User talk:Nlawrence

MATCH Update
So, do to some difficulties, I am putting recuitment on hold. AIG is not willing to be a part of MATCH, even though I did not ask them to be, I just wanted there opinion on things, and comunication was going fine before I was suddenyl cut off.

So lets focus on our introductory article getting finished and then we will storm right into the content on some of these issues. Maybe when people start to see the content, they will want to add their input.

Carl Wieland will be submitting me the results of the survey ASAP with some touches of his own on behalf of CMI. This is a big step forward I hope.--Tylerdemerchant 15:36, 9 January 2008 (EST)
 * That is great Tyler, strange that AiG was so quick to back-off, maybe because CMI is involved and they have some issues they need to resolve still? Either way, I am reading everything Tyler, still busy with school, but always watching and taking notes. Keep it up! --Tony Sommer 16:27, 9 January 2008 (EST)
 * Well Tony, we are in the same boat. I am busy with school, but I wont let this project die down. As soon as we rap up the introductory article, I know that there will be a lot for the two of you to comment on, but thanks for the reassurance.

I have learnt quite a bit lately regarding genetics and have almost finished biology 11, which is filled with evolution. Yet nothing I have seen supports the evolutionary model based on mutatation. In the same paragraph, you get things like "evolution has aloud gymnosperms to develope into angiosperms along this path" and then "flower pedals are designed to attract pollinators". What, designed? Isnt that a contradiction?--Tylerdemerchant 17:31, 9 January 2008 (EST)

So you know, I've been working on a survey of creationist journals. The questions that will be answered will be:

How many article published in creationist journal x pertain to biology? How many have to do with mutation? How many take a position of the "increase in information" debate? And so.--Nlawrence 18:10, 9 January 2008 (EST)
 * Great! that will be excellent for the introductory article. I should also mention that Dr. Wieland has responded to the survey. It is going to take some decifering because he left a lot of comments, but thats o.k.--Tylerdemerchant 14:10, 10 January 2008 (EST)

Dr Bergman is now an active member of MATCH --Tylerdemerchant 13:26, 22 January 2008 (EST)

Flank info
Not enough to help. He's a herpetologist if I remember correctly.

He joined the OriginsTalk list a few years ago, but was booted in probably under 2 weeks for personal attacks. Here's his posts to the list. Maybe it will help.

--Mr. Ashcraft - (talk) 22:01, 15 November 2007 (EST)

Mutations
Scanning journal articles is hugley valuable and shows credibility, certainly needed for what we are trying to do. --Tony Sommer 02:19, 16 November 2007 (EST)

--Tylerdemerchant 13:36, 22 January 2008 (EST)== Results from first survey on mutation(etc) ==

More are to come, but here is the first results. All of this comes from the Grisda annotations sections. They list a series of secular articles and then comment on what they are about. I hope this data will help with the mutations project proposed by Ty and some of the data can (if not all) be used for this article. The first papers start at 1988, but then will get newer as you go down. Here they are: -- Cairns, J., J. Overbaugh, and S. Miller. 1988. The origin of mutants. Nature 335:142-145.

Conventional evolutionary theory is based on the belief that variation is produced by random mutations, and that the environment acts in such a way that those individuals best adapted for survival are favored over those less well-adapted. The randomness of mutations seems intuitively obvious, but the experiments described in this paper bring this assumption into question.

In the laboratory, bacteria (E. coli) with a mutation disrupting the function of the enzyme for utilizing lactose somehow mutated to restore the lactose gene to normal function, but did so only when under selection for ability to utilize lactose. In another experiment, a bacterial strain was used that could grow in lactose only if a short DNA segment were deleted, and if grown in the presence of arabinose. Again, mutants were discovered only if lactose was present. In a third experiment, bacteria were used that lacked the normal gene for the lactase enzyme. E coli possesses a cryptic gene which can utilize lactose if two rare mutations occur together. Lactose-using colonies formed in this situation, but the process whereby this may occur is not understood.

