Watch and consider IV

[pshun2404]

Is it, or is it not consistent with the hypothesis that it is a broken gene?

Just because it is different (in form or function) does not mean it is "broken"...I gave you a couple of other examples already.

 

[46AND2]

The fact that you (or anyone) would assume these difference equal there being an ancestral creature with a consistent genome from which these all mutated is a huge leap of blind faith. It is just as likely that they are simply different unrelated organisms and that's why the genomes are different.

Quit equating the lines with ancestry. I told you the data forms nested hierarchy, regardless of of how or why. The lines simply illustrate sets and subsets. i.e., at a certain point all 4 species contain the base, until one branches off, and so on.

 

[46AND2]

Just because it is different (in form or function) does not mean it is "broken"...I gave you a couple of other examples already.

I didn't ask you if it was proof of being broken, I asked if it was consistent with it.

 

[pshun2404]

Quit equating the lines with ancestry. I told you the data forms nested hierarchy, regardless of of how or why. The lines simply illustrate sets and subsets. i.e., at a certain point all 4 species contain the base, until one branches off, and so on.

First off it is the LINES that equate them with the Common ancestry default. But fine...Branches off from what?

And yes I do keep pointing this to common ancestry, because that was the point of bringing up the GULO gene. Its alleged "broken" nature points to the Ancestor of the Gaps. So branches off from what?

 

[pshun2404]

Again...One reason for some such “differences” has been discussed here:

http://www.the-scientist.com/?articles.view/articleNo/45316/title/Same-Gene--Different-Functions/

“The researchers found that, on average, two related isoforms shared less than 50 percent of interacting proteins; 16 percent of related isoforms shared none at all. These differences in interaction partners were often associated with only tiny alterations in DNA sequence—sometimes just a single base pair.”

This reflects the importance of counting each base pair for what it actually is, and not using computer programs to split it up to create gaps that are not really there (even when it presents the illusion of insertions and deletions where these are just natural sequential “DIFFERENCES” between different organisms) Anywhere in the genome a single base pair can alter the function of a gene in different organisms or even render it appear to be functionless (but that does not make it broken just different...it may be exactly what it is supposed to be in that organism.

 

[Subduction Zone]

Again...One reason for some such “differences” has been discussed here:

http://www.the-scientist.com/?articles.view/articleNo/45316/title/Same-Gene--Different-Functions/

“The researchers found that, on average, two related isoforms shared less than 50 percent of interacting proteins; 16 percent of related isoforms shared none at all. These differences in interaction partners were often associated with only tiny alterations in DNA sequence—sometimes just a single base pair.”

This reflects the importance of counting each base pair for what it actually is, and not using computer programs to split it up to create gaps that are not really there (even when it presents the illusion of insertions and deletions where these are just natural sequential “DIFFERENCES” between different organisms) Anywhere in the genome a single base pair can alter the function of a gene in different organisms or even render it appear to be functionless (but that does not make it broken just different...it may be exactly what it is supposed to be in that organism.

Since the evidence is clearly there for it being broken, any claims that it is supposed to be that way would be claims that you need to defend.

 

[46AND2]

First off it is the LINES that equate them with the Common ancestry default. But fine...Branches off from what?

And yes I do keep pointing this to common ancestry, because that was the point of bringing up the GULO gene. Its alleged "broken" nature points to the Ancestor of the Gaps. So branches off from what?

I've told you, the pattern of differences in the genes. Sets and subsets. The organisms which fall in a subset contain a line of consistent differences/similarities with all the sets it falls under, and subsets do not attach to other subsets in different parent (not meant to imply familial relationship, just a term to refer to the set above the subset) sets. The differences and similarities, regardless of method, fall into these objective sets and subsets. And they do so with pure data, regardless of any "historical narrative."

At this point, I'm just trying to show you that these patterns exist; not what they mean. This is not my argument for common ancestry, this is my argument for patterns of similarity.

With that said, do you agree that this pattern exists, independent of placing any purpose or hypothesis as to why they exist?

 

[46AND2]

First off it is the LINES that equate them with the Common ancestry default. But fine...Branches off from what?

And yes I do keep pointing this to common ancestry, because that was the point of bringing up the GULO gene. Its alleged "broken" nature points to the Ancestor of the Gaps. So branches off from what?

