You need to site your source http://greensboring.com/viewtopic.php?f=18&t=7272

But since you are not going to say anything unique why should I.

1) http://www.talkorigins.org/indexcc/CE/CE261.html

2) http://www.talkorigins.org/indexcc/CD/CD220.html

3) http://www.talkorigins.org/indexcc/CD/CD221_1.html

4) http://www.talkorigins.org/indexcc/CD/CD701.html

5) 6) 7) http://www.talkorigins.org/indexcc/list.html#CD

8 ) http://www.talkorigins.org/indexcc/CE/CE001.html

9) http://www.talkorigins.org/indexcc/list.html#CC

10) http://www.talkorigins.org/indexcc/CG/CG041.html

11) http://www.talkorigins.org/indexcc/CG/CG040.html

What, afraid? I haven't seen you guys debating with me yet?

Well I understand, it's okay. Anybody else? 

I beg your pardon? I distinctly remember utterly rending you asunder in the previous thread you began. You copied and pasted articles from other people, since you yourself have no scientific expertise. Whereas I responded with my own writings. Yet you never returned once to that thread. Hence, you cannot possibly expect people to take you seriously if you give them a precedant whereby you

a) Copy and paste from other sources since you do not have the intellectual capacity to engage in genuine study on the matter

b) Do not return when said arguments are refuted because you cannot respond to said refutations because you do not have the expertise because you are an intellectual pygmy.

how can you possibly expect people to bother to engage in discourse with you if you front this attitude?

The first half relies entirely on the fallacy of bifurcation, or the false dichotomy. Try to poke as many holes as you like in the current scientific consensus on the age of the universe, the origins of life, or whether Hovind's frequent soap dropping can be called 'accidental' anymore, but it doesn't leave the most plausible answer whatever you want it to be. You pinheads have had centuries of nipping at science's heels, and your hypothesis, that everything was created by an overweening omnipotent agency, still has to be argued into plausibility. If you had evidence, you wouldn't have to argue against evolutionary theory, you wouldn't have to play logic games.

The second half... just look up Ken Miller on YouTube. He's a Catholic, and even he can't stand you creationist twerps.

I noticed you guys, instead of giving me a point-by-point debate on why I am saying "false" statements, you attacked the fact it was a copy/paste, too uncomfortable?

Also, you used things like:

"What is there to argue, we have already disproven this!"

REALLY? were? I would love to see.....

Then again, maybe I am wasting my time with arrogant fools..... 

Well, yet again, another one not arguing my point.

Bobby Fischer or some chess-master once said this:

"Play the board not the man"

 Revisse that statement, to:

 "debate the evidence not the source"

or can you?

And again, since I am a Christian, and know there is a God, and you are not, I am therefore the one the lives correctly (most of the time) there fore I am the one we should trust, not a atheist with not laws. Shall we? Any arguement?

Thanks, and you might noticed "bursts" of replies from me, because I have this thing called a "life" and a "job" so I don't spend all my time on foolish websites (like I am  right now) you might see me again soon. My question is, (other than the donations from RRS members) how does Brian Sapient support himself??!?!?!?!

 Does he even have a job? Who knows, who cares.I don't for al I care he could go scrub toilets for the rest of his life and I wouldn't feel sorry!

IMO anyway.

That is amazing man, 6? "you are almost certaintly lying" no lol, just joking I beieve you, but my question is, where did you go so wrong? lol, seeya probably next week, time to go to bed righ tnow. 

Which was?

OK, irrelevant. Your arguments failed on their own, apart from your poor character, sour odor and hot dog neck.

Really? Why don't you hit us with something good then, rather than a false dichotomy and argument from ignorance, you copied and pasted from some pre-fab apologetics site?

LOL, wut?

Did your oddly specific references to bricklaying betray you?

You can't have it both ways.

He issues spankings to your pastor.

You don't care, in your opinion? You're unsure what you think?

Who the hell are you talking to?!

No idiot, it's not uncomfortable... it's stupid.

 We all know how to use google.  We all know that there are thousands of sites that have plenty of information from the Christian side of this debate, we are all capable of looking them up ourselves.  If we wanted copyright laws broken and to be plagiarizers we could go to all of those sites, and steal all of their material too and post it here for us to laugh at.  

If we allowed everyone to simply cut and paste their favorite arguments from any christian site they wanted you could be posting here with nothing but other people arguments for the rest of your life.

What we want is for you to present arguments that you can actually discuss with people.  You seem to be illustrating that you are a parrot.  You can copy others but don't know how to address the issue yourself.  If you think the site(s) you reference are the best of the best, than do yourself a favor, write to the owner of the site and tell them to come over here and have a discussion with us.  

Present ideas that you are able to address without having to copy someone elses arguments verbatim.

Go ahead... get the owners of all the sites you like to come over here, we'll show you how uncomfortable we are when they get here.

If you cared so much about wasting time with arrogant fools you would've never posted the drivel you opened up with.
 

Very well, I shall put my anger on hold for the moment. This irritance springs primarily from the actions of the poster pertaining to the prior thread, but I shall forget about that. The prior thread, like this one, was a prefabricated list of arguments, which fortunately, I had written a set of responses to. To be fair, some of the responses were utter overkill and served more educational purposes than actual rebuttal purposes. There is similar merit in answering the objections in this thread in the same fashion. Some of the claims made by the OP list in this thread are obviously false. For example, it does not require massive expertise in Astrochemistry to know that the claim that comets need to be the same age as the Solar System is a non sequitur. Comets are pulled into the solar system via the Oort Cloud and Kuiper Belt. Solar Systems do not have "supplies" of comets which can be said to be "used up".

