Final Smackdown to "Evolution is a Lie"

Hambydammit's picture

This is a long entry, but this stuff needs to be preserved for posterity.  The following is from a post by some theist or another.  I'm posting his original entry, and then my reply.  Feel free to cut and paste my reply anytime someone uses the whole "Evolution is a scam" argument, or any of its corollaries.

Some Theist or Another wrote:

Do you seriously think evolution sits ontop of the mountain of logic? Look, Brian Sapient, I am not here to make you upset or angry but describe to you how you have been beleiving a lie. Did you even consider that evolution has done nothing for present day science? Science can be completely understood without "the origin of species" in the way. Science should not be revolving around the past but in the present. Even if they did find evidence for evolution, it should be included in a history curriculum only. All of you atheists are defending this theory like it is the most important one ever to be discovered. Evolution has been around for 140 years and they still cannot find solid 100% evidence for it. Ever consider throwing away the theory already because it is obviously a poorly hypothesized one? Did you know that the geologic column is based upon circular reasoning? The fossils are dated from the certain layer they lie in and the layers are dated from what types of fossils are within them. Also, did you know that all of the dating methods are subjectable to corruptable data readings? Scientists have found that something as simple as water can destory the data. The most commonly of these dating methods is carbon dating. Carbon dating in the first place only works when the atmosphere is at equilibrium. It also only works for living things. They have found just dead carcasses and dated the rear thousands of years difference than the front end of the animal. Lastly, i am sure you know, carbon dating only works for a few thousand years.

Let's describe all of these different shaped skulls you evolutionists are finding from a biblical perspective. The Bible says that the earth was in and out of the waters. There was a layer above the earth and there was a layer below the earth as well. The layer above the earth protected people from harmful UV rays and also preserved oxygen. This can explain how Adam could live up to 900 years old and can explain how reptiles got to grow so large. Now, when you grow very old, your eyebrow ridges grow very large and extend your skull forward, so you can imagine how "apelike" these skulls seem after 900-300 years of growth. The different skulls you have found are result of the amount of age the people got to live before the flood occured.

Now, i will describe how the grand canyon formed instead of saying that it has eroded from one little river over millions of years. When the layer below the earth erupted it caused rift lines all through the bottom of the sea. There used to be a lake where the grand canyon now lies called hopie lake. The overflow of water over the lake caused the sides of the lake to collapse and turn to mud and washed all of it out within a matter of weeks. Also, the grand canyon could not have eroded because the entrance of the grand canyon where they said it has been eroded is a mile lower than where it ends.
I will now tell you how we have all of these different layers throughout the world that evolutionists claim took millions of years of sediment to compact to form. The flood caused drastic effects to the world. The flood caused much of the land to turn to mud and by a process known as liquifaction, the layers sorted themselves by density and so by the different organisms as well they sorted themselves by density. This would describe generally why you have specific organisms within a specific layer of strata. Did you also know that some organisms are out of order within the geologic column? Did you know that they have found many human made artifacts within the lowest layer of the so called geologic column? Did you know that they have found petrified trees upside down and connected to the ground of one layer of the geologic column as well? The geologic column exists nowhere else but in the imagination and on paper in the textbooks.

Another embarrasing problem with the evolutionist's theory is that the earth is slowing down each year in rotation and so that must mean the earth was once faster. Well if you reverse the process millions of years, everything would be flung off the earth and destroyed in outerspace. Not only that but the sun is getting smaller two inches a year so that must mean it was once bigger. Again if you reverse the process only 25,000 years back then the earth would've been burnt to nothing. Lastly, the moon is moving away from us atleast an inch a year so that must mean it was once closer. If you reverse this again then that means the moon would be either nonexistent or the gravitational pull would've been to harsh on the earth's surface yanking everything out into space.

The theory of evolution violates many laws. Evolution automatically assumes 150 specific different amino acids got together to from a little microorganism in a hostile environment with oxygen that would've caused it to oxidize. Evolution is stating that life arose from nonlife which violates biogenesis. Another thing is that living and nonliving things alike only tend toward disorder over time so there is no way you can even come close to going from microorganism to full-fledged human no matter how many years they add onto the theory of evolution. Time is clearly the hero of the plot of evolution because without it, it would very visibly fall flat on its face. Look, if we cannot even create life with all the technology in the world then it certainly did not happen all by itself. It is funny how something so obvious can be so overlooked by many.

Another thing evolutionists argue about is since most of our DNA is similar to apes then most likely we originated from them. Just because we are similar in DNA does not mean we are related in any way,shape,or form. It only means we have to work the same way because we were created by the same Creator. There are actually millions of differences between us and primates. I think God very likely modeled us off something of a sort of prototype. Where are also all of those billions and billions of transitional forms within the geologic column? Darwin even admitted on his death bed that his entire theory was bogus and an apes eye cannot possible evolve into a human eye, yet here we are today with people beleiving this nonsense.

Now I will describe why i think some very scarcely populated dinosaurs still walk the earth today. It says in Genesis that God created all of the land animals and so when God had to flood the earth Noah took with him on his boat infant dinosaurs so they can grow within their own kind after the flood. Well after the years of the flood the oxygen died down because there was no longer a layer above the earth to keep people living to a very long age. The lowered oxygen caused the dinosaurs to die off shortly after the flood along with people killing them off. I beleive dinosaurs are still living today and they did once walk with human beings. What do you think the Loch Ness Monster is? What do you think all of those artifact and cave drawings are of people riding giant lizardlike animals in detail? Where do you think those tales of knights sleighing giant "dragons" came together from? Dragons are also known in oriental heritage also. The Bible talks of dragons 53 times. The word dinosaur did not come into play until 1841 so they called them dragons. They found just living cells of dinosaurs today and are trying to "bring dinosaurs back to life" on that program on the discovery chanell. See satan has lived with these giant creatures in the garden of eden but we arn't! Satan has used the dinosaurs to actually support the theory of evolution instead of disproove it. This may be a hole a lot to take in but it is true.

I watched your debate with The Way of The Master and i was disturbed with you and your wife pointing fingers at religion for starting many problems within the United States. I want to inform you to know that the instant evolution started to be taught, a lot of people started to lose their morals of Christianity and all havoc broke loose. Teen suicide,homicide,premaridal sex,drunk driving,teen pregnancy,pornagraphy, and many,many more wicked things sky-rocketed the minute evolution started to be taught in public schools. Another thing i was disturbed at is that you started to describe that there is certainly no hell to the viewers and we just put that fear into our children for no good reason. How could you gaurantee there is no hell if you have never died? How could you gaurantee there is no heaven if you have never been to the end of the universe? The reality is you cannot gaurantee any of these things.

You athiests all think this is such a rational world. Well there are multiple things that are not rational in this world that rationality cannot explain. There are possesions of people that mock the name of God and are mysteriously super human strength abled. There are sightings of long forgotten spirits and demons as well within old houses. The problem is you cannot explain away Christianity using rationality. I think you have a wrong idea of Christianity. I think you automatically assume Christianity is catholocism. Catholics have strayed from the central message of the Bible and have got into government,money, and sexual pervertness as well. I beleive the Catholics are one of the churches of Christ that Jesus will say depart from me for i never knew you.

Take a look at this next excerpt carefully from the King James Bible Romans 1:20... "For the invisible things of him from the creation of the world are clearly seen,(animals,water,trees,people) being understood by the things that are made, even his eternal power and Godhead; so that they are without excuse: 21 Because that, when they knew God, they glorified him not as God, neither were thankful;(athiest) but became vain in their imaginations,(thought something came out of nothing Big Bang,Evolution) and their foolish heart was darkened.(no longer had love for their creator) 22 Professing themselves to be wise, they became fools,(science calls us WISE WISE MEN) 23 And changed the glory of the uncorruptible God(HOLY) into an image made like to corruptible man,(sinners) and to birds, and fourfooted beasts, and creeping things.(Evolution) 24 Wherefore God also gave them up to uncleanness through the lusts of their own hearts,(chasing after evidence for no reason) to dishonour their own bodies between themselvesSadmade there bodies look like evolved apes) 25 Who changed the truth of God into a lie, and worshipped and served the creature(animal who evolved into us) more than the Creator,(Most High,God,Our Loving Father) who is blessed for ever. Amen." The Bible also talks of people being willingly ignorant (dumb on purpose) of the easily interpreted creation date and flood as well in the last days.

Evolution is purely a religion. There is no real correct evidence to support the theory but only very loose evidence that has no good ground at all. You have to beleive there is no God and you have to beleive we came from nothing. If you noticed nothing x nothing=nothing so using the Big Bang theory to explain it all even violates that matter cannot be created nor destroyed. What they use as an excuse is that cosmology is not related to biology or chemistry so we don't understand how the Big Bang could've occured at all. That is absolute poppycock and i cannot put it in better terms. Chemistry,cosomology,biology may be all different but they are all under the same title which is science. I am afraid you have been brainwashed over the years by being visually influenced by computer animated television programs showing us slowly evolving into an ape, watching other programs that make Creationists seem like unintelligent idiots, and reading magazines that only show one side of the argument of evolution. You are working for satan and you don't even realize it by destroying peoples faith in our loving Father.
All of this may sound very queer and laughable to you but if you look at the facts and compare it to the Bible very specifically then you may realize that the creation date is far mor plausible and relates to the real world. I like to introduce you to a very intelligent creationist that goes by the name of Kent Hovind. I like you to watch very carefully of every minute of his seven part seminars. His website is

Also watch "100 Reasons Why Evolution is Stupid" I don't want you sitting in hell someday forever realizing that God was offering his loving hands out to you all along and you ignored that. God made a way for us through the cross and you ignore that.
Let me just give you a small idea of this place called hell if God exists. Hell is a place of pitch black darkness because God is light like it says in the Bible. Hell is a place of loneliness because God gave us frienship. God gave us oxygen to breath and carry out our daily metabolic activities so there is no oxygen in hell. God gave us our lives which are full of comfort so in hell there is no comfort but only pain. You probably would not sell even one of your own eyes for 5 millions dollars because your eyes are precious to you, so certainly don't gamble your entire soul by denying the existence of God! I am telling you right now, there were millions before you that have fell into the pit of darkness and now can never get out. For the last time, we are not trying to scare anyone but warn everyone of the consequences of our sins if we don't have a relationship with Jesus Christ. Now is the time to change that because God loves you. He knows your ways and he knows every inch of your body. He knows every DNA strip within your body and every thought that goes through your mind inside and out day in and day out. These are true statements. TRUST ME ("TRUST ME" IS MY FAVORITE PART)

I heard your wife talk about a one world government in that debate with Kirk Cameron and Ray Comfort and how she would like to see that happen. Well just for so you will know, once the rapture has taken place and God has taken all of his faithful children back home, Satan will arise from the deep and set up a peace agreement between every country and God's wrath will be poured out throughout the entire world. Satan will excuse all of the people mysteriously disappearing from the earth by saying that we were abducted by aliens because we are DELUSIONAL and needed rehab assistance. Why do you think they are recently finding mysteriously shocking evidence of the possibility of there being life on another planet? He is going to force everybody to get his microchip mark just like Revelation says so you will be able to buy or sell. If you are left behind, you have to die for your faith and you will be saved by Jesus because you were a martyr. If you receive the mark, you are doomed. You have claimed loyalty to the beast that caused you pain and betrayed the loving Father that gave you life. At the conclusion of it all, people who received the mark are going to go down with satan into the lake of fire to suffer for all eternity. Jesus want's your heart right now so please don't deny his existence because he is offering you his help. How would you like it if you created someone who denied your own existence? Your pointing a gun at your head when your denying his existence because if God is real He HAS TO punish sin because he is Holy,Righteous, and Just. Jesus is trying to get your finger off that trigger and come and follow Him. Stop laughing off the Christian faith because God cares about you and doesn't want you to carry on like this. Jesus is the WAY the TRUTH and the LIFE. He is real. I GAURANTEE.


My Reply:

Do you seriously think evolution sits ontop of the mountain of logic?


No. I think evolution is a well established process by which inherited traits in a population pass from one generation to the next. I know that evolution sits on a mountain of evidence – so much that we can say that it is at least as certain to exist as gravity.


Did you even consider that evolution has done nothing for present day science?


Except for biology, biochemistry, pharmacology, modern medicine, agriculture, the cattle industry, immunology, psychology, sociology, anthropology, evolutionary psychology (more on this later), bioinformatics, resistance management, fishery management, environmental conservation, construction of bipolymers, artificial flavors, antibiotics, pigments, enzymes, bacterial strains to decompose hazardous materials...

