RSS 2.0 Feed

» Welcome Guest Log In :: Register

Pages: (58) < ... 7 8 9 10 11 [12] 13 14 15 16 17 ... >   
  Topic: Evolution of the horse; a problem for Darwinism?, For Daniel Smith to present his argument< Next Oldest | Next Newest >  
Daniel Smith



Posts: 970
Joined: Sep. 2007

(Permalink) Posted: Oct. 10 2007,03:17   

Quote (JAM @ Oct. 09 2007,18:19)
             
Quote (C.J.O'Brien @ Oct. 09 2007,17:12)
               
Quote
So when I examine the evidence, is that what I find?  Yes, that is exactly what I find.  I find complex intricate systems analogous (but far superior) to power plants, factories with automated assembly lines, communication networks, super highway systems, waste management (with recycling!), and on and on.

Bob O'H already made this point, but at some length.
For concision: None of that is evidence in the scientific sense. It's a restatement of the question in explicitly teleological terms. To consider this evidence (the result of empirical investigation beyond a cursory glance) is to beg the question.

Not only that, but most of it is false.

If our superhighway systems were anything like the cell's, trucks crashing into each other (combining their cargos), useless detours, and multiple tractors on the same cargo trailer pulling in different directions would play an integral role in every journey.

If human-designed waste management systems were designed analogously to the cell's, we'd have 20% raw sewage in our drinking water and call it delicious.

The amazing thing is that when you work in these fields, you see massive teleological biases among the scientists, so that extra data are required to overcome these analogies.

I've not seen any descriptions of any biological functions that come across as haphazard and random as you describe them.  In fact I find the opposite to be true.  Whenever I learn the details of how a biological system functions, I'm struck by the sheer brilliance of the system's design (and I'm not going to creationist sources for this info).
Take the process of protein synthesis for example.  Please explain how that process is just a hodgepodge of cobbled together mish-mash that somehow, almost by accident, gets the job done.
Or explain how the brain is just a random lucky accident, or the various visual systems, or the mammalian kidney, or the avian lung, or the central nervous system, or all the various systems of flight, or any other system.  In fact, I challenge you to provide details of how any biological system is just a cobbled together hodge-podge.

Also, explain to me how the qualities observed in an object are not evidence that can be used to determine the object's origin?

What evidence leads us to believe that Stonehenge is designed - if not the qualities of Stonehenge itself?  Do we say it is designed because there were people in the area at that time?  No.  If we did, we'd have to say that every rock, every stone, in fact everything is designed if there are people in the area at the time.  No, it's the organization of the stones and the fact that that organization is analogous to the organization of other designed objects (such as tables, chairs and benches) that leads us to believe that Stonehenge was designed.  This organization is a quality of the object in question - the object that needs explaining.  Yet we can certainly use these qualities to deduce design here.  Why not elsewhere?

Are the qualities of "the thing that needs explaining" and analogies excluded also from random or naturalistic explanations?  Do you not observe the makeup of the organism in question when trying to discern its origin?  Do you not compare the qualities of one object with another?  Do you not say that this sequence is like that one?  Is this not analogy?  If not, then what is it?

And if statements such as mine are not evidence, then why is this statement not challenged equally as vigorously?        
Quote (C.J.O'Brien @ Oct. 09 2007,17:12)
When you actually get in depth and look at some of that cellular machinery, Daniel, you'll see that it does not resemble at all the products of a rational design process. It rather resembles a Rube Goldberg-type cobbled-together mess eerily similar to the sorts of engineering solutions arrived at by evolutionary algorithms.


In short, analogies are a form of evidence.  I'm guessing that you just don't like the fact that I'm comparing biological systems to designed systems.

--------------
"If we all worked on the assumption that what is accepted as true is really true, there would be little hope of advance."  Orville Wright

"The presence or absence of a creative super-intelligence is unequivocally a scientific question."  Richard Dawkins

  
Erasmus, FCD



Posts: 6349
Joined: June 2007

(Permalink) Posted: Oct. 10 2007,07:36   

Daniel we know people make things like stonehenge.

What designer do we know of that makes cells and platypi and the grand canyon?  People?  Or something else?  I'll wait for your answer.

(sound of wind in trees)
(child farts)
(somewhere a rooster is screwing a guinea hen)
(old men die and babies born)
(cells divide under my toenails)
(republican senator somewhere taps his foot in a bathroom stall)
(snake eats a bullfrog)
(grandmaw fiddles 'Liberty' while dancing on a piece of plywood)
tick tock tick tock

That's Right!!!!  We don't know of any such designer!!!  You Lose!!!

