April 2011 Archives

Intelligent design news from the 21st of April to the 27th of April, 2011.

The Discovery Institute has been extremely relaxed with its posting over the last week - partially explaining why this is slightly late, there was no massive compulsion on my part to hastily set the record straight on certain blog posts before other new items swallowed the spotlight - and whether this is an external representation of the internal busyness of the organisation, I’m not sure. Perhaps Casey Luskin was too busy doing proper science-attorney things too blog much this week.

But it doesn’t really matter, there’s enough meat for me to sink my metaphorical blogging teeth into. Also, I remember the last time there was a slump in blogging output from the Discovery Institute: I predicted wonderful things were about to happen, but I was wrong. So, I’ll try not to read anything into it.

This week’s TWiID covers pseudogenes and “Darwinian assumptions”, enzyme evolution and ID, and the traditional religious bias of the Discovery Institute.

Blogging on Peer-Reviewed Research

I've been giving talks at scientific meetings on educational outreach — I've been telling the attendees that they ought to start blogs or in other ways make more of an effort to educate the public. I mentioned one successful result the other day, but we need more.

I give multiple reasons for scientists to do this. One is just general goodness: we need to educate a scientifically illiterate public. Of course, like all altruism, this isn't really recommended out of simple kindness, but because the public ultimately holds the pursestrings, and science needs their understanding and support. Another reason, though, is personal. Scientific results get mangled in press releases and news accounts, so having the ability to directly correct misconceptions about your work ought to be powerfully attractive. Even worse, though, I tell them that creationists are actively distorting their work. This goes beyond simple ignorance and incomprehension into the malign world of actively lying about the science, and it happens more often than most people realize.

I have another painful example of deviousness of creationists. There's a paper I've been meaning to write up for a little while, a Nature paper by David and Alm that reveals an ancient period of rapid gene expansion in the Archaean, approximately 3 billion years ago. Last night I thought I'd just take a quick look to see if anybody had already written it up, so I googled "Archaean genetic expansion," and there it was: a couple of references to the paper itself, a news summary, one nice science summary, and…two creationist distortions of the paper, right there on the first page of google results. I told you! This happens all the time: if there's a paper in one of the big journals that discusses more evidence for evolution, there is a creationist hack somewhere who'll quickly write it up and lie about it. It's a heck of a lot easier to summarize a paper if you don't understand it, you see, so they've got an edge on us.

Aurora borealis

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Photograph by Bud (Santa) Kuenzli.

KuenzliAurora.jpg

Aurora borealis. Mr. Kuenzli, who lives in North Pole, Alaska, writes that this shot “jumped out at me because it looked like a dragon breathing fire” and adds, “Pareidolia is the term for the phenomenon of seeing images like animals in clouds or Jesus’ face on a piece of toast, or a dragon in the aurora borealis.” Or cyanobacteria in a meteorite?

Late last month, Casey Luskin wrote an article advocating a positive case for ID creationism. Jack has already done a good job of refuting Casey’s wishful hand waving.

However, in the comments of the post, Casey and I had a little exchange in which I tried to get him to commit to developing a positive model of common design, and he just, well, assured me that his legal education prepared him to deal with the statistics that he was butchering left and right. Yeah, umm … anyways, my last comment was never published, and now enough time has passed that I feel I can share it with you and let you decide why it never showed up on the DI’s website.

If there’s anyone living in the Columbus, OH, area who’s interested in getting involved (or more involved) in science outreach and the Science Cafe movement, now’s your chance. The Columbus Science Pub, which I started off back in September 2010 and which now boasts over 450 fans on Facebook, is looking for new leadership to take over when Dan (the current organizer) leaves Cowtown at the end of the summer.

Anyone interested should send a note to [Enable javascript to see this email address.].

For more information on the Columbus Science Pub, go to Columbus Science Pub’s Facebook site or for information on the Science Cafe movement, check out http://www.sciencecafes.org/.

[Republished from Homologous Legs]

A well-accepted characteristic of a scientific hypothesis is that it must generate predictions about the world against which tests can be run - confirming or falsifying those predictions and thus supporting or not supporting the hypothesis in question. Understandably then, intelligent design proponents need to demonstrate that ID can produce predictions if it is to be taken seriously as a scientific hypothesis and alternative to evolutionary theory.