Oh, yeah. Also, the evolutionary principles of natural selection are the basis for genetic algorithms, which have practical applications in aerospace engineering, astrophysics, architecture, data mining, drug design, finance, geophysics, military strategy, artificial intelligence, pattern recognition software, robotics...

Oh yeah... bull semen:

Expected Progeny Differences (EPDs)
40th Annual Illinois
Performance Tested Bull Sale
EPDs offer beef cattle producers the best predictor of genetic value of a bull. EPDs combine a
bull’s individual performance with that of his ancestors and related progeny into a single estimate of
how a bull’s progeny should perform compared to the average of his breed. There will be a total of six
different traits evaluated for EPDs in the sale.
EPDs are given for the production traits of birth, weaning, yearling and maternal milk. In addition
there are two different carcass traits evaluated with EPDs with these including marbling score/%IMF,
and Ribeye Area.
In addition to EPDs there will also be accuracy levels (from .00 to .99) which express how much a
trait can deviate from a specific number. The accuracy level is dependent upon the amount of
performance information available to make the estimate. All yearling and two-year-old bulls will have
similar accuracy levels. Research studies have shown an EPD to be up to six times more accurate in
predicting progeny performance that adjusted weights. EPDs are within breed comparisons. Producers
should not compare the EPD values across breeds.

That's from cattle ranching.  Every farmer uses evolution, whether they know it or not!


Science should not be revolving around the past but in the present.


Funny you should mention this. As it turns out, the newest, and probably most exciting field of science is called Evolutionary Psychology.  You can read about it in this book:

 The New Science of Evolutionary Psychology


The Moral Animal: Why We Are, the Way We Are: The New Science of Evolutionary Psychology by Robert Wright

This new science has only been possible since we've learned to build computers powerful enough to run simulations in which interacting organisms follow the models of evolutionary theory. Through the use of these models, we've been able to verify much of what we had proposed, and even more exciting, we've been able to make predictions which have been incredibly accurate. Evolutionary psychology is the branch of science that is finally making it possible for us to explain in real, scientific terms, exactly what it means to be human, what our nature is, and why we are moral creatures.


All of you atheists are defending this theory like it is the most important one ever to be discovered. Evolution has been around for 140 years and they still cannot find solid 100% evidence for it. Ever consider throwing away the theory already because it is obviously a poorly hypothesized one? Did you know that the geologic column is based upon circular reasoning? The fossils are dated from the certain layer they lie in and the layers are dated from what types of fossils are within them. Also, did you know that all of the dating methods are subjectable to corruptable data readings? Scientists have found that something as simple as water can destory the data. The most commonly of these dating methods is carbon dating. Carbon dating in the first place only works when the atmosphere is at equilibrium. It also only works for living things. They have found just dead carcasses and dated the rear thousands of years difference than the front end of the animal. Lastly, i am sure you know, carbon dating only works for a few thousand years.


First, all these “proofs” of evolution are extraneous. If carbon dating, the fossil record, and the geologic column were taken out of the equation, evolution is still 100% proven by science. (Bet you weren't ready for me to say that, were you!)


Consider that we have demonstrated evolution in the laboratory... not just a couple of minor adaptations, but a speciation event.  Second, consider that the hard evidence of evolution comes from something called Phylogenetics.  (Bet you have never even heard of this, have you?)  I don't recommend wiki for everybody, but I think for you it will be suitable:



In biology, phylogenetics (Greek: phyle (φυλ&etaEye-wink = tribe, race and genetikos (γενετικο&sigmafEye-wink = relative to birth, from genesis = birth) is the study of evolutionary relatedness among various groups of organisms (e.g., species, populations). Also known as phylogenetic systematics or cladistics, phylogenetics treats each species as a group of lineage-connected individuals[1]. Taxonomy, the classification of organisms according to similarity, has been richly informed by phylogenetics but remains methodologically and logically distinct.[2]

Evolution is regarded as a branching process, whereby populations are altered over time and may speciate into separate branches, hybridize together, or terminate by extinction. This may be visualized as a multidimensional character-space that a population moves through over time. The problem posed by phylogenetics is that genetic data are only available for the present, and fossil records (osteometric data) are sporadic and less reliable. Our knowledge of how evolution operates is used to reconstruct the full tree.[3]

Cladistics provides a simplified method of understanding phylogenetic trees. There are some terms that describe the nature of a grouping. For instance, all birds and reptiles are believed to have descended from a single common ancestor, so this taxonomic grouping (yellow in the diagram) is called monophyletic. "Modern reptile" (cyan in the diagram) is a grouping that contains a common ancestor, but does not contain all descendents of that ancestor (birds are excluded). This is an example of a paraphyletic group. A grouping such as warm-blooded animals would include only mammals and birds (red/orange in the diagram) and is called polyphyletic because the members of this grouping do not include the most recent common ancestor.

The most commonly used methods to infer phylogenies include parsimony, maximum likelihood, and MCMC-based Bayesian inference. Distance-based methods construct trees based on overall similarity which is often assumed to approximate phylogenetic relationships. All methods depend upon an implicit or explicit mathematical model describing the evolution of characters observed in the species included, and are usually used for molecular phylogeny where the characters are aligned nucleotide or amino acid sequences.

Organisms can generally inherit genes in two ways: from parent to offspring (vertical gene transfer), or by horizontal or lateral gene transfer, in which genes jump between unrelated organisms, a common phenomenon in prokaryotes.

Lateral gene transfer has complicated the determination of phylogenies of organisms since inconsistencies have been reported depending on the gene chosen.

Carl Woese came up with the three-domain theory of life (eubacteria, archaea and eukaryotes) based on his discovery that the genes encoding ribosomal RNA are ancient and distributed over all lineages of life with little or no lateral gene transfer. Therefore rRNA are commonly recommended as molecular clocks for reconstructing phylogenies.

This has been particularly useful for the phylogeny of microorganisms, to which the species concept does not apply and which are too morphologically simple to be classified based on phenotypic traits.

Owing to the development of advanced sequencing techniques in molecular biology, it has become feasible to gather large amounts of data (DNA or amino acid sequences) to estimate phylogenies. For example, it is not rare to find studies with character matrices based on whole mitochondrial genomes. However, it has been proposed that it is more important to increase the number of taxa in the matrix than to increase the number of characters, because the more taxa, the more robust is the resulting phylogeny. This is partly due to the breaking up of long branches. It has been argued that this is an important reason to incorporate data from fossils into phylogenies where possible. Using simulations, Derrick Zwickl and Hillis[6] found that increasing taxon sampling in phylogenetic inference has a positive effect on the accuracy of phylogenetic analyses.

Another important factor that affects the accuracy of tree reconstruction is whether the data analyzed actually contain useful phylogenetic signal, a term that is used generally to denote whether related organisms tend to resemble each other with respect to their genetic material or phenotypic traits.[7]

While I'm at it, I bet you didn't know about all of this:


Introduction to Phylogenetics

Descent from a common ancestor entails a process of branching and divergence of species, in common with any genealogical process. Genealogies can be graphically illustrated by tree-like diagrams, and this is why you will hear biologists refer to the genealogy of species as the "tree of life". Diagrams such as these are known as phylogenetic trees or phylogenies. The consensus model which evolutionary biologists use to represent the well-supported branches of the universal tree of life I will refer to as the "standard phylogenetic tree". Figure 1 shows a simplified example of some of the more familiar branches of the universal phylogenetic tree. The macroevolutionary prediction of a unique, historical universal phylogenetic tree is the most important, powerful, and basic conclusion from the hypothesis of universal common descent. A thorough grasp of this concept is necessary for understanding macroevolutionary deductions.

In the following section is a brief overview of phylogenetic trees and of how biologists determine them. This overview becomes increasingly technical as it proceeds. The material up until the maximum parsimony heading is essential for understanding the rest of this FAQ. The remaining phylogenetic discussion is given for completeness and to allow the interested reader the opportunity to delve as far as is desired.

 A Consensus Phylogenety of All Life]
Figure 1. The Consensus Phylogenetic Tree of All Life.

Phylogenetic trees represent evolutionary relationships

[Trees for illustrative purposes]
Figure 2: The parts of a phylogenetic tree. The taxa in this tree are "human", "mouse", and "fly" (all of which have had their full genomes sequenced). Several nodes are indicated, such as the "fly" taxon node and an internal node that represents the common ancestor of mice and humans. The root is indicated at left, representing the common ancestor of all three taxa listed.

Phylogenetics is the scientific discipline concerned with describing and reconstructing the patterns of genetic relationships among species and among higher taxa. Phylogenetic trees are a convenient way of visually representing the evolutionary history of life. These diagrams illustrate the inferred relationships between organisms and the order of speciation events that led from earlier common ancestors to their diversified descendants.

A phylogenetic tree has several parts, shown in Figure 2. Nodes represent taxonomic units, such as an organism, a species, a population, a common ancestor, or even an entire genus or other higher taxonomic group. Branches connect nodes uniquely and represent genetic relationships. The specific pattern of branching determines the tree's topology. Scaled trees have branch lengths that are proportional to some important biological property, such as the number of amino acid changes between nodes on a protein phylogeny (see Figure 3). Trees may also be rooted or unrooted. Rooted trees have a special node, known as the root, that represents a common ancestor of all taxa shown in the tree. Rooted trees are thus directional, since all taxa evolved from the root. Unrooted trees illustrate relationships only, without reference to common ancestors.

[Trees for illustrative purposes]
Figure 3: Various representations of a 5-taxa phylogenetic tree. Each of these trees represents the same five modern taxa: A, B, C, D, and E. The tree at upper left is rooted and scaled according to evolutionary distance. The root is at left. Taxa C and E have both undergone relatively large changes since divergence from the root, in contrast to taxa B and D. The tree at lower left is rooted and unscaled. Here the branch lengths are relative indicators of time since divergence. The tree at right is scaled but unrooted. In this tree, while the root is unkown, the relationships between taxa are identical to that shown in the other two trees.

A common misconception is that some modern species are ancestral to other modern species. However, all modern species are found at the tips of the tree's branches, and one modern species is as "evolved" as any other. That is, although mammals are thought to have evolved from something that resembled modern reptiles, modern reptiles are just as "old" evolutionarily as modern mammals (Brooks 1991, p.68; Futuyma 1998, p.113).

Methods for determining phylogenetic trees: Cladistics and numerical phylogenetics

Of all clean birds ye shall eat.
But these are they of which ye shall not eat:
The eagle, and the ossifrage, and the ospray,
And the glede, and the kite, and the vulture after his kind,
And every raven after his kind,
And the owl, and the night hawk, and the cuckow, and the hawk after his kind,
The little owl, and the great owl, and the swan,
And the pelican, and the gier eagle, and the cormorant,
And the stork, and the heron after her kind, and the lapwing,
and the bat

Deuteronomy 14:11-18, KJV

If modern species have descended from ancestral ones in this tree-like, branching manner, it should be possible to infer the true historical tree that traces their paths of descent. Phylogenies have been inferred by biologists ever since Darwin first proposed that life was united by common descent over 140 years ago. Rigorous algorithmic methodologies for inferring phylogenetic trees have been in use for over the past 50 years.

In 1950, taxonomist Willi Hennig proposed a method for determining phylogenetic trees based on morphology by classifying organisms according to their shared derived characters, which are called synapomorphies (Hennig 1966). This method, now called cladistics, does not assume genealogical relatedness a priori, since it can be used to classify anything in principle, even things like books, cars, or chairs that are obviously not genealogically related in a biological sense (Kitching et al. 1998, Ch. 1, p. 26; ). Using firm evolutionary arguments, however, Hennig justified this method as the most appropriate classification technique for estimating evolutionary relationships generated by lineal descent. In fact, Hennig's cladistic method is nothing more than a formalization of the methods systematic biologists had been using intuitively ever since Linnaeus penned Systema Naturae. Biologists today construct their phylogenetic trees based on Hennig's method, and because of cladistics these phylogenetic trees are reproducible and independently testable (Brooks 1991, Ch. 2; Kitching et al. 1998).