--------------
You're obviously illiterate as hell. Peach, bro.-FtK

Finding something hard to believe based on the evidence, is science.-JoeG

the odds of getting some loathsome taint are low-- Gordon E Mullings Manjack Heights Montserrat

I work on molecular systems with pathway charts and such.-Giggles

  
JAM



Posts: 517
Joined: July 2007

(Permalink) Posted: Oct. 10 2007,10:40   

Quote (Daniel Smith @ Oct. 10 2007,02:30)
Quote (mitschlag @ Oct. 08 2007,07:02)
     
Quote (Daniel Smith @ Oct. 08 2007,04:27)
Take two members of the same species that have been geographically and reproductively isolated for a long period of time (the longer the better), sequence their genomes and compare them.

My prediction is that the coding and non-coding sequences (basically all sequences) will show an equal amount of evolutionary constraint.

Please define "evolutionary constraint."

Predict the expected results that would falsify your hypothesis.

I am using the term "evolutionary constraint" to mean a sequence that resists or rejects mutations.
As I understand it, this is the common usage of the term.

The results that would falsify my hypothesis would be if the coding sequences showed evolutionary constraint while the non-coding sequences didn't.

By "coding," do you mean more than protein-coding sequences, including things like promoters, enhancers, splicing signals, etc.?

Here's an opposing hypothesis:

Known functional sequences will be evolutionarily conserved. Most sequences will not be conserved. We will continue to find functions for some conserved sequences for which no function has been identified.

What do you think? Shall we look at the evidence to see which hypothesis is better supported?

  
JAM



Posts: 517
Joined: July 2007

(Permalink) Posted: Oct. 10 2007,11:00   

Quote (Daniel Smith @ Oct. 10 2007,03:17)
 
Quote (JAM @ Oct. 09 2007,18:19)
                 
Quote (C.J.O'Brien @ Oct. 09 2007,17:12)
                 
Quote
So when I examine the evidence, is that what I find?  Yes, that is exactly what I find.  I find complex intricate systems analogous (but far superior) to power plants, factories with automated assembly lines, communication networks, super highway systems, waste management (with recycling!), and on and on.

Bob O'H already made this point, but at some length.
For concision: None of that is evidence in the scientific sense. It's a restatement of the question in explicitly teleological terms. To consider this evidence (the result of empirical investigation beyond a cursory glance) is to beg the question.

Not only that, but most of it is false.

If our superhighway systems were anything like the cell's, trucks crashing into each other (combining their cargos), useless detours, and multiple tractors on the same cargo trailer pulling in different directions would play an integral role in every journey.

If human-designed waste management systems were designed analogously to the cell's, we'd have 20% raw sewage in our drinking water and call it delicious.

The amazing thing is that when you work in these fields, you see massive teleological biases among the scientists, so that extra data are required to overcome these analogies.

I've not seen any descriptions of any biological functions that come across as haphazard and random as you describe them.


1) Descriptions aren't evidence. Why not just be honest and admit that you avoid the actual evidence?
2) My descriptions do not imply that these systems are either "haphazard" or "random." I am accurately describing them as extremely fuzzy, with components that are related to each other with partially-overlapping functions. Therefore, they are in no way analogous to systems designed by humans, which was your preposterously ignorant claim.
 
Quote
In fact I find the opposite to be true.

But you depend on descriptions, not evidence.  
 
Quote
Whenever I learn the details of how a biological system functions, I'm struck by the sheer brilliance of the system's design (and I'm not going to creationist sources for this info).

Then show me the evidence you've examined for the cell's recycling systems and I'll show you how you are mistaken. What we real biologists find when examining the real evidence is Rube Goldberg-like, partially-overlapping complexity, with everything borrowed from something else. While this is both incredibly complex and amazing, it is in no way analogous to systems designed by humans.
 
Quote
Take the process of protein synthesis for example.

OK, but you need to explain why you are running away from the examples you initially chose.
 
Quote
Please explain how that process is just a hodgepodge of cobbled together mish-mash that somehow, almost by accident, gets the job done.

First, you are grossly misrepresenting my position by attributing "almost by accident" to me. This is a fundamentally dishonest way to discuss anything.

Second, it is a cobbled-together mish-mash, given the following evidence.

1) Please explain why ribosomal RNA is at the center of the enzymatic active site, when RNA is so much less stable than protein. Since the "RNA World" hypothesis explains this beautifully, explain how a design hypothesis explains this better.

2) Please explain third-base "wobble" and the viability of bacteria carrying amber, ochre, and opal suppressor mutations.

 
Quote
Or explain how the brain is just a random lucky accident,...

You are being dishonest. I am not claiming that the brain is "just a random lucky accident." I am claiming that the brain is not analogous to a designed mechanism.
 
Quote
... or the various visual systems, or the mammalian kidney, or the avian lung, or the central nervous system, or all the various systems of flight, or any other system.  In fact, I challenge you to provide details of how any biological system is just a cobbled together hodge-podge.

