Creationists still trying to debunk Lenski's LTEE.

... and failing.

Incl. intelligent design, belief in divine creation

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Creationists still trying to debunk Lenski's LTEE.

#1  Postby Shrunk » Feb 22, 2016 4:31 pm

Scott Minnich of the Discovery Institute has published an article in the Journal of Bacteriology that takes issue with the findings of Richard Lenski's E. coli experiment and, specifically, makes the claim that Lenski's group has failed to demonstrate that evolutionary processes can produce "new genetic information." (Any red flags going up yet?)

Lenski himself has written a response on his blog:

The authors assert repeatedly (last sentence of their Importance statement, and first and last paragraphs of their Discussion) that “no new genetic information evolved.” However, that statement flatly contradicts the fact that in their experiments, and ours, E. coli gained the new ability to grow on citrate in the presence of oxygen. We would further add (which we have not emphasized before) that these Cit+ strains can grow on citrate as a sole carbon source—when E. coli grows anaerobically on citrate, it requires a second substrate for growth in order to use the citrate (a phenomenon called “co-metabolism”).

The claim that “no new genetic information evolved” is based on the fact that the bacteria gained this new ability by rearranging existing structural and regulatory genetic elements. But that’s like saying a new book—say, Darwin’s Origin of Species when it first appeared in 1859—contains no new information, because the text has the same old letters and words that are found in other books.

In an evolutionary context, a genome encodes not just proteins and patterns of expression, but information about the environments where an organism’s ancestors have lived and how to survive and reproduce in those environments by having useful proteins, expressing them under appropriate conditions (but not others), and so on. So when natural selection—that is, differential survival and reproduction—favors bacteria whose genomes have mutations that enable them to grow on citrate, those mutations most certainly provide new and useful information to the bacteria.

That’s how evolution works—it’s not as though new genes and functions somehow appear out of thin air. As the bacterial geneticist and Nobel laureate François Jacob wrote (Science, 1977): “[N]atural selection does not work as an engineer works. It works like a tinkerer—a tinkerer who does not know exactly what he is going to produce but uses whatever he finds around him, whether it be pieces of string, fragments of wood, or old cardboards; in short, it works like a tinkerer who uses everything at his disposal to produce some kind of workable object.”

To say there’s no new genetic information when a new function has evolved (or even when an existing function has improved) is a red herring that is promulgated by the opponents of evolutionary science. In this regard, it seems relevant to point out that the corresponding author, Scott Minnich, is a fellow of the Discovery Institute and was an expert witness for the losing side that wanted to allow the teaching of “intelligent design” as an alternative to evolution in public schools in the landmark Kitzmiller v. Dover case....


Silly creationists.
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Re: Creationists still trying to debunk Lenski's LTEE.

#2  Postby Shrunk » Feb 22, 2016 4:35 pm

If you want an illustration of the term non-sequitur, you could do worse than this passage under the heading "Importance" in Minnich's article:

E. coli cannot use citrate aerobically. Long term evolution experiments (LTEE) by Lenski found a single aerobic, citrate-utilizing E. coli after 33,000 generations (15 years). This is interpreted as a speciation event. Here we show why it probably is not. Using similar media, 46 independent citrate-utilizing mutants were isolated in as few as 12 to 100 generations. Genomic DNA sequencing revealed an amplification of the citT and dctA loci and DNA rearrangements to capture a promoter to express CitT, aerobically. These are the same class of mutations identified by the LTEE. We conclude the rarity of the LTEE mutant was an artifact of the experimental conditions, not a unique evolutionary event.


:eh:
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Re: Creationists still trying to debunk Lenski's LTEE.

#3  Postby Onyx8 » Feb 22, 2016 5:10 pm

So it happened but it's not rare so it doesn't count? What?
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Re: Creationists still trying to debunk Lenski's LTEE.

#4  Postby Blackadder » Feb 22, 2016 6:00 pm

Liars for Jesus keep coming back for punishment from proper scientists and keep having their arses handed to them on a platter. Sad fucks.
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Re: Creationists still trying to debunk Lenski's LTEE.

