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Author Topic:   Dr. Schwartz' "MIssing Links"
AdminNosy
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Posts: 4754
From: Vancouver, BC, Canada
Joined: 11-11-2003


Message 76 of 86 (417346)
08-20-2007 1:01 PM
Reply to: Message 73 by Refpunk
08-20-2007 9:42 AM


Topic Warning for Refpunk
Refpunk, Several posters have noted that you are off topic in this thread. If you want to rant about the definition of animals (or any other taxonomic issue) please start a new thread on that.

You will not be allowed to post randomly so pick your posts more carefully. I also suggest that you take EvC as an opportunity to learn about many topics which you obviously know nothing about.

You next randomly off topic post will earn you a days suspension.


This message is a reply to:
 Message 73 by Refpunk, posted 08-20-2007 9:42 AM Refpunk has responded

Replies to this message:
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arachnophilia
Member (Idle past 55 days)
Posts: 9069
From: god's waiting room
Joined: 05-21-2004


Message 77 of 86 (417433)
08-21-2007 1:23 AM
Reply to: Message 73 by Refpunk
08-20-2007 9:42 AM


octopoda
Then what is an octopus?

a mollusc.

An insect?

no, insects are arthropods.

Sorry, but an octopus is a sea animal because it's a form of fish.

you can't be serious. you're putting us on, right? this is a joke? do i need to show you pictures of fish and octopodes? they're clearly not the same thing. for one, an octopus isn't even a vertebrate. actually, it's not even a CHORDATE. it has no spinal column. it has a nervous system, but it's not centralized in the same way a fish's (or a human's) is.

you'll note that tetrapods (four-legged animals) are all related to fish, but that octopodes (8 legs) and teuthoids (10 legs) are not tetrapods. neither are arthropods (number of legs varies). all are animals.

the octopus is more closely related to snails. really. here's 2/3rds of an exam question from my 2nd intro paleo course, that i just happen to have on hand. (i've labelled it for clarity)


click to expand

octopodes and teuthoids are basically the same as early nautiloids, minus the shell. early nautiloid are basically snails with snorkels an appendages. that diagram's from memory. you could easily dig up much more information (like, actual fossils) if you do some real research. and for that matter, i draw a lot better when not under pressure and time constraints.

Edited by arachnophilia, : No reason given.


אָרַח

This message is a reply to:
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Replies to this message:
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AdminNosy
Administrator
Posts: 4754
From: Vancouver, BC, Canada
Joined: 11-11-2003


Message 78 of 86 (417434)
08-21-2007 1:53 AM
Reply to: Message 77 by arachnophilia
08-21-2007 1:23 AM


back up ARCH
I think you are getting w a y ahead of refpunk. No one has justified the Linnean hierarchy to him yet.

I think if someone is patient enough (and foolish enough) they can try to explain this from a much, much simpler level.


This message is a reply to:
 Message 77 by arachnophilia, posted 08-21-2007 1:23 AM arachnophilia has responded

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arachnophilia
Member (Idle past 55 days)
Posts: 9069
From: god's waiting room
Joined: 05-21-2004


Message 79 of 86 (417435)
08-21-2007 1:55 AM
Reply to: Message 78 by AdminNosy
08-21-2007 1:53 AM


Re: back up ARCH
*shrug* i thought pictures might help.
This message is a reply to:
 Message 78 by AdminNosy, posted 08-21-2007 1:53 AM AdminNosy has not yet responded

  
Refpunk
Member (Idle past 4130 days)
Posts: 60
Joined: 08-17-2007


Message 80 of 86 (417850)
08-24-2007 10:59 PM
Reply to: Message 76 by AdminNosy
08-20-2007 1:01 PM


Re: Topic Warning for Refpunk
It doesn't take much to suspend people who don't agree with the theory of evolution. But I can assure you, that if one doesn't know why animals can't breed human descendants, then of course, he can't understand that there can be NO missing link. So my post is at the crux of the topic of this thread. So I'll wait until you evolutionists have understood the birds and the bees before you're ready to talk about what animals and humans are capable of breeding. But since I don't think that will happen any time in the near future, then you're not ready for me yet.

