Recovered: DNA Resources File

[seasmith]

3. Helical dust structures

...
Figure 3(a) illustrates double helical dust structures similar to DNA. Molecular dynamics simulations of interacting grains with an additional gas friction show that any cylindrically symmetric grain distribution converts in time into a stable self-confined helical structure [17]. ...these cylindrical crystals...
we predict the possible existence of large plasma poly-crystals in space...
These structures can have all necessary features to form `inorganic life'...

This was an important 'mainsream' paper, first contributed if i recall correctly by Kovar last year.


"From plasma crystals and helical structures towards inorganic living matter"
V N Tsytovich1,5, G E Morfill2, V E Fortov3, N G Gusein-Zade1, B A Klumov2 and S V Vladimirov4
New J. Phys. 9 (2007) 263
doi:10.1088/1367-2630/9/8/263
PII: S1367-2630(07)48657-8


http://www.iop.org/EJ/article/1367-2630 ... 8_263.html
~

[Tina]

A referance link for current information and research on the electronic structure of DNA article entitled:

"Electronic Structure of DNA revealed for the First Time at Hebrew University.......

http://www.eurekalert.org/pub_releases/ ... 022808.php

[Tina]

Hope this link works:


The DNA (or Double Helix) Nebula located near the center of our galaxy.

[seasmith]

'Selfish Gene' revisited

New Discovery Proves 'Selfish Gene' Exists

This means that the 'selfish' gene does exist, not just in theory but in reality. "We don't know exactly which gene it is, but we're getting close."
"This basically provides a validation for a huge body of socio-biology," says Thompson, who adds the completion of Honey Bee Genome Project in 2006 was crucial to this discovery.
The research will be published in the July issue of Genetics

http://www.sciencedaily.com/releases/20 ... 115905.htm

~

[seasmith]

~
Quadrupole DNA sequencing . . .

Research at Oak Ridge National Laborato ... ical care.

http://www.ornl.gov/info/ornlreview/v41 ... review.pdf
~

[Aetherisreal]

http://www.intellectuallyhonestscience. ... ave[1].doc

I will quote heavily from the above link. One of you mentioned the work of Dr. Popponin of the Russian Academy of Science. I am pleased to add the work of many of his colleagues who put together an international team of researchers inclusive of other universities (Great Britain, Germany, Canada...) and the private corporation Wave Genetics Inc.. The team is primarily interested in bioinformatics as it relates to quantum computing. Building upon volumes of prior works by the likes of Peter Mercer (a friend of mine) Peter Gariaev, W. Schempp and a host of other brilliant minds the above paper was devised.

What the team discovered is, as you gentlemen have stated at least in part, is that DNA is able to sample the environment both inside the greater organism within which it resides and also the world outside. The precise ways in which this is accomplished has been experimentally verified:

For here, as the experimental evidence now confirms, the mutual recognition of one DNA anti parallel half chain (+) by the other (-) concerns special super persistent/resonant acoustic-electromagnetic waves or solitons. Such DNA solitons have two connected types of memory. The first is typical of the phenomenon discovered by Fermi-Pasta-Ulam (FPU) [Fermi, 1972]. It concerns the capability of non-linear systems to remember initial modes of energisation and to periodically repeat them [Dubois 1992]. The DNA liquid crystals within the chromosome structure form such a non-linear system. The second is that of the DNA-continuum in an organism. Such memory is an aspect of the genome’s nonlocality. It is quasi-holographic/fractal, and relates, as is the case for any hologram or fractal, to the fundamental property of biosystems i.e. to their ability to restore the whole out of a part. This property is well known (grafting of plants, regeneration of a lizard’s tail, regeneration of a whole organism from the oocyte). And a higher form of such a biological memory would be a holographic (associative) memory of the brain cortex, i.e. of its neural network [Pribram 1991; Schempp 1992; Marcer Schempp 1997, 1998; Sutherland 1999]. Such wave sign encoding/decoding therefore, like DNA's ability to resolve "the travelling salesman’s problem", is, it can be hypothesized, an integral part of DNA's computational biofunctionality

