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Author Topic:   Does the Darwinian theory require modification or replacement?
Dr Adequate
Member (Idle past 284 days)
Posts: 16113
Joined: 07-20-2006


Message 721 of 760 (623386)
07-09-2011 9:52 PM
Reply to: Message 720 by Wounded King
07-09-2011 5:59 PM


Re: Definition of Evolution
For instance it wouldn't cover the intial events in an endosymbiosis such as that which led to the mitochondria ...
Well, it might; e.g. if the original relationship was parasitic and evolved to be endosymbiotic. But if endosymbiosis just happened one day, then it's not clear that we would want that event to be covered under the rubric of "evolution".
---
Suppose I discover that one of the weeds in my garden tastes nice. I start watering it to encourage it to grow leaves which I will then eat. At the moment I first water it, the plant and I have entered into a symbiotic relationship. But has any evolution occurred? It has not.
... it would only pertain when the genomes began interacting to enforce the symbiotic relationship ...
I think we can live with that.
Edited by Dr Adequate, : No reason given.

This message is a reply to:
 Message 720 by Wounded King, posted 07-09-2011 5:59 PM Wounded King has not replied

Replies to this message:
 Message 722 by zi ko, posted 07-10-2011 9:56 AM Dr Adequate has not replied

zi ko
Member (Idle past 3619 days)
Posts: 578
Joined: 01-18-2011


Message 722 of 760 (623425)
07-10-2011 9:56 AM
Reply to: Message 721 by Dr Adequate
07-09-2011 9:52 PM


Re: Definition of Evolution
... it would only pertain when the genomes began interacting to enforce the symbiotic relationship ...
Ithink this interacting means information flow from parasite to the host. Doesn't it lead to my theory based om information?
Edited by zi ko, : No reason given.

Information: It is time its undeservedly neglectet powerful role to evolution to be restored.

This message is a reply to:
 Message 721 by Dr Adequate, posted 07-09-2011 9:52 PM Dr Adequate has not replied

Replies to this message:
 Message 723 by Percy, posted 07-10-2011 10:35 AM zi ko has replied

Percy
Member
Posts: 22392
From: New Hampshire
Joined: 12-23-2000
Member Rating: 5.2


Message 723 of 760 (623427)
07-10-2011 10:35 AM
Reply to: Message 722 by zi ko
07-10-2011 9:56 AM


Re: Definition of Evolution
zi ko writes:
Ithink this interacting means information flow from parasite to the host. Doesn't it lead to my information theory?
You have an idea in your head that you think is information theory, but you do not yourself have an information theory, and you haven't yet acquainted yourself with the information theory used by people in that field, the one initiated by Claude Shannon.
--Percy
Edited by Percy, : Typo.

This message is a reply to:
 Message 722 by zi ko, posted 07-10-2011 9:56 AM zi ko has replied

Replies to this message:
 Message 724 by zi ko, posted 07-10-2011 2:33 PM Percy has replied

zi ko
Member (Idle past 3619 days)
Posts: 578
Joined: 01-18-2011


Message 724 of 760 (623439)
07-10-2011 2:33 PM
Reply to: Message 723 by Percy
07-10-2011 10:35 AM


Re: Definition of Evolution
Percy writes:
zi ko writes:
Ithink this interacting means information flow from parasite to the host. Doesn't it lead to my information theory?
You have an idea in your head that you think is information theory, but you do not yourself have an information theory, and you haven't yet acquainted yourself with the information theory used by people in that field, the one initiated by Claude Shannon.
You are right. I didn't know about Shannon and his theory. I think it is entirely different thing. Idont call my theory information theory , but theory of evolution based on information.
Edited by zi ko, : No reason given.

Information: It is time its undeservedly neglectet powerful role to evolution to be restored.

