Bump.

Hit.

Wow, thats long and amusing. Hm. I doubt if any theists would qoute and reply.

The theists you argue with must not be very observent of the current arguments.

The current charge against evolution is not that some mutations are good, microevolution does not occur, etc. The argument is information theory.

All mutations, good, bad, ugly, whatever, either destroy information or do not add to it. If life started as self-replicating molecules, then they would have needed a large amount of information added to become bacteria.

The problem is that no mutation has ever been observed that adds information. The closest is a mutation that copies information, not adds it, plus an information addition is against the law of entropy. Molecules tend to break down on their own, not add to.

the information theory argument rests of fundamental confusions of how scientists define Genetics as carrying information. I can simply take this from a piece I wrote called 24 answers to creationist nonsense:

Fallacy #9 (Continuation of macroevolution error): New genetic information cannot arise.
This is totally ridiculous. The assertion goes like this. Creating a new function like a wing or an eye would require the introduction of new genetic information, mutation and natural selection only changes pre-existing information”.
Adding information in DNA terms is done by the process of templated polymerization, whereby strands produce complementary strands by nucleotide bonding whereby the nucleic acids can recognize their VDW bond counterpart by the activation energy needed.
Changing information occurs when a mutation occurs by one of the mechanisms mentioned above (page 2)
The problem with this statement is that DNA genomes are extremely redundant. 91% of the human genome is redundant, if you are interested. So changing one copy will add new information. Because most of the time the polymerization works out fine. Imagine it like a library. There is only one copy of each book. You remove one book and replace it with a different, new book. Are you adding information? No. You are changing information. This is the crux of the creationist argument. But imagine you have twelve copies of each book. You replace one copy of one book with a different, new book. Now you are adding new information because the pre-existing information is still there in the form of 11 other books.

DNA defines information in a completely literal chemical makeup, with precise order of atoms and molecules representing codon order. This can be seen in the transcription cycle:

For DNA, nothing complex is required. A set of reactions that reads DNA is based on literally copying it. The key thing about DNA is that the nucleotides literally represent amino acids. One codon is identical to an amino acid. This is translation/transcription. I'll go through it step by step again.
1. A stimulus from the cell membrane causes proteins to bind to the introns flanking the necessary exon, this causes the string to unwind. This is initiated by transcriptase enzymes
2. Once unwound, the string splits
3. Through templated polymerization initiated by polymerase enzymes, free bases attach to the complementary string, producing the identical string (that which is precisely identical to the protein in question in terms of codon order), which is then tidied up using spliceosomes and ligases, enzymes that cut through the introns and glue the exons together to make the complete string.
4. The Free bases are RNA bases and attach to form the protein-identical RNA base. The reason for this is that a ribosome cannot read DNA, it must be converted into RNA. The only difference is that it has ribose instead of deoxyribose and uracil instead of thymine, but since nothing else can read thymine, that is an important difference. This string is called mRNA which is ejected from the nucleus.
5. tRNA strings which represent one amino acid bind to their corresponding amino acids on one end. On the other end they have an anticodon, which represents the base string identical to the amino acid.
6. The mRNA is captured by a ribosome, a giant macromolecular protein. The mRNA is lined up along it. The anticodon on the tRNA automatically binds to the codons on the mRNA. This forces all the amino acids to line up. They thread together automatically, which causes the now unnecessary tRNAs to detach and leave the ribosome. When the protein is finished, it is automatically detached.

Fallacy #13 The Second Law of Thermodynamics
An even worse fallacy than irreducible complexity is using The Second Law of Thermodynamics to disprove evolution, that has got to be the worst understanding of science in history. The law is:
-All systems tend to progress towards entropy
The premise of this law is that essentially all useful work will release wasted energy in the form of heat energy, which is almost impossible to reconvert into a useful form of energy again (like chemical potential). But a system which receives constant influx and outflux (a system which is not closed) will not necessarily progress towards entropy. But even the Earth itself is not a closed system. There are very few self contained systems. Almost everything receives energy from something else because everything gives off radiation heat.
Also, the implication of this ridiculous fallacy is that not that evolution cannot be sustained but rather life itself because it is complex. A seed growing into a tree supposedly breaks the second law, this is ridiculous. Even if there was a God who engineered life (there is not) there are no ad hoc little workmen running around organizing life. Life is a set of autoregulatory processes that can sustain itself. So even if we make the baseless assumption that God created life, the reproductive process where life arises from old life is natural, not supernatural. If the second law of thermodynamics extended to open systems, every function of life would be impossible, not just it’s evolution. There is nothing about it that breaks the thermodynamic law because cells take in free energy and use adenosine triphosphate to correct the entropy.

1. all of these are recombining already attained information. Duplication errors almost never survive past the embrionic state, and Horizontal transfer only recombines present alleels.

Doesnt matter, of course it recombines pre-attained information. That is the whole premise of genetics, new genes arise out of old ones. Read the paragraphs I wrote on transcription and information theory to understand why. Also, Duplication error is mitosis not meiosis, and horizontal transfer does not do that, you are thinking of vertical transfer, which, while not making new genes, promotes genetic variance, necessary for evolution.

2. All of these require a diploid or greater genome with true sexual reproduction (with the possible exception of segment shuffling, can you cite a source on that?) So we are left with how diploid eukariotic sexual reproduction can possibly arrise from prokariotic bacterial simple gene exchanges. Natural selection says that any bactreria with an added copy of it's own genome will probably be selected out because of it being inefficient. (The same thing with an incomplete flagellum)

No sir, prokaryotes have a trick known as horizontal transfer which Eukaryota cannot do. You are thinking of vertical transfer. Also, most genetic errors occur during mitosis, something prokaryotes do far more often than Eukaryotes.
The origin of Eukaryota from the protocells remains somewhat a mystery but we do know it was formed out of the punctuated equilibrium by atmospheric gas changes during the Precambrian. Studies have revealed that promiscuous gene exchange via horizontal transfer between Eubacteria and archaea developed the Eukaryota genome. The thing molecular biologists are focusing on now are the ESPs (Eukaryota specific proteins)

Generally, biological functions are very efficient. The most inefficient process in the whole human body is ATP synthesis, which is 40% efficient. Considering that the best humans can do in power plants is 33% efficient, that's still pretty good.

