I don't normally go for techno...

...but this is pretty awesome:



Nope, still not back, but at least I'm trying to give y'all some love in the meantime.

...what?

I don't even know what to do with this. Really:



Granted, the attempt to outline the message at the end is worthwhile, encourages people to be concerned with the less fortunate, and does show a degree of self-awareness, so it isn't all bad. But it also comes both after they've tried to execute a pinata with firearms, and from a guy who is wearing a shirt that implies that religious tolerance is bad. So... yeah. Mixed message, you is doing it right.

Hang around for the credits, though- they're worth it.

Happy holidays, folks.

Beautifully said.

Okay, so, yes, yesterday I said I was taking a break. I still am. But this, from the always excellent xkcd needed to be shared.



Couldn't have said it better myself.

A little too much spirit.

So, here's a question: Is anyone else bothered that some students at Liberty University changed this into this?



And on that note... I'm taking a leave of absence from the blog for my holiday travels. Updates will be sporadic and random until my eventual return. Try not to miss me too much!

A message for the holidays...

In an unusual step, I've decided to use the blog to help promote a religious message. Enjoy!



Hell, it's better than Scientology.*



* Though, I have to admit, I don't really find Scientology to be crazier than any other young religion.

As a side note: Yes, I am busy grading right now. Why do you ask?

"Deep Thought," with Richard Dawkins

I don't always agree with Dawkins, but this is just fun:



Honestly? The laugh-track makes it.

And as an unrelated side note: I freaking love this comic.

Mary Tocco Redux

So a number of years ago I wrote a post detailing my reactions to an anti-vaccine lecture delivered by Mary Tocco,* an "independent vaccine researcher," whose primary qualification appears to be that she's the business manager for a chiropractic clinic.** As you might guess, I found her lecture to be amazingly unconvincing and rather poorly informed. As such, in my view, while I absolutely believe that Ms. Tocco is acting in good faith and doing what she thinks is right, I am equally convinced that she is wrong. That's my opinion, and you're free to disagree with it, but I spent a lot of time watching her lecture and checking up on its claims, so I feel pretty secure in my opinion.

Now, interestingly enough, despite the age of that post, it still brings me a lot of traffic. In fact, "Mary Tocco" is a search term that seems to pretty regularly bring people by. I'm okay with that, not least because in the first few pages of hits on google I seem to be one of the only pro-vaccine sites. So, basically, I see it as providing some small amount of balance. Recently, however, one such visitor appeared here after having actually seen one of Tocco's more recent talks, and from the description,*** it sounds like Tocco is on about some strange stuff. And by "strange" I mean the following:

-Tocco is apparently now claiming that Bill Gates is trying to kill over one billion people in order to improve the environment. Moreover, she claims that he's trying to do it by donating $6 billion to vaccines for third world countries. And she uses this video**** as "evidence":



I think it's pretty clear from context that what Gates is actually sketching is the simple notion that as people's health situation improves and becomes more reliable, birth rates tend to drop. So, basically, making people healthy- using vaccines, etc,- is a good thing for the planet in the long run. But, what Tocco is apparently arguing now is that this is Gates admitting that vaccines are dangerous, and he's trying to poison the third world. Yikes.

-Staying on the Bill Gates angle, she is apparently also arguing that Gates' father is the reason we have abortion in the United States. Oh, yeah, and she has some kind of X-Files-ish conspiracy theory wherein the world is run by a small collection of rich people (okay, so that's sort of true, but not in the way Mary means) including the Clintons, Oprah, the Gates family and "our current president." Right, sure. Always a good sign.

-Apparently she's now also on about chemtrails, which is a level of crazy that's difficult to hold in one's mind without losing one's sanity.***** Apparently this bit concluded with her asserting that people should "LOOK IT UP!" and that chemtrails are "REAL! AND PROVEN!" She then added that, "This isn't conspiracy theory stuff, people. There is a movie coming out about it!" Indeed, anytime there's a movie about something it must be true, which, coincidentally, is why I refuse to buy a yellow car. You just never know when they'll turn out to be alien robots in disguise.

-She's still saying mean things about Paul Offit, including his claim that babies could handle up to 10,000 vaccines at one time. I'm fairly sure he's not suggesting that they could handle that many shots at once, but I digress. This isn't new, though- she's disliked Offit for some time- but it's interesting that she hasn't changed her mind.