Historically (as much as I can say “historically” in the context of such a new movement), this has not been a major goal of ID proponents. Most of their previous efforts have gone into either arguing against evolution (see Michael Behe’s Darwin’s Black Box) or trying to justify ID in a pseudomathematicophilosophical 1 way, bypassing the normal scientific process (see William Dembski’s design inference/explanatory filter). Neither of these routes have been very successful, as much as ID proponents will try to tell you otherwise, and combined with a substantial amount of scientific and philosophical attack against the ideas of the ID movement, they have begun to change tactics a little bit, and talk about predictions and testability has crept back into discussions about ID, both online and in books.

Next up on phyloseminar:

Mike Lin speaks Tuesday, April 26th at 12pm PST on “Locating protein-coding sequences under selection for additional, overlapping functions in 29 mammalian genomes”

The degeneracy of the genetic code allows protein-coding DNA and RNA sequences to simultaneously encode additional, overlapping functional elements. A sequence in which both protein-coding and additional overlapping functions have evolved under purifying selection should show increased evolutionary conservation compared to typical protein-coding genes—especially at synonymous sites. We developed a method to systematically locate short regions within known ORFs that show conspicuously low estimated rates of synonymous substitution, based on phylogenetic codon rate models and likelihood ratio tests.

We applied this method to genome alignments of 29 placental mammals, resulting in more than 10,000 “synonymous constraint elements” (SCEs) with resolution down to nine-codon windows. These are found within more than a quarter of all human protein-coding genes and contain ~2% of their synonymous sites. We collected numerous lines of evidence that the observed synonymous constraint in these regions reflects selection on overlapping functional elements including splicing regulatory elements, dual-coding genes, RNA secondary structures, microRNA target sites, and developmental enhancers. We also ruled out certain alternative explanations such as codon usage bias and neutral rate variation.

Our initial results show that overlapping functional elements are common in mammalian genes, despite the vast genomic landscape. Furthermore, anticipating the future availability of additional mammalian and vertebrate genomes, we are currently developing Bayesian codon modeling methods to measure synonymous rates at even higher resolutions, perhaps eventually allowing the detection of individual regulator binding sites embedded in protein-coding ORFs.

Japan 04:00 (04:00 AM) on Wednesday, April 27
New Zealand 07:00 (07:00 AM) on Wednesday, April 27
West Coast USA 12:00 (12:00 PM) on Tuesday, April 26
East Coast USA 15:00 (03:00 PM) on Tuesday, April 26
England 20:00 (08:00 PM) on Tuesday, April 26
France 21:00 (09:00 PM) on Tuesday, April 26

Intelligent design news from the 14th of April to the 20th of April, 2011.

Another week, another lot of ID blog posts to wade through. Not a lot I want to mention in this intro, particularly, except for perhaps this recent post of mine responding to an Uncommon Descent post about ID’s supposed scientific predictions. It was going to be included in this post, but it needed a larger amount of specific attention, given how important the topic is. It should be cross-posted on PT in a little while, but I just wanted to give you all a heads-up.

Other than that, this week wasn’t particularly noteworthy. Nothing that changed the ID/evolution game too much, just some ideas to consider. Robert Crowther wrote about the difference between promoting ID and teaching criticisms of evolution, Casey Luskin attacked the NCSE’s Steve Newton for over/misusing the word “creationist”, and Jonathan Wells’ new book on junk DNA got a flattering plug, possibly foreshadowing another book-promoting frenzy…

250 years of Bayes!

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The Reverend Thomas Bayes died 250 years ago this month, in 1761. His famous “Essay Towards Solving a Problem in the Doctrine of Chances”, from which stems “Bayes’ Rule”, was published posthumously 247 years ago in 1764 by the Royal Society. A detailed review of the argument in modern notation is Edwards (1978) in the Scandanavian Journal of Statistics. Any of us scientists working today would be beyond lucky to have our work cited 250 later!

The R Revolutions blog highlights the anniversary and is posting videos explaining the significance of Bayesian thinking. Check it out!

