5 ms·

Scientists Map 5,000 New Ocean Viruses

31 points by treefire86 11y ago

comrade1 11y ago
ugh. quanta. That, medium.com, and one other that keeps getting posted to HN news that I can't remember the name... it's all just pablum for the TED crowd. Here's the original paper which you can't read because it's behind a paywall even though it's research supported by your tax dollars: http://www.sciencemag.org/content/348/6237/1261498 http://www.sciencemag.org/content/348/6237/1261498
- FlailFast 11y ago
  Is there any group lobbying for an open source proviso from results derived from a certain threshold of government research funding? That feels like a no-brainer to me, and one which could have enormously positive economic impact.
  - dj-wonk 11y ago
    As mentioned in https://www.plos.org/open-access/ https://www.plos.org/open-access/ > There are many other organizations, such as SPARC (the Scholarly Publishing and Academic Resources Institute) and the Open Society Foundations, that work tirelessly for progress in Open Access. You can find many free resources to help you learn more or to advocate for OA journals in your institution. See also: https://doaj.org/oainfo https://doaj.org/oainfo
  - frozenport 11y ago
    >> feels like a no-brainer to me Except it creates incentives that perpetuate the publish or perish model. For example, journals no longer need to worry about if published work is interesting or has an audiance and therefore it becomes easier to publish papers of dubious value. During your annual review, you need to explain why you only published 1 paper (perhaps in the pay-walled journal of your proffesional society) when your colleague published 3 papers in some Open-Acess journal that nobody reads.
- ejstronge 11y ago
  I'm not sure who you're referring to by 'your' but it's not clear that any particular person's tax dollars were used. This work is likely government-funded but certain types of research are supported by private organizations and/or donors. EDIT: Also, this article is free provided one registers with Science/AAAS [1]. 1. http://www.sciencemag.org/content/348/6237/1261498.full http://www.sciencemag.org/content/348/6237/1261498.full
  - vixen99 11y ago
    You're not sure but most of us do understand what 'tax dollars' means and apply the 'function' according to our status. Some research supported by private organizations? I had no idea.
- mojotoad 11y ago
  Pablum? Really? I found the article to be quite fascinating, particularly the statistical methods they used.
dj-wonk 11y ago
> "In the few decades since viruses were first found in the oceans, scientists have only been able to identify a handful of species. A new survey has uncovered nearly all the rest." My first reaction was "What does 'nearly all the rest' mean and how can one come to such a conclusion?" The article is a basic but interesting writeup about Sullivan and his colleagues did to get there.
- dj-wonk 11y ago
  I'm concerned that the study may use "out of sample" reasoning in arriving at its virus population count estimate. Here is a snippet from the Quanta article showing some limitations of the sampling / collection methodology: > In addition, the scientists sequenced only viruses that use DNA to encode their genes. Some viruses, such as influenza and HIV, use RNA, a single-strand version of DNA, to encode their genes. By one estimate, as many as half of the viruses in the ocean are RNA viruses. What’s more, the Tara Oceans survey only took samples from the surface of the ocean. The deeper regions have viruses, too, as does the sediment at the bottom of the sea.

31 points by treefire86 11y ago

ugh. quanta. That, medium.com, and one other that keeps getting posted to HN news that I can't remember the name... it's all just pablum for the TED crowd. Here's the original paper which you can't read because it's behind a paywall even though it's research supported by your tax dollars: http://www.sciencemag.org/content/348/6237/1261498 http://www.sciencemag.org/content/348/6237/1261498

FlailFast 11y ago
Is there any group lobbying for an open source proviso from results derived from a certain threshold of government research funding? That feels like a no-brainer to me, and one which could have enormously positive economic impact.
- dj-wonk 11y ago
  As mentioned in https://www.plos.org/open-access/ https://www.plos.org/open-access/ > There are many other organizations, such as SPARC (the Scholarly Publishing and Academic Resources Institute) and the Open Society Foundations, that work tirelessly for progress in Open Access. You can find many free resources to help you learn more or to advocate for OA journals in your institution. See also: https://doaj.org/oainfo https://doaj.org/oainfo
- frozenport 11y ago
  >> feels like a no-brainer to me Except it creates incentives that perpetuate the publish or perish model. For example, journals no longer need to worry about if published work is interesting or has an audiance and therefore it becomes easier to publish papers of dubious value. During your annual review, you need to explain why you only published 1 paper (perhaps in the pay-walled journal of your proffesional society) when your colleague published 3 papers in some Open-Acess journal that nobody reads.
ejstronge 11y ago
I'm not sure who you're referring to by 'your' but it's not clear that any particular person's tax dollars were used. This work is likely government-funded but certain types of research are supported by private organizations and/or donors. EDIT: Also, this article is free provided one registers with Science/AAAS [1]. 1. http://www.sciencemag.org/content/348/6237/1261498.full http://www.sciencemag.org/content/348/6237/1261498.full
- vixen99 11y ago
  You're not sure but most of us do understand what 'tax dollars' means and apply the 'function' according to our status. Some research supported by private organizations? I had no idea.
mojotoad 11y ago
Pablum? Really? I found the article to be quite fascinating, particularly the statistical methods they used.

dj-wonk 11y ago

> "In the few decades since viruses were first found in the oceans, scientists have only been able to identify a handful of species. A new survey has uncovered nearly all the rest." My first reaction was "What does 'nearly all the rest' mean and how can one come to such a conclusion?" The article is a basic but interesting writeup about Sullivan and his colleagues did to get there.

dj-wonk 11y ago
I'm concerned that the study may use "out of sample" reasoning in arriving at its virus population count estimate. Here is a snippet from the Quanta article showing some limitations of the sampling / collection methodology: > In addition, the scientists sequenced only viruses that use DNA to encode their genes. Some viruses, such as influenza and HIV, use RNA, a single-strand version of DNA, to encode their genes. By one estimate, as many as half of the viruses in the ocean are RNA viruses. What’s more, the Tara Oceans survey only took samples from the surface of the ocean. The deeper regions have viruses, too, as does the sediment at the bottom of the sea.