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Messages - Testy Calibrate

I wonder what God was thinking with ferns, moss, and liverwort.
Politics and Current Events / Re: Trumpocalypse
holy fuck Kushner compromised all our assets.
Dave, how do you determine if a mutation (of any sort) is slightly deleterious or slightly beneficial?
From the way you move and sleep, to how you interact with people around you, depression changes just about everything. It is even noticeable in the way you speak and express yourself in writing. Sometimes this "language of depression" can have a powerful effect on others. Just consider the impact of the poetry and song lyrics of Sylvia Plath and Kurt Cobain, who both killed themselves after suffering from depression.

Scientists have long tried to pin down the exact relationship between depression and language, and technology is helping us get closer to a full picture. Our new study, published in Clinical Psychological Science, has now unveiled a class of words that can help accurately predict whether someone is suffering from depression.

Traditionally, linguistic analyses in this field have been carried out by researchers reading and taking notes. Nowadays, computerised text analysis methods allow the processing of extremely large data banks in minutes. This can help spot linguistic features which humans may miss, calculating the percentage prevalence of words and classes of words, lexical diversity, average sentence length, grammatical patterns and many other metrics.

So far, personal essays and diary entries by depressed people have been useful, as has the work of well-known artists such as Cobain and Plath. For the spoken word, snippets of natural language of people with depression have also provided insight. Taken together, the findings from such research reveal clear and consistent differences in language between those with and without symptoms of depression.
continued at link
Bottom line: there is a hell of a lot more genetic diversity in the human population than is represented in that outdated reference.
Yeah. The wrenches have been beat up. They aren't new any more.
See, here's where your moronic analogies serve only to reinforce your militant ignorance.
"old" or "new", shiny or "beat up" has nothing to do with it.
There are    > 2000   known alleles for a the peptidase A gene*.
You asserted that it was a "hard cold fact" that there was just one.
Almost all of those alleles are fully functional.
Nothing "beat up" about them.

* and this is just one randomly selected example.
Great. Let's compare the sequences, shall we?
"We" already did.

What's your point?
Okay you say that there are 2,000? And Cavalli Sforza just used 31? I can't remember the exact number.  Here's my prediction. I predict that 19971999 of these will be very minor variations of the 31 in Cavalli Sforza's list.  And if I am correct that there are three in his list, then I predict that there will be a wide sequence Divergence between at least two of them. Possibly a wide Divergence between all three.
So now we argue about what "very minor" means.
while still ignoring the fact that Dave has no clue what it means wrt evolution to say that a population is diverse or that a mutation can only be judged as vsdm or vsbm in the context of its environment.
The University of Wisconsin at Stevens Point has proposed dropping 13 majors in the humanities and social sciences -- including English, philosophy, history, sociology and Spanish -- while adding programs with "clear career pathways" as a way to address declining enrollment and a multimillion-dollar deficit.

Students and faculty members have reacted with surprise and concern to the news, which is being portrayed by the school's administration as a path to regain enrollment and provide new opportunities to students. Critics see something else: a waning commitment to liberal arts education and a chance to lay off faculty under new rules that weakened tenure.

Students are planning a sit-in at the campus administration building on Wednesday in a demonstration called Save Our Majors. The Stevens Point Journal said students will then deliver a list of demands and requests to school officials. The school is one of 11 comprehensive campuses in the University of Wisconsin system.

The plan to cut the liberal arts and humanities majors (see full list below) is in line with a failed attempt by Republican Gov. Scott Walker in 2015 to secretly change the mission of the respected university system -- known as the Wisconsin Idea and embedded in the state code  -- by removing words that commanded the university to "search for truth" and "improve the human condition" and replacing them with "meet the state's workforce needs."

The push away from liberal arts and toward workplace skills is championed by conservatives who see many four-year colleges and universities as politically correct institutions that graduate too many students without practical job skills -- but with liberal political views.

