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<?xml version="1.0" encoding="utf-8"?><rss version="2.0" xml:base="https://www.science20.com" xmlns:dc="http://purl.org/dc/elements/1.1/"><channel> <title>T Ryan Gregory's blog</title> <link>https://www.science20.com/genomicron</link> <description>Science 2.0® - Science for the next 2,000 years, Non-profit, non-partisan, independent.</description> <language>en</language><item> <title>Moore’s Law, The Origin Of Life, And Dropping Turkeys Off A Building</title> <link>https://www.science20.com/genomicron/moore%E2%80%99s_law_origin_life_and_dropping_turkeys_building-114220</link> <description><p>I’ve already mentioned the nonsensical paper “published” in (surprise, surprise) <em><a href="http://arxiv.org/abs/1304.3381">arXiv</a></em> in which the authors claim that the origin of life occurred long before the origin of the Earth based on the application of Moore’s Law to DNA. <br /><br />I won’t go into all the reasons that this is silly — for that, you can see critiques by <a href="http://scienceblogs.com/pharyngula/2013/04/18/graaarh-physicists-biologists/">PZ Myers</a> and <span><a href="http://rationallyspeaking.blogspot.com/2013/05/moores-law-and-origin-of-life-study-in.html" target="_blank">Massimo Pigliucci</a></span>. Suffice it to say that the data, the analysis, and the interpretation are all problematic.</p><p><a href="https://www.science20.com/genomicron/moore%E2%80%99s_law_origin_life_and_dropping_turkeys_building-114220" target="_blank">read more</a></p></description> <category domain="https://www.science20.com/humor">Humor</category> <pubDate>Mon, 10 Jun 2013 11:00:19 +0000</pubDate> <dc:creator>T. Ryan Gregory</dc:creator> <guid isPermaLink="false">114220 at https://www.science20.com</guid></item><item> <title>Genome Reduction In Bladderworts Vs. Leg Loss In Snakes</title> <link>https://www.science20.com/genomicron/genome_reduction_bladderworts_vs_leg_loss_snakes-114203</link> <description><p>In one sense, I am happy that there is enough interest in the concept of “junk DNA” (and by extension, my area of research in genome size evolution) that the subject gets regular media attention. <br /></p><p><a href="https://www.science20.com/genomicron/genome_reduction_bladderworts_vs_leg_loss_snakes-114203" target="_blank">read more</a></p></description> <category domain="https://www.science20.com/evolution">Evolution</category> <pubDate>Thu, 06 Jun 2013 11:00:20 +0000</pubDate> <dc:creator>T. Ryan Gregory</dc:creator> <guid isPermaLink="false">114203 at https://www.science20.com</guid></item><item> <title>Another Just-So Story, This Time About Fists</title> <link>https://www.science20.com/genomicron/another_justso_story_time_about_fists-101308</link> <description><blockquote><p>“It is demonstrable,” said he, “that things cannot be otherwise than as they are; for as all things have been created for some end, they must necessarily be created for the best end. Observe, for instance, the nose is formed for spectacles, therefore we wear spectacles. The legs are visibly designed for stockings, accordingly we wear stockings.”</p><p>- <em>Candide</em> by Voltaire</p></blockquote><p>Humans are unique among the great apes (of which we are one) in various ways. One of them is our possession of a very long Achilles tendon, which is quite short in chimpanzees, gorillas, and orangutans.</p><p><a href="https://www.science20.com/genomicron/another_justso_story_time_about_fists-101308" target="_blank">read more</a></p></description> <category domain="https://www.science20.com/evolution">Evolution</category> <pubDate>Mon, 21 Jan 2013 09:30:14 +0000</pubDate> <dc:creator>T. Ryan Gregory</dc:creator> <guid isPermaLink="false">101308 at https://www.science20.com</guid></item><item> <title>The Great Wrinkled Finger Debate</title> <link>https://www.science20.com/genomicron/great_wrinkled_finger_debate-100816</link> <description><p>This past May, I was fortunate enough to take part in a conference in Venice, Italy, which was a retrospective on the legacy of famous paleontologist and author Stephen Jay Gould 10 years after his death. The choice of Venice as the conference venue was a nod to one of Gould’s most famous and influential papers, “<a href="http://rspb.royalsocietypublishing.org/content/205/1161/581.abstract">The Spandrels of San Marco and the Panglossian Paradigm: A Critique of the Adaptationist Programme</a>“, which he co-authored with Richard Lewontin in 1979. </p><p><a href="https://www.science20.com/genomicron/great_wrinkled_finger_debate-100816" target="_blank">read more</a></p></description> <category domain="https://www.science20.com/evolution">Evolution</category> <pubDate>Mon, 14 Jan 2013 09:30:18 +0000</pubDate> <dc:creator>T. Ryan Gregory</dc:creator> <guid isPermaLink="false">100816 at https://www.science20.com</guid></item><item> <title>Platypus And The Problem With Primitive</title> <link>https://www.science20.com/genomicron/platypus_and_problem_primitive</link> <description>The concept of "primitive" is one that is very often misunderstood.<br /><br />Properly defined, "primitive" means "more like a particular ancestor", refers only to individual characteristics (not whole species or lineages), and is contrasted with "derived" (not "advanced" or "more evolved").