Arete

In my publications, I generally apply the generalized lineage concept which defines species as separately evolving metapopulations, and defines the properties of metapopulations as operational criteria. I generally do not use subspecies, as the definitions thereof tend to be specific to organismal groups and largely a matter of convenience. For e.g. Trypanosoma brucei brucei and T. b. rhodesiense differ at only a single gene in the genome - however that gene confers human infectivity, meaning despite no evolutionary basis for the distinction, clinically one can separate them into a "harmless" subspecies and a "lethal" subspecies based on the presence/absence of a band on an electrophoresis gel. I tend to oppose their seperation, as it implies that they are separate populations, rather than a single population with a circulating, horizontally tranferred, functional gene of importance.

This is a categorically false statement. The population genetic processes underpinned by genetic data are what is used to invalidate taxonomic assignment - not some arbitrary value.

Except those two statements are substantially different.

Could you point out where that statement occurs, please?

It's not irrelevant to use population genetics correctly - especially when it seems to be one of your fundamental criticims of everyone else. Genetic divergences are used to invalidate taxa - see the implementation of BPP here: http://www.sciencedirect.com/science/article/pii/S1055790313001085 From two pages ago:

You chose to erroneously compare Rst values from the cited paper to Fst values other studies in humans. The cited paper also includes allele frequency data, migration estimates, inbreeding coefficients and PCA analysis.

I'm not expecting to change Over 9000's mind here, but I just wanted to point out how badly incorrect this interpretation of Fixation Index is. https://en.wikipedia.org/wiki/Fixation_index 1) Fst measures the extent to which a given set of genetic data supports the division of individuals into a priori groupings. It does not measure genetic divergence. As an example, say we have two groups of organisms which are within each group, genetically identical. The two groups differ from each other at a single site. Our observed genetic divergence is perfectly explained by our clustering, resulting in a maximal Fst of 1. Despite this, our hypothetical study organism is remarkably low in genetic diversity. 2) Fst values are only comparable when the same genetic loci are being used to calculate the summary statistic. As Fst values will differ between different genetic loci and the same individuals, it is not appropriate to compare Fst's between different studies of different loci and different species. At this point, P-values become more useful than raw Fst values. 3) Genetic divergence is better assessed using average nucleotide substitutions per site, or dA. While this suffers from similar locus specific biases as Fst, fortunately whole genome calculations for both the great apes and humans have been undertaken: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4750478/ https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4750478/ http://www.nature.com/nature/journal/v499/n7459/full/nature12228.html From Bowden et al. "An equivalent analysis of the HapMap III African populations [27] showed that these African human populations are considerably less structured than the chimpanzee populations (Figures S3 and S4), as might be expected given the observation above that the chimpanzee populations are more differentiated even than continental human populations."

Humans represent a recently derived species characterized by low genetic diversity, high gene flow and clinal variation. If you examined the genetic data, naive to the origin of the data I have no doubt that any competent population geneticist would define human populations as being divergent enough to warrant taxonomic description. Chimp subspecies display orders of magnitude more divergence than human populations. http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.0030066

Indeed - a standard caveat of K means clustering http://varianceexplained.org/r/kmeans-free-lunch/ Another caveat is the vagueness of the term subspecies. "In practice, the subspecies may be a useful tool, but must be used with caution and pretty much requires familiarity with the particular species and what philosophy has been used to name the subspecies within that species." One can make an argument that human populations represent subspecies under a particular philosophy or set of operands to suit a given purpose, although I would argue that clinal variation and long term, ongoing gene flow would stand in the way of any widespread acceptance of such a proposal.

Largely from another race thread: 1) If you're talking about genetically related groups, then generally the correct terminology would be populations, rather than races. In population genetic context, the term "races" is generally used to describe different karyotypes within a species. 2) Yes, distinct human populations exist - see Rosenberg et al. 3) In some cases distinctions are useful e.g. Scandinavian populations are ~90% lactose tolerant, East Asian populations ~10%. There are some ethnically associated genetic disorders (e.g. sickle cell anemia, Tay Sachs disease, etc.) and some ethnically specific drug metabolic responses that can be quite dramatic, even fatal. So identifying distinct human populations is possible and worthwhile. 4) However differences in human populations are generally clinal, and gradients of genetic diversity exist between each genetic cluster of human populations, making the separation into discrete "races" problematic in many instances. 5) Significant, long term gene flow between populations is evident in genome comparisons of human populations. There is no such thing as "racial purity" in a genetic sense. 6) Genetic clusters of humans do not correspond well to ethnically defined "races". E.g. Most human genetic diversity is within African populations ethnically defined as "black", Mediterranean Arabic communities are genetically closer to Europeans than Middle Eastern Arabic populations, etc. 7) Intelligence is a complex trait, with both heritable and environmental components that interact dynamically. Due the fuzziness of human populations and complexity of the heritability of intelligence, saying anything concrete about the IQ of specific racial groups would be speculative and wrought with autocorrelation.

