http://www.rationalresponders.com/forum/yellow_number_five/science/9731

 My response is taken from my notes on the matter. There is no reason that I should write a response all over again since I see these arguments on a daily basis. I will not do the simpleton who wrote this article the dignity of wasting my own time doing just that. 

This sentence is a swift and immediate indication that the writer does not know anything about evolution, or indeed, biology at all. 

There is no process difference between "micro" and "macro". "Macroevolution" is just a broad term which refers to any evolutionary change which involves speciation. Although there are some creationists who challenge that speciation is impossible because species by definition can only exchange genetic material with those of the same species, such statements require egregious understanding of basic genetics. For one, the concept of "species" entails by virtue of its meaning a continuum of possible genomes with small differences such that sexual recombination is still possible (In asexual organisms, the concept of species is even more arbitrary). When examining species which have diverged from each other from a common ancestor tracing back, say, 50 million years, the intra-species genomic changes will be neglibible compared to the inter-species genomic differences. Generally speaking, when two human genomes are sequenced at random, they will differ in approximately 0.1% of the sequence. Which would compare to a much greater percentage between a human and a mouse which also needs to take chromosomal polymorphism into account. When dealing with such disparities, we refer to what is called the fixed difference, that is, the difference that will hold true of inter-species mutation for any two representatives of the two species being selected because the intra-species difference is negligible in comparison. 

So, to understand how speciation works, at least, at an extremely basic level, it is necessary to understand that any gene frequency that is now a characteristic of the whole species began as a mutation in a single organism. If this organism exists in a breeding population of size N, for sexually recombining organisms, than for diploid oragnisms, the initial allele frequency of the mutation which later spreads throughout any population is obviously (N/2). The change and rate of change of this allele will depend on consequences. If it is deleterious, like most, it will probably be eliminated quickly. If it is selectively neutral, it can spread via sampling error, the general rule is that for any neutral mutation, it will take 4N generations in a population of constant size N, to spread through the genome. As for benificial mutations, such spreads are determined by virtue of their ability to propogate, by which I mean increase the survival and procreation of the organisms which hold it, and so, itself. This holds true regardless of whether one accepts gene centers evolution. 

There is really no difference between micro and macro. When there are two species which are recently diverged from a common ancestor, their fixed difference will be hard to measure, because the intra-inter species differences will not be as clear as for a solidly established divergence that occured, say, 100 million years ago from their common ancestor. Speciation simply reflects that genome changes are continuum by nature, and there is no functional or process difference in the selection processes, it is simply the compounding effect of...well, more time, generally speaking. The laws of biology dictate that evolution will occur. Because mutation rates for each gene remain constant for that gene based on its functionality, the general rule of thumb on a molecular level is more time=more divergence. This is called the molecular clock and is firmly established by modern molecular phylogenics, making use of a class of nucleotide sequences called fibrinopeptides. 

The concept of "species", strictly speaking, is arbitrary for the bulk of the taxa in biology. A species is normally defined if we have a group of organisms N, that all organisms in population N do have the capacity for exchange of genetic material, but of course, for 99.9% of all species, this is a meaningless distinction, because about 99.9% of species reproduce asexually. 

Organisms in which the genetic material was received from two parents as opposed to just one parent passing onto progeny are called diploid organisms. We are such organisms. In humans, sexual exchange of genetic material occurs between the germ lines of males and females. In males, the germ line is formed by specialized cells called spermatozoa, and in females, by cells called egg cells or oocytes. In these organisms, all the progeny will possess two copies of the genetic material needed to encode it. One from the father, the other from the mother. The “ploidy” of the organism denotes the copies of genetic material in question. A polyploidy organism therefore has multiple copies of the genetic material that constitutes it. In a sexually reproducing organism, the fundamental laws of genetics explicitly state the each parent must make a precisely equal contribution to the genetic material of the progeny. That is, you have precisely the same contribution in terms of genetic material from the father and mother. These two copies of the genetic material are called alleles, a concept examined in greater detail next.

There is a logical consequence of this. If organisms are diploid, then each of the two germ lines must be haploid. That is, the two haploid cells are needed to make a singular diploid cell. In humans, the two haploid cells in question, are, as alluded to before, the sperm and the egg.

A haploid organism only has one copy and therefore reproduces, by definition asexually. There are some exceptions to these fundamental laws of genetics (because organisms such as yeast can switch between haploid and diploid, ie the haploid cells can fuse to become diploid cells).

