(biologist - artist - queer)

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You’re the only magician that could make a falling horse turn into thirteen gerbils

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Joined 1 year ago
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Cake day: June 10th, 2023

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  • Oooooh I have some ideas! Some of these are paid/premium (but NOT micro transactions) and some have mild ads. But I share the distaste for data-mining, money grubbing, brain-melting-ad-ridden games, so I’m certain they are on the least intrusive end of the spectrum.

    I really love biology (I’m a biologist…) so these are both pet games and usually breeding/evolution games!

    • Fish Tycoon – This one specifically. A classic! Breed and care for cute fish!
    • Niche breed and evolve – so neat and pretty educational about evolution/genetics. There’s a slightly more complicated/difficult pc game if she decides she likes the nichelings/universe.
    • Pocket Frogs – Simple, low stress collecting game. it would take years to collect all the frogs, and there’s a relatively active community of people who trade sets of frogs to other people to help them complete collections. Would be fun to play with her friends at school!
    • Reigns Her Majesty – a game about running a kingdom as a queen. When you die, you become your heir and retain some progress from your last lives. It doesn’t fit the exact criteria you mentioned, but I think she might like it anyway!

  • because the very first thing you say in this post basically amounts to “I think I have the authority to decide the basis on which we determine who deserves to vote”

    like, yeah, most people can navigate to their secretary of state websites. And it’s not really your responsibility to have to link the pages anyway.

    But doing it for that reason aligns you philosophically with people who think that the illiterate, the elderly, the poor, the disabled, the critically ill, etc. somehow don’t deserve to vote. It aligns you ideologically with other people who think they can decide who deserves to vote, with people who want to disenfranchise others-- in essence, it aligns you ideologically with many Republicans




  • As an education professional: what the hell, dude? It’s not unfortunate that we aren’t just dropping struggling students without first carefully examining why they’re not succeeding.

    You might be right that you can’t let some students detract from the class for other students, but the solution there is advocating for better funding and more staff to be able to give every student what they need, whether they’re above or below the expectation for their age.

    Saying it’s “unfortunate” that students don’t fail (read: ruin their whole god damn lives) as often anymore is blaming our most vulnerable YOUTH for the systemic problems of our society. It’s not their job to be what the school environment wants them to be, they don’t even have a choice about whether or not they are there. It’s our (as educators, and as tax paying and voting community members) responsibility to make sure they get the education they need to be functional members of our society.

    We even have huge bodies of research to reinforce this. It’s not a secret that the school environment excels at making nice workers, not critical-thinking and well-adjusted adult humans.

    Take it up with the school board! Take it up with the local, state, and federal government! Take it up with the voters!




  • When I say “the cell isn’t a machine”, it is in specific reference to the machine model of the cell, which is a previously established conceptual framework in the field of molecular biology. If you want to understand why that model is falling out of favor today, you’re invited to read the article linked by OP and/or the articles I have linked in other comments.

    The gist is that the cell is more complicated, flexible, and emergent than any machine has ever been and will be for the foreseeable future, and the idea that we can simply map the functions of each molecule in the cell to get a perfect “circuit diagram” of how everything plays together is defunct.

    I don’t have time to mess with this thread any more. You can either accept what myself (an expert in this field), the author of this publication (which happens to be one of the most prestigious journals in the world), and others who do this research daily are saying about this, or you can not. Frankly, if you are an expert also, the field, the research, and the truth barely cares about our opinion-- it certainly doesn’t care about non-expert opinions on the internet.


  • Junk DNA is repeating codons, or codons that occur in areas that are outside of the “start/stop” codon triplicate pairs.

    Those sequences do things and have effects. In fact, the coding regions are often less functional than the non-coding ones.

    They aren’t there for structural reasons, all DNA is the same 4 codons linked together over and over, all the different chromosomes are different sizes.

    Sometimes they ARE there for structural reasons? Read: enhancers, or CTCF binding sites? Among many other myriad examples of functional noncoding regions? Also, nucleotides =/= codons. There are 64 codons.

    All of this DNA is reported when the cells divide, that’s the only time those regions between the stops and starts actually come into play. This is very easily proven, we know the structure of the reading proteins down to the molecule (indeed there are starts and stops and triplicate base pairs that design these transcribing proteins).

