development https://www.scienceblogs.com/ en The marsupial placenta https://www.scienceblogs.com/lifelines/2017/09/14/the-marsupial-placenta <span>The marsupial placenta</span> <div class="field field--name-body field--type-text-with-summary field--label-hidden field--item"><p><img class="mw-mmv-final-image jpg mw-mmv-dialog-is-open" src="https://upload.wikimedia.org/wikipedia/commons/thumb/5/56/Macropus_eugenii_with_calf.jpg/800px-Macropus_eugenii_with_calf.jpg" alt="Macropus eugenii with calf.jpg" width="361" height="370" /></p> <div class="mw-mmv-wrapper"> <div class="mw-mmv-main metadata-panel-is-closed"> <div class="mw-mmv-image-wrapper"> <div class="mw-mmv-image-inner-wrapper"> <div class="mw-mmv-image">Image of a tammar wallaby and her joey By Mathae - Own work via <a href="https://commons.wikimedia.org/w/index.php?curid=1490607">Wikimedia Commons</a></div> </div> </div> </div> </div> <p> </p> <p>When I think of marsupials, what comes to mind is an image of a mother carrying her young (joey) in a pouch. Contrary to popular belief, however, mother tammar wallabies (<em>Macropus eugenii</em>) have an internal functioning placenta. Albeit, it only develops near the end of their short pregnancy (a mere 26.5 days), just before the developing offspring moves from the uterus to the pouch for further development and nursing. A new study published in <em>eLife</em> examined gene expression in both the placenta and mammary glands of mother tammar wallabies.</p> <p>What the new study found is that just before birth of the joey, the marsupial placenta begins to express genes similar to those found early on in pregnancy in placental (aka: eutherian) mammals. In contrast, gene expression patterns in the mammary glands of nursing wallabies were similar to those expressed during late stage fetal development in the placenta of eutherian mammals. Milk composition and lactation in wallabies are very complex. The idea is that lactation in marsupials may be an alternate evolutionary strategy to development within a eutherian placenta as it allows mother wallabies to regulate which molecular signals and nutrients they provide their developing offspring. In fact, mother wallabies can produce milk with different compositions from adjacent mammary glands to feed young of varying ages.</p> <p><strong>Sources:</strong></p> <div id="constrain"> <div id="main"> <div id="constrain-content" class="cleared"> <div id="content" class="col"> <article> <div id="article"> <section id="article-body"> <div class="section"> <div class="content no-heading cleared main-content"> <p>Guernsey MW, Chuong EB, Cornelis G, Renfree MB, Baker JC. Molecular conservation of marsupial and eutherian placentation and lactation. <em>eLife. </em><span class="contextual-data__cite">2017;6:e27450</span></p> <p>Nicholas K, Simpson K, Wilson M, Trott J, Shaw D. The Tammar Wallaby: A Model to Study Putative Autocrine-Induced Changes in Milk Composition. <em>Journal of Mammary Gland Biology and Neoplasia</em>. 2: 299-310, 1997.</p> </div> </div> </section> </div> </article> </div> </div> </div> </div> </div> <span><a title="View user profile." href="/author/dr-dolittle" lang="" about="/author/dr-dolittle" typeof="schema:Person" property="schema:name" datatype="">dr. dolittle</a></span> <span>Wed, 09/13/2017 - 20:19</span> <div class="field field--name-field-blog-tags field--type-entity-reference field--label-inline"> <div class="field--label">Tags</div> <div class="field--items"> <div class="field--item"><a href="/tag/life-science-0" hreflang="en">Life Science</a></div> <div class="field--item"><a href="/tag/development" hreflang="en">development</a></div> <div class="field--item"><a href="/tag/marsupial" hreflang="en">marsupial</a></div> <div class="field--item"><a href="/tag/nursing" hreflang="en">nursing</a></div> <div class="field--item"><a href="/tag/placenta" hreflang="en">placenta</a></div> <div class="field--item"><a href="/tag/pregnancy" hreflang="en">pregnancy</a></div> <div class="field--item"><a href="/tag/wallaby" hreflang="en">wallaby</a></div> </div> </div> <section> </section> <ul class="links inline list-inline"><li class="comment-forbidden"><a href="/user/login?destination=/lifelines/2017/09/14/the-marsupial-placenta%23comment-form">Log in</a> to post comments</li></ul> Thu, 14 Sep 2017 00:19:05 +0000 dr. dolittle 150518 at https://www.scienceblogs.com Tissue Organization Field Theory https://www.scienceblogs.com/pharyngula/2017/04/14/tissue-organization-field-theory <span>Tissue Organization Field Theory</span> <div class="field field--name-body field--type-text-with-summary field--label-hidden field--item"><p class="lead">It's been a while since I brought everyone up to date on the progress of my Ecological Development course, because I've been <em>busy</em>. So have the students. After our spring break I subjected them to the dreaded oral exam, which actually isn't so bad. I tried to engage them less in an adversarial role and more as a quiet conversation between two people on science. Some students took to it easily -- the more outgoing ones -- others were noticeably nervous, which was OK, and I hope they learned that it isn't that terrifying to have a discussion with a mentor.</p> <p>Then the next few weeks were a mad whirl of horrible things done to babies: teratogens, endocrine disruptors, multi-generational epigenetic inheritance, all that fun stuff. We wrapped up with the depressing stuff for me, although the young'uns were more sanguine, I think. We talked about adult onset developmental diseases (it's good to look at heart disease through the lens of developmental biology), aging, and cancer. Next week they get some time off, because I'm being drawn away to a conference on the east coast, but they're supposed to spend it preparing for their final presentations, which will consume the last two weeks of class. And then we're all done. School's out for summer!</p> <p>I'm going to say a bit about our last class discussion, because it got into some interesting territory and reflects the theme of the course well. We talked about that theory mentioned in the title of this article, and the origins of cancer, and to do that I have to give you all a little background.</p> <p><strong>Tissue Organization Field Theory (TOFT)</strong> is an alternative to what is sort of the dominant paradigm in cancer biology, the <strong>Somatic Mutation Theory (SMT)</strong>. I have to say "sort of" because what I get from the literature is that SMT is more of a working assumption, and that cancer biologists are open to new ideas. The SMT is a useful molecular perspective on carcinogenesis. It postulates that cancer is a cellular disorder in which the genetic material has been perturbed to produce a lineage of cells with aberrant characteristics, that if we want to figure out what the primary cause of a cancer was, we can trace it back to a somatic mutation, or a change in a critical gene or, more likely, multiple genes, that lead to uncontrolled proliferation. So we pursue oncogenes, genes that have the potential to acquire mutations that trigger cell division or bypass control points, and tumor suppressor genes, protective genes that, when damaged, remove essential regulators of growth.</p> <p>So, under the <strong>SMT</strong>, cancer is a disease caused by the progressive accumulation of mutations in cells of the body, as they divide. These mutations gradually strip away the normal restraints on cell division, and on immune system recognition, and on cell death activation, etc., etc., etc. until you have a rogue cell that can seed the growth of a massively disruptive tumor.</p> <p>And it's not wrong! Cancer biology has been immensely productive in identifying the enabling mutations, and even developing treatments that specifically target molecular agents of cancer. We <em>know</em> that somatic mutations are a routine part of the progression of cancer, and we also know that there heritable alleles that can affect the likelihood of the disease. The SMT is a tool to explain many of the phenomena of cancer, and it's not going to just go away. It's also a tool that is amenable to a reductionist approach to cancer biology, and is well-adapted to the utility of molecular biology. </p> <p>Tissue Organization Field Theory is an alternative explanation for the <em>origins</em> of cancer.</p> <p>TOFT argues that the focus of the SMT on single cell events is inappropriate and misses a whole range of effects at the level of tissue organization, effects which are <em>more</em> important in creating a pathological environment in which those mutations can accumulate. Further, it gets into field theory, which is important in developmental biology but isn't exactly the subject of common conversation. Here's one standard definition of a field: "<a href="https://www.researchgate.net/profile/Maria_Martinez-Frias/publication/51335730_Errors_of_morphogenesis_and_developmental_field_theory/links/0deec517527244d151000000.pdf">a morphogenetic (or developmental) field is a region or a part of the embryo which responds as a coordinated unit to embryonic induction and results in complex or multiple anatomic structures.</a>" If that's not helpful -- and it probably isn't, we'd have to go over a textbook if we wanted to explain developmental field theory -- here's a diagramatic metaphor. Do you see the field in this picture?</p> <p><img src="http://scienceblogs.com/pharyngula/files/2017/04/field-500x512.png" alt="field" width="500" height="512" class="aligncenter size-large wp-image-17651" /></p> <p>There's something special about part of that image, but it's not that the individual subunits are intrinsically different -- it's tied up in the relationships between the central set of blocks and the blocks outside of it. There's something different going on with a subset of the blocks, but it's not necessarily best described by explaining the details of single blocks, but is more easily explained at a higher level, as properties of a tissue within a tissue. Of course, what will eventually happen in a developing organism is that those central blocks will express a unique pattern of genes, so eventually it's identifiable by molecular markers, but the field first arises in a sea of genetically and epigenetically uniform cells.