The answer to your question is ... no, you don't have the slightest idea about evolution.  Back away from the creationist websites and their misinformation/lies on the topic.  Go to a bookstore or a library and pick up a book.

This is where I earn my badge title...

In my response to you, I have employed responses that I have already written myself. I have written them as templates en bloc because creationists do not have the mental capacity to write new arguments that I need to respond to. Constrast this to you, being that you do not have the intellect or capacity for original thought, I found this article from a creationist website. You are not allowed to copy and paste responses from other people, regardless of whether or not you inform us.

Nobody claims they do. Evolution is a deterministic process. You've effectively undermined all other arguments you could make because you demonstrate a fundamental misunderstanding: You don't actually know what evolution is.

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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 single cell, 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. This fundamental principle is of such simplicity that even a child could grasp it. By means of incremental change, a variation with advantage may accumulate until it produces a marked physiological and anatomical difference from the organism from which the new species immediately descends.

 

  As forthe other argument contained therein to that subsection, irreduicble complexity is an immensely poor argument, not so much a misunderstanding of molecular biology as one of evolutionary biology, believing that the process entails the addition and deletion of single components, which it usually does not. Normal 0 false false false EN-US ZH-CN X-NONE /* Style Definitions */ table.MsoNormalTable {mso-style-name:"Table Normal"; mso-tstyle-rowband-size:0; mso-tstyle-colband-size:0; mso-style-noshow:yes; mso-style-priority:99; mso-style-qformat:yes; mso-style-parent:""; mso-padding-alt:0in 5.4pt 0in 5.4pt; mso-para-margin-top:0in; mso-para-margin-right:0in; mso-para-margin-bottom:10.0pt; mso-para-margin-left:0in; line-height:115%; mso-pagination:widow-orphan; font-size:11.0pt; font-family:"Calibri","sans-serif"; mso-ascii-font-family:Calibri; mso-ascii-theme-font:minor-latin; mso-hansi-font-family:Calibri; mso-hansi-theme-font:minor-latin;} 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. 

Indicating you do not even know what DNA is, how it works, and using meaningless metaphors to cover a meaningless idea.

You are not familiar with mutation mechanisms or basic genetics.  In proteomic evolution, it is described like so:

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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. Being that this essay is about proteomics, it logically follows that the next will be about genetics. That essay, which I would describe more as a course than an essay, will be discussing in very precise detail genetic innovation mechanisms especially those related to the new field of evolutionary developmental biology and the detail we may go into when explaining the evolution of structures of multicellular Eukaryota, specifically those upheld as evidence of teleology and hence design a posteriori, such as the heart and the eye. This is the next chapter of my exploration of deriving evidence and understanding of evolution from molecular mechanisms and processes.

I think I should clarify this considering how pervasive the claim is. 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:

 

GCA GCC GCG GCU

AGA AGG CGA CGG CGU

GAC GAU

AAC AAU

UGC UGU

GAA GAG

CAA CAG

GGA GGC GGG GGU

CAC CAU

AUA AUC AUU

UUA UUG CUA CUC CUG CUU

AAA AAG

AUG

UUC UUU

CCA CCC CCG CCU

AGC AGU UCA UCC UCG UCU

ACA ACC ACG ACU

UGG

UAC UAU

GUA GUC GUG GUU

UAA UAG UGA

Ala

Arg

Asp

Asn

Cys

Glu

Gln

Gly

His

Ile

Leu

Lys

Met

Phe

Pro

Ser

Thr

Trp

Tyr

Val

Stop

A

R

D

N

C

E

Q

G

H

I

L

K

M

F

P

S

T

W

Y

V

 

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.

 

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 stopped reading after this. You should too. It is quite obvious that this poor twit knows nothing about basic science. Thermodynamics is actually an extensive topic in biology.  Nothing in biology defies thermodynamics. Nothing. Allow me to introduce the topic to you, since this fool knows nothing about it.

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!) or 500 factorial, 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

0000000000000000000000000000000000000000000000000000000000000000000000000000000

00000000000000000000000000000000000000000000000000000000000000000000000000000000

000000000000000000000000000000000000000000000000000000000000000000000000000000000

0000000000000000000000000000000000000000000000000000000000000000000000000000000

00000000000000000000000000000000000000000000000000000000000000000000000000000000

000000000000000000000000000000000000000000000000000000000000000000000000000000000

0000000000000000000000000000000000000000000000000000000000000000000000000000000000

0000000000000000000000000000000000000000000000000000000000000000000000000000000

00000000000000000000000000000000000000000000000000000000000000000000000000000000

0000000000000000000000000000000000000000000000000000000000000000000000000000000000

00000000000000

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. This is excellently indicated when you rise in the morning. The big yellow ball in the sky, which is smiling happily, as it has done for billions of years, is sitting there politely puzzled at this very odd species which appears to deny its existence (creationists). 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.

