tag:blogger.com,1999:blog-3248412803814730250.post6926570901824736662..comments2024-03-17T01:48:59.504-07:00Comments on The Theropod Database Blog: Why David Peters' analysis sucksMickey Mortimerhttp://www.blogger.com/profile/08831823442911513851noreply@blogger.comBlogger3125tag:blogger.com,1999:blog-3248412803814730250.post-8531139868085457342012-06-11T22:08:03.193-07:002012-06-11T22:08:03.193-07:00As for how to trust an analysis, you look for char...As for how to trust an analysis, you look for character and taxon number for a start. Yours is great for the latter but so-so for the former (only 99 postcranial characters across all Amniota?!). Then you see if the characters are formed well, which as I've shown, they are not. Then you see if taxa are accurately and completely coded. For the former I'm doubtful of yours due to your Photoshop method, but a glance at the matrix seems to show you were good about coding everything you thought was possible. You also check to see if characters supporting alternative topologies were included, and here I'm going to provisionally say your matrix fails. We'll see in my next post when I look at what Saurischia synapomorphies you've included. A final method is to check the CI, and I gotta say at least you haven't planned your matrix to only include characters that support your topology. Your CI of .1040 is impressively low.<br /><br />I already told you taxa that were misnested, limiting myself to dinosaurs, since I'm most familiar with that clade- http://pterosaurheresies.wordpress.com/2012/05/31/celebrating-300-taxa-in-the-large-reptile-tree/#comment-1152 .<br /><br />Look David, I don't think you're a bad person. You have noble goals, and in some respects (like including numerous genus-level OTUs) you're ahead of the pros and absolutely right to criticize them. But there's a reason the pros haven't done what you and I would like them to- it's a HUGE project. 223 characters is nothing compared to what you'd need for this analysis. At least a thousand, and we'll see why in my next post. But more than that, you need understanding. I just specialize in theropods, and I'm still finding out what certain characters mean and when the traditional knowledge about a coding is wrong. Turner in his 2008 thesis thought the obturator tuber of dromaeosaurids and birds was the same as the obturator process of avetheropods. Senter et al. in the Yurgovuchia paper thought the flat internarial bar of ornithomimosaurs, alvarezsaurs and troodontids was the dorsal curvature in lateral view as opposed to the cross section. These are professionals. To learn the details of all amniotes well enough to create and code them for an analysis would take decades. You or I could improve on Rieppel's or Mueller's just because they are so far from ideal, but neither of us could do the job justice.Mickey Mortimerhttps://www.blogger.com/profile/08831823442911513851noreply@blogger.comtag:blogger.com,1999:blog-3248412803814730250.post-62334184298439184642012-06-11T22:07:46.702-07:002012-06-11T22:07:46.702-07:00Fair enough having the email conversation continue...Fair enough having the email conversation continued here. For those following, here's what I wrote Peters that he's replying to here- "The characters themselves are too flawed to make adding or deleting taxa, recoding the matrix or constraining topologies useful. As I note in that post though, Rieppel's traditional reptile matrix suffers from similar issues, though to a lesser degree. If you have any questions on how to design character states properly, feel free to ask. Basically, every character should only score for one variable. If you have multiple states, and some are intermediate (in size, number, angle, etc.), make the character ordered. Fix it up, then we'll see what happens."<br /><br />You say that despite these problems, your analysis works. But how do you know? For fossil taxa, we have no independent method of comparison, and your reptile tree is different from both nuclear and mitochondrial results for living squamates. Your mammal results are also different from genetic analyses if I recall. You say every case has a gradual development or loss of traits, but what about... oh... hyposphene-hypantrum articulations in the dorsals? Your tree doesn't support Saurischia, so it seems like something that might perform worse in it. Traditionally, besides various crurotarsans, it evolves in Saurischia and is lost much higher up in a few clades (birds, some titanosaurs, parvicursorines). In your tree, it has to be lost in Marasuchus, silesaurids and Ornithischia, in addition to those derived clades. I went to check your tree to see how you coded it, but it's not even included. More on this later.<br /><br />Skipping over your tone argument... you said on your blog (http://pterosaurheresies.wordpress.com/2012/06/02/reptile-tree-experiments/#comment-1153) "Where’s your tree? Where’s my flawed data? So far you’re just repeating untested tradition and sniping from the sidelines. Please be specific and scientific." So you can't very well now criticize me for posting on your flawed data without discussing it with you first.<br /><br />As far as medial teeth go, I retract that criticism. My new criticism is to call these mesial or even anterior teeth to avoid confusion.<br /><br />I agree that many characters end up co-occuring often in taxa. What we have a duty to do as phylogeneticists is to eliminate characters that logically entail other included characters. Large numbers of vertebrae CAN occur without limb reduction, such as in elasmosaurs. Thus the characters are not correlated in the sense we care about. But you can't lack vomer teeth without also lacking palatal teeth, even hypothetically. So you can't have these as separate characters without coding some taxa inapplicable.Mickey Mortimerhttps://www.blogger.com/profile/08831823442911513851noreply@blogger.comtag:blogger.com,1999:blog-3248412803814730250.post-91178925315055620202012-06-11T20:33:22.146-07:002012-06-11T20:33:22.146-07:00I recently wrote Mickey, hoping for a reply after ...I recently wrote Mickey, hoping for a reply after the request for the characters. Mickey pointed me toward this blog as an answer. Here is my reply copied from my email. <br /><br />Re: Any thoughts yet on the tree?<br /><br />I understand. <br />But it works. All sister taxa look alike and one can trace the gradual development or loss of traits in a series of ancestral taxa in every case. <br />Thanks for your thoughts, Mickey. <br /><br />Your choice of words could be improved. "Sucks" comes off the street, which is inappropriate for scientific discourse. Blogging first without discussion is also bad practice in this case. It shows you can't be trusted. I'm sorry you chose to go this way. <br /><br />BTW the medial teeth in character no. 109 are the ones closest to the midline suture, the ones most medial. In character no. 108 there are indeed taxa with a medial tooth, so I can see your confusion here. <br /><br />With regard to correlated characters, it's quite hard not to correlate most characters. We already know, for instance, that large numbers in the vertebral count are correlated with small to absent limbs. Just a for instance. <br /><br />How do you "trust" an analysis? Don't trust it. Run a competing one. If an amateur like me can do it, surely any professional can. And of course, as above, if one can trace a gradual accumulation of traits without too many aberrant autapomorphies, that's another good sign. <br /><br />I also challenged you to list any genus that was mis-nested and find a better nesting closer to another genus as the beginning of a discussion. Suprageneric taxa, of course, cannot be used They're too nebulous.<br /><br />Finally, because Science is the search for the truth, very rarely does one "find" the truth. We only hope to get closer with each test and its improvements. The large reptile tree takes us that one step closer. I'm finding errors and making improvements weekly, especially when new taxa are introduced. And I'm looking forward to someone, such as yourself, taking it to the next level. <br /><br />Presently with 223 characters and 305 taxa (not counting the pterosaur tree and the therapsid tree, that comes to 68,000 matrix scores, less a certain number for headless and body-less taxa. Each score affects every other one. With such a number recovering a single tree, it's going to be hard to change the topology on a large scale. <br /><br />I'm not asking you to trust my tree. Test it and test the results. For many, trust issues go back to tradition (which are by definition trusted), affinity (professors have more of this than amateurs) and novelty (which is rarely trusted...at first.)<br /><br />DaveD.P.https://www.blogger.com/profile/13009843520057633239noreply@blogger.com