These results are based on only one species and one enzyme system, and it is not certain whether the results have a more general application. Nevertheless, this paper promises to stimulate a great deal of discussion among evolutionary theorists, and will encourage those who favor some kind of environmental influence on genetic change. If the phenomenon of non-random mutations is found among eukaryotes, it may be used to explain directionality in evolution. (For a related discussion, see Opadia-Kadima, G. Z. 1987. How the slot machine led biologists astray. Journal of Theoretical Biology 124:127-135, reviewed in Origins 14:26.) --- Hall, B. G. 1989. Adaptive evolution that requires multiple spontaneous mutations. I. Mutations involving an insertion sequence. Genetics 120:887-897.

Evolutionary biologists have assumed that spontaneous mutations occur randomly and that separate mutations occur randomly, and that separate mutations are independent and unrelated. These assumptions are challenged in this study of bacterial response to nutritional conditions. The intestinal bacterium, E. coli, possesses a set of genes (an operon) to utilize the sugar salicin, although the genes are not usually expressed. Expression cannot occur unless a mutation activates the operon. In the bacterial strain used, a second mutation — removal of an insertion sequence — is required for salicin utilization. The mutation rate at the activation site has been measured as about 4×10-8 per cell division, and the mutation rate for removal of the insertion sequence has been estimated as less than 2×10-10 per cell division. From the individual mutation rates, the expected appearance of salicin-utilizing bacteria would be about 10-17. However, under certain conditions, the actual rate of appearance of salicin-utilizing bacteria is about 10-8, which is many orders of magnitude greater than expected. It appears that mutants caused by loss of the insertion sequence occur at an unexpectedly high rate when salicin is present but other nutrients are not available. The experiments described in this paper suggest that mutations are not entirely random, but may be influenced by environmental conditions, and that the incidence of two mutations occurring together may be greater than expected on the basis of their separate mutation rates. Since insertion sequences may be responsible for a majority of mutations, the conclusions here may have general application. This calls into question the common assumption that shared derived traits indicate common ancestry, and also undermines the theoretical basis for the purported molecular clock. --- Gray, M. W., R. Cedergren, Y Abel, and D. Sankoff. 1989. On the evolutionary origin of the plant mitochondrion and its genome. Proceedings, National Academy of Sciences (USA) 86:2267-2271.

Green plants contain genetic material in three organelles: nucleus, chloroplast and mitochondrion. Ribosomal RNA (rRNA) sequences are encoded in the genomes of each of these organelles. Phylogenetic hypotheses based on chloroplast rRNA sequences suggest that green plants and green algae are most closely related to each other, and as a group most closely related to eubacteria. Proposed relationships based on nuclear rRNA are similar to those based on chloroplast rRNA. In contrast, phylogenetic hypotheses based on mitochondrial rRNA sequences suggest that green algae share a more recent ancestry with animals than with plants, and that green plants are more closely related to purple bacteria ("blue-green algae"). The explanation offered by the authors for this seeming contradiction with evolutionary theory is that mitochondria are evolved from purple bacteria which were incorporated into ancestral plant cells as endosymbionts, and that this occurred twice during the evolution of the line leading to green plants. The first endosymbiotic event occurred early in the ancestry of eukaryotes, while the second event occurred after the green plants diverged from other groups. Such ad hoc explanations are purely speculative, and should be abandoned in favor of the more parsimonious explanation of separate ancestries. -- Hall, D. H., Y. Liu, and D. A. Shub. 1989. Exon shuffling by recombination between self-splicing introns of bacteriophage T4. Nature 340:574-576.

Proteins of differing functions may have regions of similar structure. The suggestion has been made that a given coding region (exon) may be active in the production of more than one kind of protein molecule. Different proteins might be produced by different combinations of subunits, in a process dubbed "exon shuffling". This paper supports the possibility of exon shuffling by reporting the discovery of deletion mutants of phage T4 in which the deleted portion lies between two non-transcribed regions (introns) with homologous DNA sequences. It appears that the deletion occurred by recombination, resulting in a hybrid intron that connects two previously separate exons into a single transcribed unit. Exon shuffling presents some very interesting theoretical possibilities for change in species.

