USS Arizona

The USS Arizona (BB-39) is an American battleship built during World War I. It was modernized and upgraded in 1930.

The Arizona was hit by a Japanese bomb during the attack on Pearl Harbor on Dec. 7, 1941. The magazine in her forward turret exploded and the ship sank within minutes. The explosion killed 1,177 of her crew. The ship was not salvageable, unlike most of the other ships sunk on that day. The USS Arizona Memorial was built over the remains of the ship to honor the men who died in the attack. Here's an aerial view of the memorial.

We visited the USS Arizona Memorial on Thursday Feb. 14, 2013 and I've included some of my photos. Click to enlarge, especially the last two photos.

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USS Missouri

The USS Missouri is an American battleship commissioned in June 1944, toward the end of World War II. It served as the flagship of the American Third Fleet under Admiral William F. Halsey, Jr. In early August 1945, the Missouri was bombarding installations on the coast of Japan when the atomic bombs were dropped.

On September 2, 1945 the Missouri was docked in Tokyo harbor. Japanese representatives signed the surrender documents that formally ended World War II. The brass disk (below) is the site where the signing took place.

On Thursday (Feb. 14, 2013) we visited the Battleship Missouri Memorial in Pearl Harbor, Hawaii.

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Hawaiian Cuisine

I think it's important to sample the local customs whenever you travel. In this case, I'm on a mission to experience genuine Hawaiian cuisine.

We began on the first full day of our visit with a delicious spam & egg bun at a small cafe in Honolulu near the beach at Waikiki. The spam had just the right flavor (I thing it was genuine Hormel spam, probably made in the USA.) I actually prefer Prem but it's much hared to find.

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Guess Where I'm Going?

We're leaving tomorrow to visit a place I've never been. I'm really looking forward to it, especially the "red bits" in the image.

I may be too "busy" to post much in the next two weeks.

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PZ Myers Can't Write About Evolutionary Psychology

PZ Myers wants to write a serious post about evolutionary psychology but he can't.

Why not? Here's what he said on Kate Clancy tackles Evolutionary Psychology.

I’ve still got plans to post more on this subject, but an unfortunate event has blocked me. I was going to make my next post on evolutionary psychology one that focused on some of the papers, and in particular, I wanted to discuss a good paper or two, so that I could start off on the right tone. And people sent me links and papers.

Only problem: they were all awful. Every one. I couldn’t believe that even these papers that some people were telling me were the best of the bunch were so lacking in rigor and so rife with unjustified assumptions. I read through about a dozen before I gave up in disgust and decided that there were better things to do in my time.

I’d ask again, but I was burned so badly on that last go-round that I’d have a jaundiced view of any recommendation now.

I understand his pain. I've often asked for good examples of evolutionary psychology and gotten nothing but garbage. For example, an evolutionary psychologist named Gad Saad once sent me a list of The Great, Profound, and Valuable Works of Evolutionary Psychology. At some point we have to question the value of an entire field if it can't come up with even a handful of high quality papers.

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Craig Venter Discusses the Tree of Life

I don't know where this clip comes from or when it was made but it's being promoted on YouTube as "Dr. Craig Venter Denies Common Descent in front of Richard Dawkins!" The link was posted by someone in a comment to a previous post on Sandwalk.

Everything that Ventor says is correct. He didn't need to quibble about the universality of the genetic code but it's true that there are variants.

His point about the tree of life is correct, especially in a discussion about the origin of life. It's unfortunate that Richard Dawkins repeatedly makes such an issue about the tree of life because he's on shakey ground when he does that. I assume that Dawkins hasn't studied the problem. However, he's in good company since most scientists don't understand the problems with the early tree of life. The early history of life looks more like a bush with many interconnecting branches due to horizontal gene transfer [The Tree of Life].

Here's a video of the complete debate. The relevant part, according to the creationists, begins at 9 mins.

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Darwin's Dead Idea and the Man Who Helped Kill It

A new book has just been published. The title is "Darwin's Dead Idea and the Man Who Helped Kill It." Here's the description on Amazon.

