Can't speak for RSS but here are kinda some answers. 

1&2) The RSS defines the terms differently and ignore webster's dictionary. (Probably because Webster was a Christain)

3) Evolution doesn't prove or disprove God.

4) They have been told that several times as posted several times. I don't think they try to find out what passages really mean to those who practice the religion they claim is false.

5)Yep they didn't...Creation requires a creator. The way I see it the only reasonable way to go about that is to argue that "creation" isn't really a "creation" since it always existed.

6)Ok, so what is that reason?

7)I'm going to assume you mean a god and not any specific god. 

I just post here. Other than sharing many of the views these guys have, I'm not a core member of the squad, so you might not appreciate my input as much.

http://www.rationalresponders.com/am_i_agnostic_or_atheist

OK, continue.

I don't like the whole Zeus analogy as atheism normal means that one holds no god belief, not that one simply holds a different god belief than the one being discussed. It is accurate in that if only one 'god' story existed, and that was of Zeus, then your not believing in Zeus would make you an atheist. So, as far as in relation to Zeus, only, your being an atheist is true, but this is unnnecessarilly confusing and stretching the limits of reasonable discourse which I think atheists should avoid so as not to be confused with theists. 

That depends. I could possibly be agnostic on some god concepts. I would first need to hear of a god concept that was coherent. Could you tell me what exactly your god is supposed to be? Just simple things like what he exists as, where he exists, that sort of stuff.

First off, I don't choose what to believe and what not to believe. I think this is one of the oddest things that I hear theists say. I believe something when I have good reason to believe it. It is a natural occurence of receiving information that provides an answer to some unknown and does so in a way that is coherent and that I can understand. I can not understand why theists seem to think one canchoose to believe something. Go to the top of the nearest building and choose to believe you can fly. Now, are you going to jump?

Secondly, There are many theists that understand the evolutionary process and accept the obvious fact that it is the only reasonable explanation for a means by which we have arrived at the diversity of life we see on the planet today. The vast majority of theists fall into this category (though by a sample of the ones which frequent this site you would never know that). 

Thirdly, what it would take for me to believe in god is for someone to define god as a possibly existing entity and then to show me solid evidence of its existence. Its really as simple as that.

This is unimportant. The blasephmy challenge worked as the RRS was able to get their voices onto the national stage. No matter whether the challenge was accurate by any of the wildly different biblical interpretations held by different religious sects is a point I doubt the founders care anything about.

I agree that, in my opinion, the whole universe factory thing is not a very strong point against the inference of creator by creation, but your blackhawk analogy sucks for reasons that should be obvious. You can go to the factory whether it is allowed or not. It is physically possible.

The fact is that trying to infer a creator by the presence of a creation is circular, because one is referring to a creation from the outset, and it misses a fundamental difference between what it is to create as a human does and what it would be to create as a 'god' would have to do. A human simply rearranges existing physical matter to form a new 'shape'. A god, who is not bound by nature, would need to create the matter, the laws that govern it, where it exists, every parameter of existence.

In order to infer a god from this type of creation we would need to have something that was not this type of creation to contrast with. It simply makes no sense to try and equate a painting painter relationship and what would be a creator/everything relationship.

There is so much incorrect in this comment that you should really open a new thread just to discuss this one point.

Evolution is not random in the sense you use here (unguided).

Even if I walk a mile in a circle I have still walked a mile on step at a time. Evolution has no destination so it makes no difference in what direction it wlaks. It will go where the environment pushes it. 

 There are different meanings for the word faith. Religious faith is belief without, or in spite of contrary, evidence.

Intelligent design is simply god of the gaps. It makes no coherent claims. It simply says that evolution has areas that aren't completely filled in therefor creator. It is not supported by any evidence whatsoever.

No science points to the existence of a god. That is simply untrue to claim that science can lead to such a thing. When you say you have to use faith what you mean is ou have to at some point abandon the science and just suddenly insert god. If you are going to do this you might as well do  it from the start and avoid the science all together.

It is faith and faith alone that leads to a belief in a god. As can be easily shown, faith is not a reliable means to arrive at truth. In fact, the use of faith alone makes it impossible to differentiate between fact and fiction. 

Sorry. That's a stolen concept fallacy. Todangst and I blasted that out of the water

here

http://www.rationalresponders.com/forum/sapient/kill_em_with_kindness/7720

here

http://www.rationalresponders.com/forum/sapient/philosophy_and_psychology_with_chaoslord_and_todangst/6279

and here

http://www.rationalresponders.com/supernatural_and_immaterial_are_broken_concepts

Excellent! I am a molecular biologist, so evolution is my field. I have always argued that the micro/macro confusion is an argumentum ad ignoratium. Any scientist I work with will tell you it is a continuum fallacy.

Literally nothing I see would make any sense except in the context of evolution. We do not have faith that it "follows a plan". Using molecular genetics, we can show it. And this is a piece of an essay I wrote which did show just that:

As a molecular biologist, I can confimr that the evidence from molecular biology supports evolution and nothing else.

