Thanks, that was quite interesting.

I don't agree with all of their (minor) points, but it is very good.

Here are some of my highlights:

Any leader who thinks evolution is a matter of belief is arguably unfit for office. How can someone who dismisses the staggering amount of evidence for evolution assembled by researchers in myriad fields possibly evaluate more subtle scientific evidence for, say, climate change?

Those who have studied our planet and the life on it, however, have come to very clear conclusions: the Earth is around 4 billion years old and all the life on it gradually evolved from much simpler forms. There is no evidence of any kind of outside intervention, and no need to invoke it to explain what is known. Yes, there are many debates among biologists, geologists and cosmologists over the finer details, but these will be resolved sooner or later by new discoveries or experiments. Reality is the ultimate arbiter.

It also has a go at creationism.

Nice

Man, now I have to read it again to find them. Don't get me wrong, I agree with all of the headings.

"Then there's our sense of smell. Do you find the scent of roses overwhelming or do you struggle to detect it? Can you detect the distinctive odour that most people's urine acquires after eating asparagus? People vary greatly when it comes to smell, largely due to chance mutations in the genes that code for the smell receptors rather than for adaptive reasons."

I think that this is speculation... All traits have a large degree of variability built in to them (as long as it is not essential for them to stay fixed) which aides evolution (you need variety if there is going to be selection based on it). Yes, this may come about through mutaions, but also through the mixing of combinations of genes (sex, gotta love it). I would say that humans sense of smell used to be a lot stronger, in line with other animals, only we don't need it so much anymore, it is no longer a large selection criteria so it can become more variable without affecting survival.

Environment also contributes. If you have to put up with a lot of strong smells (eg, cigarette smoke) your sense of smell will decline, but you can also train your sense of smell to be better (useful in certain occupations).

"Take a look in the mirror. The face you see is rather different to that of a Neanderthal. Why? The unflattering answer could be for no other reason than random genetic drift. With features that can vary somewhat in form without greatly affecting function, such as the shape of the skull, chance might play a bigger role in their evolution than natural selection."

Genetic drift is real, but I think if you see a large drift you can't really call it random. This is speculating a bit again (as they kind of admit by using "might&quot. If you get a large genetic drift, such as a big change in shape of skull, I would argue that there is some evolutionary pressure that we aren't sure of yet such as (some speculation from me): larger (or differently shaped) brain needs different shaped skull, better brain protection(?) and don't forget the power of sexual attraction (look at bird plumage).

It's really just minor points like these, on the whole I like it.

Honestly you can talk till the cows come home and throw about paper afetr paer about evolution but it still does not explain the beginning.

There will always be new versions, theories staying steps ahead of the creationists using presuppositions in their thinking but the beginning still remains a mystery.

Wow, extensive ignorance and only 12 posts.  You rock!  Like the poster above me pointed out, abiogenesis deals with how life started.  Evolution takes off after life started.  It is a rigorously tested theory that has withstood the scientific method and there is currently no alternative which contradicts it.  The Theory of Evolution is the foundational basis of biological science.  Further, the hypothoses of abiogenesis are scientifically tested.  It may yet be a mystery as to how life formed, but that mystery would seem to be solvable.  Creationists utilize the greatest of presuppotions and offer absolutely no evidence: that god exists and created life.  I do believe that any hypothesis of abiogenesis is by far less extraordinary than the wholly unsupported belief that god exists and created life.  Spare us your ignorance and dishonesty.

Please stop confusing evolution with creationist evolution.  Creationist evolution cannot stand up against anything, just as anything creationist cannot stand up against anything.

  I think arguing with theist Lee Strobel and his gang is important to destroying dogmatic religious "creator concepts". Bring it on theists ..... let's get this bull shit over with ..... 

I have pre-written answers (which I wrote) to most of those questions since this is my area of expertise:

The process of formation of organic autocatalysis is time consuming. It begins with Piezoelectric systems on crystalline 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 which lead directly or indirectly to replication of more molecules like themselves. Catalysts with this self promoting property can use raw materials to reproduce themselves and therefore divert the same materials from the production of their substances. In modern cells the most versatile catalysts are polypeptides. However, they cannot propagate 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 similarity to polypeptides in their ability to form an active site for homogenous catalysis. It is important to note that ribozymal catalysis still exists in the most primite and ancient mechanisms common to all cellular life. Particular processes worthy of note are protein biosynthesis, snoRNA and snRNA manufacture, SSI (Self-splicing intron/exon junctions) and snRNP splicing (small nuclear ribonucleoprotein complexing), miRNA regulation of translation and RNAi mediated destruction of viral mRNA:

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 biological 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 usually have a number of highly similar correct confirmations which they can shift between on the basis of regulatory signals. This is the basis for modern biological life since it is what allows the computation of external signals. The important consideration here is that protein folding is determined by sequence, but of the vast number of possible confirmations, only a small number will actually have a particular biological function (such as possessing an active site). 

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.

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. The general properties we need concern ourselves with are as follows:

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 surface 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 undergo 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

Selection 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.

It is important to realize that vescicles which are the basis of cell membranes as well as intracellular organelle membranes, are the origin of sealed compartments holding and containing biological molecules in which segregation and selection can occur. These vesicles will spontaneously assemble because of basic thermodynamic properties. A phospholipid molecule is ampipathic because it contains a hydrophilic head group (usually choline, glycerol and phosphate) and a hydrophobic tail (fatty acyl). As such they will usually spontaneously array into a bilayer or a micelle. The former is the only geometric outcome for a bilayer such that all the hydrophobic parts are kept free from water and the hydrophilic parts are kept in contact with water. This will produce a sealed vesicle where none of the hydrophobic tails contact the water:

What is the conclusion we should draw here? Whenever we examine the requisites for certain systems in biological life, it is important to remember that because of the process of coevolution, their antecedants did not start out that way. The modern mitochondria and eukaryota both need each other because they have been in symbiosis for so long that mtDNA has ingrained itself in the nuclear genome hence making it an irreversible addition to the Eukaryota. Without it, the organelle dies. Without the organelle, the cell dies. But their antecedants, as they had not evolved "into" each other yet, did not require this relationship. This is true of many complex interlocking systems in biology, and the concept of mutual interlocking dependancy is an enormous topic on evolutionary biology and biochemistry. The mutual dependancy being discussed here is RNA with Protein and DNA and vice-versa. However, as we have seen, in the RNA world, where catalysis was run by RNA, the mutual dependancy between RNA and polypeptides did not exist. Polypeptides developed under natural selection because Ribozymes that can hold amino acids, especially those that can catalyze the peptidyl transferase reaction, have a great advantage. Eventually, polypeptides superseded ribozymes as catalysts because they are more efficient at catalysis (in biochemical terms this is due to the variance of side chains on amino acids, since biological amino acids are more diverse than biological bases). This allows for particular functions such as acid-base catalysis which are not available to ribozymes. As a result, because there was less selection pressure for ribozymal autocatalysis since that was handled by polypeptides, the ribozymes eventually became dependandt on polypeptides. A similar "outphasing" occured with the origin of DNA.  There was a reason for this:

-DNA is obviously a more advantegous molecule to use. It is more stable, but more importantly, it can form larger double-strands. The double-strand is enormously important in biology. It allows the information in DNA to be kept in two templates, the one holding the base pairs in question, and the one that can retrieve them via templated polymerization.

If you've just joined us, the smackdown was over quicker than Fedor vs. Tim Silvia.