Edited by Refpunk, : No reason given.


This message is a reply to:
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Replies to this message:
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 Message 84 by AnswersInGenitals, posted 09-24-2007 6:12 PM Refpunk has not yet responded

    
Taz
Member (Idle past 1369 days)
Posts: 5069
From: Zerus
Joined: 07-18-2006


Message 81 of 86 (417858)
08-24-2007 11:17 PM
Reply to: Message 80 by Refpunk
08-24-2007 10:59 PM


Re: Topic Warning for Refpunk
I suppose you're a college professor of biological science specializing in developmental biology and genetics?


Disclaimer:

Occasionally, owing to the deficiency of the English language, I have used he/him/his meaning he or she/him or her/his or her in order to avoid awkwardness of style.

He, him, and his are not intended as exclusively masculine pronouns. They may refer to either sex or to both sexes!


This message is a reply to:
 Message 80 by Refpunk, posted 08-24-2007 10:59 PM Refpunk has not yet responded

  
Percy
Member
Posts: 18309
From: New Hampshire
Joined: 12-23-2000
Member Rating: 2.7


Message 82 of 86 (418007)
08-25-2007 9:11 PM
Reply to: Message 80 by Refpunk
08-24-2007 10:59 PM


Re: Topic Warning for Refpunk
Hi Refpunk,

I see you believe that creationists are treated unfairly here:

Refpunk writes:

It doesn't take much to suspend people who don't agree with the theory of evolution.

This is a sentiment frequently voiced by creationists, but this site needs creationists, because without them there would be nobody to discuss with and the site would go idle. Suspending creationists for expressing creationist viewpoints would be counterproductive.

But we do have Forum Guidelines that are designed to make discussion as rewarding and informative as possible for the participants, and your suspensions result from your inability or unwillingness, I'm not sure which, to follow them. Follow the Forum Guidelines by focusing your discussion on the topic and your difficulties should cease.

--Percy


This message is a reply to:
 Message 80 by Refpunk, posted 08-24-2007 10:59 PM Refpunk has not yet responded

    
derwood
Member
Posts: 1457
Joined: 12-27-2001


Message 83 of 86 (423839)
09-24-2007 3:04 PM
Reply to: Message 67 by RAZD
08-17-2007 7:10 PM


Now I remember why I stopped coming here..
quote:
quote:
They ARE the actual amounts of change in the branch between the LCA and the taxon in question.

Not to belabor this, but they are the average rates, by definition.


Considering how I am one of the authors of the paper in question, I think I know what we were looking at, and rates - average or otherwise - had nothing to do with it. You are confusing the comparison of total changes in branch lengths to glean differences in rates of mutation accumulation to some sort of statement about the average rates of mutation.

So when you wrote: "...and then give us average rates of change for each segment in between while saying that these are the actual rates of change in those groups for those periods." you were totally off base. Nowhere did we say anything about average rates at all, in terms of absolute rates per lineage. If you read the paper, the discussion of rates entailed observations of comparisons between branch lengths of various taxa. We did not assign them any rates, we did not conclude that their rate of mutation was X, we merely compared the resulting branch lengths and described what we saw.

quote:

You do not know when each individual fixed selected mutation occurred, you don't even know if half occurred in the first half of the time period and half occurred in the second half or whether 90% occurred in the first half and 10% in the second. All you have is (n) mutations occurred in (t) time and the average rate of mutation over time (t) was (n/t). Within that time period (t) the specific rate of change could have varied considerably: you don't know.

A most astute and insightful series of proclamations. Now, if only we had done what you appear to insist we did, there might be some relevance here, but as we were not assigning rates - average or otherwise - your criticisms are still baseless and bordering on the hysterical.

What is more, the distribution of the occurrence of mutations along some spectrum is utterly irrelevant as to the analyses we performed. The observations about differences in mutation accumulation in different lineages was a by-product of what we were really interested in.

