Scientific American Chooses ENCODE Project as One of the Top Ten Science Stories in 2012

It's pretty hard to ignore the ENCODE papers if you're selecting the top ten science stories of 2012. This doesn't mean it's a "breakthrough" as Science magazine claims [Science Magazine Chooses ENCODE Results as One of the Top Ten Breakthroughs in 2012]. And it doesn't mean that the results overthrow Darwinian evolutionary theory as implied by the Intelligent Design Creationists [Intelligent Design Creationists Choose ENCODE Results as the #1 Evolution Story of 2013].

The Scientific American article was written by Bora Zivkovic, a long-time blogger who knows the difference between hype and reality. He apparently knows which scientists to believe and which ones to ignore [The Top 10 Science Stories of 2012: Publication of the ENCODE Encyclopedia: A Milestone in Genome Research].

Unfortunately, much of the discussion surrounding the publication of ENCODE failed to focus on the usefulness of the catalogue and the techniques that built it. Instead, much of the debate centered on the failure to understand that transcription does not necessarily imply meaningful biological function. Cells are messy biological entities, with lots of gunk and goo floating around, so mistakes happen all the time. Many DNA sequences get translated into RNA, only to have the cell degrade that RNA. Much, perhaps most, of the DNA in our genomes—despite being occasionally transcribed, and thus recorded in ENCODE—is still functionless “junk DNA.” That is actually not surprising; it is in fact expected from evolutionary theory. Thanks to ENCODE, though, we should eventually learn which sequences are the junk and which are the gems of cell activity.

This is a very different take on the subject than that published by the editors of Science and the Intelligent Design Creationists.

I wonder why?

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Intelligent Design Creationists Choose ENCODE Results as the #1 Evolution Story of 2012

The folks over at Evolution News & Views (sic) have selected the ENCODE papers as the Number 1 evolution-related story of 2012. Naturally, they fell for the hype of the ENCODE/Nature publicity campaign as you can see from the blog title: Our Top 10 Evolution-Related Stories: #1, ENCODE Project Buries "Junk DNA".

Most of the article is just the reposting of an article by Casey Luskin but some anonymous editor has added ...

Editor's note: For the No. 1 slot among evolution-related news stories of 2012, this one was an easy pick. The publication of the ENCODE project results detonated what had been considered among the sturdiest defenses that Darwinian evolutionary theory could still fall back upon: "Junk DNA." Casey Luskin's initial reporting is featured below. See also our response to the ensuing controversy over ENCODE ("Why the Case for Junk DNA 2.0 Still Fails").

Normally I would make fun of the creationists for misunderstanding the real scientific results in the papers that were published last September but, in this case, there are lots of real scientists who fell into the same trap.

Even Science magazine selected the ENCODE results as a top-ten breakthrough and noted that 80% of the human genome now has a function [Science Magazine Chooses ENCODE Results as One of the Top Ten Breakthroughs in 2012]. Oh well, I guess I'll just have to be content to point out that many scientists are as stupid as many Intelligent Design Creationists!

I can still mock the creationists for claiming that "Darwinian evolutionary theory" supports junk DNA.

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Science Magazine Chooses ENCODE Results as One of the Top Ten Breakthroughs in 2012

Science magazine (published by AAAS) was one of the major news sources that fell hook, line and sinker for the ENCODE/Nature publicity campaign last September [Science Writes Eulogy for Junk DNA]. It even published a laudatory three page profile of Ewan Birney, the man responsible for misrepresenting the ENCODE results as evidence that most of our genome is functional [Ewan Birney: Genomics' Big Talker].

I was somewhat apprehensive when I saw that the editors of Science had picked the ENCODE results as one of the top ten breakthroughs [Genomics Beyond Genes]. Would the editors continue to promote the idea that most of the human genome is functional?

