Supernature, Creation, and the Divine/
Is there another Creation theory?

Proteins are constructed from one or more unbranched chains of amino acids Proteins are polymers. Proteins are made when amino acids combine in a given order in chain form. No two proteins have the same sequence of amino acids Every protein has a different number and arrangement of amino acids A typical protein contains 200-300 amino acids
Protein aggregates associate & form intermolecular contacts that resemble those found in the final crystal. Aggregates reach the critical nuclear size, growth proceeds by addition of molecules to the crystalline lattice.
The processes of nucleation and crystal growth both occur in supersaturated solutions.

. The newly designed and synthesized peptide with molecular weight (MW) about 1,000 is much smaller than naturally occurring proteins with MW 5.000~150,000.  However, in view of two essential requirements for protein functioning: specific 3D structures and cooperative structural transition, the synthesized peptide may be regarded as “a smallest protein”. Protein is one of most important materials supporting life phenomena, and it has been known that for the expression of its function, the formation of specific 3D structure is playing a key role.

It has been generally conceived that for a protein keeping stable 3D structures, it has to possess at least 30~50 amino acid residues. The synthesized peptide pushes the lower limit widely downward, requesting to revise the understanding on the minimal structural unit of protein. The present study is expected to promote the progress in the studies of stabilization mechanism, folding and molecular design of proteins, and exercise a significant impact to the investigation on the origin of life.

A peptide bond is a chemical bond formed between two molecules when the carboxyl group of one molecule reacts with the amino group of the other molecule, thereby releasing a molecule of water (H2O). This is a dehydration synthesis reaction (also known as a condensation reaction), and usually occurs between amino acids. The resulting CO-NH bond is called a peptide bond, and the resulting molecule is an amide. The four-atom functional group -C(=O)NH- is called an amide group or (in the context of proteins) a peptide group. Polypeptides and proteins are chains of amino acids held together by peptide bonds, as is the backbone of PNA. Polyamides, such as nylons and aramids, are synthetic molecules (polymers) that possess peptide bonds.

The amide group has two resonance forms, which confer several important properties. First, it stabilizes the group by roughly 20 kcal/mol, making it less reactive than many similar groups (such as esters). The resonance suggests that the amide group has a partial double bond character, estimated at 40% under typical conditions. The peptide group is uncharged at all normal pH values, but its double-bonded resonance form gives it an unusually large dipole moment, roughly 3.5 Debye (0.7 electron-angstrom). These dipole moments can line up in certain secondary structures (such as the α-helix), producing a large net dipole.

In the unfolded state of proteins, the peptide groups are free to isomerize and adopt both isomers; however, in the folded state, only a single isomer is adopted at each position

Using principal component analysis (PCA) on the intrasegment C(alpha)-C(alpha) atomic distances, the conformational space of protein segments, which we call the protein segment universe, has been visualized, and three essential coordinate axes, have been identified.  radius of gyration, structural symmetry, and separation of hairpin structures from other structures.

Stem-loop intramolecular base pairing is a pattern that can occur in single-stranded DNA or, more commonly, in RNA. The structure is also known as a hairpin or hairpin loop. It occurs when two regions of the same molecule, usually palindromic (reads the same in both directions, for example AAGC in one direction would read TTCG in the other and it would be a palindrome in relation to a DNA) in nucleotide sequence, base-pair to form a double helix that ends in an unpaired loop. The resulting lollipop-shaped structure is a key building block of many RNA secondary structures. Stem-loops occur in pre-microRNA structures and most famously in transfer RNA, which contain three true stem-loops and one stem that meet in a cloverleaf pattern. The anticodon that recognizes a codon during the translation process is located on one of the unpaired loops in the tRNA. Two nested stem-loop structures occur in RNA pseudoknots, where the loop of one structure forms part of the second stem. Many ribozymes also feature stem-loop structures. The self-cleaving hammerhead ribozyme contains three stem-loops that meet in a central unpaired region where the cleavage site lies. The hammerhead ribozyme's basic secondary structure is required for self-cleavage activity. Stem-loop structures are also important in prokaryotic rho-independent transcription termination. The hairpin loop forms in an mRNA strand during transcription and causes the RNA polymerase to become dissociated from the DNA template strand. This process is known as rho-independent or intrinsic termination, and the sequences involved are called terminator sequences.

These peptide groups are not contiguous in the amino acid sequence. The first dipoles to be aligned are those that are both sufficiently close in space to be arranged in approximately linear arrays termed dipole paths. The criteria used in the construction of dipole paths are: to assure good alignment of the greatest possible number of dipoles that are close in space; to optimize the electrostatic interactions between the dipoles that belong to different paths close in space; and to avoid locally unfavorable amino acid residue conformations. The equations for dipole alignment are solved separately for each path, and then the remaining single dipoles are aligned optimally with the electrostatic field from the dipoles that belong to the dipole-path network. A least-squares minimizer is used to keep the geometry of the alpha-carbon trace of the resulting backbone close to that of the input virtual-bond chain. This procedure is sufficient to convert the virtual-bond chain to a real chain; in applications to real systems, however, the final structure is obtained by minimizing the total ECEPP/2 (empirical conformational energy program for peptides) energy of the system, starting from the geometry resulting from the solution of the alignment equations. When applied to model alpha-helical and beta-sheet structures, the algorithm, followed by the ECEPP/2 energy minimization, resulted in an energy and backbone geometry characteristic of these alpha-helical and beta-sheet structures.

All living cells have a set of special enzymes, the DNA topoisomerases, that deal with topological problems. There are two basic types that solve two major topological problems. Class I topoisomerases, solve the problems caused by the helical nature of DNA. They grasp the DNA and make an incision, cutting the strand but keeping a firm grip on one of the severed ends. The gapped helix is then free to rotate around the other strand, releasing any strain that may be present from overwinding or underwinding. Once relaxed, the topoisomerase reconnects the broken strand. DNA topoisomerase It plays an essential role in DNA replication and DNA transcription. In both cases, the DNA must be unwound to allow reading of the information held inside. Topoisomerase performs its duty nearby, releasing the stresses that occur in the process.
The class II topoisomerases, , perform an even more remarkable feat involving the juggling of two DNA strands. These topoisomerases grab a DNA double helix and break both strands, retaining a firm grip on each half. Then, a second DNA strand is passed through the gap. Finally, the first DNA is resealed behind it. Topoisomerase II plays an essential role in cell division, as the chromosomes are segregated into the two daughter cells. It releases any loops that may be linking the two chromosomes together as they separate.

The genetic code must deliver stereochemical information to peptide bond formation via tRNA-tRNA interaction.
The genetic code has an overall symmetry that represents the primary organizing force behind the code itself. The genetic code is not only an operating system that builds proteins but also a search engine that efficiently finds proteins and protein populations. The symmetry of genomes and the symmetry of their codes of translation are tightly integrated. Each successive step in the evolution of an adaptive feature must itself be adaptive.

So there is a direct relationship to be seen of motion rising up through Phi relationships from the subatomic to the molecular. From the hydrogen atom to the carbon atom to the hydrocarbon and ionic bounds to the macromolecules of life; allowing for a path of study for quantum biology and an adaptation~evolution. This is seen in three basic laws of biological systems.

1. Form and function are correlated at all levels of biological organization
2. Organisms are open systems that exchange energy with their surroundings
3. Feedback mechanisms regulate biological systems

Molecular composition of cells...
Water (H2O) 70 %
Inorganic ions (Na, K, Cl, PO4) 1 %
Small molecules (aa’s, sugar, nucleotides) 5 %
Macromolecules (protein, n.a., etc) 24 %

We can think of life as being comprised of four main types of biomolecules:  carbohydrates, lipids, proteins, and nucleic acids. The two nucleic acids with which we are most familiar are ribonucleic acid (RNA) and deoxyribonucleic acid (DNA). Just as nucleic acids and proteins are important to life, so are carbohydrates and lipids.  Because of the roles they play in all forms of life, carbohydrates make up most of the organic matter on Earth.  For instance, carbohydrates are important as fuel for living organisms, but also serve as a mechanism to store energy.  They are also important constituents of larger molecules; sugar rings are an important element of nucleic acids like DNA.  Finally, carbohydrates also function as structural elements within the cell, most commonly for cell walls.  Just as proteins are large molecules made up of smaller molecules (amino acids), carbohydrates themselves can be large molecules as well. Lipids are unusual molecules in that they have to components with different characteristics.  Part of a lipid molecule is hydrophilic, which means it is attracted to molecules such as water.  The other part is hydrophobic, which means it is repelled by water. In eukaryotic cells, lipids also form the internal membranes that define cellular organelles such as the mitochondria or chloroplasts.  there is general agreement that a localized molecular assemblage should be considered alive if it continually regenerates itself, replicates itself, and is capable of information transfer. Regeneration and replication involve transforming molecules and energy from the environment into cellular aggregations, and evolution requires heritable variation in cellular processes. The current consensus is that the simplest way to achieve these characteristics is to house informational polymers (such as DNA and RNA) and a metabolic system that chemically regulates and regenerates cellular components
 

Living cells function with such high efficiency and order that the aqueous environment within them must possess some unique spatial properties to coordinate motions and interactions between all the ionic and molecular parts.

