kyrani99 wrote:

Rumraket wrote:

Shrunk wrote:I don't think so. What he seems to be saying is that this mutation does not qualify as "new information", according to a definition of "new information" that remains mysterious and unspecified.

Well, as I've asked creationists now for about 8 years:

Define: New. Give a rigorous measure of "newness".

For example, if a gene is duplicated and mutations happen in the duplicate, is it then new?

How many mutations must happen in that gene for it to be "new"? 2% of the sequence, 10%, 100% ? Why is that new?

Answer all of these questions and explain why those are the correct answers. Be the first creationist in history to do so.

Newness would be a set of genetic change, which give a new property or function to a cell in a short period of time, say in a day or two.

I don't think that newness simply means any change but specific changes that encodes in the gene new information that is useful.

I haven't seen fully specialized cells develop new genes, but stem cells and I surmise that there were genetic changes because of the new appearances and functions as dense barrier cells (medically called cancer).
The cells I observed (using insight meditation - Vipassana) were in my ovary and bowel in the first instances. And in later stages I found the process is reversible. I cannot see down to subcellular level very well but I saw the new cells reverted back to the appearance before the changes and the new properties, such as opaque appearance, vanished.

Cai et al, 2008 wrote:Origination of new genes is an important mechanism generating genetic novelties during the evolution of an organism. Processes of creating new genes using preexisting genes as the raw materials are well characterized, such as exon shuffling, gene duplication, retroposition, gene fusion, and fission. However, the process of how a new gene is de novo created from noncoding sequence is largely unknown. On the basis of genome comparison among yeast species, we have identified a newde novo protein-coding gene, BSC4 in Saccharomyces cerevisiae. The BSC4 gene has an open reading frame (ORF) encoding a 132-aminoacid-long peptide, while there is no homologous ORF in all the sequenced genomes of other fungal species, including its closely related species such as S. paradoxus and S. mikatae. The functional protein-coding feature of the BSC4 gene in S. cerevisiae[/]i is supported by population genetics, expression, proteomics, and synthetic lethal data. The evidence suggests that [i]BSC4 may be involved in the DNA repair pathway during the stationary phase of S. cerevisiae and contribute to the robustness of [/i]S. cerevisiae[/i], when shifted to a nutrient-poor environment. Because the corresponding noncoding sequences in S. paradoxus, S. mikatae, and S. bayanus also transcribe, we propose that a new de novo protein-coding gene may have evolved from a previously expressed noncoding sequence.

Cai et al, 2008 wrote:THE total number of different proteins in all organisms on earth is estimated to be 1010–1012 (Choi and Kim 2006). How the protein repertoire evolved to this giant diversity that underlies the evolution of the complexity of life is the basis of attracting many evolutionary biologists to the field. Discussions began 40 years ago (Perutz et al. 1965); however, with the accomplishment of complete genome sequences, we have begun to get a more comprehensive view of this complex issue. Comparative genomic study supports the notion that novel protein genes derive from preexisting genes or parts of them. For example, exon shuffling, gene duplication, retroposition, and gene fusion and fission all contribute to the origin of new genes (Long et al. 2003). But the de novo gene origination process that a whole protein-coding gene evolves from a fragment of noncoding sequence is considered seldom and receives little attention. A computational analysis of several archeal and proteobacterial species’ genomes suggests that at least 240 and 320 genes, respectively, originated de novo along the branches leading to the Archea and Proteobacteria. Furthermore, there are also many de novo origination events among the species within each of the lineages (Snel et al. 2002). On the basis of the analysis, the author ranked the de novo gene origination process quantitatively the second most important process after gene loss among gene loss, de novo origination, gene duplication, gene fusion/fission, and horizontal gene transfer. This study suggests that de novo evolution not only plays an important role in generating the initial common ancestral protein repertoire but also contributes to the subsequent evolution of an organism. However, it is nearly impossible to identify the noncoding origin of the initial ancestral proteins because of long-term accumulation of mutations. Recently evolved novel protein-coding genes provide us the opportunity to investigate the de novo evolution mechanism of protein-coding genes. This methodology on gene origination has been developed in Drosophila by Long et al. (Long and Langley 1993), which has led to many advances in understanding the mechanism of new gene origination, including gene duplication, retroposition, exon shuffling, and gene fission and fusion (Nurminsky et al. 1998; Wang et al. 2002, 2004; Arguello et al. 2006; Yang et al. 2008). However, only recently did Begun et al. (2006, 2007), Levine et al. (2006), and S. T. Chen et al. (2007) find cases of whole-gene de novo origination in Drosophila melanogaster, D. yakuba, and D. erecta. The de novo genes may be functional on the basis of the RNA expression analysis, although the protein-coding potential of those de novo ORFs still needs to be proven.

