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	<title>Transitions: The Evolution of Life</title>
	<link>http://afarensis.blogsome.com</link>
	<description>Exploring the World Around Us</description>
	<pubDate>Wed, 21 Jun 2006 16:22:55 +0000</pubDate>
	<generator>http://wordpress.org/?v=1.5.1-alpha</generator>
	<language>en</language>

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		<title>Gavin de Beer and mosaic evolution</title>
		<link>http://afarensis.blogsome.com/2006/06/21/gavin-de-beer-and-mosaic-evolution/</link>
		<comments>http://afarensis.blogsome.com/2006/06/21/gavin-de-beer-and-mosaic-evolution/#comments</comments>
		<pubDate>Wed, 21 Jun 2006 16:15:02 +0000</pubDate>
		<dc:creator>Snail's Tales</dc:creator>
		
	<category>Uncategorized</category>
		<guid>http://afarensis.blogsome.com/2006/06/21/gavin-de-beer-and-mosaic-evolution/</guid>
		<description><![CDATA[	&#8220;In a broad sense, all organisms can be said to be mosaics, with some characteristics so ancient in origin that they have changed little and some so recent, geologically speaking, that they have changed more than a little. It rarely occurs to most of us that we share ancestral characters with such different organisms as, [...]]]></description>
			<content:encoded><![CDATA[	<blockquote><p>&#8220;In a broad sense, all organisms can be said to be mosaics, with some characteristics so ancient in origin that they have changed little and some so recent, geologically speaking, that they have changed more than a little. It rarely occurs to most of us that we share ancestral characters with such different organisms as, for example, a flowering shrub.&#8221;</p>
	<p><a href="http://afarensis.blogsome.com/go.php?http://snailstales.blogspot.com/2006/01/george-gaylord-simpson-1902-1984.html">George Gaylord Simpson</a>, 1983</p></blockquote>
	<p><center><a title="Photo Sharing" href="http://afarensis.blogsome.com/go.php?http://www.flickr.com/photos/salyangoz/171983418/"><img height="375" alt="focamozaik2" src="http://static.flickr.com/67/171983418_7d81e17726.jpg" width="425" /></a><br />
<span style="font-size:85%;">Detail of a mosaic from Foça (ancient Phokaia) in western Turkey. Photographed in 1995.</span></center><br />
On this date in 1972 the English evolutionary biologist <a href="http://afarensis.blogsome.com/go.php?http://www.todayinsci.com/cgi-bin/indexpage.pl?http://www.todayinsci.com/6/6_21.htm" target="_blank">Sir Gavin R. de Beer</a> died (born 1899). One lasting contribution of de Beer to evolutionary theory was the concept of mosaic evolution that he developed in a 1954 paper<sup>1</sup>.</p>
	<p>Although a mosaic-like pattern of evolution is becoming more and more apparent in many major evolutionary transitions, including the evolution of humans from ape-like ancestors, I have not been able to find a recent general review of what mosaic evolution is all about. Stebbins published a review in 1983, but he seems to have confused mosaic evolution with adaptive radiation<sup>2</sup>. Recently, Mayr<sup>3</sup> and earlier, Simpson<sup>4</sup> gave brief explanations of the concept with both authors properly distinguishing mosaic evolution from adaptive radiation. Curiously, Ridley’s textbook on evolution<sup>5</sup> doesn’t mention mosaic evolution at all.</p>
	<p>To my great satisfaction, however, I have found in de Beer’s succinctly written original paper a full explanation of his idea.</p>
	<p>As the title of his paper implies, de Beer derived the concept of mosaic evolution from his study of the fossil <i>Archaeopteryx</i> and by comparing it with the bones of reptiles and birds. He found that <i>Archaeopteryx</i> had both reptilian and avian features:</p>
	<blockquote><p>&#8220;All these are characters which would not be in the least out of place if found in any reptile. On the other hand, there are a number of features in <i>Archaeopteryx</i> which are absolutely characteristic of birds&#8221;</p></blockquote>
	<p>This comparison led him to conclude that</p>
	<blockquote><p>&#8220;…it is clear that <i>Archaeopteryx</i> provides a magnificent example of an animal intermediate between two classes, the reptiles and the birds, with each of which it shares a number of well-marked characters.&#8221;</p></blockquote>
	<p>And this led to the formulation of mosaic evolution (content in brackets mine):</p>
	<blockquote><p>&#8220;…the statement that an animal was intermediate might mean that it was a mixture and that the transition affected some parts of the animal and not others, with the result that some parts were similar to those of one type [ancestor], other parts similar to the other type [descendant], and few or no parts intermediate in structure. In such a case the animal might be regarded as a mosaic in which the pieces could be replaced independently one by one, so that the transitional stages were a jumble of characters some of them similar to those of the class from which the animal evolved, others similar to those of the class into which the animal was evolving.&#8221;</p></blockquote>
	<p>He then applied these ideas to the fossils exemplifying the transitions from fish to amphibian and from amphibian to reptile and finally, from reptile to mammal. In each case, his observations derived from specific examples can be turned into general statements of mosaic evolution.</p>
	<blockquote><p>&#8220;But the fact that an animal can be at one and the same time show so many features which would make it an ideal transitional form, and also spoil this picture by possessing one or two characters which rule it out as a direct ancestor, is itself an argument in support of the principle of mosaic evolution, with the different pieces evolving separately, and some of them too fast. This phenomenon is found again and again in the study of transitions from one type of animal to another, and appears to be of general applicability. It would be more difficult to understand if the transitions took place by a gradual and simultaneous conversion of all the parts of the animal.&#8221;</p></blockquote>
	<p>This was followed by the notion of the evolution of different organs at different rates:</p>
	<blockquote><p>&#8220;Just as in some cases…an animal may show characters which have evolved too fast relatively to the other characters, in other cases certain characters may have been left in a profoundly archaic condition.&#8221;</p></blockquote>
	<p>De Beer even dealt preemptively with potential objections to his idea:</p>
