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Thursday, July 29, 2010

Mapping the Human Genome

I searched via Google Scholar to see if it is currently possible to map the human genome or that of any other mammal. The human genome was "mapped" in terms of four bases before the discovery of another two nucleotides, viz., 5-hydroxymethylcytosine and 5-methylcytosine, which are crucial to mammalian development. I found this paper:


Nucleic Acids Research Advance Access published online on April 5, 2010
Nucleic Acids Research, doi:10.1093/nar/gkq223
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© The Author(s) 2010. Published by Oxford University Press.
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

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Methods Online



Examination of the specificity of DNA methylation profiling techniques towards 5-methylcytosine and 5-hydroxymethylcytosine
Seung-Gi Jin, Swati Kadam and Gerd P. Pfeifer*
Department of Cancer Biology, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA

*To whom correspondence should be addressed. Tel: +1 626 301 8853 begin_of_the_skype_highlighting +1 626 301 8853 end_of_the_skype_highlighting; Fax: +1 626 358 7703; Email: gpfeifer@coh.org

Received November 5, 2009. Revised March 12, 2010. Accepted March 17, 2010.

DNA cytosine-5 methylation is a well-studied epigenetic pathway implicated in gene expression control and disease pathogenesis. Different technologies have been developed to examine the distribution of 5-methylcytosine (5mC) in specific sequences of the genome. Recently, substantial amounts of 5-hydroxymethylcytosine (5hmC), most likely derived from enzymatic oxidation of 5mC by TET1, have been detected in certain mammalian tissues. Here, we have examined the ability of several commonly used DNA methylation profiling methods to distinguish between 5mC and 5hmC. We show that techniques based on sodium bisulfite treatment of DNA are incapable of distinguishing between the two modified bases. In contrast, techniques based on immunoprecipitation with anti-5mC antibody (methylated DNA immunoprecipitation, MeDIP) or those based on proteins that bind to methylated CpG sequences (e.g. methylated-CpG island recovery assay, MIRA) do not detect 5hmC and are specific for 5mC unless both modified bases occur in the same DNA fragment. We also report that several methyl-CpG binding proteins including MBD1, MBD2 and MBD4 do not bind to sequences containing 5hmC. Selective mapping of 5hmC will require the development of unique tools for the detection of this modified base.

Superconducting Graphene







Extended van Hove Singularity and Superconducting Instability in Doped Graphene

J. L. McChesney, Aaron Bostwick, Taisuke Ohta, Thomas Seyller, Karsten Horn, J. González, and Eli Rotenberg

Phys. Rev. Lett. 104, 136803 (Published April 2, 2010)






Illustration: McChesney et al., Phys. Rev. Lett. (2010)

J. L. McChesney1,2, Aaron Bostwick1, Taisuke Ohta1,3, Thomas Seyller4, Karsten Horn3, J. González5, and Eli Rotenberg1
1Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, California, USA
2Montana State University, Bozeman, Montana, USA
3Fritz-Haber-Institut der Max-Planck-Gesellschaft, Berlin, Germany
4Institut für Physik der Kondensierten Materie, Universität Erlangen-Nürnberg, Erlangen, Germany
5Instituto de Estructura de la Materia, Consejo Superior de Investigaciones Científicas, Serrano 123, 28006 Madrid, Spain

Received 18 November 2009; published 2 April 2010

See accompanying Physics Synopsis

We have investigated the effects of doping on a single layer of graphene using angle-resolved photoemission spectroscopy. We show that many-body interactions severely warp the Fermi surface, leading to an extended van Hove singularity (EVHS) at the graphene M point. The ground state properties of graphene with such an EVHS are calculated, analyzing the competition between a magnetic instability and the tendency towards superconductivity. We find that the latter plays the dominant role as it is enhanced by the strong modulation of the interaction along the Fermi line, leading to an energy scale for the onset of the pairing instability as large as 1 meV when the Fermi energy is sufficiently close to the EVHS.

© 2010 The American Physical Society

U.S. Backed Sharia Government to Destroy Temple

Science 30 July 2010:
Vol. 329. no. 5991, pp. 496 - 497
DOI: 10.1126/science.329.5991.496
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NEWS OF THE WEEK
ARCHAEOLOGY:
Copper Mine Threatens Ancient Monastery in Afghanistan
Andrew Lawler
A decade after the Taliban destroyed the famous Bamiyan Buddhas—two massive statues that have stood sentry in an Afghan valley for 1500 years—archaeologists are warning that Afghan antiquities are again at risk. This time the threat comes from a venture blessed by the Western-backed Afghan government. A Chinese company intends to blow up an ancient Buddhist monastery south of Kabul to make way for a massive copper mine. The plan has sparked outrage among Afghan and French archaeologists, who have recently uncovered more than 100 statues within a large religious complex that includes seven stupas, or tombs built to house the relics of saints.