<br /><br />I have covered this and other misunderstandings of evolutionary concepts in various articles and I try to clarify these in my courses. But the intuitive interpretation in which one species is deemed more primitive than another is very hard to shake, including in the scientific literature.<br /><br />An example:<br /><p><a href="https://www.science20.com/genomicron/platypus_and_problem_primitive" target="_blank">read more</a></p></description> <category domain="https://www.science20.com/evolution">Evolution</category> <pubDate>Mon, 26 Jul 2010 23:56:50 +0000</pubDate> <dc:creator>T. Ryan Gregory</dc:creator> <guid isPermaLink="false">70102 at https://www.science20.com</guid></item><item> <title>Primitive Frogs And Phylogenetic Fallacies</title> <link>https://www.science20.com/genomicron/primitive_frogs_and_phylogenetic_fallacies</link> <description>As I have explained in various blog posts and in <A href="http://www.gregorylab.org/reprints/UnderstandingTrees.pdf">this paper</a>, it is a fallacy to assume that any one character found in a so-called "primitive" species alive today was also found in the ancestral species. All living species are modern species, and "primitive" vs. "derived" refers to characters, not whole species.<br /><br />Anyway, <em>New Scientist</em> seems to have fallen for this in their interpretation of a recent paper.<br /><blockquote><strong><A href="http://www.newscientist.com/article/dn19221-bellyflopping-frogs-shed-light-on-evolution.html">Bellyflopping frogs shed light on evolution</a></strong><br /></blockquote><p><a href="https://www.science20.com/genomicron/primitive_frogs_and_phylogenetic_fallacies" target="_blank">read more</a></p></description> <category domain="https://www.science20.com/evolution">Evolution</category> <pubDate>Mon, 26 Jul 2010 23:55:47 +0000</pubDate> <dc:creator>T. Ryan Gregory</dc:creator> <guid isPermaLink="false">70101 at https://www.science20.com</guid></item><item> <title>Mattick On Transposable Element Function</title> <link>https://www.science20.com/genomicron/mattick_transposable_element_function</link> <description>John Mattick, University of Queensland, is one of the leading proponents of the idea that much -- <A href="http://www.science20.com/dna_and_diversity/is_most_of_the_human_genome_functional">perhaps most</A> -- of the human genome is functional. He has been making claims along these lines <A href="http://www.genomicron.evolverzone.com/2008/02/quotes-of-interest-long-neglected-some/">for at least 15 years</A>, but seems to always present it as a new idea. Readers of this blog may also remember the <A href="http://www.science20.com/genomicron/blog/hap_dap">Dog's Ass Plot</A> included in one of his publications. <br /><p><a href="https://www.science20.com/genomicron/mattick_transposable_element_function" target="_blank">read more</a></p></description> <category domain="https://www.science20.com/genetics_molecular_biology">Genetics & Molecular Biology</category> <pubDate>Mon, 26 Jul 2010 23:54:10 +0000</pubDate> <dc:creator>T. Ryan Gregory</dc:creator> <guid isPermaLink="false">70100 at https://www.science20.com</guid></item><item> <title>Does Junk DNA Protect Against Mutation?</title> <link>https://www.science20.com/genomicron/does_junk_dna_protect_against_mutation</link> <description>One of the most common hypotheses that I hear with regard to possible non-coding DNA function is that it serves to protect genes against mutation. Junk DNA, according to this proposal, is there to provide a defensive shield against mutagens (usually this includes UV, ionizing radiation, chemical mutagens, viruses, and/or oxygen radicals). I am very skeptical of this explanation, but I am willing to take it seriously if it is studied seriously. In fact, one of my current graduate students first came to talk with me when he was an undergraduate and asked me about this possible function.<p><a href="https://www.science20.com/genomicron/does_junk_dna_protect_against_mutation" target="_blank">read more</a></p></description> <category domain="https://www.science20.com/genetics_molecular_biology">Genetics & Molecular Biology</category> <pubDate>Sat, 19 Dec 2009 16:15:29 +0000</pubDate> <dc:creator>T. Ryan Gregory</dc:creator> <guid isPermaLink="false">62821 at https://www.science20.com</guid></item><item> <title>Evolution And Art</title> <link>https://www.science20.com/genomicron/evolution_and_art</link> <description>From Oct. 9-30, the University of Guelph and <a href="http://www.edvideo.org/">Ed Video</a> are hosting a special art exhibit entitled "<a href="http://www.arts.uoguelph.ca/eayd2009">This View of Life: Evolutionary Art for the Year of Darwin</a>". It was organized by professors in four departments: Integrative Biology, Philosophy, History, and English and Theatre Studies, and was curated by Scott McGovern of Ed Video. The exhibit features art by 10 artists, all inspired by the themes of evolution, Darwin, and biodiversity.<br /><br />The <a href="http://www.gregorylab.org">Gregory Lab</a> contributed some installations as well, which are shown in this brief clip from just before the opening reception on Oct. 16 (about 200 people attended the event).