tag:blogger.com,1999:blog-37148773.post3132320690820834792..comments2024-03-27T14:50:47.345-04:00Comments on <center>Sandwalk</center>: How many microRNAs?Larry Moranhttp://www.blogger.com/profile/05756598746605455848noreply@blogger.comBlogger78125tag:blogger.com,1999:blog-37148773.post-81441596642801072822014-12-13T17:53:37.432-05:002014-12-13T17:53:37.432-05:00First off, every taxon loses miRNAs. That's on...First off, every taxon loses miRNAs. That's one of the ways that development evolves. It has nothing in particular to do with "degeneracy". Note that in the study you're talking about, none of the sampled families were lost in cyclostomes, while one was lost in the ancestor of gnathostomes. Now, this is a biased sample, but it does point out that gains and losses are sprinkled all over.<br /><br />Second, I doubt that reconstructing just the ancestral miRNAs, even if possible, would produce a viable organism, as all sorts of genes and gene products interact in development. Who knows what else you'd have to reconstruct?John Harshmanhttps://www.blogger.com/profile/06705501480675917237noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-28572374161840632962014-12-13T12:57:47.445-05:002014-12-13T12:57:47.445-05:00Hi John and again thanks!
This is probably going ...Hi John and again thanks!<br /><br />This is probably going to be of my most naïve questions ever.<br /><br />It would appear Cyclostomes loss of miRNA would indicate some sort of “degeneracy” from an ancestral form given the important role miRNA plays in development.<br /><br />Is it even remotely conceivable to reconstitute the presumed ancient cyclostome miRNA repertoire by genetic engineering in vivo - and see what happens?<br /><br />Maybe considerations of expression timing and gene dosage are too crucial, making this line of conjecture more the realm of science fiction than reality.<br />Tom Muellerhttps://www.blogger.com/profile/09829281784362177069noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-83186387340988045852014-12-12T14:47:05.624-05:002014-12-12T14:47:05.624-05:00On reconsideration, i do think the fossil record m...On reconsideration, i do think the fossil record may have something to say here if judiciously combined with time-calibrated molecular trees. If jaws necessarily go along with teeth, then the absence of teeth in the first part of the Paleozoic fossil record tells us there were no jaws either, and my impression is that the cyclostome lineage goes back to before that point. Then again, you can have jaws without teeth, so this must be a tentative conclusion. <br /><br />Bones, on the other hand, have a somewhat longer record; to my knowledge the oldest bone is <i>Anatolepis</i>, a tiny fragment of dermal bone from the Late Cambrian. Clearly this record is as fragmentary as the fossil itself, but it does suggest that bone precedes teeth in evolution. And, probably, jaws. And, also probably, that cyclostomes are primitively boneless, if they're as old as trees suggest.John Harshmanhttps://www.blogger.com/profile/06705501480675917237noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-56979283949876526542014-12-12T14:23:29.726-05:002014-12-12T14:23:29.726-05:00... But rereading the above, I realize that you al...... But rereading the above, I realize that you already answered my query in the negative.<br /><br />My apologies<br /><br />Again thank you for your patience Tom Muellerhttps://www.blogger.com/profile/09829281784362177069noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-64364943530315539592014-12-12T14:19:34.477-05:002014-12-12T14:19:34.477-05:00I was hoping for something along the lines that th...I was hoping for something along the lines that the last common ancestor to both cyclostomes and gnathostomes had to be a boney fish with jaws ... That would be very nice.<br /><br />;-)<br /><br />I was wondering out loud how far "degeneration" could be pushed in this instanceTom Muellerhttps://www.blogger.com/profile/09829281784362177069noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-82667241691896491862014-12-12T13:50:57.951-05:002014-12-12T13:50:57.951-05:00What do you want? A recognition that both cyclosto...What do you want? A recognition that both cyclostomes and gnathostomes have evolved since their common ancestor? That should be obvious.John Harshmanhttps://www.blogger.com/profile/06705501480675917237noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-68026187674158831962014-12-12T13:32:15.464-05:002014-12-12T13:32:15.464-05:00Hi John
You were of great help to me earlier...
