Talk:Tree of life (biology)

Untitled
What is talked about in that article is not exactly new and is already included in the "Tree of life today" section. Do you feel that horizontal gene transfer could be somehow better discussed in this article? If so what do you feel should be included?203.213.71.221 (talk) 03:45, 24 January 2009 (UTC)

Controversy
This article also needs a "controversy" section with 2 subsections. There is a contemporary scientific controversy in which scientists such as Ford Doolittle dispute that we ought to be invoking a tree of life given that actually evolutionary history is (to a degree that is debate-able) non-tree-like due to processes such as lateral transfer. This was referenced in a comment several years ago that cites a Guardian article:
 * How about updating this with information presented here: http://www.guardian.co.uk/science/2009/jan/21/charles-darwin-evolution-species-tree-life —Preceding unsigned comment added by Wikitimi (talk • contribs) 03:25, 22 January 2009 (UTC)

There is also a minor dispute about the role of Darwin in the development of the concept that we now know as "the tree of life". Scholarship weighs on the side that Darwin did not invent the metaphor, but the idea of attributing this to Darwin just keeps popping up due to a constant stream of newcomers who think Darwin was there first because they have read Darwin but not Lamarck or other sources (e.g., this is implied in the Guardian article cited above) Dabs (talk) 15:37, 5 April 2013 (UTC)

Images
the images are not appropriate. They are history of science, not science. Can someone please get a decent image and post it. Andrewjlockley (talk) 21:05, 13 April 2009 (UTC)


 * This is an article about the Tree of Life in Science and so it describes the development of the concept and not just the latest understanding of the subject. So we have a section on the development and a section on the tree today. There is plenty of scope if you wish to improve the article . Lumos3 (talk) 23:01, 13 April 2009 (UTC)
 * I'm not really an expert on images. There's a great image I saw that's like a wheel with all the brnaches of the tree as spokes.  Can anyone stick that up, or suggest a better one? Andrewjlockley (talk) 23:21, 13 April 2009 (UTC)
 * This one? File:Tree of life SVG.svg - it's there already. Vsmith (talk) 00:41, 14 April 2009 (UTC)

How did you get away with uploading an image with 'Thor and Loki' as Eukaryotes? Can someone find a new picture? (2018) LMAO


 * There's no such image, either here or in Eukaryote. Chiswick Chap (talk) 08:36, 31 May 2018 (UTC)


 * :: The absolutely wonderful image in question is here; Loki and Thor are at the bottom right: https://upload.wikimedia.org/wikipedia/commons/9/98/A_Novel_Representation_Of_The_Tree_Of_Life.png  Here, Loki and Thor are most likely not the well known characters in Norse mythology (and the slightly more popular MCU) but in fact microbes of the Asgardarchaeota, https://en.wikipedia.org/wiki/Asgard_(archaea) https://www.sciencefocus.com/nature/thor-and-loki-microbes-hold-clues-to-origin-of-life/ - great little scientific in-joke. — Preceding unsigned comment added by 80.229.1.27 (talk)


 * They left Odin and Heimdall off the chart: (Asgard (archaea). - Donald Albury 15:12, 24 May 2019 (UTC)

Restore 12 April 2009 version?
While I understand the motivation to promote the modern diagram to the lead (per "Images" above), I think the old version (12 April) worked better. The current lead points out that the "Tree of Life" concept was originated by Darwin, so it is entirely appropriate for the lead to feature Darwin's tree. It's true that someone who never reads past the lead, and who doesn't read the image caption (with its 1859 date) might be misled about current practice, but such a reader is not going to find the new lead very enlightening.

I am in favor of restoring the old version of the article, where the modern TOL diagram was associated with the corresponding text.

As a bonus for anyone interested, I'll recommend this texscience report (News of the Death of the Tree of Life Has Been Greatly Exaggerated) that has some great info and diagrams. It's perhaps a bit focused on a particular news event for "external links", but perhaps it could be added? Johnuniq (talk) 09:11, 16 April 2009 (UTC)
 * I think you should keep the page as it is, because most people looking for the science of the 'tree of life' concept will turn up here. Andrewjlockley (talk) 18:03, 16 April 2009 (UTC)

The tree of life today
The original I edited was, in my view, too definite in describing the current position; I've added some qualifications. Hopefully there will be a consensus view soon and we can settle this section... Peter coxhead (talk) 18:52, 28 April 2010 (UTC)

Darwin's first tree of life
Please see File talk:Darwin tree of life.jpg (the image is used in this article, but the other one mentioned on that talk page might be considered a better version). - dcljr (talk) 07:29, 18 September 2012 (UTC)


 * Yes, I agree it's better; I've used it as a replacement. Peter coxhead (talk) 14:46, 18 September 2012 (UTC)

Hitchcock's Tree
I don't see the logic behind the statement that Hitchcock's tree diagrams "were not real evolutionary trees, because Hitchcock believed that a deity was the agent of change." Lots of people believe in the evolution of species from a common ancestor while also believing that a deity is controlling or influencing the process. "Biological evolution" is not synonymous with "Biological evolution by non-teleological natural selection." 206.208.105.129 (talk) 20:37, 23 January 2013 (UTC)

What is the proper scope of this article
There is a substantive question about the scope of this article. This page is titled "Tree of Life (biology)", whereas "tree of life" is also used, for instance, as a reference to the tree of knowledge in the garden of eden (Christian bible). This is why there is a disambiguation page for "tree of life".