Although most multicellular organisms pass on genetic material via gametes, both animals (sperm and egg) and plants (fertilized seeds), some plants and other multicellular organisms, even a handful of aminals do not (although the large majority of animals reproduce asexually). If this is the case, they reproduce through a variety of means. One of which is called parthenogenesis (which entails the embryo can be produced without fertilization), and another is called vegetitative parts, and the other most prevalent is called "budding". These three all have in common the lack of a gamete, and the genetic material is passed on without sexual recombination, or fertilization by the combination into diploid of the gametes of two sexually reproducing organisms (such as a seed being fertilized by pollen). In many plants, the new offspring will bud off the side of the parent plant, and become an extension of the same body. These mechanisms are common in ancient lower plants, although in higher plants, fertilization tends to be the rule of thumb. In Fungi, asexual reproduction is especially common, especially budding, although such budding often also occurs in plants, the most notable being the Hydra plant. Many fungi also propogate themsleves through the mechanism of vegetative growth, in which new individuals offshoot locally, similar to budding. Asexual reproduction such as this is not to be confused with hermaphroditism. Some species are hermaphradotic, which is to say that they contain the reproductive machinery of both genders on the same body. This is still technically sexual, for it involves the recombination of two sets of genetic material. Such reproduction, being that it does not entail the creation of an organism with a unique recombinative set of genetic material, unlike sexual reproduction, is called cloning.

 For this purpose then, genetic changes are wholly continuum. MAcroevolution simply entails more genetic changes because of more time. There is no functional distinction. The writer is simply ignorant to make this distinction, and demonstrates he should probably go back to school.

This is rather unsuprising. Fossilization is a remarkably rare process because it requires the animal to be trapped within a layer suitable for fossilization. The bulk of organic matter, including the skeletal system, decays upon death. Much of it is piled under layers of anoxic silt, in which case pressure accumulation eventually leads to the formation of oil and coal. However, it would not really matter if we had no fossils whatsoever, and indeed, such a scenario is not unlikely, we would still be able to track macroevolution by virtue of molecular phylogeny.

Again, this claim is a lie. The bulk of all life on Earth is prokaryotic, about 99.9% of it. For the vastest stretch of geologic time, our ancestors were unicellular. The original formation of progenitor cells is not a topic which is covered by evolutionary biology anyway, that is primordial chemistry, no theory explains everything. The evolution of single cells is actually something we can track in a lab, very simply, because they reproduce at a much faster rate than multicellular Eukaryota. Actually, much of our knowledge about mutation comes from single celled organisms. I imagine the writer has not spent a great deal of time in the lab.

This is utter nonsense. It is a reference to Irreducible complexity, a tired doctrine. Consider what I wrote on the matter:

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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.

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, such as, in this case, the Type III secretor system of bacterial toxin pumping).

Hence, we may conclude, that instead of this backward examination (what is the effect on X if we remove a part?), which presupposes an eschatological nature of evolution whereby the system works "towards" this goal by means of "adding parts", we view evolution, not being escathological, as using exaptation to recombine pre-existing functions to create the new mechanism. When we subdivide this not by its functional homologous relationship to other mechanisms, but rather by an arbitrary definition of a "part" is where the fallacy occurs, and the illusion of Irreducibility is generated.

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

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

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

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

∆Ssea =h/T

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

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

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

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

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

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

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

This is given by the following formula

∆G=∆G(s)+RTlog{A}/{B}

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

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

-∆G(s)=RTlog(B)/(A)

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

{B}/{A}=e^(-∆G(s)/RT)

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

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

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

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

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

-∆G= ∆Ssea +∆Sbox =∆Suniverse

A reaction will spontaneously proceed in the direction where ∆G<0, because it means that the ∆S will be >0. They are inverse functions of each other. For a complex set of coupled reactions involving many molecules, one can calculate ∆G by adding the ∆G of all the different types of molecules involved before the reaction, and comparing that to the ∆G of all the molecules produced by the end of the reaction.

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

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∆Ssea +∆Scell =∆Suniverse

The entropy of the local system can decrease, providing the entropy of the global system increases. 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.

Don't copy/paste articles, Kingdom9.

And why do you people care sooooooooo much about the theory of evolution ? Why don't you attack other theories as well ?

I never ear you complain about general relativity ! And if you ask me, general relativity is so much more weirder and less intuitive than the theory of evolution. 

That's a great fucking idea LOL !

Yeah ! Read it !

You'll be more suited to refute evolution after that. lol

I dare you to find me a single science book that says that we know what the origin of life is.

Origin of species is the name of the book, not Origin of life.

Well, you essentially copied and pasted an argument taken directly from the article I just refuted, which means you did not actually respond to my refutation to the argument, indeed I would seriously doubt that you completed or even began reading it. Approximately half an hour ago, I was only faintly amused at you. Now I am irritated.

