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Maj
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Post by Maj » Fri Dec 03, 2010 10:08 pm

> FrankTrollman wrote:OK, that's more like it. But it's also base speculation, and it is wrong. She was looking at microbes that were able to survive with very high levels of Arsenic and was speculating wildly about their contents - thinking that they might be a separate life tree. They aren't.

I have no idea what you're arguing for or against here. The idea that there is an organism that uses arsenic in its DNA didn't come out yesterday. The same NASA scientist was talking about it on a TV program five months ago. The whole tree of life bit isn't relevant to the simple fact that this news isn't breaking. It's just really cool.

> Kaelik wrote:It's not arsenic based any more than someone with screws in their arm has bones made of titanium (or whatever). You have to artificially remove the original part, and then artificially replace it with the foreign part.

In Frank's defense, regardless of the particular details of evolution, blah, blah, blah... What it means for us is that life can exist and potentially evolve in places that humans don't normally consider able to sustain life. And if there's a possibility that they can evolve past the single-celled stage, the scope of what it means to be alive is literally beyond imagining.
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Username17
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Post by Username17 » Fri Dec 03, 2010 10:29 pm

> Maj wrote:I have no idea what you're arguing for or against here. The idea that there is an organism that uses arsenic in its DNA didn't come out yesterday. The same NASA scientist was talking about it on a TV program five months ago. The whole tree of life bit isn't relevant to the simple fact that this news isn't breaking. It's just really cool.

In the video she is speculating that maybe it has arsenic in its DNA and maybe it's a separate genesis. The news this week is that it has been confirmed that arsenic is used in its DNA, but that it is not a separate genesis.
So yes, it's news. It's the difference between someone announcing that they think there might be a sasquatch and someone coming back with one in a cage.
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Prak
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Post by Prak » Fri Dec 03, 2010 10:57 pm

So, I heard about this arsenic based life yesterday, and... I find interesting, but hardly earth shaking news. More of a "huh, cool" than "holy shit that's fucking amazing!" I mean, so there's a species that can used arsenate instead of phosphate in it's DNA. um, yay? How is this honestly news in any sense other than "we now know for a fact that it works"?
Cuz apparently I gotta break this down for you dense motherfuckers- I'm trans feminine nonbinary. My pronouns are they/them.

> Winnah wrote:No, No. 'Prak' is actually a Thri Kreen impersonating a human and roleplaying himself as a D&D character. All hail our hidden insect overlords.

> FrankTrollman wrote:In Soviet Russia, cosmic horror is the default state.
> You should gain sanity for finding out that the problems of a region are because there are fucking monsters there.

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name_here
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Post by name_here » Sat Dec 04, 2010 1:59 am

See, "we now know for a fact it works" is a pretty big deal, because we no longer can say, "this planet doesn't have enough phosphorous for life, skip it," when searching space. It doesn't matter terribly much immediately, but it's useful information FOR SCIENCE!
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Sashi
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Post by Sashi » Sat Dec 04, 2010 2:05 am

It's really more exciting and mindblowing the closer you are to being a biochemist. Calling arsenic and phosphorus "similar" is almost an overstatement. Hydrogen and Deuterium differ by only a neutron, but if you drink heavy water you will die. Very small differences in bond strength and geometry can totally fuck things up.
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Kaelik
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Post by Kaelik » Sat Dec 04, 2010 9:02 am

> name_here wrote:See, "we now know for a fact it works" is a pretty big deal, because we no longer can say, "this planet doesn't have enough phosphorous for life, skip it," when searching space. It doesn't matter terribly much immediately, but it's useful information FOR SCIENCE!

A) This hasn't actually demonstrated that, because we have no more evidence that life can form without phosphorous than we did two years ago.
B) We don't skip planets for lack of element anyway, people hypothesize all kinds of things like silicate based life and such all the time. No one skips a planet just because it wouldn't be able to lead to human life.

> Sashi wrote:It's really more exciting and mindblowing the closer you are to being a biochemist. Calling arsenic and phosphorus "similar" is almost an overstatement. Hydrogen and Deuterium differ by only a neutron, but if you drink heavy water you will die. Very small differences in bond strength and geometry can totally fuck things up.

