Talk:Onion Test

Interpretation

If you have views that are disagreements of interpretation, or suggestions for improved directions, better discuss here rather than have lots of back and forth edits. Its the normal Wikipedia way. Thanks all.

I've reverted some changes that I thought made the article much less useful, happy to discuss. This is certainly not a discussion between blogs! There are citations to a number of peer reviewed joundal articles. A textbook too. It is a central concept in the junk DNA debate, which is imprtant to genomics and evolution. Lets keep this based on fact and using typical Wikipedia writing style. Again, lets discuss here if you disagree, and reach a good way forward XCalPab (talk) 10:00, 14 February 2019 (UTC)

I will have to revert to my version eventually because thus far the article looks like editorializing and not sticking to the sources content. The article as I condensed it looked more neutral and stuck to the sources without trying to make it POV pushing, which is how it looks right now. Considering that this is a minor debate that started form blogs and is not prominent in academic literature at all, it should reflect the sources, not slant them. The sources you provided were a blog, a few articles (one involving Gregory himself) and a minor textbook mention. It is not a prominent thing in the literature in evolutionary biology and certainly the point by Gregory is not unique in discussions of the C-value paradox. Gregory himself admits this: "In summary, the notion that the majority of eukaryotic noncoding DNA is functional is very difficult to reconcile with the massive diversity in genome size observed among species, including among some closely related taxa. The onion test is merely a restatement of this issue, which has been well known to genome biologists for many decades." [1] The funny thing is that Gregory just uses onions as an example of paradoxes, not an actual test. Furthermore it is not "frequently" mentioned anywhere either - all the core sources you mentioned were from 2013-2015. What about the last 4 years? It has been very quite these past few years, which implies that it is not a prominent thing among scientists.

Can you provide me a quote about the onion test in Molecular and Genome Evolution by Dan Dan Graur? I cannot see what it says, but since you put it in I assume you can provide an extensive quote about it from the textbook.

Another issue is the term "junk DNA" being thrown around too much when it refers to noncoding DNA. The term "junk DNA" amiguates the discussion since really it is about noncoding DNA and whether or not it has a function of whihc there is still lots of debate. Gregory has explained this in the article and elsewhere. But by using the terminology too much it really makes it unclear as to what is being discussed - which is noncoding DNA.

Another issue is the fact that there is some WP:OR and WP:SYN when you take sides on creationists in the criticism section and the onion/c-value paradox sections. The sources (blogs) are talking about each other and yet you downplay one and over emphasize the other. It should be neutral and to the point, not taking a side in the debate. Both blogs have their points.

The main sources for 2 sections were blogs not academic literature so that is not a good start. Looking at google scholar, the onion test is not prominent at all. There is even one scientific paper you cited seems to explain the away the onion's genome size very easily - [2]. With there being multiple views on the matter then the article should be more neutral overall.

It just looks like the article is trying too hard to oversell a simple point that that is obvious and not revolutionary and apparently solvable. Why even make an article about it in the first place?

Not to mention that the onion test is not an actual test. It is a comparative or rhetorical question that just asks stuff but does not give any answer. In fact Gregory admits in the journal article above that it is just a "restatement" not a test in the quote above - "The onion test is merely a restatement of this issue, which has been well known to genome biologists for many decades." Huitzilopochtli1990 (talk) 23:57, 14 February 2019 (UTC)

Thanks for your time considering this, and bringing it to the talk pages, this is exactly what Wikipedia is all about! To be honest I don't think we are that far apart on 90% of the issues, and I would largely agree with some of your points, but feel your outcomes regarding what is written were a bit harsh in your first edit.

Writing style: there always has to be some 'editorial' action to bring an article together, but I have spent time linking this to scientific journal articles. I think it is very factual and the style is very Wikipedia (with a few screw ups detailed below). Writing an article about something that sort-of criticises a different view cannot by definition be balanced throughout, putting equal weight on both sides, as it mainly has to describe in detail the position you are talking about. This is why I put in the criticism section to have a place for that balance. I am happy for positive suggestions but I found some of your first edits in danger of misleading a reader, and some were not correct. Some others were v good. I probably should have spent more time incorporating than reverting. Sorry, my bad.

Is it all Gregory and nobody else? No, its easily wide enough for recognition and a wikipedia article. I'll get the Graur quote sorted out. He has a subheading "The Onion Test" and three paragraphs in one of the major molecular evolutionary genetics textbooks out there. There are articles from I think four groups (not including Gregory) using this term. Thats not bad for the start of a new Wikipedia page.

Is it just blogs arguing? Yes and No. I didn't do the best job, and shouldn't have started with reference to 3 blogs, and then quietly later bring in textbooks and journal articles. I should have done it the other way. There is one very 'robust' blog back and forth. It is factually true however that the "c-value paradox" and the "Onion Test" are different. I was struggling to find clear counter arguments written down except in blogs. I'll work on this to take focus away from angry blogs and onto a clearer position. Would that help?