And before we begin, I shall introduce the terminology and the tests from which we gather our information:

Vocabulary:

Duplicative mutation: A genetic mutation where a gene string is accidentally duplicated during mitosis failure. This provides the mutation carrier with superfluous genetic baggage, basically an extra copy of a gene. This copy is free to mutate based solely on random frequency probability.

Homology: A family relationship between two or more genes (or sets of genes) as the result of a duplicative mutation. For instance, the human genome contains seven haemoglobin proteins, all of which are in a gene family called the haemoglobin family. This is part of a larger family called the globin family, under which all oxygen binding proteins are classed like myoglobins.

Paralogy: A relationship between two closely related genes in a single genome as the result of a mutation. These two genes (or sets) are said to be paralogous of each other in the same carrier species. For instance, the seven human haemoglobins are said to be paralogous of each other.

Orthology: A relationship between genes or sets of genes in different species. When two species diverge, the new genetic arm of the phylogenic tree retains much of the genetic code of it's predecessor. Any related batches of genes in two species are said to be orthologous of each other. The seven human haemoglobins are orthologous to the seven chimp ones.

Recombinative mutation: Chunks of genetic information are shuffled around. Bear this in mind for what we talk about below.

Vocabulary regarding protein organization:

Polypeptide chain: A tertiary protein is one consisting of only one polypeptide chain (one very long molecule made of many amino acid subunits all covalently bonded, usually 50-2000 amino acids long)

Tertiary domain: A recognizable subunit of a polypeptide chain. Domains are usually consistent of many alpha helices and beta sheets twisted around each other. A tertiary domain is essentially a clearly distinct building block of a polypeptide chain. When I say distinct, I mean obvious. For example, the protein nucleosaminade is constructed of four distinct regions symmetrically aligned in a tetramer (four identical domains). Perhaps telling you how obvious the domain distinct is. Perhaps a picture would help:

Domains can be aligned in stack-up formation (N-terminus to C and so on) to create long strandlike proteins as seen in fibronectin shown here

Hopefully these pictures will make you understand what I mean when I say that a domain is a “distinct region”. The technical definition of a domain is “a region of protein which folds up independent of the rest of the chain”. Thus we can see that a tertiary domain is a clear, distinct region of protein which makes up the large building subunits of polypeptide chains, a fact which will be important later.

Modular domain: A domain which pops up all over the proteome of many different proteins and many different domains in many different species, essentially a building block ubiquitous throughout evolution.

*critical note about tertiary and modular domains. When we say the domain is in many places, keep in mind that domains are not identical protein strings to the letter. Two protein strings can be 50% different in amino acid string and still be the same domain (as a domain is defined by its function). This is why the human haemoglobin alpha is a different protein string to say, the chimp haemoglobin alpha, but they are still the same domain. This is crucial for a test discussed soon called the molecular clock.

Quaternary domain: Many proteins are consistent of many polypeptide chains (tertiary proteins) noncovalently bonded together. If this is the case then it is called a quaternary protein complex, and the subunits of this large complex (called quaternary domains) are the tertiary proteins (the subunits of which of course, are tertiary domains)

Primary structure: Unfolded protein. A straight string of amino acids.

Secondary structure: The protein transforms into it’s secondary structure by folding at the kinks between the tertiary subunits.

Tertiary structure: The folding becomes further intricate during progression to tertiary structure when the folds between individual atoms and peptide bonds take shape.

Quaternary structure: Only applicable in a quaternary protein. Same as tertiary structure, except of course, with a protein complex holding multiple noncovalent bonded chains

Signature sequence: These are crucial for identifying two protein strings which are the same domain but which have very different amino acid sequences (note, the key factor in determining whether two strings are indeed the same domain is 3D geometry, aka the fold or conformation, but this can often take years to construct). For instance, two protein strings can still be considered the same domain even if, say, the match between them is 30% amino acids identical. This is because many of the mutations do not alter the geometry of the string (these neutral mutations are also called “background noise”).

So to help us tell where two protein strings are indeed the same domain, we need to find the signature sequences, conserved amino acid strings critical for the functioning of the protein (often these strings are so sensitive that they do not change whatsoever, even over two billion years). For example:

This is a comparison of the SH2 domain of the Src kinase protein (a domain which is more or less ubiquitous) between the human and the fruit fly Drosophila. Note that these are actually identical domains despite their clear differences in sequence. The results:

Homo Sapiens

WYFGKKITRRESERLLLNAERPRGTFLVRESETTKGAYCLSVSDFDNAKGL

Drosophila melanogaster:

WFFENVLREADKLLLAEENPEGTFLVRPSEHNNGYSLSVKDWEDGRKYGY

Protein Domain Signature Homologies in both: WYFGKITRRESERLL
GTFLVRESE

Side chain grouping matches:
W+F+R+E+++LLLENPRGTFLVRSEYLSVD+++_G

The reason we can ID these two strings as the same protein is due to the signature sequences which are conserved only in the SH2 domain.

