1em;"><img border="0" data-original-height="2532" data-original-width="3332" height="152" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjFLMconrRLe8XNuSbBh8cLIR1LNfTqRWKxdGAinkQZ1Lb1X63ToXlkXe0ynOB42yG987b4mjgo2eFHcRbzJyh0xJ3S2jtcqMBsp6h9ip9SXfwchqLlHKExpYONQTl3Dsx3AXJKl5rOFvjwJnZ_63yuo3Xk-Ly4A8W22DjygZS0Bs9DHaN6dIVf72anqJQ/w200-h152/Bodleian%20library%20public%20domain%20Wellcome.jpg" width="200" /></a></div>The first is the kind that we've had for millenia: a collection of books, journals, and media that is <i>ordered and curated</i> by people. These are the OG libraries, with 'book' at the very root of the word. They're rapidly evolving in our digital world, but I think they are still essentially what they've always been. Your friend the molecular biologist may not regularly go to a separate room or building to find materials, but they will use the library often.</div><div><br /></div><div>The second is an extension of the OG concept of a library, but is still called a 'library' by your friend. It contains information, perhaps in vast amounts, but is not ordered or curated. Crucially, it is a specific collection of a particular type of information: genetic information. And while it's neither ordered nor curated, it is <i>physical</i>, and is designed to be searched. The contents of the library might be DNA sequences (genes or even just chunks of some interesting genome) or protein sequences. Unlike your favorite public library, this one doesn't come with a search feature: you have to do that yourself. The process of searching a library is called screening. Your molecular biologist friend can go to the institutional library to read about these kinds of libraries, and find techniques on how to screen one, then perhaps go to a colleague or a vendor to <a href="https://www.addgene.org/crispr/libraries/" target="_blank">obtain a library</a>. Or she will obtain tools to make one herself.</div><div><br /></div><div>In my <a href="https://sfmatheson.blogspot.com/2023/08/the-library-of-possible-proteins-is.html" target="_blank">previous post</a>, I talked of an even more radical extension of the concept of a library: a collection of all the versions of any kind of text (a book, a genome, a set of proteins). <span><a name='more'></a></span>This is a library in the sense that it is a collection, and it could be ordered (alphabetically, for example) but it really can't be curated. In fact, this conception of a library is <i>not</i> curated, and that's the point. These libraries only exist in principle, because they are so incomprehensibly vast that they could not exist physically (the universe isn't nearly big enough).</div><div><br /></div><div>The canonical example of this kind of library is the <a href="https://en.wikipedia.org/wiki/The_Library_of_Babel" target="_blank">Library of Babel</a>. It was conceived in a short story (by Jorge Luis Borges), based on ideas that had existed before. What matters to us here is how the library was "constructed." The author arbitrarily defined a 'book' as a string of text of a particular length. (Information-wise, that's all any book is, if you ignore pictures.) He defined his alphabet as 25 characters. Then he envisioned <i>every single possible combination of those characters in a string of that length</i>. This means, for example, that the library contains the full text of Virginia Woolf's "<a href="https://www.google.com/books/edition/A_Room_of_One_s_Own/858oEyeN1N8C?hl=en" target="_blank">A Room of One's Own</a>," but it also contains a version with all the names changed and a version that ends with <a href="https://www.folger.edu/explore/shakespeares-works/shakespeares-sonnets/read/130/" target="_blank">Sonnet 130</a> (one of those obnoxious "Dark Lady" sonnets), and indescribably many versions with alterations that eventually obliterate the essay entirely. But importantly, the library contains almost exclusively gibberish. Borges' story describes people who navigate this universe looking for meaning. Spoiler alert: most go mad.</div><div><br /></div><div>Such a library is a useful thought experiment in contemplating the universe of possibilities in biology, and especially when considering the universe of possible texts written in DNA or in protein sequences. <a href="https://sfmatheson.blogspot.com/2023/08/the-library-of-possible-proteins-is.html" target="_blank">As I wrote yesterday</a>, Dan Dennett conceived the Library of Mendel, which is just like the Library of Babel but with a different (smaller) alphabet—the DNA alphabet of A,G,T, and C. Then I asked us to consider a library of protein sequences, with an alphabet of 20 letters (the 20 amino acids known to make up the last level of the genetic code). The message of yesterday's post was simply this: <i>all of those libraries are so large that we are tempted to invent new words to somehow communicate their vastness</i>. That vastness, I argue, can mislead us into a sense that evolution, which must explore libraries of indescribable magnitude, is so hard that it is effectively impossible.</div><div><br /></div><div>Now, in yesterday's post I suggested the "Library of Crick" as a name for the protein library, since <a href="https://profiles.nlm.nih.gov/spotlight/sc/feature/defining" target="_blank">Francis Crick was instrumental in unraveling the genetic code</a> (DNA via RNA to the amino acids that make up proteins). But the protein sequence library has <a href="https://www.nature.com/articles/225563a0" target="_blank">already been conceived</a>, by a legendary evolutionary biologist named John Maynard Smith. One of today's legendary evolutionary biologists, <a href="http://fhalab.caltech.edu/" target="_blank">Frances Arnold of Caltech</a>, wrote beautifully about the protein universe, referring to Dennett and Borges, in 2011 in the newsletter of the American Society of Microbiology (ASM). She dubbed this library the Library of Maynard Smith, and that will be its name henceforth.</div><div><br /></div><div>Prof Arnold's essay seems to have been lost when the newsletter (called <i>Microbe</i>) ceased to exist. The ASM site shows a <a href="https://asm.org/a/Microcosm-Digital-Magazine" target="_blank">new newsletter</a> and seems not to have archives of <i>Microbe</i>. I hope I'm wrong, but for now you can find <a href="http://fhalab.caltech.edu/wp-content/uploads/2017/08/Arnold_Microbe2011.pdf" target="_blank">the essay</a> on Prof Arnold's site. I can't tell whether it's licensed to share. The piece mentions that it is "one of a series that are adapted from an upcoming ASM Press book on Darwin, evolution, and microbiology." I haven't seen the book yet but would buy it the second I did!</div><div><br /></div><div><hr /></div><div>Image Credit: "The Bodleian Library, Oxford," Line engraving by J. Le Keux after F. Mackenzie, 1836. From <a href="https://wellcomecollection.org/works/u7xetmy2/images?id=mbrj8865" target="_blank">Wellcome Images</a>, public domain.</div></div>Stephen Mathesonhttp://www.blogger.com/profile/05057004085073574659noreply@blogger.com0tag:blogger.com,1999:blog-4948885059517209129.post-20850926612502407902023-08-04T23:03:00.003-07:002023-08-07T13:57:28.522-07:00The library of possible proteins is beyond vast. Does this cause us to view evolution as harder than it is?<blockquote style="border: none; margin: 0px 0px 0px 40px; padding: 0px; text-align: left;"><p></p><table cellpadding="0" cellspacing="0" class="tr-caption-container" style="float: right;"><tbody><tr><td style="text-align: center;"><a href="https://upload.wikimedia.org/wikipedia/commons/3/3f/Bates_Hall_Boston.jpg" style="clear: right; margin-bottom: 1em; margin-left: auto; margin-right: auto;"><img border="0" data-original-height="711" data-original-width="482" height="200" src="https://upload.wikimedia.org/wikipedia/commons/3/3f/Bates_Hall_Boston.jpg" width="136" /></a></td></tr><tr><td class="tr-caption" style="text-align: center;">Bates Hall at the Boston Public Library</td></tr></tbody></table><p></p></blockquote><p style="text-align: left;">One of the most effective metaphors for evolutionary change is the image of an exploration of a space, perhaps a map that shows "fitness peaks" or, better, a library of possibilities. The philosopher Daniel Dennett, writing in <i><a href="https://www.google.com/books/edition/Darwin_s_Dangerous_Idea/FvRqtnpVotwC?hl=en" target="_blank">Darwin's Dangerous Idea</a></i>, suggested The Library of Mendel as a way of thinking about the total set of possible gene sequences. He was adapting an idea famously employed in a short story by Jorge Luis Borges called "<a href="https://en.wikipedia.org/wiki/The_Library_of_Babel" target="_blank">The Library of Babel</a>," which consists of the total set of possible books of a particular length. (This "library" exists on a <a href="https://libraryofbabel.info/" target="_blank">website</a> designed for creators and researchers.)</p><p>Contemplating a space of possibilities—whether that space consists of books written in English (26 letters), or "books" written in the language of DNA (four letters), or "books" written in the language of protein (20 letters)—is both fun and dizzying. The dizziness is induced (for me, at least) by the vastness of these libraries (Babel or Mendel, doesn't matter). How vast? Here is how Dennett describes the Library of Babel's size (italics are his):</p><p></p><blockquote><p>No <i>actual</i> astronomical quantity (such as the number of elementary particles in the universe, or the amount of time since the Big Bang, measured in nanoseconds) is even visible against the backdrop of these huge-but-finite numbers. If a readable volume in the Library were as easy to find as a particular drop in the ocean, we'd be in business!</p><p>—<i><a href="https://www.google.com/books/edition/Darwin_s_Dangerous_Idea/FvRqtnpVotwC?hl=en" target="_blank">Darwin's Dangerous Idea</a></i>, p. 109</p></blockquote><p></p><p>Dennett then uses <i>Vast</i> to indicate "Very-much-more-than-astronomically" large and <i>Vanishingly</i> small to indicate the likelihood of something like discovering a "volume with so much as a grammatical sentence in it" in the Library. In other words, we lack words to adequately describe the size of the Library and the improbability of randomly discovering anything coherent inside it.<span></span></p><a name='more'></a><p></p><p></p><table cellpadding="0" cellspacing="0" class="tr-caption-container" style="float: right;"><tbody><tr><td style="text-align: center;"><a href="https://www.genome.gov/sites/default/files/media/images/tg/Genetic-code.jpg" style="clear: right; margin-bottom: 1em; margin-left: auto; margin-right: auto;"><img border="0" data-original-height="450" data-original-width="800" height="113" src="https://www.genome.gov/sites/default/files/media/images/tg/Genetic-code.jpg" width="200" /></a></td></tr><tr><td class="tr-caption" style="text-align: center;">The genetic code (from genome.gov)</td></tr></tbody></table>Now let's think about a library that is in fact a subset of the Library of Babel: a library of all possible <i>protein</i> sequences of some length. (Maybe call it the Library of <a href="https://profiles.nlm.nih.gov/spotlight/sc/feature/defining" target="_blank">Crick</a>?)<div><br /></div><div>Since the <a href="http://book.bionumbers.org/how-big-is-the-average-protein/" target="_blank">median length of a human protein</a> is about 400 amino acids, let's choose 1000 as a length (we'll exclude many human proteins but capture perhaps 80%). The size of our alphabet is 20—there are <a href="https://www.genome.gov/genetics-glossary/Genetic-Code" target="_blank">20 amino acids used to build proteins</a>. So the library's size is 20 to the 1000th power. This is Vanishingly smaller than the Library of Babel and the Library of Mendel, but still Vast. It is far larger than the total number of elemental particles in the universe.<p></p><p>And that is the library that evolution has been exploring for the last 4 billion years or so. I don't have the math handy but if you work it out, I think you will find that evolution could not have visited even a Vanishingly small subset of the library. <a href="https://www.cell.com/trends/biotechnology/fulltext/S0167-7799(98)01188-3" target="_blank">One oft-cited paper</a> compared the problem to the "problem" of Deep Blue learning chess moves. </p><p>It would be natural for this kind of reflection to cause us to think—or to feel—that evolution has accomplished something so improbable that it is effectively impossible. That accomplishment: finding and creating (or actualizing) many tens of thousands of functional proteins, some of which are undisputed marvels of design, in a Vast library of possibilities. Following the reasoning applied to the Library of Mendel and the Library of Babel, we reasonably assume that the number of functional proteins in the Library is Vanishingly small. We seem to have every reason to think and feel that evolution is hard, that it accomplishes the effectively impossible.</p><p>But let's think again about that. Do we know that functional proteins are Vanishingly rare? We have one big clear reason to doubt that: in less than a billion years, functional proteins were discovered and put to work running life on earth. This means that evolution found some jumping-off points that it could use to explore the library with some of its famous tools: small change followed by selection. In other words, as reasonable as it is for us to sense that evolution is hard, its success in finding function in the Library of Crick should make us suspect otherwise.</p><p>In fact we have new insights into the Library of Crick, some facts that erode the mythology of a vast library full of useless gibberish. We know that evolution doesn't randomly sample from the library, that its gradual and incremental nature is actually the opposite of a random sampling. But we also now know that the library itself is far richer than we used to think.</p><p>Winning the lottery at the Library of Crick is hard. Change, we all agree, is hard. Evolution is easy.</p><p><br /></p><p></p><p></p><hr />Image credits: Boston Public Library from <a href="https://en.wikipedia.org/wiki/Boston_Public_Library,_McKim_Building#/media/File:Bates_Hall_Boston.jpg" target="_blank">Wikipedia</a>; image copyright ©2005 by Daniel P. B. Smith and released under the terms of the GFDL. Genetic code from <a href="https://www.genome.gov/genetics-glossary/Genetic-Code">Genome.gov.</a></div>Stephen Mathesonhttp://www.blogger.com/profile/05057004085073574659noreply@blogger.com0tag:blogger.com,1999:blog-4948885059517209129.post-5259333939311502412023-08-03T20:48:00.004-07:002023-08-07T13:57:55.902-07:00An extrovert's response to the nightmare of remote work<p>March of 2020 seems a very long time ago. The coronavirus pandemic was roaring to life in the US, and it had arrived in Cambridge, Massachusetts where I lived and worked. I was leading an international team of editors, half of whom worked in the <a href="https://www.cell.com/" target="_blank">Cell Press</a> office in Cambridge near the MIT campus. That month, the goal was to <a href="https://www.npr.org/sections/health-shots/2020/03/13/815502262/flattening-a-pandemics-curve-why-staying-home-now-can-save-lives" target="_blank">flatten the curve</a>, so that our great hospitals and their heroic staffs would not be overwhelmed by COVID patients. There were no vaccines, and we were still wiping down grocery bags because we knew so little about the transmission of the virus. What we knew was that if we stayed away from each other, we would give the virus fewer opportunities to spread. So, early that month, I asked the team to start working from home. About a week later, the whole company moved to working from home.