ahayes

Since it seems the threads I am becoming most involved in lately are crevo threads, I have decided to archive some of my past posts or fragments of posts related to this topic in my profile.
We often hear it said that there is no mechanism for adding information (although a clear definition of "information" is not given) to a genome. Then there are others who simply say that the addition of genetic material to the genome is prohibited. For those who support these ideas, I have a quiz. If you cannot give detailed answers to these questions, I'd say you don't know enough about the mechanisms of DNA change to express an educated opinion. Without further ado. . .

Please provide three mechanisms for modifying the information content of the genome.

Provide one that involves change at one base (potentially producing a new allele, thus new information).
Provide one that involves local change and in this case addition of genetic material, i.e., undebatable new information (this should be easy because you can use any sequence from a few bases up to thousands, and there are multiple mechanisms to choose from).
Provide one that involves chromosomal change--and this is a little more specialized but please produce an example of this that gives new information not just in the form of modified gene expression but in a modified gene product.

Other posters have said that the discovery of new functions for DNA previously thought to be useless ("junk DNA") is evidence against evolution. The truth is to the contrary.

Evolutionary theory would in fact predict emerging functions for junk DNA. In all the junk DNA that accumulates through various mechanisms there is a lot of variation, and mutation occurs, and variation plus mutation is acted upon by natural selection to produce novel and unexpected functions.
Sometimes segments of the genome including genes do get duplicated. If this happens and there is a lot of that gene product needed evolution will favor the eventual emergence of a whole series of genes for this product, like the genes for ribosomes. If only a bit of the gene product is needed, the duplicate is then free to mutate and natural selection can drive a divergence between the two genes so that you get two specialized gene products fulfilling the need that was met before by a single ancestor gene product. This is what we've seen with the hemoglobin family or HOX genes. Other times a mutation kills the duplicated gene, converting it into a pseudogene, which typically is not transcribed. Usually these are relics in the genome that are not active and are only valuable to science for their use in tracing genetic phylogenies. Occasionally you'll find a pseudogene that is transcribed into RNA, but not processed into a protein. Most of these transcribed pseudogenes don't "do" anything--the RNA is degraded. However, some of them are fortuitously able to interact with the parent gene and regulate its transcription in a variety of ways.
Another example of non-coding but non-junk DNA is the palindromic sequences on the Y chromosome accumulated during its evolution. The Y chromosome is incapable of recombining with the X chromosome except at the tip, a pseudoautosomal region. Non-recombining chromosomes have a tendency to deteriorate with time as mutations build up and deletions occur. This is known as Muller's ratchet. Part of the Y chromosome's sequence is a reverse copy of important regions. The Y chromosome so far has escaped the ratchet by essentially recombining with itself. There's no guarantee for its long-term survival, though--one species of mole vole has dispensed with the Y chromosome altogether!
A final example of how junk DNA may not be junk DNA is that the three-dimensional shape of the chromosome can be important in gene transcription. A certain length of DNA may be useful between two chromosome regions for optimal transcription of these genes. Perhaps the DNA copes all right with a shorter segment in between, but when a retrotransposon (perhaps the fossil of an ancient virus?) splices itself in between these two regions and gives the chromosome some extra flexibility that aids transcription and makes the organism even more effective.
I expect we will find in future more adapted functions for junk DNA, although much of it will not yet have acquired a function.

This post traces the origins of the gamma-carboxyglutamic acid proteins. Several mechanisms for genetic change come up in this conversation, including genome duplication events and gene duplication and specialization.