The concept of "transitional form" is meaningless, and something I refuted above. I can introduce you to it very quickly:

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All life can be traced back to a common ancestor. You share a remarkable lineage, an ancient family tree that stretches back into the eons. Your friends and family share this lineage too. So does your pet, or your neighbour’s pet. The soil beneath your feet has trillions of little organisms, who also share this lineage. It connects the roaring lions on the African Savannah with the flitting birds of the moist rainforests. It binds the dog to his owner and the slave to his master. We are all part of it, and as long as life exists on this planet, none of us can escape from it. This is the lineage which leads all life to a humble proto-cell four billion years ago. 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. On the Incompleteness of the Fossil Record It is surely one of the most popular creationist absurdities to criticize the fossil record, not that animals are found in the wrong strata but rather that the record is woefully incomplete, and indeed, for the justification of this, they have invented a hitherto nonexistent term: “transitional fossils”. One may ask, well, what is a transitional fossil? The response you will undoubtedly get from these simpletons is that it is a transitional morphology between two species during a speciative split. I have no idea whatsoever what this means. 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.

Amusingly, an analogous situation is presented by Kirk Cameron, whose IQ could be unfavourably compared to that of a beet or perhaps a potato. At any rate, Cameron seems to argue, along with a group of similar minded simpletons, that if evolution were true we should see the most odd combinations of creatures such as a phrase which he apparently coined, the “crocoduck” (I assure you that I simply could not make this up if I tried). This is a very odd rehash of the transitional fossil argument. He betrays obvious ignorance regarding divergent evolution. The whole process of evolution is transition in small steps, but often two close species (measured in terms of amino acid divergences in conserved protein domains) are too alike in phenotype for there to be what anyone would consider a "transitional form". As cladogenestic speciation tends to occur when two populations become geographically seperated, the stream of genetic change that causes population X to become unable to interbreed with Y (hence called speciation) is too slow for there to be major recognizable changes within less than several thousand generations. So, supposing someone says if evolution is true we should see transitional forms such as “bird-reptiles” or something along those lines, quite frankly, that is absurd. Especially in this particular case, since Those two Orders are separated by 200 million years of divergence. Evolution does not work along such broad lines, it diverges outward, it never converges inward. Lines of cladograms never meet once they split. Birds and reptiles have a common ancestor, but the more marked the difference in phenotype for an organism is to that which we are comparing, hence, the difference in terms of genes, the farther back that ancestor is.

The three primordial cell groups used to live in primordial single cell communities, promiscuously exchanging genes. This is how the foundation genes of all life were selected. But as the three groups went their separate ways, the gene flow pump shut off, and now, it is a rare occurrence when these groups exchange genetic material. The divergence occurs long before different Orders proliferate. For instance, let us take the split on the level of Kingdoms. Plants and Animals, these are both Eukaroyta, yet their fundamental differences are much more then genetics. All plants have deep within them the result of an ancient symbioses, chloroplasts as well as Mitochondria, The truth is, all 300,000 species of plants are extremely closely related, and all have one thing in common. As explained previously, this is primarily determined via amino acid tracking. Evolution is dependent on homologous sets of genes called orthologs and paralogs. Genes in multiple organisms that obviously descended from the same common ancestor (anyone who bothers should check the amino acid tracking branching tree of hemoglobin evolution as an example) are called orthologs, while genes which occurred as the result of mutation descended from a single gene (thereby producing two or more new genes) are called paralogs. Both of these are called homologs. Indeed, all Cameron is demonstrating is that he has no idea whatsoever how allele recombination works, or how zygotes are formed, or the principle of biological gametes via vertical transfer of genetic material. It does not take transcendent intelligence to understand the principle of the self-termination of the zygote if the alleles of the vertical transfer of the two parents to the progeny are too diverged (obviously, crocodiles and ducks don't even have the same karyotype due to chromosomal polymorphism, so there is no chance such a species could be produced). This is why speciation must work along an inching continuum whereby the split between species works on the continuum principle of gene flow, that physiology and anatomy are in a continuum of morphological change, that the term “species” represents as continuous band of genetic divergence between organisms who can successfully exchange genetic material via vertical transfer, and again I simply refer the reader to the description I made of how this works. When arms of evolutionary phylogeny diverge, they will almost certainly never converge again, the principles of gene flow do not permit it. That Cameron does not understand this and yet continues to make this argument merely indicates to me that he is too ill-educated to grasp a principle which I have been versed in since the age of seven. The gene flow pump is shut off long before the divergence at order level. How can these groups interchange genetic material when only within a species can organisms breed? The different paths of evolution go their different ways. Now, as I explained before, evolution is about divergence and convergence. All life begins from the foundation, and the homologies duplicate, and diverge in function. During all this, they retain common elements (convergence), and as species get more distant from each other ("distant" merely means their most recent common ancestor is farther back, so two maximally diverged species would be two whose most recent common ancestor is the farthest back in the number of years since the divergence occured). For this reason, based on genetic homologs and the tracking of them which is based on the molecular clock technique, we can begin to glean the precise relationships between the two in terms of genetics, proteomics, anatomy and physiology, the four of which are directly tied. This allows us to draw phylogenies and cladograms, which are trees showing how, and from what organisms diverged. We can draw these in terms of specific proteins or genes to see how they have diverged (depending on the principle of "genetic conservation", all genes diverge at different rates).

 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.