	<blockquote><p>&#8220;Organisms are delicately balanced and adjusted mechanisms, and on the average, changes are more likely to upset than to strengthen them. Selection may therefore be expected to have acted with greater rigour against organisms vaying in more than one direction at a time, unless the directions were correlated…&#8221;</p></blockquote>
	<p>All of this terminated in a final conclusion:</p>
	<blockquote><p>&#8220;A necessary consequence of mosaic evolution and of the independence of characters evolving at different rates is the production of animals showing mixtures of primitive and specialised characters.&#8221;</p></blockquote>
	<p>A technical paper discussing de Beer’s significant accomplishments in embryology is available <a href="http://afarensis.blogsome.com/go.php?http://www.pitt.edu/~inb1/de_Beer.pdf" target="_blank">here</a>.</p>
	<p>Some recent technical papers on mosaic evolution:</p>
	<p><a href="http://afarensis.blogsome.com/go.php?http://www.journals.royalsoc.ac.uk/media/egehrhtrll5m0ylxjar6/contributions/j/2/0/w/j20wvank95k6x2lu.pdf" target="_blank">Andrew N. Iwaniuk, Karen M. Dean, John E. Nelson. 2004. A mosaic pattern characterizes the evolution of the avian brain. Proceedings: Biological Sciences 271, S148–151.</a></p>
	<p><a href="http://afarensis.blogsome.com/go.php?http://www.nature.com/nature/journal/v405/n6790/abs/4051055a0.html#abs" target="_blank">Robert A. Barton and Paul H. Harvey. 2000. Mosaic evolution of brain structure in mammals. <i>Nature</i> 405, 1055-1058.</a></p>
	<p><a href="http://afarensis.blogsome.com/go.php?http://www.dur.ac.uk/t.c.rae/CT/folia_rae.pdf" target="_blank">Todd C. Rae. 1999. Mosaic Evolution in the Origin of the Hominoidea. <i>Folia Primatol </i>70:125–135</a></p>
	<p><span style="font-size:85%;">1. De Beer, G.R. 1954. Archaeopteryx and evolution. <i>Advancement of Science</i> 11:160-170.<br />
2. Stebbins, G.L. 1983. Mosaic evolution: an integrating principle for the modern synthesis.<br />
<i>Experientia</i> 39:823-834.<br />
3. Mayr, E. 2001. <i>What evolution is</i>. Basic Books.<br />
4. Simpson, G.G. 1983. <i>Fossils and the history of life</i>. Scientific American Books.<br />
5. Ridley, M. 1996. <i>Evolution</i>. 2nd ed. Blackwell.</span>
</p>
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		<title>Helping Science Education</title>
		<link>http://afarensis.blogsome.com/2006/06/15/helping-science-education/</link>
		<comments>http://afarensis.blogsome.com/2006/06/15/helping-science-education/#comments</comments>
		<pubDate>Thu, 15 Jun 2006 15:41:46 +0000</pubDate>
		<dc:creator>afarensis</dc:creator>
		
	<category>Site of the Week</category>
		<guid>http://afarensis.blogsome.com/2006/06/15/helping-science-education/</guid>
		<description><![CDATA[	The ScienceBlogs/DonorsChoose raise-money-to-help-science-classrooms-a-thon!
Although I am not an educator or an academic, science education is important to me. One of the reasons I blog is to try and explain the methods and techniques of anthropology - and related subjects - to people who do not know that much about the field.  I have even started [...]]]></description>
			<content:encoded><![CDATA[	<p><b>The ScienceBlogs/DonorsChoose raise-money-to-help-science-classrooms-a-thon!</b><br />
Although I am not an educator or an academic, science education is important to me. One of the reasons I blog is to try and explain the methods and techniques of anthropology - and related subjects - to people who do not know that much about the field.  I have even started a <a href="http://afarensis.blogsome.com/go.php?http://afarensis.blogsome.com/">second blog</a> devoted to providing educational resources relating to evolution to teachers and students. So it is with great pleasure that I announce the following challange&#8230;</p>
	<p>Those of us who blog here at ScienceBlogs think science is cool, important, and worth understanding. If you&#8217;re reading the blogs here, chances are you feel the same way.</p>
	<p>A lot of us fell in love with science because of early experiences in school &#8212; teachers who made science intriguing, exciting, maybe a little bit dangerous. But tightening budgets are making it harder and harder for public school teachers to provide the books, equipment, and field trips to make science come alive for kids.</p>
	<p>DonorsChoose.org gives us a way to help teachers get the job done. A bunch of us at ScienceBlogs have set up Bloggers Challenges which will let us (and that includes you) contribute to worthy school projects in need of financial assistance. We&#8217;ll be able to track our progress right on the DonorsChoose site. And &#8212; because we like a little friendly competition &#8212; we&#8217;ll be updating you periodically as to which blogger&#8217;s readers are getting his or her challenge closest to its goal.</p>
	<p>You don&#8217;t need to give a barrel of money to help the kids &#8212; as little as $10 can help. You&#8217;re joining forces with a bunch of other people, and all together, your small contributions can make a big difference.</p>
	<p><b>Who&#8217;s In:</b></p>
	<p>Here are the ScienceBlogs bloggers who are participating with Bloggers Challenges:</p>
	<p><a href="http://afarensis.blogsome.com/go.php?http://scienceblogs.com/clock/">A Blog Around the Clock</a> (challenge here)<br />
<a href="http://afarensis.blogsome.com/go.php?http://scienceblogs.com/ethicsandscience/">Adventures in Ethics and Science</a> (challenge <a href="http://afarensis.blogsome.com/go.php?http://www.donorschoose.org/challenge.php?id=125">here</a>)<br />
<a href="http://afarensis.blogsome.com/go.php?http://scienceblogs.com/aetiology/">Aetiology</a> (challenge <a href="http://afarensis.blogsome.com/go.php?http://www.donorschoose.org/challenge.php?id=142">here</a>)<br />
<a href="http://afarensis.blogsome.com/go.php?http://scienceblogs.com/afarensis/2006/06/15/post_1/">Afarensis</a> (challenge <a href="http://afarensis.blogsome.com/go.php?http://www.donorschoose.org/challenge.php?id=63">here</a>)<br />
<a href="http://afarensis.blogsome.com/go.php?http://scienceblogs.com/cognitivedaily/">Cognitive Daily</a> (challenge <a href="http://afarensis.blogsome.com/go.php?http://www.donorschoose.org/locale0/challenge.php?id=139">here</a>)<br />
<a href="http://afarensis.blogsome.com/go.php?http://scienceblogs.com/evolgen/">Evolgen</a> (challenge <a href="http://afarensis.blogsome.com/go.php?http://www.donorschoose.org/challenge.php?id=143">here</a>)<br />
<a href="http://afarensis.blogsome.com/go.php?http://scienceblogs.com/gnxp/">Gene Expression</a> (challenge <a href="http://afarensis.blogsome.com/go.php?http://www.donorschoose.org/challenge.php?id=150">here</a>)<br />