Phylogenetic Jargon

apomorphy: A derived character of a group of organisms, not shared with ancestors of a group of organisms. Apomorphies are unique to the group, and are therefore group-defining.

bootstrap: A technical statistical procedure for estimating the variability of a measurement. In phylogenetics, bootstrapping involves the production of a new, pseudo-dataset by randomly pulling data points from the original dataset. For each pseudo-dataset, a new phylogeny is inferred. Rounds of this provide an estimation of the well- and poorly-supported regions of the original phylogeny.

character: An observable feature of an organism useful for distinguishing it from another. For example, a nucleotide in a DNA sequence, an amino acid in a protein sequence, or morphological characters like hair, feathers, or the presence or absence of certain bones.

cladistics: A class of phylogenetic techniques that construct trees (cladograms) by grouping taxa into nested hierarchies according to shared derived characters (synapomorphies). Cladistics is closely associated with the parsimony criterion.

cladogram: A hierarchical classification of taxa represented as a tree. Cladograms formally are independent of evolutionary theory, though in practice they are usually interpreted as phylogenies.

derived character: See apomorphy.

least squares: A phylogenetic distance matrix criterion. The best tree is the one with the smallest squared difference between the observed pairwise distances and the distances calculated from the inferred tree. It has a strong statistical justification, as it is based upon the common linear least squares statistical technique. Least squares is guaranteed by the Gauss-Markov theorem to converge on the correct answer as more data is included in the analysis if a proper distance metric is used, i.e. least squares is statistically consistent. Weighted versions correct for random variability and bias due to longer branch lengths.

maximum likelihood: A cladistic criterion for inferring trees with character conflict. The best tree and evololutionary model maximize the probability of the observed data. Maximum likelihood has a strong statistical foundation. Given a correct model of evolutionary change, it is guaranteed to be statistically consistent, i.e. it will converge on the correct tree as more data is added. Maximum likelihood generally performs the best of all methods in simulations, but it is very computationally expensive. Unlike parsimony, it explicitly relies upon a specific evolutionary model.

minimum evolution: A phylogenetic distance matrix criterion. The best tree is the one in which the sum of the branch lengths is smallest.

neighbor-joining: A distance matrix algorithm for inferring trees. It is an approximation to the least-squares and minimum evolution methods.

node: A point in a phylogeny where branches meet or end. Nodes at the tip or end of a branch represent taxa. In rooted trees, internal nodes represent common ancestors.

parsimony: A phylogenetic criterion for inferring trees with character conflict. Parsimony requires that the best tree is the one with the least character conflict. It is known to produce the incorrect phylogeny in certain cases, such as when evolutionary rates are high or certain branches are long.

phenetics: Sometimes known as numerical taxonomy, phenetic methods classify and group organisms based on overall similarity, usually without explicit reference to their phylogenetic relationships.

phylogeny: A branching, tree-like diagram representing genealogical relationships among taxa. Rooted phylogenies specify common ancestors and have a time axis.

plesiomorphy: A primitive character, shared with the ancestors of a group of organisms. Since it is common to more than just the group being considered, a plesiomorphy is not group-defining.

primitive character: See plesiomorphy.

root: A common ancestor of all taxa in a phylogeny. Chronologically, the root is the oldest node.

synapomorphy: A derived character that is shared between two groups of organisms.

UPGMA: A distance matrix-based clustering method for constructing trees. Rarely used, it is very fast but assumes constant evolutionary rates throughout the tree (a property called ultrametricity).

Cladistic methods are often contrasted with "phenetic" methods. Phenetic methods cluster and classify species based upon the number of identical characters that they share, that is, based upon overall similarity. Such methods can run into trouble with organisms like dolphins and tuna, which have many superficial similarities. These organisms, however, are not closely related and should not be classified together if one expects classification to reflect phylogeny.

In contrast, cladistic-based phylogenies group taxa into nested hierarchies, and they are determined using only shared derived characters of organisms, not shared primitive characters (Brooks 1991, pp. 35-36; Kitching et al. 1998, Ch. 1; Maddison and Maddison 1992, p. 49). In technical phylogenetic jargon, primitive characters are called plesiomorphies, and derived characters are called apomorphies. In cladistics, related species are grouped together because they share derived characters (i.e., apomorphies) that originated in a common ancestor of the group, but were not present in other, earlier ancestors of the group. These shared, derived features are called synapomorphies. Primitive and derived are therefore relative terms, depending upon the specific group being considered. For example, backbones are primitive characters of vertebrates, while hair is a derived character particular to mammalian vertebrates. However, when considering mammals only, hair is primitive, whereas an opposable thumb is derived.

In real-life phylogenetic analyses, shared derived characters may be in conflict with other derived characters. Thus, objective methods are required for resolving this character conflict (Kitching et al. 1998, Ch. 1; Maddison and Maddison 1992, p. 49). For instance, wings are a derived character of birds and of bats. Based upon this character alone, the cladistic method would group bats and birds together, which is how the author of Deuteronomy grouped them in the Biblical quote above. However, other shared derived characters indicate that bats should be grouped with wingless mammals, and that birds should be grouped with wingless dinosaurs.

In the past 40 years, several algorithmic methods have been devised to resolve such instances of character conflict and to infer correct phylogenetic trees (Felsenstein 2004, Ch. 10). The following sections outline some of the most successful of these methods. Each method attempts to infer a phylogeny from existing data, and each has its respective strengths and weaknesses. Years of empirical testing and simulation have shown that, in general, these different algorithms, each with very different underlying assumptions, converge on trees that are highly similar when judged statistically (Li 1997, Chs 5 and 6; Nei and Kumar 2000, Chs 6, 7, and Cool.

Maximum parsimony

One of the oldest, most basic, and most frequently used methods for character resolution is the maximum parsimony (MP) criterion (Edwards and Cavalli-Sforza 1963; Kitching et al. 1998). The parsimony criterion mandates that the best tree describing the data is the tree that minimizes the amount of character conflict. For example, consider a dataset containing 10 shared derived characters that group bats with apes (rather than with birds), and with one character that groups bats with birds (rather than apes). According to the parsimony criterion, the tree giving the first grouping should be preferred.

Currently, parsimony is the method of choice for reconstructing morphological trees (Kitching et al. 1998). It is very fast computationally, and it can be robust to differences in evolutionary rate among characters. However, maximum parsimony consistently finds the correct phylogeny only when we expect character conflict to be low or evolution to proceed parsimoniously (Felsenstein 2004, Ch. 9; Kitching et al. 1998, p. 17). If rates of evolution are slow and branches are short, character conflict will be low and parsimony will work well (Felsenstein 2004, Ch. 9; Felsenstein 1981a; Li 1997, p. 128). If character conflict is moderate or high in reality, then it is very unlikely that the true tree will have the least amount of character conflict. When rates of evolution are high, or when some branches are very long, or when the number of possible character states is limited, character conflict can be common. This is often true for nucleotide sequences, which have only four possible character states (A, C, T, or G). In cases such as these, other phylogenetic methods can be more accurate than parsimony.

Maximum likelihood

Another commonly used phylogenetic criterion is maximum likelihood (ML), an effective and robust statistical technique now used in all scientific fields (Edwards and Cavalli-Sforza 1964; Felsenstein 1981b; Fisher 1912). Many well-known statistical estimators are actually maximum likelihood estimators. For example, the common sample average as an estimate of the mean of a Gaussian distribution and the least-squares fit of a line to a set of points are both maximum likelihood estimators. Using ML, one can infer rates of evolution directly from the data and determine the tree that best describes that data given those inferred rates. In other words, ML finds the tree and evolutionary parameters that produce the observed data with the highest probability. Unlike parsimony, ML finds trees with the expected amount of character conflict given the evolutionary rates inferred from the data, even if those rates are high. ML is a computationally intensive method that can be very time-consuming.

Distance methods

Due to their computational speed, distance matrix methods are some of the most popular for inferring phylogenies (Nei and Kumar 2000, Ch. 6). All distance methods transform character data into a matrix of pairwise distances, one distance for each possible pairing of the taxa under study. Distance matrix methods are not cladistic, since the information about derived and primitive characters has been lost during this transformation. Distance methods approach phylogenetic inference strictly as a statistical problem, and they are used almost exclusively with molecular data. Although they are not cladistic, distance methods can be thought of as approximations to cladistic methods, and several of the methods are guaranteed mathematically to converge on the correct tree as more data is included.

The most simple distance metric is merely the number of character differences between two taxa, such as the number of nucleotide differences between two DNA sequences. Many other ways of calculating molecular sequence distances exist, and most attempt to correct for the possibility of multiple changes at a single site during evolution. Methods for calculating distances between sequences are usually named for their originators, such as Kimura's two-parameter (K2P), Jukes-Cantor (JC), Tamura-Nei (TN), Hasegawa, Kishino, and Yano (HKY), and Felsenstein 1984 (F84). Other important distance metrics are General Time Reversible (GTR) and LogDet (Felsenstein 2004, pp. Chs 11 and 13; Nei and Kumar 2000, Chs 2 and 3; Li 1997, Chs 3 and 4).

Once a distance matrix for the taxa being considered is in hand, there are several distance-based criteria and algorithms that may be used to estimate the phylogenetic tree from the data (Felsenstein 2004, Ch. 11; Li 1997, Ch. 5). The minimum evolution (ME) criterion finds the tree in which the sum of all the branch lengths is the smallest. Weighted and unweighted least squares criteria calculate the discrepancy between the observed pairwise distances and the pairwise distances calculated from the branch lengths of the inferred tree. Least squares then finds the tree that minimizes the square of that discrepancy. Least squares methods are some of the most statistically justified and will converge on the correct tree as more data are included in the analysis (given a mathematically proper distance metric). The neighbor-joining (NJ) algorithm is extremely fast and is an approximation of the least squares and minimum evolution methods. If the distance matrix is an exact description of the true tree, then neighbor-joining is guaranteed to reconstruct the correct tree. The UPGMA clustering algorithm (a confusing acronym) is also extremely fast, but it is based upon the unlikely assumption that evolutionary rates are equal in all lineages. UPGMA is rarely used today except as an instructional tool.

Statistical Support for Phylogenies

A phylogeny is a best approximation of the correct, historical tree using a given phylogenetic method. Some phylogenetic analyses are strongly supported by the data, some are weakly supported, and different parts of a tree may have more support than others. When comparing two independently determined phylogenies, one must take into account the statistical support assigned to each branch of the phylogenies. As with all scientific analyses, the details of a phylogenetic tree may change as new information and data are incorporated (Maddison and Maddison 1992, pp. 112-123; Li 1997, pp. 36-146; Felsenstein 1985; Futuyma 1998, p. 99; Hillis and Bull 1993; Huelsenbeck et al. 2001; Swofford et al. 1996, pp. 504-509).

Bootstrapping is the most popular statistical method for assessing the reliability of the branches in a phylogenetic tree (Felsenstein 1985). Bootstrapping is a statistical technique for empirically estimating the variability of a parameter (Efron 1979; Efron and Gong 1983). In a bootstrap analysis, a fictional dataset is created by randomly sampling data from the real dataset until a new dataset is created of the same size. This process is done repeatedly (hundreds or thousands of times), and the parameter of interest is estimated from each fictional dataset. The variability of these bootstrapped estimations is itself an estimate of the variability of the parameter of interest.

In phylogenetics, a new phylogeny is inferred from each bootstrapped dataset (Felsenstein 1985). These bootstrapped phylogenies will likely have different topologies. From these different bootstrapped trees, the variability in the inferred tree can be estimated. The parts of the bootstrapped trees that are in common are ascribed a high confidence, while the parts that vary extensively are assigned a low confidence. Trees constructed from random data do not result in high confidence trees or branches when bootstrapped. Thus, bootstrapping provides one way to test whether a phylogenetic tree is genuine.

Does Phylogenetic Inference Find Correct Trees?

In order to establish their validity in reliably determining phylogenies, phylogenetic methods have been empirically tested in cases where the true phylogeny is known with certainty, since the true phylogeny was directly observed.

  • Bacteriophage T7 was propagated and split sequentially in the presence of a mutagen, where each lineage was tracked. Out of 135,135 possible phylogenetic trees, the true tree was correctly determined by phylogenetic methods in a blind analysis. Five different phylogenetic methods were used independently, and each one chose the correct tree (Hillis et al.1992 ).

  • In another study, 24 strains of mice were used in which the genealogical relationships were known. Cladistic analysis reproduced almost perfectly the known phylogeny of the 24 strains (Atchely and Fitch 1991).

  • Bush et al. used phylogenetic analysis to retrospectively predict the correct evolutionary tree of human Influenza A virus 83% of the time for the flu seasons spanning 1983 to 1994.