From here. The conclusion:

Given the power of our prior beliefs to skew how we respond to new information, one thing is becoming clear: If you want someone to accept new evidence, make sure to present it to them in a context that doesn’t trigger a defensive, emotional reaction.

This theory is gaining traction in part because of Kahan’s work at Yale. In one study, he and his colleagues packaged the basic science of climate change into fake newspaper articles bearing two very different headlines–“Scientific Panel Recommends Anti-Pollution Solution to Global Warming” and “Scientific Panel Recommends Nuclear Solution to Global Warming”–and then tested how citizens with different values responded. Sure enough, the latter framing made hierarchical individualists much more open to accepting the fact that humans are causing global warming. Kahan infers that the effect occurred because the science had been written into an alternative narrative that appealed to their pro-industry worldview.

You can follow the logic to its conclusion: Conservatives are more likely to embrace climate science if it comes to them via a business or religious leader, who can set the issue in the context of different values than those from which environmentalists or scientists often argue. Doing so is, effectively, to signal a détente in what Kahan has called a “culture war of fact.” In other words, paradoxically, you don’t lead with the facts in order to convince. You lead with the values–so as to give the facts a fighting chance.

Grus canadensis

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Photograph by Dave Thomas.

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Grus canadensis – sandhill crane, Peralta, New Mexico, 2010.

Did language originate in Africa?

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Arguably, yes, according to an article in Science this past week. Press reports may be found in the Times and in ScienceNOW. In a nutshell, the author of the Science article, Quentin Atkinson, examined the number of phonemes in approximately 500 extant languages and found that that number was distributed geographically in a way that suggests an origin for all languages in Africa. Indeed, we might speculate that the invention of language was the breakthrough that allowed our species to expand out of Africa.

Francis Beckwith and his defender Denyse O’Leary seem to not be able to agree on what is wrong with Forrest’s critique of Beckwith in Synthese. Beckwith (2011) in Synthese:

I wish I still lived in Minnesota …

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… because then I could go to Minicon 46 and attend this bit of programming:

Creation Museum Slideshow - 8:30 PM Saturday
John Scalzi shares photos and stories from his visit to “the very best monument to an enormous load of horseshit that you could possibly ever hope to see.” Hilarity ensues.
John Scalzi, Rob Callahan moderating

Here’s Scalzi’s original report on the visit. One memorable extract:

Here’s how to understand the Creation Museum:

Imagine, if you will, a load of horseshit. And we’re not talking just your average load of horseshit; no, we’re talking colossal load of horsehit. An epic load of horseshit. The kind of load of horseshit that has accreted over decades and has developed its own sort of ecosystem, from the flyblown chunks at the perimeter, down into the heated and decomposing center, generating explosive levels of methane as bacteria feast merrily on vintage, liquified crap. This is a Herculean load of horseshit, friends, the likes of which has not been seen since the days of Augeas.

And this is, in sum, the Creation Museum. $27 million has purchased the very best monument to an enormous load of horseshit that you could possibly ever hope to see.

Just so.

Hat tip to Scalzi his own self

[Republished from Evolving Thoughts]

A while back I published a paper in a special edition of Synthese on "Evolution and its rivals". My paper was titled "Are Creationists Rational?" in which I argued that yes, in a bounded sense they are. I was very pleased to be invited to publish in this front rank journal by the special editors. However, when the printed version arrived, the editors-in-chief had inserted a rather nasty statement, a disclaimer in fact, bringing the academic standing of the contributions into disrepute. Although I do not think my paper was directly involved in this, I post below a statement about the disclaimer by the special edition's editors, Glenn Branch and James Fetzer. I fully support it.

RE: "Evolution and Its Rivals", SYNTHESE 178:2 (January 2011)

Dear Members of the Philosophy Community,

As the Guest Editors of a special issue of SYNTHESE, "Evolution and Its Rivals", we have been appalled to discover that the Editors-in-Chief added a prefatory statement to the issue that implies that the Guest Editors and their contributors have not maintained the standards of the journal. Our purpose here is to convey to you an explanation of the history of this special issue and the unusual problems we encountered in dealing with the Editors-in-Chief, in the hope that our reflections will place their statement in the proper context and guide you in future dealings with the journal.