</p><table cellpadding="0" cellspacing="0" class="tr-caption-container" style="float: right;"><tbody><tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhv0QF7UpSxAoWc7tsIelJ1ol0NW7ZOXactXoIvgN7LJ5d3P_SlnfMpILGDm7zAPsioObTMUf4dODjtiRsCQBmaSY5WiTPHyBWx-3R1OUGWDB1MMOe-A5vKLTFudhQTNlOlFQf1JxIrNJQXcOIUICll1A0DebhumgjaROieUOn97ws4aEDB38wSUxRxzrY/s4032/bike%20at%20deer%20island.jpg" style="clear: right; margin-bottom: 1em; margin-left: auto; margin-right: auto;"><img border="0" data-original-height="3024" data-original-width="4032" height="150" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhv0QF7UpSxAoWc7tsIelJ1ol0NW7ZOXactXoIvgN7LJ5d3P_SlnfMpILGDm7zAPsioObTMUf4dODjtiRsCQBmaSY5WiTPHyBWx-3R1OUGWDB1MMOe-A5vKLTFudhQTNlOlFQf1JxIrNJQXcOIUICll1A0DebhumgjaROieUOn97ws4aEDB38wSUxRxzrY/w200-h150/bike%20at%20deer%20island.jpg" title="My bike at Deer Island in Boston" width="200" /></a></td></tr><tr><td class="tr-caption" style="text-align: center;">My bike at Deer Island in Boston</td></tr></tbody></table><p>Long before March 2020, I knew I was something of a unicorn in the world of professional editorial work. My colleagues were (and are) generous and committed and brilliant. I think we all had those things in common. But one thing I didn't share with them was my extroversion. I'm a true extrovert, and as near as I can tell I am one of less than a dozen extroverts in the world who work as a journal editor. I'm joking, but I'm serious when I say that when I became a journal editor more than 10 years ago, I stood out immediately among scores of serious introverts. (True story: our open-concept office had "zones" based on noise level, and I was banned from the quiet area. Not just discouraged. Banned.) And so in March 2020, when there were cute jokes going around about how we could be "heroes" by working from the sofa (Google "couch potatriotism"), I was unamused. Working from home meant that I lost my daily bike ride through Cambridge to a bustling workplace full of my friends and colleagues.<span></span></p><a name='more'></a><p>Later that year, we moved to Tucson, Arizona partly to have more space for what had become a seemingly permanent installation of my office in our home. This solved the space problem (my wife is also a professional and also needs a workspace) but it didn't solve the extroversion problem. I realized over the last three years that I don't just prefer to have other people around. I <i>need</i> it to be at my best. It's not that I want or need someone looking over my shoulder. While it is natural and normal for people to be more effective when they are accountable in a group setting, that wasn't the thing I was missing. I was missing the presence of people, from whom I derive joy and energy. And I was missing the benefits of that bike ride, which is not just good for the heart and muscles—it's a buffer, a separation between work and home and a dedicated time for thought.</p><p>Several months ago, I started in an exciting new job with a <a href="https://plos.org/" target="_blank">great organization</a> that is fully remote, and my closest colleagues are all in the UK. So, not only am I limited to seeing my colleagues on Zoom, I'm 8 hours behind them. After about noon, it gets really quiet. I guess introverts live for that. I don't. What to do?</p><p></p><table cellpadding="0" cellspacing="0" class="tr-caption-container" style="float: right;"><tbody><tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjvKXrevTKl3wb1bWl3ooWKYwNOhWeHS06dAymQEI7bx867hSYRY60l8Fk_kBB0A4AbCuGkxtmkv7noCcmuXwdkVEln8u2c9dhnvgqBi9KoOlJAfem5nKRHwvCg7jQ50NRaMVGbDTH6rMQ6mMCXlMJFJE_f8Ozc4pXDOB3RAmegB6Dfjdxj8B3I_ovr6iA/s4032/bike%20at%20streetcar.jpg" style="clear: right; margin-bottom: 1em; margin-left: auto; margin-right: auto;"><img border="0" data-original-height="4032" data-original-width="2268" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjvKXrevTKl3wb1bWl3ooWKYwNOhWeHS06dAymQEI7bx867hSYRY60l8Fk_kBB0A4AbCuGkxtmkv7noCcmuXwdkVEln8u2c9dhnvgqBi9KoOlJAfem5nKRHwvCg7jQ50NRaMVGbDTH6rMQ6mMCXlMJFJE_f8Ozc4pXDOB3RAmegB6Dfjdxj8B3I_ovr6iA/w113-h200/bike%20at%20streetcar.jpg" width="113" /></a></td></tr><tr><td class="tr-caption" style="text-align: center;">Bike at streetcar stop,<br />temp 110F/43C</td></tr></tbody></table>Our solution is somewhat radical, at least it seems to sound that way to others. I basically recreated the "commute by bike to the office" world that worked so well for me. Every day, I commute to a <a href="https://www.lasupremaworks.com/" target="_blank">great coworking space in downtown Tucson</a>. The space is in a pleasant building that was once a tortilla factory, and bears the name of that tortilla brand: La Suprema. My bike sits safely in a courtyard while I work from a reserved desk. There's coffee and snacks and "huddle rooms" for Zoom calls and there are smart, interesting, energetic professionals sitting nearby. Just like the Cell Press offices in Cambridge. The bike ride is a bit longer, and in the afternoon it's 30 degrees hotter, but it takes me through the <a href="https://www.arizona.edu/about">campus of my beloved alma mater</a>. When the temps reach furnace levels (as they have for the past 2 weeks), I can cut the ride home in half by taking my bike on the <a href="https://www.suntran.com/routes-services/sunlink/" target="_blank">streetcar</a>.<p></p><p>To me, this all feels natural and normal. I'm an extrovert and I love my bike commute and I'm much happier now that my work schedule and environment are more tailored to who I am and how I think and work. The 10.5 mile round trip each day is keeping me young, and the coffee at La Suprema is great. The lesson, I think, is that remote work creates opportunities of various kinds for millions of people. It also creates challenges that we're <a href="https://www.theatlantic.com/newsletters/archive/2023/07/remote-work-return-to-office-policies/674736/" target="_blank">all still trying to work out</a>.</p><p></p><p></p>Stephen Mathesonhttp://www.blogger.com/profile/05057004085073574659noreply@blogger.com0tag:blogger.com,1999:blog-4948885059517209129.post-31904607445226140442023-08-02T19:44:00.004-07:002023-08-03T20:49:39.069-07:00Change is hard. Evolution is Easy. Episode 1 of many.<blockquote><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjvzWpRxCSTeULZMck1-EYKGFZXXNM3s47YnXYg4nRT8yjFezFSA_QZFOpWVE9ndwSV93JghaU6PdMKsBrUc0vRVuwPODCIYlUEoflfHTbeYy-Kn2K6i6QuYAoa2Vbw9bGnEGq1erpwmHq1z1h36h3K_02y7_71qa2dj6fCuuL-gN0mPRWoL08n2awtecA/s512/512px-Miranda_-_The_Tempest_JWW.jpg" style="clear: right; float: right; margin-bottom: 1em; margin-left: 1em;"><img alt="Miranda on a beach in a storm, looking out to sea" border="0" data-original-height="369" data-original-width="512" height="144" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjvzWpRxCSTeULZMck1-EYKGFZXXNM3s47YnXYg4nRT8yjFezFSA_QZFOpWVE9ndwSV93JghaU6PdMKsBrUc0vRVuwPODCIYlUEoflfHTbeYy-Kn2K6i6QuYAoa2Vbw9bGnEGq1erpwmHq1z1h36h3K_02y7_71qa2dj6fCuuL-gN0mPRWoL08n2awtecA/w200-h144/512px-Miranda_-_The_Tempest_JWW.jpg" title="Miranda - The Tempest, by John William Waterhouse (1916), public domain" width="200" /></a></div>ARIEL: Full fathom five thy father lies.<br />Of his bones are coral made.<br />Those are pearls that were his eyes.<br />Nothing of him that doth fade<br />But doth suffer a sea change<br />Into something rich and strange.<br />—<i><a href="https://www.folger.edu/explore/shakespeares-works/the-tempest/read/1/2/#line-1.2.474" target="_blank">The Tempest</a></i>, Act 1, Scene 2</blockquote><p>I do apologize for this dull cliche, but I know I'm right about this: change is hard. I don't mean that it's hard to adapt after someone or something forces a change on you. That's true too, but it's not my topic here. I'm talking about this: you want to change, or you need to change, or both. You know what the change has to be. Maybe you know what the first step has to be. It's change, and it's hard.</p><p>Call it personal growth or self-improvement, or maybe it's habit-breaking or demon-wrestling. Whole libraries could be stocked with materials on how to change. Even when we know we're loved, and believe we're okay, we can see opportunities and challenges that require us to change.</p><p>I won't claim to have deep knowledge of the technical literature on how people manage to change. But I do have several decades of experience in the practice of personal growth and change. I have repeatedly faced my need to change, and one of the first lessons I had to learn was the fact that effecting change is a lot harder than it sounds. It's not that easy to face one's need to change but it's vastly more difficult to make it happen. Change is hard.</p><p>But evolution is easy.<span></span></p><a name='more'></a><p></p><p>Here's what I mean. Evolution (the word means, at its root, "unrolling") is by definition a gradual process. Biologically speaking, even "rapid evolution" means a gradual stepwise process. Whether we are talking about the evolution of language, or the evolution of societies, or the evolution of one person's thought, or the evolution of animal body plans, we are talking about a process that unfolds gradually. We're talking about a process whose individual steps are likely invisible to any observer, and often discernible only in retrospect. In many cases, we're talking about a process that had no defined goal and could have ended in numerous different ways. Whatever else we might say about evolution, we ought to think of it as something that is easier than change. One obvious difference is the pace (gradual, even literally glacial) and another is the smallness of the individual steps. Change still happens, and the magnitude of the change can be extraordinary, but it feels so different. In fact, we might not feel it at all.</p><p>Evolution is easy, but it seems to me that we rarely talk about it that way. We have blind watchmakers and we climb "Mount Improbable." We envision vast and complex landscapes over which the main character (us, or a population, or a molecule, or evolution itself) must randomly "walk" in hopes of discovering a hill of treasure while avoiding or traversing valleys of death. With the help of some busy propaganda mills, we picture our world as a hellscape of lifelessness in which we and our fellow species represent impossible islands of fragile life. It seems to me that we often picture evolution as not merely hard but as effectively impossible.</p><p>Now look, I know that I'm projecting a lot onto you the reader and onto "us" as human thinkers. Maybe you have always thought that evolution was easy. I doubt it. But I'm willing to be a bit presumptuous about what "we" think and feel about evolution because I want to push all of us to think and feel differently about it. I want us to change, or at least to look at the reasons why we think evolution is so hard.</p><p>I think it's a lot easier than you think.</p>Stephen Mathesonhttp://www.blogger.com/profile/05057004085073574659noreply@blogger.com0tag:blogger.com,1999:blog-4948885059517209129.post-47874944952269808902023-08-01T21:46:00.000-07:002023-08-01T21:46:43.167-07:00A blogging festival! I'm in for Blaugust 2023<p>The <a href="https://www.theatlantic.com/technology/archive/2022/11/twitter-facebook-social-media-decline/672074/" target="_blank">messy smelly death of social media</a> is causing a few meaningful losses — most notably damage to or destruction of some online communities that really were valuable. There are some things to lament. <a href="https://www.theatlantic.com/ideas/archive/2022/11/elon-musk-black-twitter-covid-tweets/672093/" target="_blank">Black Twitter</a>, for example, was and is a vibrant and important community. In the Fediverse (aka Mastodon, which is just one part of the Fediverse, but whatever) <a href="https://fediscience.org/@sfmatheson" target="_blank">where I have been camping</a> for several months, I'm listening to and boosting voices that discourage the careless judgment and disparagement of people who want or need to stay with communities in the <a href="https://www.theatlantic.com/technology/archive/2023/07/twitter-x-rebrand-juvenile-internet-style/674875/" target="_blank">corrupt plutocrat's broken toy</a>.</p><p>But I think the world will be much, much better off without social media as we know it, and much better off without <i>anything</i> that is controlled by uberwealthy unreflective talentless techbros. We'll be better off not just because we'll be free of the immense toxicity created by these rapacious dipshits. We'll also have the chance to create — and recreate — ways of conversing and creating and sharing online. Like... blogging!</p><p></p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiLm7u8AfdNO-mRi2Yyav4Ufwe0WeprNSIbaC45X21DbVD493x6Werp2pV26dtQrT9yXmnjxN5KfLeoey6hudTUAw_N1NuAFSJKiC3ZZODnH08OTqbFvxOtSbirF_H0k4hYXsKEPOGrl-v5df9ktcSI7I9mqU3dsi2XNrmLOzsRmBrHjQgomFxWeR275hQ/s1000/blaugust2023-logo-full.webp" imageanchor="1" style="clear: right; float: right; margin-bottom: 1em; margin-left: 1em;"><img border="0" data-original-height="671" data-original-width="1000" height="134" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiLm7u8AfdNO-mRi2Yyav4Ufwe0WeprNSIbaC45X21DbVD493x6Werp2pV26dtQrT9yXmnjxN5KfLeoey6hudTUAw_N1NuAFSJKiC3ZZODnH08OTqbFvxOtSbirF_H0k4hYXsKEPOGrl-v5df9ktcSI7I9mqU3dsi2XNrmLOzsRmBrHjQgomFxWeR275hQ/w200-h134/blaugust2023-logo-full.webp" width="200" /></a></div>Today (almost too late) I learned about <a href="https://aggronaut.com/2023/07/12/blaugust-2023-is-coming/" target="_blank">Blaugust 2023</a>, a delightfully outfitted and long-running (since 2013!) blogging festival, the major goal of which is to motivate people to create. There's a <a href="https://aggronaut.com/blaugchievement-list/" target="_blank">Blaugchievement list</a>, an <a href="https://aggronaut.com/blaugust-prompt-list/" target="_blank">extensive prompt list</a>, a <a href="http://discord.gg/KAXgK2E" target="_blank">Discord server</a>, a dedicated <a href="https://gamepad.club/@blaugust" target="_blank">Mastodon account</a>, and a <a href="https://docs.google.com/spreadsheets/d/1sE2ha9oRAQk3b6EHpsPg9xJUIp9l0OUEKeFCkNUXglc/edit#gid=0" target="_blank">directory</a>. I just signed up for everything! I suggest starting at the <a href="https://aggronaut.com/blaugust-media-kit/" target="_blank">media kit</a>.<p></p><p>The basic goal is to post 31 times in August. I'm already at two! I have some topics lined up but I'll dip into the prompt list as needed, and point to interesting work by other participants. See you tomorrow.</p><p><br /></p>Stephen Mathesonhttp://www.blogger.com/profile/05057004085073574659noreply@blogger.com0tag:blogger.com,1999:blog-4948885059517209129.post-29121050075491706172023-08-01T20:04:00.003-07:002023-08-01T20:06:03.235-07:00What I'm reading in August<p>One motivation for <a href="https://sfmatheson.blogspot.com/2023/01/quintessence-of-dust-2023-restart-what.html" target="_blank">relaunching <i>Quintessence of Dust</i></a> was my desire to write about things I'm reading, whether books or articles. So here is this month's entry in my new series, <b>What I'm reading</b>, posted at the start of every month.