Carnival of Evolution #55

This month's Carnival of Evolution is hosted by Suzanne Elvidge at Genome Engineering. Read it at: Carnival of Evolution #55: New Year’s resolutions 2013 – evolution, evolution, evolution

Welcome to 2013 and to Carnival of Evolution #55, and Happy New Year to everyone from Genome Engineering. Have you made any New Year’s resolutions this year? Apart from the oft repeated ‘This year I will write my novel’, here are some of my New Year’s resolutions for 2013.

New Year’s Resolution number one: Deliver Carnival of Evolution on time

Okay – broken that one already – sorry. Hope it was worth waiting for. Now onto the rest.

There's no host yet for the next Carnival of Evolution (February, 2013). If you want to volunteer to next month or for March, April, or May, contact Bjørn Østman. Bjørn is always looking for someone to host the Carnival of Evolution. He would prefer someone who has not hosted before but repeat hosts are more than welcome right now! Contact him at the Carnival of Evolution blog. You can send articles directly to him or you can submit your articles at Carnival of Evolution although you now have to register to post a submission.

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This Is Why Christians Want Guns

I'm sure you've heard that Americans need guns so they can overthrow the government whenever it infringes on their personal beliefs. Many Americans believe they have a "right" to commit treason whenever they feel like it and, furthermore, that "right" must be protected by allowing them to bear arms, including assault weapons.

Here's what could happen. This is an interview by Janet Parshall of Mathew Staver. Believe it or not, Mathew Staver is Dean of the School of Law at Liberty University. He is also the Chair and Founder of a right-wing extremest group called Liberty Counsel. Mat is worried that the Supreme Court of the United States—the ultimate source of what's legal and what's not—could actually allow same-sex couples to get married!!!!

The consequences would be devastating, according to the Dean of Law. He says,

This is the thing that revolutions literally are made of. This would be more devastating to our freedom, to our religious freedom, to the rights of pastors and their duty to be able to speak and to Christians around the country, then anything that the revolutionaries during the American Revolution even dreamed of facing. This would be the thing that revolutions are made of. This could split the country right in two. This could cause another civil war. I’m not talking about just people protesting in the streets, this could be that level because what would ultimately happen is a direct collision would immediately happen with pastors, with churches, with Christians, with Christian ministries, with other businesses, it would be an avalanche that would go across the country.

I'm sure it's a great comfort to most Americans that these people have the weapons they need to start another civil war over legalizing gay marriage.

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[Hat Tip: Hermant Mehta: Christian Right Leader: Legalizing Gay Marriage Will Result in Another Civil War.]

The National Rifle Association: Part of the Problem

According the Toronto's Globe & Mail [NRA's call for armed guards in U.S. schools a warning for politicians].

The NRA is offering to help with the effort to put guns in schools. Mr. LaPierre named former Arkansas Republican congressman Asa Hutchinson to lead a National School Shield Program to help design security plans for every school in the country.

Because, as Mr. LaPierre put it: “The only thing that stops a bad guy with a gun is a good guy with a gun.”

If there is a one statement that sums up the political divide in America, that may be it.

Here's the video of the NRA press conference.


And here's part of the transcript ...

With all the foreign aid, with all the money in the federal budget, we can’t afford to put a police officer in every school? Even if they did that, politicians have no business — and no authority — denying us the right, the ability, or the moral imperative to protect ourselves and our loved ones from harm.

Now, the National Rifle Association knows that there are millions of qualified active and retired police; active, reserve and retired military; security professionals; certified firefighters and rescue personnel; and an extraordinary corps of patriotic, trained qualified citizens to join with local school officials and police in devising a protection plan for every school. We can deploy them to protect our kids now. We can immediately make America's schools safer — relying on the brave men and women of America’s police force.

The budget of our local police departments are strained and resources are limited, but their dedication and courage are second to none and they can be deployed right now.

I call on Congress today to act immediately, to appropriate whatever is necessary to put armed police officers in every school — and to do it now, to make sure that blanket of safety is in place when our children return to school in January.

There are about 130,000 schools in America. Let's say we find 130,000 people who are willing and able to use a gun to kill anyone who tries to get into the school. Imagine that many of them are "patriots" who belong to the National Rifle Association. They'll probably be working for close to minimum wage. A bored, underpaid, cowboy with a loaded gun in every school.

