Controlled Pathways
by BradfordTelicmeme posted Life's toolkits at his blog Teleomechanist. The blog entry references quotes about stem cells and arrives at this comment:
So stem cells have a built-in toolkit that responds to random changes, enabling then to respond to changes in their environment in a systematic and controlled way, ultimately leading to just a few endpoints. The toolkit harnesses random variation and selection to reach the same destination. The stem cells are front-loaded (provided with a toolkit) to develop along a certain path while harnessing random variation and selection.
He then cites an immunological function that entails induced mutations of the DNA of B lymphocytes and makes this comment:
B lymphocytes have a toolkit that regulates mutations for the purpose of generating antibodies. Thus, here we have another toolkit that harnesses random variation and selection to intentionally generate variety for the purpose of producing novel antibodies.
How many more toolkits that harness quantum randomness and selection to generate controlled variety will we discover?
More than we anticipate I suspect.
August 16th, 2008 at 11:15 am
Thanks for this heads-up, Bradford. A very interesting overview by Telicmeme. But I've gotta tell you, it doesn't look to me like the DD die-hards are smart enough to follow this sort of evidence for front-loading, self organization, and self-imposed constraints on the direction evolution takes and the constructs it can achieve.
The most compelling lure of NDS pablum is that it's… pablum. Soft, easy-to-digest mush that claims to explain literally everything while actually explaining nothing. "RM-NS did it" is just as much an intellectually stifling pronouncement as "God did it." The more you look into how and with what the more things look to be designed with tight constraints. While the random damage end starts looking more like "what goes wrong" in violation of those constraints.
So long as biology can't tell the difference between what goes right and what goes wrong (NDS insists it's the same process either way), evolutionary theory isn't going to help us out much in learning to mitigate what goes wrong. Thus isn't very useful as anything but ideological 'orthodoxy'. Humanity has had too many of those already. It didn't need another.
Comment by Joy — August 16, 2008 @ 11:15 am
August 16th, 2008 at 12:33 pm
Joy:
Yes, but curiously an alternative is suggested by the critics themselves albeit unintentionally. When I bring up origins issues it becomes clear that random mutations cannot suffice as the initial cause of a chain of events. So critics are willing to resort to alternatives when backed up against the wall.
Constraints are largely ignored because they don't bode well for standard interpretations. Samsen brought that matter to our attention and there will be follow-ups.
Comment by Bradford — August 16, 2008 @ 12:33 pm
August 16th, 2008 at 2:00 pm
Interesting post, Bradford.
Comment by Bilbo — August 16, 2008 @ 2:00 pm
August 16th, 2008 at 2:05 pm
Bilbo:
Thanks, but the credit goes to an interesting guy- Telicmeme.
Comment by Bradford — August 16, 2008 @ 2:05 pm
August 19th, 2008 at 11:11 am
Joy, in the Open Thread (where I'm banned):
Nope, [3] refers to a Science paper. Also, anybody even slightly familiar with Nature journals knows that a 'letter' therein is a peer-reviewed research paper.
Comment by Raevmo — August 19, 2008 @ 11:11 am
August 19th, 2008 at 12:37 pm
Raevmo:
Cool.
Did they do knockout humans, Raevmo? They obviously didn't do knockout mice, since the knockout mice that were done demonstrated that their conclusion is erroneous.
I have no doubt these things duly pass muster with the orthodoxen posing as gatekeepers today. What I've said is that real experimental evidence contradicts the assumption from theory, and that evidence cannot be waved away with the assertion of more assumption from theory. That isn't how science works. Didn't they teach you that in school?
Comment by Joy — August 19, 2008 @ 12:37 pm
August 19th, 2008 at 1:02 pm
Joy:
Forgive for me taking your lectures on science with several enormous grains of salt, you being an uneducated amateur and all.
As pointed out repeatedly by myself, by Zachriel, and last but not least by the authors of the knockout paper themselves, their experiment does not rule out selection except in the most extreme form. For example, 16 mice were used to detect effects on longevity, while statistical theory guarantees us that hundreds of mice are needed to detect even a 10% difference in mortality rate, 10% being more than enough to conserve a DNA sequence.
Other independent studies indicate that selection is responsible (e.g., Drake et al. 2006, Conserved noncoding sequences are selectively constrained and not mutation cold spots, Nature Genetics 38, 223-227).
Having said that, I fully expect that you will continue to claim that the knockout paper has falsified NS, per your usual MO.
Comment by Raevmo — August 19, 2008 @ 1:02 pm
August 19th, 2008 at 1:49 pm
Raevmo:
Um… can you define the term "ultraselection," Raevmo? Do you know the parts of the genome to which this assumption has been applied as theoretical prediction? Are you able to understand what has been falsified by this excellent scientific work?