  • In 1998, researchers used 111 modern HIV-1 (AIDS virus) sequences in a phylogenetic analysis to predict the nucleotide sequence of the viral ancestor of which they were all descendants. The predicted ancestor sequence closely matched, with high statistical probability, an actual ancestral HIV sequence found in an HIV-1 seropositive African plasma sample collected and archived in the Belgian Congo in 1959 (Zhu et al.1998 ).

  • In the past decade, phylogenetic analyses have played a significant role in successful convictions in several criminal court cases (Albert et al. 1994; Arnold et al. 1995; Birch et al. 2000; Blanchard et al. 1998; Goujon et al. 2000; Holmes et al. 1993; Machuca et al. 2001; Ou et al. 1992; Veenstra et al. 1995; Vogel 1997; Yirrell et al. 1997), and phylogenetic reconstructions have now been admitted as expert legal testimony in the United States (97-KK- 2220 State of Louisiana v. Richard J. Schmidt [PDF]). The legal test in the U. S. for admissibility of expert testimony is the Daubert guidelines (U. S. Supreme Court Case Daubert v. Merrell Dow Pharmaceuticals, Inc., 509 U.S. 579, 587-89, 113 S. Ct. 2786, 2794, 125 L. Ed. 2d 469, 1993). The Daubert guidelines state that a trial court should consider five factors in determining "whether the testimony's underlying reasoning or methodology is scientifically valid": (1) whether the theory or technique in question can be and has been tested; (2) whether it has been subjected to peer review and publication; (3) its known or potential error rate; (4) the existence and maintenance of standards controlling its operation; and (5) whether it has attracted widespread acceptance within the relevant scientific community (quoted nearly verbatim). Phylogenetic analysis has officially met these legal requirements.

Caveats with Phylogenetic Inference

As with any investigational scientific method, certain conditions must hold in order for the results to be reliable. A common premise of all molecular phylogenetic methods is that genes are transmitted via vertical, lineal inheritance, i.e. from ancestor to descendant. If this premise is violated, gene trees will never recapitulate an organismic phylogeny. This assumption is violated in instances of horizontal transfer, e.g. in transformation of a bacterium by a DNA plasmid, or in retroviral insertion into a host's genome. During the early evolution of life, before the advent of multicellular organisms, horizontal transfer was likely very frequent (as it is today in the observed evolution of bacteria and other unicellular organisms). Thus, it is questionable whether molecular methods are applicable, even in principle, to resolving the phylogeny of the early evolution of life near the most recent common ancestor of all living organisms (Doolittle 1999; Doolittle 2000; Woese 1998).

The list below gives some of the more important caveats that scientists must keep in mind when interpreting the results of a phylogenetic analysis (Swofford 1996, pp. 493-509). In general, the contribution of each of these concerns will be "averaged out" by including more independent characters in the phylogenetic analysis, such as more genes and longer sequences.

  • Correlated characters: each character used in the analysis optimally should be genetically independent. Characters that are strongly functionally correlated are better thought of as a single character. There are statistical tests that can help control for unrecognized character correlation, such as the block bootstrap and jackknife.

  • True structural convergence: structures that have undergone convergent evolution can artificially result in incorrect tree topologies. Including more characters in the analysis also aids in overcoming convergent effects.

  • Character reversals: characters that revert to an ancestral state pose a challenge similar to convergence. Because DNA and RNA only have four different character states, they are especially prone to reversals during evolution.

  • Lost characters: lineages that have lost characters (such as whales and their hindlimbs) can also pose cladistic problems. Often, if a cladistic analysis indicates strongly that a certain character has been lost during evolution, it is best to omit this character in higher resolution analyses of that lineage.

  • Missing characters: incomplete fossils are problematic, since they may lack important characters. Better fossils are the answer.

  • Intractable number of possible phylogenetic trees: for computational reasons, this is one of the most important phylogenetic challenges to overcome. The goal of a phylogenetic reconstruction is to determine the best tree that the data supports. For an analysis of only five species, there are 15 possible trees. For an analysis of 50 species, there are over 1074 possible trees that must be searched—which is computationally impossible. This problem is not as bad as it first sounds, since narrowing down the number of reasonable trees can be trivial in many cases (for instance, using the branch and bound algorithm). Several methods have been developed to work around this issue successfully, and ultimately more powerful computers are better.

  • Maximum Likelihood assumptions: the maximum likelihood method makes explicit assumptions about the pattern of nucleotide substitutions based upon a given model of nucleotide evolution. These assumptions are based upon a solid statistical foundation; however, the validity of the models must be considered when evaluating the results.

  • Long branch attraction: lineages that diverged relatively long ago will tend to "cluster" together in a phylogenetic reconstruction under the appropriate conditions. The mathematical reasons are somewhat complicated, but using more slowly evolving genes (or regions of genes) helps overcome the problem.

  • Rate variation between lineages: rates of nucleotide substitution may differ between lineages; this can contribute to long branch attraction and result in incorrect tree topologies. However, maximum likelihood and least squares methods are particularly useful here.

  • Rate variation within a single gene: rates of nucleotide substitution can vary along the length of a single gene—this also exacerbates long branch attraction.

  • Gene trees are not equivalent to species trees: from simple Mendelian genetics we know that genes segregate individually, and that throughout time individual genes do not necessarily follow organismic genealogy (Avise and Wollenberg 1997; Fitch 1970; Hudson 1992; Nichols 2001; Wu 1991). An obvious example is the fact that while you may have brown eyes, your child may have the genes for blue eyes—but that does not mean your child is not your descendent, or that your brown-eyed children are more closely related to you than your blue-eyed children. Including multiple genes in the analysis is a solution to this conundrum. Based upon simple genetic calculations, an analysis of more than five genes is usually necessary to accurately reconstruct a species phylogeny (Wu 1991).

For more information on cladistics, you can consult one of several excellent online cladistic resources, such as the SASB Introduction to Phylogenetics, UC Berkeley's Integrative Biology Phylogenetics Lab, or Diana Lipscomb's stellar Basics of Cladistic Analysis, downloadable in Adobe Acrobat PDF format. A good, concise description for the layperson can be found at the Journal of Avocational Paleontology. Finally, you can read Charles Darwin's explanation in The Origin of Species of the "Tree of Life", where the concept of a phylogenetic tree was first introduced.





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That's one page from this handy explanation of all the different ways we know evolution to be true:



Scientific Evidence and the Scientific Method

Phylogenetics introduction

Part I. A unique, historical phylogenetic tree

  1. Unity of life

  2. Nested hierarchies

  3. Convergence of independent phylogenies

  4. Transitional forms

  5. Chronology of common ancestors

Part 2. Past history

  1. Anatomical vestiges

  2. Atavisms

  3. Molecular vestiges

  4. Ontogeny and developmental biology

  5. Present biogeography

  6. Past biogeography

Part 3. Evolutionary opportunism

  1. Anatomical parahomology

  2. Molecular parahomology

  3. Anatomical convergence

  4. Molecular convergence

  5. Anatomical suboptimal function

  6. Molecular suboptimal function

Part 4. Molecular evidence

  1. Protein functional redundancy

  2. DNA functional redundancy

  3. Transposons

  4. Redundant pseudogenes

  5. Endogenous retroviruses

Part 5. Change

  1. Genetic

  2. Morphological

  3. Functional

  4. The strange past

  5. Stages of speciation

  6. Speciation events

  7. Morphological rates

  8. Genetic rates

Closing remarks


Let's describe all of these different shaped skulls you evolutionists are finding from a biblical perspective.

Let's not.  The bible doesn't mention anything about DNA or selection pressure, so I doubt that it would have much to say on the subject of common descent.  After all, this is the book that recommends giving women poison to see if they've been cheating on their husband, right?  If it's ok with you, I'm going to trust the empirical evidence instead of a bronze age collection of superstition.

Now, i will describe how the grand canyon formed instead of saying that it has eroded from one little river over millions of years.

Did you want to talk about evolution or geology?  As far as I know, the formation of the Grand Canyon is not included in any evolution textbooks.  It simply has nothing to do with the passing of genetic traits between generations.

Another embarrasing problem with the evolutionist's theory is that the earth is slowing down each year in rotation and so that must mean the earth was once faster. Well if you reverse the process millions of years, everything would be flung off the earth and destroyed in outerspace.



I can't think of anything constructive to say about this.  Nothing at all.  This is the single dumbest thing I've ever heard, and that's saying a lot.  There's a certain level of credulity with which I cannot compete.

Not only that but the sun is getting smaller two inches a year so that must mean it was once bigger. Again if you reverse the process only 25,000 years back then the earth would've been burnt to nothing.

Oh, my...

25,000 years X 2 inches = 50,000 inches... divided by 12 = 4,166.67 feet... divided by 5280 = 0.78914 miles.

Current distance from the sun to the earth = 93 million miles

0.78914 divided by 93 million = 00000000084853915 = 000000008% of a change in overall distance from earth.  Now consider that in reality, the earth's orbit is not circular, so the actual range is between 91 and 93 million miles.  Two million is a little less than 2% of 93 million, so we move two percent closer every year, and then move back out again.  Would you care to revise your theory a little bit?

Lastly, the moon is moving away from us atleast an inch a year so that must mean it was once closer. If you reverse this again then that means the moon would be either nonexistent or the gravitational pull would've been to harsh on the earth's surface yanking everything out into space.

I'm guessing you're not familiar with the current theory on the formation of the moon.


The Giant Impact, as pictured in a painting by William K. Hartmann on the cover of Natural History Magazine in 1981. Copyright William K. Hartmann

The idea in a nutshell:

At the time Earth formed 4.5 billion years ago, other smaller planetary bodies were also growing. One of these hit earth late in Earth's growth process, blowing out rocky debris. A fraction of that debris went into orbit around the Earth and aggregated into the moon.

Half an Hour After the Giant Impact, based on computer modeling by A. Cameron, W. Benz, J. Melosh, and others. Copyright William K. Hartmann

Why this is a good hypothesis:

  • The Earth has a large iron core, but the moon does not. This is because Earth's iron had already drained into the core by the time the giant impact happened. Therefore, the debris blown out of both Earth and the impactor came from their iron-depleted, rocky mantles. The iron core of the impactor melted on impact and merged with the iron core of Earth, according to computer models.

  • Earth has a mean density of 5.5 grams/cubic centimeter, but the moon has a density of only 3.3 g/cc. The reason is the same, that the moon lacks iron.

  • The moon has exactly the same oxygen isotope composition as the Earth, whereas Mars rocks and meteorites from other parts of the solar system have different oxygen isotope compositions. This shows that the moon formed form material formed in Earth's neighborhood.

  • If a theory about lunar origin calls for an evolutionary process, it has a hard time explaining why other planets do not have similar moons. (Only Pluto has a moon that is an appreciable fraction of its own size.) Our giant impact hypothesis had the advantage of invoking a stochastic catastrophic event that might happen only to one or two planets out of nine.



Evolution automatically assumes 150 specific different amino acids got together to from a little microorganism in a hostile environment with oxygen that would've caused it to oxidize.

No, it doesn't.  Evolution explains how traits are passed genetically between generations.  It does not address abiogenesis.  The most compelling current theories of abiogenesis make no such claim:


Every so often, someone comes up with the statement "the formation of any enzyme by chance is nearly impossible, therefore abiogenesis is impossible". Often they cite an impressive looking calculation from the astrophysicist Fred Hoyle, or trot out something called "Borel's Law" to prove that life is statistically impossible. These people, including Fred, have committed one or more of the following errors.


Acyl transferase:
An enzyme or ribozyme that synthesizes peptides.
An enzyme or ribozyme that adds a monomer to a polymer, or links two shorter polymers together.
Any single subunit of a polymer. An amino acid is a monomer of a peptide or protein, a nucleotide is a monomer of an oligonucleotide or polynucleotide.
Adenine, Guanine, Cytosine and Uracil. These are the monomers that make up oligo- or polynucleotides such as RNA.
A short polymer of nucleotide subunits.
A enzyme or ribozyme that makes a polymer out of monomers. For example, RNA polymerase makes RNA out of single nucleotides.
A biological catalyst made from RNA.
A molecule which can make an identical or near-identical copy of itself from smaller subunits. At least four self-replicators are known.

Problems with the creationists' "it's so improbable" calculations

1) 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.

2) They assume that there is a fixed number of proteins, with fixed sequences for each protein, that are required for life.