Cai et al, 2008 wrote:In this study, we identified a novel protein-coding gene BSC4 that completely evolved from a noncoding sequence in S. cerevisiae. This gene first caught our attention as a species-specific protein-coding gene in our genome comparison analysis among Saccharomyces species (H.-F. Jiang and W. Wang, unpublished data). Previously the BSC4 gene was found as one of the stop codon readthrough genes in baker’s yeast by Namy et al. (2003). They found that BSC4 has a typical readthrough nucleotide context around its stop codon and its readthrough frequency is 9% when cloned into a plasmid with reporter genes (Namy et al. 2003). Although the BSC4 gene has been included in many large-scale studies, no specific study has been done with an aim to characterize it. The Saccharomyces Genome Database (SGD) (http://www.yeastgenome.org/) curates dozens of data sets, most of which were carried out using the gene chips of S. cerevisiae. In all the gene chips there are probes designed against the BSC4 gene along with other genes in S. cerevisiae. These data sets provide much expression information for BSC4 under different culture conditions. This gene was also included in the systematic gene deletion project in which ORFs of yeast genes were deleted and subsequent phenotypic analyses were carried out on those derived gene deletion strains (Saccharomyces Genome Deletion Project, http://wwwsequence.stanford.edu/group/y ... ions3.html). On the basis of the panel of those gene deletion strains, whole-genome synthetic lethal analyses were carried out by Pan et al. (2006) that deleted two genes to see if that would be lethal to S. cerevisiae. Their result shows that deletion of gene DUN1 or RPN4 is lethal to S. cerevisiae if BSC4 is also deleted (Pan et al. 2006). In addition, there are multiple tandem mass-spectrometry analysis results of yeast protein samples deposited into the ‘‘Peptide Atlas’’ (http://www.peptideatlas.org/repository). Our analysis of these proteomics data supports the existence of the BSC4-coded peptides and our population genetic analysis suggests that the ORF of this novel protein-coding gene is under strong negative selection at the nonsynonymous sites. Our expression data show that its orthologous noncoding sequences have detectable expression at the RNA level, across the closely related species of baker’s yeast. On the basis of these data, we suggest that a novel protein gene can wholly evolve from a noncoding sequence.

Cai et al, 2008 wrote:RESULTS

Origin of the de novo gene BSC4: BSC4 is a S. cerevisiae gene, which has an ORF of 132 amino acids, and with no apparent similarity to any previously characterized protein. BSC4 has no significant homolog when we used tBLASTN to search against genome sequences of S. bayanus, S. kudriavzevii, S. mikatae, and S. paradoxus under the standard parameters. Even if we use the putative translation product of the stop codon bypass event predicted by Namy et al. (2003), which is a peptide of 237 amino acids, there is still no significant homolog in these sibling species. The absence of homolog might be the false negative result due to incompleteness of the genomic databases of those species. However, the multiple-species search makes this possibility less likely, and the genome databases of Saccharomyces species are widely considered as the most reliable compared with genome databases of other species. These results suggest that BSC4 may be a newly evolved gene in S. cerevisiae. To further rule out possible spurious results caused by sequencing gaps in the outgroups, we conducted a genomic Southern blot with the probe designed against BSC4. The southern blot result shows that only the S. cerevisiae genome exhibits obvious hybridization signals (Figure 1). We also carried out a further tBLASTN search against genome sequences of other fungal species to exclude the probability of multiple-gene loss in the four outgroup species. The results showed that this ORF has no homolog in any other fungal species. However, the origination mechanism still remains to be clarified until we find its ancestral sequence because horizontal gene transfer or high divergence of sequences can both explain the above results.

In addition to sequence similarity, the chromosomal context–synteny relationship is another important piece of information for identification of gene relationships. A pair of sequence fragments in two related species can be supposed to be in orthologous relationship if they have weak homology and their flanking genes are in orthologous status, when they do not have BLAST hits of a higher score in other regions of the genome. The Synteny Viewer on the Saccharomyces Genome Database website indicates that the flanking genes of BSC4 have their orthologs in the same synteny blocks of S. bayanus, S. mikatae, and S. paradoxus (Kellis et al. 2003). We cut the intergenic region between the two flanking genes and manually aligned them with BSC4 of S. cerevisiae (Figure 2). Because S. kudriavzevii is not covered in the Synteny Viewer on the Saccharomyces Genome Database website, we did not include it in Figure 2, although we also found by genome comparison that the synteny relationship of the locus in this species is also conserved (data not shown). The alignment shows that there are tracts of homologous sequences and the overall identity across those four Saccharomyces species is 35.71%. Data on the UCSC genome browser also indicate the same orthologous relationship, which is consistent with our analysis. These orthologous regions in the sibling species of S. cerevisiae have very low probability to code for proteins even if we consider stop codon readthrough in those species, because of the existence of a number of premature stop codons (supplemental Figure 1).

The flanking genes of BSC4 in the S. cerevisiae genome, ALP1 and LYP1, are a pair of paralogs lined in an inverted direction. This gene order also remains conserved in the more distant yeast genomes of Ashbya gossypii, Kluyveromyces lactis, and S. castelli beyond Saccharomyces sensu stricto complex species (Figure 3). In addition, the length of this intergenic region does not change much across all those species (713 bp in A. gossypii and 889 bp in S. cerevisiae). From these results, we can make an estimate that the origin of the BSC4 ancestral sequence can be dated back at least to the last common ancestor of A. gossypii and S. cerevisiae, i.e., .100 million years ago (Dietrich et al. 2004) when an inverted gene duplication event formed the syntenic orthologs flanking the ancestor of BSC4. However, only after the divergence from S. paradoxus the ancestral noncoding sequence evolved into a protein-coding gene in S. cerevisiae. On the basis of these pieces of evidence, it is very likely that this is a real de novo origination case with clearly defined lineage.