For example, the lines which you wanted to make disappear actually represent data. Take the line segment from the picture above between the orangutan node and where the chimp breaks off from that line. That line segment represents the total of the overall base differences which are shared by both chimps and humans, including, most importantly, the ones which are unique to humans and chimps.

The line labelled "chimp" is the line which represents differences which are not found in any of the other three species. Likewise, the one labelled "human" represents differences not found in any other species.

And when you compare larger segments of our respective genomes, adding more primates, the observation holds true, and indeed, is more detailed.

The lines don't need to represent ancestry. They represent data.

Can you predict where the rat sequence would be placed, if it were included in that diagram? If the pattern is really there, it can only be placed in one spot.

 

[pshun2404]

Since the evidence is clearly there for it being broken, any claims that it is supposed to be that way would be claims that you need to defend.

Here I actually thought I was. So by this logic then, the same gene that helps reduce cholesteral in Humans and Rats which appears to have no function in D. Melongaster must be "broken" in the fly and shows that this fly not only developed later than humans, but from a common ancestor. Hmmm? Interesting!

So then a difference in form (number or letter of base pairs) in the same gene, and the same gene not sharing the same function in different organisms (maybe not having that function in one or the other) equals "broken"!!! OR is there a double standard and these rules only apply to such difference when they fit the model (so we can point them out when they support our designated Hierarchies and ignore the same things when they may not).

 

[pshun2404]

I've told you, the pattern of differences in the genes. Sets and subsets. The organisms which fall in a subset contain a line of consistent differences/similarities with all the sets it falls under, and subsets do not attach to other subsets in different parent (not meant to imply familial relationship, just a term to refer to the set above the subset) sets. The differences and similarities, regardless of method, fall into these objective sets and subsets. And they do so with pure data, regardless of any "historical narrative."

At this point, I'm just trying to show you that these patterns exist; not what they mean. This is not my argument for common ancestry, this is my argument for patterns of similarity.

With that said, do you agree that this pattern exists, independent of placing any purpose or hypothesis as to why they exist?

Actually I know and agree that these can be placed in sets and subsets based on similarity, that they cannot has never been my argument (though you may think it has been) when the GULO was brought up it was brought up as support for the idea of ancestry (not by me). My issues were does difference equal "broken"? And the article in Cell indicated in the link (and work in Encode) shows how a difference as small as a single base pair can effect function and purpose. And my second issue has been, does similarity implicate a familial lineage? And I see no reason for either conclusion. But as for grouping things that show similarity for categorization is fine (there are all kinds of reasons we do that) but that does not mean they are related in the sense of family (and I am not speaking about Taxa).

 

[pshun2404]

For example, the lines which you wanted to make disappear actually represent data. Take the line segment from the picture above between the orangutan node and where the chimp breaks off from that line. That line segment represents the total of the overall base differences which are shared by both chimps and humans, including, most importantly, the ones which are unique to humans and chimps.

The line labelled "chimp" is the line which represents differences which are not found in any of the other three species. Likewise, the one labelled "human" represents differences not found in any other species.

And when you compare larger segments of our respective genomes, adding more primates, the observation holds true, and indeed, is more detailed.

The lines don't need to represent ancestry. They represent data.

Can you predict where the rat sequence would be placed, if it were included in that diagram? If the pattern is really there, it can only be placed in one spot.

The line labelled "chimp" is the line which represents differences which are not found in any of the other three species. Likewise, the one labelled "human" represents differences not found in any other species.

Exactly! All they REALLY represent is an indication that these differences exist (exactly what I have been saying)...but in principle (and you know this) those places of alleged similarity (the points where they meet in the picture) are interpreted as places where they split off from earlier creatures. What creature was that?

So chimps and humans (that come out of a small area in Africa) allegedly split from orangutan (which comes from a small area in Asia) and they both from an alleged ancestor from where? And then, what is this creature? Some form of old world monkey that was in both locations? Which one? OR perhaps the orangs migrated away leaving no trace in Africa or vice versa? Hmmm?

IMO such a model should elicit so many questions that apparently must be ignored or discredited by those trying to defend the already presupposed (since Darwin) "belief"!

 

[46AND2]

The line labelled "chimp" is the line which represents differences which are not found in any of the other three species. Likewise, the one labelled "human" represents differences not found in any other species.

Exactly! All they REALLY represent is an indication that these differences exist (exactly what I have been saying)...but in principle (and you know this) those places of alleged similarity (the points where they meet in the picture) are interpreted as places where they split off from earlier creatures. What creature was that?