 

 

Sorry, don't have time to log in. You guys have proved nothing except Creationism to me so far, I am fine with evolution. And I will be happy to sing it around a campfire along with other fables and myths. I think YOU guys need to search some websites. I would like to point out that I personally (I haven't read the whole thing) have read certain parts of the book "Origin of species" and found it amusing as well as hilarious! The greatest hoax of our life lifetime is the theory of evolution. Nothing can exceed the scope and
size of this scheme to dupe the public into accepting what cannot be proven (i.e. life began from
nonliving matter and slowly developed into thousands of insects, fish, fowls, animals and humans
that live on the earth today). Evolution has been popularized by a propaganda campaign second
to none. A steady stream of unfounded assumptions flow from the mouths of evolutionists via
universities, television, news media, Hollywood, science books and in schoolrooms around the
world. Young, impressionable minds are constantly fed this information from grammar school all
the way through college. Basically, these evolutionists are atheists, and because of their rejection
of God they resort to this conjectured theory. And because they have bought into the theory, they
want to sell it to everyone else.
They use every conceivable angle to promote evolution. A few years back some educators were
claiming that Americans were scholastically falling behind other industrialized nations because
evolution had not been stressed enough in our public school system. Question: how can the
theory of evolution possibly enhance a child’s advancement in the subjects of math, reading,
literature, history, or computer science? I personally think it strange that school children possess
a greater knowledge of extinct animals than they do about animals that still walk the earth. For
example, school children know much more about the size, diet, and environment of dinosaurs
than they know about the common chicken or cow. Ask a kid how fast a dinosaur can run and they
can tell you. However, they do not know the same information about the horse. They know what
dinosaurs ate, but they do not know what food keeps pigs alive or what helps egg production in
chickens. How can this lack of knowledge be helpful to society?
The evolutionary scientists understand the financial windfall evolution can be to their
pocketbooks. It is a virtual gold mine. It is relatively a ripe field for sensational books, magazines,
movies, television and the lecture circuit. The more popular evolution becomes the more lucrative
are their opportunities. Scientists can take in millions of dollars by exciting the public with
sensational theories about dinosaurs and searching for the missing link. It creates many job
opportunities for them in museums and universities. It makes raising funds for expeditions to
search for more fossils easier. The media too has learned that television specials, magazine
articles and movies can make big bucks. It behooves them to keep evolution as glamorous and
as exciting as they can. The movie series Jurassic Park has now reached three full-length
productions. They have proven that powerfully, huge, vicious dinosaurs connected with an
The “Missing Links” Of Evolution Richard Massey
Christian Evidences – 19th Annual Mid-West Lectures Page 2
©2001 – This material may be freely distributed as long as it remains unchanged and proper credit is given for source. It is
not be be sold. For information contact the 39th Street church of Christ, 15331 East 39th Street, Independence, MO 64055.
evolutionary theme can bring in multiplied millions of dollars at the box office. Keeping this hoax
alive is good for their pocketbooks. Public education has, for decades, been in full support of
espousing evolutionary assumptions.
GLARING GAPS
During World War II America tried to keep their work on the atomic bomb a total secret. They
endeavored to stop all leaks of information about this project top secret. Understandably they did
not want their own super weapon to be used against them. Darwinists are also trying to keep
some things a secret about evolution, therefore they rarely speak of them. There are major flaws
in their theory. They prefer not to reveal them. There are gaps in their theory that demolish the
idea of evolution. These enormous gaps could also be seen as impassable chasms. It is
impossible to get from one point in their theory to another. Getting from one-celled creatures to
enormous dinosaurs is one huge gap. Can they bridge the gap? Or does it present a situation
where egg can be seen on the face of some pretty learned men?
THE GAP OF SPONTANEOUS GENERATION
Evolution is based upon a theory that at some point in time, billions of years ago, no life existed
upon the earth, not even one trace of life could be found. But, somehow, a miracle occurred when
just the right mixture of gases and acids mingled themselves together and microscopic organisms
begin to develop. It was impossible, but it happened just the same. In a swamp somewhere on
earth, it is conjectured that non-living matter gave birth to that which was alive. It sounds very
romantic and has captured the interest of thousands, however there is just one major flaw in the
whole scenario. The fundamental laws of science contradict this basic evolutionary premise. The
fundamental law of biology is the Law of Biogenesis. This scientific law upholds that all life must
come from preceding life, and that of its kind. Science teaches that life does not come from
nonliving matter. Dr. Lazzaro Spallanzani and Louis Pasteur proved in the middle of the
eighteenth century that the concept of “spontaneous generation” was indeed false. Dr. Pasteur
in his “victory speech” to the French Academy of Science stated, “The theory of spontaneous
generation will never recover from the mortal blow dealt it by this simple experiment.” The
experiment of which he spoke proved the formerly held theory of spontaneous generation false.
Scientists that promote evolution cannot get their theory to harmonize with this known law of
science. They have a dilemma; their theory contradicts science. Notice the following statement
by Dr. George Wald of Harvard:
The reasonable view was to believe in spontaneous generation; the only
alternative, to believe in a single, primary act of creation. There is no third
alternative. For this reason, many scientists a century ago chose to regard the
belief in spontaneous generation as a philosophical necessity. (Wald 45)
Again, from Dr. Wald,
The “Missing Links” Of Evolution Richard Massey
Christian Evidences – 19th Annual Mid-West Lectures Page 3
©2001 – This material may be freely distributed as long as it remains unchanged and proper credit is given for source. It is
not be be sold. For information contact the 39th Street church of Christ, 15331 East 39th Street, Independence, MO 64055.
Most modern biologists, having reviewed with satisfaction the downfall of the
spontaneous generation hypothesis, yet unwilling to accept the alternative belief in
special creation, are left with nothing…To make an organism demands the right
substances in the right proportions and in the right arrangement. We do not think
anything more is needed—but that is problem enough. One has simply to
contemplate the magnitude of this task to concede that the spontaneous generation
of a living organism is impossible. Yet here we are—as a result, I believe, of
spontaneous generation. (Ibid)
Can you believe the irrationality of that statement? Evolutionists try to bridge this enormous gap
by just ignoring the distance across it. It is like trying to cross the Atlantic Ocean in one