<a href="http://afarensis.blogsome.com/go.php?http://scienceblogs.com/goodmath/">Good Math, Bad Math</a> (challenge <a href="http://afarensis.blogsome.com/go.php?http://www.donorschoose.org/challenge.php?id=147">here</a>)<br />
<a href="http://afarensis.blogsome.com/go.php?http://scienceblogs.com/islandofdoubt/">Island of Doubt</a> (challenge here)<br />
<a href="http://afarensis.blogsome.com/go.php?http://scienceblogs.com/mikethemadbiologist/">Mike the Mad Biologist</a> (challenge <a href="http://afarensis.blogsome.com/go.php?http://www.donorschoose.org/challenge.php?id=154">here</a>)<br />
<a href="http://afarensis.blogsome.com/go.php?http://scienceblogs.com/neurotopia/">Neurotopia, version 2.0</a> (challenge <a href="http://afarensis.blogsome.com/go.php?http://www.donorschoose.org/challenge.php?id=151">here</a>)<br />
<a href="http://afarensis.blogsome.com/go.php?http://scienceblogs.com/pharyngula/">Pharyngula</a> (challenge <a href="http://afarensis.blogsome.com/go.php?http://www.donorschoose.org/challenge.php?id=148">here</a>)<br />
<a href="http://afarensis.blogsome.com/go.php?http://scienceblogs.com/purepedantry/">Pure Pedantry</a> (challenge here)<br />
<a href="http://afarensis.blogsome.com/go.php?http://scienceblogs.com/authority/">The Questionable Authority</a> (challenge <a href="http://afarensis.blogsome.com/go.php?http://www.donorschoose.org/challenge.php?id=144">here</a>)<br />
<a href="http://afarensis.blogsome.com/go.php?http://scienceblogs.com/scientificactivist/">The Scientific Activist</a> (challenge <a href="http://afarensis.blogsome.com/go.php?http://www.donorschoose.org/challenge.php?id=138">here</a>)<br />
<a href="http://afarensis.blogsome.com/go.php?http://scienceblogs.com/strangerfruit/">Stranger Fruit</a> (challenge <a href="http://afarensis.blogsome.com/go.php?http://www.donorschoose.org/challenge.php?id=152">here</a>)<br />
<a href="http://afarensis.blogsome.com/go.php?http://scienceblogs.com/terrasig/">Terra Sigillata</a> (challenge here)<br />
<a href="http://afarensis.blogsome.com/go.php?http://scienceblogs.com/principles/">Uncertain Principles</a> (challenge <a href="http://afarensis.blogsome.com/go.php?http://www.donorschoose.org/challenge.php?id=146">here</a>)<br />
<a href="http://afarensis.blogsome.com/go.php?http://scienceblogs.com/worldsfair/">The World&#8217;s Fair</a> (challenge <a href="http://afarensis.blogsome.com/go.php?http://www.donorschoose.org/challenge.php?id=149">here</a>)</p>
	<p><b>How It Works</b></p>
	<p><a href="http://afarensis.blogsome.com/go.php?http://www.donorschoose.org/challenge.php?id=63"> Follow these links to the DonorsChoose website.</a></p>
	<p>Pick a project from the slate the blogger has selected (or more than one).</p>
	<p>Donate.</p>
	<p>(If you&#8217;re the loyal reader of multiple participating blogs and you don&#8217;t want to play favorites, you can donate to multiple challenges!)</p>
	<p>When Donors Choose sends you a confirmation email, forward it to:</p>
	<p>sb.donorschoose.bonanza@gmail.com</p>
	<p>This is your contest entry.</p>
	<p>Sit back and watch the little donation thermometers inch towards 100 percent. Once the Challenge ends, we&#8217;ll select winners at random.</p>
	<p><b>Contest you say? What&#8217;s that about?</b></p>
	<p>Just in case you&#8217;re on the fence about helping the kids, we thought we&#8217;d provide some incentives. They are:</p>
	<p>Subscriptions to <i>Seed</i> magazine</p>
	<p>ScienceBlogs mugs</p>
	<p><i>What We Believe But Cannot Prove</i>, edited by John Brockman</p>
	<p><i>The Republican War on Science</i>, by Chis Mooney</p>
	<p><i>Rebuilt: My Journey Back to the Hearing World</i>, by Michael Chorost</p>
	<p>Subscriptions to <i>TIME</i> magazine</p>
	<p><a href="http://afarensis.blogsome.com/go.php?http://bloggerinasnap.blogspot.com/">Blogging in a Snap</a>, by Julie Meloni</p>
	<p><i>Galileo&#8217;s Daughter</i>, by Dava Sobel</p>
	<p><i>The Scientific Renaissance: 1450-1630</i>, by Marie Boas Hall</p>
	<p><i>Paleoanthropology</i> (1st ed) by Milford Wolpoff (gently used)</p>
	<p><b>Administrative Details</b></p>
	<p>The contest will run from June 15 to July 1. Email your entries by July 1! Prize notification will start by July 5. </p>
	<p><a href="http://afarensis.blogsome.com/go.php?http://www.donorschoose.org/challenge.php?id=63" title="Help public school kids through my DonorsChoose challenge!"><img border="0" src= "http://www.donorschoose.org/images/link/link_donorschoose_small.gif"/></a>
</p>
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		<title>Learn the controversy: sympatric versus allopatric speciation</title>
		<link>http://afarensis.blogsome.com/2006/05/17/learn-the-controversy-sympatric-versus-allopatric-speciation/</link>
		<comments>http://afarensis.blogsome.com/2006/05/17/learn-the-controversy-sympatric-versus-allopatric-speciation/#comments</comments>
		<pubDate>Wed, 17 May 2006 14:40:55 +0000</pubDate>
		<dc:creator>Snail's Tales</dc:creator>
		
	<category>Uncategorized</category>
		<guid>http://afarensis.blogsome.com/2006/05/17/learn-the-controversy-sympatric-versus-allopatric-speciation/</guid>
		<description><![CDATA[	&#8220;When one looks carefully at a biological problem, one can usually discover more than one casual explanation&#8230;Indeed, it is quite possible that in biology the majority of phenomena and processes must be explained by a plurality of theories.&#8221;
	Ernst Mayr This is Biology (1997)
	One long standing controversy in evolutionary biology is about the respective contributions sympatry [...]]]></description>
			<content:encoded><![CDATA[	<blockquote><p>&#8220;When one looks carefully at a biological problem, one can usually discover more than one casual explanation&#8230;Indeed, it is quite possible that in biology the majority of phenomena and processes must be explained by a plurality of theories.&#8221;</p>
	<p>Ernst Mayr <em>This is Biology</em> (1997)</p></blockquote>
	<p>One long standing controversy in evolutionary biology is about the respective contributions sympatry and allopatry have made during the origins of the millions of species that now exist.</p>
	<p>A new species (or 2 new species) can develop if gene flow between 2 populations ceases or slows down to permit the independent evolution of the 2 populations.</p>