Other claims, such as the decay of the magnetic field, require a lot of technical expertise to even understand let alone refute. Fortunately, I am in possession of such expertise and am therefore preparing a series of physics lectures in which the topic of magnetic fields is very thoroughly treated. My writing on that subject in particular for educational purposes is extensive and goes beyond the Jifemko equations and the Lorentz Law. However, this demonstrates a key issue pertaining to the debate: In order to even begin to have discourse on these matters, a vast amount of background knowledge is necessary. Most creationists do not possess this background knowledge and therefore do not have the capacity to make an informed decision on the matter. Creation "science" arguments are generally aimed at the average person who is not technically trained in the matters at hand, and indeed, Creationism in general is more concerned with appealling to those without technical training in the fields which are necessary to understanding evolutionary theory. 

In order to properly understand the merits of evolutionary theory, it is probably best to be familiar with more or less every single disciple in biology, since evolution is the Unifying Theory of Biology and therefore unifies all distinct fields. However, to be familiar with all these fields is untentable. Therefore, my suggestion is that a core set of four fields is absolutely necessary to comprehend evolution. Those four fields are molecular biology, developmental biology, genetics and evolutionary biology. I suggest that our interlocutor hence research these topics from textbooks and following that, science journals and published papers. 

On the other hand, I am happy to educate. My interlocutor claimed he could not access his previous thread. I accused him of lying. But I am reasonable. Perhaps he was not lying. Hence I shall rescind my statement. Indeed, to be even more fair, I shall re-post my response to the arguments that he pasted, in this thread, so that discourse on both matters can be opened simultaneously, and that our interlocutor and all others in the room can be offered some proper education in these matters.

Hence:

An introduction to what evolution is is first necessary.

Evolution is the process of environmental non-random selection of random fluctuations in biological replicators, a strive to adapt the genes to the environment by which variations are propogated. Every organism in existence has had a direct lineage to a common ancestor, the mutations of whose offspring have produced life’s diversity.

The etymological roots of evolution come from evolvres, in Latin, meaning "to roll out". Today, it simply means change. Presumably, you are referring to biological evolution, also called organic evolution. Evolution in this sense refers to the change in frequency of genes down a lineage. Evolution is not concerned with ontogeny, the development of an individual organism. Organisms do not evolve by themselves. What is occuring is descent with modification, where the variations in any population have selective pressure against them, pressure which is dictated by the environment, which results in the alteration of gene frequencies through a lineage. In this regard, evolution is determinstic, in that the process is not guided by luck or chance.

Evolution is essentially this. Systems of biological life by definition replicate and passes on hereditary information to their progeny. But the progeny never posess a carbon copy of the genetic information which conceived them, rather, there are variations in a population without which we would all still be single celled organisms. These variations produce different organisms with different traits, these different traits may provide advantage and disadvantage in the struggle for resources upon which life is based, as a result, organisms with advantegous traits for the environment may reproduce more hence the advantageous trait flourishes and multiplies at the expense of the weaker organisms, which perish as they cannot match up in the struggle for resources. As time goes on, the variability accumulates and hence marked changes in phenotype and morphology may be observed to the repeated cumulative effect of the advantage of the variation in question causing those possessing it to have more offspring, as a result, the variation becomes more prominent in the pool of organisms until it is a dominant feature of the organism.

Therefore, organisms, by means of reproduction and the variation produced in gene pool, generate variability which accumulates by means of increased prominence in the pool due to the reproductive advantage it offers. The vast array of different advantages by which an organism may elevate itself and hence its offspring in the struggle for resources is so utterly vast that a literal infinitude of possible different phenotypic traits and hence a vast number of distinct phylogenies may proliferate. This is the principle of natural selection, that favorable traits are propagated simply because the organism in question will have an increased chance of survival and reproduction.

The next section therefore concerns a basic course in molecular evolution. Life began humble and meagre, nothing more then a flexible bag of fluid enclosing some precious molecules encoding self-replicating information. And yet, in that time, life has grown to all the fantastic variety and complexity we see around us. Through endless duplication, mutation and selection, life has ultimately diverged into countless distinct branches. This is the molecular biology behind evolution. As a result of this, all life is homologous, which is to say that there is a lineage relationship between all organisms that diverges as the time between the development of the organisms being compared increases, and converges as this time length decreases. This is embodied in the biochemical and anatomical similarities which underlie all life, beginning from those gene families in the table upon which every known organism is based, from that base of operations, the process of evolution, using that foundation, may spring forth and diverge along different phylogenies. The result is that phylogenic trees linking organisms and their constituents (genes and proteins) may be drawn for any cataloged relationship. Indeed, I provided some in my proteomics essay, which I direct the reader to for a much more technical account of molecular evolution. Using the outlined techniques, we can track macroevolution, which is to say that we can track large-scale speciation and common descent despite having not observed it. The duplicative mechanisms for creating the raw material for all homologies from the molecular to the anatomical and physiological level that encompass the whole spectrum of life are so obvious when we examine arrayed and compared genomes that we have a very accurate picture, more so than can be delivered by the rare event of fossilization. These mutations leave very distinct signs which leave it obvious to anyone who observe them that the homology is the result of common descent, not common design.

It is now time to consider molecular mechanisms associated.  It is first necessary to consider a basic fact about DNA. 

The claim “DNA is a language” is probably the result of pop-science, which tries to reduce concepts to simple single words or phrases. That’s how the myth “you only use ten percent of your brain” started (Complete nonsense. The confusion arises because only 10% of brain cells are neuronal, the rest are glial cells like oligodendrocytes and astrocytes). It is also how the Second Law of thermodynamics became reduced to “everything progresses towards disorder” with the result that many creationists are confused about thermodynamics, and labour under the delusion that entropy can never decrease in a system. Nonsense, again. But it does reveal troubling ignorance about science, a few names, some general concepts, that’s it. The claim “DNA is a language” is a meaningless allusion, even if construed as metaphorical. DNA is no more a language than a telephone book is a computer. DNA is a cipher, that is to say that it is a direct substitution representation of the sequential structure of another unbranched polymer, polypeptide (some DNA, however, codes for RNA genes), constructed of a different monomer class, amino acids. The order of the amino acids will determine the structure and function of the final product for which the DNA codes, the protein. In this regard, DNA does not function, even analogously, as a language, it is a substitution cipher. A substitution cipher is one in which one set of functional expressions is replaced with another. For example:

A=1

B=2

C=3

D=4

E=5

F=6

Etc

If I transcribed this to write: 85(12)(12)(15)=HELLO, which was then decoded by another conscious being with the same understanding, then it would become a language. This does not analogously occur in DNA. The DNA is a substitution of DNA bases grouped in to codon triplets, which are transcribed and translated to make functional polypeptides. This is not a language. A substitution cipher per se does not qualify as a language.

