The Disordered Mind…, Eric R. Kandel

The Disordered Mind: What Unusual Brains Tell us about Ourselves, Eric R. Kandel, 2018.

Kandel is an eminent neuroscientist, known for his work on the low-level mechanisms of learning and memory as demonstrated in Aplysia. He’s won a host of prizes, including the Nobel for this work. Interestingly, as an undergraduate he majored in humanities, and afterwards became a psychiatrist, before migrating into neuroscience. Now in his 90’s, he is writing about larger themes, and addressing himself to more general audiences.

Continue reading The Disordered Mind…, Eric R. Kandel

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Snow Crystals, Kenneth Libbrecht

Snow Crystals: A Case Study of Spontaneous Structure Formation, Kenneth Libbrecht, 2022

This is Libbrecht’s magnum opus, at least on snow; this goes deep into the science. …and I love that he has ordered the references by date, so you can see the history of the science leading up to Libbrecht’s work.

Notes still in progress

Continue reading Snow Crystals, Kenneth Libbrecht

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Why Machines Learn*

November 2024 – April 2025

* Why Machines Learn: The Elegant Math Behind Modern AI, Anil Ananthaswamy, 2024. (Ananthaswamy is a science journalist, not an AI person, as I initially assumed. That said, he’s quite good.)

My Take on the Book

As discussed below, this is not the sort of book I’d usually read — my interest stops at the level or algorithms, and understanding the underlying math just doesn’t grab me. This really is a book for people interested in the math. But I learned some interesting, mostly-meta things from it.

  • Early learning systems. Early research focused on using simple networks (e.g. Perceptrons) to recognize fuzzy inputs like hand-written letters. This involved presenting a system with an input, having it try to map that input to a category, and then providing feedback to the system based on the mismatch between the input and the right (label for the input) result. Much of the math to do with measuring and tracking the degree of error.
    Even though they sound different things, this is also how adaptive filters: they try to learn the characteristics of noise so as to minimize it.
  • Matrices model networks! More generally, matrices and linear algebra are exceptionally useful for modeling networks.
  • A Lot of AI learning is just gradient descent. A lot of the math involves figuring out multi-dimensional spaces that characterize a domain, and using some sort of algorithm, usually involving gradient descent, to find the minima. The minima, of course, being where error is minimized, meaning that the system is performing as well as possible at its learning task.
  • People made jaw-droppingly crude simplifications, and yet the math still worked! Something I found very interesting was that, once you have an algorithm that appears to do what you want, you can make shockingly crude simplifications to it that (1) make it possible to run it in very high dimensional spaces, and (2) it will still work well.
    For example, if you are doing gradient descent in a multi-dimensional space, you can get away with finding the gradient for a randomly chosen single dimension (stochastic gradient descent), rather than in all dimensions.
    I still don’t get why that works, but it does. Not only does god play dice with the universe, but he’s OK with kludges tool.
  • Adding ‘noise’ can improve learning. Adding noise to data sets on which machines are trained can make the learning more robust. To me this seems sensible, in that, especially if you add different amounts of noise to the same features, you can multiply the training set and counter the tendency to overfit.
    Of course the noise ought to be ‘natural,’ which is to say that it ought to be native to the distribution from which you are sampling. I presume it is possible to figure that out for particular domains, but don’t actually know.
  • Monty Hall as Enabling Inside Trading. Hurrah. I finally understand the Monty Hall problem. In my defense, I will note that the ‘story problems’ I had in my primary education worked against my ability to solve it. In story problems, the stories didn’t actually matter, they were just frameworks for presenting a math problem. But in the Monty Hall problem, the key bit is Monty — he has inside information and will not choose to spoil the game by revealing where the prize is. Thus his action is not random, and provides additional information. If the Monty Hall problem were instead re-presented as an earthquake or windstorm accidentally revealing a goat behind one of the doors, the answer would be different.
  • WTF? — Why does deep learning work so well? We don’t, currently, really understand why deep learning works as well as it does. Spooky.,
  • Why do deep neural nets keep learning new things after they’ve overfit their training data? In particular, there is the paradox of benign overfitting / harmless interpolation: a deep neural network has so many parameters that it should perfectly overfit the training data, but — after enough training — it is able to generalize correctly to new data, something that it would not do if it had overfit. So what is going on?
    You’d think that once it was able to model the training data perfectly, it would stop learning. But perhaps the continued ‘training’ is introducing some kind of ‘noise’ or fluctuation which keeps perturbing the neural net?
  • Is something happening in the hidden layers??? I feel like there must be interesting stuff going on in the hidden layers of deep neural networks as their training continues beyond the point of benign overfitting/harmless interpolation. I don’t really understand what continued training of a deep neural net does — either directly or via back propagation. I have a vague idea idea that structure of the hidden layers undergoes some kind of phase change, in an analog to fractional crystallization. (In a magma chamber, where when the magma cools to a certain point a particular mineral crystalizes and precipitates, changing the nature of the magma and enabling further crystallization (and/or re-solution of prior crystalites) as the mix changes.)
  • In the epilogue the author raises the questions of whether LLMs have really learned, or are just doing statistics. I’m in the “stochastic parrot” camp.
Continue reading Why Machines Learn*

