Open Thread

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This entry was posted on Saturday, August 16th, 2008 at 11:06 pm and is filed under Random Stuff. You can follow any responses to this entry through the RSS 2.0 feed. You can leave a response, or trackback from your own site. The trackback link is: http://telicthoughts.com/open-thread-4/trackback/

81 Responses to “Open Thread”

Thought Provoker Says:
August 17th, 2008 at 12:30 am
Hi Bradford,

For what it is worth, I'm impressed.

Your last couple of threads focused on science and now and Open Thread.

Since I have often been critical with you, I thought it appropriate to express this positive opinion. I hope it doesn't come across a condensending.

And please don't take my lack of comments on you threads as a sign of a lack of interest. It is more a lack of time.

I thought the Teleomechanist blog was intriguing. Especially his positive and lengthy post on Penrose/Hameroff's Orch OR.

I case anyone is interested, Joy and I had a minor skirmish with the folks over at AtBC. Link

It isn't that interesting, but I felt Joy and I did fairly well and there was even a little evidence of some independent thinking being provoked (see midwifetoad's questions to Oleg).

It's wishful thinking on my part, but I actually hope for more direct dialog between the sides. My compliments to Joy for making the attempt.

Comment by Thought Provoker — August 17, 2008 @ 12:30 am

Doug Says:
August 17th, 2008 at 12:34 am
Chase Ted Thompson out of town.

Comment by Doug — August 17, 2008 @ 12:34 am

Thought Provoker Says:
August 17th, 2008 at 1:30 am
Hi Bradford,

For what it is worth, I'm impressed.

Your recent threads have focus on science and now a Open Thread.

Considering how often I have been critical with you, I felt it appropriate to mention these observations.

Comment by Thought Provoker — August 17, 2008 @ 1:30 am

Bradford Says:
August 17th, 2008 at 11:24 am
TP:

Hi Bradford,

For what it is worth, I'm impressed.

Your last couple of threads focused on science and now and Open Thread.

Since I have often been critical with you, I thought it appropriate to express this positive opinion. I hope it doesn't come across a condensending.

And please don't take my lack of comments on you threads as a sign of a lack of interest. It is more a lack of time.

I thought the Teleomechanist blog was intriguing. Especially his positive and lengthy post on Penrose/Hameroff's Orch OR.

Thanks for the kind words TP. I know you have more interest in posting comments than time allows. I like Telicmeme's writings and hope he shows up at TT in the near future.

Every so often I come across something about Penrose/Hameroff's Orch in the course of looking for something else. I'll have to create a folder and file the links for future use. It generates much interest.

You are a good example of one who can critique while setting the personal attacks aside.

Comment by Bradford — August 17, 2008 @ 11:24 am

Joy Says:
August 17th, 2008 at 1:06 pm
TP:

It isn't that interesting, but I felt Joy and I did fairly well and there was even a little evidence of some independent thinking being provoked (see midwifetoad's questions to Oleg).

Oh, good grief! You may want to fool yourself into believing a gaggle of minor league gangstas are capable of "independent thinking," but don't be attributing any such foolishness to me. My brief appearance was just me busting into their filthy treehouse to yell at them about the trash they threw in the front yard. I've zero tolerance for pasty creeps pitifully trying to make up for substandard man-parts with macho posturing.

I made that point perfectly clear in my LHC post as well. There's no arrogance quite as arrogant as the socially inept who insist no one but themselves is qualified to opine about science – then pretend, as Zach pretended here, that specializing in one branch of science automatically qualifies them to police the gates of all other branches of science on their own authority too.

These are not people who can ever 'win' a culture war. They don't know enough about culture to find the arena with a map. Why you'd waste your time with them is a mystery, but please leave me out of it.

The Swamp is where the teenage hoodlums from II go when they finally get kicked out of their mother's basement. It is not a place for adults.

Comment by Joy — August 17, 2008 @ 1:06 pm

Bradford Says:
August 17th, 2008 at 3:26 pm
Rock, where are you? Tell us more about:

An intense selective regime for any function should reveal the irreducible core of the function. If the concept of a biological function means anything then there must be some irreducible, some definitive statement of what that function is and how it is minimally actualized (materialized).

Comment by Bradford — August 17, 2008 @ 3:26 pm

Thought Provoker Says:
August 17th, 2008 at 3:48 pm
Hi Joy,

Are you trying to spoil my fun?

Yes, I continue my Don Quixote quest of provoking independent thinking.

As to who will win the culture war, I suspect you know my position is that no one will win, just like no one won the culture war waged in Alexandria in 400 AD. (Although Cyril did become “St. Cyril”).

P.S. if this is a duplicate, I am sorry. I have been having trouble posting to TT

Comment by Thought Provoker — August 17, 2008 @ 3:48 pm

Rock Says:
August 17th, 2008 at 8:50 pm
A general purpose RNA-cleaving DNA enzyme
Santoro & Joyce
http://www.pnas.org/content/94...

Schlosser & Li
http://yingfulilab.org/Papers/...

(There are a couple of versions of this paper and I was really thinking of one entitled "Tracing Sequence Diversity," which may be more apropos to what you guys were arguing about. I'm too lazy to look for it.)

See also the hammerhead
http://pubs.acs.org/cgi-bin/ab...

and hairpin

http://www.nature.com/nature/j...

Not quite sure if that's what you may have expected or if it works for you.

Comment by Rock — August 17, 2008 @ 8:50 pm

Rock Says:
August 17th, 2008 at 8:55 pm
Well, that didn't work the first time so let me try again.

Not quite sure if this is what you expected or how it works out for you, but see

A general purpose RNA-cleaving DNA enzyme
Santoro & Joyce
http://www.pnas.org/content/94...

Schlosser & Li
http://yingfulilab.org/Papers/...

(See also "Tracing Sequence Diversity" by the same pair.)

And the hammerhead

http://pubs.acs.org/cgi-bin/ab...

and hairpin

http://www.nature.com/nature/j...

Comment by Rock — August 17, 2008 @ 8:55 pm

Rock Says:
August 17th, 2008 at 8:56 pm
Does this thing work?!

Comment by Rock — August 17, 2008 @ 8:56 pm

Rock Says:
August 17th, 2008 at 8:57 pm
Apparently. Don't know what I'm doing wrong here. Let me try it one step at a time

A general purpose RNA-cleaving DNA enzyme
Santoro & Joyce
http://www.pnas.org/content/94...

Comment by Rock — August 17, 2008 @ 8:57 pm

Rock Says:
August 17th, 2008 at 8:58 pm
Tracing Sequence Diversity
Schlosser & Li
http://yingfulilab.org/Papers/...

Comment by Rock — August 17, 2008 @ 8:58 pm

Rock Says:
August 17th, 2008 at 8:59 pm
See also hammerhead
http://pubs.acs.org/cgi-bin/ab...

Comment by Rock — August 17, 2008 @ 8:59 pm

Rock Says:
August 17th, 2008 at 8:59 pm
and hairpin

http://www.nature.com/nature/j...

Comment by Rock — August 17, 2008 @ 8:59 pm

Rock Says:
August 17th, 2008 at 9:02 pm
LOL They work seperately, but not altogether.

Don't know if that's anything like what you expected or how that's going to work out for you.

I don't have access to all my servers, but I've got "DNA-World" files on this one, so its a bit skewed and maybe not as general as my statement. But I think you'll get the point, which seemed to be one of common knowledge.

Comment by Rock — August 17, 2008 @ 9:02 pm

Thought Provoker Says:
August 17th, 2008 at 9:11 pm
Rock,

I was having trouble posting too.

Comment by Thought Provoker — August 17, 2008 @ 9:11 pm

Bradford Says:
August 17th, 2008 at 9:23 pm
Rock and TP, your comments were caught up in the spam detector for some reason. I even had to liberate my own response to TP. It also got caught.

Comment by Bradford — August 17, 2008 @ 9:23 pm

johnnyb Says:
August 18th, 2008 at 12:22 am
I just recently posted links to some of my current work on the theoretical aspects of the production of variability on my blog. I'd be interested for any reactions. It might even be worth its own discussion.

