Total Drek

Or, the thoughts of several frustrated intellectuals on Sociology, Gaming, Science, Politics, Science Fiction, Religion, and whatever the hell else strikes their fancy. There is absolutely no reason why you should read this blog. None. Seriously. Go hit your back button. It's up in the upper left-hand corner of your browser... it says "Back." Don't say we didn't warn you.

Sunday, June 29, 2008

There are no words.

Folks who read this blog have been following the Richard Lenski foolishness. To wit, Richard Lenski and colleagues published an article on evolution which was subsequently "challenged" by Andrew Schlafly, as recounted earlier. Schlafly e-mailed Lenski insinuating wrongdoing and Lenski responded quite politely. Schlafly then compounded his idiocy by questioning Lenski's basic honesty in even more strident terms. This attack did not go unanswered, as Lenski proceeded to administer the beatdown. One would think that would be the end of it but, sadly... not so much.

So far, Schlafly hasn't sent any new e-mails to Lenski but, having reviewed the earlier posts, check on Schlafly's newest claims:





Yes folks, that's right: according to Schlafly, Lenski is the problem here. Sure he is. And the Sun orbits around the Earth every day.

I'm still on my Misery Journey and don't have a lot of time so, really, I think this little number I whipped up over at Dinosaur Comics says it best:



Nuff Said.

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Saturday, June 28, 2008

Blogiversary IV: The Return of Drek's Deadly Spawn

Yes, ladies and gentlemen, it's true: today, June 28th, 2008, is Total Drek's Four-Year Blogiversary.* It was four years ago that I started this particular e-cesspool and I have, for reasons mysterious even to me, kept it going for four long, wearying trips around the sun.**

One is forced to ask, of course, what lessons we have perhaps learned in all that time? Well, really, none at all. Seriously. Nothing useful has ever come out of this project. Still, I like to think that we have been at least slightly entertained. We have, for example,*** slapped Conservapedia around, discussed evolution, engaged with religion, explored advertising talked about sociology, ranted about tech support and even been skeptical of skepticism. Sadly, this year has been fairly short on my favorite blog topic- boobs- but there are easy solutions for that little deficiency. It has been, in short, a year about as productive as any other year of my blogging.

So what can we look forward to in the next year? Well, doubtless I'll finish my series on atheism, which I have certainly not forgotten about. Otherwise, you can expect the same sort of juvenile humor and "analysis" you have grown so familiar with. You know, the typical stuff:



But hey, that's why you hate love me, right?

Right?

Crap.


* For those who are curious, no, this does not signal the end of my Misery Journey. I pre-loaded this post before departure because, really, who can stand to miss something like this?

** Yeah? So what if you're one of the ignorant fucks from the Flat Earth Society? You ain't gonna stop ME from telling the truth about astronomy! Turtles all the way down, biatch!

*** For the record, I have way more posts that fall into these categories than the tags reveal for the simple reason that this blog was around for years before tagging even became an option on blogger.

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Tuesday, June 24, 2008

Holy enraged biologist, Batman!

Many of you may remember my ongoing coverage of the Richard Lenski nonsense over at Conservapedia. It began with a report on Lenski's fascinating research and the insane response from Andrew Schlafly. Specifically, a demand via e-mail for Lenski's data. Lenski responded to this request by indicating- politely- that Andy should read the f-ing paper because it was all contained therein. Things might have calmed down but, as Schlafly was involved, they did not. Instead, the "controversy" continued with Schlafly claiming the data weren't supplied and overtly disparaging Lenski's integrity both on Conservapedia and in an e-mail to the Proceedings of the National Academy of the Sciences. In other words, this was quite an escalation.

Well, ladies and gentlemen, the unbelievable has happened: Lenski has responded.

And man is he pissed!

The following is drawn from the relevant page over on RationalWiki as Conservapedia seems to be mysteriously offline. No doubt they're busy shooting the messengers or something.

So, without further ado, Richard Lenski:

Dear Mr. Schlafly:
I tried to be polite, civil and respectful in my reply to your first email, despite its rude tone and uninformed content. Given the continued rudeness of your second email, and the willfully ignorant and slanderous content on your website, my second response will be less polite. I expect you to post my response in its entirety; if not, I will make sure that is made publicly available through other channels.

I offer this lengthy reply because I am an educator as well as a scientist. It is my sincere hope that some readers might learn something from this exchange, even if you do not.

First, it seems that reading might not be your strongest suit given your initial letter, which showed that you had not read our paper, and given subsequent conversations with your followers, in which you wrote that you still had not bothered to read our paper. You wrote: “I did skim Lenski’s paper …” If you have not even read the original paper, how do you have any basis of understanding from which to question, much less criticize, the data that are presented therein?

Second, your capacity to misinterpret and/or misrepresent facts is plain in the third request in your first letter, where you said: “In addition, there is skepticism that 3 new and useful proteins appeared in the colony around generation 20,000.” That statement was followed by a link to a news article from NewScientist that briefly reported on our work. I assumed you had simply misunderstood that article, because there is not even a mention of proteins anywhere in the news article. As I replied, “We make no such claim anywhere in our paper, nor do I think it is correct. Proteins do not ‘appear out of the blue’, in any case.” So where did your confused assertion come from? It appears to have come from one of your earlier discussions, in which an acoltye [sic] (Able806, who to his credit at least seems to have attempted to read our paper) wrote:

"I think it might be best to clarify some of Richard's work. He started his E.Coli project in 1988 and has been running the project for 20 years now; his protocols are available to the general public. The New Scientist article is not very technical but the paper at PNAS is. The change was based on one of his colonies developing the ability to absorb citrate, something not found in wild E.Coli. This occurred around 31,500 generations and is based on the development of 3 proteins in the E.Coli genome. What his future work will be is to look at what caused the development of these 3 proteins around generation 20,000 of that particular colony."

As further evidence of your inability to keep even a few simple facts straight, you later wrote the following: “It [my reply] did clarify that his claims are not as strong as some evolutionists have insisted.” But no competent biologist would, after reading our paper with any care, insist (or even suggest) that “3 new and useful proteins appeared in the colony around generation 20,000” or any similar nonsense. It is only in your letter, and in your acolyte’s confused interpretation of our paper, that I have ever seen such a claim. Am I or the reporter for NewScientist somehow responsible for the confusion that reflects your own laziness and apparent inability to distinguish between a scientific paper, a news article, and a confused summary posted by an acolyte on your own website?

Third, it is apparent to me, and many others who have followed this exchange and your on-line discussions of how to proceed, that you are not acting in good faith in requests for data. From the posted discussion on your web site, it is obvious that you lack any expertise in the relevant fields. Several of your acolytes have pointed this out to you, and that your motives are unclear or questionable at best, but you and your cronies dismissed their concerns as rants and even expelled some of them from posting on your website. [ http://rationalwiki.com/wiki/Expelled:_No_Intelligence_Allowed] Several also pointed out that I had very quickly and straightforwardly responded that the methods and data supporting the evolution of the citrate-utilization capacity are already provided in our paper. One poster in your discussions, Aaronp, wrote:

“I read Lenski's paper, and as a trained microbiologist, I thought that it was both thorough and well done. His claims are backed by good data, namely that which was presented in the figures. I went through each of the figures after Aschlafly said that they were uninformative. Actually, they are basic figures that show the population explosion of the bacterial cultures after the Cit+ mutation occurred. These figures show that the cultures increased in size and mass at a given timepoint, being able to do so because they had evolved a mechanism to utilize a new nutrient, without the assistance of helper plasmids. … Lenksi’s paper, while not the most definite I’ve seen, is still a very well-researched paper that supports its claims nicely.”

(As far as I saw, Aaronp is the only poster who asserted any expertise in microbiology.) As further evidence of the absence of good-faith discussion about our research, in the discussion thread that began even before you sent your first email to me, I counted the words “fraud” or “fraudulent” being used more than 10 times, including one acolyte, TonyT, who says bluntly that I am “clearly a fraudulent hack.” In the discussion thread that also includes comments after my first reply, the number of times those same words are used has increased to 20, with the word “hoax” also now entering the discussion. A few posters wisely counseled against such slander but that did not deter you. I must say, it is surprising that someone with a law degree would make, and allow on his website, so many nasty comments that implicitly and even explicitly impugn my integrity, and by extension that of my collaborators, without any grounds whatsoever and reflecting only your dogmatic adherence to certain beliefs.