</p> <p><img src="http://scienceblogs.com/pharyngula/files/2017/04/polarcoords-145x150.jpeg" alt="polarcoords" width="145" height="150" class="alignright size-thumbnail wp-image-17652" /></p> <p>Another important property of a field is that it is not itself uniform. It's going to acquire complex spatial properties over time. Insect limbs, for instance, arise from a disc-shaped field with extensive patterning information within them, so the central region will become the distal tip of the limb, and there is information that is interpreted as polar coordinates that specifies what portion of the limb is anterior, posterior, medial, and lateral (the limb is not a uniform cylinder). Similarly, vertebrates have a limb field represented in the limb bud, with gradients of morphogens specifying the orientation of the limb, and with re-expression of Hox genes used to specify longitudinal positions. Hox genes in a limb field are interpreted in different ways than Hox genes along the body axis, obviously.</p> <p>The key factor here is that in field theory cells are not simply independent units -- they are part of a larger assemblage, a tissue, that has complex fates that are not easily summarized by individual gene expression. They have to be understood as a network.</p> <p>That's the first thing to remember: TOFT is treating a cancer as a field, with field properties, which are not adequately described if you only look at cancer as a collection of autonomous cells all doing their own thing at the command of their broken genes. Aberrant disruption of the field can produce aberrant structures <em>without</em> requiring any genetic changes.</p> <p>This is the difference between a mutagen and a teratogen. The effects of a <strong>mutagen</strong> are caused directly by damage to the structure or sequence of DNA; they produce heritable changes to the cells of an organism. <strong>Teratogens</strong>, on the other hand, are not necessarily mutagenic at all -- they disrupt the normal pattern of development without changing genes at all. Thalidomide babies, for example, had some extreme morphological changes, like phocomelia or truncated limb development, but those are <em>not</em> heritable, and the people affected by thalidomide can grow up to have normal, healthy children.</p> <p>TOFT argues something similar, that there is a disruption of a <em>tissue</em> that initializes aberrant growth, that may then be an enabling precondition for the accumulation of mutations. One piece of evidence for this is a set of experiments on tissues, illustrated below.</p> <p>Most cancers arise in epithelial tissues, like the sheets of cells that line glands or your organs, in large part because those are the cells that divide most frequently. These epithelial cells, also called parenchyma, do not typically grow in isolation, but on a substrated of connective tissue, extracellular matrix, and other cell types, called stroma. The stroma supports and signals the overlying epithelium, and vice versa, and together they make a coherent functional tissue.</p> <p>The theory suggests that cancers can arise in epithelia by way of disruptions in signaling in the stroma. A carcinogen could distort the interactions between stroma and epithelium at the level of the stroma, and the epithelium then goes nuts and proliferates to produce a pre-cancerous mass.</p> <p><img src="http://scienceblogs.com/pharyngula/files/2017/04/toftdiag.png" alt="toftdiag" width="306" height="498" class="aligncenter size-full wp-image-17653" /></p> <p>One test of the theory would be to separate stroma and epithelium, expose the stroma to a short-lived teratogen, and then after the teratogen was washed out, re-associate the two and determine whether there was an increase in the frequency of cancers <em>in the epithelium</em>, which has not been exposed to teratogens.</p> <p>The experiment has been done. Here are the results for rat mammary gland tissue in which the epithelium was exposed to the solvent vehicle but no N-methyl nitorsourea (a potent mutagen), while the stroma was soaked in NMu, labeled VEH/NMu. The numerator describes the epithelial condition, and the denominator is the stroma condition, so NMu/NMu means both were hit with the mutagen, VEH/VEH means both were exposed only to the vehicle, and NMu/VEH means the epithelium was poisoned with NMu, while the stroma was not.</p> <p><img src="http://scienceblogs.com/pharyngula/files/2017/04/epistromaexp-500x398.png" alt="epistromaexp" width="500" height="398" class="aligncenter size-large wp-image-17654" /></p> <p>There's an awfully strong positive correlation between exposing the stroma to mutagens and getting tumors, and a negative correlation with exposing epithelia to mutagens and tumors.</p> <p>You want more evidence? Here's a very interesting experiment. Start with aggressively metastatic melanoma cells from a human patient (labeled in green, below). Inject them into a completely different environment, the neural crest pathway in a developing chick embryo. Surprisingly, if you accept the SMT, the cancer cells calm right down and are conditioned by their environment to participate in normal development in the chick and get incorporated into the facial cartilages and sympathetic ganglia.</p> <p><img src="http://scienceblogs.com/pharyngula/files/2017/04/melanoma.jpg" alt="melanoma" width="479" height="480" class="aligncenter size-full wp-image-17655" /></p> <p>I suspect those melanoma cells do carry somatic mutations, and are not actually "cured" of a predisposition to cancer. What the experiment says, though, is that environmental influences are extremely important in regulating the behavior of these cells, and that modifying the cells communicating with the cancerous cells can have a profound effect on how they act.</p> <p>Note that this is not a pathway to a cure. It's all well and good to say that if we could break up a tumor, separate the individual cells and put them in a more nurturing, embryo-like environment, they'll stop acting up and resume normal, regulated growth, but if we could do that, slicing out the tumor and tossing it in an incinerator would also be effective. The problem is that in a human patient we do not and cannot have such precise control of the micro-environment of the cancer, and in fact, the tumor itself is a kind of bubble of micro-environment that actively reinforces cancer growth.</p> <p>My students and I read a paper from Carlos Sonnenschein, who is a major proponent of TOFT, as well as our textbook summary. The paper was titled <a href="https://www.ncbi.nlm.nih.gov/pubmed/21503935"><i>The tissue organization field theory of cancer: a testable replacement for the somatic mutation theory</i></a>. They're a smart bunch, and they see the promise of the idea, in part because this whole course is about thinking a level above reductionist cell biology, but they also found the word "replacement" off-putting. It doesn't invalidate everything about the SMT, but it does support an important alternative route for carcino<em>genesis</em>. They also weren't impressed by the rather aggressive insistence by some TOFT proponents that they have the One True Explanation, and that their observations are sufficent to explain cancer -- we came up with a few alternative interpretations of their own favorite experiments that they haven't nailed down completely just yet.</p> <p>One thing that amused me is that the class consensus actually converged on the views of another paper by Bedessem and Ruphy, which I did not assign them to read, largely because of its more philosophical argument (I've focused on empirical/experimental papers in the class). This is how I feel about it, too.</p> <blockquote><p>The building of a global model of carcinogenesis is one of modern biology's greatest challenges. The traditional somatic mutation theory (SMT) is now supplemented by a new approach, called the Tissue Organization Field Theory (TOFT). According to TOFT, the original source of cancer is loss of tissue organization rather than genetic mutations. In this paper, we study the argumentative strategy used by the advocates of TOFT to impose their view. In particular, we criticize their claim of incompatibility used to justify the necessity to definitively reject SMT. First, we note that since it is difficult to build a non-ambiguous experimental demonstration of the superiority of TOFT, its partisans add epistemological and metaphysical arguments to the debate. This argumentative strategy allows them to defend the necessity of a paradigm shift, with TOFT superseding SMT. To do so, they introduce a notion of incompatibility, which they actually use as the Kuhnian notion of incommensurability. To justify this so-called incompatibility between the two theories of cancer, they move the debate to a metaphysical ground by assimilating the controversy to a fundamental opposition between reductionism and organicism. We show here that this argumentative strategy is specious, because it does not demonstrate clearly that TOFT is an organicist theory. Since it shares with SMT its vocabulary, its ontology and its methodology, it appears that a claim of incompatibility based on this metaphysical plan is not fully justified in the present state of the debate. We conclude that it is more cogent to argue that the two theories are compatible, both biologically and metaphysically. We propose to consider that TOFT and SMT describe two distinct and compatible causal pathways to carcinogenesis. This view is coherent with the existence of integrative approaches, and suggests that they have a higher epistemic value than the two theories taken separately.</p> </blockquote> <p>Anyway, keep an eye open for more on the tissue organization field theory -- there seems to be a fair bit of ongoing debate in the scientific literature about it. I'll keep telling everyone cancer is a developmental disease, so you need more developmental biologists to study it. Or, alternatively, every cancer biologist is already a developmental biologist.</p> <hr /> <p class="ref">Bedessem B, Ruphy S. (2015) SMT or TOFT? How the two main theories of carcinogenesis are made (artificially) incompatible. Acta Biotheor. 63(3):257-67.</p> <p class="ref">Soto AM, Sonnenschein C (2011) The tissue organization field theory of cancer: a testable replacement for the somatic mutation theory. Bioessays. 33(5):332-40.