	<p><strong>Allopatric</strong> (or geographic) speciation takes place when 2 populations are geographically isolated from each other by, for example, a mountain chain, or an ocean. Because the members of the 2 populations cannot mate and exchange genes with each other, the populations may start to diverge genetically and phenotypically and eventually end up being 2 separate species. In extreme cases of allopatry, there will be no gene flow between the diverging populations.</p>
	<p>The opposite of this is <strong>sympatric</strong> speciation, which takes place in 2 populations whose distribution ranges are largely overlapping. Individuals initially belonging to the same species may begin to differentiate from each other when they start eating different foods or living in different habitats. If the slight genetic differences that may exist between such individuals are reinforced by assortive mating<sup>1</sup>, 2 populations may emerge and begin to diverge genetically and phenotypically to eventually become separate species. New species may originate even when there is some gene flow between the 2 populations.</p>
	<p>An intermediate mechanism is <strong>parapatric</strong> speciation, which takes place in contiguous, but otherwise geographically isolated (allopatric) populations.</p>
	<p><center><img src="http://home.earthlink.net/~snailstales2/speciation.JPG" /><br />
Diagrammatic representation of population divergence in allopatric and sympatric speciation. The vertical axis represents time, running from older, below, to younger, above. The circles and crosses represent the different genotypes. Darkening of the symbols symbolize new species. Modified from a drawing in G.G. Simpson. 1983. <i>Fossils and the History of Life</i>. Scientific American Books.</center><br />
The late Ernst Mayr was a strong proponent of allopatric speciation and for most of his long career, he discounted sympatric speciation as a viable mechanism. However, an increasing number of studies have been demonstrating that sympatric speciation is possible and may have taken place more often than traditionally believed.</p>
	<p>A well-written short essay by Chris D. Jiggins<sup>2</sup> in the 9 May issue of <a href="http://afarensis.blogsome.com/go.php?http://www.current-biology.com/" target="_blank">Current Biology</a> reviews some recent studies and presents a good argument in favor of sympatric speciation, while pointing out that the usual division of speciation events along a strict line as either sympatric or allopatric creates an “artificial dichotomy”. In line with Mayr’s opinion about the necessity to explain biological processes by more than one theory, Jiggins suggests that in most cases of speciation, sympatric and allopatric processes may both have been reponsible.</p>
	<blockquote><p>&#8220;…allopatric and sympatric speciation lie at the opposite ends of a continuum, which runs from zero to maximal gene flow between diverging populations. These new studies provide good evidence that fully sympatric speciation can occur, but most examples probably lie somewhere in between these two extremes.&#8221;</p></blockquote>
	<p>As is usually the case with any genuine scientific controversy, this one will continue to inspire further research and lead to better understandings of the many-faceted speciation events in nature. Jiggins ends his paper by laying out potential paths for future research.</p>
	<blockquote><p>&#8220;…we should abandon the common assumption that allopatric speciation is the ‘null hypothesis’ with all the burden of proof lying on the hypothesis of speciation with gene flow. Instead, speciation research should concentrate on the more proximal causes of speciation, rather than intractable questions of geography. Key questions that we can answer include whether speciation results from natural selection and/or genetic drift, and what traits and genetic architectures are causal in divergence.&#8221;</p></blockquote>
	<p>1. The mating of individuals preferentially with others of their own genotype is called assortive mating. The opposite of assortive mating is random mating.<br />
2. Chris D. Jiggins. Sympatric Speciation: Why the Controversy? <i>Current Biology</i>, Vol 16, R333-R334, 09 May 2006.</p>
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		<title>Explorations In Time</title>
		<link>http://afarensis.blogsome.com/2006/05/04/explorations-in-time/</link>
		<comments>http://afarensis.blogsome.com/2006/05/04/explorations-in-time/#comments</comments>
		<pubDate>Thu, 04 May 2006 16:37:03 +0000</pubDate>
		<dc:creator>afarensis</dc:creator>
		
	<category>Interactive Web Sites</category>
	<category>Site of the Week</category>
		<guid>http://afarensis.blogsome.com/2006/05/04/explorations-in-time/</guid>
		<description><![CDATA[	I haven&#8217;t picked a site of the week in awhile, so it is time to remedy that neglect. This week I have choosen Explorations in Time.
This is an extremely interesting interactive web site with modules for both students and teachers. I worked my way through the What did T-Rex taste like? module. The module uses [...]]]></description>
			<content:encoded><![CDATA[	<p>I haven&#8217;t picked a site of the week in awhile, so it is time to remedy that neglect. This week I have choosen <a href="http://afarensis.blogsome.com/go.php?http://www.ucmp.berkeley.edu/education/explotime.html">Explorations in Time</a>.<br />
This is an extremely interesting interactive web site with modules for both students and teachers. I worked my way through the <a href="http://afarensis.blogsome.com/go.php?http://www.ucmp.berkeley.edu/education/explorations/tours/Trex/index.html">What did T-Rex taste like?</a> module. The module uses phylogeny to answer the question. Along the way you learn about to construct a phylogenetic tree and use it to ask further questions about the history of life. The module is easy to understand and the concepts are explained in a clear and easily understandable fashion - even for those who know nothing about biology. There is also a selection of questions at the end that you can use the data, from your work in the module, to answer.  (You will have to work through the module to find out what T-Rex would taste like&#8230;)<br />
As mentioned there are a number of other modules to work through at the site. Each is accompanied by a recommended grade level - which is extremely useful. The modules are designed for K-12 but I think several of them could be used in introductory biology classes (for non-majors for example) at the university level.<br />
The page itself is part of University of California, Berkeley<br />
Museum of Paleontology website and they to be commended for coming up with such a great resource!