Comment by johnnyb — August 18, 2008 @ 12:22 am

Alan Fox Says:
August 18th, 2008 at 3:17 am
@ Johnnyb

Bruce Fast's gentle chiding that you have an engineer's take on evolution and are attacking a strawman is worth taking on board. If you are YEC, as your site suggests on a quick perusal, I doubt many will spare you much time.

Comment by Alan Fox — August 18, 2008 @ 3:17 am

johnnyb Says:
August 18th, 2008 at 7:50 am
Alan -

Bruce Fast was agreeing with me – he was just pointing out the futility of arguing with Darwinists. I'm not sure how I'm attacking a straw man – these are general principles of open-ended systems. Please expound.

"If you are YEC, as your site suggests on a quick perusal, I doubt many will spare you much time."

It is true that many are guilty of genetic fallacies, but I don't see how it is relevant to the discussion.

Comment by johnnyb — August 18, 2008 @ 7:50 am

Bradford Says:
August 18th, 2008 at 12:29 pm
johnnyb at UD:

So this is why (in fairly simplistic terms) the production of structures is a bigger problem than most neo-Darwinists realize. If we want the structures to be produceable, then we have to assume that the system is parameterized (as in our first few example systems), and not open-ended (as in our last example system). However, this would mean that the majority of the interesting parts of organisms are actually pre-coded, as well as the lines for which they are variable (the number of lines of variability is probably enormous, but yet it is not open-ended – this would mean that evolution does not increase complexity). Open-ended evolution, however, cannot happen because it requires as its substrate a type of system that is too chaotic to be manipulated ad-hoc, but instead requires coordination of parts to move between functional areas.

Do you see a strawman in there Alan?

Comment by Bradford — August 18, 2008 @ 12:29 pm

Bradford Says:
August 18th, 2008 at 12:41 pm
From a link supplied by Rock:

It is clear that the hammerhead must have a fairly precise sequence requirement for cleavage. All three helices and thirteen conserved nucleotides appear in the seven available natural examples of hammerheads (Forster & Symons, 1987a,b). A limited number of mutagenesis experiments have confirmed the need for complementary base pairs in the helices and for specific nucleotides at several of the single-stranded positions (Sampson et al., 1987; Koizumi et al., 1988, 1989: Sheldon & Symons, 1989; Ruffner et al., 1989). Presumably the essential nucleotides could either participate in tertiary interactions, coordinate catalytically important divalent metal ions, or provide functional groups necessary for activation of the labile bond. The intent of this paper is to systematically determine the sequence requirements of the hammerhead domain by changing each of the nucleotides in the conserved or semiconserved positions of the hammerhead to each of the other nucleotides and examining their activity.

It looks as if IC can be empirically determined does it not?

Comment by Bradford — August 18, 2008 @ 12:41 pm

Rock Says:
August 18th, 2008 at 12:47 pm
I'm gratified that you could find some use for it, Bradford, because I thought you might start reading one of the papers and realize that it belongs in the spam bin.

I didn't think the examples would fit prior notions of complexity. (They fit quite nicely with my own idea "Irreducible Simplicity (IS)." But strangely, that idea never had much appeal beyond myself. LOL Oh, well. Someday my genius will be truly appreciated.)

Comment by Rock — August 18, 2008 @ 12:47 pm

Alan Fox Says:
August 18th, 2008 at 4:39 pm
Do you see a strawman in there Alan?

Yes, Bradford.

Comment by Alan Fox — August 18, 2008 @ 4:39 pm

Joy Says:
August 18th, 2008 at 5:28 pm
fmm:

I can't post to that other too-long thread, but can pull up the comments from the admin page. In that thread per those ultraconserved regions, don't let Zach and Levin pull one on you. Ask 'em about this…

Mice Thrive Missing Ancient DNA Sequences

"These and other highly conserved sequences are thought to have persisted with little or no change because they are indespensable, performing functions vital for viability or reproduction.

This is what they mean by "ultraselected" – the expectation that without these sequences the critter won't be born at all, or won't participate in the reproduction game. When knockout mice showed almost no ill effects at all, the researchers were (as becomes more and more common these days) "surprised"…

"For us, this was a really surprising result," says Nadav Ahituv of Berkeley Lab's Genomics Division and DOE's JGI, a human geneticist who led the experiment. "We fully expected to demonstrate the vital role these ultraconserved elements play by showing what happens when they are missing. Instead, our knockout mice were not only viable and fertile but showed no critical abnormalities in growth, longevity, pathology, or metabolism."

Comment by Joy — August 18, 2008 @ 5:28 pm

Alan Fox Says:
August 18th, 2008 at 5:43 pm
I can't post to that other too-long thread,…

Well, why not start another on the topic if you want to join in.

Comment by Alan Fox — August 18, 2008 @ 5:43 pm

Bradford Says:
August 18th, 2008 at 5:44 pm
Do you see a strawman in there Alan?

AF: Yes, Bradford.

Specify what it is please.

Comment by Bradford — August 18, 2008 @ 5:44 pm

Bradford Says:
August 18th, 2008 at 5:48 pm
Joy:

This is what they mean by "ultraselected" – the expectation that without these sequences the critter won't be born at all, or won't participate in the reproduction game. When knockout mice showed almost no ill effects at all, the researchers were (as becomes more and more common these days) "surprised"…

Ultraselected; knockouts… Sounds familiar. That's it! Irreducible complexity without the auto-hostility.

Comment by Bradford — August 18, 2008 @ 5:48 pm

Alan Fox Says:
August 18th, 2008 at 5:50 pm
Specify what it is please.

OK, but it's nearly midnight here, so you'll have to wait till tomorrow at least.

Comment by Alan Fox — August 18, 2008 @ 5:50 pm

Joy Says:
August 18th, 2008 at 5:58 pm
Alan Fox:

Well, why not start another on the topic if you want to join in

I've no desire to jump on that merry-go-round. The boyz are just spouting junk they'd already know is junk if they were keeping up with the research.

We went round and round on this when the research was first reported. We got a lot of "but… but… they're LAB mice! They live cushy lives! Out in the wild I bet those sequences would contribute to 'fitness' somehow!" Which of course doesn't address the actual findings at all. Those are:

Some significant amount of the ultraconserved DNA (in this case, the sequences tested via knockouts) are *NOT* "ultraselected." Thus the assertion that ultraconserved DNA is ultraconserved because it's "ultraselected" has been soundly falsified.

That's not IDers talking, it's scientists. The dirty deed is done, what Zach and Levin are asserting is now known to be false. Some parts of the genome are exempted from 'normal' mutation rates and mechanisms, and also are exempted from strong (or even apparent) viability/sexual selection.

Comment by Joy — August 18, 2008 @ 5:58 pm

Raevmo Says:
August 18th, 2008 at 6:04 pm
Joy:

This is what they mean by "ultraselected" – the expectation that without these sequences the critter won't be born at all, or won't participate in the reproduction game. When knockout mice showed almost no ill effects at all, the researchers were (as becomes more and more common these days) "surprised"…

Do you have some time series statistics on researchers being "surprised", or are you just blowing smoke about a topic you are ignorant about, as usual?

A few percent difference in survival is enough to guarantee conservation of a DNA sequence, but not enough to be detected in a single lab trail with a small sample size.

Comment by Raevmo — August 18, 2008 @ 6:04 pm

Bradford Says:
August 18th, 2008 at 6:14 pm
This is what they mean by "ultraselected" – the expectation that without these sequences the critter won't be born at all, or won't participate in the reproduction game. When knockout mice showed almost no ill effects at all, the researchers were (as becomes more and more common these days) "surprised"…

Raevmo: Do you have some time series statistics on researchers being "surprised", or are you just blowing smoke about a topic you are ignorant about, as usual?

Raevmo, self-censure yourself and eliminate this type of trash from your comments. Your second paragraph sufficed to make your point.

Comment by Bradford — August 18, 2008 @ 6:14 pm

Joy Says:
August 18th, 2008 at 6:24 pm
Raevmo:

Do you have some time series statistics on researchers being "surprised", or are you just blowing smoke about a topic you are ignorant about, as usual?