</p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh2OekO0UOGfXYKbzXUwwPPtQaOBq4DkArptCfwv3ZYAbAvsWfnUHC25itlLRIedLv-Ol_ywAN2Jyb8IOnIrj5a5lulN5O-JiagejCI4Kij4Cna9jvXvUVl5Wtm_UpVLWrONPMmGLA7SL2XJB1Ua4escf5Zvo7tgLwUnyzjWU1TLMnyJE1GEyKcTzLi28k/s4032/Aug%202033%20reading.jpg" style="clear: right; float: right; margin-bottom: 1em; margin-left: 1em;"><img border="0" data-original-height="2268" data-original-width="4032" height="113" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh2OekO0UOGfXYKbzXUwwPPtQaOBq4DkArptCfwv3ZYAbAvsWfnUHC25itlLRIedLv-Ol_ywAN2Jyb8IOnIrj5a5lulN5O-JiagejCI4Kij4Cna9jvXvUVl5Wtm_UpVLWrONPMmGLA7SL2XJB1Ua4escf5Zvo7tgLwUnyzjWU1TLMnyJE1GEyKcTzLi28k/w200-h113/Aug%202033%20reading.jpg" width="200" /></a></div><p></p><div><hr /><cr><b>Fiction</b><p><a href="https://us.macmillan.com/books/9781250278555/hester" target="_blank"><i>Hester</i> by Laurie Lico Albanese</a></p></cr></div><blockquote style="border: none; margin: 0px 0px 0px 40px; padding: 0px;"><p>I bought this book in March at the <a href="https://tucsonfestivalofbooks.org/" target="_blank">Tucson Festival of Books</a> after a fascinating event called "She persisted". Even got my copy signed! <a href="https://www.wbur.org/news/2022/10/04/laurie-lico-albanese-hester-book-review" target="_blank">WBUR loved it</a>. I asked the author whether it would matter that I (unlike, I think, everyone else at the event) have never read <i>The Scarlet Letter</i> and was assured that it would not. I'm a little more than halfway through and I love the book. I think I've read actual accounts of the Salem Witch Delusions (I haven't looked up the history to compare with the book's narrative), and I like the cadence of switching between centuries. A recurring theme is <a href="https://doi.org/10.1371/journal.pbio.1001205">synesthesia</a>, which the central character refers to as "the colors," and there are detailed descriptions of needlework that are a bit challenging.</p></blockquote><p> </p><div><hr /><b>Non-fiction</b><p><a href="https://press.princeton.edu/books/hardcover/9780691236544/complicit" target="_blank"><i>Complicit</i> by Max Bazerman</a></p></div><blockquote style="border: none; margin: 0px 0px 0px 40px; padding: 0px;"><p>I <a href="https://sfmatheson.blogspot.com/2023/04/thoughts-on-complicity-before-reading.html" target="_blank">wrote about this book</a> and my experiment (before and after reading). The first chapter was harrowing and introduced me to the term "complicitor" and outlines Bazerman's approach, which is case-based and more "practical" than what philosophers do. I should have known that Aquinas was an original source of instruction on complicity, but I didn't. I'm about halfway through.</p></blockquote><div><p><a href="https://www.google.com/books/edition/A_Humanist_Path/rFG_zgEACAAJ?hl=en" target="_blank"><i>A Humanist Path: Confucius and Lao Zi for Today</i> by Wei Djao</a></p></div><blockquote style="border: none; margin: 0px 0px 0px 40px; padding: 0px;"><p>This book was strongly recommended to me by a friend here in Tucson. My friend has studied with the author, who was partly Tucson-based (and perhaps still is). I'm excited to finally experience the wisdom of these ancient teachers. <a href="https://gingerpostworld.com/?page_id=1239" target="_blank">The publisher's page</a> has a little more information.</p></blockquote><p>You know the ancient struggle between chance and contingency vs. design/structuralism (aka necessity) in evolutionary explanation? How's this for a provocative title of a research paper: "<a href="https://elifesciences.org/articles/67336" target="_blank">Contingency and chance erase necessity in the experimental evolution of ancestral proteins</a>." <span></span></p><a name='more'></a>The abstract:<p></p><p></p><blockquote>The roles of chance, contingency, and necessity in evolution are unresolved because they have never been assessed in a single system or on timescales relevant to historical evolution. We combined ancestral protein reconstruction and a new continuous evolution technology to mutate and select proteins in the B-cell lymphoma-2 (BCL-2) family to acquire protein–protein interaction specificities that occurred during animal evolution. By replicating evolutionary trajectories from multiple ancestral proteins, we found that contingency generated over long historical timescales steadily erased necessity and overwhelmed chance as the primary cause of acquired sequence variation; trajectories launched from phylogenetically distant proteins yielded virtually no common mutations, even under strong and identical selection pressures. Chance arose because many sets of mutations could alter specificity at any timepoint; contingency arose because historical substitutions changed these sets. Our results suggest that patterns of variation in BCL-2 sequences – and likely other proteins, too – are idiosyncratic products of a particular and unpredictable course of historical events.</blockquote><p>This brilliant paragraph comes from the Introduction (emphasis is mine):</p><p></p><blockquote><i><b>The ideal experiment to determine the relative roles of chance, contingency, and necessity in historical evolution would be to travel back in time, re-launch evolution multiple times from each of various starting points that existed during history, and allow these trajectories to play out</b></i> under historical environmental conditions (Gould, 1989). By comparing outcomes among replicates launched from the same starting point, we could estimate the effects of chance; by comparing those from different starting points, we could quantify the effects of contingency that was generated along historical evolutionary paths (Figure 1). Necessity would be apparent if the same outcome recurred in every replicate, irrespective of the point from which evolutionary trajectories were launched and changes that occurred subsequently: in that case, evolution would be both deterministic (free of chance) and insensitive to initial and intervening conditions (noncontingent). <i><b><span style="color: red;">Although time travel is currently impossible</span>, we can approximate this ideal design by reconstructing ancestral proteins as they existed in the deep past (Thornton, 2004) and using them to launch replicated evolutionary trajectories in the laboratory under selection to acquire the same molecular functions that evolved during history.</b></i> </blockquote><p></p><p></p>Stephen Mathesonhttp://www.blogger.com/profile/05057004085073574659noreply@blogger.com0tag:blogger.com,1999:blog-4948885059517209129.post-39892675845500884512023-07-04T20:35:00.006-07:002023-07-04T20:39:53.135-07:00What I'm reading in July<div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj7HNVX6xEgEqmImuUDFYM-dO0w1LZlyjNo5Q2GhymgkO-lL3ru_LOMMJuUx0HUbjwaBB4BdcKkeMg6EfaQSPDpXf9cUOP1EbnZ1nSdnIPpSClLyOVpAt4TCm2h2c2pRluUB6rDfb-IWQRZCyg6JzGkpDI3idmcv2xZkEHcC0NCVAreKrKsCxebG7i5/s4032/PXL_20230305_002323397.jpg" style="clear: right; float: right; margin-bottom: 1em; margin-left: 1em;"><img border="0" data-original-height="4032" data-original-width="3024" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj7HNVX6xEgEqmImuUDFYM-dO0w1LZlyjNo5Q2GhymgkO-lL3ru_LOMMJuUx0HUbjwaBB4BdcKkeMg6EfaQSPDpXf9cUOP1EbnZ1nSdnIPpSClLyOVpAt4TCm2h2c2pRluUB6rDfb-IWQRZCyg6JzGkpDI3idmcv2xZkEHcC0NCVAreKrKsCxebG7i5/w150-h200/PXL_20230305_002323397.jpg" width="150" /></a></div><p>One motivation for <a href="https://sfmatheson.blogspot.com/2023/01/quintessence-of-dust-2023-restart-what.html" target="_blank">relaunching <i>Quintessence of Dust</i></a> was my desire to write about things I'm reading, whether books or articles. So here is this month's entry in my new series, <b>What I'm reading</b>, posted at the start of every month.</p><div><hr /><b>Fiction</b><p><a href="https://us.macmillan.com/books/9781250278555/hester" target="_blank"><i>Hester</i> by Laurie Lico Albanese</a></p></div><blockquote style="border: none; margin: 0px 0px 0px 40px; padding: 0px;"><div><p style="text-align: left;">I bought this book in March at the <a href="https://tucsonfestivalofbooks.org/" target="_blank">Tucson Festival of Books</a> after a fascinating event called "She persisted". Even got my copy signed! <a href="https://www.wbur.org/news/2022/10/04/laurie-lico-albanese-hester-book-review" target="_blank">WBUR loved it</a>. I asked the author whether it would matter that I (unlike, I think, everyone else at the event) have never read <i>The Scarlet Letter</i> and was assured that it would not. Just started (finally).</p></div></blockquote><div><p><a href="https://www.google.com/books/edition/Fragile_Things/NoFHsQiguDIC?hl=en&gbpv=1" target="_blank"><i>Fragile Things</i> by Neil Gaiman</a></p></div><blockquote style="border: none; margin: 0px 0px 0px 40px; padding: 0px;"><div><p style="text-align: left;">Continued from June. I only recently read <i><a href="https://www.google.com/books/edition/_/XpYXARD6BjYC?hl=en&gbpv=1">American Gods</a></i> (I know, I know!) and of course loved it. (I was late to the party but at least I read the "author's preferred text.") My brother's favorite book by Gaiman is <i><a href="https://www.google.com/books/edition/Neverwhere/PqlwZikOXLIC?hl=en&gbpv=1&dq=neverwhere&printsec=frontcover" target="_blank">Neverwhere</a></i>, and I'll get there, but I grabbed this nice collection of stories and poems at <a href="https://bookmans.com/" target="_blank">Bookmans</a> and am almost through.</p></div></blockquote><div><hr /><b>Non-fiction</b><p><a href="https://press.princeton.edu/books/hardcover/9780691236544/complicit" target="_blank"><i>Complicit</i> by Max Bazerman</a></p></div><blockquote style="border: none; margin: 0px 0px 0px 40px; padding: 0px;"><div><p style="text-align: left;">I <a href="https://sfmatheson.blogspot.com/2023/04/thoughts-on-complicity-before-reading.html" target="_blank">wrote about this book</a> and my experiment (before and after reading). The first chapter was harrowing and introduced me to the term "complicitor" and outlines Bazerman's approach, which is case-based and more "practical" than what philosophers do. I should have known that Aquinas was an original source of instruction on complicity, but I didn't.<span></span></p><a name='more'></a><p></p></div></blockquote><div><p><a href="https://www.google.com/books/edition/A_Humanist_Path/rFG_zgEACAAJ?hl=en" target="_blank"><i>A Humanist Path: Confucius and Lao Zi for Today</i> by Wei Djao</a></p></div><blockquote style="border: none; margin: 0px 0px 0px 40px; padding: 0px;"><div><p style="text-align: left;">This book was strongly recommended to me by a friend here in Tucson. My friend has studied with the author, who was partly Tucson-based (and perhaps still is). I'm excited to finally experience the wisdom of these ancient teachers. <a href="https://gingerpostworld.com/?page_id=1239" target="_blank">The publisher's page</a> has a little more information.</p></div></blockquote><p>I <a href="https://sfmatheson.blogspot.com/2023/06/design-without-designer-british.html" target="_blank">recently wrote about</a> two main tendencies (or schools, or emphases) in evolutionary biology: the American interest in diversity and the British interest in design. This distinction seems to roughly parallel another dichotomy based on structuralism and adaptationism. I've never really gotten my head around biological structuralism but I'm very familiar with a lot of the ideas and writing<span style="font-family: Arial; font-size: 11pt; white-space-collapse: preserve;">—</span><a href="https://www.pnas.org/doi/10.1073/pnas.94.20.10750" target="_blank">Gould</a>, <a href="https://www.google.com/books/edition/_/g7vzAgAAQBAJ?hl=en&sa=X&ved=2ahUKEwjj4_HizPb_AhVAJ0QIHYcYBi8Qre8FegQIDxAF" target="_blank">Wagner</a>, <a href="https://books.google.com/books?id=_9NMM9l5FMUC&newbks=0&hl=en&source=newbks_fb" target="_blank">D'Arcy Thompson</a>, they're all in my library). While looking for readings on these concepts and disputes, I found a <a href="https://www.sciencedirect.com/journal/seminars-in-cell-and-developmental-biology/vol/145/suppl/C" target="_blank">special issue of <i>Seminars in Cell & Developmental Biology</i></a> that seems devoted to them and will start with <a href="https://doi.org/10.1016/j.semcdb.2022.02.022" target="_blank">Structuralism and Adaptationism: Friends? Or foes?</a> by Rachael L. Brown. Here's the abstract:</p><p></p><blockquote>Historically, the empirical study of phenotypic diversification has fallen into two rough camps; (1) "structuralist approaches" focusing on developmental constraint, bias, and innovation (with evo-devo at the core); and (2) "adaptationist approaches" focusing on adaptation, and natural selection. Whilst debates, such as that surrounding the proposed "Extended" Evolutionary Synthesis, often juxtapose these two positions, this review focuses on the grey space in between. Specifically, here I present a novel analysis of structuralism which enables us to take a more nuanced look at the motivations behind the structuralist and adaptationist positions. This makes clear how the two approaches can conflict, and points of potential commensurability. The review clarifies (a) the value of the evo-devo approach to phenotypic diversity, but also (b) how it properly relates to other predominant approaches to the same issues in evolutionary biology more broadly.</blockquote><p></p><p> </p>Stephen Mathesonhttp://www.blogger.com/profile/05057004085073574659noreply@blogger.com0tag:blogger.com,1999:blog-4948885059517209129.post-48238959926688354092023-06-06T13:22:00.010-07:002023-06-07T13:44:58.844-07:00Design without a designer: explaining and answering some questionsI've been writing and thinking about design in biology since I started <i>Quintessence of Dust</i>. I want to write and think about it a lot more, so <a href="https://sfmatheson.blogspot.com/2023/06/design-without-designer-british.html" target="_blank">in my last post</a> I introduced my view of the concept and pointed ahead to this post, which consists of edited excerpts from some conversations at a discussion forum at the Peaceful Science site. You will find links to those conversations in the <a href="https://sfmatheson.blogspot.com/2023/06/design-without-designer-british.html" target="_blank">previous post</a>. I have removed people's names and lightly edited for clarity. Other people’s words are indented; the rest are mine.<div><hr /><br /><div><div><blockquote>I would like to understand better how you think about it because it seems quite different from the way I normally think about it. I would really like learn more about how you see it and expand my understanding of "design".</blockquote></div><div>This is a potentially big interesting deep conversation that is worthy of a dedicated thread with some clear goals. Someday I’ll propose that, since I believe that we can improve the quality and tone of conversations about biological design by getting at least some unbelievers to agree that design in biology is an interesting and worthy question that need not and should not have inherent religious overtones.</div><div><br /></div><div>I guess my first question for you as you compare your conception of 'design' to mine is this: do you think design is something that is <i>done</i> (by a designer) or do you think it is something that <i>exists</i> and can be detected by humans? Obviously both can be true, but as long as a person believes that 'design' necessitates a 'designer', then they won’t see design the way I do. Because my view is that design exists whether or not it is linked to a designer. To me, it is axiomatic that a mindless process can generate design, not only because we have seen it happen but because there is no good argument to the contrary. It is instructive, IMO, that the "argument" offered to the contrary is something like "all of our examples of design can be traced back to a mind." This is not even an argument.</div><div><br /></div><div>But what do we mean by 'design'? Here I think we can look at some of the definitions and conceptions offered by the ID movement. I think Behe’s "purposeful arrangement of parts" is a nice start, because it captures something that we all detect when we consider (for example) a molecular machine. Was a bacterial flagellum designed by a designer? I don’t know. Does a bacterial flagellum evince design? To me, the answer is obviously yes. <span><a name='more'></a></span>So, I disagree with many fellow unbelievers (materialists for the most part) who use phrases like "apparent design" or words like 'designoid' to describe the biological world. My view is that design is design. If I see it, I should call it design. This doesn’t imply a designer. That simply doesn’t follow.</div><div><blockquote>How do you manage the distinction between design as a "process of making" vs. "plan or schematic" vs. "product of a designing process"?</blockquote></div><div>I don’t manage that. Those are all conceptions of design, but they’re not what we see when we look at ATP synthase or a flagellum. I think those things are all distractions away from what I (personally) care about, especially since they all assume the presence of a designer.</div><div><blockquote>Is that last one even rightly called design?</blockquote></div><div>Sure, why not? Anyone who believes otherwise would have to claim that the sentence "I see design in this thing" is linguistically incorrect. I can respect that, but then it ends the conversation.</div><div><blockquote>So you are trying to legitimize one understanding of design in its own right, separate from other definitions.