Finally, let me now turn to our data. As I said before, the relevant methods and data about the evolution of the citrate-using bacteria are in our paper. In three places in our paper, we did say “data not shown”, which is common in scientific papers owing to limitations in page length, especially for secondary or minor points. None of the places where we made such references concern the existence of the citrate-using bacteria; they concern only certain secondary properties of those bacteria. We will gladly post those additional data on my website.

It is my impression that you seem to think we have only paper and electronic records of having seen some unusual E. coli. If we made serious errors or misrepresentations, you would surely like to find them in those records. If we did not, then – as some of your acolytes have suggested – you might assert that our records are themselves untrustworthy because, well, because you said so, I guess. But perhaps because you did not bother even to read our paper, or perhaps because you aren’t very bright, you seem not to understand that we have the actual, living bacteria that exhibit the properties reported in our paper, including both the ancestral strain used to start this long-term experiment and its evolved citrate-using descendants. In other words, it’s not that we claim to have glimpsed “a unicorn in the garden” – we have a whole population of them living in my lab! [ http://en.wikipedia.org/wiki/The_Unicorn_in_the_Garden] And lest you accuse me further of fraud, I do not literally mean that we have unicorns in the lab. Rather, I am making a literary allusion. [ http://en.wikipedia.org/wiki/Allusion]

One of your acolytes, Dr. Richard Paley, actually grasped this point. He does not appear to understand the practice and limitations of science, but at least he realizes that we have the bacteria, and that they provide “the real data that we [that’s you and your gang] need”. Here’s what this Dr. Paley had to say:

“I think there’s a great deal of misunderstanding here from the critics of Mr. Schlafly and obfuscation on the part of Prof. Lenski and his supporters. The real data that we need are not in the paper. Rather they are in the bacteria used in the experiments themselves. Prof. Lenski claims that these bacteria ‘evolved’ novel traits and that these were preceded by the evolution of ‘potentiated genotypes’, from which the traits could be ‘reevolved’ using preserved colonies from those generations. But how are we to know if these traits weren’t ‘potentiated’ by the Creator when He designed the bacteria thousands of years ago, such that they would eventually reveal themselves when the time was right? The only way this can be settled is if we have access to the genetic sequences of the bacteria colonies so that we can apply CSI techniques and determine if these ‘potentiated genotypes’ originated through blind chance or intelligence. But with the physical specimens in the hands of Darwinists, who claim they will get around to the sequencing at some unspecifed future time, how can we trust that this data will be forthcoming and forthright? Thus, Prof. Lenski et al. should supply Conservapedia, as stewards, with samples of the preserved E. coli colonies so that the data can be accessible to unbiased researchers outside of the hegemony of the Darwinian academia, even if it won’t be put to immediate examination by Mr. Schlafly. This is simply about keeping tax-payer-funded scientists honest.”

So, will we share the bacteria? Of course we will, with competent scientists. Now, if I was really mean, I might only share the ancestral strain, and let the scientists undertake the 20 years of our experiment. Or if I was only a little bit mean, maybe I’d also send the potentiated bacteria, and let the recipients then repeat the several years of incredibly pain-staking work that my superb doctoral student, Zachary Blount, performed to test some 40 trillion (40,000,000,000,000) cells, which generated 19 additional citrate-using mutants. But I’m a nice guy, at least when treated with some common courtesy, so if a competent scientist asks for them, I would even send a sample of the evolved E. coli that now grows vigorously on citrate. A competent microbiologist, perhaps requiring the assistance of a competent molecular geneticist, would readily confirm the following properties reported in our paper: (i) The ancestral strain does not grow in DM0 (zero glucose, but containing citrate), the recipe for which can be found on my web site, except leaving the glucose out of the standard recipe as stated in our paper. (ii) The evolved citrate-using strain, by contrast, grows well in that exact same medium. (iii) To confirm that the evolved strain is not some contaminating species but is, in fact, derived from the ancestral strain in our study, one could check a number of traits and genes that identify the ancestor as E. coli, and the evolved strains as a descendant thereof, as reported in our paper. (iv) One could also sequence the pykF and nadR genes in the ancestor and evolved citrate-using strains. One would find that the evolved bacteria have mutations in each of these genes. These mutations precisely match those that we reported in our previous work, and they identify the evolved citrate-using mutants as having evolved in the population designated Ara-3 of the long-term evolution experiment, as opposed to any of the other 11 populations in that experiment. And one could go on and on from there to confirm the findings in our paper, and perhaps obtain additional data of the sort that we are currently pursuing.

Before I could send anyone any bacterial strains, in order to comply with good scientific practices I would require evidence of the requesting scientist’s credentials including: (i) affiliation with an appropriate unit in some university or research center with appropriate facilities for storing (-80ºC freezer), handling (incubators, etc.), and disposing of bacteria (autoclave); and (ii) some evidence, such as peer-reviewed publications, that indicate that the receiving scientist knows how to work with bacteria, so that I and my university can be sure we are sending biological materials to someone that knows how to handle them. By the way, our strains are not derived from one of the pathogenic varieties of E. coli that are a frequent cause of food-borne illnesses. However, even non-pathogenic strains may cause problems for those who are immune-compromised or otherwise more vulnerable to infection. Also, my university requires that a Material Transfer Agreement be executed before we can ship any strains. That agreement would not constrain a receiving scientist from publishing his or her results. However, if an incompetent or fraudulent hack (note that I make no reference to any person, as this is strictly a hypothetical scenario, one that I doubt would occur) were to make false or misleading claims about our strains, then I’m confident that some highly qualified scientists would join the fray, examine the strains, and sort out who was right and who was wrong. That’s the way science works.

I would also generally ask what the requesting scientist intends to do with our strains. Why? It helps me to gauge the requester’s expertise. I might be able to point out useful references, for example. Moreover, as I’ve said, we are continuing our work with these strains, on multiple fronts, as explained in considerable detail in the Discussion section of our paper. I would not be happy to see our work “scooped” by another team – especially for the sake of the outstanding students and postdocs in my group who are hard at work on these fronts. However, that request to allow us to proceed, without risk of being scooped on work in which we have made a substantial investment of time and effort, would be just that: a request. In other words, we would respect PNAS policy to share those strains with any competent scientist who complied with my university’s requirements for the MTA and any other relevant legal restrictions. If any such request requires substantial time or resources (we have thousands of samples from this and many other experiments), then of course I would expect the recipient to bear those costs.

So there you have it. I know that I’ve been a bit less polite in this response than in my previous one, but I’m still behaving far more politely than you deserve given your rude, willfully ignorant, and slanderous behavior. And I’ve spent far more time responding than you deserve. However, as I said at the outset, I take education seriously, and I know some of your acolytes still have the ability and desire to think, as do many others who will read this exchange.

Sincerely,

Richard Lenski

P.S. Did you know that your own bowels harbor something like a billion (1,000,000,000) E. coli at this very moment? So remember to wash your hands after going to the toilet, as I hope your mother taught you. Simple calculations imply that there are something like 10^20 = 100,000,000,000,000,000,000 E. coli alive on our planet at any moment. Even if they divide just once per day, and given a typical mutation rate of 10^-9 or 10^-10 per base-pair per generation, then pretty much every possible double mutation would occur every day or so. That’s a lot of opportunity for evolution.

P.P.S. I hope that some readers might get a chuckle out of this story. The same Sunday (15 June 2008) that you and some of your acolytes were posting and promoting scurrilous attacks on me and our research (wasn’t that a bit disrespectful of the Sabbath?), I was in a church attending a wedding. And do you know what Old Testament lesson was read? It was Genesis 1:27-28[1], in which God created Man and Woman. It’s a very simple and lovely story, and I did not ask any questions, storm out, or demand the evidence that it happened as written at a time when science did not yet exist. I was there in the realm of spirituality and mutual respect, not confusing a house of religion for a science class or laboratory. And it was a beautiful wedding, too.

P.P.P.S. You may be unable to understand, or unwilling to accept, that evolution occurs. And yet, life evolves! [ http://en.wikipedia.org/wiki/E_pur_si_muove] From the content on your website, it is clear that you, like many others, view God as the Creator of the Universe. I respect that view. I find it baffling, however, that someone can worship God as the all-mighty Creator while, at the same time, denying even the possibility (not to mention the overwhelming evidence) that God’s Creation involved evolution. It is as though a person thinks that God must have the same limitations when it comes to creation as a person who is unable to understand, or even attempt to understand, the world in which we live. Isn’t that view insulting to God?