This message is a reply to:
 Message 723 by Percy, posted 07-10-2011 10:35 AM Percy has replied

Replies to this message:
 Message 725 by Wounded King, posted 07-10-2011 3:08 PM zi ko has replied
 Message 726 by Percy, posted 07-10-2011 6:17 PM zi ko has not replied

Wounded King
Member
Posts: 4149
From: Cincinnati, Ohio, USA
Joined: 04-09-2003


Message 725 of 760 (623445)
07-10-2011 3:08 PM
Reply to: Message 724 by zi ko
07-10-2011 2:33 PM


Zi Ko's definition of information
I think you should coherently define information for us or just stop posting here. At the moment you are in three different threads promoting exactly the same nonsense.
TTFN,
WK

This message is a reply to:
 Message 724 by zi ko, posted 07-10-2011 2:33 PM zi ko has replied

Replies to this message:
 Message 730 by zi ko, posted 07-16-2011 11:14 AM Wounded King has not replied

Percy
Member
Posts: 22392
From: New Hampshire
Joined: 12-23-2000
Member Rating: 5.2


Message 726 of 760 (623466)
07-10-2011 6:17 PM
Reply to: Message 724 by zi ko
07-10-2011 2:33 PM


Re: Definition of Evolution
zi ko writes:
I think it is entirely different thing. Idont call my theory information theory , but theory of evolution based on information.
I was going to suggest that you propose a new thread. Then I read WK's message, and he has noticed that you're trying to shift discussion onto this topic in three different threads, so now I think that proposing a new thread is an even better idea. You can do that over in Proposed New Topics.
--Percy

This message is a reply to:
 Message 724 by zi ko, posted 07-10-2011 2:33 PM zi ko has not replied

Replies to this message:
 Message 727 by Wounded King, posted 07-10-2011 6:35 PM Percy has replied

Wounded King
Member
Posts: 4149
From: Cincinnati, Ohio, USA
Joined: 04-09-2003


Message 727 of 760 (623468)
07-10-2011 6:35 PM
Reply to: Message 726 by Percy
07-10-2011 6:17 PM


Re: Definition of Evolution
For heaven's sake Percy, at least one of those threads is one he specifically opened to discuss Information's role in evolution.Should we put it more in the picture?. The last thing we need is for him to open up yet another one for exactly the same topic! Perhaps instead the moderators could reccommend he confine his theories to just one of the 2 threads, the other being New theory about evolution between creationism and evolution., he already has specifically to discuss them.
TTFN,
WK

This message is a reply to:
 Message 726 by Percy, posted 07-10-2011 6:17 PM Percy has replied

Replies to this message:
 Message 728 by Percy, posted 07-10-2011 7:39 PM Wounded King has not replied

Percy
Member
Posts: 22392
From: New Hampshire
Joined: 12-23-2000
Member Rating: 5.2


Message 728 of 760 (623473)
07-10-2011 7:39 PM
Reply to: Message 727 by Wounded King
07-10-2011 6:35 PM


Re: Definition of Evolution
Sorry, I researched it as much as I had time for.
--Percy

This message is a reply to:
 Message 727 by Wounded King, posted 07-10-2011 6:35 PM Wounded King has not replied

Taq
Member
Posts: 9972
Joined: 03-06-2009
Member Rating: 5.6


Message 729 of 760 (623494)
07-11-2011 12:28 AM
Reply to: Message 713 by shadow71
07-08-2011 4:09 PM


Re: Natural Engineering
NO I was discussing possible new discoveries in the CRISPR System.
You mean discoveries that have not been made yet?
If I was a prosecuting attorney, could I convict someone on the claim that I will find evidence in the future?
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.
And I have already addressed this multiple times. Retroviral insertions will produce neutral, beneficial, and detrimental mutations. Inserting upstream of genes, even with a slight bias, does not guarantee that they will be beneficial. Therefore, retroviral insertions are random with respect to fitness in line with the Modern Synthesis.
Also Barbara Wright's paper that both I and Ziko cited discusses directed, non-random mutations for fitness.
And I have discussed one of Wright's papers with you where I demonstrated that the mutations Wright references are in fact random with respect to fitness. I believe it was this paper. I would be happy to go through this paper again with both you and zi ko if you would like.