</blockquote></div><div>Yes, though I think the work of "legitimizing" this understanding is already done. To reject this use of the word/concept is defensible in principle, but there’s nothing revolutionary about saying "design is detectable without knowledge of a designer."</div><div><blockquote>Seems like the same thing would have to be done with the term "purpose."</blockquote></div><div>Maybe. [shrug]</div><div><blockquote>I don’t think science recognizes design without a model of a designer. So this would be pretty revolutionary.</blockquote></div><div>Science has never spoken on this, since it can’t do that. But scientists have. Here are just a few examples from places I know well.</div><div><a href="https://www.cell.com/molecular-cell/fulltext/S1097-2765(13)00004-X" target="_blank">Design Principles of Regulatory Networks: Searching for the Molecular Algorithms of the Cell</a></div><div><a href="https://www.cell.com/cell/fulltext/S0092-8674(20)30277-4" target="_blank">Defining the Design Principles of Skin Epidermis Postnatal Growth</a></div><div><a href="https://www.cell.com/cell-reports/fulltext/S2211-1247(18)30188-8" target="_blank">Quantitative Operating Principles of Yeast Metabolism during Adaptation to Heat Stress</a></div><div><blockquote>I tend towards notion of "appearance of design," and trying to make sense of what defines that appearance. That is, I think, closely aligned with what you are after.</blockquote></div><div>I don’t see that as closely aligned, because I don’t assume that design requires a designer. "Appearance of design" downgrades ATP synthase to an "appearance" of something I consider obvious. I understand why people do this, and especially why naturalism leads people to do it (that infamous quote about a "divine foot in the door") but I’m with Dan Dennett here. The biological world is overflowing with design. Calling it "apparent" just encourages the madness of attempting to find the "real" design that isn’t just "apparent" design. Does this give some kind of comfort to ID creationists and their propaganda machines? Maybe, but that just means that they didn’t read to the end of the sentence: "…without a designer."</div><div><br /></div><div>But here’s the thought experiment. Suppose I sit down at my supercomputer to predict ways to build a much better version of enzyme Z; let’s even say that my enzyme has a new substrate specificity and is orders of magnitude more stable than enzyme Z. I synthesize the gene and insert it into bacteria. Does this enzyme evince design? Or only apparent design? Is there any way to tell the difference, without knowing that I designed the new enzyme on my supercomputer? Are we going to actually say, "well I can’t tell whether this is design or apparent design until I investigate supercomputer user patterns?"</div><div><br /></div><div>Just a couple of quick thoughts at this point.</div><div style="text-align: left;">🌵In a universe that includes one or more omnipotent gods, it is impossible to argue persuasively that <i>anything</i> came about without a designer, for the straightforward reason that such beings can make anything they want, and make it look any way they want.<br />🌲To me, the fundamental first question is not "can we have design without a designer?" but "does design detection imply knowledge or assumptions about possible designers?" I am saying an emphatic ‘no’ to that question, but one can coherently circumscribe ‘design’ to essentially require the answer to be ‘yes.’ I think that creates problems, which I’ve mentioned above, but it’s coherent and defensible to limit ‘design’ in that way. I will grant that once you answer ‘no’ to the fundamental question then it’s hard (maybe impossible) to answer ‘no’ to the first question.</div><div><blockquote>What would you suggest as terminology for the two cases?</blockquote></div><div>I don’t need any new words and I don’t share the premise of "design implies a designer" with you. I have tried to document the fact that design is a pretty integrated concept in biology, such that many biologists talk about design and design principles with no worry that they will be misunderstood. I’m afraid I don’t see how the concept of design without a designer is either hard to grasp (conceptually) or hard to understand (linguistically).</div><div><br /></div><div>People have tried words like 'designoid' and phrases like 'apparent design.' The subtitle of Dawkins’ <i>The Blind Watchmaker</i> is "Why the Evidence of Evolution Reveals a Universe without Design." I’m well aware that many believers and unbelievers alike are stuck with the word 'design' linked to 'designer'. I have seen only one argument for this approach so far, which is the dictionary. Maybe there are other things going on. But here is Dennett (from <a href="https://www.edge.org/conversation/the-false-allure-of-group-selection#dd" target="_blank">this piece</a>) on one reason why it might not be a good idea to refuse to give ATP synthase the honor of showing design:</div><div><br /></div><div><blockquote>The second misplaced emphasis is Pinker’s phrase 'the illusion of design in the natural world." Richard Dawkins, in a similar vein, says "the illusion of design conjured by Darwinian natural selection is so breathtakingly powerful" in <i>The Ancestors’ Tale</i> (p 457), and elsewhere proposes to speak of "designoid" features of the natural world (eg., <i>Climbing Mount Improbable</i>, p 4). I disagree with this policy, which can backfire badly. I recently overheard a conversation among some young people in a bar about the marvels of the nano-machinery discovered inside all cells. "When you see all those fantastic little robots working away, how can you possibly believe in evolution!" one exclaimed, and another nodded wisely. Somehow these folks had gotten the impression that evolutionary biologists thought that the intricacies and ingenuities of life’s processes weren’t all that wonderful. These evolution-doubters were not rednecks; they were Harvard Medical students! They hugely underestimated the power of natural selection because they had been told by evolutionary biologists, again and again, that there is no actual design in nature, only the appearance of design. This episode strongly suggested to me that one of the themes that has been gaining ground in "common knowledge" is that evolutionary biologists are reluctant to "admit" or "acknowledge" the manifest design in nature. I recommend instead the expository policy of calling nature’s marvels design, as real as any design in the universe, but just not the products of an intelligent designer.</blockquote></div><div>You can read how Dennett describes design <a href="https://books.google.com/books?id=PEp8DAAAQBAJ&lpg=PP1&pg=PT46#v=onepage&q&f=false" target="_blank">here</a>, in his recent cool book <i>From Bacteria to Bach and Back</i>.</div><div><br /></div><div>Biology shows design. I don’t think that’s confusing or unclear, and I think it’s a mistake to make distinctions based on old dictionaries. YMMV.</div><div><br /></div></div></div>Stephen Mathesonhttp://www.blogger.com/profile/05057004085073574659noreply@blogger.com0tag:blogger.com,1999:blog-4948885059517209129.post-54058357307793853732023-06-06T12:44:00.003-07:002023-08-07T14:04:13.463-07:00Design without a designer: the "British tendency" and introductionOne of the most interesting books I've read in the last few years was <i><a href="https://global.oup.com/academic/product/the-genes-eye-view-of-evolution-9780198862260?cc=us&lang=en&" target="_blank">The Gene's-Eye View of Evolution</a></i> by <a href="https://arvidagren.com/about-2/" target="_blank">J. Arvid Ågren</a>. The author explains the gene's-eye view both scientifically and historically, and I hope to write about the book sometime soon. But for now there's one point he makes that I found fascinating. Citing Kim Sterelny (an Australian philosopher of science who has written on personalities in evolutionary biology, esp. Gould vs. Dawkins), he identifies two major emphases (<a href="https://www.google.com/books/edition/The_Evolution_of_Agency_and_Other_Essays/Fx7JTzcbBosC?hl=en&gbpv=1" target="_blank">Sterelny calls them "tendencies"</a>) in evolutionary biology: the American interest in diversity and the British interest in design. These are pretty crude distinctions, at least because examplars of the "British tendency" include Americans like Dan Dennett. But the point is that one of two major streams of thought in evolutionary science is the challenge Paley made famous and that inspired Darwin<span id="docs-internal-guid-cb95b673-7fff-2235-b63e-bcae1e12b210"><span style="font-family: Arial; font-size: 11pt; font-variant-alternates: normal; font-variant-east-asian: normal; font-variant-numeric: normal; vertical-align: baseline; white-space: pre-wrap;">—</span></span>the one that inspired <i><a href="https://www.google.com/books/edition/The_Blind_Watchmaker/sPpaZnZMDG0C?hl=en" target="_blank">The Blind Watchmaker</a></i> and its author. It's the challenge of explaining design in the biological world, and the most notable characters in that story are Brits from three very different generations.<div><br /><div><table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto;"><tbody><tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg_3Fu8zrmxLGFEbHBfpSJ7WBamQr2vfhH0DxuEN43JXax46IEHcWiCMEBBNWN1sNshEhA41WWENMVzw8LT_1jIF7Jq3pfXq2IFapupCOQsJELkmVxHyGoj6_tvmWi5EfJ7tHgETfrBc5oiExExr1mdf-JZGHtPi5RI1jTUMivg-rBocqgdOOxuyGYZ/s2074/TFF%20superfamily%20PLOS%20Biol%202019%20--%20cropped%20to%20diagrams.png" style="margin-left: auto; margin-right: auto;"><img border="0" data-original-height="417" data-original-width="2074" height="80" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg_3Fu8zrmxLGFEbHBfpSJ7WBamQr2vfhH0DxuEN43JXax46IEHcWiCMEBBNWN1sNshEhA41WWENMVzw8LT_1jIF7Jq3pfXq2IFapupCOQsJELkmVxHyGoj6_tvmWi5EfJ7tHgETfrBc5oiExExr1mdf-JZGHtPi5RI1jTUMivg-rBocqgdOOxuyGYZ/w400-h80/TFF%20superfamily%20PLOS%20Biol%202019%20--%20cropped%20to%20diagrams.png" width="400" /></a></td></tr><tr><td class="tr-caption" style="text-align: center;">Schematic representations of the type IV filament superfamily of nanomachines, from Figure 1 of Denise et al. 2019</td></tr></tbody></table><br /><div><div>I'm not British (I'm just a wannabe) but I'm drawn to that question too. My interest is probably partly due to my time served as a Christian believer, since the Christian god is a common unworthy beneficiary of the curiosity and wonder that nature inspires in humans. I have always objected to the whole construction: we see cool and extraordinary stuff in nature, we don't seem to have an explanation, so we turn to a god as an "answer." Nothing about those stories appealed to me, not when I was a committed believer and not now that I am an emancipated apostate. One problem, that I've mentioned before, is that I am apparently of the British tendency: I see the design, and I want to <b>explain</b> it. Design is the question, and not the answer to any interesting question. Design is what I see. I don't need a religious apologist to convince me that it exists.<span><a name='more'></a></span></div><div><br /></div><div>The figure above is an example of the kind of design I see. The diagrams depict various members of a superfamily of protein-based machines (that's the word used by the authors in the <b>title</b> of <a href="https://doi.org/10.1371/journal.pbio.3000390" target="_blank">the 2019 <i>PLOS Biology</i> paper in which the figure appears</a>). This is the type IV filament (TFF) superfamily and it includes components related to (in fact, derived from) the <a href="https://doi.org/10.1016/j.cub.2007.05.003" target="_blank">bacterial flagella of Intelligent Design fame</a>. A commentary on the 2019 <i>PLOS Biology</i> paper is titled "<a href="https://doi.org/10.1371/journal.pbio.3000405" target="_blank">Evolution of a family of molecular Rube Goldberg contraptions</a>." Machines! <b>Contraptions!</b> That's the language of design, and I think it's perfect.</div><div><br /></div><div>But I know that "design without a designer" is hard for many people to process. It seems wrong.</div><div><br /></div><div>A few years ago, I was a regular participant in discussions at Peaceful Science, a <a href="https://peacefulscience.org/" target="_blank">website</a> and <a href="https://discourse.peacefulscience.org/" target="_blank">discussion forum</a> built around the ideas of <a href="https://peacefulscience.org/authors/swamidass/" target="_blank">Joshua Swamidass</a>. <a href="https://discourse.peacefulscience.org/t/how-to-have-a-fruitful-and-respectful-conversation/11131/1" target="_blank">In one thread</a>, I mentioned the design-without-a-designer concept in response to a typically confused Christian. Others started asking for more detail, <a href="https://discourse.peacefulscience.org/t/design-without-a-designer/11227" target="_blank">spawning a second thread</a> about my position on design that gave me a chance to answer questions and write some organized thoughts.</div><div><br /></div><div>I've taken my writing on that thread and excerpted it with some editing to make the questions (from others) a bit clearer and to remove people's names. The intent is not to protect identities, since the whole discussion is public<span id="docs-internal-guid-ff74568c-7fff-285e-a204-4b9eb643ea15"><span style="font-family: Arial; font-size: 11pt; font-variant-alternates: normal; font-variant-east-asian: normal; font-variant-numeric: normal; vertical-align: baseline; white-space: pre-wrap;">—</span></span>the goal is just to provide a clear and somewhat smoothly-flowing discussion of the question. That question is: what does it mean to talk of design without a designer?</div><div><br /></div><div>That's for the next post.</div></div></div><div><br /></div><div><hr />Image credit: Revised (cropped) from <a href="https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3000390" target="_blank">Figure 1</a> of <a href="https://doi.org/10.1371/journal.pbio.3000390" target="_blank">Diversification of the type IV filament superfamily into machines for adhesion, protein secretion, DNA uptake, and motility</a> by Denise et al., <i>PLOS Biology</i> (2019).</div></div>Stephen Mathesonhttp://www.blogger.com/profile/05057004085073574659noreply@blogger.com0tag:blogger.com,1999:blog-4948885059517209129.post-9495230159984968302023-06-04T11:01:00.003-07:002023-07-04T20:40:33.302-07:00What I'm reading in June<div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj7HNVX6xEgEqmImuUDFYM-dO0w1LZlyjNo5Q2GhymgkO-lL3ru_LOMMJuUx0HUbjwaBB4BdcKkeMg6EfaQSPDpXf9cUOP1EbnZ1nSdnIPpSClLyOVpAt4TCm2h2c2pRluUB6rDfb-IWQRZCyg6JzGkpDI3idmcv2xZkEHcC0NCVAreKrKsCxebG7i5/s4032/PXL_20230305_002323397.jpg" style="clear: right; float: right; margin-bottom: 1em; margin-left: 1em;"><img border="0" data-original-height="4032" data-original-width="3024" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj7HNVX6xEgEqmImuUDFYM-dO0w1LZlyjNo5Q2GhymgkO-lL3ru_LOMMJuUx0HUbjwaBB4BdcKkeMg6EfaQSPDpXf9cUOP1EbnZ1nSdnIPpSClLyOVpAt4TCm2h2c2pRluUB6rDfb-IWQRZCyg6JzGkpDI3idmcv2xZkEHcC0NCVAreKrKsCxebG7i5/w150-h200/PXL_20230305_002323397.jpg" width="150" /></a></div>One motivation for <a href="https://sfmatheson.blogspot.com/2023/01/quintessence-of-dust-2023-restart-what.html" target="_blank">relaunching <i>Quintessence of Dust</i></a> was my desire to write about things I'm reading, whether books or articles. So here is this month's entry in my new series, <b>What I'm reading</b>, posted at the start of every month.<div><hr /><b>Fiction</b><p><a href="https://www.google.com/books/edition/Tomorrow_and_Tomorrow_and_Tomorrow/JrpHEAAAQBAJ?hl=en" target="_blank"><i>Tomorrow, and Tomorrow, and Tomorrow</i> by Gabrielle Zevin</a></p><p>Recommended by colleagues on our PLOS Slack channel and in a <a href="https://www.npr.org/2022/07/28/1114196664/video-game-novel-tomorrow-and-tomorrow-and-tomorrow-gabrielle-zevin" target="_blank">great review at NPR</a>. Plus, as a bardolator I am doctrinally obligated to read a book with a title like that. I'm deliberately reading the last few chapters slowly; this is something I do when I love a book so much that I don't want it to end.