For example, we wrote:

"We further utilized the percentages of nucleotide change on the branches of the phylogenetic trees in Figs. 3 and 4 along with the estimated ages of the branch points (Table 4) to obtain estimates of evolutionary rates for noncoding DNA. These results are presented in Table 5. They indicate that noncoding DNA accumulated change at a slower rate."

See? We were concerned with rates of accumulation, we were not postulating anything about the rate of occurrance:

"It has been observed that during primate evolution the rate of accumulation of nucleotide substitutions in noncoding DNA markedly slowed in anthropoids and..."

It simply does not matter when the rates of occurrance might have been faster or slower. We were looking at the total - the end results.

quote:
quote:

I fail to see the relevance of this.
["this" refers to: "My main criticism of molecular clocks is that it cannot differentiate between survival selection and sexual selection. In the case of human evolution there is pretty good evidence for fisherian runaway sexual selection,..."]

They would de facto have different rates of fixing selected mutations.

And it would still be irrelevant for the our purposes.
quote:
quote:

This is irrelevant to the general 'accuracy' of local clock calculations. The goal of such calculations is not to make such differentiations. Your criticisms seem similar to Paul Nelson's criticism of molecular phylogenetics as being a diversion because they do not explain what the mechancim behind the changes is.

Again the rate of fixing selected mutations would be de facto different under punctuated versus stasis conditions.


And it would still be irrelevant to the study in question.
quote:
quote:

Well of course, but criticising a paper in which the goal was not to do that for not doing that seems superfluous.

You were the one that introduced the paper in answer to my criticism. If it doesn't do that it is not my fault.

Um, well, OK, but I recall introducing the paper to address this:

Now when we compare "molecular clocks" for mtDNA Eve and yChrom Adam what do we see? More change in Eve than in Adam? Longer change in Eve than in Adam or slower change in Adam than in Eve? We don't know. There is no connection to fossils, hard data, to be able to say at this point.

In my reply, I wrote:

"Again, that is not always the case. Local molecular clocks use fossil divergence dates as calibration points. This paper, for example, employs such clocks and its results are quite congruent with dates inferred from fossil data when applicable. "

So, I think it pretty clear why I introduced it and in reference to what, and it was not inreference ot criticisms about knowing when mutations took place of whether or not the mutations were in coding DNA or not and whether they were beneficial or not, etc.

quote:
quote:

Yes. Since local molecular clocks do not rely on any assumptions about mutation rates or rate differentials, a sufficiently large data set will not suffer from potential short term bursts of mutation and selection or the lack thereof.

Nor will it be able to identify short term bursts or conditions under which they may apply.


Totally insightful! And here is more shocking news - shovels don't work well when you want to chop down trees...

quote:

Thus it will be unable to identify when a period could be high rate or low rate. By identifying average rates as uniform rates over long periods it also ignores the fact that different rates occur during different times.


No, it does not. If for the sake of discussion we adopt your forced position that we were assigning average rates, the very term 'average' means that such differences have been taken into account. That is how one gets averages. Again, for the purposes of the paper in question, such criticisms are superfluous and irrelevant.

quote:

One thing I do note from your paper is that the different rates are significantly different even in spite of the averaging of the rates over the time periods involved. To me this is validation that different rates occur regularly during evolution. I would think that the question of rate changes and maximum rates of change would be of high interest.


They may well be for some, but it is a mistake to presume that all researchers are interested in and will devote time to all things that appear to be of interest.

quote:
It is logical for me that the rates of selecting and fixing change away from other daughter species would be higher for one or both than the average rate of selecting and fixing change.

This would make understanding the magnitudes of different rates of fixing selected mutations fairly critical to the understanding of speciation and the causes of different rates. Especially if you are doing studies involving multiple speciation events or periods of intense selection pressure.

Different rates of selecting and fixing mutations is part of evolution, and understanding those different rates, and the conditions under which they occur, is also part of understanding evolution.


That may well be, but such understanding is not required when doing analyses in which such differentiations are irrelevant.

Perhaps an analogy is in order.

