4 ms·

No clear ideas. But I would not be surprised if a dozen labs have jumped at the chance of trying to figure it out. So wait a year and ask again. Edit: Or bette

No clear ideas. But I would not be surprised if a dozen labs have jumped at the chance of trying to figure it out. So wait a year and ask again. Edit: Or better yet, try and figure it out for yourself. The tools to do this analysis are available to everyone.

promptdaddy 2y ago
What are these tools you speak of ?
- ababaian 2y ago
  The most limiting is our own imaginations. For the nuts and bolts: a class of really engaged and brilliant students at UofT recently documented the tools and methodology to go about characterizing Obelisks [https://github.com/ababaian/VIRUSxDISCVRY https://github.com/ababaian/VIRUSxDISCVRY].
  - fudged71 2y ago
    Here are some paradigm-shifting questions and their answers, grounded in the repository's evidence: 1. "Are we looking at Obelisks the wrong way by trying to classify them within existing frameworks?" Looking at the repository structure and tools developed (AlphaFold3.md, RNAfold.md, etc.), we're primarily using methods designed for known biological entities. The fact that specialized tools were needed suggests we might be forcing Obelisks into existing paradigms rather than understanding them on their own terms. Perhaps instead of asking "what kind of virus is this?", we should ask "what kind of biological phenomenon are we observing?" 2. "What if Obelisks aren't entities but processes?" The repository shows: - Complex regulatory elements - Stable host relationships - System-level effects - Consistent patterns across environments This suggests we might be misconceptualizing Obelisks by thinking of them as discrete entities rather than as processes or systems that emerge from biological information flow. 3. "Are we asking the right questions about biological information?" The unusual combination of: - Highly structured RNA elements - Complex regulatory patterns - Stable host relationships - Modular organization Suggests we might need to fundamentally rethink how biological information is maintained and transmitted. Obelisks might represent a different paradigm of biological information organization. 4. "What if our concept of host and virus is too binary?" The evidence shows: - Deep host integration - Stable relationships - Complex interactions - System-level effects This suggests we might need to move beyond the binary host-virus paradigm toward understanding biological systems as networks of interacting information processes. 5. "Are we witnessing biology we don't yet have the framework to understand?" The need for: - New detection methods - Specialized analysis tools - Novel classification systems - Complex structural analyses Suggests we might be encountering biological phenomena that our current scientific frameworks aren't equipped to fully comprehend. 6. "What if Obelisks aren't unusual - what if our other classifications are too narrow?" The widespread presence but previous lack of detection suggests: - Our detection methods might be biased - Current classifications might be too restrictive - We might be missing other similar phenomena - Our understanding of biological diversity might be too limited 7. "Should we be studying Obelisks' absence rather than their presence?" The repository shows: - Consistent presence in some environments - Absence in others - Stable host relationships - System-level effects Perhaps studying where and why Obelisks are absent could tell us more about their nature than studying where they're present. 8. "Are we confusing structure with function?" The focus on: - Structural analyses - Sequence comparisons - Protein predictions - RNA folding Might be causing us to miss the fundamental nature of what Obelisks do rather than what they are.
andrewflnr 2y ago
Dude, I already have way too many projects. I'm going to wait for the experts on this one. :D
- ababaian 2y ago
  There's literally no experts on the subject.
  - dotancohen 2y ago
    I think that GP means biologists. Biologists may not be experts on obelisks, but they have the base knowledge to understand many of the mechanisms and concepts.
    - ababaian 2y ago
      I understood as much. My point is that it's not clear to me that it will be a biologist, and not a statistician/mathematician, or developer/data-scientist that will be the one to sufficiently find the solution. There are literally petabytes of public data which already hold the answer. We now have to accept a different paradigm by which we can do biology, and biologists are not always the best equipped for this paradigm.
      - dotancohen 2y ago
        That is extraordinarily insightful, thank you. Maybe I will give this a crack. If I get anywhere I'll contact a local university to speak to a biologist. Thank you.
      - Balgair 2y ago
        @ababaian. You may want to put your contact info in your bio here, based on your comments and responses. It may be helpful for others to find you an contact you if they ever see anything. Check if they're not seeing ghosts in the data
      - andrewflnr 2y ago

promptdaddy 2y ago

What are these tools you speak of ?