As for details, let's use the cell's waste management system. The details show that there is no single pure membranous compartment anywhere in the cell. Even the proteins that help to specify what we call separate compartments overlap with each other.

How's that?
 
Quote
Also, explain to me how the qualities observed in an object are not evidence that can be used to determine the object's origin?

They are. You're just completely wrong about the qualities because you've not bothered to look at real evidence.

Your need to grossly misrepresent my position speaks volumes about your confidence in your own position, too.
 
Quote
No, it's the organization of the stones and the fact that that organization is analogous to the organization of other designed objects (such as tables, chairs and benches) that leads us to believe that Stonehenge was designed.  This organization is a quality of the object in question - the object that needs explaining.  Yet we can certainly use these qualities to deduce design here.  Why not elsewhere?

Then tell me about the qualities of the cell's recycling system that lead you to believe that it was designed. You have to go to the primary data, not anyone's interpretation of them.
 
Quote
Are the qualities of "the thing that needs explaining" and analogies excluded also from random or naturalistic explanations?

Analogies are explanatory devices. They are not evidence.
 
Quote
Do you not observe the makeup of the organism in question when trying to discern its origin?  Do you not compare the qualities of one object with another?  Do you not say that this sequence is like that one?  Is this not analogy?  If not, then what is it?

Mostly, it's homology, not analogy.
 
Quote
In short, analogies are a form of evidence.  I'm guessing that you just don't like the fact that I'm comparing biological systems to designed systems.

We don't like the fact that you are ignoring the actual evidence and promoting fake analogies.

  
C.J.O'Brien



Posts: 395
Joined: Aug. 2005

(Permalink) Posted: Oct. 10 2007,12:35   

Quote
I've not seen any descriptions of any biological functions that come across as haphazard and random as you describe them.  In fact I find the opposite to be true.  Whenever I learn the details of how a biological system functions, I'm struck by the sheer brilliance of the system's design (and I'm not going to creationist sources for this info).
Take the process of protein synthesis for example.  Please explain how that process is just a hodgepodge of cobbled together mish-mash that somehow, almost by accident, gets the job done.
Or explain how the brain is just a random lucky accident, or the various visual systems, or the mammalian kidney, or the avian lung, or the central nervous system, or all the various systems of flight, or any other system.  In fact, I challenge you to provide details of how any biological system is just a cobbled together hodge-podge.

Daniel appears to be running TurboGoalposts v.3:16.

First, we were talking about biochemistry, not how the brain (or anything else) is "just a random lucky accident," which is a straw-man representation of evolutionary theory as well as off the subject.

That there is a certain kind of elegance to biochemical processes is not in question. They work well enough to have sustained evolving life on Earth for billions of years, and are perfectly capable of supporting the functions of big, complex animals like ourselves. So I am not saying that they barely "get the job done." I am saying, though, that all of the highly-touted complexity of the cell, when it is actually investigated, not simply remarked upon, seems to owe its existence to a maddeningly short-sighted designer --one that seems incabable of building a structure or pathway using anything other than pre-existing components, often themselves integral parts of other, fully functioning systems. But you challenged me for examples.

Here is Ken Miller on the vertebrate blood-clotting cascade

Here is a TalkOrigins summary of several articles on the evolution of the Krebs Cycle

Here is an abstract of a Science paper on the evolution of a steroid-hormone receptor

--------------
The is the beauty of being me- anything that any man does I can understand.
--Joe G

  
mitschlag



Posts: 236
Joined: Sep. 2006

(Permalink) Posted: Oct. 10 2007,12:47   

Quote (Daniel Smith @ Oct. 10 2007,02:30)
The results that would falsify my hypothesis would be if the coding sequences showed evolutionary constraint while the non-coding sequences didn't.
There's a fair amount of evidence showing that (contrary to expectation) non-coding sequences have fewer base changes than coding sequences, see, for example:
http://www.biomedcentral.com/1471-2148/7/66
Quote
The primary result is that the mean rate of intergenic nucleotide substitution is two-thirds that of the synonymous coding data, with an absolute rate estimated to be 1.05 × 10-8 substitutions per site per year. This result holds with alternative nucleotide models (see Methods), and thus does not appear to be solely an issue of estimation procedures.

Slower rates in non-coding regions relative to synonymous sites are becoming a surprisingly frequent observation. For example, a recent study of Drosophila demonstrated that non-coding DNA evolves considerably slower than synonymous sites in terms of both divergence between species and polymorphism within species [16]. By comparing studies, one can also make the case that pseudogenes [32,33] and introns [34,35] evolve more slowly than synonymous sites in apes and other mammals [13,36-38]. Studies of mammalian intergenic regions have also found slower rates than synonymous sites [35,39,40]. Although most of these studies encompass only a handful of genes, an overall picture of relatively slow non-coding rates is emerging.

