Sal

@Sal@mander.xyz

• ⁨Comment⁩ on ⁨DNA cassette tapes could solve global data storage problems⁩ ⁨⁨4⁩ ⁨days⁩ ago⁩:

  Fair point - I completely forgot to take the 3D geometry into account. I guess this could be solved by either making both sp³ (sub the Si-O with Si-Cl) or both sp² (sub the H-O-Si with H-N=Si)? But then writing data becomes more complicated than just adding or removing hydrogens that, as you said, isn’t as simple as it looks like.

  I think that the solution that life came up with - making a flexible double helix-forming backbone from which base pairs hang is actually a pretty good way of going about it. Similar as with proteins - a standard flexible backbone with different groups hanging off the chain and influencing how it folds. In your proposition you have the silicon backbone and a single atom as the ‘side chain’, so there is no separation between the backbone and the pairing elements to add this flexibility.

  There are also some other details to consider. For example, the amount of data you can store in a given chain length changes depending on how many different types of chemistry you have. In your example, you are using only one type of ‘base’ because the only options are ‘hydrogen bond donor’ or ‘hydrogen bond acceptor’. If you have a chain length of 3, you get only 3 bits, which can store one of 2^3 = 8 values from 0 to 7 (000 to 111). With DNA, you have 4 different base pairs, so a chain length of three can encode 4^3 = 64 values.

  That means that, to get a good information density, you would also want to increase the number of possibilities. The challenge here is that you need to tune the set of possibilities so that the thermodynamics are balanced. You don’t want some pairs to stick very strongly while others stick only loosely, and you also don’t want certain bases to be able to pair with each other. See: en.wikipedia.org/…/Nucleic_acid_thermodynamics

  You can perhaps dispense with some of the thermodynamic tuning if you don’t need to be able to easily replicate the data through a process similar to DNA replication, as you don’t actually need to ‘pair’ at all - you have a single string of data. But in that case you lose a very powerful method as you are forced to re-synthesize every data chain from scratch - I think that with such a system you lose too many benefits.

  If you go through the steps of creating a system of molecular data storage from scratch, I think it is easy to converge towards something similar to DNA. A lot of ‘origin of life’ research is actually about this - thinking about these systems and how to engineer them from scratch, and… DNA is pretty good at this. When you consider that early chemical evolution was an optimization algorithm to solve this problem, it makes sense that DNA is a good choice.

  I do think it is good and fun to explore this. We do have at least some advantages over nature - for example, we have managed to purify many compounds that were not abundant in early chemical soups. So, perhaps we can find something.

  Like the dNaM / dTPT3 pair, right? That’s perhaps more viable, at least to increase information density.

  Yeah, like those. In this recent paper, for example, researchers sequenced a chain of four anthrophogenic base pairs that they refer to as ‘ALIEN bases’: www.nature.com/articles/s41467-025-61991-9

  Image

• ⁨Comment⁩ on ⁨DNA cassette tapes could solve global data storage problems⁩ ⁨⁨5⁩ ⁨days⁩ ago⁩:

  The R2S=O case is closer to a trigonal planar geometry, the other silicon is tetrahedral. The silicon-silicon distances for different pairs of adjacent molecule types will be different. In a very very rough forcefield optimization I see about 3% difference. I don’t think this one will work out structurally because the chains will become unable to pair after a short length as the chain will not have the flexibility to create the O–H bond without adding too much strain.

  Image

  But, that’s just one thing. You then need to consider how to actually selectively place/remove the hydrogen atoms, how to avoid the molecule from chemically reacting, and how to read out the data.

  So, yes, eventually it would be nice to have a fully orthogonal system. There are already several synthetic DNA base pairs that can be used instead of the naturally present bases. But these would still be susceptible to DNAses or RNAses.

  The way I see it is that the chemistry of living things is currently centuries ahead of human tech. A large portion of the techniques used in biochemistry rely on using living things to produce the components, and then we purify those components and use them. It makes a lot of sense to make use of that toolkit because the amount of challenges that need to be solved to create this system from scratch is massive.

  Your proposal of your silicon chain reminds of the Ferroelectric RAM, where the state is encoded by the polarity of a cell that is changed by moving a zirconium or titanium cation:

  Image

  This does work, but it works because the crystal is contained within a semiconductor scaffold, and this is something that we do have a good handle on.