3) They calculate the probability of sequential trials, rather than simultaneous trials.

4) They misunderstand what is meant by a probability calculation.

5) They seriously underestimate the number of functional enzymes/ribozymes present in a group of random sequences.

I will try and walk people through these various errors, and show why it is not possible to do a "probability of abiogenesis" calculation in any meaningful way.

A primordial protoplasmic globule

So the calculation goes that the probability of forming a given 300 amino acid long protein (say an enzyme like carboxypeptidase) randomly is (1/20)300 or 1 chance in 2.04 x 10390, which is astoundingly, mind-beggaringly improbable. This is then cranked up by adding on the probabilities of generating 400 or so similar enzymes until a figure is reached that is so huge that merely contemplating it causes your brain to dribble out your ears. This gives the impression that the formation of even the smallest organism seems totally impossible. However, this is completely incorrect.

Firstly, the formation of biological polymers from monomers is a function of the laws of chemistry and biochemistry, and these are decidedly not random.

Secondly, the entire premise is incorrect to start off with, because in modern abiogenesis theories the first "living things" would be much simpler, not even a protobacteria, or a preprotobacteria (what Oparin called a protobiont [8] and Woese calls a progenote [4]), but one or more simple molecules probably not more than 30-40 subunits long. These simple molecules then slowly evolved into more cooperative self-replicating systems, then finally into simple organisms [2, 5, 10, 15, 28]. An illustration comparing a hypothetical protobiont and a modern bacteria is given below.

[Ur Cell figure]

The first "living things" could have been a single self replicating molecule, similar to the "self-replicating" peptide from the Ghadiri group [7, 17], or the self replicating hexanucleotide [10], or possibly an RNA polymerase that acts on itself [12].

[Self-replicator figure]

Another view is the first self-replicators were groups of catalysts, either protein enzymes or RNA ribozymes, that regenerated themselves as a catalytic cycle [3, 5, 15, 26, 28]. An example is the SunY three subunit self-replicator [24]. These catalytic cycles could be limited in a small pond or lagoon, or be a catalytic complex adsorbed to either clay or lipid material on clay. Given that there are many catalytic sequences in a group of random peptides or polynucleotides (see below) it's not unlikely that a small catalytic complex could be formed.

These two models are not mutually exclusive. The Ghadiri peptide can mutate and form catalytic cycles [9].

No matter whether the first self-replicators were single molecules, or complexes of small molecules, this model is nothing like Hoyle's "tornado in a junkyard making a 747". Just to hammer this home, here is a simple comparison of the theory criticised by creationists, and the actual theory of abiogenesis.

[Two views of abiogenesis]

Note that the real theory has a number of small steps, and in fact I've left out some steps (especially between the hypercycle-protobiont stage) for simplicity. Each step is associated with a small increase in organisation and complexity, and the chemicals slowly climb towards organism-hood, rather than making one big leap [4, 10, 15, 28].

Where the creationist idea that modern organisms form spontaneously comes from is not certain. The first modern abiogenesis formulation, the Oparin/Haldane hypothesis from the 20's, starts with simple proteins/proteinoids developing slowly into cells. Even the ideas circulating in the 1850's were not "spontaneous" theories. The nearest I can come to is Lamarck's original ideas from 1803! [8]

Given that the creationists are criticising a theory over 150 years out of date, and held by no modern evolutionary biologist, why go further? Because there are some fundamental problems in statistics and biochemistry that turn up in these mistaken "refutations".

The myth of the "life sequence"

Another claim often heard is that there is a "life sequence" of 400 proteins, and that the amino acid sequences of these proteins cannot be changed, for organisms to be alive.

This, however, is nonsense. The 400 protein claim seems to come from the protein coding genome of Mycobacterium genetalium, which has the smallest genome currently known of any modern organism [20]. However, inspection of the genome suggests that this could be reduced further to a minimal gene set of 256 proteins [20]. Note again that this is a modern organism. The first protobiont/progenote would have been smaller still [4], and preceded by even simpler chemical systems [3, 10, 11, 15].

As to the claim that the sequences of proteins cannot be changed, again this is nonsense. There are in most proteins regions where almost any amino acid can be substituted, and other regions where conservative substitutions (where charged amino acids can be swapped with other charged amino acids, neutral for other neutral amino acids and hydrophobic amino acids for other hydrophobic amino acids) can be made. Some functionally equivalent molecules can have between 30 - 50% of their amino acids different. In fact it is possible to substitute structurally non-identical bacterial proteins for yeast proteins, and worm proteins for human proteins, and the organisms live quite happily.

The "life sequence" is a myth.

Coin tossing for beginners and macromolecular assembly

So let's play the creationist game and look at forming a peptide by random addition of amino acids. This certainly is not the way peptides formed on the early Earth, but it will be instructive.

I will use as an example the "self-replicating" peptide from the Ghadiri group mentioned above [7]. I could use other examples, such as the hexanucleotide self-replicator [10], the SunY self-replicator [24] or the RNA polymerase described by the Eckland group [12], but for historical continuity with creationist claims a small peptide is ideal. This peptide is 32 amino acids long with a sequence of RMKQLEEKVYELLSKVACLEYEVARLKKVGE and is an enzyme, a peptide ligase that makes a copy of itself from two 16 amino acid long subunits. It is also of a size and composition that is ideally suited to be formed by abiotic peptide synthesis. The fact that it is a self replicator is an added irony.

The probability of generating this in successive random trials is (1/20)32 or 1 chance in 4.29 x 1040. This is much, much more probable than the 1 in 2.04 x 10390 of the standard creationist "generating carboxypeptidase by chance" scenario, but still seems absurdly low.

However, there is another side to these probability estimates, and it hinges on the fact that most of us don't have a feeling for statistics. When someone tells us that some event has a one in a million chance of occuring, many of us expect that one million trials must be undergone before the said event turns up, but this is wrong.

Here is a experiment you can do yourself: take a coin, flip it four times, write down the results, and then do it again. How many times would you think you had to repeat this procedure (trial) before you get 4 heads in a row?

Now the probability of 4 heads in a row is is (1/2)4 or 1 chance in 16: do we have to do 16 trials to get 4 heads (HHHH)? No, in successive experiments I got 11, 10, 6, 16, 1, 5, and 3 trials before HHHH turned up. The figure 1 in 16 (or 1 in a million or 1 in 1040) gives the likelihood of an event in a given trial, but doesn't say where it will occur in a series. You can flip HHHH on your very first trial (I did). Even at 1 chance in 4.29 x 1040, a self-replicator could have turned up surprisingly early. But there is more.

1 chance in 4.29 x 1040 is still orgulously, gobsmackingly unlikely; it's hard to cope with this number. Even with the argument above (you could get it on your very first trial) most people would say "surely it would still take more time than the Earth existed to make this replicator by random methods". Not really; in the above examples we were examining sequential trials, as if there was only one protein/DNA/proto-replicator being assembled per trial. In fact there would be billions of simultaneous trials as the billions of building block molecules interacted in the oceans, or on the thousands of kilometers of shorelines that could provide catalytic surfaces or templates [2,15].

Let's go back to our example with the coins. Say it takes a minute to toss the coins 4 times; to generate HHHH would take on average 8 minutes. Now get 16 friends, each with a coin, to all flip the coin simultaneously 4 times; the average time to generate HHHH is now 1 minute. Now try to flip 6 heads in a row; this has a probability of (1/2)6 or 1 in 64. This would take half an hour on average, but go out and recruit 64 people, and you can flip it in a minute. If you want to flip a sequence with a chance of 1 in a billion, just recruit the population of China to flip coins for you, you will have that sequence in no time flat.

So, if on our prebiotic earth we have a billion peptides growing simultaneously, that reduces the time taken to generate our replicator significantly.

Okay, you are looking at that number again, 1 chance in 4.29 x 1040, that's a big number, and although a billion starting molecules is a lot of molecules, could we ever get enough molecules to randomly assemble our first replicator in under half a billion years?

Yes, one kilogram of the amino acid arginine has 2.85 x 1024 molecules in it (that's well over a billion billion); a tonne of arginine has 2.85 x 1027 molecules. If you took a semi-trailer load of each amino acid and dumped it into a medium size lake, you would have enough molecules to generate our particular replicator in a few tens of years, given that you can make 55 amino acid long proteins in 1 to 2 weeks [14,16].

So how does this shape up with the prebiotic Earth? On the early Earth it is likely that the ocean had a volume of 1 x 1024 litres. Given an amino acid concentration of 1 x 10-6 M (a moderately dilute soup, see Chyba and Sagan 1992 [23]), then there are roughly 1 x 1050 potential starting chains, so that a fair number of efficent peptide ligases (about 1 x 1031) could be produced in a under a year, let alone a million years. The synthesis of primitive self-replicators could happen relatively rapidly, even given a probability of 1 chance in 4.29 x 1040 (and remember, our replicator could be synthesized on the very first trial).

Assume that it takes a week to generate a sequence [14,16]. Then the Ghadiri ligase could be generated in one week, and any cytochrome C sequence could be generated in a bit over a million years (along with about half of all possible 101 peptide sequences, a large proportion of which will be functional proteins of some sort).

Although I have used the Ghadiri ligase as an example, as I mentioned above the same calculations can be performed for the SunY self replicator, or the Ekland RNA polymerase. I leave this as an exercise for the reader, but the general conclusion (you can make scads of the things in a short time) is the same for these oligonucleotides.

Search spaces, or how many needles in the haystack?

So I've shown that generating a given small enzyme is not as mind-bogglingly difficult as creationists (and Fred Hoyle) suggest. Another misunderstanding is that most people feel that the number of enzymes/ribozymes, let alone the ribozymal RNA polymerases or any form of self-replicator, represent a very unlikely configuration and that the chance of a single enzyme/ribozyme forming, let alone a number of them, from random addition of amino acids/nucleotides is very small.

However, an analysis by Ekland suggests that in the sequence space of 220 nucleotide long RNA sequences, a staggering 2.5 x 10112 sequences are efficent ligases [12]. Not bad for a compound previously thought to be only structural. Going back to our primitive ocean of 1 x 1024 litres and assuming a nucleotide concentration of 1 x 10-7 M [23], then there are roughly 1 x 1049 potential nucleotide chains, so that a fair number of efficent RNA ligases (about 1 x 1034) could be produced in a year, let alone a million years. The potential number of RNA polymerases is high also; about 1 in every 1020 sequences is an RNA polymerase [12]. Similar considerations apply for ribosomal acyl transferases (about 1 in every 1015 sequences), and ribozymal nucleotide synthesis [1, 6, 13].

Similarly, of the 1 x 10130 possible 100 unit proteins, 3.8 x 1061 represent cytochrome C alone! [29] There's lots of functional enyzmes in the peptide/nucleotide search space, so it would seem likely that a functioning ensemble of enzymes could be brewed up in an early Earth's prebiotic soup.

So, even with more realistic (if somewhat mind beggaring) figures, random assemblage of amino acids into "life-supporting" systems (whether you go for protein enzyme based hypercycles [10], RNA world systems [18], or RNA ribozyme-protein enzyme coevolution [11, 25]) would seem to be entirely feasible, even with pessimistic figures for the original monomer concentrations [23] and synthesis times.


The very premise of creationists' probability calculations is incorrect in the first place as it aims at the wrong theory. Furthermore, this argument is often buttressed with statistical and biological fallacies.

At the moment, since we have no idea how probable life is, it's virtually impossible to assign any meaningful probabilities to any of the steps to life except the first two (monomers to polymers p=1.0, formation of catalytic polymers p=1.0). For the replicating polymers to hypercycle transition, the probability may well be 1.0 if Kauffman is right about catalytic closure and his phase transition models, but this requires real chemistry and more detailed modelling to confirm. For the hypercycle->protobiont transition, the probability here is dependent on theoretical concepts still being developed, and is unknown.

However, in the end life's feasibility depends on chemistry and biochemistry that we are still studying, not coin flipping.


[1] Unrau PJ, and Bartel DP, RNA-catalysed nucleotide synthesis. Nature, 395: 260-3, 1998

[2] Orgel LE, Polymerization on the rocks: theoretical introduction. Orig Life Evol Biosph, 28: 227-34, 1998

[3] Otsuka J and Nozawa Y. Self-reproducing system can behave as Maxwell's demon: theoretical illustration under prebiotic conditions. J Theor Biol, 194, 205-221, 1998

[4] Woese C, The universal ancestor. Proc Natl Acad Sci USA, 95: 6854-6859.

