I'll nominate him for troll status in the Mod forum.

Forensic entomology.

So? I'm illustrating a point, which you admittedly just ignored by discounting it simply because it's a parable.

The point is, you can't stand at the end result of a largely improbable event and say it didn't happen just because it's too improbable! I can deal out a stack of 6 decks of cards one after the other, and stand there and say "Wow, what are the chances I would have dealt out this order? It must be one in a million.... impossible." Try and think of all the hands of cards I didn't deal out, and you'll get the point... one of the possible outcomes had to happen, no use drawing attention to it as something special.

rugerac,

     The basic question here is... Which is more likely?:

A) An omniscient, omnipresent, omnipotent, etc. being created himself, or always existed

or

B) one day, after billions of years of nothing happening, something small happend. Something so small that we wouldn't be able to see it happend: the smallest most fundamental tiniest building block of life came in existence by itself, or always existed.

B could also be rephrased back farther if you like:

     B) one day after trillions of years of nothing... Something was there. This something was the smallest block of anything possible to ever exist, and was as dense as possible. It came into existence by itself, or always existed.

-To reword this, we are comparing more unlikely events... which is more likely... Something very complex (God) created itself? or Something very simple (The first building block of life or the universe) created itself? 

In the case of B, we simply need to try our best to trace back the steps by which we got something big from something small. Of course this is such a long history that it seems being our understanding, but we can at least try.

In the case of A, we presupose that everything zapped into existence 6,000 years ago. POOF!

*Throws the ball to rugerac for a quick one line response*

What was that dude's name who did that show... "The System"?  He correctly picked the winners of something like 5 horse races in a row and mailed the winning name to this woman -- before the race -- every time.  After the 5th correct guess in a row, which is so statistically improbable as to be considered impossible, he had her convinced that he had a real system and could correctly pick the winner.

So, she came on the show, and they went to the horse race together, and he told her which horse to pick.  She bet $4000 of her own money on it.  After she placed the bet, he explained the system to her.  It's simple math.  In each race, you send out one letter for each horse in the race, each to a different person.  I don't remember the number because I don't know how many horses in a race, but suppose there are 8 horses.  In the last round, he sent only 8 letters, guaranteeing that one person will win and seven will lose.   So, you just do the math, and when you have enough people so that each of the five rounds, 7/8 of the pool are eliminated, you guarantee with 100% certainty that someone will get all five horses right.

Highly improbable events must not be viewed as one shot deals because that's not how the math works.  In this case, it only takes 8000 or so tries before you are guaranteed a result.  Similarly, if there are a billion billion planets, that must be taken into account. 

No, because IAGAY has to be high and drink a lot to get down to the mental retardation of Rugarac.  Without those indulgences IAGAY is perfectly normal.  It speaks volumes about Rugarac where, in his case, I'm sure he needs no assistance in being stupid.

Hello. It is good to be back. I extend my thanks to Hamby for resetting my password. Before reading the answer which is to follow, readers should consider the following picture:

  This is an M6 Anti-Tank Bazooka, for which my tag label is named. It propels a rocket grenade out a launch tube designed to penetrate the armor of Tiger Tanks. Now imagine you have the misfortune to be a housefly, and that the grenade which is propelled from this rocket happens to be travelling towards your fragile organism. This would undoubtably be an extremely unpleasant experience, as we shall soon see. (PS, if you didn't follow, please refer to the tag on the upper left of my avatar.

Since our interlocutor appears to have a general communication problem, I shall remind everyone of what the questions at hand are thus.

What is the probability that the sun is the "correct temperature" for biological life to occur?

What is the probability that the Earth has the correct gravitational conditions for its current state (its orbit, its spin etc.)

What is the probability that "gravity" is exactly the correct amount (as we shall see, this question has no meaning)

What is the probability that a DNA Helix assembles?

What is your theory on the origin of life?

This is how a star is born. A cloud of diffuse hydrogen undergoes gravitational instability, hence forming a gravity well, it begins to spin and acts like a gas jet, accumulating hydrogen. The gas cloud begins to take shape as it collapses under its own gravitational force. When the cloud has finally achieved hydrostatic equilibrium (unidirectional equivalent pressure), a protostar, the precursor of a star, forms in the centre of the cloud, and these newly born stars continually emit huge jets of gas from their core.

The main sequence of a star’s life cycle is the achievement of a high enough temperature that fusion may begin, whereby it begins to burn all of it’s hydrogen and fuse it to make helium. Our sun is currently halfway through this process. The star spends this time converting all the hydrogen to helium, and the length of time it spends doing this depends on how much hydrogen it has to burn, which depends on the Hertzsprung Russell class of the star. 