No, I read the press release. Where the leader of the experiment – Nadav Ahituv of Berkeley Lap's Genomics Division and DOE's JGI [Joint Genome Institute] – expressed his and his fellow researchers' surprise. His words: "really surprising result." That three-word clause is not at all difficult to parse, even if English isn't your first language. The Director of BLGD and JGI and director of this research Edward Rubin explained WHY their "surprise" -

"Many scientists had speculated that the reason for absolute identity of sequences over the 80 million years since humans and rodents diverged was that these sequences are crucial for life: if a base changes, the organism would die, so that's why we see absolutely no sequence changes in these regions."

Followed immediately with the rest of the quotation…

"The results of this study clearly show that this is not the case."

That's not hard to parse either. But fear not, you can still claim that they simply chose the "wrong" ultraconserved sequences to knock out, that if they'd chosen other, realer ultraconserved sequences they'd have confirmed the – RESEARCHERS' WORD – "speculation."

Thus does what was once a firm and confident prediction of the NDS theoretic magically become a mere "speculation" when it's finally falsified. THAT's some handy semantic sleight of mind right there! §;o)

Comment by Joy — August 18, 2008 @ 6:24 pm

Bradford Says:
August 18th, 2008 at 6:44 pm
Do you have some time series statistics on researchers being "surprised", or are you just blowing smoke about a topic you are ignorant about, as usual?

No, I read the press release. Where the leader of the experiment – Nadav Ahituv of Berkeley Lap's Genomics Division and DOE's JGI [Joint Genome Institute] – expressed his and his fellow researchers' surprise. His words: "really surprising result." That three-word clause is not at all difficult to parse, even if English isn't your first language. The Director of BLGD and JGI and director of this research Edward Rubin explained WHY their "surprise" -

Good smackdown Joy.

Comment by Bradford — August 18, 2008 @ 6:44 pm

Raevmo Says:
August 18th, 2008 at 7:02 pm
Joy, Bradford,

You missed my points. I asked Joy, but not clearly enough obviously, to substantiate her claim that researchers are more and more surprised these days compared to the good old days (that's why I asked about time series).

You ignored my second point, which was that even small (hardly measurable) differences in survival can lead to conserved sequences. That's a mathematical fact.

Comment by Raevmo — August 18, 2008 @ 7:02 pm

Joy Says:
August 18th, 2008 at 7:10 pm
Bradford:

Good smackdown Joy.

Oh, I expect Raevmo wants backup for my statement that researchers are being surprised quite often these days. So here's some statistics, Raevmo can parse them however he likes on that score…

A search on ScienceDaily (science news release service) over a 1-year period returns:

2,408 results on the terms "surprising finding"
861 results on the terms "surprising conclusion"
748 results on the terms "challenge dogma"
and
1,033 results on the terms "central dogma"

Thus it is not difficult to see how someone who follows the science news on a daily basis (as I do) would encounter "surprising" new findings that challenge NDS orthodoxy's "central dogma" on a regular basis.

Comment by Joy — August 18, 2008 @ 7:10 pm

Bradford Says:
August 18th, 2008 at 7:13 pm
Raevmo: You missed my points. I asked Joy, but not clearly enough obviously, to substantiate her claim that researchers are more and more surprised these days compared to the good old days (that's why I asked about time series).

That's her perception and I've also noticed surprise among researchers who encounter unexpected evidence. So what? Do you think I'm obligated to statistically back up what I would admit is a subjective perception on my part?

I did not miss the point of your gratuitous insult though.

You ignored my second point, which was that even small (hardly measurable) differences in survival can lead to conserved sequences. That's a mathematical fact.

Did I dispute that somewhere?

Comment by Bradford — August 18, 2008 @ 7:13 pm

Bradford Says:
August 18th, 2008 at 7:18 pm
Grow up Raevmo.

Comment by Bradford — August 18, 2008 @ 7:18 pm

Joy Says:
August 18th, 2008 at 7:20 pm
Raevmo:

You ignored my second point, which was that even small (hardly measurable) differences in survival can lead to conserved sequences. That's a mathematical fact.

But entirely irrelevant to the issue being addressed here. Zach and Levin have repeatedly asserted the tenet that derives from the "central dogma" that predicted ultraconserved sequences are ultraconserved because they are ultraselected. This is what was falsified by the knockout mice and "surprised" the researchers, who were operating on the very same assumptive tenet when they undertook the experiment.

Still, have you a source for the completely different assumption that hardly measurable differences in reproductive contributions to the pool lead to conserved sequences? And if they're not ULTRAconserved, why do you think this pertains to the subject?

Comment by Joy — August 18, 2008 @ 7:20 pm

Joy Says:
August 18th, 2008 at 8:33 pm
Raevmo, while you're here, did you miss the thread
We Were Absolutely Stunned? That's a quote from the researchers too, after finding a more elaborate and diverse signaling network in Monosiga brevicollis than in any multicellular organism. Pretty nifty, a bit stronger than mere "surprise."

Comment by Joy — August 18, 2008 @ 8:33 pm

Bradford Says:
August 18th, 2008 at 8:58 pm
Joy: Raevmo, while you're here, did you miss the thread
We Were Absolutely Stunned?

It matters not. There are a large number of ideological extremists numbered among TT commenters who don't care a whit about evidence that militates against their cherished beliefs. The defender of science mantel they sport is a sham.

Comment by Bradford — August 18, 2008 @ 8:58 pm

Todd Berkebile Says:
August 18th, 2008 at 9:54 pm
So Joy has some "recent" research received May 15, 2007 and accepted July 3, 2007 about Deletion of Ultraconserved Elements Yields Viable Mice. Zach has some "outdated" research from March 12, 2007 published June 28, 2007 about Human Genome Ultraconserved Elements Are Ultraselected. I guess April of 2007 must have been a break-through sort of month that changed everything. Two clearly conflicting results were generated at approximately the same time, so obviously Joy claims the conclusion supporting her side is clearly authoritative and the other side is just "junk" for the "boyz". Seems to me like further studies are required to resolve the apparent conflict. If the knockout study holds and further studies confirm the long term viability of the mice is not effected that certainly presents a challenge to MET.

Comment by Todd Berkebile — August 18, 2008 @ 9:54 pm

johnnyb Says:
August 18th, 2008 at 10:39 pm
Todd -

Two things:

1) Joy was not saying that ultraselection doesn't exist, just that the presumption of ultraselection has been shown to be wrong
2) I don't have access to the paper, but based on the abstract it seems that the "ultraselection" in this case is based on weaker data than the mouse one – it looks like it is based on the assumption of ultraselection by comparing with nearby protein-coding genes. The mouse data was determined by actually snipping out the section and seeing what happens

Note that there are LOTS of biologists who work and publish based on outdated paradigms. In addition, there is always a variable level of testability to different claims. It is important to know for each claim how well-tested each one is, and whether it is a best-guess inference or an experimentally-validated hypothesis. There is no problem with people making and using best-guess inferences, it is just problematic to equate them to experimentally-validated hypotheses.

The issue with the mice is that based on the best-guess inferences they were assuming that the region should be ultraselected, but when they managed to experimentally validate their hypothesis, it turned out to be false. This is actually an illustration of the problem with assuming that the one equals the other.

Comment by johnnyb — August 18, 2008 @ 10:39 pm

Joy Says:
August 18th, 2008 at 10:56 pm
Todd B.:

Seems to me like further studies are required to resolve the apparent conflict. If the knockout study holds and further studies confirm the long term viability of the mice is not effected that certainly presents a challenge to MET.

LOL!!! Their "research" is behind a firewall, Todd. Mine came from PLoS, where science is free. But I can tell you right now that nobody who signed off on the human pronouncement examined any knockout humans to reach their entirely orthodox 'conclusion'. They were just reasserting the prediction entailed from the dogma. Again. It's been asserted thousands of times. Zach and Levin have been asserting it all day.

The prediction from NDS orthodoxy that ultraconserved elements are ultraconserved by ultraselection has been falsified by actually existent knockout mice. Who were "not only viable and fertile but showed no critical abnormalities in growth, longevity, pathology, or metabolism."