Do we need this article? Yes. I feel strongly that Wikipedia has to have as much knowledge as humanly possible. Is it notable? Yes, by Wikipedia definitions it is. That is demonstrated I feel. I'm not hearing different in your critique, just that you think the words make it sound more important than it is. That can be fixed.

Is this a major thing? Here we disagree a bit, depending on what 'major' means. 1) It does not have to be major to be on wikipedia, only notable 2) It is a major thing in evolutionary genomics? It is a very significant, important (=major, maybe) thing even though the phrase "Onion Test" is not as frequent as many other topics. Let's not conflate what Gregory says with the bigger picture of the C-value paradox. Yes that's been discussed for years. This different Onion Test rationale made a contribution to the ENCODE genome function debate, which was all through the news a few years back. This logical "test" is common in the field even if the name is perhaps less common. I admit. Even more reason to have the article! How about we modify my language to make its frequency a bit more downplayed?

Is it just re-stating stuff, and other examples before onions. Yes I agree. Nothing is truly new. There is another paper I meant to include talking about lungfish vs zebrafish rather than onions. Same thing. Also I think history will show there are earlier people saying similar things to Gregory. I'll try to put something about that this is a restatement of other ideas. Yes?

Is it a test? Is it a (c-value) paradox? Good points, probably they're bad names, but they are names that actually exist and are used by people. Nothing can be done about those names.

Is "junk DNA" being used too much, and junk is a term linked to non-coding DNA. I agree, lets fix that.

Do I take sides with creationism? Yes and no. I do take a side, because confusion about what the onion test really is, is a demonstrable thing. Saying the onion test is the c-value paradox is not true, thats not taking sides its not true. I don't take a side, or discuss, bigger arguments. If you think I should remove "particularly by creationists", yes maybe a good idea, maybe that appears unhelpful?

Suggestion: Lets start making incremental changes and if anyone disagrees its only one thing to swap out/revert and discuss in more detail. I'll start with some of the issues you were right on outlined above. Thoughts or suggestions? I'll do my edits as outlined above in next 48 hours probably, unless you have better suggestions. XCalPab (talk) 14:54, 15 February 2019 (UTC)

Glad to hear your comments. I agree with many of your observations. I understand that there is some confusion because of all the charged terms and findings from ENCODE that created a wide debate about terms and what the evidence means. It is dicey stuff. Too bad the terminology in these debates are so polarizing and cause issues of ambiguity like this.

You can incorporate some of the wording I used to try to make this article better. The worries of misleading disappear when we stick to the sources and what they actually say instead of making claims in the voice of wikipedia - as if the issue was already settled. Clearly there is no closure in the research on this and the debates do continue (this is normal in evolutionary research) so this article should have nuanced and careful wording - like the sources do. Here are some thoughts in consideration of what you replied above:

I look forward to the quote from Graur's textbook. It is one out of many textbooks on the topic and that one does not stand out to me. I just want to know what he discusses and how relevant it really is.

Not sure if you can actually say that "It is factually true however that the "c-value paradox" and the "Onion Test" are different." There isn't much clarity on the issue and only the 2 blogs (Johnathan M. and Larry Moran) seem to mention it and disagree with each other on this point - both claim misunderstanding or hidden assumptions. We should just present the views and leave it at that without saying one side misunderstands the issues because both blogs claims they both misunderstand the issues or implications of the arguments, etc. Interestingly, Gregory seems to clearly involve the onion test with the c-value paradox when he says "In summary, the notion that the majority of eukaryotic noncoding DNA is functional is very difficult to reconcile with the massive diversity in genome size observed among species, including among some closely related taxa. The onion test is merely a restatement of this issue, which has been well known to genome biologists for many decades." in the PLos article. Clearly he is talking about genome sizes and organism complexity - which is the c-value paradox. If it is unclear then it is best to leave that up to the reader to decide, not us to make the claim in wikipedia's voice.

We should eliminate any mention of the frequency of the term "onion test" since it is not a prominently used term like you mentioned. It is not unique idea either and similar comparisons have certainly been discussed for decades. Let the reader decide if it is prominent or not. Besides, other science wikipages don't mention about how widely a term is used or not. It looks like fluffing or trying too hard to oversell otherwise. It is not even a test really, since Gregory himself says it is a "The onion test is merely a restatement of this issue, which has been well known to genome biologists for many decades." It is a restatement of things previously discussed - lack of correlation between genome sizes and organisms complexity and the implications for functionality of noncoding DNA. For the real impartant stuff is there already with many more useful studies on "c-values" and "c-paradoxes", discussion of organism complexity, etc. You many add the stuff on lungfish and zebrafish since it is a similar thing.

Lets fix the "junk dna" term and use it very rarely. Noncoding DNA is less ambiguous and to the point for all readers.

On creationism, lets remove all such references, including ""particularly by creationists", from the article since it is not helpful. It muddles the debate which is not about creationism, but about how much noncoding DNA has a function.

Hope this helps. Huitzilopochtli1990 (talk) 04:04, 16 February 2019 (UTC)

capitalisation

this is a common noun, is it not? Arlo James Barnes 17:35, 13 December 2023 (UTC)