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Four Billion Years and Counting…

Four Billion Years and Counting: Canada’s Geological Heritage. Produced by the Canadian Federation of Earth Sciences, by seven editors and dozens of authors. 2014.

November-December, 2024.

I am reading this with CJS. It is a nice overview of regional geology, and it is nice that all the examples come from Canada, and at least some of the discussion is relevant to Minnesota Geology. The book is notable for its beautifully done pictures and diagrams.

Continue reading Four Billion Years and Counting…

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Through the Language Glass

by Guy Deutscher

October 2024

This is an excellent book; interesting well-documented science, and some beautiful and erudite writing as well. The basic argument — that grammar determines what must be specified, rather than what can be specified, and in that manner instills certain habits of mind that effect how people see the world — seems correct, if not quite living up to the subtitle of the book: Why the World Looks Different in Other Languages.

Perhaps the most interesting and fun part of the book was to be introduced to languages that work very differently from English: The Mates language (in Peru) that requires speakers to specify whether the fact they report is based on personal observation, indirect evidence, or hearsay; and the Australian language that has no egocentric prepositions, but requires all positional information to be reported in terms of the cardinal directions, thus requiring their speakers to always be oriented.

This book was a pleasure to read. I plan to seek out other work by this writer. 

Contents

Front Matter

On whether languages reflect the characteristics of their speakers, he writes:

Many a dinner table conversation is embellished by such vignettes, for few subjects lend themselves more readily to disquisition than the character of different languages and their speakers. And yet should these lofty observations be carried away from the conviviality of the dining room to the chill of the study, they would quickly collapse like a soufflé of airy anecdote-at best amusing and meaningless, at worst bigoted and absurd.

— p. 2

The basic argument of the book is this:

The effects that have emerged from recent research, however, are far more down to earth. They are to do with the habits of mind that language can instill on the ground level of thought: on memory, attention, perception, and associations. And while these effects may be less wild than those flaunted in the past, we shall see that some of them are no less striking for all that.

I think it is correct, but that the subtitle of the book – Why the World Looks Different in Other Languages – is a bit of an exaggeration.

C1-5: <Reprise of history and status of color terms>

C1: Naming the Rainbow

This chapter reprises now-unknown work by William Gladstone (now remembered as an English prime minister) on Homer and his writings, and focuses in on particular on one chapter in Gladstone’s monumental 3,000 page work: a chapter on Homer’s use of color terms.

Gladstone’s scrutiny of the Iliad and the Odyssey revealed that there is something awry about Homer’s descriptions of color, and the conclusions Gladstone draws from his discovery are so radical and so bewildering that his contemporaries are entirely unable to digest them and largely dismiss them out of hand. But before long, Gladstone’s conundrum will launch a thousand ships of learning, have a profound effect on the development of at least three academic disciplines, and trigger a war over the control of language between nature and culture that after 150 years shows no sign of abating.

Gladstone notes that Homer uses color terms in odd ways — the famous “wine dark sea” (really “wine-looking” sea) being just one example.