Kawaguchi, Y., H. Honda, J. Taniguchi-Morimura, and S. Iwasaki. 1987. The codon CUG is read as serine in an asporogenic yeast Candida cylindracea. Nature 341:164-166.

The genetic code is virtually the same for all organisms. Each codon, or base triplet, specifies the same amino acid in nearly all species. However, a few exceptions are known in certain microorganisms, including Paramecium, Mycoplasma, Tetrahymena, and Eschericia coli. This paper reports another exception, a yeast. The codon CUG specifies the amino acid leucine in all known organisms, except in Candida, where it specifies serine. The authors are looking for CUA codons in Candida to determine whether they also code for serine. Exceptions to the universality of the genetic code pose interesting questions for evolutionary theory.

Fleischer, R. C., S. Conant, and M. P. Morin. 1991. Genetic variation in native and translocated populations of the Laysan finch (Telespiza cantans). Heredity 66:125-130.

Much theoretical work has been done on the concept of genetic bottlenecks and founder effects, but little actual field evidence is available. This paper reports genetic differences among populations of Laysan finches on four islands. Contrary to expectations, population bottlenecks did not result in reduced levels of genetic variation. In fact, genetic variation appears possibly to have increased after the bottleneck. The differences are relatively minor, but occurred in less than twenty years. This result is contrary to the conventional wisdom, and may have important implications for models of speciation. --- Jablonka, E., M. Lachmann, and M. J. Lambs. 1992. Evidence, mechanisms and models for the inheritance of acquired characters. Journal of Theoretical Biology 158:245-268.

Evidence is presented that certain changes in organisms may be transmitted through several generations of offspring even when no change in DNA sequence has occurred. An example is the degree of methylation of DNA. The addition of methyl groups to cytosine in a DNA sequence generally causes the DNA sequence to become inactive. During DNA replication, the pattern of methylation is preserved in the DNA copies. Thus the gene will also be inactive in the new cell. In unicellular organisms, the new individual will inherit the methylation pattern, and its gene will be inactive, despite the lack of change in DNA sequence. A similar argument would apply to genes that have been turned on by removal of the methyl group. Inheritance of the condition of a gene rather than the sequence of the gene can be attributed to the presence of epigenetic inheritance systems (EIS). EISs may be based on chromatin marking, such as methylation, by positive feedback regulatory loops, or, in a few cases, by structural inheritance. Positive feedback regulatory loops occur when a protein product stimulates further production of the protein. If the protein is transmitted to the daughter cell, the daughter cell will continue to produce the protein. Such inheritance does not depend on the sequence of the DNA, but on the presence of the regulatory protein. Structural inheritance occurs when a cellular structure is used as a template for constructing the daughter cell. EISs seem more common in unicellular organisms and in plants than in animals. This is believed to be a result of the early separation of the germ-line during development in animals. Heritable epigenetic variations have been called "epimutations," which are believed to be considerably more frequent than DNA sequence mutations. Many inherited changes that are now thought to be caused by DNA mutations may actually be caused by epimutations.

Dessauer, H. C., G. F. Gee, and J. S. Rogers. 1992. Allozyme evidence for crane systematics and polymorphisms within populations of sandhill, sarus, Siberian and whooping cranes. Molecular Phylogenetics and Evolution 1:279-288.

There are 15 living species of cranes, all of which were sampled for this study. Based on protein electrophoresis, the two species of African crowned cranes are distinct from the remaining species, which are themselves divided into two groups. The "sandhill group" consists of seven species, and is distributed across the Old World, with the sandhill crane reaching North America. The "whooper group" consists of six species which are all restricted to the northern continents. Single species diversity was also analyzed. A significant result was the discovery that genetic diversity among whooping cranes was surprisingly high, similar to that for the six other species with which it was compared. This is contrary to expectations of genetic loss due to a population bottleneck of some 15 individuals in the 1940s. The possibility should be explored that some mechanism exists for rapidly restoring genetic variability after population bottlenecks. --- Ohta, T. and C. J. Basten. 1992. Gene conversion generates hypervariability at the variable regions of kallikreins and their inhibitors. Molecular Phylogenetics and Evolution 1:87-90.