I didn't mean inefficient in terms of physics, I meant it in terms of biological structures.

We will continue to say new information cannot arise out of mutation until a difinitive mutation produces new information. Calling us names and saying that a long list of mutations can give new information isn't enough. If 4.5 billion years is all it took for the information in the bacterial genome to self-assemble, there should be plenty of specific mutations that increase information rather than just recombining present information.

I did not call you names. You have not responded to my second post about information theory. And perhaps you should study prokaryotes as I have, they have vastly more genetic diversity than Eukaryotes.

And for the second law, I point out again that if that were actually true for open systems, life would be impossible, not just it's evolution.

I fail to see why. All that would suggest is life could only have not arisen from non-life. Correct me if it is wrong.

The topic of entropy and life has been studied for decades. Life feeds on a reverse system called negentropy, where being expressed by an axiom of the second law of thermodynamics called Gibbs Free Energy. I suggest you put more study into entropy and life. It is an extensive topic in biophysics.

You still have not responded to my information theory post.

Term nagging: Bacteria do not go through mitosis at all. Mitosis requires a nucleus and protein spools. Bacteria just have fission because their genes never assemble into chromosomes like diploid eukariotes.

Sorry, early and no coffee. correct, bacteria lack centrioles. Actually, fission creates more opportunity as the DNA is not packaged in closed compartments.

I am not sure about the mutation rates of fission as compared to mitosis, but as everything is more hectic with bacteria, I would bet that its higher.

It is.

I did. That (new genes arising out of old genes) is an assumption of Darwinian evolution. If it could be proven, I would not be arguing with you about science, but metaphysics.

I suggest you study orthologs, paralogs and homeoboxes, as good proof of genetic origin from predecessors

It can. Depends, of course, which one you are looking for.

horizontal transfer: Easily proven. We have lots of pretty pictures from SEM
Intragenetic mutation: Easily proven again, now that we can decode genomes
Recombination: Again, proven by genome decoding
Duplication: This one we can, again, phyiscally see happening

[i]Now let's assume that negentropy somehow also implies information growth of the genome (even though this contradicts information theory: new information must be intelligently assembled or derrived from existing information, this is supplimental information.) You still have to accept the astronomically small probabilities of an evolvable life form being created in the first place that creationists -and even evolutionists- have been computing for decades.[/i]

You still have not responded to my post refuting the confusion of genetic encoding with information theory.

growth of the genome is meaningless in your terms. growth is accomplished by polymerase functions. Change is accomplished by mutation. If you are still confused, read the post on information theory. It does not have to be intelligently assembled. It is derived from existing information.

Furthermore:
Fallacy #15 Abiogenesis

One of the greatest mysteries in all of science is how the first life arose. Of course, here it is important to define life. Life is a set of autocatalytic chemical processes aimed at reproduction of the self. Unlike other chemical complex systems like crystals, biochemical molecules are remarkable for the reproductive capabilities. I suppose, by that definition, that Ribonucleic Acid is probably life. It is the building block from which all life was originally based, before being gradually phased out by DNA, although obviously RNA still retains a critical place in biochemistry.

The attempt to answer that has come in the form of a hypothesis known as abiogenesis . How did the organic polymerated strings of nucleic acids or indeed any necessary function of life arise? Whoever answers it will probably receive a Nobel prize from every field imaginable, although I imagine the awards will have to go to a great many people. There are numerous hypotheses out there, autocatalysis, RNA world, lipid-based world.

All The hypotheses begin with the Earth’s hydrogenesis, the formation of the oceans. Due to the polar nature of water, dissolving free ions with its slightly polar configuration, it is an ideal “primordial soup” to use the phrase, for the formation of simple self-replicating abiotic molecules. Due to the atmospheric difference of the Earth at the time, the Primordial Soup was very different. It was much warmer, an ideal incubator for the development of simple biomolecules. Experiments have shown that these simple amino and nucleic acids can arise in a hydrated anoxic environment provided there is sunlight. Molecules like Cytosine and Adenine are reasonably simple and will reassemble. This is not probable, but considering the vast size of the ocean and the span of time, the Law of Averages states it will eventually happen. The first abiotic reassembling molecules will vastly increase the chance that they will form life components like RNA; this is the basis of the RNA world Hypothesis.

Regarding the origin of life and RNA...evolution cannot answer that. The theory does not extend that far back. From the moment RNA appeared on Earth, evolution provides a god-free explanation. At the moment there are hypothesis on life's origin, including abiogenesis, Panspermia...and god. All three are assertions, so none have weight. However, science operates on an Occam’s Razor principle regarding hypotheses. Panspermia would require you to assume the existence of alien life that came to earth, the probabilities of which are astronomical. God requires you to believe that there is a extramaterial out of space and time deity who infused the primordial soup with RNA. The odds again, are astronomical. Abiogenesis on the other hand...merely requires you to assume that ancient molecules obeyed chemical law. Thus it is the most widely assumed.

But really it is a non-issue. Evolution does not deal in primordial chemistry. Primordial chemists deal in primordial chemistry.

[i]Allow me to rephrase my position. Mutation (point or otherwise) creates new aleels or a new reordering of the genome. Usually the latter is fatal or extensively debilitating.[/i]

The operative word being usually.

[i]What you are calling "new information" is, according to your own position, modified old information. For an introduced gene (not a new alleel, but a new gene being introduced into the system to constitute net information growth) to function, it must be introduced at the right point, with not just a copy of the old information, but functional application of new information that must work or natural selection will select them out.[/i]

Not necessarily. Most mutations dont do anything. Only bad mutations are selected out.