</p> </div> <span><a title="View user profile." href="/pharyngula" lang="" about="/pharyngula" typeof="schema:Person" property="schema:name" datatype="">pharyngula</a></span> <span>Fri, 04/14/2017 - 12:06</span> <div class="field field--name-field-blog-tags field--type-entity-reference field--label-inline"> <div class="field--label">Tags</div> <div class="field--items"> <div class="field--item"><a href="/tag/development" hreflang="en">development</a></div> </div> </div> <section> </section> <ul class="links inline list-inline"><li class="comment-forbidden"><a href="/user/login?destination=/pharyngula/2017/04/14/tissue-organization-field-theory%23comment-form">Log in</a> to post comments</li></ul> Fri, 14 Apr 2017 16:06:21 +0000 pharyngula 14361 at https://www.scienceblogs.com How to grow a bigger heart... https://www.scienceblogs.com/lifelines/2016/10/18/how-to-grow-a-bigger-heart <span>How to grow a bigger heart...</span> <div class="field field--name-body field--type-text-with-summary field--label-hidden field--item"><p>...in alligators at least.</p> <div style="width: 285px;"><img title="Photograph showing alligator hatchling and eggs" src="https://www.nps.gov/ever/learn/nature/images/alligatorbabyeggs.jpg" alt="Photograph showing alligator hatchling and eggs" width="275" height="250" /> Image of alligator eggs and hatchling from National Park Service. </div> <script src="//embedr.flickr.com/assets/client-code.js" async="" charset="utf-8"></script><p>Researchers from the University of Manchester, University of North Texas - Denton, and the Rockefeller Wildlife Refuge - Grand Chenier, Louisiana teamed up to explore the effects of exposure to low oxygen on embryonic American alligators (<em>Alligator mississippiensis</em>). Alligator eggs are often laid in nests where oxygen concentrations can reportedly vary between 11-20% (21% is normal atmospheric levels). This is really important as issues related to embryonic development could continue to affect animals throughout their adult lives as well.</p> <p>The results of the study were recently published in the <em>American Journal of Physiology - Regulatory, Integrative and Comparative Physiology. </em>The researchers found that embryos exposed to low oxygen were smaller and had larger hearts even into their juvenile years. In addition, the mitochondria of juvenile alligators that had been exposed to low oxygen were more efficient at using oxygen. These adaptations may help the animals adjust well to low oxygen environments.</p> <p>In contrast, a recent review article written by Patterson and Zhang suggests that human embryos exposed to low oxygen do not fare as well as alligators. While a period of hypoxia is important in normal development, prolonged exposure of embryos to low oxygen can result abnormal heart structure and function. In fact, it is thought that these embryos may be more prone to heart disease as adults.</p> <p><strong>Sources:</strong><br /> Galli GLJ, Crossley J, Elsey R, Dzialowski EM, Shiels HA, Crossley II DA. Developmental Plasticity of Mitochondrial Function in American Alligators, <em>Alligator mississippiensis</em>. <em>American Journal of Physiology - Regulatory, Integrative and Comparative Physiology. </em>In press. doi:10.1152/ajpregu.00107.2016</p> <div class="inline_block eight_col va_top"> <div>Patterson AJ, Zhang L. Hypoxia and fetal heart development. <em>Current Molecular Medicine. </em>10(7): 653-666, 2010.</div> </div> </div> <span><a title="View user profile." href="/author/dr-dolittle" lang="" about="/author/dr-dolittle" typeof="schema:Person" property="schema:name" datatype="">dr. dolittle</a></span> <span>Tue, 10/18/2016 - 12:19</span> <div class="field field--name-field-blog-tags field--type-entity-reference field--label-inline"> <div class="field--label">Tags</div> <div class="field--items"> <div class="field--item"><a href="/tag/life-science-0" hreflang="en">Life Science</a></div> <div class="field--item"><a href="/tag/alligator" hreflang="en">alligator</a></div> <div class="field--item"><a href="/tag/development" hreflang="en">development</a></div> <div class="field--item"><a href="/tag/egg" hreflang="en">egg</a></div> <div class="field--item"><a href="/tag/embryo" hreflang="en">embryo</a></div> <div class="field--item"><a href="/tag/hatchling" hreflang="en">hatchling</a></div> <div class="field--item"><a href="/tag/heart" hreflang="en">Heart</a></div> <div class="field--item"><a href="/tag/hypoxia" hreflang="en">hypoxia</a></div> <div class="field--item"><a href="/tag/oxygen" hreflang="en">oxygen</a></div> </div> </div> <section> </section> <ul class="links inline list-inline"><li class="comment-forbidden"><a href="/user/login?destination=/lifelines/2016/10/18/how-to-grow-a-bigger-heart%23comment-form">Log in</a> to post comments</li></ul> Tue, 18 Oct 2016 16:19:40 +0000 dr. dolittle 150433 at https://www.scienceblogs.com Limb regeneration in brittle stars https://www.scienceblogs.com/lifelines/2016/04/30/limb-regeneration-in-brittle-stars <span>Limb regeneration in brittle stars</span> <div class="field field--name-body field--type-text-with-summary field--label-hidden field--item"><div style="width: 594px;"><a href="https://upload.wikimedia.org/wikipedia/commons/c/c1/Brittle_Star_%282388531935%29.jpg"><img src="https://upload.wikimedia.org/wikipedia/commons/thumb/c/c1/Brittle_Star_%282388531935%29.jpg/1200px-Brittle_Star_%282388531935%29.jpg" alt="File:Brittle Star (2388531935).jpg" width="584" height="387" data-file-width="4304" data-file-height="2852" /></a> Image of brittle star by Jerry Kirkhart from Los Osos, Calif. [CC BY 2.0 (<a href="http://creativecommons.org/licenses/by/2.0">http://creativecommons.org/licenses/by/2.0</a>)], via Wikimedia Commons </div> <p class="Heading">A new study published in <em>Frontiers in Zoology</em> examined the developmental process involved in regulating limb regeneration in brittle stars (<i>Amphiura filiformis</i>) following amputation of an arm. Limb regeneration is a multi-stage process involving initial healing and repair of the wounded site, initial growth of the limb followed by development of more complex layers of cells until ultimately the limb has been fully regenerated. Understanding this process in brittle stars may lead to better understanding of limb regeneration in other echinoderms or at least methodologies that can examine the process in other animals.</p> <p class="Heading">The ability for brittle stars to regenerate limbs so readily is more than likely an adaptation to avoid predation.</p> <h3 class="Heading"><strong>Source:</strong></h3> <p><span class="AuthorName">A Czarkwiani</span>, <span class="AuthorName">C Ferrario</span>, <span class="AuthorName">DV Dylus</span>, <span class="AuthorName">M Sugni, P</span><span class="AuthorName"> Oliveri. </span>Skeletal regeneration in the brittle star <em class="EmphasisTypeItalic">Amphiura filiformis. </em><span class="ArticleCitation"><em><span class="JournalTitle">Frontiers in Zoology. </span></em><span class="ArticleCitation_Volume"><strong>13</strong>:18, 2016. </span></span><strong>DOI: </strong>10.1186/s12983-016-0149-x</p> <p> </p> </div> <span><a title="View user profile." href="/author/dr-dolittle" lang="" about="/author/dr-dolittle" typeof="schema:Person" property="schema:name" datatype="">dr. dolittle</a></span> <span>Sat, 04/30/2016 - 14:12</span> <div class="field field--name-field-blog-tags field--type-entity-reference field--label-inline"> <div class="field--label">Tags</div> <div class="field--items"> <div class="field--item"><a href="/tag/life-science-0" hreflang="en">Life Science</a></div> <div class="field--item"><a href="/tag/amputation" hreflang="en">amputation</a></div> <div class="field--item"><a href="/tag/brittle-star" hreflang="en">brittle star</a></div> <div class="field--item"><a href="/tag/development" hreflang="en">development</a></div> <div class="field--item"><a href="/tag/limb" hreflang="en">limb</a></div> <div class="field--item"><a href="/tag/regeneration" hreflang="en">Regeneration</a></div> <div class="field--item"><a href="/tag/wound-healing" hreflang="en">wound healing</a></div> </div> </div> <section> <article data-comment-user-id="0" id="comment-2510208" class="js-comment comment-wrapper clearfix"> <mark class="hidden" data-comment-timestamp="1462052074"></mark> <div class="well"> <strong></strong> <div class="field field--name-comment-body field--type-text-long field--label-hidden field--item"><p>“The ability for brittle stars to regenerate limbs so readily is more than likely an adaptation to avoid predation.”</p> <p>Dear Dr. Dolittle,</p> <p>Why didn’t we human’s adapt this same survival-enhancing ability?</p> <p>What do you do with your time when you’re not writing science fiction?</p> </div> <drupal-render-placeholder callback="comment.lazy_builders:renderLinks" arguments="0=2510208&amp;1=default&amp;2=en&amp;3=" token="ma1QkPxkz3uwpazH0e6I31MG5xJosNIt-CKLw2l-PAM"></drupal-render-placeholder> </div> <footer> <em>By <span lang="" typeof="schema:Person" property="schema:name" datatype="">See Noevo (not verified)</span> on 30 Apr 2016 <a href="https://www.scienceblogs.com/taxonomy/term/17/feed#comment-2510208">#permalink</a></em> <article typeof="schema:Person" about="/user/0"> <div class="field field--name-user-picture field--type-image field--label-hidden field--item"> <a href="/user/0" hreflang="und"><img src="/files/styles/thumbnail/public/default_images/icon-user.png?itok=yQw_eG_q" width="100" height="100" alt="User Image" typeof="foaf:Image" class="img-responsive" /> </a> </div> </article> </footer> </article> <article data-comment-user-id="0" id="comment-2510209" class="js-comment comment-wrapper clearfix"> <mark class="hidden" data-comment-timestamp="1462171380"></mark> <div class="well"> <strong></strong> <div class="field field--name-comment-body field--type-text-long field--label-hidden field--item"><p>"Why didn’t we human’s adapt this same survival-enhancing ability?"</p> <p>Well, you dishonest little science denier, why don't try to do some research and find out?</p> <p>Oh, because that would require work on your part? I forgot, you're a fundamentalist and creationist - work and education aren't things your type do.