The mice work just fine for the purpose of falsification, as the 80 million years' ultraconserved segments that were knocked out in the knockouts are identical in mice and humans. It doesn't matter what the orthodoxen confidently said or say about how ultraconserved DNA is ultraconserved. Ultraselection is *NOT* the mechanism.

Comment by Joy — August 18, 2008 @ 10:56 pm

Zachriel Says:
August 19th, 2008 at 7:22 am
Joy: The prediction from NDS orthodoxy that ultraconserved elements are ultraconserved by ultraselection has been falsified by actually existent knockout mice.

Not quite. What we have is an apparent anomaly and additional research is required. Any new scientific understanding has to be able to explain *both* findings. And that is exactly what scientists are attempting to do. Clinging to one result while waving away the other will not lead to any resolution of the conundrum.

Comment by Zachriel — August 19, 2008 @ 7:22 am

Zachriel Says:
August 19th, 2008 at 8:03 am
Bradford, on the meta-side, you might consider giving Open Threads unique names. It makes it easier to maintain bookmarks. Thanks!

Comment by Zachriel — August 19, 2008 @ 8:03 am

Joy Says:
August 19th, 2008 at 10:43 am
Zach:

Clinging to one result while waving away the other will not lead to any resolution of the conundrum.

One is the result of actual scientific experimentation returning objectively empirical evidence. The other is just another pronouncement from the orthodoxen. I'll take evidence over orthodoxy any day, and can pretty much guarantee the pronouncement from the orthodoxen didn't come from studying knockout humans.

From the Introduction to the mouse experiment in PLoS:

Several hypotheses have been proposed to explain the extreme sequence constraint of ultraconserved elements, including strong negative selective pressure and/or reduced mutation rates [3]. The negative selection hypothesis postulates that crucial functions such as vital gene regulatory information is embedded within these sequences, while the reduced mutation rate hypothesis suggests that these sequences exist in a hyperrepaired or hypomutable state [3].

Reference [3] refers to a letter ('letter', not research) published in Nature Genetics in 2005 and written by 11 duly authoritative scientists insisting that these ultraconserved elements are "selectively constrained" (i.e., ultraselected) instead of being somehow protected from mutation. Which, according to theory, are the only possibilities. So it's not like the mouse experimenters weren't aware of what the theoretical prediction was, or that it was made specifically to counter the 'other' possibility – that such segments are somehow not subject to "random" mutations.

Edict-based reinforcement of your cool Uber-Theoretic may sound satisfyingly science-like, but it's not nearly as science-like as real evidence. So go ahead and read the mouse paper. Point out the experimental flaws, the materials cheats and the heretical findings that make it fall short of actual physical evidence against the pronouncements of dogma.

Comment by Joy — August 19, 2008 @ 10:43 am

Zachriel Says:
August 19th, 2008 at 11:50 am
Joy: Reference [3] refers to a letter ('letter', not research) published in Nature Genetics in 2005 and written by 11 duly authoritative scientists insisting that these ultraconserved elements are "selectively constrained" (i.e., ultraselected) instead of being somehow protected from mutation. Which, according to theory, are the only possibilities.

The authors point out that ultraconservation could be due to "a highly elevated negative selection rate" *or* "a highly reduced mutation rate" *or* a combination. They end their edict-based reinforcement of their cool Uber-Theoretic satisfyingly science-like pronouncements with a question.

Ultraconserved Elements in the Human Genome: In any case, the questions remain: What kind of elements associated with these processes would have arrived relatively early in chordate evolution and then become practically frozen in birds and mammals? And what mechanisms would underlie this, allowing them to resist virtually all further change?

Joy: Edict-based reinforcement of your cool Uber-Theoretic may sound satisfyingly science-like, but it's not nearly as science-like as real evidence. So go ahead and read the mouse paper.

Okay.

Deletion of Ultraconserved Elements Yields Viable Mice: It is possible that our assays were not able to detect dramatic phenotypes that under a different setting, for instance, outside the controlled laboratory setting, would become evident. Moreover, possible phenotypes might become evident only on a longer timescale, such as longer generation time. It is also possible that subtler genetic manipulations of the ultraconserved elements might lead to an evident phenotype due to a gain-of-function-type mechanism. All four elements examined in this study demonstrated in vivo enhancer activity when tested in a transgenic mouse assay, which would suggest regulatory element redundancy as another possible explanation for the lack of a significant impact following the removal of these specific elements.

There are still a lot of unanswered questions.

Comment by Zachriel — August 19, 2008 @ 11:50 am

Todd Berkebile Says:
August 19th, 2008 at 11:59 am
Joy: LOL!!! Their "research" is behind a firewall, Todd. Mine came from PLoS, where science is free.

FYI: The site I linked requires a sign-up, but access is free. If sharing your address and email to too much of a wall to finding the facts (as opposed to some journalist's summary of the research) then that's your choice.

Comment by Todd Berkebile — August 19, 2008 @ 11:59 am

Joy Says:
August 19th, 2008 at 12:33 pm
Zach:

There are still a lot of unanswered questions.

No doubt. But one of them is NOT whether the four 100% ultraconserved sequences knocked in the mice out are 'ultraselected' due to being absolutely vital to survival or reproduction. That supposition has been falsified.

So when you're making off-the-cuff assertions about why ultraconserved elements are ultraconserved, don't be asserting already falsified assumptions drawn purely from theory and not supported by physical evidence.

Now, this doesn't falsify the 'ultraselected' status of DNA that encodes for ribosome pieces-parts, expression and assembly, as these are in fact vital for basic survival. Deal is, the status has been found not to apply to ultraconserved elements across the board. Thus it is no longer acceptable to make blanket statements about such things as if they are all of a kind. They most obviously are not.

Comment by Joy — August 19, 2008 @ 12:33 pm

Zachriel Says:
August 19th, 2008 at 12:40 pm
Joy: But one of them is NOT whether the four 100% ultraconserved sequences knocked in the mice out are 'ultraselected' due to being absolutely vital to survival or reproduction. That supposition has been falsified.

Even if the sequences are not required for viability, that doesn't mean they aren't under selection. As the researchers point out, there are still unanswered questions before that can be determined with any certainty.

Joy: So when you're making off-the-cuff assertions …

Please don't refer to my statements obliquely. Be specific.

Comment by Zachriel — August 19, 2008 @ 12:40 pm

Thought Provoker Says:
August 19th, 2008 at 1:02 pm
I would like to point out, while there is still the undercurrent of philosophical bias and strong opinions, this thread has mostly been arguing science.

Comment by Thought Provoker — August 19, 2008 @ 1:02 pm

Todd Berkebile Says:
August 19th, 2008 at 2:19 pm
Joy: No doubt. But one of them is NOT whether the four 100% ultraconserved sequences knocked in the mice out are 'ultraselected' due to being absolutely vital to survival or reproduction. That supposition has been falsified.

The claim in the paper is that these regions have a 3x selective pressure compared even to protein coding regions. The claim is not that any change in these regions means 100% instant death. I'm glad that some strawman has been falsified though.

Comment by Todd Berkebile — August 19, 2008 @ 2:19 pm

Joy Says:
August 19th, 2008 at 3:49 pm
Todd B.:

The claim in the paper is that these regions have a 3x selective pressure compared even to protein coding regions.

And the claim in the paper is not that these regions have no function -

To maximize the likelihood of observing a phenotype, we chose to delete elements that function as enhancers in a mouse transgenic assay and that are near genes that exhibit marked phenotypes both when completely inactivated in the mouse and when their expression is altered due to other genomic modifications.

They chose elements of the ultraconserved regions based on the likelihood that, a) they'd get a live or near-live birth to enable pinpointing of the presumed missing vital function, and b) they'd have a clue as to what to look for in terms of abnormality.

The presumption of function is given in the definition of ultraconserved. These sequences haven't changed in 80 million years. At all. In order to retain 100% fidelity over 80 million years' worth of mammalian evolution (and possibly going all the way back to the establishment of vertebrates), any changes that might get to sexual maturity must either render the organism sterile or be repaired in an unusual way (for the genome). Changes simply weren't allowed to happen for some reason.

