[{"content":"","date":null,"permalink":"https://mdonertas.github.io/scratchpad/en/tags/biological-frames/","section":"Tags","summary":"","title":"Biological Frames"},{"content":"","date":null,"permalink":"https://mdonertas.github.io/scratchpad/en/categories/","section":"Categories","summary":"","title":"Categories"},{"content":"","date":null,"permalink":"https://mdonertas.github.io/scratchpad/en/tags/identity/","section":"Tags","summary":"","title":"Identity"},{"content":"","date":null,"permalink":"https://mdonertas.github.io/scratchpad/en/posts/","section":"Posts","summary":"","title":"Posts"},{"content":"","date":null,"permalink":"https://mdonertas.github.io/scratchpad/en/tags/reading/","section":"Tags","summary":"","title":"Reading"},{"content":"\u0026ldquo;To read\u0026rdquo; is a verb. \u0026ldquo;Well-read\u0026rdquo; is an adjective. One is work done; the other is a badge worn. In Turkish they share a root — okumak and okumuş — but they trade in different markets.\nTurkish offers a useful opening here. Okumak isn\u0026rsquo;t applied only to text. You can read a situation, read an event, read a person. So the skill is wider than pages — parsing what\u0026rsquo;s in front of you, looking at the detail, trying to understand before concluding. Being okumuş / well-read is supposed to cover all of these: not just books, but events and phenomena too, read and understood. At least that\u0026rsquo;s what the word claims.\nIn practice it usually runs the other way. If being well-read were held as a skill — actually looking, questioning, withholding judgment — then \u0026ldquo;don\u0026rsquo;t speak before reading\u0026rdquo; would be the basic rule of that identity. But when it\u0026rsquo;s held as a position, as belonging, the rule inverts: judging without reading doesn\u0026rsquo;t damage the identity, it reinforces it. Verdict first, reading (maybe) second. Often the second step never even happens.\nCould this be the patterns that \u0026ldquo;being well-read\u0026rdquo; calcifies over time? A particular vocabulary, a particular frame of reference, a particular \u0026ldquo;I already know what this means\u0026rdquo; reflex. These patterns help at first — they build context fast — then they outlive their use and become shortcuts, maybe. Instead of reading what\u0026rsquo;s in front of you as it appears, you drop it into the pattern and read the result, maybe. A headline, a sentence, an event, a person — all run through the same operation. No text, just pattern. Maybe this is how human thinking works; maybe we need a shortcut like this.\nThe reaction economy accelerates it. Social media rewards the fast reply — slowness loses its voice. Reading takes time; reacting doesn\u0026rsquo;t. They don\u0026rsquo;t fit the same economy. Something gets cut. Usually reading does, because looking well-read is a much faster job than reading.\nAcademia isn\u0026rsquo;t immune to this speed; if anything, maybe more prone. Skipping from abstract to argument, taking positions from titles, fitting a phenomenon to a familiar frame and thinking you\u0026rsquo;ve seen it, dismissing out-of-field work as \u0026ldquo;not serious\u0026rdquo; — these are operational shortcuts that time pressure forces, but they keep legitimizing themselves as long as the \u0026ldquo;knowing\u0026rdquo; identity stays intact. Same reflex, better vocabulary.\nWhat\u0026rsquo;s interesting is the crack inside the word \u0026ldquo;well-read\u0026rdquo; — or, in Turkish, okumuş. The word carries a claim: someone who reads, thinks, waits before judging. The action often says otherwise. Nobody endorses this contradiction out loud, but nobody suspends the identity to repair it either. The protective function of the identity outweighs the obligations the skill would impose.\nSo what would reading-as-skill actually look like if it were owned? Small, boring, invisible work, I think. Probably without the instant identity-badge or the dopamine hit. But I think it\u0026rsquo;s also the only thing that closes the gap between being well-read and reading.\n","date":"24 Apr 2026","permalink":"https://mdonertas.github.io/scratchpad/en/posts/okuma-yetisi-okumus-kimligi/","section":"Posts","summary":"On the gap between reading as a verb and being well-read as an identity — and how calcified patterns short-circuit the reading of texts, events, and situations alike.","title":"reading as skill, being well-read as identity"},{"content":"Now #I\u0026rsquo;m a research group leader at the Leibniz Institute on Aging (FLI) — computational biology, aging, age-related disease. Outside of that, these days I\u0026rsquo;m learning German, starting A Little History of Science and listening to 36 Books That Changed the World on Audible (bookshelf →), and writing code for fun.