Mostly Homer, as well as other Greek authors of the period, use color very little in their descriptions: mostly they use black or white; terms for colors are used infrequently and inconsistently. For example, the only other use of “wine-looking” is to describe the color of oxen.

Gladstone’s fourth point is the vast predominance of the “most crude and elemental forms of color”-black and white-over every other. He counts that Homer uses the adjective melas (black) about 170 times in the poems, and this does not even include instances of the corresponding verb “to grow black,” as when the sea is described as “black-ening beneath the ripple of the West Wind that is newly risen.” Words meaning “white” appear around 100 times. In contrast to this abun-dance, the word eruthros (red) appears thirteen times, xanthos (yellow) is hardly found ten times, ioeis (violet) six times, and other colors even less often.

C6: Crying Whorf

This chapter describes the origin, rise and fall of linguistic relativity. Sapir is depicted as respectable but making over-stated claims; Whorf comes across as a charlatan, for example, making claims to have deeply studied Hopi, when he only had access to a single informant in New York – and making broad claims that are entirely wrong (e.g. that the Hopi language does not have a future tense). 

Deutscher traces the origin of linguistic relativity to Wilhelm von Humboldt in 1799,  whose “linguistic road to Damascus led through the Pyrennes.” Deutscher encountered the Basque language, and found that it was radically different from the languages linguists tended to study. He then sought out other ‘more exotic’ languages, which he found by going to the Vatican library and studying the notes of Jesuit missionaries to South and Central America: “…Humboldt was barely scratching the surface. But the dim ray of light that shown from his materials felt dazzling nonetheless because of the utter darkness in which he and his contemporaries had languished.” p. 135 Although Humboldt’s ideas led to linguistic relativity, it should be noted that he had a much more nuanced and correct view: In principle, any language may express any idea; the real differences among languages are not what they are able to express but in “what it encourages and stimulates its speakers to do from its own inner force.” But this view was not carried forward, and instead: “The Humboldtian ideas now underwent a process of rapid fermentation, and as the spirit of the new theory grew more powerful, the rhetoric became less sober. ”

All that said, Deutscher argues it is a mistake to dismiss the idea that language has no influence over thought. But rather than taking the strong case the language constrains thought, he instead argues the habits of language may lead to habits of mind. In the case of the influence of language, and refers to the idea that Boas introduces and that Jakobson crystalized into a maxim: “Languages differ in what they must convey, and not in what they may convey.”

Phrases I like

“…has still the power to disturb our hearts.” [Sapir, referring to Homer, Ovid, etc.] p. 129

“[His] linguistic road to Damascus led through the Pyrennes.” p. 134

“…Humboldt was barely scratching the surface. But the dim ray of light that shown from his materials felt dazzling nonetheless because of the utter darkness in which he and his contemporaries had languished.” p. 135

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The Light Eaters…, Zoë Schlanger

September 2024 – January 2025

These are notes on “The Light Eaters: How the Unseen World of Plant Intelligence Offers a New Understanding of Life on Earth“, by Zoë Schlanger (read with Rachel). On the positive side, it changed my perspective on ‘plant behavior’ — I knew about some tropisms, but it introduced me to a whole range of ways in which plants sense and respond to their environment and surroundings. Schlanger also writes clearly, and has some lovely turns of phrase, some of which I list below. On the negative side, I think the book is marred by attempts to make it overly dramatic or paradigm-shifting — or perhaps she really buys the claim that plants can be seen as having nervous systems, agency and even consciousness. I don’t think that’s supportable, unless one really wants to broaden (and weaken) the criteria by which we assess such things, and I don’t see the value in that.

Continue reading The Light Eaters…, Zoë Schlanger

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w/CJS: Best Science & Nature Writing, 2022

Reading The Best American Science and Nature Writing , 2022 (ed. Ayaba Elizabeth Johnson) with CJS.

So far, as of May 2024, this is a very enjoyable read. I particularly appreciate the efforts of the editor to create a nice progression of topics, giving what is essentially an eclectic sampling of articles a higher level narrative.

September 2024: Nearing the end; still an enjoyable read.