    That’s bull. You’re out of your depth. A contemporary college molecular biology course would show your examples to the contrary.

    The “important” junk DNA that has significance while not being in a “start->stop” zone are the codons that occur before the first start codon on either side of a DNA strand, when DNA is replicated the protein that starts replicating it has to start at 1 end of 1 side of the DNA in order to be able to read it

    I feel like a broken record but Enhancers! lncRNAs! siRNAs! Binding sites! Other gene regulatory regions! Epigenetic nucleosome modifications! Chromatin remodeler sites!

    except it needs to find the end first, and to make sure it’s all the end it “clips” the first 6 (? Maybe more maybe less, it’s been decades since I’ve studied this)

    Oh, there’s your problem. A lot has changed. You refuse to see the sea change happening around you because it means you’re out of date.

    Sorry for the wall of text, but there’s plenty of examples of blatantly junk DNA, and there are known methods of how it occurs. Anyone who says every codon pair has a purpose has a screw loose and is ignorant to the mechanics of evolution.

    I was happy to reply to you and engage pleasantly originally but you are only engaging with people that know less about biology than you do. You are not an expert if you last studied biology decades ago and can’t remember the details. You certainly aren’t enough of an authority on the subject to question a contemporary article published in Science or the work of other researchers currently in the field.

    I really, really encourage you to read these papers thoroughly. You are the target audience-- people who learned the machine model of the cell and who are gripping it so tightly that they are blind to the nuance that we’ve uncovered. I also encourage you to not write insults about people who disagree with you, especially people with more domain knowledge than you have.


  • This is a funny comment though, because “junk” DNA is involved with epigenetic regulation and cellular behavior.

    “It’s there so it must have function”, “it’s still in the genetic code so it must have been selected for” is the least nuanced take,

    “It’s there just randomly and therefore is junk”, and “evolution does not select for efficiency” is an improvement,

    But “it’s there and it’s doing something despite not having a bespoke, prescribed function” and “evolution is a cascade of emergent effects and random chance, none of our genome is non-functional even though it is random” is the most up to date take

    You seem like a biologist, why not go read some of these papers? Like the one I linked by Dan Nichols? Most people don’t have the background necessary to understand the language (no shade) but you seem to!


  • I would encourage you to read the linked Science paper and Dan Nichol’s paper, Is the Cell Really a Machine?

    You feel that if a codon isn’t meant for something, if it doesn’t have a purpose– then it is junk. This is a mindset that is reflective of the machine model of the cell. We used to expect that each protein was bespoke for a function, each transcript necessary.

    The whole paradigm shift at hand is this model falls flat, even for coding regions. I think you’re actually very spot in here with the prokaryotic DNA or the plant genomes (love me some violets for their weird genomes). Some parts of a genome will rapidly change and appear to serve no real purpose, but the next bite is the important one: even if it seems like there isn’t a purpose, like a top-down prescription for functionality, those regions are still doing something while they are present.

    For example, some long non-coding regions affect the likelihood that a person will develop Parkinson’s disease, or in the case of plants with various polyploidies, the relative expression of their genes won’t necessarily change, but the absolute expression may.

    Basically, you aren’t wrong that these regions dont have a purpose, because no genes have a purpose. The cell isn’t a machine.



  • So I think I can make the claim that I am an expert in this, at least compared to 95%+ of biological researchers. My research foci include epigenetic and emergent interactions like the ones discussed in the article, and although I am not going to back this up by identifying myself, please believe me when I say I’ve written some papers on the topic.

    The concept of junk DNA is perhaps the problem here. Obviously there are large swaths of our genome that do not encode anything or have instructions for proteins. However, dismissing all non-coding DNA as “junk” is a critical error.

    Your telomeres are a great example. They don’t contain vital information so much as they serve a specific function-- providing a buffer region to be consumed during replication in place of DNA that does contain vital information. Your cells would work less well without telomeres, so calling them junk is inaccurate.