impossible giant step. You cannot get living organisms from spontaneous generation. Nonliving
matter cannot produce anything, due to the fact that it is not alive. This is a proven and accepted
scientific law, and yet they completely ignore it.
What is the probability of spontaneous generation happening just once in history. Consider the
basic law of probability formulated by Dr. Emile Borel,
This law states that the occurrence of any event where the chances are beyond one
in one followed by 50 zeros is an event which we can state with certainty will never
happen, no matter how much time is allotted and no matter how many conceivable
opportunities could exist for the event to take place. (27)
Dr. Carl Sagan of Cornel University calculated the probability of life evolving on one planet to be
one chance in one followed by TWO BILLION ZEROS! In other words, the odds of spontaneous
generation occurring even one time are literally impossible. Life could not have simply occurred
by accident.
THE GAP OF MISSING LINKS IN ANIMALS
Evolutionists propose that over the course of billions of years all life evolved from single cell
organisms. They tell us that the whales, elephants, giraffes, hippopotamus, dinosaurs, mammoth
elephants, rhinoceros and walrus were at one point little small creatures. They want us to believe
their theory that small animals slowly mutated and change many, many times over billions of
years. Their theory is that these mutated animals slowly increased in size until huge mammals
and reptiles roamed the earth and all sizes of sea creatures developed in the oceans. Just
thinking about that is an incredible, mind-boggling thought. There is one problem with which these
evolutionists must cope—no evidence. If their theory is true then there ought to be literally
millions of fossils that show thousands of transitional forms of all of these animals. There should
be thousands upon thousands of bones that became fossilized during those billions of years
which record the necks, legs and bodies of the giraffes slowly getting bigger and longer. There
should also be plenty of fossil evidence showing the development of dinosaurs, horses, cows,
alligators and all of the other animals known to man. However, there are none. Absolutely no
transitional fossils exists to prove their theory.
The “Missing Links” Of Evolution Richard Massey
Christian Evidences – 19th Annual Mid-West Lectures Page 4
©2001 – This material may be freely distributed as long as it remains unchanged and proper credit is given for source. It is
not be be sold. For information contact the 39th Street church of Christ, 15331 East 39th Street, Independence, MO 64055.
This theory also calculates that reptiles gave rise to birds. That millions of years ago a baby
alligator (or similar dinosaur-type reptile) hatched from an egg with feathers growing on its rough
skin. Then slowly, over millions of years, the alligator with feathers developed a beak. If the fully
feathered bird evolved from the reptile family, then we politely ask, where is the evidence? Where
is the proof that will substantiate this assumption? The fact of the matter is, no proof at all exists.
There are millions upon millions of missing links throughout the animal kingdom. Missing links for
ostrich, tigers, brontosaur, seal, octopus, bat and all other creatures. No fossil proof has shown
transitional forms in any of the species. The fossil record does show the sudden appearance of
the dinosaur, the horse, the birds, as well as all of the other animals of the world. The lack of
transitional forms in the fossil record actually strengthens the creation account of the Bible. The
Bible explains that God created all things fully developed in six literal days (Genesis 1-2; Exodus
20:11).
Postulate all they might, they still have no hard evidence that any animal evolved from another.
They rely solely upon similarities. They conjecture that since a man looks similar to a monkey,
he must have evolved from one. That is the only proof that they can offer for evolution. That
proves nothing. Because football stadiums in America have similarities to the ancient coliseum
in Rome does not prove they evolved from one another. Because clouds can have the shape of
an elephant does not mean that elephants came from clouds. Anyone can see that. The
similarities in animals can also prove that the one and same being—God, created them all.
THE GAPS OF MISSING LINKS IN HUMANS
Since Darwin published his book, The Origin Of Species, a frantic search has been made to find
the “missing link” between primates and man. Scientists have been searching endlessly for any
kind of evidence that would help bridge the gap and show their theory to be true. According to
Darwinists, man evolved from the apes and so any suspicious bone fragments or unidentifiable
teeth they find are usually hailed as the illusive missing link. Their supposed “missing links” so
far have either been simple cases of mistaken identity or a hoax.
Java Man was named from skull fragments of a gibbon found in 1891 by Dutch physician, Eugene
Dubois. Fifty feet away were found other bone fragments of a human. They put them together and
gave it the name of Java Man. A decade before he died, Dubois admitted that Java man appeared
to be nothing more than a large gibbon. Piltdown Man. Bone fragments found in 1912 were
thought to be that of a cave man. Scientists were fooled by alterations someone had done to the
bones to make them appear older. After testing in 1953 it was admitted that the skull was human
to which someone had attached the jaw of an orangutan. Peking Man. Dr. Davidson Black
discovered some teeth and bone fragments in a cave. Though he classified it as a possible
“missing link” his bone fragments and 147 teeth he found have all disappeared. Therefore, they
are no longer available for examination. However, in the same cave there were also found many
more human skulls which presents a dating problem for Peking man being the ancient “the
missing link.” Other scientists have claimed to have found the link between primate and humans,
The “Missing Links” Of Evolution Richard Massey
Christian Evidences – 19th Annual Mid-West Lectures Page 5
©2001 – This material may be freely distributed as long as it remains unchanged and proper credit is given for source. It is
not be be sold. For information contact the 39th Street church of Christ, 15331 East 39th Street, Independence, MO 64055.
but not one of them has been able to pass the test of approval under scientific scrutiny. Dr. Lyall
Watson, an evolutionist, stated that the fossil record does not support evolution:
Modern apes, for instance, seem to have sprung out of nowhere. They have no
yesterday, no fossil record. And the tru origin of modern humans—of upright,
naked, tool-making, big-brained beings,– is, if we are to be honest with ourselves,
an equally mysterious matter. (Moore)
At least a few honest ones of their number will speak frankly about the lack of evidence. Quite
frankly, we need more admissions of this type in books that the public school use.
CONCLUSION
Evolution contends that life first came from nothing. Then it claims simple celled animals gave rise
to higher life forms. Finally it postulates that man evolved from the ape. This theory can never
have any legitimacy until it has some evidence to back it up. It presents no proof to substantiate
these major premises. As a matter of fact, the evidence happens to point convincingly toward the
fact of creation and not evolution. We would hope that each reader would simply examine the
evidence and reach the logical and reasonable conclusion regarding evolution.