Tests used (need to know about these):

Sequencing: Very simple. Run a gene sequence through a sequencer and determine the string of nucleotides that make up the gene.

Proteomic Sequencing: A protein’s amino acid string can be immediately determined through gene sequencing. This is really boring, so we just run it through a proteomic sequencer and the codons are matched with the correct amino acid.

Microarray: Crucial test to measure how mutations affect gene expression. A Microarray is a tiny square on which we can array the genome or a section of genome of any organism we care to test. Each gene is arrayed on it’s own tiny glass square subunit within the array. A mixture of nucleotides is then passed over the array, which bond to the ones aligned on the array. These nucleotides have fluorescent chemical tags attached to them, and thusly, they light up. The rate of gene expression can be monitored based on the fluorescence of the nucleotides to which a particular gene is tagged. In this way, thousands of genes can be monitored simultaneously, the effect of adding or removing any gene can be monitored, different conditions on the gene set can be monitored, and the entire GRNP (Gene Regulatory Node Pathway) can be completely constructed, and the result of evolutionary changes on the GRNP can be monitored to a degree of exact detail. The evolutionary relationship between organisms becomes immediately clear as we can observe the effect of mutations on the organism as a whole (making this test much more accurate than knockout selective mutation test), albeit much more difficult to read).

Genetic engineering knockout: When we want to find out what a certain gene does, we can do this:

a) Knockout test. Engineer an organism with one and only one specific gene removed by a process called recombinative deleting. Observe effect on the phenotype to conclude what this gene does. By breeding many mutant versions of an organism with one particular gene, any gene that we wish to test, knocked out of it, we can discern what the missing gene does.

b) Engineered insertion: To help discern what the gene knocked out of one organism does, we can insert it into another and find out exactly how it works. A memorable example, I recall, is the removal of pax6 gene from a mouse, which is a master gene that commands a set of genetic instructions to make an eye. We only discovered this when we inserted it into a fly and astonishingly discovered a perfectly formed fly eye growing on the fly’s leg.

What this means is that we inserted pax6 next to the gene expression regulators responsible for coordinating development of the leg. This is the other useful piece of data obtained from an engineered insertion test. For instance, I trust you have all heard of the famous “glowing green monkey”, where researchers inserted a fluorescent green protein gene into a monkey genome and discovered that it was now glowing green, thus indicating that the gene had been inserted next to the one responsible for skin pigmentation.

Homologous match comparison:

Molecular Clock: A crucial test. The necessity of a protein domain for survival will affect the rate of mutation and change of that gene. Critical genes that are absolutely necessary for survival do not change very easily and are thusly called conserved genes. The rate at which mutations in domains occurs is measured by observing the rate of change of a domains by comparing the amino acid divergence in different species. For instance, haemoglobin changes at a rate of 6% every 100 million years. Due to the fact that the homologous domains are identical, this divergence would only exist if the species in question are descendants of a common ancestor. If ID, creationism, sponataneous appearance of complex life by God waving his magic finger, then these divergences should not eixst. An example of how this can be used to rip Behe's Irreducibile complexity a new asshole shown here:

[Digression]

Blood Clotting Claimed Irreducible By Behe: False.

It might be best to step back and first determine how the metabolic pathways to blood clotting work. It is a complex process indeed. At the heart of blood clotting is a substance in your blood called fibrin. Fibrin is a sticky molecule soluble in water which has the natural tendancy to form a clot. The mesh which it forms stops haemopoitic cells from escaping. Fibrin forms about 3% of the blood. However, it obviously cannot exist normally as fibrin, or it would simply block up the vessels, hence when in the blood, fibrin exists as part of a larger molecule called fibrinogen. Fibrinogen is a complex, amino-acid rich macromolecular complex, which at it’s center contains the fibrin molecule. Surrounding it are many amino acid side chains, which have a negative charge (at the pH of blood, amines and side chains always have a charge). This causes them to repel each other, thus they exist as independent molecules in the blood, without clotting.

This changes when a wound initiates the metabolic pathways known as the blood clotting cascade. A protease enzyme has to catalyze the removal of the side chains, thus exposing the fibrin. This enzyme is called thrombin. But obviously thrombin has to exist as an inactive enzyme otherwise it would simply initiate the reaction whenever. It exists as protothrombin, and has to be activated to become the catalysis enzyme. A tiny additional chain on the protothrombin fold renders it inactive. This has to be removed by another clotting serine factor, Factor X. This too, as a serine, must be activated in the same manner. And so, the blood clotting cascade has four steps more until we reach the beginning. Factor X is activated by Factor XI, which is activated by Factor IX, which is activated by Factor XII, Which is activated by the Kininogen-Kallikrein system of co-activation, which is triggered by external stimuli. This is where the process starts.