What could possibly go wrong?

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Michael Ruse Defends the Cosmological Argument

Here's a video of Michael Ruse criticizing Richard Dawkins for being too simplistic in his attack on belief in god(s). What Ruse is saying is that theologians have a much more sophisticated view of religion than Dawkins admits. It goes without saying that really good philosophers, like Ruse, understand the sophisticated version of Christian apologetics so they would never write a book like The God Delusion.

Ruse gives us an example of the worst form of accomodationism. Beginning at 2:11, Ruse treats us to a defense of the cosmological argument for the existence of god. Here's his (Ruse's) brief description.

1. Everything has a cause.
2. The world is a thing therefore the world must have a cause.
3. Call it god.

This is somewhat simplistic (), a more sophisticated version can be found on Wikipedia (above) or at the Stanford Encyclopedia of Philosophy: Cosmological Argument.

IDiots at Evolution News & Views Defend Ann Gauger's Video

I few days ago I posted a video by Ann Gauger where she criticizes population genetics. Sandwalk readers recognized right away that she doesn't understand population genetics, or phylogenetics. Read the comments on: Ann Gauger Describes the Intelligent Design Creationist Version of Population Genetics.

I've been waiting for a response from Ann Gauger or any of the other IDiots. I've been waiting to see how they twist the meaning of "population genetics" to fit what she says in the video. I've been waiting to see how they defend her words on tree-making given the criticism on Sandwalk and elsewhere.

Incidentally, it turns out that the "laboratory" in the background of the video is a stock photo from Shutterstock and not an actual lab where Ann Gauger works. Here's the video so you can see what I'm talking about.

David Klinghoffer has finally responded to the criticism in a post on Evolution News & Views: Scandal! Gauger Filmed in Front of Green Screen. As you can see from the title, he is most upset about the use of a fake lab ... or rather he's upset about being discovered and exposed by Richard B. Hoppe at Panda's Thumb and Casey Johnston at Ars Technica.

But what about the scientific criticism of what Ann Gauger is actually saying in the video?

Klinghoffer has an answer ....

It's hard to believe that Miss Johnson, who writes for Ars Technica ("a trusted source for technology news, tech policy analysis, breakdowns of the latest scientific advancements"), is unaware of these things. So too Richard Hoppe. The most likely explanation for their posing at the game of "Gotcha!" is that they can't answer Dr. Gauger's arguments, which are given in full in a recent brief book co-authored by Gauger, Doug Axe and Casey Luskin, Science and Human Origins. We would be happy to send a review copy to Ars Technica.

Gauger, a PhD in developmental biology who was a post-doctoral fellow at Harvard, has the science on her side. It's a typical Darwinist feint: When you don't have the arguments and you don't have the science, change the subject and pile on the red herrings. Casey Johnson, who dismisses our little video as a "nonsensical rant," can't reply to Dr. Gauger on the merits. If she could, she would.

David Klinghoffer reads Sandwalk so he knows how real scientists deal with the nonsense being spouted by Ann Gauger. I suspect he would rather focus on the "red herring" than defend the bad science in the video.

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A Course on Intelligent Design in the Natural Sciences

Want to learn more about Intelligent Design Creationism? The Center for Science & Culture in Seattle, Washington (USA) is offering a course next summer: The CSC Seminar on Intelligent Design in the Natural Sciences.

