Talk:Junk DNA

Overlinking

I propose to revert most of the links that were recently added by Melosina because, in my opinion, it's an example of overlinking (too much blue). I don't think it's necessary to link to terms such as "DNA," "genes," "protein," "natural selection," "eukaryotic," "nucleus," "expression," "geneticists," "evolutionary biologists," molecular biologists," "evolution," and "Nobel." Some of the links they inserted are not at all helpful in the context of an article on junk DNA and may even be counter-productive (e.g. "functional," and "mutation"). The problem of overlinking has been covered many times in the past few years. For example, the essay on the overlink crisis says,

Overlinking is the characteristic of having too many internal wikilinks or hyperlinks to external webpages. Editors should use an appropriate number of wikilinks in an article's text. In addition to providing relevant navigation opportunities, an appropriate number of blue links makes articles easier to read, especially in long paragraphs or sections.

The issue concerns readability. Too many Wikilinks (too much blue) makes the article less attractive to readers without adding any significant value. This is a serious problem in science articles where the leads can look overwhelmingly complex to the average reader because of excessive Wikilinks (e.g. Human genome).

The Wikipedia:Manual of Style/Linking makes the following wise suggestions concerning links.

An article is said to be overlinked if it contains an excessive number of links, making it difficult to identify those likely to aid a reader's understanding. A good question to ask yourself is whether reading the article you're about to link to would help someone understand the article you are linking from. Unless a term is particularly relevant to the context in the article, the following are usually not linked: -Everyday words understood by most readers in context

Perhaps we can find a happy medium where unusual terms that are essential to understanding are given links but commons scientific words that should be familiar to anyone reading this article are not? Genome42 (talk) 14:26, 29 April 2023 (UTC)

I agree with you. Some terms are super obvious like DNA, expression, genomes, natural selection that they do not to be wikilinked. Feel free to clean it up. Ramos1990 (talk) 18:21, 29 April 2023 (UTC)

Minor tense suggestion

Perhaps having the word YET used more frequently, as well as having as a second point if not the first, a clarification clarifying / a differentiation differentiating between,..

.

1 matched-with-others-in-surpassed-evolutionary-progressions-and-so-redundant(true junk) DNA,

2 assumed-no-function junk from genetic processes (high confidence - temporary retentions kept longer than needed if needing to be kept at all), and

3 theorised to have no function but of more compatible DNA-chemistry -combinations ... junk (ones that have still matching after-activation matching chemistry with organelles or functional materials in plasma/interstitial spaces, but are without 'context' in nearby genes along the chains, and so seem pointless, despite chemical-compatibility. Compared to things like say, immune system instructions or embryonic stages, ones with clear-purpose) (less-confidence / more reasonable uncertainty - the chemistry suggests a high likelyhood if not outright proof, of past usefullness) ...

.

... could help to introduce the concept FIRST?

Rather than finding the contrast or inferred-problems with the single concept or inferred consistency, further down the page, and the static tense (scientific conclusion-ary) avoiding the still-new problems of the field? i.e. using YET, adds necessary cautionary relativity to a solid concept, but a phenomenon that is sometimes irreversibly presumed static.

---

i.e. when something THOUGHT junk, is 'let-back-in', at the PREVIOUS time of it being labelled junk, the static nature was less correct, than saying "YET", so,.. yet-confirmed as junk, or yet-re-included back into unknown status rather than confirmed-junk or certified-junk, etc. A big part of that problem is WHO certifies, but that might end up making the page much larger than it should be if that kind of debate/issue should be on a separate page or is not subjectively purposed - i.e. at least the 'YET' nature of both corrective processes, reveals just HOW-new, this science is. Sort of like if you re-wrote it entirely, and re-wrote it with constant inferred STATUS inferences, to keep reminding the reader, that DNAs classification can rapidly CHANGE, that DNA is only sometimes statically clearly-purposed, nature's IMperfections, compared to imaginary ideals, etc. That's not opinion, that's hard-science. Human DNA for tails, for example, are recent, but HAD function. Tense with it as an example, would be an easy example to demonstrate the principle of CAUTION with DNA's classification as junk or not-junk. 120.21.106.152 (talk) 15:13, 30 June 2023 (UTC)

I don't understand your point. Could you give a specific example of something you think should be changed? Genome42 (talk) 22:10, 30 June 2023 (UTC)

The function wars

Junk DNA is DNA that does not have a function so the entire debate hinges on determining which part of the genome is functional. You can't do that unless you can define function in some meaningful way. The debate over the proper meaning of function is called the "function wars" and since 2012 it has almost exclusively been about the best way to describe a selected effect function. I think the "maintenance" function definition is the best one.

This is 2024. There are no other definitions of function that are actively defended in the scientific literature. The causal role function (biochemical activity) was thoroughly debunked a decade ago and I'm not aware of any serious publication that defends biochemical activity as a viable definition of function. In order for biochemical activity to be a serious contender, there would have to be numerous examples of genuine functional regions of the genome that exhibit biochemical activity but are not under purifying selection. In the absence of such examples, the maintenance function definition covers all examples of genuine biochemical activity plus functional regions that don't exhibit traditional biochemical activity.

Ramos1990 insists on inserting a reference to the ENCODE 2014 paper that casts doubt on the maintenance function by claiming that there are "diverse understandings of 'function' in different fields." The three diverse understandings are genetic, evolutionary, and biochemical.