The following statement was published in the printed but not the on-line version of this issue:

Statement from the Editors-in-Chief of SYNTHESE

This special issue addresses a topic of lively current debate with often strongly expressed views. We have observed that some of the papers in this issue employ a tone that may make it hard to distinguish between dispassionate intellectual discussion of other views and disqualification of a targeted author or group.

We believe that vigorous debate is clearly of the essence in intellectual communities, and that even strong disagreements can be an engine of progress. However, tone and prose should follow the usual academic standards of politeness and respect in phrasing. We recognize that these are not consistently met in this particular issue. These standards, especially toward people we deeply disagree with, are a common benefit to us all. We regret any deviation from our usual standards.

Johan van Benthem
Vincent F. Hendricks
John Symons
Editors-in-Chief / SYNTHESE

First and foremost, we deeply regret the decision to insert this disclaimer, which insults not only us but also the contributors to the special issue. It was inserted without our consent or approval, without our being directly notified by the Editors-in-Chief, and despite our having been assured twice by one of the Editors-in-Chief that it would not be inserted (as we will explain below). In retrospect, we perhaps should have warned the contributors when the proposal to insert such a disclaimer was broached, but it did not occur to us that the Editors-in-Chief would renege on their assurances that no disclaimer would be inserted. Nevertheless, we would like to take this opportunity to reiterate our sincerest apologies to the contributors.

The background to the disclaimer involves Barbara Forrest's contribution to the special issue, "The Non-Epistemology of Intelligent Design," which vigorously critiqued the work of Francis Beckwith. Shortly after the papers were published on-line in advance of publication by SYNTHESE in 2009, friends of Beckwith began to protest -- not to the Guest Editors, but to the Editors-in-Chief -- about Forrest's article, one even going so far as to claim that it was "libelous."

In response, the Editors-in-Chief discussed the matter with Jim Fetzer, who has an extensive history with the journal, including serving as one of its co-editors from 1990 to 1999 and editing six previous special issues. In preparation for this discussion, Fetzer solicited the opinion of another former editor of SYNTHESE, who regarded the paper as unproblematic with the minor exception of Forrest's mention of Beckwith's recent return to the Catholic Church, a matter that has not surfaced in any of the discussion that has followed.

The outcome of the discussion was that Beckwith would be allowed a chance to respond in a later issue of SYNTHESE (which he has now taken; his response has already been published on-line in advance of publication), but that "[n]othing is to be done to the special issue" (as Fetzer summarized his understanding of the discussion to the Editors-in-Chief, none of whom expressed any disagreement).

Subsequently, in September 2010, Forrest advised Glenn Branch that she had been asked by two of the Editors-in-Chief to revise her paper -- which, again, had already been published on-line -- on pains of an editorial disclaimer being added to the issue. This condition was not, as would have been appropriate, discussed with or even divulged to the Guest Editors. Branch passed this news on to Fetzer, who protested vehemently to the Editors-in-Chief; it appears that the third was not aware of the demand from the other two. In November 2010, the third Editor-in-Chief assured us that both the request for a revision and the idea of an editorial disclaimer had been dropped. (We should also mention that the publisher of the journal was by no means enthusiastic about the idea of revising an already published paper.) With that, we believed we had resolved any issues between the parties involved.

It therefore came as a complete -- and most unwelcome -- surprise to discover such a statement included in the printed edition.

Several of the contributors have informed us and/or the Editors-in-Chief that they would have withdrawn their papers from the issue had they known that they would have been published under the shadow of such a disclaimer. (Note that the disclaimer speaks of "some of the papers," in the plural, suggesting that Forrest's was not the only paper that is supposedly objectionable.) We ourselves would have reconsidered our proposal to edit a special issue on this subject had we any idea that such opprobrium might attach to our efforts, which have conformed to appropriate standards of scholarship and publication in general, and with the standards of SYNTHESE in particular, with which we are very familiar.