The activation of the serine cofactors is a similar process. For XI to become XIa (Activated Factor 11), a side chain must be cut removing the ionic charge, which allows it to cascade into the next step. It seems unnecessary complex, almost like an infinite regress of serine-cofactor activation steps. But it makes sense, because for every step that is taken, an exponential signal transduction increase occurs. If it was just a very short pathway, say a single cofactor triggered by external stimuli to start the thrombin conversion, then the clot would be far too small, and would take hours to form. Thus, the six-step amplification works best.

In others words, blood coagulation is a complex and beautiful process. But does that mean it is irreducible and could not have evolved? One of the key establishment requisites of Behe’s irreducible complexity is that a mechanism could not evolve by gradual evolutionary steps. But I beg to differ. The implication that he made clear in Darwin’s Black Box was that the designer would have to put all the parts together at once, otherwise it would not really be irreducible or a challenge to evolution. But unfortunately, genetic analysis of the cofactor cascade tells us otherwise. Thus we return to my previous comment about the homologous nature of the cascade.

So how could this function have evolved, and how can we trace it? Typically, when we start looking at a biomolecular function, we have a base from which to start. We never start from scratch. Only primordial chemists deal in that. This base function might be exteremly primitive, almost bound by basic laws of chemistry. For instance, when we look at the eye in all it’s glory, we see that all nine divergences that have taken their course come from a highly simplified patch of light-sensitive cells. Likewise, when we observe the fantastic complexity and variation of the Eukaroytic cell membranes, with all their complex ion channels and protein transport functions, we see that in common they are all bound a very simple chemical law known as ampipathism, the tendency of hydrophilic/phobic molecules to align in a bilayer. The membrane’s composition resembles a flagellum in molecular shape, with a long twin hydrophobic fatty acid tail and a stubby hydrophilic choline-phosphate-glycerol head.

What similar base function might we find in blood clotting? Studying the evolution of metabolic pathways is different to studying other molecular functions. The job is made significantly easier by the Autocatalytic nature of the pathways as described in my previous link. Much of the steps in coagulation work like that too. The serine proteases that form the original primitive life forms (as being detected on the long arms of chromosomes 1 and 5) were not originally designed for blood clotting, but they were there. In his book Finding Darwin’s God, Ken Miller suggests that cAMP (that’s cyclic adenosine monophosphate) would be a significant launch pad to build up the homologous set of serine cofactors that make the cascade. He’s correct here. cAMP is cellular transduction molecule that acts somewhat like a neurotransmitter, smoothing muscular tissue around vascular epithelial tissue, and inhibiting blood flow. A damaged cell, spilling all of it’s contents, would pour the cAMP out along with it. Evolution could work with that. Cellular mechanisms already possess, for unrelated reasons, white blood cells, whose adhesive nature allowed them to clump the wound

From the rudimentary system, where several factors are in place and a simple automatic system of clumping exists, a highly complex multilayered system of cascading can accumulate by two well-known evolutionary processes. One is called duplicate error from which the various homologies are formed, and the other is exon shuffling as done by spliceosomes. From the receptors point of view, we could see how the repeated duplication and slight mutation of the serine cofactors would work, for reasons not the least of which that we can track it’s paralogies. For the most part, coagulation is autocatalytic, it just needs the materials to initiate. If the progenitors are already in place, then well…all that is needed is time for the duplicative errors to occur. If we have primordial serine cofactors (we do), the rudimentary single layer is pre-existing (ie, primordial enzyme A is cleaved to make Aa, which actives the thrombin). This would initiate itself. And we can imagine the naturally selective benefits that would come from the repeated duplication of the serine, as this would make clotting more efficient.

It is in no way Irreducible. You can be sure that we would notice it in the genome if it was (as it turns out, they are strewn all over the genomes across the strata, XII is in Chromosome 5, VII is on 13, Factor VIII is on the sex chromosome etc)

Blood clotting is an example of a zymogen cascade pathway, and any metabolism generated by zymogenes can be generated by duplication and homology. This particular cascade is composed almost exclusively of serine proteases. Surely, serine protease zymogenous cascade is the worst example of "intelligent design", not because it is poor, but because the homology in this particular protein family is more obvious than any other family, kinase domains, homeodomains, Cro repressor dimers, you name it, this is the textbook example of a protein family in an obvious homology. This particular domain is so close in amino acid structure of the proteases that some of the serines are nearly indistinguishable without close scrutiny of the difference in signature sequences. (Sig sequences are tiny stretches of amino acids 10-30 amino acids long used to ID domain stretches that have diverged alot). Of course, the serines haven't exactly diverged alot. In fact, they are one of the most conserved families in the whole proteome. They are the nemesis of intelligent design, an obvious example of duplication and homology.