Unfortunately since it has been so many billions of years not all genes can be traced back to their origin in prokaryotes (although this can be done with some metabolic and DNA management genes). However, this one can be traced back quite far enough to cause any young earth creationist great discomfort.
MGP and BGP are matrix and bone gamma-carboxyglutamic acid proteins. BGP is osteocalcin.
"Origin and Evolution of BGP and MGP—It is quite clear that BGP and MGP have a common origin and that they are more closely related to each other than to any other VKD protein. This is well supported by the data base searching, the exon patterns, and protein sequence alignments showing that 1) BGP and MGP genes share the same simple gene organization and protein structure and 2) the C-terminal domain signature is similar in MGP and BGP. It is also clear that BGP and MGP are nearly if not completely absent in most non-vertebrate taxa. Levels of sequence similarity between BGP and MGP are much higher than one would expect to occur by convergence, suggesting that this gene group originated through gene duplication followed by subsequent sequence divergence. This duplication (gene, chromosome, or genome duplication) probably occurred very early in vertebrate evolution, being almost certainly an ancient event. Strong evidence for whole genome duplication has been shown for vertebrates (57). After the divergence of the cephalochordates from the chordate line, a genomic duplication occurred before jawless fish evolved around 500 Myr ago (Fig. 7). Another genomic duplication event probably led to the evolution of jawed fish around 400 Myr ago (Fig. 7). These two duplications led to the development of many distinctive vertebrate features, such as cartilage and bone. We hypothesize that the first genome duplication (before the branching of jawless fish) originated the ancestor gene of MGP, and the second genome duplication (before the branching of cartilaginous fish) would have produced the BGP ancestor gene. The BGP (380 Myr ago) and MGP (480 Myr ago) emergence times estimated from the evolutionary rate agree well with this conjecture. The appearance of MGP would be followed by cartilage formation and that of BGP by bone formation. After duplication, gene duplicates (BGP in this case) often experience relaxed evolutionary constraints. This promotes functional diversification of duplicates and biochemical innovation through mutations and recombination. In other words, duplicates evolve to acquire new functions. Several more speculative lines of evidence for BGP being a duplicate of MGP have been collected: 1) the presence of a MGP-like immunoreactive protein has been observed in lamprey (the more ancient species tested), whereas BGP was not detected7; 2) MGP is associated with cartilage, which appeared with the first vertebrates, whereas BGP is only associated with bone, a structure that appeared later in evolution; and 3) BGP seems to be better conserved than MGP."
The precursor to MGP did not have the same function that MGP has and unfortunately has been lost forever. Interestingly, the fruit fly protein Msp-300 (muscle-specific protein 300) C-terminus has some homology to well-conserved (and therefore required for function) regions of MGP. Msp-300 and MGP may have had a common origin in a gene existing prior to the evolution of the vertebrates.
http://www.jbc.org/cgi/content/abstract/280/29/26659
"Evolution of Matrix and Bone g-Carboxyglutamic Acid Proteins in Vertebrates." Vincent Laizé, Paulo Martel, Carla S. B. Viegas, Paul A. Price, and M. Leonor Cancela. Journal of Biological Chemistry, 2005, 289, 26659-26668.

Creationists often say that we all have the same evidence, we just interpret it differently. Unfortunately creationists really don't do much interpreting of the evidence because it doesn't make any sense from a young-earth creationist point of view. This post gives examples of some problems with creation "science" and actual evidence.

I've seen the "philosophical underpinnings" from both sides. As a young-earth creationist I found that those underpinnings were secured embarrassingly poorly. You say both sides have the facts and the differences are in the interpretation. Why, then, is it impossible to find scholarly articles explaining the whole of the natural evidence from a young earth creationist viewpoint? Creationists can't even determine among themselves which strata were laid down by the Flood and which are post-Flood, and that's a rather critical point.
I discovered years ago as a creationist that creationism is not about examining the evidence and drawing conclusions from it. It's about concluding creationism based on faith, ignoring the evidence, and then attempting to poke holes in the theory of evolution as if debunking that would leave young earth creationism as the only alternative (it wouldn't).
There are as many lines of evidence as there are journal articles all pointing towards a universe about 13.7 billion years old with our solar system being 4.5 billion years old, life originating on earth over 3 billion years ago, metazoans (multicellular organisms) appearing about 600 million years ago, tetrapods colonizing land 365 million years ago, the sauropsids (leading to reptiles) and therapsids (leading to mammals) diverging about 340 million years ago, mammals appearing about 220 million years ago, primates 60 million years ago, apes diverging 25 million years ago, the human line diverging from the chimpanzee line between 5 and 7 million years ago, and anatomically modern humans appearing 130,000 years ago.
From an old earth, evolutionary perspective evidence from astronomy, physics, chemistry, and biology make perfect sense and repeatedly corroborate each other. From a young earth perspective none of this evidence lines up, explaining creation "scientists"' failure to provide a cohesive model of the history of the earth.
For some examples of evidence that young earth creationism cannot address:

When magma seeps up from the earth and solidifies, paramagnetic atoms oriented with the earth's magnetic field are trapped in their original orientation. From examining continental plates and these magnetic lines we know that the earth's magnetic field has oscillated repeatedly every few tens to thousands or millions of years. We can use these records on the continental plates to cross-reference contemporary magnetic records and plot the positions of the continental plates over geological time. Creationism would suggest that during the Flood (when these strata were supposedly laid down) the earth's magnetic field oscillated wildly, reversing rapidly many times. Creationism can't make sense of the orientation of magnetic field lines in different layers of rock and can't cross-reference these to plot the movement of continental plates.
As long as we're talking about continental plates, many fragments of continental plates that are known to have been in contact because of their magnetic record also align well with the types of rock layers present, occurring in the same order and with similar thicknesses. This is a second line of evidence corroborating the magnetic data and indicating continental plates drift over long periods of time. Creationism can't do anything but suggest that the plates cruised to their present positions over a matter of months during the Flood, in spite of the fact that this would have destroyed all life due to the heat flow into the ocean from exposed mantle and massive volcanism.
The orderly progression of fossil types did not escape scientists even before the theory of evolution was formulated. In centuries past scientists put forth successive creationist models, with God creating one type of life, then after a time destroying it and replacing it with one more advanced. Many of these men were sincere Christians, and the evidence did not lead them to the conclusion that the first two chapters of Genesis are a literal account. Creationism cannot explain why some organisms are never found together in spite of occupying similar habitats.
Radioisotopes decay with known half-lives. We can observe "fossil" decay in light from supernovas. The spectra produced corroborate constant decay rates billions of years into the past. When a sample is radiometrically dated different dating methods, as long as appropriate for the age and type of material tested, produce corroborating ages. Creationism cannot deal with anything dated over 6,000 years old, and thus creationists have had to provide various challenges to radiometric dating (which, once again, do not support their model, but just try to poke holes in the physicists' model) such as suggesting decay rates are nonconstant in spite of the evidence, and in spite of the fact that decay rates proposed would have cooked the newly created earth.
Returning to fossil sorting, microfossils are tiny fossils that should not sort appreciably. In spite of this, we have sea cores holding fossils of Foraminifera going back millions of years and showing greater complexity of the test (shell) evolving over time. This falls completely in line with what evolution would suggest, but creationism cannot explain how the Flood waters managed to sort such tiny fossils so meticulously. And, of course, the creationists don't even try.
Most strata are assumed by creationists to have been laid down during the Flood. Among these strata are layers of lava from volcanic eruptions. During the Flood these would have been extruded into water and should have formed characteristic pillow lavas. Instead, we have many layers of volcanic rock that have characteristics of lava laid down on dry land.
There are fossils that indicate organisms were going about their normal lives during the supposed time of the Flood. Layers of coal hold animal trackways and vertical stumps, sometimes with the roots attached and twining through undisturbed coal. In the Joggins Fossil Cliffs multiple hollow lycopod stumps have been found to contain fossils of primitive amphibians and reptiles that used the stumps for shelter--in strata supposedly laid down during the middle of the Flood. In Triassic strata fossils of the dicynodont Diictodon have been found curled up in their helical riverbank burrows after flash floods drowned and buried them. Creationists are unable to explain how these animals managed to dig burrows when they should have been underwater and the only substrate present should have been liquified mud.