Based on current concepts, motion and order within molecules in living cells are controlled by transitions between specific thermodynamic states. However, water within cells is dynamic - it does not undergo specific transitions and its molecules do not bind tightly together. Instead, it appears that environmental order is provided by the transient, dipolar-alignment of water molecules between ions and charge-centers on molecules to permit proton pulses to oscillate back and forth to delocalize charge. Although the alignments have preferred lengths for maximum charge stabilization, the water molecules composing them are still dynamic - only the short, linear units that propagate the proton charge are ordered. By repeatedly defining preferred distances between oppositely-charged centers as multiples of hydrogen-bonded water molecules to minimize energy potential, motions and interactions are quantized. Thus,  the high efficiency and order evident within living cells can be seen to be provided by the dynamic, repetitive, linear quantization of aqueous space by the transient alignment of water molecules between the ionic and molecular parts.

However, One of the wonders of life is that all cells undergo continual turnover, and sustain their structure and function through continuous molecular self assembly.  This dynamic renewal process is commonly viewed from the bottom-up, by focusing on the properties and interaction functions of individual molecular components. In reality, all cells form from other cells using preexisting structures, such as the cytoskeleton, as orienting scaffolds that guide replication and formation of new cellular components.

The ratio 'Phi' appears in certain very important structures of the cell. The hexagonal pattern of microtubules exhibits the Fibonacci feature and it is found that this pattern is made up of 5 right-handed and 8 left-handed helical arrangements

The angle is determined by the number phi, often also called the 'golden section' or 'golden mean'. There are actually two numbers called phi, one with and one without a capital 'p'. Phi is just phi inverse (and interestingly Phi and phi have the same fractional part). phi * 360 degrees yields 222.49°, sometimes (in simulation *and* in real plants) 360° - 222.49° is used instead. Plants seem to have a preference for one or the other value depending on which hemisphere they grow in.

The number phi appears to produce the best packing that can be produced by a constant offset. The constant offset is important for plants as once an organ grows at a certain place it cannot be rearranged easily. What nature seems to use is the same pattern to place seeds on a seedhead as it used to arrange petals around the edge of a flower *and* to place leaves round a stem. What is more, *all* of these maintain their efficiency as the plant continues to grow and that's a lot to ask of a single process!

The amazing thing is that a single fixed angle can produce the optimal design no matter how big the plant grows. So, once an angle is fixed for a leaf, say, that leaf will least obscure the leaves below and be least obscured by any future leaves above it. Similarly, once a seed is positioned on a seedhead, the seed continues out in a straight line pushed out by other new seeds, but retaining the original angle on the seedhead. No matter how large the seedhead, the seeds will always be packed uniformly on the seedhead.

And all this can be done with a single fixed angle of rotation between new cells? Yes! This was suspected by people as early as the last century. The principle that a single angle produces uniform packings no matter how much growth appears after it was only proved mathematically in 1993 by Douady and Couder, two french mathematicians.



Trying other numbers tends to always converge to a pattern with a number of 'arms' going from the center outwards. Depending on the number the pattern may need longer to exhibit these arms, but all number will eventually end up with a fixed number of arms.

Actually it turns out that: "No number which can be written as an exact ratio (a rational number) would be good as a turn-per-seed angle. If we use p/q as our angle-turn-between-successive-turns, then we will end up with q straight arms, the seeds being placed every p-th arm."



So what is a "good" value? One that is *not* an exact ratio - an irrational number such as sqrt2, Phi, phi, e, pi and any any multiple of them. Still not all of these values work very good.

While still being irrational some of these values can be approximated by rational fractions pretty good. 355/113 is already a very good approximation to pi, the error is only 0.000000266. The best approximation to sqrt(2) with a denominator less than 200 is 239/169 and has an error or 0.0000124. This is much less satisfactory.

Observations like these have led mathematicians to set up a hierarchy among irrational numbers, according to how difficult they are to approximate with rationals. It is in this sense that one irrational is more irrational than another.

What is "the best" irrational number? One that never settles down to a rational approximation for very long. Number having this property are called continued fractions. Phi is such a number.


"An interesting fact is that, for ALL series that are formed from adding the latest two numbers to get the next, and, starting from ANY two values (bigger than zero), the ratio of successive terms will ALWAYS tend to Phi!" (definition of continued fractions?)



Another model which tries to be less descriptive and more explanatory has been introduced by Fowler in 1992. It works on abitrary surfaces of revolution. Basically the organs grow at the top of the 'meristem' and then fall down the outline curve until they collide with an existing organ. They are then placed tangential to the organ they hit. The line each organ falls down at is rotatet by phi.

This is a somewhat explanatory model as it actually considers the size of the organs and their interaction. Still the rotation of phi for each succeeding organ is not explained by the model and the pattern forming the plant is in reality determined when the early form of the plant organ (the primordium) is first created at the tip of the 'meristem'. Also this model has some practical modeling drawbacks. It is for example hard to estimate the actual number of plant organs on the receptacle one ends up with. If one wants to create a certain number of organs/visual appearance one has to change the parameters, run the simluation, change the parameters again and so on.



Ridley presented a model in 1986. It's similar to the former in that it also operates on abitrary surfaces of revolution, but it's completely descriptive again. Here each plant organ is rotated by phi against it's predecessor (around the axis of revolution of the underlying surface of revolution). The distance along the outline curve from the start to the position of each organ is brought into relation with the radius of the supporting surface as well as to the size of the organs. Both the Outline curve and the organ size can be defined as abitrary functions.

Let (fx(s), fy(s)), s e [0, L] be a parametric planar curve C that generates the receptacle (supporting surface) when rotated around the y axis of the coordinate system. We assume chord-length parametrization of the curve C, which means that parameter s is the arc-length distance of point (fx(s), fy(s)) from the origin of the curve. The area dA of the infinitesimal slice of the receptacle generated by the arc [s, s+ds] is then equal to 2*pi*fx(s)*ds. We denote by pi*ro^2(s) the area occupied by an organ placed on the receptacle at a distance of s from the origin of the generating curve C. => We can interpret 1/pi*ro^2(s) as the organ density at s. The integer part of the Integral

[INTEGRAL]

is then equal to the total number of organs placed in the portion [0, s] of the receptacle. Consecutive organs are placed at locations that increment N(0,s) by one.


So do plants know math?
It has been talked a lot about why these patterns turn out to be very good, but how do these patterns actually develop? This is going to be a short paragraph because there's no definite answer to that, yet.

Botanists have shown that plants grow from a single tiny group of cells right at the tip of any growing plant, called the meristem. There is a separate meristem at the end of each branch or twig where new cells are formed. Once formed, they grow in size, but new cells are only formed at such growing points. Cells earlier down the stem expand and so the growing point rises.

Even though the phenomenon of phyllotaxis has been observed for hundreds of years and studied by many botanists and mathematicians, only recently has there been a begining of an answer. There is a model by the french physicists Stephane Douady and Yves Couder, who came up with a simple model for the formation of these spiral patterns, which they implemented both physically and on the computer. This model, based on assumptions made by the botanist Hofmeister, spontaneously generates the Fibonacci spiral patterns. The three basic principles of Hofmeister on which this model is based are the following:

A new dot is formed periodically in the place around the central disk where it is least crowded by the others dots.
Once they form, the dots move radially away from the center.
As time increases, the rate at which new dots move away decreases
The dots represent the center of microscopic bulges of cells (primordia) that occur at the growing tip (meristem) of the plant. These bulges eventually differentiate to become the leaves, petals, sepals, flowerets or scales of the plant.

Fractal-like networks effectively endow life with an additional fourth spatial dimension. This is the origin of quarter-power scaling that is so pervasive in biology. Organisms have evolved hierarchical branching networks that terminate in size-invariant units, such as capillaries, leaves, mitochondria, and oxidase molecules. Natural selection has tended to maximize both metabolic capacity, by maximizing the scaling of exchange surface areas, and internal efficiency, by minimizing the scaling of transport distances and times. These design principles are independent of detailed dynamics and explicit models and should apply to virtually all organisms.

NATURE KNOWS
Fibonacci sequences appear in biological settings, such as branching in trees, the spiral of shells, the curve of waves, the fruitlets of a pineapple, an uncurling fern and the arrangement of a pine cone. As the Fibonacci sequences progresses it approximates the Golden Mean.

Why does Phi appear in plants?
The answer seems to be, at least in some cases, evolution: survival of the fittest. The geometrical structures that contain the number Phi = 1.618034 are usually the best structures in terms of “use of available space”, therefore plants and animals have evolved to have that kind of structures in their bodies.

The arrangements of leaves is the same as for seeds and petals. All are placed at 0.618034  leaves, (seeds, petals) per turn. In terms of degrees this is 0.618034 of 360° which is 222.492°.  However, we tend to "see" the smaller angle which is (1 - 0.618034) x 360 = 0.381966 x 360 = 137.50776..°.