-Interestingly, she seems to be defending Andrew Wakefield, arguing that the whole reason he was discredited is because of a recent study on vaccinating primates. You know, rather than because of blatant ethical and scientific problems. We've talked about Dr. Wakefield before, so I'll decline to go off on that again just now. See also here.

-Mary is also invoking some funny logic about VAERS, the Vaccine Adverse Event Reporting System. For those who don't know, if something happens to you- anything, really- soon after you received a vaccine, that event may be reported to VAERS. Importantly, however, reports to VAERS can be- and often are- unverified, and there's no confirmation that the event is at all due to the vaccination. Put differently, it is somewhat dependent on classic post hoc ergo propter hoc logic, and all the inaccuracies that implies. So, reports to VAERS do NOT equal confirmed problems stemming from vaccines. Rather, reports to VAERS are efforts to make sure that any previously unknown problems from vaccines can be detected, and the threshold for inclusion is ridiculously low out of an abundance of caution. In any case, and keeping all this in mind, she apparently claims that because "only about 10% of doctors report vaccine issues via VAERS" the true number of adverse reactions is nine times larger (i.e. accounting for the 90% of doctors who don't report anything). Obviously, this logic suffers from the assumption that all doctors see the same rate of adverse events, but more importantly it essentially assumes that all doctors who don't report adverse events are suppressing the reports, rather than simply not observing any adverse events. And when you make an assumption like that, what kind of proof could ever convince you otherwise?

Fortunately for us all, my reader seems to think that as this littany of madness continued to pour forth, most of her audience became more and more convinced that she wasn't as in command of the facts as she claimed. This makes me hope that, perhaps, some of the anti-vaccine hysteria may be self-limiting. But, even if it's not, it's both terrifying, and inescapably funny.

But mostly terrifying.


* Her website appears to be down lately, but you can see a brief bio here.

** I mention this because being the business manager for a surgeon doesn't qualify you to take a scalpel to anyone, so I fail to see how this particular qualification should make us value her advice about vaccines.

*** It goes without saying that I cannot confirm what my reader has told me, and as such I make no guarantee as to its accuracy.

**** I find it more than a little disquieting that the person who posted this video quoted Conservapedia's article on fair use in the description of the video. Leaving aside the issue of whether or not Conservapedia understands fair use (they don't), I gotta say, anyone who uses Conservapedia as a source in anything other than jest is probably not playing with a full deck.

***** For those of you who are wondering: yeah, I pretty much feel that some conspiracy theories are on a par with a Lovecraftian Elder God. One cannot behold them full-on without slipping the bonds of mere sanity.

As a final note: Special thanks to my unnamed correspondent, who was kind enough to send me several long e-mails on the subject.

I can't believe anyone didn't know this already.

As we approach the holidays, I just want to share a quick public service tip. When putting on a nativity play at your local church it is never a good idea- no matter how awesome it might sound at the planning session- to use a live camel:



And before you feel guilty for laughing, nobody- not even the camel- was harmed. Likewise, a motorcycle is right out:



That is all.

UPDATE: Camel video is fixed... for NOW.

Way to prove your opponent's point.

From time to time I teach a class wherein my students and I discuss a number of theories dealing with the determinants of economic success. These sorts of theories, and their supporting articles, are often interesting but, at the same time, frequently approach the world from the perspective of an educated individual who is trying to maximize his or her utility. So, for example, we might read extracts from Ron Burt's "Structural Holes," which has some great stuff to say, but seems more like advice to MBAs than anything else. What I often think is lacking in such discussions, however, is an examination of what things are like for those who don't have a lot of education and options. You know, the people who lack the freedom of choice that much of the academic literature on strategic action presumes. And this is where Barbara Ehrenreich comes in.

See, Ehrenreich wrote a book called "Nickel and Dimed," which details her efforts to live as a member of the working poor for three months. Now, it goes without saying that her "experiment" lacks the sort of rigor that good social science demands, and there are huge, gaping flaws in her reasoning and argumentation that make me flinch every time I read the book. At the same time, it's an evocative look at what life can be like when you don't start out with advantages and assets, and provides a useful counterpoint to academic work that seems more interested in how executives can become even more successful, rather than those at the bottom of the income spectrum. And realistically, even (perhaps especially) when I have students who violently disagree with Ehrenreich's arguments, it turns out to be an interesting reading.