P.P.P.P.S. I noticed that you say that one of your favorite articles on your website is the one on “Deceit.” That article begins as follows: “Deceit is the deliberate distortion or denial of the truth with an intent to trick or fool another. Christianity and Judaism teach that deceit is wrong. For example, the Old Testament says, ‘Thou shalt not bear false witness against thy neighbor.’” You really should think more carefully about what that commandment means before you go around bearing false witness against others.




UPDATE: The stupidity continues!


Special thanks to loyal reader cpcolumn for bringing this to my attention during my Misery Journey.

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Monday, June 23, 2008

It's back and it's pissed off!

Longtime readers of this blog probably remember the semi-annual excursion that has come to be known as the "Misery Journey." The name derives from the often amusing webcomic "College Roomies From Hell" and has been written about several times before. In short, I sometimes need to leave town for an ongoing research effort and, despite last year's reprieve, that time has come again.

These trips, as the name suggests, are something less than fully enjoyable most years. I have a good time, but they are accompanied by significant physical discomfort. As such, they are both looked forward to and dreaded in equal measures. It is for certain that they are not as uplifting as the trips some other people get to take:



Sadly, this year's trip promises to be even more uncomfortable because my return will be followed immediately by a move to a new apartment where the utilities will not yet be fully connected. As such, much as I am sorry about this, you should all be prepared for an unusally lengthy hiatus in my blogging. My esteemed co-bloggers, of course, may well post but I think most of them have far, far better things to do with their time. You know... like pick lint out of their belly-buttons.

So, aside from the possible, though unlikely, on-the-road post, you shouldn't expect to see anything here for a while. I appreciate your patience, and I'll "see" you if when I return.*

Ciao!


* For those who are curious, my wife is also accompanying me, which will surely improve my lot substantially while worsening hers.

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Friday, June 20, 2008

I just couldn't resist.

For those who are fans of R.K. Milholland's Something*Positive and related web comics, this will be immensely funny. For the rest of you... it'll probably still be funny.

Enjoy!



Sometimes I'm really glad to be from the South, so that shit like this seems normal to me.

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Thursday, June 19, 2008

Double-down

Some of you may remember a few days back when I posted on Richard Lenski's exciting research and, in turn, on Andrew Schlafly's demand to be given access to the data. To wit, Schlafly doubted the veracity of the research since "evolutionists have a long history of deceit" and insinuated that Lenski would not be cooperative.

Well, as you may recall, Lenski responded to Schlafly's rather insulting e-mail in a very gracious manner, correcting Schlafly's misconceptions and directing him to numerous papers relating to the subject. This has not, however, satisfied Schlafly who appears to want access to the complete twenty-year database of Lenski's research. And, as long as we're on the subject, Schlafly seems undeterred by the fact that said database is not only likely to be in excess of one terabyte in size but also that it is likely to be entirely uninterpretable to someone who lacks Lenski's training. So, you might wonder, what is Schlafly going to do about it?

Staying true to form, he has decided to send another e-mail. And not just any e-mail! Oh, no! This e-mail is not only more insulting that the last one, implying that Lenski has been uncooperative, but it has also been CC'ed (allegedly) to the Proceedings of the National Academy of the Sciences and New Scientist. Check it out:



Or, in super neat texty format:

Dear Prof. Lenski,

This is my second request for your data underlying your recent paper, "Historical contingency and the evolution of a key innovation in an experimental population of Escherichia coli," published in PNAS (June 10, 2008) and reported in New Scientist ("Bacteria make major evolutionary shift in lab," June 9, 2008).
http://myxo.css.msu.edu/lenski/pdf/2008,%20PNAS,%20Blount%20et%20al.pdf
http://www.newscientist.com/channel/life/dn14094-bacteria-make-major-evolutionary-shift-in-the-lab.html

Your work was taxpayer-funded, and PNAS represents that its authors will make underlying data available. I'd like to review the data myself and ensure availability for others, including experts and my students. Others have expressed interest in access to the data in addition to myself, and your website seems well-suited for public release of these data.

If the data are voluminous, then I particularly request access to the data that was made available to the peer reviewers of your paper, and to the data relating to the period during which the bacterial colony supposedly developed Cit+. As before, I'm requesting the organized data themselves, not the graphs and summaries set forth in the paper and referenced in your first reply to me. Note that several times your paper expressly states, "data not shown."

Given that this is my second request for the data, a clear answer is requested as to whether you will make the key underlying data available for independent review. Your response, or lack thereof, will be posted due to the public interest in this issue. Thank you.

Andy Schlafly, B.S.E., J.D.
www.conservapedia.com
cc: PNAS, New Scientist publications


Now, a couple of observations here. First, Richard Lenski is not just some random-ass biologist. He's an elected member of the U.S. National Academy of the Sciences and a recipient of a MacArthur "Genius" Grant. For those who don't know, the "Genius Grant" is basically an award of a helluva lot of money so you can research whatever the hell you feel like for a few years- it's a huge honor and Lenski won it in 1996. So, on the most basic level, I seriously doubt that Lenski* is going to be all that impressed by "Andy Schlafly, B.S.E., J.D."

Secondly, however, let's consider what has just happened. Schlafly has just been quite rude to a guy who has racked up enough scientific accolades that, were there to be a Science All-Star Team to play an exhibition match against the Zion Zealots,** he would stand a good chance of being in the starting lineup. Had Schlafly just sent this e-mail to Lenski, I suspect he may have just ignored it but Schlafly didn't just send it to Lenski, he also sent it to important folks in science. And while I suspect that PNAS and New Scientist will laugh themselves incontinent at Schlafly, I would not be surprised if Lenski were a bit pissed. So, in short, I am really curious to see what happens next. Stay tuned.

As for me, I am proud to report that I have at last earned my first blocking on Conservapedia:



Cheap shot? Sure but, after a while, I just get so sick of not having people respond to actual points, that I get kinda antsy. Who can blame me? I admit, however, that I wonder if XKCD isn't right about this situation as well as many others.

Eh. Oh well. Until magic flying girls arrive, I guess we'll just have to muddle through.


UPDATE: No word from Lenski, who is probably lost in the usual Schlafly-inspired What-the-fuckery. Andy, however, is apparently feeling emboldened by Lenski's silence:



Or, in text form:

Aaronp, either you're naive or you're engaging in bullying if you maintain that Lenski plans to release his raw data soon for independent, public review. I asked him last Friday to release it, and his reply declined to do so. I asked him again yesterday, and he predictably has not replied. It now seems to me to be likely that the peer reviewers for his paper did not even see the raw data. I think it's likely that only Lenski and his grad student have seen the raw data underlying that paper (note its footnote). Don't pretend that Lenski welcomes independent review of the data.--Aschlafly


And thus we answer the question "Does Schlafly have any decency left" with a resounding "no." I admit, I'm actually disappointed.


UPDATE TO THE UPDATE: As Lenski has not yet replied (though it hasn't even been 48 hours yet) Schlafly is concluding that Lenski really is concealing fraud. His newest schtick is that the peer review at PNAS was obviously inadequate and he claims to be asking the editors some stern questions. Seriously:



Or, in texty format (FYI: Schlafly is in plain text, another Conservapeon is in bold):

Lenski has essentially refused my request that he make his underlying data available for public scrutiny, despite his use of public funding. Given the remarkably short time between submission of his PNAS manuscript and its acceptance (only 14 days), I doubt his paper even had meaningful peer review.