The next sequence of the star’s life is required for the generation of the elements necessary for biology, Carbon, oxygen, nitrogen and iron. When the star has exhausted it’s ignition hydrogen it begins to expand into a Red giant, and tremendous heat and pressure is applied to the core area of the star, which allows the process of helium fusion to begin, to create heavier elements. Heavier elements still must be generated by the largest stars, which expand into Red hypergiants (Betelgeuse is a good example). The temperatures here are sufficient to fuse carbon, and continue the nucleosynthesis bridge up to iron. This is an obvious consideration. According tho this equation:

E=mc^2, there is a direct proportionality between the mass deficit of a nucleus versus its nucleon constituents at an infinite distance from each other. That is, the breaking of a nucleus releases a certain amount of energy which is interconverted to mass. The following argument will help make this clear. Consider this diagram:

Being that iron has the greatest binding energy per nucleon, the process of fission of nuclei less massive than Fe-56 will decrease the binding energy per nucleon of the products, and the fission of those much more massive than Fe-56 will increase the binding energy per nucleon. Iron, being the most bound, requires the greatest temperature and pressure conditions to form.

 However, it is the collapse of the star which generates the necessary temperature and pressure conditions necessary to distribute this material. The destroyed layers of the dying star are stripped off and recycled to make new stars and planets, while a glowing pulsar is left in its place.

This will be important in our discussion later on. Now back to the question. What is the probability that the Sun is "exactly the right temperature". I would estimate about 80%, since the Sun belongs to the common Main sequence of stars. To understand why, we must consider the Hertzsprung-Russell diagram:

Now, to interpret this digram, we must understand two things:

1. Apparant brightness of an observed stellar body is inversely proportional to the square of the distance between the the observing body and the stellar body. This is obvious when we think about it. Apparent brightness. is given in terms of the amount of wattage recieved over a certain area, or Wm^-2. Let us say that when the star is a distance x from the body a, its brightness is b. Now consider that the distance doubles, as such, the area will increase by a factor of 4. As such, the brightness will decrease by a factor of four, being that the wattage is now more spread out. Hence:

b=L/[4pi(r^2)]

Now, stars are classified as well based on their light spectra. Once shifting is factored into the spectral anaylsis, we can analyze the surface temperature based on the color, to give the main Surface temperature. For this, refer to the x-axis of the graph. The letters run O,B,A,F,G,K,M. These are the primary spectral classes in decreasing order of temperature. Class O has a blue absorption. As such, its surface temp. is 28000K-50,000K. Compare to M, which has a surface temperature of 2000-3500K. If the reader wishes to find out the temperature for every spectral class, they may do so themselves. It's on the graph.

M=5log(d/10)-m

M, the absolute magnitude, is an important class measure of stars by how much power they radiate, and as well as spectral class, is the primary measure of stars.

This we must clearly understand. The largest proportion of stars, the "normal stars", will fall in the main sequence. As such, if we consider a band of planets that orbit a star, the "Goldilocks Zone" for a Main sequence star will differ. For a star with a high temperature spectral class and hence a higher magnitude in the main sequence, the Goldilocks zone will be further from that star than for a cooler star with a smaller magnitude. Our sun is in the lower quadrant of the main sequence, and therefore is in a density of stars such that it is very common. I estimated 80% before. I suppose this needs to be revised. The real question is, what percentage of stars have a Goldilocks Zone, or a chance to support a terrestrial planet that could support life. This is a much more meaningful question than the one you asked. Most stars require a precise Zone, since they are in binary orbit. A reasonable estimate would be 10% of stars. It is also important to remember that all the giant stars were once in the Main sequence too, before they ran out of hydrogeN, and the dwarfs, before they ran out of hydrogen, and then ran out of helium, and this shall be taken into consideration. Additionally, there is no reason to say that only the main sequence can support a Goldilocks zone. And this shall also be taken into consideration. It is also important to consider that within a certain range of the mutual orbit of a binary star, protoplanet formation can be induced more rapidly, and in fact, that it would indeed be possible for such a system to support terrestrial planets. This would raise the estimate a great deal. However, since a binary star orbit is much more sensitive to ejection of a planet, it limits the range of orbital viabilities greatly. As such, we shall be fair, and assume that only 10% of stars have the capacity to support plantary systems. This is a reasonable estimate based on our current understanding of Astrophysics. 10% of stars is approximately 600,000,000,000,000,000,000, or, more accurately 6x10^20 stars. I trust that this is a high enough probability for you?

Now, let us consider the next question. It is linked to the previous one:

What is the probability that the sun is the "correct temperature" for biological life to occur?

