Creation: May Math Lessons

Hmmm, my comment on the blind darwinist post also relates to this. The idea of evolution and abiogenesis does not include the idea that particular proteins are goals. The idea is that selection is involved in which proteins ultimately became established in early cells.
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You may still argue that abiogenesis is not possible, but the idea that each protein in a cell must have resulted from a probability of all amino acid combinations being tested does not fit with how abiogenesis is thought to have happened.
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(As I’ve said before, abiogenesis is still a hypothesis without a clear chain of events and you could legitimately call it muddy. But also it is not baseless hand-waving – there are actual chemical ideas being investigated. Since we can’t go back and see what was going on billions of years ago at the molecular level necssary to find out how life could have formed, and since the conditions on earth have changed greatly since then, there are necessarily gaps and lack of precision.)

Your math is off.
15 billion years = 4.7335389 × 10^17 seconds
=1.31487192 × 10^14 hours
= 5.47863298 × 10^12 days
= 7.82661855 × 1011 weeks
= 180 000 000 000 months
= 1 500 000 000 decades
= 150 000 000 centuries

Its easy to calculate the probabilities associated with proteins . 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 calculations in the possibility of stable biological proteins arising, because the calculations, as was pointed out by the TalkOrigins archive:

· You 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.

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

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

· You misunderstand what is meant by a probability calculation.

· You 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