It's unscientific for others to repeat as true an unverified claim based on concealed data. I wonder if PNAS violated its own stated policies by publishing Lenski's paper, and I'm going to email its Editor-in-Chief to request an explanation.--Aschlafly 11:19, 20 June 2008 (EDT)

How long does peer review normally take? And what PNAS policies do you think may have been violated? Philip J. Rayment 11:32, 20 June 2008 (EDT)

Other articles in the same issue of PNAS:

Effective tumor treatment targeting a melanoma/melanocyte-associated antigen triggers severe ocular autoimmunity approved April 14, 2008 (received for review November 18, 2007)

Localized and extended deformations of elastic shells approved March 11, 2008 (received for review August 7, 2007)

Characterization of the structure–function relationship at the ligament-to-bone interface approved April 11, 2008 (received for review December 28, 2007)

Mutations in the telomerase component NHP2 cause the premature ageing syndrome dyskeratosis congenita approved April 14, 2008 (received for review January 3, 2008)

Experimental evidence for negative selection in the evolution of a Yersinia pestis pseudogene approved April 15, 2008 (received for review February 13, 2008) --Aschlafly 11:36, 20 June 2008 (EDT)

The average length of peer review for PNAS, based on a sample, is over 120 days. Lenski's paper was accepted within only 14 days of submission.--Aschlafly 11:53, 20 June 2008 (EDT)


I concede I'm curious about the difference in review times BUT I very much doubt anything nefarious is afoot. Can't wait to see what, if anything, Schlafly finds out- especially since his own determined ignorance will always get in the way. Not to mention his typical mean-spiritedness, but I digress.

In more amusing news, however, my resolute following of this insanity has earned Total Drek a very peculiar honor. It appears that, for the moment, if you enter the search terms "Schlafly" and "Lenski" into google, we're the very first hit. We even edged out Conservapedia itself! Seriously:



And as we know from Conservapedia, being rated highly by search engines means that you're totally right!


UPDATE TO THE UPDATE TO THE UPDATE: Just noticed this over on the usual den of iniquity:



Or, in text form:

I have to run an errand but want to you everyone know, as I've said before, that it's only productive to discuss something with somebody who has an open mind. If you agree with my statement that "It's unscientific for others to repeat as true an unverified claim based on concealed data," then let's talk. If not, then please rant somewhere else. Thanks.--Aschlafly


Translation: "It's pointless to talk to people who aren't willing to consider alternative viewpoints so, if you don't agree with my narrow framing of this issue, I won't talk to you." Huh-WHA?!

Hey, Andy? Yeah. I don't think what word means what you think it means.

But, then again, you and I have talked about openmindedness before, albeit without much success.


UPDATE TO THE UPDATE TO THE UPDATE TO THE UPDATE: Richard Lenski responds and it's f-ing beautiful!


* And in a totally awesome twist, Richard Lenski is also the son of Sociologist Gerhard Lenski.

** Their mascot is a burning bush. Looks totally awesome on the sidelines, but the costume sure seems like it'd be uncomfortable to wear.

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Wednesday, June 18, 2008

It's hypnotic.

In lieu of a post today, allow me to suggest that you watch this. Now, I know, I know: it's going to look like something tawdry at first. Seriously, though, let it get a minute or two in and then tell me if the coordination alone isn't cool as hell:



I don't even know how to describe it.

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Tuesday, June 17, 2008

It's all so clear to me now.

Longtime readers* know that I keep an eye on the whole intelligent design fiasco. There are a number of reasons for this but, given that I'm not interested in discussing them at length, let's just say it's because I think Wild Bill Dembski is a sexy bitch. Mmmmmmmm.... fivehead!**

In any case, given my interest in ID I have not only developed a comprehension of the arguments of the "theory" but have also come to understand a fair amount about their rhetorical strategies. These are, of course, different in that the way you talk about a set of ideas can have a fairly large impact on how those ideas are received.*** As a consequence, no matter how brilliant your ideas, you must develop at least a rudimentary command of rhetoric if you are to be heard. What makes rhetoric so interesting, however, is that it can be used to get an idea about what's going on in someone's head. Partly, this is because when a person advances an argument for their own ideas, there's a natural tendency to try and advance defenses against anticipated criticisms. Whether these defenses are successful or not, they end up cluing the audience in as to where possible deficiencies may lie.****

With this in mind I have long been perplexed by one particular obsession of the ID crowd: front-loading. Now, if you haven't heard about this before, front-loading is the idea that the DNA sequences for all organisms on Earth were somehow loaded into the very first organisms by that mysterious intelligent designer. Thus, while it may appear that life has evolved over millions upon millions of years, in fact each new species has been a deterministic result of the DNA "program" executing itself in the previous species. In a sense, speciation events are pre-planned. When confronted with the point that the DNA of early bacteria and such do not appear to contain all the sequences in modern higher critters, proponents of this idea are quick to observe that the earlier DNA represents a program for producing the next stage, not necessarily a copy of that stage. This is, of course, very similar to my discussion of information theory a while back: sometimes you can have a program to write a particular line even if the line is not contained within the program.

The thing is, why all the concern with front-loading? I mean, really, it's one of the most scientifically problematic arguments advanced by the ID folks. Aside from being almost entirey unverifiable, there are huge potential issues with it: mutation, DNA transcription errors, etc. I get that it enables one to mesh intelligent design with an old Earth, thus saving some ID proponents from having to travel the way of madness to its conclusion, but it still seems so dreadfully unnecessary. So what is the deal?

Well, as it happens, thanks to Mark Perakh, I finally understand the reason. To get it yourself, you first need to understand the idea of "irreducible complexity." IC is the idea that some complex systems serve a functional purpose which they would be unable to continue serving were even one part removed from them. While Michael Behe, the originator of the concept, likes to invoke an analogy to a mousetrap I actually prefer the analogy used by David Berlinski: a chair serves a valuable purpose as a place to sit, but a chair with one leg removed no longer serves this purpose. It is, in effect, irreducibly complex. A system that is irreducibly complex, it is argued, cannot be the result of natural processes and so must be the result of design. And, it is said, since a number of biological structures are horrendously complex, they must have been designed.

Now, Perakh has observed that there's a major problem with this argument. The issue is that- despite the inclusion of the term "complex"- the major way that Behe and his ilk are identifying design is by function. Analogy to the contrary, a chair is not a particularly complex structure but it serves a specific purpose and does so well. Therefore, we conclude that a chair may be a product of design. Perakh thus proposes that design is more likely to be the case in an instance of simplicity and functionality than it is in a case of complexity and functionality. And the reason, to summarize his argument as succinctly as possible, is that while there is only one simplest way, there are a wide variety of complex, convoluted ways. Thus, a probabalistic process is much more likely to find one of the many complex ways rather than the one simple way.

A crude analogy can be drawn, for all the quantoids out there, to writing code in Stata. Let's say that a first-year grad student, just barely familiar with Stata, is given a task: define a variable that contains the sum of three other variables. Let's call the first variable "output" and the other variables "input1", "input2" and "input3." How might our rookie grad student handle this problem?

Well, if they're not thinking particularly clearly they might try:

gen output=input1+input2+input3


The problem here, however, is that if any of those three input variables are missing***** then the value of output will also be set to missing. As it turns out, this is not acceptable. What to do?

Eventually, they would no doubt think to try something a little more complex:******

gen output=.
replace output=input1+input2+input3 if (input1~=. & input2~=. & input3~=.)
replace output=input1+input2 if (input1~=. & input2~=. & input3==.)
replace output=input2+input3 if (input1==. & input2~=. & input3~=.)
replace output=input1+input3 if (input1~=. & input2==. & input3~=.)
replace output=input1 if (input1~=. & input2==. & input3==.)
replace output=input2 if (input1==. & input2~=. & input3==.)
replace output=input3 if (input1==. & input2==. & input3~=.)


This code would work, but it's a horrible pain in the ass to write- especially if you need to sum up, say, nine variables instead of three. Now, the thing is, the above code serves a purpose, is arguably complex, and is irreducible (i.e. removing any line will screw up the function). Therefore, it fits (weakly) Behe's definition of "irreducible complexity."

Yet, the thing is, let's say that this same grad student tries to perform the same task a few years later when they know Stata better and can design- rather than kludge- their programs. At that point the entire program would most likely read:

egen output=rsum(input1 input2 input3)


See, the egen/rsum command combination tells Stata to sum up all the non-missing values of the variables inside the parentheses for each respondent and put the result in a variable named "output." In other words, our more advanced grad student can do the same thing with a one-line program that used to require eight lines. Arguably, this program is simpler but, nevertheless, remains functional. And I think most of us would argue that the last program is better evidence of deliberate planning and design than either of the first two. And if you think about longer programs executing a variety of functions, the more advanced grad student will almost certainly be able to do the same functions while using far fewer lines than the less advanced grad student. Design, in this case, equates to simplicity not complexity.