As we have seen before, the Goldilocks Zone henceforth referred to as GZ, can vary depending on the position of the star in question on the HR diagram. What we really want to know is, given a random sample of Solar systems, what is the probability that the system contains one planet within the GZ? This again, is a much more meaningful question to ask. It is also part of the Drake Equation. There is not enough data to answer this question meaningfully, since the only solar system about which we have assembled a complete picture is our own. On the other hand, terrestrial planets within the respective GZ have been discovered. Firstly, we should consider that in total there are approximately 5,000,000,000,000,000,000 planets or, 5x10^18 planets. However, given the information above about stars with the capacity, even a relatively tiny estimate would yield at least one quadrillion planets. This has also been considered within the Drake equation. The key thing to understand is that the pictures we are beginning to form of other solar systems indicates that ours is not remarkable. The HR indicates our star is of the most common type, and planetary formation is a common occurence (mostly among singular orbit stars). The formation of planets is under a process similar to that of stars. Stars, being the result of gas clouds which collapsed under a gravity well to produce a nuclear furnace. All stars begin as a diffuse cloud of hydrogen gas which starts to collapse as driven by gravity. As hydrogen accumulates, the gravity increases, and it starts to condenses faster and faster, acting like a gas jet, sucking in hydrogen, at which point it is called a protostar, a phase which lasts 100,000 years. The cloud starts to spin rapidly (this often results in binary star systems), before condensing into the core, and the star's dense core heats up so much due to the kinetic energy of stellar gas being forced into the star's core, it starts fusing hydrogen atoms together to make the next heaviest element, helium. The process of converting hydrogen to helium is called "ignition", because the star starts to burn it's hydrogen. Planets form in a very similar way, especially the gas giants. Smaller terrestrial planets will form from a different element set, since supernovae allow the completion of the nucleosynthesis chain up to Fe-56. Terrestrial planets, being primarily made of oxygen, hydrogen, nitrogen, carbon and iron, will condense "inside-out" from a distributed cloud of such materials, to form a protoplanet. These planets will not be randomly arranged either. Because of the stronger exertion of gravitational field strength inversely proportional to the distance from the stellar body in question, terrestrial planets will condense closer to the star in question, and the less dense gas giants will condense further away from it. The key thing to take away from this section, and as we shall see, the one below, is that the formation of solar systems is a process determined by physical laws, and there is nothing in particular remarkable about our Solar system, or our GZ. All stars have a GZ, although it is difficult to ascertain precisely what is the probability of a terrestrial planet forming within that band, although it is probably not too low given that we have discovered exoplanets within their respective GZs. As stellar spectroscopy improves, we will probably discover more terrestrial exoplanets within the GZ.

Moving to the next question

What is the probability that "gravity" is exactly the correct amount (as we shall see, this question has no meaning)

The answer to this is much shorter given that the question does not meaningfully express any proposition.  I shall reword it to make it meaningful.The question means for gravity to be the correct amount such that planets in question have the angular momentum to maintain a stable orbit around a star in question. It is important to understand that Solar systems do not assemble chaotically. That is, the dynamics of the protosystems are ordered, although you seem unable to understand this. The formation of a protoplanet will depend on the gravity of the star in question. Planets form precisely because of the gravitational equilibriation that occurs in a solar system. As such, given the inverse square law:

Think of it like this. Between any two bodies x and y there will be a point of equilibrium such that the gravitational forces between them are static. We shall call this point b, and we shall say the the distance from b to x is r1, and that from y to b is r2. Now, given the inverse square law, and that the resultant field of gravitation at such a point is zero. This means that the pull in each direction is equivalent. This will depend on the respective masses of the two bodies. If the two bodies are of identical mass, then this point will be equidistant from both bodies, if not, it will be closer to the less massive body, like this:

At gravitational equilibrium Gm1/r1^2=Gm2/r2^2

In the same way, a body which is orbiting around an object which is stationary relative to it follows similar mathematics. For simplicity in demonstrating this principle, let us say that the body is orbiting in a circle, which the Earth pretty much is. Now, this means that the gravitational force exerted on the body is equivalent at every single point of its orbit, as given by the inverse square law. To understand how Earth and all the other planets maintain their orbit, and how this forms when Solar systems form, that is, that it is not "set up" by a designer, we need to understand Newton's first and second Law in considerable detail. Now, the formal statement of Newton's first law is that a body at constant speed or at rest will continue to move at a constant speed until some other force acts upon it. Since there is no meaningful distinguishing between constant speed and rest in Newtonian mechanics, this is better stated as a body with no net resultant force will continue as it was until a resultant force acts upon it. Newton's second law follows from this, that is, that a resultant force will cause acceleration. More formally, Force is proportional to rate of change of momentum. The following argument will help make this clear.