</p> </div> <drupal-render-placeholder callback="comment.lazy_builders:renderLinks" arguments="0=2510209&amp;1=default&amp;2=en&amp;3=" token="ledqSOHvZ_8G2BOKAD_v1OkDDilq25WM6n4sruKRohs"></drupal-render-placeholder> </div> <footer> <em>By <span lang="" typeof="schema:Person" property="schema:name" datatype="">dean (not verified)</span> on 02 May 2016 <a href="https://www.scienceblogs.com/taxonomy/term/17/feed#comment-2510209">#permalink</a></em> <article typeof="schema:Person" about="/user/0"> <div class="field field--name-user-picture field--type-image field--label-hidden field--item"> <a href="/user/0" hreflang="und"><img src="/files/styles/thumbnail/public/default_images/icon-user.png?itok=yQw_eG_q" width="100" height="100" alt="User Image" typeof="foaf:Image" class="img-responsive" /> </a> </div> </article> </footer> </article> </section> <ul class="links inline list-inline"><li class="comment-forbidden"><a href="/user/login?destination=/lifelines/2016/04/30/limb-regeneration-in-brittle-stars%23comment-form">Log in</a> to post comments</li></ul> Sat, 30 Apr 2016 18:12:06 +0000 dr. dolittle 150392 at https://www.scienceblogs.com Exercise grows bigger fish https://www.scienceblogs.com/lifelines/2016/02/28/exercise-grows-bigger-fish <span>Exercise grows bigger fish</span> <div class="field field--name-body field--type-text-with-summary field--label-hidden field--item"><div style="width: 509px;display:block;margin:0 auto;"><img class="mw-mmv-final-image mw-mmv-dialog-is-open" src="https://upload.wikimedia.org/wikipedia/commons/9/95/Sparus_aurata_Sardegna.jpg" alt="Sparus aurata Sardegna.jpg" width="499" height="375" /> Image of gilthead sea bream By Roberto Pillon - <a href="http://www.fishbase.us/photos/UploadedBy.php?autoctr=13070&amp;win=uploaded">http://www.fishbase.us/photos/UploadedBy.php?autoctr=13070&amp;win=uploaded</a>, CC BY 3.0, <a href="https://commons.wikimedia.org/w/index.php?curid=20825139">https://commons.wikimedia.org/w/index.php?curid=20825139</a> </div> <p>A new study published in the <em>American Journal of Physiology - Regulatory, Integrative and Comparative Physiology</em> explored the effects of exercise on growth and hormone regulation in gilthead sea bream (<em><span class="highlight">Sparus</span> <span class="highlight">aurata</span></em>). The main hormones that regulate growth are, perhaps not surprisingly, growth hormone and insulin-like growth factor. Researchers discovered young gilthead seam bream that underwent sustained moderate exercise for 5 weeks gained more weight than fish that were not exercised. The exercised fish also had higher levels of the hormone insulin-like growth factor in their blood along with higher levels of a hormone associated with increased protein synthesis in their muscles (i.e. the production of new muscle cells). This is interesting as plasma levels of growth hormone actually decreased with exercise.</p> <p>Aside from understanding the effects of exercise on the growth and development of fish, this research has important implications for developing or improving the sustainability of aquaculture.</p> <p><strong>Source:</strong></p> <p><span class="highwire-citation-authors"><span class="highwire-citation-author first has-tooltip hasTooltip" title="" data-delta="0"><span class="nlm-given-names">EJ</span> <span class="nlm-surname">Vélez</span></span>, <span class="highwire-citation-author" data-delta="1"><span class="nlm-given-names">S</span> <span class="nlm-surname">Azizi</span></span>, <span class="highwire-citation-author has-tooltip hasTooltip" title="" data-delta="2"><span class="nlm-given-names">A</span> <span class="nlm-surname">Millán-Cubillo</span></span>, <span class="highwire-citation-author" data-delta="3"><span class="nlm-given-names">J</span> <span class="nlm-surname">Fernández-Borràs</span></span>, <span class="highwire-citation-author" data-delta="4"><span class="nlm-given-names">J</span> <span class="nlm-surname">Blasco</span></span>, <span class="highwire-citation-author" data-delta="5"><span class="nlm-given-names">SJ</span> <span class="nlm-surname">Chan</span></span>, <span class="highwire-citation-author" data-delta="6"><span class="nlm-given-names">JA</span> <span class="nlm-surname">Calduch-Giner</span></span>, <span class="highwire-citation-author" data-delta="7"><span class="nlm-given-names">J</span> <span class="nlm-surname">Pérez-Sánchez</span></span>, <span class="highwire-citation-author has-tooltip hasTooltip" title="" data-delta="8"><span class="nlm-given-names">I</span> <span class="nlm-surname">Navarro</span></span>, <span class="highwire-citation-author has-tooltip hasTooltip" title="" data-delta="9"><span class="nlm-given-names">E</span> <span class="nlm-surname">Capilla</span></span>, <span class="highwire-citation-author" data-delta="10"><span class="nlm-given-names">J</span> <span class="nlm-surname">Gutiérrez. Effects of sustained exercise on GH-IGFs axis in gilthead sea bream (<em>Sparus aurata</em>). </span></span></span><span class="highwire-cite-metadata-journal-title highwire-cite-metadata"><em>American Journal of Physiology - Regulatory, Integrative and Comparative Physiology.</em></span><span class="highwire-cite-metadata-volume highwire-cite-metadata"> 310(</span><span class="highwire-cite-metadata-issue highwire-cite-metadata">4): </span><span class="highwire-cite-metadata-pages highwire-cite-metadata">R313-R322, 2016. </span><span class="highwire-cite-metadata-doi highwire-cite-metadata"><span class="label">DOI:</span> 10.1152/ajpregu.00230.2015 </span></p> </div> <span><a title="View user profile." href="/author/dr-dolittle" lang="" about="/author/dr-dolittle" typeof="schema:Person" property="schema:name" datatype="">dr. dolittle</a></span> <span>Sun, 02/28/2016 - 17:52</span> <div class="field field--name-field-blog-tags field--type-entity-reference field--label-inline"> <div class="field--label">Tags</div> <div class="field--items"> <div class="field--item"><a href="/tag/life-science-0" hreflang="en">Life Science</a></div> <div class="field--item"><a href="/tag/aquaculture" hreflang="en">aquaculture</a></div> <div class="field--item"><a href="/tag/development" hreflang="en">development</a></div> <div class="field--item"><a href="/tag/exercise" hreflang="en">exercise</a></div> <div class="field--item"><a href="/tag/fish" hreflang="en">fish</a></div> <div class="field--item"><a href="/tag/gilthead-sea-bream" hreflang="en">gilthead sea bream</a></div> <div class="field--item"><a href="/tag/growth" hreflang="en">growth</a></div> <div class="field--item"><a href="/tag/meat" hreflang="en">meat</a></div> <div class="field--item"><a href="/tag/sustainability" hreflang="en">sustainability</a></div> </div> </div> <section> <article data-comment-user-id="0" id="comment-2510200" class="js-comment comment-wrapper clearfix"> <mark class="hidden" data-comment-timestamp="1456713283"></mark> <div class="well"> <strong></strong> <div class="field field--name-comment-body field--type-text-long field--label-hidden field--item"><p>This is a really strange phenomenon, which is different from human beings. I think this project must find out more about the fish. I want to know more about it. Thanks for sharing this.</p> </div> <drupal-render-placeholder callback="comment.lazy_builders:renderLinks" arguments="0=2510200&amp;1=default&amp;2=en&amp;3=" token="Yf8MFqmy21pPeQ-sm73GHb0qN8KRJlby1puPA6_wr5I"></drupal-render-placeholder> </div> <footer> <em>By <span lang="" typeof="schema:Person" property="schema:name" datatype="" content="amino acids determination">amino acids de… (not verified)</span> on 28 Feb 2016 <a href="https://www.scienceblogs.com/taxonomy/term/17/feed#comment-2510200">#permalink</a></em> <article typeof="schema:Person" about="/user/0"> <div class="field field--name-user-picture field--type-image field--label-hidden field--item"> <a href="/user/0" hreflang="und"><img src="/files/styles/thumbnail/public/default_images/icon-user.png?itok=yQw_eG_q" width="100" height="100" alt="User Image" typeof="foaf:Image" class="img-responsive" /> </a> </div> </article> </footer> </article> </section> <ul class="links inline list-inline"><li class="comment-forbidden"><a href="/user/login?destination=/lifelines/2016/02/28/exercise-grows-bigger-fish%23comment-form">Log in</a> to post comments</li></ul> Sun, 28 Feb 2016 22:52:50 +0000 dr. dolittle 150372 at https://www.scienceblogs.com The structuralist heresy https://www.scienceblogs.com/pharyngula/2016/02/12/the-structuralist-heresy <span>The structuralist heresy</span> <div class="field field--name-body field--type-text-with-summary field--label-hidden field--item"><p class="lead">Larry Moran has heard the words of Michael Denton, and has <a href="http://sandwalk.blogspot.ca/2016/02/what-is-structuralism.html">come away with a creationist interpretation of structuralism</a>. I have to explain to Larry that Denton, as you might expect of a creationist, is distorting the whole idea. Here's the Denton/Intelligent Design creationism version of structuralist theory.</p> <blockquote><p>As Denton says, the basic idea is that the form (structure) of modern organisms is a property of the laws of physics and chemistry and not something that evolution discovered. He would argue that if you replay the tape of life you will always get species that look pretty much like the species we see today because the basic forms (Baupläne) are the inevitable consequences of the underlying physics. </p> </blockquote> <p>Say what? Look, I'm a developmental biologist; I was baptized in the Stygian stream of structuralism by D'Arcy Wentworth Thompson, I reacted and diffused with Alan Turing, I danced disco by the light of the Belousov–Zhabotinsky reaction, and no, that is not the structuralism I have studied. There is a grain of truth to it, in that structuralism does imply that there are physical/chemical constraints on form, but only the extremists would suggest that that means life on Mars would evolve to look like life on earth. That overlooks the fact that structuralists are thoroughly familiar with the diversity of life on this one planet, and since those physical laws can generate both mushrooms and monkeys, it's clear that there is some room for exploration of form.</p> <p>I can see, though, why creationists would gravitate towards structuralism. Here's Rudy Raff in <a rel="nofollow" href="http://www.amazon.com/gp/product/0226702669/ref=as_li_tl?ie=UTF8&amp;camp=1789&amp;creative=390957&amp;creativeASIN=0226702669&amp;linkCode=as2&amp;tag=pharyngula0e-20&amp;linkId=UDBLWIOHHTUZBTFQ"><i>The Shape of Life: Genes, Development, and the Evolution of Animal Form</i></a><img src="http://ir-na.amazon-adsystem.com/e/ir?t=pharyngula0e-20&amp;l=as2&amp;o=1&amp;a=0226702669" width="1" height="1" border="0" alt="" style="border:none !important; margin:0px !important;" /> (a most excellent book on evolution and development, I recommend it highly), where he contrasts it with modern molecular genetic approaches.