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Member (Idle past 2961 days) Posts: 706 From: Joliet, il, USA Joined: |
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Author | Topic: Does the Darwinian theory require modification or replacement? | |||||||||||||||||||||
shadow71 Member (Idle past 2961 days) Posts: 706 From: Joliet, il, USA Joined: |
Shadow71 writes:
Do you disagree with the findings that the CRISPR System discussed in the paper is dedicated, nonrandom and beneficial If someone would ANSWER the question I would not have to repeat it.There seems to be on this board scientists who refuse to acknowledge scientific findings that go against the grain of evolutionary dogma of today. Let me rephrase. Does the modern evolutionary theory accept findings of "mutations that are dedicated, nonrandom and beneficial?
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shadow71 Member (Idle past 2961 days) Posts: 706 From: Joliet, il, USA Joined: |
Taq writes:
So you admit that there is no known mechanism for directed mutations outside of CRISPR domains? NO I was discussing possible new discoveries in the CRISPR System. Shapiro has already discussed, even on this board, his findings in his 2010 paper (biasing retrovirus insertion upstream of coding regions) that are non-random with respect to their potential biological utility.CRISPR seem to be a continuation of these discovries. Also Barbara Wright's paper that both I and Ziko cited discusses directed, non-random mutations for fitness. So this area of evolutionary mechanisms is opening quite nicely.
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shadow71 Member (Idle past 2961 days) Posts: 706 From: Joliet, il, USA Joined: |
I have been meditating on my OP and I really need a good definition of evolution. As many have pointed out on this board, my referals to the MS, Darwin's theory, the modern theory have been not as explicit as they should be.
So as I read the posts and papers etc. it appears that evolution as defined today contains many aspects that were not usually cited when I began my reading on evolution. Here is a definition I came across on the web. Would like your thoughts on this so it can be determined if in fact the OP can be correctely addressed. Here is the definition of Laurence Moran. Taking these ideas into account I propose the following definition; Biological evolution is the process of change in the geneticmakeup of a population. This definition is necessary and sufficient (IMHO). Laurence A. Moran (Larry)Dept. of Biochemistry University of Toronto
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shadow71 Member (Idle past 2961 days) Posts: 706 From: Joliet, il, USA Joined: |
Dr Adequate writes:
That seems reasonable. To which one might add: the theory of evolution is the set of known mechanisms by which evolution takes place. Darwinism might then be defined as the theory of evolution plus the principle of common descent. It would be nicer to have a better word than "Darwinism", but it'll have to do. Thanks Dr A.
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shadow71 Member (Idle past 2961 days) Posts: 706 From: Joliet, il, USA Joined: |
Percy writes:
It's ironic that the very next message is you once again quoting someone. Instead of you polling us over and over again about whether we agree with this quote or that quote, perhaps you could present evidence and argument supporting the quote and then discuss the answers. Don't get so bent out of shape Percy. Just wanted to clarify something for myself.Dr. Adequate helped me with his reply. So now I am rereading papers on CRISPR System and will reply to WK and your responses.
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shadow71 Member (Idle past 2961 days) Posts: 706 From: Joliet, il, USA Joined: |
Wounded King writes:
think I have made a reasonable case that the choice of sequences incorporated is not non-random in any meaningful sense, beyond perhaps a variable specificity for certain common motifs occurring hundreds of times even in the small genomes of bacteriophages. I think this paper disagrees with your opinion; "RNA-guided complex from a bacterial immunesystem enhances target recognition through seed sequence interactions" Blake Wiedenhefta,b, Esther van Duijnc,1, Jelle Bultemad,1, Sakharam Waghmaree,1, Kaihong Zhoua,1, Arjan Barendregtc,Wiebke Westphalb, Albert Heckc, Egbert Boekemad, Mark Dickmane, and Jennifer A. Doudnaa,b,f,g,2 aHoward Hughes Medical Institute; bDepartment of Molecular and Cell Biology, University of California, Berkeley, CA 94720; fPhysical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720; Department of Chemistry, University of California, Berkeley, CA 94720; gDepartment of Chemistry, University of California, Berkeley, CA 94720; cBiomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research, Utrecht Institute for Pharmaceutical Sciences, and The Netherlands Proteomics Center, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands; dElectron Microscopy Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands; and eDepartment of Chemical and Biological Engineering, ChELSI Institute, University of Sheffield, Mappin Street, Sheffield S1 3JD, United Kingdom Contributed by Jennifer A. Doudna, February 24, 