Given that the differentials for Newtonian mechanics indicate that instantaneous velocity is equivalent to the instantaneous change in displacement:

ds/dt

Then the instantaneous change in velocity will be the differential of the instantaneous velocity with respect to time. Hence:

ds^2/d^2t

So we have a formal definition for acceleration:

a= dv/dt

F=Ma

Given that the momentum of an object is also proportional to mass, but by velocity:

p=mv

This can be stated as:

p=m(ds/dt)

I=dp=mdv

Recall the identity:

F=ma

a=dv/dt

Then we substitute in to find Newton's second law:

F=dp/dt

We need to understand this to consider how orbit works. Now, consider a cannon. More specifically, consider Newton's cannon. According to Newton, in projectile motion, the horizontal projection of a body should not affect the vertical projection for two bodies which are launched the same vertical distance and being acted upon by the same gravitational force. To put it another way, if I was standing on a high cliff, and dropped a bullet off the cliff in one hand, and fired the other horizontally in the other, they will hit the ground at precisely the same time. Additionally, for two objects in free fall, the mass does not affect the acceleration. Both objects will accelerate by precisely the same amount. On Earth, this is 9.81ms^-2. And by this, a cannonball and a feather would hit the ground at the same time, if there were no air resistance. We need to understand this when we consider how orbit works. To fully understand the ramifications of this, however, we also must understand UCM (Uniform Circular Motion).

Uniform circular motion is the motion at constant velocity of a body around a fixed point such that each point on the path taken by the body is equidistant from the point around which the body is moving. In one dimensional projection, this is usually given as a cosine or sine wave:

The graph is in degrees but it is more coherent to speak of circular motion in terms of radians. The angular velocity is therefore given as the number of radians displaced per unit time. Or:

d(theta)/dt

Now, even though the body moves at a constant velocity, it is changing direction at every instant and as such under Newton's definition it is acceleration. This means a force is required to accelerate it, called the centripidal force. Given as the sum of two vectors from the radius, the centripidal acceleration is given as

a=v^2/r

where r is the radius. Or, using Newton's law:

Centripidal force=ma, or:

Centripidal force=mv^2/r.

This is crucial to understand. If I fire a bullet horizontally off a cliff, and drop another bullet off the cliff at the same time, they will hit the ground at exactly the same time. But the bullet fired will transverse a much greater horizontal distance before falling, since in the time in flight, its horizontal speed is much greater. The horizontal speed is not "keeping it up" but rather allows it to displace a greater horizontal distance in the time in flight. Newton realized, therefore, that a cannonball fired fast enough should come straight back around the Earth and strike the cannon. Take a cannonball of mass 50kg. How fast would it have to be travelling in order to displace the Earth's circumfrence if fired approximately 50m above ground level?

Well, we know that the time taken to fall to the ground is given as:

s=0.5at^2

Hence sqr rt. (s/0.5a)=t

Given that a=9.81ms^-2

Then:

t=sqr rt (50/4.905)=3.2 seconds

Given that the Earth's circumfrence is 40,000km or 40,000,000m, then the cannonball must transverse 40,000,000m in 3.2 seconds which is a velocity of 12,540,000 ms^-1. This is much greater than Earth's escape velocity and as such, it would impossible to have a satellite at 50m above the Earth's surface. Additiionally, we can work out the centripidal force needed in this case, given that the radius of Earth is 6,000km or 6,000,000m. Then the centripidal force is:

(50)(12,540,000^2)/6,000,000 = 131000000N

This principle tells us how Satellites work. It also explains why geosynchronous satellites travel slower the higher in orbit from Earth they are. The satellites do not fall back down to Earth because of the centripidal force which keeps them in orbit, this is the principle of angular momentum. It is the same reason why Earth retains its stable orbit. In general, planets closer to the sun must travel faster in order to maintain orbit. It is again important to understand that there are viable orbit points at any distance within the escape radius of the Sun, depending on the velocity of the body rotating around it. Again, it is not the case that the Earth was crafted and then propelled at just the right velocity for this to occur. Rather, the velocity at which an orbiting body travels is determined by its formation and distance from the Sun. Again, this is a simple physical causality process. The physical laws enable the process to set itself up. To fully appreciate this, we must understand Kepler's Third Law, which is directly related to the aforementioned principle.