And let's consider some other odd features of young earth creationism. Most creationists think that God made two animals of each kind, usually interpreted as genera, and then these evolved (!!) to produce all living organisms over a period of 4000-6000 years. This would require rates of evolution much faster than any evolutionist would suggest. So why do historical records not show new species popping into existence every few centuries? And why has this runaway creationist evolution apparently stopped? Then also creationists tend to think that only extant creatures would have to have been preserved on the ark, plus some that have gone extinct in the past 4000 years. In actuality 80% of the mammal genera that have ever lived are extinct. Major groups have come and gone--primitive tetrapods, primitive synapsids, primitive archosaurs, dinosaurs (with the exception of birds), all but two genera of monotremes, most of the marsupials, many placental mammals, and others. And that's just the tetrapods, which I am admittedly biased towards. Pull out a paleontology book--there will be placental mammals in it that you won't even recognize. Supposedly representatives of all of these genera were present at Creation, most lost at the Flood (goodbye dinosaurs (-birds)--not one creationist can explain why they all died off), others dying off in whole clades after the Flood--in between evolving at breakneck speed. The creationist God is massively incompetent. Creationists object to the process of evolution as wasteful, but the evolution of metazoans took place over the last half-billion plus years, and the creationist God managed to burn through the majority of all of the metazoans he ever made in only 6,000 years. Ouch.
These are just a few of the dilemmas that creationism is unable to address. Once I realized the complete lack of corroborating evidence I abandoned young earth creationism and determined God must have used evolution over billions of years to make living organisms.

And finally this is my (as yet unanswered) letter to Answers in Genesis regarding their biased coverage.