"Darwin’s Dead Idea and the Man Who Helped Kill It" makes for highly engaging reading. Witness the fascinating journey of a smart, inquisitive adolescent rejecting his school’s ask-no-questions religious indoctrination into a mathematician, philosopher, and scientist of the highest order, one who today is powerfully and persuasively challenging academia’s reigning answer to the questions that haunt us all: Where did we come from? Why is there something rather than nothing? A leading spokesman for the scientific theory that is shattering materialist assumptions about reality and the origin of life, Dr. William Dembski responds to probing questions from James Barham, general editor of TheBestSchools.org. That interview forms the core of DDI. Dembski’s forthright and humbly restrained responses reveal the courage, perseverance, and original thinking that have made him a lightning rod in the scientific community. The heated controversy surrounding intelligent design theory dramatically confirms Machiavelli’s observation that there is nothing more difficult to carry out nor more doubtful of success, nor more dangerous to handle, than to initiate a new order of things. DDI introduces readers to one of the stellar lights of the new order of things now emerging on the horizon.

I'm speechless.

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Why Do University Press Releases Continue to Spread Misinformation?

There's a very interesting paper that's just been published online in ScienceExpress. The work is by Haung et al. (2013) from the Broad Institute at Harvard and MIT (Boston, Massachusetts, USA). These workers looked at the genomes of 70 different malignant melanomas and discovered that fifty (50) of them had mutations in the promoter region of the gene TERT (telomerase reverse transcriptase). The mutations created a new binding site for transcription factors resulting in a 2-4 fold increase in transcription of the gene.

Here's a picture of the gene from the Ensembl website [TERT]. The position of the transcription start site (P) is shown and the approximate position of the two mutations (M) is just upstream.

It's good that mutations affecting melanomas have been identified but the result isn't totally unexpected. We've known for fifty years that mutations in the promoter regions of genes can affect expression. Even in humans, such mutations have been widely studied; for example, lactase persistence is due to mutations in enhancer regions of the lactase gene.

Let's look at the press release from the Broad Institute [Genomic "dark matter" yields major melanoma discovery]. It's written by Paul Goldsmith who writes ...

"This new finding represents an initial foray into the 'dark matter' of the cancer genome," said Levi Garraway, senior associate member of the Broad, and associate professor of medicine at Dana-Farber, the article’s senior author.

WTF! Since when have promoters and enhancers been called "dark matter"? And why isn't it mentioned, or even hinted at, in the published paper?

Only about 1% of the human genome provides the blueprint for the body’s proteins. The remaining "non-coding" portion of the genome, sometimes referred to as dark matter, is poorly understood. Scientists have only recently begun exploring the relationship between these regions and the body’s cellular structure and processes.

We have an excellent understanding of the human genome [What's in Your Genome?]. This press release implies that only 1% of the genome is understood and the rest is mysterous "dark matter." We've known for decades that most of this DNA is junk (defective transposons). We know about pseudogenes, genes that encode functional RNAs, regulatory regions (including enhancers), introns, centromeres, defective viruses, telomeres, origins of replication, and several other functional parts of the genome.

I don't believe that the senior author of this study, Levi Garraway, actually believes what he is quoted as saying. If it were true then why didn't he put it in the paper? Why is there nothing in the paper about the importance of revealing mysterious "dark matter"?

Why do press releases have to be so misleading?

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Huang, F.W., Hodis, E., Xu, M.J., Kryukov, G.V., Chin, L., and Garraway, L.A. (2013) Highly Recurrent TERT Promoter Mutations in Human Melanoma. Science published online January 24 2013 [doi: 10.1126/science.1229259

IDiot Quote of the Day

This is for all of you who really miss Saturday morning cartoons. It's from a post by David Klinghoffer who is upset about the way some people are treating Thomas Nagel [New York Times on Thomas Nagel's "Dangerous Sympathy for Intelligent Design"].