h...Hi John<br /><br />You were of great help to me earlier...<br />http://sandwalk.blogspot.ca/2014/04/asbmb-core-concepts-in-biochemistry-and.html<br /><br />I was wondering about more reinterpretation along these lines extended to include cyclostoma <br /><br />http://www.scientificamerican.com/article/modern-sharks-may-not-be-living-fossils-after-all/?&WT.mc_id=SA_WR_20140423<br />Tom Muellerhttps://www.blogger.com/profile/09829281784362177069noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-28868578620165213422014-12-12T13:22:24.278-05:002014-12-12T13:22:24.278-05:00I don't see that this paper, or the one it pri...I don't see that this paper, or the one it primarily references, says anything much about the common ancestor. Nor do the fossil data. The record is highly biased toward bones. Euconodonts have something resembling bone and perhaps calcified cartilage. "Agnathans" have dermal bone and sometimes perichondral bone, but never teeth or endochondral bone. Hard to make much of that. But there is no fossil record of bony jaws before gnathostomes.John Harshmanhttps://www.blogger.com/profile/06705501480675917237noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-64703606708906770002014-12-12T13:09:18.020-05:002014-12-12T13:09:18.020-05:00Hi again Larry
I was surprised by your answer and...Hi again Larry<br /><br />I was surprised by your answer and needed to think it over some more<br /><br /><i> If you want to refer to single-cell eukaryotes as "protists" then that's okay with me. <br /><br />The important point is that students learn of their existence and their diversity. Quibbling about cladistics and the exact relationship of some multicellular algae is distracting and counter-productive for high school students. </i><br /><br />The problem with over-simplification is that students walk away with the erroneous notion there exists a Scala Naturae and that modern single cell Protists are primitive ancestors to more evolved animals plants and fungi.<br /><br />Of course you would never allow such error in your class, but I assure you: many teachers, when left to their own devices with current textbook resources allow exactly those kinds of ignorachio elenchi to occur.<br /><br />Tom Muellerhttps://www.blogger.com/profile/09829281784362177069noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-21311659322555331912014-12-12T11:42:26.086-05:002014-12-12T11:42:26.086-05:00High school students need to learn that there'...<i>High school students need to learn that there's a lot more to life than mushrooms, maple trees, and moose.</i><br /><br />LOL!<br /><br />Bravo!!!<br /><br /><i> If you want to jump into that morass then you'd be better off discussing the Three Domain Hypothesis and whether archaebacteria really represent a distinct domain of life that gave rise to eukayotes.</i><br /><br />As a matter of fact - that is exactly what I do. My students actually can briefly justify that distinction in biochemical terms. Ex phospholipid ether bonds vs. ester bonds etc making Archaea appear almost alien. Of course eukaryotic ribosomes in organelles vs cytoplasm and the intron/exon story common to Archaea and Eukaryotes etc etc justifying the endosymbiotic story is also emphasized.<br /><br /><i> Or, for that matter, whether humans are a form of fish. </i><br /><br />I often awarded bonus marks for proof demonstrating students have independently read Neil Shubin's book.<br /><br />Nowadays, I just show the video in class.<br /><br />I am delighted to confirm you and I are on the same page<br /><br /><br /><br /><br /><br />Tom Muellerhttps://www.blogger.com/profile/09829281784362177069noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-69437142929433227342014-12-12T11:23:21.680-05:002014-12-12T11:23:21.680-05:00... I mean I understand the point about "deg...... I mean I understand the point about "degeneration". I just want to know if this "degeneration" also included the loss of jaws and what evidence would support that contention.<br /><br />I do hope I am not betraying hopeless confusion again.Tom Muellerhttps://www.blogger.com/profile/09829281784362177069noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-64867426290098169692014-12-12T11:20:48.327-05:002014-12-12T11:20:48.327-05:00I have a naïve question tangential to miRNA
I am ...I have a naïve question tangential to miRNA<br /><br />I am rereading this paper and wonder out loud…<br />http://www.pnas.org/content/107/45/19137.full.pdf<br /><br />What is the latest we know regarding the status of the common ancestor to gnathostomes & cyclostomes?<br /><br />Is there credible evidence that modern so-called jawless fish in fact had a jawed and perhaps even boney fish ancestor?