This team of researchers was able to map the frequency of cellular reproduction and project said frequency onto a dead seed (died under conditions of radioactive poisoning) causing it to spring to life and grow into a healthy plant. They conducted other suc frequency mapping with sometimes bazaar results. The point is that DNA is able to speak and comprehend its own genomic language. See here how they describe ths:

1) That the evolution of biosystems has created genetic "texts", similar to natural context dependent texts in human languages, shaping the text of these speech-like patterns.
2) That the chromosome apparatus acts simultaneously both as a source and receiver of these genetic texts, respectively decoding and encoding them, and
3) That the chromosome continuum of multicellular organisms is analogous to a static-dynamical multiplex time-space holographic grating, which comprises the space-time of an organism in a convoluted form.
That is to say, the DNA action, theory predicts and which experiment confirms,
i) is that of a "gene-sign" laser and its solitonic electro-acoustic fields, such that the gene-biocomputer "reads and understands" these texts in a manner similar to human thinking, but at its own genomic level of "reasoning". It asserts that natural human texts (irrespectively of the language used), and genetic "texts" have similar mathematical-linguistic and entropic-statistic characteristics, where these concern the fractality of the distribution of the character frequency density in the natural and genetic texts, and where in case of genetic "texts", the characters are identified with the nucleotides, and ii) that DNA molecules, conceived as a gene-sign continuum of any biosystem, are able to form holographic pre-images of biostructures and of the organism as a whole as a registry of dynamical "wave copies" or "matrixes”, succeeding each other. This continuum is the measuring, calibrating field for constructing its biosystem.

This team demonstrate that DNA and other constituents of living cells are able to modulate light and sound and convert them into broadband signals for the purpose of sending, receiving and storing information (owing to the properties of liquid crystal mirroring).

I encourage folks to give a careful read of this paper and offer your comments here for us to ponder. As for myself, I would prefer this paper written in an aether physics paradigm rather than the mass=energy paradigm but it is what it is and one must convert the processes in ones own mind as necessary to comprehend the underlying truths discovered in this remarkable work.

[seasmith]

The DNA-wave Biocomputer


Aetherisrael,

Greetings, just getting back on line.
This work, and translation, is from the last decade and is an ambitious (and learned) agglutination of theory from a number of fields; which, imo, ultimately intends to garner patronization for more research in the big-budget realm of “bio-computing”; under the hot-button banner of the ‘DNA Archetype'.

Getting past the odd use of “laser mirror”, where I assume is meant laser recording function, there are a number of very good concepts.
ie: Continuity of energy spectrum including ‘photonic’ (the slightest ‘quantum’ so far detectable) though radio wave and acoustic, Semantic and semiotic parallels between genetic and grosser forms of communication, Transmitting/receiving function of DNA, Simultaneous signal reception/recognition on a vast ‘scalable’ scale,
and others.

From your cited paper above:

«1. The DNA-wave Biocomputer


« It can therefore be asserted, that this phenomenon concerns a new type of a computer (and biocomputer) memory, and also a new type of EPR spectroscopy, namely one featuring photon-laser-radiowave polarization spectroscopy. The fundamental notion is, that the photon-laser-radiowave features of different objects (i.e. the Fourier-spectra of the radiowaves of crystals, water, metals, DNA, etc) are stored for definite but varying times by means of laser mirrors, such that the "mirror spectra" concern chaotic attractors with a complex dynamic fractal dynamics, recurring in time. «»

«A soliton is an ultra stable wave train often with a seemly simple closed shape, which can arise in the context of non-linear wave oscillations. It actually consists of a rather complexly interrelated assembly of sub wave structures, which keep the whole solitonic process in a stationary state over a comparatively long time. In the literature, a soliton is often described as an entity, which is neither a particle nor a wave in much the same way as is a quantum, for it, too has wave/particle duality. It can also be a means to carry information.»

OR ....