[End of digression]

when I read your first thought was...that's it? Thats your response to 16,000 homology catalogues, Endogenous Retroviral insertions, and Mitochondrial DNA transfers? Sir, this relationship is extremely obvious, and it is not one, it is tens of thousands of homologies which clearly diverge as separation widens and close as it narrows, as indicated by time length separation. This test will come up on any protein domain I pick. It clearly indicates that life began a primordial genome, and as the genome duplicated, parts diverged and it expanded thusly. Genetic duplication error and polyploids are set in stone fact, and no geneticist would say otherwise. I can even watch gene duplication myself, using a microarray, although I hardly think it is worth the trouble. Using decoders, microarrays, and homology databases, geneticists have now catalogued evolutionary relationships between vast swaths of life, and the effects of these changes.

The existence of paralogies of genetics across the families in the proteome, even diverged as far as separations between the three domains themselves, and the fact that amino acid tracking reveals this to narrow as the organisms in question become more closely related (a fact which is reinforced by advanced radiometry) can only be possible via repeated duplication and divergence of genes, thusly bearing gene families which in turn branched out depending on the survival requisites of the organism and location, the lack of originality in the proteome, especially the vertebrae proteome, which can be explained entirely in terms of domain shuffling and protein string recombination can only be explained by origin from a common descent, a primordial genome who bore only the survival requisites for the simplest of life. What this genome may have looked like is mysterious, but insight into a small bacteria called Mycoplasm genitalium can give us the answer, when computationally recombined with cross-references of genes exclusive to archae, eubacteria and eukaryotes (Excluding ESP proteins of course) we arrive at an answer of roughly 200 genes dedicated to basic metabolic and structural proteins, rRNAs and mitosis control gates. Ad it is from this humble beginning that life evolved. A fact which is correlated 100% by genomic/proteomic analysis and ortholog/paralog/xenolog tracking.

Quite simply, molecular genetics tracking, ERVs and mtDNA, in addition to computational searches for paralogies across the spectrum, leads us inevitably to the conclusion that the whole swath of life arose from a single, simple, primodial cell.

It is about duplicative mutations, followed by recombinative mutations, or shuffling mutations. For instance, A protein is not subdivided merely by it’s amino acid. It is grouped into large subunits called polypeptides, regional stretches of protein subunit roughly 100 amino acids long. In this way we can see that massive proteins (>1000 amino acids) are not only defined by their individual, but ultimately, the order of different units created by smaller strings of amino acids within the complex. The protein transforms into it’s secondary structure by folding at the kinks between the subunits. The shape, therefore, of a protein is directly determined by it’s chemical sequence. The folding becomes further intricate during progression to tertiary structure when the folds between individual units take shape. Finally, the protein reaches it’s quaternary structure or it’s native state, with the intricate system of folds.

there is almost nothing original in the vertebrae genome. It is the result of multiple whole-global duplications throughout evolution. Even in humans, the proteome contains only 7% vertebrae-specific proteins. The only place we really seem to have any originality is in domain shuffling (Im pretty sure that the human tyrpsin can bind to at least 18 domains, while in drosophilia it's only 5). As I said about protein structure, much of the innovation merely comes from rearrangement of subunits, which is beneficial in terms of the shuffling mutation quite often.

These are divergences found in an identical protein domain confirmed exactly by molecular clock tracking against the known divergence rate of the domain and the orthologous seperation of these two species. If (as you claim) these species were created within days of each other, or had no common ancestor, this divergence would not exist. This is the same domain for each animal, which I took the liberty of sequencing myself. Because I can.

Orthologous Divergence of the haemoglobin chain of various vertebrae correlated by molecular tracking:

Percentage divergence in amino acids between conserved domain of haemoglobin

Human/Lamprey (divergence: 550 million years ago) 35%

Human /Shark (Divergence: 520 million years) 51%

Human/tuna fish (450 million years) 55%

Human/frog (350 million years) 56%

Human/chicken (320 million years) 70%

Human/lizard (270 million years) 77%

Bird/Crocodile (220 million years) 76%

Human/Kangaroo (170 million years) 81%

Human/Sloth/Mouse/Elephant/Rabbit/Pig/Sheep/Whale/Cat/Dog/rat

All between 150 and 50 million years, all 80-85% related in this domain

Human/orangutang (10 million years) 98%

and finally...human/chimp (7 million years) 100%

All this in turn is corroborated by ERV tracking and the vertical transfers in Mitochondrial DNA

How do you explain and account for mitochondrial DNA horizontal transfer migration without common descent?

Endogenous retroviral insertion occurs when a retrovirus reverse transcribes it's own RNA into a host's DNA by means of polymerase RNA-DNA conversion, 3' and 5' enzymatic degradation and intergrase fusion. Retroviruses are the only organisms that can do this. That is what makes HIV so deadly. The ERV insertions are rare and very random. Although complementation ensures they can only bind to specific points on the host's genome, the amount of possible insertions that the ERV could transcribe, not to mention the fact that this has to be to the power of seven to account for all seven retroviruses, and of course, the fact that it is a very rare occurrence and the fact that even a single transcribed piece has numerous choices of insertion due to multiple duplication errors that exist in Eukaryotic genomes means the odds of finding even just one insertion (let alone 8% of the genome for humans alone) on one identical position in the chromosomal karyotype would be astronomical. And then, that number has to be raised to the power of seven, then multiplied by several thousand to account for all the possible transcribable genes, which has to multiplied by 10 again to account for the duplicative errors, and that doesn't even factor in how rare the insertions are.