It sounds really interesting. Here's the description.

he CSC Seminar on Intelligent Design in the Natural Sciences will prepare students to make research contributions advancing the growing science of intelligent design (ID). The seminar will explore cutting-edge ID work in fields such as molecular biology, biochemistry, embryology, developmental biology, paleontology, computational biology, ID-theoretic mathematics, cosmology, physics, and the history and philosophy of science. The seminar will include presentations on the application of intelligent design to laboratory research as well as frank treatment of the academic realities that ID researchers confront in graduate school and beyond, and strategies for dealing with them. Although the primary focus of the seminar is science, there also will be discussion of the worldview implications of the debate over intelligent design. Participants will benefit from classroom instruction and interaction with prominent ID researchers and scholars. Past seminars have included such speakers as Michael Behe, Stephen Meyer, William Dembski, Jonathan Wells, Paul Nelson, Jay Richards, Douglas Axe, Ann Gauger, Richard Sternberg, Robert Marks, Scott Minnich, and Bruce Gordon. The seminar is open to students who intend to pursue graduate studies in the natural sciences or the philosophy of science. Applicants must be college juniors or seniors or already in graduate school.

Do you have a commitment to truth and to following the evidence where it leads? Do you have the desire, the vision and the determination necessary to breathe new purpose into the scientific enterprise and influence its self-understanding in ways that will benefit both science and humanity? Apply to become one of a select group of students participating in this exciting workshop.

This is your chance to get up-to-date information on biochemistry and population genetics from Michael Behe and Ann Gauger! You can learn about evolution from Young Earth Creationist Paul Nelson and anti-evolutionist Jonathan Wells.

What an opportunity! I'm sure there are many Sandwalk readers who would welcome the chance to learn about Intelligent Design directly from its main proponents. This is bound to be a marvelous course, even if you're a skeptic.

The application process seems pretty straightforward. It looks like they're open to all points of view so they can have a healthy debate in a critical thinking environment.

Admission Requirements: You must be currently enrolled in a college or university as a junior, senior, or graduate student. Required application materials include (1) a resume/cv, (2) a copy of your academic transcript, (3) a short statement of your interest in intelligent design and its perceived relationship to your career plans and field of study, and (4) either a letter of recommendation from a professor who knows your work and is friendly toward ID, or a phone interview with the seminar director.

Just ignore the fact that you need a letter from a professor who's ID-friendly. I'm sure they don't mean that as way of eliminating skeptics and evolutionists. I'm sure that the phone interview is just a way of confirming that you are really interested in learning about Intelligent Design Creationism no matter what your religion.

I'm sure that any organization promoting critical thinking and "teach the controversy" would never choose their students based on whether they are already proponents of Intelligent Design Creationism.

Same goes for any organization that would support a movie like Expelled: No Intelligence Allowed ("Big science has expelled smart new ideas from the classroom.") Especially since Richard Sternberg might be one of the lecturers.

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This Is What a Culture of Guns and Violence Looks Like

The man who is advocating gun culture is Louie Gohmert, a Republican member of the United States Congress representing the 1st Congressional District of Texas. Gun control will never be successful as long as a substantial number of Americans think like this. Gohmert won the last election (Nov. 2012) with 72% of the vote.

Change the culture. Violence is never the answer and more violence will never fix the problem. Change the culture and gun control automatically follows, as in most other countries. It's unlikely that tweaking a few gun laws will make much of a difference as long as everyone thinks it's okay to act like a gun-toting vigilante.

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Monday's Molecule #196

Last week's molecule was tetrahydrofolate, an essential cofactor in several reactions; notably the synthesis of thymidine. The winner was Jacob Troth [Monday's Molecule #195]. He should contact me by email.

This week's molecule is a very important molecule. I'm showing you two different conformations of the same molecule. You need to identify this molecule using its full and complete common name. I'm going to be strict about this, if you give me an ambiguous name you will not win.

Post your answer as a comment. I'll hold off releasing any comments for 24 hours. The first one with the correct answer wins. I will only post mostly correct answers to avoid embarrassment. The winner will be treated to a free lunch.

There could be two winners. If the first correct answer isn't from an undergraduate student then I'll select a second winner from those undergraduates who post the correct answer. You will need to identify yourself as an undergraduate in order to win. (Put "undergraduate" at the bottom of your comment.)

Ann Gauger Describes the Intelligent Design Creationist Version of Population Genetics

In lieu of Saturday morning cartoons, I offer this video. David Klinghoffer likes it [The Awkward Secret that Plagues Population Genetics and Darwinian Evolutionary Theory]. Enjoy.