Now, Ehrenreich is essentially an atheist, but at one point in the book she goes to a tent revival- in no small part because it's a type of entertainment that she can afford. And while there, after noticing all the haranguing for people to donate to the church/traveling religious carnival, she thinks about the message that the preachers are pitching and how it differs in some ways from what Jesus might have said. Particularly, if you check out pages 68 and 69 in the edition available from Google Books, you'll find this:

The preaching goes on, interrupted with dutiful "amens." It would be nice if someone would read this sad-eyed crowd the Sermon on the Mount, accompanied by a rousing commentary on income inequality and the need for a hike in the minimum wage. But Jesus makes his appearance here only as a corpse; the living man, the wine-guzzling vagrant and precocious socialist, is never once mentioned, nor anything he ever had to say. Christ crucified rules, and it may be that the true business of modern Christianity is to crucify him again and again so that he can never get a word out of his mouth.

The interesting thing about this passage is that Ehrenreich isn't insulting Christ or Christianity per se, but rather a practice of it that ignores Jesus' deep concern for the poor and less fortunate. In other words, she's making an admittedly flowery argument that one can't be Christian and holy and yet unconcerned with the deep and serious economic inequalities that characterize American society. It's a provocative point and my students and I often have an interesting time discussing it. Often one or more students ask whether anyone is really like this, whether anyone can consider themselves a devout and committed Christian and yet miss the essential need for concern for the poor.

And now, when that comes up, I get to mention this:

A New Hampshire couple has pulled their son out of his local high school after the teen was assigned a book that refers to Jesus Christ as a "wine-guzzling vagrant and precocious socialist."

Aimee Taylor says her oldest son, 16-year-old Jordan Henderson, was required to read "Nickel and Dimed: On (Not) Getting By in America," this fall for Bedford High School's personal finance class.

The book is a first-person account of author Barbara Ehrenreich's attempts to make ends meet while working minimum wage jobs in Florida, Maine and Minnesota.

...

Taylor asked her son to show her what was so bad about the book and after he pointed out a few controversial excerpts she decided to read it in full.

"I finished the book that night, I could not put it down because I was just mortified by the take on this book as well as the language, and the Jesus Christian bashing was unbelievable to me, and that it was in our school was just amazing to me," she said.

...

Assistant Superintendent Chip McGee told the Union Leader that the district still plans to evaluate the personal finance class to see if "Nickel and Dimed" can be replaced with a less controversial book and will require teachers to notify parents from now on before assigning the book and offer an alternative should they object.

But Taylor says that's not enough.

"We've eliminated Christmas, we've eliminated all these things because we don't want to step on anyone's toes but here we're going to hand out this book? … This is anti-God, anti-religion, it's racial, I mean it crosses a wide spectrum of very touchy and very insulting issues to most human beings and I think that even with a parental consent it's not enough. They need to boot that book out of there," Taylor said.

The Taylors, who have since begun home schooling their son at his request, plan to attend the Dec. 13 Bedford School Board meeting to ask that the book be yanked entirely so taxpayers are no longer forced to pay for it. They have five other children, including a freshman at Bedford High School.

And all this is just amazing to me. First off, because it's not anti-Christian and there isn't any "Jesus Christian bashing" therein. No, rather, what's going on is that Ehrenreich is suggesting that Jesus had good ideas but that some modern Christians are not doing so well at following them. That is complimentary to Christ, but perhaps less so to Christianity. Second... racial? Is Christian a race now? Granted, Ehrenreich does talk about racial issues a bit, but talking about race isn't necessarily a bad thing. Or, put differently, you can talk about race without being racist. Granted, I think 16 may be a bit young to be reading "Nickel and Dimed," but, that said, by the time I was 16 I had read things that were way, way more advanced and risque than a simple book about income inequality.

But in the end, the thing I find most amazing is this: the student, and the parents, noticed the suggestion that Jesus was a wine-guzzling vagrant, but completely missed the substance of what she was saying. More importantly, they seem to have missed the substance of what Jesus was saying. And honestly, there's no better way to support Ehrenreich's point than that.

Arsenic again

Just in case you weren't tired of the arsenic-based life story from a while back,* we now have some arsenic-based controversy. Specifically, a number of scientists who seem to think that the discovery was... well... bogus:

On Thursday, Dec. 2, Rosie Redfield sat down to read a new paper called "A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus." Despite its innocuous title, the paper had great ambitions. Every living thing that scientists have ever studied uses phosphorus to build the backbone of its DNA. In the new paper, NASA-funded scientists described a microbe that could use arsenic instead. If the authors of the paper were right, we would have to expand our notions of what forms life can take.

