• 0 Posts
  • 100 Comments
Joined 1 year ago
cake
Cake day: July 18th, 2023

help-circle
  • I’m going to hazard a guess it’s a combination of falling budget and an over reliance on autocorrect. If it’s like other industries, they’re trying to get more articles out with fewer people.

    I know that I often have an atrocious number of typos - but some are entirely the fault of autocorrect either changing a correct word to something else or correcting a typo to a word that makes no sense in the context of the sentence. I’m hoping that the next generation will improve this.

    If anything a now - not typo at least indicates that it was written by a human. LLM errors generally don’t involve that sort of thing.



  • I can’t say what their corporate culture is like now, but they’ve had a pretty poor reputation in the past, including the notion that the lowest performing 10% should be fired every year. The Amazon folks I’ve known have been great people - not at all the Gordon Gecko types you’d imagine from that - but culture in large corporations varies a lot by the team you’re in.

    I came up with a saying back in the 90s when I was doing the startup scene - “Do you want it right, or by Tuesday?” Sometimes they do indeed need it by Tuesday. More of the time they have no idea why you need the extra days to get it right. But it’s really important for those in a leadership position - whether they’re managers or senior engineers - to push back and set expectations.



  • Personally, I do think of viruses as a form of life, and although it’s not universally held by any means, I think there’s a growing consensus around the idea.

    That’s probably as minimalistic as I would go, though. I mean, you can make a similar argument to some extent about prions, but prions are too close to being “just chemistry” for me.

    Viruses on the other hand cooperate and compete in complex ecosystems, which in my opinion magnifies the complexity of a virus as an element of a complex adaptive system. They don’t have a metabolism as such (which is why so many don’t consider them living), but their ability to conduct theft of resources of more complex and obviously living systems makes me push them to group of living things.

    One of the nearest things about biology is that there’s always an exception to the rules and examples, and the simplifications we make when teaching bio 101 are really best learned as rules of thumb. Things like what a “gene” really is, the operation of selection, and even what constitutes a “species” can lead to some really interesting discussions.


  • Theoretical biologist here. I’m going to push back on that just a bit. I think that you might have mentioned Selfish Gene, too. That was not the best book even at the time of publication (most biologists had a number of problems with it oversimplifying in a way that’s probably similar to what anthropologists think about Guns Germs and Steel). It also has been getting worse the more we learn.

    Evolution acts on the phenotype, not the genotype. It affects the gene makeup of the population through differential reproduction rates. “Fitness” can be measured as a value relative to the rest of the population specifically by using the number of offspring. So what I’m saying here is that all factors that affect phenotype, whether genes or other factors, affect evolution.

    So, of course genes are important. But you have epigenetic factors, too. link here You also have extensive non-coding regions that regulate transcription. You have rna editing. And so on.

    If you’re interested, I would highly recommend a book called How Life Works by Phillip Ball. It was just published in November and is an outstanding summary of how much our understanding of life has evolved (heh) in the last 20 years or so.


  • I can give you my impression and that of the people I spoke to about it. I’m coming from the perspective of a theoretical biologist who was heavily involved with computational models of complex systems - particularly ones with biological foundations. I worked with simulations ranging from molecular cell biology up to ecosystems.

    I don’t want this to sound dismissive, but CA are cartoonishly simple versions of complex systems. Once you get past illustrating the idea that simple rules can give rise to complex behaviors, that they’re Turing complete, and that there are neat and interesting phenomena that can arise, I think you’re pretty much done. They’re not going to show you anything about the evolutionary dynamics that drive carcinogenesis. They’re not going to let you explore the chemistry that might have given rise to the origin of life. They’re not going to let you model how opinions and behaviors cascade on social networks.

    Topics like emergence are core to complexity theory, but CA can only illustrate that it exists, and it does so in such an abstract way that it doesn’t really translate into an understanding of how emergence is grounded in real world systems.

    Wolfram’s problem, in my opinion, is that he was largely disconnected from the complex adaptive systems community, and for some reason didn’t realize we had largely moved on. I don’t know anyone in the CAS community that thought his work was groundbreaking.