Kallikreins are a group of serine proteases found in mammals. A family of genes codes for these enzymes. DNA sequences in the active region of the proteins' sites are more variable than in neutral sites between genes, suggesting that some mechanism is causing a higher rate of mutation in the region coding for the active site. Kallikrein genes are believed to engage in frequent exon shuffling, but gene conversion seems to be the mechanism involved here. Gene conversion occurs when one sequence is copied to match a second, usually similar, sequence. Some gene copies may act as reservoirs of genetic variability by retaining alternative sequences which may be substituted into a transcribed gene. Thus, gene conversion may be an important source of genetic variability. -- Nilsson, D.-E. and S. Pelger. 1994. A pessimistic estimate of the time required for an eye to evolve. Proceedings of the Royal Society of London B 256:53-58.

The origin of the vertebrate eye has been a conundrum for evolutionary biologists ever since Darwin. Nilsson and Pelger tackled the problem with a computer simulation in which the starting point is a flat patch of light-sensitive, pigmented epithelium. They then proceeded to cause the shape of the patch to vary by "mutations" of 1%, followed by "selection" of the most functional shape. Each step in the process was called a "generation." They counted the number of "generations" required for the flat patch on the computer screen to change to the shape of the vertebrate eye. Along the way, they introduced a variation in refractive index, which eventually "developed" into a "lens." The number of "generations" required to effect the change from a flat patch of photosensitive cells to a vertebrate eye with functional lens was calculated as about 364,000. This report was received approvingly by Richard Dawkins (Nature 368:690-691). Various types of eyes are present in at least 40 independent "lineages," which Dawkins believes shows that evolution of the eye cannot be terribly difficult. Nevertheless, both Dawkins and the authors of the report note that the model does not take certain features into consideration, such as the origins of the photosensitive patch of cells, the variable iris, or variable focusing. Perhaps analysis of these features will be forthcoming. What is one to make of all this? First, comparing the evolution of the eye to shape changes on a computer screen seems rather far-fetched. The entire project seems closer to an exercise in geometry than in biology. Second, the exercise assumes a functional starting point. Thus it has nothing to do with the origin of the biochemical systems of vision or the requisite neural network. Third, Nilsson and Pelger's computer exercise operates as if each 1% change in morphology can be accounted for by a single gene mutation. They do not consider the effects of pleiotropy, genetic background, or developmental processes. Fourth, an important part of the model relies on the special circumstance of a layer of clear cells covering the "retina." This layer somehow assumes the proper shape of a lens. Fifth, as noted by the authors, several features of the eye remain unaccounted for, such as the iris. Basically, the only result achieved was to show that two light-sensitive surfaces that differ in shape by 1% will have different efficiencies in photoreception, and that an uninterrupted series of 1% improvements is possible. The failure of scientists to produce new structures in selection experiments illustrates the implausibility of Nilsson and Pelger's "just so" story. -- Wilson R, et al. (55 authors). 1994. 2.2 Mb of contiguous nucleotide sequence from chromosome III of C. elegans. Nature 368:32-38.