</p>
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		<title>Tiktaalik roseae and the Origins of Tetrapods</title>
		<link>http://afarensis.blogsome.com/2006/04/19/tiktaalik-roseae-and-the-origins-of-tetrapods/</link>
		<comments>http://afarensis.blogsome.com/2006/04/19/tiktaalik-roseae-and-the-origins-of-tetrapods/#comments</comments>
		<pubDate>Wed, 19 Apr 2006 19:03:07 +0000</pubDate>
		<dc:creator>afarensis</dc:creator>
		
	<category>Vertebrates</category>
	<category>Amphibians</category>
	<category>Fish</category>
		<guid>http://afarensis.blogsome.com/2006/04/19/tiktaalik-roseae-and-the-origins-of-tetrapods/</guid>
		<description><![CDATA[	
	The above is a picture of a new fossil, called Tiktaalik roseae, that was recently discovered on Canada. The fossil is important because it fills in a gap in the transition from fish to amphibians and provides clues as to how the transition took place. The picture below is of a Coelacanth
	
	Coelacanths are often called [...]]]></description>
			<content:encoded><![CDATA[	<p><img src='/images/T1b.JPG' alt='' /></p>
	<p>The above is a picture of a new fossil, called <em>Tiktaalik roseae</em>, that was recently discovered on Canada. The fossil is important because it fills in a gap in the transition from fish to amphibians and provides clues as to how the transition took place. The picture below is of a <em><a href="http://afarensis.blogsome.com/go.php?http://sacoast.uwc.ac.za/education/resources/fishyfacts/coelacanth.htm">Coelacanth</a></em></p>
	<p><img src="http://sacoast.uwc.ac.za/education/resources/fishyfacts/images/coelacanth_fins.gif"/></p>
	<p><em>Coelacanths</em> are often called living fossils. They are generally considered to be somehow related to the groups that gave rise to <a href="http://afarensis.blogsome.com/go.php?http://www.ucmp.berkeley.edu/vertebrates/tetrapods/tetrafr.html">tetrapods</a>. In reality this is somewhat inaccurate. <em>Coelacanths</em> are actually highly specialized derivatives of groups common in the <a href="http://afarensis.blogsome.com/go.php?http://www.ucmp.berkeley.edu/paleozoic/paleozoic.html">Paleozoic</a> and <a href="http://afarensis.blogsome.com/go.php?http://www.ucmp.berkeley.edu/mesozoic/mesozoic.html">Mesozoic</a> eras. In particular, they are <a href="http://afarensis.blogsome.com/go.php?http://www.palaeos.com/Vertebrates/Units/140Sarcopterygii/140.100.html#Sarcopterygii">sarcopterygians</a>. Another name for them are lobe finned fishes (as opposed to ray finned). The lobe fins seem to be an adaptation to life on or near the bottom where they can be used to push against the bottom. Because of this research has focused on their relationship to early tetrapods. Over the years a number of important fossils have been discovered that are important to the issue.</p>
	<p><img src='/images/tiktaalik_phylo.jpg' alt='' /></p>
	<p><em>Panderichthys</em> - the fish second from the bottom in the above picture - dates to about 385 million years ago. Prior to the discovery of <em>Tiktaalik roseae</em> the earliest tetrapods dated to about 376 million years ago. <em>Tiktaalik roseae</em> dates to somewhere around 382 million years ago. Why is this important? Ahlberg and Clack, in thier recent Nature commentary, explain it the best:</p>
	<blockquote><p>The gap was bounded at the top by primitive Devonian tetrapods such as Ichthyostega and Acanthostega from Greenland, and at the bottom by Panderichthys, a tetrapod-like predatory fish from the latest Middle Devonian of Latvia &#8230; Ichthyostega&#8230;and Acanthostega5 retain true fish tails with fin rays but are nevertheless unambiguous<br />
tetrapods with limbs that bear digits&#8230; Panderichthys&#8230; is vaguely crocodile-shaped and, unlike the rather conventional osteolepiform fishes farther down the tree, looks like afish–tetrapod transitional form. The shape of the pectoral fin skeleton and shoulder girdle are intermediate between those of osteolepiforms and tetrapods, suggesting that Panderichthys was beginning to ‘walk’, but perhaps in shallow water rather than on land&#8230;</p></blockquote>
	<p>Into this drops <em>Tiktaalik roseae</em>. Like <em>Panderichthys</em>, <em>Tiktaalik</em> has pelvic fin rays, retain fin rays in paired appendages and has well developed gill arches. On the other hand, <em>Tiktaalik</em> is more tetrapodlike in its feeding and breathing apparatus:</p>
	<blockquote><p>These changes probably relate to breathing and feeding, which are linked in fishes because the movements used for gill ventilation can also be used to suck food into the mouth. A longer snout suggests a shift from sucking towards snapping up prey, whereas the loss of the gill cover bones (which turned the gill cover into a soft flap) probably correlates with reduced water flow through the gill chamber.
</p></blockquote>
	<p><em>Tiktaalik</em> also has some interesting features of its postcranial anatomy which link it to later tetrapods. Especially in its fins. The fins are adapted to flex gently upwards - as if the fin were being used to support the body. One of the interesting differences between fins and <em>Tiktaalik</em> limbs is that the later contain bones that comprise mobile wrist and ankles:</p>
	<p><img src='/images/tiktaalik_limb.jpg' alt='' /></p>
	<p>Another interesting feature is the central axis formed by the some of the long bones (red arrow in the picture below):</p>
	<p><img src='/images/Fin1.JPG' alt='' /></p>
	<p>As Shubin et al point out in their article on the pectoral fin of <em>Tiktaalik</em>:</p>
	<blockquote><p>A fin axis that extends distal to the ulnare has been unknown in any tetrapodomorph&#8230; until the discovery of Tiktaalik. As in porolepiforms and dipnoans, the axis of Tiktaalik lies in the centre of the fin. If the five radials of Tiktaalik are homologous to digital rays, then the axis of the tetrapod limb would extend from the humerus through digit three. Unfortunately, the absence of a well-defined axis in other tetrapodomorphs leaves uncertain whether a central axis is primitive for tetrapods or if it evolved separately in Tiktaalik. Testing these competing hypotheses awaits the discovery of other tetrapodomorph fins with axes that project into the distal<br />
fin.<br />
The pectoral skeleton of Tiktaalik is transitional between fish<br />
fin and tetrapod limb. Comparison of the fin with those of related<br />
fish reveals that the manus is not a de novo novelty of tetrapods;<br />
rather, it was assembled in fishes over evolutionary time to meet<br />
the diverse challenges of life in the margins of Devonian aquatic<br />
ecosystems.
