To me, these responses re-iterate my statement: “This is a challenging topic…”
First, let me clarify what I meant by that statement: (1) “Challenging to come to a holistic decision on”, and subsequently (2) “Challenging to convince either side.” We’re dealing with a seriously large set of data, as well as two conclusions that have a great deal of overlap: descent vs design. The holistic binary answer doesn’t just emerge.
In the process of studying this topic, I’ve found there to be a lot more than “a single dot” of data opposing common descent. I know this because I’ve spent time researching it.
However, I do have to say that since I’ve posted my “Help me see what you see” question, and followed up on the responses, I have gained insight into what evolutionists ‘see’. There was more data supporting a tree than I previously was privy to. I know this because I’ve spent time researching that also.
In regard to (1) above:
Despite all this (continual) research, that binary answer to this individual topic hasn’t totally emerged.
In regard to (2) above:
What of those who consider me “contradicting physical reality”? I question whether they are trying to ‘see what I see’. But should I try? How successful would that endeavor be? Even if they seem to agree, is it genuine? Will any cognitive bias in them alter what they ‘see’? With this large of a data set, it’s too easy for each side to focus only on their supporting evidence.
This gets me back to my statement:
With respect to phylogenies, there is no overlap. There is no reason why we would expect a phylogenetic signal in this data if design is true.
Incongruencies don’t oppose common descent. Noise is expected in these data sets. What you need to address is the signal, not the noise. When you have a signal in the data set that is way, way stronger than the noise then you have a well supported hypothesis. We see both the signal and the noise, but you seemed focused on just the noise.
Added in edit:
TalkOrigins has a page on the statistics of incongruent trees, including a chart and calculator for p values. As an example, a phyogeny of 13 taxa can have 5 incongruencies and still be statistically significant with a p value of 0.0095.
I also noticed that the TalkOrigins page has this interesting reference:
Harshman, J., Huddleston, C. J., Bollback, J. P., Parsons, T. J., and Braun, M. J. (2003). “True and false gharials: a nuclear gene phylogeny of crocodylia.” Syst Biol. 52: 386-402.
Yes, and among other reasons both because it is rather technical, but also because it is very wide in scope. There are so many kinds of data to draw from. But we’ve all mostly been speaking in generalities so far, and in particular you’ve stated that one way that you’d evaluate the common descent vs creation hypothesis is to try to evaluate how good the tree is “outside of kinds”, but you’ve so far not responded to calls for you to explain how you determine what is or isn’t a kind.
At some point, if we are to make any headway in this discussion at all, we should start to look at real data, and compare models to data. To do that we need a creationist model, and yet I know of none. And I know of no way to determine what is or isn’t a kind.
If I may jump in here a moment and help out @jeffb, (something he will doubtless reject). This argument of @Rumraket is erected as a false dilemma. Creationists do not have to produce anything except an appeal to the Supreme Intelligence quite capable of creating all we see via a miraculous intervention into the nature he created first, then Life second. The reason @Rumraket does not “yet know of” a creationist model is because one is not needed. God was here first, and his creative powers brought all we see into being. It is the evolutionist, the latecomer, who needs to produce a viable model, and he needs the persuasive ability to leverage that model against the First Cause - namely, God, and how that First Cause declared all of Life to have come about.
What the evolutionist is seeing in his “data” is simply an artifact of God’s creative process and reading into it the paradigm of his own choosing. If Life is young, which it is as the Bible declares, then there is really only one reason the evolutionist’s “data” exists or seems to exist. And that reason is that it is simply an artifact, a misreading of the truth about creation.
If creationists argue that separate creation would also produce a phylogenetic signal then they would need to produce a creationist model to support that assertion. Earlier, @jeffb stated:
" “Challenging to convince either side.” We’re dealing with a seriously large set of data, as well as two conclusions that have a great deal of overlap : descent vs design."
In order for us to look at the overlap between descent and design we need a scientific model for design. In order to answer questions about created kinds we need to know how we can determine which species belong in a created kind.
Such a claim would require a creationist model and evidence.
On the contrary, I appreciate @r_speir 's refreshing honesty in admitting YEC does not even try to be scientific, and is just an expression of dogmatic faith. I don’t often encounter this.
On the issue of whether we get nearly-the-same trees from different parts of the genome, one simple way you can investigate this yourself is to get data sets of aligned DNA sequences from one of the online sites that supply that. For example, from OrthoMam (which will be found at https://orthomam.mbb.cnrs.fr/ ). It has alignments for 116 mammalian species for 14,509 coding sequences, basically loci. After a slight struggle with specifying which species have to be present, you can download aligned sequences and also estimated phylogenies for any loci you want. One can compare the phylogenies by looking for incongruent branches (program Consense in my PHYLIP package can do that). Or you can write scripts to copy the aligned sequences so as to concatenate them, and then use any phylogeny program to infer trees for data sets of L loci, where L is a number like 10. Then you can see whether the trees for groups of 10 loci are more similar to each other then trees of L=1, L=2, L=5, where the two groups compared for each L value do not contain the same loci. I have done exercises for my undergraduate classes to show the result, which is as we would predict.
The belief in evolution requires dogmatic faith. The god of abiogenesis has not yet been found to exist, yet so many believe dogmatically in it. Evolution at its foundation is a religion all its own.
So choose your god. Mine has a Name, a Personality, inspired a Writ about his Character that we study to this day, and even left Traces of his Existence at keys point throughout human history. Your god is a phantom, a wispy dream, a fanciful hope.
Perhaps you could address the topic of the thread.
We are saying that a phylogenetic signal is evidence of evolution so that we don’t have to use dogmatic faith. Why are we wrong? Why wouldn’t evolution produce the evidence we see?
You’ll never find an evolutionary biologist who confirms this. For the very good reason that it is simply not true.
OTOH, you have just admitted that “Creation Science” is nothing more than dogmatic faith, yet there are entire well-funded conglomerates pushing the idea that YEC is science. Should you not perhaps call them out on this deception.
You should ask yourself why there are no clear boundaries. I would expect that if there were indeed separate kinds, the boundaries ought to be obvious in a host of ways. Yet we see none, and that’s good evidence against the notion. In particular, since nested hierarchy is an expectation of common descent alone, we should see nested hierarchy within but not between kinds. And yet it’s hierarchy all the way down. Why?
You sound like one antivaxxer who believes those who advocate for or receive vaccines practice a form of religion called “vaccinianity”.
Evolution is a scientific fact, same as gravity (of course, many flat-earthers believe otherwise). Deal with it or continue to delude yourself with fantasy.
No one cares, same way you don’t care about Amadioha, the Igbo (my tribe) God of Thunder.
If the scientific method is a god, then I would say its the best god out there. It gave us evolutionary theory, germ theory and gravitational theory which are undoubtedly important in our modern world.