So chimps and humans (that come out of a small area in Africa) allegedly split from orangutan (which comes from a small area in Asia) and they both from an alleged ancestor from where? And then, what is this creature? Some form of old world monkey that was in both locations? Which one? OR perhaps the orangs migrated away leaving no trace in Africa or vice versa? Hmmm?

IMO such a model should elicit so many questions that apparently must be ignored or discredited by those trying to defend the already presupposed (since Darwin) "belief"!

So, then you now agree that through pure data, we objectively see a pattern of similarities, correct? No interpretation is necessary at this point, the pattern is there. Can we agree on that?

 

[pshun2404]

So, then you now agree that through pure data, we objectively see a pattern of similarities, correct? No interpretation is necessary at this point, the pattern is there. Can we agree on that?

I have repeatedly pointed our from the beginning of our discussion that all that these show are our differences and similarities, so I do not get your point, unless YOU are finally coming around. We are different types of creatures with different genomes (as we would expect). Differences are not always indicators of mutation or brokeness of one or the other, and the different base pairs do not HAVE TO mean an insertion or deletion took place.

None of these necessitate that one came from or became another...just that we share some characteristics in common and differ in others.

 

[46AND2]

Dude, we'll get to the point. I just want to make sure we are on common ground about the actual data we see.

Do you agree that the pattern exists, independent of any kind of interpretation?

 

[pshun2404]

Dude, we'll get to the point. I just want to make sure we are on common ground about the actual data we see.

Do you agree that the pattern exists, independent of any kind of interpretation?

The various areas that show differences in different creatures are a reality, and the various areas that show similarity in different creatures DO IN FACT EXIST...without interpretation and in spite of it.

Are you familiar with the notions of homological taxonomy, cladistic parsimony, distance measures, maximum likelihood and other approaches that have come up with DIFFERENT nested hierarchy models? Did you know that many types of creatures we have found do not really fit?

Marketa Zvelebil and Jeremy O. Baum in, Understanding Bioinformatics (New York: Garland Science, 2008), p. 239, tell us that cladists, for example depend on certain assumptions. Number one is that “Any group of organisms are related by descent from a common ancestor.” Another is that any set of sequences that match (that are homologous) derive from a single ancestor. You see they do not demonstrate it they assume it before they begin classification.

Michael Syvanen, “Evolutionary Implications of Horizontal Gene Transfer,” Annual Review of Genetics, 46:339-356 (2012), reveals that “Because tree analysis tools are used so widely, they tend to introduce a bias into the interpretation of results. Hence, one needs to be continually reminded that submitting multiple sequences (DNA, protein, or other character states) to phylogenetic analysis produces trees because that is the nature of the algorithms used.” And with this I 100% agree, making the idea of this indicating a Common Ancestor a precursor to analysis of the “patterns” you speak of NOT the evidential conclusion.

 

[46AND2]

The various areas that show differences in different creatures are a reality, and the various areas that show similarity in different creatures DO IN FACT EXIST...without interpretation and in spite of it.

Are you familiar with the notions of homological taxonomy, cladistic parsimony, distance measures, maximum likelihood and other approaches that have come up with DIFFERENT nested hierarchy models? Did you know that many types of creatures we have found do not really fit?

Marketa Zvelebil and Jeremy O. Baum in, Understanding Bioinformatics (New York: Garland Science, 2008), p. 239, tell us that cladists, for example depend on certain assumptions. Number one is that “Any group of organisms are related by descent from a common ancestor.” Another is that any set of sequences that match (that are homologous) derive from a single ancestor. You see they do not demonstrate it they assume it before they begin classification.

Michael Syvanen, “Evolutionary Implications of Horizontal Gene Transfer,” Annual Review of Genetics, 46:339-356 (2012), reveals that “Because tree analysis tools are used so widely, they tend to introduce a bias into the interpretation of results. Hence, one needs to be continually reminded that submitting multiple sequences (DNA, protein, or other character states) to phylogenetic analysis produces trees because that is the nature of the algorithms used.” And with this I 100% agree, making the idea of this indicating a Common Ancestor a precursor to analysis of the “patterns” you speak of NOT the evidential conclusion.

We just went over the pattern shown by differences in the gulo gene of four species. Do you deny that the lines represent actual data?

 

[46AND2]

I promise this is not a gotcha! question. By saying yes, you by no means are agreeing with evolution.