What do you make of that?

--------------
"You can establish any “rule” you like if you start with the rule and then interpret the evidence accordingly." - George Gaylord Simpson (1902-1984)

  
jeannot



Posts: 1201
Joined: Jan. 2006

(Permalink) Posted: Oct. 10 2007,13:55   

Quote (mitschlag @ Oct. 10 2007,12:47)
Quote (Daniel Smith @ Oct. 10 2007,02:30)
The results that would falsify my hypothesis would be if the coding sequences showed evolutionary constraint while the non-coding sequences didn't.
There's a fair amount of evidence showing that (contrary to expectation) non-coding sequences have fewer base changes than coding sequences...

...at synonymous sites.

  
Henry J



Posts: 5786
Joined: Mar. 2005

(Permalink) Posted: Oct. 10 2007,15:00   

What's makes a site synonymous?

  
mitschlag



Posts: 236
Joined: Sep. 2006

(Permalink) Posted: Oct. 10 2007,15:47   

Quote (Henry J @ Oct. 10 2007,15:00)
What's makes a site synonymous?

 
Quote
Nucleotide substitutions in genes coding for proteins can be either synonymous (do not change amino acid), alternatively called silent substitutions, or non-synonymous (changes amino acid). Usually, most non-synonymous changes would be expected to be eliminated by purifying selection, but under certain conditions Darwinian selection may lead to their retention. Investigating the number of synonymous and non-synonymous substitutions may therefore provide information about the degree of selection operating on a system.
From http://pubmlst.org/software/analysis/start/manual/dsdn.shtml

--------------
"You can establish any “rule” you like if you start with the rule and then interpret the evidence accordingly." - George Gaylord Simpson (1902-1984)

  
JAM



Posts: 517
Joined: July 2007

(Permalink) Posted: Oct. 11 2007,11:00   

Quote (Daniel Smith @ Oct. 08 2007,02:18)
3.  What are presently considered neutral sites will be found to be "instructional" - that is, they will carry the instructions that tell the various proteins, RNA and enzymes where to go, when to go and what to do when they get there.

This is testable. It makes clear predictions about what will happen when we remove the nucleus, for example by cutting off a part of the cell with a laser, creating a cytoplast, or if we sever the axon tethering a neuronal growth cone to its cell body.

It predicts that these proteins will no longer "know what to do." Do you agree, Daniel?

  
Wesley R. Elsberry



Posts: 4991
Joined: May 2002

(Permalink) Posted: Oct. 12 2007,07:35   

ISI's Web of Knowledge says, on search for "linkage disequilibrium" in papers of the last 5 years,

Quote

9,966 results found


Hmmm. The crickets seem to have come out.

--------------
"You can't teach an old dogma new tricks." - Dorothy Parker

    
Alan Fox



Posts: 1556
Joined: Aug. 2005

(Permalink) Posted: Oct. 13 2007,03:52   

Quote
Hmmm. The crickets seem to have come out.


Daniel tells me that he finds this site "too combative", so I am not sure if he will be continuing here.

I do wonder whether posts can sometimes be a little too waspish, but maybe that's just me.

Edited by Wesley R. Elsberry on Oct. 13 2007,05:21

  
Wesley R. Elsberry



Posts: 4991
Joined: May 2002

(Permalink) Posted: Oct. 13 2007,05:23   

Quote (Alan Fox @ Oct. 13 2007,03:52)
Quote
Hmmm. The crickets seem to have come out.


Daniel tells me that he finds this site "too combative", so I am not sure if he will be continuing here.

I do wonder whether posts can sometimes be a little too waspish, but maybe that's just me.

The "edit" and "quote" buttons are right next to each other. I ought to wake up sometime along here. Anyway, my reply that I inadvertently dropped into Alan's comment follows:

I asked,

 
Quote

So, why does the term "linkage disequilibrium" seem to get used by geneticists? Wouldn't your prediction mean that we should see the same degree of linkage disequilibrium everywhere we look? If not, what consequences do you think your "prediction" actually has?


After another page of back-and-forth, there was no indication that Smith was going to address work that was highly relevant to his claim. I think the degree of waspishness in my follow-up was quite in line with the context. I think that one can look at Smith's replies and see that he doesn't consider waspishness a bad thing, when he gets to be the wasp.

--------------
"You can't teach an old dogma new tricks." - Dorothy Parker

    
Alan Fox



Posts: 1556
Joined: Aug. 2005

(Permalink) Posted: Oct. 13 2007,05:43   

Quote
I think the degree of waspishness in my follow-up...