The only way it is possible that we can find large strings of ERV's on identical interspersals throughout the genome of species throughout every eon is because of common descent.

It is empirically demonstratable that mitochondria are the result of billion year old symbiosis between ancient oxyphobic bacteria and proto-eukaryotes. This is the reason they have their own little genome. The mtDNA genome in humans is only 16,000 base pairs. Prokaryotes have a remarkable ability to exchange genetic material by a different process which is critical to bacterial evolution. This is called horizontal transfer. Vertical transfer is an ability eukaryotes do not have because their DNA is enclosed in an intercellular packaged membrane (hence the name eukaroyote). Vertical transfer occurs when bacteria simply exchange genes by passing them through the cell membrane to each other. This can occur either by direct junction fusing or literally uptaking of the new material. Prokaryotes can take any peice of nucleic acid string and simply incorporate it immediately because their DNA is not kept in an intercellular membrane.

So, mitochondria, as ancient prokaryotes, of course keep their DNA is a loop strand like every other bacteria. Indeed, mtDNA also undergoes transfer. This is very rare and obviously useless. In this case, it is intracellular thus the transfer is into the nucleus of the host cell, where the master genome is stored. Such is termed mtDNA migration.

I think mtDNA migration is even better than ERV because the probability is even lower by several orders of magnitude that we could find mtDNA on identical positions of the genotypes of multipe species throughout multiple eons without common descent whereby the offspring would inherit the mtDNA. The best part is that obviously, as time passes, the amount of mtDNA in the master genomes should accumulate, since more horizontal transfer is taking place over longer periods of time, and this should still turn up on the same positions in the genotype. What a surprise! It does.

Without common descent, the probability of individual horizontal transfers accounting for entire species inheriting identical mtDNA which remains so throughout geological eons and continues to accumulate and end up in the same places is so low the number is unfathomable.

And now to recall the discussion about protein domains is the clincher, namely the fact that there are no original protein domains in the whole proteomic spectrum makes it very obvious that they evolved by duplication and blind guidance. The entire vertebrae genome was created by shuffling mutations which rearranged domains into novel combinations. The human genome contains only 7% vertebrae specific protein, and differs in terms of size from a fruit fly by only a factor of 1.2, yet the fact that much more novel and complex arrangements of the same protein domains means the construction of a much more complex organism. There is nothing original about the vast diverstiy of life. It all came from very simple, repeating, diverging, primordial, protein domains.

HOWEVER, if your argument is one from thermodynamics, that the "order" necessary to drive evolution is impossible on a macro scale, I have refuted that here:

This is a lengthy explanation of the entropy laws, and how they relate to life. I understand that many people have been using the Second Law of Thermodynamics as if it were a challenge to evolution. You can imagine how amusing I find this.

At any rate, we need to understand some basic concepts first. These are The laws of thermodynamics, entropy, enthalpy and free energy.

Let us imagine a box, a system closed off from the universe, with a cell inside it. The cell in a box is a closed system with a fixed amount of free energy. This system will have a total amount of Energy denoted E. Let us suppose the reaction A to B occurs in the box and releases a great deal of chemical bond energy as heat. This energy will increase the rate of molecular motions (transitional, vibrational and rotational) in the system. In other words it will raise the temperature.

However, the energy for these motions will soon transfer out of the system as the molecular motions heat up the wall of the box and then the outside world, which is denoted sea. Eventually, the cell in a box system returns to it’s initial temperature, and all the chemical bond energy released has been transferred to the surroundings. According to the first law of thermodynamics, the change in energy in the box (denoted ∆Ebox or just ∆E) must be equal and opposite to the amount of heat energy transferred out, denoted as h. Therefore ∆E=-h.

E in the box can also change during a reaction due to work done in the outside world. Suppose there is a small volume increase in the box (∆V) which must decrease the energy in the box (∆E) by the same amount. In most reactions, chemical bond energy is converted to work and heat. Enthalpy(H) is a composite function of work and heat, (H=E+PV). Technically it is the Enthalpy change (∆H) is equal to the heat transferred to the outside world during a reaction.

Reactions with a -∆H are exothermic, and ones with +∆H are endothermic. Therefore –h=∆H. The volume change in reactions is so negligible that this is a good approximation.

-h≈∆H≈∆E

The Second Law of Thermodynamics allows us to predict the course of a reaction.

Let us consider 1000 coins in a box, all facing heads. It is a closed system, which, by definition, does not exchange energy input or output with the rest of the universe. States of high order have low probability. For instance, if we imagine a box with 1000 coins lying heads up, and we shake it twice, it is vastly more probable that we will end up with a chaotic arrangement of coins than the arrangement that we had previously. Thus, the law can be restated closed systems tend to progress from states of low probability to high probability. This movement towards high probability in a system where the energy is E, is progressive. In order for the entropy (the progression towards high probability) to be corrected, there must be periodic bursts of energy input, which would break the closed nature of the system. In this case, it would require someone to open the box and rearrange the coins.