2011 (sent for review January 5, 2011) In the abstract they write; Prokaryotes have evolved multiple versions of an RNA-guidedadaptive immune system that targets foreign nucleic acids. In each case, transcripts derived from clustered regularly interspaced short palindromic repeats (CRISPRs) are thought to selectively target invading phage and plasmids in a sequence-specific process involving a variable cassette of CRISPR-associated (cas) genes. and; Here we showthat the Csy proteins (Csy1C4) assemble into a 350 kDa ribonucleoprotein complex that facilitates target recognition by enhancing sequence-specific hybridization between the CRISPR RNA and complementary target sequences. Target recognition is enthalpically driven and localized to a seed sequence at the 5 end of the CRISPR RNA spacer. and; These repetitive elements rapidly expandin response to phage challenge by site-specifically integrating short fragments of the foreign DNA at one end of the evolving CRISPR (3C5). CRISPR adaptation results in sequence-specific resistance to genetic parasites containing a complementary sequence. and; Here we report the discovery of a CRISPR-associated complexfrom the PA14 strain of P. aeruginosa. The complex is composed of a unique set of proteins, which have previously been shown to be exclusive to and conserved in the Csy subfamily (CRISPR system yersinia) of CRISPR-mediated immune systems (7, 9). We show that this complex participates in target recognition by facilitating sequence-specific hybridization between the crRNA and complementary targets. Similar to mRNA recognition by Argonaute proteins during RNA interference (RNAi) in eukar- yotes, CRISPR target selection is governed by a seed sequence at the 5 end of the crRNA spacer. Although comprised of distinct proteins, the stoichiometry and the morphology of the Csy complex resemble the architecture of the Cascade complex from E. coli. These findings suggest that large CRISPR-associated ribonucleoproteins mediate surveillance and target recognition in diverse CRISPR-mediated immune systems. Also Shapiro in his book "Evolution a view from the 21st century"wrote aboult the famous Luria-Delbruck fluctation test that purported to prove that infection could not induce resistance. In fact Shapiro states that what Luria and Delbruck: " demonstrated was that mutations conferring resistance to a virus that is invariably lethal immediately upon infection do occur prior to selection. They never could disprove the operation of a CRISPR or other infection-triggered resistance mechanism for other viruses, such as temperate bacteriophages. The incorporation of fragments from invading DNA elements for the purpose of self-defense (the CRISPR system has been described as a genomic immune system is a precise example of the kind of dedicated, nonrandom, beneficial change specifically excluded by generations of evolutionary theorists." In the Kafginov paper http:http://www.ncbi.nih.gov/pmc/articles/PMC2819186/ The authors wrote; Thus, during the acquisition of a defensive repertoire, the CRISPR machinery appears to select sequences from the phage genome and incorporate these as novel spacers (Fig. 2B). The selection is not random. Instead, sequence motifs can be detected in proximity to those regions that ultimately become part of the CRISPR, termed proto-spacers. Analysis of spacers newly added to the CRISPR1 locus of independently selected S. thermophilus phage-insensitive mutants identified a short motif (NNAGAAW) directly downstream of the proto-spacer in the phage genome (Deveau et al., 2008). A similar motif was independently observed by Bolotin and colleagues (Bolotin et al., 2005). Interestingly, spacers from CRISPR3, a locus with some divergence from CRISPR1, showed a different downstream motif, NGGNG, near proto-spacers (Horvath et al., 2008). In S. mutans, one CRISPR locus displayed a preference for a short motif 3′ of the proto-spacer, while another CRISPR locus favored a 5′-adjacent motif (van der Ploeg, 2009). Similarly, three different CRISPR families in the archaeal Sulfolobales have distinct 5′ proto-spacer adjacent motifs (PAMs) (Lillestol et al., 2009). Like the repeat and leader sequences, distinct PAMs correspond to specific CRISPR/cas subtypes (see the section on CRISPR/cas co-evolution below). This suggests that spacer acquisition is driven by recognition of phage sequences by subtype-specific proteins in different species (Mojica et al., 2009). However, it also implies that when an individual species harbors multiple CRISPR loci from different subtypes, these represent distinct and compartmentalized resistance systems. In addition to its suggested role in spacer selection, the PAM also appears to be important at the effector stage of defense, since phage can evade resistance to a particular spacer by mutating this nearby motif (Deveau et al., 2008). And at p.13 However, armed with knowledge of the molecular basis of this response, CRISPR-cas does seem to fit more firmly with a Lamarckian paradigm, in essence because increases in fitness do not rely on random mutations but on a much more specific acquisition of genetic information from environmental sources. Based on what I have read I believe it shows that the CRISPR System is nonrandom for fitness.