No, Wesley, I certainly didn't mean you, here. I quoted you thinking you were alluding to Daniel's absence. I don't think I have seen a comment of yours that was in any way less than polite. I was thinking of the name-calling that sometimes seems unnecessary to make a point. It can allow the recipient to avoid the substantive issue.

  
Wesley R. Elsberry



Posts: 4991
Joined: May 2002

(Permalink) Posted: Oct. 13 2007,05:56   

Quote

It can allow the recipient to avoid the substantive issue.


That's absolutely right. I've seen that happen a lot.

--------------
"You can't teach an old dogma new tricks." - Dorothy Parker

    
Erasmus, FCD



Posts: 6349
Joined: June 2007

(Permalink) Posted: Oct. 13 2007,13:07   

I'd just rather assume that everyone had read Hume and Kant's criticism of arguments from design.  It is rather strange that 200 years later rudimentary errors in reasoning continue to perpetuate themselves.  as fascinating as 'the complexity of life and nature' is, it is only evidence for 'the complexity of life and nature'.

category errors and crap analogies irritate me.  is that waspish?

--------------
You're obviously illiterate as hell. Peach, bro.-FtK

Finding something hard to believe based on the evidence, is science.-JoeG

the odds of getting some loathsome taint are low-- Gordon E Mullings Manjack Heights Montserrat

I work on molecular systems with pathway charts and such.-Giggles

  
Daniel Smith



Posts: 970
Joined: Sep. 2007

(Permalink) Posted: Oct. 13 2007,13:22   

Quote (Wesley R. Elsberry @ Oct. 12 2007,07:35)
ISI's Web of Knowledge says, on search for "linkage disequilibrium" in papers of the last 5 years,

 
Quote

9,966 results found


Hmmm. The crickets seem to have come out.

I've been trying to wrap my head around the concept of linkage disequilibrium but am not having much luck.  It's a bit over my head - which is why I haven't responded to your post yet.  Perhaps if you could explain the concept in layman's terms I could give you an answer.  Either that, or you'll have to wait awhile.

--------------
"If we all worked on the assumption that what is accepted as true is really true, there would be little hope of advance."  Orville Wright

"The presence or absence of a creative super-intelligence is unequivocally a scientific question."  Richard Dawkins

  
JAM



Posts: 517
Joined: July 2007

(Permalink) Posted: Oct. 13 2007,13:49   

Quote (Daniel Smith @ Oct. 13 2007,13:22)
Quote (Wesley R. Elsberry @ Oct. 12 2007,07:35)
ISI's Web of Knowledge says, on search for "linkage disequilibrium" in papers of the last 5 years,

   
Quote

9,966 results found


Hmmm. The crickets seem to have come out.

I've been trying to wrap my head around the concept of linkage disequilibrium but am not having much luck.  It's a bit over my head - which is why I haven't responded to your post yet.  Perhaps if you could explain the concept in layman's terms I could give you an answer.  Either that, or you'll have to wait awhile.

Maybe while you're trying to wrap your head around linkage disequilibrium, you can point us to a designed mechanism involving large numbers of similar, but not identical, parts, that have only partially overlapping functions.

That mechanism would be analogous to living ones.

Also, you can directly test your hypothesis that noncoding regions are conserved by peeking at the VISTA genome browser:

http://pipeline.lbl.gov/cgi-bin/gateway2?bg=hg16

You're not gonna like what you see, so you probably should blow it off and not try to grapple with any real evidence. Here's an idea--pretend that our calling you out on your false claims is mean, which automatically makes your false claims correct (at least in your mind).

  
Daniel Smith



Posts: 970
Joined: Sep. 2007

(Permalink) Posted: Oct. 13 2007,13:50   

Quote (Erasmus @ FCD,Oct. 10 2007,07:36)
Daniel we know people make things like stonehenge.

What designer do we know of that makes cells and platypi and the grand canyon?  People?  Or something else?  I'll wait for your answer.
That's Right!!!!  We don't know of any such designer!!!  You Lose!!!

I'm proposing that the designer is not human but has qualities similar to human qualities (intelligence, free agency, etc.).

I am proposing this entity has infinite intelligence and that it would require intelligence of that kind to design the universe and life.

IOW, if all this is designed (including us), whatever designed it is as far above us intellectually as the cosmos are above us physically.

