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Messages - teeming brown mass

2
Politics and Current Events / Re: Comey
So articles of impeachment:

Witness tampering
Obstruction of justice (probably several)
Public corruption

What else?
3
Science / Re: New fossil caecilians!
That moment where you realise you started a interdepartmental fight...

<-first author
Neat paper. Looks like it was written by a third grader. :stuckup:

Agreed
4
Science / Re: early tetrapods got weird
Ooooh!
Nature, even!

:notworthy:

Per only publishes in Nature. We're just along for the ride ;)
5
Science / early tetrapods got weird
some dummies wrote a paper:

http://www.nature.com/nature/journal/vaop/ncurrent/full/nature22966.html

Quote
Phylogenetic analysis of early tetrapod evolution has resulted in a consensus across diverse data sets1, 2, 3 in which the tetrapod stem group is a relatively homogenous collection of medium- to large-sized animals showing a progressive loss of 'fish' characters as they become increasingly terrestrial4, 5, whereas the crown group demonstrates marked morphological diversity and disparity6. The oldest fossil attributed to the tetrapod crown group is the highly specialized aïstopod Lethiscus stocki7, 8, which shows a small size, extreme axial elongation, loss of limbs, spool-shaped vertebral centra, and a skull with reduced centres of ossification, in common with an otherwise disparate group of small animals known as lepospondyls. Here we use micro-computed tomography of the only known specimen of Lethiscus to provide new information that strongly challenges this consensus. Digital dissection reveals extremely primitive cranial morphology, including a spiracular notch, a large remnant of the notochord within the braincase, an open ventral cranial fissure, an anteriorly restricted parasphenoid element, and Meckelian ossifications. The braincase is elongate and lies atop a dorsally projecting septum of the parasphenoid bone, similar to stem tetrapods such as embolomeres. This morphology is consistent in a second aïstopod, Coloraderpeton, although the details differ. Phylogenetic analysis, including critical new braincase data, places aïstopods deep on the tetrapod stem, whereas another major lepospondyl lineage is displaced into the amniotes. These results show that stem group tetrapods were much more diverse in their body plans than previously thought. Our study requires a change in commonly used calibration dates for molecular analyses, and emphasizes the importance of character sampling for early tetrapod evolutionary relationships.
6
Science / Re: New fossil caecilians!
That moment where you realise you started a interdepartmental fight...

<-first author
7
Science / Re: New fossil caecilians!
Just in time for Bili's birthday, although I should have posted it yesterday.

So maybe Lissamphibia is polyphyletic after all. Or at least crown Lissamphibia has to include a whole bunch of other stuff if you want to keep it monophyletic. Maybe. I'd be interested in any criticisms anyone has on that.

Stem caecilian from the Triassic of Colorado sheds light on the origins of Lissamphibia Jason D. Pardo, Bryan J. Small,and Adam K. Huttenlocker (2017) PNAS, doi:10.1073/pnas.1706752114

Quote
The origin of the limbless caecilians remains a lasting question in vertebrate evolution. Molecular phylogenies and morphology support that caecilians are the sister taxon of batrachians (frogs and salamanders), from which they diverged no later than the early Permian. Although recent efforts have discovered new, early members of the batrachian lineage, the record of pre-Cretaceous caecilians is limited to a single species, Eocaecilia micropodia. The position of Eocaecilia within tetrapod phylogeny is controversial, as it already acquired the specialized morphology that characterizes modern caecilians by the Jurassic. Here, we report on a small amphibian from the Upper Triassic of Colorado, United States, with a mélange of caecilian synapomorphies and general lissamphibian plesiomorphies. We evaluated its relationships by designing an inclusive phylogenetic analysis that broadly incorporates definitive members of the modern lissamphibian orders and a diversity of extinct temnospondyl amphibians, including stereospondyls. Our results place the taxon confidently within lissamphibians but demonstrate that the diversity of Permian and Triassic stereospondyls also falls within this group. This hypothesis of caecilian origins closes a substantial morphologic and temporal gap and explains the appeal of morphology-based polyphyly hypotheses for the origins of Lissamphibia while reconciling molecular support for the group's monophyly. Stem caecilian morphology reveals a previously unrecognized stepwise acquisition of typical caecilian cranial apomorphies during the Triassic. A major implication is that many Paleozoic total group lissamphibians (i.e., higher temnospondyls, including the stereospondyl subclade) fall within crown Lissamphibia, which must have originated before 315 million years ago.


Okay so summary here:

If we're right, Lissamphibia is still monophyletic. This is consistent with the molecular phylogenies and the age of Lissamphibia is right in the middle of modern molclock estimates for the origin of the amphibian crown.

Again, if we're right, Lissamphibia is a LOT more inclusive, and most "temnospondyls" are actually true lissamphibians. Small size in caecilians and salamanders is convergent rather than a shared, derived characteristic. Soft tissue features shared between caecilians and frogs/manders can probably be extended downward into most fossil amphibians. The evolutionary history of the pedicellate bicuspid tooth is unclear; it would seem to be convergent based on the distribution of unicuspid nonpedicellate teeth across total-group amphibians, but there may be some "deep homology" there.