The reason arsenic is deadly is because it is so close to phosphorous that your body tries to use it as phosphorous, and fails, and dies.
They are very similar, they have the the same valence electrons, and therefore have the potential to act very similarly.
Yes, being different is a big deal, but being roughly the same is also a big deal, since this can theoretically work with arsenate, but no one has yet theorized DNA based on uranium.

> DSMatticus wrote:Kaelik gonna kaelik. Whatcha gonna do?

The U.S. isn't a democracy and if you think it is, you are a rube.
That's libertarians for you - anarchists who want police protection from their slaves.
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Koumei
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Post by Koumei » Sun Dec 05, 2010 1:52 am

> Kaelik wrote: The reason arsenic is deadly is because it is so close to phosphorous that your body tries to use it as phosphorous, and fails, and dies.

Cool, I didn't know that.

> but no one has yet theorized DNA based on uranium.

Until NOW, that is.

> Count Arioch the 28th wrote:There is NOTHING better than lesbians. Lesbians make everything better.

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Maj
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### If You Like It, The You Should'a Put a Ring On It...

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Post by Maj » Tue Dec 07, 2010 3:16 am

Palmreaders weren't reading your palms...

> [url=http://www.dailymail.co.uk/health/article-1335155/What-length-index-finger-says-you.html wrote:Daily Mail[/url] {OK, Hands, Fingers, Testosterone}]What the length of your index finger says about you
> By Michael Hanlon
> Last updated at 8:48 AM on 3rd December 2010
> The idea that the shape of your hands indicates something profound about your sexual proclivities, the films you like, your athletic ability and your prowess on the stock market seems bizarre.
> And yet for many decades now, scientists have noticed an extraordinary link between the ratio of two digits on the hand — the ring and index fingers, known in scientists’ jargon as 2D and 4D — and a whole host of seemingly unrelated traits.
> Evidence is growing that this ‘digit ratio’, especially when applied to the right hand, is a fundamental indicator of sexuality, aggression and diseases suffered by men.
> Pointing the finger: Scientists have noticed a relationship between finger measurements and a host of unrelated traits
> This week, for example, strong evidence has emerged of a link between the ‘2D:4D finger ratio’ and a man’s likelihood of developing prostate cancer.
> Specifically, men whose index fingers are longer than their ring fingers are significantly less likely to develop the disease, according to scientists at the Institute Of Cancer Research.
> Working out your digit ratio is not simply a matter of looking at your hand and comparing the position of the tips of the fingers. You must measure the distance from the midpoint of the lowest crease at the base of the finger, on the palm side, to the very end of the fleshy tip (obviously the fingernail does not count!).
> A long index finger also correlates strongly with a lower risk of early heart disease and, in women, a higher risk of breast cancer and greater fertility.
> People with relatively long index fingers are also more likely to suffer from schizophrenia, allergies, eczema and hay fever.
> Young boys are more likely to be clingy and anxious than their low-ratio peers but also, ultimately, less attention-seeking and better behaved in school.
> While a long index finger is considered a more feminine hand — men who have them are more likely to be homosexual — a short index finger relative to the ring finger is a more masculine hand.
> It correlates with higher male fertility and sperm counts, higher levels of aggression and increased aptitude for both sport and music.
> Women who have this masculine finger pattern are more likely to be lesbians than those who don’t, and display higher levels of aggression — as well as enjoy greater professional success.
> The extraordinary thing is that these assertions are based on serious scientific evidence. It was as long ago as the late 1700s that people noticed that a greater proportion of men have shorter index fingers than do women.
> But it was not until the 1980s that scientists began to wonder if the digit ratio could be linked to more than simply being male or female.
> The first such study was conducted on women, and found a link between a short index finger — or more ‘masculine’ ratio — and female assertiveness. Since then, the floodgates have opened, showing links between the digit ratio and more than 100 psychological traits and propensities to various illnesses.
> So what is going on? Can finger length really determine your behaviour and vulnerability to certain diseases? The truth is that it is not finger-length per se that is having all these profound and dramatic effects.
> According to developmental biologist Dr John Manning, who has been analysing digit ratios for more than 20 years, this subtle difference in finger lengths is linked to a foetus’s exposure in the womb to sex hormones, notably the ‘masculine’ hormone testosterone.
> Put simply, more testosterone equals a greater chance of a more ‘masculine’ hand, i.e. one with a relatively short index finger.
> And it is this exposure to testosterone in the womb that has very profound effects on our behaviour and susceptibility to diseases.
> Studies have found that foetuses which have had a high exposure to testosterone — and have short index fingers — tend to be associated with an extroverted personality, a willingness to take risks, higher levels of aggression, stronger muscles and, interestingly (because musical ability is not commonly identified as particularly ‘masculine’), a much greater likelihood of playing an instrument well.
> Of course, the rules are not hard and fast, but people of both sexes with relatively short index fingers tend to be more sexually adventurous. They are more likely to experiment with drugs; they like watching violent movies and become addicted to alcohol more easily.
> People with short index fingers make better soldiers, engineers, speculators and chess players, and are better at solving problems such as crosswords. They are also more likely to be left handed.
> But short index fingers have also been linked to a higher chance of ending up in prison, being murdered, going mad — and in children higher rates of hyperactivity and attention deficit disorder.
> People with short index fingers may be poorer and find it harder to hold down a job. They suffer more infectious diseases and probably, on average, do not live as long.
> What is a mystery is why this relationship between testosterone levels in the womb and finger length evolved.
> What Professor Manning and others have noticed is that there may be an element of ‘sex selection’ going on with hands as well. Women often remark on ‘masculine’ hands and Manning speculates that this might be a subconscious assessment of the digit ratio.
> It may be, as Manning says, that a long index finger in men evolved for purely functional reasons. Many evolutionary anthropologists have speculated that, along with our ability to manipulate fire, one of the key reasons why humans became so successful was our ability to project our strength from a distance by using weapons such as the spear, slingshot and the bow-and-arrow.
> Scientists have found that a longer wedding ring finger can help increase accuracy when throwing objects. And men who could throw well killed more animals, ate better and thus made better mates. So they would have been preferred as partners by the available females, thus ensuring that the masculinity-long ring finger link was passed on.