There has been some disagreement about this on the talk page, with some folks complaining that the historical material is inappropriate. I'm not going to take a position on that, but I think the article needs to be more clear, using consistent language and section headings.

I'm going to put this in the form of some questions for those who are interested in offering an opinion.


 * 1) should the main focus of this article be on the contemporary meaning of "tree of life" in biology?
 * 2) is "a broad phylogeny of species" the *only* contemporary meaning, or are there other contemporary meanings?
 * 3) how much attention should be given to taxonomic trees of life, as distinct from phylogenetic trees of life?
 * 4) should this article address uses of "tree of life" to refer to the connectedness of life where this is not proposing a concrete hierarchy of living things?

As a scientist indirectly involved with the "tree of life" project, I can attest that contemporary usage is roughly as follows. THE tree of life is a hypothetically comprehensive tree, covering all the millions of species that exist. Some people want to include extinct species as well (the tree of all things that have lived). Any attempt to produce a broad or comprehensive phylogeny qualifies as *A* tree of life. Woese's rRNA tree with 3 "urkingdoms" (later called "domains"), or the ToLWeb tree, are trees of life. The number of published trees of life is not huge. Haeckel's tree is a tree of life.

However, that meaning only became common since about ~2000 AD as the result of NSF's "assembling the tree of life" project. Before that, the tree of life might have referred to a taxonomic tree, i.e., a hierarchy of relationships of similarity without any explicit assumption that the relationships are evolutionary. And even before that, people were using "tree of life" as a metaphor to refer to the connectedness of life, without necessarily thinking about hierarchy in the way that we do today. — Preceding unsigned comment added by Dabs (talk • contribs) 15:49, 3 April 2013 (UTC)

Darwin did not invent the tree of life
The first sentence, "The Tree of Life is a metaphor proposed by Charles Darwin to express the concept of phylogeny" is wildly incorrect. First, Darwin did not propose the metaphor "tree of life". This phrase had existed for centuries as a reference to the biotic world (and also as a reference to the biblical tree of knowledge of life and death). Second, while Darwin used the expression "tree of life" 1 time in the Origin of Species, he did not use it to refer to a phylogeny.

These two points are explained in the following article:

http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001096#s4

Penny (above article) explains that Darwin's reference to "tree of life" is not a reference to phylogeny, so the section quoting this passage from Darwin is not relevant to this article. I'm going to delete it.

Third, regardless of whether one calls it a "tree of life", Darwin did not invent the use of a branching diagram to unite all of life into a branching (hierarchical) classification. Many others had done that. Fourth, Darwin did not invent the use of a branching diagram to represent a historical process, i.e., *evolutionary* relationships of organisms. Lamarck thought of this before Darwin was born-- it appeared in his 1809 Philosophie Zoologique. These points are easily verified and are mentioned in the following article:

http://roughguidetoevolution.blogspot.com/2009/08/lamarck-darwin-and-tree-of-life.html