«3. Another Theoretical but Experimentally Validated Perspective - Quantum Holography
.....
The quantum holographic DNA-wave biocomputer model describes the morphology and dynamics of DNA, as a self-calibrating antenna working by phase conjugate adaptive resonance capable of both receiving and transmitting quantum holographic information stored in the form of diffraction patterns (which in MRI can be shown to be quantum holograms). The model describes how during the development of the embryo of the DNA's organism, these holographic patterns carry the essential holographic information necessary for that development. This would explain the almost miraculous way the multiplying assembly of individual cells is coordinated across the entire organism throughout every stage of its development - in complete agreement with the explanation arrived at in Moscow by Gariaev and his co-workers»

See also:

A condensation of this paper by the BCS
http://www.bcs.org.uk/siggroup/cyber/dna.htm

and

“The transfer of energy from the first pulse to the second one is actually described by a frequency-dependent phase shift (i.e., a change of the spectral phase), which can be calculated with Kramers-Kronig relations.”

http://www.rp-photonics.com/spotlight_2007_10_11.html

What is your take?

s
~

[junglelord]

I was considering how many atoms in a simple bacteria. I came across this. I was trying to see how many atoms to create consciousness. Like a critcal limit. I think we could determine that even a virus is in some type of consciousness.

Our own cells contain about 3 billon base pairs, that´s about 150 billon atoms. Interesting.

--------------------------------------------------------------------------------

Re: How many atoms are in a cell?
Date: Mon May 24 23:57:14 1999
Posted By: Talia Arcari, Undergraduate, Bioquemistry, State University
Area of science: Cell Biology
ID: 927183560.Cb
--------------------------------------------------------------------------------
Message:


Dear Paul,

Thanks for your question.
I hope my explanation is clear enough for you to understand it.

You probably know all living organisms are made of cells. Some cells are
complete organisms, such as bacteria and others, such as muscle cells, are
specialized components of multicelular organisms.

Cells vary greately in their composition and size. For example: the
smallest bacteria is about 0.1 micrometres in diameter (that´s
the 10,000,000 of a meter) and egg yolks of ostriches are about 8 cm (0.08 m)
in diameter (really big, don´t you think!?)Although cells might differ
widely in size, appearence and functions, they are all composed primarily
by 4 different types of atoms: Oxygen, Hydrogen, Carbon and Nitrogen.
These four elements make up the majority of organic compounds. The most
important organic compounds in a cell are:

1.Proteins

They are very large molecules, ranging in molecular weight from a few
thousand to more than a million, and they are specific for each species and
for each organ of each species. Humans have an estimated 30,000 different
proteins.

Proteins are composed of units of about 20 different amino acids, which, in
turn, are composed of carbon, hydrogen, oxygen, nitrogen, and often
sulfur. In a protein molecule these amino acids form peptide bonds. The
almost numberless combinations in which the acids line up, and the helical
and globular shapes into which the strands coil, help to explain the great
diversity of tasks that proteins perform in living matter.


2.Nucleic Acids

Nucleic acids have at least two functions: to pass on hereditary
characteristics from one generation to the next, and to trigger the
manufacture of specific proteins. All living cells contain the genetic
materials DNA (deoxyribonucleic acid) and RNA (ribonucleic acid). One cell
has about one meter of DNA. The complete set of genes in each of your cells
is 3 billon base pairs. (that´s about 150 billon atoms)

3.Lipids (oil)

Lipids are distinguished from other classes of organic compounds in that
they do not dissolve in water but are soluble in organic solvents.
Among the most important lipids are the phospholipids, which are major
components of the cell membrane. (1 single fatty acid is made of
aproximately 50 atoms)

4.Polysaccharides (sugar)

Compounds in the carbohydrate group that are readily soluble in water; are
colorless, odorless, and usually crystallizable; and are more or less sweet
in taste.


Water makes up to 60-65% of an average cell, because it´s a favourable
environment for biochemical reactions.


Well, as you can see, cells are quite complex tiny structures. You can´t
possibly know the exact number of atoms in a cell but let´s say you can
find as many atoms in a cell as stars in the sky...

Hope my answer will help.

Just in case you want to know more about cells:

http://library.advanced.org/3564/
http://www.mblab.gla.ac.uk/dictionary/
or if you have Microsoft´s Encarta Encyclopedia 98-99 you can look for the
information given under cell.

Talia Arcari
State University
Montevideo
Uruguay

[junglelord]

I also saw this as a way to extrapolate the number of atoms by the amount of atoms per mole.