...

As soon as Redfield started to read the paper, she was shocked. "I was outraged at how bad the science was," she told me.

Redfield blogged a scathing attack on Saturday. Over the weekend, a few other scientists took to the Internet as well. Was this merely a case of a few isolated cranks? To find out, I reached out to a dozen experts on Monday. Almost unanimously, they think the NASA scientists have failed to make their case. "It would be really cool if such a bug existed," said San Diego State University's Forest Rohwer, a microbiologist who looks for new species of bacteria and viruses in coral reefs. But, he added, "none of the arguments are very convincing on their own." That was about as positive as the critics could get. "This paper should not have been published," said Shelley Copley of the University of Colorado.

None of the scientists I spoke to ruled out the possibility that such weird bacteria might exist. Indeed, some of them were co-authors of a 2007 report for the National Academies of Sciences on alien life that called for research into, among other things, arsenic-based biology. But almost to a person, they felt that the NASA team had failed to take some basic precautions to avoid misleading results.

The rest of the article is worth reading, although I wouldn't read too much into this yet. Scientists love to disagree- I mean, seriously, we can argue about damned near anything. So, as a result, the presence of controversy surrounding such a new and radical finding is only to be expected. By the same token, however, new and radical results are often not everything we think or hope they will be. So, there's both a good chance that the critics are right, and a good chance that the critics are wrong. Only time, and further study, will reveal the truth. But, then, that's the beauty of the scientific approach: all arguments are, eventually, settled by the data.**

Needless to say, the science reporters over at the "Trustworthy" encyclopedia are all over a story of this magnitude, and with their usual flair for the dramatic to boot:



Or, in plain text:

"This Paper Should Not Have Been Published": NASA claims new discovery of arsenic-based life proves the possibility of life on other planets. Others are so critical that they say that the paper should not have been published. The authors are distributing press releases and doing friendly interviews, but refusing to address any of the criticisms because they say that would be inappropriate. There is a lot of gullibility for anything promoting extraterrestrial life.

If you're wondering why Conservapedia of all groups is so down on NASA over this, you should check out their page on extraterrestrial life, which has on a number of occasions dismissed arguments for such critters as unChristian. Oh, and UFO sightings are actually evidence for demonic visitation:



This is not to say that I believe we're being visited by aliens, but dismissing UFOs by saying, "That's implausible; we're really being tormented by demons," is a response so ludicrous it boggles the mind.

So, hey, at least the maybe-arsenic-based microbes are keeping everyone busy, right?


* I know I'm not. That was some cool shit right there.

** Although careers may be destroyed and lives ruined in the interim but, hey, there you go.

Apparently the evil secular conspiracy fell down on this one

I sometimes see people argue that the U.S. has been taken over by secularism. Granted, these people are often at Conservapedia, and thus arguably crazy, but that isn't the point. The point is that I find such arguments completely absurd, given the immense amount of deference that religion receives in the U.S., and this incident is just a case in point:



So, just to reiterate, a father who happens to be a veteran apparently lost custody of his children because he is an agnostic.* Well, not necessarily because he's an agnostic, but at least because he isn't Christian. Now, it is possible to make the argument that this isn't a discriminatory decision. From the article:

Madison County Superior Court 2 Commissioner George G. Pancol told The Herald Bulletin that his decision was based on the children's best interest and that Indiana law requires courts to determine whether divorced parents can agree on education, religious upbringing and other issues.

"The case law requires me to make a decision whether or not the parties can communicate effectively about these matters and others concerning their children," he said. "I have never rendered a decision concerning custody on the basis of one of the parents' religious beliefs."

Leaving aside the question of whether that aspect of the law is just- or even constitutional- I think it's worth pointing out that in a case of disagreement over religion, presumably the courts may have to choose one way or the other.** So it's interesting to note that when disagreement appears, it is clearly the agnostic who is "in the wrong."

And honestly the saddest thing is that this doesn't surprise me at all.


* I'll note here that I obviously don't have access to the court documents, and so acknowledge that there may be some other reason why he had his custody reduced.