[i]Occam's Razor+ natural selection= loss of genetic information, not gaining it. This is not irreducable complexity, it is raw inefficiency. The new gene will almost certaintly not last long enough to be point mutated upon enough for it to work. It is theoretically possible, but at our modern rate of mutation rates, 4.5 billion years is many hundreds of orders of magnitude too short a time period for information growth.[/i]

What? There are two types of genes. Introns and exons, which have these separate functions. Exons code for proteins. Introns are mostly junk or redundant, but they flank all the exons. Sometimes they are just punctuation, dictating where a gene starts and stops, but their most important function by far is to regulate the speed of protein transcription, a mechanism we will look at it more detail later. Exons dictate how a protein will be assembled. They do this because a protein is essentially a string of amino acids or a polypeptide. Therefore, exons dictate the order of amino acids in a protein. They do this by representing each amino acid with a codon. A codon is three nucleotides. Three nucleotides make up an amino acid. There are 20 possible amino acids, but 64 possible codons, therefore, exons are highly sensitive. They are also sensitive because they are ordered very precisely. For instance, let’s look at a simple string of three codons in a gene: AGG CTT GCC. Now let’s assume that an extra base is accidentally inserted (Like a G for example). The new string would be totally different, it would look like this. GAG GCT TTG CC, so every base would be shifted down one, and the entire gene would change. This would be completely devastating. This is why DNA repair mechanisms quickly target such errors.

On the other hand, Introns, which are not so sensitive or precisely executed, or are sometimes just junk or redundant, mutate based solely on random frequency. As there are 44 codons that don't correspond to an amino acid, these are used in introns. Therefore, the next axiom of evolution is that evolution is driven by the Introns. Obviously it is more complicated, Introns can become exons during shuffling/shifting, and exons can become Introns, and sometimes exons can be mutated harmlessly, so long as the mutation changes only a tiny chunk of the gene, but this rule still applies.

Now that you understand genetic mutation mechanisms, this can be applied to how advantage mutation works.

Intron mutation can change more than just transcription rate. It can change the protein fold. So, in all likelihood an organism won’t end up with one enzyme or protein morphing into another, but an identical polypeptide folding into a new enzyme. Only exon mutation will "change" an enzyme because it will change some codons, thereby changing the protein string order. From a probability standpoint, the odds of gaining a useful mutation because you can fold a protein in a new way vastly outweigh the possibility that you can get from producing a new protein. Mutations can have chain reactions on the cycle. Same string but different protein will produce a different catalytic function therefore will change another intron somewhere else down the line, or perhaps change an exon and make a new protein which, because it is bound to the cycle, not random, will be useful. If mutations operated independently, and outside the cycle, evolution would never get off the ground.

It can be understand like this:

A useless mutation occurs: Nothing happens

A bad mutation occurs: The cell dies, or the error is targeted because it is disrupting the cycle

A good mutation occurs: A new protein, rate of transcription or fold function is made. This is useful. It alters the cycle, producing a knock on effect.

For a mutation to occur which can be preserved, junk must be turned into non-junk. It is really easy to play with the introns. The prokaryotes that are the basis of life have almost no junk DNA. It is evident that such small organisms evolved to have conservative genomes. They have useful introns. It may seem extremely unreasonable in terms of probability but DNA mutates all the time. If the shift is Duplicate error, a popular method, then the gene advantage can be conserved, because it is a redundant piece. Evolution is just mathematics. As long as a gene exists, it will fight to survive...at the chemical level there exists a ruthless primal battle in which the best of the best are constantly being selected, and the weak crushed. The only phenotype affecting genes that are conserved are the ones that affect reproductive capacity. That will cause it to be conserved and cumulatively mutated upon. This is the mathematics of evolution.

Genetic drift drives evolution. Some mutations are good, some are bad, most do nothing, but through the endless cycles, organisms evolve. The analogy I like to use is the telemarketer. About 90% of people hang up on them, but the 10% who say yes make the enterprise quite profitable.

The statement advantage mutation is impossible is a confusion of possibility and probability. Advantage mutation almost never happens…the operative word being ALMOST. But if you have mutations working at quantum speed and three billion years on your hand, your odds improve dramatically.

he knock-on effect is a good demonstrator. All proteins do only one thing, they act as a catalyst for the body's catabolic chemical reactions. Without proteins, you would have to set yourself on fire to release enough energy to perform respiration. This is obviously not practical. All proteins lower the activation energy for a chemical reaction by providing an active site which works like a lock and key model. The chemical fits into the protein receptor and is broken into smaller molecules. Therefore, one can imagine that a different fold will mean that protein will have a different catabolic function which could offer a significant advantage if it allows an organism to synthesize a new chemical. The most effective way to do this would probably be base-pair swap exon mutation, which will only change a small chunk of an exon. Normally, the amino confirmation will predispose a protein to fold in a certain way, although this process is not understood (that would be the Levinthal Paradox). Natural selection, it seems, has selected a chemical interaction set which encourages the protein to fold, because in it's primary and secondary state, it is useless.

Protein folding is also a useful demonstrator of life's autoregulatory weirdness. They fold into elegant shapes after being translated from mRNA only for a tiny piece of it to serve as an active site. The hemoglobin molecule is the bizarre case and point. It is a colossal macromolecular protein snugly wrapping a single haemite (iron). This is somewhat akin to building a nuclear powered transformer to plug in a lamp.
There are 100 nucleic acids and 300 amino acids that exist in nature, we use only 4 and 22. The sugars and phosphates snap together to form the base backbone in the exact same way that nucleic acids bond together. From a chemical standpoint, the phosphorylate-saccharide (ribose)-nucleic acid structure is sensible. There are 100 nucleic acids and 300 amino acids that exist in nature, we use only 4 and 22. There is no reason why life could not be based on other amino acids and nucleic acids. The sugars and phosphates snap together to form the base backbone in the exact same way that nucleic acids bond together. From a chemical standpoint, the phosphorylate-saccharide (ribose)-nucleic acid structure is sensible.

We can look at the knock-on effect with respect to folding like this:

1) A small mutation changes a few codons

2) A different protein is made with a new fold

3) This catalyzes a chemical in a different fashion, most likely a new product

4) This new product has a different effect on the cell membrane receptors, which keep up the autocatalytic cycle. It causes a different command to be followed, as transcription is driven when a stimuli causes a protein to bind to the introns that flank the necessary exon.