[ How Gov. Walker tried to quietly change the mission of the University of Wisconsin ]

The administration at the University of Wisconsin at Stevens Point recently issued a statement detailing the plan, which still must be approved by a campus governance committee as well as the University of Wisconsin system's chancellor and Board of Regents.

It said that the school faces a $4.5 million deficit over two years because declining enrollment has led to lower tuition revenue, and proposes adding or expanding 16 programs in areas "with high-demand career paths as a way to maintain and increase enrollment." Last fall, the school saw an enrollment decrease of 5.4 percent from the year before. That was on top of a 6.8 percent drop the previous year.

"To fund this future investment, resources would be shifted from programs with lower enrollment, primarily in the traditional humanities and social sciences," the school statement says. "Although some majors are proposed to be eliminated, courses would continue to be taught in these fields, and minors or certificates will be offered."

Programs that would be expanded, which "have demonstrated value and demand in the region," include marketing, management, graphic design, fire science and computer information systems.

The student newspaper, the Pointer, quoted Samantha Stein, a 2017 graduate, as opposing the plan. Stein, who earned a bachelor's degree in biology and had a minor in biomedical writing through the English department, said:

    "The shift away from the humanities and from the opening of one's mind to other cultures, languages, the arts, political science and so much more is one that universities will not return from, and we are giving up what a college education is all about if we do this."

Inside Higher Education quoted Michael Williams, chair of English at Stevens Point, as saying, "Well, you can imagine the mood in the College of Letters and Science, which houses the humanities."

The Republican-dominated legislature in Wisconsin weakened tenure in 2015, removing it from state law. Lawmakers also changed the traditional power-sharing arrangement at public universities that had long given students, faculty and staff an important role in governance, instead giving more power to administrators and the governor-appointed Regents. The Regents then set new policies that made it easier for public universities to lay off tenured faculty.

Here's the school's full message:

    The University of Wisconsin-Stevens Point outlined a plan today to address fiscal challenges by shifting resources to invest in areas with growth potential.

    UW-Stevens Point faces a deficit of $4.5 million over two years because of declining enrollment and lower tuition revenue. It proposes adding or expanding 16 programs in areas with high-demand career paths as a way to maintain and increase enrollment.

    To fund this future investment, resources would be shifted from programs with lower enrollment, primarily in the traditional humanities and social sciences. Although some majors are proposed to be eliminated, courses would continue to be taught in these fields, and minors or certificates will be offered.

    This repositioning is necessary because of declining financial resources, demographic changes with fewer students in K-12 schools and rising competition among public and private universities, said Greg Summers, provost and vice chancellor for academic affairs. A significant increase in graduation rates recently has also contributed to overall enrollment declines.

    A broad, liberal arts education continues to be critical, UW-Stevens Point Chancellor Bernie Patterson said in messages to students, faculty and staff today. "Importantly, we remain committed to ensuring every student who graduates from UW-Stevens Point is thoroughly grounded in the liberal arts, as well as prepared for a successful career path. It is critical our students learn to communicate well, solve problems, think critically and creatively, be analytical and innovative, and work well in teams. This is the value of earning a bachelor's degree."

    UW-Stevens Point proposes expanding academic programs that have demonstrated value and demand in the region, including:

    • Chemical Engineering
    • Computer Information Systems
    • Conservation Law Enforcement
    • Finance
    • Fire Science
    • Graphic Design
    • Management
    • Marketing

    These programs have existed as options and would expand to majors. In addition, new bachelor's (or advanced) degree programs are proposed in:

    • Aquaculture/Aquaponics
    • Captive Wildlife
    • Ecosystem Design and Remediation
    • Environmental Engineering
    • Geographic Information Science
    • Master of Business Administration
    • Master of Natural Resources
    • Doctor of Physical Therapy

    The recommendations recognize a growing preference among students for majors with clear career pathways, Summers said. "UW-Stevens Point is committed to strengthening our academic offerings while improving our liberal arts core to ensure students graduate with the knowledge and skills they will need to be successful in the future."