The small, free-living roundworm, Caenorhabditis elegans, has a genome of about 100 million base pairs. An attempt is underway to sequence the entire genome of this worm. The DNA sequence reported, about 2% of the genome, is one of the largest contiguous DNA sequences known. Perhaps unsurprisingly, the data has revealed some surprises. First, genes are more numerous than expected. On average, one gene was found for about every 5000 base pairs. Assuming this is characteristic of the entire genome, the total number of genes in the genome is estimated at nearly 18,000. Second, a much higher than expected proportion of the genome is involved in coding. Putative coding sequences account for 29% of the sequenced genome. When introns are included, the total rises to 48%. This is perhaps ten times the proportion previously estimated as typical. Third, the number of genes not shared with other phyla appears to be larger than previously thought. The authors estimate that at least 60% of the genes are unique to roundworms. Fourth, inverted repeats are the most common type of repeat, and are located in introns twice as frequently as in other parts of the genome. Most of the inverted repeats have characteristics that suggest they may be remnants of mobile elements. By contrast, most tandem repeats were located between genes. Fifth, some sequences with 98% similarity are found widely separated on the chromosome. These might be duplicated genes, but how they became so widely separated is not clear. This report, together with advances in other genome studies, demonstrates that we still have a great deal to learn about how the genome operates. - Farabaugh PJ. 1993. Alternative readings of the genetic code. Cell 74:591-596.

The genetic code has been known for twenty years or so. The code is based on groups of three DNA nucleotides (a codon), which either codes for a specific amino acid or is a start or stop signal. By determining the DNA sequence of a gene, one is theoretically able to predict the amino acid sequence of its product. There are some complications to this standard scenario. Intervening sequences (introns) are well-known, in which portions of the messenger RNA are spliced out before decoding and protein synthesis begins at the ribosome. There are other rare phenomena that indicate the potential for altering the conventional message of a DNA sequence during the process of decoding. For example, termination codons are sometimes ineffective in stopping the cell from continuing to add amino acids to the protein being manufactured. Thus a codon that appears to be a stopping point may not function as a stopping point. Another unusual observation is frameshifting. In this situation, the predicted grouping of nucleotides into codons is altered so that the message is read in a completely different way. A third type of alteration is hopping, in which large DNA segments may simply be skipped. These observations indicate that the operation of the genetic system is much more complex than a simple understanding of the genetic code would indicate.

Hall BG. 1994. On alternatives to selection-induced mutation in the Bgl operon of Escherichia coli. Molecular Biology and Evolution 11:159-168.

The assumption that mutations were random was challenged in 1988 by experiments that appeared to show that mutations occurred more rapidly than expected under conditions favoring the mutant phenotype. The suggestion that mutations might somehow be directed touched off a controversy that has not yet been resolved. Other researchers challenged the conclusion that mutations may be directed, reporting tests that explained the previous results without recourse to directed mutation. In this paper, Hall expands the experimental protocol to include tests of his own previous interpretations as well as those of his challengers. The mutation in question involves excision of a movable element, resulting in the ability of the cell to utilize the sugar salicin. Hall provides an explanation for his own previous results, his present results, and those of his challengers that involves directed mutation, and concludes that mutations may be directed, contrary to conventional wisdom. - Zhu N, Liggitt D, Liu Y, Debs R. 1994. Systemic gene expression after intravenous DNA delivery into adult mice. Science 261:209-211.

Under the right conditions, genes can be transferred into mice by intravenous injection. The injection includes an expression plasmid and a cationic liposome in a preferred ratio. Depending on the DNA dosage, the gene may be expressed in a few or many tissues, and over a period of time ranging from a few days to at least several months. This technique could facilitate gene therapy and other forms of genetic engineering. Gene transfer has frequently been proposed as an agent of morphological change. Transfer of genes is generally thought to be rare. If gene transfer is not so difficult as thought, its significance in morphological change is likely to be enhanced.

Fraser CM, Gocayne JD, White O, Adams MD, Clayton RA, Fleischmann RD, Bult CJ, Kerlavage AR, Sutton G, Kelley JM + 18 other authors + Venter JC. 1995. The minimal gene complement of Mycoplasma genitalium. Science 270:397-403.

