Talk:Hazards of synthetic biology

Mirror life dangers, including "kill us all", 2016 synthesized mirror polymerase

We are slowly approaching synthesis of first mirror-image cells ( https://wiki.riteme.site/wiki/Mirror_life ) - built of mirror versions of standard molecules (enantiomers). For example while functional large mirror proteins seemed a big difficulty a few years ago, in 2016 there was synthesized first functional mirror polymerase: https://www.nature.com/news/mirror-image-enzyme-copies-looking-glass-dna-1.19918

Here is 2010 Wired article: "Mirror-image cells could transform science - or kill us all" regarding dangers of mirror cyanobacteria, which due to nearly incompatible natural enemies could dominate e.g. our oceans: https://www.wired.com/2010/11/ff_mirrorlife/

As mirror versions of biomolecules are often toxic due to unpredictable interactions, like in thalidomide case, other mirror microbes might already turn out extremely dangerous. Bacteria are known to be able to adapt to consumption of opposite chirality sugars (e.g. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4160389/ ), and mirror ones could populate some ecological niches due to nearly no natural enemies.

Mirror life needs a special attention regarding "Hazards of synthetic biology" - maybe it deserves a separate section in this article? Jarek Duda (talk) 12:14, 2 April 2019 (UTC)

@Jarek Duda: Mirror life would fall under the category of xenobiology and would have much of the same impacts, both in terms of hazards and for use as intrinsic biocontainment. The sources I've looked at tend to emphasize xeno nucleic acids and I haven't seen much treatment of mirror life. If you could suggest a source I'll take a look at it. Due to Wikipedia's content guidelines (see Wikipedia:Reliable_sources#Scholarship), secondary sources such as review articles in peer-reviewed journals, or guidance documents from government health agencies, are strongly preferred. Popular science articles and even primary research articles aren't preferred, which is much different from writing in other contexts. John P. Sadowski (NIOSH) (talk) 08:00, 21 May 2019 (UTC)

There are peer-reviewed articles regarding realized synthesis of e.g. mirror polymerase in 2016. There are authorities warning about this possibility in popular science articles, like Jack Szostak and George Church in the 2010 Wired article. However, reliable understanding of consequences of synthesizing e.g. the first mirror cells, seems extremely difficult, we might wait for such peer-reviewed papers more than for this synthesis. Should it be ignored since then? Jarek Duda (talk) 08:34, 21 May 2019 (UTC)

GA Review

This review is transcluded from Talk:Hazards of synthetic biology/GA1. The edit link for this section can be used to add comments to the review.

Reviewer: Ajpolino (talk · contribs) 22:26, 2 December 2019 (UTC)

Pinging @John P. Sadowski (NIOSH): (nom) and @Antony-22: (main account) to notify you since this nomination has languished so long in the GAN cue. Sorry for the wait. It may take me the week to get through this, but wanted to signal my intention to make it through this review asap. Ajpolino (talk) 22:29, 2 December 2019 (UTC)

Ok, made my first pass through. Kudos for taking on a topic that's the topic of both public interest and frequent misunderstanding/hyperbole. The article is generally good, with the two main problems (in my opinion) being (1) frequent unattributed opinions in Wikipedia's voice, and (2) prose that is sometimes unclear and wordy. I hope both will be relatively easy fixes, and am happy to help out if you're short on time/interest. I've posted slightly more-detailed comments below. Feel free to mark them with a comment, strike them through, or mark with {{done}} as you get to them. Also I'm just as prone to mistakes as anyone else, so if you think I've misjudged something, feel free to push-back and I'm happy to talk about it. Thanks for the interesting read! Ajpolino (talk) 23:17, 3 December 2019 (UTC)

GA review – see WP:WIAGA for criteria

1. Is it well written?

   A. The prose is clear and concise, and the spelling and grammar are correct:

   •The article could use a copyedit. It's at times unecessarily wordy which makes it slow to read through. I'm happy to give it a copyedit as well, but would prefer to wait until you're definitely around so you can make sure I don't change the intended meaning of anything.