#5  Postby Shrunk » Feb 22, 2016 6:10 pm

But just watch: This will be cited by creationists for years to come as an example of "ID research" that was published in the peer reviewed literature.
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Re: Creationists still trying to debunk Lenski's LTEE.

#6  Postby tolman » Feb 25, 2016 1:59 am

On the other hand, creationists do seem to be living embodiments of survival while producing no new information over several generations.
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Re: Creationists still trying to debunk Lenski's LTEE.

#7  Postby Animavore » Feb 25, 2016 8:01 am

They couldn't debunk an IKEA bed set.
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Re: Creationists still trying to debunk Lenski's LTEE.

#8  Postby felltoearth » Feb 25, 2016 1:17 pm

Sorry about my ignorance but is Minnich saying "yeah, its a mutation but its not a *real* mutation?"
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Re: Creationists still trying to debunk Lenski's LTEE.

#9  Postby Shrunk » Feb 25, 2016 4:47 pm

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. :dunno:

Biologos actually has a very fulsome discussion of Michael Behe's attempts, which seem related to Minnich's, to hand wave away the results of Lenski's work:

http://biologos.org/blogs/dennis-venema ... -evolution
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Re: Creationists still trying to debunk Lenski's LTEE.

#10  Postby Rumraket » Feb 26, 2016 10:16 am

Onyx8 wrote:So it happened but it's not rare so it doesn't count? What?

Yeah that doesn't make sense to me either.

Evolution in our direct-selection for certain outcomes experiments is faster than evolution without direct selection, also in some of our experiments the mutation happened within a few days, in others it still took a few months, therefore your evolution experiment without deliberate selection for certain outcomes is not good evidence for evolution.

W... w... wat? :crazy:
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Re: Creationists still trying to debunk Lenski's LTEE.

#11  Postby Rumraket » Feb 26, 2016 10:19 am

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. :dunno:

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.


Never recieved an answer. Most don't bother to even try and obfuscate, immediately after me asking this question I'm simply ignored.

In a thread on Larry Moran's blog where I ask the question, a creationist answers me by copy-pasting the answer given by an evolutionary biologist to a question about what constitutes a functional novelty, which is ironic both because itøs irrelevant to the creationist claim about informational novelty, but also apparently not knowing that by using the definition given by evolutionary biologists and applying it to information, he's fucking up his own case. Seriously. :picard:
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Re: Creationists still trying to debunk Lenski's LTEE.

#12  Postby Fuxino » Feb 27, 2016 9:48 am

Creationists misrepresenting science and getting their arses kicked by actual scientists. Nothing new here. :P
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Re: Creationists still trying to debunk Lenski's LTEE.

#13  Postby GenesForLife » Mar 06, 2016 11:49 pm

I laugh at any creationist who things rearrangements/copy number information is not meaningful, biologically because cancers are full of them, and guess what, a lot of them are under selective pressure, and actually *do stuff* in cancer cells.
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Re: Creationists still trying to debunk Lenski's LTEE.

#14  Postby kyrani99 » Mar 10, 2016 3:56 pm

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. :dunno:

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.
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Re: Creationists still trying to debunk Lenski's LTEE.

#15  Postby Shrunk » Mar 10, 2016 4:10 pm

:eh:
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Re: Creationists still trying to debunk Lenski's LTEE.

#16  Postby Calilasseia » Mar 10, 2016 4:30 pm

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. :dunno:

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.


Actually, de novo gene origination has been documented frequently in the scientific literature. Viz:

De Novo Origination Of A New Protein-Coding Gene In Saccharomyces cerevisiae by Jing Cai, Ruoping Zhao, Huifeng Jiang and Wen Wang, Genetics, 179: 487-496 (May 2008) [full paper downloadable from here]

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.


The paper continues with:

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.


In more detail:

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.


The authors cite their results thus:

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.