<br /><p><a href="https://www.science20.com/genomicron/evolution_and_art" target="_blank">read more</a></p></description> <category domain="https://www.science20.com/science_society">Science & Society</category> <pubDate>Sat, 17 Oct 2009 16:43:16 +0000</pubDate> <dc:creator>T. Ryan Gregory</dc:creator> <guid isPermaLink="false">60592 at https://www.science20.com</guid></item><item> <title>Humans Vs. Chimps -- Neither Is An Offshoot Of Ardipithecus Ramidus</title> <link>https://www.science20.com/genomicron/humans_vs_chimps_neither_offshoot_ardipithecus_ramidus</link> <description><A href="http://i.usatoday.net/tech/_photos/2009/10/01/ardix.jpg"><img src="http://i.usatoday.net/tech/_photos/2009/10/01/ardix.jpg" alt="" border="0" /></a>Tomorrow's <span><A href="http://www.sciencemag.org/ardipithecus/">Science</a> </span>will be a special issue reporting tons of new information on the fossil hominid <em>Ardipithecus ramidus </em>("Ardi"), which is really exciting (though not as much as <span>Darwinius</span>, which was "<A href="http://www.revealingthelink.com/">like a meteor hitting the Earth</a>" or whatever).<br /><br /><br /><p><a href="https://www.science20.com/genomicron/humans_vs_chimps_neither_offshoot_ardipithecus_ramidus" target="_blank">read more</a></p></description> <category domain="https://www.science20.com/evolution">Evolution</category> <pubDate>Thu, 01 Oct 2009 17:30:53 +0000</pubDate> <dc:creator>T. Ryan Gregory</dc:creator> <guid isPermaLink="false">60241 at https://www.science20.com</guid></item><item> <title>Omnigenomics</title> <link>https://www.science20.com/genomicron/omnigenomics</link> <description>Sometimes it is helpful to have a catchy word to describe one's type of research. I think that's why "omics" words are so popular -- they encapsulate a complex combination of approaches (usually something + genomics, or something-more-than-genomics) in a memorable way that immediately conveys the gist of the field.<br /><br />"Metagenomics" is a good example -- it's the study of a larger assemblage of genomes than just one, usually from an environmental sample of microbes. "Proteiomics" is another, or "transcriptomics". Of course, this can get out of hand (see <A href="http://phylogenomics.blogspot.com/2009/01/worst-new-omics-word-award-museomics.html">here</a>).<br /><p><a href="https://www.science20.com/genomicron/omnigenomics" target="_blank">read more</a></p></description> <category domain="https://www.science20.com/evolution">Evolution</category> <pubDate>Thu, 01 Oct 2009 00:13:00 +0000</pubDate> <dc:creator>T. Ryan Gregory</dc:creator> <guid isPermaLink="false">60232 at https://www.science20.com</guid></item><item> <title>Does Evolutionary Biology Make Predictions?</title> <link>https://www.science20.com/genomicron/does_evolutionary_biology_make_predictions</link> <description>A commenter on a <a href="http://www.scientificblogging.com/genomicron/breaking_news_evidence_evolution_found">previous post</a> seems to have objected to the claim that evolutionary science makes predictions.<br /><blockquote>gimme 5 examples of predictions, i mean real predictions: not fit the model hogwash<br /><br /> <span class="submitted">Marilyn</span></blockquote>Here's a list that I put together in around 10 minutes.<br /><br />1) That a transitional fossil linking fishes and tetrapods would be found in rocks of a specific age (from the Devonian) and formed in freshwater environments. <a href="http://tiktaalik.uchicago.edu/">CONFIRMED</a>.<br /><p><a href="https://www.science20.com/genomicron/does_evolutionary_biology_make_predictions" target="_blank">read more</a></p></description> <category domain="https://www.science20.com/evolution">Evolution</category> <pubDate>Thu, 24 Sep 2009 21:20:32 +0000</pubDate> <dc:creator>T. Ryan Gregory</dc:creator> <guid isPermaLink="false">60005 at https://www.science20.com</guid></item><item> <title>Are We Descended From Monkeys?</title> <link>https://www.science20.com/genomicron/are_we_descended_monkeys</link> <description>Today I gave my lecture on mammal diversity and evolution in the 4th year vertebrate course. We have been talking a fair bit about <A href="http://en.wikipedia.org/wiki/Paraphyly">paraphyletic</a> groups, common vs. scientific names, and so on. Within this context, we explored the issue of whether we're "descended from monkeys", by taking a look at a phylogeny of relevant primates:<br /><p><a href="https://www.science20.com/genomicron/are_we_descended_monkeys" target="_blank">read more</a></p></description> <category domain="https://www.science20.com/evolution">Evolution</category> <pubDate>Thu, 24 Sep 2009 20:47:41 +0000</pubDate> <dc:creator>T. Ryan Gregory</dc:creator> <guid isPermaLink="false">60003 at https://www.science20.com</guid></item><item> <title>Breaking News: Evidence For Evolution Found!</title> <link>https://www.science20.com/genomicron/breaking_news_evidence_evolution_found</link> <description>One of Doug Futuyma's great quotes is this one:<br /><blockquote>"...no biologist today would think of publishing a paper on ‘new evidence for evolution’... it simply hasn’t been an issue in scientific circles for more than a century."<br /> - Futuyma, 1998 <span>Evolution Biology</span>, 3rd edition</blockquote>Press officers are a different story. <A href="http://esciencenews.com/articles/2009/09/03/molecular.decay.enamel.specific.gene.toothless.mammals.supports.theory.evolution">Here's one</a> from the University of California, Riverside:<br /><blockquote><span>Molecular decay of enamel-specific gene in toothless mammals supports theory of evolution</span><br /></blockquote><p><a href="https://www.science20.com/genomicron/breaking_news_evidence_evolution_found" target="_blank">read more</a></p></description> <category domain="https://www.science20.com/evolution">Evolution</category> <pubDate>Fri, 11 Sep 2009 12:12:04 +0000</pubDate> <dc:creator>T. Ryan Gregory</dc:creator> <guid isPermaLink="false">59414 at https://www.science20.com</guid></item><item> <title>Small Genomes In Pterosaurs Too.