In this case, each amino acid is read as a triplet group of nucleotides called a codon, with other codons dictating the stop and start of translation. As shown in this table, DNA is a substitution cipher like so:

However, DNA is not a language, in any sense, because it does not represent concepts or meanings, a language entails that abstracts represent concretes, such as a number 5 written on a piece of paper, which has “meaning” to an entity which can understand what “5” means. Nothing analogous is found in DNA, since it is only a substitution cipher, which represents the order of amino acids in a protein, or RNA nucleotides in an RNA molecule. There is no abstract representation or assigned meaning going on with a direct physical substitution cipher, like DNA. When a stop codon orders a ribosome to stop transcribing, the ribosome does not “understand” that it has to stop transcribing, because it is just a ribosome. Nor does the nascent polypeptide “understand” that it is being hydrolyzed. Nor do tRNA “understand” that they must bind to their respective codons on mRNA. There is no transmission of conscious understanding, no abstract communication that entails one entity interprets symbols because it has the same understanding as the entity which communicated them. In this regard, DNA is not a language by definition. All that is happening is that the stop codon does not contain the binding site for any tRNA, but it does contain the binding site for the release factors which terminates translation because it causes the nascent polypeptide to hydrolyze an ester bond as they catalyze this hydrolysis reaction and release from the subunits of the ribosome.

 Proteins are the physical product of the genome, and are, analogous to the genes, represented in a linear fashion by chemical encoding. Whilst homology in genes is determined by sequence, homology in proteins is determined by structure and function. It is established that we can find a gene's function by means of working in reverse, which is to discover what the organism in question lacks when this gene is deleted artificially. We can also conclude that homologous genes retain the same function, and there is directly proportional relationship between divergence of function and divergence of base pairs.

The gene families are all homologous, which is to say that they are all built from duplication, which increases the raw material of genetics, and divergence of the different new orthologous and paralogous arms of a set which were created by said mutations. The proteome is the physical expression of such and as such it has precisely the same homologous properties. In evolutionary terms, we examine proteins by their higher subdivisions. We can divide a protein into quaternery domains. We can divide quaternery domains into polypeptide chains, or tertiary domains, which we can divide into batches of supersecondary structures, which we can divide into patterns of secondary structures, which can be explained in terms of primary structure (sequence)

. Once we get to a high enough level, often the section of the protein in question is simply self-assembling and is not affected by other domains on the same protein. In other words, the building blocks of proteins as we measure them at higher levels are the functional modules by which evolutionary mechanisms occur, not the deleterious lower level changes. Since at higher levels, the functional units of proteins fold up utterly independantly, the result is simply that we have modular functional domains that are interchangeable throughout a wide range of proteins and retain their preexisting function. In this way, we can see that the bulk of evolutionary innovation comes from the reshuffling of such domains at higher levels. Since there is a directly inverse relationship between diversity of organisms and complexity (by which I mean that prokaryota are by far the most simple, and hence the most diverse, while protozoa are much more constrained, and muilticellular Eukaryota are the most constrained by far, due to limits on physiology and anatomy). Hence, originality decreases as we travel up the taxonomy. By the time we reach the least diverse groups, such as mammals (by far the least diverse Class in the whole animal Kingdom), we find that the vast bulk of changes are little more than quantitative tweaks in Hox genes, as opposed to actual innovation.

At any rate, the result of such a relationship is that the vertebrae in particular are noted for having no proteomic originality, which is to say that the proteins of the vertebrae proteome are always found everywhere else, hence any innovation in the vertebrae proteome occurs by means of simple reshuffling of the modular domains. Since the relationship between time divergence and amino acid divergence is directly proportional, we find that noise mutations which alter the sequence but not the structure or function of proteins are an indicator of time/divergence relationships in a proteomic homology, since the rate at which the sequences diverge is calculable, and is different for each protein depending on the conservation of the protein in question. In every protein, we invariably find sequences of amino acids 10-30 long which are so highly conserved due to the fact that they are absolutely necessary for the function of the protein that they do not change over evolutionary history, and hence, by means of comparing such sequences to the noise mutation which operates on the probability of just random frequency and is neutral, we find the rate of divergence, which tells us the time separation associated with the arising of two species. But this would only work if the species arose in a continuum from a common ancestor, since the homology indicates that all proteins are the result of recombination following duplication and the reassembly of modular domains to produce novel structures (the originality of which lessens as the organisms in question become more complex), and that the lack of originality in such a domain indicates that the entire proteome originates from a common ancestral proteome, whose appearance we can shed light on by means of cross-referencing universal domains with the most simple and, in terms of genome hence proteome size, the smallest organism in existence, the Mycoplasma genitalium bacteria.

The noise mutations found in the homologous sets of proteins which do not affect structure and function serve as the markers by which we may catalogue evolutionary relationships. Indeed, without the process of evolution, the existence of such markers would be absurd since they indicate a directly proportional relationship between sequence and time of divergence, which must indicate that such mutations occurred in a continuum nature reaching from a common ancestor all the way across the lineage to the organisms in question. Were the organisms designed, or created spontaneously or without a line of descent from such a common ancestor, such a distinct molecular trail would not exist, since there would be no familial relationship by lineage from the organism to the marker organism the noise mutations on which are the ones being compared. So, we have a homologous protein set the result of common descent, that we can determine was clearly the result of duplication and divergence which most certainly indicates common descent, and then we may track the progress of such divergence by means of the direct relationship between amino acid noise mutation, or non-deleterious neutral mutations which do not alter either structure or function, which, again, would be impossible without common descent. The innovation of creating new proteins is only a small portion of the genetic mechanism by which evolution may occur, however. We need to consider systems of genetic control, the workings of regulatory DNA, the Hox genes and how changes in utero by means of alteration of the Hox genes and the associated node pathway may produce novel structures in multicellular Eukaryota, and at a more simple level, how changes in regulatory DNA as well as protein innovation may produce novelties in protozoa and prokaryota, since they lack Hox genes being that they are not multicellular and do not need such control systems.