Absolute conservation requires that variants NOT find their way into the gene pool. They can suffer no replication accidents or crossover 'oops' events without perfect repair during regular reproduction either. We can probably figure out HOW DNA gets perfectly preserved over millions of years. WHY some DNA enjoys this stability is still a mystery. It is not because the organism can't survive and reproduce if changes in this DNA occur.

Once they can rule out one presumptive mechanism, they can focus on testing other possibilities the theoretical framework could be tweaked to encompass. Of those, mutational 'cold spots' ('signaling' barrier?) is as likely as a preferentially-deployed absolute repair mechanism of some variety.

The claim is not that any change in these regions means 100% instant death.

I didn't say that. The expectation, which as you can see from the already provided pronouncements was the preferred prediction of theory, is that some abnormality would result that prevented successful reproduction by adversely influencing survival, virility, growth, longevity, pathology and/or metabolism.

These results, while not inclusive of all the possible phenotypic impact of the deleted sequences, indicate that extreme sequence constraint does not necessarily reflect crucial functions required for viability.

Or, from the 'Author Summary' -

It is widely believed that the most evolutionarily conserved DNA sequences in the human genome have been preserved because of their functional importance and that their removal would thus have a devastating effect on the organism. To ascertain this we removed from the mouse genome four ultraconserved elements—sequences of 200 base pairs or longer that are 100% identical among human, mouse, and rat. To our surprise, we found that the mice lacking these elements are viable, fertile, and show no apparent abnormalities. This completely unexpected finding indicates that extreme levels of DNA sequence conservation are not necessarily indicative of an indispensable functional nature.

See how apologetic they are for finding something nobody expected to find? You can almost feel sorry for these folks. The paper is very clear in what it's saying. It's meticulous in its methodology, confirmations, etc., as it must be because it's challenging a "widely believed" assumption.

I'm glad that some strawman has been falsified though.

Yeah, me too. I was getting really tired of trying to explain it to you. Zach and Levin asserted the "widely believed" theoretical assumption yesterday as if it were entirely self-evident. Ultraconserved elements are ultraconserved because they're ultraselected. Some vital function or developmental grotesquery that prevents successful reproduction.

I called 'em on it, because that is no longer the automatic assumption. It has been experimentally demonstrated wrong for four of these ultraconserved elements of more than 200 bp., and while it may still be true for other specific elements (as for ribosomes), it's not a general fact about ultraconserved elements.

Comment by Joy — August 19, 2008 @ 3:49 pm

fifth monarchy man Says:
August 19th, 2008 at 5:17 pm
Zach:

Not quite. What we have is an apparent anomaly and additional research is required. Any new scientific understanding has to be able to explain *both* findings.

One possible solution to the conundrum is that there is a yet unknown mechanism that maintains the integrity of information in certain DNA sequences with out subjecting them to the normal selection pressure.

That’s my prediction and it flows from a frontloading perspective. Such a mechanism would be tailor-made for frontloading things in a genome that are not immediately necessary for the fitness of an organism.

What’s your prediction and does it flow directly from MET or is it just another epicycle.

Here is your chance to shine. Make a prediction. It’s what real scientists do.

Clinging to one result while waving away the other will not lead to any resolution of the conundrum.

No the only way to do that is with research and you can’t have scientific research with out predictions.

I’ve got mine

Peace

Comment by fifth monarchy man — August 19, 2008 @ 5:17 pm

Zachriel Says:
August 19th, 2008 at 8:00 pm
Joy: The presumption of function is given in the definition of ultraconserved.

Not by definition. However, the Theory of Evolution would imply that ultraconserved regions would be under selection.

Joy: In order to retain 100% fidelity over 80 million years' worth of mammalian evolution (and possibly going all the way back to the establishment of vertebrates), any changes that might get to sexual maturity must either render the organism sterile or be repaired in an unusual way (for the genome).

Not necessarily. Strong selection doesn't equate to non-viability.

Joy: Absolute conservation requires that variants NOT find their way into the gene pool.

There is some variation across populations. However, these variations tend not to become fixed. That implies the regions are "strongly constrained functional elements".

Joy: Zach and Levin asserted the "widely believed" theoretical assumption yesterday as if it were entirely self-evident.

I asked you to be specific when indicating disagreement with any statement of mine. I don't remember ever using the phrase "widely believed".

Joy: It has been experimentally demonstrated wrong for four of these ultraconserved elements …

The authors of the study don't think they have eliminated the role of selection in ultraconserved regions. They even suggested possible areas of weakness in their findings that would warrant additional study.

Comment by Zachriel — August 19, 2008 @ 8:00 pm

Zachriel Says:
August 19th, 2008 at 8:02 pm
fifth monarchy man: One possible solution to the conundrum is that there is a yet unknown mechanism that maintains the integrity of information in certain DNA sequences with out subjecting them to the normal selection pressure.

Hypomutable or hyperrepaired regions were already suggested in the original 2004 paper. I don't think you will find that Front Loading guided their thinking. Nor have you responded to the data which indicates the sequences are under strong selection.

Comment by Zachriel — August 19, 2008 @ 8:02 pm

matt_b Says:
August 19th, 2008 at 8:02 pm
This is a bit of a nit-pick, but this point:

Reference [3] refers to a letter ('letter', not research) published in Nature Genetics

misunderstands the meaning of the term "Letter" as used in most scientific journals (including the Nature journals). It's not correspondence, but rather a report that is smaller than an "Article". The standard of peer review is as harsh as (or harsher than, given that more has to be said in less space) that of an article. There is no sense in which a "letter" does not represent research: Watson and Crick's 1953 paper would certainly be published as a Letter in Nature today.

As you were.

Comment by matt_b — August 19, 2008 @ 8:02 pm

fifth monarchy man Says:
August 19th, 2008 at 8:26 pm
I don't think you will find that Front Loading guided their thinking.

You don’t think it was MET do you?

Please describe why MET would lead you to predict a mechanism that defeats natural selection. Before you were forced to do so by observations.

Nor have you responded to the data which indicates the sequences are under strong selection.

Once again is there any data that suggests these regions are under strong selection pressure besides the fact that there is little variation or drift in them?

To say that data like this “indicates strong selection” is to beg the question IMHO.

It does nothing of the sort unless I’m misunderstanding something it merely means that the regions are protected from decay in some way. That’s what ultaconserved means!!!!

This protection could be the result of the mechanism that I’m predicting in fact such a thing would be required if the goal was to preserve information.

If the DNA in question showed lots of variation due to drift it would falsify my prediction not confirm it. It looks like The data supports me. What am I missing.

Peace

Comment by fifth monarchy man — August 19, 2008 @ 8:26 pm

Zachriel Says:
August 20th, 2008 at 8:27 am
fifth monarchy man: Once again is there any data that suggests these regions are under strong selection pressure besides the fact that there is little variation or drift in them?

Did you bother to read the paper on hyperselection? There is variation in populations, but the phylogenetic evidence indicates that the variation doesn't become fixed. The narrow range of this variation is consistent with hyperselection.

fifth monarchy man: This protection could be the result of the mechanism that I’m predicting in fact such a thing would be required if the goal was to preserve information.

As I mentioned, the possibility of a hypomutable or hyperrepair mechanism was discussed in the original 2004 paper on ultraconservation. We already know about genetic repair mechanisms. Even if a novel mechanism were found, you haven't shown how it would be uniquely entailed in the Front Loading hypothesis —especially considering that the possibility was noted by evolutionary biologists. (You must apparently accept Common Descent, including humans.)

Comment by Zachriel — August 20, 2008 @ 8:27 am

Thought Provoker Says:
August 21st, 2008 at 7:41 pm
Hi DaveScot,

I posted this here in case you decided not to allow it at Uncommon Descent. I didn't want to lose it.

Allow me to point out the Vernanimalcula guizhouena.

If you are not familiar with this interesting creature, allow me to point out some of its features.

Vernanimalcula guizhouena – which was about the size of four human hairs laid side by side – is thought to have survived that period of extreme cold, Bottjer said.

"It was a little button-shaped organism that probably scooted along the sea floor," he said. "It had a little mouth, sort of like a vacuum cleaner. It was tiny, but microbes are even smaller so it probably sucked them up so it could eat them."