</title> <link>https://www.science20.com/genomicron/small_genomes_pterosaurs_too</link> <description>My colleagues Chris Organ and Andrew Shedlock, who provided evidence that theropod dinosaurs already had (somewhat) reduced genome sizes prior to the evolution of birds (Organ et al. 2007) have followed up their study by estimating the genome sizes of several species of pterosaurs.<br /><br />Pterosaurs were the first vertebrates to evolve powered flight, having taken to the air 70 million years before birds and 150 million years prior to bats. Interestingly (though perhaps not surprisingly at this point), they seem to have possessed reduced genome sizes, and these downsizings of DNA amount began before flight arose.<br /><p><a href="https://www.science20.com/genomicron/small_genomes_pterosaurs_too" target="_blank">read more</a></p></description> <category domain="https://www.science20.com/evolution">Evolution</category> <pubDate>Thu, 23 Oct 2008 15:25:03 +0000</pubDate> <dc:creator>T. Ryan Gregory</dc:creator> <guid isPermaLink="false">33880 at https://www.science20.com</guid></item><item> <title>Evolution: Education And Outreach Special Issue - Eye Evolution</title> <link>https://www.science20.com/genomicron/evolution_education_and_outreach_special_issue_eye_evolution</link> <description><p>I was planning to wait until the issue was actually in print, or at least until all the articles were available in preprint, but there is already some buzz starting so here it is. The upcoming issue of <A href="http://www.springer.com/life+sci/journal/12052"><span>Evolution: Education and Outreach</span></a>, of which I was editor, is a special issue dedicated to eye evolution. The table of contents:</p><p><span>Evolution: Education and Outreach</span><br />Volume 1 Issue 4<br /><span>The evolution of eyes</span><br />Edited by T. Ryan Gregory</p><p><span>Editorial</span></p><p><a href="https://www.science20.com/genomicron/evolution_education_and_outreach_special_issue_eye_evolution" target="_blank">read more</a></p></description> <category domain="https://www.science20.com/evolution">Evolution</category> <pubDate>Wed, 22 Oct 2008 20:54:11 +0000</pubDate> <dc:creator>T. Ryan Gregory</dc:creator> <guid isPermaLink="false">33837 at https://www.science20.com</guid></item><item> <title>A Pronounced Affection For Parasites</title> <link>https://www.science20.com/genomicron/a_pronounced_affection_for_parasites</link> <description><a href="http://environment.newscientist.com/channel/earth/dn14393-many-little-parasites-add-up-to-one-big-biomass.html">According to Peter Olson</a> of the Natural History Museum in London, &quot;All free-living organisms host one or more parasites.&quot; This can be taken two ways, both of them generally true: a) that each individual multicellular organism hosts at least one individual parasite within its body, and b) that each free-living species plays host to at least one species of parasite that attacks it exclusively. Consider this second point for a moment. For each free living species there is one or more (usually several more) parasite species -- that is, as a category (polyphyletic, obviously), parasites may very well be the most diverse types of organisms on the planet.<p><a href="https://www.science20.com/genomicron/a_pronounced_affection_for_parasites" target="_blank">read more</a></p></description> <category domain="https://www.science20.com/ecology_zoology">Ecology & Zoology</category> <pubDate>Thu, 24 Jul 2008 11:35:54 +0000</pubDate> <dc:creator>T. Ryan Gregory</dc:creator> <guid isPermaLink="false">30898 at https://www.science20.com</guid></item><item> <title>Gecko Genome Size And Cell Size</title> <link>https://www.science20.com/genomicron/gecko_genome_size_and_cell_size</link> <description><p>One of the many aggravations I encounter when reviewing manuscripts is that some authors greatly overstate the applicability of statistically significant patterns they report. For example, a statistically significant pattern in a small comparison of a few animals may be extrapolated in the discussion to the kingdom at large. </p><p>Today I was disappointed to see a paper that is soon to come out in <em>Zoology </em>that does the opposite -- i.e. takes a non-significant relationship in a handful of species and pretends that it challenges the importance of broad relationships that have been considered important for decades. </p><p>The paper in question is: </p><p><a href="https://www.science20.com/genomicron/gecko_genome_size_and_cell_size" target="_blank">read more</a></p></description> <category domain="https://www.science20.com/genetics_molecular_biology">Genetics & Molecular Biology</category> <pubDate>Sat, 05 Jul 2008 15:12:40 +0000</pubDate> <dc:creator>T. Ryan Gregory</dc:creator> <guid isPermaLink="false">30293 at https://www.science20.com</guid></item><item> <title>Natural Selection Before Darwin</title> <link>https://www.science20.com/genomicron/natural_selection_before_darwin</link> <description><p align="justify"><a href="http://en.wikipedia.org/wiki/Charles_Darwin">Charles Darwin</a> (1809-1882) opened his <a href="http://darwin-online.org.uk/content/frameset?itemID=CUL-DAR121.