[5] Varetto L, Studying artificial life with a molecular automaton. J Theor Biol, 193: 257-85, 1998

[6] Wiegand TW, Janssen RC, and Eaton BE, Selection of RNA amide synthases. Chem Biol, 4: 675-83, 1997

[7] Severin K, Lee DH, Kennan AJ, and Ghadiri MR, A synthetic peptide ligase. Nature, 389: 706-9, 1997

[8] Ruse M, The origin of life, philosophical perspectives. J Theor Biol, 187: 473-482, 1997

[9] Lee DH, Severin K, Yokobayashi Y, and Ghadiri MR, Emergence of symbiosis in peptide self-replication through a hypercyclic network. Nature, 390: 591-4, 1997

[10] Lee DH, Severin K, and Ghadri MR. Autocatalytic networks: the transition from molecular self-replication to molecular ecosystems. Curr Opinion Chem Biol, 1, 491-496, 1997

[11] Di Giulio M, On the RNA world: evidence in favor of an early ribonucleopeptide world. J Mol Evol, 45: 571-8, 1997

[12] Ekland EH, and Bartel DP, RNA-catalysed RNA polymerization using nucleoside triphosphates. Nature, 383: 192, 1996

[13] Lohse PA, and Szostak JW, Ribozyme-catalysed amino-acid transfer reactions. Nature, 381: 442-4, 1996

[14] Ferris JP, Hill AR Jr, Liu R, and Orgel LE, Synthesis of long prebiotic oligomers on mineral surfaces [see comments]. Nature, 381: 59-61, 1996

[15] Lazcano A, and Miller SL, The origin and early evolution of life: prebiotic chemistry, the pre- RNA world, and time. Cell, 85: 793-8, 1996

[16] Ertem G, and Ferris JP, Synthesis of RNA oligomers on heterogeneous templates. Nature, 379: 238-40, 1996

[17] Lee DH, Granja JR, Martinez JA, Severin K, and Ghadri MR, A self-replicating peptide. Nature, 382: 525-8, 1996

[18] Joyce GF, Building the RNA world. Ribozymes. Curr Biol, 6: 965-7, 1996

[19] Ishizaka M, Ohshima Y, and Tani T, Isolation of active ribozymes from an RNA pool of random sequences using an anchored substrate RNA. Biochem Biophys Res Commun, 214: 403-9, 1995

[20] Mushegian AR and Koonin, EV, A minimal gene set for cellular life derived by comparison of complete bacterial genomes. Proc. Natl. Acad. Sci. USA, 93: 10268-10273.

[21] Ekland EH, Szostak JW, and Bartel DP, Structurally complex and highly active RNA ligases derived from random RNA sequences. Science, 269: 364-70, 1995

[22] Breaker RR, and Joyce GF, Emergence of a replicating species from an in vitro RNA evolution reaction.Proc Natl Acad Sci U S A, 91: 6093-7, 1994

[23] Chyba C and Sagan C, Endogenous production, exogenous delivery and impact-shock synthesis of organic molecules: an inventory for the origins of life. Nature, 355: 125-32., 1992

[24] Doudna JA, Couture S, and Szostak JW, A multisubunit ribozyme that is a catalyst of and template for complementary strand RNA synthesis. Science, 251: 1605-8, 1991

[25] Lahav N, Prebiotic co-evolution of self-replication and translation or RNA world? J Theor Biol, 151: 531-9, 1991

[26] Stadler PF, Dynamics of autocatalytic reaction networks. IV: Inhomogeneous replicator networks. Biosystems, 26: 1-19, 1991

[27] Eigen M, Gardiner W, Schuster P, and Winkler-Oswatitsch R, The origin of genetic information. Sci Am, 244: 88-92, 96, et passim, 1981

[28] Eigen M, and Schuster P, The hypercycle. A principle of natural self-organization. Springer-Verlag, isbn 3-540-09293, 1979

[29] Yockey HP, On the information content of cytochrome c. J Theor Biol, 67: 345-76, 1977


Evolution is stating that life arose from nonlife which violates biogenesis.

No, evolution makes no such statement.  Evolution describes how genes pass traits from one generation to the next.  It does not address abiogenesis.

Theists, on the other hand, claim that in the beginning, there was nothing, and god made everything.  That, I'm afraid, is abiogenesis.  At least scientists admit that life came from something... it's called "elements."  You may have heard of them...


So you see, life did not come from nothing.  It came from matter.

Another thing is that living and nonliving things alike only tend toward disorder over time so there is no way you can even come close to going from microorganism to full-fledged human no matter how many years they add onto the theory of evolution.


Ever notice this thing in the sky?  It's a star, and it is the source of this thing called ELECTROMAGNETIC RADIATION.  This is a form of ENERGY.  The earth is not a closed system.

Cosmic rays from space hit Earth's atmosphere all the time. When a high-energy cosmic ray enters the atmosphere, it can cause an "air shower". The cosmic ray hits a molecule in the atmosphere and "breaks up", producing lots more sub-atomic particles. A real air shower can make millions of particles. This picture shows a simple version of an air shower. The cosmic ray (in red, at the top) makes lots of other particles, many with odd names. The sub-atomic particles shown here include protons (green), neutrons (orange), pions (yellow), muons (purple), photons (blue), and electrons & positrons (pink).
Click on image for full size (43 Kb)
Windows to the Universe original artwork by Randy Russell using a photo courtesy UCAR (Nicole Gordon).



Another thing evolutionists argue about is since most of our DNA is similar to apes then most likely we originated from them. Just because we are similar in DNA does not mean we are related in any way,shape,or form.

Ok, for comparison, think of War and Peace.  It's a monumental piece of literature, to be sure.  So is On the Origin of Species.  With the exception of illustrations, both books are written using the same set of characters -- 26 letters, spaces, ten numbers, and a handful of punctuation marks.  Yet, despite being made from exactly the same substances, the two books are completely different in content.  In fact, aside from saying that they are both books, we can hardly say that they are the same kind of thing.  So it is with life.

Consider:  The gene for a protein called brain-derived neurotrophic factor (BDNF) is located on chromosome 11 in humans.  It is only 1,335 letters long, which is quite short for a gene.  It spells out the recipe for a protein that encourages the growth of neurons.  In most animals, including humans, the 192nd letter is a G, but in about 25% of humans, it's an A.  This very slight difference makes a very big difference in the organism.  Those with G's form the chemical valine, and those with A's form methionine.  Since each human has two copies of each gene, there are three types of people -- met/met, val/val, and met/val (val/met).  It turns out that met-mets are significantly less neurotic than val-mets, who are statistically less neurotic than val-vals.  This tiny difference -- one letter in one gene on one chromosome -- makes a huge impact on a person's personality.  Imagine how much difference 2% of an entire genome could make!  (This, by the way is the highest estimate of our similarity with chimps -- 98%.)

Now I will describe why i think some very scarcely populated dinosaurs still walk the earth today.


(Someone get the straight jacket... we've got a live one...)


I watched your debate with The Way of The Master and i was disturbed with you and your wife pointing fingers at religion for starting many problems within the United States.

They're not married.  They do fuck often, and from what Brian tells me, it's a lot of fun.

Well there are multiple things that are not rational in this world that rationality cannot explain.

Please don't make the mistake of thinking that because you cannot explain something rationally, that it cannot be explained.  You are not the most rational person I've encountered.

Take a look at this next excerpt carefully from the King James Bible Romans 1:20...

I did.  It's very poetic.  Is that what I was supposed to say?  Can we go back to talking about science now?

Evolution is purely a religion.

No.  Evolution is the process of passing genes between generations in a population.  A religion is something else.

There is no real correct evidence to support the theory but only very loose evidence that has no good ground at all.
The following was compiled by Yellow_Number_Five:
On Observed Speciation and Speciation Models:

Salamanders and Songbirds

More details on the salamanders, with additional links

London mosquitos

Another article on Himalayan song birds

Speciation by reinforcement

Lots of examples here

More examples

Speciation models

Links on examples and models

More on the London mosquitos

Ringed-speciation model and examples, plus links

In Drosophila (fruit flies)

On Behavior, Reciprocal Altruism and the Evolution of Behavior:

Behavior models (registration required)

The Origins of Right and Wrong in Humans and Other Animals

Chimps show sense of fair play

Genes, altruism and evolution (with more links)

Reciprocal altruism

Kin selection and reciprocal altruism

On the Evolution of Complexity


Evolution of human intellect and diet

Evolution of language

Music and the relation to language (registration required)

Evolution of religious memes

Bacteria flagella

Avida Digital evolution

More on the evolution of religion

Complex evolution in the laboratory

The eye

The brain
You have to beleive there is no God and you have to beleive we came from nothing.

Actually, evolution doesn't address the question of god at all.  As I've already explained, evolution doesn't deal with abiogenesis, nor do scientists claim that life came from nothing.  They claim it came from matter.

I don't want you sitting in hell someday forever realizing that God was offering his loving hands out to you all along and you ignored that.

That's mighty neighborly of you.  I don't want you operating heavy machinery near me.  I fear for your ability to read complex sets of instructions.

Let me just give you a small idea of this place called hell if God exists.

SCARE ME BABY!!!!  DO IT!!!!!  SCARE ME!!!!!!    That'll prove to me that evolution is wrong!!

Well just for so you will know, once the rapture has taken place and God has taken all of his faithful children back home, Satan will arise from the deep and set up a peace agreement between every country and God's wrath will be poured out throughout the entire world.

Scary stuff.... When does that girl spin her head around and vomit pea soup?

Stop laughing off the Christian faith because God cares about you and doesn't want you to carry on like this. Jesus is the WAY the TRUTH and the LIFE. He is real. I GAURANTEE.

Atheism isn't a lot like religion at all. Unless by "religion" you mean "not religion". --Ciarin
Books about atheism

Kay Cat's picture

Some Theist or Another

Some Theist or Another wrote:

Stop laughing off the Christian faith because God cares about you and doesn't want you to carry on like this. Jesus is the WAY the TRUTH and the LIFE. He is real. I GAURANTEE.



wow... just wow... to your rebuttal. If this individual bothers to read this, I'm sure Linda Blair will have nothing on him in regards to head spinning.



dunnow if I'd want his guar ant tea, sounds pretty nasty.



Vote for McCain... ...and he'll bring Jesus back

Rook_Hawkins's picture

Wow, Hamby.  Just wow. 

Wow, Hamby.  Just wow.  Well done.

Cool ... Hamby brings out

Cool ... Hamby brings out tank, kills fly. Be on the fly lookout, and call in the big guns .... I am feeling safer this day, ..... as god of wounded Abe, takes another blow ....    

       I got a bb gun ! .... Next is ammo .... throw what ya got .... Rum bombs too ....

                  Sending this via e-mail ....     


deludedgod's picture

(No subject)

*Buries hands in face*. You know what, read my signature. I’m sick of telling people they need to “at least know some basic evolutionary biology” in order to create an informed argument. From now on, I will be perfectly clear: In order to make strongly backed up claims about evolution, it is necessary for the claimant to be intimately familiar with developmental, molecular and evolutionary biology, and genetics. Achieving a state where I was intimately familiar with all these disciplines took…10 years. To put it another way, there are a lot of people with a lot of serious reading to do. I swear, I’m going to start testing people before they come to me with arguments against evolution, and if they can’t answer a basic question like “what is a clade?” then they can just go away. Call me elitist if you want. I don’t care at this point. I’m damned sick of reading assertions about evolution and thermodynamics from people who would be unable to solve an integration problem or assertions about abiogenesis from people who don’t even know what an “oligonucleotide” is.

PS: Good job on the rebuttal Hamby. I'd pitch in, but as you know, virtually everything here has already been argued to which I have already responded. Creationists are not known for originality. However, if he comes back, I shall be waiting with a smile and artillery, as I always do.

Actually, why not? Here, for the 17th time on this board, is my official encapsulation on abiogenesis:


The process of formation of organic autocatalysis is time consuming. It begins with Piezoelectric systems on crystalline surfaces, which form the precursors of ribozymes. The first biological molecules on Earth may have been formed by metal based catalysis on the crystalline surface of minerals.