Favorites

After finishing the book, here are my favorites

Top Five Six

  • C2 – What Slime Knows. Really gave me a new view of slime molds. I hadn’t realized the degree of intelligence a seemingly simple colonial organism can possess. Offers a counter-narrative to the usual ideas about what is necessary for intelligence.
  • !! C7- Rising Groundwater. This is the biggest eye-opener in the book, at least for me. While sea level rise will have very obvious impacts on costal regions, this makes the point that sea water will also cause a rise in ground water and, with or without infiltrating it, will cause a lot of problems for a lot more people than are effected directly by sea level rise. Think corroding water and gas pipes, malfunctioning sewage systems, and failing electical systems. This is one I’ll tell other people about.
  • C15: Poisoned—Part I: The Factory. Not a pleasant story. Talks about working conditions in a battery recycling factory, the horrible degree of exposure to lead, and the toll it takes on the workers. Shocking for two reasons: one is that the company behind this is based in Minnesota, and is in theory doing good things (recycling lead from batteries); second, that the industry and factories are regulated, but that in spite of that conditions are horrible.
  • !! C25 – Why Combining Farms & Solar Panels Could Transform How We Produce Both Food and Energy. A hopeful and plausible tale about how we can do better quite easily. A win-win. Perspective shifting and positive. I’ll mention this to others.
  • : – ) C28 – Beavers Are Firefighters Who Work for Free (Sierra) A perspective shifting article on role beavers can play in making land more resistant to wildfires, and also points out that the autonomy of tribes can allow them to take the forefront in experimenting with more sustainable approaches to environmental problems.
  • : – ) C32 – A River Reawakened (Orion). Not a perspective shifter, but just a very pleasant positive piece on what happens when a river is undammed, the problems that need to be addressed, and the rapidity of recovery. This was going to be an honorable mention, but I liked it too much!

Honorable Mentions

Continue reading w/CJS: Best Science & Nature Writing, 2022

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w/RB: The Master Builder: How the New Science of the Cell is Rewriting the Story of Life, Alfonso Martinez Arias

* The Master Builder: How the New Science of the Cell is Rewriting the Story of Life, Alfonso Martinez Arias, 2023

March 2023…

I am reading this book with RB, a chapter or two at a time. My first impression is that it is going to be a great read. It has interesting and new-to-me science straight from a scientist who has spent his career studying this area, and it is well written too.

The premise of the book is that DNA gets too much credit for its role in shaping organisms, and that it is also important to pay attention to the ways in which cells carry out the ‘instructions’ of DNA. Unlike DNA, cells can respond to their environment, sense ambient conditions at the cellular level, and respond to distance and orientation. Quite a number of things that we would presume would be determined by genetics — everything from finger prints and retinal patterns to birth defects, propensity to diseases, and the location of organs in the human body — are determined by cells rather than DNA.

Continue reading w/RB: The Master Builder: How the New Science of the Cell is Rewriting the Story of Life, Alfonso Martinez Arias

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LS: A Wilder Time,* William E. Glassley

*A Wilder Time: Notes from a Geologist at the Edge of the Greenland Ice. William E. Grassley, 2018.

A lyrical book that provides an account of a geologic expedition to gather evidence for a 1.8 Ga collision between continents that resulted in a series of shear zones in western Greenland. Also important for providing evidence that plate tectonics has been going on for a long time, something that has been contested. Content is quite interesting, but I also appreciate it for its lyrical writing about landscape and geology, which is this focus of my “LS” project.

Continue reading LS: A Wilder Time,* William E. Glassley

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EP#14: 2023 Best Science & Nature Writing–Overview

* The Best American Science and Nature Writing of 2023 (ed. Carl Zimmer)

February – March 2024

CT and I selected this book to continue our essay project. However, after reading the first three pieces, we have reconsidered. Although the articles are interesting, they are not what either of would call essays. It’s really journalism, with the focus on ideas. The prose is generally clear and workman like, but as yet we have not encountered any writing that makes us pause to savor the phrase. We intend to look through the book, and — by paying attention to where the piece was originally published – see if we can come up with more essay-like pieces. However, we both suspect, that the book will not past muster vis a vis our project, and that we will move on to something else following our next meeting.