For one, the concept of theory in scientific methodology is not synonomous with the layman's definition. A theory represents an experimentally tested and confirmed hypothesis by proper method, theory in layman's terminology is to what hypothesis is in science. This means that every time somebody acknowledges that evolution is a theory, they are acknowledging it has been confirmed. Hence those who make such statements as if they were arguments against a proposition on grounds that it is a "theory" are actually affirming it. 

Of course, you have the obligatory Godwin violation, which means you lose the debate immediately, being that in any thread, in any forum the law explicitly states that any comparison with the Nazis' or Hitler that is not justified causes a swift and immediate loss of the debate for that participant. Your comment regarding Hitler and Joseph Goebbel's was meant to evoke emotional response and was not actually a reasoned argument which had anything to do with the topic at hand. For this very standard violation you lose the debate immediately.

From whence did the person from whom you took that quote derive the statement that sexual changes in original diploid organisms were rapid and drastic? The origin of diploid organisms is very, very recent in the evolutionary time scale, but that is the geologic time scale, for comparitive purpose. The original sexually reproducing organisms were haploid-diploid, for example, the common yeast. 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;} A set of GRP Determines Cell type in a Budding Yeast. The yeast can differentiate into three distinct cell types. It is a singe celled eukaryota that exists in either a haploid or diploid state. Diploid cells form by a process called mating, two hapoloid cells fuse. In order for such fusion, the two haploids must be of different mating type (sex). In yeast, there are two mating types, alpha and a, which are specialized for mating with each other. Each produces a specific diffusible signaling molecule called a mating factor. They also produce a specific cell surface receptor protein. These jointly enable the cell to recognize and be recognized by the opposing type, and then they fuse. The resulting diploid called alpha/a. They are distinct from either parent. They cannot mate, but they can sporulate. When they run out of food, sporulation gives rise to more haplods and the cycle repeats by meiosis. The mating type of the haploid cell is determined by a single LCR, called the MAT or maying type locus. In an a-type cell this is encoded as a single GRP, a1 and in an alpha-type cell is encoded in two GRP, Mat alpha 1 and 3. The a1 has no effect in the a haploid that produces it but becomes important in the diploid. In the alpha haploid produces the proteins specific to its mating type by default. The alpha 2 protein acts in the cell as a transcription repressor which turns of a-specific genes while alpha 1 acts as an activator turning on alpha specific genes. Some strains isolated from the wild can swithce between a and alpha cell types of gene rearrangement. On either site of the MAT locus there is a silent locus encoding the mating type GRP. The silent locus on one side encoding the alpha one and two, on the other, a1.Every other cell division, the active gene in MAT locus is excesived and replced by a newly synthesized copy of the silent locus which puts it in the active slot. This is called a cassette mechanismThe silent “cassettes” are maintained as transcriptionally inactive by the same means that is responsible to silencing genes in chromosomes, it is packaged into heterochromatin. Control of Cell types in Yeast is determined by three GRP, alpha one, two and a1. These are controlled by the MAT locus. Different sets of genes transcribed in a haploid cell a, in haploid cells alpha, and diploid cells. The haploid cells express haploid specific genes, hSG and either a set of alpha specific genes (alphaSG) or a-speific genes (aSG). Diploid cells express none of these. Alpha 1 is an activator, alpha 2 a repressor. Both work in combination with something called Mcm1 that is present in all three cell types. In a diploid cell, a1 and alpha 2 form a heterodimer that turns off a set of genes (including the one encoding the alpha 1 activator gene). This is an example of combinatortial control. a1 and alpha 2 use a DNA binding site recognized via a homeodomain motif

If somebody considers this a point or an argument, they should probably concede that they have lost the debate.

Lastly, you posted Irreducible complexity again, something I already refuted. Please acknowledge your interlocutors.

This animated GIF has two functions. It represents my frustration at seeing the same arguments presented by a creationist for the 1,297,432nd time and also how deludedgod must have felt the last time he responded with original material and realized it would be easier to write stock essays:

Kingdom9, for Christ's sake learn something about evolution before you attempt to disprove it. I didn't even really read your post. I just glanced over it, saw the words "macroevolution" and "2nd Law of Thermodynamics" and knew you just regurgitated the same crap I was taught in fundy high school over 20 years ago, crap that has been thoroughly and soundly refuted.

Just seeing those words clued me in that you don't know the first thing about evolution.

Read some books.

The Blind Watchmaker: Why the Evidence of Evolution Reveals a Universe Without Design by Richard Dawkins

The Making of the Fittest: DNA and the Ultimate Forensic Record of Evolution by Sean B. Carroll (Paperback - Sep 10, 2007)

Seriously, dude, doubting evolution is equivalent to claiming the earth is flat.  Evolution has been proven over and over and over again. It has been observed.  It has been documented. In the natural world, nothing makes sense unless viewed through the lens of evolution.