If there are Phi (1.618034) leaves per turn (or, equivalently, Phi = 0.618034 turns per leaf ), then we have the best packing so that each leaf gets the maximum exposure to light, casting the least shadow on the others. This also gives the best possible area exposed to falling rain so the rain is directed back along the leaf and down the stem to the roots. For flowers or petals, it gives the best possible exposure to insects to attract them for pollination.

Fibonacci numbers in flower petals

3 Lilies
5 Buttercups, Roses
8 Delphinium
13 Marigolds
21 Black-eyed susans
34 Pyrethrum
55/89 Daisies

Also, many plants show the Fibonacci numbers in the arrangements of the leaves around their stems. If we look down on a plant, the leaves are often arranged so that leaves above do not hide leaves below. This means that each gets a good share of the sunlight and catches the most rain to channel down to the roots as it runs down the leaf to the stem.

The DNA molecule, the program for all life, is based on the Golden section. It measures 34 angstroms long by 21 angstroms wide for each full cycle of its double helix spiral.34 and 21, of course, are numbers in the Fibonacci series and their ratio closely approximates Phi,

This shows that the phyllotactic occurrence of Phi may have very deep roots, deep inside the genetic codes of organisms. Conclusion All these evidences and several more that are yet to be discovered make the golden ratio an indispensable number. We began showing evidences for occurrence of the golden ratioin the DNA and cell structure. Towards the end we were able to show how certain changes in the DNA sequence actually disrupts the Phi pattern. Thus when information is transferred form the molecular level to the macro level, there is one thing that is conserved- Phi. The journey ahead will be interesting as we try and fill the gaps in the translation process. Phi may in future give rise to a new branch of non reductionist science where correlation between entities is far more important than understanding their discrete functions. Already, we have been able to show the strong correlation the genome sequence has with phi. A correlation was also be made between Fibonacci Numbers and the ways of operation of Nature. In Fibonacci numbers each number owes its identity to what has occurred before it. Thus the series is self forming. Similarly in nature operates on this very same principal of self organization. Hence Phi is a number which becomes conspicuous in both.

Life has her own set of  'Phi' relationships as does thermodynamics and vector field power equations!!!

the shape is shared by things as diverse as a seashell, water going down a drain and the path of a falcon on the hunt.

In terms of origin, development and general physics, there is typically little or nothing that binds these various spirals. Behind them all, however, is a magical number.

"The Golden Ratio:  Phi, describes among other things the remarkable connection between avian flight patterns, stormy weather and cosmic pinwheels.


Phi (not pi) is the number 1.618 followed by an infinite string. Take a rectangle whose sides conform to this Golden Ratio, carve from it a square, and the remaining rectangle still follows the ratio.

The Golden Ratio also describes the ever-expanding nature of what is termed a logarithmic spiral, logarithmic spirals appear in totally unrelated phenomena.

"They also appear, interestingly enough, when a falcon dives toward its prey,". The flight pattern allows the bird to maintain a constant angle. Head cocked, its eyes never waver. "It allows the falcon to keep its prey continuously in sight."




 

Plants and trees grow in the Phi ratio. The Earth and Moon have this same relationship. The sunflower is a wonderful example of the spiraling effect of Phi. Look at a pine cone and find the same relationship of Phi... in two directions at the same time

The Flower of Life (FOL) is a geometrical figure composed of multiple evenly-spaced, overlapping circles, that are arranged so that they form a flower-like pattern with a sixfold symmetry like a hexagon. The center of each circle is on the circumference of six surrounding circles of the same diameter. The FOL symbol is over six thousand years old. Throughout human history, philosophers, artists, and architects around the world have known the FOL for its perfect form, proportion, and harmony. It is considered by many to be a symbol of sacred geometry, said to contain ancient, religious value depicting the fundamental forms of space and time. In this sense, it is a visual expression of the connections life weaves through all mankind, believed by some to contain a type of Akashic Record of basic information of all living things.There are many religious beliefs associated with the FOL; for example, depictions of the five Platonic Solids are found within the symbol of Metatron's Cube, which may be derived from the FOL pattern. These platonic solids are geometrical forms which are said to act as a template from which all life springs.

The "Flower of Life" can be found in all major religions of the world.
It contains the patterns of creation as they emerged from the "Great Void". Everything is made from the Creator's thought.
After the creation of the Seed of Life the same vortex's motion was continued, creating the next structure known as the Egg of Life.
This structure forms the basis for music, as the distances between the spheres is identical to the distances between the tones and the half tones in music. It is also identical to the cellular structure of the third embryonic division (The first cell divides into two cells, then to four cells then to eight). Thus this same structure as it is further developed, creates the human body and all of the energy systems including the ones used to create the Merkaba. If we continue creating more and more spheres we will end up with the structure called the Flower of Life.

In the early 20th century, Ernst Haeckel described (Haeckel, 1904) a number of species of Radiolaria, some of whose skeletons are shaped like various regular polyhedra. Examples include Circoporus octahedrus, Circogonia icosahedra, Lithocubus geometricus and Circorrhegma dodecahedra. The shapes of these creatures should be obvious from their names. Circogonia Icosahedra from Haeckels 1904 Kunstformen der Natur. 157 by 175 pixels, 6172 bytes. ... Possible classes Polycystinea Acantharea Taxopodea Radiolaria are amoeboid protozoa that produce intricate mineral skeletons, typically with a central capsule dividing the cell into inner and outer portions, called endoplasm and ectoplasm. ... Ernst Haeckel. ... Possible classes Polycystinea Acantharea Taxopodea Radiolaria are amoeboid protozoa that produce intricate mineral skeletons, typically with a central capsule dividing the cell into inner and outer portions, called endoplasm and ectoplasm

Most radially symmetric animals are symmetrical about an axis extending from the center of the oral surface, which contains the mouth, to the center of the opposite, or aboral, end. This type of symmetry is especially suitable for sessile animals such as the sea anemone, floating animals such as jellyfish, and slow moving organisms such as starfish (see special forms of radial symmetry). Animals in the phyla cnidaria and echinodermata exhibit radial symmetry (although many sea anemones and some corals exhibit bilateral symmetry defined by a single structure, the siphonoglyph)

Symmetry in biology is the balanced distribution of duplicate body parts or shapes. The body plans of most multicellular organisms exhibit some form of symmetry, either radial symmetry or bilateral symmetry or glide symmetry.

it is becoming recognised that DNA sequences and other molecular information are only one aspect of the understanding of biological systems. Organisms make use of DNA in highly dynamic contexts. For example there is no doubt that DNA has a significant role in organising the development of an organism, but that very little information about the form of the organism and its developmental path can be 'read off' from its DNA sequence. Genetics acts in concert with dynamical physical and chemical processes. The more we learn about genes, the more evident becomes the need for a good understanding of dynamic effects in biology--- in growth, in development, in the regulation of genetic networks, in ecosystems, and in evolution.

The mathematics of dynamical systems has undergone its own revolution, as the need to consider nonlinear effects has become clear. The theory of dynamical systems is one of the major growth areas of today's mathematical research, and one of its strengths is a strong conenction with applied science.

There are two distinct ways to encourage interaction between mathematics and biology. 'Horizontal' programmes select specific problems in biology (such as protein-folding) and bring many different mathematical methods to bear. What we propose is the other kind of meeting: a 'vertical' program organized around a package of general methods that apply to many different biological problems. In this case, the package is the exploitation of symmetries in nonlinear dynamial systems, and the strong relation between symmetry and pattern formation.
 

exploring a far more active role for symmetry, in the context of nonlinear dynamical systems. It has become apparent that the symmetries of a system of nonlinear ordinary or partial differential equations can be used, in a systematic and unified way, to analyze, predict, and understand many general mechanisms of pattern-formation.

It is important to understand that 'pattern' here is not restricted to visual patterns such as shape or pigmentation. The structure and function of the visual cortex involves patterns, and can be modelled by a symmetric network of neurons. The formation of new species is a pattern: one group of organisms, a highly symmetric situation, splits into two groups--- a less symmetric one. Synchronous firing of neurons, which seems to be an important feature of brain function, is a pattern. Phase relations in biological oscillators are patterns.

In physics, patterns can often be understood by writing down very specific and accurate mathematical models --- equations. Few areas of biology are yet equipped with equations of comparable accuracy. It is here the the symmetry approach has major advantages: it is a general method that applies to a variety of models. It can lead to general conclusions even when specific models are unknown, or controversial, or of limited accuracy.

The point here is not the literal symmetry of a biological system, or an organism, or a process. Hardly anything in biology is exactly symmetric. But a huge range of biological systems possess approximate symmetries (for example all organisms in a species are approximately identical), and the best way to model such systems is to exploit the symmetry of an idealized model, and then consider what changes might occur to the conclusions if the symmetry is close, but not exact.

. ...

the space time of living things

Living organisms come in a vast range of sizes--from microbes to whales, they span at least 21 orders of magnitude.


