Tangled Bank #79

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Over the past two weeks, dozens of writers in their own shabby huts across the globe have toiled for countless hours to share their unique perspective on issues affecting all areas of science. Now you’re being given an opportunity to read all of that hard work, in one simple place.

Welcome to the 79th edition of the Tangled Bank.

Before we get started, I would like to welcome all of the new visitors to Epigenetics News. I encourage you to check out what this newfangled “epigenetics” thing is all about — maybe hit the “random post” link over to the right a few times to get an idea.


The evolution of wings, based on an accumulation of evidence from dinosaur fossils, is reviewed in an excellent post at Duo Quartunciae, a new blog from “Sylas” on science, mathematics, and unbelief.

Mary Hrovat of The Thinking Meat Project provides a synopsis of a two-day symposium on brain evolution in “I think I can feel my brain evolving.”

Sarda Sahney of Fish Feet asks and answers the question, “Why does a platypus lay eggs anyway?

John Beetham of A DC Birding Blog summarizes the latest research into the evolution of duck phalluses and other strange genitalia.

Monado of Science Notes provides a nice history lesson (with excellent illustrations from Charles Darwin’s own handwritten notebooks) on Darwin and punctuated equilibrium.

And in a different sort of evolution, Coturnix of A Blog Around the Clock goes above and beyond to explain the evolution of the modern chronobiology field and reviews a recent seminal paper that provides conclusive evidence that a pacemaker is a network.


A drug now in clinical trials offers hope for treating hundreds of diseases caused by nonsense mutations, including cystic fibrosis and muscular dystrophy, reports Orac at Respectful Insolence.

GrrlScientist of Living the Scientific Life (Scientist, Interrupted) provides a glimpse of the groundbreaking research in regenerative medicine, which allowed researchers to give paralyzed mice the chance to walk again.

Dan Rhoads of Migrations points out a review and primary article on hypoxia-inducible cancers and selections for malignancy in tumor masses.

The long shadow of smallpox from Tara C. Smith of Aetiology describes the recent phenomena of contact transmission of the vaccinia virus following vaccinations given to service men and women.


Jeremy Bruno at The Voltage Gate is questioning the sincerity of evangelical environmentalists after reviewing the conservation book: Serve God, Save the Planet: A Christian Call to Action by J. Matthew Sleeth.

Tim Abbott of Walking the Berkshires takes some time to review the evolution of The Nature Conservancy logo and reflects on how each logo change coincided with remarkable transformations in the organization over its recent history.

Jennifer Forman Orth of Invasive Species remarks on the impact that certain invasive species of fish may have on the sport fishing industry at Lake Michigan.

The tactics of companies using the heightened awareness of consumers to global conservation in designing product marketing is the topic of discussion at _Paddy K_.

Mike Bergin of 10,000 Birds writes convincingly about the “eerie, sinister, unnaturally still” bird, the night heron.


A brief review of research into erectile dysfunction that aims to better define the force needed to collapse an “apparatus” is the topic of discussion by Mark A. Rayner at the skwib.

Martin Rundkvist of Aardvarchaeology discusses the impact of essentialism on archaeological interpretation.

Obligatory Administrative Details

The next Tangled Bank will be available on May 23, 2007 at geek counterpoint. To submit a post, e-mail host@tangledbank.net.

Epigenetics in Focus at Nature Reviews Genetics

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Following closely on the heels of the special issue of Cell on epigenetics, Nature Reviews Genetics today published its own focus issue on epigenetics (April 2007), with reviews from some of the most prominent experts in several sub-disciplines within epigenetics, including stem cell research, cancer epigenomics, and environmental epigenetics. The editors of the journal open the issue with a brief introduction:

The explosion of interest in epigenetics over the past few years has had an impact on many branches of genetic and genomic research. One of the hottest topics in the field of gene regulation relates to the role of epigenetic modifications in dictating the expression output of the genome. In genomics, the advent of technologies for the large-scale profiling of these marks has made the characterization of epigenomes a coveted goal. And chromosome biologists are increasingly learning how epigenetic modifications contribute to the structural packaging of the genetic material at various levels.

The cover of the issue, pictured below, is a cartoon sketchboard by the journal’s art editor, Patrick Morgan.