Transgenic technology has revealed that changing a gene can start making a gene down the line do bizarre things. Why? Simple. Genes can control each other. The knock-on is established by introns controlling exons which in turn produce proteins which control introns which control exons which… you understand. If evolution operated like individual genes doing individual things, it would not get on the ground.

Knock-on effects work all across the genome. After all, what do genes do, they produce proteins, or they regulate the production of proteins. What do those proteins do? Well...everything: The big functions are of course:

-Catabolism of biochemical families (nucleotides, coenzyme factors, carbohydrates)

-Anabolism (glycogen synthesis, lipid synthesis)

-RNA synthesis control

-Ion channels and membranes (cell membranes, nerve membranes, particularly oligolipoproteins for myelin) , transport mechanisms including inorganic transport, ion flux and carrying

-Exocrine systems and secretory pathways/chemical production

-endocrine systems and hormone control Autocatalysis

-Maintenance of cell signal transduction and energy release metabolic pathways

The thing to notice about all of these is they are all dependant on biochemical triggers. You change one thing, you change a cascade. Making a new ion channel will change the electrochemical gradient or allow a different material influx, which will affect how protein receptors bind to introns. A new ion channel could trigger a hitherto unused intron. There are so many complex factors to genetic evolution, it is not a clear cut process.

The discovery of genes was probably one of the most important in the history of science. Before genomic sequencing, the human body or indeed any organism or indeed a single celled organism seemed unbearably complex. Of course, with the advent of new molecular biology techniques that was swept away. Everything can be explained in terms of metabolic pathways building macromolecules with remarkable properties. There are only thirteen families of Biochemicals (Terpenoids, Flavanoids, Carotenoids, Polyketides, Alkaloids Peptides, Polypeptides, Amino Acids, Nucleic Acids, Steroids, Enzyme Cofactors, Carbohydrates, Lipids and Tetrapyrroles). Everything can be explained in terms of these, and the manufacture, regulation, secretion and synthesis of these…can be explained by DNA. This explains everything from simple sugar metabolism all the way to the Progenitor…the stem cell with the potential to make a human body.

With regard to probability, think about this. Things work at quantum speed at the size of molecules. Cells are always undergoing mitosis, copying, shifting, transcription, translation, receiving and processing chemical signals. Imagine the genome as a supercomputer and the environment, the determinate of what constitutes a genetic advantage that causes more reproduction like the password. The supercomputer has to guess the password. It does so by brute force. Go through the permutations. Mutations are happening so fast, so often, some are being chucked out in a blur, some are useless and ignored, the ones that are chucked out are automatically repaired because they are getting in the way, and then finally, the computer finds a permutation. Since this is not a disruptor, it is retained in much the same way that a useless mutation would be, passed on to children, who reproduce more...etc etc.

The environment is always playing around with genes, it just takes millions of years to nurture the ones it likes.

In terms of probability, evolution is actually extremely generous. Think about this. There are 25 speciative links between monkey (the pan genus) and man (Homo Sapiens). Every Hominid before us went extinct. We killed them all, that is what happens when an organism is too successful. Man may be the most genocidal creature nature ever produced, but I digress. There are 5000 different genes in the monkey/man split. The absolutely most closely related species differ in 200 genes. 200 genes is not enough to give massive difference in phenotype, but it is enough to prevent interbreeding. Anyway, there are 4 million years of gradual evolution to produce the last Hominid, the third chimpanzee. 4 million years and 5000 genes and two amino acids. One thousand years for billions of organisms to cumulate in just one helpful gene. 1000 years and one gene. Not a big stretch.

[i]No, it doesn't extend that far back. You outright assume it.[/i]

Assume what?

[i]Might I remind you of my pointing out that genetic redundancy (which you said was 90%, so any mutation in the redundant segment is new information) was a prevention of mutations rather than an assistance to it. The redundant information is used as an error check to eliminate mutations wherever possible, not as a cesspool for mutations to accumulate.[/i]

What? How old are you? Do you understand proofreading mechanisms? Proofreading mechanisms only work because bad genes are destroying a metabolic cycle. The proofreading mechanisms that occur during the polymerase are anything but infallible, as they depend on the constant influx of ATP, and only work because nucleotides bind more tightly to their counterpart. After that, a corrupted cell which is doing something "bad" is destroyed by phagocytosis. Most redundant genes are not in use. They will go unnoticed. That's the premise of duplication error.

44 leftover codons??? I hate to have to be the one to tell you, but you are dead wrong here. Most amino acids have several codons that the tRNA will attach to. There are about 5 stop codons for instance. This is another aspect of the genome being redundant to retard mutations, not assist in procreating them

When did I say anything about leftovers? The real issue with exons/introns in their sensitivity. There are codons dedicated to spliceosomics of course (which are still proteins dedicated to the enzymatic catalyzation of removing the introns from a mRNA string), but the real problem with exon mutation is the sensitivity of the codon order. Also, stop codons are not exons technically as they are punctuation which does not code for protein. Since codons are triple-based, the extras create mutation opportnity (especially point mutation as opposed to base insertion). That's what I mean by "extra codons". If we had doublet-based codons we could only make 16 amino acids.

I'm sorry it wasnt clear, I shouldn't have used the term genes, base pairs is more clear. Humans and chimps are about 80,000,000 base pairs different. Many of these were not even produced by genetic mutation or drift, they were produced by karyotype fusion. If we are to look at the amount of new information produced by genetic mutation. The difference between humans and monkeys in terms of the product of genes, is only 160 enzymes. 160 new enzymes is nothing.

Reading my post again, I must have been extremely drunk. Nearly all of the mutations that were passed on are useless. If we remove all of the junk mutations, the amount of useful mutations becomes about a 0.4% difference between men and chimps. Depending, of course on how you define it. Percentage is typically taken to mean base-pairs because using the term genes simply is not clear. That's 12,000,000 base-pairs of helpful genetic material. A significant percentage of that was not borne out of genetic mutation but karyotype fusion anyway.