Viruses are just an assembly of nucleic acids wrapped by a protein coat (or 'capsid'). When frozen, their readiness to crystallize in highly ordered patterns was taken as a key cross-over between the purely chemical and the biological. Many viruses,  have the shape of a regular icosahedron. Viral structures are built of repeated identical protein subunits and the icosahedron is the easiest shape to assemble using these subunits. A regular polyhedron is used because it can be built from a single basic unit protein used over and over again; this saves space in the viral genome. .they have highly symmetrical crystalline structures,.. 
 

Nanobes call into question the minimum size requirements for life; Roughly the same size as viruses, which are considered only half alive because they need hosts to reproduce.  Dissective cuts through the axes of some of the filaments ''demonstrate that nanobes have an amorphous membrane structure,''  Such an outer covering, ''is consistent with biological material and excludes the presence of crystalline mineral compounds. ''They're alive...
Examination revealed the structures to be tiny irregular shaped filaments less than 1/100,000 mm (millimetres) wide. Further experimentation and observation in the laboratory showed that the structures were capable of growing and increasing in number spontaneously on freshly fractured rock  As  the smallest known living organisms they will break not just the small size record but also the record for hyperthermophiles since at the depth they were found the temperature is more than 150°C. In trying to nail down the life issue, the team treated the nanobes with three kinds of DNA stains, in each case getting positive results.


Biologists have successfully revived a bacterium after it apparently remained dormant for 250 million years encased in a salt crystal,. The previous record-holder was a bacterium living inside a bee that had been encased in amber for 25 million to 40 million years. Researchers have known for some time that bacterial spores can live for long periods of time in a so-called "cryptobiotic" state, meaning the hardy spores remain alive, but do not feed or reproduce.

halobacteria may be the oldest life form on earth. DasSarma and his team have recently sequenced the genome of the extreme halophile called Halobacterium NRC-1. When compared with the genes of other organisms, Halobacterium NRC-1 appears to be the most ancient of the archaean group. Comparisons of small ribosomal RNA sequences indicate that halophilic bacteria are closely related to the methanogens. Both types of bacteria are now classified in the kingdom Euryarchaeota within the Archaea domain. Halophiles need oxygen while methanogens are anaerobic; however, halophiles can produce energy without oxygen in two ways: from the degradation of arginine, and by using the photosynthetic molecule bacteriorhodopsin A remarkable pigment in the cell membrane of halobacteria called (bacteriorhodopsin) enables them to utilize sunlight for energy. Like photosynthetic chloroplasts in plant cells, the halobacteria produce their own ATP; but unlike green plants, they utilize bacteriorhodopsin instead of chlorophyll. The bacteria survive inside the salt crust, even though it has been exposed to sun-baked summers and freezing winters.

Extreme thermophilic bacteria live in boiling water of hot springs where no other living cells can possibly survive (i.e. without their proteins becoming completely denatured). They have also been discovered in (or near) hot water emanating from sulfide chimneys ("black smokers") thousands of feet deep at the bottom of the ocean (near the Galapagos Islands). Surviving in the wild near steam vents where the temperature reaches 350 degrees Celsius under tremendous pressure, the bacteria have also been cultured under extreme heat and pressure in the laboratory. Although their optimal "operating temperature" is just over 100 degrees Celsius, no one would have believed that a living cell containing DNA, RNA and protein could survive anaerobically in a pressure cooker at 250 degrees Celsius, more than twice the temperature of boiling water. These cells could easily have flourished on a young earth under conditions previously thought to be uninhabitable to all known life forms.

Acid hot springs in Yellowstone National Park with a pH of below 4.0 support the eukaryotic alga Cyanidium caldarum. This remarkable photosynthetic alga can even survive in a pH approaching zero! Some acidophilic hot springs bacteria utilize the oxidation of sulfur and iron for the synthesis of ATP. Alkaline hot springs support colonies of bacteria that utilize hydrogen sulfide for their energy source.

In 2002, bearing her microscope on a microbe that lives in the gut of fish, Bonnie Bassler isolated an elusive molecule called AI-2, and uncovered the mechanism behind mysterious behavior called quorum sensing -- or bacterial communication. She showed that bacterial chatter is hardly exceptional or anomolous behavior, as was once thought -- and in fact, most bacteria do it, and most do it all the time. (She calls the signaling molecules "bacterial Esperanto.")

The discovery shows how cell populations use chemical powwows to  forge slimy defenses called biofilms.
 

bacteria spore, which can live much longer lives than the parent bacteria. If a bacteria senses bad times (for example, a drought), says Sullivan, it forms spores to suspend animation and wait out the life-threatening conditions.

Spore found recently in New Mexico may have waited 250 million years for the right conditions reports John Fleck in the Albuquerque Journal and others in national news. Pennsylvania biologists William Rosenzweig and Russell Vreeland and New Mexico biologist Dennis Powers announce an amazing feat. Two thousand feet under the ground at Carlsbad, New Mexico, they found spore in tiny water bubbles contained in 250-million-year-old rock salt from a vanished inland sea. They brought the spore back to life and grew bacteria from them!

The oldest rocks sufficiently unaltered to retain cellular fossils - African and Australian sediments dated to 3.5 billion years old - do preserve prokaryotic cells (bacteria and cyanophytes) and stromatoIites (mats of sediment trapped and bound by these cells in shallow marine waters). Thus, life on the earth evolved quickly and is as old as it could be. This fact alone seems to indicate an inevitability, or at least a predictability, for life's origin from the original chemical constituents of atmosphere and ocean.
 

Driving the first step in evolution A possible candidate for Shapiro's driver reaction might have been recently discovered in an undersea microbe, Methanosarcina acetivorans, which eats carbon monoxide and expels methane and acetate (related to vinegar). Biologist James Ferry and geochemist Christopher House from Penn State University found that this primitive organism can get energy from a reaction between acetate and the mineral iron sulfide. Compared to other energy-harnessing processes that require dozens of proteins, this acetate-based reaction runs with the help of just two very simple proteins.
 

Stanley Miller In 1953  creating a chamber with only hydrogen, water, methane, and ammonia. To speed up "geologic time" in his experiment, he boiled the water and instead of exposing the mix to ultraviolet light he used an electric discharge something like lightning. After just a week, Miller had a residue of compounds settled in his system. He analyzed them and the results were electrifying: Organic compounds had been formed, most notably some of the "building blocks of life," amino acids.  Miller found the amino acids glycine, alanine, aspartic and glutamic acid, and others. Fifteen percent of the carbon from the methane had been combined into organic compounds. As amazing as discovering amino acids at all was how easily they had formed.

 

It has been known that in some protein, specific sites of chain polymer called “nucleus” begins to form 3D structure prior to other sites in the earlier phase of folding. If there is any correlation between the initial process of folding and the earlier phase of molecular evolution, it may be expected that the “nucleus” structure is conserved better than other parts. Segments of 3D structure similar to that in “nucleus” of certain protein were extracted from a protein structure database. Since no software for this operation was available at the time of starting the work, an original algorithm was created to develop a special purpose computer program. Through the statistical analysis for a number of extracted segments, it was found that there was a significant bias in amino acid sequence of these segments, and that the bias reflected the stability of the partial structures concerned semi-quantitatively. With such an original computer analysis, some novel amino acid sequences were designed in expectation of forming stable structures, and named “chignolin”. The detailed analysis revealed cooperative response of entire molecule and two-state structural transition. The transition occurred broadly over a wide range of temperatures. About 20 % of chignolin molecules in equilibrium state hold 3D structures even at temperatures around 100 °C. It is very interesting that this small peptide, chignolin can persist stably under higher temperatures in view of “deep sea hydrothermal vents” hypothesis of origin of life.

An endolith or cryptoendolith is an organism (archaea, bacterium, or fungus) that lives inside rock, coral, animal shells, or in the pores between mineral grains. Many are extremophiles; living in places previously thought inhospitable to life.  As water and nutrients are rather sparse in the environment of the endolith, they have a very slow procreation cycle. Early data suggests that some only engage in cell division once every hundred years. As most endoliths are autotrophs, they can generate organic compounds essential for their survival on their own from inorganic matter.

Nanoarchaeum
Nanoarchaeum equitans is a species of tiny microbe discovered in 2002 in a hydrothermal vent off the coast of Iceland by Karl Stetter. A thermophile that grows in near-boiling temperatures, Nanoarchaeum appears to be an obligatory symbiont on the archaeon Ignicoccus; it must be in contact with the host organism to survive. Its cells are only 400 nm in diameter, making it the smallest known living organism, with the possible exception of nanobes (if they are considered to be living). Its genome is only 490,885 nucleotides long; as of 2005 it remains the smallest non-viral genome ever sequenced.