\nAbout →\n","date":null,"permalink":"https://mdonertas.github.io/scratchpad/en/","section":"Scratchpad","summary":"\u003ch2 id=\"now\" class=\"relative group\"\u003eNow \u003cspan class=\"absolute top-0 w-6 transition-opacity opacity-0 -start-6 not-prose group-hover:opacity-100\"\u003e\u003ca class=\"group-hover:text-primary-300 dark:group-hover:text-neutral-700\" style=\"text-decoration-line: none !important;\" href=\"#now\" aria-label=\"Anchor\"\u003e#\u003c/a\u003e\u003c/span\u003e\u003c/h2\u003e\u003cp\u003eI\u0026rsquo;m a research group leader at the Leibniz Institute on Aging (FLI) — computational biology, aging, age-related disease. Outside of that, these days I\u0026rsquo;m learning German, starting \u003cem\u003eA Little History of Science\u003c/em\u003e and listening to \u003cem\u003e36 Books That Changed the World\u003c/em\u003e on Audible (\u003ca href=\"/scratchpad/en/books/\"\u003ebookshelf →\u003c/a\u003e), and writing code for fun.\u003c/p\u003e\n\u003cp\u003e\u003ca href=\"/scratchpad/en/about/\"\u003eAbout →\u003c/a\u003e\u003c/p\u003e","title":"Scratchpad"},{"content":"","date":null,"permalink":"https://mdonertas.github.io/scratchpad/en/tags/social-media/","section":"Tags","summary":"","title":"Social Media"},{"content":"","date":null,"permalink":"https://mdonertas.github.io/scratchpad/en/tags/","section":"Tags","summary":"","title":"Tags"},{"content":"","date":null,"permalink":"https://mdonertas.github.io/scratchpad/en/categories/thinking/","section":"Categories","summary":"","title":"Thinking"},{"content":"Populist waves keep recurring. 1890s America, 1930s Europe, almost everywhere since the 2010s. The form changes — leader, slogan, enemy — but the wave itself isn\u0026rsquo;t new. Historians have read it this way for a long time.\nAnd yet every time, we do the same thing: we find a person. A leader\u0026rsquo;s personality, a party\u0026rsquo;s strategy, an electoral mistake. We pin the responsibility to one spot. \u0026ldquo;Get rid of them, it\u0026rsquo;ll sort itself out.\u0026rdquo; Then the wave comes back and we say the same sentence again.\nI find this interesting. If a dynamic has been repeating for a hundred and fifty years, the single-person story stops holding water at some point. The individuals change, the wave stays. So the real question isn\u0026rsquo;t a person — it\u0026rsquo;s: what conditions keep producing this wave over and over?\nThat\u0026rsquo;s a shared question across economics, sociology, history, psychology. Not my field — I\u0026rsquo;m a computational biologist, my contact with these waves is mostly living inside them. But looking from outside, I\u0026rsquo;ve noticed a link: how little the fields that study these questions are funded, and how we keep repeating the same reflex, seem connected. We\u0026rsquo;ve narrowed what counts as \u0026ldquo;real science\u0026rdquo; — and what didn\u0026rsquo;t make it in is causal understanding of a phenomenon that\u0026rsquo;s been repeating for a hundred and fifty years. It didn\u0026rsquo;t make it in, so every new wave gets the same sentence.\nThen I started thinking about something else. Why is looking for a single person to blame so attractive? Maybe the brain works by parsimony — a preference for explaining the most with the fewest causes. Systemic, interactional explanations are expensive. Many parameters, uncertain, not catchable in one go. If the brain can say \u0026ldquo;this guy did it,\u0026rdquo; it relaxes. A shortcut for meaning-making.\nAnd there\u0026rsquo;s a small irony here. The moment I take the question why do we keep looking for a single person? seriously, the answer pulls me through social psychology, into cognitive science, down into basic brain function. A thought that starts with \u0026ldquo;let\u0026rsquo;s take social science seriously\u0026rdquo; ends in a place where the boundary between social and biological is already very faint. Understanding one phenomenon isn\u0026rsquo;t enough for a single discipline — even the word \u0026ldquo;field\u0026rdquo; starts to feel too sharp.\nI suppose, for now, my takeaway is this: to stop repeating the same reflex in the face of repeating social dynamics, we have to wonder why that reflex is there in the first place.\n","date":"20 Apr 2026","permalink":"https://mdonertas.github.io/scratchpad/en/posts/cevap-sosyal-bilimler-mi/","section":"Posts","summary":"Populist waves have been recurring for a hundred and fifty years, and each time we reach for a single person to blame. Where does this reflex come from — and where does taking it seriously lead?","title":"Is the answer social science?"