** This choice is interesting to me, as a side note, because it creates a mechanism through which the state can judge between different religions. So, for example, what if the disagreement was between a devout Jew and a devout Christian? Whose faith wins then, eh?

I did not know this.

Ever heard of Hedy Lamarr? If you're a cinema buff, the answer is almost certainly "yes," since Lamarr was quite the success in Hollywood back in the day, not to mention a popular pinup in World War II:



Rawr!

What you may not realize, however, is that Lamarr was more than just a starlet- she was also a successful inventor who pioneered, among other things, spread spectrum communications technologies:

Perhaps it was those restrictions that made Hedy an inventor, or perhaps it was just her intellectual curiosity. Either way, Hedy was inventing things, big and small, right up until she died. There were many utilitarian, small inventions, like a box of tissues that had its own pocket to store used tissues in. And then there was the showstopper: With musician George Antheil, she patented the 'secret communication system' in 1942. The frequency hopping, spread-spectrum invention allowed its users to manipulate radio frequencies. The earliest one used a piano roll to guide the hopping between frequencies. In World War II, it was used to keep torpedoes from being detected or manipulated by enemy forces.

Decades later on, the wide spectrum aspect of the invention formed the basis for the communications boom. Cell phones, Wi-Fi, the modern world as we know it, it all flowed from the original patent that Hedy came up with to fight Nazis.

Pretty neat, eh?

You don't even want to know what they do to contractions

Dear Students,

I realize that we're approaching the end of the semester and I, like all of you, am very tired. Indeed, I feel like a dehydrated man crawling painfully through a desert lusting after the cool, refreshing waters of yon oasis. Granted, yon oasis is, in my case, a mirage since the end of the semester is always punctuated by a hurricane of grading, but I digress. My point is that I understand and, indeed, sympathize with your exhaustion. All that having been said, there is a small matter that we really need to discuss- a problem that I have noticed several times over the course of the semester. A problem that I have actually explicitly addressed with the class as a whole and with several of the more egregious offenders in person. That problem is simply this:

The words that you use to describe the reasoning process? Yeah- they do not mean what you think that they do.

Let's start with the word "assume". To assume does not mean "To make an ass out of you and me" as many hackneyed grammar teachers might quip, but rather is to take something for granted, as if it were true, based upon presupposition without the preponderance of facts. In other words, an assumption can be thought of as something we accept as given, even though we can't prove it, so that we can move our logical reasoning forward. Assumptions are a necessary part of logical reasoning- for example, I assume that I am communicating with someone just now rather than simply rambling in my own demented fever dream*- but nevertheless, we must always keep in mind their status as unproven beliefs.

Next, let's consider the word "conclude". A conclusion is a logical consequence of some thing or things that we know to be true. So, for example, if the statement "All frogs are green" were true,** then the statement "Kermit the Frog is green" would have to also be true. In the context of a social science or, indeed, any science, conclusions are generally based on evidence- so, in other words, rather than deriving from formal logical statements, our conclusions reflect the quality and nature of the empirical evidence we have produced. The critical point here is that, unlike an assumption, a conclusion is something we take to be true based upon explicit evidence. Thus, in this case a conclusion might be something like, "Given that we found using a large, nationally-representative data set that female incomes tend to be lower than male even while controlling for a variety of confounding factors, we conclude that gender plays a role in determining compensation." Note than a conclusion can be erroneous while, yet, remaining a conclusion.

Finally, let's consider the term "inference". To "infer" something is to make a guess based on the balance of evidence, but regarding a subject about which you do not have direct evidence. So, in other words, an inference is sort of mid-way between an assumption and a conclusion- it's supported by some evidence, and therefore isn't an assumption, but the evidence doesn't support it directly, and thus it is not a conclusion. An example of an inference is something like, "One of my students was doing consistently poorly and then, before the last test, came to tell me that he needed to take it late because his grandmother had died. Given my knowledge of the Dead Grandmother/Exam Syndrome, I infer that this student is most likely lying to me." I don't know that the student is lying to me- my evidence doesn't speak directly to that point- but I have evidence that leads me to infer that he most likely is.