Aside from a mouth, Vernanimalcula guizhouena had an anus and paired external pits that the researchers theorized it used to sense environmental conditions, such as light.

link

The Vernanimalcula guizhouena were early descendents of Urbilateria which makes this find relevant…

It is likely that [two types of hormone-secreting nerve cells] existed already in Urbilateria, the last common ancestors of vertebrates, insects and worms.
…
Both of the cell types…are multifunctional: they secrete hormones and at the same time have sensory properties. The vasotocin-secreting cells contain a light-sensitive pigment, while RF-amide appears to be secreted in response to certain chemicals. The EMBL scientists now assume that such multifunctional sensory neurons are among the most ancient neuron types. Their role was likely to directly convey sensory cues from the ancient marine environment to changes in the animal's body. Over time these autonomous cells might have clustered together and specialised forming complex brain centres like the vertebrate hypothalamus.

link

This tiny "spring animal" had organs, skin and a hormonal-based signaling system that allowed it to see, touch, taste and smell.

The Vernanimalcula guizhouena existed 50 million years prior to the Cambrian.

Comment by Thought Provoker — August 21, 2008 @ 7:41 pm

Bradford Says:
August 21st, 2008 at 8:55 pm
TP:

Allow me to point out the Vernanimalcula guizhouena.

OK TP, you provoked my curiosity. What was the purpose of that comment and why was it directed at Dave Scot?

Comment by Bradford — August 21, 2008 @ 8:55 pm

Thought Provoker Says:
August 21st, 2008 at 9:23 pm
Hi Bradford,

Every once in a while I test the waters at Uncommon Descent by submitting a relevant comment. I understand thread's authors have the authority to allow comments they see fit to publish.

DaveScot just posted a thread titled Universal Genome in the Origin of Metazoa at Uncommon Descent.

It has an underlying suggestion that the Cambrian Explosion might be supporting evidence for front loading including the possibility that pre-Cambrian life was more complicated than needed (had preloaded features).

The Vernanimalcula guizhouena is my favorite example for showing how organized life was prior to the Cambrian. Of course, I suggest the organization comes from quantum effects interconnected in space and time (the latter explaining foresight).

However, I am willing to share.

I would think the Vernanimalcula guizhouena would be very relevant to DaveScot's thread.

It will be interesting to see if he is willing to take advantage of the science I offer, even if it means giving credit to a vocal critic of the ID Movement.

Comment by Thought Provoker — August 21, 2008 @ 9:23 pm

Bradford Says:
August 22nd, 2008 at 12:46 pm
Since this is an open thread I'll link to this viewpoint which offers some timely thoughts on events ocurring in the world.

Comment by Bradford — August 22, 2008 @ 12:46 pm

Rock Says:
August 24th, 2008 at 6:09 pm
You asked me, Raevmo, I recall, if I had a “superior theory” in mind, and I do, but I don’t recall and cannot find the topic in which you asked the question.

In Neo-Darwinism adaptation is the purely coincidental, random, matching of variation to an a priori (and ever changing) pattern of conditions; which conditions and coincident matching (and non-matching) we call “natural selection.” I don’t believe it.

I.e., I don’t believe it is a coincidence (the matching). I certainly do believe in the occasional coincidence, but not billions of years of billions of coincidences. As a physicist I don’t believe in coincidences (of such magnitude and duration), as a mathematician I don’t believe in coincidences, as a computer scientist I don’t believe in coincidences, but biological theory expects me to! I don’t. I don’t believe it! Evolution is not a coincidence. Its not random, chance, circumstance or happenstance. It doesn’t “just happen.” Whether evolution was planned or designed is an open question in my mind. A question I’m not so prepared, trained, educated, or experienced to deal with, at least in the terms of these discussions.

But I am prepared, trained, educated, and experienced to deal with it! It’s what I did for 25 years. Design complex adaptive systems. Coincidence played virtually no role. Design did. In design one of the problems to be solved is the systematic elimination of “coincidence.” We didn’t design systems to coincidently adapt. We designed systems to adapt. Which is not easy to do. Indeed, the theoreticians in my own field insist that it cannot be done.
So much for theory! LOL

Self-Adaptation

http://ml.cs.tu-berlin.de/~mto...

It leads to a fundamentally different “philosophical” perspective on biological evolution. One in which evolution is not something that “just happens” (Dawkins) to life forms. Evolve is what life forms do. As I’ve said before, what they were “designed” to do (?!). Life forms are not simply the pawns of forces beyond their control. Evolution is an intrinsically controlled experiment. Evolution is a process in self-adaptation.

This is the basic premise (usually left implicit) of just about all evolutionary computing. (Revealing my purely parochial perspective.) It is about the design of systems that self-adapt. Are not adapted under continual monitoring, supervision, or intervention of the designer or slavishly to conditions. Adaptation is evolution to a state independent of conditions (including the designer).

As I suggested, we need to re-examine our presumptions about what is “adaptation.”

Comment by Rock — August 24, 2008 @ 6:09 pm

Thought Provoker Says:
August 31st, 2008 at 12:22 am
I noticed a comment from Raevmo on the Open Thread before I went to the fair where he claimed Bradford DELETED a comment instead of sending it to the memory hole. I now notice that it appears that comment is deleted as well and does not show up in the memory hole.

Has Telic Thoughts' policy changed? From the Comment Guidelines…

"Every public forum has to consider the bounds in which discourse is to take place. At Telic Thoughts, we've chosen a form that will hopefully live up to our vision of "a pleasant and fruitful atmosphere." Inspired by the good folks at The Panda's Thumb, who have a similar system, we're introducing The Memory Hole, into which comments, that we, for one reason or another, find inappropriate, will be dumped. Although its name comes from George Orwell's novel 1984, in which The Party used the memory holes to destroy unwanted documents, a comment in our Memory Hole will still be accessible to anyone caring to wade through the piles.

As the crew of this blog, it is entirely our call what gets moved."
…
"Of course, any spam, threats, and material of a pornographic or violent nature will be deleted entirely."

Did Raevmo's first e-mail contain "spam, threats, and material of a pornographic or violent nature"?

If you are changing TT's policy, I suggest the ethical thing would be to update the words to match the actions.

P.S. If the TT Crew happens to get together to change the written policy, I humbly suggest that would be a good time to vote on my request to join said crew.

Comment by Thought Provoker — August 31, 2008 @ 12:22 am

Rob R. Says:
September 1st, 2008 at 7:04 pm
Hello TP,

Is the Brain a Quantum Computer?(.pdf)

Critique of Orch OR (and ideas like it) from '06. Thought I'd pass it along.

Abstract
We argue that computation via quantum mechanical processes is irrelevant to explaining how brains produce thought, contrary to the ongoing speculations of many theorists. First, quantum effects do not
have the temporal properties required for neural information processing. Second, there are substantial physical obstacles to any organic instantiation of quantum computation. Third, there is no psychological
evidence that such mental phenomena as consciousness and mathematical thinking require explanation via quantum theory.We conclude that understanding brain function is unlikely to require quantum computation or similar mechanisms.

May be old news but, I'd be curious as to what you (or Joy/whomever) thought about it.

Comment by Rob R. — September 1, 2008 @ 7:04 pm

Thought Provoker Says:
September 1st, 2008 at 7:55 pm
Hi Rob,

I'm impressed that you took the effort to find this paper.

Yes, it is old news to me. I have read quite a bit both Pro and Con on Orch OR. But, please, present anything you want on the subject. The more the better.

Most critique's of Orch OR heavily depend on Tegmark. This paper is no exception. Tegmark is very much in opposition to this. First, he embraces the Many Worlds quantum interpretation (which opposes Penrose's Copenhagen like OR interpretation) and he is convinced the brain is too wet and noisy for quantum computation. Tegmark has presented his calculations showing quantum collapse would occur on the order of microseconds, not milliseconds as required by the Orch OR model.

Hameroff has refuted this essentially pointing out Tegmark's calculations are based on Tegmark's incorrect assumptions.

Penrose isn't a biologist. He admits that he isn't certain of how, but it is obvious that he is quite convinced that somehow, someway consciousness and quantum effects are interconnected. It's necessary to complete the QM puzzle.