<span></span></p><p><a href="https://us.macmillan.com/books/9781250278555/hester" target="_blank"><i>Hester</i> by Laurie Lico Albanese</a></p><p>I bought this book in March at the <a href="https://tucsonfestivalofbooks.org/" target="_blank">Tucson Festival of Books</a> after a fascinating event called "She persisted". Even got my copy signed! <a href="https://www.wbur.org/news/2022/10/04/laurie-lico-albanese-hester-book-review" target="_blank">WBUR loved it</a>. I asked the author whether it would matter that I (unlike, I think, everyone else at the event) have never read <i>The Scarlet Letter</i> and was assured that it would not. I'll start as soon as I finish <i>Tomorrow, and Tomorrow, and Tomorrow</i>.</p><p><a href="https://www.google.com/books/edition/Fragile_Things/NoFHsQiguDIC?hl=en&gbpv=1" target="_blank"><i>Fragile Things</i> by Neil Gaiman</a></p><p>Continued from May. I only recently read <i><a href="https://www.google.com/books/edition/_/XpYXARD6BjYC?hl=en&gbpv=1">American Gods</a></i> (I know, I know!) and of course loved it. (I was late to the party but at least I read the "author's preferred text.") My brother's favorite book by Gaiman is <i><a href="https://www.google.com/books/edition/Neverwhere/PqlwZikOXLIC?hl=en&gbpv=1&dq=neverwhere&printsec=frontcover" target="_blank">Neverwhere</a></i>, and I'll get there, but I grabbed this nice collection of stories and poems at <a href="https://bookmans.com/" target="_blank">Bookmans</a> and am almost through.</p><hr /><b>Non-fiction</b><p><a href="https://press.princeton.edu/books/hardcover/9780691236544/complicit" target="_blank"><i>Complicit</i> by Max Bazerman</a></p><p>I <a href="https://sfmatheson.blogspot.com/2023/04/thoughts-on-complicity-before-reading.html" target="_blank">wrote about this book</a> and my experiment (before and after reading). The first chapter was harrowing and introduced me to the term "complicitor."</p><p><a href="https://www.google.com/books/edition/A_Humanist_Path/rFG_zgEACAAJ?hl=en" target="_blank"><i>A Humanist Path: Confucius and Lao Zi for Today</i> by Wei Djao</a></p><p>This book was strongly recommended to me by a friend here in Tucson. My friend has studied with the author, who was partly Tucson-based (and perhaps still is). I'm excited to finally experience the wisdom of these ancient teachers. <a href="https://gingerpostworld.com/?page_id=1239" target="_blank">The publisher's page</a> has a little more information.</p></div>Stephen Mathesonhttp://www.blogger.com/profile/05057004085073574659noreply@blogger.com0tag:blogger.com,1999:blog-4948885059517209129.post-66397984259154337642023-05-31T18:47:00.005-07:002023-05-31T18:47:41.594-07:00Beshrew my heart but I pity the man. Final reflections on From Extraterrestrials to Animal Minds by Simon Conway Morris<p>I've reviewed a few books over the years here at <i>Quintessence of Dust</i>, but <i><a href="https://www.google.com/books/edition/From_Extraterrestrials_to_Animal_Minds/xwZXEAAAQBAJ?hl=en&gbpv=1&dq=extraterrestrials+animal+minds&printsec=frontcover" target="_blank">From Extraterrestrials to Animal Minds: Six Myths of Evolution</a></i> by Simon Conway Morris was the first book I blogged through that I was genuinely excited about reading. I bought it sight unseen, new and in hardcover, from a publisher of dubious reputation, because I was beguiled by the author and the title and what I mistakenly believed that title to mean. I have already written that <a href="https://sfmatheson.blogspot.com/2023/05/confusion-and-convergence-but-no-myth.html" target="_blank">I regretted paying money for the book</a> once I read the first couple of chapters and realized I'd been had. <i>From Extraterrestrials to Animal Minds</i> isn't about myths, nor is it about interesting controversies, and its ideas/claims are mostly recycled from previous works by the author. In retrospect, the book didn't merit the attention I gave it, and it doesn't merit yours.</p><p></p><table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto;"><tbody><tr><td style="text-align: center;"><a href="https://pics.filmaffinity.com/William_Shakespeare_s_a_Midsummer_Night_s_Dream-872517850-large.jpg" style="margin-left: auto; margin-right: auto;"><img border="0" data-original-height="342" data-original-width="800" height="137" src="https://pics.filmaffinity.com/William_Shakespeare_s_a_Midsummer_Night_s_Dream-872517850-large.jpg" width="320" /></a></td></tr><tr><td class="tr-caption" style="text-align: center;">David Strathairn and Sophie Marceau as Theseus and Hippolyta in A Midsummer Night's Dream (1999)</td></tr></tbody></table><br />But that doesn't mean I regret the exercise as a whole. Writing my way through the book helped me clarify some of my own thoughts and ideas. So this post is as much about me and my ideas as it is about the book.<p></p><p><span></span></p><a name='more'></a>🌵 Reading about evolutionary convergence again<span style="font-family: Arial; font-size: 11pt; white-space: pre-wrap;">—</span>and specifically reading Conway Morris as he enthused chaotically about the latest examples of convergence<span style="font-family: Arial; font-size: 11pt; white-space: pre-wrap;">—</span>reinforced my deep interest in <a href="https://doi.org/10.1073/pnas.0904433106" target="_blank">Design Space</a>. Evolution is (among other things) an exploration of Design Space, and I share with Dan Dennett a desire to explore<span style="font-family: Arial; font-size: 14.6667px; white-space: pre-wrap;">—</span>not avoid<span style="font-family: Arial; font-size: 14.6667px; white-space: pre-wrap;">—</span><a href="https://www.google.com/books/edition/From_Bacteria_to_Bach_and_Back_The_Evolu/PEp8DAAAQBAJ?hl=en&gbpv=1&dq=dennett%20%22why%20shrink%20from%20the%20pedagogical%20task%22&pg=PT49&printsec=frontcover" target="_blank">what it means to see design in the biological world</a>. Evolutionary convergence, to me, is a clear picture of a process that is guided by design. <a href="https://www.edge.org/conversation/the-false-allure-of-group-selection#dd" target="_blank">Design does not require a designer</a>. That claim, by the way, simply does not mean that there isn't a designer or a god or a million of them. It means that design is a question, not an answer.<p></p><p>It's hard to tell whether Conway Morris agrees with that last part (about the necessity of a designer). <i>From Extraterrestrials to Animal Minds</i> ends in a Funhouse of the Paranormal but is otherwise vague about whether a deity is loading the dice. What is clear to me is that the author wants evolution to sit in a wacky supernatural cosmic tableau, and I think (but I'm still unsure) that his choices to propound "rebuttals" to non-issues like "no limits" and to shallow misconstruals of "random" suggest that he seeks to infuse the world with supernatural nonsense. I don't care about his preference for haunted worlds, but I was shocked and disappointed to see how eager he was to twist science and to sneer at his non-religious colleagues who do the work. Selfishly, I'm keen to explore design and evolution with a religious person, and I am lucky enough to have other places I can do that. Simon Conway Morris is not qualified.</p><p>👎 The book has a discernible trajectory that makes it even less worthy of consideration, in my view. Consider that the last two chapters<span style="font-family: Arial; font-size: 14.6667px; white-space: pre-wrap;">—</span>one a <a href="https://sfmatheson.blogspot.com/2023/05/a-gruesome-autopsy-of-chapter-5-of-from.html" target="_blank">misleading crapfest about non-human animal minds</a> and the other a <a href="https://sfmatheson.blogspot.com/2023/05/do-not-infest-your-mind-with-beating-on.html" target="_blank">shambling entrance to paranormal woo</a><span style="font-family: Arial; font-size: 14.6667px; white-space: pre-wrap;">—</span>are in the title. If (and this is a guess) the goal was to get us there, then the silly stuff that came before<span style="font-family: Arial; font-size: 14.6667px; white-space: pre-wrap;">—</span>the <a href="https://sfmatheson.blogspot.com/2023/04/superheroes-and-nonexistent-myth-of-no.html" target="_blank">non-myth of no limits</a>, the <a href="https://sfmatheson.blogspot.com/2023/05/confusion-and-convergence-but-no-myth.html" target="_blank">red herrings about randomness</a>, the <a href="https://sfmatheson.blogspot.com/2023/05/missing-links-are-myth-but-whose.html" target="_blank">odd little chapter about missing links</a><span style="font-family: Arial; font-size: 14.6667px; white-space: pre-wrap;">—</span>served some kind of purpose in the author's mind. Even the <a href="https://sfmatheson.blogspot.com/2023/05/mass-extinction-as-acceleration-chapter.html" target="_blank">good chapter about mass extinctions</a> looks different from the vantage point of the last two chapters. He (er, Mortimer) <a href="https://sfmatheson.blogspot.com/2023/04/reviewing-from-extraterrestrials-to.html" target="_blank">says the book is about confronting "received wisdom"</a> but I'm not convinced this was ever the aim. One possibility is that Conway Morris is more interested in the paranormal portals of the final chapter than he is in evolution itself, and so he sought to downgrade evolution to something pedestrian and prefigured. I might be very wrong about that, but the book made little sense to me otherwise.</p><p>🎭 And now I should explain this post's title. I felt bad about not letting Hippolyta give the benediction in <a href="https://sfmatheson.blogspot.com/2023/05/do-not-infest-your-mind-with-beating-on.html" target="_blank">the post on the final chapter</a>, so she gets the final word. The context is yet another play-within-a-play, this time the presentation of the "rude mechanicals" at the end of <i><a href="https://www.folger.edu/explore/shakespeares-works/a-midsummer-nights-dream/read/" target="_blank">A Midsummer Night's Dream</a></i>. Her point (and mine) is that the acting is so bad that she has moved from scorn ("This is the silliest stuff that ever I heard") to pity. Bottom the Weaver, as Pyramus, has just completed a hilariously histrionic speech. I don't suggest that <i>From Extraterrestrials to Animal Minds</i> is nearly as funny as Pyramus, or that we should mock it the way Theseus heckles Bottom. But I did think the whole thing sad enough to end with this:</p><p></p><blockquote><p>THESEUS: This passion, and the death of a dear friend,<br />would go near to make a man look sad.<br />HIPPOLYTA: Beshrew my heart but I pity the man.</p><p><span style="font-family: Arial; font-size: 14.6667px; white-space: pre-wrap;">—</span><a href="https://www.folger.edu/explore/shakespeares-works/a-midsummer-nights-dream/read/5/1/#line-5.1.303" target="_blank">A Midsummer Night's Dream, Act 5, Scene 1</a></p></blockquote><p><br /></p><p><a href="https://www.folger.edu/explore/shakespeares-works/a-midsummer-nights-dream/read/5/1/#line-5.1.303" target="_blank"></a></p><hr />Image credit: <a href="https://www.filmaffinity.com/us/filmimages.php?movie_id=713806">Filmaffinity</a>Stephen Mathesonhttp://www.blogger.com/profile/05057004085073574659noreply@blogger.com0tag:blogger.com,1999:blog-4948885059517209129.post-56617535806905490192023-05-30T19:28:00.011-07:002023-06-01T08:59:34.218-07:00Reviewing From Extraterrestrials to Animal Minds by Simon Conway Morris: Full series<p></p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhAjd2XaVxT4cJieR3PE_IaQ_MguQM1_8fad2RJCUa6ngOIGfx847s90l0dcXTZfTVc403aqzq36rpsxfCdt_-y5HQbrw57qqGRKR1IdZOFGVU1dGkPsJz1bok-B43eTx51F8QlQG-4gHfZc7xFfaIUpZ7Kic96BHtdFo057roE_Ft4ZWV8dX6owyKR/s1920/SixMythsCover.jpeg" style="clear: right; float: right; margin-bottom: 1em; margin-left: 1em;"><img border="0" data-original-height="1920" data-original-width="1280" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhAjd2XaVxT4cJieR3PE_IaQ_MguQM1_8fad2RJCUa6ngOIGfx847s90l0dcXTZfTVc403aqzq36rpsxfCdt_-y5HQbrw57qqGRKR1IdZOFGVU1dGkPsJz1bok-B43eTx51F8QlQG-4gHfZc7xFfaIUpZ7Kic96BHtdFo057roE_Ft4ZWV8dX6owyKR/w133-h200/SixMythsCover.jpeg" width="133" /></a></div>Full series on <i><a href="https://www.google.com/books/edition/From_Extraterrestrials_to_Animal_Minds/xwZXEAAAQBAJ?hl=en&gbpv=1&dq=extraterrestrials+animal+minds&printsec=frontcover" target="_blank">From Extraterrestrials to Animal Minds: Six Myths of Evolution</a></i> by Simon Conway Morris.<p></p><p><a href="https://sfmatheson.blogspot.com/2023/04/reviewing-from-extraterrestrials-to.html" target="_blank">Introduction and overview</a></p><p>Chapter 1: The Myth of No Limits <span style="font-family: Arial; font-size: 11pt; white-space: pre-wrap;">—</span> <a href="https://sfmatheson.blogspot.com/2023/04/superheroes-and-nonexistent-myth-of-no.html" target="_blank">Part 1</a> <span style="font-family: Arial; font-size: 11pt; white-space: pre-wrap;">—</span> <a href="https://sfmatheson.blogspot.com/2023/04/superheroes-and-limits-more-on-chapter.html" target="_blank">Part 2</a></p><p><a href="https://sfmatheson.blogspot.com/2023/05/confusion-and-convergence-but-no-myth.html" target="_blank">Chapter 2: The Myth of Randomness</a></p><p><a href="https://sfmatheson.blogspot.com/2023/05/mass-extinction-as-acceleration-chapter.html" target="_blank">Chapter 3: The Myth of Mass Extinctions</a></p><p><a href="https://sfmatheson.blogspot.com/2023/05/missing-links-are-myth-but-whose.html" target="_blank">Chapter 4: The Myth of Missing Links</a></p><p>Chapter 5: The Myth of Animal Minds — <a href="https://sfmatheson.blogspot.com/2023/05/the-author-doth-protest-too-much.html" target="_blank">Part 1</a> — <a href="https://sfmatheson.blogspot.com/2023/05/a-gruesome-autopsy-of-chapter-5-of-from.html" target="_blank">Part 2</a></p><p><a href="https://sfmatheson.blogspot.com/2023/05/do-not-infest-your-mind-with-beating-on.html" target="_blank">Chapter 6: The Myth of Extraterrestrials</a></p><p><a href="https://sfmatheson.blogspot.com/2023/05/beshrew-my-heart-but-i-pity-man-final.html" target="_blank">Final comments and reflections</a></p>Stephen Mathesonhttp://www.blogger.com/profile/05057004085073574659noreply@blogger.com0tag:blogger.com,1999:blog-4948885059517209129.post-3630732805388395632023-05-29T22:34:00.011-07:002023-06-19T10:12:43.690-07:00Do not infest your mind with beating on the strangeness of this business. Chapter 6 of From Extraterrestrials to Animal Minds<blockquote><p>ALONSO: This is as strange a maze as e’er men trod,<br />And there is in this business more than nature<br />Was ever conduct of. Some oracle<br />Must rectify our knowledge.</p><p><span style="font-family: Arial; font-size: 11pt; white-space: pre-wrap;">—</span><a href="https://www.folger.edu/explore/shakespeares-works/the-tempest/read/5/1/#line-5.1.293" target="_blank"><i>The Tempest</i>, Act 5, Scene 1</a> </p><p></p></blockquote><p></p><p></p><div class="separator" style="clear: both; text-align: center;"><a href="https://upload.wikimedia.org/wikipedia/commons/6/6a/William_Hamilton_Prospero_and_Ariel.jpg" style="clear: right; float: right; margin-bottom: 1em; margin-left: 1em;"><img border="0" data-original-height="764" data-original-width="543" height="200" src="https://upload.wikimedia.org/wikipedia/commons/6/6a/William_Hamilton_Prospero_and_Ariel.jpg" width="142" /></a></div>That's one of two epigraphs at the beginning of Chapter 6 of <i><a href="https://www.google.com/books/edition/From_Extraterrestrials_to_Animal_Minds/xwZXEAAAQBAJ?hl=en&gbpv=1&dq=extraterrestrials+animal+minds&printsec=frontcover" target="_blank">From Extraterrestrials to Animal Minds: Six Myths of Evolution</a></i>, "The Myth of Extraterrestrials," by Simon Conway Morris. It seemed odd to me when I started reading the book, but it makes some sense now that I've made it to the end. Conway Morris wants (or needs) there to be more to this business than nature "was ever conduct of." This final chapter makes that clear, and by that I mean that it makes the author's desire/need clear. It is, sadly, a fitting end to the book.