We need to consider this, for example, in relation to arguments about Irreducible Complexity. The recombination of genetic material can extend far above the level of single proteins or domains. Indeed, enormous chunks of genetic material may be recombined. Hence, when examining homologies, we can examine relationships that go up to the quaternary level, caused by large order duplications or recombination. Indeed, we are often tempted to think of evolutionary increment as “adding parts” or something of that like. This is a very primitive design-style worldview of looking at evolution. Indeed, the process can add parts and delete parts via these mechanisms, but this is a rare occurrence (begging the question of what a single “part” is anyway). Many complex biomolecular structures can generated by the recombination of pre-existing structures into a new role, which is a rapid-order mutation, instead of incrementation to generate the whole structure in question, incrementing generates some of the underlying mechanisms of the structure in question, and then these underlying protein structures may recombine to rapidly form the product structure. If only two or three pre-existing major components are required to generate the new and supposedly “irreducible” function, then it can be generated by what is called exaptation which is, as described, a process by which major structures (which may have no relevance per se to the function which they recombine to form) recombine and create something, which, when broken down into its fundamental constituents, appears irreducible. However, this misses the big picture of how evolution works and how functions often coalesce to form new ones by recombination, since this is generated in one or two steps, selective pressure all the way is still achieved. Now, this is true of many structures and functions, such as blood clotting (the whole chain is homologous and formed by serine duplication) or the flagellar motor (all homologous proteins, but comprised of the recombination not of individual proteins, but rather pre-existing structures.

The real fallacy in Behe's argument is how he examines a function  to conclude it is Irreducible. We have established, firstly, that the proteins are homologous and hence arose by means of duplication and divergence, but this is not enough. What we need to understand is that Behe's argument relies on circular reasoning that involves looking that the subdivisions of the function in question as "parts" where a "part" in this case is defined as a single protein cofactor. In other words, Behe miscontrues evolution as being a system working towards an "objective' by means of adding "parts" to the system. Yet this is not the case. This not being the case, he is forced to work backwards, presupposing that a function was actually worked towards and then required simultanous generation by virtue of that fact that the system could not function without either. Yet evolution does not work like that, there is no eschatology. When homologous duplication takes place, a not so uncommon phenomenon is called double-deleterious incapacitation, that is if the homologous copy does not form a psuedogene, then often, since neither is being heavily conserved by virtue of the fact that a copy can assume the function in question, if a homologous gene had multiple functions such as if it is a gene command locus, then if both copies suffer a deleterious mutation that forces certain functions of the locus into incapacitation, then suddenly both copies are conserved, and so the homologous gene is propogated and cannot become a psuedogene. A molecular biologist who was naive might conclude that the system was "irreducible" by virtue of the fact that both parts are required, but homologous duplication contributes the bulk of evolutionary novelty, and such irreducibility is an illusion because the system was never working towards the current system in the first place. 

It is also necessary to consider recombinative mechanisms: 

In other genetic disciplines, different mechanisms of construction of novel genetic material occurs, but all are fully known. Consider TSSR and meiotic recombination:

An overview of genetic recombination. There are two principle pathways. The first is meiotic recombination. The second is repair-based recombination, and the two pathways have different outcomes. In meiosis, the genome of a diploid organism  is duplicated, and then undergoes two rounds of division. The cells that result each have one complete set of chromosomes, or half the genetic content of the cell. These then fuse during fertilization to form the gametes

 Homologous chromosomes will pair, or synpase, during meiosis. Homologous chromosomes are not the same thing as sister chromatids. Sister chromosomes are copies of the same chromosome caused by replication, whereas homologous chromosomes are different copies of the same chromosome which are inherited from each parent.

 Genetic recombination occurs when a strand of genetic  material from one chromosome is broken off and attached at the homologous site on the other. In meiosis, this occurs when a double strand break in one of the two homologous chromosomes is induced by the Spo11 protein. The 5' ends of the strands are then chewed back by exonucleases. This generates the free 3' ends which can then begin strand invasion and DNA synapsis on the complementary sites on the homologous chromosomes. The DNA synapsis is mediated by the RecA protein. The free 3' ends of the two strands bind to their complementary sequences as shown:

The Holliday Junction that forms as shown can be pulled along the DNA. After RecBCD helicase-exonuclease complex creates the free 3' ends, RecA proteins will bind to them forming nucleoprotein filaments which act as recombinases, catalyzing the invasion of the ssDNA into the homologous dsDNA.

 Chromosomal recombination occurs before the double-cell division of meiosis, when the homologous chromosomes are held tightly together. This produces a unique blueprint for the gametes. Recombination hence explains something that hitherto puzzled scientists: Why is it that offspring of the same parents do not all look alike? The difference and variety of phenotype that can be generated by the recombination of genes is testimony to the advantageous nature of recombination, and hence of the principle upon which it is built: diploid genomes.

For recombinative repair, the 3' ends need to be created by the RecBCD complex, which is unique among the helicases in that it actually recognizes a specific sequence, called the Chi sequence, these being interspersed throughout the genome. The RecBCD acts as a helicase-exonuclease in the 5' to 3' direction, destroying DNA along ssDNA to create a protruding 5' end until it encounters the Chi sequence, at which point the DNA-binding causes a functionally induced change in the exonuclease function, also note that RecBCD is an ATP-dependant motor protein as it moves along the ssDNA. When this occurs, the RecBCD works on the other ssDNA strand, causing a protruding 3' end. RecBCD also serves to load the ATP-dependant RecA onto the protruding 3' end so that it can facilitate DNA invasive synapsis.