But yeah.
8
Science / Re: New fossil caecilians!
First author is a grade-A douche
9
Gotta think the GOP will consider this when deciding whether to work with or against the Trump impeachment.
10
why do you guys even bother?
11
94 jackknife just means that 94% of random character deletions do not affect the recovery of the node.
12
anyone trying to use bootstrap/jackknife as a measure of clade support is wrong. that's not what it means. hth.

Thanks, that's good to know.  What statistical metric(s) would be appropriate to use as a measure of clade support?

realistically you need to make a constraint tree and then test it against random trees using I dunno a KH or something. Node support is ridiculously hard to calculate in a meaningful way and most of the methods used to generate node support do not actually do this.

Bootstrapping and Jackknifing basically estimate how well the universe of characters that inform a specific node have been sampled. They are notoriously easy to calculate and notoriously difficult to interpret. It definitely doesn't reflect how much you should trust a node per se and doesn't tell you anything about broader trends in treespace, though.

Basically trying to treat any of these numbers as having mathematical or biological meaning is difficult to justify though.
13
Feedback loop. people who grow up rural are more likely to have shitty opinions about cooperative tolerant modern societies, and people who have shitty opinions about cooperative tolerant modern societies are more likely to either move away from cities or stay rural when the job market calls for moving to a city. There's a social filter that is concentrating shitty people into rural areas and helping them become more and more shitty.
14
anyone trying to use bootstrap/jackknife as a measure of clade support is wrong. that's not what it means. hth.
15
Politics and Current Events / Re: Trumpocalypse
it's not about having a good case. it's about convincing enough republican congressmen that they can vote against impeachment and justify it to their electorate.
16
Politics and Current Events / Re: Trumpocalypse
the only option at this point is to try to establish that Trump did not think he was under investigation at the time of the firing and therefore was not intentionally obstructing an investigation.
17
As I keep saying. Rural people are morally deficient and should all be sent to reeducation camps.
18
lol this thred
20
I think Testy would chalk this up to karma
21
or things went bad during surgery.
22
really we're only a few years away from going full-on Lebanon.
23
this is about a mile from our apartment.  not a ton of details or hard facts yet.

the house gop baseball team was having practice when the shooting happened.  scalise, the house gop whip, was reportedly hit in the hip.

given scalise's flirtation with white supremacists, it's tempting to think he was targeted over that.  however, it sounds like this was a generalized shooting spree (50 shots fired), so maybe he wasn't specifically a target.

between the facts that an (apparently semiautomatic) rifle was used, and the shooter is in custody rather than dead, I am going to guess the shooter is white.
here's an instant-migraine inducing thought.  if and when the police determine that the person who was asking questions was not the same person as the shooter, and say so, the alt-right  will assume the original identification was true and that the police are engaged in a cover-up.
it's a completely irrelevant detail. like it doesn't seem to make sense for the shooter to ask that beforehand but the shooting could still be politically motivated.
Sure it does. He was double checking that he didn't get it wrong. Dumbass couldn't even kill one of them and he had a damn rifle.

Anyway, it seems pretty reasonable to me to assume he was an antifa type. There's a lot of hate out there right now directed at the gop.

He wasn't anti-fa. He was a bernie-bro who was apparently having health issues and who, based on his personal history of domestic violence, seems to respond violently to conflict. The dysfunction that led to this shooting seems pretty clear.
24
this is why conspiracy theories and opposition derangement syndrome are dangerous.  if you convince yourself someone is the devil, then anything you do to them will seem justified.

it's trickier to make this point with trump in office, because he is legitimately scary in a lot of ways, and his personality and track record make it realistic to worry about him abusing his power.  but we are dealing with that possibility, and the situation is more or less under control.  contrary to what this shooter thinks, trump has not crowned himself dictator.  he's not the next hitler.  those ideas have grown out of control because of people being dumb and conspiratorial in the far left bubble.

Well, given the rate of ICE detainments, I'm not sure I necessarily agree. We've seen some major concerted pushes by Trump to dismantle a lot of the civil rights protections within the US, including a consistent assault on the free media. Saying "well, Trump's just a corrupt grifter" ignores the fact that Trump absolutely is waging an aggressive policy war against civil rights and we don't really know what that endgame will look like.

I don't disagree that buddy here definitely had problems and that definitely led to both the fanatical political viewpoints and the subsequent political violence, and I agree that right now is not necessarily the time for political violence, but we really are in dangerous territory and saying "well, Trump is not bad enough to warrant assassination" probably is a statement that depends a lot on the relative security of your personal demographic.
25
Politics and Current Events / Re: corbyn won
How is that a walkback?
because 4 years ago is not "at this point" or "current conditions."

what i'm getting at is that you're kinda just going off the cuff here to rationalize a lazy smear job rather than actually paying attention.

Conditions were bad four years ago, when there were massive shortages of all sorts of essential goods. It wasn't the current situation where there's been an average of 10 kilos lost per person due to starvation, but it was bad and the dismantling of checks and balances had already gone ahead ~5 years prior.

Anyone who was backing Chavez after ~2008 is an idiot or a piece of shit.