So how does this get us to front-loading? Well, you see, the DNA of Humans and most other species is littered with all kinds of DNA that we just don't seem to use. This is often referred to as "junk DNA" even though this is an oversimplification- it isn't that it definitely has no function, we just haven't discovered one yet. The thing is, since evolution is a probabalistic process, we shouldn't expect it to come up with efficient solutions to problems. It should act like the immature grad student in our earlier example: cobbling together complex structures out of a myriad of basic sub-parts. Our DNA should, more or less, be somewhat of a kludge. And, as it happens, that's more or less the way our DNA looks right now. If DNA is a computer program, then it's a computer program that has huge swathes commented out (i.e. inactivated) and much of the rest thrown together out of a little of this and a little of that.

Ah, but what about this front-loading business? Well, you see, in that case all of that kludged DNA program is, in fact, just part of an overall design meant to produce new species. See, front-loading isn't meant to account for the complexity of the genome at all. Instead, it's meant to explain how the non-coding gobbledegook we keep finding is, in fact, a very simple way of accomplishing an additional function. In an ironic twist, front-loading is a way to save the "design inference" from the naturalistic demon of complexity.

And I find that awfully funny.


* Hell, let's face it: if you read this blog for, like, a week you probably realize this.

** For those who are unfamiliar with the term, when someone's forehead is truly gigantic and prominent- like the melon on a dolphin- it is referred to as a "fivehead."

*** I think this is one of the more difficult lessons grad students have to learn, actually.

**** This is, as a side note, why I sometimes recommend against trying to protect yourself from criticism too early in a debate. At best it makes you look defensive. At worst, it makes your audience suspicious and deprives you of an opportunity to rebut an opponent's claim.

***** "Missing" simply means that there is no value assigned to that variable- like leaving a test question blank.

****** FYI: "~=" is read as "is not equal to" and "." is read as a missing value. "==" just means "is equal to".

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Monday, June 16, 2008

Advice for new parents...

In honor of Father's Day, which we celebrated this past weekend, I'd just like to direct you to a post over at the delightful Skepchick. They provide an important public service by publishing a simple set of "dos" and "don'ts" for taking care of a new baby. I have to admit, some of these I would not have figured out on my own.*



Remember: The air horn should be kept at least twelve inches from the baby's head. This produces a maximally room-filling sound and will prove most effective in waking the child.



Salt lick and water? Good. Lack of a hamster Baby-wheel? Bad.



Most babies will not be ready for free weights until they are at least six months old. Start with some pilates first.



Last year over three million shoes were prematurely destroyed by babies. Help us reduce this alarming statistic.

So head on over and read the rest. Your children will be glad you did!


* ...if I were profoundly stupid.

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Friday, June 13, 2008

Science: 1, Intelligent Design: 0

Folks who follow the ongoing slapfight between science and intelligent design are probably aware that evolutionary theory is sometimes criticized on the grounds of being non-falsifiable. Since we can't observe evolution occurring, the story goes, evolution is little more than a tautology. Perhaps worse, characters like Wild Bill Dembski even argue that random mutation and selection is incapable of producing new and useful features and will, instead, simply degrade an organism over time. Well, today science has an exciting new response.* And that response is: blow me.

Over at Michigan State University** fashion model/biologist Richard Lenski and his lab have made a very exciting discovery. See, they've been running an experiment over there for about twenty years. In this experiment, he and his team took a single sample of E. Coli and derived twelve different study populations. They then watched them reproduce- over and over and over. Now, this wasn't some kind of unicellular pornography,*** but a study in evolution. See, given time it was thought that random mutations from a variety of sources might build up in these bacteria and produce some noticeable changes. And, as it happens, they have:

Mostly, the patterns Lenski saw were similar in each separate population. All 12 evolved larger cells, for example, as well as faster growth rates on the glucose they were fed, and lower peak population densities.

But sometime around the 31,500th generation, something dramatic happened in just one of the populations – the bacteria suddenly acquired the ability to metabolise citrate, a second nutrient in their culture medium that E. coli normally cannot use.

Indeed, the inability to use citrate is one of the traits by which bacteriologists distinguish E. coli from other species. The citrate-using mutants increased in population size and diversity.

"It's the most profound change we have seen during the experiment. This was clearly something quite different for them, and it's outside what was normally considered the bounds of E. coli as a species, which makes it especially interesting," says Lenski.


But wait, that's not all! As it turns out, Lenski's team has been storing samples of the different populations every few generations which allows them to, in effect, rewind biological time. And the outcome was, indeed, cool:

Would the same population evolve Cit+ again, he wondered, or would any of the 12 be equally likely to hit the jackpot?

The replays showed that even when he looked at trillions of cells, only the original population re-evolved Cit+ – and only when he started the replay from generation 20,000 or greater. Something, he concluded, must have happened around generation 20,000 that laid the groundwork for Cit+ to later evolve.

Lenski and his colleagues are now working to identify just what that earlier change was, and how it made the Cit+ mutation possible more than 10,000 generations later.


The significance here is real: it is experimental evidence not only of evolution, but that mutations can accumulate over time- perhaps innocuous and useless in and of themselves- suddenly becoming helpful when a given set of them have appeared. It is, in effect, a direct challenge to Behe's craptacular "irreducible complexity" idea. And, given the amount of time during which the only life on Earth was microbial, there was a lot of time for mutations and variations to accumulate, bequeathing a wealth of variation to macroscopic species like our own. Many of our adaptations may have been made possible by the bounty of mutations built up in the genomes of our bacterial progenitors.

It goes without saying that science-haters are already hard at work either ignoring or castigating this research. Nevertheless, this is an important finding and one that will no doubt teach us a great deal both about evolution and about the lengths one must go to in order to pretend it doesn't work.



UPDATE: Andy Schlafly over at Conservapedia tries to call Richard Lenski out:



Or, more accurately, sends him an impolite e-mail demanding that Lenski defend his work against the top scientific mind of "Andy Schlafly, B.S.E, J.D.":



Or, in textual form:

June 13, 2008

Dear Professor Lenski,

Skepticism has been expressed on Conservapedia about your claims, and the significance of your claims, that E. Coli bacteria had an evolutionary beneficial mutation in your study. Specifically, we wonder about the data supporting your claim that one of your colonies of E. Coli developed the ability to absorb citrate, something not found in wild E. Coli, at around 31,500 generations. In addition, there is skepticism that 3 new and useful proteins appeared in the colony around generation 20,000. A recent article about your claims appears in New Scientist here: http://www.newscientist.com/channel/life/dn14094-bacteria-make-major-evolutionary-shift-in-the-lab.html

Submission guidelines for the Proceedings of the National Academy of Science state that "(viii) Materials and Data Availability. To allow others to replicate and build on work published in PNAS, authors must make materials, data, and associated protocols available to readers. Authors must disclose upon submission of the manuscript any restrictions on the availability of materials or information." Also, your work was apparently funded by taxpayers, providing further reason for making the data publicly available.

Please post the data supporting your remarkable claims so that we can review it, and note where in the data you find justification for your conclusions.

I will post your reply, or lack of reply, on www.conservapedia.com . Thank you.

Andy Schlafly, B.S.E., J.D. Conservapedia


To be totally honest I hope Lenski does provide the data just so we can see Schlafly try to interpret it. Actually, scratch that: his ignorance will simply cause him to exclaim that the dreaded "evolutionists" are presenting the data in a confusing way to obfuscate their failure. Yeah. Right. Because science is that fucking easy.

Stay tuned.


UPDATE TO THE UPDATE: Richard Lenski replies and, as it turns out, is quite the gentleman:



Dear Mr. Schlafly:

I suggest you might want to read our paper itself, which is available for download at most university libraries and is also posted as publication #180 on my website. Here's a brief summary that addresses your three points.

1) "... your claims, that E. Coli bacteria had an evolutionary beneficial mutation in your study." We (my group and scientific collaborators) have already published several papers that document beneficial mutations in our long-term experiment. These papers provide exact details on the identity of the mutations, as well as genetic constructions where we have produced genotypes that differ by single mutations, then compete them, demonstrating that the mutations confer an advantage under the environmental conditions of the experiment. See papers # 122, 140, 155, 166, and 178 referenced on my website. In the latest paper, you will see that we make no claim to having identified the genetic basis of the mutations observed in this study. However, we have found a number of mutant clones that have heritable differences in behavior (growth on citrate), and which confer a clear advantage in the environment where they evolved, which contains citrate. Our future work will seek to identify the responsible mutations.