 The DNA synapsis leads to branch migration, in which the Holliday junctions are pulled along the DNA:

 The RuvABC complex can resolve the Holliday junction, as shown. The Holliday junction is the four strand intermediate that forms due to the pairing as shown above. After ligation, the junction can be pulled across the synapse by virtue of the RuvA/B complex (which also mounts a DNA helicase onto the strands to resolve any ssDNA structures). The branch migration is facilitated by ATP-dependant proteins, in humans called RAD51.

 RuvA and RuvB can pull the Holliday junctions along, whereas RuvC will resolve the strand by means of strand cutting:

 The Holliday junction isomerizes by rotating, at which point the joints are resolved by strand cutting:

 The two outcomes of meiotic recombination as shown. Gene conversion results from SDM after incorrect base pairing due to an overt difference in the two alleles. It is for this reason that gene-conversion represents non-Mendelian inheritance. Crossovers result from standard synapsis in which the Holliday junction is resolved by isomerization. If the Watson-Crick base pairing of the two alleles is not substantive enough, then the MutS-MutL complex will destroy one strand (the MutL as usual mounting a helicase onto the DNA and the MutS binding to the muTL dimer to loop out the DNA as an endonuclease trails behind). If this is the case, then the strand that was originally from the other parent will be used as a template for the mounting of DNA Polymerase onto the strand (to be then sealed by the ligase). If this is the case, then a chunk of information that was originally from the allele of one parent will be converted into that of another. This violates a fundamental law of genetics that both parents make a precisely equal contribution to the genome of the offspring and is hence non-Mendelian inheritance (this is contrast to ). (This is again constrast to recombinative repair, where one chromosome is not changed and the other is repaired by means of using the information of the  other as a template by which the synapsis does not alter the sequence of the donor chromosome, as opposed to meiotic recombination, which does. This constitutes roughly 99% of the recombination that occurs in meiotic cells).

I also wish to cover horizontal and vertical transfer and transition:

 There is no such thing as a “transition” between species, because there is no fixed anatomical description of what a species actually is. In terms of physiology and anatomy, a species is a broad, encompassing taxanomical term which encompasses a range of slightly differing anatomy and physiology between a group of organisms whose only unifying definition is their ability to exchange genetic material and procreate to form progeny (at least in the case of organisms whose reproductive transfer is genetically vertical), and this definition only applies to sexual species, regarding asexual species, the concept of species is utterly arbitrary, and hence the concept of microevolution, that of intraspecies change, that far from being just an extrapolation of microevolution, macroevolution is actually a necessary corollory, because it is functionally identical, it simply entails more time, and since the laws of genetics and biology say that variation must occur and must have selection acting upon it, if evolutionary divergence is functionally proportional to time at the molecular level, then macroevolution is not merely a good idea, it actually must take place, it follows directly from observation of small scale evolution, since it is given that

(A) It is functionally identical, ie there is no process difference and

(B) It must take place (the laws of biology explicitly state that variations under selection must occur)

then the immediate corollary given that nucleotide sequences change at a rate which is directly proportional to time, then it is an iron corollory that macroevolution will occur. It tumbles straight out of the observations, just like the expanding universe comes out of the Einstein field equations.

Hence, the word species is a continuum term, the boundaries of which are marked only by the points at which the genetic differences underlying organisms X and Y are just too great to allow vertical transfer. So, presumably, by transitional fossil, they would mean an organism whose genetic material is at such a precise equilibrium between two species that it is very difficult to class it. Needless to say, the probabilities of finding such an organism are ridiculous, even without the incompleteness in the fossil record. On the incompleteness of the fossil record, this is merely a state the obvious claim. The fossil record is not a videotape of evolution. The utterly vast majority of animals and indeed physiologically distinct species are lost forever to human knowledge for reasons that fossils are such a rarity anyway. It is pure happenstance than an organism may be trapped in an anoxic environment such that they will be fossilized. The utterly and truly vast majority of all organisms are being siphoned out of the ground and burned to power our machines including the one on which I am typing- they become oil (and coal). It is utterly unreasonable to expect that fossils will provide us with a complete account of evolution anyway, that is impossible. Fossils help us greatly by providing a general account of the phyla, anatomy and physiology of organisms in particular strata, they are not a book which utterly accounts for the steps of incremental change in biological life. That is why more research is being put into my field (this may be my bias as a molecular biologist, but...), of proteomics and molecular genetics, which is helping to provide a very accurate account of macroevolution.

An Introduction to Thermodynamics and Entropy/Enthalpy:

 We need a quantitative unit to measure entropy, 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 ∆S is measured in entropy units (eu). But that equation is normally used for chemical reactions which change the entropy of a system because they change the energy distribution, from highly ordered packets of free energy in reactive chemical bonds to vastly more disordered, probable heat energy released. On Boltzmann’s tomb there is a famous epitaph:

S=klogW

That equation is simply a rewording of the one above, where the entropy of a system is the gas constant multiplied by the natural logarithm multiplied by W, the number of possible microstates in question.