   •Hazards>Biosafety - the first paragraph here seems to belabor the point such that it's very slow to read. Can you re-word and trim this paragraph so it doesn't read "Hazardous chemicals include [list]. Biological hazards include [list], present in [list]. Routes of exposure include [list]. Physical hazards include [list]. Additional hazards include [list including hazards not-at-all unique to synthetic biology]."? Maybe less detail will suffice?  Done

   •Risk assessment - "Synthetic organisms also may not be included in existing risk groups." It's not clear what this means.  Done

   •Risk assessment - "An additional challenge is that syntehtic biology engages a wide range of disciplines outside of biology who may be less familiar with microbiological risk assessment." Weird phrasing. "disciplines... who..." doesn't really make sense. Could you rephrase it somehow?  Done

   •Risk assessment - "Some researchers have sugggested... its amount and properties." - It's not clear what you're getting at here. Maybe you could clarify that somehow?  Done

   B. It complies with the manual of style guidelines for lead sections, layout, words to watch, fiction, and list incorporation:

2. Is it verifiable with no original research?

   A. It contains a list of all references (sources of information), presented in accordance with the layout style guideline:

   •Minor question: at the end of paragraph one of the Risk assessment section, the reference call is marked as bold and italics (i.e. in the non-visual editor it shows up as '''''<ref name=":1" />'''''). Is that intentional? I've never seen that before. I can't tell if it actually changes the appearance of the reference at all...  Done

   B. All in-line citations are from reliable sources, including those for direct quotations, statistics, published opinion, counter-intuitive or controversial statements that are challenged or likely to be challenged, and contentious material relating to living persons—science-based articles should follow the scientific citation guidelines:

   C. It contains no original research:

   •Hazards>Biosecurity - "Bacteria are considered to be a higher risk than viruses because they are easier to manipulate and their genomes are more stable over time." I skimmed the NASEM report pages you cite, and I'm not sure this broad a statement is supported. They have four risk categories for each hazard they assess: usability of technology, usability as a weapon, requirements to use, and mitigation potential. They rank viruses on these four: Med-Low, Med-High, Med, Med. They rank bacteria: High, Med, Med, Med. Perhaps I missed a place where they make a more outright statement? If not, I'd suggest re-phrasing this.  Comment.

   •Hazards>Biosafety - I'm a little confused as to the definition of biosafety. The biosafety Wikipedia article describes it (opaquely enough) as prevention of the "loss of biological integrity". The source you use the most in that section ([1]), sadly, I don't have access to. But the other sources make it sound like "biosafety" refers to the risk that the biological entities being worked on in the lab will either harm laboratory workers or harm ecosystems outside the laboratory. Is that correct? If so, it's confusing that you lump in safety hazards of working in the lab (i.e. chemical exposure, autoclaves, centrifuges, et al) under the subsection "biosafety". Maybe there should be a distinction between the biosafety hazards of synthetic biology, and the safety hazards of working in synthetic biology? Or maybe I'm just not understanding the definition of biosafety and that should be clarified instead? Either way, some clarity would be appreciated.  Comment.

   D. It contains no copyright violations nor plagiarism:

3. Is it broad in its coverage?

   A. It addresses the main aspects of the topic:

   B. It stays focused on the topic without going into unnecessary detail (see summary style):

4. Is it neutral?

   It represents viewpoints fairly and without editorial bias, giving due weight to each:

   •I don't really think this is the right section for this, but since WP:WIKIVOICE redirects to the WP:NPOV page I'll put it here: there are several places in the article where the article states an opinion in Wikipedia's voice when it should either be attributed to the actual opinion's source, or cited to an authoritative reference that clearly states that the opinion is widely held. Examples: "Which is considered possible but unlikely given...", "Creating existing bacteria... are considered a low risk.", "There is also the possibility of novel threats that are considered lower risks due to their technical challenges...".