</p> <blockquote><p>One school of developmental biologists derides this gene-focused program as epiphenomenological. These "structuralists" envisage morphology as arising from the properties of physical rules that generate structure in developing systems. This is a long-standing perspective on development that arises from pre-Darwinian idealistic morphology and continued to be held by anti-Darwinists. J. Bell Pettigrew published a wonderfully illustrated three-volume treatise in 1908 entitled <i>Design in Nature</i>. Unlike modern structuralists, Pettigrew was arguing on behalf of "First Cause and Design." Pettigrew based his argument for common rules of form in nature, such as the spirals present in nonliving and living structures. Thus, "the dendrites of minerals and metals, the frost pictures on window-panes and pavements in winter, the lightning flash, &amp;c., are amazingly like the arborescent forms seen in the branches and leaves of plants and trees, the division and subdivision of blood-vessels and lymphatics, the branching of nerve cells…" and so on.</p> </blockquote> <p>The core idea in structuralism is the importance of phenotypic interactions, rather than genetic control. Why do isolated cells tend to round up into spherical forms? It's not because there are genes instructing them to do so, but because that's a form that minimizes energy. Why do they flatten when they contact an adhesive surface? For the same reason. You don't need to even mention genes. (Except, of course, that the adhesivity of certain surfaces is going to vary with the expression of specific cell surface molecules).</p> <p>No modern structuralist would deny the importance of genetic regulation, but a lot of the old ones did. D'Arcy Wentworth Thompson pretty much denied this new-fangled genetics stuff any relevance at all -- it's all mathematical interactions all the way down -- but let's cut him some slack. He was schooled in biology <em>before</em> the rediscovery of Mendel, and published <a rel="nofollow" href="http://www.amazon.com/gp/product/0486671356/ref=as_li_tl?ie=UTF8&amp;camp=1789&amp;creative=390957&amp;creativeASIN=0486671356&amp;linkCode=as2&amp;tag=pharyngula0e-20&amp;linkId=72DJC4C5OBFAQP4C"><i>On Growth and Form</i></a><img src="http://ir-na.amazon-adsystem.com/e/ir?t=pharyngula0e-20&amp;l=as2&amp;o=1&amp;a=0486671356" width="1" height="1" border="0" alt="" style="border:none !important; margin:0px !important;" /> in 1917, when biologists were in the middle of a brawl over how genetics worked at all, and he was deep into his alternative model for the inheritance of form.</p> <p>There was, after Thompson, a long period where many were seduced by the elegance of structuralism. It offered an explanation for how simple processes could generate complex and diverse patterns. Look at snowflakes, for instance: simple rules, simple molecules, all assembling into complex symmetrical patterns. If mere water can do that, then maybe there's something equally simple underlying us…a kind of seed crystal for a human being.</p> <p>One example for how people were thinking: many animals are segmented, that is, they have this repeating pattern of body elements reiterated sequentially along the length of the animal. Maybe, just maybe, there's a molecule, a morphogen, that is expressed in an oscillating pattern, a kind of standing wave of simple molecule X that would explain the whole morphology. Wouldn't that be cool? Turing's reaction-diffusion model showed one way you could spontaneously generate a repeating pattern of stripes with just two molecules, and that was temptingly elegant. I've got a small collection of papers from the 1950s that are just that, theoretical explanations for how the whole insect body plan could be set up with a source at one end, a sink at the other, and a couple of simple, unidentified molecules diffusing and interacting chemically to make the pattern, with minimal genetic interaction. </p> <p>These models all got blown to flinders as the actual mechanisms emerged: it was all differential gene expression controlled by intricate, Rube-Goldbergian regulatory logic. I'd argue that there are still vestiges of physical/chemical phenotypic interactions in the importance of epistatic interactions between genes products and genes, but it's impossible to deny the centrality of genetic control any more.</p> <p>I have another complaint about Larry's treatment of structuralism. This is just plain wrong.</p> <blockquote><p>One of the problems with structuralist explanations is that they are very animal-centric. </p> </blockquote> <p>No, they're not. The most persuasive examples focus on single cells, which clearly have structure and form, but you can't fall back on patterns of differential gene regulation to explain them. One of the late Brian Goodwin's favorite examples was <i>Acetabularia</i>. Here's what it looks like:</p> <p><img src="http://scienceblogs.com/pharyngula/files/2016/02/Acetabularia-500x375.jpg" alt="Acetabularia" width="500" height="375" class="aligncenter size-large wp-image-17396" /></p> <p>The mind-blowing thing about it is that that slender mushroom-shaped thing is a <em>single algal cell</em>. How does that work? You're not going to be able to address it by just looking at what genes are present in the nucleus, down in the rhizoid. It's going to demand a structuralist approach to puzzle out what kinds of interactions are going on inside the cell -- there has to be some kind of patterning information being propagated through the cytoplasm. Reaction-diffusion, maybe? Some kind of radial streaming to make the cap?</p> <p>But of course there is some kind of genetic control. There are also different species of <i>Acetabularia</i>, with different morphologies. One cool experiment that has been done is to snip off the caps of two species with distinctive shapes, and swap them. Gradually, the transplanted cap will assume the species-specific morphology of the host nucleus. So some genetic factors are clearly being transported from the rhizoid to the cap, where they then dance together to make a characteristic parasol.</p> <p>That's the interesting part about structuralism. The old-school extremist version is pretty much dead, along with Thompson and Goodwin, but there are valid questions still waiting to be answered. They just aren't the questions creationists are asking.</p> <p>Now evo-devo, though, does have a distinct bias towards multi-cellular animals (and <i>Arabidopsis</i>). But evo-devo isn't really a descendant of structuralist thought -- it's more a scion of comparative molecular genetics. It's a bit more mainstream. Likewise, the people I've known who have structuralist leanings (hi, <a href="https://mcb.illinois.edu/faculty/profile/mitten/">Jay</a>!) don't deny genetics or evolution -- far from it -- but like to point out that there are patterning mechanisms beyond genetic switches, and that there are physical constraints on possible forms.</p> <p>Caricaturing modern structuralism as being all about constraints that force humans to evolve on every planet is even more ridiculous than caricaturing modern molecular biologists as people who claim that biochemistry is irrelevant. I suppose people like that exist, but no one takes them even as seriously as they do Michael Denton.</p> </div> <span><a title="View user profile." href="/pharyngula" lang="" about="/pharyngula" typeof="schema:Person" property="schema:name" datatype="">pharyngula</a></span> <span>Fri, 02/12/2016 - 10:48</span> <div class="field field--name-field-blog-tags field--type-entity-reference field--label-inline"> <div class="field--label">Tags</div> <div class="field--items"> <div class="field--item"><a href="/tag/development" hreflang="en">development</a></div> <div class="field--item"><a href="/tag/evolution" hreflang="en">evolution</a></div> </div> </div> <div class="field field--name-field-blog-categories field--type-entity-reference field--label-inline"> <div class="field--label">Categories</div> <div class="field--items"> <div class="field--item"><a href="/channel/life-sciences" hreflang="en">Life Sciences</a></div> </div> </div> <section> <article data-comment-user-id="0" id="comment-830346" class="js-comment comment-wrapper clearfix"> <mark class="hidden" data-comment-timestamp="1455300396"></mark> <div class="well"> <strong></strong> <div class="field field--name-comment-body field--type-text-long field--label-hidden field--item"><p>"As Denton says, the basic idea is that the form (structure) of modern organisms is a property of the laws of physics and chemistry and not something that evolution discovered. He would argue that if you replay the tape of life you will always get species that look pretty much like the species we see today because the basic forms (Baupläne) are the inevitable consequences of the underlying physics"</p> <p>Hm. Seems somewhat similar to the views of Simon Conway Morris, actually.</p> </div> <drupal-render-placeholder callback="comment.lazy_builders:renderLinks" arguments="0=830346&amp;1=default&amp;2=en&amp;3=" token="oA_0uXRzWFRrSNBsDNfH-PTjno3m_DWkfp1CuwOHINE"></drupal-render-placeholder> </div> <footer> <em>By <span lang="" typeof="schema:Person" property="schema:name" datatype="">llewelly (not verified)</span> on 12 Feb 2016 <a href="https://www.scienceblogs.com/taxonomy/term/17/feed#comment-830346">#permalink</a></em> <article typeof="schema:Person" about="/user/0"> <div class="field field--name-user-picture field--type-image field--label-hidden field--item"> <a href="/user/0" hreflang="und"><img src="/files/styles/thumbnail/public/default_images/icon-user.png?itok=yQw_eG_q" width="100" height="100" alt="User Image" typeof="foaf:Image" class="img-responsive" /> </a> </div> </article> </footer> </article> </section> <ul class="links inline list-inline"><li class="comment-forbidden"><a href="/user/login?destination=/pharyngula/2016/02/12/the-structuralist-heresy%23comment-form">Log in</a> to post comments</li></ul> Fri, 12 Feb 2016 15:48:19 +0000 pharyngula 14233 at https://www.scienceblogs.com A tale of three arms https://www.scienceblogs.com/pharyngula/2016/01/06/a-tale-of-three-arms <span>A tale of three arms</span> <div class="field field--name-body field--type-text-with-summary field--label-hidden field--item"><p><a href="http://scienceblogs.com/pharyngula/files/2016/01/octopusarm.jpg"><img src="http://scienceblogs.com/pharyngula/files/2016/01/octopusarm-150x138.jpg" alt="octopusarm" width="150" height="138" class="alignright size-thumbnail wp-image-17364" /></a><br /> </p><p class="lead">Once upon a time, deep in the Precambrian, this was the planet of worms. Well, actually, this was, is, and always will be the planet of bacteria, but if you filter your perspective to just organisms above a particular size, and if you're an animal writing about it in the modern day with a chauvinistic attitude that allows you to ignore that it was also a planet of algae, that would become a planet of plants, on a world that also is built of soil formed by lichens and saturated with fungus…if you ignore all that, OK, it was a planet of worms.