    Other examples of important non-coding regions are enhancer and promoter regions. Papers describing the philosophical developments of stochasticity in cellular function note how enhancers are vital for increasing the likelihood of transcription by making it more likely that specific proteins floating in the cellular matrix interact with each other. Promoter regions are something most biologists understand already, so I won’t describe them here (apologies for anyone who needs to go read about them elsewhere!). Some regions also inform the 3D structure of the genome, creating topological associated domains (TADs) that bring regions of interest closer together.

    Even the sequences with less obvious non-coding functions often have some emergent effect on cellular function. Transcription occurs in nonsense regions despite no mRNA being created; instead, tiny, transient non-coding RNAs (ncRNAs) are produced. Because RNA can have functional and catalytic properties like proteins, these small RNAs “do jobs” while they exist. The kinds of things they do before being degraded are less defined than the mechanistic models of proteins, but as we understand more stochastic models, we are beginning to understand how they work.

    One last type of DNA that we used to consider junk: binding sites for transcription factors, nucleosome remodelers, and other DNA binding proteins. Proteins are getting stuck to DNA all the time, and then doing things while they’re stuck there. Sometimes even just being a place where a nucleosome with a epigenetic flag can camp out and direct other cellular processes is enough to invalidate calling that region “junk”.

    Anyway I’m done giving my spiel but the take home message here is that all DNA causes stochastic effects and almost all of it (likely all and we haven’t figured it out yet) serves some function in-context. Calling all DNA that doesn’t encode for a protein “junk” is outdated-- if anything, the protein encoding regions are the boring parts.


  • Pretty much every day, multiple times a day, with strangers, acquaintances, and friends. I think it usually brightens people’s day, and with strangers, I think delivery and content is much more important than what I look like or who I am.

    For content, I only compliment choices, not attributes:

    “Cool shirt!” is good, “Nice legs!” is not

    “I love your haircut!” is good, “Your hair has such a nice texture!” is not

    Tailored compliments are even better, ex. “That book (or other media) is awesome!” is great, if I really do like it, and it can start a conversation, but obviously I don’t lie and pretend I know it when I don’t.

    For delivery, I keep it light and casual. I am mindful to only do it when they aren’t preoccupied, like on the phone or reading something. For tone, I guess I pop the compliment, smile, and movie on. For example, if we’re walking past each other-- I don’t slow down, and I look away immediately after giving a friendly smile. I don’t mean that I don’t care about their response, because of course I’m mindful to be sure I didn’t offend them, but I don’t burden them with needing to respond with gratitude or happiness. I think of it as, I want this person to have the (hopefully pleasant) information that their choice was seen and respected by a stranger. I don’t want anything back from them.

    I would say 95-100% of the people I compliment seem to be genuinely happy I did, and of the ones who don’t react positively, I’d say the vast majority react neutrally. In the rare case where my compliment has totally failed, I usually go “Oh! I’m sorry” and again, disengage.

    Obviously, with friends and acquaintances the options open up a little more, and usually I do follow up/continue the conversation instead of moving on. But it’s similar in the philosophy that I’m usually just trying to give them positive information, and not seeking anything in return. Compliments are not a tool to get people to talk to me or be friends with me. That can and does happen, but it’s not the point. Honestly, I think that’s the part that most people struggle with, if they feel like they don’t get good responses with compliments. It’s not for us.

    I do think I’m probably an outlier, because I give compliments a lot. But I continue to do it because it seems to really make people smile!



  • It’s fine if you want to draw some conceptual comparisons between biological and synthetic polymers, but it’s 100% not true that “plastics” as defined as synthetic, organic polymers (I.e. acrylics, silicones, polyesters, polyurethanes, halogenated plastics, thermosets, thermoplastics et al.) are the same on a chemical basis as most biological polymers.

    Like… where are you drawing the line? Are proteins a plastic? Is starch plastic? Is DNA plastic? RNA? Clearly not, by multiple definitions (bioavailability, reactivity, structure and function, persistence in the environment, etc.). Even biological compounds closer to synthetic polymers (cellulose, chitin, etc.) are definitively different, even if they do have longer persistence, lower reactivity, etc. And bioplastics (like what people mean when they say biodegradable plastics) are heat-modified biological polymers. They don’t come out of a living thing that way; they are fundamentally altered from their previous form.

    I guess I just… disagree that the distinction is “arbitrary semantics”?