"Evolution" to the extent to which it has been applied today is not a fact of nature but and idea which exists in the minds of the evolutionists. They assume man evolved from apes without any proof. They TRUST the words of their teachers. They TRUST the pictures in their science books. They BELIEVE without seeing it happen. They have FAITH in the evolutionary tale.

Doubting EVOLUTION? WHAT DO YOU MEAN by that? I think you mean the variations within a kind of animal. We observe that kind of "evolution" which is not evolution at all really. I call this MICRO-EVOLUTION not MACRO-EVOLUTION. The leap of faith people want you to take is the leap from micro to macro evolution. Why do people want you to believe this theory of evolution? I think it has to do with control. They don't want you to know the God who created you.

ANSWER THIS: Name one transitional form. There is not one animal that has changed into another kind of animal. There are limits.

The problem with molecules-to-man evolution is that it is not observable and is not possible. What I find is that people ASSUME it happened. If we did evolve from lower life forms there would have to be thousands and thousands and thousands of transitional forms. There is not one.

Fortunately, the God who created us in His image let us know exactly how He did it.

Every animal is transitional. Your rejection of evolutionary theory is based on a misunderstanding of it.

Take my challenge, damn it.

Creationist Challenge: Read the damn book.

You Christians are always griping that everyone needs to read the bible. Why don't you read the book you revile?

Again, why pick the evolution theory ?

Why not pick on Quantum Mechanics or General Relativity instead ? Two theories that goes against what is written in The Fucking Bible as well. There is a "missing link" between QM and GR, but I never ear you guys complain about it... why ?

You see what is really going on here, is that you let your HUGE ego get in the way of your objectivity.

You guys think humans are SOOOOOO special that they HAVE to be the direct creation of God. Do you realize how big your ego as to be to hold such a view of the world ?

You creationists don't give a fuck about quantum mechanics and general relativity simply because you think that matter and gravity is far away from what you are, you think that you are from out of this world, where Angels flies and where God plays the harp on fucking could. But when it comes to Darwin... Oh!!!!!! you guys go nuts ! Because you percieve his theory to be closer to what you are than the other 2, which is completely false.

Guess what ? You are not from out of this world buddy ! Welcome in the universe ! How cool is that ?

Apes don't evolve into humans? Correct. Why are you correct? Humans are apes. Please read one or more of the books that have been suggested.

Why can't you and your ilk understand the difference between a scientific theory and the use of the word "theory" as a synonym for "hypothesis" or "conjecture"?  Why?  Because you don't want to understand the difference, it's much easier to shamelessly spread ignorance than pick up a book and fucking learn something.

So no, evolution is not "just a theory", it is a fucking SCIENTIFIC THEORY.  Stop spreading your uneducated, uninformed, bull-shit lies.

GRRRRRRRRR! 

Can you please give me one scientific reference that is peer reviewed by the scientific community that says they believe humans evolved from apes?  Please cite the exact page and paragraph if you can.  Demonstrate that you got this information from a credible source.  Humans and apes came from a common ancestor not from one another. 

Missing links in the fossil record are expected, however fossils are not the best nor only information we have to support the theory of evolution.  Fossils are rare, we are not going to have one for every single generation.  Just think any relatives of your that are cremated are missing links in your family history (as far as fossils are concerned).

Kingdom9, you obviously don't understand what you are arguing against.

Am I going to sit here and argue about the correct spelling of Russian words?  No!  Why?  Because I don't know anything about the Russian language.

Please stop being an idiot by continuing to keep ignoring what everyone is saying.

Either refute their arguements piece by piece or leave.  You're just wasting everyone's time here.

Visual Paradox wrote: 

If your argument about the second law of thermodynamics held true, it would be impossible for humans to have children, lackwit.

Visual Paradox: I understand--to some extent, anyway--why Kingdom9's claim about this law doesn't work; what I don't understand is how this translates into a problem with procreation.  Could you either explain a bit further, or at least link to an explanation?

Thanks in advance

Conor

_________________________________________________________________________________________

"Faith does not fear reason."--Pope Pius XII

"But it should!"--Me

You forgot the "Someone's lying, Lord" stanza. 

That's because bush is a complete and total fucking moron. How can you even believe the bull shite you're trotting out?

Take it from me it has way more to do with our inability to believe how fucking stupid you people are than any shift in thinking.

To the community at large, please excuse my foul mouth. These fucking idiots just seem to bring it out in me

Now is it just me, or is this language scary? "round earth theory"? The earth is round; it is confirmed scientific fact.

Oh and if you are still around Kingdom9, take all the guys' suggestions and read a book on evolution. It will make your mind feel better. If you don't want to read Darwin's primary text, then may I suggest this book: Darwin's Dangerous Idea by Daniell Dennett.