Ignicoccus is a genus of Archaea living in marine hydrothermal vents.  The archebacteria of the genus Ignicoccus have tiny coccoid cells with a diameter of about 2 µm, that exhibit a smooth surface, an outer membrane and no S-layer. They have a previously unknown cell envelope structure - a cytoplasmic membrane, a periplasmic space (with a variable width of 20 to 400 nm, containing membrane-bound vesicles), and an outer membrane (approximately 10 nm wide, resembling the outer membrane of gram-negative bacteria). The latter contains numerous tightly, irregularly packed single particles (about 8 nm in diameter) and pores with a diameter of 24 nm, surrounded by tiny particles, arranged in a ring (with a diameter of 130 nm) and clusters of up to eight particles (each particle 12 nm in diameter) They gain energy by reduction of elemental sulfur to hydrogen sulfide using molecular hydrogen as the electron donor. A unique symbiosis with (or parasitism of) nanoarchaea has also been reported




Nanobes may even outnumber bacteria by an order of magnitude!  In addition, they appear to be membrane-bound structures that are possibly surrounded by cytoplasm and nuclear area and are composed of C, N, and O, chemical constituents associated with living biota

the size of a single ribosome (site of protein synthesis) is roughly the same as the smallest nanobes. Equally as amazing, the nanobes most likely came from a sandstone rock sample retrieved from 3-5km below the ocean bed, where the pressure is around 2,000 atmospheres and the temperature ranges from 115-170°C.
 

The tests showed the nanobes fulfilled the following criteria to qualify as life: -

their colonies grew spontaneously;
they contained genetic material (DNA);
they were composed of biological material such as carbon, oxygen and nitrogen;
ultra-thin sections showed an outer layer or membrane that could represent a cell wall, surrounding a possible cytoplasm and nuclear area.
Further, they tested a variety of plausible non-biological explanations for the nanobes, gradually discounting materials such as crystalline materials, carbonates, fullerenes, carbon nano-tubes and non-living polymers.

Folk asserts that nanobacteria are key players in mineral formation and that their activities aid in the formation of geological strata (e.g. soil formation). Using acid etching and gentle gold shadowing techniques, he was the first to demonstrate the presence of 0.05-0.2 µm spherical structures in an assortment of geologic materials. Folk is credited with discovering nanobe structures in carbonate rocks, which he attributes to biomineralization processes by tiny life forms.

shale/clay rich in trace elements and minerals.

studies have shown that the nanobe culturing media has been found to spontaneously generate particles that resemble nanobe cells and "dwelling structures" when inorganic calcium and phosphate salts are combined with organic materials. Nanobacteria may mediate processes currently thought to be controlled by inorganic chemical reactions, such as low-temperature precipitation of dolomite, oxidation of iron, and the formation of clay minerals.

Nanobes may also exist on other planets! Martian meteorites such as ALH84001 have been speculated to contain trace fossils of nanobacteria.

Microbes make up the foundation of the biosphere and sustain all life on earth.

**

In another step toward understanding the origin of Earth's biological molecules, two independent laboratory experiments have produced amino acids--the building blocks of proteins--by simulating conditions in icy, interstellar space; ie..  on interstellar ice particles that are exposed to ultraviolet light,

Saturn's smoggy moon Titan has hundreds of times more natural gas and other liquid hydrocarbons than all the known oil and natural gas reserves on Earth, scientists said today.The hydrocarbons rain from the sky on the moon, collecting in vast deposits that form lakes and dunes. This much was known. But now the stuff has been quantified using observations from NASA's Cassini spacecraft. "Titan is just covered in carbon-bearing material — it's a giant factory of organic chemicals,"

Although Titan is classified as a moon, it is larger than the planets Mercury and Pluto. It has a planet-like atmosphere which is more dense than those of Mercury, Earth, Mars and Pluto. The atmospheric pressure near the surface is about 1.6 bars, 60 percent greater than Earth's. Titan's air is predominantly made up of nitrogen with other hydrocarbon elements which give Titan its orange hue. These hydrocarbon rich elements are the building blocks for amino acids necessary for the formation of life. Scientists believe that Titan's environment may be similar to that of the Earth's before life began putting oxygen into the atmosphere.

Titan's surface temperature appears to be about -178°C (-289°F). Methane appears to be below its saturation pressure near Titan's surface; rivers and lakes of methane probably don't exist, in spite of the tantalizing analogy to water on Earth. On the other hand, scientists believe lakes of ethane exist that contain dissolved methane. Titan's methane, through continuing photochemistry, is converted to ethane, acetylene, ethylene, and (when combined with nitrogen) hydrogen cyanide. The last is an especially important molecule; it is a building block of amino acids.
 

Saturn's largest satellite has a predominantly nitrogen atmosphere containing a few percent of methane. Both of these compounds are being continuously broken apart by solar UV photons, precipitating electrons from Saturn's magnetosphere, and cosmic rays. The fragments of the parent molecules recombine to make new compounds, while the liberated hydrogen escapes into space (to become a species in Saturn's magnetosphere). Six simple hydrocarbons in addition to methane and five nitriles have been identified, as well as CO and a tiny trace of CO₂. Titan's visible atmosphere is filled with smog, which must be a mixture of simple condensates of the identified gases and polymers that have built up from molecules such as HCN and C₂H₂.  Water ice is almost certainly the main constituent of Titan's crust and upper mantle,

Jupiter's moon Europa is slightly smaller than Earth's Moon and is the sixth-largest moon in the Solar System. Though by a wide margin the least massive of the Galilean satellites, its mass nonetheless significantly exceeds the combined mass of all moons in the Solar System smaller than itself. It is primarily made of silicate rock and likely has an iron core. It has a tenuous atmosphere composed primarily of oxygen. Its surface is composed of ice and is one of the smoothest in the Solar System. This young surface is striated by cracks and streaks, while craters are relatively infrequent. The apparent youth and smoothness of the surface have led to the hypothesis that a water ocean exists beneath it, which could conceivably serve as an abode for extraterrestrial life.Heat energy from tidal flexing ensures that the ocean remains liquid and drives geological activityAntarctic Lake Vostok. Life in such an ocean could possibly be similar to microbial life on Earth in the deep ocean. So far, there is no evidence that life exists on Europa, but the likely presence of liquid water has spurred calls to send a probe there.

Until the 1970s, life, at least as the concept is generally understood, was believed to be entirely dependent on energy from the Sun. Plants on Earth's surface capture energy from sunlight to photosynthesize sugars from carbon dioxide and water, releasing oxygen in the process, and are then eaten by oxygen-respiring animals, passing their energy up the food chain. Even life in the ocean depths, where sunlight cannot reach, was believed to obtain its nourishment either from consuming organic detritus rained down from the surface waters or from eating animals that did. A world's ability to support life was thought to depend on its access to sunlight. However, in 1977, during an exploratory dive to the Galapagos Rift in the deep-sea exploration submersible Alvin, scientists discovered colonies of giant tube worms, clams, crustaceans, mussels, and other assorted creatures clustered around undersea volcanic features known as black smokers.[55] These creatures thrive despite having no access to sunlight, and it was soon discovered that they comprise an entirely independent food chain. Instead of plants, the basis for this food chain was a form of bacterium that derived its energy from oxidization of reactive chemicals, such as hydrogen or hydrogen sulfide, that bubbled up from the Earth's interior. This chemosynthesis revolutionized the study of biology by revealing that life need not be sun-dependent; it only requires water and an energy gradient in order to exist. It opened up a new avenue in astrobiology by massively expanding the number of possible extraterrestrial habitats. Europa's unlit interior is now considered to be the most likely location for extant extraterrestrial life in the Solar System.
 

The theory of abiogenic petroleum origin holds that natural petroleum was formed from deep carbon deposits, perhaps dating to the formation of the Earth. The ubiquity of hydrocarbons in the solar system is taken as evidence that there may be a great deal more petroleum on Earth than commonly thought, and that petroleum may originate from carbon-bearing fluids which migrate upward from the mantle. Some scientists (mostly Russian and Ukrainian geologists) believe that oil wasn't produced from any living thing at all. This abiogenic petroleum origin hypothesis claims that oil was formed from deep carbon deposits dating from as early as the formation of Earth. Within the mantle carbon may exist as hydrocarbon molecules, chiefly methane..  Methane .. The simplest hydrocarbon, methane, is a gas with a chemical formula of .CH_4.. .. It is the simplest alkane, and the principal component of natural gas. Natural gas occurs in reservoirs beneath the surface of the earth. It is often found in conjunction with petroleum deposits.

, and as elemental carbon, carbon dioxide and carbonates. The abiotic hypothesis is that a full suite of hydrocarbons found in petroleum can be generated in the mantle by abiogenic processes, and these hydrocarbons can migrate out of the mantle, into the crust until they escape to the surface or are trapped by impermeable strata, forming petroleum reservoirs.
 

Hydrogen gas and water have been found more than 6 kilometers deep in the upper crust,
 

Everything is alive... life' on its most fundamental level was to small to see before.. and its processes at this level to fast or slow to be observed readily.. life exists everywhere it is not excluded..   its initial formation is in even higher pressures, temperatures and chemical extremes then thought possible before.. the term 'natural selection' by definition implies the exclusion of too many life forms.. and also implies 'punctuated equilibrium'..  once a life expression is found and becomes self sustaining there is no need to redo it.. as seen by the whole system.. 'holistic'.. until the organisms and the environmental homeostasis require it.. Further, there will be cross over states between life and non life seen at the 'elementary' levels and 'is' what is seen in viruses and naobes..