--------------
"If we all worked on the assumption that what is accepted as true is really true, there would be little hope of advance."  Orville Wright

"The presence or absence of a creative super-intelligence is unequivocally a scientific question."  Richard Dawkins

  
Daniel Smith



Posts: 970
Joined: Sep. 2007

(Permalink) Posted: Oct. 13 2007,13:53   

Quote (mitschlag @ Oct. 10 2007,12:47)
 
Quote (Daniel Smith @ Oct. 10 2007,02:30)
The results that would falsify my hypothesis would be if the coding sequences showed evolutionary constraint while the non-coding sequences didn't.
There's a fair amount of evidence showing that (contrary to expectation) non-coding sequences have fewer base changes than coding sequences, see, for example:
http://www.biomedcentral.com/1471-2148/7/66
   
Quote
The primary result is that the mean rate of intergenic nucleotide substitution is two-thirds that of the synonymous coding data, with an absolute rate estimated to be 1.05 × 10-8 substitutions per site per year. This result holds with alternative nucleotide models (see Methods), and thus does not appear to be solely an issue of estimation procedures.

Slower rates in non-coding regions relative to synonymous sites are becoming a surprisingly frequent observation. For example, a recent study of Drosophila demonstrated that non-coding DNA evolves considerably slower than synonymous sites in terms of both divergence between species and polymorphism within species [16]. By comparing studies, one can also make the case that pseudogenes [32,33] and introns [34,35] evolve more slowly than synonymous sites in apes and other mammals [13,36-38]. Studies of mammalian intergenic regions have also found slower rates than synonymous sites [35,39,40]. Although most of these studies encompass only a handful of genes, an overall picture of relatively slow non-coding rates is emerging.

What do you make of that?

If this is true, then it would be a confirmation of my hypothesis with better than expected results.

--------------
"If we all worked on the assumption that what is accepted as true is really true, there would be little hope of advance."  Orville Wright

"The presence or absence of a creative super-intelligence is unequivocally a scientific question."  Richard Dawkins

  
Daniel Smith



Posts: 970
Joined: Sep. 2007

(Permalink) Posted: Oct. 13 2007,14:00   

Quote (JAM @ Oct. 10 2007,10:40)

Here's an opposing hypothesis:

Known functional sequences will be evolutionarily conserved. Most sequences will not be conserved. We will continue to find functions for some conserved sequences for which no function has been identified.

What do you think? Shall we look at the evidence to see which hypothesis is better supported?

Yes, let's look.  But be warned, I'll be approaching the evidence from a different perspective than you and won't accept any preconceived ideas as part of the interpretation.  What I mean is that the perceived "rate of mutation" is often calculated by a comparison of species that are assumed to have evolved from a common ancestor via an accumulation of random mutations.  Since I am opposing that theory, I won't accept that assumption.  You must show me that the evidence supports this assumed buildup of random mutations first, then we can move on from there.

Fair enough?

--------------
"If we all worked on the assumption that what is accepted as true is really true, there would be little hope of advance."  Orville Wright

"The presence or absence of a creative super-intelligence is unequivocally a scientific question."  Richard Dawkins

  
Daniel Smith



Posts: 970
Joined: Sep. 2007

(Permalink) Posted: Oct. 13 2007,14:17   

Quote (JAM @ Oct. 11 2007,11:00)
 
Quote (Daniel Smith @ Oct. 08 2007,02:18)
3.  What are presently considered neutral sites will be found to be "instructional" - that is, they will carry the instructions that tell the various proteins, RNA and enzymes where to go, when to go and what to do when they get there.

This is testable. It makes clear predictions about what will happen when we remove the nucleus, for example by cutting off a part of the cell with a laser, creating a cytoplast, or if we sever the axon tethering a neuronal growth cone to its cell body.

It predicts that these proteins will no longer "know what to do." Do you agree, Daniel?

Well, I'm not sure what affect removing the nucleus would have on existing, functioning proteins - since they should already know what to do.  If however, you were able to remove non-coding regions (by this I mean supposed neutral sequences) while leaving the coding sequences intact, then (according to my prediction) the proteins produced would not know what to do.

--------------
"If we all worked on the assumption that what is accepted as true is really true, there would be little hope of advance."  Orville Wright

"The presence or absence of a creative super-intelligence is unequivocally a scientific question."  Richard Dawkins

  
Daniel Smith



Posts: 970
Joined: Sep. 2007

(Permalink) Posted: Oct. 13 2007,14:41   

Quote (C.J.O'Brien @ Oct. 10 2007,12:35)
That there is a certain kind of elegance to biochemical processes is not in question. They work well enough to have sustained evolving life on Earth for billions of years, and are perfectly capable of supporting the functions of big, complex animals like ourselves. So I am not saying that they barely "get the job done." I am saying, though, that all of the highly-touted complexity of the cell, when it is actually investigated, not simply remarked upon, seems to owe its existence to a maddeningly short-sighted designer --one that seems incabable of building a structure or pathway using anything other than pre-existing components, often themselves integral parts of other, fully functioning systems. But you challenged me for examples.

Here is Ken Miller on the vertebrate blood-clotting cascade

Here is a TalkOrigins summary of several articles on the evolution of the Krebs Cycle

Here is an abstract of a Science paper on the evolution of a steroid-hormone receptor

The articles and abstracts you cite are just explanations of how such systems theoretically could have evolved - not evidence that these systems are cobbled together "Rube Goldberg" type systems.