This is the second organism to have its entire genome sequenced, Mycoplasma genitalium is thought to have the smallest genome for a self-replicating organism. Its genome is about 580,000 base pairs, and contains 470 predicted genes. Of the 470 genes identified, 318 represented known proteins and another 56 had been discovered in other organisms. The remaining 96 were previously unknown, and may represent genes unique to mycoplasmas. This species is missing several genes, but can survive because it is parasitic. The genome sequence of this species may help in estimates of the minimum genome size needed for independent life. It seems likely that independent life is not possible with fewer than perhaps 250 or 300 genes. This estimate constrains explanations of the origin of life, making a naturalistic origin seem highly implausible. Another feature that may contribute to a better understanding of life is the possibility of identifying the number of gene families present, and comparing this with the numbers of gene families present in other types of organisms. New gene families require an explanation as to their origin, and it seems likely that a better understanding of the magnitude of this problem will show naturalistic processes to be implausible.

Andersson DI, Hughes D. 1996. Muller's ratchet decreases fitness of a DNA-based microbe. Proceedings of the National Academy of Sciences (USA) 93:906-907.

Since it appears that most mutations are harmful, it would seem that organisms would tend to degenerate. This has been proposed to happen unless variation is provided by sexual reproduction. Examples of degeneration are known among RNA viruses, which have unusually high mutation rates. This is the first report to show spontaneous degeneration among DNA-based organisms, specifically the bacterium Salmonella typhimurium. Cells were grown asexually, with repeated bottlenecking to promote random accumulation of mutations. After 1700 generations, 1% of the 444 lineages showed decreased growth rate. During the experiment, the mutation rate for a group of about 200 genes was calculated to be about 10-9 per base per pair per generation. This experiment suggests that species tend to degenerate genetically, but the process is slowed by natural selection.

Kordis D, Gubensek F. 1998. Unusual horizontal transfer of a long interspersed nuclear element between distant vertebrate classes. Proceedings of the National Academy of Sciences (USA) 95:10704-10709.

LINEs, or long interspersed nuclear elements, are segments of DNA found repeated in many copies in a genome. One particular LINE, called ART-2 retroposon, was previously found first in cattle, then throughout the ruminants. It was thought to be specific to the ruminants until it was discovered also in vipers. This appeared to be a case of horizontal genetic transfer, perhaps by a common parasite. This possibility was tested by surveying 22 species of snakes, 17 species of lizards, 2 crocodilians, and 2 turtles. ART-2 retroposons were discovered in all the snake species and a majority of the lizard species, but not in the crocodilians or turtles. Horizontal transfer appears to be the best explanation for this pattern. Horizontal transfer is common among bacteria, but it is thought to be rare among multicellular organisms. If horizontal transfer is much more common among multicellular organisms than currently believed, inferences from similarities in molecular sequences might be greatly weakened. -- Nurminsky DI, Nurminskaya MV, De Agular D, Hartl DL. 1999. Selective sweep of a newly evolved sperm-specific gene in Drosophila. Nature 396:572-576.

The fruit fly, Drosophila melanogaster, belongs to a group of very similar flies, but it has a unique DNA sequence located between the genes for the cell-adhesion protein annexin and the cytoplasmic dynein intermediate chain protein. In the other species, these two genes are adjacent, but in D. melanogaster they are separated by ten copies of a hybrid gene. The hybrid gene consists of a portion of the annexin gene combined with a portion of the dynein gene. The hybrid gene has a function — it produces a protein used in dynein in the sperm axoneme. A portion of the hybrid gene acts as a promoter, permitting regulation of the gene's activity. It is not known whether the new gene is essential, or how it functions. The appearance of the new gene can be explained by a series of duplications and deletions. Some intronic sequences were included in the functional portion of the hybrid gene. This explanation contrasts with widely held views of how genes evolve. First, the promoter region did not "evolve," it appeared fortuitously in a single step. Second, regulatory and coding sequences were not conserved, but a new regulatory sequence formed from a previous coding sequence, while a new coding region formed from a previous intronic sequence. Third, similarities among the promoter sequences of the genes involved are not due to common ancestry, but are of independent origin.

Assuming this interpretation is correct, this is a remarkable discovery. Evidence that a complex series of mutations may be preserved and produce new functional sequences may help creationists explain how species could change rapidly in a much shorter time span than commonly thought. Although it is stretching the point to call the hybrid gene a new gene, the production of newly functional sequences through apparently random mutations does seem to fly in the face of some probability arguments used by creationists to reject evolutionary claims. The bottom line may be that the genome contains many surprises for everyone. --- Finkel SE, Kolter R. 1999. Evolution of microbial diversity during prolonged starvation. Proceedings of the National Academy of Sciences (USA) 96:4023-4027.