What I want to know is what correlations are present when/if the ratio is 1:1.
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Username17
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Post by Username17 » Tue Dec 07, 2010 6:08 am

> Maj wrote:What I want to know is what correlations are present when/if the ratio is 1:1.

No idea. My own fingers are the same length.
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Maxus
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Post by Maxus » Tue Dec 07, 2010 8:41 am

My index finger is about an eighth of an inch shorter.
Also, I have funky-shaped hands. My palm is about four and a quarter inches wide across the widest point (above the thumb, from that web to the side), and four-and-a-quarter from the base of my bird finger to the crease where my wrist meets my hand.
Except my ring finger is basically three inches on the dot.
Geez, I've got a big palm and some little fingers. It sort of makes sense--my mom has small hands but my dad has hands like a welder's mitt. I just wouldn't expect mom-sized fingers on dad-sized palms.
He jumps like a damned dragoon, and charges into battle fighting rather insane monsters with little more than his bare hands and rather nasty spell effects conjured up solely through knowledge and the local plantlife. He unerringly knows where his goal lies, he breathes underwater and is untroubled by space travel, seems to have no limits to his actual endurance and favors killing his enemies by driving both boots square into their skull. His agility is unmatched, and his strength legendary, able to fling about a turtle shell big enough to contain a man with enough force to barrel down a near endless path of unfortunates.
--The horror of Mario
Zak S, Zak Smith, Dndwithpornstars, Zak Sabbath. He is a terrible person and a hack at writing and art. His cultural contributions are less than Justin Bieber's, and he's a shitmuffin. Go go gadget Googlebomb!
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Maj
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Post by Maj » Tue Dec 07, 2010 6:46 pm

Mine are the same length, too - as are my son's.
Random musing... Isn't baldness associated with testosterone levels? If that's the case, can finger length predict baldness?
My son makes me laugh. Maybe he'll make you laugh, too.
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Sashi
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Post by Sashi » Tue Dec 07, 2010 7:34 pm

Male pattern baldness is slightly linked to higher levels of testosterone (actually a derivative, DHT), but the primary cause is having hair follicles that responsd to DHT and die off. That's why men develop that horseshoe pattern: the follicles that are left don't respond in the same way.
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Kaelik
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Post by Kaelik » Wed Dec 08, 2010 10:27 pm

In further pissing all over Frank's happiness news:
Turns out, the general consensus of the scientific community is that the NASA articles evidence that arsenic was incorporated into the DNA is unconvincing.
Oops. I guess it's even less impressive then I thought.