-&amp;viewtype=text&amp;pageseq=1">first notebook</a> about &quot;the species question&quot; in 1837, not long after his return from the voyage of the <em>Beagle</em>. By 1838, he had developed the basic outline <img src="http://upload.wikimedia.org/wikipedia/commons/7/74/Alfred_Russel_Wallace.jpg" alt=" " width="110" height="132" align="right" /><img src="http://upload.wikimedia.org/wikipedia/commons/thumb/4/42/Charles_Darwin_aged_51.jpg/225px-Charles_Darwin_aged_51.jpg" alt=" " width="115" height="141" align="left" />of his theory of natural selection to explain the evolution of species. He spent the next 20 years developing the theory and marshalling evidence in favour of both the fact that species are related through common descent and his particular theory to explain this. After receving word that another naturalist, <a href="http://en.wikipedia.org/wiki/Alfred_Russel_Wallace">Alfred Russel Wallace</a> (1823-1913), had independently come upon the same theory, he assembled his work for publication, first in a joint <a href="http://www.linnean.org/index.php?id=380">paper with Wallace</a> presented to the Linnean Society of London in 1858 and then his &quot;abstract&quot;, <a href="http://darwin-online.org.uk/content/frameset?itemID=F373&amp;viewtype=side&amp;pageseq=1"><em>On the Origin of Species</em></a>, in 1859. </p><p align="justify">Some authors have argued that <a href="http://en.wikipedia.org/wiki/Edward_Blyth">Edward Blyth</a> (1810-1873), an <a href="http://www.darwinproject.ac.uk/darwin/search/advanced?query=author%3A%22Blyth%2C+Edward%22+addressee%3A%22Blyth%2C+Edward%22&amp;targetResult=1&amp;maxresults=50">acquaintance of Darwin&#39;s</a>, developed the central idea of selection in <a href="http://www.wku.edu/~smithch/biogeog/BLYT1835.htm">an 1835 paper</a> in the <em>Magazine of Natural History</em>. For example, <a href="http://www.jstor.org/pss/985383">Eiseley and Grote (1959)</a> claimed that &quot;the leading tenets of Darwin&#39;s work -- the struggle for existence, variation, natural selection and sexual selection are all fully expressed in Blyth&#39;s 1835 paper&quot;, from which they then quoted the following: </p><p><a href="https://www.science20.com/genomicron/natural_selection_before_darwin" target="_blank">read more</a></p></description> <category domain="https://www.science20.com/evolution">Evolution</category> <pubDate>Wed, 02 Jul 2008 15:03:24 +0000</pubDate> <dc:creator>T. Ryan Gregory</dc:creator> <guid isPermaLink="false">30211 at https://www.science20.com</guid></item><item> <title>Massive Moths! (Genomes, Not So Big)</title> <link>https://www.science20.com/genomicron/massive_moths_genomes_not_so_big</link> <description><p>Like several other insect orders, the Lepidoptera is staggeringly diverse -- there are about 180,000 described species in the order and an untold number that remain unknown to biologists. (For comparison, there are about 5,000 mammal species). </p><p>Most people know the Lepidoptera (&quot;leps&quot; to entomologists) as moths and butterflies. The incompleteness of their taxonomic descriptions reflects their sheer diversity rather than academic neglect -- leps have been collected and studied for centuries. As it turns out, the distinction between moths and butterflies probably is not phylogenetically meaningful, as the &quot;butterflies&quot; (which includes three superfamilies: true butterflies, skipper butterflies, and moth-butterflies), though probably monophyletic as a group, may represent a clade nested within the other moths. However, I won&#39;t complain if these terms survive as they are useful in non-phylogenetic contexts. </p><p><a href="https://www.science20.com/genomicron/massive_moths_genomes_not_so_big" target="_blank">read more</a></p></description> <category domain="https://www.science20.com/ecology_zoology">Ecology & Zoology</category> <pubDate>Sun, 22 Jun 2008 13:35:39 +0000</pubDate> <dc:creator>T. Ryan Gregory</dc:creator> <guid isPermaLink="false">29846 at https://www.science20.com</guid></item><item> <title>Learning Versus Evolution In Microbes.</title> <link>https://www.science20.com/genomicron/learning_versus_evolution_in_microbes</link> <description><p>One of my pet peeves is the common description in the media of bacteria &quot;learning&quot; to &quot;outsmart&quot; antibiotics. As anyone with a basic comprehension of evolution knows, learning has nothing to do with it. Learning is what happens during the lifetime of an individual, and it occurs in direct response to some information that the individual encounters. When bacteria become resistant to antibiotics, it is not by learning. The individual bacteria do not sense the antibiotic and change to become resistant. Rather, individual bacteria in a population that happen to be resistant because of some genetic difference (or in whom a mutation conferring resistance arises by chance or through gene transfer from another population) will survive and reproduce more effectively than individuals lacking the genetic characteristic that confers resistance. Over many generations of this process, the gene providing resistance to