</p></blockquote>
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		<item>
		<title>Taxonomy and Carnivorus Dinosaurs</title>
		<link>http://afarensis.blogsome.com/2006/02/19/taxonomy-and-carnivorus-dinosaurs/</link>
		<comments>http://afarensis.blogsome.com/2006/02/19/taxonomy-and-carnivorus-dinosaurs/#comments</comments>
		<pubDate>Sun, 19 Feb 2006 17:16:07 +0000</pubDate>
		<dc:creator>afarensis</dc:creator>
		
	<category>Vertebrates</category>
	<category>Reptiles</category>
	<category>Dinosaurs</category>
		<guid>http://afarensis.blogsome.com/2006/02/19/taxonomy-and-carnivorus-dinosaurs/</guid>
		<description><![CDATA[	I have come across a good example of how paleontologist use character traits to classify dinosaurs. The example is short and simple and could be used - with a few modifications in a biology class.
The example comes from Thomas Holtzs&#8217; article Chasing Tyrannosaurus and Deinonychus Around the Tree of Life: Classifying Dinosaurs
 If you look [...]]]></description>
			<content:encoded><![CDATA[	<p>I have come across a good example of how paleontologist use character traits to classify dinosaurs. The example is short and simple and could be used - with a few modifications in a biology class.<br />
The example comes from Thomas Holtzs&#8217; article <a href="http://afarensis.blogsome.com/go.php?http://www.geol.umd.edu/~tholtz/tyrdeintree.pdf">Chasing Tyrannosaurus and Deinonychus Around the Tree of Life: Classifying Dinosaurs</a><br />
 If you look at the list below you will see four dinosaurs and nine traits listed. With these nine traits we can create a simple cladogram for the four dinosaurs. Traits or characters fall into four different catagories: primitive, unique, shared derived and convergent.<br />
If you look at the chart below, you will notice that all four dinosaurs have three traits in common: hinge in lower jaw, wishbone and bipedality. These are considered the primitive traits that are found in the common ancestor of all four dinosaurs (if you assume the common ancestor did not have the three traits then each would have had to evolve independently in all four dinosaurs - which is a much more complicated scenario). Unfortunately, the three primitive traits do not tell us much, so lets look at unique traits. There are two unique traits in the list (retractable sickle claw and backward pointing pubis) found only in Deinonychus. While these distinguish Deinonychus they don&#8217;t help us learn which of the other three dinosaurs was the closest relative of Deinonychus. So we seem to be at an impass.</p>
	<p>Allosaurus	Deinonychus	Albertosaurus	Tyrannosaurus<br />
Hinge in lower jaw	Yes	Yes	Yes	Yes<br />
Wishbone	Yes	Yes	Yes	Yes<br />
Bipedal	Yes	Yes	Yes	Yes<br />
Retractable sickle claw	No	Yes	No	No<br />
Backawards-pointing pubis	No	Yes	No	No<br />
Number of fingers	3	3	2	2<br />
Third metatarsal in foot	Unpinched	Unpinched	Pinched	Pinched<br />
Astragalus (ankle bone)	Short	Tall	Tall	Tall<br />
Tip of ischium	Expanded	Pointed	Pointed	Pointed</p>
	<p>Let&#8217;s look at the chart again. There are several traits on the list that are shared between two or more - but not all - of the dinosaurs. These are two fingers (rather than three) on the hand, pinched third metatarsal (rather than unpinched), tall astragalus (rather than short) and pointed ischium (rather than expanded). None of these traits occur in Allosaurus (or meat eaters previous to Allosaurus). At this point we can say that the condition seen in Allosaurus is the ancestral condition (although this does not mean Allosaurus was the actual ancester of the other three). At this point then, we can say we have two clade, one composed of Allosaurus and the other composed of the other three dinosaurus:</p>
	<p><img src='/images/Allosaurus.JPG' alt='' /><br />
 This leaves the relationships between Deinonychus, Albertosaurus and Tyrannosaurus to work out. There are three posibilities. First, Deinonychus could be more closely related to Albertosaurus. Second, Deinonychus could be more closely related to Tyrannosaurus. Third, Tyrannosaurus is more closely related to Albertosaurus. Lets go back and look at our trait list. We have determined that the hinge in the lower jaw, the wishbone and bipedality are primitive traits shared by all four dinosaurs. We have also determined the tall astragalus and pointed tip of the ischium evolved after the lineages for Deinonychus, Albertosaurus and Tyrannosaurus split from the Allosaurus lineage. We have also determined that the retractable claw and the backward pointing pubis separate Deinonychus from the others. Let&#8217;s look at the second option above (that Deinonychus is more closely related to Tyrannosaurus). </p>
	<p><img src='/images/Third.JPG' alt='' /></p>
	<p>In order for this to be the case 11 evolutionary changes would have had to take place: one change for the three primitive features shared by all, one for each of the unique traits in Deinonychus and 2 for the remaining two traits in Albertosaurus and Tyrannosaurus (which would have evolved independently in each lineage). There is a simpler explanation - one involving fewer evolutionary changes. This is the third option listed above, that Albetosaurus and Tyrannosaurus are more closely related to each other which requires only nine evolutionary changes, which I will leave to the reader to work out (consult the article by Holtz, linked to above, for a more detailed explanation and better cladograms).