I am in the business of starting with endpoints and trying to figure out starting points, or stops along the way to the end point, say for cars in a road race. When the cars get to the finish line, I try to figure out where they started from (crazy road race). Upon discerning a starting point for the race, we can observe that car A took much longer than car B to reach the end, even though they started from the same place. I might then conclude that car A drove more slowly than car B. Now, car A might have gone full speed for several miles, then pulled off the side of the road for a rest, then coasted for a time, etc., while car B drove at a steady pace for the entire race.
Would that really matter if my only concern was how long it took each car to get to the end? Regardless of car A's driver's habits, it still took longer to get to the end, even if car A drove super fast for a long tiome and only then slowed down.
Your complaint seems to be that because I did not map out when and for how long car A went super fast then slow, that I cannot draw conclusions about who won the race.


This message is a reply to:
 Message 67 by RAZD, posted 08-17-2007 7:10 PM RAZD has responded

Replies to this message:
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AnswersInGenitals
Member
Posts: 509
Joined: 07-20-2006
Member Rating: 3.4


Message 84 of 86 (423877)
09-24-2007 6:12 PM
Reply to: Message 80 by Refpunk
08-24-2007 10:59 PM


Re: Topic Warning for Refpunk
...if one doesn't know why animals can't breed human descendants...

There is (at least) one species of animal that is capable of breeding human descendants.


This message is a reply to:
 Message 80 by Refpunk, posted 08-24-2007 10:59 PM Refpunk has not yet responded

  
RAZD
Member
Posts: 19757
From: the other end of the sidewalk
Joined: 03-14-2004
Member Rating: 5.8


Message 85 of 86 (423927)
09-24-2007 8:38 PM
Reply to: Message 83 by derwood
09-24-2007 3:04 PM


What's the problem?
Considering how I am one of the authors of the paper in question, I think I know what we were looking at, and rates - average or otherwise - had nothing to do with it. You are confusing the comparison of total changes in branch lengths to glean differences in rates of mutation accumulation to some sort of statement about the average rates of mutation.

So when you wrote: "...and then give us average rates of change for each segment in between while saying that these are the actual rates of change in those groups for those periods." you were totally off base. Nowhere did we say anything about average rates at all, in terms of absolute rates per lineage.

So when you say "rate" you don't mean rate as in X/Y, but the total change? If I misunderstood your use of terms then I apologize for that. You can put me down as totally confused by your use of "rate" to mean "total".

(you quoting the paper)
"We further utilized the percentages of nucleotide change on the branches of the phylogenetic trees in Figs. 3 and 4 along with the estimated ages of the branch points (Table 4) to obtain estimates of evolutionary rates for noncoding DNA. These results are presented in Table 5. They indicate that noncoding DNA accumulated change at a slower rate."

"It has been observed that during primate evolution the rate of accumulation of nucleotide substitutions in noncoding DNA markedly slowed in anthropoids and..."

Now when I substitute "total" for "rate" I am even more confused. "Total" does not make any sense. If you do mean "rate" as in X/Y, I have no idea what your Y is anymore if it does not refer to the length of time for the branch.

See? We were concerned with rates of accumulation, we were not postulating anything about the rate of occurrance

It simply does not matter when the rates of occurrance might have been faster or slower. We were looking at the total - the end results.

Now you are drawing a distinction between all mutations and accumulation (fixation) of mutations, point taken, and if I misrepresented that mea culpa because I should (do) know better. Obviously you could not know what the number of mutations would be, as only the fixed ones are remaining in the DNA of today.

(you quoting me}
Again the rate of fixing selected mutations would be de facto different under punctuated versus stasis conditions.

See? Fixed mutations. You can put me down for not being specific in talking about mutations in other places then.

However ... if anything, this just changes (refines) the X, and I am having a real hard time understanding what your Y is, for if you are talking about an X/Y rate of change, and if it is not the time period of the branch, then what is it? Substituting total for rate does not make any sense.

(you quoting me back at the start of this issue):
Now when we compare "molecular clocks" for mtDNA Eve and yChrom Adam what do we see? More change in Eve than in Adam? Longer change in Eve than in Adam or slower change in Adam than in Eve? We don't know. There is no connection to fossils, hard data, to be able to say at this point.