the antibiotic will be found in the majority of bacteria -- not because it &quot;spreads&quot; and not because individual bacteria develop resistance, but because the bacteria that are the most abundant in the population after many generations are obviously the descendants of the ancestors that left the most offspring, namely those who survived the antibiotics. </p><p><a href="https://www.science20.com/genomicron/learning_versus_evolution_in_microbes" target="_blank">read more</a></p></description> <category domain="https://www.science20.com/applied_physics">Applied Physics</category> <pubDate>Fri, 20 Jun 2008 11:55:02 +0000</pubDate> <dc:creator>T. Ryan Gregory</dc:creator> <guid isPermaLink="false">29810 at https://www.science20.com</guid></item><item> <title>Junk DNA And The Onion Test</title> <link>https://www.science20.com/genomicron/junk_dna_and_the_onion_test</link> <description><p>One copy of the human genome is more than 3 billion nucleotides in length, and weighs in at about 3.5 picograms (pg, or trillionths of a gram). Only about 1.5% of this is composed of our 20,000 or so protein-coding genes, though other data suggest that at least 5% has been conserved by natural selection, suggesting that a notable portion of the non-coding majority is also functional. On the other hand, it is now apparent that much of the genome residing in our cells is made up of sequences like transposable elements -- &quot;parasites&quot; of the genome that can move about wwithin and be copied independently of the &quot;host&quot; genome -- and especially their extinct remnants. One such element, <em>Alu</em>, is present in more than one million copies.</p><p><a href="https://www.science20.com/genomicron/junk_dna_and_the_onion_test" target="_blank">read more</a></p></description> <category domain="https://www.science20.com/evolution">Evolution</category> <pubDate>Sun, 01 Jun 2008 10:00:00 +0000</pubDate> <dc:creator>T. Ryan Gregory</dc:creator> <guid isPermaLink="false">29099 at https://www.science20.com</guid></item><item> <title>Platypus Sex Chromosomes And Basal-Equals-Primitive</title> <link>https://www.science20.com/genomicron/platypus_sex_chromosomes_and_basal_equals_primitive</link> <description><p>There has been considerable interest in the publication of the platypus genome, which is good. Unfortunately, much of the reporting has been distorted, which is bad. However, rather than picking on the press, I want to focus on an example from the scientific literature where a misconception about evolutionary relationships seems to creep in and generate confusion. Consider the following line, from a soon to be published paper about platypus sex chromosomes (Veyrunes et al. 2008). </p> <blockquote> <p>As the most basal mammal group, the egg-laying monotremes are ideal for determining how the <a href="http://en.wikipedia.org/wiki/Theria">therian</a> <a href="http://en.wikipedia.org/wiki/XY_sex-determination_system"> XY</a> system evolved. </p></blockquote><p><a href="https://www.science20.com/genomicron/platypus_sex_chromosomes_and_basal_equals_primitive" target="_blank">read more</a></p></description> <category domain="https://www.science20.com/science_education_policy">Science Education & Policy</category> <pubDate>Fri, 09 May 2008 16:17:52 +0000</pubDate> <dc:creator>T. Ryan Gregory</dc:creator> <guid isPermaLink="false">28379 at https://www.science20.com</guid></item><item> <title>Phylogenetic Fallacies: Branching From A Main Line</title> <link>https://www.science20.com/genomicron/phylogenetic_fallacies_branching_from_a_main_line</link> <description><p>In <a href="/genomicron/phylogenetic_fallacies_early_branching_must_mean_primitive">Phylogenetic Fallacies: Early Branching Must Mean Primitive</a> I focused on the misconception that an &quot;early branching&quot; lineage was necessarily &quot;primitive&quot; (i.e., very similar to a distant ancestor). This time, I want to discuss something slightly more subtle, but nonetheless important, with regard to interpreting phylogenies. Specifically, I want to note a problem with the very concept of one lineage &quot;branching off from&quot; another lineage. There can be a tendency to consider evolutionary trees as reflecting a main line with a series of &quot;side branches&quot;. This is especially true when the tree is &quot;unbalanced&quot; (lineages are depicted with uneven amounts of diversity) and &quot;ladderized&quot; (the more diverse branches are placed on the same side of each node). The following is a general unbalanced, right-ladderized tree. <a href="http://bp3.blogger.com/_KQSgvOOpF1I/SAVsbqOq7OI/AAAAAAAAAVE/jS0GimHYqns/s1600-h/tree1.jpg"><img src="http://bp3.blogger.com/_KQSgvOOpF1I/SAVsbqOq7OI/AAAAAAAAAVE/jS0GimHYqns/s400/tree1.jpg" /></a></p><p><a href="https://www.science20.com/genomicron/phylogenetic_fallacies_branching_from_a_main_line" target="_blank">read more</a></p></description> <category domain="https://www.science20.com/science_education_policy">Science Education & Policy</category> <pubDate>Thu, 01 May 2008 12:14:16 +0000</pubDate> <dc:creator>T. Ryan Gregory</dc:creator> <guid isPermaLink="false">28128 at https://www.science20.com</guid></item><item> <title>Whose Genome?