Thanks for TRYING to disprove Creationism, but you once again failed, and I would like you to know I will try to pray for all of you!

Ilikegod

You claim to have read the posts of your interlocutors in this conversation, and presumably you are pertaining to mine.

Your post occured at 1134 (GMT +8), precisely nine minutes after mine. Nine minutes is not nearly enough time to read, respond and comprehend a post of that length, especially since you do not have technical training. The only reason I responded so quickly to the OP was because I had already read the article he has posted.

Secondly, the post-format pattern in your post indicates copy-and-pasting, and unless you list the source, unless you are the source (which you are not) then that is plaigarism and you get two warnings before the mods terminate your welcome. You did not write that post. The lack of spacing indicates incorrectly formatted copy-and-paste. 

So, not only did you not read my response, you actually plaigarised from somebody else. You did not construct arguments, you listed reading materials. A proper argumentative response entails line-by-line response. Since my response was tailored specifically to the Original Post article, I have obeyed all of these common courtesies...you, you have not. The mods do not like kindly on those who copy and paste from others, and have nothing to contribute. we have bandwith problems as it is. 

http://www.rationalresponders.com/irreducible_complexity_reduced_to_absurdity



This claim is just so ludicrous I don't know where to start.  You honestly think scanning space for signal patterns has something to do with DNA?



Shame it was proven by a creationist just recently.

http://www.rationalresponders.com/forum/yellow_number_five/evolution_of_life/12425



http://www.rationalresponders.com/forum/yellow_number_five/science/101



Once a fossil is found, it is given a name.  If there's no life form to associate it to, one is created for it.  Evolution does not claim that one day a creature will give birth to another.  It's more the case that gradual changes happen slowly over time through THOUSANDS of generations until eventually there's been enough changes that a creature will have to be classified differently.  In other words, ALL fossils are transitional forms as they ALL have minor changes from their parents.  Even YOU are a transitional form.



http://www.rationalresponders.com/forum/yellow_number_five/evolution_of_life/8571

Horses and Zebras are considered different species, yet right here we see a cross.  This is due to the two species not being seperated that far via gradual changes that they cannot inter breed.  So, your claim that modern humans would be able to breed with "ape-men" makes these ape-men actually human is false.  



http://www.rationalresponders.com/forum/yellow_number_five/science/3445

Refer to the post from deludedgod.



I fail to see your point here.  It just shows a lack of understanding in medicine.  Not all vestigal body structures have had uses found.  Whales still have hip bones, some dolphins are still born with hind legs etc etc.  



Evolution has got nothing to do with the creation of life.  Evolution is simply about the changes of life over time, from one form to another.  The creation of life is called abiogenesis.

http://www.rationalresponders.com/compilation_of_works_from_deludedgod



http://www.rationalresponders.com/forum/yellow_number_five/science/11875

Macro evolution is just a term invented and thrown around by creationists.  It is nothing more than a large number of micro evolutionary changes.



Charles Darwin proposed a new idea, a new concept.  He did not have the knowledge or equipment to figure out every single fact about evolution - only the starting blocks.  If evolution was false, we would not be able to use it in a practical sense today as we do.  Evolutionary biology and chemistry are used on a daily basis to produce new drugs and medical procedures.



Copied from AiG, yes.  The biggest perveyors of bad science, misinformation and lies on the internet.  Nothing you stated is new, it's just a shame that I couldn't find earlier refutations from some of them (there's only so much a google search can do).

Depressing...read a book and form your own opinions you forum ninja.

Have you ever thought why evolution has never been disproven? BECAUSE EVERY TIME IT IS THE "THEORY" IS REVISED TO FIT THE NEEDS OF ATHEISTS AND KEEP THE "THEORY" ALIVE!

Do you want to believe in a hypothesis like that?

You mean like the hypothesis you follow:

Magic->"goddidit"->Creationism->Creation Science->Intelligent Design?

Yes, because this is how science works!! Do any Creationists even know what the scientific method is??? Jesus F'n Christ man!! read a basic 2nd grade science  book.