   •On this note, perhaps you could consider rephrasing things like "One capability of concern is the recreation of known pathogens from scratch" (confusingly vague. Concern to whom? Wikipedia?) to things more like "Synthetic biology tools make it possible to recreate known pathogens from scratch" (which is explicitly supported and discussed by pg3-4 of the NASEM report you cite)... I mean you can re-word things however you'd like. But just a suggestion.  Done

   •Why are lentiviral vectors derived from HIV-1 of "special interest"? The CDC blogs source just uses them as an example, but doesn't give a reason they'd be of any more special interest than other novel viruses (you also cite the Journal of Occupational and Environmental Hygiene paper, but I don't have access to it, so I'm not sure if that makes it more clear. If so, could you clarify?).  Done

5. Is it stable?

   It does not change significantly from day to day because of an ongoing edit war or content dispute:

6. Is it illustrated, if possible, by images?

   A. Images are tagged with their copyright status, and valid fair use rationales are provided for non-free content:

   B. Images are relevant to the topic, and have suitable captions:

7. Overall:

   Pass or Fail:

@Ajpolino: Thanks for the thorough review; I know this is a long and technical article and I appreciate the time spent reviewing it. Comments below:

• I'm happy for you to give it a copyedit at your leisure, I can go back and revise anything that needs it.
• Hazards>Biosafety: Good point; I've cut it down and moved the full laundry list over to the Biosafety article.
• Hazards>Biosecurity: This statement is based on the overall ranking on p. 5 and elsewhere; "making existing bacteria more dangerous" is on the top level, while "making existing bacteria more dangerous" is on the second level down.
• WP:WIKIVOICE: I'll try to find time to find and reword these statements.

John P. Sadowski (NIOSH) (talk) 02:51, 20 December 2019 (UTC)

@John P. Sadowski (NIOSH): Just a note that I'll be traveling in real life this week, so it may take me 7-10 days to get back to this review. Just wanted to let you know I haven't forgotten about it. Cheers! Ajpolino (talk) 16:15, 21 December 2019 (UTC)

No worries! John P. Sadowski (NIOSH) (talk) 04:49, 25 December 2019 (UTC)

@John P. Sadowski (NIOSH): Ok, starting to work my way through this again. I'll try to break up any larger edits into digestible chunks. Don't be shy about complaining, changing, or undoing any of my edits. Ajpolino (talk) 18:56, 31 December 2019 (UTC)

@John P. Sadowski (NIOSH): Just a note to say I added a couple more comments today. The big remaining thing is the WP:WIKIVOICE concern (but there's also some minor things above). Feel free to strike through my comments as you get to them. I'll mark this review as on-hold for now. There's no rush here. If I haven't heard from you in a few months, I'll close this review and you can put it back in the queue any time (but if you need more time than that, just comment here). Happy editing! Ajpolino (talk) 17:42, 24 January 2020 (UTC)

Thanks for the extra points; I've dealt with the additional explicit ones, and will look for others in the article later. For the biosafety item, I agree that the Biosafety article is poorly written; for the purposes of this article, the "Biosafety" section deals with hazards to workers, while there's a separate "Environmental" section for hazards to the environment. John P. Sadowski (NIOSH) (talk) 14:39, 30 January 2020 (UTC)

@Ajpolino: I have given the article another round of copyedits in addition to correcting the issues above. I'm ready for you to take another look at it. John P. Sadowski (NIOSH) (talk) 05:41, 11 March 2020 (UTC)

@John P. Sadowski (NIOSH): Great! I took another look through and it looks much-improved. I'm happy to mark this as a pass. Thanks for the interesting read. I hope all is well; happy editing! Ajpolino (talk) 22:15, 12 March 2020 (UTC)

@Ajpolino: Thanks for sticking through this! I know technical articles like this are not easy to review, and I appreciate the time and effort you spent with it. John P. Sadowski (NIOSH) (talk) 05:34, 13 March 2020 (UTC)