 

[pshun2404]

We just went over the pattern shown by differences in the gulo gene of four species. Do you deny that the lines represent actual data?

The lines of the base pairs of GULO do represent real data (I see no reason you would make them up). And I do believe in evolution, just not in everything evolutionists claim or say these things mean.

However the lines I was referring to which I said are nothing, are the ones drawn into the Tree picture you had previously presented. The Chimp and Human nests go back to an imagined point (with no knowable examples) that stems off of the Orangutan and Gorilla nests common unknowable (assumed) meeting point, all of which go back even further to a completely unidentifiable (but assumed) meeting point of origin. This is not remotely established to be real or true but ASSUMED (caps always only for emphasis not emotion)...

 

[46AND2]

The lines of the base pairs of GULO do represent real data (I see no reason you would make them up). And I do believe in evolution, just not in everything evolutionists claim or say these things mean.

However the lines I was referring to which I said are nothing, are the ones drawn into the Tree picture you had previously presented. The Chimp and Human nests go back to an imagined point (with no knowable examples) that stems off of the Orangutan and Gorilla nests common unknowable (assumed) meeting point, all of which go back even further to a completely unidentifiable (but assumed) meeting point of origin. This is not remotely established to be real or true but ASSUMED (caps always only for emphasis not emotion)...

No worries, I use caps for emphasis, too.

I know what you object to. A lot of information gets lost when people speak in hyperbole during these discussions. All I wanted to establish is that the lines are not just drawn through assumption. They represent real data.

I have one more item to clear up before we get to interpretation, but it will have to wait till I get home, instead of on my phone.

 

[pshun2404]

Nested Hierarchies have changed over time. Some creatures and varieties have been moved to completely different areas, and even the order previously believed in has been re-ordered.

Consider birds for example. We were pretty sure we had it all figured and presented it many times as settled in many textbooks and courses (perhaps one you have studied and believed). But new information has arisen from fresh eyes, and the whole Nested Hierarchy for birds is being re-drawn as we learned in Nature as far back as 2014 (Flock of geneticists redraws bird family tree )...and this not from the information of one study but from many geneticists.

You see there is much incongruence discovered in phylogenetic analysis conveniently left out in one’s training and in popular presentations. Here is a paper you should read about this phenomenon:

Understanding phylogenetic incongruence: lessons from phyllostomid bats. - PubMed - NCBI

Phylogenetic Incongruence: Window into Genome History and Molecular Evolution

Or perhaps

Evaluating Phylogenetic Congruence in the Post-Genomic Era

Which reveals the new struggle with incongruence and how strategy is being developed to deal with the reality so it still fits the hypothesis...this article suggests “The extent to which characters in a data set are incongruent (i.e., disagree with one another), given the inferred phylogeny, can be assessed via a number of statistics, such as the consistency and retention indices (Kluge and Farris 1969; Farris 1989), as well as a number of statistics that have been developed specifically for partitioned data (Farris et al. 1994; Huelsenbeck and Bull 1996; Waddell et al. 2000).

(Again, read How to Lie with Statistics which teaches us it is all about purpose driven presentation and emphasis when selling an idea or product)

A third camp of scientists argued that neither the taxonomic congruence nor character congruence method was always the best approach. Instead, they suggested “conditional data combination” (Huelsenbeck and Bull 1996). This strategy involves first testing the data to determine whether they are significantly heterogeneous (i.e., whether they reject the hypothesis that they evolved along the same tree). If the different data appear to be heterogeneous, they are then subjected to separate phylogenetic analysis using a taxonomic congruence approach. As with any taxonomic congruence analysis, the resulting trees are often then either inspected to identify discordant relationships implied by the different trees or tested statistically to evaluate whether they are more similar than expected by chance. If there is no evidence that the data evolved along different trees, they are instead combined using a character congruence approach.” But I must ask, sincerely, do you believe for one minute if the data suggests the possibility of different interacting trees or even only organism specific trees that they will even see it? If they do, being already convinced, will they be objective or interpret the data THROUGH the hypothesis? If their presentations of the data bring the hypothesis into serious question will they still be funded to study further?

These new approaches may very well (and probably will) once again re-Nest and maybe re-Hierarch....or maybe how one sees or presents the patterns may also be inaccurate (or contain a bias) giving just cause for reasonable doubt of any and all. Clearly there is a new jury, and they are still out, and this is still an in-house jury of your own camp.