Posted by: Dan | July 21, 2006

Link Digest (7/16-7/21)

The quote for the week comes from J.B.S. Haldane (HT: PZ):

My practise as a scientist is atheistic. That is to say, when I set up an experiment I assume that no god, angel, or devil is going to interfere with its course; and this assumption has been justified by such success as I have achieved in my professional career. I should therefore be intellectually dishonest if I were not also atheistic in the affairs of the world. And I should be a coward if I did not state my theoretical views in public.

And now the recommended reading:



  1. Atomic-resolution Structure Of A Ribozyme Yields Insights Into RNA Catalysis And The Origins Of Life

    I understand that Science Daily articles are rehashed press releases, but they do give enough info to track down the peer-reviewed papers on which they are based.

    “The structure illustrates unambiguously how functional groups of the RNA mediate acid-base chemical catalysis, permitting us to suggest that acid-base chemistry is so fundamental to enzyme catalysis that it predates the origin of protein enzymes,” Scott said.

    Tertiary Contacts Distant from the Active Site Prime a Ribozyme for Catalysis
    Monika Martick and William G. Scott
    (online, no volume and page numbers at present)

    Minimal hammerhead ribozymes have been characterized extensively by static and time-resolved crystallography as well as numerous biochemical analyses, leading to mutually contradictory mechanistic explanations for catalysis. We present the 2.2 Å resolution crystal structure of a full-length Schistosoma mansoni hammerhead ribozyme that permits us to explain the structural basis for its 1000-fold catalytic enhancement. The full-length hammerhead structure reveals how tertiary interactions occurring remotely from the active site prime this ribozyme for catalysis. G-12 and G-8 are positioned consistent with their previously suggested roles in acid-base catalysis, the nucleophile is aligned with a scissile phosphate positioned proximal to the A-9 phosphate, and previously unexplained roles of other conserved nucleotides become apparent within the context of a distinctly new fold that nonetheless accommodates the previous structural studies. These interactions permit us to explain the previously irreconcilable sets of experimental results in a unified, consistent, and unambiguous manner.

  2. Thanks for posting this. It is almost as much an honor to be featured on an atheist website as it is to get death threats from creationists.

    The link gets you to some more information and molecular structures that you can actually play around with in your web browser (assuming it has javascript). The paper itself by the way is freely available on I am not sure if that will persist, but if not I will make a pdf available to anyone from our website.

  3. You’re most certainly welcome! I’ve integrated your link and comments to the post that I put up, after becoming aware of the paper:

  4. It is almost as much an honor to be featured on an atheist website as it is to get death threats from creationists.
    I am SHOCKED! SHOCKED! I say, to discover thatthis is an atheist web site!

  5. Scientists Discover Evolutionary Origin Of Fins, Limbs

    “…This midline — think of the dorsal, tail and anal fins of a fish – is where the genetic template to produce fins originated, about 100 million years before paired fins evolved and about 200 million years before paired fins evolved into limbs, according to University of Florida genetics researchers. The findings, published online today in the journal Nature,…”

  6. The power of Hox genes in the bilateral body form is fascinating, isn’t it? I assume there are orthologs to HoxD, Fgf8 and Tbx18 in other bilaterals, like Arthopods and Annelids, also…

  7. Male Praying Mantids Prefer Not To Be Victims Of Sexual Cannibalism


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