I am writing to you because I feel that your coverage of Dr. Schweitzer's dinosaur fossil research has been grossly unfair and misleading. AIG has misrepresented Dr. Schweitzer's research, slandered Dr. Schweitzer and her colleagues by accusing them of attempting to "explain away" their findings, and swept under the rug a follow-up paper published by Dr. Schweitzer which presents some inconvenient evidence indicating that birds and theropod dinosaurs are genetically related.
My letter is prompted by your March 6 article "The Scrambling Continues" regarding Dr. Schweitzer's discovery last year of an unusually well-preserved Tyrannosaurus rex fossil femur. When the fossil was retrieved the femur was broken. The internal cavity had an unusual porous appearance, so Dr. Schweitzer took some small fragments of the bone and soaked them in a solution that removed all of the minerals. It is important for the sake of accuracy to emphasize that the samples removed from the fossil were indeed hard and mineralized, not soft like raw marrow as some sources have stated (based I believe on your misleading commentary). After the minerals were removed the end products were tiny fragments (most less than 1/8 inch in diameter) of a network, with some fragments (or sections of a fragment) brittle and fragile while other fragments were spongy and flexible, resembling connective tissue and blood vessels. Under the microscope in the vessels Dr. Schweitzer could see structures resembling cells and with some type of internal structure. I'll quote the conclusion of Dr. Schweitzer's paper (1):
"The elucidation and modeling of processes resulting in soft-tissue preservation may form the basis for an avenue of research into the recovery and characterization of similar structures in other specimens, paving the way for micro- and molecular taphonomic investigations. Whether preservation is strictly morphological and the result of some kind of unknown geochemical replacement process or whether it extends to the subcellular and molecular levels is uncertain. However, we have identified protein fragments in extracted bone samples, some of which retain slight antigenicity (3). These data indicate that exceptional morphological preservation in some dinosaurian specimens may extend to the cellular level or beyond. If so, in addition to providing independent means of testing phylogenetic hypotheses about dinosaurs, applying molecular and analytical methods to well-preserved dinosaur specimens has important implications for elucidating preservational microenvironments and will contribute to our understanding of biogeochemical interactions at the microscopic and molecular levels that lead to fossilization."
AIG has reported this recovered material as strictly organic. This is a conclusion not warranted by the evidence, as a close reading of Dr. Schweitzer's original article and even a cursory reading of the accompanying commentary article (2) in the same issue of Science would show:
"Hendrik Poinar of McMaster University in Hamilton, Ontario, cautions that looks can deceive: Nucleated protozoan cells have been found in 225-million-year-old amber, but geochemical tests revealed that the nuclei had been replaced with resin compounds. Even the resilience of the vessels may be deceptive. Flexible fossils of colonial marine organisms called graptolites have been recovered from 440-million-year-old rocks, but the original material--likely collagen--had not survived."
Some of the tougher biopolymers (especially chitin, lignins and proteins) may degrade very slowly in a fossil. Some arthropod fossils from 25 million years ago contain a small amount of chitin (3), although insects preserved in amber from about the same time period show complete diagenetic alteration (fossilization) in spite of the superb morphological preservation (4). Likewise, in spite of the excellent morphological preservation of this fossil Dr. Schweitzer clearly states that it is unknown at this time whether the actual original cellular and organic material is present. The preservation of intact organic material from a long-extinct species would be a wonderful scientific find, however it is most likely that Dr. Schweitzer and other molecular paleontologists will have to settle for studying the typical biomolecule degradation products found in fossils (5). It may actually be that some fraction of organic matter was preserved, and the supplemental material Dr. Schweitzer published indicates that this may be true as the sample extracts showed some affinity for antibodies against bovine osteocalcin and chicken type I collagen. This leads to the exciting possibility of extracting collagen or other structural proteins from the T. rex sample and comparing these to avian proteins to help clarify the evolutionary relationship between birds and theropod dinosaurs. However, it is unfortunately more likely that the sample will prove to be fully mineralized and lacking any utilizable amount of untransformed biomolecules. If this is so AIG will have egg in its face after its trumpeting of the T. rex sample as "unfossilized soft tissue" ("Still Soft and Stretchy," 25 March 2005).