Once we begin to consider the nature of ordered systems, the probabilities in question become mind boggling. Consider a book with 500 pages, if unbound, and tossed into the air, what is the entropy change associated? The 500 pages all in correct order represent a single ordered state. 1/W. The number of disordered states is vast, truly and utterly beyond comprehension, for the number in question is 500 product, which means 500 x 499 x 498 x 497....x 1, where n! is expressed as n x (n-1) x (n-2) x (n-3)...(n-(n-1)) This number is 1.2 x 10^1134, or to make it more visually holding:

1220136825991110068701238785423000000000000000000000000000000000000000000000000

00000000000000000000000000000000000000000000000000000000000000000000000000000000

00000000000000000000000000000000000000000000000000000000000000000000000000000000

000000000000000000000000000000000000000000000000000000000000000000000000000000

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Entropy therefore is a measure of the probability associated with a system, and an increase in entropy in invariably a tend towards more probable states, by which we mean less ordered states. When we consider entropy in relation to Enthalpy, we realize that highly disorderd states are vastly more probable than highly ordered states, since there are simply so many more than there are ordered states. At any rate, when we consider that it is the nature of all things to head probabilistically towards the lowest energy state, one might ask why, in fact, all things do not immediately do so. Why does paper not spontaneously combust? Paper is an ordered state. Ash and gas, disorder and vastly more probable. The oxidized ash and the escaping carbon dioxide never reconstitute themselves into paper. Clearly, there is vast favorability associated with this combustion? So why do we not all spontaneously combust. The answer is activation energy, for a reaction to occur requires a certain energy level be reached that systems in their stable state normally do not attain unless prompted to do so, such as by being supplied by a fire, in this case. Activation energies are the principles upon which catalysis work. Most reactions in the body could only take place inside an oven without catalysis. Occurances into lower-probability states still need energy inputs into the system in order to coax the reaction to fall towards the lower probability state. In the case with a bound book, the book will not spontaneously disorder itself, but once given the necessary energy (unbind it and toss it into the air). For any reaction where the Free-energy change is positive, which thence cannot proceed with spontaneity, not only a vault over an energy barrier required, but also then, state B is less probable than state A, as opposed to a favourable reaction, where upon the completion of an energy barrier, the free energy drops such that the reaction proceeds spontaneously, hence, if I toss a book, unbound, into the air, I have provided the activation energy, and the rest proceeds spontaneously. If I drop an egg off a table, I have provided that activation energy such that the reaction may proceed spontaneously, but I cannot do the same for attempting to reconstruct the shattered egg, for such is expressly forbidden by the laws of probability.

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 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.

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.

This allows us to predict the nature and course of reactions, and also the free energy associated with the reactant and product in question. For a reaction to proceed, at the end of it, as a result of the reaction, there must be an increase in disorder in the universe, even if the reaction itself produces an island of order inside the cell. The laws of probability do not allow for this to be reversed. It would be analogous to eggs unbreaking. When we consider that a reaction can be predicted like this, if the ∆G of the product is greater than the reactant, the reaction will proceed spontaneously. If not, the reaction must be coupled to one which is, and that drives biological life.

This is given by the following formula

∆G=∆G(s)+RTlog{A}/{B}

What this basically says is that the change in free energy in a reaction will be equivalent to the free energy change under standard conditions for the products and reactants (available to be consulted in any data booklet), where R is Boltzmann’s constant (the universal gas constant), T is the temperature in Kelvin, and {A} and {B} are the concentration of A and B in mol/liter respectively.

Many chemical reactions are wholly reversible. If A can become B, there is no reason that B cannot become A, it’;s just that for many reactions, B has a much lower G value than does A, and so is more probable, whilst B becoming A again is improbable. On the other hand, in biochemistry, reactants and products are violently colliding in the cytoplasm all the time, and this can provide the activation energy necessary such that B might return to A even though this is normally impossible because of the activation energy barrier. Consider a reaction with 100 molecules of A and 100 molecules of B. As A favourably turns into B, there will begin to be a large excess of B over A, and therefore, with the random collisions associated with molecules, a small amount of B will turn back into A. When the concentrations of the two are such that the rate of conversion of A to B is exactly the same as B to A, we say the reaction is in thermodynamic equilibrium. This is very useful because it allows us to calculate the concentrations of A and B and the standard free energy change if we so desire. Because thermodynamic equilibrium means ∆G=0, then the equation becomes:

-∆G(s)=RTlog(B)/(A)

For which we can rearrange to make the concentration the subject, where (A)/(B) would now represent the equilibrium constant. The ratio of B over A such that the reaction proceeds in equilibrium. The greater this ratio, the greater the free energy loss, and the more favorable hence probable A to B becomes. Now:

{B}/{A}=e^(-∆G(s)/RT)

For example, if a reaction A to B had an equilibrium constant of 10^5, it would mean that 10,000 times the number of molecule B would be needed over molecule A in order that the precise rate of A to B is equivalent to the rate of change of B to A, and then the two would be considered in chemical equilibrium. And, in that case, the free energy change would be precisely zero. The concept of free energy, or G, is what will be examined next.

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 (mc∆T) 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.

In this regard, there is a central distinguishing in chemistry between two types of reaction, endothermic and exothermic. When bonds are broken, heat energy is released, and so such reactions are considered exothermic, and such reactions hence are thermodynamically favorable, as has already been established, whilst those that make bonds are endothermic, and hence thermodynamically unfavorable, and occur as described. Since certain bonds have certain amount of energy associated with them, it takes a certain amount of energy to break certain chemical bonds. This is called the bond energy and is measured in kJ/mol, meaning the number of kilojoules required to break one mole of said bonds. So, a bond with a bond energy of 20 kJ/mol entails that it requires 20 kJ to break 6.02x10^23 of said bonds.

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∆Ssea +∆Scell =∆Suniverse

The entropy of the local system can decrease, providing the entropy of the global system increases. In a nutshell, It was Schrodinger who realized that decreases in entropy and the construction of high-order information patterns (measured by Gibb's Free Energy) are the result of a very important function in the second law of thermodynamics which dictates that for any concentric set of systems, decreases in entropy in local systems can be attained by a correspondingly larger increase in entropy in the total system. These entropy decreases and high-order systems are not random quantum fluctuations but precise mathematically equatable systems which can be measured very precisely using the basic formulae of thermodynamics (Hemholt'z equations, Gibb's equations, entropy, negentropy, Enthalpy etc).

Entropy is in effect a measure of probability states and it has a proportional relationship to temperature (that is, the tend towards disorder is accelerated at higher temperatures).

But all high-order systems are open, otherwise they would be unsustainable. A closed system does not allow the crossing of heat, matter, energy etc across the boundary from the surrounding to the system. The necessity of all low-entropy systems is an influx of free energy, the expenditure of which is always compliant with thermodynamic, which allows for "order islands", that is, pockets of increasingly high order called the local system where the whole system (assuming closed) tends towards disorder. This is why the net entropy is always >0.