</p> <p>Late in the Precambrian, the oceans were full of accumulated muck and it was a good time to be a worm -- a slender, plastic body, able to burrow and plunder the detritus of it's nutrients, digging shelters or writhing in the freshest debris up top. Worms were everywhere, and the family was diverse. There were hairy ones, thick ones, slender ones, spiky ones. There were worms beginning to assemble bits of armor, either extracting calcium from their environment or crosslinking stable sugars to create chitin, because there were also worms that were developing the habit of eating other worms, rather than farming the muck.</p> <p>Worms were and are diverse. One successful subfamily of worms were segmented -- they had begun to evolve more elaborate mechanisms of specializing body parts, so instead of just a simple tube, they had ways of setting aside regions for essential functions, like a head end for eating, a tail end for excreting and reproducing, and a means of making lots of repetitive copies of subunits of their bodies. So, for instance, when they evolved a way to make a bristle at one place, it would be repeated in a whole chain of bristles down the length of the body.</p> <p>Now as I said, these worms were diverse -- they'd been proliferating and diverging for hundreds of millions of years, and each new kind of worm created a more complex environment that permitted even more kinds of worms to flourish. Different lineages of worms had different histories and different sets of attributes. At the end of the Precambrian, not only had they fueled their own diversification, but they'd also changed the planet. They'd stirred up long-buried nutrients and brought about a population explosion, and other organisms (you know, those neglected algae) had been changing the atmosphere, and it was a different world, ripe with opportunity for even more novel forms and opening up new environments, and there were worms fortuitously endowed with traits to take advantage of those opportunities.</p> <p>In this vast family of worms, I'm going to mention just three cousins -- three Precambrian worms that were going to found new dynasties in the Cambrian and on.</p> <p>One cousin had inherited a couple of extraordinarily useful endowments. She had limbs. Lots of limbs. She was segmented, and initially had figured out how to sprout muscular appendages from each segment, and so she had an extravagant superfluity of limbs, and each could be specialized in novel ways. She was a walking Swiss army knife. She also had acquired bits of chitinous armor, which would also serve her family in good stead -- she was the armored and armed cousin, who would found the great family of arthropods.</p> <p>If she'd had foresight, she would have smiled wolfishly at the prospects for her descendants, if she'd had the kind of mouth that could smile. Instead, she had a face full of legs, each one already specializing into stabbing needles and gnashing blades and pulverizing clubs, which, come to think of it, is even better than a smile for communicating wolfishness.</p> <p>The second cousin had not inherited any limbs or armor at all. She was smooth and torpedo-shaped. Her endowment was the beginnings of an internal skeleton, a notochord, which made her a fast and efficient swimmer. She was the mother of chordates, and she was the swift cousin -- what she gave to her descendants was the ability to run away quickly. In contrast to her armed cousin, she also had a purty mouth, a delicate basket of rods and cilia and membranes, a pharynx that was an efficient filter feeding tool. Someday, her descendants would be able to smile, but only after radically rearranging that complex endowment.</p> <p>The third cousin…well, I'm going to call her the humble cousin. She had no arms, either, just one big muscular foot that she could use to crawl about on the bottom of the ocean. She had a gland to secrete a shell, but it wasn't articulated like that of her armored cousin, so it really was a purely defensive structure -- she couldn't shape it into knives and spears. She also had a talent for mucus, which is not usually the kind of thing to make one popular at parties. She's not so obvious as the founder of a successful family, but she was. She was the mother of molluscs. She didn't have much of a face -- a sheet of muscle with a muscular sphincter -- so she wasn't much for smiling.</p> <p>Time passes. Arthropods flourish and take over the world -- in the modern day we'd have to say we're living on the Planet of the Insects, except that that external armor turned out to impose some limitations on size so they never got big enough to support a large brain, didn't invent the internet, and aren't writing the story of history. But that doesn't matter much when they're the first to invade the land, first to take to the skies, and are filling practically every ecosystem on the planet. Those limbs turned out to be a really lucky and extremely handy if you wanted to interact with the environment in complex ways. Eating, walking, flying…limbs make those behaviors relatively easy, and enable all kinds of specialization.</p> <p>Limbs do have a limitation -- they're a real drag for swimming, where simple, streamlined torpedos rule. The swift cousin does well in the open sea, and builds a huge clan of fish. Evolution tinkers with them, too, though. Even a torpedo can benefit from fins, so those fish that can manage a little fin-fold swim straighter, and those that can flex a fin become more maneuverable. The heavy duty modifications occur in the pharynx. The bigger the animal, the less useful a delicate ciliated basket is for feeding, so it's dismantled, rearranged, repurposed. It's used for respiration; parts of it are beefed up and turned into a grasping clamp, the jaws; it becomes a key element of the blood circulation; its membranes are used for ion exchange, and some of the tissue is specialized for managing salt balance; in fact, the whole front end of the chordate -- now vertebrate -- gets massively renovated, not just to recycle elements of the pharyngeal apparatus, but to build a bigger brain and a sensitive sensory apparatus.</p> <p>But jaws don't quite have the versatility of limbs. It took almost a hundred million years after the beginning of the Cambrian for vertebrates to scrape together a kludge to give some of their members a small set of manipulatory/locomotor appendages. This process involved localizing four patches of epidermal thickening<sup>1</sup>, reusing signals to recruit mesodermal tissue into the zones, and then recycling signals used for patterning the longitudinal axis of the animal to pattern the length of the limb. It's an amusing glimpse into the way evolution tinkers to see how vertebrate limbs are such perfect examples of bricolage: a piece here, a piece there, jigger them about and reassemble them to make a protruding limb, with the same Hox genes used to specify the organization of the hindbrain lifted wholesale and used in new ways to organize upper arm, forearm, and digits of the hand.</p> <p>It's also a testimony to the utility of limbs that they've evolved multiple times. There must be considerable incentive for some lineages to reach out and touch the world somehow, as these projecting bulges keep popping out. But they also reveal the other side of convergent evolution: we can get similar function by very different mechanisms, and internal structure reveals historical differences. Here's a cartoon of cross sections of various limbs to expose those differences.</p> <p><a href="http://scienceblogs.com/pharyngula/files/2016/01/limbcomp.png"><img src="http://scienceblogs.com/pharyngula/files/2016/01/limbcomp-500x501.png" alt="limbcomp" width="500" height="501" class="aligncenter size-large wp-image-17362" /></a></p> <p>So arthropods had limbs from the earliest times in their history, and are a defining character of the clade. They also acquired an armored exoskeleton made of chitin. When we look at their limbs in cross-section (top left), what we see is a strong, supportive skeletal tube with muscles (in yellow) on the inside. Those muscles are primarily longitudinal -- that is, they attach to the inner wall of the tube and extend the length of that tube to attach to the inner wall of the next tube in sequence (or to internal protrusions called apodemes), and the tubes are linked by articulating joints.</p> <p>The subgroup of the vertebrates, the tetrapods, that finally got around to evolving jointed limbs, have a mechanically different solution (top right). Their limbs have a central bony rod to which longitudinal<sup>2</sup> muscles attach, and extend down to the next rod in sequence. Each bone is articulated with the next with joints made of cartilage. Vertebrates and arthropods have come up with roughly similar solutions to movement, constructing rigid structual elements that can be flexed relative to each other by the actions of muscles, but they're inside out relative to one another. As it turns out, having an internal structural support is arguably better engineering at large sizes, while having an external support that doubles as armor is arguably more efficient at smaller sizes, which is one reason arthropods rule the animal domain below about 10cm in size, while tetrapods are living in lonely majesty above that size.<sup>3</sup></p> <p><a href="http://scienceblogs.com/pharyngula/files/2016/01/Berghia_coerulescens.jpg"><img src="http://scienceblogs.com/pharyngula/files/2016/01/Berghia_coerulescens-150x84.jpg" alt="Berghia_coerulescens" width="150" height="84" class="alignright size-thumbnail wp-image-17363" /></a></p> <p>But wait! What about that homely cousin, the molluscs? I was wrong to call them homely. They blossomed. The nudibranchs are really the most spectacularly colorful animals in the ocean, and they used a body that, thanks to that muscular foot, is practically a solid wall of intricately controlled muscle fibers in multiple orientations. They have a muscular versatility that puts <a href="https://www.youtube.com/watch?v=XslSXVYru4s">Terry Crews' pecs</a> to shame, but one thing they lack is a rigid skeletal framework. No bones or exoskeleton to tug on! All they can do is exert force on other muscles and on the flexible dermal connective tissue, which sounds as if it would be a serious limitation, but then you watch a sea slug dance through the water, and you have to rethink that assumption.