},{"content":"","date":null,"permalink":"https://mdonertas.github.io/scratchpad/en/tags/populism/","section":"Tags","summary":"","title":"Populism"},{"content":"","date":null,"permalink":"https://mdonertas.github.io/scratchpad/en/tags/social-science/","section":"Tags","summary":"","title":"Social Science"},{"content":"","date":null,"permalink":"https://mdonertas.github.io/scratchpad/en/categories/book/","section":"Categories","summary":"","title":"Book"},{"content":"","date":null,"permalink":"https://mdonertas.github.io/scratchpad/en/tags/consciousness/","section":"Tags","summary":"","title":"Consciousness"},{"content":"","date":null,"permalink":"https://mdonertas.github.io/scratchpad/en/tags/evolution/","section":"Tags","summary":"","title":"Evolution"},{"content":"I read Peter Godfrey-Smith\u0026rsquo;s Living on Earth. The author of Other Minds and Metazoa, but this time pulling the lens out from animal minds to planet scale. The book reads organisms not as evolution\u0026rsquo;s passive products but as active causes that shape the atmosphere, soil, other species and their evolution — coral polyps building their reefs, photosynthesis redrawing the gas balance of the surface. From there it moves to animal minds where sensing and acting meet, and ends on the ethics of humans being one of those Earth-shaping forces.\n","date":"18 Apr 2026","permalink":"https://mdonertas.github.io/scratchpad/en/posts/living-on-earth/","section":"Posts","summary":"Peter Godfrey-Smith\u0026rsquo;s \u003cem\u003eLiving on Earth\u003c/em\u003e — a book that reads life not as evolution\u0026rsquo;s passive product but as an active cause shaping the planet.","title":"living on earth"},{"content":"","date":null,"permalink":"https://mdonertas.github.io/scratchpad/en/tags/ethics/","section":"Tags","summary":"","title":"Ethics"},{"content":"Peter Godfrey-Smith\u0026rsquo;s Living on Earth. Author of Other Minds and Metazoa; professor of History and Philosophy of Science at the University of Sydney. It had been sitting on my reading list for a long time; I finally started it. Already at the beginning, it triggered a few thoughts\u0026hellip;\nTwo perspectives. On one side, we too are a creature inside the evolutionary process — a species that has evolved traits affecting other species\u0026rsquo; evolution, but not the only one. The book actually opens with the cyanobacteria example — by polluting the atmosphere with oxygen, they had a catastrophic effect on species that had no oxygen tolerance at the time, while shaping the world we now live in, the world we need in order to live. What we do is, in the end, a \u0026ldquo;natural\u0026rdquo; process. On the other side, as conscious creatures we\u0026rsquo;re somehow responsible. We can question what we do, change it, weigh it against our conscience.\nAt first glance the two perspectives look separate. The more I think about it, the less sure I am they are.\nWhat is consciousness, exactly? I don\u0026rsquo;t fully know. It\u0026rsquo;s something I want to read more about. But my current sense: a complex phenomenon that emerges from the interaction of hormones, chemicals, electrical currents. Not something apart from biology — an output of biological processes. If that\u0026rsquo;s right, then \u0026ldquo;consciously taking responsibility\u0026rdquo; is also a biological behavior. Not a separate category outside the evolutionary process — a layer within it.\nConscience fits into this whole too. We experience the discomfort of polluting the environment as \u0026ldquo;responsibility\u0026rdquo; — but conscience isn\u0026rsquo;t a separate biological component. It\u0026rsquo;s a product of our evolution as a social species. The social structure itself is also evolutionary. So conscience too, and the sense of responsibility, don\u0026rsquo;t step outside the evolutionary process. They\u0026rsquo;re its outputs. One more layer.\nHere\u0026rsquo;s something interesting. Could it be that having different moral positions, different value judgments within a population — the way genetic diversity provides resilience against environmental change — makes that population more resilient too? Imagine, all at once, everyone rejecting a particular behavior — the ecological and societal consequences would be extreme, maybe \u0026ldquo;good\u0026rdquo; maybe \u0026ldquo;bad\u0026rdquo; but extreme. 1 Just as genetic diversity is a kind of insurance, moral diversity might be too. If differences in height, color, disease resistance can be an evolutionary advantage, maybe differences in value judgments belong in the same category?\nBut right here, one thing ends and another begins. \u0026ldquo;Evolutionarily advantageous\u0026rdquo; and \u0026ldquo;morally right\u0026rdquo; aren\u0026rsquo;t the same thing. That diversity is advantageous for the long-term persistence of a population doesn\u0026rsquo;t say other views are right. It only explains why that diversity exists. Past this point, I think, it\u0026rsquo;s no longer biology\u0026rsquo;s subject — it\u0026rsquo;s philosophy\u0026rsquo;s. We live inside certain social norms. Different social structures produce different \u0026ldquo;truths.