</title> <link>https://www.science20.com/genomicron/whose_genome</link> <description>The term &quot;genome&quot; is oft-heard but seldom defined, and indeed has more than one meaning. Little wonder, then, that discussions about genome sequences and comparisons thereof can leave otherwise interested audiences more frustrated than enlightened. &quot;What is a genome?&quot; and &quot;whose genome was sequenced?&quot; are legitimate questions, and what follows is an attempt at clarification that is, by necessity, as much philosophical as scientific.<strong> </strong><p class="MsoNormal"><strong>Definition #1:</strong> In a broad sense, a genome can be considered as the collective set of genes, non-coding DNA sequences, and all their variants that are located within the chromosomes of members of a given species.</p><p><a href="https://www.science20.com/genomicron/whose_genome" target="_blank">read more</a></p></description> <category domain="https://www.science20.com/science_education_policy">Science Education & Policy</category> <pubDate>Wed, 30 Apr 2008 12:31:07 +0000</pubDate> <dc:creator>T. Ryan Gregory</dc:creator> <guid isPermaLink="false">28099 at https://www.science20.com</guid></item><item> <title>Guide To Translating Scientific Papers Into Plain English</title> <link>https://www.science20.com/genomicron/guide_translating_scientific_papers_plain_english-28033</link> <description><P align="left">Believe it or not, scientists do not always take themselves too seriously. We can laugh at ourselves and the sometimes rigid conventions of our profession. Take, for example, this guide to translating the formal language of scientific articles into plain English. (Note: This has circulated on email among scientists a number of times over at least a 10 year period; I remember taping it on the door when I was a grad student. An astute reader pointed out that it is originally from Graham, CD. 1957. <A href="http://www.astro.rug.nl/~terlouw/glossary.html">A glossary for research reports</a>. Metal Progress 71: 75, though it has mutated somewhat in the interim).</p><p><a href="https://www.science20.com/genomicron/guide_translating_scientific_papers_plain_english-28033" target="_blank">read more</a></p></description> <category domain="https://www.science20.com/humor">Humor</category> <pubDate>Tue, 29 Apr 2008 01:25:47 +0000</pubDate> <dc:creator>T. Ryan Gregory</dc:creator> <guid isPermaLink="false">28033 at https://www.science20.com</guid></item><item> <title>Phylogenetic Fallacies: Early Branching Must Mean Primitive</title> <link>https://www.science20.com/genomicron/phylogenetic_fallacies_early_branching_must_mean_primitive</link> <description><p>Evolutionary trees, or "phylogenies", are a major part of modern evolutionary science. They depict hypotheses regarding the relationships among taxa, and are therefore important in reconstructions of the historical path of evolution (Gregory 2008a,b).</p><p>Various approaches can be taken to formulating phylogenetic hypotheses, including analyses based on morphological, fossil, and/or molecular data. These methods often agree well, but sometimes one or another can throw up some surprises and challenge previous hypotheses about the relationships among groups of organisms.<p> Reconstructing the tree of life is a difficult and complicated process, and one should expect there to be significant refinements and revisions along the way. This is especially true of the deepest branches of the tree, which are often the most difficult to resolve.</p><p>Case in point, the<a href="http://tolweb.org/"> Tree of Life Web Project</a> gives the following summary of deep branches among major animal lineages:<br /><a href="http://bp2.blogger.com/_KQSgvOOpF1I/SAIa_KOq7LI/AAAAAAAAAUs/nT6jfO2Epvo/s1600-h/Phyl1.jpg"><img src="/files/deep branches among major animal lineages.jpg" width="380" alt="" id="BLOGGER_PHOTO_ID_5188739393064201394" border="0" /></a></p><p><a href="https://www.science20.com/genomicron/phylogenetic_fallacies_early_branching_must_mean_primitive" target="_blank">read more</a></p></description> <category domain="https://www.science20.com/science_education_policy">Science Education & Policy</category> <pubDate>Sat, 26 Apr 2008 11:50:00 +0000</pubDate> <dc:creator>T. Ryan Gregory</dc:creator> <guid isPermaLink="false">27928 at https://www.science20.com</guid></item><item> <title>Non-functional DNA: Non-functional Vs. Inconsequential</title> <link>https://www.science20.com/genomicron/nonfunctional_dna_nonfunctional_vs_inconsequential-26384</link> <description>Each copy of the human genome consists of about 3,200,000,000 base pairs, and includes about 500,000 repeats of the <em>LINE-1</em> transposable element (a <a href="http://sandwalk.blogspot.com/2007/10/junk-in-your-genome-lines.html">LINE</a>) and twice as many copies of <em>Alu</em> (a <a href="http://sandwalk.blogspot.com/2007/10/junk-in-your-genome-sines.html">SINE</a>), as compared to around 20,000 protein-coding genes. <br /><br />Whereas protein-coding regions represent about 1.5% of the genome, about half is made up <em>LINE-1</em>, <em>Alu</em>, and other transposable element sequences. These begin as parasites, and some continue to behave as detrimental mutagens implicated in disease. However, most of those in the human genome are no longer mobile, and it is possible that many of these persist as commensal freeloaders. <br /><br />Finally, it has long <a href="http://genomicron.blogspot.com/2008/02/non-functional-dna-quantity.html">been expected</a> that