I found this item from the article on blood clotting interesting:  
Quote
If the modern fibrinogen gene really was recruited from a duplicated ancestral gene, one that had nothing to do with blood clotting, then we ought to be able to find a fibrinogen-like gene in an animal that does not possess the vertebrate clotting pathway. In other words, we ought to be able to find a non-clotting fibrinogen protein in an invertebrate. That's a mighty bold prediction, because if it could not be found, it would cast Doolittle's whole evolutionary scheme into doubt.

Not to worry. In 1990, Xun Yu and Doolittle won their own bet, finding a fibrinogen-like sequence in the sea cucumber, an echinoderm. The vertebrate fibrinogen gene, just like genes for the other proteins of the clotting sequence, was formed by the duplication and modification of pre-existing genes.

This prediction does not seem that "bold" to me - since we already know that convergent evolution produces analogous sequences in unrelated animals.  In fact, I'll be even bolder and predict that you can take any gene and find something "like it" somewhere in some unrelated organism's genome.

--------------
"If we all worked on the assumption that what is accepted as true is really true, there would be little hope of advance."  Orville Wright

"The presence or absence of a creative super-intelligence is unequivocally a scientific question."  Richard Dawkins

  
jeannot



Posts: 1201
Joined: Jan. 2006

(Permalink) Posted: Oct. 13 2007,14:57   

Quote (Daniel Smith @ Oct. 13 2007,13:53)
Quote (mitschlag @ Oct. 10 2007,12:47)
 
Quote (Daniel Smith @ Oct. 10 2007,02:30)
The results that would falsify my hypothesis would be if the coding sequences showed evolutionary constraint while the non-coding sequences didn't.
There's a fair amount of evidence showing that (contrary to expectation) non-coding sequences have fewer base changes than coding sequences, see, for example:
http://www.biomedcentral.com/1471-2148/7/66
   
Quote
The primary result is that the mean rate of intergenic nucleotide substitution is two-thirds that of the synonymous coding data, with an absolute rate estimated to be 1.05 × 10-8 substitutions per site per year. This result holds with alternative nucleotide models (see Methods), and thus does not appear to be solely an issue of estimation procedures.

Slower rates in non-coding regions relative to synonymous sites are becoming a surprisingly frequent observation. For example, a recent study of Drosophila demonstrated that non-coding DNA evolves considerably slower than synonymous sites in terms of both divergence between species and polymorphism within species [16]. By comparing studies, one can also make the case that pseudogenes [32,33] and introns [34,35] evolve more slowly than synonymous sites in apes and other mammals [13,36-38]. Studies of mammalian intergenic regions have also found slower rates than synonymous sites [35,39,40]. Although most of these studies encompass only a handful of genes, an overall picture of relatively slow non-coding rates is emerging.

What do you make of that?

If this is true, then it would be a confirmation of my hypothesis with better than expected results.

Daniel, you still need explain what your hypothesis is.
You merely provided one prediction, which is a totally different thing. Without your hypothesis clearly detailed, a prediction is useless.

I still don't see why you'd expect similar "evolutionary constraint" in coding and non coding sites.

  
Daniel Smith



Posts: 970
Joined: Sep. 2007

(Permalink) Posted: Oct. 13 2007,14:58   

Quote (JAM @ Oct. 13 2007,13:49)
Maybe while you're trying to wrap your head around linkage disequilibrium, you can point us to a designed mechanism involving large numbers of similar, but not identical, parts, that have only partially overlapping functions.

That mechanism would be analogous to living ones.

So we're accepting analogies as evidence now?  
Quote


Also, you can directly test your hypothesis that noncoding regions are conserved by peeking at the VISTA genome browser:

http://pipeline.lbl.gov/cgi-bin/gateway2?bg=hg16

You're not gonna like what you see, so you probably should blow it off and not try to grapple with any real evidence. Here's an idea--pretend that our calling you out on your false claims is mean, which automatically makes your false claims correct (at least in your mind).

I went to the vista site, but I'm not sure how to use it.  I'll have to read the help file I guess.

BTW, you are generally mean - but I'm still here.
Your meanness has nothing to do with your rightness.

--------------
"If we all worked on the assumption that what is accepted as true is really true, there would be little hope of advance."  Orville Wright

"The presence or absence of a creative super-intelligence is unequivocally a scientific question."  Richard Dawkins

  
Daniel Smith



Posts: 970
Joined: Sep. 2007

(Permalink) Posted: Oct. 13 2007,15:02   

Quote (Wesley R. Elsberry @ Oct. 13 2007,05:23)
The "edit" and "quote" buttons are right next to each other.