One more thing I can mention is that the thermodynamics equations that allow for evolution operate on the same mathematical principles that allow for other order-generating systems like reproduction etc. Entropy measures probability associated with ordered systems, but ordered systems, far from being random results of a vat number of possible microstates, are forced to be created as pockets of order, like us, in a disordering universe, because, ironically, of precisely the same principles. This is, in essence, what entropy is, a probability measure, but the probability only matters when the system is closed, which is why anyone who wishes to understand the principles must first understand that:

∆Ssea+∆Scell=∆Suniverse, whereby:

∆Suniverse>0

But the entropy of the local system can decrease, as long as a corresponding increase in entropy in the whole system obeys the second law, which dictates that ∆Suniverse for every reaction always>0. When S=KlogW, wherever W is vastly higher than the number of ordered states, it indicates, when ordered states are discovered, the entropy is lower. That’s what ordered states are, low entropy, hence low probability. But that probability function applies to a system where the total energy is increasingly progressing towards uniform distribution, the lowest energy state, like the universe. We do not live in such a system. Our system is supplied by a constant influx of free energy by a massive free energy generator which simultaneously generates vastly more entropy into the surrounding environs: A sun.

The mathematics, in short that dictate that you can drop salt into water and increase its order are the same mathematics which allow for the replication of DNA, the generation of a tree from a seed, the evolution of life. The Earth is an island of order fed by a huge system of dG (Gibb's Free energy), which, if you understand the logarithmic relationship between it and entropy, it should be easy to understand that the precise and quantifiable mathematics which allow for the coexistence of order-generators (like life) in an increasingly disordered universe is permitted. It is to these principles that you owe your very existence, since if they did not hold, a device of monstrously low entropy like a cell let alone a multicellular organism could never be generated:

Biological Life is a system of very high order, generating very high order, but at the expense of the universe overall. Without the laws of thermodynamics forcing things to take their lowest energy states, biology could not possibly functions. Proteins would not fold properly. Enzyme catalysis would not work. Bonds couldn’t form, reactions could not proceed. The Second Law of Thermodynamics and the functions associated make systems of extremely high order maintaining and producing this high order bound to expend a great deal of disordered heat energy into the surrounding system in order to continue functioning. This is the basis upon which carrier packets like NAD and ATP work. Systems of very high order can be generated in a universe which must progress towards disorder. Free energy can be created within a local system (like a cell) so long as the reaction required to do this forces the expenditure of significantly more disorder into the universe than order is produced in the local system. Without this, not only could evolution not occur, nothing could occur. Gas clouds would not collect, stars would not form, planets would not form, life would not form. Biological life is utterly forcibly complied with thermodynamics. Allow me to demonstrate:

The concept of an energy carrier molecule is very central in biochemistry. We have discussed before the concept of reactive bonds and groups in chemicals, that is, certain bonds and groups in certain molecules are very reactive, and when broken, release a great deal of energy, and such reactions are exothermic. Here, this is precisely what is employed. Eventually, the stepwise oxidation of glucose produces a set of energy carrier molecules which are used to drive biosynthetic reactions in a manner that we shall soon see. These energy carriers therefore act as the principle metabolic “currency” of the cell, distributing energy to where it is needed across the cell to fuel its processes and sustain its existence. We will be examining how energy carriers are produced from the stepwise oxidation of glucose after discussing what energy carriers are.

How do Energy Carriers Work? It is probably best to describe the universal principles upon which they work before going into each individual energy carrier molecule.

We have already met the concept of activation energy, and that the key purpose of catalysts, of which the biological ones are called enzymes, is to lower the free activation energy. However ,catalysts can only do that. That is, if the free energy of the product is still greater than a reactant, they cannot force such a reaction to occur. They cannot make a thermodynamically unfavorable reaction favorable, they can only make favorable reactions occur spontaneously. Or, rather, Imagine a dam which holds water back from a waterfall. The catalyst can remove the dam, thereby making the water flow downward, but cannot force the water to flow upwards.

However, energy carriers, technically, can do something similar to what I just described. That is, they can make a thermodynamically unfavorable reaction favorable. We have already met this entropy equation:

-∆G= ∆Ssea +∆Sbox =∆Suniverse

That is to say, therefore, that in any reaction, the overall result of the reaction must be to increase the disorder in the universe, or it cannot occur. However, providing that the system in which the reaction occurs is open, an ordering reaction (ie an endothermic one) can occur, just so long as the reaction causes a larger increase in entropy in the whole system than the decrease in the local system.

This central principle underlies biology. In this way, we can view ordered systems as pockets of order contributing to and in a universe progressing towards disorder.

Energy carriers will be the principle driving force behind the thermodynamically unfavorable reaction by ensuring that its occurances entails a release of greater disorder in the universe a a whole. The principle reactions that such energy carriers drive are polymerization reactions, and they often do so by means of contributing a reactive bond or chemical group which releases a great deal of energy, thereby contributing to the disorder of the universe, while simultaneously creating local order within the cell. Such a principle is called coupling reactions. To get a better understanding of coupling reactions, imagine rocks which fall off a cliff. No useful work is obtained by rocks falling off a cliff, but such a reaction is favorable and will occur spontaneously, that is, once pushed, rocks will fall off a cliff of their own accord. Now consider lifting a bucket of water. A bucket of water rising off the ground is thermodynamically unfavorable, and will never occur spontaneously.

But now imagine that a paddle wheel is placed on the ground which raises the buckets of water when the wheel is turned. Imagine now that the rocks falling from the cliff turn the paddle wheel and so raise the bucket of water.

In this analogy, the paddle wheel plays the role of the energy carrier molecule, the unfavorable reaction such as polymerization is represented by the bucket being raised off the ground. The favorable reaction represented by the rock falling is the breaking of the reactive bond on the energy carrier, which releases a great deal of energy.