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shadow71 Member (Idle past 2961 days) Posts: 706 From: Joliet, il, USA Joined: |
I am reading Ernst Mayr's book "What evolution Is" 2001, and he states in the conclusion of chapt 7 p. 157 Adaptedness and Natural Selection: Anagensis:
"Genetic material (nucleic acids) is constant and impervious to any influence from the environment. No genetic information can be transmitted from proteins to nucleic acids, and so the inheritance of acquired characters is therefdore impossible. This provides an absolute refutation of all Lamarckian theories of evolution. The Darwinian model of evolution, based on random variation and natural selection, explains satisfactorily all phenomena of evolutionary change at the species level, and in particular adaptation." This to me seems to be statement that the "Central Dogma" is in fact correct and that Shapiro et al. are wrong. Any comments on the accurracy of Mayr's statement? If he is incorrect doesn't this in fact support this thread? "Does the Darwinian theory require modification or replacement?"
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shadow71 Member (Idle past 2961 days) Posts: 706 From: Joliet, il, USA Joined: |
Taq writes:
Not without reading more of the book to understand what he is getting at. Does Mayr deal with transposons, retrotransposons, or the process of mutagenesis at all in the book? He devotes one paragraph to transposable elelments and then suggest the reader confer a genetics textbook for detailed treatment on the manifold manifestations of transposable elements. He does write at p100 "No selectively valuable contributions are known for any of the TEs."
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shadow71 Member (Idle past 2961 days) Posts: 706 From: Joliet, il, USA Joined: |
Taq writes:
From that quote, do you think Mayr is happy with the current Modern Synthesis? yes he seems to be, but is he up to date and correct in that quote? --------------------------------------------------------------------------------
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shadow71 Member (Idle past 2961 days) Posts: 706 From: Joliet, il, USA Joined: |
Malcom writes:
That depends, do you think Shapiro or Wright are suggesting that genetic information is being transmitted from proteins to nucleic acid, and if so can you quote the relevant data? Shapiro sets out the data in this paper. NATURAL GENETIC ENGINEERING AND NATURAL GENOME EDITINGRevisiting the Central Dogma in the 21st Century James A. Shapiro Department of Biochemistry and Molecular Biology, University of Chicago, Gordon Center for Integrative Science, Chicago, IL, USA Edited by AdminModulous, : summaries only now please. content hidden. You can use peek to view contents.
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shadow71 Member (Idle past 2961 days) Posts: 706 From: Joliet, il, USA Joined: |
SUMMATION. DOES THE DARWINIAN THEORY REQUIRE MODIFICATION OR REPLACEMENT?
I have to admit I have failed. The Darwinian theory from Darwin to Neo-Darwinism to the Modern Synthesis are perfectly correct. All who talk about Molecular biology, information exchange in the cells, Genetic changes that are non random and driven by the enviroment, stavation etc. are fools.The Cental Dogma is correct, there is not information exchange from proteins to DNA, RNA, ect. Endosymbiosis Reticulate evolution Evo-Devo Phenotypic Plasticity Gene flow genetic drift Fusion of genomes and gene fragaments methylation of DNA hybridization Polyploidy CRISPS Epigenetics THATS ALL BULLSHIT. As Mayr says Medelian genetics, by proving the constancy of genes, completely contraticts soft inheritance. Finally it was shown by molecular biology that NO INFORMATION CAN BE TRANSMITTED FROM THE PROTEINS OF THE BODY TO THE NUCLEIC ACIDS OF THE GERM CELLS, IN OTHER WORDS, THAT AN INHERITANCE OF ACQUIRED CHARACTERS DOES NOT TAKE PLACE, THIS IS THE CENTRAL DOGMA OF MOLECULAR BIOLOGY. Anyone who argues against this should be drawn and quartered. Let us open minded Darwin believers rest in peace. Let Shapiro and those heretics be banned from the kingdom.Let Nobles et. al. be banned from the Kingdom. We will not take dissent.Nothing is planned. Nothing is directed. All is random, unplanned, and if it were to happen again, it would all be different. Long live Dawkins. Edited by shadow71, : No reason given.
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