Satellites of bodies, such as the moon to Earth, or the Earth to the sun, are kept in stable orbit by their centripidal force. In general:

Gravitational attraction to the body of the satellite= centripidal force on the body. Hence:

GM1m2/r^2=mv^2/r Hence, the velocity of orbit is given as:

v= sqr rt. GM/r

Given that the body orbits in one whole revolution in time T, then given that v is the number of radians displaced per second:

v=2pi r/T

Then:

GM=4pi^2 r^3/T^2

This applies to any circular orbit, and explains how orbits form. The Earth maintains its orbit not because it is "gravity is just right for it to happen", but because it formed the distance from the sun that it did. All planets follow this principle. The orbit depends on the formation of the planet, not some careful "setting up" of said planet. Nor does their have to be some very precise "just right" distance for the angular orbit to maintain itself given that the centripidal force provided depends on the distance. Its exactly the same as our satellites. The higher ones travel slower not because we "set" them to do so but because gravity determines it as per Kepler's Third Law. Your causal understanding of the process is backwards.

You seem to think that astrophysicists think that because these are natural events that are not at the hands of a designer, that they are chaotic and random. Well, they are not. Au contraire, the events follow a coherent sequence which can be explained solely in terms of physical causality, as I have already demonstrated. If you wish to know more on this matter, I leave it an exercise to you to open an Astrophysics textbook. 

Moving to the next two questions:

What is the probability that a DNA Helix assembles?

What is your theory on the origin of life?

This question is worded poorly as it implies that our current scientific understanding of polynucleotides is that they are the result of a rapid, spontaneous process of chance. This is not the case. The process of chemical evolution by which the current order of biological life, universally based on the transcription of codons from a set of four bases, is founded, was not always the case, and arose by a slow and arduous process of chemical evolution similar to the process of biological evolution which followed it. I shall point out that these questions are more or less the same, and treat them as such. My suggestion is as follows:

The process of formation of organic autocatalysis is time consuming. It begins with Piezoelectric systems on crystallien surfaces, which form the progenitors of ribozymes. The first biological molecules on Earth may have been formed by metal based catalysis on the crystalline surface of minerals.

In principle, an elaborate system of molecular synthesis and breakdown called metabolism could have existed as such long before the first cells. Life requires molecules which catalyze reactions hsih lead directly or indirectly to replication of more molecules like themselves. Catalysts with this self promoting propertycan use raw materials to reproduce themselves and therefore divert the same materials from the production of ther substances. In modern cells the most versatile catalysts are polypeptides. However, they cannot propogate self-replication, they do not replicate. There needs to be a molecule which can act as a catalyst and guide its own replication. Such a molecule does exist: RNA.

To understand this more fully, we must understand the relation between protein, DNA, and RNA. Now, the key principle to grasp is the central dogma of molecular biology. Note that the word dogma is not used because the principle has religious adherence, but rather because it seems to be obeyed by all biological life.

Proteins, being the primary structure and material of all cellular life, are encoded by the information in DNA, which is transcribed to an RNA intermediate before being translated into protein. This process is central to all biological life and is universal in its usage. However, it was not always the case. Prior to the existence of DNA, RNA was used as a ribozyme, prior to the usage of protein as the catalytic compound which would be necessary for the self-replicative properties of biological life. Hence:

Pre-RNA>Pre-RNA

would eventually be superseded by:

RNA>RNA

The manner in which this could occur and form has been detailed above, since RNA have a similiarity to polypeptides in their ability to form an active site for homogenous catalysis.

The process of natural selection would naturally favor those RNA which could hold amino acids or small stretches of such at their active sites, by the process detailed above. Hence, eventually the order above would have been superseded by the following:

RNA>RNA and RNA>Protein

DNA has several advantages over RNA. The superseding of RNA as the primary encoder of the codons for polypeptides would have been a slower process. In modern organisms, translation is done by virtue of a set of RNA molecules which hold amino acids and match them to the mRNA called tRNA adaptors. As mentioned previously, RNA molecules that could hold information to guide polypeptide synthesis would have had a massive advantage over its catalytic counterparts because polypeptides are much more efficient at catalysis. Now, ribozymes can perform the function of tRNA-like molecules called psuedo-tRNAs. Finally, this crude form of the peptidyl-transferase would have been naturally selected for its ability to hold the amino acid at the catalytic side of the string of RNA that can hold its code. This development was probably what led to the modern system of codons. Hence we have the following:

mRNA (via psuedo-ribosomes)> translates Protein

Finally, the sequence we see today:

DNA>RNA>Protein

Would have arisen later. The chemical similarities between the two molecular chains, that is, DNA and RNA, allows for the superseding to occur without interrupting the central processes of this primitive form of biological life. But DNA would be naturally selected for as the primary sequence for the transcription of chains to hold the codons because deoxyribose is more stable than ribose and thymine more so than uracil.