We have already met the concept of reactive bonds being used to push reactions in one direction. We met it in lecture two, at the very end, regarding hydrocarbon polymerizations. The reactive double bonds of the monomers opened to link to form polymers. Because this reaction stabilizes the molecules by creating single covalent bonds, the reaction is favorable and will occur spontaneously. A similar idea is used with energy carriers being used to drive polymerization.

All energy carriers are molecules of which one part or group has a highly reactive group or bond which is donated to the monomer subunits undergoing polymerization. This bond does something similar to the reactive double bonds on the hydrocarbon subunit monomers discussed in lecture 2. The release of energy exothermically makes the polymerization energetically favorable.

Since energy carrier molecules carry a single reactive bond or group, the rest of the molecule can be thought of as a “handle”, so to speak. This being the case, one of the principle outcomes of stepwise oxidation to produce energy packets is to “replenish” the molecule by means of the addition of the reactive group on that molecule. That reactive group is then used to drive anabolic processes. This can be schematically represented like this:

Figure 1.27 A Schematic representation of how energy carrier cycles work, the central feature of metabolism

I suppose now is a better time than ever to consider what precisely these molecules are, and what their handles are. Let us consider what is surely the most ubiquitous energy carrier, an energy currency used by virtually all known biological life, and the main product of the stepwise oxidation of glucose, a molecule called adenosine triphosphate.

This molecule consists of three groups we are already familiar with. The base (adenine), the sugar (ribose) and the phosphate group (triphosphate). The reactive group that provides the energy packet is the third phosphate. The phosphate bond in question is called a phosphodiester bond. The breaking of one phosphodiester bond releases a large amount of energy, roughly 11kJ/mol. It is used to power a large amount of cellular reactions. Let us take a simple example. The release of the energy willbreak off the last phosphate group, thereby leaving:

ATP=> ADP + Pi

WHere Pi is inorganic phosphate

ADP is adenosine diphosphate and ATP is broken into ADP + Pi via the opposite of condensation, that is, we already met condensation discussing polymerization. When polymerized bonds are formed, water is expelled, but when bonds are broken, water is consumed. Hence the central reaction of ATP breaking into ADP + Pi is termed hydrolysis, since it is "splitting by water", as shown:

Note that the consumed water molecule is incorporated into the inorganic phosphate and the ADP. That is, when the Pi splits off, it leaves exposed chemical groups that are polar, and will pull a water molecule apart, to form an OH group and an H group, that will "seal the gap" so to speak on the exposed faces of ADP and Pi.

Suppose I wanted to form a bond beween molecules A and B. Typically, in biology, bonds are formed between an exposed OH group on one molecule, and an H group on another molecule, so the two molecules would be denoted A-H and B-OH.

This reaction is unfavorable. Bonds like this are thermodynamically unfavorable and cannot occur spontaneously. The reactant has a lower free energy than the product. In this case, the energy carriers play the role of the waterwheel already described. The energy carrier reactive group’s bond is broken from the handle, which forms an inorganic phosphate, and so the reactive bond displaces the OH group on molecule B, forming this: B-O-PO3.

The bond between molecule B and the phosphate is very reactive. That is why it will form spontaneously, since the product has a lower free energy than the reactant, since the splitting of ATP releases a great deal of energy. And so, the reaction will proceed via the reactive intermediate phosphate bond. That is to say, the following reaction:

A-H + B-OH => A-B + H2O

Is an unfavorable condensation reaction. We already met the concept of condensation. It is the method of polymerization of all types of biological polymers. It cannot occur by itself. However, via an intermediate, the following reaction occurs:

ATP => ADP + Pi

B-OH + Pi => B-O-PO3

B-O-PO3 + A-H => A-B + H2O + Pi

Note that “Pi” is the denotation for inorganic phosphate.

The Pi is then used again, being joined back to ADP to form ATP. However, this condensation reaction of ADP + Pi => ATP is energetically unfavorable, since ATP has a higher free energy than ADP. The replenishment of the ADP handle is done through the central metabolic pathway of the stepwise oxidation of glucose.

I now wish to introduce a short course about the origin of life:

The wost argument as it pertains to your above post is the one regarding the origin of life, which is biochemically an unrelated topic to evolutionary biology. Biogenesis is directed against the old doctrine of spontaneous generation.People used to believe, for example, that maggots were generated by rotting meat, called spontaneous generation. A long and complex process of chemical evolution to lead to the first cells is not something that abiogenesis comments on.

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 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.

-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

-he 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 AM JESUS , what do you want to debate ?

   yeah evolution sucks, Damn,  no sky daddy. I hate the truth too .... 

God sucks. It ain't fair, I never want to die ..... so heaven I say ....

I must believe !

  ......  these following videos are from a Christian ,

Definitive Proof of Evolution  10 min http://www.youtube.com/watch?v=i1fGkFuHIu0&feature=related

Proof of Evolution Part II - Summation  10 min  http://www.youtube.com/watch?v=-CvX_mD5weM

Top Myths About Evolution - I   10 min   http://www.youtube.com/watch?v=SJQFp0IfZ1Q

Creationism,   

Creationism's Damage to Christianity  8 min  http://www.youtube.com/watch?v=zBoqKF52FU8&feature=related

Creationism's Damage to Christianity II   10 min   http://www.youtube.com/watch?v=vBaOFKoLlZk&feature=related

Why Teaching Creationism is a Horrible Idea  8 min  http://www.youtube.com/watch?v=dYphna9UTCk

Creationism Dishonesty and Immorality, Part I.  7 min  http://www.youtube.com/watch?v=FoZW7-3YSns&feature=PlayList&p=6818DF8C6AB4A0DF&index=0

Creationism Dishonesty and Immorality, Part II.  6 min http://www.youtube.com/watch?v=bZjxBdyu10A&NR=1

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From another source ,

19 videos on,   Why do people laugh at creationists?    http://www.youtube.com/profile_videos?user=Thunderf00t&p=r

        Want more ??????  people make me