• ⁨Comment⁩ on ⁨DNA cassette tapes could solve global data storage problems⁩ ⁨⁨5⁩ ⁨days⁩ ago⁩:

  Very cool!

• ⁨Comment⁩ on ⁨Coprinus comatus painted with the blood of Coprinus comatus.⁩ ⁨⁨6⁩ ⁨days⁩ ago⁩:

  I love this!!! That’s a very cool technique and you draw very well! 😄

• ⁨Comment⁩ on ⁨I think I found our community icon? Shaggy mane (Coprinus comatus)⁩ ⁨⁨1⁩ ⁨week⁩ ago⁩:

  Hahaha, didn’t mean to send a message 😆

  Whether it “spoils” is a matter of perspective, this guy has a recipe on making a Shaggy Ink Sauce: foragerchef.com/shaggy-mane-ink/

  It reminds of huitlacoche. I am curious if it equally delicious. I have only foraged them once and ate them fresh, but next time I want to try out this recipe.

• ⁨Comment⁩ on ⁨I think I found our community icon? Shaggy mane (Coprinus comatus)⁩ ⁨⁨1⁩ ⁨week⁩ ago⁩:

  Yes, you did!! 😀

  I think this was the photo that I sketched on top of:

  Image

• ⁨Comment⁩ on ⁨Baby sized bolete of some sort⁩ ⁨⁨1⁩ ⁨week⁩ ago⁩:

  Some of these terms I am not yet familiar with, so I will need to do some reading. I’ll save this comment and come back during the week. It seems like you are very knowledgeable about display technologies! Very cool

• ⁨Comment⁩ on ⁨Baby sized bolete of some sort⁩ ⁨⁨1⁩ ⁨week⁩ ago⁩:

  Why not RGBW with some interesting wavelength response of the white subpixel?

  Hmm, I’m not really sure. A monochrome pixel would be much more sensitive, but without a neutral density filter it might saturate when the RGB pixels are well-exposed. With a neutral density filter I think it could resolve better the variation of light intensities of very small features.

  Same with LCDs. It wouldn’t take much change in the manufacturing process much to create a WWW or YWB 1080p LCD that has less or no color but passes way more light, allowing less backlight or even a reflective mode, while still being driven with conventional electronics

  So, would the WWW be a monochrome LCD? Wouldn’t these be similar to the ones sometimes used in small electronic displays like this one:

  Image

  I am not sure of what the YWB would do.

  These could be used in public transport signage etc. In some cases, a monochrome LCD with RGB backlight could also come in handy.

  I am also interested in the use of the ‘E-Ink’ displays for public signage in well-illuminated places. I found a few examples online:

  Image

  Also not really related but it infuriates me that Samsung turned the Bayer filter 45°, halved the pixel count and patented it as an OLED pattern so nobody can make similar displays.

  I am not familiar with this… I looked it up and I think it is this? en.wikipedia.org/wiki/PenTile_matrix_family

  I’ll look into it. Interesting!

• ⁨Comment⁩ on ⁨Baby sized bolete of some sort⁩ ⁨⁨1⁩ ⁨week⁩ ago⁩:

  Interesting examples, we’re really splitting hairs here.

  Haha, maybe 😜 I did some reflection about why the term ‘artificial’ in the context of photography made me want to jump into the conversation in the first place. I think that the reason is that the term ‘artificial’ implies that there is a boundary between what corresponds to a ‘natural’ photograph and an ‘artificial’ photograph.

  Thanks for responding to those examples and giving a definition, I think now I better understand what you mean when you say ‘artificial’. I was interpreting it from a universal point of view of ‘natural/artificial’, but I see now that you meant it in the sense of the camera’s nature. So, if one simply takes a photo with the camera, it is ‘natural’ in the sense that the camera’s nature was enough to capture that image. When a human applies uses a technique that creates an image cannot be captured by the camera itself, then it is ‘artificial’.

  No need to continue discussing the semantics of ‘artificial’, I think we both know what each other means now 😄

  Still, always to chat more about these things as I enjoy talking about techniques. I am actually considering getting a monochrome industrial camera to create some color images manually. I already have filters from UV to the near-IR. Like what I mentioned in example 4. I am curious about whether I can capture noticeably better luminances throughout by using the filters manually. I’m also keeping an eye for an affordable camera with this sensor type: www.sony-semicon.com/en/…/multispectral.html …

• ⁨Comment⁩ on ⁨Baby sized bolete of some sort⁩ ⁨⁨1⁩ ⁨week⁩ ago⁩:

  Ah, alright! My reason for describing the details of the process was primarily to emphasize the parallels along the processing chain between different techniques.