So, I live on 12 acres in the Sierras. We are relatively tapped in to our local agricultural industry. I shoot around 4-6 mule deer a year on our property and 6-10 turkeys. We have a 1 acre orchard. We raise two dozen broiler chickens a year, We buy a cow, a pig and three sheep a year from local farms. We get our vegetables from a local CSA and I am personal friends with the dairy I get my milk and cheese from, and my wife bakes bread from scratch. I am very lucky to live in a rural setting where I can know pretty much precisely where all my food. Venison is healthy, low fat meat either cook it rare, or for a long time ( e.g curry) to get the best out of it.

1963 Mercury Comet, and a 1927 T roadster in bits all over my garage.

While I share your displeasure at the fact that this election has sunk to the level of monkeys flinging poo at each other, one of the reasons personal attack has featured so heavily is the fact that Trump is hopelessly outgunned in matters of policy. Many of his policy positions are naive and juvenile. For e.g. 1) Immigration policy that is unconstitutional and financially unfeasible. 2) Taxation policy that would cause spiraling national debt. 3) Foreign policy that would significantly weaken the US strategically and destabilize the global economy etc. Many of his policies are so bad that his own party disavows them and he would likely face bipartisan opposition if elected. His politics are fundamentally flawed. The only logical argument I can see for a Trump vote is as a middle finger to the Washington establishment, I get it, partisan politics and special interest lobbyists seem to matter more than the people, and you want to throw a delusional, narcissistic orange wrench into the machine and shake that thing up. However as someone who works on old cars as a hobby - throwing your tools at things tends to make it worse, rather than better. Facilitating change would best done strategically, with bipartisanship and expertise. Trump represents none of these attributes.

I believe you are mistaken. The affidavit was to request the evaluation. The request was denied. The evaluation never took place, and was never entered as evidence. The only place the quoted statements appear is in the affidavit, and not in evidence presented to a jury in court. It was never used as evidence to determine the defendant's guilt or innocence, simply to justify the exam. You seem to be a little confused in that an affidavit requesting a psychological exam to a judge is a different document to a testimony submitted as evidence in a court. All the affidavit implies is that Clinton had been told that "that the complainant is emotionally unstable with a tendency to seek out older men and to engage in fantasizing. I have also been informed that she has in the past made false accusations about persons, claiming they had attacked her body.” The psychological exam was intended to determine if there was any factual basis to the claim. Clinton did not claim the above was fact, nor did she submit it as evidence. All she did was state that it had been said to her by parties named in the affidavit, and asked for a psychological evaluation be undertaken to determine its veracity. All subsequent vetting of that affidavit have determined it to be a part of due diligence in providing the defendant with a just and fair trial. It was a lot more convoluted than is being presented - there were two defendants, one also a minor, and all parties involved were intoxicated. The defendant pleaded out to a lesser crime - which is not Clinton's decision, but the prosecutor's and likely based on the available (and demonstrably flawed) physical evidence. There's no wrongdoing present in her actions - all it really shows is that the job of a defense attorney is distasteful at times. Now I'm no Clinton fanboy, but my family is full of lawyers, and this hatchet job does a major disservice to the role of the defense. If the defendant is guilty, the defense should make sure all reasonable doubt has been exhausted by the prosecution prior to conviction. If Clinton felt that the plaintiff's testimony might have represented reasonable doubt, even if she personally believed it, it's her duty to not only the defendant, but the people, to verify it.

I highly doubt it was. I cannot fathom that a judge would deny a psychiatric exam and then allow fabricated evidence from that exam that never took place to subsequently be presented as evidence in the case. Do you have anything that indicates that this happened?

The quote is from an affidavit requesting a psychiatric evaluation, not evidence given in court. Also, her sources were cited in the affidavit. http://www.snopes.com/hillary-clinton-freed-child-rapist-laughed-about-it/

Clinton did not say the "victim was _____", she said she HAD BEEN INFORMED that the victim was ____ .

Not sure... the nets are usually funded by state governments but I'm not entirely sure what the legislation is. Or as I anecdotally witnessed in when pit bulls were banned but Staffies weren't in South Australia, suddenly everyone had a really big-boned Staffordshire terrier (which bring us back to the ambiguity issue). Breed/bad owners are not the only issues involved - 30% of dogs involved in fatal attacks were chained and 60% were un-neutered males.

The closest I can think of is shark netting in Australia. 35 -50% of sharks found entangled in the nets have come from the beach side of the net. 50 years of data shows mixed results on the impact the incidence of attacks, largely due to extremely small sample sizes. Not enough people get attacked by sharks to work out if nets work, but they sure make people feel better about taking their kids to the beach.

Perhaps the climate change debate would be a better analogy.