Cultures of Escherichia coli were incubated for more than a year without adding nutrients or removing bacteria, leading to starvation conditions. Comparison of bacterial samples showed that different mutants arose in different cultures, despite identical culture conditions. Rapid changes in DNA sequence were detected even after several months of incubation. As no single mutant strain took over a culture completely, genetic diversity was always present.

Apparently, genetic variability is not lost during starvation conditions. Other experiments indicate that stress conditions may stimulate mechanisms that produce genetic variation. Maintenance of high levels of genetic variability may make it possible for species to change rapidly. --- Papadopoulos D, Schneider D, Meier-Eiss J, Arber W, Lenski RE, Blot M. 1999. Genomic evolution during a 10,000 generation experiment with bacteria. Proceedings of the National Academy of Sciences (USA) 96:3807-3812.

Twelve populations of the bacterium E. coli were established from a single common ancestor. For two populations, samples were chosen at intervals and analyzed for mutations using restriction enzymes. The other 10 populations were not analyzed until generation 10,000. Numerous mutant strains were detected. Some strains increased in number, then disappeared as new strains appeared. The phylogeny has the shape of a single trunk, with all branches attenuated. Most detected mutations were probably due to transpositions and chromosomal rearrangements rather than to point mutations. At the end of 10,000 generations, nearly every sample had a unique genotype. These results show that the bacterial genome undergoes significant changes over relatively short time spans. Many creationists believe that biodiversity has increased significantly in a relatively short time, which suggests that genomic changes may occur rapidly. This experiment supports that idea, although it is uncertain whether conclusions drawn from bacterial genomes can be applied to genomes of multicellular animals. --- Cronn RC, Small RL, Wendel JF. 1999. Duplicated genes evolve independently after polyploid formation in cotton. Proceedings of the National Academy of Sciences (USA) 96:14406-14411.

Current evolutionary theory predicts that new genes may arise when genes are duplicated, producing extra gene copies that are free to mutate and evolve new functions. Alternatively, the extra gene copies may degenerate into functionless pseudogenes. A third possibility is that each of the gene copies may continue to function as before the duplication event. The relative frequency of these various fates is unknown. Polyploidy produces extra copies of every gene in the genome. Polyploids may form when two slightly different species hybridize. This has happened in cotton, and the ancestral species have been identified. Sixteen genes were studied in the polyploid cotton and its ancestral species. In nearly all the comparisons, the duplicated copies continued their original function. Although the gene sequences had diverged, there was no evidence that the rate of divergence was affected by the presence of duplicated gene copies. A high rate of divergence has been previously reported among duplicated highly repetitive DNA sequences, but there are no such reports from duplicated nuclear genes.

These results do not support the theory that gene duplication accelerates the process of pseudogene formation and evolution of new gene functions. Further studies are needed to see how widely these results apply. --- Visscher PM, Smith D, Hall SJG, Williams JA. 2001. A viable herd of genetically uniform cattle. Nature 409:303.

Inbreeding is generally considered harmful, due to accumulation of deleterious alleles. However, if inbreeding were combined with selection, deleterious alleles might be purged. Support for this idea comes from the Chillingham cattle, a feral herd of some 49 individuals living in a park in northern England. This herd is thought to have been isolated for at least 300 years, and is almost genetically uniform. The Chillingham cattle might provide a model for study of the bovine genome and the genetics of disease resistance.

This example suggests that inbreeding would not be harmful in a world without deleterious mutations. Small population sizes, such as after the creation or after the Biblical flood, would not necessarily cause genetic deterioration leading to extinction.

I this enough? lol I still have to go through the post-2001 material, but all of that is on PDF. So I can't copy and paste it here.--Nlawrence 21:18, 16 November 2007 (EST)


 * I am still looking for some journal work that is pro-neodarwinism.

