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Topics - Kai

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Techmology and Scientism / 168 retractions = world record.
« on: April 13, 2012, 10:08:22 pm »

Editors representing 23 journals have publicly asked officials at seven Japanese institutions to investigate the integrity of 193 publications authored by anesthesiologist Yoshitaka Fujii.

As reported yesterday by Retraction Watch, questions were first raised about Fujii's work a decade ago. Tokyo-based Toho University, his most recent employer, dismissed him in February for not following ethical review procedures in producing eight of nine papers investigated by an internal committee. (Fujii agreed to retract those papers, according to a statement on the university's Web site.)

On 8 March, the journal Anaesthesia published an analysis questioning data in 168 of Fujii's papers. Now the group of editors, mostly from journals focusing on anesthesiology, is planning to retract what may be Fujii's entire English language body of work if the institutions with which he was affiliated cannot confirm that the studies took place, that the original research data have been verified, and that the studies had been properly reviewed in advance for ethical considerations.

Oh boy.  :lulz: And for anesthesiology too! It's not like this is taxonomy here, which, while loads of made up new species descriptions would be a horrible mess to clean up, the mistakes generally are not used in medical policy that may kill people.

Techmology and Scientism / 'Academic Publishing is Broken'
« on: March 22, 2012, 09:32:53 pm »
The best damn summary of everything that is wrong with scientific publishing:

Let’s take a look at the flow of money in the production of research. The government takes tax revenue from citizens and uses it to fund university research groups and libraries. Researchers obtain government grants and use the money to conduct experiments. They write up the results in manuscripts that are destined to become published papers. Manuscripts are submitted to journals, where they are handled by other researchers acting as unpaid volunteer editors. They co-ordinate the process of peer-review, which is done by yet other researchers, also unpaid. All these roles—author, editor, reviewer—are considered normal responsibilities of researchers, funded by grants.

At this point, researchers have worked together to produce a publication-ready, peer-reviewed manuscript. But rather than posting it on the Web, where it can contribute to the world’s knowledge, form a basis for future work, and earn prestige for the author, the finished manuscript is then donated gratis to a publisher: the author signs away copyright. The publisher then formats the manuscript and places the result behind a paywall. Then it sells subscriptions back to the universities where the work originated. Well-off universities will have some access to the paper (though even they are denied important rights such as text-mining). Less well-off universities have access to varying selections of journals, often not the ones their researchers need. And the taxpayers who funded all this? They get nothing at all. No access to the paper.

Let's say, you give me the goods, and then I give it back to you for a one time low fee, and to anyone else for the same. I'm sure you'll see this is an offer you can't refuse.


Discordian Recipes / Recipes for the future.
« on: March 19, 2012, 03:13:58 pm »
Here's the situation:

The last 4 months have been a huge renovation project. I'm staying with my parents currently, and in October my dad got the idea to check what the original ceiling looked like above the then current ceiling in the kitchen. This may or may not have been a mistake, depending on how you feel about 40 thousand dollar kitchen renovations. To make a long story short, the contractors will soon be finishing their part, the last coat on the floor will be put down, the counter tops measured, cut, and affixed, and the appliances. This includes a top of the line gas range and gas convection oven. This kitchen is going to be like a dream. The whole thing is beautiful. (I will post pictures upon completion.)

Here's where you come in. You post recipes that I should try in this new, amazing kitchen. I will post a few recipes that run in the family, as well (including my Great Grandma Burington's chicken pot pie recipe). Then I post pictures of how they turn out, in this kitchen, when it is completed.

Principia Discussion / Any relevance for religion?
« on: March 13, 2012, 11:11:23 pm »
Talking with an old friend yesterday, he brought up that he thought religion, despite being pretty much false, has a necessary place in the human world. I immediately disagreed, but I wanted to ask that question here, because I'm looking for new insights.

Does religion serve a necessary place in the human world? Is it relevant in an age of science where what were formerly the most profound questions are now answered (e.g. where does the sun go at night?)?