<p></p><p>Recall that <i><a href="https://www.google.com/books/edition/Life_s_Solution/EdQLAQAAQBAJ?hl=en&gbpv=0" target="_blank">Life's Solution</a></i>, the author's 2003 book that made convergence a household word, is subtitled <i>Inevitable Humans in a Lonely Universe</i>. The notion that our species (or something very much like it) is "inevitable" is (in my view) a reasonable conjecture once one is faced with the pervasiveness of evolutionary convergence. I enjoyed that book when I read it all those years ago, and became convinced that evolution was not merely blundering around finding the weird and wonderful<span id="docs-internal-guid-4766ffa7-7fff-2d3c-22ca-8685c2a22e12"><span style="font-family: Arial; font-size: 11pt; font-variant-alternates: normal; font-variant-east-asian: normal; font-variant-numeric: normal; vertical-align: baseline; white-space: pre-wrap;">—</span></span>it was algorithmically churning toward design, and then toward better design. I was then in a Christian world where it seemed that "adaptationism" was a Bad Thing embraced by extremists and (oh god) atheists, but here was a rock-star Christian paleontologist who was all in on adaptation. I loved that rebel vibe, then and now. But then, and also now, I was baffled by his apparent desire to be alone. Not alone in his office, but alone in the universe.<span></span></p><a name='more'></a><p></p><p>This odd preference is starkly incongruent with convergence and certainly with inevitability. To me, it was weird in 2003 to argue that we are both inevitable and universally unique. Today, now that our <a href="https://www.theatlantic.com/science/archive/2023/03/jwst-earthlike-trappist-1-exoplanet-system/673559/" target="_blank">estimates of the amount of habitable space</a> in our cosmos are vastly larger than they were back then, the claim strikes me as, well, a myth. Not a myth as in "falsehood" but as in an aging truism, linked to crumbling religion, that dissolves when immersed in facts. I'm not saying that I know or even firmly believe that extraterrestrial intelligence exists. I'm saying that human uniqueness is now playing the role of the old legend. Conway Morris (<a href="https://sfmatheson.blogspot.com/2023/04/reviewing-from-extraterrestrials-to.html" target="_blank">er, I mean Mortimer</a>) wants us to believe that he's critiquing "received wisdom" but in this chapter and <a href="https://sfmatheson.blogspot.com/2023/05/a-gruesome-autopsy-of-chapter-5-of-from.html" target="_blank">in the train wreck of Chapter 5</a>, he's guarding graveyards of ancient dogma.</p><p>I couldn't read Chapter 6 without wondering what it was like to write it. Scientifically, it's weak and unconvincing. Sadly, the author subjects us to his typical disparaging and disingenuous dismissal of fellow scholars using the kind of "what a bunch of elitists" language endemic to the American Christian Right. (I doubt the British Christian Right is doing better, but I don't yet live there.) To try to make his case against the existence of extraterrestrial intelligence, he writes stuff like this:</p><p></p><blockquote>As Dr. Johnson stated, "All argument is against it, but all belief is for it." He, of course, was talking about ghosts, but to invert his remarks the widespread intuition is that despite there not being a shred of evidence there <i>must</i> be extraterrestrials. (pp. 209-210)</blockquote><p></p><p>Let's think about what we just read. The author repurposes a quote about ghosts, using the phrase "not being a shred of evidence," as a <i>Christian</i> who is about to discuss the <i>paranormal</i> in a book that claims to be critical of "<i>myths</i>." No irony meter could withstand this, so please use caution if you intend to read it aloud.</p><p>Right after that, he is forced to admit that "the vital statistics appear to be on the side of the believers." He spends much of the following section(s) reprising the "yes but" rejoinders to science, the ones that made <a href="https://sfmatheson.blogspot.com/2023/05/a-gruesome-autopsy-of-chapter-5-of-from.html" target="_blank">Chapter 5 a convincing argument against ever reading his writing again</a>. The topic is the <a href="https://www.theatlantic.com/technology/archive/2018/06/but-seriously-where-is-everybody/563498/" target="_blank">so-called Fermi Paradox</a>, maybe better phrased as a question: Where are they?</p><p>I can confirm there is no "myth" here, nor is there clear orthodoxy. Writings about the question are necessarily speculative and seem to span the spectrum of possible positions, from "seems very likely they're out there" to "I think we're alone." When Conway Morris described one position as "home to all those <i>bien-pensants</i>, their reassuring murmur arising from the university faculty clubs, North Oxford, and other zones of intellectual rectitude," he finalized (for me) his status as a disgrace.</p><p>The rest of the chapter is about what I will call the paranormal, because Conway Morris calls it the paranormal and because it is the paranormal. Uber kooky. Complete with a few of his signature sneers at "the materialists," the sections are unworthy of further comment. The book ends with a coda that includes our old marionette Mortimer. I was just so happy to be done.</p><p>My first thought was to let Hippolyta have the last word, since I so love <i>A Midsummer Night's Dream</i>:</p><p></p><blockquote><p>DEMETRIUS: No remedy, my lord, when walls are so
willful to hear without warning.<br />HIPPOLYTA: This is the silliest stuff that ever I heard.</p><span style="font-family: Arial; font-size: 14.6667px; white-space: pre-wrap;">—</span><a href="https://www.folger.edu/explore/shakespeares-works/a-midsummer-nights-dream/read/#line-5.1.223" target="_blank"><i>A Midsummer Night's Dream</i>, Act 5, Scene 1</a></blockquote><p><a href="https://www.folger.edu/explore/shakespeares-works/a-midsummer-nights-dream/read/#line-5.1.223" target="_blank"></a></p><p>But I think it best to let the Bard finish the conversation that Conway Morris started with. That expression of wonderment by Alonso, above, was answered by Prospero thus:</p><p></p><blockquote><p>PROSPERO: Sir, my liege,<br />Do not infest your mind with beating on<br />The strangeness of this business.</p><p><span style="font-family: Arial; font-size: 11pt; white-space: pre-wrap;">—</span><a href="https://www.folger.edu/explore/shakespeares-works/the-tempest/read/5/1/#line-5.1.297" target="_blank"><i>The Tempest</i>, Act 5, Scene 1</a></p></blockquote><p><a href="https://www.folger.edu/explore/shakespeares-works/the-tempest/read/#line-5.EPI.1" target="_blank"></a></p><p>There. <a href="https://www.hp-lexicon.org/magic/voldemorts-cave-potion/" target="_blank">I drank the whole potion</a> and have survived. My last post in this series will include some general thoughts and responses.</p><p><br /></p>
<hr />
Image credit: Prospero and Ariel (from Shakespeare's <i>The Tempest</i>), 1797 by William Hamilton. From <a href="https://ia.wikipedia.org/wiki/File:William_Hamilton_Prospero_and_Ariel.jpg" target="_blank">Wikipedia</a>.Stephen Mathesonhttp://www.blogger.com/profile/05057004085073574659noreply@blogger.com0tag:blogger.com,1999:blog-4948885059517209129.post-11111694996821522832023-05-29T01:43:00.008-07:002023-06-28T10:52:07.097-07:00A gruesome autopsy of Chapter 5 of From Extraterrestrials to Animal Minds<p>Before I explain the rot at the heart of this chapter (Chapter 5 of <i><a href="https://www.google.com/books/edition/From_Extraterrestrials_to_Animal_Minds/xwZXEAAAQBAJ?hl=en&gbpv=1&dq=extraterrestrials+animal+minds&printsec=frontcover" target="_blank">From Extraterrestrials to Animal Minds: Six Myths of Evolution</a></i>, "The Myth of Animal Minds," by Simon Conway Morris), I'd like to show you my workspace as I sullenly trudge toward the end of this task.</p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiOtHfKI7oUTEXE2y70WZxKX-Zq_NP7YcHQK5VGX_OxczSSNTLibpLrG1RMJhg7ZYcD3oUFJdF5bujhkzIPEQcHfc6W57qqQWF2APv0tcsOTvLVKvEiuPhYDlVtpG0cnqGUQQilAKMlqeZmARyspFPmK5HLmBWNlpPnCfq4SWZRQDBp2NnpDSqCDRbw/s4032/workspace.jpg" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="2268" data-original-width="4032" height="180" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiOtHfKI7oUTEXE2y70WZxKX-Zq_NP7YcHQK5VGX_OxczSSNTLibpLrG1RMJhg7ZYcD3oUFJdF5bujhkzIPEQcHfc6W57qqQWF2APv0tcsOTvLVKvEiuPhYDlVtpG0cnqGUQQilAKMlqeZmARyspFPmK5HLmBWNlpPnCfq4SWZRQDBp2NnpDSqCDRbw/s320/workspace.jpg" width="320" /></a></div><p>That's my fun little Chromebook 2-in-1, and the barely-visible tartan mouse pad is from my dad. You'll see my toolkit of sticky notes and a stack of (some of) my books on consciousness and human cognition. Conway Morris' book is open to the pages (155-157, in a section called "An unbridgeable gulf?") <a href="https://sfmatheson.blogspot.com/2023/05/the-author-doth-protest-too-much.html" target="_blank">that stopped me in my tracks</a>.<span></span></p><a name='more'></a><p></p><p>See all the sticky notes in the book? There's a big blue one in the upper right that marks my current place in the Notes section (it's 170 pages long). When I'm reading a book like this one, with a lot of notes and references, I need to be able to flip back and forth between text and notes. Why even mention this? Because in this crucial section of <a href="https://sfmatheson.blogspot.com/2023/05/the-author-doth-protest-too-much.html" target="_blank">the disastrous Chapter 5</a>, the notes help reveal the rot. They are few in number but<span id="docs-internal-guid-0a89f2ec-7fff-6f8a-2ce8-9de71563add4"><span style="font-family: Arial; font-size: 11pt; font-variant-alternates: normal; font-variant-east-asian: normal; font-variant-numeric: normal; vertical-align: baseline; white-space: pre-wrap;">—</span></span>worse<span style="font-family: Arial; font-size: 11pt; white-space: pre-wrap;">—</span>are misleadingly cherry-picked or curiously irrelevant. The diagram on the left is chaotic and uninformative, seemingly a sketch in someone's notebook, and neither the diagram nor the discussion in the text is accompanied by a citation. If you look carefully, you'll see why: the diagram is bafflegab labelled as "the cognitive architecture of humans." Even if it were properly labelled as "Simon's conception of human cognitive architecture," it would be an embarrassment.</p><p></p><p><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEijXQFpV3o4AJ4bAdbeoI16BTyUVHwb6gwrtExWK3nd1aI4WPf160J1voycuEb95bZrZCG2XdUP-plRgL5utg8bPvtuCKHF8kppxWl7WNpj-iW-_hif6NYg4ExzmRwWJbCMpAsF0_PiWhGHM2JZXTZuTYA0gTZRlmZZM2mQVU1q9jU3mRZYtj8Q9AAm/s2166/fig%205-1.jpg" style="clear: right; float: right; margin-bottom: 1em; margin-left: 1em; text-align: center;"><img border="0" data-original-height="2041" data-original-width="2166" height="189" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEijXQFpV3o4AJ4bAdbeoI16BTyUVHwb6gwrtExWK3nd1aI4WPf160J1voycuEb95bZrZCG2XdUP-plRgL5utg8bPvtuCKHF8kppxWl7WNpj-iW-_hif6NYg4ExzmRwWJbCMpAsF0_PiWhGHM2JZXTZuTYA0gTZRlmZZM2mQVU1q9jU3mRZYtj8Q9AAm/w200-h189/fig%205-1.jpg" width="200" /></a>The silly diagram is cited in the text in support of this claim: "the capacities that make us human are intimately intertwined and very deeply rooted." That's blandly true, but the diagram doesn't help us understand. Then, yikes, here's the next sentence: "It is almost as if we were parachuted onto the planet." Sorry, what? I don't see 'non sequitur' on the diagram, but that's just the beginning of the problem with this section. In support of that sentence, Conway Morris cites an <a href="https://doi.org/10.1080/21582041.2012.691989" target="_blank">obscure sociology paper</a> that's not about sudden evolutionary change (or teleportation) but about how culture drives human evolution.</p><p>The next paragraph is worse. Conway Morris tries to establish that the "intertwined" nature of human cognition is "robust to insult," meaning that it can persist in the presence of major damage. He provides <a href="https://doi.org/10.1080/21582041.2012.691989" target="_blank">a single cherry-picked case</a> to support this claim. First, note that the authors of that report suggest precisely the opposite of what Conway Morris wants us to believe, writing (emphasis mine):</p><p></p><blockquote>Therefore, the pattern of responses revealed in this case of severe agrammatic aphasia attests to a dissociation between grammar and cognition and to <b>the modular nature of mature brain functioning</b>. Grammar may play a vital role in configuring cognitive processes, but once these processes have been established, cognition can operate without grammar.</blockquote><p></p><p>But the more troubling problem with this section should be obvious to anyone who's read <a href="https://www.google.com/books/edition/The_Man_Who_Mistook_His_Wife_For_A_Hat_A/nc2dE9swe0sC?hl=en" target="_blank">Oliver Sacks</a> or <a href="https://www.google.com/books/edition/_/hSswinQcxY8C?hl=en&gbpv=0" target="_blank">V.S. Ramachandran</a> or <a href="https://www.google.com/books/edition/Descartes_Error/twcjEAAAQBAJ?hl=en&gbpv=1&dq=damasio&printsec=frontcover" target="_blank">Antonio Damasio</a>. Conway Morris is wrong when he writes that "the associated gallimaufry of cognitive capacities that enshrine causal reasoning and theory of mind lie far deeper and stay operative in the face of serious injuries."</p><p>Why is he making that claim in the first place? Why should it matter that humans <a href="https://www.theatlantic.com/science/archive/2016/09/hemispatial-neglect/500000/" target="_blank">can lose their connection to half of their world, after a particular brain injury</a>? The answer is in the following paragraph, on page 157, in the sentence that is the heart of the rot. Conway Morris writes (italics are his):</p><p></p><blockquote>Equally trying to persuade ourselves that animal A has this nascent cognitive capacity or animal B has another one is to miss the point. If beast A or B had language or any other part of our cognitive battery (figure 5.1), it would have <i>all</i> of them, either directly expressed or with the obvious potential for expression.</blockquote><p></p><p>Uh, bullshit. <a href="https://www.annualreviews.org/doi/10.1146/annurev-psych-062220-051256" target="_blank">We know this is false</a>. Conway Morris should know that it's false, but it's hard to tell whether he's actually read much on the topic<span id="docs-internal-guid-02d8b031-7fff-0c26-803f-ae48682b21e0"><span style="font-family: Arial; font-size: 11pt; font-variant-alternates: normal; font-variant-east-asian: normal; font-variant-numeric: normal; vertical-align: baseline; white-space: pre-wrap;">—</span></span>this kind of malpractice is usually the result of mining, not reading.</p><p>Unfortunately, this flaw in the chapter is not just a mistake. It is the backdrop, the <i>raison d'être</i>, of the 40+ pages that follow. In those pages, Conway Morris tours numerous experiments and observations in non-human animal cognition, probing for weaknesses but mostly just chanting the mantra about the vast gulf between non-human animals and humans. Without the central falsehood about "it would have <i>all</i> of them," readers might correctly perceive that the chapter is nothing more than a recitation of how one particular professor reckons the size of the gulf to be.</p><p>I guess my hope for readers is that they'll see the game even without the insight into the flaw at the heart, since the bulk of the chapter is a teeter-totter of "look at this cool thing" followed by "yes but"<span style="font-family: Arial; font-size: 14.6667px; white-space: pre-wrap;">—</span>enough yesbuttery to perhaps trigger the <a href="https://sfmatheson.blogspot.com/2023/05/the-author-doth-protest-too-much.html" target="_blank">Gertrude reflex</a>. Let's hope. </p><p>The final sad point to make about the chapter is that, to my mind, Conway Morris vandalized his own good work in order to dig his moat. All of the preceding chapters have reinforced the power of evolutionary algorithmic "creativity." (Those are my words, to be clear.) Think of Chapter 1, where the <a href="https://sfmatheson.blogspot.com/2023/04/superheroes-and-limits-more-on-chapter.html" target="_blank">author argued that evolution has discovered all there is to discover</a>. Or of Chapter 3, where he <a href="https://sfmatheson.blogspot.com/2023/05/mass-extinction-as-acceleration-chapter.html" target="_blank">convincingly argues that mass extinctions speed innovation</a> because so much of the discovery has already been done. How about Chapter 4, in which our hero <a href="https://sfmatheson.blogspot.com/2023/05/missing-links-are-myth-but-whose.html" target="_blank">dynamites a myth of "missing links" that mostly churchgoers repeat</a>, but in the process helps us all see that innovations generally bubble up from tools established long before? Why on earth is everything suddenly different when the topic is human cognition?