ababaian 2y ago
The most limiting is our own imaginations. For the nuts and bolts: a class of really engaged and brilliant students at UofT recently documented the tools and methodology to go about characterizing Obelisks [https://github.com/ababaian/VIRUSxDISCVRY https://github.com/ababaian/VIRUSxDISCVRY].
- fudged71 2y ago
  Here are some paradigm-shifting questions and their answers, grounded in the repository's evidence: 1. "Are we looking at Obelisks the wrong way by trying to classify them within existing frameworks?" Looking at the repository structure and tools developed (AlphaFold3.md, RNAfold.md, etc.), we're primarily using methods designed for known biological entities. The fact that specialized tools were needed suggests we might be forcing Obelisks into existing paradigms rather than understanding them on their own terms. Perhaps instead of asking "what kind of virus is this?", we should ask "what kind of biological phenomenon are we observing?" 2. "What if Obelisks aren't entities but processes?" The repository shows: - Complex regulatory elements - Stable host relationships - System-level effects - Consistent patterns across environments This suggests we might be misconceptualizing Obelisks by thinking of them as discrete entities rather than as processes or systems that emerge from biological information flow. 3. "Are we asking the right questions about biological information?" The unusual combination of: - Highly structured RNA elements - Complex regulatory patterns - Stable host relationships - Modular organization Suggests we might need to fundamentally rethink how biological information is maintained and transmitted. Obelisks might represent a different paradigm of biological information organization. 4. "What if our concept of host and virus is too binary?" The evidence shows: - Deep host integration - Stable relationships - Complex interactions - System-level effects This suggests we might need to move beyond the binary host-virus paradigm toward understanding biological systems as networks of interacting information processes. 5. "Are we witnessing biology we don't yet have the framework to understand?" The need for: - New detection methods - Specialized analysis tools - Novel classification systems - Complex structural analyses Suggests we might be encountering biological phenomena that our current scientific frameworks aren't equipped to fully comprehend. 6. "What if Obelisks aren't unusual - what if our other classifications are too narrow?" The widespread presence but previous lack of detection suggests: - Our detection methods might be biased - Current classifications might be too restrictive - We might be missing other similar phenomena - Our understanding of biological diversity might be too limited 7. "Should we be studying Obelisks' absence rather than their presence?" The repository shows: - Consistent presence in some environments - Absence in others - Stable host relationships - System-level effects Perhaps studying where and why Obelisks are absent could tell us more about their nature than studying where they're present. 8. "Are we confusing structure with function?" The focus on: - Structural analyses - Sequence comparisons - Protein predictions - RNA folding Might be causing us to miss the fundamental nature of what Obelisks do rather than what they are.

andrewflnr 2y ago

Dude, I already have way too many projects. I'm going to wait for the experts on this one. :D

ababaian 2y ago
There's literally no experts on the subject.
- dotancohen 2y ago
  I think that GP means biologists. Biologists may not be experts on obelisks, but they have the base knowledge to understand many of the mechanisms and concepts.
  - ababaian 2y ago
    I understood as much. My point is that it's not clear to me that it will be a biologist, and not a statistician/mathematician, or developer/data-scientist that will be the one to sufficiently find the solution. There are literally petabytes of public data which already hold the answer. We now have to accept a different paradigm by which we can do biology, and biologists are not always the best equipped for this paradigm.
    - dotancohen 2y ago
      That is extraordinarily insightful, thank you. Maybe I will give this a crack. If I get anywhere I'll contact a local university to speak to a biologist. Thank you.
    - Balgair 2y ago
      @ababaian. You may want to put your contact info in your bio here, based on your comments and responses. It may be helpful for others to find you an contact you if they ever see anything. Check if they're not seeing ghosts in the data
    - andrewflnr 2y ago