In principle, an elaborate system of molecular synthesis and breakdown called metabolism could have existed as such long before the first cells. Life requires molecules which catalyze reactions which lead directly or indirectly to replication of more molecules like themselves. Catalysts with this self promoting property can use raw materials to reproduce themselves and therefore divert the same materials from the production of their substances. In modern cells the most versatile catalysts are polypeptides. However, they cannot propagate self-replication, they do not replicate. There needs to be a molecule which can act as a catalyst and guide its own replication. Such a molecule does exist: RNA.

To understand this more fully, we must understand the relation between protein, DNA, and RNA. Now, the key principle to grasp is the central dogma of molecular biology. Note that the word dogma is not used because the principle has religious adherence, but rather because it seems to be obeyed by all biological life.

Proteins, being the primary structure and material of all cellular life, are encoded by the information in DNA, which is transcribed to an RNA intermediate before being translated into protein. This process is central to all biological life and is universal in its usage. However, it was not always the case. Prior to the existence of DNA, RNA was used as a ribozyme, prior to the usage of protein as the catalytic compound which would be necessary for the self-replicative properties of biological life. Hence:


would eventually be superseded by:


The manner in which this could occur and form has been detailed above, since RNA have a similarity to polypeptides in their ability to form an active site for homogenous catalysis. It is important to note that ribozymal catalysis still exists in the most primite and ancient mechanisms common to all cellular life. Particular processes worthy of note are protein biosynthesis, snoRNA and snRNA manufacture, SSI (Self-splicing intron/exon junctions) and snRNP splicing (small nuclear ribonucleoprotein complexing), miRNA regulation of translation and RNAi mediated destruction of viral mRNA:


The process of natural selection would naturally favor those RNA which could hold amino acids or small stretches of such at their active sites, by the process detailed above. Hence, eventually the order above would have been superseded by the following:

RNA>RNA and RNA>Protein

DNA has several advantages over RNA. The superseding of RNA as the primary encoder of the codons for polypeptides would have been a slower process. In modern organisms, translation is done by virtue of a set of RNA molecules which hold amino acids and match them to the mRNA called tRNA adaptors. As mentioned previously, RNA molecules that could hold information to guide polypeptide synthesis would have had a massive advantage over its catalytic counterparts because polypeptides are much more efficient at catalysis. Now, ribozymes can perform the function of tRNA-like molecules called psuedo-tRNAs. Finally, this crude form of the peptidyl-transferase would have been naturally selected for its ability to hold the amino acid at the catalytic side of the string of RNA that can hold its code. This development was probably what led to the modern system of codons. Hence we have the following:

mRNA (via psuedo-ribosomes)> translates Protein

Finally, the sequence we see today:


Would have arisen later. The chemical similarities between the two molecular chains, that is, DNA and RNA, allows for the superseding to occur without interrupting the central processes of this primitive form of biological life. But DNA would be naturally selected for as the primary sequence for the transcription of chains to hold the codons because deoxyribose is more stable than ribose and thymine more so than uracil.

We will now consider the precise manner in which this process occurred. First we must understand proteomics in some detail:

Essentially, a protein is a string of amino acids, usually 500-2000 amino acids long. The whole of life depends on proteins. Everything else, save the genes, is a mere passive bystanders in biological life. When we observe the cell, we are in essence observing proteins. Proteins control movement (motor proteins), the control structure (structural proteins), they control concentration (transmembrane proteins), they control ion gradients (pump proteins), and most importantly, they control every single chemical reaction in the body (enzymes). Proteins don't just control the body, they are the body. All proteins fold up tightly into one highly preferred conformation. There is no limit to the number of tasks they do in the cell. Proteins can be subdivided into two large classes, the globular proteins fold up into irregular ball-like shapes and fibrous proteins. Nearly all globular proteins are allosteric, which means they can adopt two slightly different conformations, this means they have two binding sites, one of which is for a regulatory molecule, and the other is for the substrate. Allosteric control is very complex. Suffice it to say for now that it works on either negative or positive feedback (ie the regulatory molecule increases the protein's affinity for the substrate, and the other way around, or the opposite, the regulatory molecule decreases protein affinity for the substrate, which of course, would be reciprocal. In this way, regulatory molecules can turn the protein on or off, and in negative control, there is a tug of war between the regulatory ligand and substrate which are reciprocally affected by each others concentration in the cell.

A protein is a specific type of biological polymer made up a specific family of chemical subunits called amino acids. There are 20 biological amino acids, and they are distinguished by the fact that they all have a central alpha carbon, which is attached to an amine group (-NH2), a Carboxyl group (-COOH), a hydrogen, and a side chain. It is the side chain that gives each amino acid its properties, and each of the 20 has a different side chain. Proteins can be anything in length. Usually it is 50-2000 amino acids long, and the longest ones can 7000 amino acids long. The interaction between the side chains (which is determined by charge, since three are basic, four are acidic, nine are nonpolar and five are polar but uncharged) determines the shape of the protein. For instance, the nonpolar side chains are all hydrophobic (water hating) which means the protein will fold up in a manner where the nonpolar side chains are facing inwards and not exposed to water (this is the most energetically favorable conformation). This is just one of many different subtle interplays between amino acids that determine a proteins shape. However, nearly all proteins fold spontaneously in a solution, indicating that all the information necessary to fold it is stored in the amino acids.

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

Now, for the number of possible combinations of amino acid, such calculations are easy to make. With just two amino acids joined in a row, we have 20^2, or 400 possibilites. With three we have 20^3 or 8000 possibilities, with ten, we have 10240000000000 possibilities, with the average protein having several hundred amino acids up to a thousand, we have vastly more conformations than there have been seconds or atoms in the universe.

There is an evolutionary advantage to stable conformations forming, and stable conformations, in turn, are the ones which give rise to biological functions. There is an obvious reason for this. The general properties we need concern ourselves with are as follows:

All Proteins Bind to Other Molecules

· Properties of proteins depend on their interactions with other molecules

  • Eg. Antibodies attach to viruses to mark them for destruction, the enzyme hexokinase binds glucose and ATP to catalyze the reaction between them
  • Actin molecules bind to each other to produce actin filaments etc
  • All proteins stick or bind to other molecules
  • Sometimes tight binding, sometimes weak and short lived
  • Binding is always highly specific. Each protein can usually only bind to one type of molecule out of the thousands it encounters
  • The substance bound to a protein, be it an ion, a macromolecule, a small molecule etc is referred to as the ligand of that protein
  • Region of the protein associating with the ligand is known as the binding site
  • Usually a cavity in the protein surface caused by a particular chain of amino acids
  • These can belong to different portions of the polypeptide chain brought together when the protein folds
  • Separate regions of the protein surface generally provide binding sites for different ligands.


The Details of a Protein’s Conformation Determine It’s Chemistry

· Proteins chemical capability comes in part because neighboring chemical groups on the protein’ surface often interact in ways which enhance the reactivity of amino acid side chains

· Two categories of this: Neighboring parts of the chain may interact in a way that restricts water molecules access to the ligand binding site.

· Because water molecules tend to form hydrogen bonds, they can compete with the ligands for sites often the protein surface

· Therefore, the tightness of the protein-ligand bonding is greatly increased if water molecules are excluded

· Water molecules exist in large hydrogen bonded networks, and inside the folds of a protein a ligand can be kept dry because it is energetically unfavorable for water molecules to break from this network

· Clustering of neighboring polar amino acid side chains together can alter reactivity. If the way the protein folds forces many negative side chains together that would otherwise not associate due to their mutual repulsion, the affinity of this new pocket for a positive ion is greatly increased

· Sometimes, when normally unreactive groups like CH2OH interact with each other because the side chains on which they are on form Hydrogen bonds with each other they can become reactive, allowing them to enter reactions making/breaking covalent bonds

· Therefore the surface of each protein has a unique chemical reactivity that depends on which side chains are exposed and their exact orientation relative to each other.

Sequence Comparisons Between Protein Family Members Highly Crucial Ligand Binding Sights

  • Many domains in proteins can be grouped into families showing clear evidence of evolution from a common ancestor
  • Genome sequence reveal a large number of proteins with one or more common domains
  • 3D structures of members of same domain family remarkably similar
  • Even when the amino acids identity match falls to 25% the backbone atoms in two members of the same domain family have the same fold within 0.2nm
  • These allow a method called “evolutionary tracing” to determine which sites in the protein domain which are most crucial to the function of said domain
  • For this, the most conserved amino acids stretches are mapped onto structural model of the known structure of one family member
  • The SH2 domain is a module that functions in protein-protein interactions. It binds the protein containing it to a second protein containing a phosphorylated tyrosine side chain in a specific amino acid context
  • The amino acids on this binding site have been slowest to change in the evolutionary history of SH2

We must understand all of this. Biology is highly modular. It is all about the assembly of large structures from smaller ones. Polypeptides are modularly assembled from amino acids hence determining its structure hence its chemistry and binding. Proteins are modularly assembled from polypeptides, and supramolecular structures from polypeptides, therefore, the evolution of proteins will be forced in the direction of stable amino acid conformations not random possibilities associated with amino acids. This becomes evident when we consider proteomic supramolecular structures:

Protein Molecules Ofter Serve as Subunits for the Assembly of Large Structures

· Noncovalent bonding allows proteins to generate supramolecular structures like construction of giant enzyme complexes, ribosomes, proteasomes, protein filaments, and viruses

· These are not made by one giant single covalent molecule, instead by noncolvalent assembly of many giant subunits

· Advantages of this building technique: Large structure built from a few repeating subunits requires little genetic information

· Both assembly and disassembly are easily controlled and reversible

· Errors in structural synthesis are easily avoided as proofreading mechanisms can operating during the course of the assembly

· Some protein subunits assemble into flat sheets, on which the subunits are arranged in a hexagonal pattern

· Slight changes in the subunit geometry can turn the sheet into a tube, or with slightly more changes, into a hollow sphere

· Protein tubes and spheres which bind to RNA form the coats of viruses

· Formation of these closed structures provides additional stability because it increases the number of covalent bonds

· This principle is illustrate by the protein coat or capsid of may viruses

· Capsids are often made of hundreds of identical protein subunits enclosing and protecting the viral nucleic acid code

· The proteins of capsid must have particularly adaptable structure. Not only must it have multiple contact points to make a stable sphere but also must be able to change to let the nucleic acid out to initiate viral replication in a cell. This is shown here by the construction of a capsid from monomer protein subunits, which connect into dimers, then trimers, then into the intact sphere with the addition of more free dimers

Polynucleotides Can Both Store Information and Catalyze Chemical Reactions. RNA can propagate itself by means of complementary base pairing. However, this process without catalysis is slow, error prone and inefficient. Today, such processes are catalyzed by a massive battery of complex interactions of RNA and proteins.

In the RNA world, the RNA molecules themselves would have acted as catalysts. A pre-RNA world probably Predates the RNA One. It is unlikely RNA was the first self-replicating propogater. It is difficult to imagine that they could form through nonenzymatic means. The ribonucleotides are hard to form enzymatically, also RNA polymers entail a 5 to 3 chain which must compete with other linkages that are possible including 2 to 5 and 5 to 5. It has been suggested that RNA was preceded by molecules with similar properties, but that were similar. Candidates for pre-RNA include p-RNA and PNA (peptide nucleic acid)

The transition from pre-RNA to RNA would have occurred through the synthesis of RNA via these simpler components as template and catalyst. Laboratory experiments demonstrate this as plausible. PNA can act as a template for RNA molecules. Once the first RNA molecules had been produced, they could have outphased their antecedents leading to the RNA world

Single-Stranded RNA molecules can fold into highly elaborate structures Comparisons between many RNA structures reveal conserved motifs, short structural elements used over and over again as part of larger structures. Common motifs include

Single strands, double strands, single nucleotide bulges, triple nucleotide bulges, hairpin loops, symmetric internal loops, asymmetric internall loops, two stem junction, three stem junctions and four stem junctions. RNA molecules can also form common conserved interactions such as psuedoknots and “kissing hairpins” and hairpin-loop bulge contacts, like in this picture:

-Protein catalysts require a surface of unique countours. RNA molecules with appropriate folds can also served as enzyme. Many of the ribozymes work by positioning metal ions at the catalytic sites. Relatively few catalytic RNA exist in modern day cells, being the polypeptides work much better.