This is an argumentum ad consequentiam and is therefore completely and utterly irrelevant to the topic at hand. Please stop issuing random red herrings and focus on the topic at hand.

All of the following utterances by you:

All of this is completely and utterly irrelevant to this topic. What's the matter? Can't take that I exposed you for the incoherent, plaigarising simpleton that you are? I suggest you start focusing here, because you are, at this point, derailing the thread with random, preachy nonsense as a cover up for the fact that you don't have the first damned clue what you are talking about. Sit down, shut up, read the posts of your interlocutors, and then you can stay. Otherwise, do not waste my time and the time of everyone else here with random babble, idiocy and nonsense. 

Everything I quoted from you above directly is your personal opinion, emotion and feelings. These are completely worthless in the debate we are having, which is meant to be pertaining to the validity of evolution. You have no training or expertise in these matters. You probably would not be able to answer the most basic questions pertaining to evolutionary biology, such as what the three principles of natural selection are, or what Muller's Ratchet is, or an example of Non-Mendelian inheritance, or what the transcriptome is, or what meiotic recombination is, or what a heterozygous allelle is...all high school level questions. Now, unless you can think of something intelligent to contribute, I suggest that if your posting quality is to continue in the manner it thus far, that you stop posting lest you be laughed out of the room. 

You have the gall to ask me to study physics? This coming from you? Dear sir, my physics education surely supersedes your own by orders of magnitude. Do you know the formula for the Lorentz contraction, or the Einstein-Polodsky-Rosen thought experiment, or the zeroth law of thermodynamics is? What about superposition, or relativity of simultaniety, or the Relativistic Doppler effect?  Do you know the answer to any of these?

Lastly, pertaining to the question of which I would pick...I would rather that which the evidence demonstrates than that which makes me feel better. For the purpose of gleaning objective knowledge, it is necessary to divorce yourself emotionally. Your emotional stance on a matter is utterly irrelevant to its empirical truth. Your rhetorical ploy is just an appeal to ad consequentiam combined with a non sequitur to make a meaningless rhetorical appeal. Indeed, your entire post is a clever piece of irrelevant misdirection. We are in a debate pertaining to the validity of evolution, and you walk in and announce that you'll pray for us? Dear sir, you are truly sunk here. You are ignorant, uneducated, arrogant, vapid, mendacious, pernicious, noxious, virulent and insipid. Now start addressing the arguments of your interlocutors or get the hell out.

 

 

 

DG do you mind if I repost or use any of your materials on another website and for an upcoming debate? I will cite you and post a link as well, ofc.

Ok Mr. Evolutionsucks.

Let's say that everything  you said in the opening post is true, which is hilariously not but let's say that it is.

Let's say that evolution is a huge scam that the entire scientifique community have build up in order to confuse us, miserable laymen...

So what ?

Let me rephrase...

So fucking what ?

Disproving evolution doesn't prove creation, period !

Why don't you guys try to prove creation instead of disproving evolution ?

Oh !!!!! I know I know.... Cause you can't !

Life's a bitch isin't it ?

Ah ah !!!! I have disproven the flat earth theory... As written in my divine Book, the earth is thus conic ! Take that you evil flat earth theorist !!! 

Absurd logic isin't it ?

 

 

 

And now I continue.  In what way is a gene or chromosome duplication event followed by mutations on the duplicated gene or chromosome not adding information to the genome?  How are mutations in general not adding information to the genome?  Esspecially insertion mutations.  We know for a fact that such mutations happen, so if they do (and they do) count as adding information to the genome, then we do know of mutations that add information to the genome.  Also a bunch of wonderful examples, most of them not at all relevant to your question, then there's the evolution of bacterium who could digest nylon and the waste products of nylon production.  They evolved novel enzymes, known collecvtively as Nylonase.  Analysis of the Nylonase genes shows that Nylonase actually did evolve through mutation, the ability was in no way present previously.  The evolution of another way to do the same thing was also reproduced in a laboratory setting with a different species of bacteria.

http://en.wikipedia.org/wiki/Nylonase

 

I have to be honest this is one of my favorite questions.  Everyone who asks this demonstrates immediately that they know almost nothing at all about physics.  The second law of thermodynamics actually states:

"The total entropy of any isolated thermodynamic system tends to increase over time, approaching a maximum value. "

Entropy is just a measure of how close a thermodynamic system is to equilibrium.  As it turns out entropy has little to do with disorder.  It has everything do with the fact that everything in the universe in a vacuum of external energy will tend toward its lowest energy state, at that point the system will be at equilibrium.  As the universe, or any given thermodynamic system, is attempting to reach equilibrium all sorts of complexity is allowed.  Even thermodynamic systems at equilibrium may be more complex or ordered than they were with lower entropy.  Now since it would require the addition of enormous amounts of energy to prevent stars from collapsing stellar formation in no way violates the law of entropy.  And then we come to life.  The second law of thermodynamics applies as a barrier only to closed systems.  The earth is not a closed system.  We recieve energy from the sun.  Organisms on earth are also not closed systems.  We maintain a lower entropy level by eating.  This helps us to maintain the constant chemical reactions going on within all of our cells.  If we stop consuming food we stop slowing down our increase in entropy and our chemical reactions will eventually reach equilibrium and when they happens we die.  Also important to know is that only chemical reactions that result in a net energy loss or no energy loss are permissible due to the second law of thermodynamics.  This is also why we need to constantly consume food. 

http://en.wikipedia.org/wiki/Gibbs_free_energy

Yay!  Isn't finding accurate information fun?