We are both shocked and chagrined that a journal of SYNTHESE's stature should have sunk so low as to violate the canons of responsible editorial practice as the result of lobbying by a handful of ideologues. This tells us -- as powerfully as Forrest's work -- that intelligent design corrupts. We regret the conduct of the Editors-in-Chief and the unwarranted insult to the contributors and ourselves as Guest Editors represented by the disclaimer. We are doing our best to make the misconduct of the Editors-in-Chief a matter of common knowledge within the philosophy community in the hope that everyone will consider whatever actions may be appropriate for them to adopt in any future associations with SYNTHESE.

Sincerely,

Glenn Branch
Deputy Director
National Center for Science Education, Inc.

James H. Fetzer
McKnight Professor Emeritus
University of Minnesota Duluth

(Institutions are listed for the purposes of identification only.)

It looks very much like Francis Beckwith's sympathisers' objections were unilaterally accepted without question by the editors-in-chief. One can only wonder why. Perhaps threats of legal action were made against the journal or the editors? If so, this action is execrable and should be withdrawn. The proper forum for academic dispute is in debate, not attack based on fear of litigation. Beckwith has his forum, and readers can decide for themselves whether they think he has a case. One wonders whether or not a similar disclaimer will accompany his contribution.

Is this what the academy has been reduced to? In the light of recent attempts to silence or discourage criticisms by certain allied political interests, this looks very bad.

Intelligent design news from the 6th of April to the 13th of April, 2011.

This week was fairly interesting with regards to the online ID movement. However, it wasn’t a great week for author diversity. Yes, all the posts I’ll be talking about were written by Casey Luskin, everyone’s favourite non-scientist attorney. What I want to know is: how does he find the time to write so much? Surely his work as Program Officer in Public Policy & Legal Affairs at the Discovery Institute occupies much of his time, so where does all of this time come from to discuss so many different topics relating to ID? As a full-time student I barely have enough time to scrape this together every week… (And I’ve been sick and quite busy, which is why this post is a day late, I apologise.)

Anyway, this week’s posts are about Lynn Margulis and academic “status”, the Tennesse academic freedom bill and language in biology. Let’s get into it.

Freshwater: Rutherford Institute joins the case

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As I noted in a comment a few days ago, federal judge Gregory Frost remanded John Freshwater’s appeal of his terrmination back to the Knox County Court of Common Pleas. Now according to a press release today, April 11, the Rutherford Institute has agreed to assist Freshwater in the appeal of his termination.

The press release says

The Rutherford Institute is defending a Christian teacher who was allegedly fired for keeping religious articles in his classroom and for using teaching methods that encourage public school students to think critically about the school’s science curriculum, particularly as it relates to evolution theories.

More below the fold.

Tenodera sinensis

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Photograph by Burt Humburg.

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Tenodera sinensis – Chinese (praying) mantis, Michigan, 2010. Identification courtesy of Eric Eaton, author of Kaufman Field Guide to Insects of North America.

Margulis does it again

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We all know of once-respected scientists who ended up going off the deep end, adhering to an unproven idea despite massive evidence to the contrary. Linus Pauling and his advocacy of megadoses of Vitamin C, or Peter Duesberg’s descent into HIV denial. It’s all the more disappointing when the one taking a dive is a woman, since there are, compared to men, relatively fewer female “big names” in the sciences. So when one goes from views that were outside of the mainstream (but later proven largely correct) to complete science denialism, it makes it all the more depressing. Even worse, mainstream popular science magazines like Scientific American (with this article by Peter Duesberg) and Discover (Duesberg again) give these ideas reputable press. And now Discover has done it again by giving “maverick” biologist Lynn Margulis a profile in their latest issue. More over at Aetiology.

According to a recent tally by the ever-vigilant National Center for Science Education, nine anti-science bills have been introduced in various states since January. Most of them use the “critical analysis” ploy, also known as the “strengths and weaknesses” ploy. Some bills specifically state that teachers may not be penalized in any manner for “helping” students to understand the strengths and weaknesses of evolution. Most recently, the Tennessee House passed a bill that would allow teachers to “help students understand, analyze, critique, and review … the scientific strengths and scientific weaknesses of existing scientific theories.” By an odd coincidence, the scientific theories with which students evidently need the most help include evolution, global warming, origin of life, and human cloning, just those topics which so bemuse the extreme right. Where, you may ask, is homeopathy or “alternative” medicine, subjects that are desperately in need of critical analysis? Certainly not singled out in any of the bills. You may read more details and find relevant links at the NCSE website.

