Recovered: DNA Resources File

[junglelord]

I just opened the PDF of that link. I am forever working on the structure of these different domains and how they scale.
http://arxiv.org/PS_cache/arxiv/pdf/080 ... 1048v1.pdf

It seems that geometry was not accounted for with hydration and DNA geometry and charge transfer.
Again vivid proof of the role of geometry and charge and the nanoworld rules with structure and function.

We suggest that the reason for the underestimation
of the humidity effect lies in the fact that the
DNA geometry transformation from B to A forms with
dehydration of DNA is not taken into account.

In our present work we report on our investigation of
the impact of humidity on the orbital interaction and
charge transfer between two base pairs if they are stacked
according to the structural parameters of B-DNA and
A-DNA. The aspects of the orbital interaction of the unbound
electrons are considered also for an explanation
of the magnetic properties of the B-DNA molecule, exhibiting
the paramagnetic behavior in a magnetic field

Our findings that hydration of DNA activates the occurrence
of the unbound π electrons, which can easily
participate in conductance because of narrowing of the
band gap to ∼ 3.0 eV in comparison to ∼ 8.0 eV for dehydrated
DNA, allow us to characterize the DNA molecule
as a narrow band gap semiconductor. The main factors
enhancing the appearance of these unbound electrons are
linking of the nucleobases with water molecules and intrastrand
interactions between neighboring nucleobases.
The main contribution to the conductivity comes from
the intrastrand transfer of unbound π electrons between
purines because of quite strong overlapping of their orbitals

The more I learn the more I see that indeed the diry word in science circles of sacred geometry is really the Holy Grail of physics. Within the platonic solids was my first clue back in 1994 and my journey into fascial science, tensegrity and the world of structure and function of Ida Rolf. A Zome Tools kit is the opportunity to approach the nanoworld in our dimensions. Pi, PHI, e are the source of the missing direction of modern math. This must relate to Hydrogen atoms, and hydrogen bonding and therefore DNA replication. I see DNA as a triple helix at this point with the missing 120 phase being the aether. It models the Tesla three phase motor, a three force universe, and a triple helix is I believe the second archetype after the spiral.

[seasmith]

junglelord wrote:

I see DNA as a triple helix at this point with the missing 120 phase being the aether.

Hmmmn....
~

[junglelord]

Yeah that one blows the mind. We come back full circle to Tesla and his triple phase system.
We start to see the triple helix everywhere, the third one invisible but fitting perfectly.
Each one 120 degrees out of phase.
So a Birkeland current is really a triple helix and so is DNA.
It goes back to vortex math and geometry.

[junglelord]

Gene2Music! This is just awsome! After hearing the musics of plants and stones and planets I have now listened to the music of the 20 amino acids. Take a listen to a gnome sequence that codes for a prototype human protein, ThyA.

SUMMARY
The primary goal of this work is to convert genome-encoded protein sequences into musical notes in order to hear auditory protein patterns. Although there have been previous efforts to do this, one of the main problems has involved the large jumps between consecutive notes in a 20 note range (2.5 octaves) that results from a one-to-one amino acid-to-musical note assignment. Some other concerns include assigning rhythm, dynamics, and accompaniment according to the characteristics of the protein sequence.

We derived a reduced 13 base note range according to hydrophobicity and pairing of similar amino acids. The amino acid pairs were differentiated using variants of three-note chords, namely the root position and first inversion chords. A rhythm has been encoded into the musical sequence according to the organism’s codon distribution used in the genome-encoded protein sequence. Such a designation allows each amino acid to be represented by different note durations. The result is a set of rules that produces musical compositions that can be applied to any protein sequence [1]. As an example, we have used a prototype human protein, Thymidylate Synthase A (ThyA). A detailed description of our coding assignment can be found in the Project Evolution.

In addition to the primary goal, we also aim to use this conversion to help make protein sequences more approachable and tangible for the general public and children. The project also opens opportunities for visually impaired scientists to access protein sequences more readily. We show and allow one to listen to examples of several proteins translated into music by these methods and also provide the opportunity for others to convert their own gene of interest using our GENE2MUSIC program.

Takahashi R, Miller, JH: Conversion of Amino Acid Sequences in Proteins to Classical Music: Search for Auditory Patterns. Genome Biology 2007.

http://www.mimg.ucla.edu/faculty/miller ... /home.html

[junglelord]

I have a strong association with Colour and Pitch.

Brain & Music
Synesthesia refers to a neurological condition in which there is a union of two or more physical senses. Commonly, a person will associate unique colors with specific letters. There are also cases of strong associations between color and pitch or less frequently taste and pitch. Multiple groups have investigated this phenomenon to better understand cross-modal associations in the brain. There is speculation that well-known artists and scientists such as Wassily Kandinsky, Alexander Scriabin, and Richard Feynman were synesthetes. Daniel Tammet has a rare form of synesthesia known as Savant syndrome. Not only can he visualize prime numbers as smooth and round, but he also has the ability to become fluent in difficult languages, such as Icelandic, in a matter of days. All numbers have a specific shape, color, and sometimes tone.

http://www.mimg.ucla.edu/faculty/miller ... ience.html

[seasmith]

Trapping of DNA in nonuniform oscillating electric fields.

Asbury CL, van den Engh G. 2008

Department of Molecular Biotechnology, University of Washington, Seattle 98195, USA.

