3 ms·

Does their on-ship wet lab not include genome sequencing equipment? If not, why not? It feels very weird when both phys.org and NOAA pump up the mystery by for

Does their on-ship wet lab not include genome sequencing equipment? If not, why not? It feels very weird when both phys.org and NOAA pump up the mystery by for now temporarily pretending they never heard of genome sequencing.

webmobdev 3y ago
Cut them some slack please - even they need the occasional PR hype to ensure funding.
DoctorOetker 3y ago
[flagged]
- Sunhold 3y ago
  I don't know why you are assuming it is standard, expected or necessary to have genome sequencing equipment on the ship. There's no doubt that they've brought it back to land and are working to identify it now.
  - DoctorOetker 3y ago
    Do you accept or deny the desirability of on-ship genome sequencing equipment? Nobody knows the sum total of all observations made by mankind. If one can effectively sequence immediately, one can quickly how novel the genome is, and if its not novel, if its a novel lifestage. On the way to land the specimen (if alive) may die, or (if dead) be consumed and rot on the way to land. If the species or closest known artificially sustainable life-form can be identified on-ship, probability to keep it alive can be increased. I don't doubt they are working to identify it, and I wouldn't be surprised if they already did (perhaps on-ship). What disturbs me is major popular science platforms are pro-actively feeding mysticism and trolls by staying mute on the most obvious next logical step. I do not at all assume it is standard: I assume the number of nation-state actors investing resources in exploring the deep sea ecology (to this depth) constitutes a very small list. So by no means can any of this research be taken for granted and assumed standard. The mere activity of this type of research is already non-standard. Genome sequencing equipment has been highly miniaturized and become a lot more affordable. So yes, I do expect a wet-lab on this vessel to actually have genome sequencing equipment. If not, I think the researchers have a right to lament it publically.
    - dlor 3y ago
      Have you ever been on a boat? It's not safe to assume the existence of anything, including a toilet, on them.
      - DoctorOetker 3y ago
        have you ever seen a picture of this mothership? I think it's pretty safe to assume it has toilet... https://oceanexplorer.noaa.gov/okeanos/collaboration-tools/EX_Capabilities_Overview.pdf https://oceanexplorer.noaa.gov/okeanos/collaboration-tools/E...
    - aydyn 3y ago
      Even if you were able to start sequencing immediately, standard sequencing alone takes on the order of a day. And then depending on your computational methods, could take another few hours. Remember that it's not just the sequencer, you also need extraction, so you need to add a centrifuge, a vortex, a pipetting station, a PCR machine, a -20 C freezer, a spectrophotometer and a whole lot of reagents, additional personnel, and probably tons of other things I'm forgetting. Also I doubt most instruments are specced to be able to handle ship sway on the open sea. It really just isn't practical.
      - yreg 3y ago
        There are portable devices for sequencing out in the field, like MinION. https://www.youtube.com/watch?v=6RRSxWtJPUw https://www.youtube.com/watch?v=6RRSxWtJPUw https://nanoporetech.com/products/minion https://nanoporetech.com/products/minion
        aydyn 3y ago
        Nanopore has a much, much higher error rate and you still need sample extraction / sample prep all the same.
        yreg 3y ago
        The error rate is low enough for plenty of tasks. E.g. DoctorOetker's goal of finding out how novel the collected genome is. If you can do the extraction / prep with a briefcase you bring to a jungle, then you can do it on a boat as well.
gopher_space 3y ago
https://oceanexplorer.noaa.gov/okeanos/collaboration-tools/EX_Capabilities_Overview.pdf https://oceanexplorer.noaa.gov/okeanos/collaboration-tools/E... I'm still reading but it looks like they're sailor/pilot oriented thanks to their telepresence capabilities. Land lubbers get to stay ashore.
- DoctorOetker 3y ago
  thanks for the link, it mentions the wet lab but not the equipment it entails.
jsndidneske 3y ago
[flagged]

webmobdev 3y ago

Cut them some slack please - even they need the occasional PR hype to ensure funding.

DoctorOetker 3y ago

[flagged]

Sunhold 3y ago
I don't know why you are assuming it is standard, expected or necessary to have genome sequencing equipment on the ship. There's no doubt that they've brought it back to land and are working to identify it now.
- DoctorOetker 3y ago
  Do you accept or deny the desirability of on-ship genome sequencing equipment? Nobody knows the sum total of all observations made by mankind. If one can effectively sequence immediately, one can quickly how novel the genome is, and if its not novel, if its a novel lifestage. On the way to land the specimen (if alive) may die, or (if dead) be consumed and rot on the way to land. If the species or closest known artificially sustainable life-form can be identified on-ship, probability to keep it alive can be increased. I don't doubt they are working to identify it, and I wouldn't be surprised if they already did (perhaps on-ship). What disturbs me is major popular science platforms are pro-actively feeding mysticism and trolls by staying mute on the most obvious next logical step. I do not at all assume it is standard: I assume the number of nation-state actors investing resources in exploring the deep sea ecology (to this depth) constitutes a very small list. So by no means can any of this research be taken for granted and assumed standard. The mere activity of this type of research is already non-standard. Genome sequencing equipment has been highly miniaturized and become a lot more affordable. So yes, I do expect a wet-lab on this vessel to actually have genome sequencing equipment. If not, I think the researchers have a right to lament it publically.
  - dlor 3y ago
    Have you ever been on a boat? It's not safe to assume the existence of anything, including a toilet, on them.
    - DoctorOetker 3y ago
      have you ever seen a picture of this mothership? I think it's pretty safe to assume it has toilet... https://oceanexplorer.noaa.gov/okeanos/collaboration-tools/EX_Capabilities_Overview.pdf https://oceanexplorer.noaa.gov/okeanos/collaboration-tools/E...
  - aydyn 3y ago
    Even if you were able to start sequencing immediately, standard sequencing alone takes on the order of a day. And then depending on your computational methods, could take another few hours. Remember that it's not just the sequencer, you also need extraction, so you need to add a centrifuge, a vortex, a pipetting station, a PCR machine, a -20 C freezer, a spectrophotometer and a whole lot of reagents, additional personnel, and probably tons of other things I'm forgetting. Also I doubt most instruments are specced to be able to handle ship sway on the open sea. It really just isn't practical.
    - yreg 3y ago
      There are portable devices for sequencing out in the field, like MinION. https://www.youtube.com/watch?v=6RRSxWtJPUw https://www.youtube.com/watch?v=6RRSxWtJPUw https://nanoporetech.com/products/minion https://nanoporetech.com/products/minion
      - aydyn 3y ago
        Nanopore has a much, much higher error rate and you still need sample extraction / sample prep all the same.
        yreg 3y ago
        The error rate is low enough for plenty of tasks. E.g. DoctorOetker's goal of finding out how novel the collected genome is. If you can do the extraction / prep with a briefcase you bring to a jungle, then you can do it on a boat as well.

gopher_space 3y ago

https://oceanexplorer.noaa.gov/okeanos/collaboration-tools/EX_Capabilities_Overview.pdf https://oceanexplorer.noaa.gov/okeanos/collaboration-tools/E... I'm still reading but it looks like they're sailor/pilot oriented thanks to their telepresence capabilities. Land lubbers get to stay ashore.

DoctorOetker 3y ago
thanks for the link, it mentions the wet lab but not the equipment it entails.

jsndidneske 3y ago

[flagged]