No one here argues that selection doesn't shape the landscape of evolution. It is simply hypothesized that because selection doesn't create anything, the actual raw material of evolution are the genomes, expression profiles/phenomes and reproductive fitness of organisms. Whole living systems, which are selected or not selected as whole organisms in the game of change over generational time. Individual stretches of DNA are not selected on this basis, the organism in which it functions is (or is not) selected.
The notion of "ultraselection" holds for those elements of the genome that the organism cannot live (or reproduce) without. You know this as well as I do (or, by your own measure, should know it better than I do). Absolute fidelity in elements of DNA close to coding elements that are observably 'normal' in their accumulation of SNPs and such mutations indicates that something is maintaining those elements perfectly. There are three possibilities that NDS could tolerate -
1. Ultraselection. As with DNA associated with things so vital as ribosomes, the organism without these – or with disabling mutations in these – will never be born, will never reproduce, can never be a playa in the evolution game.
2. Mutational Cold Spots. Despite proximity to 'normally' mutating coding or expression elements, the ultraconserved elements experience NO mutations. Perhaps the Yin to mutational hot spots' Yang.
3. Absolute Repair. Perhaps some epigenetic mechanism that focuses intense DNA conservation measures to these particular elements (but not others).
What's your favorite?
I have never claimed NS has been (or ever could be) falsified, Raevmo. Despite your personal dislike of me, I know you can refrain from lying if you really try. It won't hurt, I promise.
Comment by Joy — August 19, 2008 @ 1:49 pm
August 19th, 2008 at 2:25 pm
Joy,
But individual stretches do get selected, for example as transposable elements. Interestingly, many ultraconserved sequences seem related to such jumping genes (see, e.g., Pennisi 2007, Science 317: 894-895.)
Your #1 is wrong, as pointed out before, but you just keep repeating it like a broken record. Again, it doesn't require such extreme selection to conserve a sequence. For example, ten percent reduced viability will do the job just fine.
Numbers 2 and 3 are possibilities, but so far there is no evidence for them, unlike selection (see paper I referred to before). There might be more possibilities, like extreme horizontal transfer.
Comment by Raevmo — August 19, 2008 @ 2:25 pm
August 19th, 2008 at 5:42 pm
Hi Bradford,
Thanks for the airtime.
Cytosine deamination, controlled variation and the immunological functions are nicely linked and analogous systems in unicellular organisms can be found. Should be interesting to see research on DNA replication, gene expression, and variation and how it is linked to epigenetic factors. And why not simulate a front-loaded state to see if a cyberpspace intelligence can evolve. Maybe it will solve the "number 42" question?
Comment by Telicmeme — August 19, 2008 @ 5:42 pm
August 19th, 2008 at 6:36 pm
Raevmo:
I saw an allusion to that somewhere recently, sounds intriguing. Can you give me the gist?
No, that's the existing prediction that's been demonstrated wrong in this case. The authors describe it quite well as "widely believed," I think.
Do tell. I like X-Games almost as well as I like Vaudeville. Describe this 100% successful (for 80+ million years) maneuver for me, please!
Comment by Joy — August 19, 2008 @ 6:36 pm
August 19th, 2008 at 7:13 pm
From Pennisi 2007:
Joy:
The authors would say that to make their findings sound more impressive. The fact is that their findings only rule out short-term extreme selection. I'm getting tired of repeating this, and I won't do it again.
Comment by Raevmo — August 19, 2008 @ 7:13 pm
August 19th, 2008 at 7:21 pm
Raevmo:
What is the difference between ultra-selection and extreme- selection?
From webster
extreme
a: existing in a very high degree
ultra:
: going beyond others or beyond due limit : extreme
Peace
Comment by fifth monarchy man — August 19, 2008 @ 7:21 pm
August 19th, 2008 at 10:08 pm
This thread looks thoroughly derailed. I see Telicmeme weighed in.
Telicmeme:
You're welcome. I'm trying to get you a syndicated show.
Cytosine deamination is a topic near and dear to Mike's heart if I recall. Controlled varaition has an unmistakable telic ring to it.
METers tell us that if it replicates it evolves. Doe that apply to cyber viruses?
Comment by Bradford — August 19, 2008 @ 10:08 pm
August 19th, 2008 at 11:46 pm
Bradford:
I apologize for my part in derailment, I kinda hoped there's a segue from controlled pathways to ultraconservation of non-coding DNA. It just kerfluffles me that these people would defend assertions after they've been demonstrated erroneous. It's entirely understandable if they hadn't heard about the falsification. It's just garbage when they try to pretend the falsification isn't what it demonstrably *is*.
Sorry. I know better than to waste time on Raevmo.
Comment by Joy — August 19, 2008 @ 11:46 pm
August 20th, 2008 at 12:07 am
Not a problem Joy. In the future though if I'm not around and you think commenters are abusing a thread I started take whatever action you believe is appropriate. I trust your judgement.
Comment by Bradford — August 20, 2008 @ 12:07 am