Discrete Landau Levels In Graphene

Graphene ordinarily has continuous energy levels. However, as was recently shown that by adding strain, one can easily produce discrete landau levels. This achieved the equivalent of a 300 tesla magnetic field which is 10 times larger than any steady state magnetic field ever produce in a laboratory. This pivotal research paves the way to a future in which graphene will be used in optoelectronics.








Strain-Induced Pseudo–Magnetic Fields Greater Than 300 Tesla in Graphene Nanobubbles
N. Levy,1,2,*, S. A. Burke,1,*, K. L. Meaker,1 M. Panlasigui,1 A. Zettl,1,2 F. Guinea,3 A. H. Castro Neto,4 M. F. Crommie1,2,




Recent theoretical proposals suggest that strain can be used to engineer graphene electronic states through the creation of a pseudo–magnetic field. This effect is unique to graphene because of its massless Dirac fermion-like band structure and particular lattice symmetry (C3v). Here, we present experimental spectroscopic measurements by scanning tunneling microscopy of highly strained nanobubbles that form when graphene is grown on a platinum (111) surface. The nanobubbles exhibit Landau levels that form in the presence of strain-induced pseudo–magnetic fields greater than 300 tesla. This demonstration of enormous pseudo–magnetic fields opens the door to both the study of charge carriers in previously inaccessible high magnetic field regimes and deliberate mechanical control over electronic structure in graphene or so-called "strain engineering."

1 Department of Physics, University of California Berkeley, Berkeley, CA 94720, USA.
2 Materials Science Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
3 Instituto de Ciencia de Materiales de Madrid (CSIC), Madrid 28049, Spain.
4 Department of Physics, Boston University, Boston, MA 02215, USA.
* These authors contributed equally to this work.

Present address: Center for Nanoscale Science and Technology, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA.

Present address: Department of Physics and Astronomy and Department of Chemistry, University of British Columbia, Vancouver, BC V6T 121, Canada.

Friday, July 23, 2010

My Laptop


This is the current layout of my computer. The Windows taskbar is on the far left. The language taskbar is on the very top. The recycle bin is behind the VMware Player window running the 6th beta release of Dream Linux 4. I displayed the menus for Gimp to make it more interesting. Any comments or questions?

Wednesday, July 21, 2010

The latest meaning for the word "go".

The pratice of giving new, unrelated meanings to common words and the invention of new rules when to capitalize words never ends. They picked on "go" because it is the first two letters of "Google". Compilers are supposed to be an easy way for people to talk to computers, but always end up being written for the benefit of the computers.

Saturday, July 17, 2010

Matthew 16:19

I thought of Mathew 19:16 as an admonition from the Lord about the repercussions of one’s actions. When I read it, I thought it meant something to this effect: I give you access to the reign of the spiritual, your physical actions whether pro or con with be mirrored in the spiritual. I know that others think it means someone been granted divine authority to run the church and doubt anyone else holds my view.
Here is the translation I use:


καὶ δώσω σοι τὰς κλεῖς τῆς βασιλείας τῶν οὐρανῶν καὶ ὃ ἐὰν δήσῃς ἐπὶ τῆς γῆς ἔσται δεδεμένον ἐν τοῖς οὐρανοῖς καὶ ὃ ἐὰν λύσῃς ἐπὶ τῆς γῆς ἔσται λελυμένον ἐν τοῖς οὐρανοῖς

και conjunction
kai kahee: and, also, even, so then, too, etc.; often used in connection (or composition) with other particles or small words

δωσω verb - future active indicative - first person singular
didomi did'-o-mee: to give (used in a very wide application, properly, or by implication, literally or figuratively; greatly modified by the connection)

σοι personal pronoun - second person dative singular
soi soy: to thee -- thee, thine own, thou, thy.

τας definite article - accusative plural feminine
ho ho: the definite article; the (sometimes to be supplied, at others omitted, in English idiom) -- the, this, that, one, he, she, it, etc.

κλεις noun - accusative plural feminine
kleis klice: a key (as shutting a lock), literally or figuratively -- key.

της definite article - genitive singular feminine
ho ho: the definite article; the (sometimes to be supplied, at others omitted, in English idiom) -- the, this, that, one, he, she, it, etc.