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Texas Wants to Protect the IDiots in Universities

As most of you know, there's a reason why we call them IDiots. There's a reason why faculty members in a biology department might not get tenure if they believe most of the things you read on Evolution News & Views (sic). There's a reason why a student might get a low grade for questioning the existence of natural selection or for thinking that skin cells don't accumulate mutations.

The elected members of the Texas legislature are well aware of this discrimination against stupidity so they've taken steps to stop it. Bill HB285 "Relating to prohibiting discrimination by public institutions of higher education against faculty members and students based on their conduct of research relating to intelligent design" should do the trick, if it becomes law.

Here's the key provision,

An institution of higher education may not discriminate against or penalize in any manner, especially with regard to employment or academic support, a faculty member or student based on the faculty member’s or student’s conduct of research relating to the theory of intelligent design or other alternate theories of the origination and development of organisms.

I suppose it was inevitable that politicians in Texas would finally recognize that their children might flunk out of university.

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Fallout from the ENCODE Fiasco Makes It into the Globe & Mail

Most of us are aware of the ENCODE publicity fiasco. The leaders of the project made some outlandish claims about the function of most of our genome in order to attract attention and make their work seem much more significant than it really is [see Sean Eddy on Junk DNA and ENCODE].

Many scientists tried to set the record straight and they pretty much succeeded, at least in the scientific community. Most scientist now know that the case for junk DNA is a lot stronger than they thought.

Unfortunately, the criticisms didn't get much publicity and the average person is left with the impression that most of our genome has an important function, even if we don't know exactly what that function is. This means that good science writers have to work harder to educate the public about the true state of our genome.

Timothy Caulfield is a Professor in the Faculty of Law and the School of Public Health at the University of Alberta in Edmonton, Alberta, Canada. He's also Canada Research Chair in Health Law and Policy, a very prestigious award. He writes the following in today's issue of The Globe & Mail, Canada's most important newspaper [We’re overselling the health-care 'revolution' of personal genomics].

The relationship between our genome and disease is far more complicated than originally anticipated. Indeed, the more we learn about the human genome, the less we seem to know. For example, results from a major international initiative to explore all the elements of our genome (the ENCODE project) found that, despite decades-old conventional wisdom that much of our genome was nothing but “junk DNA,” as much as 80 per cent of our genome likely has some biological function. This work hints that things are much more convoluted than expected. So much so that one of ENCODE’s lead researchers, Yale’s Mark Gerstein, was quoted as saying that it’s “like opening a wire closet and seeing a hairball of wires.”

Statements like this from someone who is supposed to be knowledgeable about such issues show us that the ENCODE fiasco has far-reaching consequences. The misleading statements by Ewan Birney and others will take years to undo. It's all the more reason to criticize Nature and Science for aiding and abetting the spread of this false information.

How can we expect people like Timothy Caulfield to understand the science if the leading journals get it wrong?

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[Hat Tip: Ryan Gregory, "The Bullshit Continues to Spread" on Facebook.]

Do Some IDiots Actually Question the Existence of Natural Selection?

Paul Nelson has been challenging the pervasiveness of adaptationism by pointing out that many evolutionary biologists promte nonadaptive evolution. See the discussion and comments on Jerry Coyne's blog website: A Marshall McLuhan moment with creationist Paul Nelson. Nelson has been accused, falsely, of claiming that some evolutionary biologists deny that natural selection is an important mechanism in evolution.

Paul Nelson doesn't deny that natural selection is a real phenomenon. He may be an IDiot (and a YEC) but he's not THAT stupid. On the other hand, one didn't have to wait too long before getting confirmation that some other IDiots really are THAT stupid.

And guess what? They are allowed to post on the main Discovery Institute blog, Evolution News & Views (sic)!!! You have to read How "Real" Is Natural Selection? by Tom Bethell ... otherwise you'd never believe me.

Here's what Tom Bethell says about natural selection.