I see no "Edit" button with my browser (Mozilla Firefox).  All I see is a question mark (?) next to the "Quote" button - even on my own posts.

--------------
"If we all worked on the assumption that what is accepted as true is really true, there would be little hope of advance."  Orville Wright

"The presence or absence of a creative super-intelligence is unequivocally a scientific question."  Richard Dawkins

  
Daniel Smith



Posts: 970
Joined: Sep. 2007

(Permalink) Posted: Oct. 13 2007,15:07   

Quote (jeannot @ Oct. 13 2007,14:57)
Daniel, you still need explain what your hypothesis is.
You merely provided one prediction, which is a totally different thing. Without your hypothesis clearly detailed, a prediction is useless.

I still don't see why you'd expect similar "evolutionary constraint" in coding and non coding sites.

Because my hypothesis - which I have already explained here - is that most (if not all) of the genome is used (non-neutral), and so because of this, there are not a bunch of random mutations accumulating in non-coding (neutral) sites.
I've restated it several times, I'm not sure how I can make it any clearer.

--------------
"If we all worked on the assumption that what is accepted as true is really true, there would be little hope of advance."  Orville Wright

"The presence or absence of a creative super-intelligence is unequivocally a scientific question."  Richard Dawkins

  
jeannot



Posts: 1201
Joined: Jan. 2006

(Permalink) Posted: Oct. 13 2007,15:16   

Quote (Daniel Smith @ Oct. 13 2007,15:07)
Quote (jeannot @ Oct. 13 2007,14:57)
Daniel, you still need explain what your hypothesis is.
You merely provided one prediction, which is a totally different thing. Without your hypothesis clearly detailed, a prediction is useless.

I still don't see why you'd expect similar "evolutionary constraint" in coding and non coding sites.

Because my hypothesis - which I have already explained here - is that most (if not all) of the genome is used (non-neutral), and so because of this, there are not a bunch of random mutations accumulating in non-coding (neutral) sites.
I've restated it several times, I'm not sure how I can make it any clearer.

So what about the fact that mutation rates are far higher at synonymous sites?

  
Wesley R. Elsberry



Posts: 4991
Joined: May 2002

(Permalink) Posted: Oct. 13 2007,16:36   

Quote

I see no "Edit" button with my browser (Mozilla Firefox).


You should see an edit button on your own posts, but not other people's posts.

With moderator privileges, the edit button is on every comment.

--------------
"You can't teach an old dogma new tricks." - Dorothy Parker

    
JAM



Posts: 517
Joined: July 2007

(Permalink) Posted: Oct. 13 2007,17:14   

Quote (Daniel Smith @ Oct. 13 2007,14:00)
 
Quote (JAM @ Oct. 10 2007,10:40)

Here's an opposing hypothesis:

Known functional sequences will be evolutionarily conserved. Most sequences will not be conserved. We will continue to find functions for some conserved sequences for which no function has been identified.

What do you think? Shall we look at the evidence to see which hypothesis is better supported?

Yes, let's look.  But be warned, I'll be approaching the evidence from a different perspective than you and won't accept any preconceived ideas as part of the interpretation.

Daniel, this is why real, honest scientists make predictions BEFORE they get the data.

My hypothesis predicts that when we graph position on the x axis and % identity on the Y axis, we will see this, with the high points representing conserved sequences, which include, but are definitely not limited to, protein-coding sequences:
/\_/\___

Your hypothesis predicts that we will see a flat line wherever we look:

--------------
Quote
What I mean is that the perceived "rate of mutation" is often calculated by a comparison of species that are assumed to have evolved from a common ancestor via an accumulation of random mutations.

Not even remotely close, Daniel. Mutation rates are much more directly measured by quantitating new mutations; for example, we can measure the rate of new cases of autosomal dominant diseases that aren't inherited from parents. No assumptions are necessary to distinguish between our hypotheses. We are simply looking at differences between lineages for orthologous regions of the genome.
Quote
Since I am opposing that theory, I won't accept that assumption.

I'm not making any such assumption, so your desperate evasion won't work. You might want to reread the hypothesis we're testing.
Quote
You must show me that the evidence supports this assumed buildup of random mutations first, then we can move on from there.

Nope. That's not how science works. We use hypotheses to make predictions, and then we look at the evidence to see whether it is consistent or inconsistent.

Only pseudoscientists who have zero confidence in their hypotheses make petulant demands like yours.

  
  1733 replies since Sep. 18 2007,15:27 < Next Oldest | Next Newest >  

Pages: (58) < ... 7 8 9 10 11 [12] 13 14 15 16 17 ... >   


Track this topic Email this topic Print this topic

[ Read the Board Rules ] | [Useful Links] | [Evolving Designs]