In my reply, I wrote:

"Again, that is not always the case. Local molecular clocks use fossil divergence dates as calibration points. This paper, for example, employs such clocks and its results are quite congruent with dates inferred from fossil data when applicable. "

So, I think it pretty clear why I introduced it and in reference to what, and it was not inreference ot criticisms about knowing when mutations took place of whether or not the mutations were in coding DNA or not and whether they were beneficial or not, etc..

So your whole point was that in some studies the "molecular clock" is calibrated against the fossil record? I have not questioned that in any way, and am actually impressed by it. Good work etc etc. I think it was a great study and we need more like it.

I also noted that you showed different rates of accumulation of mutations in different lineages -- assuming (as I did) that you meant number of fixed changes per time period of each branch as the "rate" of change. This supports my criticism of "molecular clocks" for assuming constant or average rates of change rather than noting that there is a lot of variation in rates of change.

I further noted that your study is subject to the same problem, and you readily admit that this is the case:

quote:
quote:
(you) Yes. Since local molecular clocks do not rely on any assumptions about mutation rates or rate differentials, a sufficiently large data set will not suffer from potential short term bursts of mutation and selection or the lack thereof.

(me) Nor will it be able to identify short term bursts or conditions under which they may apply.

(you) Totally insightful! And here is more shocking news - shovels don't work well when you want to chop down trees...

What's the big deal? It's not like you were capable of finer resolution of the data, you only had a certain small number of fossils that could be used. So let's agree that the study could not possibly have measured any instantateous rates of accumulation of mutations at any time in the whole study. I am not criticising you for failure to do that.

No, it does not. If for the sake of discussion we adopt your forced position that we were assigning average rates, the very term 'average' means that such differences have been taken into account. That is how one gets averages. Again, for the purposes of the paper in question, such criticisms are superfluous and irrelevant.

Precisely. And my point was that not using "average" in the terminology leads to the impression that there are no significant changes in rates of accumulation of change inside those periods. You have valid reasons for this in the limitations of the study. Why the fuss over using average if that is in fact what you were ending up with? Particularly if it is the correct terminology?

Perhaps an analogy is in order.

I am in the business of starting with endpoints and trying to figure out starting points, or stops along the way to the end point, say for cars in a road race. When the cars get to the finish line, I try to figure out where they started from (crazy road race). Upon discerning a starting point for the race, we can observe that car A took much longer than car B to reach the end, even though they started from the same place. I might then conclude that car A drove more slowly than car B. Now, car A might have gone full speed for several miles, then pulled off the side of the road for a rest, then coasted for a time, etc., while car B drove at a steady pace for the entire race.
Would that really matter if my only concern was how long it took each car to get to the end? Regardless of car A's driver's habits, it still took longer to get to the end, even if car A drove super fast for a long tiome and only then slowed down.
Your complaint seems to be that because I did not map out when and for how long car A went super fast then slow, that I cannot draw conclusions about who won the race.

No, my point is that you don't know what maximum speeds the cars are capable of or what kind of sustained high speed they can travel at, and thus if you are looking at a shorter or less intensive race course, or just any different race course, you have no idea whether car A or car B will win. You have no real predictive ability, because all you have is the average speed of each car from that one race. You may have an educated guess, but that is the best it is.

They may well be for some, but it is a mistake to presume that all researchers are interested in and will devote time to all things that appear to be of interest.

That may well be, but such understanding is not required when doing analyses in which such differentiations are irrelevant.

Until you do deal with the variability of rates of accumulation of mutations, you will not have any real predictive ability.

That was my criticism of "molecular clocks" in general and the "adam" and "eve" studies in specific -- that they were making predictions of their age on insufficient information and assumptions of uniformity that don't necessarily apply -- and I see absolutely no reason (yet) to change my mind on this issue.

But it seems that your whole problem is over the use of average in the terminology, and I really have to wonder what the big deal is on this issue.

Enjoy.


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This message is a reply to:
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derwood
Member
Posts: 1457
Joined: 12-27-2001


Message 86 of 86 (430927)
10-28-2007 11:23 AM


Some people are just uberexperts in everything, I guess...
    
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