Therefore, for a living organism to maintain order and increase order, there must be a useful energy input. For that to happen, there will be a useless energy output. Thus increasing the order in the cell will increase the disorder of the entire universe. In this way, we can imagine life forms and other complexities as islands of order in a universe progressing towards disorder. For this to happen, there must be a colossal influx of free energy all the time. This is one the requisites for life. As luck would have it, we have such a system: The sun.

We need a quantitative unit to measure this, and to measure the degree of disorder or probability for a given state (recall the coins in a box analogy). This function is entropy (denoted S) The change in entropy that occurs when the reaction A to B converts one mole A to one mole B is

∆S= R log PB/PA

PA and PB are probabilities of states A and B. R is the gas constant (2 cal/deg^-1/mole-¹⁾ ∆S is measured in entropy units (eu).

In an example with a box containing one thousand coins all facing heads, the initials state (all coins facing heads) probability is 1. The state probability after the box is shaken vigorously is about 10^298. Therefore, the entropy change when the box is shaken is R log 10^298 is about 1370eu per mole of each container (6.02x10^23 containers). ∆S is positive in this example. It is reactions with a large positive ∆S which are favorable and occur spontaneously. We say these reactions increase the entropy in the universe.

Heat energy causes random molecular commotion, the transfer of heat from the cell in a box to the outside increases the number of arrangements the molecules could have, therefore increasing the entropy (analogous to the 1000 coins a box).The release of X amount of heat energy has a greater disordering effect at low temp. than at high temp. therefore the value of ∆S for the surroundings of the cell in a box denoted ∆Ssea is equal to the amount of heat transferred divided by absolute temperature or

∆Ssea =h/T

We must now look at a critical concept: Gibbs Free Energy (G)

When observing enclosed bio-systems, we need to know whether or not a given reaction can occur spontaneously. The question regarding this is whether the ∆S for the universe is positive or negative for the reaction, as already discussed.

In the cell in a box system there are two separate components to the entropy change in the universe. The ∆S for the inside of the box and the ∆S for the surrounding sea. These must be added together.

For example, it is possible for an endothermic reaction to absorb heat therefore decreasing the entropy of the universe (-∆Ssea) but at the same time cause such a large disorder in the box (+∆Sbox) that the total ∆S is greater than zero. Note that ∆Suniverse=∆Ssea+∆Sbox. 13

For every reaction, ∆Suniverse must be >0. We have just encountered another way to restate the Second Law of Thermodynamics

In this case, the reaction can spontaneously occur even though the sea gives heat to the box during the reaction. An example of this is a beaker of water (the box) in which sodium chloride is dissolving. This is spontaneous even though the temp of the water drops as it is occurring.

The most useful composite function is Gibbs Free Energy (G) which allows one to deduce ∆S in the universe due to the reaction in the box. The formula is: G=H-TS.

For a box of volume V, H is the Enthalpy (E+PV), T is the absolute temperature and S is the entropy. All of these apply to the inside of the box only. The change in free energy in the box during a reaction is given as the ∆G of the products minus the ∆G of the reactants. It is a direct measure of the disorder created in the universe when a reaction occurs. At a constant temp, ∆G= ∆H+T∆S. ∆H is the same as –h, the heat absorbed from the sea. Therefore

-∆G= -∆H +T∆S or -∆G=h+T∆S Therefore -∆G/T=h/t+∆S

h/T still equals ∆Ssea but the ∆S in the above equation is for the box. Therefore.

-∆G= ∆Ssea +∆Sbox =∆Suniverse

A reaction will spontaneously proceed in the direction where ∆G<0, because it means that the ∆S will be >0. They are inverse functions of each other. For a complex set of coupled reactions involving many molecules, one can calculate ∆G by adding the ∆G of all the different types of molecules involved before the reaction, and comparing that to the ∆G of all the molecules produced by the end of the reaction. For example, comparing the ∆G of the passage of a single proton through the inner mitochondrial membrane across the electrochemical proton gradient to the ∆G for ATP hydrolysis, we can conclude that ATP synthase requires the passage of more than one proton for each molecule of ATP synthesized.

Let’s review:

2^nd Law: Basically an expression dictating that the whole universe progresses towards disorder, and any reaction must contribute to that disorder. Disorder is energetically favorable and probability-wise favorable.

Heat Energy: The energy in the random motion and hubbub of molecular jostling and movement. This is basically a measure of temperature, but all reactions give off heat energy, which is irretrievable (another way to restate the second law). Heat energy is denoted h.