</p><p>I think I know the answer to that last question. That we have ended up with that question, and that answer, in a book that <a href="https://sfmatheson.blogspot.com/2023/04/reviewing-from-extraterrestrials-to.html" target="_blank">purports to oppose myths and "received wisdom"</a> ... is irony that would make Shakespeare blush.</p>Stephen Mathesonhttp://www.blogger.com/profile/05057004085073574659noreply@blogger.com0tag:blogger.com,1999:blog-4948885059517209129.post-70995145175189357832023-05-28T22:13:00.009-07:002023-06-19T10:14:30.848-07:00The author doth protest too much, methinks. The disastrous Chapter 5 of From Extraterrestrials to Animal Minds<div style="text-align: right;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEimBHuGeGJfshUWPZ815wug29kjgnSC0unwMQFLTy1Vjzg1M8sVLEG0NFADmV4PkDWofoyw27JRzG9BbLwv4X8O-sR4XvwAB_xs0LnntNtatWu4y0ajKf1s3rYdq7RCDqQPsxwxvz8powq3N-baaApYr3z44wB0lUuvoWrYpn-ARHi1GrRvd8nGy0eQ/s1400/Abbey_-_The_Queen_in_Hamlet.jpg" style="clear: right; float: right; margin-bottom: 1em; margin-left: 1em;"><img alt="The Queen in Hamlet, by Edwin Austin Abbey" border="0" data-original-height="1400" data-original-width="1073" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEimBHuGeGJfshUWPZ815wug29kjgnSC0unwMQFLTy1Vjzg1M8sVLEG0NFADmV4PkDWofoyw27JRzG9BbLwv4X8O-sR4XvwAB_xs0LnntNtatWu4y0ajKf1s3rYdq7RCDqQPsxwxvz8powq3N-baaApYr3z44wB0lUuvoWrYpn-ARHi1GrRvd8nGy0eQ/w153-h200/Abbey_-_The_Queen_in_Hamlet.jpg" width="153" /></a></div>It's one of the most famous misquoted lines in the English language, spoken by Lady Gertrude (Hamlet's mom) during the <a href="https://www.folger.edu/explore/shakespeares-works/hamlet/read/3/2/" target="_blank">intense scene</a> featuring a play ("The Mousetrap" aka The Murder of Gonzago) within a play, intended by Hamlet to be "<a href="https://www.folger.edu/explore/shakespeares-works/hamlet/read/2/2/#line-2.2.624" target="_blank">the thing wherein I’ll catch the conscience of the King</a><span>." The character in "The Mousetrap" has delivered some sappy lines about commitment and widowhood, designed to flush out the King and Gertrude. But you know all that. The frequently-mangled line is "The lady protests too much, methinks." It's a great line and it works out to something like "she's overdoing it" spoken by a person who is literally the subject being portrayed. When we say "the lady doth protest too much" we usually mean "they're overacting so much that now it seems even <i>they</i> don't believe what they're saying."</span><p></p><p>That's how Chapter 5 of <i><a href="https://www.google.com/books/edition/From_Extraterrestrials_to_Animal_Minds/xwZXEAAAQBAJ?hl=en&gbpv=1&dq=extraterrestrials+animal+minds&printsec=frontcover" target="_blank">From Extraterrestrials to Animal Minds: Six Myths of Evolution</a></i>, "The Myth of Animal Minds," felt to me. Simon Conway Morris is hellbent on digging a conceptual moat around human cognition, desperate to isolate it from non-human cognition so that it can receive metaphysical shipments from on high. If that sounds harsh, it is<span id="docs-internal-guid-d0710ed5-7fff-b74b-0d19-e1a30e8a78e5"><span style="font-family: Arial; font-size: 11pt; font-variant-alternates: normal; font-variant-east-asian: normal; font-variant-numeric: normal; vertical-align: baseline; white-space: pre-wrap;">—</span></span>and it is exactly what the chapter is about. <span></span></p><a name='more'></a>Tragically, in his zeal to dig that moat, he:<p></p><p></p><ul style="text-align: left;"><li>unweaves the tapestry he wove himself in the previous chapter, which correctly dispensed with "missing links" through convergence and evolution-as-a-bushy-tree;</li><li>separates <i>himself</i> (not just his audience) from the threatening facts of non-human cognition; and far worse,</li><li>separates himself from his colleagues, whom he disparages with <a href="https://doi.org/10.1098/rstb.2011.0195" target="_blank">poop-flinging</a> like this:</li></ul><p></p><p></p><blockquote>Rather than seeking a mysterious factor X, a grafting on of some strange capacity, or trying to maintain the fiction that whatever separates us from animals is only a matter of degree, we need to take a metaphysical perspective. (p. 204)</blockquote><p></p><p>If you unwisely read this book, you'll be accustomed by Chapter 5 to Conway Morris' disingenuous conversion of big questions and unresolved disagreements into "myths." That quote is just one more canard in this cringe-inducing cavalcade, so maybe you're not yet impressed by how dismissive he really is. Consider, then, the next couple of sentences.</p><p></p><blockquote>Entirely alien to the materialist, this viewpoint insists that humans have entered new realms. These are ones of ideas and imagination where the unobservable is real, a world of concepts and generalizations working in easy harmony.</blockquote><p></p><p>Yeah, so after reducing one legitimate position in a robust, deeply interesting <a href="https://doi.org/10.1098/rstb.2012.0211" target="_blank">ongoing debate about human cognition</a> to "maintaining a fiction," the author asserts that the "realms" of ideas and imagination are "entirely alien to the materialist." That slur is aimed at many (maybe most) of his colleagues, and it's aimed at me and at every other person who is unconvinced by stories of the supernatural. Either the author doth protest too much, or... he's portraying an ignorant, arrogant ass in a farcical play. I expected better from Simon Conway Morris, and now I regret that.</p><p>Notice that I haven't yet written about what he explores, biologically, in the chapter. As in the rest of the book, the chapter is a deep dive into current science with characteristically energetic excursions into behavior and cognition of diverse non-human animals. Which is mostly good. But there is a big ugly flaw in the middle of the argument. It's bad enough that it stopped me cold, and it's worrying enough that I briefly wondered if the whole book contains contagion like it. After all, I'm a neuroscientist and thus able to follow the details of the chapter (which is another way of saying that I'm hard to fool when it comes to cognitive science). Might I have missed other big flaws in chapters outside my expertise? (Remember the <a href="https://sfmatheson.blogspot.com/2023/05/confusion-and-convergence-but-no-myth.html" target="_blank">blooper about mutation hotspots</a>? That's also an area I know well.) I've read the whole book, and I'm reasonably confident that there aren't any more. (The final chapter is flat-out kooky, but not built on falsehoods that I could identify.) But this one is bad, and I'll discuss it in the next post.</p><p><br /></p><hr /><p>Image credit: Edwin Austin Abbey, The Queen in "Hamlet", 1895, <a href="https://americanart.si.edu/artwork/queen-hamlet-3" target="_blank">Smithsonian American Art Museum</a>.</p>Stephen Mathesonhttp://www.blogger.com/profile/05057004085073574659noreply@blogger.com0tag:blogger.com,1999:blog-4948885059517209129.post-55768399197213369642023-05-26T23:18:00.006-07:002023-06-19T10:20:21.931-07:00Missing links are a myth, but whose? Chapter 4 of From Extraterrestrials to Animal Minds<p>There are some truly vexing and annoying myths of evolution. They are almost exclusively recited and embellished by religious propagandists, some of whom actually know what they're doing. Rarely but notably, there are myths that are gleefully repeated by creationists while being amplified by scientists who should know better. The clearest example of this is the <a href="https://whatsinyourgenome.blogspot.com/" target="_blank">mythology and nonsense surrounding "junk DNA.</a>"</p><p>Missing links are not an example of this.</p><p>The phrase "missing link" is <a href="https://www.smithsonianmag.com/science-nature/whats-missing-link-180968327/" target="_blank">so dated and so scientifically laughable</a> that it could only be seriously discussed in a book about myths that circulate among laypeople who watch YouTube videos about Sasquatch, refuse vaccines to own the libs, and go to church. What is it doing in a book by Simon Conway Morris, a <a href="https://sfmatheson.blogspot.com/2023/04/reviewing-from-extraterrestrials-to.html#more" target="_blank">book that claims to address "areas of received wisdom that are long overdue for careful reexamination"</a>? It's the subject of the fourth chapter of <i><a href="https://www.google.com/books/edition/From_Extraterrestrials_to_Animal_Minds/xwZXEAAAQBAJ?hl=en&gbpv=1&dq=extraterrestrials+animal+minds&printsec=frontcover" target="_blank">From Extraterrestrials to Animal Minds: Six Myths of Evolution</a></i>, "The Myth of Missing Links."</p><p></p><table cellpadding="0" cellspacing="0" class="tr-caption-container" style="float: right;"><tbody><tr><td style="text-align: center;"><a href="https://upload.wikimedia.org/wikipedia/commons/1/1a/Morrigan.jpg" style="clear: right; margin-bottom: 1em; margin-left: auto; margin-right: auto;"><img border="0" data-original-height="648" data-original-width="500" height="200" src="https://upload.wikimedia.org/wikipedia/commons/1/1a/Morrigan.jpg" width="154" /></a></td></tr><tr><td class="tr-caption" style="text-align: center;">The Mórrígan. A myth.</td></tr></tbody></table>This question summarizes one source of my deep disappointment in this book, a work that has lowered my opinion of its author. I have no right to blame my disappointment on the author, and I know that my feelings betray an expectation on my part that the professor has no obligation to even consider. That expectation: that Christian scientists acknowledge and consider resisting the mountains of lies that their fellow believers dump into the world. <span><a name='more'></a></span>I expect to introspect and learn about this frustration of mine when I get to <a href="https://sfmatheson.blogspot.com/2023/04/thoughts-on-complicity-before-reading.html" target="_blank"><i>Complicit</i> by Max Bazerman</a>. For now, I think it's only fair to confess that this chapter pissed me off not because it's wrong about "missing links" but because it suggests that there is a myth of missing links among the people who Conway Morris used to call colleagues: biologists. It's a myth all right<span style="font-family: Arial; font-size: 11pt; white-space: pre-wrap;">—</span>but it's someone else's.<p></p><p>If we were to move this chapter to a book it seems Simon Conway Morris will never write, about Facebook crap that Christians feast on, it would be a pretty good exploration of two concepts that don't fit into the old fables about ladders of progress:</p><p>1) <a href="https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.0040352" target="_blank">Natural history is the unfolding of a tree, and not the ascending of a ladder</a>. Even big events like the emergence of tetrapods from fish, or the invention of feathers, are characterized by parallel innovations in lineages that have accumulated tools and ingredients. Here's the author actually naming the myth:</p><p></p><blockquote>This is the myth of a missing link: long before the final breakthrough, the seeds of success were not only being sown, but multiple times. (p. 117)</blockquote><p></p><p>This alone makes the metaphor of a "missing link" nonsensical.</p><p>2) Organisms are often "mosaics" of features that are "advanced" and "primitive." This is <a href="https://elifesciences.org/articles/74159" target="_blank">true today</a> and it was true hundreds of millions of years ago. As Conway Morris writes about the era of "<a href="https://shubinlab.uchicago.edu/research-2-2/" target="_blank">fishapods</a>":</p><p></p><blockquote>Although the overall story of tetrapodization is clear enough, in detail the story is very far from some sort of monotonic narrative. This is because the fossils in question are almost always a puzzling muddle of characters, revealing a striking degree of mosaic evolution. In other words, in any given species we see relatively archaic features co-occurring with more advanced ones. (p. 114)</blockquote><p></p><p>These two concepts are interesting, and Conway Morris takes us on a tour of convergence and parallel evolution with moderate panache. He ends with <i>H. sapiens</i> and family, with little to add conceptually but with an increasing frequency of interjections about "the numinous" and other themes that form the obvious goal of the book. Myths, I assure you, are not the topic.</p><p><br /></p><hr /><p>Image credit: Detail of Battle Crow from "Cú Chulainn riding his chariot into battle" by Joseph Christian Leyendecker. From <a href="https://en.wikipedia.org/wiki/The_Morr%C3%ADgan#/media/File:Morrigan.jpg" target="_blank">Wikipedia</a>.</p>Stephen Mathesonhttp://www.blogger.com/profile/05057004085073574659noreply@blogger.com0tag:blogger.com,1999:blog-4948885059517209129.post-75591826770501004252023-05-24T21:25:00.005-07:002023-06-19T10:21:02.278-07:00Mass extinction as acceleration: Chapter 3 of From Extraterrestrials to Animal Minds<p>If you read about natural history, even just popular accounts, you know about the <a href="https://www.nhm.ac.uk/discover/what-is-mass-extinction-and-are-we-facing-a-sixth-one.html" target="_blank">epic mass extinctions</a> visited on the living world throughout life's tenure on Earth. Words like 'devastating' and 'catastrophic' barely capture their scale<span style="font-family: Arial; font-size: 11pt; white-space: pre-wrap;">—</span>the most thorough purge is called The Great Dying and extinguished at least 95% of the species on the planet. And this isn't just animals dying. It's whole <i>lineages</i> dying. As our host writes, these things are "extremely nasty and most definitely to be avoided."</p><div class="separator" style="clear: both; text-align: center;"><a href="https://upload.wikimedia.org/wikipedia/commons/thumb/8/8c/Chicxulub_impact_-_artist_impression.jpg/1024px-Chicxulub_impact_-_artist_impression.jpg" style="clear: right; float: right; margin-bottom: 1em; margin-left: 1em;"><img alt="Artistic impression of the asteroid slamming into tropical, shallow seas of the sulfur-rich Yucatán Peninsula" border="0" data-original-height="640" data-original-width="800" height="160" src="https://upload.wikimedia.org/wikipedia/commons/thumb/8/8c/Chicxulub_impact_-_artist_impression.jpg/1024px-Chicxulub_impact_-_artist_impression.jpg" width="200" /></a></div>It's tempting to picture these epochs as the <a href="https://www.americanscientist.org/article/vestiges-of-james-hutton" target="_blank">erasure of worlds</a>, with new worlds taking their place. Lots of death means lots of vacant niches means lots of opportunity, for animal lineages to expand and diversify, and for humans to weave gripping tales of fortune and fate. Or even myths. If, like me, you read this book to learn about myths of evolution, you had to slog through <a href="https://sfmatheson.blogspot.com/2023/05/confusion-and-convergence-but-no-myth.html" target="_blank">two chapters of chaos and blather</a> to get to something that finally resembles one.<p></p><p>The third myth in <i><a href="https://www.google.com/books/edition/From_Extraterrestrials_to_Animal_Minds/xwZXEAAAQBAJ?hl=en&gbpv=1&dq=extraterrestrials+animal+minds&printsec=frontcover" target="_blank">From Extraterrestrials to Animal Minds: Six Myths of Evolution</a></i> by Simon Conway Morris, the subject of Chapter 3, is "The Myth of Mass Extinctions." The chapter is long and detailed, clogged with taxonomic jargon in places, sparkling with typical mischief in others. (Page 76: "Not for a moment am I suggesting that the early Triassic is a preferred destination for the time traveler. Your tour group would be greeted by shocking scenes, but the cognoscenti would see which way the wind was blowing.") By now we know we have to ask: what exactly is the myth? Conway Morris isn't questioning the occurrence of mass extinctions, nor does he doubt their apocalyptic power. He's attacking a somewhat specific view of their effects on the biosphere.