> DSMatticus wrote:Kaelik gonna kaelik. Whatcha gonna do?

The U.S. isn't a democracy and if you think it is, you are a rube.
That's libertarians for you - anarchists who want police protection from their slaves.
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Username17
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Post by Username17 » Thu Dec 09, 2010 7:41 am

Well, you get some angry tirades like from Rosie Richardson, but I wouldn't call that any kind of scientific consensus. Her tirade is full of crap, is not internally consistent, and her suggestions of things that they absolutely should have done before publication are retarded and would not have shown anything.
Here is the bottom line:

- The organism survives and grows in an environment that is much higher in Arsenate than any other creature we have. Thus we know 100% that it does not do the thing that normal organisms do, which is to incorporate Arsenate into nucleotides (mostly ATP) and then die.
- GC and X-ray studies demonstrate the distinct lack of Arsenite, which means that it doesn't survive by an analogous method to what, for example, Arsenic resistant E. coli does, which is to reduce Arsenate to Arsenite and then excrete it before it can do too much genetic damage.
- mass spec and GC studies demonstrate that when you purify the DNA, that there is Arsenate there (though not very much - itself unsurprising since you purify the DNA into an aqueous environment, which tears Arsenic-containing DNA to pieces in minutes).
- The Synchrotron X-ray work demonstrates that the Arsenate is esterated into some ogragnic molecules, though not necessarily nucleotides.

So when Richardson goes off on a tirade about how they should have mixed Arsenate with E. coli and then run the same purifications to see if they got a negative result - she is either being a moron or is deliberately being obstructive. If you mix non-resistant E. coli with Arsenate, you will find Arsenate incorporated into nucleotides and it will fucking die. So they'd get the same results, but they'd have gotten them from dead microbes instead of live ones. If they used resistant microbes at a concentration that wouldn't kill them, they'd find a bunch of Arsenite, and thus the GC would have been totally different.
The available null hypothesis of this study is that the organism uses their weird vacuoles in some unknown way to sequester Arsenate in some new esterated organic molecule without reducing it to Arsenite and without incorporating it into their functional organic molecules. The null hypothesis is not that Arsenate contaminated the sample (they ran controls for that, although hilariously Richardson condemns these controls for being pointless - on the grounds that they only would have shown anything if the samples were contaminated!), it is not that the Arsenate is free floating and unincorporated (that never happens, and in any case the Arsenate is demonstrated to have been in an Ester by bond length analysis), and it is not that the organism uses a previously known system of Arsenic resistance (because the metabolites are not present).
Here are the dots:

- The chemical results are consistent with the incorporation of Arsenic into nucleotides.
- Arsenic is incorporated into nucleotides in normal cells.
- The chemical results are inconsistent with previously identified systems of sequestering and excluding Arsenic from inclusion into nucleotides.
- Purifying the DNA did not remove all of the Arsenate.
- Mass spectrometry proves that Arsenic was inside the cell and not excluded or secreted.

So Arseno-DNA is an answer that neatly draws a line through all of the data points. However, there are other answers that could also fit all of the data points. But remember: when detractors are jumping up and saying "Not necessarily!" they are really saying "There could still be an entirely different new and novel biochemical system in use that is preventing the nucleotides from having Arsenic incorporated into it while still leaving the Arsenic in a chemical form that that would normally be incorporated into nucleotides and forming bond lengths that are consistent with forming nucleotides!" Which when you say it out loud, sounds like kind of a stretch. But people are saying it because A) that is factually true, and B) an organism incorporating Arsenic into nucleotides and not dying is kind of a stretch too.
Still, the most likely answer is still the one PZ Myers proposed: where the vacuoles are filled with a non-aqueous environment that Arsenic infused nucleotides can be in without breaking. Richardson's rant comes off like a stream of consciousness temper tantrum. I am actually embarrassed for her having read her diatribe.
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Zinegata
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Post by Zinegata » Thu Dec 09, 2010 8:00 am

http://www.slate.com/id/2276919/
I think the issue is more than just one angry tirade by Richardson (which, upon review, is actually pretty high on signal).
It's more of a lot of scientists (including folks who did arsenic bacteria studies before) finding that the testing methodology left a lot to be desired and the conclusions had far more noise than signal.
Anyway, the article concludes that NASA is willing to hand out the poor microbes to other researchers so they can validate/disprove the paper.
Edit: Okay, Kaelik and I just posted the exact same link. Don't feel obligated to click on both.
Last edited by Zinegata on Thu Dec 09, 2010 8:11 am, edited 3 times in total.
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Kaelik
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Post by Kaelik » Thu Dec 09, 2010 8:03 am

If it were just one PhD biologist, I might be inclined to take your word, but when nearly every single one says that they have failed to present their case...
I'm going to assume that at least some of those PhD research biologists know more about the accompanying tests than you.