</p> <p>This is where convergence gets interesting: some members of the molluscan clade also evolved limbs <i>de novo</i>. Cephalopods are simply slugs with ambition. They also evolved new limbs, which had to be even more difficult than the path tetrapods took -- molluscs lack any kind of articulated skeleton at all, so there aren't many conveniently rigid structural elements to act upon. So they resorted to a different solution. Tentacles.</p> <p>The bottom illustration in the diagram above is a cross-section through an octopus arm. There is no skeleton. It's just layers of muscles, some longitudinal, some transverse, some circumferential, all pulling in complex ways to change the shape of the appendage. The closest thing we humans have to something like that is our tongue, which contains intrinsic muscles that do not have a bony attachment, and which can change the organ's shape in interesting ways. But look at that diagram! They have all kinds of muscles in all kinds of orientations, and also unlike the arthropod or tetrapod, a robust central nervous organ with chains of ganglia extending the length of the arm. It takes a lot of local circuitry to control something as complex as a cephalopod arm.</p> <p>That's <em>three different ways</em> to make a limb right here on our one solitary planet. That's interesting in both a developmental and evolutionary way. Do all three use similar processes? We know quite a bit about tetrapod and arthropod limb development, and they aren't homologous at all. Primitively, every segment in an arthropod has a limb; vertebrates had none. As is typical, limbs had to be built using the common molecular toolkit, and we find that homologous genes are used in similar ways. Insects use a gene called <i>decapentaplegic</i> as a morphogen to organize their limb fields. Vertebrates use the <i>decapentaplegic</i> homolog <i>Bone Morphogenetic Protein</i> to regulate skeletal formation in the embryo. We know that molluscs also have <i>decapentaplegic</i> -- they use it as a morphogen to control shell shape. Does it get recycled into cephalopod arm formation?</p> <p>We also know how squishy vertebrate limbs grow. There is an epidermal thickening called the apical ectodermal ridge that secretes a morphogen, <i>FGF</i> to induce proliferation and extension, and another part of the limb bud called the zone of polarizing activity that uses another morphogen, <i>Shh</i>, to induce polarity (the dorsal side of your arm is different than the ventral). How do cephalopod arms develop? Is it similar, with the same kinds of patterns of proliferation and extension, and do they also recruit the same or similar molecules to do the job?</p> <p>People are always asking me why I'm known for my fascination with cephalopods, when I work on a limbless vertebrate, the zebrafish, and this is why. Because asking why things are the way they are <em>requires</em> asking about the way they are not. Understanding how our biology came to take one particular path should involve looking at all the different paths, and thinking about alternatives. So if you want to really understand vertebrate limb development, it's important to compare it with <strong>in</strong>vertebrate limb development.</p> <p>My introduction has gone on way too long, so I'll post the answers (and mostly, lack of answers) to my questions later. For now, just remember that the issue is how different organisms build a protruding appendage, a very general question, and we want to know more about how a group very different from our own, that has diverged from the vertebrate lineage for at least 600 million years, has constructed their unique version of an arm.</p> <hr /> <p class="ref">Nödl et al. (2015) <a href="http://evodevojournal.biomedcentral.com/articles/10.1186/s13227-015-0012-8">The making of an octopus arm</a>. EvoDevo 6:19</p> <hr /> <p class="ref"><sup>1</sup>One of the things that always annoys me in SF movies is the ubiquity of bipeds tottering about. That we only have four limbs is entirely a historical accident of our clade -- and bipeds like us are the result of a clumsy evolutionary effort to free up a pair from locomotory duties to be more manipulatory. We're weird! Why do we keep unthinkingly imposing our historical limitations on every alien species we imagine, especially when our own planet is so rich in species that have no such arbitrary constraint?</p> <p>And don't use that "movie budget" excuse: we have CGI aliens all over the place, and even there they simply map them onto distorted bipedal forms. We even have movies like <i>Avatar</i> which imagines an entire diverse alien ecosystem with diverse body plans, and then chickens out and turns the intelligent aliens into slender big-eyed anime models<sup>4</sup>.</p> <p class="ref"><sup>2</sup>Of course we have some greater complexity than just longitudinal muscles -- obliques, for instance, that rotate the radius and ulna, or the layered sheets of muscle that make up the abdominal wall.</p> <p class="ref"><sup>3</sup>On the topic of imaginary aliens -- use our extant patterns as a guide. Imagine an equivalent Precambrian world elsewhere, where one group gets a mix of traits, a complex oral structure plus an exoskeletal armor, whie another group gets a different mix, multiple segmented limbs plus an internal skeleton. Work forward. Later, you've got small heavily armored snake-like things with intricate mouthparts, and giant fleshy beasts with limbs sprouting all over the place.</p> <p>And of course, the creatures with all the feet evolve into galactic imperialists, conquering the universe to accumulate enough real estate to house all their shoe stores.</p> <p class="ref"><sup>4</sup>Also chickening out: I liked the diversity of limb structure in the <a href="http://www.imdb.com/title/tt0401729/"><i>John Carter</i></a> movie, but once again, the hero species defaulted to fully humanoid, to the point where a human would find them sexually attractive. Which is bizarre -- the Red Martians in Burroughs' stories <em>lay eggs</em>. Somebody needs to write the story of John Carter and Dejah Thoris's wedding night, when the wife disrobes and reveals to her husband…a cloaca. Does the sexual attraction endure?</p> </div> <span><a title="View user profile." href="/pharyngula" lang="" about="/pharyngula" typeof="schema:Person" property="schema:name" datatype="">pharyngula</a></span> <span>Wed, 01/06/2016 - 11:50</span> <div class="field field--name-field-blog-tags field--type-entity-reference field--label-inline"> <div class="field--label">Tags</div> <div class="field--items"> <div class="field--item"><a href="/tag/development" hreflang="en">development</a></div> <div class="field--item"><a href="/tag/evolution" hreflang="en">evolution</a></div> </div> </div> <div class="field field--name-field-blog-categories field--type-entity-reference field--label-inline"> <div class="field--label">Categories</div> <div class="field--items"> <div class="field--item"><a href="/channel/life-sciences" hreflang="en">Life Sciences</a></div> </div> </div> <section> <article data-comment-user-id="0" id="comment-830254" class="js-comment comment-wrapper clearfix"> <mark class="hidden" data-comment-timestamp="1452103026"></mark> <div class="well"> <strong></strong> <div class="field field--name-comment-body field--type-text-long field--label-hidden field--item"><p>That was fun, thanks.</p> </div> <drupal-render-placeholder callback="comment.lazy_builders:renderLinks" arguments="0=830254&amp;1=default&amp;2=en&amp;3=" token="MOBWT888SXmeENKhKxwMwQlfmp8Hx_Lhs0im-3-dvG0"></drupal-render-placeholder> </div> <footer> <em>By <span lang="" typeof="schema:Person" property="schema:name" datatype="">GregH (not verified)</span> on 06 Jan 2016 <a href="https://www.scienceblogs.com/taxonomy/term/17/feed#comment-830254">#permalink</a></em> <article typeof="schema:Person" about="/user/0"> <div class="field field--name-user-picture field--type-image field--label-hidden field--item"> <a href="/user/0" hreflang="und"><img src="/files/styles/thumbnail/public/default_images/icon-user.png?itok=yQw_eG_q" width="100" height="100" alt="User Image" typeof="foaf:Image" class="img-responsive" /> </a> </div> </article> </footer> </article> <article data-comment-user-id="0" id="comment-830255" class="js-comment comment-wrapper clearfix"> <mark class="hidden" data-comment-timestamp="1452103449"></mark> <div class="well"> <strong></strong> <div class="field field--name-comment-body field--type-text-long field--label-hidden field--item"><p>That was the most interesting thing I've read in a long time. Thanks for sharing!</p> </div> <drupal-render-placeholder callback="comment.lazy_builders:renderLinks" arguments="0=830255&amp;1=default&amp;2=en&amp;3=" token="OlF_ua7fzZES88UlqCjiw3mHGg1fVTVu-NbKzQw9_Rw"></drupal-render-placeholder> </div> <footer> <em>By <span lang="" typeof="schema:Person" property="schema:name" datatype="">Chris (not verified)</span> on 06 Jan 2016 <a href="https://www.scienceblogs.com/taxonomy/term/17/feed#comment-830255">#permalink</a></em> <article typeof="schema:Person" about="/user/0"> <div class="field field--name-user-picture field--type-image field--label-hidden field--item"> <a href="/user/0" hreflang="und"><img src="/files/styles/thumbnail/public/default_images/icon-user.png?itok=yQw_eG_q" width="100" height="100" alt="User Image" typeof="foaf:Image" class="img-responsive" /> </a> </div> </article> </footer> </article> <article data-comment-user-id="0" id="comment-830256" class="js-comment comment-wrapper clearfix"> <mark class="hidden" data-comment-timestamp="1452113537"></mark> <div class="well"> <strong></strong> <div class="field field--name-comment-body field--type-text-long field--label-hidden field--item"><p><a href="http://throughpassion.weebly.com/jesus-christ-meant-to-return-a-long-time-ago.html">http://throughpassion.weebly.com/jesus-christ-meant-to-return-a-long-ti…</a> </p> <p>I once saw Christopher Hitchens say something to this affect after having written my book. I wondered with incredulity how he could not have written a book about this. It's probably because it does not take a book to prove this, but in my own I give plenty of passages and historical examples to do so. Still, why did he in the least not write an article about this if he cared so much about ending religion?