I don't think that it's a very sensible comparison: 1) Around 40% of US households have guns, and there are around 34,000 gun related deaths in the US each year. Around 37% of US households own a dog, and there are 20-30 dog related fatalities per year (of which about 30% are caused by pit breeds) The CDC concludes that the number is too small to make robust, empirical statements about the danger of specific breeds. To put that into context, around 350 Americans drown in bathtubs each year, 100 die of honey bee stings and 400 are killed by space heaters. In the grand scheme of things, dogs of any breed - including pit bulls are very safe. the same thing can obviously not be said about firearms. 2) Again the ambiguity surrounding what a pitbull is, and the inclusion of everything from 150 pound dog breeds through to 30 pound breeds make breed specific statistical comparisons apples to oranges comparisons. If you combine German Shepards, rottweilers, dobermans and dachshunds together, they now become the most dangerous breed. If gun bans were the comparison we'd be lumping in water pistols and bb guns with AR15's. 3) People can't identify mixed breed dogs with any accuracy. As previously cited, visual identification is incorrect in 85% of cases. Therefore many dogs involved in attacks that are visually confirmed as being pitbull type dogs are in all likelihood, not. If someone has been shot it is usually fairly unequivocal that a gun was involved. Breed specific legislation is like shark nets at the beach - the fear of being killed vastly outweighs the actual statistical probability of being killed, and the resultant "measures" to prevent statistically anomalous events are usually of limited effectiveness, but make people feel better.

Evolutionary just so stories should generally be considered suspect until causation is verified. In this case, we have data - pretty good data given the sample size of 870 pitbulls (of which 86.8% passed the test) that they do not have an abnormally aggressive temperament (compare dobermans (n=1,655 78.5%) and golden retrievers (n= 785, 85.2%). Therefore the argument that they have been (successfully) bred to be "naturally" more aggressive than other breeds doesn't hold up to empirical testing.

So we have 2 Staffordshire bull terriers, and an 18 month old human, When my son was coming along I tried to thoroughly research the issue in a quantitative manner, with an open mind. What I discovered was that: a) "Pit bull" is an ambiguous term which refers to a suite of breeds known as "bully breeds" which range from our 35 pound dogs, up to 150 pound bull mastiffs -arguably also including Boston terriers and boxers. Therefore the first issue with a "pit bull" ban is that it is ambiguous as to what exactly a pit bull is. b) Bully breeds do not have more propensity to attack than other breeds, in fact the American Staffordshire terrier scores better in the AKC temperament test than the Labrador. c) Bully breeds don't generate any more bite force than breeds of similar size. d) HOWEVER "pit bulls" are over-represented in fatal dog attacks . So there appears to be a conundrum - pit breeds don't actually have the propensity or capacity to do more damage than similarly sized breeds, but appear to do so anyway. One possible explanation is that people are really terrible at visually identifying dog breeds - getting it incorrect over 85% of the time. That said ANY dog is capable of attacking and larger dogs are more likely to cause injury. Fatal dog attacks are exceedingly rare, making up 0.0007% of dog attacks. Statistically, bathtubs and ladders kill far more people than pit bulls, or any other dog breed. Anecdotally, here's Huxley and Wallace - our two:

Yeah, I guess I'm thinking about a scenario where Trump brings something like this up at a G8 summit - tries to extort negotiate more "protection money" from Japan for the US presence in Okinawa. Japan takes offense, scraps the security treaty, tells the US to pack up and get out. Now the US foots the bill for relocating 50,000 troops and associated hardware, loses the $2 billion contribution per year from Japan to upkeep, and has some of the worst EPA superfund sites to clean up before giving the land back to Japan, and loses possibly its most important strategic military position in the Asia Pacific region. Does Trump just not know that a) Japan pays a bunch for the US presence there, or b) The US doesn't have troops in Japan to protect its little buddy out of the goodness of its heart? If so, it's terrifying that I as an Australian citizen and a biologist know more than a presidential nominee about US foreign policy, and he brought it up as a talking point in the debate? Or alternatively, he does know all this and insinuated that Japan doesn't contribute to US military efforts because he didn't think the voters would know he was lying, and thought it would score points? Or maybe he just thinks, as he constantly says, he could get a "better deal" than Eisenhower, Kennedy, Johnson, Nixon, Ford, Carter, Reagan, Bush I, Clinton, Bush 2 or Obama? In my mind it's simply a case among the multitude of others that demonstrates the potential for a Trump presidency to be a disaster. Edit: Can has no spull gud.

One thing that's been bothering me is that there's been limited discussion of this quote by Trump: Under the Japan-US security treaty, the US agrees to defend Japan against its foreign adversaries, and Japan agrees to help support a US force on Japanese soil, which they spend about US $2 billion a year doing. Similarly, South Korea contributes US $808 million a year to the upkeep of US troops and is paying over US $9 billion to build new US bases in South Korea. It would be considerably more costly for the US to house those troops in the US than in Japan and South Korea. So Trump's comment is comprehensively false - Japan contributes considerably to US military operations in Asia, and in return the US maintains a presence of about 80,000 troops right on China and North Korea's doorstep - a massive military advantage if there was ever a conflict, and a huge economic advantage in being able to control and protect trade routes in the Eastern Pacific. So the open questions become - is Trump (supposedly a savvy businessman with dealings in Asia) simply that clueless about US foreign policy and diplomacy, or is he just assuming the voters are and he can dupe them? How would it go down if he brought something like that up in a discussion with a foreign president, and how would it damage US trade and security interests?