  I am curious about how you draw the line between ‘artificial’ and ‘not artificial’, hope you don’t mind me asking.

  • Is a black-and-white image produced by a camera without the color filter artificial?
  • Is a landscape photograph generated by sticking multiple images together artificial?
  • Is a long exposure image artificial?
  • What about placing a monochromatic camera into a tripod, taking three different photos - one with a green, one with a blue, and one with a red filter, and then creating a color image using these three different images as an input?
• ⁨Comment⁩ on ⁨Baby sized bolete of some sort⁩ ⁨⁨2⁩ ⁨weeks⁩ ago⁩:

  It is not about colorspace conversion. Most color cameras today use a bayer filter: en.wikipedia.org/wiki/Bayer_filter . The camera captures 3 almost-overlapping images, one green, one blue, one red. Using data from these three images, it calculates the red,green,blue values for each pixel. This combines a physical technique (the byer filtering) with digital software algorithms to produce the final image.

  In focus stacking, one generates a set of overlapping images while scanning the focal plane. Software is then used to combine the in-focus slices to produce an image that is in focus. So, again, we combine a physical process (movement of the focal plane) with a digital processing method.

  In the first case you have a technique that has been implemented at the hardware level by camera sensor engineers. The second is a technique that is implemented at the photographer level. I see both techniques as equally ‘artificial’. In the first case the filters scan through colors. In the second case the focal plane is scanned. In the first case the people who developed the camera firmware did the work of automated processing, in the second case the photographer needs to do the processing themselves.

  I don’t mean to debate your definition, I just wanted to jump in and share my perspective.

• ⁨Comment⁩ on ⁨Baby sized bolete of some sort⁩ ⁨⁨2⁩ ⁨weeks⁩ ago⁩:

  I understand where you are coming from, but I think that - perhaps without realizing it - you are using a definition of ‘artificial’ that practically categorizes all photography as ‘artificial’.

  For example: Camera sensors and also the older types of photographic film usually do not discriminate color directly. Techniques are used to combine multiple layers of color data together in order to replicate colors as we see them. Inside of modern a digital camera, for example, this is generally done my using a variable color filter grid on top of a monocromatic pixel array and then applying an algorithm to smooth out color data. Many camera users today may completely oblivious to this kind of processing, but the camera is making a lot of different choices for them and performing different kinds of processing. There are also other built-in features to removing aliasing, optical aberrations, color correction, etc…

  Old school photographers would also need to combine filters or different material films together to create color renditions. It is just that, today, the camera does it for us. But photography is actually all about these ‘artificial’ methods to capture an image.

  Focus stacking is a technique in which one expands the range of an optical system by capturing multiple slices and combining them optically together to recreate a larger depth of field. This is technical photography.

  So, when you call this ‘artificial’, well… The act of projecting an image into some kind of film and then somehow preserving that image either directly on the film or as a digital representation is an artificial process. All photography is artificial.

• ⁨Comment⁩ on ⁨Gomphidius subroseus and Suillus lakei⁩ ⁨⁨2⁩ ⁨weeks⁩ ago⁩:

  Wow! really really cool!!

  Near my place there is a spot where the ‘Yellow Stainer’ (Agaricus xanthodermus) fruits. The yellow stainer becomes yellow when you cut it, and what makes it especially interesting is that the yellow pigment is an azobenzene derivative (4,4’-dihydroxy-azobenzene). Azobenzene is very well known in the field of photochemistry because it is a light-driven switch. But, in nature, it is extremely rare. I actually only know of this specific example…

  So I am very curious about what the bright yellow is in this fungus…

  According to this review on fungal pigments: Pigments of Higher Fungi: A Review

  It appears that the main component of the yellow pigment could be a compound called ‘gomphidic acid’

  Image

  Image

  This molecule is very similar to the molecule from the lichen that you posted a few months ago, vulpinic acid, except that one of the phenyls has 1 hydroxide group and the other contains 3 hydroxides.