We will now consider the precise manner in which this process occured. First we must understand proteomics in some detail:

Essentially, a protein is a string of amino acids, usually 500-2000 amino acids long. The whole of life depends on proteins. Everything else, save the genes, is a mere passive bystanders in a biological dance of life. When we observe the cell, we are in essence observing proteins. Proteins control movement (motor proteins), the control structure (structural proteins), they control concentration (transmembrane proteins), they control ion gradients (pump proteins), and most importantly, they control every single chemical reaction in the body (enzymes). Proteins don't just control the body, they are the body. All proteins fold up tightly into one highly preferred conformation. There is no limit to the number of tasks they do in the cell. Proteins can be subdivided into two large classes, the globular proteins fold up into irregular ball-like shapes and fibrous proteins. Nearly all globular proteins are allosteric, which means they can adopt two slightly different conformations, this means they have two binding sites, one of which is for a regulatory molecule, and the other is for the substrate. Allosteric control is very complex. Suffice it to say for now that it works on either negative or positive feedback (ie the regulatory molecule increases the protein's affinity for the substrate, and the other way around, or the opposite, the regulatory molecule decreases protein affinity for the substrate, which of course, would be reciprocal. In this way, regulatory molecules can turn the protein on or off, and in negative control, there is a tug of war between the regulatory ligand and substrate which are reciprocally affected by each others concentration in the cell.

A protein is a specific type of biological polymer made up a specific family of chemical subunits called amino acids. There are 20 biological amino acids, and they are distinguished by the fact that they all have a central alpha carbon, which is attached to an amine group (-NH2), a Carboxyl group (-COOH), a hydrogen, and a side chain. It is the side chain that gives each amino acid its properties, and each of the 20 has a different side chain. Proteins can be anything in length. Usually it is 50-2000 amino acids long, and the longest ones can 7000 amino acids long. The interaction between the side chains (which is determined by charge, since three are basic, four are acidic, nine are nonpolar and five are polar but uncharged) determines the shape of the protein. For instance, the nonpolar side chains are all hydrophobic (water hating) which means the protein will fold up in a manner where the nonpolar side chains are facing inwards and not exposed to water (this is the most energetically favorable conformation). This is just one of many different subtle interplays between amino acids that determine a proteins shape. However, nearly all proteins fold spontaneously in a solution, indicating that all the information necessary to fold it is stored in the amino acids.

Proteins have only one or a second highly similar conformation, that is how they work.

Now, for the number of possible combinations of amino acid, such calculations are easy to make. With just two amino acids joined in a row, we have 20^2, or 400 possibilites. With three we have 20^3 or 8000 possibilities, with ten, we have 10240000000000 possibilities, with the average protein having several hundred amino acids up to a thousand, we have vastly more conformations than there have been seconds or atoms in the universe.

However, the Hoyle Fallacy occurs here, in making our calculatiosn in the possibility of stable biological proteins arising, because the calculations, as was pointed out by the TalkOrigins archive:

· They calculate the probability of the formation of a "modern" protein, or even a complete bacterium with all "modern" proteins, by random events. This is not the abiogenesis theory at all.

· They assume that there is a fixed number of proteins, with fixed sequences for each protein, that are required for life.

· They calculate the probability of sequential trials, rather than simultaneous trials.

They misunderstand what is meant by a probability calculation.

· They seriously underestimate the number of functional enzymes/ribozymes present in a group of random sequences.

Now, proteins do not form in this way. There is an evolutionary advantage to stable conformations forming, and stable conformations, in turn, are the ones which give rise to biological functions. There is an obvious reason for this. In my notes on the matter, I wrote:

All Proteins Bind to Other Molecules

· Properties of proteins depend on their interactions with other molecules

• Eg. Antibodies attach to viruses to mark them for destruction, the enzyme hexokinase binds glucose and ATP to catalyze the reaction between them
• Actin molecules bind to each other to produce actin filaments etc
• All proteins stick or bind to other molecules
• Sometimes tight binding, sometimes weak and short lived
• Binding is always highly specific. Each protein can usually only bind to one type of molecule out of the thousands it encounters
• The substance bound to a protein, be it an ion, a macromolecule, a small molecule etc is referred to as the ligand of that protein
• Region of the protein associating with the ligand is known as the binding site
• Usually a cavity in the protein surface caused by a particular chain of amino acids
• These can belong to different portions of the polypeptide chain brought together when the protein folds
• Separate regions of the protein surface generally provide binding sites for different ligands.

The Details of a Protein’s Conformation Determine It’s Chemistry

· Proteins chemical capability comes in part because neighboring chemical groups on the protein’ surface often interact in ways which enhance the reactivity of amino acid side chains

· Two categories of this: Neighboring parts of the chain may interact in a way that restricts water molecules access to the ligand binding site.

