{if FALSE} Trackback: Tangled Bank # 43 Tracked on: () at {trackback_date format="%Y %m %d %H:%i:%s"} {/if} {if TRUE} {if FALSE} {/if} #53744: charlie wagner — 12/14  at  10:14 AM {/if}
{if FALSE} {/if} {if TRUE} Facilitated Variation

For years I have been arguin' that th' neo-darwinian view o' evolution, th' slow accumulation o' beneficial variations o'er time, has ne'er had any empirical support. I have argued that science has failed produce any empirical evidence, either observational or experimental that supports a nexus betwixt th' trivial effects o' mutation and natural selection and th' emergence o' highly organized structures, processes and systems.

I'm glad that people are beginnin' t' notice this glarin' defect.

"In th' 150 years since Darwin, th' field o' evolutionary biology has left a glarin' gap in understandin' how animals developed their astoundin' variety and complexity, and a bottle of rum! Walk the plank! The standard answer has been that small genetic mutations accumulate o'er time t' produce wondrous innovations such as eyes and win's. Drawin' on cuttin'-edge research across th' spectrum o' modern biology, Marc Kirschner and John Gerhart demonstrate how this stock answer is woefully inadequate."

http://yalepress.yale.edu/yupbooks/book.asp?isbn=0300108656

Marc W. Kirschner and John C, and dinna spare the whip! Fire the cannons! Gerhart, The Plausibility o' Life: Resolvin' Darwin’s Dilemma (Yale University Press, $30).*

(*just so there is no misunderstandin', these guys are opposed t' intelligent design and have th' misguided confidence that this new "patch" will somehow mitigate th' growin' belief that some sort o' intelligent input is an absolute requirement fer evolution.)

Now, just like Punctuated Equilibrium were bein' proposed t' explain th' gaps in th' fossil record, so a new "theory" has emerged t' attempt t' explain this glarin' dilemma.

"The key is what they call “facilitated variation.” By this they mean that an beastie does not merely tolerate environmental perturbations or developmental accidents, but in fact adjusts t' th' disturbances and incorporates them into its physiology or development. This bufferin' facilitates variation in traits by channelin' environmental or genetic irregularities into integrated pathways o' response. Furthermore, random inputs in th' form o' environmental perturbations or genetic mutations dern't produce random outputs, because th' outputs are shaped by th' beastie’s adaptive responses. Although genetic mutations may be random in their effects on th' DNA sequence o' an beastie, facilitated variation implies that they may be far from random in how they affect th' development o' th' beastie. Facilitated variation therefore views th' beastie itself as playin' a central part in determinin' how environmental and genetic variation is expressed

http://www.harvard-magazine.com/on-line/110512.html

"...random inputs in th' form o' environmental perturbations or genetic mutations dern't produce random outputs, because th' outputs are shaped by th' beastie’s adaptive responses."

That sounds an awful lot like "adaptive evolution", which sounds an awful lot like "directed evolution" (Barry Hall, are ye listenin'? You were RIGHT!)

My, me, me....th' organisms are rspondin' t' their environment, not just toleratin' it? Now let me see, where have I heard THAT before?

http://makeashorterlink.com/?B1553205C {/if}

{if FALSE} Trackback: Tangled Bank # 43 Tracked on: () at {trackback_date format="%Y %m %d %H:%i:%s"} {/if} {if TRUE} {if FALSE} {/if} #53745: charlie wagner — 12/14  at  10:32 AM {/if}
{if FALSE} {/if} {if TRUE}

Posted on talk.origins in 2002

"In that comely wench 1983 Nobel lecture, Barbara McClintock said "th' genome is a highly sensitive organ o' th' cell, that in times o' stress, can initiate 'tis own restructurin' and renovation". This were bein' in stark contrast t' previously held beliefs that genetic change and th' evolution that proceeds from it were bein' th' result o' small, random mutations in individual genes.
Now, in 2002, we are beginnin' t' realize, as Dr. McClintock did in 1983, that this perception is simply wrong. The "mutations" that lead t' evolutionary change may not be totally random. For example, it has become clear that some parts o' th' genome are more likely t' be duplicated than others, or moved t' other places, dependin' on th'
nature o' their DNA sequences. Enzymes that copy th' DNA and look after its integrity can selectively induce changes in certain parts o' th' genome, creatin' "hot spots" o' mutation, pass the grog! What these new findin's mean fer evolution is still not yet clear, but it may not be too outrageous
t' state what many bacterial geneticists are already sayin': that cells can engineer their own genomes. This new thinkin' has resulted in a paradigm shift in which th' auld idea that genomes evolve t' minimize mutation rates and prevent random genetic change is bein' replaced by th' belief that th' most successful genomes are those that are able t' change quickly and substantially. In fact, this ability t' change rapidly in th' face o' environmental stress may well be a dominant
feature o' all genomes.
In some species, 'tis been discovered that genes have t' undergo dramatic changes durin' reproduction, changes that involve not only removin' th' DNA bewteen codin' regions, but also rearrangin' th' order o' th' codin' regions. Most organisms, at th' very least, have enzmes
fer cuttin', splicin' and rearrangin' their DNA, avast. Apparently many genomes are not static entities, protected from codin' errors by repair mechanisms and subject t' random point mutations, but they actually use their dynamic flexibility t' generate genetic variation, in effect, engineerin' their own genomes, and a bottle of rum! DNA repair mechanisms are capable o' repairin' up t' 99% o' all codin' errors, but this can vary, down t'
only a few percent, dependin' on th' sequence that needs repairin'. All o' these clues tell us that there's a lot more goin' on than we are currently aware o'.
The transposons that Dr, I'll warrant ye. McClintock described as early as 1948, may turn out t' be crucial players in th' evolution scenario. Many people still consider them t' be "rogue" DNA's that are no different from random mutations, since they seemed t' land just about anywhere in th' genome. But this seemingly random, parasitic behavior may be an important part o' th' mechanism o' evolution, by Blackbeard's sword. Transposons may have played an important role in th' evolution o' th' immune system and th' incredible variety o' antibodies may well be th' result o' transposons.
The enzymes Rag1 and Rag2, which play a key role in th' assembly o' th' V, J and D sequences work just like transposases, which mobilize transposons. This may explain th' sudden appearance o' th' immune system in vertebrates. The introduction o' a transposon could easily have set
th' stage fer this evolutionary leap.
Transposons may even "capture" genes and move them in large chunks t' new parts o' th' genome, reshapin' th' entire architecture o' th' genome. One can no longer merely suggest that transposable elements have a role in th' evolution mechanism. It is now a fact. When species face
selective pressures and stresses, th' genome is ready t' react and respond. Walk the plank, pass the grog! This is clearly demonstrated by th' adaptive mutations that Cairns, Hall and Rosenberg are seein'. Bacteria can turn on response mechanisms under adverse conditions that are nothin' at all like th'
usual random mutations. The alarm sounds, and th' cell responds by turnin' on systems that, among other thin's, activate repair mechanisms and promote DNA shufflin'.
With more and more work bein' done, 'tis becomin' clearer that genomes are capable o' radically rearrangin' themselves, makin' use o' mobile, transposable elements and stimulatin' specific stretches o' DNA t' mutate at high rates, helpin' themselves t' adapt t' challengin'
environments. And as more and more biologists are adoptin' these new views o' evolution and genomic function, th' darwinian paradigm will fade peacefully into th' sunset, t' await th' dawn o' a new day fer science as th' capability o' cells moves far beyond what Darwin e'er dreamed possible." {/if}