2. "Specifically, we wonder about the data supporting your claim that one of your colonies of E. Coli developed the ability to absorb citrate, something not found in wild E. Coli, at around 31,500 generations." You will find all the relevant methods and data supporting this claim in our paper. We also establish in our paper, through various phenotypic and genetic markers, that the Cit+ mutant was indeed a descendant of the original strain used in our experiments.

3. "In addition, there is skepticism that 3 new and useful proteins appeared in the colony around generation 20,000." We make no such claim anywhere in our paper, nor do I think it is correct. Proteins do not "appear out of the blue", in any case. We do show that what we call a "potentiated" genotype had evolved by generation 20,000 that had a greater propensity to produce Cit+ mutants. We also show that the dynamics of appearance of Cit+ mutants in the potentiated genotypes are highly suggestive of the requirement for two additional mutations to yield the resulting Cit+ trait. Moreover, we found that Cit+ mutants, when they first appeared, were often rather weak at using citrate. At least the main Cit+ line that we studied underwent an additional mutation (or mutations) that refined that ability and led to a large improvement in growth on citrate. All these issues and the supporting methods and data are covered in our paper.

Sincerely,

Richard Lenski


Gotta love it. Now to see how Schlafly handles the matter...


UPDATE TO THE UPDATE TO THE UPDATE: The stupidity continues! Check out the latest news!


* Actually, this has been the response for some time. It's just that we've recently added some new evidence to the already mammoth pile of it.

** Rock on, Trojans!

*** "Oh, wow! Check out the flagellum on that! Raarrr!"

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Thursday, June 12, 2008

Forget science, what the hell is a human?

Taking a break from the interesting conversation sparked by yesterday's post, I'd like to direct your attention to a bit of news coming to us from Europe. It appears that a very, very interesting human rights trial is in the works over there. Interesting because, in this case, the question at hand is just what it is that defines a human:

Matthew, a 26-year-old chimp, is headed to court in Europe as part of a human effort to classify him as a person.

Beyond the legal challenges, anthropologists say chimpanzees are not humans, though without a clear definition of what it means to be human, backing that claim up is a challenge perhaps fit for some great courtroom drama.

Animal rights activist and teacher Paula Stibbe, along with the Vienna-based Association Against Animal Factories (AAAF), says she wants the chimpanzee, named Matthew Hiasl Pan, declared a person. That way, Stibbe says she can become the primate's legal guardian if the bankrupt animal sanctuary where Matthew lives closes. (Under Austrian law, only humans are entitled to have guardians.)

The appeal has been filed in the European Court of Human Rights in Strasbourg, France. The case comes after Austria's Supreme Court upheld a lower court ruling in January, which rejected a request to appoint the chimp with a legal guardian. The rulings did not address whether a chimpanzee could be declared a person.


Now, this case may strike some of you as ridiculous, but I want you to hang in there, because it's quite the opposite. Chimpanzees are our closest relatives in the animal kingdom, they share a wide variety of traits in common with us including tool use, some communication, sociability, and a propensity for intra-species violence. That last similarity isn't really to our credit or theirs but, in perfect honesty, I suspect that any species as advanced as ours will almost certainly exhibit the same tendency. At the same time, however, most of us probably react to this story in a fairly predictable way:

"Granted, chimpanzees show many similarities with us as humans," said John Mitani, a primate behavioral ecologist at the University of Michigan, "but they are nonetheless chimpanzees, not humans, and are obviously different as well."


Yeah, I sympathize with this perspective but, unfortunately, get very nervous when people invoke that "obviously" line. There was a time when it was "obvious" that Africans were not the equals of white folk. There was a time when it was "obvious" that women couldn't be trusted in positions of power and authority. All too often "obvious" in a context like this is really just a code phrase for "this goes against my culturally determined beliefs." Perhaps fortunately for us all, however, our cultures are not the final arbiters of what is or is not true. Women and those of African-descent are the equals of whites and men and a large number of us would now claim that as being "obvious."

So on what basis can we make a decision here? Chimpanzees are, without question, a different species but in trying to decide if they're "human" we're not actually meaning human in a biological sense. Rather, we're asking if they should be treated as independent members of our society. Must one be human in order to earn such a privilege? Probably not. If a team of aliens from another star visited tomorrow we would likely treat them as equals- as though they were odd looking humans- rather than as animals. As such, biological similarity is not necessary to be treated as human. Thus, from here on in, I would say we should rephrase the question to "Should chimpanzees be classed as humankind?"

Once we get our terms straight, we need to come up with a basis for discrimination. We've already eliminated genetics through our alien example, so we need something else. Perhaps we can discriminate humankind from non-humankind based on intelligence? Well, maybe, but that's a tough position to take: there are a number of individuals who were born from human parents but whose intelligence is substantially below the norm. If chimps are non-humankind because they're not as smart, what does that mean for those persons? Hard to say- comparing human and non-human intelligence is notoriously difficult- but it's probably not good. Besides, is intelligence the best determinant of whether something is worthy of mercy and compassion? In the event that the technological singularity is possible, I sure as hell hope not.

The path I ventured down in an effort to resolve this question is suggested by something I brought up above: should chimps be given the privilege of membership in our society? The thing is, in my ethical worldview, privilege always comes paired with responsibility and vice versa. It is, to me, a sort of social or ethical law on par with the thermodynamic laws of physics. Thus, if you have the privilege of acting independently in a society, then you must also assume responsibility for the consequences of that freedom. Obligation, as a responsibility that attaches without an associated privilege, simply doesn't exist. There is always, always a pairing. So, in this case, I was forced to ask: can chimpanzees, if granted the privilege of membership in our civilization, also manage to shoulder the responsibilities that come with it? Indeed, I suspect they cannot and I'm not alone:

If Matthew the chimp were declared a person, scientists foresee it would open a messy can of worms.

"In general, I don't think that it's a good idea to grant chimpanzees legal human rights," Mitani said. "Chimpanzees are well-known to kill each other. What would we do to perpetrators of those 'crimes?'"


Indeed, this is a real problem although more for us than for the chimps. Based on this logic, it appears that we should not extend membership to chimps because they cannot execute all of the necessary responsibilities. Yet, again, there are problems here. Many impaired individuals are unable to take full responsibility for their own actions and yet, nevertheless, remain humankind. Perhaps the argument can be made that those persons are impaired whereas chimps, at their best, are still unable to accept responsibility, but that's also not really helpful. Children are, as a group, assumed to be incapable of accepting adult responsibility and are still humankind. Perhaps chimps could be integrated in a similar way?

Ultimately, I have no answer to this question. It will require a great deal of thought and effort and perhaps even research by the Animals and Society Section.* The thing is, however, that we had better start working on this question soon. The issue of what makes one humankind is not going to be limited to just chimps and primates for all that much longer. Leaving aside issues like artificial intelligence, which we touched on earlier this week, there's also the impending possibility of fashioning new forms of human existence. Take, for example, the recent and very overblown news, that it may soon be possible to fashion a child who has three parents. Okay, wait, that's not totally accurate- it's possible now, we just aren't allowed to do it:

A child with three genetic parents could be born within the next three years, scientists have predicted.

A team of scientists from Newcastle University have successfully created embryos containing DNA from one man and two women.

Under the current law, these embryos must be destroyed after fourteen days. However, new measures in the Human Fertilisation and Embryology Bill mean these embryos could soon be allowed to develop into children.

The technique aims to prevent certain hereditary diseases being passed from mother to child.


I said that this case was overblown and it is. In fact, what is being done is that the nucleus from a fertilized egg is removed and then inserted into another egg cell that does not have a nucleus.** Thus, the DNA that produces the human child derives from only two parents (i.e. the ones that contributed to the nucleus) and the third parent contributes her mitochondria. Mitochondria are funny little critters that help produce cellular energy, but contain their own DNA and act as independent, albeit subsidiary, organisms. Indeed, one hypothesis is that they used to be separate critters that eventually developed a symbiotic relationship with us. In any case, scientists are not engaging in full-on DNA tinkering here.

Yet, at the same time, this shows that we are moving closer to being able to engineer people. We could eliminate many forms of genetic disease and perhaps even build enhancements into our genome. What then? Are the results of such efforts humankind or are they artifice? We're going to need answers, and we're going to need them soon.