On this basis I'm going to delete the misattribution of "tree of life" to Darwin, and delete the section on the diagram that appears in the Origin of Species. This is not relevant because it is not a broad tree of actual species (a tree of life in the modern scientific sense of the term) but a diagram of a hypothetical process. That is, while Lamarck referred to branches with actual groups of organisms, Darwin's diagrams (in his notebook and his OOS) is a purely hypothetical process diagram, which is why the entities are labeled with numbers or letters. Haeckel's tree fits in this article because it purports to show the evolutionary relationships of the known biological world, whereas Darwin's diagram is intended to illustrate a hypothetical process and is not a tree of life in the sense in which this article clearly intends. Dabs (talk) 15:06, 3 April 2013 (UTC)
 * The section in OtOOS is clearly about the metaphor, and as such belongs in this article so I've restored it. The idea of a tree of life predated Darwin, but there's clearly an innovation in treating it as an evolutionary tree. I've removed the spaces from the start of lines which affected the formatting of your comment, and will review the sources., . . dave souza, talk 16:00, 3 April 2013 (UTC)
 * You are right that it is clearly a use of a "tree" metaphor. But that isn't enough to quality it for inclusion in this article.  Penny, in the published scholarly article cited above, quotes exactly the same passage and explains that this single occurrence of the words "tree of life" in the Origin of Species are not a reference to a tree of relationships, and thus not about what scientists mean when they invoke "the tree of life" as a phylogeny of all things (the topic of this wikipedia article).  As Penny notes, Darwin says elsewhere that relationships "have sometimes been represented by a great tree", indicating that the metaphor was already familiar to Darwin and his readers.  QED, Darwin did not invent this.  Here is what Penny writes:   In contrast to the 21 occurrences of the theory of descent, in the Origin of Species there is only a single usage of the Tree of Life. However—and this is my third point—it is not used as a description of relationships, but rather as an analogy for competition between species (and groups of species) during evolution. It is the analogy of a branch of the tree overgrowing, and supplanting a “feebler branch” (see Darwin [9], p. 148). The full quote is “buds give rise by growth to fresh buds, and these, if vigorous, branch out and overtop on all sides many a feebler branch, so by generation I believe it has been with the great Tree of Life, which fills with its dead and broken branches the crust of the earth, and covers the surface with its ever branching and beautiful ramifications”. As such, it is not a description of the relationship between taxa, but rather a suggestion that a living tree analogy can be applied to lineages of species competing (and supplanting) other lineages or groups of species—whether fungi, plants, or animals. In other words, microevolutionary processes are similar in principle to macroevolutionary processes, a central part of his thinking [7]. He also comments that “the affinities of all the beings of the same class have sometimes been represented by a great tree”, and immediately follows with the sentence “I believe this simile largely speaks the truth”. And that is the usage that is best used today: the tree of life is a useful simile. But the context in the Origin shows that readers were already expected to know about the tree simile; it was neither a novel nor a central part of his theory. Dabs (talk) 15:23, 5 April 2013 (UTC)
 * Certainly Darwin was drawing on a pre-existent metaphor while giving it new meaning: he doesn't just show a branching form, he explicitly refers to a "tree of life" and as such was influential. He used the same term in 1837, and this should be shown. As Archibald indicates, some earlier versions had less influence, and this context should be made clear. Similarly, Bowler is explicit that Lamarck was thinking of parallel lines of development with no extinction, with occasional branches. A very different concept. Penny focusses on competition, but Darwin's original branching "tree of life" predates his ideas of Malthusian competition. Something to improve, but not delete altogether. . . dave souza, talk 17:05, 5 April 2013 (UTC)
 * I agree entirely that deleting the whole section is clearly wrong. Darwin did use the metaphor of a tree of life, so his use should be covered here, based on a variety of reliable sources not one article. It's equally clear that he was not the first to use this metaphor, and the article needs to amended. I have reverted the deletion, pending appropriate amendments. Peter coxhead (talk) 09:24, 7 April 2013 (UTC)

Amendments
I have now amended the article in the following way: I hope this approach finds consensus. Peter coxhead (talk) 10:23, 7 April 2013 (UTC)
 * It no longer says that Darwin first used the term; this is clearly wrong.
 * I have made the first part of the section on Darwin's use of the term into a neutral description of what he says. This article can't possibly omit this material given that it's one of the better known passages in the Origin of Species and constantly quoted.
 * I've then started a "discussion" part where more should be added on what people have written about Darwin's use of the term, including Penny's recent paper, which is clearly something of a minority view, regardless of whether it is correct. We must maintain WP:NPOV!
 * Thanks, that's a good start and we can cite various views of Darwin's tree as well as others. On the first illustration, it's based on Interactive Tree Of Life, an online tool for the display and manipulation of phylogenetic trees so it really refers to phylogenetic tree rather than this article. Evidently the term remains in use as a common name for what are properly called phylogenetic trees, but it's not clear how widespread this use is in published papers.
 * Our inclusion of earlier trees seems to lack any confirmation that these trees were actually called a "tree of life" rather than taking their metaphor from family trees based on the ancient concept of genealogy.  We also seem to be blurring the intention of earlier non-evolutionary trees which were of "affinities" of created forms, trees of transmutation showing branches on lines of parallel development from Lamarck's scheme, and Darwin's evolutionary concept of divergence and extinction which explicitly drew on the tree of life simile from the outset. . dave souza, talk 11:44, 7 April 2013 (UTC)

When was the sketch published after 1837?
In the year 1837, Darwin entered his sketch into his notebook. But since when is the copy of that sketch available to the public? What is the first publishing date e.g. of a facsimile in a magazin or some other prined publication? Did Darwin himself show it (or a facsimile) to the public?

The image is very popular, but I don't find the publishing date given together with any reproduction of that sketch. It woud be interesting to specify that date in the article --DL5MDA (talk) 18:44, 9 June 2013 (UTC)
 * The essential answer is that we don't know, because as far as I can find the question of the first publishing date of a facsimile hasn't been discussed by a published source. It does go back at least as far as De Beer's 1960 paper, see pp. 45–46. You could try hunting elsewhere on Darwin Online, perhaps starting with Freeman. . . dave souza, talk 07:53, 10 June 2013 (UTC)

At least an inaccuracy should be corrected?
The text "have the ability to transfer genetic information between unrelated organisms through horizontal gene transfer" is inaccurate: horizontal gene transfer occurs all the time between all sorts of organisms. Maybe "tends more than most organisms"? 120.18.115.178 (talk) 06:34, 7 October 2023 (UTC)


 * Not sure what "most" would imply but we needn't go there. I've tweaked the text. Chiswick Chap (talk) 06:58, 7 October 2023 (UTC)