  This is the structure of vulpinic acid, for comparison:

  Image

  I still don’t understand why Gomphidius has a yellow base, what about the metabolism of fungi makes them choose vulpinic acid-like molecules as pigments, and whether there is a functional reason why the yellow stainer uses an azobenzene derivative and this one a vulpinic acid… My current guess is that the metabolism to produce vulpinic acid evolved and is often recycled for pigment production, and that the yellow’s stainer is using the azobenzene as some form of defense mechanism (it would be very cool if it turns out to be a phototoxic one) and the yellow color is merely accidental in that case.

• Bright yet dark: how strong coupling quenches exciton-polariton radiationarxiv.org ↗
  Submitted ⁨⁨2⁩ ⁨weeks⁩ ago⁩ to ⁨physics@mander.xyz⁩ | ⁨0⁩ ⁨comments⁩
• The Dry-Climate Hypothesis: Identifying the Environmental Drivers of Terrestrial Viviparous Salamandersonlinelibrary.wiley.com ↗
  Submitted ⁨⁨2⁩ ⁨weeks⁩ ago⁩ to ⁨herpetology@mander.xyz⁩ | ⁨0⁩ ⁨comments⁩
• ⁨Comment⁩ on ⁨⁩ ⁨⁨2⁩ ⁨weeks⁩ ago⁩:

  Wow. This is really magnificent work!! I just had a look through the Wikipedia article of Platynereis dumerilii and I can see from the citation list that you have quite a story with these guys 😁 It is very neat to see how you were figuring out this worm’s phototaxis in 2008 and by now you have figured out a map of the whole thing.

  Looking at the movie and the paper I am very intrigued and also a bit intimidated by the complexity! I would really like to get five minutes to experience this worm through your eyes. I will set some time to go through this paper carefully and try to benefit a little bit from your insight.

  Thanks a lot for sharing this here, it really is a privilege! Very very cool stuff.

• ⁨Comment⁩ on ⁨I keep⁩ ⁨⁨2⁩ ⁨weeks⁩ ago⁩:

  This may also be of interest to you, even though they do not use this specific mushroom: www.youtube.com/watch?v=T4TjnxFO3yw

• ⁨Comment⁩ on ⁨I keep⁩ ⁨⁨2⁩ ⁨weeks⁩ ago⁩:

  From: fungusfactfriday.com/119-pisolithus-arrhizus/

  The Dyeball, as its common name implies, can also be used for dyeing wool. P. arrhizus is counted among the best mushrooms for dyeing and imparts wool with a deep brown to reddish-brown to blackish color. The pigments come from the tar-like gel between the peridioles, so younger Dyeballs work better.

• ⁨Comment⁩ on ⁨I keep⁩ ⁨⁨2⁩ ⁨weeks⁩ ago⁩:

  Hmm, I’m not so sure, I think that for Scleroderma the inside is a lot denser.

  To me, these larger granules look more like a dyeball, Pisolithus arhizus: www.jungledragon.com/specie/8966/dyeball.html

• ⁨Comment⁩ on ⁨The pointiest Chroogomphus I have ever come across⁩ ⁨⁨2⁩ ⁨weeks⁩ ago⁩:

  Cool! That is quite pointy.

  Is the spotty pattern on the Suillus normal? Or is it showing signs of being parasitized?

• ⁨Comment⁩ on ⁨Scientists found the missing nutrients bees need — Colonies grew 15-fold⁩ ⁨⁨3⁩ ⁨weeks⁩ ago⁩:

  That’s awesome! And the paper is open access :)

• ⁨Comment⁩ on ⁨[PSA] Watch for the antiyanks troll and consider adjusting your rate limits⁩ ⁨⁨3⁩ ⁨weeks⁩ ago⁩:

  Haha, yeah, trusting ChatGPT with how to manipulate the database and change config files is a risky move 😆 I did use it myself to remind me of the postgresql syntax to find and alter the field.

• [PDF] Discovery of the eggs of Bolitoglossa pandi with observations on its reproductive biologyherpetologia.fciencias.unam.mx ↗
  Submitted ⁨⁨3⁩ ⁨weeks⁩ ago⁩ to ⁨herpetology@mander.xyz⁩ | ⁨0⁩ ⁨comments⁩
• ⁨Comment⁩ on ⁨[PSA] Watch for the antiyanks troll and consider adjusting your rate limits⁩ ⁨⁨3⁩ ⁨weeks⁩ ago⁩:

  Sorry, I went to sleep. Glad you were able to sort it out 😄

• ⁨Comment⁩ on ⁨[PSA] Watch for the antiyanks troll and consider adjusting your rate limits⁩ ⁨⁨3⁩ ⁨weeks⁩ ago⁩:

  😁 👍

• ⁨Comment⁩ on ⁨[PSA] Watch for the antiyanks troll and consider adjusting your rate limits⁩ ⁨⁨3⁩ ⁨weeks⁩ ago⁩:

  So, ultimately my problem was that I was trying to set all of the limits to what I thought were “reasonable” values simultaneously, and misunderstood what ‘Message’ meant, and so I ended up breaking things with my changes without the reason being obvious to me. I looked into the source code and I can see now that indeed ‘Messages’ refer to API calls and not direct messages, and that there is no ‘Direct Message’ rate limit.

  If I let ‘Messages’ stay high I can adjust the other values to reasonable values and everything works fine.

  Thanks a lot for your help!! I am surprised and happy it actually worked out and I understand a little more 😁

• ⁨Comment⁩ on ⁨[PSA] Watch for the antiyanks troll and consider adjusting your rate limits⁩ ⁨⁨3⁩ ⁨weeks⁩ ago⁩:

  Thanks!

  I was able to crash the instance for a few minutes, but I think I have a better idea of where the problem is. Ths $emote_addr variable seems to work just the same.

  In the rate limit options there is a limit for ‘‘Message’’. Common sense tells me that this means ‘direct message’, but setting this to a low number is quite bad. While testing I eventually set it to ‘1 per minute’ and the instance became unresponsive until I modified the settings in the database manually. If I give a high number to this setting then I can adjust the other settings without problem.

• ⁨Comment⁩ on ⁨[PSA] Watch for the antiyanks troll and consider adjusting your rate limits⁩ ⁨⁨3⁩ ⁨weeks⁩ ago⁩:

  Yes, I see this there. Most of the nginx config is from the ‘default’ nginx config in the Lemmy repo from a few years ago. My understanding is somewhat superficial - I don’t actually know where the variable ‘$proxy_add_x_forwarded_for’ gets populated, for example. I did not know that this contained the client’s IP.

      # backend
      location ~ ^/(api|pictrs|feeds|nodeinfo|.well-known) {
        proxy_pass http://0.0.0.0:8536/;
        proxy_http_version 1.1;
        proxy_set_header Upgrade $http_upgrade;
        proxy_set_header Connection "upgrade";
  
        # Rate limit
        limit_req zone=mander_ratelimit burst=30000 nodelay;
  
        # Add IP forwarding headers
        proxy_set_header X-Real-IP $remote_addr;
        proxy_set_header Host $host;
        proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;
      }
  
  

  I need to do some reading 😁

• ⁨Comment⁩ on ⁨[PSA] Watch for the antiyanks troll and consider adjusting your rate limits⁩ ⁨⁨3⁩ ⁨weeks⁩ ago⁩:

  Thanks! Yes, I saw both messages and I am now going through the NGINX config and trying to understand what could be going on. To be honest, Lemmy is the hobby that taught me what a ‘reverse proxy’ and a ‘vps’ are. Answering a question such as ‘Are you sending the client IP in the X-Forwarded-For header?’ is probably straight forward for a professional but for me it involves quite a bit of learning 😅

  At location /, my nginx config includes:

        proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;
  

  So, I think that the answer to your question is probably ‘yes’. If you did have these rate limits and they were stable, the more likely explanation is that something about my configuration is sub-optimal. I will look into it and continue learning, but I will need to keep my limits a bit high for the time being and stay alert.

• ⁨Comment⁩ on ⁨[PSA] Watch for the antiyanks troll and consider adjusting your rate limits⁩ ⁨⁨3⁩ ⁨weeks⁩ ago⁩:

  I don’t recall any of them being from mander (unless they were dealt with before I started testing?), but thanks for taking preventative measures :)

  I don’t know what ‘Antiyanks’ is
  

  It’s the codename for a particular long-term troll and is based off of their original username pattern (which they still use sometimes). I have reason to believe it’s also the same troll that used to spam the racist stuff in Science Memes.

  These are most of today’s batch (minus the JON333 which was just a garden-variety spammer that made it into the last screenshot).

  No, they were not in mander.xyz. But I am generally quite relaxed when it comes to accepting applications. I mostly reject an applicant if it is very clear it is not an actual user, and then actively follow up on recent accounts for a short time. So the possibility of silent spammer accounts accumulating over time is always a concern.