Rucas's edits on EvoWiki
''Should we add a rebuttal to Rucas's edits on EvoWiki? This would be a excellent example of the double handed tactics used by EvoWiki.--Nlawrence 18:04, 19 January 2008 (EST)''


 * No. Personally I dont think he was an imposter - just someone who has a problem working under authority. Its a problem we've had before. Because the CW is open to public editing, people seem to think they should be able to do anything they want.


 * Note that he (Rolloffle) was doing the same thing at EvoWiki. He edited the CreationWiki article yesterday and the day before, re-deleting page content twice more after it was restored by administrators. Thats the same thing that originally got him into trouble on the CW.


 * Now of course he's banned for undermining the CW on EvoWiki (whether its permanent or not is up to him). --Mr. Ashcraft - (talk) 18:24, 19 January 2008 (EST)

Hey
Hey. I have started a website and we can use it for MATCH. Its called creationsciencegroup. It is at creationsciencegroup.freehostia.com. E-mail me if you would like a user account. With it, you can submit articles or papers of your own, submit news, use the project center or a developement wiki. Let me know.--Tylerdemerchant 15:20, 3 March 2008 (PST)

suggestion for project
Remember a awhile back when I tried starting an Index of New Age Claims? If you give me permission, I would like to start one now since the New Age article has been written.--Nlawrence 11:10, 23 April 2008 (PDT)


 * Fine by me, but the New Age article is far from written. Its just a stub.

--Mr. Ashcraft - (talk) 19:55, 23 April 2008 (PDT)

Criticisms
Such a criticism is blatantly false and does not deserve a formal response from us, and should not be given advertisement on our site. In addition, titles containing CreationWiki are likely to be called up as a secondary to the main page in search engine results, and therfore, should be used with great reservation and cleared by the admin. I'll want to delete that page. --Mr. Ashcraft - (talk) 02:40, 1 May 2008 (UTC)

Copyright violation
This article - John Whitmore - contains text that was copied verbatim from another site in violation of U.S. copyright law. While there is public domain and GNU licensed text on the web that may be used to help build articles, the use of copyright material is not permitted. --Ashcraft - (talk) 00:08, 1 December 2008 (UTC)

Journal lists
A common title scheme should be used for the lists - that is all lowercase/singular as per convention. I would propose something like the following - with Creation in secular publication being the leading or main menu page.


 * Creation in secular journal (biology)
 * Creation in secular journal (cosmology)
 * Creation in secular journal (geology)

Limiting the lists to a single topic may be best - and you may want to consider broadening the individual page titles to "publication" rather than only "journal". You can then create separate journal/magazine headings....

--Ashcraft - (talk) 22:13, 4 December 2008 (UTC)

''reply on journal lists I'm am happy to see that you have an interest in my newest project. I don't know how to rename pages, so can you do it please? I should stress that the biology article should not renamed intelligent design. It is more inclusive to just call it biology. Also, cosmology and physics should remain together. --Nlawrence 03:28, 5 December 2008 (UTC)''


 * OK - I renamed the 3 lists I could find to the above titles, and added a link to the main "secular publications" page in the resource navbox.


 * BTW - the publications in each list should be alphabetized by author name. Also - instead of numbering each item - use the number sign instead ( # ) that way the numbers will automatically update with any new addition.


 * Good job - they make excellent resources...

--Ashcraft - (talk) 18:49, 7 December 2008 (UTC)

Discussion
CreationWiki:Discussion: ''The CreationWiki is not a discussion forum or bulletin board and we discourage our editorial staff from using it as such. The discussion pages are only to be used for CreationWiki article reviews or other topics specifically related to CreationWiki content.''


 * You appear to have redirected discussion away from a topical page to a usertalk page. Discussion not specifically related to a CreationWiki article or content should be done on an appropriate discussion forum like OriginsTalk.

--Ashcraft - (talk) 15:57, 16 December 2008 (UTC)