I really don't know how we're going to solve these sorts of issues but I'm not too worried. We're a smart species and as often as we make mistakes, we're also capable of stunning compassion. I'm proud of my species and, indeed, of all humankind.

Whatever the hell exactly it turns out that is.


* Is it just me, or does that logo make it look like that dude ate a cat?

** That egg's nucleus was also removed earlier.

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Wednesday, June 11, 2008

"And the great fleas themselves, in turn, have greater fleas to go on..."

This was just too good not to post more or less on its own:



Oddly, I feel satisfied with my place in the scheme of things. I don't think my field is just applied psychology but, hey, who wants to have an inter-disciplinary slap fight first thing in the morning?

Given the things I see written about us,* I'm just happy to see XKCD classing us as a science, you know?


* For example, I recently noticed a sociologist critiquing a textbook because it "...had a heavy focus on sociology as a science, which painted a very unidimensional picture of the discipline." Perhaps I'm in the minority,** but the whole reason I did sociology rather than, say, literary theory is that I want to study human society scientifically. That's kinda the whole point of the field.***

** Also, I'm a cranky bastard. I have no grudge against the "offending" sociologist and rather think she's promising... insofar as a moron like me can say that, anyway.

*** I'm suddenly reminded of a story from a conference I attended in my subject area. We'll call that area "wanking" for simplicity's sake. Anyway, I was talking to this guy who was attending for the first time and he said, "This wanking conference is great but all of the papers keep talking about wanking." And that's odd... why?

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Tuesday, June 10, 2008

Sometimes I just don't understand...

Some of you may have heard the recent news of a baby that was born twice. No, I don't mean "born again"- for the moment it appears that infants remain beyond the reach of the religious right.* No, in this case, I am referring to an infant who was partially removed from her mother so that doctors could operate on her, before replacing her in the womb. It's a pretty cool story, actually:

Four months into Keri McCartney's pregnancy, doctors reportedly noticed a tumor growing on the baby's tailbone.

Doctors discovered that the tumor was stealing blood from the fetus and weakening her heart. So, at 25 weeks, surgeons at Texas Children's Fetal Center cut into McCartney's abdomen in an effort to remove the life-threatening mass, according to a CBS News report.

...

Once the abdomen was open, doctors pulled out the entire uterus — and then half of the baby.

At that point, surgeons carefully cut away the non-cancerous tumor, which reportedly was the size of a grapefruit. ...“Half of the baby is extracted — only the part that needs to be operated on. And then she is put back into the womb," he said. "The womb is then closed and carefully monitored for signs of premature labor and other complications.”


So, not so much a child who was "born twice" as one that underwent a pretty sophisticated surgical intervention. I have never heard of something like this before and I am, to be totally honest, really impressed. Something I noticed however, as an afterthought, was this:

"We definitely had hope, but at the same time there are those times things don't go your way and God has other plans," [Keri] McCartney told CBS News.


And here the wheels just completely come off of my cognitive wagon. See, I understand the argument that contraception is wrong because it interferes with god's plan that a child be conceived. I get the argument that abortion is wrong because, likewise, it interferes with god's plan for a baby to be born.** I disagree with both of these arguments but I understand the logic behind them. The thing is, however, let's say that your child, in the womb, starts growing a giant tumor. Let's say that tumor might kill the child. By extension, doesn't that suggest that god wants your child to die? And if so, doesn't that mean that a surgical intervention to save the child is- in effect- a deliberate effort to thwart god's will?

Don't get me wrong, I have no idea if Ms. McCartney subscribes to any of the beliefs above but her remark that maybe "god has other plans" kinda implies that she thinks it's possible that god might have meant for her child to die. And if so, then trying to avert that outcome is, pretty much by definition, working to thwart god's intentions. Much like the Sago mine disaster, about which I have written previously religious faith often seems to make the world a sort of rorschach test. We perceive in the world what we are prepared to based on our preconceptions, even if those perceptions aren't particularly consistent with logic or objective reality. Granted, often the ambiguous world we live in does throw a signal or two our way, but I think we ignore the genuine signals as often as we latch onto the fake ones.

I'm not condemning, I'm sure I miss things due to my preconceptions on a fairly regular basis too. I have little doubt that my wife could even ennumerate specific examples. I just have to admit that this particular potential source of bias*** always leaves me baffled.

Whether I get it or not, though, I would like to offer my deepest congratulations to Ms. McCartney and her family for their heart-warming success. I would also like to express my genuine admiration and respect for the physicians, nurses, technicians, engineers, and scientists who developed the equipment and techniques that allowed this to happen. Your success gives me a sense of profound awe, pride, and satisfaction.

And I think that feeling is something we can all understand.


* Not least because a good number of Protestant doctrines deny that a child is able to receive baptism until such time as their faculties are sufficiently developed to do so willingly.

** I'm not referring to, nor will I touch, the argument that abortion is wrong because it is murder. I have an opinion on that but, at the moment, I am dealing entirely with the argument that it is wrong because it thwarts god's will.

*** Given that I am an atheist I have little choice but to view it as bias but, all the same, I must concede in all honesty that Ms. McCartney may be correct- it may be that god is responsible in some inscrutable way for the ultimate health of her child. I don't find that account at all plausible but, hey, there you go.

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Monday, June 09, 2008

The Measure of a Man

Recently just to pass the time I've been doing a bit of light reading. Specifically, I've been working my way through Mark Perakh's intriguing book Unintelligent Design. As you might guess, it's a critique of the ideas of Wild Bill Dembski generally, and his books Intelligent Design, The Design Inference, and No Free Lunch in particular. One of the arguments centers around the area of information theory and has really got me thinking.

To begin, let's consider information theory. This is, as you might guess, a sort of interdiciplinary area studying signals and communication. It is generally considered to have been founded by Claude Shannon back in 1948 and employs a definition of information that may seem a little counter-intuitive to many of us. Specifically, it regards a text (for example) as having an information content equal to the shortest possible computer program required to reproduce it. So, the easier the text is for a computer to generate, the less information that text carries. To make this a little more explicit, let's consider a pair of examples. The first example is a string of numbers like this "5696585638565615275755151850760772515." I produced this string more or less at random by slapping keys on my keyboard. This of course means that it is not truly random- given my hand placement the middle keys were struck rather a lot- but it provides a simple example of an otherwise unordered string of numbers. On the other hand, let's consider a different string of numbers: "1 11 21 1211 3112 132112 312213 232221 134211." Now, believe it or not, this second string of numbers is not random. Instead, it is derived from a simple rule that, after the first entry, each successive entry describes the previous. So, for example, "11" would be read as "one-1" and "21" would be read as "two-ones," and so on. Now, because the second string of numbers is a deterministic result of a simple rule, a computer program needs only that rule in order to accurately reproduce this string and, indeed, extend it to any arbitrary length we should require. In a sense the only information in the second string is carried by the first number which determines the remainder of the sequence- other than it, all other numbers are simply logical consequences of the first number and the rule. In contrast, the first string is effectively random and no number can be used to deduce the next in the sequence. Thus, to reproduce this sequence in a computer program you would effectively have to simply record the sequence in full and read it back out of memory. Thus, according to Shannon, the first sequence contains more "information" because it requires more computer space and effort to produce while the second sequence contains less.

This may seem highly counter-intuitive because most of us are used to employing the word "information" to refer to "meaningful content." Indeed, the random hash that we hear on an untuned radio station would likely be ignored as containing no information by most people despite the fact that- like the random series of numbers- it would be more difficult to reproduce than the content of a radio signal. In other words, static is regarded as containing more information than meaningful communication. The explanation for this, however, is that the meaningfulness of a signal is not necessarily inherent in that signal. Consider, for a moment, a police drama in which an agreement is made that when one character coughs twice the rest of the police squad will storm a building. Is there any way that those two coughs could be analyzed and dissected so as to reveal an unequivocal command to storm the building? Obviously not- in this case the meaningfulness is derived from properties of the sender (i.e. the cougher) and the receiver (i.e. the rest of the police) but is not otherwise inherent. Likewise, the meaningfulness of a text written in a language we cannot read is exceedingly low. Certainly we surmise that it must mean something, but we are incapable of distinguishing a meaningful sentence in, say, cyrillic from a random hash of letters unless we can actually read that alphabet and the relevant language.* As a result of all this, we cannot quantify the meaningfulness of a message with any ease but can quantify information in Shannon's sense. It is this distinction between meaning and information that, as a side note, proves so useful to Perakh in slapping the shit out of Dembski.