Enthalpy: A composite function of heat and work, but since ∆V is always next to nothing, we can regard it as the inverse of heat. Enthalpy is a measure of heat energy lost or ∆H=-h

Gibbs Free Energ

The total ∆G for a reaction measures how far from equilibrium the reaction is. The large negative ∆G for ATP hydrolysis means that the cell keeps it very far from equilibrium. Equilibrium is reached when the forward and backward rates of each reaction are precisely equal and the ∆G is zero. For ATP hydrolysis, this occurs when the vast majority of ATP has been hydrolyzed (because ATP hydrolysis is much more favorable than ATP synthesis), like in a dead cell.

What we can conclude is that every reaction must have a negative ∆G to occur.

But how? What about anabolism, free energy creation, energy stores? Many reactions in cells are energetically unfavorable. Most polymerizations are, oxaloacete generation, ADP condensation etc as well as supramolecular operation like ribosomal assembly, mitosis, mRNA synthesis etc

These seemingly impossible reactions make use of a key concept covered earlier. Let us return to our cell in the sea scenario. Except the cell is not in the box, it is in the sea, receiving free energy from the sun.

Recall: ∆Ssea +∆Sbox =∆Suniverse

Except now it becomes: ∆Ssea +∆Scell =∆Suniverse

For an unfavorable reaction to occur, it must be coupled to a favorable reaction of higher magnitude. IN this way, even the order in the cell increases, the disorder in the sea increases by a greater amount therefore the ∆S is still positive and the ∆G is still negative, leaving the laws of thermodynamics intact.

There are a vast number of examples to choose from. Let us consider a typical unfavorable condensation reaction

A-H+ B-OH = A-B + H20

This reaction will not occur spontaneously. It cannot. It will create free energy of its own accord. That’s impossible. Fortunately there is a mechanism to bypass this.

A favorable reaction is coupled to it. ATP Hydrolysis is a favorable and readily occurring reaction where ATP splits one phosphanhydride to ADP, leaving a very reactive inorganic phosphate. This bond, because it is highly reactive, readily bonds with B-OH forming B-O-PO3.

This is called a high-energy intermediate. Because the bond is so high-energy, it will immediately react with B-H producing A-B + H2O + Pi + ADP

This concept exists in a huge number of reactions. Many reactions involve critical stepwise passing of high energy intermediate chains.

The cells must maintain order by maintaining a constant stream of biochemical catabolism and anabolism being driven by enzymes which lower the activation energy. Food is broken down from macromolecular giant biological polymers like polysaccharides, polypeptides, proteins and giant fatty acids by oxidation, electron carrying, and catalysis of favorable reactions into simple molecules like glucose, amino acids and glycerol. Some of this is in turn, catabolized to break the phosphate bonds which release heat energy to power the cell (and increase entropy in the universe). The rest of it is used to be anabolized again into giant structures in glycogen or lipid storage for later consumption or construction into cellular structures like ribosomes. All of these highly intricate metabolic pathways that do these things must be set in motion by thermodynamically favorable events.

For instance, imagine rocks falling off a cliff onto the ground. The kinetic energy is being converted into heat and sound. This is useless. But if we set up a turbine underneath the rock which powers a small hydraulic pump, we are obtaining useful work from free energy.

Seems like you can point to all sorts of "things" that require no "creator" all the time.  There's no reason to assume that if you run across a tree in the woods that a group of builders put it there.  You know in all known cases of natural tree growth, you need the same basic requirements.   A seed in the ground, water, sunlight, time, correct climate conditions, etc.   Someone could have planted the seed in the ground or the seed could have been placed there from the wind or other natural occurances.   Simply seeing a tree, actually doesn't give you definitive proof that someone planted it or not. (or that someone used magic to "make it grow&quot
It's like looking at a photo of the world and thinking "the shape of the world is similar to a scoop of ice cream, therefore there must be a giant worldly ice cream scoop somewhere." The only fact here is that you can observe a shape, but the conclusion from it is a simple fantasy.

I love this guy. I read everything he and toddangst have written. Is he married?

Wait if you think zeus(or whoever you all were talking about) is mythological then wouldn't that mean by definition that you think he isn't real.

Definition of mythological-

imaginary; fictitious.

Anyways, how is the community doing today?

Not to any scholar worth his salt.

Ugh. I detest prescriptionists. 

Lol, I got the difinition from dictionary.com.  You know because i don't feel like getting up and finding a dictionary at 3 in the mourning, but whatever here is the definition pasted from dicitionary.com.

     /ˌmɪθəˈlɒdʒɪkəl/ Pronunciation Key - Show Spelled Pronunciation[mith-uh-loj-i-kuhl] Pronunciation Key - Show IPA Pronunciation

myth·o·log·i·cal       (mĭth'ə-lŏj'ĭ-kəl)  Pronunciation Key  adj.   Of, relating to, or recorded in myths or mythology. Fabulous; imaginary. myth'o·log'i·cal·ly adv.

mythological

mythological: in CancerWEB's On-line Medical Dictionary

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Anyways if you don't think their definition is correct then could you give me what "you" think mythological means? 

Jesterhawk I am a Christian Theist by the way.