I bring all this up because you are driving me to madness by insisting upon writing things like, "Based on her evidence Bethany Bryson assumed that people avoid liking the musical styles of lower-status individuals." And you see that's just not right- if it's based on evidence, it's not an assumption. It might be a conclusion, or it might be an inference- depending on the nature of the evidence and the claim- but it isn't an assumption. This may seem like a trivial matter, but these terms denote very different parts of the reasoning process and very different levels of certaintly. And, frankly, it distresses me more than a little that college students- even advanced college students- cannot discern the difference between a claim that is taken to be true, despite a lack of evidence, in order to facilitate reasoning and a claim that has strong evidentiary support. I realize that a variety of media outlets seem almost to be conspiring to stamp out good, rigorous thinking,*** but that is no excuse. And frankly, every time I read a paper where someone says "assume" when they mean "conclude," or "infer" where they mean "assume," my train of thought spectacularly derails, killing masses of helpless neurons.

Please, please stop.

All the best,

Drek the Uninteresting


* Given the quality of my writing, the fever dream option may be far more parsimonious.

** In point of fact, all frogs are NOT green, but give me a break here.

*** I'll decline to specify whom I am referring to here. Fill in your own preferred villain at your leisure.

As a side note: No students were directly quoted in this post.

More on arsenic...

Well, my totally awesome friend from yesterday's post is back with some analysis, and I thought y'all might be interested. Enjoy!

Hello again all. Just a quick update with my reaction to what today's NASA press conference actually said. Due to my sometimes-exceptionally-poor time management skills, I didn't get to see the press conference myself, but I've been following the news coverage, and I skimmed the Science paper announcing the results.

To summarize: the researchers collected bacteria from mud at the bottom of Mono Lake and brought them into the lab. They put them into petri dishes containing arsenic but no phosphorous, then transferred the microbes to new petri dishes until the phosphorous level was down to nearly zero. The bacteria thrived. When the researchers looked at important biological molecules in the bacteria (DNA and ATP), they saw that where you would normally find phosphorous, there was arsenic. This is the first time anyone has found an organism where one of the six major biological elements ("CHNOPS") were swapped out for another element. It shows that the possibilities for life are not as narrow as we previously thought.

Professional science writers have explained it more clearly than I just did. Here are a few examples from the Washington Post, the New York Times, the BBC, Wired (with an awesome analogy in the lede), LiveScience, and, of course, Phil Plait's Bad Astronomy (which is actually not bad).

Places you might not think to look for science articles, which shows how widely-covered this result include: Fox News, and hyperbolic as usual, Al-Jazeera (with video), and The Sun.

My quick-hit reactions:

1a) Of the possibilities I mentioned, #2 comes closest. It's different than I expected, and slightly less impressive. I had expected them to announce the discovery of life that incorporates arsenic in its DNA/RNA/ATP in the wild. Instead, it was a lab-based discovery.

1b) If I'm understanding correctly, the arsenic-incorporating bacteria evolved from the wild bacteria through artificial selection introduced by the researchers reducing the amount of phosphorous in their environment and increasing the amount of arsenic. Evolution = awesome.

1c) But that evolution likely would have never happened without the "head start" of the bacteria living in an arsenic-rich environment in Mono Lake.

2a) It's not accurate to say this is "arsenic-based life." Rather, it's life that looks biochemically just like the rest of life on Earth, just with most of the phosphorous atoms switched out for arsenic.

2b) Therefore, my possibility #3 is not true. These bacteria are a branch of the same tree of life as everything else is, and have already been placed into a Family in the Linnean classification system. We're still waiting for a genus-species name for them (as in Canis familiaris or Alces alces). May I suggest Horta californius?

3a) All that said, this is the closest example yet to "life as we don't know it." It's a fairly small substitution from the rest of life, but the shift from "life can only exist if it contains mostly the CHNOPS elements" to "hey, that could totally be CHNOAsS instead" is a profound one. (Although CHNOAsS would be a particularly unfortunate acronym.) If As can substitute for P, what else could be switched out?

3b) ...although, it should be noted that the bacteria still prefer "eating" phosphorous to eating arsenic. If you put phosphorous in the petri dish, they'll gobble up all the phosphorous and switch to arsenic only when they have to.

4) Switching carbon for silicon would be harder, because carbon and silicon are chemically more different than arsenic and phosphorous.

5) Picking up on one of the things a friend of mine wrote, an obvious implication is that these bacteria would be a great way to clean up arsenic spills. Consider that arsenic is a deadly poison to us, but is actually food to the bacteria. It's as if some actual intelligent aliens from another planet were looking for a species to clean up a highly toxic pecan pie spill. I'd totally volunteer for that job.