Only a very small amount of each gene changes. The absolutely largest change was identified by a computer in a tiny region of only 118 nucleotides called HAR1 (an RNA gene involved in cortical development of the neocortex) 18 nucleotides changed, amounting to a 10% change. That was the largest change found in a single gene (note, a gene is usually about 1000 base pairs, but is defined as having a stop codon/intron punctuation at either end, producing just one protein).

I hope it is more clear now. 80,000,000 nucleotide changes over four million-eight million years (the exact time is unknown), most of which were not created by mutation conservation.

Ignore my statement about "5000 genes", it is ridiculous, makes no sense, is unclear and Im sorry.

Some clarification. Obviously introns are important. They serve useful functions regarding punctuation, stop codons, and of course, they control transcription rate. Not all junk DNA are introns, and defintitely not all introns are junk DNA. Introns are simply genes flanking exons that do not code for protein.

However one looks at it, introns make up the vast majority of the Eukaryotic genome. Small, conservative prokaryotes tend to have a nearly fully-functioning genome. The average bacteria has only a 90% functioning rate. Incredible by Eukaryota standards. For instance, in our own genome, only 2.5% are exons.

Anyway. There are multiple ways to define "junk"
-Redundancy. This is quite a big one. Not a useless gene but rather an extra copy of a useful one which comes about by duplication error. this creates problems for geneticists trying to determine functionality, but creates opportunities for evolution.

-Migrating genes. These are the holy grail of the common descent study. There are two biggies: Endogenous Retrovirals and MtDNA migration. ERVs are the result of ancient Retroviral reverse transcription. The same reverse transcription process by which the HIV virus infects our CD4 T-Cells. They become fused into the genome and passed on for millions of years. They make up around 8% of the human genome, but don;'t worry, they can't make viruses. They have something called nonsense mutations that make them harmless. The other migrating gene comes from within every cell in our body. Every Eukaryotic cell has mitochondrion to power them by metabolizing food breakdown. the mitochondrion are actually bacteria, the result of an ancient evolutionary symbiosis which I can go into more detail about if you ask me to. Because they are bacteria, the Mt have their own tiny little genome, around 16000 base pairs. mtDNA is useful for evolution and genetic tracking because it never changes, because there is no gamete fusing. It's also useful evidence of common descent because sometimes MtDNA migrates into the full genome in the nucleus. I cannot recall off the top of my head how much of the human genome is useless mtDNA.

Yeah, I can back up the appendix statement. I used to study endocrinology, so I know it is useful lymph tissue.

The rate of mutation is not too high, not when you consider that there are millions of mutations per day. Polymerase is far from perfect.

what do you mean just as likely, the genome contains both. The threemain genetic waste products are mtDNA insertions, Endogenous retrovirals, redundancies. Junk DNA is just useless DNA.

The reason Endogenous Retrovirals are so useful is because when we find the Endogenes discovered on identical fusings in the genomes of different organisms, especially of different eons, it provides very useful indication of the common descent. The process is rare and random, so the probability of the event occuring twice without common descent, let alone thousands or millions of times, would be astronomical

The only other explanation for Endogenes is that God deliberately inserted them to fool us and test our faith.

Yeah, yeah, yeah.

You said you caught [i]viruses[/i]. I'm talking about retroviruses. Have you ever caught a retrovrisus? I doubt it unless you have HIV. Ancient retroviral insertion proves common descent unless you have a rebuttal.

By the way, please tell me you aren't a young Earth creationist are you? Please tell me you are not!

Your previous post about retroviral infection of species is idiotic. Most viruses commandeer the cellular mechanisms to make copies. A retrovirus on the other hand, reverse transcribes in RNA into the host genome (hence reverse transcriptase inhibitors as drugs against HIV). Now, like I said, retroviral insertion is both random and rare. That means that finding identical retroviral positions ON IDENTICAL POSITIONS IN THE GENOME of multiple species would be all but impossible without genetic descent. Viruses go extinct, but I dont think you understand that they leave their genomes inside their host organisms.

If you are young Earth creationist, yes, that does frighten me. Furthermore, I have read scripture, but obviously I dont believe that Jesus made wine out of water (does it frighten you that I dont believe in God).

Im not going to use that argument you suggested against young Earth creationism, but it will be interesting to see how you respond to this.