Systems biology

Systems biology focuses on the systematic study of complex interactions in biological systems, thus using a new perspective (integration instead of reduction) to study them. "The reductionist approach has successfully identified most of the components and many of the interactions but, unfortunately, offers no convincing concepts or methods to understand how system properties emerge...the pluralism of causes and effects in biological networks is better addressed by observing, through quantitative measures, multiple components simultaneously and by rigorous data integration with mathematical models"
"Systems biology...is about putting together rather than taking apart, integration rather than reduction. It requires that we develop ways of thinking about integration that are as rigorous as our reductionist programmes, but different....It means changing our philosophy, in the full sense of the term"

Revolutionary Change in Biology Scientific revolutions are difficult to predict, but two conditions often precede them. The first is along period during which large amounts of data are gathered that cannot be accommodated within traditional conceptual frameworks. The second is a period of substantial influx of ideas and methodologies from other fields. Both conditions apply to biology today. Interestingly, the last revolution in biology happened not long ago: Molecular Biology emerged in the 1950’s, and over several decades re-oriented much biological research toward elucidating the fundamental biochemical and genetic machinery underlying life. A legacy of molecular biology—the cataloguing of DNA sequences of human, animal and plant genomes—has recently given us a comprehensive view of all of the components of life and how they interact with each other. The results have been at once exhilarating and terrifying. Armed for the first time with the ability to interrogate living systems in a comprehensive way, we biologists are finding increasing frustration in our inability to fit life into neat linear pathways that do well-defined jobs. We have been forced to confront the fact that the building blocks of life are interconnected through vast layers of structural and functional interaction, wherein every input triggers hundreds or thousands of outputs. Complexity, of course, is not new in biology. In the molecular biology tradition, one strives to reduce complexity by focusing on elucidating underlying physical and chemical mechanisms. Yet the “new” complexity in biology does not stem from a lack of mechanistic detail. In fact, it is in areas in which we possess the most mechanistic knowledge that our lack of real understanding has become obvious. What so often eludes us is not how molecules and assemblies work in isolation, but how they work together in useful networks

The growth rate parameter in models of certain classes of dynamical systems in biology satisfies a variational principle which is formally analogous to the minimization of the free energy in statistical thermodynamics. This principle implies a precise correspondence between certain concepts in thermodynamic theory, and certain macroscopic variables that characterize the behavior of dynamical systems in biology. The evolutionary formalism has led to a descriptor of the structure and behavior of certain classes of biological systems at the molecular, cellular and population levels. The variational principle entails that the methods of equilibrium statistical mechanics, which revolve around thermodynamic concepts such as free energy and temperature, can be used to study the non-equilibrium behavior of biological systems, which are described by processes defined by parameters such as growth rate and cycle time.

 Biological systems are interconnected dynamical processes, where myriads of cells and molecules interact with each other to create elaborate biological functions. Their collective behaviors are highly robust and sustainable even in a hostile environment. Analytical and computational studies have shown that  a quantitative measure of the rate of information flow within the network is a precise measure of the property of homeostasis. This relation is used to explore the relation between the structure and function of biological networks.


 

Cybernetics is the interdisciplinary study of the structure of complex systems, especially communication processes, control mechanisms and feedback principles. Cybernetics is closely related to control theory and systems theory, but both in its origins and in its evolution in the second-half of the 20th century, cybernetics is equally applicable to social (that is, language-based) systems. Cybernetics is always and only involved when the system under scrutiny is involved in a closed loop, where action by the system in an environment causes some change in the environment AND that change is manifest to the system via information/feedback that causes changes in the way the system then behaves, and all this in service of a goal or goals. This "circular causal" relationship is necessary and sufficient for a cybernetic perspective.

 

The term symbiosis (from the Greek: σύν syn "with"; and βίωσις biosis "living") commonly describes close and often long-term interactions between different biological species. The term was first used in 1879 by the German mycologist, Heinrich Anton de Bary, who defined it as: "the living together of unlike organisms"

The definition of symbiosis is in flux and the term has been applied to a wide range of biological interactions. The symbiotic relationship may be categorized as being mutualistic, parasitic, or commensal in nature . Others define it more narrowly, as only those relationships from which both organisms benefit, in which case it would be synonymous with mutualism.

Hummingbirds and ornithophilous flowers have evolved to form a mutualistic relationship. It is prevalent in the bird’s biology as well as in the flower’s. Hummingbird flowers have nectar chemistry associated with the bird’s diet. Their color and morphology also coincide with the bird’s vision and morphology. The blooming times of these ornithophilous flowers have also been found to coincide with hummingbirds' breeding seasons.

In a broad sense, biological co-evolution is "the change of a biological object triggered by the change of a related object". Coevolution can occur at multiple levels of biology: it can be as microscopic as correlated mutations between amino acids in a protein, or as macroscopic as covarying traits between different species in an environment. Each party in a co-evolutionary relationship exerts selective pressures on the other, thereby affecting each others' evolution. Species-level co-evolution includes the evolution of a host species and its parasites, and examples of mutualism evolving through time.

Symbiotic relationships included those associations in which one organisms lives on another (ectosymbiosis, such as mistletoe), or where one partner lives inside another (endosymbiosis, such as lactobacilli and other bacteria in humans or zooxanthelles in corals). Symbiotic relationships may be either obligate, i.e., necessary to the survival of at least one of the organisms involved, or facultative, where the relationship is beneficial but not essential to survival of the organisms.

Symbiosis played a major role in the co-evolution of flowering plants and the animals that pollinate them. Many plants that are pollinated by insects, bats or birds, have very specialized flowers modified to promote pollination by a specific pollinator that is also correspondingly adapted. The first flowering plants in the fossil record had relatively simple flowers. Adaptive speciation quickly gave rise to many diverse groups of plants, and at the same time, corresponding speciation occurred in certain insects groups. Some groups of plants developed nectar and large sticky pollen while insects evolved more specialized morphologies to access and collect these rich food sources. In some taxa of plants and insects the relationship has become dependent, where the plant species can only be pollinated by one species of insect.

Symbiosis is a major driving force behind evolution. Darwin's notion of evolution, driven by competition, are incomplete, and evolution is strongly based on co-operation, interaction, and mutual dependence among organisms, "Life did not take over the globe by combat, but by networking While historically, symbiosis has received less attention than other interactions such as predation or competition, it is increasingly recognized as an important selective force behind evolution, with many species having a long history of interdependent co-evolution. In fact the evolution of all eukaryotes (plants, animals, fungi, protists) is believed to have resulted from a symbiosis between various sorts of bacteria.
 

Homeostasis is a system that makes the organism - up to a certain level - independent of its environment. (Homeostasis is: the possibility every living system has to keep its inner system balanced, like our body keeps its temperature constant, independently of the outside temperature). Of course each living system must at the same time adapt to its environment. Many processes happen adapted to day or night, or to the seasons. This is not strange. Life has from the beginning been submitted to day and night. Often organisms are so adapted to day and night that they have a system that causes the adaptation already before night falls or morning begins. Biological clocks take care that things happen at the right time. Homeostasis is nowadays seen as one of the fundamental aspects of life, having a biological clock may be as fundamental

The tendency of people to see purpose in symmetry suggests at least one reason why symmetries are often an integral part of the symbols of world religions. Just a few of many examples include the sixfold rotational symmetry of Judaism's Star of David, the twofold point symmetry of Taoism's Taijitu or Yin-Yang, the bilateral symmetry of Christianity's cross and Sikhism's Khanda, or the fourfold point symmetry of Jain's ancient (and peacefully intended) version of the swastika. With its strong prohibitions against the use of representational images, Islam, and in particular the Sunni branch of Islam, has developed intricate and visually impressive use of symmetries.

The ancient Taijitu image of Taoism is a particularly fascinating use of symmetry around a central point, combined with black-and-white inversion of color at opposite distances from that central point. The image, which is often misunderstood in the Western world as representing good (white) versus evil (black), is actually intended as a graphical representative of the complementary need for two abstract concepts of "maleness" (white) and "femaleness" (black). The symmetry of the symbol in this case is used not just to create a symbol that catches the attention of the eye, but to make a significant statement about the philosophical beliefs of the people and groups that use it.

hurricanes display regular geometry in their eyes.