βασιλειας noun - genitive singular feminine
basileia bas-il-i'-ah: royalty, i.e. (abstractly) rule, or (concretely) a realm -- kingdom, + reign.

των definite article - genitive plural masculine
ho ho: the definite article; the (sometimes to be supplied, at others omitted, in English idiom) -- the, this, that, one, he, she, it, etc.

ουρανων noun - genitive plural masculine
ouranos oo-ran-os': the sky; by extension, heaven (as the abode of God); by implication, happiness, power, eternity; specially, the Gospel (Christianity) -- air, heaven(-ly), sky.

και conjunction
kai kahee: and, also, even, so then, too, etc.; often used in connection (or composition) with other particles or small words

ο relative pronoun - accusative singular neuter
hos hos: the relatively (sometimes demonstrative) pronoun, who, which, what, that -- one, (an-, the) other, some, that, what, which, who(-m, -se), etc.

εαν conditional
ean eh-an': before, but, except, (and) if, (if) so, (what-, whither-)soever, though, when (-soever), whether (or), to whom, (who-)so(-ever).

δησης verb - aorist active subjunctive - second person singular
deo deh'-o: to bind (in various applications, literally or figuratively) -- bind, be in bonds, knit, tie, wind.

επι preposition
epi ep-ee': meaning superimposition (of time, place, order, etc.), as a relation of distribution (with the genitive case), i.e. over, upon, etc.; of rest (with the dative case) at, on, etc.; of direction (with the accusative case) towards, upon, etc.

της definite article - genitive singular feminine
ho ho: the definite article; the (sometimes to be supplied, at others omitted, in English idiom) -- the, this, that, one, he, she, it, etc.

γης noun - genitive singular feminine
ge ghay: soil; by extension a region, or the solid part or the whole of the terrene globe (including the occupants in each application) -- country, earth(-ly), ground, land, world.

εσται verb - future indicative - third person singular
esomai es'-om-ahee: will be -- shall (should) be (have), (shall) come (to pass), may have, fall, what would follow, live long, sojourn.

δεδεμενον verb - perfect passive participle - nominative singular neuter
deo deh'-o: to bind (in various applications, literally or figuratively) -- bind, be in bonds, knit, tie, wind.

εν preposition
en en: in, at, (up-)on, by, etc.

τοις definite article - dative plural masculine
ho ho: the definite article; the (sometimes to be supplied, at others omitted, in English idiom) -- the, this, that, one, he, she, it, etc.

ουρανοις noun - dative plural masculine
ouranos oo-ran-os': the sky; by extension, heaven (as the abode of God); by implication, happiness, power, eternity; specially, the Gospel (Christianity) -- air, heaven(-ly), sky.

και conjunction
kai kahee: and, also, even, so then, too, etc.; often used in connection (or composition) with other particles or small words

ο relative pronoun - accusative singular neuter
hos hos: the relatively (sometimes demonstrative) pronoun, who, which, what, that -- one, (an-, the) other, some, that, what, which, who(-m, -se), etc.

εαν conditional
ean eh-an': before, but, except, (and) if, (if) so, (what-, whither-)soever, though, when (-soever), whether (or), to whom, (who-)so(-ever).

λυσης verb - aorist active subjunctive - second person singular
luo loo'-o: to loosen -- break (up), destroy, dissolve, (un-)loose, melt, put off.

επι preposition
epi ep-ee': meaning superimposition (of time, place, order, etc.), as a relation of distribution (with the genitive case), i.e. over, upon, etc.; of rest (with the dative case) at, on, etc.; of direction (with the accusative case) towards, upon, etc.

της definite article - genitive singular feminine
ho ho: the definite article; the (sometimes to be supplied, at others omitted, in English idiom) -- the, this, that, one, he, she, it, etc.

γης noun - genitive singular feminine
ge ghay: soil; by extension a region, or the solid part or the whole of the terrene globe (including the occupants in each application) -- country, earth(-ly), ground, land, world.

εσται verb - future indicative - third person singular
esomai es'-om-ahee: will be -- shall (should) be (have), (shall) come (to pass), may have, fall, what would follow, live long, sojourn.

λελυμενον verb - perfect passive participle - nominative singular neuter
luo loo'-o: to loosen -- break (up), destroy, dissolve, (un-)loose, melt, put off.

εν preposition
en en: in, at, (up-)on, by, etc.

τοις definite article - dative plural masculine
ho ho: the definite article; the (sometimes to be supplied, at others omitted, in English idiom) -- the, this, that, one, he, she, it, etc.