<br />Tom Muellerhttps://www.blogger.com/profile/09829281784362177069noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-19069861547537530592014-12-12T11:17:27.111-05:002014-12-12T11:17:27.111-05:00High school students need to learn that there'...High school students need to learn that there's a lot more to life than mushrooms, maple trees, and moose. They need to learn about bacteria and single-cell eukaryotes. If you want to refer to single-cell eukaryotes as "protists" then that's okay with me. <br /><br />The important point is that students learn of their existence and their diversity. Quibbling about cladistics and the exact relationship of some multicellular algae is distracting and counter-productive for high school students. <br /><br />If you want to jump into that morass then you'd be better off discussing the Three Domain Hypothesis and whether archaebacteria really represent a distinct domain of life that gave rise to eukayotes. Or, for that matter, whether humans are a form of fish. Larry Moranhttps://www.blogger.com/profile/05756598746605455848noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-32560820596109540292014-12-12T11:07:22.120-05:002014-12-12T11:07:22.120-05:00I was using "size" as a convenient way o...<i>I was using "size" as a convenient way of expressing whether the common ancestor is recent or ancient. I was thinking of the length of the branches which indicates the depth as well as the total number of nodes in a typical tree. I think you knew that. </i><br /><br />No, I didn't. That was a very poor way of expressing yourself, especially when I had previously made the distinction between age and size. If you want to be understood, say what you mean, not something else entirely.<br /><br />And Simon Gunkel makes a fine point. The total time covered by all branches of a tree is what you need to assess when deciding on sequence conservation. And it does seem to me that 100 million years is more than enough branch length to distinguish "converged" from "highly conserved". 100 million years total branch length is more than enough branch length to distinguish "conserved" from "highly conserved", much less "evolving neutrally". So all this talk about phyla, and assertions that Cnidaria is a "small clade" seem to show a serious misunderstanding.John Harshmanhttps://www.blogger.com/profile/06705501480675917237noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-15402439203863237112014-12-12T08:45:10.482-05:002014-12-12T08:45:10.482-05:00Needless to say, this must have devastating impact...Needless to say, this must have devastating impact on the understanding of evolution. All of the examples you posted present a progressive view of evolution. And we know all the things that follow from that view :(Georgi Marinovhttps://www.blogger.com/profile/12226357993389417752noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-90921998445892676222014-12-12T08:38:40.031-05:002014-12-12T08:38:40.031-05:00Reality Check:
Not too long ago, Larry asked the ...Reality Check:<br /><br />Not too long ago, Larry asked the question:<br /><br /><i> That curriculum looks pretty impressive to me. What's the point of teaching "AP" biology in Canada?</i><br />http://sandwalk.blogspot.ca/2014/04/core-concepts-in-genetics.html<br /><br />The best answer I can muster is that I inflicted much error upon my students until I signed on for AP. I blush to admit that I also taught that <i>… large multicellular creatures are only offshoots in the three eukaryote branches founded by protists</i><br /><br />AP Biology imposes a quality control on teachers. AP teachers have to get with the program and stay current. For example, textbooks must be less than 10 years old and must be approved.<br /><br />With that in mind – allow me to present the most recent edition of one approved text that still employs the term “Protist” but in much modified context than other texts such as the Miller & Levine version cited above.<br /><br />http://highered.mheducation.com/sites/0073383074/student_view0/chapter29/image_powerpoint_for_students.html<br /><br />AP Biology only endorses the highest quality university-level texts. <br /><br />Typical high school texts (like Miller & Levine) are quite a different story all together.<br /><br />Sadly, the Raven phylogeny would be very unfamiliar to the majority of high school teachers who continue to espouse naïve a 6-kingdom mythology as found in all typical high school texts.<br />http://www2.estrellamountain.edu/faculty/farabee/biobk/kingdoms.gif<br />Tom Muellerhttps://www.blogger.com/profile/09829281784362177069noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-13609773590402665292014-12-12T07:44:26.556-05:002014-12-12T07:44:26.556-05:00@Larry:
It's not completely irrelevant. Let...@Larry:<br />It's not completely irrelevant. Let's say you have a sequence of length 22 in two species that diverged 60 million years ago and there is one difference. On the other hand, you have 4 species, the first of which diverged 40 million years ago from the others, one diverged 25 million years ago from the others, and the last two split 15 million years ago and in one of them there is one difference. Which sequence is less conserved? In both cases the total time in the phylogeny is 120 million years, in both cases one substitution occured. The degree to which they are conserved is the same.<br />Anonymoushttps://www.blogger.com/profile/04521153536420798640noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-90509505350024449242014-12-12T07:23:21.739-05:002014-12-12T07:23:21.739-05:00re judmarc's quote above:
"[E]ukaryotic...re judmarc's quote above:<br /><br /><br /><i>"[E]ukaryotic life is mainly defined by the enormous diversity of unicellular forms, whereas the conspicuous, large multicellular creatures are only offshoots in the three eukaryote branches founded by protists."</i><br /><br />Sadly, that is an exact description of how phylogeny is typically taught!<br /><br />http://www2.estrellamountain.edu/faculty/farabee/biobk/kingdoms.gif<br /><br />I for one would like to know what would constitute an example of a modern "fungus-like" Protist?!<br /><br />The problem is that high school texts are hanging on to tradition:<br /><br />(Domain)<br />Kingdom<br />Phylum<br />Class<br />Order<br />Family<br />Genus<br />Species<br /><br />So when do we study red and brown algae? Hmmm... Not with Plants - so Protists it is!<br /><br />I argue that the easiest fix is to abolish the taxon "Kingdom" and be done with it.<br /><br /><br /><br />Tom Muellerhttps://www.blogger.com/profile/09829281784362177069noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-33900425932655087312014-12-12T07:13:41.456-05:002014-12-12T07:13:41.456-05:00@ Larry & @ Larry
Let's say you discover ...@ Larry & @ Larry<br /><br /><i>Let's say you discover a gene that's only found in humans and chimps but it's almost identical in both species. Is that a "highly conserved" gene? </i><br /><br />Instead of Chimps & Humans, how about Lampreys and Humans?<br /><br />...or how about Tunicates & Humans?<br /><br />What if sequence homology is almost identical in these instances? <br /><br />I think I must be missing something.Tom Muellerhttps://www.blogger.com/profile/09829281784362177069noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-18430469666732903762014-12-12T02:47:47.917-05:002014-12-12T02:47:47.917-05:00See here, for example. The history of the terms Pr...See <a href="http://www.ncbi.nlm.nih.gov/pubmed/6395918" rel="nofollow">here</a>, for example. The history of the terms Protista, Protictista, Protozoa, etc. is discussed at some length by <a href="http://www.im.microbios.org/08december99/03%20Scamardella.pdf" rel="nofollow">Scamardella (1999)</a>.<br /><br />As noted above, some red algae (for example) are unicellular and look like <a href="http://www.shigen.nig.ac.jp/algae_tree/CyanidiophyceaeE.html" rel="nofollow">this</a>. If unicellularity is treated as a diagnostic criterion, Rhodophyta should be split between two "kingdoms" (or, alternatively, be regarded as "ambiregnal", the way the ICN and the ICZN treat slime moulds). But then Protista reduces to a purely descriptive label (= unicellular eukaryotes). One could just as well define "Bipedalia" as any tetrapods that use two legs for walking (birds, pangolins, humans, and possibly miscellaneous others).Piotr Gąsiorowskihttps://www.blogger.com/profile/06339278493073512102noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-60312866753361635022014-12-11T21:47:54.001-05:002014-12-11T21:47:54.001-05:00@John Harshman
For sure. So why are you bringing ...@John Harshman<br /><br /><i>For sure. So why are you bringing up the sizes of clades? That's irrelevant.</i><br /><br />I was using "size" as a convenient way of expressing whether the common ancestor is recent or ancient. I was thinking of the length of the branches which indicates the depth as well as the total number of nodes in a typical tree. I think you knew that. <br /><br />You and I both know that different phyla, for example, have differing numbers of species ranging from one to millions. Give me a little credit. Larry Moranhttps://www.blogger.com/profile/05756598746605455848noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-2673533975930855482014-12-11T20:14:05.472-05:002014-12-11T20:14:05.472-05:00That seems odd. By the usual 5-kingdom classificat...That seems odd. By the usual 5-kingdom classification, brown and red algae are, I believe, plants. But-but-but, you sputter, that's polyphyly! Not a big matter of concern to those who came up with it, apparently.John Harshmanhttps://www.blogger.com/profile/06705501480675917237noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-18007938147126147302014-12-11T19:41:46.746-05:002014-12-11T19:41:46.746-05:00That same Miller& Levine high school text for ...That same Miller& Levine high school text for example.Tom Muellerhttps://www.blogger.com/profile/09829281784362177069noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-43644421120575546032014-12-11T19:33:18.965-05:002014-12-11T19:33:18.965-05:00I have seen it many times but I can't find an ...I have seen it many times but I can't find an example right nowGeorgi Marinovhttps://www.blogger.com/profile/12226357993389417752noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-47400706770493370362014-12-11T19:32:01.595-05:002014-12-11T19:32:01.595-05:00Who is it tossing brown and red algae into the sam...Who is it tossing brown and red algae into the same bin as Protista? I haven't seen such a classification. John Harshmanhttps://www.blogger.com/profile/06705501480675917237noreply@blogger.com