When I read "The Scrambling Continues" it led me to see if any new papers on this fossil have been published since last year. Sure enough, my search revealed a Science paper from June 2005 (6). This paper is foreshadowed by a line in the initial paper: "In addition to the dense compact bone typical of theropods, this specimen contained regions of unusual bone tissue on the endosteal surface." I'll quote from the June paper:
"The location, origin, morphology, and microstructure of the new T. rex tissues support homology with ratite MB [medullary bone]. The T. rex tissues line the medullary cavities of both femora of MOR 1125, suggesting an organismal response. The tissues are similar in distribution to those of extant ratites, being more extensive in proximal regions of the bone. They are clearly endosteal in origin, and the microstructure with large vascular sinuses is consistent with the function of MB as a rapidly deposited and easily mobilized calcium source. The random, woven character indicates rapidly deposited, younger bone. Finally, the robustly supported relationship between theropods and extant birds (15–18, 24, 25) permits the application of phylogenetic inference to support the identification of these tissues (26, 27)."
Medullary bone is a particular type of bone laid down in the endosteal cavities of female birds to allow storage and rapid mobilization of calcium for egg-laying. This type of bone has only been found in birds, so its discovery in a dinosaur fossil ought to be noteworthy to anyone interested in science. This uniquely avian trait in T. rex adds another piece of evidence supporting the evolutionary origin of birds from theropod dinosaurs. I'm certain that your researchers must have run across this article while checking to see if Dr. Schweitzer had published a follow-up paper. Your failure to mention this article's findings in your rather snide article indicates to me that AIG is not so much interested in the pursuit of knowledge as the promulgation of anti-evolutionary propaganda.
Now I have the benefit of prior knowledge of your likely response to this finding of medullary bone in a dinosaur. I mentioned my complaints about your coverage to a young-earth creationist, and he emailed you asking about this. He shared with me your response, which was that medullary bone was indeed found in other species besides birds, providing these links as support: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=1790209&dopt=Abstract, http://cal.vet.upenn.edu/saortho/chapter_53/53mast.htm. These links can be easily found by either searching Google for "medullary bone" and ignoring the multiple hits saying it is uniquely avian or by searching for "medullary bone" and excluding "avian" and "bird." The first example given is actually a misunderstanding by your staff member of basic bone growth--in a young mammal the interior of the bone is filled with spongy bone which recedes to leave a medullary cavity as the bone grows. The second example is talking about the medullary cavity and adjacent structures--it describes "medullary bone infarct," which usually occurs in the medullary cavity near the end of a long bone and results in bone marrow and trabecular bone necrosis. Both of these instances have nothing to do with avian medullary bone. Genuine medullary bone is produced by a genetically encoded organismal response to gonadal hormones in an adult female bird, leading to the deposition of bone in the medullary cavity. The gross and microscopic appearance of medullary bone is unique, and the structural composition is quite different from other types of bone (7). Indeed, osteoblasts isolated from hen medullary bone show different expression patterns of genes than osteoblasts isolated from rats, indicating that avian medullary osteoblasts are uniquely differentiated and the process of medullary bone deposition is different than mammalian bone formation (8). The fossilized bone recovered from this T. rex show unequivocal avian medullary bone, and pose quite a conundrum for those who deny evolutionary relationships.
I can hardly expect AIG to suddenly embrace an old earth and common descent. However, I'm sure that AIG would want to be seen as a trustworthy organization that can be relied upon to present the facts accurately. In light of this I am requesting that you publish a correction stating that the T. rex fossil discovered was extensively fossilized, did not have a "raw" appearance, and that the flexible fragments recovered are tiny (on the order of 1/8 inch). Additionally I request an acknowledgment of the existence of Dr. Schweitzer's paper reporting the discovery of avian medullary bone in the T. rex fossil. Finally, I request that my letter in whole be published on your site. These steps will go far towards correcting AIG's superficial coverage of Dr. Schweitzer's findings.
Thank you for your attention to these matters.

