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Topics - socrates1

1
http://datadryad.org/resource/doi:10.5061/dryad.84t75
Brusatte et al
Supplementary Appendix 1: Character List
Character 1: Feathers, vaned feathers on forelimb, form:
0: symmetric
1: asymmetric


http://www.ivpp.cas.cn/qt/papers/201403/P020140314389417822583.pdf
Xu et al
Character list (Characters 1-363 are from Hu et al. (2009), whereas 364-374 are newly
added).
1. Vaned feathers on forelimb symmetric (0) or asymmetric (1). The barbs on opposite
sides of the rachis differ in length; in extant birds, the barbs on the leading edge of flight
feathers are shorter than those on the trailing edge.

Odd. No value for lack of feathers.

2
Alternative Reality Science Extravaganza / Bremer
Notice the abysmally low Bremer support values:
http://www.cell.com/cms/attachment/2019474733/2039573094/mmc1.pdf

Maniraptoriformes--is only poorly supported (Bremer support of 1 and jackknife percentage of less than 50%), and relationships at its base are unresolved. There is a basal polytomy consisting of four clades: Ornitholestes, Compsognathidae, Ornithomimosauria, and Maniraptora (i.e., the clade of all taxa more closely related to birds than to Ornithomimus: [S52]).

Maniraptora--the clade defined as all taxa closer to birds than to Ornithomimus--is comprised in the present study of Alvarezsauroidea, Therizinosauroidea, Oviraptorosauria, and Paraves. This clade is supported by a Bremer value of 2 but a jackknife percentage of less than 50%.

Oviraptorosauria and Paraves is supported by a Bremer value of 1 and a jackknife percentage of less than 50%.

Paraves--consisting of dromaeosaurids, troodontids, and avialans--is also poorly supported, as it also has a Bremer value of 1 and a jackknife of less than 50%.

http://ib.berkeley.edu/courses/ib200a/labs/ib200a_lab10_bootstrap_jackknife_bremer.pdf
As a rule of thumb, a Bremer score of 3 is good and a score of 5 is "highly supported."

3
http://reptilis.net/2017/03/27/new-study-shreds-the-dinosaur-family-tree-and-exposes-double-standards-in-phylogenetic-nomenclature/
Unfortunately, some ardent supporters of cladistics thought that this method might work well in terms of classification.
Now some of you might be shaking your head right now thinking that phylogeny and classification are the same thing. They are not.
Classification is the act of categorization. It is an arbitrary way for humans to order what they see in the world around them. We classify everything!
4
https://en.wikipedia.org/wiki/Computational_phylogenetics#Bootstrapping_and_Jackknifing
The statistical rigor of the bootstrap test has been empirically evaluated using viral populations with known evolutionary histories,[35] finding that 70% bootstrap support corresponds to a 95% probability that the clade exists. However, this was tested under ideal conditions (e.g. no change in evolutionary rates, symmetric phylogenies). In practice, values above 70% are generally supported and left to the researcher or reader to evaluate confidence. Nodes with support lower than 70% are typically considered unresolved.

Anyone notice the support value below 70% on the Brusatte et al cladogram between tyrannoraptora and paraves? The entire dinosaur to bird theory is based on this unresolved node.
5
Imaginary nodes
6
https://en.wikipedia.org/wiki/Yi_(dinosaur)
Yi qi, and presumably other scansoriopterygids, possessed a type of wing unknown among any other [dinosaur] prehistoric bird  relatives. Unlike other paravian dinosaurs, they seem to have replaced bird-like feathers with membranous wings, in what may have been one of many independent evolutionary experiments with flight close to the origin of birds.[1]

A variant of the bat model might be the "pterosaur model" in which the styliform bone would have been directed obliquely to the outside, with a narrower wing as a result.

Other vertebrate fossils found in the same rock quarry as Yi qi, which would have been close contemporaries, included salamanders like Chunerpeton tianyiensis, the flying pterosaurs Changchengopterus pani, Dendrorhynchoides mutoudengensis, and Qinglongopterus guoi, as well as the early tree-dwelling mammal species Arboroharamiya jenkinsi.[1]
7
Which is more parsimonious?
Oviraptorids as ground based, feathered dinosaurs? Or secondarily flightless members of Paraves?
8
http://ib.berkeley.edu/courses/ib200a/labs/ib200a_lab10_bootstrap_jackknife_bremer.pdf
Bootstrapping calculates a support value for each node based on the fraction of samples that support that node. The highest support value is 100, while values below 70 are usually considered weak. Values below 50 aren't shown; in fact, branches below 50 are collapsed and shown as a polytomy.
9
https://en.wikipedia.org/wiki/File:Archaeo-deinony_hands.svg
The similarity of the forelimbs of Deinonychus (left) and Archaeopteryx (right) led John Ostrom to revive the link between dinosaurs and birds.
10
http://www.xinglida.net/pdf/Xu_et_al_2012_Yutyrannus.pdf

"Filamentous integumentary structures are preserved in all three [Yutyrannus]
specimens. Those preserved in ZCDM V5000 are evidently associated
with the posterior caudal vertebrae. As preserved, they are parallel to
each other and form an angle of about 30u with the long axis of the tail.
The filaments are at least 15 cm long. They are too densely packed for it
to be possible to determine whether they are elongate broad filamentous
feathers (EBFFs) like those seen in the therizinosauroid Beipiaosaurus,
slender monofilaments, or compound filamentous structures."

Yutyrannus is often referenced as having feathers. In fact what they had was simply filaments.
11
https://www.vox.com/science-and-health/2017/6/7/15745714/nature-homo-sapien-remains-jebel-irhoud

I ran Hublin's paper and conclusions by two other anthropologists -- Ian Tattersall, the curator emeritus of human origins at the American Museum of Natural History, and John Hawks, a professor at the University of Wisconsin. And while they don't doubt the dating of these findings, they do question whether we can really call these specimens Homo sapiens.

After all, they do have some significant differences with us when it comes to the shape of their brains, which is a defining characteristic of our kind.

"I think you have to be fairly rigorous [with] what you admit into Homo sapiens," Tattersall says. "There are plenty of people out there who are willing to take a much looser view of what Homo sapiens is, and would be happy to cram this into Homo sapiens as a matter of convenience, or a matter of philosophy even. I wouldn't go along with that."

https://cdn.vox-cdn.com/thumbor/jgZHREv6tVX-AEKL3QX8L1Hz-1U=/0x0:2048x982/920x613/filters:focal(80x142:406x468):format(webp)/cdn.vox-cdn.com/uploads/chorus_image/image/55140151/Figure_11__1_.1496853535.jpg

https://cdn.vox-cdn.com/thumbor/2oMOhoxq7dpK2crWx4vpmmblluk=/0x0:912x495/720x0/filters:focal(0x0:912x495):gifv():no_upscale()/cdn.vox-cdn.com/uploads/chorus_asset/file/8645949/irrhound_3.gif