This is not helpful since we have highlighted the serious shortcomings of biochemical activity as a definition of function and provided references to 10 papers that discuss these shortcomings. There's no good explanation of "genetic" function in this article. (The section under "Genetic function" is useless and should be deleted.) Readers will be left wondering why there are still "diverse understandings" of function when the only one supported by data and logic is the one based on conservation and purifying selection.

The only reason for bringing up biochemical function in this article is to alert readers to the false claim made by the ENCODE researchers in 2012. That claim received such massive coverage in the popular press that there are still many readers (and many scientists) who think that the idea of junk DNA has been abandoned by the experts in the field. By putting undue emphasis on the excuses and rationalizations made by the ENCODE workers in 2014 we are contributing to the misconceptions that they promoted in 2012. Genome42 (talk) 14:42, 2 May 2024 (UTC)

I did not cite the 2014 paper. You added it there. Have to stick to what the sources actually say. Also you mentioned that other researchers understand function differently (e.g. Mattick, Kellis, Abascal, etc). Even Linquist 2020 acknowledges different understandings of function are in the literature and that it is unclear much of the time when it is used. Ramos1990 (talk) 00:47, 3 May 2024 (UTC)

The two most important points in the 2014 paper are: (1) that the ENCODE researchers admit that biochemical activity on its own is not a reliable indicator of function and (2) there is evidence for junk DNA that they did not mention in their 2012 papers.

We all know what this means. It means that they were wrong to claim that their data refuted junk DNA and that at least 80% of the human genome is functional. These are the important points that readers need to know since there is still a widespread belief that the ENCODE data refuted junk DNA.

I recently added the following description of the Kellis et al. (2014) paper.

"The challengers argued that biochemical activity is not a reliable indicator of function and in 2014 the ENCODE researchers agreed with the challengers and abandoned their claim that 80% of the human genome was functional. They also presented evidence for junk DNA that was missing in their 2012 papers.(Kellis et al., 2014)"

You deleted that description and restored the previous version which says,

"In 2014, ENCODE researchers responded that there are both limitations and advantages to the different approaches (genetic, evolutionary, biochemical) used to get estimates of functional elements, that there are diverse understandings of "function" in different fields, and that integration of genetic, evolutionary, and biochemical approaches should be used to better define function. (Kellis et al., 2014)"

I maintain that your version misrepresents the significance of the ENCODE retraction and perpetuates the myth that their data still refutes junk DNA. Your version makes it look like the ENCODE researchers are defending the notion that biochemical activity could still be a legitimate definition of function in "their" field.

Let me remind you of what the ENCODE researchers said in 2012, "These data enabled us to assign biochemical functions for 80% of the genome." That's the conclusion that was promoted in the university press releases and the popular press articles where it was taken to mean that junk DNA was refuted. Many of the ENCODE researchers are on record as supporting the idea that most of the genome is functional and not junk.

And here's what those same researchers said in 2014, "The major contribution of ENCODE to date has been high-resolution, highly-reproducible maps of DNA segments with biochemical signatures associated with diverse molecular functions. We believe that this public resource is far more important than any interim estimate of the fraction of the genome that is functional."

That's a clear repudiation of their earlier claim that 80% of the genome is functional. How should we explain this to our readers? I look forward to your suggestions. Genome42 (talk) 14:08, 3 May 2024 (UTC)

Ramos1990 said, "Even Linquist 2020 acknowledges different understandings of function are in the literature ..."

This is correct. Linquist mentions that biochemical activity is a causal role (CR) function. Here's what he says,

"I have argued that in the discipline of genomics, component-driven functional investigation runs the risk of causal-role myopia. The tendency to posit one organism-level capacity after another as the putative CR function of some genetic element can proceed indefinitely because (1) the genome is littered with TEs and their partially deactivated descendants which (2) masquerade as components with interesting CR functions and (3) it is experimentally onerous to determine whether a given element lacks any such function. The fact that ENCODE appears to have fallen victim to this kind of reasoning suggests that CR myopia is not a hypothetical concern."

Do you think we should put this quotation into the article in order to demonstrate the consensus view of most experts in the field of genomic function? Genome42 (talk) 14:18, 3 May 2024 (UTC)

The 2014 paper highlighted strengths and weaknesses of all 3 methods. They stated that "absence of conservation cannot be interpreted as evidence for the lack of function." as well and also noted that conservation estimates provide a lower bound estimate (with problems), not the complete estimate of functional elements. They argue for biochemical activity as a powerful tool and emphasize molecular function in the quote you quoted. They concluded that all 3 approaches should be used to get a more comprehensive understanding of elements in biology and disease. In Abiscal 2020, ENCODE still uses biochemical activity for molecular functionality proxy. In terms of Linquist, he clearly states "However, as a number of authors have noted, the problem is also partly due to a confusion about the various possible meanings of “function” in biology [3–5]." and also acknowledges differing practices of evolutionary biologists, experimental biologists, and genomicists; each with different sets of assumptions, often adaptionist. Of course Abascal and Mattick show different views of function too. I don't think there is a consensus across these fields of what constitutes function. Otherwise there would be no debates of articles seeking clarification on the term (e.g. Kellis, Linquist, Doolittle). Ramos1990 (talk) 02:48, 4 May 2024 (UTC)