M. Schweitzer, J. Wittmeyer, J. Horner, J. Taporski, Science 307, 1952-1955, (2005).
E. Stokstad, Science 307, 1852, (2005).
M. Flannery, A. Stott, D. Briggs, R. Evershed, Organic Geochemistry 32, 745-754, (2001).
A. Stankiewicz, H. Poinar, D. Briggs, R. Evershed, G. Poinar, Proceedings: Biological Sciences 265, 641-647, (1998).
M. Schweitzer, Annals of Paleontology 90, 81-102, (2004).
M. Schweitzer, J. Wittmeyer, J. Horner, Science 308, 1456-1460, (2005).
C. Dacke, S. Arkle, D. Cook, I. Wormstone, S. Jones, M. Zaidi, Z. Bascal, Journal of Experimental Biology 184, 63-88, (1993).
S. Hiyama, T. Sugiyama, S. Kusuhara, T. Uchida, Comparative Biochemistry and Physiology, Part B 142, 419-425, (2005).

Here's a short primer on DNA, RNA, and protein:

DNA is formed of nucleotides linked together. In DNA the nucleotides are made from phosphate-bearing deoxyribose linked to one of the four DNA bases (adenine, thymine, guanine, and cytosine, symbolized by A, T, G, and C). The nucleotides are named after their bases as adenosine, thymidine, guanosine, and cytidine. Each nucleotide sugar is linked to the sugar of the adjacent nucleotides through the phosphate. The order of these nucleotides is unconstrained--you can have any imaginable DNA sequence. However, some sequences will produce transcripts and others will not. Each strand of DNA in everything but some viruses is duplexed with the complementary strand. (Genes occur on either side of the duplex, and usually if a gene occurs on one strand that stretch of DNA on the complementary strand will be noncoding.) So along the link of the chain the nucleotides of A, T, G, and C are bound together quite tightly by covalent bonds, but when each base binds to the complementary one in the opposite strand of the duplex (A to T, G to C) the bonds there are hydrogen bonds, which are more like an electrostatic interaction of positive charge adhering to negative charge. Because these hydrogen bonds are much weaker than covalent bonds, the two strands of the duplex can easily be peeled apart when needed to allow duplication or transcription.
The simplest explanation of a gene is what is called an open reading frame (orf), a DNA sequence beginning with the "start codon," the sequence ATG, and ending with a stop codon, which can be TGA, TAG, or TAA. When a ribosome reaches the ATG sequence and when the gene has been turned on by regulatory components, transcription begins. The ribosome copies the DNA strand carrying the start codon into RNA. It stops (in our ideal definition) when it reaches the stop codon. The RNA transcript is complementary to the DNA (where the DNA had T, RNA has A, etc.) except that in RNA the thymines are replaced with uracil (an additional important difference is that the sugar here is ribose).
After the RNA transcript (messenger RNA or mRNA) has been made, it needs to be translated into protein. Beginning at the start of the RNA transcript each set of three bases makes up a codon. Each codon corresponds to a particular amino acid. There is redundancy in the code so each amino acid is represented by two to four different codons. The translation is done by transfer RNA or tRNA, which bears an anticodon that is complementary to a particular codon, and the amino acid that corresponds to this codon. The anticodon hydrogen bonds with the codon. When the adjacent tRNA binds to the next codon, the two amino acids are linked and the first tRNA falls off. In this way the peptide chain is lengthened up to the end of the transcript. The peptide product is then modified in various ways to produce the final gene product.
Because of the way the coding works, it takes a DNA sequence 240 bp long to produce an 80 aa protein. Because of the redundancy of the code, swapping one base in the DNA for another does not necessarily change the output protein. Even if it does, protein tends to be pretty tolerant of amino acid changes--the 3-d structure of the protein often is unchanged. Bad things can happen, though, when this change occurs at an active site, where a chemical reaction of a substrate is triggered and where the locations of positive and negative charge and acidity and basicity need to be precise. If a protein has no catalytic activity often the sequence can vary pretty widely without affecting function.
This is ignoring all sorts of fun stuff like alternative splicing, genes continuing transcribing sometimes into other orfs, and viral DNA that is packed so tightly with information that often sequences complementary to a gene also contain genes as well.

Finally, a post describing how my analysis of morality led me away from Christianity, since this topic keeps coming up.

Unfortunately the background I came from is pretty fundamentalist, so I was taught that the Bible including OT was inspired and that God really did speak to various prophets. In the past year or so I've been trying to reconcile that with the sketchy morality depicted in the OT.
There seem to be two different ideas of morality among Christians (although a lot of times they coexist in the mind of a person even though they're contradictory. . .) The first is that morality is derived from the nature of God, and God is immutable, thus morality is absolute and never changes. Therefore it ought to be always wrong to murder an innocent, yet God is said to have told Joshua to eradicate the Canaanites down to the babies.
The second idea of morality is that our moral laws are just made up by God (possibly completely arbitrarily) and that God is not bound to those rules at all and can change them at any time. I think this is an attempt to detour around the problem of God ordering acts that we would all say are evil. At the same time they say that God is Good, not because we can look at his actions and judge them as being good (God is said to be beyond human understanding and judging his actions is presumptuous), but because God says of himself that he is good. I find this very distasteful because it renders God completely incomprehensible and untrustworthy. Perhaps God really has a personality more like Satan, has handed us moral laws to follow just to play with us, and is telling us that he is good while planning a surprise for those who choose to follow him into the afterlife. . .
So from my point of view either the Judeo-Christian God exists but is too incompetent to transmit his will to his followers, or he exists but is possibly really evil or completely amoral and definitely untrustworthy, or he does not exist and the Bible comes about from human beings gradually building onto a framework of myth. My fundamentalist background makes me unwilling to accept the first, the second I really hope is not true and I wouldn't want to serve that God anyway, and the third I find the most reasonable conclusion, unfortunately.