It's because of the nature of fossilization that fossils of transitional forms are so hard to find.  On the other hand we are surrounded by zoos of living transitional forms.  In fact every person living is a transitional form.  Ebery animal living as well.  Evolution is descent with modification.  Every organism born is a slightly evolved member of its species in some small usually undetectable way.  It's the evolutions that confer advantages to an organism in its environment that in most cases are passed to future generations because the organism with the beneficial mutation is the organism that is most likely to survive to breed.

Back to the fossil record, because of the nature of the process of fossilization scientists would consider it miraculous and completely unexplanable by anything we knew if every relevant transitional form were represented in the fossil record.  By relevant I mean every transitional form that resulted only in a species that lives today rather than the many mutations that didn't survive because they proferred no benefit, or were actually detrimental.  It is interesting to note that the fossil record shows many branches of this nature, branches of species which just died off completely contributing nothing to the diversity of species alive today.

If every transitional form of every species were represented in the fossil record, for one thing the vast majority would be indistinguishable, because fossils only preserve the major morphological changes that are reflected in the skeleton, not the minor cellular changes or the changes to any soft tissue at all.  Then there is the fact that we would almost be forced to conclude miracle.  The process of fossilization makes that physically impossible.

http://en.wikipedia.org/wiki/Fossilization

And remember there's no such thing as macro vs micro evolution.  "macroevolution" is only the gradual accumulations of "microevolutions" over time.  If you want to assert that that can't happen you should read up on the Continuum Fallacy (http://en.wikipedia.org/wiki/Continuum_fallacy).

Now all that being said you also ignore the fact that many transitional forms have already been found, and significant ones.  The transition from fish to amphibian, fish to reptile, reptile to mammal, reptile to bird, and land mammal to sea mammal are, with teh exception of the reptile to bird transition, very well documented in the fossil record.  The fossils we have of these transitions are more then sufficient to show that this evolutionary pattern happened, and the missing transitional forms can only tell us more about the order of certain even smaller changes that are interesting but will never invalidate what we know.

http://en.wikipedia.org/wiki/List_of_transitional_fossils

This is actually wishful thinking on your part.  They use the exact same method we use to reconstruct faces on discovered skeletons for the purpose of trying to identify john or jane does.  The method involves looking at the groves and other markings that muscle material wore into the skeletons in order to rebuild the musculature and then place body tissue on top of that.  The method for determining what the skin looked like is a little more guesswork, but is generally based on how much more similar the specimen is to one species as opposed to another.  If the specimen is more similar to an ape then they guess that the specimen will have skin and hair that is more similar to an ape's.

It all comes down to one thing, though, all of the aspects that are mostly guesswork are entirely superficial.

Everything in this "objection to evolution" is false.  Decay rates have been shown to have nothing at all to do with the chemical makeup of the environment an element is found in.  the only thing that matters to the decay rate of an atom is it's nucleus's stability.  I would bet that you couldn't produce the scientific experiment that showed that decay rates were dependant on anything else.  Decay rates were also shown to have been constant for hundreds of thousands of years relatively recently when we observed a supernova hundreds of thousands of light years away.  Scientists observed certain radioactive clouds within the nebular aftermath and were able to predict and then measure their rate of decay and that rate of decay matched up with the predictions. 

http://www.talkorigins.org/indexcc/CF/CF210.html

http://www.talkorigins.org/faqs/hovind/howgood-c14.html#R2

The second link addresses a lot of young earth creationist arguments in general in a very detailed and interesting manner.

This is just an example of evolution at work.  The appendix is a good example of this specifically.  Our appendix is derived from an organ that is fully functional in chimps and used to digest plant matter that we no longer eat.  Our appendix no longer serves its original purpose at all, but it seems that it is slowly being coopted by our immune system.  Recent studies suggest that the appendix produce some immune system proteins.  Currently, however, our appendix is anything but necessary for any purpose at all and can be safely removed with absolutely no adverse effects.  This is because the appendix no longer performs its original function at all, and it doesn't yet perform its new function in any way that makes it important.  It is a true vestigial form.  The appendix had two possible evolutionary paths available to it from the time when it became useless.  It could disappear, or it could become adapted to a new purpose.  It would seem that it is going along that second path, at this point, however, only time will tell.

http://www.talkorigins.org/faqs/vestiges/appendix.html

But if you really want to talk useless vestigial forms, why do some whales or dolphins still have leg buds sometimes, and in at least one documented case, fully formed feet?

http://www.msnbc.msn.com/id/15581204/

http://www.talkorigins.org/features/whales/

Spontaneous generation was the rediculous idea that if you left out some meat maggots and other parasites would just spontaneously appear on the meat.  Also if you eft out garbage the rats would spontaneously generate.  Yes spontaneous generation is a ridiculed, and rightly so, idea.  It's entirely impossible by what we know about science.  As for the origin of life, that is an entirely different field of science, a branch of chemistry known as abiogenesis.  Abiogenesis is not all rediculous.  It takes into account what we know from biochemistry, that life at the biochemical level, obeys all of the laws of chemistry.  It also takes into account the fact that all of the materials needed to make life were present in the early earth.  The fact that we know now that organic compounds can be formed through simple reactions from nonorganic compounds.  The fact that asteroid and comets that have impacted earth or been probed by satellites show that the necessary compounds for life, amino acids and nucleotides, exist all through our solar system.  And the fact that evolutionary theory shows us that all of life on earth shares a single common ancestor.  Abiogenesis needs only account for the generation of one single celled organism that reproduced.  Not at all similar to spontanous generation.