a significant subset of non-coding elements would be co-opted by the host and take on functional roles at the organism level, and there is increasing evidence to support this. A notable fraction of the non-genic portion of human DNA is undoubtedly involved in regulation, chromosomal function, and other important processes, but based on what we know about non-coding DNA sequences, it remains a reasonable <a href="http://genomicron.blogspot.com/2008/02/non-functional-dna-burden-of-proof.html">default</a> assumption -- though one that should continue to be tested empirically -- that much or perhaps most of it is not functional at the organism level. <br /><br />This does not mean that a search for the functional segments is futile or irrelevant -- far from it, as many non-genic regions are critical for normal genomic operation and some have played an important role in many evolutionary transitions. It simply means that one must not extrapolate without warrant from discoveries involving a small fraction of sequences to the genome as a whole.<br /><p><a href="https://www.science20.com/genomicron/nonfunctional_dna_nonfunctional_vs_inconsequential-26384" target="_blank">read more</a></p></description> <category domain="https://www.science20.com/genetics_molecular_biology">Genetics & Molecular Biology</category> <pubDate>Mon, 14 Apr 2008 14:55:07 +0000</pubDate> <dc:creator>T. Ryan Gregory</dc:creator> <guid isPermaLink="false">26384 at https://www.science20.com</guid></item><item> <title>Do You Understand Evolutionary Trees? (Part Two)</title> <link>https://www.science20.com/dna_and_diversity/do_you_understand_evolutionary_trees_part_two</link> <description><p>In the <a href="/dna_and_diversity/do_you_understand_evolutionary_trees_part_one" target="_blank">first installment of this series</a>, we encountered the common misconception that the order of the terminal nodes (&quot;tips&quot;) on an evolutionary tree reflects the actual relatedness among the species represented. Simply rotating some internal nodes without affecting the branching order (&quot;topology&quot;) of the tree -- and thus, making no change to the relationships among species -- showed that that the order of tips on a tree is actually arbitrary. What matters is the way that the species are connected through their common ancestors. </p><p><a href="https://www.science20.com/dna_and_diversity/do_you_understand_evolutionary_trees_part_two" target="_blank">read more</a></p></description> <category domain="https://www.science20.com/science_education_policy">Science Education & Policy</category> <pubDate>Tue, 11 Mar 2008 18:55:35 +0000</pubDate> <dc:creator>T. Ryan Gregory</dc:creator> <guid isPermaLink="false">9174 at https://www.science20.com</guid></item><item> <title>Should Evolution Be Taught In High School?</title> <link>https://www.science20.com/dna_and_diversity/should_evolution_be_taught_in_high_school</link> <description>Microbiologist <a href="http://en.wikipedia.org/wiki/Carl_Woese">Carl Woese</a> is well known as an iconoclast. Indeed, few biologists have so thoroughly shaken the tree of life as he did when he proposed that there are not two major branches -- <a href="http://en.wikipedia.org/wiki/Prokaryote">prokaryotes</a>, whose cells lack nuclei, and <a href="http://en.wikipedia.org/wiki/Eukaryote">eukaryotes</a> who possess nuclei, including all animals, plants, fungi, and protists -- but rather <a href="http://en.wikipedia.org/wiki/Three-domain_system"><em>three</em></a>. &quot;Prokaryotes&quot;, Woese argued, do not represent a cohesive category, and should be split into two deeply divergent lineages: the <a href="http://en.wikipedia.org/wiki/Bacteria">Bacteria</a>, with which everyone is reasonably familiar, and the <a href="http://en.wikipedia.org/wiki/Archaea">Archaea</a>, superficially similar organisms that are less commonly encountered as many of them reside in extreme environments. What&#39;s more, studies of genetic data suggested that the Archaea are actually more closely related to eukaryotes -- including humans -- than they are to bacteria. <img src="http://upload.wikimedia.org/wikipedia/commons/thumb/7/70/Phylogenetic_tree.svg/320px-Phylogenetic_tree.svg.png" alt="Three-domain tree" width="320" height="216" /><p>Woese&#39;s three-domain tree of life. From <a href="http://en.wikipedia.org/wiki/Image:Phylogenetic_tree.svg">Wikimedia Commons</a>.</p>At 79 years of age, Woese is still shaking things up. Most recently, he stated in an interview with <a href="http://blog.wired.com/wiredscience/2008/02/famed-microbiol.html"><em>Wired</em></a> that,<blockquote><p>My feeling is that evolution shouldn&#39;t be taught at the lower grades. You don&#39;t teach quantum mechanics in the grade schools. One has to be quite educated to work with these concepts; what they pass on as evolution in high schools is nothing but repetitious tripe that teachers don&#39;t understand. </p></blockquote><p><a href="https://www.science20.com/dna_and_diversity/should_evolution_be_taught_in_high_school" target="_blank">read more</a></p></description> <category domain="https://www.science20.com/science_education_policy">Science Education & Policy</category> <pubDate>Sun, 24 Feb 2008 16:37:38 +0000</pubDate> <dc:creator>T. Ryan Gregory</dc:creator> <guid isPermaLink="false">8600 at https://www.science20.com</guid></item></channel></rss> 