And on that note, would Discordianism fit into that necessity or lack thereof and why?

Full summary over here:

Basically, John Bargh, a researcher at Yale, conducted a psychological experiment to see if by talking about old age he could prime people to feel the effects of age (aka walking slower). This was back in 1996.

Just recently, Stephane Doyen attempted to replicate this study, but with blinding in some units, something that the original study did not have. Which ended up showing that the individuals walked slower "only when they were tested by experimenters who expected them to move slowly". A basic case of blinding revealing unconscious bias.

Bargh then wrote a blog post where he proceeded to throw a fit. Mind you, it's the sort of gentlemanly like fit that you see in academic circles, but most obviously a case of a grown man loosing it because he wasn't right. He attacks the journal, the authors, and Ed Yong as well. The last was a particularly dumb move, since Yong is probably the best damn science journalist out there, and wasn't exactly going to let it go at that.

This all illustrates that scientists aren't really different than other people when it comes to territoriality, and that replication, /published/ replication studies, are needed now more than ever. Until a study is replicated, it's a sample size one.

Aneristic Illusions / "Scientific" Racism.
« on: March 03, 2012, 11:26:03 pm »
I'm currently reading The Mismeasure of Man by SJ Gould, which is about the historical use of quantitative measures of intelligence (through brain size, skull size, IQ, and other numbers) to justify racism, sexism, and classism.

I am finding myself entirely fascinated by this, partly because just about every scientist of the 19th century (including Charles Darwin, a known abolitionist) was racist to some degree, and used evolutionary argument to support these social constructions. And the way they went about it was the backwards version of scientific method, despite these being scientists in all other respects. They started with socially generated racial stereotypes and then, more or less unconsciously, found their data to fit the conclusions. I'm not saying they fabricated the data, rather, they inserted ad hoc hypotheses to explain why the data didn't fit with their conclusions in an effort of immense cognitive bias. The anthropologists were the worst of them; if I'm to understand correctly, the whole field was originally created as unconscious think tank to justify Caucasian male superiority. It was almost evangelical, with evolutionary theory twisted to support a "hierarchy of man" with very precise, yet ultimately mishandled, measurements. Some of the worst offenders being Louis Agassiz, who was otherwise a world renowned glacial geologist and morphologist of fishes, and Paul Broca, the neuroanatomist who discovered the speech center of the brain.

Despite scientific racism being put out of style in the last 50 years (most scientists these days would be horrified at the idea), I can still see these same issues going on in medicine and psychology to target other groups, including women, homosexuals, and other "social deviants".

Take the Duesberg anti-AIDS type schtick. It is almost formulaic of Broca's style: take a social stereotype ("homosexuality is not innate, it is a lifestyle choice, and furthermore immoral"), choose an area of measurement (in this case, African population dynamics), pick the data for measurements that support the stereotype, and present the argument so it leads to the conclusions you desire ("since HIV doesn't lead to AIDS, it must be a disease in gay men brought on by drug use"). Shift the argument as needed to account for refuting evidence. This is not science, yet it looks scientific because there are numbers involved. And people take it seriously because it supports their prejudices.

You can even find these sorts of arguments outside of social concerns. Those people who still deny that birds are dinosaurs, for example. They start with a conclusion ("only birds have feathers"), see fossils with feathers (even Dromaeosauridae fossils), and present their argument ("they can't be dinosaurs [even though we labeled them such before we knew they had feathers] because they have feathers, therefore they are birds"). Shift the argument for every new feathered fossil found. Or, for example, when that T-rex hemoglobin was discovered, and found to be very similar to chicken hemoglobin.

The worst part about all of this is that the manipulation, the self-deception, is largely unconscious on the part of the people involved. They do not see how their own biases are shaping their conclusions. They think they are just following data.

Techmology and Scientism / 'Better living through electrochemistry'
« on: March 03, 2012, 07:16:38 pm »
AKA, 9 volt battery a day keeps the voices of doubt away.

Not in the least bit clear how it works. Yes yes, it's 9 volts of current coursing through your brain, but how is it interfering with the connectome specifically?