· Because water molecules tend to form hydrogen bonds, they can compete with the ligands for sites often the protein surface

· Therefore, the tightness of the protein-ligand bonding is greatly increased if water molecules are excluded

· Water molecules exist in large hydrogen bonded networks, and inside the folds of a protein a ligand can be kept dry because it is energetically unfavorable for water molecules to break from this network

· Clustering of neighboring polar amino acid side chains together can alter reactivity. If the way the protein folds forces many negative side chains together that would otherwise not associate due to their mutual repulsion, the affinity of this new pocket for a positive ion is greatly increased

· Sometimes, when normally unreactive groups like CH2OH interact with each other because the side chains on which they are on form Hydrogen bonds with each other they can become reactive, allowing them to enter reactions making/breaking covalent bonds

· Therefore the surface of each protein has a unique chemical reactivity that depends on which side chains are exposed and their exact orientation relative to each other.

Sequence Comparisons Between Protein Family Members Highly Crucial Ligand Binding Sights

• Many domains in proteins can be grouped into families showing clear evidence of evolution from a common ancestor
• Genome sequence reveal a large number of proteins with one or more common domains
• 3D structures of members of same domain family remarkably similar
• Even when the amino acids identity match falls to 25% the backbone atoms in two members of the same domain family have the same fold within 0.2nm
• These allow a method called “evolutionary tracing” to determine which sites in the protein domain which are most crucial to the function of said domain
• For this, the most conserved amino acids stretches are mapped onto structural model of the known structure of one family member
• The SH2 domain is a module that functions in protein-protein interactions. It binds the protein containing it to a second protein containing a phosphorylated tyrosine side chain in a specific amino acid context
• The amino acids on this binding site have been slowest to change in the evolutionary history of SH2

We must understand all of this. Biology is highly modular. It is all about the assembly of large structures from smaller ones. Polypeptides are modularly assembled from amino acids hence determining its structure hence its chemistry and binding. Proteins are modularly assembled from polypeptides, and supramolecular structures from polypeptides, therefore, the evolution of proteins will be forced in the direction of stable amino acid conformations not random possibilities associated with amino acids. This becomes evident when we consider proteomic supramolecular structures:

Protein Molecules Ofter Serve as Subunits for the Assembly of Large Structures

· Noncovalent bonding allows proteins to generate supramolecular structures like construction of giant enzyme complexes, ribosomes, proteasomes, protein filaments, and viruses

· These are not made by one giant single covalent molecule, instead by noncolvalent assembly of many giant subunits

· Advantages of this building technique: Large structure built from a few repeating subunits requires little genetic information

· Both assembly and disassembly are easily controlled and reversible

· Errors in structural synthesis are easily avoided as proofreading mechanisms can operating during the course of the assembly

· Some protein subunits assemble into flat sheets, on which the subunits are arranged in a hexagonal pattern

· Slight changes in the subunit geometry can turn the sheet into a tube, or with slightly more changes, into a hollow sphere

· Protein tubes and spheres which bind to RNA form the coats of viruses

· Formation of these closed structures provides additional stability because it increases the number of covalent bonds

· This principle is illustrate by the protein coat or capsid of may viruses

· Capsids are often made of hundreds of identical protein subunits enclosing and protecting the viral nucleic acid code

· The proteins of capsid must have particularly adaptable structure. Not only must it have multiple contact points to make a stable sphere but also must be able to change to let the nucleic acid out to initiate viral replication in a cell. This is shown here by the construction of a capsid from monomer protein subunits, which connect into dimers, then trimers, then into the intact sphere with the addition of more free dimers

Polynucleotides Can Both Store Information and Catalyze Chemical Reactions. RNA can propagate itself by means of complementary base pairing. However, this process without catalysis is slow, error prone and inefficient. Today, such processes are catalyzed by a massive battery of complex interactions of RNA and proteins.

In the RNA world, the RNA molecules themselves would have acted as catalysts. A pre-RNA world probably Predates the RNA One. It is unlikely RNA was the first self-replicating propogater. It is difficult to imagine that they could form through nonenzymatic means. The ribonucleotides are hard to form enzymatically, also RNA polymers entail a 5 to 3 chain which must compete with other linkages that are possible including 2 to 5 and 5 to 5. It has been suggested that RNA was anteceteded by molecules with similar properties, but that were similar. Candidates for pre-RNA include p-RNA and PNA (peptide nucleic acid)

The transition from pre-RNA to RNA would have occurred through the synthesis of RNA via these simpler components as template and catalyst. Laboratory experiments demonstrate this as plausible. PNA can act as a template for RNA molecules. Once the first RNA molecules had been produced, they could have outphased their antecedents leading to the RNA world

Single-Stranded RNA molecules can fold into highly elaborate structures Comparisons between many RNA structures reveal conserved motifs, short structural elements used over and over again as part of larger structures. Common motifs include

Single strands, double strands, single nucleotide bulges, triple nucleotide bulges, hairpin loops, symmetric internal loops, asymmetric internall loops, two stem junction, three stem junctions and four stem junctions. RNA molecules can also form common conserved interactions such as psuedoknots and “kissing hairpins” and hairpin-loop bulge contacts, like in this picture:

-Protein catalysts require a surgace of unique countours. RNA molecules with appropriate folds can also served as enzyme. Many of the ribozymes work by positioning metal ions at the catalytic sites. Relatively few catalytic RNA exist in modern day cells, being the polypeptides work much better.