Let's guess that a crumb of toast weighs a hundredth of a gram, that is 0.00001 kg. Let's also assume that, being organic, toast is mostly made of carbon, oxygen and hydrogen, with an average atomic weight of about 8. (C=12, O=16, H=2, but there are more hydrogen atoms than carbon or oxygen). So let's simplify our toast by pretending that it's made up of atoms with atomic weight 8. By definition, one mol of anything weight as much in kg as the atomic weight of the things, so a mol of toast atoms weighs 8 kg; and one mol is a number of things equal to Avogadro's constant, which is 6 x 10^23, or 600,000,000,000,000,000,000,000. But we don't want 8 kg of toast, we only want 0.00001 kg, so we divide that number by 8 and multiply by 0.00001 and we get a rough answer: 75 x 10^16 = 750,000,000,000,000,000 atoms, or 750 quadrillion.

That should be correct within a few orders of magnitude -- that is, the right answer could easily be a hundred times more or less, but probably not much more than a thousand times more or less.

But ... is that, in fact, more than all the grains of sand in the sea? How many grains of sand are there in the sea? Anyone?

[junglelord]

The DNA molecule is comprised from only five different atoms; carbon, hydrogen, oxygen, nitrogen and phosphorous but it is still an enormous molecule with thousands and thousands of atoms.

To give an idea of the size of a DNA molecule, the longest human DNA molecule, when fully stretched out, spans about 9 cm! Chemically, DNA is a long polymer of simple units called nucleotides, with a backbone made of sugars and phosphate groups joined by ester bonds. Attached to each sugar is one of four types of molecules called bases. As an example, the largest human chromosome (chromosome number 1) is approximately 220 million base pairs long. The human DNA does not exist as a single molecule, but instead as a tightly-associated pair of molecules which entwine in the well known double helix shape.

The backbone of the DNA strand is made from alternating phosphate and sugar residues. The sugar in DNA is 2-deoxyribose (C5H10O4) which is joined together by phosphate groups that form ester bonds between the third and fifth carbon atoms of adjacent sugar rings.

The DNA double helix is stabilized by hydrogen bonds between the bases attached to the two strands. The four bases found in DNA are adenine (C5H5N5), cytosine (C4H5N3O), guanine (C5H5N5O) and thymine (C5H6N2O2). These four bases are attached to the sugar/phosphate to form the complete nucleotide.

A nucleotide is made up of 30 atoms, plus or minus a few, depending on the base. It's no wonder that determining the sequence of bases in the human genome -- all three billion of them -- was such a monumental accomplishment. And though the task of determining the sequence is over, that of understanding the sequence is just beginning. Figuring out how these three billion bases code for a human being will keep researchers busy for many decades to come.


http://www.pbs.org/wgbh/nova/genome/dna_sans.html

We often hear about how the deoxyribonucleic acid (DNA) macro-molecule that contains the human genome has about 3 billion base pairs, but we rarely hear about the atoms. I was curious to know how many such a complex structure required…

Warning: Back of the envelope calculations.

Here we go:

3 billion base pairs equals 6 billion nucleotides.

The human genome uses 4 types of nucleotides:

Adenine (A)
Guanine (G)
Cytosine (C)
Thymine (T)
‘T’ is always associated with ‘A’, and ‘G’ with ‘C’.

Each of these nucleotides is composed of a nitrogen-containing base, a five-carbon sugar, and a phosphate group.

To simplify, we’ll only look at Thymine, which is pretty representative of the others in size.


Thymine’s base is a pyrimidine ring compound and it contains 15 atoms. Its pentose sugar has 15 atoms also (the 5-carbon sugar used for ribonucleic acid (RNA) is very similar, but it has an extra oxygen atom). The phosphate group contains 4 atoms.

Total for a thymine nucleotide: 34 atoms.

Multiply that by 6 billion nucleotides and you get 204 billion atoms.

Of course, that’s just an estimate since human DNA isn’t composed of only ‘T’ nucleotides, and I think some of them can have more than one phosphate group (not sure). But it should be in the right ballpark.
http://michaelgr.com/2008/04/06/how-man ... an-genome/

[junglelord]

I find it interesting at this time of my learning curve to review the amount of atoms and molecules to make up our systems via DNA. The critical mass for these different domains is something I wish to pursue until I have some bell curve of these ratios in different organisms.

I am interested in if anyone has ever done a study that looked at the amount of atoms it takes to achieve consciousness.