    To create programs that meet the evolving needs of students, UW-Stevens Point proposes shifting resources from programs where fewer students are enrolled. Discontinuing the following programs is recommended:

    • American Studies
    • Art - Graphic Design will continue as a distinct major
    • English - English for teacher certification will continue
    • French
    • Geography
    • Geoscience
    • German
    • History - Social Science for teacher certification will continue
    • Music Literature
    • Philosophy
    • Political Science
    • Sociology -- Social Work major will continue
    • Spanish

    Students enrolled in any major that is eventually discontinued will have the opportunity to complete their degrees. This includes students who enroll in fall 2018. Courses would continue to be taught in these fields. Minors in English, Art, History and Philosophy are among those continuing.

    Additional programs in humanities and social sciences that have clear career pathways will provide opportunities to major in liberal arts fields, Summers said.

    The proposal to discontinue programs must be reviewed by a campus governance committee, then the chancellor and UW System Board of Regents. Because possible program elimination may result in the layoff of some tenured faculty members, a new UW Board of Regents policy will be followed. This process is expected to begin in August. If a reduction in tenured faculty positions is recommended, cuts would occur no sooner than June 2020.

    Summers described program discontinuation as difficult, painful and necessary. "If we accept the need for change, and we confront and solve the financial issues currently facing the institution, we can create a new identity for the regional public university. UW-Stevens Point can move forward with fiscal stability, new opportunities to build programs and grow enrollment, and renewed capacity to improve our service to the students and communities of central and northern Wisconsin, which are complex, diverse and ever changing."

Despite state public access laws, Colorado law enforcement agencies routinely refuse to release internal files related to police misconduct, according to a new report.

Independent researchers Bridget DuPey, Margaret B. Kwoka and Christopher McMichael from the University of Denver Sturm College of Law tried to collect internal affair files during 2015 and 2016 from law enforcement agencies across Colorado--but to little avail.

More than half of the 43 agencies they reached out to either did not respond or rejected their request.

Twenty-four of the agencies provided no responsive records. Only five of the law enforcement agencies queried supplied files that were deemed to be "substantially transparent."

Under The Colorado Criminal Justice Records Act (CCJRA), discretionary release of investigation files against police officers is permitted.

The intent of Colorado's open-record laws is to promote the public's interest in holding government accountable by requiring transparency, the study said.

One court noted that "transparency enhances public confidence in the police department and is constituent with community policing concepts and represents the more modern and enlightened view of the relationship between police departments and the communities they serve."

But the study found this is hardly the case, and custodians generally deny all requests for files, regardless of the situation or outcomes.

The authors followed up with a second wave of requests to agencies that responded the first time, asking for more specific internal affairs documents.

Forty percent of agencies did not respond at all. Seven percent offered a duplicate of their first response, and thirteen percent asked for a prohibitive access fee.
A Superior Court judge in Newark on Wednesday took away subpoena and investigatory powers from the city's Civilian Complaint Review Board but said it could still conduct oversight of the police department.

Mayor Ras Baraka called Judge Donald Kessler's oral decision "a setback to criminal justice reform in America and to the critical need for citizens to have complete trust that incidents of police misconduct will be dealt with fairly, appropriately and impartially."

"For now, our CCRB will continue to move forward using its power of oversight, but Newark will appeal the court's decision," the mayor said in a statement.

The board was conceived following a damning report released by the U.S. Department of Justice in July 2014 that found Newark police failed to provide sufficient constitutional reason for about 75 percent of pedestrian stops and that despite hundreds of citizen complaints from 2007 to 2012, just one complaint of excessive force was sustained.

It was designed to provide additional civilian oversight of a beleaguered police department that federal investigators found routinely engaged in acts of excessive force and violations of residents' constitutional rights.

The creation of the 11-member board to review police misconduct allegations was met with resistance from police unions.

The Fraternal Order of Police challenged the civilian review board's subpoena powers in court, arguing it violated state statute, an officer's due process rights and the attorney general guidelines.