<span></span></p><a name='more'></a><p></p><p><a href="https://www.google.com/books/edition/_/4T6fQgAACAAJ" target="_blank">That view is most commonly associated with Stephen Jay Gould</a> and is linked (inextricably, in my opinion) to Gould's preference for the contingent and the "random" as major forces in the unfolding of life. The Gouldian view is something like this: mass extinctions redirect evolution, pushing life in new directions that would not have been pursued without the cataclysmic erasure of lineages and ecosystems. This is the overly famous "replay the tape of life" metaphor, now focused on what Gould saw as random reboots caused by catastrophes. And the upshot that matters most to Conway Morris is this one: if the asteroid zigs instead of zags and misses our blue planet, then the dinosaurs still "rule the earth" while the mammals cower in the bushes and get eaten. And that means the mammals don't take over and evolve along lineages that lead to humans. Put more precisely and technically: major radiations of new species/lineages, like the one that led to us, wouldn't have happened without the cataclysms.</p><p>My retelling doesn't do justice to this position, which is not a silly fable but a hard-nosed scientific view based, at least until fairly recently, on an informed reading of natural history. Conway Morris acknowledges this, though perhaps not clearly enough. His view is that yes, there were great dyings, and yes, these erased lineages and whole ecosystems, and yes, these dyings were followed by radiations of new lineages. But these radiations were going to happen anyway, and once the smoke cleared and a bazillion dead animals returned to the dust, the effect of the cataclysm was to speed up the process.</p><p>Conway Morris marshals considerable evidence making this case. The chapter is convincing, partly because it is well organized, partly because there really is a myth to be opposed and corrected, and (I suspect) partly because this is the author's area of legendary expertise. Versions of the myth, by the way, <a href="https://www.washington.edu/news/2019/06/20/mammaliaforms-ecological-radiation/" target="_blank">cause annoyance and distraction in other paleontologists as well</a>.</p><p>I do think there is a weakness in his argument: a lineage that has been erased is a lineage whose prior accomplishments no longer count. This matters because Conway Morris rests his case on the fact that innovations that occurred after a cataclysm, during a post-apocalyptic radiation, nearly always existed before the apocalypse. I agree with him that this suggests that the Gouldian view is largely wrong and that dyings lead to birthings and expansions that are not "random," but we have to acknowledge that a complete extinction of a vast lineage can determine winners and losers by destroying whole clubs of future potential winners.</p><p>But I liked the chapter a lot and was much less grumpy about the money I spent on the book when I finished Chapter 3. The biology is fascinating, the story is compelling, and the need for correction and rebuttal (of Gouldian replaying of tapes and such) is clear. Plus, the author's cheekiness works well for the first time in the book. Here's a favorite passage, on the end-Cretaceous extinction event that ended the dinos:</p><p></p><blockquote>Some groups seemed to have looked up and said, "Oh, another mass exctinction?" and carried on. Spiders, for example, continued to spin and lice to infest. Meanwhile out in the oceans, the pelagic fish swam on unconcerned.</blockquote><p></p><p>Humor in mass extinction? I like it, even if <a href="https://humag.co/features/the-dark-ecology-of-the-far-side" target="_blank">Gary Larson was doing it decades ago</a>.</p><p><br /></p><hr /><p>Image credit: Artistic impression of the asteroid slamming into tropical, shallow seas of the sulfur-rich Yucatán Peninsula in what is today Southeast Mexico. From <a href="https://en.wikipedia.org/wiki/Cretaceous%E2%80%93Paleogene_extinction_event#/media/File:Chicxulub_impact_-_artist_impression.jpg" target="_blank">Wikipedia</a>.</p>Stephen Mathesonhttp://www.blogger.com/profile/05057004085073574659noreply@blogger.com0tag:blogger.com,1999:blog-4948885059517209129.post-85909338891709392122023-05-14T22:56:00.009-07:002024-01-22T12:51:52.912-07:00Confusion and convergence, but no "myth of randomness." Chapter 2 of From Extraterrestrials to Animal Minds<p>The concept of randomness is caught up in evolution, in two broad ways. The first and most famous aspect is the oft-misunderstood randomness of mutation. The second aspect is the role of chance in the trajectory of evolution. It is this question<span style="font-family: Arial; font-size: 11pt; white-space: pre-wrap;">—</span>is evolution predictable, or is it a random "drunkard's walk"<span style="font-family: Arial; font-size: 11pt; white-space: pre-wrap;">—</span>that Conway Morris tackles in the second chapter of <a href="https://www.google.com/books/edition/From_Extraterrestrials_to_Animal_Minds/xwZXEAAAQBAJ?hl=en&gbpv=1&dq=extraterrestrials+animal+minds&printsec=frontcover" style="font-style: italic;" target="_blank">From Extraterrestrials to Animal Minds: Six Myths of Evolution</a>. The chapter is called "The Myth of Randomness."</p><p>The chapter is a chaotic mess and ends without a clear argument, much less a convincing one. Conway Morris wants to tip the scales away from "randomness" and toward "cyclicity." From the second paragraph of the chapter (page 43):</p><p></p><blockquote>Although through geological time increasing degrees of biological complexity and integration are undeniably the case, superimposed on this is an intriguing cyclicity: <i>plus ça change, plus c'est la même chose</i>. It transpires that evolutionary history is very far from random.</blockquote><p></p><p></p><table cellpadding="0" cellspacing="0" class="tr-caption-container" style="float: right;"><tbody><tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgeEoUEyonNoYJMBojwTh4d4h7ohQCwAaQlBQD3iqsy3O2cIkwb6Cm2bDKEaiTazznOXAjUfWWhJiO9Y2y-8MqRoArJEo4rZ7HllrnpWq4PvO8PG3eV4Gug3PKndVyNZfAoYTSomytVy-oOJdTEf85_sj7uOahrmBy71XuyIqpxkmq0X8vbjaIEHqVP/s1024/NPS_saguaro-rincon-mountain-district-trail-map1024_1.jpg" style="clear: right; margin-bottom: 1em; margin-left: auto; margin-right: auto;"><img alt="Map of the Rincon Wilderness in Arizona" border="0" data-original-height="640" data-original-width="1024" height="125" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgeEoUEyonNoYJMBojwTh4d4h7ohQCwAaQlBQD3iqsy3O2cIkwb6Cm2bDKEaiTazznOXAjUfWWhJiO9Y2y-8MqRoArJEo4rZ7HllrnpWq4PvO8PG3eV4Gug3PKndVyNZfAoYTSomytVy-oOJdTEf85_sj7uOahrmBy71XuyIqpxkmq0X8vbjaIEHqVP/w200-h125/NPS_saguaro-rincon-mountain-district-trail-map1024_1.jpg" title="The Rincon Mountain Wilderness of Arizona" width="200" /></a></td></tr><tr><td class="tr-caption" style="text-align: center;">Rincon Mountain Wilderness</td></tr></tbody></table><a href="https://sfmatheson.blogspot.com/2023/04/superheroes-and-nonexistent-myth-of-no.html" target="_blank">Like he did in Chapter 1</a>, Conway Morris takes a profoundly interesting, long-standing question in science, a question that currently inspires brilliant writing and experimentation by evolutionary biologists, and paints one of the possibilities as a "myth." Like he did in Chapter 1, he erects a strawperson. Unlike in Chapter 1, the strawperson is not a laughable nonexistent entity but instead a fuzzy caricature of a major factor in evolutionary history<span style="font-family: Arial; font-size: 11pt; white-space: pre-wrap;">—</span>the combination of chance and contingency. Fortunately, unlike in Chapter 1, Conway Morris provides a poorly integrated amalgam that few laypeople will understand. Thus, even those inclined to cheer the immolation of the strawperson will find little more than stuff like this (p. 56): "The clear implication is that beneath these entirely plausible factors there are deeper organizational principles at work and of which we know very little at present." That sentence is typical of the chapter, which reaches its nadir at an invocation of "particle physics or the periodic table" as evidence that physicists embrace the notion of "a deeper order of the world" while biologists struggle to do the same. In his ardor to preach on these "deeper" things, Conway Morris obscures the grandness of the question and at times distorts what working scientists know and do. It was on finishing this chapter, a few weeks ago, that I regretted buying and reading the book.<span><a name='more'></a></span><p></p><p>This chapter (and perhaps the whole book) seems to lack an identifiable audience. Lay readers will not follow his reasoning and will not understand why his examples are even relevant to a "myth of randomness." On the other hand, those who know the literature on this fascinating topic will already know that randomness is not a "myth" in any sense of that word, and will already know that we have excellent evidence for both "sides" of the question. Inconveniently for ideologues and religious apologists, this is not a debate that a doctrinal faction gets to win. Randomness is a major factor but convergence shows that adaptation and principles of design are deeply involved in evolutionary trajectories. Reasonably well-informed people already know this.</p><p>So, is there anything new or interesting in the chapter? "Cyclicity," what Conway Morris calls "the eternal return," is a bit more than mere convergence. It is <i>repeated</i> convergence, in which evolution returns to the same solution over and over. A classic example is C4 photosynthesis, which has been invented/discovered more than 60 times. This is an interesting subject, but Conway Morris rambles through the topic with no apparent question or purpose beyond asserting a "clear implication" that there are "deeper organizational principles at work." He seems impressed by the fact that there are evolutionary "hotspots" in the tree of life, and points briefly and vaguely to "Vermeij's observation that some niches appear to be potentially available but remain unoccupied" while avoiding <a href="http://dx.doi.org/10.1098/rsfs.2015.0028" target="_blank">what Vermeij thinks this might mean</a>. The uneven occupation of Design Space is indeed interesting, but it's not a new subject for Conway Morris or anyone else.</p><p>Okay, but does Conway Morris have interesting takes on randomness? Sadly no: he is mistaken about the meaning of work on <i>genetic</i> hotspots of phenotypic variation; he writes that "in at least some cases mutations are very far from random but rather tend to be concentrated in so-called hot spots." This is a garbled misstatement, both of what "random" means in the context of mutation and of <a href="https://onlinelibrary.wiley.com/doi/10.1111/evo.12081" target="_blank">what the cited work is actually about</a>. Indeed "randomness," evidently the topic of the chapter, is a term Conway Morris at times seems not to understand. For example, from different work than I just cited, we know that mutations are not equally distributed in genomes<span style="font-family: Arial; font-size: 11pt; white-space: pre-wrap;">—</span>indeed it has long been known that there are particular mutations that happen far more often than "normal" and many of these are well understood (keyword: <a href="https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1008749" target="_blank">breakpoints</a>). This says nothing about whether mutations are random, because the term was never meant to claim that all mutations in a genome are equally likely. That quote about "concentrated in so-called hotspots" suggests that Conway Morris doesn't know what random mutation means.</p><p>Maybe that doesn't matter, because this chapter is really not about randomness. A clue to the source of confusion can be found in the strange introduction on page 43, wherein the author takes us to a casino where some countess is playing the Game of Life. She loses ("a gasp of surprise") then "walks into the darkness of extinction." (Those are high stakes!) This happens next:</p><p></p><blockquote>...hitherto shadowy figures now join the game. But they are very far from being unexpected arrivistes<span style="font-family: Arial; font-size: 14.6667px; white-space: pre-wrap;">—</span>rather, they were not only waiting in the wings but turn out to be yet more accomplished players. The rules remain the same but at a yet faster pace.</blockquote><p></p><p>This is really not relevant to randomness. But it helps us understand the author's project, because the casino depicts the theme of the <i>next</i> chapter (the "creative" role of mass extinctions). What Conway Morris wants us to imagine is that the Game of Life is somehow rigged<span style="font-family: Arial; font-size: 11pt; white-space: pre-wrap;">—</span>that success involves following established pathways through Design Space, pathways so vanishingly rare that they render nearly all of Design Space uninhabitable. And he wants us to believe this is true in organism Design Space <i>and</i> in molecule (protein) Design Space. I see two obvious problems with his reasoning:</p><p></p><ul style="text-align: left;"><li>Rarity of "good design" is both relativistic (what is "rare"?) and expected.</li><li>Neither contingency nor chance is relevant to the question of the "density" of Design Space. Those are concepts about <i>how evolution explores Design Space</i>, whether that space is overflowing with viable options or resembles a <a href="https://www.nps.gov/sagu/planyourvisit/maps.htm" target="_blank">trail map of an Arizona wilderness</a>.</li></ul><p></p><p>Once we identify the author's misconceptions about randomness, the chapter resolves into these themes:</p><p></p><ul style="text-align: left;"><li>a nice exploration of some examples of convergence, which surely suggest tracks through Design Space but are simply the latest writings by Conway Morris on a now well-established topic; and</li><li>a flawed attempt to establish evolution, including molecular evolution, as a journey on a "knife-edge of biological existence, the narrowest of tracks that thread their way across an otherwise desolate landscape of nonviability."</li></ul><p></p><p>With the caveat that it's not clear how to dispute terms like "knife-edge" and "narrowest of tracks," I think we can now say that Conway Morris is wrong about that second theme in the realm of protein evolution. It was dubious when he wrote it*, but <a href="https://doi.org/10.1126/science.abn6895" target="_blank">as of May 2022</a> it became nearly indefensible. Molecular evolution, it turns out, is easy. I'm writing a book about that, and I'll start writing about it here, soon.</p><p>So finally, is there some orthodoxy that Conway Morris is challenging in this chapter? No. He's staking out a position that seems extreme, and that is flimsy in important ways, in a subfield of evolutionary biology that already knows that both extremes are wrong. It looks bad and is reason enough for you to avoid reading the book. But is there some interesting biology in the chapter? Yes, of course, and my favorite stuff was about convergence and innovation in the proteins that carry and store oxygen in animal bodies. The section on the machinery of photosynthesis was chaotic and, like everything else in this chapter, an expansion of the author's previous writings on exactly the same topics. But who doesn't love photosynthesis?</p><p>Next up is the first chapter that was worth reading, about mass exctinctions. As I'm sure you could guess by now, there's no "myth" exposed in the chapter, but finally Conway Morris succeeds in making a case for an adjustment in our thinking.</p><p></p><hr /><p></p><p>*He doesn't say when he was writing but there are citations to 2021 papers. The book was published in mid-2022.</p><p>Image credit: Rincon Mountain district trail map. From <a href="https://commons.wikimedia.org/wiki/File:NPS_saguaro-rincon-mountain-district-trail-map.pdf" target="_blank">Wikipedia</a>.</p><p><br /></p>Stephen Mathesonhttp://www.blogger.com/profile/05057004085073574659noreply@blogger.com0