RationalWiki has posted an exhaustive list of evidence that evolution is a hoax.

Thanks to Mike Klymkowsky for the tip.

Intelligent design news from the 30th of March to the 5th of April, 2011.

Sometimes, keeping up with the intelligent design movement can feel like a full-time job. Other times… not so much. While some of the output by the Discovery Institute and its related organisations is somewhat novel, most of it is simply rehashed ideas from a limited pool. This week was a fairly good example of the latter. We had copy-and-paste arguments for the positive nature of the design argument, as well as an unsurprising plug for a blatantly religious debate, not to mention many, many posts on Uncommon Descent about- well, I don’t really know. The words just tend to blend together after a while, forming a soup of pseudo-philosophy and rhetoric.

The only really “novel” thing this week was something to do with April Fool’s Day… and it wasn’t novel in a good way.

The headline says it all. See here for the latest article by Adam Liptak in the Times. To put it as briefly as possible, the Court seems to think that a tax expenditure is not an expenditure. My earlier posting on the topic is here.

Thanks to Jim Lippard for lighting a fire under me.

IMG_0300_Enoplognatha ovata_Chlorochroa_600.jpg

Enoplognatha ovata – candystripe or polymorphic spider – dancing with Chlorochroa sp. – stink bug. Identifications courtesy of Eric Eaton, author of Kaufman Field Guide to Insects of North America.

34th Carnival of Evolution

The newest edition of the Carnival of Evolution is up at Quintessence of Dust. Support your local carnival, especially if you’re curious about chemotaxis, pit vipers, kin selection, or human penises. Yes, it’s the 1 April edition. No, that last entry is not a joke. But it should get you moving.

Testing Common Design

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Recently I’ve been thinking that it might be possible to test a subset of creationist arguments: that molecular similarities are better explained by common design than common descent.

I believe that using a Bayes factor-based analysis along the lines of Theobald (2010) would be the appropriate approach. Not only would this force the construction a positive model of design (a first in creationism), but one can also integrate over the different intelligent designers that the DI likes to throw out there. So whether Hanuman, God, Jesus, God, the Holy Ghost, God, Richard Dawkins, God, Moses, God, Uranus, God, Thor, God, Prof. X, or God is the true common designer (or a mixture of the ones above), they all can be included in the model.

Of course, ID advocates would probably insist on using a Dirac delta function as the prior.

Green dandelions at last!

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Natural selection seems to have overshot the mark just a little bit, but, as I predicted, last summer I began to see a few green dandelions in my lawn.

IMG_0279_GreenDLion_600.png

Taraxacum officinale viride – green dandelion. The visitor is a longhorn beetle, Crossidius sp., according to Eric Eaton, author, Kaufman Field Guide to Insects of North America.

Does religion make you fat?

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Well, no, not exactly, maybe, but a recent article in the Los Angeles Times cites a study to the effect that young adults who participate regularly in religious activities are more likely to become obese than those who do not. Specifically, people with very high involvement in religious activities were 50% more likely to become obese than those who did not participate at all, even after the data were controlled for such factors as age, sex, race, income, and what I will call the initial condition, that is, the body-mass index of the subjects at the beginning of the study.

Why? The principal investigator, Matthew Feinstein, would not commit himself, but thought it might be the weekly potluck dinners. The LA Times worries about the future of the Jell-O salad. I immediately thought of the movie where Woody Allen decides to become a Catholic and brings home a loaf of white bread and a jar of mayonnaise.

iConfess. Speaking of Catholicism, this month’s issue of The Progressive cites a Reuters dispatch to the effect that the Catholic Church in the United States has approved an iPhone app for confession. Priests need not worry about technological unemployment, however; there is, at least so far, no app for absolution – or is that iAppsolution? – so Catholics will still have to get absolution from a priest.

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