6a) As for the astrobiology implications, another of my buddies had another very insightful comment. He says: I was just telling [someone] something the other night actually, my long-time complaint about "what's this 'planets that can support life' business anyway?  Life evolves to the environment, not the other way around."  And here we are!

6b) That's obvious when you think about it, and it suggests that life could be even more common in the universe than we ever thought.

Science may make the research paper available to the public, outside their subscription firewall, tomorrow. There are actually two papers, both short. One is the full research report, written by the team and intended for biochemists. The other is a more journalistic article, written by a science writer for all practicing scientists, including non-biologists.

Lastly, I should have mentioned earlier, please forward this or my previous E-mail to any family, friends, co-workers, drinking buddies, or frenemies that you think might be interested. The more people hear about cool science, the better.

Actually, someone's thoughtful forwarding of yesterday's E-mail led to a friend-of-a-friend E-mailing me, which means I got to meet a cool person also. They also told me that their kidneys were stolen by a man with a hook for a hand that called in sick to work on 9/11. (That last part is a joke - see the third paragraph of this article).

So that turned into another very long, very geeky E-mail. Hope you enjoyed reading it at least 1/42 as much as I enjoyed writing it. :)

-Drek's awesome friend, whose DNA still contains boring old phosphorous

Boring or not, we're all just as happy he's around! As for me, I'll just note that this discovery is so cool, it made xkcd:



Now that's awesome.

Too cool not to share...

So I hang out with some pretty neat people and one of them sent me something that, I think, many of you would be interested in. And so, without further interruption, take it away Drek's friend:

Hi friends-interested-in-space,

I don't normally send mass E-mails, but something very cool is happening tomorrow (Wednesday) that I wanted to share with all of you. NASA is holding a press conference at 2 PM Thursday to announce something that, in their words, "will impact the search for evidence of extraterrestrial life."

The press conference will be airing live on NASA TV here.

If you're able to multitask at work, this could be a cool thing to watch. If not, it should be all over the science news by Thursday evening.

Internet rumors that they are announcing the discovery of life elsewhere in the solar system are sadly not true. But NASA has announced the lineup of scientists speaking at the press conference, and some Google sleuthing by me and other space geeks suggests what the discovery will be. Most likely, scientists studying a lake in the California desert have discovered a type of bacteria that uses arsenic instead of phosphorous in its biochemistry. More information on the research is available via the London Times, as well as via a paper by one of the scientists on the panel, Felisa Wolfe-Simon of the United States Geological Survey (USGS), describing the context of the research. This will give all the technical details if you have a background in biochemistry.

Oh, and here is the lake.

So that is the context, but there is still some suspense. The suspense is - how exactly does this bacteria use arsenic? And what does this mean for the search for extraterrestrial life? There are three possibilities, ranging from "hey, that's really cool" to "OMG, that totally revolutionizes our understanding of life."

Remember that arsenic and phosphorous are chemically very similar, but phosphorous is a key ingredient of every cell in the body, and arsenic is a deadly poison.* This leads to the three possibilities:

1) These bacteria are similar to, and evolved from, other bacteria; but have evolved the ability to use arsenic to keep themselves alive. This would merit a "hey, that's really cool," because something that's a deadly poison to everything else on Earth would be food to these creatures. But that's not the really exciting possibility...

2) It's also possible that, rather than just metabolizing arsenic, these bacteria are in a real sense made of arsenic. Meaning that, in molecules where other organisms (from bacteria to humans) have phosphorous, these bacteria would have arsenic.*** That would make them different from every other species on the planet.

3) If they do announce possibility (2), there could be something even more exciting in store. Evolution can produce a wide variety of adaptations, but it's hard to imagine evolution making such a basic structural change through natural selection based on mutations. That means that these bacteria could have formed from the inorganic primordial ooze independently from everything else on the planet - a second "creation event," if you like. Instead of being our evolutionary "cousins," they would be strangers. But even if this is objectively true, how would we prove it?

So what does this mean for astrobiology, the search for extraterrestrial life?

If they announce that they have discovered possibilities (2) or (3), it has major implications. We've looked all over the solar system for life, but we've always been looking for "life as we know it." These humble bacteria could be the first example of "life as we don't know it." There could be lots of possible ways to make life work. Non-DNA-based life? Life that doesn't have cells? The sky's the limit. Here is a very readable paper outlining the possibilities, but these are just the possibilities we can imagine.