And if that wasn't enough, you can make your own.. If electrocuting your brain is the sort of crazy thing you like to do, anyway.

Techmology and Scientism / THE FUTURE IS NOW MAKE YOUR TIME.
« on: February 20, 2012, 12:30:48 am »

a little gadget that can sequence DNA while plugged into your laptop

the DNA does not need to be amplified

can sequence DNA strands as long as 10,000 bases continuously

the MinION would take about 6 hours to complete a human genome

Each unit is expected to cost $900 when it goes on sale later this year

WhattheIdon'teven. No PCR, no shotgun sequencing, speed comparable to pirosequencing, fits in the palm of your hand, and COSTS LESS THAN 1000 DOLLARS.

How it works -

Oxford Nanopore is also building a larger device, GridION, for lab use. Both GridION and MinION operate using the same technology: DNA is added to a solution containing enzymes that bind to the end of each strand. When a current is applied across the solution these enzymes and DNA are drawn to hundreds of wells in a membrane at the bottom of the solution, each just 10 micrometres in diameter.

Within each well is a modified version of the protein alpha hemolysin (AHL), which has a hollow tube just 10 nanometres wide at its core. As the DNA is drawn to the pore the enzyme attaches itself to the AHL and begins to unzip the DNA, threading one strand of the double helix through the pore. The unique electrical characteristics of each base disrupt the current flowing through each pore, enough to determine which of the four bases is passing through it. Each disruption is read by the device, like a tickertape reader.

This is science fiction territory, people. Combine one of these with an iphone, and you have damn near a tricorder.

My only question in this is "are the MinIONs one time use or mult-use?" Because if they are multi-use /I. Want. One./

either exposure to pesticides and herbicides or chronic dehydration.

And I thought, really, chronic dehydration? Seems far more likely to be toxin related.

Techmology and Scientism / 'God Hates Checkered Whiptail Lizards'
« on: February 14, 2012, 09:49:47 pm »
An obvious parody, but hilarious all the same.

In the science section because this are parthenogenic species, without males, the females laying clonal eggs. And before egg laying they engage in homosexual pseudocopulation. A whole species of lesbian lizards. And god hates them.  :lulz:

of North America.

New DNA analysis of ethnic groups living in the Altay Mountains (see map) revealed a unique genetic mutation that also occurs in modern-day northern Native Americans.

A possible link between Siberians and Native Americans is an "age-old question" that was first raised by European explorers in the New World, said study leader Theodore Schurr, an anthropologist at the University of Pennsylvania in Philadelphia.

That's because some of those early explorers had also been to Asia, and they noticed physical similarities between the two populations.


The scientists received written consent to take DNA samples from nearly 500 people, many of whom were living in remote areas and had never met Americans. As part of ongoing genetic research, the team had previously taken samples from close to 2,500 Native Americans in the U.S., Canada, and Mexico.

Depending on the location and individual preferences, the researchers collected DNA via cheek swabs, mouthwash samples, or blood samples.

In their analyses of Altay and Native American DNA, the scientists focused on two parts of the human genome: mitochondrial DNA, which is passed down through mothers, and the Y chromosome, which is passed down through fathers....

Over time, mutations accumulate in these part of the genetic code that can help scientists pinpoint when populations branched off and migrated to new places, said Schurr, who is also the North American director for the National Geographic Society's Genographic Project, which is conducted independently from the Altay DNA project. (The Society owns National Geographic News.)

In the case of the Altay people, the scientists found a mutation in one paternal lineage that arose about 18,000 years ago—a genetic marker that's also found in modern-day Native Americans.

The finding dovetails with previous studies, including some by Schurr, that found a shared mutation in the two groups' mtDNA, one that arose around the same time as the newfound Y chromosome mutation.

As we talked about this before on these forums and the discussion was controversial (albeit less so than discussions on drug legalization ethics), I should mention that this is support, not confirmation, that other populations in East Asia also show these traits, and that molecular clock dating is notorious for large confidence intervals. Algorithm calibration for these tests at best uses a good series of fossil evidence, and at worst is a just so story of average mutation rates.