The unions later obtained an injunction in December 2016 to prevent the board from exercising its investigatory power.

Since then the board has largely reviewed changes in police department policies but has not conducted any investigations, a city official said.

The official said Kessler ruled that any investigations by the civilian board would violate due process rights; Newark police already have an internal affairs department to handle such complaints.

The unions argued the board's investigative powers undermine the police department's disciplinary process.

"The FOP has said since day one that the powers given to the proposed CCRB by executive order were far too broad. We are not against reform or transparency, but it has to be within the confines of the law," James Stewart Jr., president of the FOP said in a statement. "We always said we would lay our cards on the table and let a judge decide the issue based on the merits of the case and today he made reference to many of our points in his decision."
I think it's pretty amazing that Dave has yet to even acknowledge, let alone answer, the question about whether he understands that a deleterious mutation can be beneficial in a different environment. 4th Law reigns supreme on that one.
And, at this point in his flailing, it's probably the only question that matters.
Dave, this is another "I didn't realize Lenski's bacteria were clonal" moment.  There are FAR more than 4 alleles per gene in the human genome.  Best you move on back to explaining "genetics" to us without this nonsense, if you can.
Look, idiot.  I know that.  Woodmorappe knows that.  Cavalli-Sforza knows that.  Jesus Christ.

We're talking about MAJOR difference, not SNP differences.

Here's a link to a Preview of Cavalli-Sforza's tome.  You can see part of Table 1.3.1 referenced by Woodmorappe ...

Most well studied loci ... which are given in this table have - as "W" points out -  between 1 and 4 common alleles.

Deal with it.
Pulling this forward
Quote from: Dave Hawkins
The best way for you to prove that my insinuations are not founded [...] would be for you to demonstrate that here by actually doing those things that good scientists would normally do.

I mean, I'm only using misogyny to try to bully you into agreeing with me. It's cool, though, because some people judge me based on my actions, history, and beliefs, which is the same as me dismissing you due to an accident of birth.
Her gender was not an "accident of birth."  Its a great thing to be born a woman. Or a man.

It's her sciencyness I have a problem with. And yes I sometimes bully and taunt and caricature - both men and women - for impact.

The only 'impact' it has is that people regard you with disgust every time you do it. It is not appropriate at all. It is stark misogyny, and sometimes you toss in a little racism, as you did this time.

Perhaps you've noticed that every time members taunt you with veiled accusations of child abuse, I have intervened, because it is not right to make such remarks when there is no indication that they are in any sense true.

The same goes for your nasty little misogynist remarks, usually tossed at Pingu or me at the same moment you are accusing us of lying or being stupid or incompetent.

This is ugly behaviour, Dave, and undeserved, not only by the women you interact with, but by all women.

Think before you jeer about women and minorities. If nothing else moves you to quit your gendered sneering, remember you're supposed to be some version of a Christian. I spend every Sunday morning in church. I'm pretty sure I've never heard there that women and minorities are lesser beings. If that's what you hear in your church, it's time to look for salvation somewhere else.
This is just Borealis spin ... again.  I've never once hinted that women or minorities are lesser beings.   The latest of many examples of my impartiality toward women is my high praise for Barbara McClintock. 
And some of your best friends are black, amirite?
Funny you should mention that. Dave's black friends are also from the hood!
Like I've said to many people before you for the past 12 years ... If you don't like me, go away. There's plenty of "adult" science threads for you to participate in.

I took a swipe at quotas. Looks like I might have struck a nerve.

Yeah, you did. 

The nerve of any Native American person here, plus the nerve of mine you repeatedly bang whenever you tell me that I only got my job because I am a woman.

So yeah, you did.
And by the way, people, don't let Pingu spin you here.  I've never claimed to KNOW how she got her job.  I've only speculated.  What I DO know is how she "does science" HERE, which in my opinion is pretty lame. 