Now, pausing information theory for a moment, let's talk about Alan Turing. The father of computer science, Turing developed a method for determining when a computer should be regarded as intelligent or sentient, a test that has become known as the Turing test. I've discussed his ideas before but the basic logic of the test is simple: place a human in a room and allow them to correspond with several entities. Some of those entities are other humans but others are computers. To the extent that the first human cannot reliably distinguish the humans from the machines, you must consider the machine to be sentient. This may seem a little simplistic but, really, it just mirrors the process we use when talking to other humans. We cannot directly observe each other thinking but, because we speak and act in a manner that implies that we are intelligent and sentient,** we generally assume that other humans are intelligent and sentient. The Turing test simply makes it possible for a machine- an artificial construct- to be given the same benefit of the doubt that we normally give to other hominids.

So how does all this come together? Well, here's the thing: let's say that we managed to put together an artificial intelligence that could replicate, but not exceed, the mental capabilities of the average human. It passes the most stringent Turing test, or derivative examination, we can construct with flying colors. That A.I. would, presumably, be defined at least in part by a series of software commands.*** Interestingly enough, we can precisely measure and quantify the length and complexity of a computer program. More simply, we could calculate the amount of "information" contained in that program in Shannon's terms. And if this computer program is capable of mimicking a human, if it must be regarded as intelligent and sentient, then we have a way of measuring the "information" content of a single human individual.

And that, when you get right down to it, is pretty f-ing cool.


* Actually, information theory would provide a way to distinguish nonsense from a message but, sadly, it would not get us any closer to desiphering said message.

** The folks on Conservapedia being a notable exception.

*** For those not used to thinking about issues like this, I'm engaging in a lot of handwaving here. A functional A.I. would probably not rely on software as usually conceived any more than human thought depends on a hand calculator.

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Friday, June 06, 2008

Maybe it's just me...

...but has anyone else noticed that John McCain:



Sounds an awful lot like Andy Rooney?



It's just... creepy.

What slogan will they use?

"Old, Crazy Lunatic for President!"

"John McCain: Ask me about my grandkids!"

"Napping our way to prosperity!"

Yeesh.

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Thursday, June 05, 2008

Pants on Fire!

You probably heard the news that Barack Obama Tuesday acquired enough delegates to be the presumptive winner of the democratic presidential primary. This was long-expected, of course. Mathematically, a win by Hillary Clinton has been a near impossibility for months. Everybody, it seems, had known this, though Hillary stayed in the race for reasons of her own. She never “said die”, even though she’d already drunk the hemlock. I can’t speak to the wisdom of her choice, honestly. I assume it was a power play, and that her control of so many delegates puts her in a stronger position to demand a cabinet position (attorney general?) or even the vice presidency. The more of a pain you are, the more someone will pay you to have you go away. I really can’t say. But she stayed in the race long after it became clear she could not win the nomination.

To reasonably stay in the race, of course, she had to deny or ignore these facts. The legitimacy of her continued candidacy depended upon projecting the belief that she still had a chance. She went from town to town on the campaign trail voicing this false belief – and often declaring her expectation that she will in fact win. Since she’s an intelligent, rational person, I have to question whether this was a truthful statement – whether she in fact believed it—and I have serious doubts. And I am not alone in this.

But of course, she’s safe in declaring any belief she wants because we do not have a way to conclusively verify her intention or her true beliefs. So we in a sense are forced to give her the benefit of the doubt, even when all evidence points to artifice. In political circles, this realm of personal belief is a recognized contradiction-free zone. A savvy politician is stupid not to take advantage of this loophole in fact-checking. They learn to say they believe whatever is most expedient to be seen to believe. What they really believe is largely independent from their public statements about it, and is protected within their inner circle.

I watched some of the election punditry Tuesday during the final primaries. Even before the polls closed in Montana, the news organizations had declared Obama the presumptive nominee. Clinton then gave her final speech of the primary campaign, scheduled an hour before Obama’s, to an audience of supporters who, we were told, were not allowed to have cell phones or blackberries so that they would remain unaware of the fact that the networks had already pronounced the race over. It’s hard to imagine that Clinton herself was kept unaware of the facts, but she chose not to mention it. She—and everyone else there-- seemed to believe she was still in the race.

Of course, the plausibility of this “belief” that Clinton would win has been waning steadily since “super Tuesday”, and on this day, it was literally a foregone conclusion that she was out of it. Clinton would have had to win both the final primaries in South Dakota and Montana by about a hundred points just to keep Obama from acquiring the number of delegates he needed to clinch the nomination that night. No informed person could reasonably still hold out any hope for a Clinton victory. The only issue was whether or not she would acknowledge this. She chose rather to portray a person still with hope for victory. The pundits withheld their determination of whether this was dishonest, delusional, or just pathetic.

The Daily Show with Jon Stewart of that day taped at 5, before the returns came in, but aired at 11. I tuned in to watch it just after Obama’s speech and found that the guest was Clinton’s campaign committee chairman Terry McAuliffe. There is no one who has recently exploited the free zone of personal belief more than he. Long after a Clinton victory was possible, he prognosticated with practiced confidence and enthusiasm not that she could but that she would win the nomination. Stewart treated us to a video “greatest hits” of McAuliffe making such ridiculous statements on various news outlets, time and time again. And here he was on the very day that he KNEW it would all end-- that all these fanciful assertions would be exposed and knocked down like a house of chimerical cards – taping a show that he KNEW would not air until AFTER Obama had already won (and had given a speech claiming this). And yet, he took that moment to categorically reassert his claim that Clinton would win the nomination. It was so brazenly false as to be shocking. Stewart could barely believe it was happening – he asked “How do you DO that?”

What he meant of course is “How can you sit there and lie to my face?” Because that’s what he was doing. Lying. We know it and they know it. But since we can’t demonstrate the falsity of prediction, a form of belief, we silently grit our teeth, and they continue to do it.

He’ll no doubt be working for the Obama campaign in a month or two, using the same dishonest tactics against republican operatives like Karen Hughes doing the same thing. After each public debate or speech, some news organization will put a microphone in his face so he can look America in the eye and say whatever he wants us to think he believes. We’ve come to refer to this as “spin”, but that implies we think they’re just engaging in wishful thinking or biased perception, when really it’s clearly unprincipled “lying”.

OK, I know lying in politics isn’t exactly new. But haven’t we reached something of a crescendo lately? It seems to me that public figures used to keep their lying to a plausible minimum, largely because being found to be a liar used to have adverse consequences for the public trust and one’s career. But now it’s in many cases expected. It’s shocking when somebody tells the truth, even under oath, when they could conceivably, if disingenuously, claim to not know, not to remember, or not to not mean what they knew, remembered, or meant. Evidence may rebut such assertions, but no one has the balls to try to attach the “liar” label when there is the slimmest colorable claim that they are being genuine.

I understand this reluctance, but a person is only entitled to this benefit of the doubt until they demonstrate they don’t deserve it. Once you’re caught in a probably lie, this ought to presumptively discredit your future statements. Really, once someone like McAuliffe or Hughes has demonstrated not just bias but clear disregard for truth, how can a news organization continue to give them a platform to speak and pretend it’s still plausible that they’re speaking from their honest opinions? Wouldn’t it be more honest to introduce these people as “professional liar James Carvell” or “cynical misinformation expert Karl Rove”? or “White House propaganda conveyer Dana Perino”

The fact that no one does this suggests that lying in this way is accepted as business as usual, even when the campaign is over. Sadly, this was confirmed recently by former White House propaganda conveyer Scott McClellan’s new book. In it, McClellan criticizes the current administration for being in “perpetual campaign mode”, and it’s clear by this, he means “constant lying”. Although he gives his old boss (Bush) the benefit of the doubt as to whether he really believes what he’s saying, he describes a White House that said and did whatever was necessary to have the impact it desired, to leave the impressions of facts it wanted to leave, irrespective of reality.

How far can this go? How much latitude do we allow a public figure to deny reality if they express the falsities as their opinion or belief with sufficient brazenness, even though it strains credulity? How many times do we let such people do this before we publicly dismiss them? Our forbearance is seemingly infinite.

Isn’t it time we called liars liars?

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