Large atoms with concentrated, crowded nuclei are highly unstable. To correct the instability, they will either
a) Release a highly ionizing but low energy particle consisting of a helium nucleus with two protons and neutrons. This is called alpha radiation.
b) If the nucleon number is isotopically unstable, the atom will change a proton into a neutron or vice versa allowing an electron to be released or a positron depending on beta minus versus positive.
Another thing they can do is released an ultra-high energy wave called gamma which is irrelevant to my question below.
For instance, a carbon-14 isotope. 99.999% of all carbon is stable carbon-12. but carbon-14 isotopes are not stable and make up 1ppt (part per trillion) of all carbon. They release beta radiation to correct the nucleon instability by firing off an electron. This causes it to decay into Nitrogen-14. The great thing about radioactive decay is that it is a random process that obeys probability laws. The other good thing about it is that you can dip a radioactive material in molten lead, in acid, shoot it, burn it, fire particles at it, try to irradiate it again, pass a current through it...and none of these things will change the isotope clocks. They are fixed.
Now let me explain how we use this to measure the age of the Earth and organic material. Radioactive half-life is the amount of time it takes for the Geiger counter count rate (CPS) to fall by half. Radioactivity is a Zeno's paradox, because it falls to 1/2 then 1/4 then 1/8, but never to 0. It takes the same amount of time to fall from full to half as from half to quarter because the probability remains the same, because radioactive decay is an elemental nuclear cycle.
Depending on their isotopic properties, different isotopes and elements decay at different rates. Uranium 238 has a half life of 4500 million years...almost exactly the age of the Earth. Certain Thorium isotopes, and Polonium 221 for example, half in hours to seconds.
All life is made out of carbon, and all life is made out of roughly the same percentage of carbon-14, which is 1ppt (part per trillion). When something is alive, the amount of carbon-14 it has remains at a constant 1ppt, but once it decays, biological processes stop so the carbon influx/outflux stops too, and the C-14 starts to decay into N-14 and is not replaced. So if we examine a dead plant by giving it a radiocarbon test, and we find the amount of carbon 14 (can be calculated using the mass of total carbon) and the amount of C-14 has reduced to 1/8, it means that the plant is 18,000 years old roughly, because C-14 has a half life of 6000 years (actually about 5300 years). The N-14 that C-14 decays into is simply released into the atmosphere.
If you don’t like Carbon 14 dating, there are over 20 types of radioisotope dating, including Pb-Ur, Ar-Ar, K-Ar etc. Some of which can date back millions and billions of years because the isotope is more stable.
To prove that the dinosaur bones are 6000 years old, you would need to find some rocks in ancient geological striation, among the dinosaurs, and test them using multiple isotope tests, which should give you a dating of between 3000 and 10,000 years if you are right.
Radiometric dating is not exact science. However, dinosaur bone dating never drops below 65 million years. They cannot provide exact answers for ancient (millions to billions of years) dating, but using a range establishes consensus. If the Earth was only 6,000 years old, the radioactivity emitted by unstable materials would be huge. We would immediately notice it because almost none would have decayed...in fact, we would not be here because life could not survive in that environment.
Creationists typically answer this with two fallacious arguments:
1. Radiometric dating is erratic, different techniques give you totally different numbers. It cannot be trusted
2. Scientists assume uniformitarianism, while radiometric dating might have been greatly speeded up in the past.
Both of these are ridiculous. The error in the spectrum of radiometric dating is normal experimental error. Radioactivity, after all, is a completely random process. However, the use of multiple isotope tests is not designed to establish a precise age. It is meant to establish the magnitude. If you have three tests, one which says 50 million years, another says 70 million and another says 92 million, then that is your age range. Radiometric errata does not help creationists, because it is used only to establish the magnitude of age. Even with such error, we would notice if the Earth was 6000 years old because the spectrum would bluntly stop between 2000 years and 12000 years. Radiometric errata is not an argument for creationism. The magnitude of age always comes up on the order of millions and billions.
Uniformitarianism. Firstly, this argument is self-defeating. To assume anti-uniformitarianism (a legitimate scientific debate) one must assume the Earth is millions or billions of years old. We can measure the conditions of the last 10 000 years so accurately now that we can be certain that the cataclysm of the conditions necessary to increase radioactivity that much could only have existed long before advanced life, as such bombardment would have inevitably shut down any evolutionary projects. Anti-uniformitarianism only calls into question the accuracy of ultra-slow isotopes like U238, which halves in over 4.5 billion. years. It does not affect fast isotopes like C-14, which we can measure only to the past 60,000 years. Going back this recently, radioactivity could not have increased at all in such a short time span unless our Neanderthal ancestors were performing atomic blast tests.
Obviously, insisting the universe is 6,000 years old is completely ridiculous. As is the idea that the world was created in six days. I could present literally thousands of arguments from every scientific field in existence. Gaseous shifts, atmospheric depletion, spectroscopy, radioactive decay…all impossible if the universe is so young. At 6,000 years of age the universe was barely a tiny baby, and stellar evolution had not yet taken place with the result that matter was simple quark soup and dark energy. On the other hand, when the Earth was 6,000 years old, the Universe was fully mature. Hydrogenous ionization that had taken place during what cosmologists and astrophysicists call the “dark ages” had formed every element imaginable, and had created the fusion process necessary for the creation of stellar bodies and galactic clusters. The sun was still a little sun, because it was created roughly the same time as Earth was pulled together by it’s gravity. When Earth hit it’s 6,000th birthday, it was a lifeless boiling radioactive rock and an immature, barely existent atmospheric layer of carbon dioxide.

I did not write it in eight minutes. I took it from an essay that I wrote called twenty two answers to creationist nonsense. I did not copy it from anyone else.

[i]Next time can we be so kind as to respect my intelligence. I think you knew very well that I know what uniformitarianism and radioactivity are. My positions are not held out of a lack of education and I feel somewhat insulted that you are handing me a paper of definitions that I learned in 6th grade.[/i]

I wrote this essay generically, you idiot. It was meant to be a general response to creationists, very few of whom are scientifically literate. You think I would take the time to write a full response to this pointless debate? I know that you know. Most dont.

[i]Radioactivity: U 235 accounts for about 1/150th of the naturally occuring Uranium on Earth, and it's half-life is half an order of magnitude less than U-238. If the earth was really 4.5 billion years old, then there would need to be a cosmic abundance of about 1/30th the natural Uranium. We don't see that.[/i]

What are you talking about? We use these to measure the ages of objects, not the Earth. For that we use zircon dating. The amount of radioactive elements remains constant due to decay cycles. That is why we use them to measure objects (from which radioactivity does escape). With a half-life of 700 million years, Any U235 that was around at 4.5 billion years ago should have deacyed by six half lives, or to about 1/32 of the original amount. Pu-239 decays into U235. The amount of radioactive elements is cylical. What do you mean "we should see 1/30", that does not make sense. We should see 1/30 of the amount of U235 in an object that is 4.5 billion years old obviously, assuming we know how much it had to begin with, and we do. But we can use it certainly to prove that the Earth is billions of years old. It is used for relative, not absolute dating.

