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Topics - socrates1

3
https://www.nature.com/articles/ncomms14229
Functional roles of Aves class-specific cis-regulatory elements on macroevolution of bird-specific features
Quote
Abstract
Unlike microevolutionary processes, little is known about the genetic basis of macroevolutionary processes. One of these magnificent examples is the transition from non-avian dinosaurs to birds that has created numerous evolutionary innovations such as self-powered flight and its associated wings with flight feathers. By analysing 48 bird genomes, we identified millions of avian-specific highly conserved elements (ASHCEs) that predominantly (>99%) reside in non-coding regions. Many ASHCEs show differential histone modifications that may participate in regulation of limb development. Comparative embryonic gene expression analyses across tetrapod species suggest ASHCE-associated genes have unique roles in developing avian limbs. In particular, we demonstrate how the ASHCE driven avian-specific expression of gene Sim1 driven by ASHCE may be associated with the evolution and development of flight feathers. Together, these findings demonstrate regulatory roles of ASHCEs in the creation of avian-specific traits, and further highlight the importance of cis-regulatory rewiring during macroevolutionary changes.
4
https://www.theguardian.com/science/2013/dec/02/men-women-brains-wired-differently
Male and female brains wired differently, scans reveal
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Scientists have drawn on nearly 1,000 brain scans to confirm what many had surely concluded long ago: that stark differences exist in the wiring of male and female brains.

Maps of neural circuitry showed that on average women's brains were highly connected across the left and right hemispheres, in contrast to men's brains, where the connections were typically stronger between the front and back regions.

Ragini Verma, a researcher at the University of Pennsylvania, said the greatest surprise was how much the findings supported old stereotypes, with men's brains apparently wired more for perception and co-ordinated actions, and women's for social skills and memory, making them better equipped for multitasking.
5
https://www.realclearscience.com/blog/2017/11/25/the_worst_theoretical_prediction_in_the_history_of_physics.html
The Worst Theoretical Prediction in the History of Physics
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Quantum mechanics has a dark energy problem.
When it comes to scientifically mysterious concepts that begin with the word "dark," dark matter attracts most of the public attention. Dark energy, however, constitutes 68.3% of the mass of the universe compared to dark matter's paltry 26.8% (and normal matter's minuscule 4.9%). It is truly the more consequential of the two "dark" concepts.
Yet we'll never likely be able to "catch" a particle of dark energy as scientists are striving to do with dark matter. That's because dark energy is - most likely - just the energy inherent to space, itself, perhaps arising from Quantum foam, composed of virtual particles that flit in and out of existence. As Einstein reminds us, the energy delivered by these virtual particles briefly protruding into space has mass.
When astronomers attempt to measure dark energy's density in space, they come up with roughly 10^−9 joules per cubic meter, a microscopic but influential amount. However, this observed value, known as the cosmological constant, isn't remotely close to that which is predicted by the time-tested quantum field theory. As detailed in the textbook General Relativity: An Introduction for Physicists:
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"The simplest calculation involves summing the quantum mechanical zero-point energies of all the fields known in Nature. This gives an answer about 120 orders of magnitude higher than the upper limits... set by cosmological observations. This is probably the worst theoretical prediction in the history of physics! Nobody knows how to make sense of this result. Some physics mechanism must exist that makes the cosmological constant very small."
6
http://www.dailymail.co.uk/sciencetech/article-5113687/Is-smarter-chimps.html
How humans became so smart: Huge dose of the 'feel-good' chemical dopamine may be responsible for our intelligence
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It's a chemical known to play a key role in pleasure and reward, and now it seems that dopamine may also play a part in human intelligence.
A new study has found that the dopamine system evolved differently in humans than it did in great apes.
The researchers found that humans have a generous supply of dopamine in the brain regions that help us think and plan - which could explain why we are more intelligent than other primates.


8
http://www.alfredwallace.org/intelligent-evolution.php
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Alfred Russel Wallace advocated what is best described as a theory of "intelligent evolution."

Intelligent Evolution Defined
Intelligent evolution is a theory of common descent based upon natural selection strictly bounded by the principle of utility (i.e. the idea that no organ or attribute of an organism will be developed and retained unless it affords it a survival advantage). Where utility cannot be found in a known organ or attribute, some other cause--an intelligent cause--must be called upon.

In sum, intelligent evolution is directed, detectably designed, and purposeful common descent.

Wallace's Intelligent Evolution Contrasted with Darwinian Evolution
Both forms of evolution describe change through time, but only Wallace's intelligent evolution limits the power of natural selection to effect biological change. It suggests that in those areas of the biological world beyond the scope of natural selection's operations, some purposive intelligence must be called upon to explain their existence. In contrast, Darwinian evolution claims that all biological life can be explained through a directionless process of "survival of the fittest" and random mutation.

Wallace, basing his theory on Darwin's own principle of utility (the cornerstone of natural selection that says attributes in an organism will only develop when they accord the organism a survival advantage), insisted that where no clear survival advantage can be found some teleological (purposive) and intelligent agency must be the cause.

Both Wallace and Darwin were committed to science, but their conceptions of science were dramatically different: for Wallace science was simply the search for truth in the natural world; for Darwin science must invoke only natural processes functioning via unbroken natural laws in nonteleological ways. Wallace's view of science was unencumbered by philosophical assumptions whereas Darwin's science was pigeonholed by the philosophical presumption known as methodological naturalism (or methodological materialism).
9
Alternative Reality Science Extravaganza / A blue halo
Fascinating subject:

https://apnews.com/95b0bcb8e7174459aa2df36ab1e66a3d/Some-flowers-create-blue-halo-to-say-hello-to-foraging-bees

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Some flowers have found a nifty way to get the blues.They create a blue halo, apparently to attract the bees they need for pollination, scientists reported Wednesday. Bees are drawn to the color blue, but it's hard for flowers to make that color in their petals.
Instead, some flowers use a trick of physics. They produce a blue halo when sunlight strikes a series of tiny ridges in their thin waxy surfaces. The ridges alter how the light bounces back, which affects the color that one sees.
10
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.

11
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."

12
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!
13
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.
14
Imaginary nodes
15
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]
16
Which is more parsimonious?
Oviraptorids as ground based, feathered dinosaurs? Or secondarily flightless members of Paraves?
17
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.
18
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.
19
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.
20
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