Lol. For any casual reader, it is perfectly clear that pingu is not only well versed in the pedagogy, she has been incredibly patient in trying to teach you even though you are too dumb to learn.
Do you deny that there are problems with members of protected groups getting unfair promotions?
Define "problem here.
We must look forward,  not back.
Politics and Current Events / Re: Trumpocalypse
More innovative ideas from the Republicans:
This sounds like they want access to the evidence Mueller has gathered.
I'm going to limit my review to bacterial genetics and human genetics for now. I'm going to try to limit my discussion to "how things are" and try not to get too much into "how things came to be" and I think that would be best if we all tried to do that.
How about starting with a demonstration that you actually understand what "evolution" actually is, as understood by population geneticists. The following is one operational definition:

Changes in allele frequency among generations

This is fairly uncontroversial. Do you agree or disagree? Can you offer an alternative operational definition? Do you recognize that populations change over time, and that this is a currently operating process? Do you agree that these changes are the result of 'mutations' on a genetic level, and that these changes propagate through populations of organisms by selection and drift?

Note that this is all a description for "how things are" and shouldn't be a problem for your high-speed mind at this point.
You need to add "in populations".
And if they aren't beneficial now, they may be in some future environment.  Which is why genetic diversity is important for adaptation.

Dave is STILL struggling with this concept.  It's not that he doesn't agree with it.  He doesn't even get it.
No. He doesn't get it. It's weirdly similar to the question "why do the curves agree".
That's because of your conditioning to think errors are the ultimate source of variation.  Which is bullshit. And even Shapiro SAYS (politely( that it's bullshit. You are seeing only what you want to see.

FFS Dave.  "Errors", like "random" is not a precise term.  Different people mean different things by it.  In the context of evolution, it usually means some process of replication or repair that results in a sequence different from the parent sequence.

Nobody now thinks that all mutations result from duplication or repair processes, because lots of other mutagenic processes have been discovered.  So that is a straw man. Many of them, when they happen in animals, result in cancer.

And some of the errors that DO arise during the process of replication are actually recombination - so it's not as though "copying error" and "recombination" are even mutually exclusive categories.

The person who is only seeing what they want to see is you.  I've said something like the above several times now, and you just dismiss it.  But it's not even controversial. It's all in Shapiro for a start.

Of course Shapiro, unlike you, understands the basic principles of evolution. He understands that the errors NHEJ and other processes produce can be either good or bad, depending on the environment, and the ones the environment selects are the good ones.
Sure but he recognizes that they are mostly VSDMs.

Dave!!!!! I thought you said you understood adaptation and natural selection!  Yes, in a well-adapted population they ARE "mostly VSDMs. That's because once a genome has been optimised for an environment, most variants will be worse.  By definition.

But if the ENVIRONMENT CHANGES,  as Ben is talking about, then what was a VSDM can become a VSBM, and vice versa. So the prevalence of those old VSDMs increases, and the prevalence of the "originals" decreases. 

That's. What. Adaptation. IS.

It's a pretty blatant mental block.
"Although the phenomenon and the term 'adaptive' have proved controversial (Roth et al. 2006), I argue that the term is appropriate in two senses: (i) increased mutability occurs as an adaptive response to starvation conditions, and (ii) among the resulting mutations, there are invariably some that provide adaptation to the selective conditions."

Yes if course mutability increased. It's an energy thing.  Already discussed. Yes some mutations might be adaptive. But the % that are is miniscule as we know from other authors.
It only needs to be miniscule. Individuals don't matter in evolution. Populations do.
Yes, that's exactly what he means. So it's a cell-directed process that nonetheless generates errors, and these errors are an important source of genetic change. So he's clearly not making a distinction where "random," "error," and "not cell-directed" are all always on one side with "non-random," "non-error," and "cell-directed" on the other. This is clearly a process he considers both cell-directed and error-producing.
What a fucking wonky way of seeing things.  The cell isn't trying to generate errors in NHEJ as you make it sound. The cell is trying to repair the damage.  Period. But it's not possible to make repairs error free, so naturally errors happen.
So there isn't a bright line differentiating "cell-mediated" and "error-prone".