On the other hand, Zircon dating is almost impossible to refute. Or isochrons, if you want. Also, how do you explain:
a) Diamonds
b) Oil
c) Any sort of atmospheric gas shift
d) Cosmological observation of distant galaxies
or anything else

[i]First of all, it is quite probable that God could not have created an earth that was immediately sustainable for life unless He had created it so that some of the systems had appeared to have been running for some time. There would have been no soil for plants if the erosion cycle had not apparently been running for quite some time.[/i]

Sounds to me like you are making stuff up. Provide some evidence. You are hypothesizing out of thin air.

b) You can read it for yourself. I don't mind using biased sources.
http://www.icr.org/index.php?module=articles&action=view&ID=259

yikes. The Creation Institute. An organization with 600 members who spend their time pretending to research science. You may not, but I mind biased sources. I have a few insignificant little organizations on my side too, like the American Society of Biochemistry and Molecular Biology, The American Association for the Advancement of Science (10 million members), the American Chemical Society (160,000) the American Society of....etc etc ad infinitum.

When we synthesize diamonds, we can do it far more optimally than nature can. The oldest diamonds that are not synthesized allotropes are one billion years old.
[i]
c) If the Earth is really 10,000 years old, what makes you think that any of your dating proceedures are accurate or that those gas bubbles weren't made that way? (see opening paragraph)[/i]

that does not make any sense. You assume the conclusion than try to distort facts to fit it. We drew the conclusion of the age of the earth only after using dating methods to confirm it. Your logic is the precise antithesis of science. You still have not countered zircon dating or indeed any non-carbon radiometry except to say that it might be wrong. Of course it might, but that does not mean that creationists are right by reductio ad absurdum. Can you provide a shred of evidence that the Earth is 10000 years old?

Here is the problem with creationists. They assume they have the truth (the bible) then they try to force science to conform to that model. In other words, they have the conclusions and try to make up facts to support it.

In realityland (not fairyland where they reside) the scientific induction process is the precise opposite. You find facts and draw conclusions from them.

[i]d) How do you explain the Big Bang in the first place, concidering that space, time, and mass are all interdefined, there was none of any to produce a naked singularity by a quantum flux in the first place?[/i]

You are leaving the topic and trying to change subjects. This is not a discussion about energy-matter condensation. This does not explain how we can see stars billions of light years away.

[i]Prove it.[/i]

The person who thinks the Earth was created after the Sumerians learned to brew beer wants proof? Fine.

forcing the carbon bonds to adopt a four-way covalency requires very specific temperature/pressure relationship that is found only at certain deep points within theupper mantle. Whereas synthesis is done under HTHP conditions, diamond formation occurs at relatively low temperature. Diamond formation occurs not in the crust, which only extends to 70km in depth, but through to 150km up to 320 km below the surface, where the pressure is great enough to force the formation of diamond. Inside the mantle where the diamonds are formed, small minerals reside within the surrounding rocks. these contain ancient isotopes that reveal that diamonds are very old, 3.5 billion years in some cases. They cannot form on land, as they will quickly decay into graphite, and can only reach the surface through volcanic blasts. The conditions in which the diamonds reside for most of their history is ideal for measuring very long lengths of time using isochrons or ultra-slow isotopes that cannot be explained by creationists.

In addition, I only felt it necessary to invoke the organizations on my side since you decided to post a link from the creation institute. You may understand why I find this insulting.

You still have not responded to my challenge regarding
a) tracking of distant galaxies/stars
b) Endogenous retroviral gene insertion
c) MtDNA tracking

You have not responded to my posts regarding daimonds, ERVS, MtDNA or galactic clusters.

Furthermore, the argument from the link you posted rests on circular reasoning. The Earth is 6000 years old because it says so in the Bible, and it also says there is a flood, which might be consistent with the anoxic formation of oil if it happened hypothetically assuming we ignore all the other evidence we have gathered to state the age of the Earth.

You can see the insult to scientific induction this is. Creationists do not draw conclusions by gathering facts, they make up facts to support conclusions which were preexisting.

You want links from these sites? My favorite personally is the AAAS. They publish the elite magazine Science, which is read by scientists of every field around the world. I myself subscribe to this magazine.

Science publishes articles of biochemical evolution and cosmological age in nearly every article. you can try to access it online but I think you need a password. This is the very best source for science in the entire world. All of the world's most elite scientists write and contribute in this magazine. The results of the most recent experiments, tests and findings are published in this magazine.

Might I remind you that everyone does.

Milikan, the American student of J. J. Thompson, when he was getting an exact measurement of the charge of the electron used J. J. Thompson's cloud experiments to give a gague of what he should look for. If the charge was not close enough, he would pour over all the equiptment to find an excuse to throw the answer out. If he got a result about where he wanted, he bookmarked the solution and gave the equiptment a lick and a promise because he didn't care to find out what went right.

I can even quote his personal log book if you want.

An evolutionist actually said that "If science were not done in this way, we could not do anything." about this.

Everybody is biased. It is purely hipocritical to say anything otherwise.

**SIGH**

I already have delt with all of them, you just refused to allow the arguments. (That is not unexpected. If you cannot deal with an argument you dissagree with, call it a non-argument.)

As that you wish, though, I will give short, succinct answers that, in honor of your sophomoric style, give no sources at all.

A and B: Uranium and Zircon (cycle) decays both yeild lead and helium. Lead (and similar elements like argon) is used in radioactive dating because it isn't going to go anywhere, even though there is no effective method for determining what isotope of lead is being delt with and how much lead was in the rock to begin with. Helium is ignored because it is supposed to diffuse out of the rock as fast as it is produced. In actuality, there is a little Helium in rocks. Based on the decay rate and labratory tests on actual rock effusion rates, the actual rock ages around diamonds and fossils usually corresponds to a rock that is 6-10 thousand years old.

C: I fail to see the argument here, unless it is more on the 98% of the non-coding human genome, which we already know has some other purpouses other than protein synthesis. This is more of an assumption of useless DNA than a real argument. I have already listed a bunch of organs that were falsely assumed to be vestigial which later proved to be wrong.

D: Again, I fail to see the argument Mitochondrial DNA (I just now found out that that is what mtDNA stands for, thanks a lot.) There is no way I can tell what your argument is if all you give me is one term with no substance.

E: All proteins and genetic matterials degrade to total illegibility at a conjectured rate. The age of the rocks used to assess that rate are dated with radioactive dating, which, as seen above, does not give the full story. This is circular reasoning.