This message is a reply to:
 Message 713 by shadow71, posted 07-08-2011 4:09 PM shadow71 has not replied

zi ko
Member (Idle past 3619 days)
Posts: 578
Joined: 01-18-2011


Message 730 of 760 (624167)
07-16-2011 11:14 AM
Reply to: Message 725 by Wounded King
07-10-2011 3:08 PM


Re: Zi Ko's definition of information
I think you should coherently define information for us or just stop posting here. At the moment you are in three different threads promoting exactly the same nonsense.
You can find more about information in my provisional work: (http://www.sleepgadgetabs.com)

This message is a reply to:
 Message 725 by Wounded King, posted 07-10-2011 3:08 PM Wounded King has not replied

Replies to this message:
 Message 731 by Percy, posted 07-17-2011 6:32 AM zi ko has replied
 Message 737 by zi ko, posted 07-22-2011 3:24 PM zi ko has not replied

Percy
Member
Posts: 22392
From: New Hampshire
Joined: 12-23-2000
Member Rating: 5.2


Message 731 of 760 (624300)
07-17-2011 6:32 AM
Reply to: Message 730 by zi ko
07-16-2011 11:14 AM


Re: Zi Ko's definition of information
You don't define information here, and when requested to do so you refer us to your webpage where you also don't define information.
Just as here, you're still confusing information with knowledge.
Why can't you just use Shannon information?
--Percy

This message is a reply to:
 Message 730 by zi ko, posted 07-16-2011 11:14 AM zi ko has replied

Replies to this message:
 Message 732 by zi ko, posted 07-17-2011 9:50 AM Percy has replied

zi ko
Member (Idle past 3619 days)
Posts: 578
Joined: 01-18-2011


Message 732 of 760 (624326)
07-17-2011 9:50 AM
Reply to: Message 731 by Percy
07-17-2011 6:32 AM


Re: Zi Ko's definition of information
I can't understand what Shannon says. To me information is what the senses bring in from outside or inside word. Knowledge is the understanding of meaning of what senses bring in.

This message is a reply to:
 Message 731 by Percy, posted 07-17-2011 6:32 AM Percy has replied

Replies to this message:
 Message 733 by Larni, posted 07-17-2011 12:59 PM zi ko has not replied
 Message 734 by Percy, posted 07-17-2011 9:06 PM zi ko has replied

Larni
Member (Idle past 164 days)
Posts: 4000
From: Liverpool
Joined: 09-16-2005


Message 733 of 760 (624345)
07-17-2011 12:59 PM
Reply to: Message 732 by zi ko
07-17-2011 9:50 AM


Re: Zi Ko's definition of information
To me information is what the senses bring in from outside or inside word.
What you are talking about is perception, not information.

This message is a reply to:
 Message 732 by zi ko, posted 07-17-2011 9:50 AM zi ko has not replied

Percy
Member
Posts: 22392
From: New Hampshire
Joined: 12-23-2000
Member Rating: 5.2


Message 734 of 760 (624431)
07-17-2011 9:06 PM
Reply to: Message 732 by zi ko
07-17-2011 9:50 AM


Re: Zi Ko's definition of information
zi ko writes:
To me information is what the senses bring in from outside or inside word.
Yes, that's correct, but everything in the universe is exchanging information with everything else all the time, not just with our senses. Light brings information, whether it strikes a leaf or an eye. Sound brings information, whether it causes vibration in a champagne glass or an eardrum. Fumes bring information, whether they react with curing meat or your nose.
Shannon information isn't hard to understand. If you understand binary then you can understand Shannon information. If you needed to transmit one of 4 different digits to someone (0, 1, 2, 3), how many binary bits would it take? If you know the answer to that question then you can understand Shannon information.
--Percy

This message is a reply to:
 Message 732 by zi ko, posted 07-17-2011 9:50 AM zi ko has replied

Replies to this message:
 Message 738 by zi ko, posted 07-22-2011 3:46 PM Percy has replied

shadow71
Member (Idle past 2934 days)
Posts: 706
From: Joliet, il, USA
Joined: 08-31-2010


Message 735 of 760 (625117)
07-21-2011 1:22 PM
Reply to: Message 714 by Wounded King
07-08-2011 5:12 PM


Re: Natural Engineering
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 immune
system 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-guided
adaptive 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 show
that 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 expand
in 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 complex
from 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.

This message is a reply to:
 Message 714 by Wounded King, posted 07-08-2011 5:12 PM Wounded King has replied

Replies to this message:
 Message 736 by Wounded King, posted 07-21-2011 1:50 PM shadow71 has not replied

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