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Author Topic:   Are mutations truly random or are they guided?
Wounded King
Member
Posts: 4149
From: Cincinnati, Ohio, USA
Joined: 04-09-2003


Message 44 of 134 (548751)
03-01-2010 3:19 PM
Reply to: Message 40 by Species8472
03-01-2010 2:44 PM


A much better analogue for those 'commented out' bits of code would be pseudogenes. These are what appear to be copies of genes that have mutated in such a way as to become non-functional, or at least to have lost their original function.
An analogue for your habit of reusing code would be the conserved binding domains which turn up in very diverse families of proteins, such as the homeodomain (HOX), the paired box domain (PAX), Zinc Finger domains and many others. There are molecular mechanisms which allow these domains, or modules of more than one of these domains, to be swapped between proteins with distinct functional domains to produce novel combinations of binding and functional domains.
A neutral mutation is more like if you changed the way the code was typed but not its functionality, for a bash example it is like changing ' if test $i -ge 10' into 'if [ $i -ge 10 ]'.
TTFN,
WK

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


Message 48 of 134 (548758)
03-01-2010 4:17 PM
Reply to: Message 42 by slevesque
03-01-2010 3:09 PM


Re: Neutral mutations
And also since the vast majority of mutations are only slightly deleterious
This has of course long been the received wisdom, but there is actually some doubt as to whether it actually holds up. There is experimental evolution research on mutation accumulation which suggests that in fact the rate of slightly deleterious mutations is only around 10% of all mutations and that most mutational load is caused by larger effect mutations which are much more easily removed by selection (Eyre-Walker et al., 2002). Looking at almost any paper with Adam Eyre-Walker or Peter Keightley on will reveal interesting research into the natural and frequency of deleterious and beneficial mutations.
TTFN,
WK

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


Message 64 of 134 (548783)
03-01-2010 7:27 PM
Reply to: Message 53 by slevesque
03-01-2010 4:40 PM


Re: Neutral mutations
This would mean that of all the mutations I have from my parents, only 10% are slightly deleterious and the rest are detectable by selection ?
Obviously it doesn't mean this at all, for the reasons that Dr. A went into, some of those mutations will be genuinely neutral and some may be slightly beneficial, others will have larger effects on fitness and will be suitable targets for selection.
As to how natural selection will ever sort them, once again you are following the same song sheet as Smooth Operator in the other thread. Has no one in the ID/Creationist camp ever looked into basic genetics? Things like genetic recombination and the effects of sexual reproduction? That is how nature sorts them out, random assortment allowing the segregation of few or many deleterious mutations to one chromosome, and at a higher level amongst genomes, where they may be more prone to selection due to the cumulative or combinatorial effects of the deleterious mutations (Keightley and Otto, 2006).
TTFN,
WK

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


Message 82 of 134 (548927)
03-02-2010 2:53 PM
Reply to: Message 79 by AZPaul3
03-02-2010 2:04 PM


Re: Neutral mutations
What Taq is saying is that RNA polymerases, the proteins which bind to DNA and make mRNA from the DNA template, have specific patterns of DNA which they recognise and bind to when transcription is initiated. These proteins don't have a 100% perfect ability to bind only to those exact sequences so they may well bind to sequences which happen to be similar in other non biologically functional regions of the genome and transcribe that sequence into mRNA, even though the resulting mRNA serves no purpose.
This seems reasonable, but I would also add another factor which is that many transcription factor binding motifs are comparatively simple, like the common TATA box with the sequence TATAAA. So rather than the potentially non functional transcripts being the result of non-specific binding they are rather the result of binding to specific sequences which simply occur by chance in the genome in some cases.
TTFN,
WK

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


Message 111 of 134 (549126)
03-04-2010 7:50 AM
Reply to: Message 108 by RAZD
03-03-2010 11:35 PM


Cairnsian Adaptive mutation and Paper availability
There is no doubt that there are stress induced mechanisms that increase mutation rates, but there is little or no evidence of the sort of specific targeting that Cairns' model hypothesised.
With regard to Herebedragons problem with the availability of the primary literature, one big advantage in recent years to the lay person with an interest is the increasing availability of Open Access publications of high quality research such as PLOS and the BioMedCentral publications. Along with this many traditional journals are now making their articles Open Access after a given period of time.
Two examples of open access material dealing with adaptive mutation are a review of various forms of stress induced mutatgenesis (Foster, 2007), and some recent primary research on how a specific form of stress can lead to adaptive mutations when one major element of one of the most common stress induced mutational pathways is knocked out (Stoebel et al., 2009).
The Entrez database has a whole collection of searchable Open Access articles known as 'Pubmed Central'. So while access to any specifc article on a topic may be a problem there is certainly a good chance you will be able to find many papers on a topic available under some sort of Open Access.
TTFN,
WK

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


Message 133 of 134 (550992)
03-20-2010 5:44 AM
Reply to: Message 132 by kalimero
03-20-2010 4:41 AM


Re: Guided mutations
This is true but as you suggest the existence of somatic hypermutation in immune cells no more shows a role for guided mutation causing evolution than the epigenetic changes which lead to lineage differentiation in development show a role for Lamarckian mechanisms in evolution.
It is also important to bear in mind that while somatic hypermutation is restricted to specific regions the actual mutations and rearrangements themselves are still essentially random, especially with regard to the immunological challenges they are going to face. Somatic hypermutation is not targeted in such a way as to respond to a specific immunological challenge, it depends on the generation of vast amounts of random variation followed by selection to find suitable antibodies.
It is definitely worth noting though that where such a guided mechanism exists it has been identified and characterised, unlike the cryptic mechanisms of guidance so many ID supporters postulate.
TTFN,
WK
Edited by Wounded King, : No reason given.

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