According to anthropologist Connie Mulligan, the new paper—to be published in the February 10 issue of the American Journal of Human Genetics—offers the most detailed genetic picture yet of ethnic Altay peoples.

Yet she thinks Shurr is "a little overly specific" in saying that Native Americans' founding DNA comes from the Altay region.

"I would broaden [that] to say [it's] that general region of central East Asia," said Mulligan, of the University of Florida in Gainesville.

That's because the mitochondrial and Y chromosome mutations that Schurr identified are also found together elsewhere in Asia, for instance, in China and Mongolia, she said.

The bottom line is that it's important to keep other Asian "populations in the running, and [it] means we should do dating studies on those populations as well," Mulligan said.

Stephen Zegura, a professor emeritus of anthropology at the University of Arizona in Tucson, thinks Schurr and colleagues have a strong case for pinpointing Altay. But he added that, ultimately, it'll be difficult to tease out exactly how the New World was peopled.

"We don't have definitive information, like remains of people from the Beringia land bridge with ancient DNA," he said.

"This is one of the problems—we have hypotheses, but we don't have strong confirmation."

Techmology and Scientism / Uncanny valley turned up to eleven.
« on: February 12, 2012, 12:26:16 am »

It may seem like videos of robots folding laundry, and an all terrain robot "mule", but the movements and the corrections the robots make, and how they were trained to do these things makes their movements almost biological. Especially when the robot mule stumbles. It just about freaked me out how much that looks like a cow stumbling and attempting to get up.

Technology Review magazine says "Abbeel taught one robot how to fold laundry by giving it some general rules about how fabric behaves, and then showed it around 100 images of clothing so it could analyze how that particular clothing was likely to move as it was handled." No live human instruction. Just pictures.

In this towel-folding video, you can almost feel the robot studying the cloth, trying to figure out which two points are farthest apart and therefore the best places to grasp and fold. It's spooky.

Spooky is right. My whole response during the video was laughter and "Oh my god..."

Techmology and Scientism / Nine Lost Treasures that science wants back.
« on: February 09, 2012, 11:03:02 pm »

The Maxberg Archaeopteryx- One of 11 complete specimens, first to show that the bones were hollow. Lost after the death of the owner, now for 20 years.

Musaeum regalis societalis
- A specimen of long neck seal showing natural variation that may in part have been responsible for myths of long necked marine creatures. Lost since the 17th century.

The Apollo Plaques - Brought back to Earth from the Moon during the Apollo missions, many of the moon rocks were gifted to foreign nations and US states. While the vast majority of the moon rocks are protected, many of the plaques have been stolen or lost.

The Peking Man - Discovered in 1921, these were the oldest homonid bones known at the time, and very clearly were that of a Homo but not of Homo sapiens that used tools and fire. Lost in 1941.

Greek Fire - A secret weapon of the Byzantine Empire, it was shot from the bow of ships and struck terror into the hearts of their enemies. The recipe is lost.

The Soviet Seed Bank - A collection of 250,000 seeds and plant samples from Soviet Russia, meant to contain varieties enough to feed a vast empire. A large portion were stolen by the NAZIs during WWII and taken to Lannach Castle in Austria. Now destroyed, lost, or misplaced in Russian university collections.

The Mars Polar Lander
- Sent to Mars' south pole in 1999 to study climate, lost connection upon landing. People are still searching from photographs.

Damascus Steel - Crucible steel produced by Middle Eastern smiths in the middle ages, with high flexibility and strength. The recipe was a guarded secret and is lost.

The Moon Trees
- In 1971 Stuart Roosa carried "roughly 500 pine, sycamore, sweetgum, redwood and Douglas fir seeds" with him on Apollo 14 to lunar orbit and returned with to Earth. Most germinated and were given to people in North America and around the world to plant, but no one kept track of where. The locations of ~80 are now known, most of which are still alive.

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