</p>
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	</item>
		<item>
		<title>Transitions Site of the Week</title>
		<link>http://afarensis.blogsome.com/2006/01/08/transitions-site-of-the-week-3/</link>
		<comments>http://afarensis.blogsome.com/2006/01/08/transitions-site-of-the-week-3/#comments</comments>
		<pubDate>Sun, 08 Jan 2006 16:49:43 +0000</pubDate>
		<dc:creator>afarensis</dc:creator>
		
	<category>Interactive Web Sites</category>
	<category>Site of the Week</category>
		<guid>http://afarensis.blogsome.com/2006/01/08/transitions-site-of-the-week-3/</guid>
		<description><![CDATA[	This week I have chosen The Paleontology Portal as the site of the week. The Paleontology Portal contains a wide variety of resources. For example, there are pages for K-16 teachers and students, fossil galleries and collections (on the collections page you can search collections in Museums and Universities).
Some pics from the site:
	Eucrotaphus trigonocephalus
	Dromomeryx borealis
	Nothrotheriops
	And [...]]]></description>
			<content:encoded><![CDATA[	<p>This week I have chosen <a href="http://afarensis.blogsome.com/go.php?http://www.paleoportal.org/">The Paleontology Portal</a> as the site of the week. The Paleontology Portal contains a wide variety of resources. For example, there are pages for <a href="http://afarensis.blogsome.com/go.php?http://www.paleoportal.org/audience/k16.php">K-16 teachers and students</a>, fossil galleries and collections (on the collections page you can search collections in Museums and Universities).<br />
Some pics from the site:</p>
	<p><img src="http://www.paleoportal.org/media/submissions/6/24076_submission_image_641_medium.jpg"/>Eucrotaphus trigonocephalus</p>
	<p><img src="http://www.paleoportal.org/media/submissions/6/66498_submission_image_645_medium.jpg"/>Dromomeryx borealis</p>
	<p><img src="http://www.paleoportal.org/media/submissions/7/18109_submission_image_726_medium.jpg"/>Nothrotheriops</p>
	<p>And thousands more!<br />
If you ever encounter someone who says we don&#8217;t have a lot of fossils - this would be one site to send them to!<br />
Additionally, the site contains hundreds of links:</p>
	<p><a href="http://afarensis.blogsome.com/go.php?http://www.paleoportal.org/fossil_gallery/more_submissions.php?taxon_id=91">Mammals</a> or <a href="http://afarensis.blogsome.com/go.php?http://www.paleoportal.org/fossil_gallery/more_submissions.php?taxon_id=134">Reptiles</a> for example. Speaking of reptiles here are a few fossils:</p>
	<p><img src="http://www.paleoportal.org/media/submissions/8/50532_submission_image_898_medium.jpg"/>Pachyrhinosaurus</p>
	<p><img src="http://www.paleoportal.org/media/submissions/6/16269_submission_image_672_medium.jpg"/>Chelydridae</p>
	<p>And here are a few amphibians:</p>
	<p><img src="http://www.paleoportal.org/media/submissions/7/85860_submission_image_755_medium.jpg"/>Milneria</p>
	<p><img src="http://www.paleoportal.org/media/submissions/7/77254_submission_image_773_medium.jpg"/>Trimerorhachis</p>
	<p>Also, some fish:</p>
	<p><img src="http://www.paleoportal.org/media/submissions/5/3783_submission_image_576_medium.jpg"/>Priscacara liops</p>
	<p><img src="http://www.paleoportal.org/media/submissions/8/45231_submission_image_863_medium.jpg"/>Heliobatis radians</p>
	<p>There is much, much more at the site. Check it out!
</p>
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		<item>
		<title>Barnacles: Darwin&#8217;s old buddies</title>
		<link>http://afarensis.blogsome.com/2005/12/29/barnacles-darwins-old-buddies/</link>
		<comments>http://afarensis.blogsome.com/2005/12/29/barnacles-darwins-old-buddies/#comments</comments>
		<pubDate>Thu, 29 Dec 2005 20:08:51 +0000</pubDate>
		<dc:creator>Snail's Tales</dc:creator>
		
	<category>Uncategorized</category>
		<guid>http://afarensis.blogsome.com/2005/12/29/barnacles-darwins-old-buddies/</guid>
		<description><![CDATA[	
I am holding in my hand a cluster of fossil barnacles, Balanus concavus1, from the Miocene (5-23 million years ago). I found this specimen at a location along the Calvert Cliffs, Maryland, an area famous for its fossils.
	
Compiled from Lippson &#038; Lippson2.
Barnacles (Cirripedia) are marine invertebrates. A barnacle starts out as a free-swimming larva, called [...]]]></description>
			<content:encoded><![CDATA[	<p><center><img src="http://home.earthlink.net/~snailstales/balanus.JPG" /></center><br />
I am holding in my hand a cluster of fossil barnacles, <i>Balanus concavus</i><sup>1</sup>, from the Miocene (5-23 million years ago). I found this specimen at a location along the Calvert Cliffs, Maryland, an area famous for its <a href="http://afarensis.blogsome.com/go.php?http://www.mgs.md.gov/esic/brochures/fossils/index.html" target="_blank">fossils</a>.</p>
	<p><center><img src="http://home.earthlink.net/~snailstales/barncycle.jpg" /><br />
<span style="font-size:85%;">Compiled from Lippson &#038; Lippson<sup>2</sup></span>.</center><br />
<a href="http://afarensis.blogsome.com/go.php?http://www.ucmp.berkeley.edu/arthropoda/crustacea/maxillopoda/cirripedia.html" target="_blank">Barnacles (Cirripedia)</a> are marine invertebrates. A barnacle starts out as a free-swimming larva, called a <i>nauplius</i>, (plural <i>nauplii</i>) . The nauplius grows a pair of shells around its body. At this stage it is called a <i>cypris</i> larva. The cypris larva attaches itself permanently to a rock, a mollusk shell, an adult barnacle or any other hard structure. The larva, now sessile, starts to develop into an adult. It casts off its shells and begins to secrete several calcareous plates that end up completely surrounding its body. The fossil in the picture above consists of the shells of adult barnacles.</p>
	<p><center><img src="http://home.earthlink.net/~snailstales/barnfeedin.jpg" /><br />
<span style="font-size:85%;">A barnacle feeding. From Lippson &amp; Lippson<sup>2</sup></span>.</center><br />
A barnacle feeds by opening its shell and unfolding its appendages that are covered with fine hairs. The appendages sweep tiny particles of food suspended in the water into the barnacle&#8217;s mouth. </p>
	<p>Because of their calcareous shells, until the early 19th century people thought barnacles were mollusks. It was finally determined around 1819 that barnacles were actually crustaceans.</p>