F: Another case of circular reasoning. You have already said that the difference between humans and apes is 80 million base pairs. Is God supposed to give completely different metabolisms for all of his creatures? How would the food chain function if each creature had to break down all of what it ate into atoms to process it? Digestion already claims half the body's energy, and that is with the help of enzymes already present in food we eat before we eat it. To not have similar metabolisms would mean a nill of leftover energy.

G: 2 points:

1. If God created the universe 6-10 thousand years ago, do you really think that He would bother making stars millions of light years away and not have a stream of light made flowing between here and there? To create one and not the other would be pointless.

2.Do we know the fundamental shape of space-time curvature? All we know is that the Hubble constant is positive, so our best guess is that space-time curvature is negative. This would mean that as light travels furhter, it encounters more resistance from space-time itself via gravitational redshift, so we really have no clue as to even if the galaxies are really moving away from us at all, or if the universal space-time is just negatively curved to begin with.

Now, will you answer my question on the Big Bang or not?

As that I am in a bit of a time pinch, I will only deal with a few:

1. Retroviral Gene Insertion: Retroviruses do insert Genes into the Host's genome. The occurence is rare and random, but also the site of insertion is only possible in a few places.

What information you leave out can be more importiant than the included information. The idea that Retroviruses can only insert specific information into very specific places is the entire concept of Gene Therapy. Also, these "inserted genes" have purpouses within the hosts themselves.

[quote]Most insertions have no known function and are often referred to as "junk DNA". However, many endogenous retroviruses play important roles in host biology, such as control of gene transcription, cell fusion during placental development in the course of the germination of an embryo, and resistance to exogenous retroviral infection.[/quote]

About the Radioactive dating: The Lead isotopes we are talking about are all stable. I did not use the word effuse for no reason, I was talking about how fast the Helium produced by the decay effuses from the rock.

[quote] Space-time is empirically demonstrable to be hyperbolic. [/quote]

Really? I am sure that astronomers will be shocked at that, concidering that the hyperbolic curvature is deduced from the Hubble Constant. Funny that a hyperbolic space-time curvature would cancel the effects of the redshift by having the light constantly compressed by the space-time curvature.

Orthologs and paralogs are little more than genetic forms of the vestigial organ argument. A common example is Hemoglobin (Blood O2 carrier), Myoglobin (muscle protein), and Chlorophyll (photosynthesis) as being two paralogs and an ortholog off the same structure.

If this were really the case, then we could probably think of a place where all three of these would have had a common function in evolution, after all, a plant must have chloryphyll to live as the human would need both Myoglobin and Hemoglobin to survive.

If Both Hemoglobin and Myoglobin were not fully functional in a very primitive form of life, evolving to the point of being a Nemotode is impossible. Impressive, concidering that anything smaller would have had no use for either. Far from proving evolution, you just run into irreducible complexity again.

Due to the vast and technical nature of the above debate, I shall offer only 2 small points.

1) what is meant by 'new' information. There is Guanine, Adeninie, Thymine, and Cytosine. What new can be added? It all comes down to arrangement, which can easily be created through vertical transcription, copying errors etc...

2) as to mutations, regardless of which has a higher propensity to survive, 'good' mutations propagate themselves better, and thus will come to dominate populations.

[quote=Egann]Point 1

New information: a gene that has not been in the population before or has recently exited the intron pool constitutes [i]new genetic matterial,[/i] but not new information. new information also implies that the protein produced by the gene is functional or fully capable of functionality, even if it is not specifically put to the exact task it would be best at immediately.

New genetic matterial is a net increase of the geneome. New information is an increase in the net used gene pool (not a new aleel, but a new opening for aleells to form.)

New information also has a requirement instated by Intelligent Design: It must constitute a comprehensible net of material enough to not be attributable to chance. While the exact statistical limit for the Universal Probability Bound is still under debate, the present bounds proposed are between 10^50 bits (proposed by Emile Borel) and 10^150 (proposed by Dembski.)

In other words, because genes are so long, all newly introduced functional genes must be concidered new information.

Point 2:

Good mutations will propogate themselves. I know better than to argue with microevolution (ie limited flexibility of the species development.) But the possibilities are inherently limited without [i]new information[/i] (as defined earlier.) If all beneficial mutations either diminish or do not increase the information (as is the case with all observed mutations: silent, detrimental, or beneficial) the evolutionary possibilites of the initial bacteria from the primordial goo is severely limited to less and less information only.

Believe it or not, deludedgod did not prove that genome increasing mutations occur above. All he proved was that net genetic increases were possible, not that either they are observed, or that those would eventually constitute new information.[/quote]

Well, yes, assuming the precepts of Intelligent Design, that seems a problem. However, structures do not have to be built up in a flash. Rome wasn't built in a day, and neither was the human genome.

Three already existing forms whose use has since been eliminated may combine to create 'new' information. Or, the same forms, being used for something else might be duplicated, and changed in such a way that they now do something different.

I know that creation was not created 2 seconds ago because God says he created it millenia ago. That simple. Now how do you know that you didn't come into existance 2 seconds ago either? How do you know that you exist at all?

Arbitraryness is bad for a very simple reason: it negates reason. All philosophical systems must have at least one arbitrary point: the ultimate self-attesting authority (in my case, God, and in your case, probably your own reason.) that one point must be arbitrary, but beyond that, all arbitrartion constitutes suggestion that the view is wrong, because it leans less and less on empirical evidence and logical flow, and more and more upon assumptions.

Inconsistancy is like arbitraryness, but proves that the worldview is metaphysically impossible rather than unlikely.

In other words, everyone is entitled to an opinion, but no one is entitled to a wrong opinion.

Generally, inconsistancy and arbitrariness go hand-in-hand. If you find one, usually with a bit of digging you will find the other.

Finally, God's statements (assume He exists for this instance) while ethically, logically, and authoritatively complete even if they are arbitrary, are almost never. God is bound by His own nature, which I assume is mostly described in th Bible, so His decisions can be called circular (which is justified because we are talking about the ultimate self-attesting authority) but not arbitrary.