An example of In vitro selection of synthetic ribozymes:

-A large pool of dsDNA each with a randomly generated sequence. Transcription and folding into randomly generated RNA molecules. Addition of ATP derivative containing a sulfer in place of oxygen Only a rare RNA has the ability to phosphorylate itself. This is captured by elution of the phosphorylated material

These experiments and others like them have created RNAs that can catalyze a wide variety of reactions:

Peptide bond formation in protein synthesis, RNA cleavage and DNA ligation, DNA cleaving, RNA splicing, RNA polymerization, RNA and DNA phosphorylation, RNA aminoacylation, RAN alkylation, Amide bond formation, amide bond cleavage, glycosidic bond formation and porphyrin metalation, since, like proteins, ribozymes undergo allosteric conformation change

Self-Replication Molecules Undergo Natural Selection

-The 3D structure is what gives the ribozyme chemical properties and abilities. Certain polynucleotides therefore will be especially successful at self-replication. Errors inevitably occur in such processes, and therefore variations will occur over time. Consider an RNA molecule that helps catalyze template polymerization, taking any RNA as a template

-This molecule can replicate. It can also promote the replication of other RNA. If some of the other RNA have catalytic activity that help the RNA to survive in other ways, a set of different types of RNA may evolve into a complex system of mutual cooperation.

One of the crucial events leading to this must have been the development of compartments. A set of mutually beneficial RNA could replicate themselves only if the specialized others were to remain in proximity

Selection of a set of RNA molecules according to the quality of replication could not occur efficiently until a compartment evolved to contain them and therefore make them available only to the RNA that had generated them. A crude form of this may have simply 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 arisen this way. Any RNA that guided the synthesis of a useful polypeptide would have a great advantage.

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

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

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

And of course, my official encapsulation of evolution and thermodynamics. I've posted this nearly 50 times across the boards over the last year. Theists are so unoriginal.


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

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

E in the box can also change during a reaction due to work done in the outside world. Suppose there is a small volume increase in the box (∆V) which must decrease the energy in the box (∆E) by the same amount. In most reactions, chemical bond energy is converted to work and heat. Enthalpy(H) is a composite function of work and heat, (H=mc∆T). Technically it is the Enthalpy change (∆H) is equal to the heat transferred to the outside world during a reaction, since Enthalpy is the composite function in question. In the equation above “c” simply refers to the specific Heat Capacity of the Material in question, such that the SHC is the amount of energy required to be inputted into the system to raise the temperature of one gram of the substance in question by one Kelvin (note that we can also measure this in terms of moles instead of mass, termed molar heat capacity). In the language of the First Law of Thermodynamics, we would express such like this:

Where Q=∆U-Wo, Q=mc∆t or (for molar heat capacity) Q=nc∆T

So, ∆H is a quantity expressing the SHC multiplied by the temperature change and by the mass of the substance in question. Since SHC is simply a measure of Energy change per Kelvin per Gram (or per mole), ∆H is simply a quantity expressing the change in energy of a system in question, where ∆H is roughly equivalent to the heat energy lost in a reaction.

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

Let us consider 1000 coins in a box, all facing heads. It is a closed system, which, by definition, does not exchange energy input or output with the rest of the universe. States of high order have low probability. For instance, if we imagine a box with 1000 coins lying heads up, and we shake it twice, it is vastly more probable that we will end up with a chaotic arrangement of coins than the arrangement that we had previously. Thus, the law can be restated closed systems tend to progress from states of low probability to high probability. This movement towards high probability in a system where the energy is E, is progressive. In order for the entropy (the progression towards high probability) to be corrected, there must be periodic bursts of energy input, which would break the closed nature of the system. In this case, it would require someone to open the box and rearrange the coins. The second Law of thermodynamics is a probability function dictating that energy, regardless of how hard we try, always “spreads out” by which we mean that it becomes converted into less useful forms that are probabilistically very, very difficult to retrieve back into ordered states. This governs our lives. Eggs do not unbreak, glasses do not unshatter, entropy is highly directional, for it predicts, in any given system, there to be only one ordered state and a vast amount of disordered states, such that the probability of a disordered state is logarithmically greater than those of ordered states. Specifically, heat, being random hubbub of molecular motion, is the most singularly chaotic and disordered form of energy, and ultimately, therefore, almost impossible to retrieve into ordered states. There is a critical equation governing this to be described below.

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:


Note that k and R should not be confused.

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:
















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.

All this means is that the probability distribution for a set of particles in a system is given as that most particles do not have enough energy to complete a chemical reaction. This graph, called the Maxwell-Boltzmann Distribution, is central to chemistry and statistical mechanics. The number of particles that have a certain range of energies is given by integrating the area between the two values we want to measure.

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 k log 10^298, ∆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.

Ultimately, regardless of whether we are talking about gas molecules or coins in a box, or book pages, the reason for the increase in entropy will come, as mentioned, because high entropy states are states with a greater probability. To understand this it is necessary to distinguish between microstates within a closed system and macrostates. The former are measures of the particles themselves, velocity, position, etc. Macrostates are measures of variables of the system, temperature, pressure, volume, etc. Pressure serves as an easy variable to explain. Imagine a box with a slit in the center where both sides are of equal volume and are filled with gas molecules, one side having 6 times the number of molecules than the other. Thus, assuming constant temperature, it follows that by the combined gas law, that side will have 6 times the pressure of the other. This is effectively a restriction on the number of possible microstates that the system could take, because there are fewer ways to arrange the molecules such that one side has six times the pressure of the other. This is called a potential or a thermodynamics inequilibrium. It is the basis of our understanding of S=klogW. Once the barrier is released, the molecules will tend to equilibriate, since this represents the macrostate where the greatest number of microstates, hence the greatest probability, could represent, one of equal pressure throughout the system. Hence we say the system moves towards equilibrium. As we shall soon see, so do chemical reactions, and this is the basis of all chemistry, including that of biological life. A diagram works well to illustrate this principle:

The number of microstates for the given macrostates is given in the diagram. Establishing them ourselves is a simple exercise in combinatorial mathematics.However, whoever made the image is probably using a different criterion for permutations, since it seems obvious at first sight that for the first example, there should be (8!) permutations, or 40,320 possibilities, and the other number of microstates should increase accordingly (it may be that the image-makers have excluded the order-criterion, while I have incorporated it, resulting in my computing of (10!) combinations for the final macrostate. The point to take away is that high entropy states have a greater number of microstates corresponding to a single macrostate. This, basic probability, is the reason that things tend towards disorder.

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


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 the gas constantt, 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. Indeed, most reactions do not go onto completion. They reach a point where the rate of backward reaction and forward reaction are equivalent (this can only be established in a closed system), and thus the concetration of product does not increase. Such a system is said to be in a system of dynamic equilibrium and the ratio with which the products are in with the reactants at the point of equilibrium is called the equilibrium constant or the Kc. The magnitude of the Kc will determine the free energy change. For some reaction aA+bB=>cC, then


Note that this also depends on the molecularity of the reaction, which in turn determines the stoichiometric coefficients of the reaction.The higher this ratio, the more product is needed over reactants to establish dynamic equilbrium, meaning the probability of A becoming B is high, whilst that of B becoming A is low. We say that this reaction tends to completion and that it has a negative free energy change in the forward direction. Thus it has an equal and opposing free energy change in the back direction.

If 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:


For which we can rearrange to make the concentration the subject, where (B)^b/(A)^a would now represent the equilibrium constant for some reaction aA=>bB. The ratio of B over A such that the reaction proceeds in equilibrium raised to the power of the respective stoichiometric coefficients is this Kc. The greater this ratio, the greater the free energy loss, and the more favorable hence probable A to B becomes.



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.

∆Ssea +∆Scell =∆Suniverse

The entropy of the local system can decrease, providing the entropy of the global system increases. It was Schrodinger who realized that decreases in entropy and the construction of high-order 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.

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.

Now that we know all that we do about entropy, we must ask ourself precisely what the argument is and how entropy has anything to do with evolution. Although evolution is not directional, the history of life on Earth observes a general trend via which more biologically complex creatures, like humans, are the distant descendants of less complex ones, those that came first, prokaryota, etc. To someone who misunderstands the principles just outlined, this is a very crude analogy to the unshattering of an egg. However, this is not the case. Biological evolution is a generalized process that operates on entities which already generate order from disorder, biological entities. Yet as has just been exhaustively detailed, these entities existence are perfectly compliant with the laws of thermodynamics. All cells, in effect, are in a race against time, the inevitable disordering that occurs as a result of probability. If a bacterial cell dies, the processes running which generate order within the cell at the expense of order in the universe stop, and so the cell rapidly becomes disordered. The DNA starts to break and fragment and knot, the cell starts to swell due to osmosis since the pumps are no longer operating, and it will either reach a new osmotic equilbrium or burst. Live cells will order their internal components, and maintain an ordered system and generate more ordered systems out of less ordered ones, at expense of the surroundings. Thus to state that evolution violates thermodynamics would be redundant if true (it isn't). Life is an order generating process which works against the grain of thermodynamics because it contributes to the entropy of the surroundings. This process is only possible because biological life in turn operates via a series of chemical reactions that allow for order generation via intermediate reactions which contribute more disorder to the universe. The sustaining power behind this is the sun. It is no coincidence that the first life forms that appeared were cyanobacteria. Phototropism necessarily predates organotrophism, since the latter requires a preexisting stock of organic material which in turn must be generated in an order-generated process fed by an external source of energy. Photons are the stores of energy allowing for this process to occur, for via photosynthesis the plant produces glucose, via which it in turn runs the necessary mechanisms to stay ordered. This in turn allows for the development of organotrophes. It is no exaggeration to say that virtually all biological life depends on phototrophes. Evolution is simply a process operating on these order-generating systems. To state it would be in violation of thermodynamics would thus be redundant since it operates by definition upon processes which generate order, which, as we have seen, is permissible.

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:


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 influx of 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. 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 ( an endothermic reaction will disorder the system and order the surroundings and vice-versa for an exothermic reaction) 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. The release of energy makes the polymerization energetically favorable. The chemical potential energy in the ATP is used to drive a polymerization which could otherwise not occur and simultaneously cause such a large disordering effect on the universe as to increase the total entropy in the universe, in the form of heat energy released. So it is that everything your body does, replication of DNA, production of gametes, transcription, translation, nerve cell firing, etc. serves to increase the entropy of the universe. 

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.


"Physical reality” isn’t some arbitrary demarcation. It is defined in terms of what we can systematically investigate, directly or not, by means of our senses. It is preposterous to assert that the process of systematic scientific reasoning arbitrarily excludes “non-physical explanations” because the very notion of “non-physical explanation” is contradictory.


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Hambydammit's picture

Oh... damn... he's fighting

Oh... damn... he's fighting a two front war now, and all he came armed with was a Nerf (TM) Gun.

Thanks, DG


Atheism isn't a lot like religion at all. Unless by "religion" you mean "not religion". --Ciarin
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deludedgod's picture

Don't thank me, I didn't do

Don't thank me, I didn't do anything. I wrote that summary piece months ago. It was no effort on my part to retrieve it. You sort of know what to expect after a while. "Hmmm, another argument from thermodynamics. Go into the "physical chemistry" folder and retrieve the file I wrote last year on entropy and life" What's that? Another argument from incredulity? Just go into the "molecular evolution" folder and retrieve the file on "modularity and the evolution of large scale biological structures". Maybe I can hire someone to write a program that does this form me and therefore stands in for me. Of course, the frustrating thing is the prerequisite knowledge. What I wrote above, which I retrieved from the file marked "biochemistry" under the file for "primordial chemistry" will appear gibberish unless the OP knows biochemistry. Let's find out.

"Physical reality” isn’t some arbitrary demarcation. It is defined in terms of what we can systematically investigate, directly or not, by means of our senses. It is preposterous to assert that the process of systematic scientific reasoning arbitrarily excludes “non-physical explanations” because the very notion of “non-physical explanation” is contradictory.


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DG with atomic bazooka on

DG with atomic bazooka on our side , yanking all chains. Gawed love ....

Fuck Abe's God .....  

      ....  just comes to mind,  ..... post a song DG !!!!      LOL

       Saxon, Power and the Glory

                    "Fix the words" , said a buddha ....

JillSwift's picture

I envy Hamby's patience. I

I envy Hamby's patience. I could not read that whole post, never mind follow it up with such a thorough rebuttal.

"Anyone can repress a woman, but you need 'dictated' scriptures to feel you're really right in repressing her. In the same way, homophobes thrive everywhere. But you must feel you've got scripture on your side to come up with the tedious 'Adam and Eve not Adam and Steve' style arguments instead of just recognising that some people are different." - Douglas Murray