The issue is packed with five reviews on epigenetics topics of interest:

  • Environmental epigenomics and disease susceptibility by Jirtle RL and Skinner MK. Epigenetic modifications provide a possible link between the environment and disease-causing alterations in gene expression. Evidence from animal studies increasingly supports this theory, including recent findings of epigenetically mediated transgenerational alterations in phenotype that are caused by environmental exposure. Link
  • Epigenetic signatures of stem-cell identity by Spivakov M and Fisher AG. How do stem cells keep the genes that drive differentiation in a repressed state, while maintaining the ability to express them in the future? Increasing evidence indicates that distinctive epigenetic traits underlie this unique aspect of stem-cell biology. Link
  • Transposable elements and the epigenetic regulation of the genome by Slotkin RK and Martienssen R. Cells use a range of increasingly well understood epigenetic mechanisms to keep transposable elements under control. These silencing mechanisms have been co-opted during the course of evolution to contribute to key aspects of chromosome biology and gene regulation. Link
  • Cancer epigenomics: DNA methylomes and histone-modification maps by Esteller M. Recent technological advances allow epigenetic alterations in cancer to be studied across the whole genome. These approaches are being used to answer key outstanding questions about cancer biology, and to provide new avenues for diagnostics, prognostics and therapy. Link
  • The epigenetic regulation of mammalian telomeres by Blasco MA. Epigenetic modifications are key players in the regulation of fly and yeast telomeres, and recent studies indicate that the same applies in mammalian cells. These findings have implications for our understanding of the roles of telomeres in ageing and cancer. Link

The recent surge of coverage by high impact journals in the area of epigenetics likely reflects the major advances and discoveries made in recent years, and will hopefully provide renewed interest among scientists, funding bodies, and most importantly, the general public.

First Look at Cold Spring’s Epigenetics

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When Cold Spring Harbor Laboratory Press announced the release of the new epigenetics textbook, I knew that I had to get my hands on it. After receiving it earlier this month and getting a chance to read specific portions, I am going to offer some initial, “first look” comments on this highly specialized textbook.

For starters, the textbook is about the same size as your average genetics textbook: 24 chapters, 502 pages. While the book has its fair share of diagrams and illustrations, it is fair to say that the book is dominated by text. Perhaps the best way to describe much of the book would be to call it a fantastic compilation of reviews in every specialized area of epigenetics.

The book’s contributors are largely the foremost experts in their various fields. Cancer, small and interfering RNAs, epigenetics research specialized for various model organisms — these topics are all covered in CSHL’s Epigenetics. It is clear that the editors did a fantastic job of recruiting the best and the brightest to bring their expertise to a wide audience of researchers and students.

Even better, the text is still very approachable for even the novice undergraduate. The authors do an admirable job of educating the reader about important background information necessary to understanding the concepts presented. And the book has already attracted attention from postdocs and other researchers in my lab, who are intrigued by all of the specialized areas of epigenetics that fall outside their own knowledge of this rapidly expanding field.

With that said, I plan to share additional thoughts on the book as I am able to read more of its contents. Until then, I would highly recommend that anyone interested in the field of epigenetics grab the new “must-have” for your reference book shelf. Link

Review of New Paid Reviewing System

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Note: The following is a paid review.

ReviewMe is a new service that offers bloggers an opportunity to receive paid offers from advertisers to review a Web site on their blog. I decided to give the service a try because there are some clear-cut rules that must be adhered to when a blogger accepts a paid review offer from an advertiser.

For instance, the review must be identified as a paid review. As you may see at the top of this post, there is no confusion that it is a paid review. However, advertisers are told up-front that they may not stipulate that a review be positive. That means that I’m free to review the site honestly and openly criticize a site as I see fit. I don’t see any problem with this kind of service when both of these guidelines are in place.

The real benefit to advertisers for this service is that rather than being placed as an ad on a site, your site will be linked as part of the “normal” content of the blog. That means that your Web site will show up in the RSS feed, for example, and the review of the site will likely be indexed by Google. The review will also contain a link to your site, and the backlink may provide a boost to your own page ranking at Google.

Based upon this site’s Technorati ranking and other criteria, the price that the site is asking for a paid review at Epigenetics News is US$60. The “ranking” of this site will be monitored over time and the price will be adjusted as needed.

ReviewMe will not accept all bloggers that apply, but right now they have set aside $25,000 to give to those that sign up, are accepted, and review their service on their blog. Link