> DSMatticus wrote:Kaelik gonna kaelik. Whatcha gonna do?

The U.S. isn't a democracy and if you think it is, you are a rube.
That's libertarians for you - anarchists who want police protection from their slaves.
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Zinegata
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Post by Zinegata » Thu Dec 09, 2010 8:48 am

> FrankTrollman wrote:If you mix non-resistant E. coli with Arsenate, you will find Arsenate incorporated into nucleotides and it will fucking die.

I actually took a look at the Richardson doc again for a careful reading, and bluntly, I think Frank's pretty wrong on this one.
Apparently, NASA just dumped the bacteria in an arsenic solution, took them out of it, didn't wash them, dumped them into a mass spectrometer, and said "Woo! We found arsenic!".
Again, think about that carefully.
* They dumped something into an arsenic solution.
* Took the stuff out.
* Didn't wash the stuff.
* Then the mass spectrometer said "It has arsenic!"
That's why Richardson is calling for dumping other bacteria into the same solution. The "regular" bacteria are the control group to see if the methodology actually works at all.
And yes, it's totally valid to have a control group like this. You can't just invent new methodologies without demonstrating that it works.
Because if turns out that E Coli survive (or even thrive) in the solution (which apparently isn't 100% arsenic and has some salts that could contain phosphates - so E Coli won't necessarily die), and then the mass spec has the same results, then NASA is indeed guilty of some exceedingly retarded science.
Last edited by Zinegata on Thu Dec 09, 2010 8:52 am, edited 2 times in total.
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Username17
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Post by Username17 » Thu Dec 09, 2010 9:42 am

> Kaelik wrote:If it were just one PhD biologist, I might be inclined to take your word, but when nearly every single one says that they have failed to present their case...
> I'm going to assume that at least some of those PhD research biologists know more about the accompanying tests than you.

The first half of that article was rantings by and about Richardson, whose tirades are so nonsensical that someone needs to call her a proctologist for her case of severe butthurt. The rest is clipped and cherry picked. As for a critique that I am genuinely interested in, I'll look at the samplings from Here over something on Slate any day. Again, Richardson is getting more time than she deserves, but the section from the X-Ray specialist is genuinely interesting:

> To learn more about arsenic's chemical environment, the team performed X-ray studies. Extended X-ray absorption fine structure spectroscopy, one technique the team used, can reveal arsenic's oxidation state and average distances of any bonds it's making, explains Keith O. Hodgson at Stanford University, an expert on X-ray techniques. In its report, the team "looks at the average distances, they make comparisons, and they conclude that it's a reasonable assumption that arsenic could be part of a DNA backbone," Hodgson says. However, "there's no direct proof in the X-ray absorption data that the arsenic is a part of the DNA backbone."
> The team "has not conclusively proven, in my view, that arsenic has been incorporated into DNA," Hodgson says. It'll take studies on isolated molecules with techniques such as X-ray crystallography or NMR to unambiguously prove that, he says.

That's relevant and interesting. Richardson's tirade is neither relevant nor interesting, because her suggestion of:

> Richardson wrote:They should have mixed pregrown E. coli or other cells with the arsenate supplemented medium and then done the same purifications.

indicates that she isn't thinking clearly about this at all, and that her hate parade is largely powered by sour grapes. Because that thing she just said? That's fucking retarded. Because when you mix Arsenate medium with normal cells you do get Arsenate in nucleotides!
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Kaelik
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Post by Kaelik » Thu Dec 09, 2010 10:00 am

That's great Frank, but I wasn't talking about Richardson. Because Richardson is one person, who's article was already published when we were discussing this last time, but I didn't bring it up then, because one person could easily be a retard. But when literally everyone says that there isn't enough evidence to support the assertion that it's part of DNA, and some people explicitly say that the tests they did indicate it couldn't have even been part of the DNA, I'm willing to believe "every single expert that has posted on the study" over "the people who did the study." I'm not saying it's impossible. I'm not even saying it's not true. I'm just saying that apparently the study doesn't sufficiently support the assertion that it is true.