Volcanic plumes have been known to spawn waterspouts and dust devils, as well as sheaths of lightning around their roiling debris clouds, but scientists didn't know why. Images of the 2008 eruption of Mount Chaiten in Chile and a 200-year-old report of an eruption in the Azores by a sea captain that described these features have helped scientists at the University of Illinois solve the puzzle. This evidence indicates that the volcanic plume rotates like a tornado system, a phenomenon the researchers call a "volcanic mesocyclone. "What happens in tornadic thunderstorms is analogous to what happens in strong volcanic plumes," said lead author of the study, Pinaki Chakraborty, a postdoctoral researcher at Illinois. A volcanic plume consists of a vertical column of hot gases and dust topped by an umbrella-like structure. A volcanic mesocyclone sets the entire plume rotating, causing it to spawn waterspouts or dust devils and group together the electric charges in the plume to form a sheath of lightning. Satellite images of the 1991 eruption of Mount Pinatubo in the Philippines confirm the rotation of strong volcanic plumes,

The Gaia hypothesis is an ecological hypothesis proposing that the biosphere and the physical components of the Earth (atmosphere, cryosphere, hydrosphere and lithosphere) are coupled to form a complex interacting system. This coordinated system of living organisms maintains the climatic and biogeochemical conditions on Earth in a preferred homeostasis. Gaia theory simply maintains that Earth's natural cycles work together to keep the Earth healthy and support life on Earth. Overall, the Gaia Theory is a compelling new way of understanding life on our planet. It argues that we are far more than just the "Third Rock from the Sun," situated precariously between freezing and burning up. The theory asserts that living organisms and their inorganic surroundings have evolved together as a single living system that greatly affects the chemistry and conditions of Earth’s surface. Gaia philosophy (named after Gaia, Greek goddess of the Earth) is a broadly inclusive term for related concepts that living organisms on a planet will affect the nature of their environment in order to make the environment more suitable for life. This set of theories holds that all organisms on an extraterrestrial life giving planet regulate the biosphere to the benefit of the whole. The Gaia concept draws a connection between the survivability of a species, (hence its evolutionary course) and its usefulness to the survival of other species. While there were a number of precursors to Gaia theory, the first scientific form of this idea was proposed as the Gaia hypothesis by James Lovelock, a UK chemist, in 1970. The Gaia hypothesis deals with the concept of homeostasis, and claims the resident life forms of a host planet coupled with their environment have acted and act as a single, self-regulating system. This system includes the near-surface rocks, the soil, and the atmosphere.

James Lovelock defined Gaia as: a complex entity involving the Earth's biosphere, atmosphere, oceans, and soil; the totality constituting a feedback or cybernetic system which seeks an optimal physical and chemical environment for life on this planet. His initial hypothesis was that the biomass modifies the conditions on the planet to make conditions on the planet more hospitable – the Gaia Hypothesis properly defined this "hospitality" as a full homeostasis. Lovelock's initial hypothesis, accused of being teleological by his critics, was that the atmosphere is kept in homeostasis by and for the biosphere.
Lovelock suggested that life on Earth provides a cybernetic, homeostatic feedback system operated automatically and unconsciously by the biota, leading to broad stabilization of global temperature and chemical composition. With his initial hypothesis, Lovelock claimed the existence of a global control system of surface temperature, atmosphere composition and ocean salinity. His arguments were:

The global surface temperature of the Earth has remained constant, despite an increase in the energy provided by the Sun.
Atmospheric composition remains constant, even though it should be unstable.
Ocean salinity is constant.

Evolution is less a matter of species competing for inadequate food supplies than a question of species evolving to increase the total food supply and thereby their own share in the total .food supply

 In effect, entire ecosystems evolve, not just individual species. Thus a competition does indeed exist, but it is a competition between ecosystems to enlarge energy flows, rather than a fight over existing energy flows; it naturally leads to environmental changes that favor the further development of life.

There is a spectrum of Gaia hypotheses, ranging from the undeniable to radical. At one end is the undeniable statement that the organisms on the Earth have radically altered its composition. A stronger position is that the Earth's biosphere effectively acts as if it is a self-organizing system which works in such a way as to keep its systems in some kind of equilibrium that is conducive to life. Biologists usually view this activity as an undirected emergent property of the ecosystem; as each individual species pursues its own self-interest, their combined actions tend to have counterbalancing effects on environmental change. Proponents of this view sometimes point to examples of life's actions in the past that have resulted in dramatic change rather than stable equilibrium, such as the conversion of the Earth's atmosphere from a reducing environment to an oxygen-rich one.

An even stronger claim is that all life forms are part of a single planetary being, called Gaia. In this view, the atmosphere, the seas, the terrestrial crust would be the result of interventions carried out by Gaia, through the coevolving diversity of living organisms. Many scientists deny the possibility of this view; however, such a view is considered within scientific possibility.

The most extreme form of Gaia theory is that the entire Earth is a single unified organism; in this view the Earth's biosphere is consciously manipulating the climate in order to make conditions more conducive to life. Many non-scientists see homeostasis as a process that requires conscious control. The more speculative versions of Gaia, including versions in which it is believed that the Earth is actually conscious, sentient, and highly intelligent, are usually considered outside the bounds of science.
 

The question of "what is an organism" and at what scale is it rational to speak about organisms vs. biospheres, give rise to a semantic debate. We are all ecologies in the sense that our (human) bodies contain gut bacteria, parasite species, etc., and to them our body is not organism but rather more of a microclimate or biome. Applying that thinking to whole planets:

The argument is that these symbiotic organisms, being unable to survive apart from each other and their climate and local conditions, form an organism in their own right, under a wider conception of the term organism than is conventionally used. It is a matter for often heated debate whether this is a valid usage of the term, but ultimately it appears to be a semantic dispute. In this sense of the word organism, it is argued under the theory that the entire biomass of the Earth is a single organism (as Johannes Kepler thought).

The Gaia Theory posits that the organic and inorganic components of Planet Earth have evolved together as a single living, self-regulating system. It suggests that this living system has automatically controlled global temperature, atmospheric content, ocean salinity, and other factors, that maintains its own habitability. In a phrase, “life maintains conditions suitable for its own survival.” In this respect, the living system of Earth can be thought of analogous to the workings of any individual organism that regulates body temperature, blood salinity, etc. So, for instance, even though the luminosity of the sun – the Earth’s heat source – has increased by about 30 percent since life began almost four billion years ago, the living system has reacted as a whole to maintain temperatures at levels suitable for life.

Our home solar system forms a complex, harmonically interrelating, multi-octave musical instrument composed of great number of octaves of vibrational interplay. Your brain and body structures resonate to those continually fluctuating field patterns as they beat against the Earth', Moon's, and Sun's natural rhythms.
 

The Cassini division in the rings of Saturn falls at the Golden Section of the width of the ring.
A closer look at Saturn's rings reveals a darker inner ring which exhibits the same golden section proportion as the brighter outer ring.

Earth and the Relationship to Phi
As shown on the Distance Calculation page, the distance of the Earth from the Sun, where Mercury is 1, is computed as follows:

((½ ( Ö3 + 1 )) ^ (½ ( Ö4 + 1 ))) * (½ ( Ö5 + 1 ))

Note: Öx indicates the square root of x

There is something quite incredible about this derivation for Earth.

Note the repeating term ½ ( Öx + 1 ) with 3, 4, and 5

First, it is quite amazing that the same form of:
½ ( Öx + 1 )

would appear in three successive terms using the integers 3, 4, and 5 for x.

3, 4 and 5 are, of course, the key integers used in the most elementary example of the Pythagorean theory for right triangles, where

32 + 42 = 52.


The third term, ½ ( Ö5 + 1 ), is Phi!

More incredible yet is that the third term, ½ ( Ö5 + 1 ), is none other than the ubiquitous number 1.6180339..., better known as phi, or Ø. Phi has mathematical properties unlike any other number. The reciprocal of Ø is Ø-1, or 0.6180339... . When a line is divided at 1/Ø, the ratio of the small section to the large section will be identical to the ratio of the large section to the entire line.


This results in the incredible relationship of 1 and Ø between Venus (to the ¾ power) and Earth:


Similarities in the derivation of Phi and the Earth's distance.


It is also interesting that the derivation of Phi is so similar to the derivation of the distance of the Earth from the Sun. Consider the similarity in the formulaic construction, where the first two terms use an exponent and then a multiplier.

Phi is derived from:

Ø = 5 ^ .5 * .5 + .5 = 1.6180339...

While the distance of the Earth from the Sun, where Mercury = 1 is:

½ ( Ö3 + 1 ) ^ ½ ( Ö4 + 1 ) * ½ ( Ö5 + 1 ) = 2.583306...

The Earth embodies the two treasures of geometry


It's as though Earth embodies the Pythagorean theory and the Golden Section in one beautiful construction.

Perhaps Johannes Kepler (Mathematician and Astronomer, 1571-1630) had greater insight into the universe than we may have suspected when he said:

"Geometry has two great treasures: one the Theorem of Pythagoras; the other, the division of a line into extreme and mean ratio. The first we may compare to a measure of gold; the second we may name a precious jewel."
 

Relative planetary distances average to Phi

The average of the mean orbital distances of each successive planet in relation to the one before it approximates phi:

Clouds of interstellar material have been observed throughout the universe. These clouds spin, causing them to flatten along their rotational axis. This accounts for the planets forming in the same plane. Gravity also causes the cloud to collapse. During this process, the center contracts into a ball of hot gas and dust. This will become the sun; in this stage it is called a protosun.

The next process is accretion, which results in planet formation. First, the gases outside of the sun condense into solid materials. These particles collide and are held together by electrostatic forces, gravity and magnetism, forming larger particles called planetesimals, which in turn collide and form protoplanets. These protoplanets then become planets. The composition of the planets is a result of the order of the solid materials that formed from the gases outside of the sun.