One of the take-aways here is not only the progress ID is making in scientific and general culture, but specifically among liberal thinkers. That makes it a lot harder to pigeonhole us in time-honored Darwinian fashion as right-wing Christian fundamentalists, creationists and the like. This may be the chief source of outrage from the Darwin community. Deprived of that old crutch, these guys will be forced to argue with us and explain in detail why ID, not creationism yet again, is wrong. Of course that's something that most have stubbornly, and tellingly, refused to do.

I have been arguing with these IDiots for over twenty years. They stubbornly, and tellingly, refuse to listen. Isn't that strange?

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Coming Soon to a Theater Near You - "The Unbelievers"

I wonder if Richard Dawkins and/or Lawrence Krauss will win an Academy Award?

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Not All Atheists Are Skeptics

PZ Myers posted an article last week that was part of an ongoing discussion about the role of atheism in the skepticism movement. The title of his post was: Atheists are skeptics. I covered that debate in an earlier post [Skeptics Must Be Atheists].

Now I want to discuss whether all atheists must be skeptics.

The answer is "no." Atheists are people who don't believe in any god(s). There are millions of atheists all around the world who have grown up without any belief in god(s). Their parents didn't believe, their grandparents didn't believe, and they live in a secular culture. Many of these atheists are taken in my homeopathy, fear of GMOs, and various conspiracy theories. They aren't critical thinkers and they aren't skeptics.

Let's not fall into the trap of assuming that all atheists have grown up as believers and have recently lost their faith. That's just not accurate.

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Skeptics Must Be Atheists

The skeptic movement has been in a bit of a turmoil over the past few years. One of the problems concerns the role of atheism in the movement. Many people think that outspoken criticism of religion (i.e. Gnu Atheism) is not a necessary part of skepticism. I agree—just as you don't have to be an outspoken critic of chiropractors to be a skeptic.

However, that doesn't mean that belief in god(s), or belief in the grandiose claims of chiropractors, is compatible with skepticism. They aren't.

PZ Myers and Steve Novella are debating this issue. The latest round is from last week on Pharyngula: Atheists are skeptics. (His title is wrong ... more about that in another post.¹) Novella is one of those skeptics who think that skepticism requires scientific thinking [Bigfoot Skeptics, New Atheists, Politics and Religion] but he also believes that the scientific way of knowing has limits and that belief in god(s) falls outside of those limits. The "limit" is, as we all know, methodological naturalism. (Novella's main interest is quack medicine.) Here's how he describes one of the attributes of a skeptic ...

Skip the Acknowledgements Slide!

Joshua Schimel blogs at Writing Science. His latest post recommends that we stop ending our talks with a boring slide that lists all funding sources and everyone who may have contributed to the project [Why do people blow the punchline in scientific talks? The destructive effect of acknowledgements slides].

I never thought about this before. He makes a good point.

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[Hat Tip: Mike the Mad Biologist ]

The Proper Role of Scientific Societies

Scientific societies are made up of groups of scientists who band together for various legitimate purposes such as organizing meetings, publishing journals, promoting their speciality, and lobbying for funds. The credibility of a society depends on its area of expertise. They lose credibility when they take positions on issues outside of their discipline.

That's why many of us have been opposed to the accommodationist positions of the American Association for the Advancement of Science (AAAS) and other societies. These societies have no special expertise in epistemology/philosophy or religion yet they openly proclaim that science and religion are compatible. They should be neutral on that question. A (slight) majority of Sandwalk readers agree, according to a poll I took a few years ago [What Should Scientific Organizations Say about Religion?].

I wasn't alone in adopting this position. Jerry Coyne and PZ Myers also think that scientific societies should keep their nose out of areas that are outside of their mandate. We are united when it comes to opposing accommodationism.

“This House Believes Religion Has No Place In The 21st Century”

Here's the video of last week's debate at the Cambridge Union debating society. The main event pitted Richard Dawkins against Rowan Williams, former Archbishop of Canterbury. The motion was that "This House Believes Religion Has No Place In The 21st Century." At the end of the debate a majority decided that religions does, indeed, have a place in the 21st century.

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