\u0026rdquo; These truths are, for me, the frame I build my own life around. When I live by my own truths, I\u0026rsquo;m a happier person. But my truths don\u0026rsquo;t have to match anyone else\u0026rsquo;s. Environment, personal history, lived experience — all of these shape what any given person calls \u0026ldquo;right.\u0026rdquo; I can encourage others toward what I see as right, argue my case. But what\u0026rsquo;s happening is argument. Not an absolute truth — a perspective, a view.\nAnd maybe a capacity for persuasion, itself shaped by a gene × environment interaction, is one more biological layer underneath view-diversity, and through that, behavioral diversity?\nI\u0026rsquo;m early in the book. I don\u0026rsquo;t know where the author ends up. Maybe what I\u0026rsquo;m thinking doesn\u0026rsquo;t fit there at all; maybe it\u0026rsquo;s getting close\u0026hellip;\n","date":"17 Apr 2026","permalink":"https://mdonertas.github.io/scratchpad/en/posts/bir-katman-daha/","section":"Posts","summary":"Godfrey-Smith\u0026rsquo;s \u003cem\u003eLiving on Earth\u003c/em\u003e triggered a thought: are being an evolutionary creature and carrying conscious responsibility two layers of the same whole? And might moral diversity function like genetic diversity?","title":"one more layer?"},{"content":"","date":null,"permalink":"https://mdonertas.github.io/scratchpad/en/tags/beginning/","section":"Tags","summary":"","title":"Beginning"},{"content":"","date":null,"permalink":"https://mdonertas.github.io/scratchpad/en/tags/blog/","section":"Tags","summary":"","title":"Blog"},{"content":"printf(\u0026#34;hello, world\\n\u0026#34;); A new programming language, a new development environment, a new computer — this is the first thing I run whenever I set something up. Is the compiler working? Is the interpreter alive? Does the screen produce output? If you see \u0026ldquo;hello, world\u0026rdquo;, good — the system is alive.\nThis post is an extension of that. I set up a new blog, the theme settled in, two languages are working, the post flow looks clean. Something comes out — you\u0026rsquo;re reading this. So it works.\nWhat comes next? Notes, thoughts, experiments. I wrote about what I\u0026rsquo;ll be writing about on the About page; the only goal here is \u0026ldquo;hello\u0026rdquo;.\nhello, world.\n","date":"16 Apr 2026","permalink":"https://mdonertas.github.io/scratchpad/en/posts/merhaba-dunya/","section":"Posts","summary":"First post — blog is up, system is alive. What comes next: notes, thoughts, drafts.","title":"hello, world"},{"content":"","date":null,"permalink":"https://mdonertas.github.io/scratchpad/en/categories/meta/","section":"Categories","summary":"","title":"Meta"},{"content":"Why I write here #To learn. And to share what I learn.\nAbout fifteen years ago my first blog was called compbio scratchpad — back then I wrote about my own process of learning computational biology. It turned out to help friends around me, and beyond that, trying to explain something in my own words helped me too. A win-win — and it still makes me happy.\nThis blog won\u0026rsquo;t stay strictly within computational biology anymore. I want to share what I learn and think about life too — in scratchpad mode. Not polished ideas and claims like I\u0026rsquo;m writing a book; the environment I want is one where I\u0026rsquo;m genuinely thinking aloud, sharing the process of thinking itself. Because that same process is what helps me shape my own thinking.\nShort bio #I\u0026rsquo;m a computational biologist running my own research group at the Leibniz Institute on Aging (FLI) in Jena. We work on understanding aging, measuring it, and slowing it down — leaning heavily on AI and computational methods. Group page: donertas-group.github.io.\nI might write the story behind some of these turning points as a separate post later.\n","date":null,"permalink":"https://mdonertas.github.io/scratchpad/en/about/","section":"Scratchpad","summary":"\u003ch2 id=\"why-i-write-here\" class=\"relative group\"\u003eWhy I write here \u003cspan class=\"absolute top-0 w-6 transition-opacity opacity-0 -start-6 not-prose group-hover:opacity-100\"\u003e\u003ca class=\"group-hover:text-primary-300 dark:group-hover:text-neutral-700\" style=\"text-decoration-line: none !important;\" href=\"#why-i-write-here\" aria-label=\"Anchor\"\u003e#\u003c/a\u003e\u003c/span\u003e\u003c/h2\u003e\u003cp\u003eTo learn. And to share what I learn.\u003c/p\u003e\n\u003cp\u003eAbout fifteen years ago my first blog was called \u003cstrong\u003ecompbio scratchpad\u003c/strong\u003e — back then I wrote about my own process of learning computational biology. It turned out to help friends around me, and beyond that, trying to explain something in my own words helped me too. A win-win — and it still makes me happy.\u003c/p\u003e","title":"About"},{"content":"","date":null,"permalink":"https://mdonertas.github.io/scratchpad/en/books/","section":"Scratchpad","summary":"","title":"Bookshelf"}]