	<p>During the 19th century, the world&#8217;s leading authority on barnacles was none other than Charles Darwin. Darwin spent 8 years studying, dissecting and classifying barnacles. The outcome of his efforts was a set of authoritative books. (Links to complete texts and scanned plates of Darwin&#8217;s barnacle books and other publications are available on <a href="http://afarensis.blogsome.com/go.php?http://pages.britishlibrary.net/charles.darwin2/texts.html" target="_blank">this page</a>.)</p>
	<p>His work on barnacles exposed Darwin to the extent of variation that exists in nature within and between species. Later, in <a href="http://afarensis.blogsome.com/go.php?http://pages.britishlibrary.net/charles.darwin/texts/origin_6th/origin6th_fm.html" target="_blank"><i>On the Origin of Species</i></a>, Darwin developed the idea that one species gradually evolves into another one. According to Ernst Mayr<sup>3</sup>, Darwin&#8217;s studies of barnacles may have influenced the development of his ideas on speciation. Darwin himself noted this in his <a href="http://afarensis.blogsome.com/go.php?http://www.gutenberg.org/etext/2010" target="_blank">autobiography</a>:</p>
	<blockquote><p>&#8220;<em>The Cirripedes form a highly varying and difficult group of species to class; and my work was of considerable use to me, when I had to discuss in the &#8216;Origin of Species&#8217; the principles of a natural classification</em>.&#8221;</p></blockquote>
	<p><span style="font-size:85%;">1. Harold E. Vokes, John D. Glaser and Robert D. Conkwright. Bulletin 20: Miocene fossils of Maryland. Second Edition January, 2000. Electronic Publication No. 00-1. Available as a CD-ROM from the <a href="http://afarensis.blogsome.com/go.php?http://www.mgs.md.gov/esic/publications/new/b20.html" target="_blank">Maryland Geological Survey</a>.<br />
2. Lippson, A.J. &amp; Lippson, R.L. 1984. <i>Life in the Chesapeake Bay</i>. Johns Hopkins University Press.<br />
3. Mayr, E. 1991. <i>One long argument</i>. Harvard University Press.</span></p>
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		<item>
		<title>Transitions Site of the Week</title>
		<link>http://afarensis.blogsome.com/2005/11/25/transitions-site-of-the-week-2/</link>
		<comments>http://afarensis.blogsome.com/2005/11/25/transitions-site-of-the-week-2/#comments</comments>
		<pubDate>Fri, 25 Nov 2005 19:59:28 +0000</pubDate>
		<dc:creator>afarensis</dc:creator>
		
	<category>General Evolution</category>
	<category>Site of the Week</category>
		<guid>http://afarensis.blogsome.com/2005/11/25/transitions-site-of-the-week-2/</guid>
		<description><![CDATA[	This Week&#8217;s Site of the Week is Dean Falk&#8217;s Brain Dance. An excellent website that contains an overview of her research and a gallery of endocasts! You will also find an overview of Endocasts, reconstructions and 3-D morphometrics as well as references to the literature on these techniques. There are also links to some interesting [...]]]></description>
			<content:encoded><![CDATA[	<p>This Week&#8217;s Site of the Week is Dean Falk&#8217;s <a href="http://afarensis.blogsome.com/go.php?http://www.anthro.fsu.edu/research/falk/braindance.html">Brain Dance</a>. An excellent website that contains an overview of her research and a gallery of endocasts! You will also find an overview of Endocasts, reconstructions and 3-D morphometrics as well as references to the literature on these techniques. There are also links to some interesting websites. I would recommend visiting the endocast section, if you visit nothing else. It&#8217;s cool!
</p>
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	</item>
		<item>
		<title>Transitions Site of the Week</title>
		<link>http://afarensis.blogsome.com/2005/11/19/transitions-site-of-the-week/</link>
		<comments>http://afarensis.blogsome.com/2005/11/19/transitions-site-of-the-week/#comments</comments>
		<pubDate>Sat, 19 Nov 2005 14:14:31 +0000</pubDate>
		<dc:creator>afarensis</dc:creator>
		
	<category>Site of the Week</category>
		<guid>http://afarensis.blogsome.com/2005/11/19/transitions-site-of-the-week/</guid>
		<description><![CDATA[	This is the first in a semi-regular series higlighting informative and interesting sites related to evolution. This week I have picked The Museum of Science website Human Evolution: Interpreting Evidence. The site has several interesting features including: fossil fact sheets with pictures that can be printed, an interactive comparison of three different views on hominin [...]]]></description>
			<content:encoded><![CDATA[	<p>This is the first in a semi-regular series higlighting informative and interesting sites related to evolution. This week I have picked The Museum of Science website <a href="http://afarensis.blogsome.com/go.php?http://www.mos.org/evolution/main/">Human Evolution: Interpreting Evidence.</a> The site has several interesting features including: fossil fact sheets with pictures that can be printed, an interactive comparison of three different views on hominin phylogenetic relationships, advice on how to teach human evolution and educator resources. From Human Evolution: Interpreting Evidence:</p>
	<blockquote><p>There are three major issues we will address:</p>
	<p>· With any scientific discovery come facts and interpretations. It is important to distinguish what is a fact and what is an interpretation and how evidence plays a role in each case. It is important to recognize that scientific interpretations are very often supported by a wealth of evidence, and are not just wild guesses.</p>
	<p>Fact: K. Kimeu discovered the individual who is represented by skull KNM-WT 15000 in East Africa in 1984.<br />
Interpretation: This skull is of an 8-year old Homo erectus who lived 1.6 million years ago.</p>
	<p>· Science is not a belief system; it is rooted in doubt. Science embraces and thrives on skepticism, challenge, and debate. We present on this web site three different interpretations of the human family tree (or phylogeny). These are fiercely debated in the scientific community. We suggest that this scrutiny is a healthy part of science and should not be avoided in the classroom. What is important to teach students is why scientists disagree (or agree) about particular interpretations of the human fossil record.</p>
	<p>· Science is dynamic and incorporates new discoveries into what is already known about the world. Every year, new hominid discoveries complicate our understanding of human evolution and force scientists to readdress hypotheses about our ancestry. Keep visiting this site to see how new discoveries alter our family tree.</p></blockquote>
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