Just to tie up a loose end....
As for molecular Phylogenetics, first they expect that sequences conserved in various organisms will accumulate mutations over time, but this is not always the case, because many alleged differences interpreted to be mutations (indicated by the assignment of the term insertion or deletion once the separating sequence alignment has been applied) may not be mutations just differences between these unique equally possibly unrelated organisms.
Great - provide your evidence. To include evidence that mutations in intergenic non-regulatory DNA affect phenotype.
Can't wait!
I say this because they cannot demonstrate these alleged mutations were once something different in the same type of organism (one thing mutating into another).
Can you demonstrate that they were always like that - that mutations don't occur? We can (and have) sequenced genomes of 'parent' and 'offspring' and seen that there are nucleotide differences. Why make special rules for how we apply genetics knowledge when it concerns your pet beliefs?
What is your evidence that this somehow ceases when looking at more than 1 lineage?
Your ad hoc desperation is interesting in its psychology, but I am guessing that were someone to apply the same sort of escapism to YEC cult beliefs or the question of the Inspiration of the bible (we know how you dealt with that in 2014) you would sing a different (double standards) tune.
Second there is an assumption of “constant rate of mutation” that simply does not exist.
Then you must be able to provide evidence that this is an assumption.
a) There are real mutations and those alleged to be as a result of noted differences
Please condescend from on high to explain how one identifies the difference?
b) We KNOW the rate is not actually constant so this assumption biases the interpretation of data
Since we know this, why do you assume that this knowledge is not applied to molecular phylogenetics?
Is this part of your brainwashing plan?
I mean, in your 30 years of in-depth study on molecular phylogenetics did you never once read about the Maximum Likelihood method? Did your studies not find that the method, by "design", does NOT assume constant mutation rates?
What can we conclude from you claim that there is an assumption of constant rates? Was it purposeful deception on your part? Or ignorance? Or a mere desire for it to be so?
Did you never read about how this was applied to phylogenetics because earlier methods did not take it into account (interestingly, the outcomes of algorithms such as maximum parsimony, which to not generally consider mutation rate differences nevertheless produce outcomes that are typically identical to those of ML methods, at least in my experience)?
Most interesting how confidence in erroneous claims shows a positive correlation with those being creationists.
And also please explain how this truly causes a big problem for phylogenetics?
Especially when the methods have been tested on knowns and shown to be accurate? Could it be that in most cases, your concerns are irrelevant?
From this assumption they devise imagined molecular clocks that are based on this misinformation and from this they devise their evolutionary or phylogenetic “trees” believing and most stating these to be probable.
Oh right - this dopey erroneous canard. I forgot you tried this one before.
No, molecular phylogenetics is NOT premised on the universal molecular clock. Never was - this is just a creationist lie.
In fact, in Hall's "Phylogenetic Trees Made Easy", 'molecular clock' does not even appear in the index. You'd think if the concept of the universal molecular clock was a foundational assumption of molecular phylogenetics, it might, maybe, be mentioned in a book about generating phylogenetic trees?
Clock concepts are used in inferring dates/timeframes of things, but not for phylogenies.
Or maybe if this was a big assumption that nobody wants to talk about, you can explain why there are 23 pages on the subject in Li's "Molecular Evolution" book? To include entire sections dedicated to rate differences? Nah - it is all just a big assumption of the universal molecular clock... Yup... Who are we to disbelieve documentably false assertions churned out by Dr.Plagiarism....
Only this “probable” is based on the assumptions mentioned above.
Which is false...
Therefore it may be likely only IF
a) All the alleged mutations actually are mutations (which is not factually known, many existing in those organisms as far back as we can determine)
b) If the various organism’s mutation rates are actually constant (which we KNOW they are not)
It is so precious how you actually seem to believe your false propaganda.
Of course, if your claims had merit, you have to explain to us how they can re-create known phylogenies, and also why Creation Scientists would use the same programs as real scientists do when assessing 'baraminological phylogenies'...
But you are in error, so it doesn't matter.
Let’s face it, the whole evidential implication is drawn from the homological aspects of the sequences that the program searches and for and aligns (which do not occur naturally in sequence).
Ah yes - the other old Gish claim about gaps. So sad and desperate.
These areas do not occur in the natural sequence of each type of organism in the same place, and often have different sequences preceding and/or following (and we all know what just a couple of actual mutant base pair differences can do let alone how the sequences preceding and/or following can effect function of the similar sequences in different organisms).
You write as if you are some sort of world-renowned expert on this and nobody else knows anything about it. Sadly, as usual you are wrong.
Believe it or not, we actually know about things like insertions, deletions, tandem duplications, etc. Just because YOU don't is no reason to assume that nobody else does.
Sorry.
In some organisms different sequences perform similar functions and same sequences can and sometimes do perform different functions. So in the end we know we can use this to see phylogeny (paternity and maternity) in a given species and its subsequent sub-species but that is it. Nothing more about historical transformations can be factually implied only speculated based on the pre-held conviction (which existed and was believed from before Darwin without a hint of evidence except hypothesis based interpretation of fossils and geological layers).
Ah - so in addition to throwing everything but the kitchen sink at molecular phylogenetics in your desperation, you are also of the opinion that only functional sequence is used in such analyses.
Cool how you unwittingly admit that you actually don't understand how any of this works.
Because in reality, we actually LIKE noncoding, non-regulatory DNA for phylogenetic analyses. I know you don't know why that might be, but I do hope you try to explain it to me. Because I've done LOTS of these sorts of anaylses. And you've done none, and seem to get all of your information about these processes from YEC websites, which you then try to gussy-up by doing keyword searches for non-YEC sources to use and often take out of context and misrepresent.
And do not forget the new discovery of horizontal gene transfer, and commonality of biogeographic factors influencing multiple life forms simultaneously.
Yes, so new - only about 50 years old. But do throw more sinks at us!
Maybe one day you will find one that actually works!
So this particular cladistics approach MUST ASSUME:
a) Classification must be arranged to support the presupposition of phylogenetic descent, and
The same presupposition used by creationists, you mean? The horror!
b) That all the taxa deemed to be valid for the study must be monophyletic (all are ancestors of a common descendent)
Ancestors of a common descent [sic]?? You mean like how you believe with no evidence that all canids are derived in an ancestor-descendant fashion from an original dog-kind make from dust of the ground? Except without the artificial constraints? Can't have that!
Neither of which are conclusions one can draw FROM the data but effect construction and interpretation of the data.
Right.
So cool how you totally ignore the fact that your own statement from that other site proves you don't know how to interpret cladograms (you know, the actual topic of this thread?), so awesome that you really seem so confident in your erroneous beliefs about phylogenetics, extra cool that you diss the "assumption" of ancestor-descendant relationships when your own belief system REQUIRES it, just with constraints premised on the rantings of ancient numerologists and mystics.
Yeah, your arguments are totally awesome and convincing!
LOL!!!!!