The press conference is intended to support a paper in the journal Science, coming out tomorrow. Lastly. for those of you who are science fiction fans, I realized that the Star Trek original series episode "Devil in the Dark" [SPOILER ALERT] features the "Horta," an intelligent, misunderstood creature in which molecules in Earth-based life that contain carbon instead contain silicon, the element below carbon in the periodic table. If tomorrow we hear about possibility (2), then it's the same principle but with arsenic instead of phosphorous. [END SPOILER ALERT]

So, in summary, this is way cool. Thanks for reading as I geek out on it. I'll be watching tomorrow if I'm not in meetings, and you should too. If you do, send me a Gmail or Facebook chat.

Enjoy!

-Drek's Awesome Friend

I have the coolest friends ever.

UPDATE: You can find NASA's article on the talk here. It doesn't clarify the issue of whether the arsenic-using bacteria derive from an independent abiogenesis event or not, but the description of the bacteria as otherwise part of a very common family of bacteria makes me suspect that isn't the case. Sadly, I wasn't able to stream the conference so I can't speak to that. Nevertheless, so very freaking cool.


*Geek note: Phosphorous is an important part of all three of the key molecules of life - DNA (genetic code), RNA (transmitter of genetic information), and ATP (provider of energy to cells). Arsenic is a deadly poison, and has been a choice murder weapon from the middle ages to today.**

**Geek note #2: Phosphorous (symbol P) is directly above arsenic (As) in the periodic table (in the same "group" - (see here.), meaning they are chemically very similar. In fact, this is why arsenic is a poison - arsenic "tricks" your body into thinking it is phosphorous, but they are chemically just different enough that arsenic can't substitute for phosphorous, and your body breaks down.

***Geek note #3: Phosphorous is part of the "backbone" of DNA and RNA, the thing that the information-carrying ACTG/ACUG bases attach to; and also part of the structure of ATP; in fact, the "P" in ATP stands for "phosphate." If arsenic were swapped with phosphorous, the structure of all three molecules would be the same, but they would be chemically different. ATP would be ACTAs instead.

What goes around, comes around.

If you're a bible-believing fundamentalist Christian, you stand a decent chance of believing that the universe is a paltry 6,000 years old. If you're a science-loving empirically-minded person, you likely think that the universe is much, much older (e.g. around 14 billion years old). But in either case, you believe that our universe had a distinct beginning- a starting point from which everything we see derives. And, as it turns out, it might just be that we've all been wrong about that:

Most cosmologists trace the birth of the universe to the Big Bang 13.7 billion years ago. But a new analysis of the relic radiation generated by that explosive event suggests the universe got its start eons earlier and has cycled through myriad episodes of birth and death, with the Big Bang merely the most recent in a series of starting guns.

That startling notion, proposed by theoretical physicist Roger Penrose of the University of Oxford in England and Vahe Gurzadyan of the Yerevan Physics Institute and Yerevan State University in Armenia, goes against the standard theory of cosmology known as inflation.

The researchers base their findings on circular patterns they discovered in the cosmic microwave background, the ubiquitous microwave glow left over from the Big Bang. The circular features indicate that the cosmos itself circles through epochs of endings and beginnings, Penrose and Gurzadyan assert. The researchers describe their controversial findings in an article posted at arXiv.org on November 17.

The circular features are regions where tiny temperature variations in the otherwise uniform microwave background are smaller than average. Those features, Penrose said, cannot be explained by the highly successful inflation theory, which posits that the infant cosmos underwent an enormous growth spurt, ballooning from something on the scale of an atom to the size of a grapefruit during the universe’s first tiny fraction of a second. Inflation would either erase such patterns or could not easily generate them.

It's worth reading the rest of the article to hear about the methodology, as well as its potential faults, but this is pretty neat news both because of its implications for our understanding of where our current universe came from, and for the suggestion that there might be ways to peer back before that "first cause" to see what came before. And honestly, this is one of those moments that really demonstrates the bizarre nature of a scientist's mind- when news comes out that suggests we may have been fundamentally wrong about something, the reaction tends to be something like this: "Oh, COOL! Is this real? Because if it is... WOW! That is so interesting! What else will chance now?" When life is a quest for knowledge, the entire universe becomes your playground.


As a side note: Does this mean that the crazy lady with the circles was onto something?