How do this play into the way consciouness develops? At what level can we take a wholistic approach with modern knowledge? Ovbiously the reduction approach is finished. We can count the amount of atoms and the configurations are known. How do these structures relate to consciouness? What is it about consciouness and structure that has not been recognized that is staring us in the face? Why does the carbon atom create life? Its ability to construct structure is really quite amazing
http://en.wikipedia.org/wiki/Carbon

Human DNA is divided into 23 paired chromosomes, 22 pairs of autosomes and 1 pair of sex chromosomes. There are about 3 Billion nucleotide pairs packed away in there, most of it inactive at any one point in time. It's believed that much of the DNA is inactive, meaning that it is not currently expressed, and therefore not responsible for creating proteins. However, the inactive DNA could be responsible for early fetal development; we aren't entirely sure what all of the DNA does, although all of it has been mapped out...

Now back to the initial question. A molecule is defined as 2 or more atoms connected by chemical bonds. Each DNA strand is comprised of two Phosphate Deoxyribose backbones, held together by nucleotides (Adenine, Cytosine, Guanine, and Thymine), bound by Hydrogen bonds. So technically, every DNA segment that's connected is one molecule...therefore, there are 46 molecules of DNA in each human cell.

But, if what you were asking how many molecules are assembled for the DNA in each cell, I'd bet 4 per each nucleotide, 1 for each side of the backbone, and 1 for each nucleotide pair. That's about 12 Billion molecules, but they are joined by chemical bonds, and therefore are not individual molecules anymore once assembled.

[seasmith]

~ For reference only, w/o comment [pay site]

Copyright © 2008 American Chemical Society
How the Surrounding Water Changes the Electronic and Magnetic Properties of DNA

Julia Berashevich and Tapash Chakraborty*

Department of Physics and Astronomy, The University of Manitoba, Winnipeg, Canada R3T 2N2

Received: July 11, 2008
Revised Manuscript Received: August 20, 2008

Abstract:

We study the influence of humidity on the transport and magnetic properties of DNA within the quantum chemistry methods. Strong influence of water molecules on these properties, observed in this study, opens up opportunities for application of DNA in molecular electronics. Interaction of the nucleobases with water molecules leads to breaking of some of the π bonds and appearance of unbound π electrons. These unbound electrons contribute significantly to the charge transfer at room temperature by up to 103 times, but at low temperature the efficiency of charge transfer is determined by the spin interaction of two unbound electrons located on the intrastrand nucleobases. The charge exchange between the nucleobases is allowed only when the spins of unbound electrons are antiparallel. Therefore, the conductance of DNA molecule can be controlled by a magnetic field. That effect has potentials for applications in developing nanoscale spintronic devices based on the DNA molecule, where efficiency of spin interaction will be determined by the DNA sequence.

http://www.globalspec.com/engnews/detail?t=469409
~

[junglelord]

Wow, nice post. That is really compelling information that is perfect timing right now.
H2O and DNA and the relationships of geometry and spin are fascintating.
Thanks.

[seasmith]

~
J,

Would be interested to read your synopsis of the H2O - DNA relations, at some point in time.

Cheers,
s

[seasmith]

From DNA to Domains
"Groundbreaking study led by an eminent molecular biologist at Florida State University..."

"We know that all the information (DNA) required to take on the identity of any tissue type is present in every cell, because we already can, albeit very inefficiently, create whole animals from adult
tissue through cloning," Gilbert said. "We also can make a kind of artificial embryonic stem cells, called induced pluripotent stem cells, out of many adult cell types, but there are two major hurdles remaining. First, the methods currently used rely on the unnatural retroviral insertion of genes into patients' cells, and these genes are capable of forming tumors. Second, this method is very inefficient as well because only one in 1,000 cells into which the genes are inserted becomes pluripotent.

But, Gilbert noted, one time that the cell "shows its cards" is during DNA replication.

"During this process, which was the focus of our FSU research, it's not just the DNA that replicates," he said. "All the packaging must be replicated as well in each cell division cycle."

He explained that embryonic stem cells have many more, smaller "domains" of organization than differentiated cells, and it is during differentiation that they consolidate information.

"In fact, 'domain consolidation' is what we call the novel concept we discovered," he said.

http://www.physorg.com/news142876340.html