Continue reading EP#14: 2023 Best Science & Nature Writing–Overview

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LS: Land Above the Trees: A Guide to American Alpine Tundra, Ann Zwinger & Beatrice E. Willard

February 2024…

This book was recommended in Kim Stanley Robinson’s The High Sierra: A Love Story, as a good guide to the ecology and botany of the Sierra Nevada (and the upper portions of other North American ranges). And, indeed, it is beautifully written with a narrative style in which the reader moves through landscapes with the authors, looking at this and that, in contrast to what I had expected would be more of a catalog or encyclopedic approach. The book is divided into two principle parts: part 1 examines elements of ‘above the trees’ ecosystems, like fellfields or krumholtz; part 2 looks at particular North American tundra ecosystems, with one chapter being on the Sierra Nevada.

Continue reading LS: Land Above the Trees: A Guide to American Alpine Tundra, Ann Zwinger & Beatrice E. Willard

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w/CS: Gulp: Adventures on the Alimentary Canal, Mary Roach

January-February 2024

Gulp: Adventures on the Alimentary Canal, Mary Roach, 2022. I am reading the with CS. Mary Roach is a popular science writer who has developed a ‘brand’ of doing popular science books with toungue-in-cheek titles like Gulp, Stiff, Bonk, and so forth.

My impression after the first two chapters is that it will be a fun, fairly light read. She is very good at tossing in the amusing descriptive phrase.

Continue reading w/CS: Gulp: Adventures on the Alimentary Canal, Mary Roach

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EP #`13: Awakenings, Oliver Sacks

January 2024

Entry 13 in the Essays Project with CT; this is the seventh book we’ve read by Oliver Sacks. This is the book that, with the help of a documentary and then movie, transformed him into something of a celebrity. It is an account of the experience of ‘awakening’ patients with Parkinson’s induced by Encephalitis Lethargia by administering L-Dopa, their experiences of returning to a sort of normal life, and then their declines due to the follow-on negative effects of L-Dopa.

Continue reading EP #`13: Awakenings, Oliver Sacks

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LS*–The High Sierra: A Love Story, Kim Stanley Robinson

November 2023

The High Sierra: A Love Story, by Kim Stanely Robinson. 2022.

* I was reading this for other reasons, but nevertheless it fits well into my project to read essays that focus on landscape and natural history.

TL;DR: I love this book. But it is not for everyone. On the other hand, it is organized in such a way that readers interested in particular topics — geology, history, etc. – could skip through the book attending to one or a few themes that interest them. It has great pictures, too.

#

I’m a big fan of KSR, and think it likely that I’ve read everything he’s written, although it is possible that that omits a few early science fiction novels that were retroactively published after he became better known. I like the complex characters he develops, the intensely developed worlds he portrays, and especially his attention to geology, climate, economics, politics, and the role of large institutions – themes that are uncommon in much science fiction. Also unusual is that he sometimes ventures beyond the borders of SF, as with his novel Years of Rice and Salt, and especially with this book, which is multi-threaded work the interweaves memoir, geology, natural history and history.

Continue reading LS*–The High Sierra: A Love Story, Kim Stanley Robinson

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w/CS: Elixir: A History of Water and Humankind*, Brian Fagan

November 2023…

*Elixir: A History of Water and Humankind, Brian Fagan. Reading with CJS.

Comment after finishing seven chapters:
There is interesting material here, and I am happy to be reading it. However, the writing is not grea: it is difficult to follow if you are really trying to get a deep sense of what is going on.

  • The same date is sometimes referred to as 4,000 BCE, 6,000 years ago, or a millennia after another event. I can do the math, but pausing to do so drops me out of the flow of the text.
  • The maps helpfully included in the chapters lack many of the places referred to in the text: Where are the Taurus mountains? Are they the same as the mountains near Cudi Dag (not shown on the map either). Clearly, neither writer nor editors ever tried referring to the associated map…
  • Places are also referred to with different names: The Lands of Enlil; Southern Mesopotamia; the lands to the south of modern-day Bagdad; the Fertile Crescent refer, I think, to the same area. But it is difficult to be sure.
  • Often it is unclear what the relationship between sequential examples are — are they supposed to reinforce one another, or complement one another, or are they being presented for some other reason? Sign-posting would be really helpful.