DNA molecules can be manipulated in aqueous solution in a manner analogous to optical trapping. Due to the induction of an electric dipole, DNA molecules are pulled by a gradient force to regions of high electric field strength. Molecules can be locally trapped in an oscillating field using strips of very thin gold film to generate strong electric fields with steep gradients. Spatial control over the trapped molecules is achieved because they are confined to a width of approximately 5 microm along the edges of the gold-film strips. By mixing static and oscillating electric fields, trapped molecules can be moved from one edge to another or made to follow precise trajectories along the edges. This phenomenon should be useful in microdevices for manipulation of small quantities or single molecules of DNA.

http://www.ncbi.nlm.nih.gov/sites/entre ... 00m,isrctn



Detection of DNA Sequences Using an Alternating Electric Field in a Nanopore Capacitor

Molecular dynamics simulations revealed that back-and-forth motion of DNA strands through a 1 nm diameter pore exhibits sequence-specific hysteresis that arises from the reorientation of the DNA bases in the nanopore constriction. Such hysteresis of the DNA motion results in detectable changes of the electrostatic potential at the electrodes of the nanopore capacitor and in a sequence-specific drift of the DNA strand under an oscillating transmembrane bias. A strategy is suggested for sequencing DNA in a nanopore using the electric field that alternates periodically in time.

http://pubs.acs.org/doi/abs/10.1021/nl071890k

[junglelord]

Thanks for those links. Geometry is a central concept that is going to guide us into the nanotechnology of Biophysics.


Wonderful to see its all capacitance, E fields, and geometry.

[seasmith]

JL

~ This one is probably even more up your alley.
Pity i'm too cheap to get the full article


Protein and DNA Reactions Stimulated by Electromagnetic Fields
Author: Martin Blank a
Affiliation: a Department of Physiology and Cellular Biophysics, Columbia University, New York, New York, USA


Abstract

The stimulation of protein and DNA by electromagnetic fields (EMF) has been problematic because the fields do not appear to have sufficient energy to directly affect such large molecules. Studies with electric and magnetic fields in the extremely low-frequency range have shown that weak fields can cause charge movement. It has also been known for some time that redistribution of charges in large molecules can trigger conformational changes that are driven by large hydration energies. This review considers examples of direct effects of electric and magnetic fields on charge transfer, and structural changes driven by such changes. Conformational changes that arise from alterations in charge distribution play a key role in membrane transport proteins, including ion channels, and probably account for DNA stimulation to initiate protein synthesis. It appears likely that weak EMF can control and amplify biological processes through their effects on charge distribution.
Keywords: Electric fields; Magnetic fields; Charge transfer; Protein; Hydration energy; DNA

Schumann resonances anybody ?

http://www.informaworld.com/smpp/conten ... 868~db=all

[junglelord]

Charge transfer is best connected to Fuller Synergetics I believe.
This would relate to quantum and atomic and molecular levels very well.
The structural protein and the structural framework must control charge transfer via their own confirmation activity.
This has been pointed out by myself and the gentleman who did the 2.5 hrs video on quantum biology that Divinty had posted in another thread. The fact it is very low levels and that the threshold is within only biolgical ranges is well document by Robert Becker and the Body Electric. Still on target.

[seasmith]

by StefanR on Wed Jan 21, 2009 1:01 pm

Molecular Visualizations of DNA
http://www.youtube.com/watch?v=4PKjF7OumYo

http://www.wehi.edu.au/WEHI_Groups/inde ... php?id=151

[junglelord]

Everything in the universe vibrates and oscillates. Therefore the connecting link between all forms of energy is vibration, sympathetic harmony, and resonance. Dr. Dan Burisch, David Wilcock, and others have discovered that a simply quartz crystal, electricity, and water are all the ingredients needed to create a medium for spontaneous DNA to appear in the vacuum..

http://www.youtube.com/watch?v=wbewGohc ... re=related

[webolife]

That video is full of garbage and science fiction (note I distinguish between the two) and is not based on any real scientific studies or experiments. The salamander to frog laser experiment mentioned therein is a figment of someone's active imagination. DNA cannot and does not spontaneously assemble in any kind of environment, let alone a vacuum. DNA can only be produced from DNA, albeit it undergoes some mutation through reverse transcription by retroviruses (w/RNA) and the like.

[seasmith]

Lamark Redux
Jean-Baptiste Lamarck (1744-1829)
What Lamarck Believed
Lamarck had to postulate that simple organisms, such as protists, were constantly being spontaneously generated.

Lamarck is best known for his Theory of Inheritance of Acquired Characteristics, first presented in 1801 (Darwin's first book dealing with natural selection was published in 1859): If an organism changes during life in order to adapt to its environment, those changes are passed on to its offspring. He said that change is made by what the organisms want or need. For example, Lamarck believed that elephants all used to have short trunks. When there was no food or water that they could reach with their short trunks, they stretched their trunks to reach the water and branches, and their offspring inherited long trunks. Lamarck also said that body parts that are not being used, such as the human appendix and little toes are gradually disappearing. Eventually, people will be born without these parts. Lamarck also believed that evolution happens according to a predetermined plan and that the results have already been decided.

http://www.ucmp.berkeley.edu/history/lamarck.html

~s~

[bboyer]

That video is full of garbage and science fiction (note I distinguish between the two) and is not based on any real scientific studies or experiments.

That would, indeed, appear to be the case. Just Google "Dan Burisch" (mentioned at the start).

Never heard of him before but, offhand, the word "gullibility," for one, in terms of the intended audience comes to mind. Haven't spent any time on it other than a quick Google as above but other probable words like fraud and con come to mind, too.

[GaryN]

David Icke thinks sound creates everything. (I'm still not sure about this guy!) If the Sun puts out so many frequencies with so many harmonics, then I'm sure some very interesting self-assembly would occur in the surrounding medium.

http://uk.youtube.com/watch?v=oCmGjD9j9bU