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?
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
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?
I wonder if Richard Dawkins and/or Lawrence Krauss will win an Academy Award?
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.
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 ...
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.
[Hat Tip: Mike the Mad Biologist ]
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.
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.
Jonathan Wells has just been named to the Encyclopedia of American Loons: #409: Jonathan Wells. He joins another Discovery Institute Fellow, #411 John West.
Appallingly inane crackpot, infuriatingly dense, and reprehensibly dishonest, Wells’s lack of insight and inability to even pretend to begin to understand anything before he starts criticizing it based on personal dislike, is of almost epic proportions. Yet he continues to be shockingly influential.
Less than ideally honest chucklehead, and a prime case of every strand of cognitive bias channeled into a single-minded force of rage against reality. West should not be underestimated, however, as he has made serious contribution to undermining science and education.
I received this email message today from Leslie Maloy, (lmaloy@hastingsgroup.com). It's stupid. It's an example of scientific illiteracy. There's no chance than food from genetically modified crops will do you any harm. You may want to oppose GMO crops for other reasons but to pretend that GMO crops will endanger your health is a lie.
It's stuff like this that's giving the environmental movement a bad reputation. Their anti-science positions are losing them support from the scientific community.
National Coalition Calls on Hershey and Mars to Label GMOs in Chocolates, Other Candy . Or Get Them Out Completely.
Washington DC -- February 7, 2013 -- What will you get your loved one this Valentine's Day? If genetically modified organisms (GMOs) in chocolates are not on your shopping list, you will want to know about GMO Inside's new push to get the nation's largest candy manufacturers-Hershey and Mars-to break up with GMOs in 2013.
GMO Inside, a campaign dedicated to advancing the right of consumers to know whether or not foods are genetically engineered, is calling on Hershey and Mars to either stop putting GMOs in Valentines candy and other products . or to start labeling the products as containing GMOs.
Hershey and Mars combined comprise nearly 70 percent of the U.S. chocolate market. The two companies are not shy about their love affair with GMOs; together they spent more than a million dollars to oppose GMO labeling in California in the November 2012 election. Hershey is reported to have spent $518,900 to defeat Prop 37 and Mars spent $498,350.
The reason these companies oppose GMO labeling so strongly is due to the fact that GMO ingredients are in their sweets; a label would surely make a consumer think twice about eating their favorite candy bar.
For example, these popular candies contain the following GMO-risk ingredients:
* Reese's Peanut Butter filled Hearts (Hershey) contain sugar, soy lecithin, and cornstarch
* Hershey Hugs contain sugar, soy lecithin and corn syrup solids
* Valentine's Colored M&M's (Mars) contain sugar, soy lecithin, cornstarch, and corn syrup
* Valentine's Snickers (Mars) contain soy lecithin, corn syrup, sugar, and partially hydrogenated soybean oil
GMO Inside also released a "Valentine's Day Villains" shopping guide for consumers who want to avoid GMOs treats for their Valentines. Go to www.GMOinside.org to get a list of candies to watch out for and also some non-GMO alternatives for your loved one
Genetically modified organisms have never been proven safe for consumption, and a growing body of studies is raising concerns around the health effects of eating them. GMOs are also increasing the use of toxic herbicides and causing harm to farmers in the US and abroad.
In Europe, where genetically modified ingredients are already required to be labeled, Hershey and Mars have adapted their recipes to formulate Kisses and M&Ms without GMOs. According to Confectionery News, Hershey products made for distribution in Europe will be formulated without GMO ingredients, in order to meet the requirements of major retailers which ban the sale of products with genetically modified ingredients and to satisfy increasing consumer concern about the safety of GMOs.
"Unless you can buy Hershey or Mars products in Europe, there is a high chance you could be giving your Valentine a treat with GMOs that endanger their health and the environment," said GMO Inside Campaign Director Elizabeth O'Connell, "To be safe, you should choose organic certified or Non-GMO Project Verified chocolate to show the loved ones in your life you really care."
Beyond the issue of GMOs, Hershey also has problems with child labor in the cocoa it sources. Though the company committed to certify its supply chain as 100 percent sustainable in October of 2012, there has been no further information about how the company plans to deliver on its promise to remove forced child labor from its supply chain over the next seven years.
"Consumers have a choice -- there is delicious chocolate from companies that are organic or verified through the Non-GMO Project, said Alisa Gravitz, president of Green America. "And you can make it doubly sweet by also looking for fair trade options. You'll be showing your sweetheart you care in every way. Refuse to buy GMO-laden chocolate this Valentine's Day."
Climate change has been very good to Toronto because the increase in temperature during the winter is just enough to avoid snow. In the past decade we've had several winters where I hardly ever had to shovel.
That's all about to change. Tomorrow we're going to get hit with a big storm that's supposed to dump about 25 cm of snow. It's another one of those situations where bad things come from our neighbor to the south.
The city can cope—this is, after all, Canada—but it's probably not going to be a pleasant day. I'm planning to declare a personal snow day and stay home.
That means I won't be able to attend our meeting tomorrow evening [see, Join Us on Friday to Discuss "Thoughts on Science: Evolution versus Intelligent Design (Part I of an indefinite number of parts)"]. Check the Facebook page [Thoughts on Science 2: Evolution VS. Intelligent Design (Part I of an indefinite number of parts)] to see if Rufina is going to cancel the event.
Professor Richard Dawkins debated Professor John Lennox at Oxford University. This is an old debate from about five years ago. I find it very frustrating because both sides frequently drift off-message. All of the arguments from Lennox seem to be of two sorts: (1) the argument from personal incredulity, or (2) the argument from personal satisfaction (i.e. I believe in god(s) because it makes me feel good).
I don't think Dawkins does a good enough job of ignoring or discounting these arguments. They are irrational and deserve no place in debates like this. Dawkins does say, on several occasions, that just because a belief makes you feel good doesn't mean that it's true. He should have kept on saying that, and nothing else, every time Lennox brought it up.
Biochemistry students have been learning this little bit of history for over fifty years. I discovered, quite by accident, that there's a video of Linus Pauling telling the story ...
[Hat Tip: The Biochemistry Questions Site]
There's a conference in April called the Westminster Conference on Science and Faith. It takes place in a church in Philadelphia. Here's the trailer. How many of you just can't wait to register?
The Department of Ecology & Evolutionary Biology and the Royal Ontario Museum present the Annual Darwin Lecture: Darwin, Lizards, and Evolutionary Biology in the 21st Century. The speaker is Jonathan Losos and the lecture takes place tomorrow, Thursday, February 7, 2013 in the Earth Science Centre Auditorium, Room 1050, at 8pm.
Brief Description: Modern day evolutionary biologists combine DNA studies with field experiments that can detect Darwinian evolution in real time. Lizards are an ideal subject for such research.