So, we have hard scientific evidence for the de novo origination of protein-coding genes. The above paper isn't the only one by the way. Other appropriate papers on de novo gene origination include:

Extensive De Novo Genomic Variation In Rice Introduced By Introgression From Wild Rice (Zizania latifolia Griseb.) by Yong-Ming Wang, Zhen-Ying dong, Zhoing-Juan Zhang, Xiu-Yun Lin, Ye Shen, Daowei Zhou and Bao Liu, Genetics, 170: 1945-1956 (August 2005) [full paper downloadable from here]

Novel Genes Derived From Noncoding DNA In Drosophila melanogaster Are Frequently X-Linked And Exhibit Testis-based Expression by Mia T. Levine, Corbin D. Jones, Andrew D. Kern, Heather A. Lindfors and David J. Begun, Proceedings of the National Academy of Sciences of the USA, 103(26): 9935-9939 (27th June 2006) [full paper downloadable from here]

Evidence For De Novo Evolution Of Testis-Expressed Genes In The Drosophila yakuba/Drosophila erecta Clade by David J. Begun, Heather A. Lindfors, Andrew D. Kern and Corbin D. Jones, Genetics, 176: 1131-1137 (June 2007) [full paper downloadable from here]

Evolution Of Enzymes For The Metabolism Of New Chemical Inputs Into The Environment by Lawrence P. Wackett, Journal of Biological Chemistry, 279(40): 41259-41264 (1st October 2004) [full paper downloadable from here]

Evolution Of Hydra, A Recently Evolved Testis-Expressed Gene With Nine Alternative First Exons In Drosophila melanogaster by Shou-Tao Chen, Hsin-Chien Cheng, Daniel A. Barbash and Hsiao-Pei Yang, PLoS Genetics, 3(7): 1131-1143 (July 2007) [full paper downloadable from her]

Recently Evolved Genes Identified From Drosophila yakuba And D. erecta Accessory Gland Expressed Sequence Tags by David J. Begun, Heather A. Lindfors, Melissa E. Thompson and Alisha K. Holloway, Genetics, 172: 1675-1681 (March 2006) [full paper downloadable from here]

Also, this article may prove useful.

Incidentally, I covered the Wackett paper on new enzymes cited above in more detail in this post over at the old Richard Dawkins website.
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Re: Creationists still trying to debunk Lenski's LTEE.

#17  Postby kyrani99 » Mar 10, 2016 6:01 pm

Hi Calilasseia and thank you for those papers and links. I'll start reading them soon.

I can't get anything from the Richard Dawkins site (I get a 404) probably because I was banned forever from his site for discussing my finding with cancer and saying that they were not consistent with evolutionary theory on the "Disproving Intelligent Design with a mouse trap" thread. I didn't see that I said anything offensive but they got very upset. The put a public warning notice on the thread and sent me an email without any prior warning that I was banned forever.

I am a theist but not a Christian (I believe Jesus was a prophet and I see a lot of corruption in the Bible). I believe that some sort of creationism takes place but so far I haven't seen anything that convinces me. However I don't agree with evolutionary theory.

Am I right to say these de novo gene origination are part of the dynamic genome as first seen and described by the American cytogeneticist Barbra McClintock? These are the sort of changes that I believe are involved in cancer.
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Re: Creationists still trying to debunk Lenski's LTEE.

#18  Postby Rumraket » Mar 10, 2016 6:54 pm

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. :dunno:

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.

You can't use the word you are trying to define in your definition of that word.

You are trying to define 'new', that means you can't change it from new information to new function. What makes it NEW ? What property of "newness" makes it new instead of same?

Try to answer the specific example I have with gene duplication and subsequent accumulation of mutations. Make it universally applicable within the context of biological information.

If you are going to define 'new information' terms of function, then you must also supply a criterion for delineating functions from each other. At what point does one function become different enough from another function to qualify as 'new'?
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Re: Creationists still trying to debunk Lenski's LTEE.

#19  Postby Shrunk » Mar 10, 2016 6:58 pm

Silly! If we actually see something arise, and God didn't do it, then it's obviously not "new", since only God can create "new" things. QED.
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Re: Creationists still trying to debunk Lenski's LTEE.

#20  Postby Calilasseia » Mar 10, 2016 7:07 pm

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