Atoms and molecules within the nebula combined to form larger particles. The Sun determined what kinds of particles could exist. where, in effect acting like a sluice box. The jovian planets are large, with high gravitational fields, so they accumulated much of the Hydrogen and Helium and may be viewed as the beginnings of  a binary or trinary solar sytem. As can be seen by comparing the Earth-Sun formation to Jupiter-Europa and Satarn-Ttitan; there are (Phi) forces that define planetary distance to molecular densities producing planetary bodies in zones favorable to life!

An interesting fact is that, for ALL series that are formed from adding the latest two numbers to the following, and, starting from any two values (larger than zero), the ratio of successive terms will always tend to Phi! The varieties of symmetries of crystals of various minerals is a corollary of a varieties of chemical elements and various versions of their spatial packing, which generate a delightful symmetry of an exterior form and symmetry of physical properties of crystals. The varieties of chemical substances is a corollary of a varieties of chemical elements and various combinations of their spatial packing. The stationarity of a structure of steady chemical substances is provided with various kinds of chemical connections. By analogy, the stationarity of structures to gravitational systems should be provided with various kinds of gravitational connections

It has long been recognized that the Phi and the Fibonacci Series are intimately related to the subject of natural growth. The Phi, the Fibonacci, Lucas and related series, far from being confined to plant and animal natural growth alone, occur in numerous diverse contexts over an enormous range that extends from the structure of quasi-crystals out to the very structure of spiral galaxies. And this being so, should there really be any great surprise if Phi should also prove to be an underlying element in the structure of planetary systems?".
 

Conforming to the Golden Ratio, hurricanes and galaxies share physical traits. Gravity and angular momentum, play a role in both cases. Masses of material from which galaxies were formed had an initial amount of angular momentum,". As a developing galaxy's gas, dust and stars contract into a smaller region of space, it all spins faster -- just as a skater twirls more rapidly by pulling her arms in.

 Gravitational disturbances called density waves, rippling slowly through a galaxy, are thought to cause it to wind up and generate the spiral appearance.
The spiral arms of a galaxy are places where gas piles up at the wave crests. The material does not move with the spirals, but rather is caught up in them.

 Meaning there is an Intergalactic Flux of Gravitational Waves

For more than 10 years plasma physicists have had an electrical model of galaxies. It works with real-world physics. The model is able to successfully account for the observed shapes and dynamics of galaxies without recourse to invisible dark matter and central black holes. It explains simply the powerful electric jets seen issuing along the spin axis from the cores of active galaxies. Recent results from mapping the magnetic field of a spiral galaxy confirm the electric model. More recently, inter-galactic magnetic fields have been discovered

Plasma has been called the "fourth state" of matter, after solids, liquids and gases. Most of the matter in the universe is in the form of plasma. A plasma is formed if some of the negatively charged electrons are separated from their host atoms in a gas, leaving the atoms with a positive charge. The negatively charged electrons, and the positively charged atoms (known as positive ions) are then free to move separately under the influence of an applied voltage or magnetic field. Their net movement constitutes an electrical current. So, one of the more important properties of a plasma is that it can conduct electrical current. It does so by forming current filaments that follow magnetic field lines. Filamentary patterns are ubiquitous in the cosmos.

Intergalactic space is the physical space between galaxies. Generally free of dust and debris, intergalactic space is very close to a total vacuum. Some theories put the average density of the Universe as the equivalent of one hydrogen atom per cubic meter. The density of the Universe, however, is clearly not uniform; it ranges from relatively high density in galaxies (including very high density in structures within galaxies, such as planets, stars, ) to conditions in vast voids that have much lower density than the Universe's average. The temperature is only 2.73 Kelvin. as 2.725 +/- 0.002 K

Surrounding and stretching between galaxies, there is a rarefied plasmathat is thought to possess a cosmic filamentary structure and that is slightly denser than the average density in the Universe. This material is called the intergalactic medium (IGM) and is mostly ionized hydrogen, i.e. a plasma consisting of equal numbers of electrons and protons. The IGM is thought to exist at a density of 10 to 100 times the average density of the Universe (10 to 100 hydrogen atoms per cubic meter). It reaches densities as high as 1000 times the average density of the Universe in rich clusters of galaxies.

The heliosphere is a bubble in space "blown" into the interstellar medium (the hydrogen and helium gas that permeates the galaxy) by the solar wind. Although electrically neutral atoms from interstellar space can penetrate this bubble, virtually all of the material in the heliosphere emanates from the Sun itself.

For the first ten billion kilometres of its radius, the solar wind travels at over a million kilometres per hour. As it begins to collide with the interstellar medium, it slows down before finally ceasing altogether. The point where the solar wind slows down is the termination shock; the point where the interstellar medium and solar wind pressures balance is called the heliopause; the point where the interstellar medium, travelling in the opposite direction, slows down as it collides with the heliosphere is the bow shock.
The solar wind consists of particles, ionized atoms from the solar corona, and fields, in particular magnetic fields. As the Sun rotates once in approximately 27 days, the magnetic field transported by the solar wind gets wrapped into a (Phi) spiral.

The shape of galactic rotation curves (i.e. the galactic rotation velocity as a function of the distance from the galactic center), has led astronomers to the conclusion that galaxies must be surrounded by an invisible massive halo of 'dark matter' which exceeds the visible mass by up to 10 times However, even a large additional amount of dark matter would not exclusively determine the galactic gas dynamics.

Their underlying assumption with the old model is that gravity is the only force determining the dynamics of the galaxy. However, practically all rotation curves indicating the existence of dark matter have been obtained by observing the Doppler shift of gas (usually the 21 cm line of hydrogen) rather than of stars. It is generally assumed that the gas provides a tracer for the motion of the stars, but this assumption neglects the fact that ionized atoms are very much affected by electromagnetic forces: it is easy to show that with the generally assumed galactic magnetic field of 10-6 Gauss, the Lorentz force on a thermal proton is about 10 orders of magnitude stronger than the gravitational force (assuming a galaxy of the mass and size of the Milky Way) and should therefore completely determine the dynamics of the plasma, which in turn should also have an impact on the neutral gas because of recombination.

magnetic fields are a key part of the interstellar medium and scientists are finding they may play a major role in galactic formation, such as helping to form the (Phi) spiral arms of galaxies

rotation is a large part of the higher velocities inside the galaxy, and this is perhaps some of our missing energy; and note there is also rotation within the rotation being an expression for the rotation of plane of polarization, of an electromagnetic wave, induced by the field of a gravitational wave propagating along the same direction [(Gμd²Ω⁴)/(3ω)], ω and Ω being their respective frequencies.  Plane-parallel magnetic fields with a dominant azimuthal component 'Phi" prevail in spiral galaxies. This can be easily understood because differential rotation is strong in spiral galaxies

the recursive irony of which is that they are themselves the primary thing that is pulling and twisting themselves together in this definite, time-space spiral galaxy pattern . . . . . their motion is "fixed", within a loose envelope . . . . time dependent . . . on a well-defined galaxy spiral clock cycle (non-linear, with varying time rate/s); that is, it has a definite sequence as measured by it's (non-linear) space dragging and time warping characteristics, over time and space (see spiral arm pair magnetic fields above)

Amazingly, recent galaxy-cluster mapping has shown geometry!
Microwave data gathered by the WMAP satellite indicates the Larger Universe may be in the shape of a polyhedron with a Phi symmetry ; due to gravitational / expansive forces finding equilibrium in minimum-energy vectors. Close packing is the full pattern implied by the supercluster geometry,
It's the most economical, space/energy conserving arrangement of equal size spheres.


 

A GREAT MOTHER !

Thanks for your reply. I'm aware of the uniform background radiation issue. I think it is fascinating that Genesis says in the beginning, the world was without form and void, i.e., nothing. That God created the universe out of nothing, that the universe had a beginning, an unintuitive idea not anticipated by science, and come the 20th century, science tells us that, by their methods, it looks to be true. Otherwise, I'm not an astronomer, I leave scientific issues to experts.
My question is why is this topic important to your beliefs? If not Big Bang, then what, and how does this bring us closer to knowledge of the feminine Person of the Godhead? ...

Thanks for your reply back.. Actually I think the question is more important then the answer.. which is why it is important to me..
The real importance to me is the discovery that the universe is alive and not a clock; which seems to be a left over from a totally objective science. Also, there are many things left over regarding women's connection with Nature/Creation as separate from a God/Creator which are in need of repair on a social level. It is a matter of creating complementary world views along a living ethic which is not found in gasoline alley. In a view where an explosion replaces what may perhaps be better pictured by a birth, is not the Mother aspect of Creation also lost? I simply do not know how God created everything, but I know I am alive in a living universe with a Mother and Father, I see people being married and having children. I believe this same living intelligence I see in Nature to be the source of life and all things....

Thanks again. I definitely agree, the universe is not a clock as in the old deterministic viewpoint. You make a good point about semantics; creation could just as easily, and perhaps better, be imagined as a birth rather than an explosion. It wasn't really an explosion in the ordinary sense of the word. It was an as yet not understood, difficult to imagine, Becoming. I will reflect on your message