Your coin toss example is completely rediculous.  A better analogy to what scientists think about evolution and abiogenesis would be a state lottery.  If you look at the odds of an individual winning they aren't so good.  However that is the most common way creationists look at the lottery analogy and it is another wrong way to look at it.  If you look at the odds that a given state lottery will be won given enough people playing it you start to approach a more valid analogy.  A state lottery with enough players will almost inevitably eventually see a jackpot winner.  That's how evolution works.  There's a lot of genomes playing that lottery, one of them is going to hit the jackpot.

I also thought it was funny when your analogy went from saying one thing irrelevantly but almost tangentially relevantly to saying something completely different in a completely irrelevant way.  Bravo.  I laughed out loud when the coin sprouted arms and legs.

The scientific method reasons from existing information about what isn't already existing information.  It then attempts, by experimentation, to test the hypothesis we derive by reasoning from what we know to what we don't know.  The scientific method is not at all limited to what we have information about, it's a method that tells us what we should be seeking new information about and a method that tells us how best to do that in order to ensure the accuracy and integrity of that information.  Conclusions about what happened in the past don't have to be based on direct observation of those events in the past.  Only direct observation of the modern results of those events in the past.  How do you know that the american revolution ever took place?  You weren't there?  But you can see the modern results of that revolution.  Just a simple example.  First thing that came to my mind.

I wonder what evidence you've looked at.  It seems clear to me from your apparent lack of understanding of any aspect of science that you brought up, that you did not research what actual scientists have to say on any of these topics.  I wonder if you didn't start your research from a conclusion and look only at sites, sources and information that confirmed the conclusion you already decided was true?  If that's the case how do you determine that your conclusion is actually true if you never look at sources that call it into question and then rationally answer those objections?

Darwin's theory of natural selection is referred to almost constantly, but his book itself not so much because new information which confirms and adds to his original work has been uncovered and is more relevant now.  Since most papers are far more specific and detailed and references to On Origins of Species are generally considered unnecessary in a peer reviewed biological paper.  Darwin doesn't need credit for specific aspects of a biologist's discovery because anything based on Natural selection, and that's almost everything about evolution, though not actually everything, is based on Darwin's book primarily with more information later added.  We don't need to constantly refer back to his specific words, though, because he was only describing what he observed and has since been independantly verified by observations made by many other scientists in every other related field.  Darwin is not the only or primary source of information about natural selection as the bible is about god.  Honestly if Darwin came back to life today he'd be absolutely shocked to discover exactly how much MORE reason there is to believe his theory than there was when he died.

Well I hope that helped, though experience tells me you'll special plead away everything I've said rather than even for an instant consider any of it.  It doesn't confirm your presupposed conclusion so it must automatically be false.  That's no way to determine truth, but let's face it, truth has almost nothing to do with these questions.

This OP is a flaming troll and probably, also, a Poe.

Why is it afforded any bandwidth?

Goo or dirt ? hmm... I don't remember what the bible said.

Wasn't it dirt ?

Yeah, I think it was dirt...

You are right !

Dirt is way far better than goo. If I had to choose between coming out of divine dirt or from yukky smelly goo stuff... I would choose magical.. I'm sorry... Divine Dirt.

I am now a born again Christian...

Let me share the joy that was brought upon me by becoming this enlightened God fearing woman. I now have the priviledge to act as a slave to this Monster that will torture me for eternity if I ever question the nature of the universe... ... I am now accomplished. Feel the monster's luuuuuuuuuuuv !

HE GOT US MAN! DAMN, GOD IS GONNA GET PISSED AT ME JUDGMENT DAY!

EVERYONE PRAY PRAY PRAY!

 ................zzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzz................

Nope, havent see this junk crap before.

This moron obviously thinks we have NEVER run into the "Pay no attention to my mythology" bait and switch distraction.

Now, EVEN IF, one could debunk evolution, it would not default to Jesus over Yahwey over Vishue or Allah.

This is just Christian backpeddling trying to retrofit science after being caught in a lie.

Hate to burst your bubble, but if EVERYTHING IS DISIGNED like you say, then that means nasty bugs and viruses like AIDS and Ecoli and Cancer, are disigned as well. Is your fictional sky daddy willing to take responsibility for "designing" such nasty things?

You just cant stand the fact that you have no ghostsperm and cant get a 3 day old dead body to dance the jig.That is why you attack solid science by twisting it and basterdizing it in a pathetic attempt to distract us away from your absurd superstition.

Evolution IS  fact otherwise scientists would not be having to year after year come up with new flu vaccines. BECAUSE THE FLU VIRUS KEEPS EVOLVING. 

Insted of buying the fairy tales your preacher sells you, pick up a biology textbook and learn. 

19 hijackers put faith in the "revealed Word" of Allah, and we all know the unfortunate effect of their "faith".

Keep your head in the sand. I can see that not being a puppet is too difficult for you. 

 

 

 

 

 

 

You would only be censored if you insist on posting anonymously.  Otherwise you can feel free to call them morons as long as you have more to say.