Hello all, I’m here for the moment.
As a general policy, I don’t engage in comment/forum threads. My problem is that once I start posting I very quickly become this guy:
And that’s just not helpful to anybody. If (probably when) I find myself becoming that guy I’m going to have stop participating in this thread both not posting and not reading it. That will not mean I’m not interested in well articulated carefully reasoned critiques. If you write one, feel free to e-mail them to me at email@example.com.
I will also note that BioComplexity would love to publish an official critique to my paper if anyone is interested.
I’m also going to have a zero-tolerance policy towards insults. If anyone starts calling me names, attacking me on irrelevant issues, etc, I’m going to leave. Putting up with abuse just isn’t worth my time.
Josh, thanks for your respect and acknowledgment of me actually trying to a build a scientific model. Although I’m sure we disagree on a lot, we probably largely agree as to this being a problematic deficit in the current state of intelligent design. In fact that respect you are showing is the big reason I’m breaking my general rule and engaging in this thread. Let’s hope I don’t regret that!
However, I must make one point of objection to Josh’s statements so far. He uses the word “ignore” repeatedly to describe factors/data I did not take into account. I’m not ignoring them, I’ve just limited the scope of what is being looked at in this first presentation of the model.
For any serious objection to my hypothesis, I probably won’t dispute it in this thread. If its a worthwhile objection I will want to take the time to think about, come up with a hypothesis to explain it, test that hypothesis etc. That will take time. I’m less interested in arguing the point as in understanding the objections to it so that it can guide where work on this hypothesis needs to go.
Josh states that I ignore much stronger evidence for common descent. I find that different people rank different lines of evidence differently. Some do seem to think nested clades is the strongest evidence. Regardless, it doesn’t matter. There many lines of evidence I have not attempted to touch. If my model is to succeed it does need to be developed to explain all those lines of evidence. I appreciate that’s a daunting task. But, my current paper only deals with nested hierarchy, and I’m going to ignore, for this thread, any bringing up over other lines of evidence.
To clarify this, common design is an alternative to common descent not an addition to it. The phrase common design is used by intelligent design proponents to refer to the idea that commonalities in different living things can be explained by a common designer instead of common descent. When I talk about common design not being a “critique of common descent” my point is that I’m not interested in simply pointing out places where common descent has trouble explaining the data. I’m interested in developing common design as positive model in its own right.
This is a good suggestion, its on my list of potential future related projects.
This is certainly true. In my paper I called it a “tree model” rather than a “common descent model” for exactly this reason. What I’ve shown is that the data fits a dependency graph better than a tree. But this could be explained if there is some mechanism operating in common descent that produces data that looks kinda like modules that are being picked up by my analysis.
My question for you is: what mechanisms do you see as good candidates?
I’m not sure here whether you are referring to:
- Lines of evidence for common descent besides nested hierarchy
- Data besides gene families that fit a nested hierarchy
In either case, it is true. I fully acknowledge there is a lot more data and evidence that needs to be taken account of. If 2, I’d be curious to know which data you think has the best chance of falsifying my hypothesis.
Here I’d like to know what you are referring to since selection of any sort didn’t enter into the analysis. Perhaps something about genes drifting through sequence space in a neutral fashion?