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“Miracle,” “miraculously” used to describe reassembled … bacteria

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Here in our combox, bornagain77 notes a very interesting find, “Lazarus” bacteria”*:

If its naming had followed, rather than preceded, molecular analyses of its DNA, the extremophile bacterium Deinococcus radiodurans might have been called Lazarus. After shattering of its 3.2 Mb genome into 20–30 kb pieces by desiccation or a high dose of ionizing radiation, D. radiodurans miraculously reassembles its genome such that only 3 hr later fully reconstituted nonrearranged chromosomes are present, and the cells carry on, alive as normal. In its ability to repair severe DNA damage, D. radiodurans is similar to several bacterial species (Cox and Batista, 2005) and the bdelloid rotifers (Gladyshev and Meselson, 2008), which also periodically contend with the DNA-shattering effects of desiccation. In this issue of Cell, Slade et al. (2009) provide the most comprehensive picture to date of how such miracles are wrought.

D. radiodurans cells are more than 200 times better able to repair and survive DNA breakage than Escherichia coli, which by comparison has a moderate capacity for repair (Cox and Batista, 2005 and references therein). Some of the prowess for repair displayed by D. radiodurans may result from having more complementary or homologous DNA fragments to engage as repair partners. Whereas E. coli carries 1–4 identical chromosomes per cell, D. radiodurans carries 4–10 copies of its two chromosomes per cell. Beyond this difference, the steps of repair in D. radiodurans appear to be conspicuously normal.

“Miracles?” “Miraculously?” Well, we can’t rule out that it is a miracle, of course, but perhaps there is a layer of organization in a life form that is more basic than DNA as we know it. Perhaps it provides information that enables the DNA to reassemble correctly. Having more identical chromosomes won’t necessarily account for the observation if those chronmosomes don’t know what to do either. And if they know, how do they?

Note: This article is NIH Public Access. That terminology might have been stuck from the version that appeared in Cell, but we’d have to pay to find out.

* The term has nothing to do with “Lazarus species”: Those are species ruled extinct that turn up again decades later. Their demise, like Mark Twain’s, was greatly exaggerated …

a few related notes:
“Live memory” of the cell, the other hereditary memory of living systems - 2005 Excerpt: To understand this notion of “live memory”, its role and interactions with DNA must be resituated; indeed, operational information belongs as much to the cell body and to its cytoplasmic regulatory protein components and other endogenous or exogenous ligands as it does to the DNA database. We will see in Section 2, using examples from recent experiments in biology, the principal roles of “live memory” in relation to the four aspects of cellular identity, memory of form, hereditary transmission and also working memory. http://www.ncbi.nlm.nih.gov/pubmed/15888340 An Electric Face: A Rendering Worth a Thousand Falsifications - September 2011 Excerpt: The video suggests that bioelectric signals presage the morphological development of the face. It also, in an instant, gives a peak at the phenomenal processes at work in biology. As the lead researcher said, “It’s a jaw dropper.” https://www.youtube.com/watch?v=wi1Qn306IUU http://darwins-god.blogspot.com/2011/09/electric-face-rendering-worth-thousand.html What Do Organisms Mean? Stephen L. Talbott - Winter 2011 Excerpt: Harvard biologist Richard Lewontin once described how you can excise the developing limb bud from an amphibian embryo, shake the cells loose from each other, allow them to reaggregate into a random lump, and then replace the lump in the embryo. A normal leg develops. Somehow the form of the limb as a whole is the ruling factor, redefining the parts according to the larger pattern. Lewontin went on to remark: "Unlike a machine whose totality is created by the juxtaposition of bits and pieces with different functions and properties, the bits and pieces of a developing organism seem to come into existence as a consequence of their spatial position at critical moments in the embryo’s development. Such an object is less like a machine than it is like a language whose elements... take unique meaning from their context.[3]",,, http://www.thenewatlantis.com/publications/what-do-organisms-mean Epigenetics and the "Piano" Metaphor - January 2012 Excerpt: And this is only the construction of proteins we're talking about. It leaves out of the picture entirely the higher-level components -- tissues, organs, the whole body plan that draws all the lower-level stuff together into a coherent, functioning form. What we should really be talking about is not a lone piano but a vast orchestra under the directing guidance of an unknown conductor fulfilling an artistic vision, organizing and transcending the music of the assembly of individual players. http://www.evolutionnews.org/2012/01/epigenetics_and054731.html Do Physical Laws Make Things Happen? - Stephen L. Talbott Excerpt: While there are many complex and diverse movements of mind as we speak, it is fair to say very generally that we first have an idea, inchoate though it may be, and then we seek to capture and clothe this idea in words. Each word gains its full meaning — becomes the word it now is — through the way it is conjoined with other words under the influence of the originating idea. The word simply didn't exist as this particular word before — as a word with these nuances of meaning. So an antecedent whole (an idea) becomes immanent in and thereby transforms and constitutes its parts (words), making them what they are. In terms of active agency, it is less that the parts constitute the whole than the other way around. http://www.natureinstitute.org/txt/st/mqual/ch03.htm#fn3.0 Alexander Tsiaras: Conception to birth — visualized – video http://www.youtube.com/watch?v=fKyljukBE70 Comment on preceding video: Mathematician and medical image maker Alexander Tsiaras offers a stunning visualization of the process that in nine months takes an emerging human life from conception to birth. He speaks of “the marvel of this information,” “the mathematical models of how these things are done are beyond human comprehension,” “even though I look at this with the eyes of mathematician I look at this and marvel. How do these instruction sets not make mistakes as they build what is us?” To Model the Simplest Microbe in the World, You Need 128 Computers - July 2012 Excerpt: Mycoplasma genitalium has one of the smallest genomes of any free-living organism in the world, clocking in at a mere 525 genes. That's a fraction of the size of even another bacterium like E. coli, which has 4,288 genes.,,, It took a cluster of 128 computers running for 9 to 10 hours to actually generate the data on the 25 categories of molecules that are involved in the cell's lifecycle processes.,,, ,,the depth and breadth of cellular complexity has turned out to be nearly unbelievable, and difficult to manage, even given Moore's Law. The M. genitalium model required 28 subsystems to be individually modeled and integrated, and many critics of the work have been complaining on Twitter that's only a fraction of what will eventually be required to consider the simulation realistic.,,, "Right now, running a simulation for a single cell to divide only one time takes around 10 hours and generates half a gigabyte of data," lead scientist Covert told the New York Times. "I find this fact completely fascinating, because I don't know that anyone has ever asked how much data a living thing truly holds." One cell. One division. Half a gig of data. Now figure that millions of bacteria could fit on the head of a pin and that many of them are an order of magnitude more complex than M. genitalium. Or ponder the idea that the human body is made up of 10 trillion (big, complex) human cells, plus about 90 or 100 trillion bacterial cells. That's about 100,000,000,000,000 cells in total. That'd take a lot of computers to model, eh? If it were possible, that is. http://www.theatlantic.com/technology/archive/2012/07/to-model-the-simplest-microbe-in-the-world-you-need-128-computers/260198/ Psalm 139:15 My frame was not hidden from You, When I was made in secret, And skillfully wrought in the depths of the earth;
Music and quote:
Evanescence - My Heart Is Broken http://www.vevo.com/watch/evanescence/my-heart-is-broken/USWV41100052 "I ain't got enough faith to be an atheist!" Frank Turek

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