From the paper you found…

Although the hypothesis that the brain is a quantum computer is biologically and computationally implausible, there might be psychological phenomena not amenable to a neurocomputational
explanation that are explicable by appeal to quantum theory. Penrose (1994, 598 A. Litt et al./Cognitive Science 30 (2006) 1997) and Hameroff (1998a, 1998b) argued that mathematical thinking and conscious experience are two such phenomena.

The Penrose–Hameroff “Orch OR”model for brain function describes consciousness as depending fundamentally on the orchestrated, noncomputable wave-function collapse (reduction) of coherent quantum states in neural microtubules (Hameroff, 1998b). The collapse must not be completely random, as would be the case with environmental decoherence, so Penrose (1997) postulated the existence of an objective reduction (OR) phenomenon based on “self-collapse” due to quantum gravitational effects on space time. Before the coordinated collapse that signifies conscious processing, quantum-coherent states within different microtubules are thought to interact with one another, thus achieving a sort of rudimentary quantum computation in the brain for preconscious processes.

There are many problems with this theory, beginning with the OR conjecture. Penrose’s (1994, 1997) idea that superpositional collapse happens on its own, independent of environmental interaction, is an extremely controversial one. Hawking (1997) voiced opposition to the idea, arguing “that warping [of space-time under OR] will not prevent a Hamiltonian evolution with no decoherence” (p. 170). More general resistance centers on the implications of the hypothesis. The existence of OR in the manner described by Penrose and Hameroff (1998b) would require fundamental and far-reaching revisions to quantum theory itself. Although Penrose freely accepted this fact, such a significant claim requires substantial supporting evidence. Even discounting the lack of direct empirical support, however, the main theoretical arguments for the necessity of OR are also critically flawed.

This is the part I find rather amusing. People need to rationalize that Penrose has lost it. If you note the reference to Hawking. You might want to look up the 1994 debate between Penrose and Hawking. For most of the debate they agree. The major disagreements revolved around Schrödinger's cat. Basically, Hawking argued to ignore the cat. The ramifications that consciousness and quantum outcomes are linked are just unacceptable to a lot of people.

I don't believe Penrose's logic is "critically flawed". Penrose presented his logic in his 1000 page book The Road to Reality. Just as controversial as his OR quantum interpretation is his Twistor Theory (both are in the book). I see them as very much related. Penrose's Twistor Theory had been pretty much ignored for 30 years. Lately, Twistor Strings is becoming the latest grand unifying theory and things are following into place.

It is an interesting time to watch how people react when the unacceptable becomes seen as reality.

Comment by Thought Provoker — September 1, 2008 @ 7:55 pm

Rob R. Says:
September 1st, 2008 at 9:51 pm
I'm impressed that you took the effort to find this paper.

It's thanks to you I even look at it at all. Not exactly the kind of thing your average schmuck [:waves:] knows about.

Yes, it is old news to me. I have read quite a bit both Pro and Con on Orch OR. But, please, present anything you want on the subject. The more the better.

Lol! I'm quite sure I couldn't add a thing. :average-schmuck-wave: My eyes are bigger than my intellect when it comes to Orch OR.

Penrose isn't a biologist. He admits that he isn't certain of how, but it is obvious that he is quite convinced that somehow, someway consciousness and quantum effects are interconnected. It's necessary to complete the QM puzzle.

From the paper:

Humans and our closest relatives can perform these tasks better than other animals, and spindle neuron concentration among hominid species seems strongly correlated with such success as well. In contrast to this well-supported neuronal explanation, quantum–microtubule theorists have yet to outline plausible mechanisms by which species differ in their abilities. In this absence, are we to believe that carrots and rutabagas also exhibit quantum computation, or are conscious?

I was wondering if you thought of this as an issue (i.e., it seems, so far as I understand it, that he's arguing that (higher?) consciousness is a product of evolution, and therefore, not a mechanism for abiogenesis or even pre-mammalian evolution)? Is this a big deal wrt Orch OR? Or is it along the lines of that whole 'effects can precede causes – retrocausality thing'? Seems, to me, that they're saying that the neurological abilities needed for Orch OR to work weren't present in life until just (relatively) recently. Where'd I go wrong here?

This is the part I find rather amusing. People need to rationalize that Penrose has lost it. If you note the reference to Hawking. You might want to look up the 1994 debate between Penrose and Hawking. For most of the debate they agree. The major disagreements revolved around Schrödinger's cat. Basically, Hawking argued to ignore the cat. The ramifications that consciousness and quantum outcomes are linked are just unacceptable to a lot of people.

For me it's an issue of understanding. I'm still in the 'getting it' phase. I never got the 'cat' thing either. Me and Hawking, peas in a pod (I get that ALL the time.) No issues accepting it. . . I don't think. I'm certainly in no position to be reading Penrose's book yet. . . I'm certain. I've noticed that Oleg wasn't very impressed and Heddle hasn't shown much interest either (thought it'd be his kind of [i][d]). I'm sure they can handle the math and the concepts without much trouble, and arguments from authority are all a layman like me can work with. Then again, it's Penrose. I'd be sitting on the fence on this one, but I can't even find that!

It is an interesting time to watch how people react when the unacceptable becomes seen as reality.

Good luck with that! Seriously. I'll be cheering from the cheap seats.

Comment by Rob R. — September 1, 2008 @ 9:51 pm

Thought Provoker Says:
September 1st, 2008 at 10:06 pm
Hi Rob,

What's the matter, you don't like that idea of having your food be conscious?

Here is Dr. Hameroff's answer to this.

Litt et al. ask: “Are we to believe that carrots and rutabagas also exhibit quantum computation, or are conscious?” (p. 597). No, we are not. Plant cells have very few microtubules (very small E); whether they have quantum isolation and quantum computation is unknown. But, assuming they did, by E =h¯/t a carrot or rutabaga (small E, long t ) might have a single, very low intensity conscious moment once per month or so.

You may want to read this paper. Dr. Hameroff's papers aren't always the most readable, but he is better than most. http://www.hameroff.com has a lot more papers to look at.

Comment by Thought Provoker — September 1, 2008 @ 10:06 pm

Thought Provoker Says:
September 1st, 2008 at 10:40 pm
Hi Rob,

Rereading your comment, I'm not sure I answered your question. Dr. Hameroff has this paper on how Orch Or fits in with evolution.

As to Schrödinger's cat. Here is my short version.

Reality can be split up into three areas of study. The very small, quantum. The very large, relativistic. And the everyday Macro world we experience.

Scientists have pretty much mathematically modeled each of the three areas of study. The models are consistent and understandable with Quantum Mechanics lagging behind because scientists refused to accept what the experiments were showing them ("God doesn't play dice").

The interface between the macro and relativistic is understand. By interface, I mean it can be shown how the relativistic equations could be modified to match Macro World observations. I'm of the opinion that Penrose has shown how the relativistic/quantum interface works. This is at the base of the arguments between Oleg and I. He won't say Penrose is wrong, He just insists that Penrose's math is an interesting exercise unrelated to reality. Yea, right, just like Penrose's previous exercise in modeling Black Holes. The final interface is the one between the Macro and the Quantum. This is where Schrödinger's cat comes in. The answer to the Schrödinger's cat paradox is the key to understanding this last interface.

Buckyballs are like soccer balls made up of 60 atoms. They exhibit quantum level behavior such as wave/particle behavior in dual slit experiments. Penrose asks why don't real soccer balls act like Buckyballs?

The answer Penrose is given by the likes of Tegmark and Hawking is that the real world is too messy and noisy. Penrose rejects that answer. Because there are a lot of large objects in isolation in space that don't exhibit quantum behavior either. He thinks he has the answer. He has been refining this answer for 30 years. I think he is right because all the other alternatives sound like non-answers. "It's too complicated to understand" is usually a dead giveaway.

Comment by Thought Provoker — September 1, 2008 @ 10:40 pm

Rob R. Says:
September 2nd, 2008 at 1:00 am
Hi TP,

Rereading your comment, I'm not sure I answered your question. Dr. Hameroff has this paper on how Orch Or fits in with evolution.

