Editing 3010: Geometriphylogenetics

{{comic
| number    = 3010
| date      = November 11, 2024
| title     = Geometriphylogenetics
| image     = geometriphylogenetics_2x.png
| imagesize = 316x391px
| noexpand  = true
| titletext = There's a maximum likelihood that I'm doing phylogenetics wrong.
}}

==Explanation==
{{incomplete|Created by CLOSE BOT RELATIVE - Please change this comment when editing this page. Do NOT delete this tag too soon.}}

{{w|Phylogenetics}} refers to the practice of examining relationships among things that follow the principle of "descent with modification of progeny". In the course of descent with modification, one thing may give rise to two (the progeny), different modifications happen to each, and those modifications become established. Iterated "splits" over time yield a tree of objects; it is the purpose of phylogenetics to recover ("reconstruct") these trees, and use the information gained to inform study of the things contained. Phylogenetics has been most commonly applied to the classification/taxonomy of biological species and investigations of their evolutionary history, but it has also been used to examine the evolution of genes and biosynthetic pathways. Similar conceptual approaches have been used in the study of human languages and their evolution. 

Data for phylogenetic analyses may come from any attributes ("characters") of the things being examined. {{w|Computational_phylogenetics|Rigorous techniques}} for these analyses became available starting in the {{w|Willi_Hennig|1950s}}, and these replaced earlier methods based largely on the individual judgement of experts. In phylogenetic studies of organisms, their DNA is far and away the most data-dense source of information, and consequently, most present-day investigations are based on analyses of selected genes and, increasingly, whole genomes. Thanks to the advent of more robust datasets, and more robust methods of data analysis, it is now commonplace for studies, especially on relatively understudied creatures, to reconstruct an evolutionary history (a phylogeny) that is radically different from what had previously been assumed. This is the "phylogenetic revolution" referred to in the caption. One example is the genus {{w|Hippopotamus|<em>Hippopotamus</em>}}, which had been considered a relative of pigs, which the animals somewhat resemble, until modern data and methods revealed it to be more closely related to whales, despite the animals being very different physically (hippos spend time in water, but [https://www.youtube.com/watch?v=X-YRJCSZRJU can't swim]).
 
This comic presents a tree, which resembles and purports to be a phylogenetic tree, in which the endpoints ("terminal taxa") are geometric shapes. This has been given the name "geometriphylogenetics" — a portmanteau of "{{w|geometry}}" and "phylogenetics". The claim is that triangles have been moved from the lower part of the tree (where they would be closely related to squares, rectangles, pentangles, and the like) to the upper part (placing them closer to circles and ellipses). This is a riff on the findings, and even the wording, of authentic phylogenetic research papers that report "revolutionary" results. The absurdity, and the joke, is that geometries do not change over time. Human understanding might change, but triangles and circles and rectangles themselves did not evolve or descend from ancestors, they are not progeny of some other geometries of ages past, and therefore phylogenetic principles and techniques don't apply to their study. Moreover, geometries do not contain DNA,{{cn}} so genetic analysis, even if it was ever relevant, is impossible. 

The title text alludes to {{w|Computational_phylogenetics#Maximum_likelihood|maximum likelihood}}, one of the most robust, and most frequently used, methodologies for phylogenetic analysis. The method builds a number of trees from the data, assigns to each a probability that it conforms to a pre-selected model of evolution, and then selects the tree that has the highest (maximum) likelihood of conformity to the model. In this case, though, the statement "There's a [high probability] that I'm doing phylogenetics wrong" doesn't just have the maximum probability of the available options; it has the maximum ''possible'' probability of 1, because it is definitely the case.

==Transcript==
{{incomplete transcript|Do NOT delete this tag too soon.}}

:[A tree diagram, or a dendrogram is shown, consisting of lines that branch off from left to right, starting with one horizontal line on the left. Eight results are shown on the right: ellipse on Path 1, circle on Path 2, triangle on Path 3, parallelogram on Path 4, trapezoid on Path 5, square on Path 6, rectangle on Path 7, and a pentagon on Path 8. The paths are listed in order top to bottom.]
:[Path 3 and the triangle are bold black, while the other branches are dimmer. The paths are connected as follows: Path 2 and 3 are connected, then both connect together to Path 1; Path 4 and 5 are connected, as are Path 6 and 7, and these two paths are connected altogether; Path 8 is then connected to the branch containing Paths 4 to 7. All of Paths 1 to 3 are then connected to Paths 4 to 8, the branches all culminating in a single line on the left.]

:[Caption below the panel:]
:The phylogenetic revolution continues:
:Triangles were long believed to be related to squares, but genetic analysis proves that they are actually very pointy circles.

{{comic discussion}}

[[Category:Geometry]]
[[Category:Biology]]
[[Category:Charts]]
[[Category:Statistics]]