An example of In vitro selection of synthetic ribozymes:

-A large pool of dsDNA each with a randomly generated sequence. Transcription and folding into randomly generated RNA molecules. Addition of ATP derivative containing a sulfer in place of oxygen Only a rare RNA has the ability to phosphorylate itself. This is captured by elution of the phosphorylated material

These experiments and others like them have created RNAs that can catalyze a wide variety of reactions:

Peptide bond formation in protein synthesis, RNA cleavage and DNA ligation, DNA cleaving, RNA splicing, RNA polymerization, RNA and DNA phosphorylation, RNA aminoacylation, RAN alkylation, Amide bond formation, amide bond cleavage, glycosidic bond formation and porphyrin metalation, since, like proteins, ribozymes undero allosteric conformation change

Self-Replication Molecules Undergo Natural Selection

-The 3D structure is what gives the ribozyme chemical properties and abilities. Certain polynucleotides therefore will be especially successful at self-replication. Errors inevitably occur in such processes, and therefore variations will occur over time. Consider an RNA molecule that helps catalyze template polymerization, taking any RNA as a template

-This molecule can replicate. It can also promote the replication of other RNA. If some of the other RNA have catalytic activity that help the RNA to survive in other ways, a set of different typers of RNA may evolve into a complex system of mutual cooperation.

One of the crucial events leading to this must have been the development of compartments. A set of mutually beneficial RNA could replicate themselves only if the specialized others were to remain in proximity

Selelection of a set of RNA molecules according to the quality of replication could not occur efficiently until a compartment evolved to contain them and therefore make them available only to the RNA that had generated them. A crude form of this may have simly been simple absorption on surfaces or particles.

The need for more sophisticated containment fulfilled by chemicals with the simple physiochemical properties of ampipathism. The bilayers they form created closed vesicles to make a plasma membrane. In vitro RNA selection experiments produced RNA molecules that can tightly bind to amino acids. The nucleotide sequence of such RNA contains a disproportionate number of codons corresponding to the amino acid. This is not perfect for all amino acids, but it raises the possibility that a limited genetic code could have arised this way. Any RNA that guided the synthesis of a useful polypeptide would have a great advantage.

I trust this is sufficient detail to answer your question.

So which would you prefer DG , Rum or Sake , for trying to deeply understand all that you just posted about GAWED ?      An important experiment is now being conducted by me and Hamby, ... I think?   ...... gulp ......    

WE BOTH WIN !

*Loads another one of deludedgod's rounds into his bazooka*

Theist!  3 o'clock!

i get so fucking SICK of this argument, i.e., "what are the chances the universe could have produced the perfect conditions for life on its own?"

one, this presupposes a teleological position that somehow our chance creation was the "right" way for the universe to work out.  in other words, it "worked," it "did what it was supposed to do."  this a purely subjective position.  there would still be a universe if your fucking hairless monkey ass didn't exist and i doubt it would shed a tear over a lost opportunity.

two, there could ALWAYS be conditions for life in the universe.  just not YOUR life.  for example, let's imagine all the possible confugurations of the universe put into one handy knob.  this knob has to be set in JUST the right position for HUMAN life.  if it were to be turned by GOD or, let's say, a leprechaun, a little to the left, humanity is fucked.  but BOOM, this other race pops up: a race of people with blue skin who breathe sulphur.  they build houses from smoke and their women have eight boobs like that dancer in jabba the hutt's palace.  they're a very sophisticated race of people who don't even have to take a shit, and one day they say, "WOW, what are the odds the EXACT fucking conditions worked out that allowed LIFE in the universe?"  they come to the only logical conclusion: it must've been GOD.  this really pisses off the leprechaun, btw.

you see?  basically you're just really happy YOU got lucky enough to exist and don't want to face the fact that things might've been nicer without you: eight-boobed women and so forth.

Yeah, Nigel. With even a little understanding of what's out there, WE HAD TO BE, as is carbon based life else where.

I think it's also amusing that people think our big bang universe is special and rare, and even the only one. Think much MUCH BIGGER, no Bigger yet, NO BIGGER , ahhhh keep going .....

mindspread to the rescue !  Great Video ..... thanks