Which is what we've been telling you. Repeatedly.
There is s bright line between ...



Non errors
Yes. That line is called the frame of reference.
It may make your head spin. Those 'flexible responses' are not news to the scientists you label 'neo Darwinists', and it makes perfect sense that cells must have evolved to have such protections, otherwise life would not have survived.
This is the annoying thing about Shapiro and some of his fellow "mavericks".
They encourage idiots like Hawkins to think that there's some sort of "revolution" with "Third Wayers" storming the barricades of dead-ender "Neo-Darwinists".  This view, of course, appeals to Hawkins, who sees all of science as competitive cheerleading (or jeerleading/sneerleading, as the case may be).

It's not like that.
Science is a continuous dialectic.
When Mendelian genetics was discovered, it was reconciled with Darwin's descent with modification.
When the nature of DNA was elucidated, it was incorporated into the, yes, evolving understanding of how genetics and evolution worked. This is around the point, in retrospect, labeled the start of "Neo-Darwinism".
But that's an arbitrary label applied to a period with arbitrary start and end periods.
Hawkins can't help but see science in terms of religion, but in fact it's not like the Council of Nicaea, where the bishops get together and decide what everyone is supposed to believe, forever.
The discovery of recombination, transposons, transducing viruses, epigenetics... all changed the understanding of how genetics and evolution work, but these are not "Christianity displaces Paganism" moments. No one of these discoveries - or its general acceptance in consensus science - marks the End of the Neo-Darwinist Era. These are incremental changes. It's Einstein / Newton, not Copernicus / Ptolemy.

Consilience simply doesn't work for dave.
Dave:  I accept that you think your model is true.  I also accept that it makes some kind of internal sense.

I can also see that, with that model as your starting point, you can see things in what Shapiro and Noble write that could make you think that some of the evidence they present is consistent with it.

But can I suggest you turn this round:  ask yourself: what evidence would FALSIFY that model?

Lol. You can ask. Sure. If wishes were ...
But he most definitely makes a clear distinction between types of mutations... Random versus non-random. Error versus non error.
:no: He most definitely does not. He talks about processes that work to prevent mutations and processes that work to produce them, but he does not refer strictly to the mutations that escape the prevention processes as "errors" and the mutations that arise from other processes as "non errors." Remember, he specifically describes NHEJ as an "error-prone process" and yet talks about it as an important source of variation. He does not make the distinction you think he does.

Yes he does.

I will dig them up again in the morning.
It's quite obvious to me that Ben has not even bothered to read Shapiro ... because to anyone who HAS read his stuff about the R/W genome and NGE and such it is obvious that what Ben says above is just flat wrong.  Shapiro does indeed make a clear distinction between "random / accident" and "cell directed change."  Here's one that says it clearly right in the damn abstract ... you don't even have to get into the paper at all ...

The genome has traditionally been treated as a Read-Only Memory (ROM) subject to change by copying errors and accidents. In this review, I propose that we need to change that perspective and understand the genome as an intricately formatted Read-Write (RW) data storage system constantly subject to cellular modifications and inscriptions. Cells operate under changing conditions and are continually modifying themselves by genome inscriptions. These inscriptions occur over three distinct time-scales (cell reproduction, multicellular development and evolutionary change) and involve a variety of different processes at each time scale (forming nucleoprotein complexes, epigenetic formatting and changes in DNA sequence structure). Research dating back to the 1930s has shown that genetic change is the result of cell-mediated processes, not simply accidents or damage to the DNA. This cell-active view of genome change applies to all scales of DNA sequence variation, from point mutations to large-scale genome rearrangements and whole genome duplications (WGDs). This conceptual change to active cell inscriptions controlling RW genome functions has profound implications for all areas of the life sciences.
How you can misunderstand such a straightforward statement is a testament to the power of Morton's demon.
Arts and Entertainment / Re: Harvey Weinstein
Oh that will make things interesting