    I do have to say that Robert Sapolsky seems to have found his work interesting, and I am very deeply interested in Sapolsky’s work. But he’s a neurobiologist, not a complexity scientist, and he doesn’t draw a concrete connection between Wolfram’s work and his own, other than the generic connection that complex systems can arise from simple rules. That’s something we’ve known since Conway and Lorenz.

    My mind is open to counter arguments, but that was my impression and as far as I could tell, the same was true of my colleagues. I think that the general academic reception to his book bears this analysis out. It’s like if someone wrote a comprehensive book about all kinds of Prisoner’s Dilemma models long after we’ve moved on from PD to modeling more complex and accurate depictions of cooperative versus competing interactions. Students should absolutely study PD, and they should study CA. It’s just not something you want to hang your academic hat on at this point.

    Mathematica, on the other hand, is pretty neat.



  • I am a biologist but I’m warning you up front that I’m going off of memory on this one, and animal vision was never my area of specialization (except in evolutionary models, which I can get into but which don’t apply to your specific question).

    Cat vision, as I recall, is optimized around two things - seeing in low light conditions and seeing motion. Cats can have a harder time focusing on stationary objects and I don’t believe they have a particularly high level of processing for visual detail.

    It’s important to remember - especially when we’re talking about trying to reverse engineer what another species sees - that the phenomenon we refer to generally as “vision” is an incredibly complex process. It involves multiple cell types, chemical and physical processes, and things like memory, taste, and smell. You’ve probably seen comments on nasty rooms where people say “I can smell this picture,” or caught a whiff of a cologne or perfume that evoked powerful memories including being able to visualize the person you associated it with, even though they’re not actually in front of you.

    The visual parts of your brain can be activated absent any input from your eyes (something those with PTSD can know all too well), and your eyes take in a huge amount of information that never makes it to the visual processing layers of your brain, because you simply disregard it.

    So when we look at the cells in a cat’s eye, we’re only seeing (so to speak) a very tiny part of the story. We learn more when we start to study how cats respond to visual stimuli - how they hunt, how they play, how they explore their worlds - but it’s all a blind men and the elephant kind of thing. Plus, I have to imagine it’s pretty hard to get that kind of research funded.

    Anyway, I’d keep that in mind when you do start finding papers on cat vision, and I’d recommend more comprehensive works on cat behavior in general, from which you can infer things about vision but will provide a more full context like I’m talking about.

    If you’re thinking about building Rube Goldberg type machines for keeping cats entertained, I think you should just go for it. Experiment. Do note that cats have a huge amount of variability in what they find interesting or fun. Some will watch tv, others will chase a laser pointer or a feather on a string. I had one that would just sit and stare at absolutely nothing all day long and couldn’t be bothered with anything but head scratches and the occasional piece of chicken.

    One thing that seems to be pretty popular is having a ball or something that skitters around while under a blanket or towel, but do be aware that you’re basically training them to bite your toes really really hard while you’re trying to fall asleep. I speak from experience on that.


  • Let’s say you were an expert in epidemiological modeling, and you and a modestly sized group of your fellow researchers had been working on an approach that demonstrated what should have been done in 2020, and what a shitshow it would be if it wasn’t done. Then, of course, it wasn’t done. Then one of your fellow travelers wrote a book saying what should have been done. You know the work - you’d contributed to it yourself - but you think other people should know about it.

    Would you consider that book “very important?”




  • There are several. One is the gene-centric theory of biology, which carries less weight in biology itself than it does in how biological sciences are communicated to laypersons - eg the Selfish Gene, which I could rip on for pages - and others include ideas that are considered contentious within biology, such as multilevel selection theory that extends beyond kin selection. I can’t begin to tell you about the number of arguments I’ve gotten into on that subject alone. I will frequently bring up that there is confusion as to what a “gene” actually is, and how it’s really determined by the context in which we’re using the word. There’s really just so much that needs to be re-evaluated.


  • Theoretical biologist here. This is an incredibly important book. I just bought it a few minutes ago and so I’m only partway through the beginning, but it’s summarizing everything people from my school of thought (complex adaptive systems theory, multilevel selection models, and so on) have been arguing for two or three decades. It’s a very fast read so far (probably less so if you’re less familiar with the points the author is making), but I really hope that this book has an impact that’s reflective of the timeliness and cohesiveness (as I am reading into what the author is preparing to argue) deserves.