Thanks for that, it does help put a timeline to things. So Orch OR isn't really about origins or even typical ID evolution arguments (flagellum, ATP, DNA etc) – all of that stuff is already in place when Orch OR does its thing. Is that correct? I like it more as an inflationary epoch event. Take care of fine-tuning and all while it's at it. Easier to deal with the retrocausality thing too, with space/time so compact and infinitely curved then suddenly and very quickly stretched out. If, as the paper you linked cites: "consciousness derives from an experiential medium which exists as a fundamental feature of reality." Then why not way before the Cambrian, or even the first life. Like I said already, I'm still trying to get it.

As to Schrödinger's cat. Here is my short version.

Shorter version: Size matters?

The cat's too big. There was no paradox to begin with, a cat would have never been in that situation. The small stuff probably can't do it either, it's just too small and too fast to measure properly… says I.

This is at the base of the arguments between Oleg and I. He won't say Penrose is wrong, He just insists that Penrose's math is an interesting exercise unrelated to reality.

Isn't that an appropriate criticism? My understanding was that he felt you were going beyond what Penrose was saying because you weren't understanding the (mathematical) nuances. Not that I could judge that for myself mind you, but how would you (did you?) respond to the idea that Penrose's model doesn't correspond to reality?

Buckyballs are like soccer balls made up of 60 atoms. They exhibit quantum level behavior such as wave/particle behavior in dual slit experiments. Penrose asks why don't real soccer balls act like Buckyballs?

Mass?

Because there are a lot of large objects in isolation in space that don't exhibit quantum behavior either.

What sort of 'isolated' objects?

He thinks he has the answer. He has been refining this answer for 30 years. I think he is right because all the other alternatives sound like non-answers. "It's too complicated to understand" is usually a dead giveaway.

Complicated is relative I guess.

I appreciate the help, TP.

Comment by Rob R. — September 2, 2008 @ 1:00 am

Thought Provoker Says:
September 2nd, 2008 at 4:59 pm
help, I have several comments stuck in the spam filter.

Comment by Thought Provoker — September 2, 2008 @ 4:59 pm

Guts Says:
September 2nd, 2008 at 5:19 pm
Sorry, currently doing some work on the site and haven't de-spammed in a while (busy at work), hopefully the system learns you're not a bot.

Comment by Guts — September 2, 2008 @ 5:19 pm

Thought Provoker Says:
September 2nd, 2008 at 5:40 pm
Hi Rob,

To Schrödinger's cat, you wrote…

Shorter version: Size matters?

The cat's too big. There was no paradox to begin with, a cat would have never been in that situation. The small stuff probably can't do it either, it's just too small and too fast to measure properly… says I.

You are not alone in wanting to deny the reality of superposition. However, the reality is becoming so undeniable inventors are starting to build computers and secure communication devices which based on it.

Try reading think link

To my "Penrose asks why don't real soccer balls act like Buckyballs?"

You responded with…

Mass?

Congratulations. That is what Penrose says.

Penrose says larger objects have more mass and, therefore, more self-induced gravitational energy. Small objects like photons and electrons can stay in superposition for a very long time. Cat sized objects can't. While they can go into superposition, the multiple states self-collapse into one state that we experience in the Macro World (i.e. undergo Objective Reduction "OR") very quickly.

Simple right? I think it is. It is the ramifications that make it unpalatable to some. For example…

Why does conscious observation effect how Quantum OR happens.

Comment by Thought Provoker — September 2, 2008 @ 5:40 pm

Thought Provoker Says:
September 2nd, 2008 at 5:43 pm
Thanks Guts

Comment by Thought Provoker — September 2, 2008 @ 5:43 pm

Telicmeme Says:
September 3rd, 2008 at 2:37 pm
Hi Zachriel,

Could you please comment on the following trees of life and say which one of them best describes the current understanding of the evolution of life. I am looking for an accurate and graphical representation of the tree. Which one do you (or anyone else) think is he best (at present) and could you perhaps point to a better one if you know of any?
1
2
3
4
5
6

Thank you. Much appreciated.

Comment by Telicmeme — September 3, 2008 @ 2:37 pm

Zachriel Says:
September 3rd, 2008 at 7:43 pm
Telicmeme: I am looking for an accurate and graphical representation of the tree.

It depends on what you are trying to represent, and that can mean a trade-off with accuracy or completeness. Most people like to see the evolution of animals, particularly vertebrates, even more particularly mammals and hominids. Dhushara (#2) provides this, but with so much clutter as to be difficult to discern the patterns. Other times, we might want to grasp the whole picture at once. The one created with iTOL (#6) gives a lot of detail and uses a cool, modern cladogram to organize the data. But I rather like the Nature Reviews Genetics (#4). It doesn't have the clutter and shows a couple of interesting features, such as the horizontal transfer of mitochondria and chloroplasts from Bacteria to Eukaryota. Here's a rather simple and elegant tree, if you just want to show the basic concept.

None of these diagrams tell the whole story, though. A tree is a particular mathematical pattern called the nested hierarchy. It's amazing that such a simple pattern applies so broadly across so many biological taxa. But nothing in life is ever so simple as that.

There are several problems. The first and most important is that the story is being told by the survivors. For every lineage shown, there are hundreds that went extinct and left no trace.

And there is an awful lot being represented with each node. Many times, when a new niche opens up, there is a rapid radiation of new forms. This happens so fast in geological terms, that it can be very difficult to discern what branched before what. And many of these lineages may also have gone extinct. All that is being represented with just a single dot. (This may not be a problem as long as you realize that from a certain vantage, humans are 'just' elaborated Deuterostomes. A tube with appendages to stuff food into one end.)

And the node of most interest is at the root of the tree. The universal ancestor, if it existed, may have coexisted with many other organisms that left no descendents. And extensive horizontal evolution may mean a naïve view of descent doesn't properly describe what happened. Various organisms may have lived in communities, trading back and forth until one became predominant or the collective became stabilized into a few forms.

So we might have something like this with several lineages (blue lines) forming a common ancestral population. Or even more boldly. Or with artistic license. In this latter view, the distinction between biological domains is arbitrary and a result of our look-back.

Diagrams are tools for understanding. So, it depends on what you are trying to express which diagram will be best for your purposes. For many uses, a simple Tree of Life can express much of interest and importance (keeping in mind the several caveats).

For fun, here's a cladogram of just dinosaurs.

Comment by Zachriel — September 3, 2008 @ 7:43 pm

Telicmeme Says:
September 5th, 2008 at 11:14 am
Thank you Zachriel. I like the Doolittle graphic.

Would it be safe to assume that the genetic code arose in a common ancestor of the Common Ancestral Community of Primitive cells? Or can it be viewed as another example of convergent evolution on a molecular level?

Comment by Telicmeme — September 5, 2008 @ 11:14 am

Zachriel Says:
September 5th, 2008 at 11:53 am
Telicmeme: Would it be safe to assume that the genetic code arose in a common ancestor of the Common Ancestral Community of Primitive cells?

There are a variety of theories, including that the genetic code may have evolved before a true cell. However, there is evidence that the genetic code also has an evolutionary history.

Brooks et al., Evolution of Amino Acid Frequencies in Proteins Over Deep Time: Inferred Order of Introduction of Amino Acids into the Genetic Code, Molecular Biology and Evolution 2002.

Comment by Zachriel — September 5, 2008 @ 11:53 am

Zachriel Says:
September 5th, 2008 at 12:15 pm
Telicmeme: Or can it be viewed as another example of convergent evolution on a molecular level?

Common Descent is the most plausible explanation, but that doesn't mean that during the time of the origin of the Common Ancestor, it was the only variant. Indeed, there is evidence that the Genetic Code is the result of natural selection among competitors.

Freeland et al., Early Fixation of an Optimal Genetic Code, Molecular Biology and Evolution 2000.

And also evidence that the genetic code is not the best of all possible codes, but a balance between adaptation and frozen accident.

Novozhilov et al., Evolution of the genetic code: partial optimization of a random code for robustness to translation error in a rugged fitness landscape, Biology Direct 2007.

This would also argue against convergence.

Comment by Zachriel — September 5, 2008 @ 12:15 pm

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