> DSMatticus wrote:Kaelik gonna kaelik. Whatcha gonna do?

The U.S. isn't a democracy and if you think it is, you are a rube.
That's libertarians for you - anarchists who want police protection from their slaves.
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Zinegata
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Post by Zinegata » Thu Dec 09, 2010 10:19 am

> FrankTrollman wrote: That's relevant and interesting. Richardson's tirade is neither relevant nor interesting, because her suggestion of:

> > Richardson wrote:They should have mixed pregrown E. coli or other cells with the arsenate supplemented medium and then done the same purifications.

> indicates that she isn't thinking clearly about this at all, and that her hate parade is largely powered by sour grapes. Because that thing she just said? That's fucking retarded. Because when you mix Arsenate medium with normal cells you do get Arsenate in nucleotides!
> -Username17

I'm almost tempted to post Frank's own sour graping tirade to one of these journals just to see how much weight it actually holds.
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Username17
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Post by Username17 » Thu Dec 09, 2010 11:16 am

> Kaelik wrote:That's great Frank, but I wasn't talking about Richardson. Because Richardson is one person, who's article was already published when we were discussing this last time, but I didn't bring it up then, because one person could easily be a retard. But when literally everyone says that there isn't enough evidence to support the assertion that it's part of DNA, and some people explicitly say that the tests they did indicate it couldn't have even been part of the DNA, I'm willing to believe "every single expert that has posted on the study" over "the people who did the study." I'm not saying it's impossible. I'm not even saying it's not true. I'm just saying that apparently the study doesn't sufficiently support the assertion that it is true.

If literally everyone was saying that, sure. But Here's a followup article by the person who wrote the Slate Article you linked:

> A lot of people are interested in my Slate story yesterday on the arsenic aliens. It’s still the most-read story of the site at the moment, Slashdot and others have linked to it, and I’m doing some more radio and maybe other media (details to come).
> I think that what has gotten so much attention to the story is just how many scientists had such critical things to say. The verdict was not unanimous, but the majority was large.

Here's the thing though: "critical" responses run the range from "Blargh! Bad Science!" (Richardson) to "the team has not conclusively proven that the Arsenate is incorporated into the DNA" (Hodgson). The first kind of "critical" is a negative review, but the second kind of "critical" is not.
The team did not show that there was definitively Arsenic in the DNA of living microbes. They really honestly didn't show that. What they showed was results consistent with there being Arsenic in the DNA of living microbes. And inconsistent with results that would have been shown by exposing previously cataloged microbes (Arsenic resistant or not) to high levels of Arsenate.
Yes, there could be other explanations, but providing that kind of criticism is what science is all about.
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Zinegata
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Post by Zinegata » Fri Dec 10, 2010 3:14 am

Two things:
1) I did just post in the blog asking Frank's question, because Rosie seems to be answering people's concerns without flying into rages.
2) It's actually Rosie Redfield, not Richardson.
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Post by CatharzGodfoot » Fri Jan 07, 2011 4:42 am

Anti-vaccination Asshole Gets Smacked Down by BMJ
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Post by mean_liar » Fri Jan 07, 2011 6:13 pm

Your job doesn't suck as much as you think it does, and some people would do anything to keep making six figures.[/url]
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Post by Prak » Mon Jan 10, 2011 5:04 pm

So, apparently, some researchers are suggesting that dolphins are intelligent enough to qualify as "non-human persons" for moral standing in interactions.
Times Online UK Article
I find it interesting that the first species we extend personhood to may be one of the more rapey.
Cuz apparently I gotta break this down for you dense motherfuckers- I'm trans feminine nonbinary. My pronouns are they/them.

> Winnah wrote:No, No. 'Prak' is actually a Thri Kreen impersonating a human and roleplaying himself as a D&D character. All hail our hidden insect overlords.

> FrankTrollman wrote:In Soviet Russia, cosmic horror is the default state.
> You should gain sanity for finding out that the problems of a region are because there are fucking monsters there.

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