Preface

The three themes of this book are (1) gravity and its fundamental impact on the flow of water; (2) the relationship between ritual and water management; and (3) sustainability. One point the book will take up is the way in which the invention of the mechanical pump transformed the mining and movement of water.

The book takes an anthropological perspective, closely examining the relationships between water technologies and human usage and management practices, and looking at the role rituals play. It looks at both historical examples — even reaching into the deep past where the primary source of information is archeological work — and present day examples. And of course the book addresses the ongoing crisis in water sourcing and distribution, and the question of sustainability.

Continue reading w/CS: Elixir: A History of Water and Humankind*, Brian Fagan

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EP#12: The Mind’s Eye, Oliver Sacks

Entry 12 in the Essays Project with CT; and this is the sixth book we’ve read by Oliver Sacks. Here we take up the neurological case account essays for which he is best known, after reading his two autobiographies, and other writings ranging from general essays to an account of his travels in Oaxaca. This book, published in 2010, explores cases in which people have lost visual abilities that we all take for granted – not so much blindness (although maybe there will be some essays on that), but rather the consequences of some of the many ways in which the complex and intertwined elements of the visual processing system may be disrupted.

Continue reading EP#12: The Mind’s Eye, Oliver Sacks

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w/CS: Islands of Abandonment: Nature Rebounding in the Post-human Landscape, by Cal Flyn

September 2023

Islands of Abandonment: Nature Rebounding in the Post-human Landscape, by Cal Flynn, 2021.* This book looks at how nature — fungi, plants, animals – are re-colonize landscapes that have been destroyed and abandoned by humans. Examples include massive slag piles, nuclear test grounds, etc. It examines both how primary succession occurs in unpromising circumstances, and how the absence of human presence facilitates re-wilding. In the introduction, the author notes that we are now in the midst of a vast self-directed experiment in re-wilding, driven in part by the concentration of people in cities (and a soon-to-be-decreasing population), and in part by the depletion of non-sustainable natural resources that leave ‘waste lands’ behind.

Post-reading comment: There are three or four chapters in the book that are great, and really align with the aims laid out above. Unfortunately, more of the chapters, particularly as one progresses in the book, are more in the line of what I would call disaster tourism: lyrical descriptions of degraded environments and terrible situations, with little or no mention of how the ecosystem has adapted or not.

* Reading with CJS, fall of 2023

Continue reading w/CS: Islands of Abandonment: Nature Rebounding in the Post-human Landscape, by Cal Flyn

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w/RB: An Immense World: : How Animal Senses Reveal the World Around Us, Ed Yong

An Immense World: How Animal Senses Reveal the World Around Us, Ed Yong, 2022.

Overall, a good book. Yong writes well, and sometimes has very nice turns of phrase, though I’d say his gift is more for clarity and content than lyricism. The downsides of the book — small ones but nevertheless there — is that he often doesn’t go as deeply into the mechanisms and neurophysiology of sensing as I would like. It is also the case that one gets a bit of whiplash from looking first at this organism, and then at that, and then at that — but I don’t see how that could have been avoided in this sort of book.

To summarize briefly and incompletely, here are some of the points I found most interesting:

  • What we think of as a single sense (e.g., vision) can be quite complex. All of the following can be separate: distinguishing light from dark areas; color vision (and bi- tri- and tetra-achromatism); ability to see polarized and/or UC and/or infrared light; and more.
  • Also, the same sense can be configured and deployed in different ways: the shape of an organism’s visual field is tightly bound with its role in the food web; an organism may have one, two or multiple eyes, and may be able to move them independently; and so on.
  • Some senses seem easy to evolve, in that they have been independently evolved at many different points in time. And then lost, and then re-evolved.

April 2023 – February 2024

Introduction

The book begins with a fanciful description of a room with different creatures in it, including a human, a robin, an elephant, a spider, and so on. It uses this to make the point that the different creatures, although all in the same room, have radically different impressions of the room and its occupants. What is evident to one is invisible to another. An organism’s very particular view of its environment – is referred to as its umveldt, coined by Jacob Uexkull in 1909.

Continue reading w/RB: An Immense World: : How Animal Senses Reveal the World Around Us, Ed Yong

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