ουρανοις noun - dative plural masculine
ouranos oo-ran-os': the sky; by extension, heaven (as the abode of God); by implication, happiness, power, eternity; specially, the Gospel (Christianity) -- air, heaven(-ly), sky.

Oil Spill Info




Corexit EC9500A the newer formulation, is made without 2-butoxyethanol and is mainly comprised of hydrotreated light petroleum distillates, propylene glycol and Dioctyl sodium sulfosuccinate.

Symptoms of Dioctyl sodium sulfosuccinate Exposure
- Severe eye irritation.
- Skin irritation.
- Ingestion causes diarrhea, intestinal bloating, cramps, nausea.
- Cytotoxic effects on liver cells in tissue culture have been observed.

NEUROTOXICITY
type of concern product conditions reference
One or more animal studies show brain and nervous system effects at moderate doses RTECS®- Journal of Industrial Hygiene and Toxicology 1943
show more

DEVELOPMENTAL/REPRODUCTIVE TOXICITY
type of concern product conditions reference
One or more animal studies show reproductive effects at high doses RTECS®- Fundamental and Applied Toxicology 1990

IRRITATION (SKIN, EYES, OR LUNGS)
type of concern product conditions reference
One or more animal studies show skin irritation at low doses RTECS®- Journal of Pharmacology and Experimental Therapeutics 1944


Cleaning an oil spill.




Thursday, July 15, 2010

Attested Languages

I read the Russian research on hypthetical proto-languages and became confused as to what languages we really have examples of. Here is my quick list. I know there must be more, but do not plan to research it more. If you know where other languages fit in, then post a comment. Personally, I do not plan to learn any proto-languages in which nothing is ever known to have been written. Better to spend your time writing in category theory is my view.

Prehistoric attested languages: None (by definition, if a language is prehistoric, then,there is no historical evidence. So,it is unattested).

Ancient Languages:
Sumerian, Akkadian/Eblaite, Egyptian/Elamite, Hittite/Luwian/Hattic/Hurrian, Canaanite/Hebrew, Minoan/Greek

Classical languages:
Cham, Chinese, Korean, Mayan/Olmec, Bactrian, Sanskrit/Prakrit, Latin/Faliscan/Gaulish/Hispano-Celtic/Celtic/Galatian, Proto-Norse


Relationship to Modern languages

Egyptian:Elamite :: Arabic:Persian

Reconstructed Languages(more precisely, dead languages which have been revived): Egyptian, Greek, Hebrew

Constructed, but incomplete languages: Mathematics, Phonetics, Computer Programming and Scientific Languages

English comes from Proto-Norse, the reconstructed languages, the constructed languages and borrowings from all the other languages. It has too many words for any one person to know. That is why we have computers I guess.


The moral of the story. It is impossible to translate a word a basic as graphene into other languages, because it does not exist in them. Graphene is not graphite. So why do you keep inventing new synonyms just so others cannot understand. Likewise it is impossible to write category theory in any of them, so why do you think you understand anything.

Monday, July 12, 2010

Jantelagen

1. Du skal ikke tro at du *er* noe.
Thou shalt not presume that thou art anyone [important].
2. Du skal ikke tro at du er like saa meget som *oss*.
Thou shalt not presume that thou art as good as us.
3. Du skal ikke tro at du er klokere en *oss*.
Thou shalt not presume that thou art any wiser than us.
4. Du skal ikke innbille deg du er bedre enn *oss*.
Thou shalt never indulge in the conceit of imagining that thou art
better than us.
5. Du skal ikke tro du vet mere enn *oss*.
Thou shalt not presume that thou art more knowledgeable than us.
6. Du skal ikke tro du er mere enn *oss*.
Thou shalt not presume that thou art more than us [in any way].
7. Du skal ikke tro at *du* duger til noe.
Thou shalt not presume that that thou art going to amount to
anything.
8. Du skal ikke le av *oss*.
Thou art not entitled to laugh at us.
9. Du skal ikke tro at noen bryr seg om *deg*.
Thou shalt never imagine that anyone cares about thee.
10. Du skal ikke tro at du kan lære *oss* noe.
Thou shalt not suppose that thou can teach us anything.

Festivalen Frizon 2010

Festivalen Frizon är Sveriges bästa festival du inte visste om. År 2010 arrangeras festivalen 11-15 augusti.

Måndag 12 juli 2010 på Liseberg

Music is good for the soul and the epigenome!

Lotta på Liseberg - Del 4 av 8. På scen står Kalle Moraeus, Sanna Nielsen och Timo Räisänen