</p> </div> <drupal-render-placeholder callback="comment.lazy_builders:renderLinks" arguments="0=830256&amp;1=default&amp;2=en&amp;3=" token="e0yfDzEV-sDuFZ1OY61SqUgiKjEcvhIR2sTqRTchSWs"></drupal-render-placeholder> </div> <footer> <em>By <span lang="" typeof="schema:Person" property="schema:name" datatype="">Desiderus Lachrimae (not verified)</span> on 06 Jan 2016 <a href="https://www.scienceblogs.com/taxonomy/term/17/feed#comment-830256">#permalink</a></em> <article typeof="schema:Person" about="/user/0"> <div class="field field--name-user-picture field--type-image field--label-hidden field--item"> <a href="/user/0" hreflang="und"><img src="/files/styles/thumbnail/public/default_images/icon-user.png?itok=yQw_eG_q" width="100" height="100" alt="User Image" typeof="foaf:Image" class="img-responsive" /> </a> </div> </article> </footer> </article> <article data-comment-user-id="0" id="comment-830257" class="js-comment comment-wrapper clearfix"> <mark class="hidden" data-comment-timestamp="1452114519"></mark> <div class="well"> <strong></strong> <div class="field field--name-comment-body field--type-text-long field--label-hidden field--item"><p>best read i've had since "the Ancestor's Tale"</p> <p>be great if English teachers used this in some sort of comprehension exercise(s). Nice way to sneak in some really interesting evolutionary science</p> <p>good job PZ</p> </div> <drupal-render-placeholder callback="comment.lazy_builders:renderLinks" arguments="0=830257&amp;1=default&amp;2=en&amp;3=" token="gjig6OZhZNealBAQsHplcVbkVnQSxKydjqbHbOwrAig"></drupal-render-placeholder> </div> <footer> <em>By <span lang="" typeof="schema:Person" property="schema:name" datatype="">The Peak Oil Poet (not verified)</span> on 06 Jan 2016 <a href="https://www.scienceblogs.com/taxonomy/term/17/feed#comment-830257">#permalink</a></em> <article typeof="schema:Person" about="/user/0"> <div class="field field--name-user-picture field--type-image field--label-hidden field--item"> <a href="/user/0" hreflang="und"><img src="/files/styles/thumbnail/public/default_images/icon-user.png?itok=yQw_eG_q" width="100" height="100" alt="User Image" typeof="foaf:Image" class="img-responsive" /> </a> </div> </article> </footer> </article> <article data-comment-user-id="0" id="comment-830258" class="js-comment comment-wrapper clearfix"> <mark class="hidden" data-comment-timestamp="1452117221"></mark> <div class="well"> <strong></strong> <div class="field field--name-comment-body field--type-text-long field--label-hidden field--item"><p>Of course,as usual, absolutely no evidence for 99% of this "I can just imagine " story.<br /> Even getting to sound like Dawkins.</p> </div> <drupal-render-placeholder callback="comment.lazy_builders:renderLinks" arguments="0=830258&amp;1=default&amp;2=en&amp;3=" token="Md5c_U1QPq8XlKN0jHPmDlL92ZxamZ3xMU18_S65iYg"></drupal-render-placeholder> </div> <footer> <em>By <span lang="" typeof="schema:Person" property="schema:name" datatype="">Barrie Lewis (not verified)</span> on 06 Jan 2016 <a href="https://www.scienceblogs.com/taxonomy/term/17/feed#comment-830258">#permalink</a></em> <article typeof="schema:Person" about="/user/0"> <div class="field field--name-user-picture field--type-image field--label-hidden field--item"> <a href="/user/0" hreflang="und"><img src="/files/styles/thumbnail/public/default_images/icon-user.png?itok=yQw_eG_q" width="100" height="100" alt="User Image" typeof="foaf:Image" class="img-responsive" /> </a> </div> </article> </footer> </article> <article data-comment-user-id="0" id="comment-830259" class="js-comment comment-wrapper clearfix"> <mark class="hidden" data-comment-timestamp="1452128023"></mark> <div class="well"> <strong></strong> <div class="field field--name-comment-body field--type-text-long field--label-hidden field--item"><p>Voilà!<br /> “… they had begun to evolve more elaborate mechanisms of specializing body parts…”</p> <p>Zowie!<br /> “…they evolved a way to make a bristle at one place…”</p> <p>Pow!<br /> “…the tetrapods, that finally got around to evolving jointed limbs…”</p> <p>Boffo!<br /> “…some members of the molluscan clade also evolved limbs de novo…”</p> <p>How fitting that you end with a footnote about science fiction.</p> </div> <drupal-render-placeholder callback="comment.lazy_builders:renderLinks" arguments="0=830259&amp;1=default&amp;2=en&amp;3=" token="NITe1pSRsblhW6AL70KQARSuC5k8TCG5u5j3x-LHrRI"></drupal-render-placeholder> </div> <footer> <em>By <span lang="" typeof="schema:Person" property="schema:name" datatype="">See Noevo (not verified)</span> on 06 Jan 2016 <a href="https://www.scienceblogs.com/taxonomy/term/17/feed#comment-830259">#permalink</a></em> <article typeof="schema:Person" about="/user/0"> <div class="field field--name-user-picture field--type-image field--label-hidden field--item"> <a href="/user/0" hreflang="und"><img src="/files/styles/thumbnail/public/default_images/icon-user.png?itok=yQw_eG_q" width="100" height="100" alt="User Image" typeof="foaf:Image" class="img-responsive" /> </a> </div> </article> </footer> </article> <article data-comment-user-id="0" id="comment-830260" class="js-comment comment-wrapper clearfix"> <mark class="hidden" data-comment-timestamp="1452179882"></mark> <div class="well"> <strong></strong> <div class="field field--name-comment-body field--type-text-long field--label-hidden field--item"><p>Torpedo fast? Like they say in the NFL, " You can't teach speed." </p> <p> Excellent class on evolution of worms. I enjoyed every bite. I too feel peeved at the plethora of bipedal-centric aliens populating the Sci-Fi universe. For a penny plus postage you buy a copy of Robert Mccammon's novel "Stinger". The alien is a super intelligent segmented worm with a bad attitude.</p> <p>I'm glad I stumbled across your blog.</p> </div> <drupal-render-placeholder callback="comment.lazy_builders:renderLinks" arguments="0=830260&amp;1=default&amp;2=en&amp;3=" token="0cddskApwaC7H91EWvXUTtgNoY3gCjZ8-zizoUQk9sI"></drupal-render-placeholder> </div> <footer> <em>By <span lang="" typeof="schema:Person" property="schema:name" datatype="">Ramsey Glissadevil (not verified)</span> on 07 Jan 2016 <a href="https://www.scienceblogs.com/taxonomy/term/17/feed#comment-830260">#permalink</a></em> <article typeof="schema:Person" about="/user/0"> <div class="field field--name-user-picture field--type-image field--label-hidden field--item"> <a href="/user/0" hreflang="und"><img src="/files/styles/thumbnail/public/default_images/icon-user.png?itok=yQw_eG_q" width="100" height="100" alt="User Image" typeof="foaf:Image" class="img-responsive" /> </a> </div> </article> </footer> </article> <article data-comment-user-id="0" id="comment-830261" class="js-comment comment-wrapper clearfix"> <mark class="hidden" data-comment-timestamp="1452185347"></mark> <div class="well"> <strong></strong> <div class="field field--name-comment-body field--type-text-long field--label-hidden field--item"><p>@See Noevo: Can you do anything else besides sneer at the articles? It's pretty lame.</p> </div> <drupal-render-placeholder callback="comment.lazy_builders:renderLinks" arguments="0=830261&amp;1=default&amp;2=en&amp;3=" token="zpTulH3a0g4fR2XvftiJYwPhOrLiXPB6N-thwrqLuQo"></drupal-render-placeholder> </div> <footer> <em>By <span lang="" typeof="schema:Person" property="schema:name" datatype="">Chris (not verified)</span> on 07 Jan 2016 <a href="https://www.scienceblogs.com/taxonomy/term/17/feed#comment-830261">#permalink</a></em> <article typeof="schema:Person" about="/user/0"> <div class="field field--name-user-picture field--type-image field--label-hidden field--item"> <a href="/user/0" hreflang="und"><img src="/files/styles/thumbnail/public/default_images/icon-user.png?itok=yQw_eG_q" width="100" height="100" alt="User Image" typeof="foaf:Image" class="img-responsive" /> </a> </div> </article> </footer> </article> <article data-comment-user-id="0" id="comment-830262" class="js-comment comment-wrapper clearfix"> <mark class="hidden" data-comment-timestamp="1452196046"></mark> <div class="well"> <strong></strong> <div class="field field--name-comment-body field--type-text-long field--label-hidden field--item"><p>Ah, dopey old creationists. There is evidence for this story: the fossils and the molecular history.</p> </div> <drupal-render-placeholder callback="comment.lazy_builders:renderLinks" arguments="0=830262&amp;1=default&amp;2=en&amp;3=" token="oSfOnPYqrNifB_ME6RW_CAdaXi_xwBMeGE_b9S8sVGE"></drupal-render-placeholder> </div> <footer> <em>By <span lang="" typeof="schema:Person" property="schema:name" datatype="">PZ Myers (not verified)</span> on 07 Jan 2016 <a href="https://www.scienceblogs.com/taxonomy/term/17/feed#comment-830262">#permalink</a></em> <article typeof="schema:Person" about="/user/0"> <div class="field field--name-user-picture field--type-image field--label-hidden field--item"> <a href="/user/0" hreflang="und"><img src="/files/styles/thumbnail/public/default_images/icon-user.png?itok=yQw_eG_q" width="100" height="100" alt="User Image" typeof="foaf:Image" class="img-responsive" /> </a> </div> </article> </footer> </article> <article data-comment-user-id="0" id="comment-830263" class="js-comment comment-wrapper clearfix"> <mark class="hidden" data-comment-timestamp="1452261333"></mark> <div class="well"> <strong></strong> <div class="field field--name-comment-body field--type-text-long field--label-hidden field--item"><p>Who needs evidence when you can have <a href="https://vimeo.com/28280553">highly evolved worms in your aquarium</a>.</p> </div> <drupal-render-placeholder callback="comment.lazy_builders:renderLinks" arguments="0=830263&amp;1=default&amp;2=en&amp;3=" token="r83SECIv50_WK9jfiCFlpNs7vu0abJk2zhlF8wAOnss"></drupal-render-placeholder> </div> <footer> <em>By <span lang="" typeof="schema:Person" property="schema:name" datatype="">GregH (not verified)</span> on 08 Jan 2016 <a href="https://www.scienceblogs.com/taxonomy/term/17/feed#comment-830263">#permalink</a></em> <article typeof="schema:Person" about="/user/0"> <div class="field field--name-user-picture field--type-image field--label-hidden field--item"> <a href="/user/0" hreflang="und"><img src="/files/styles/thumbnail/public/default_images/icon-user.png?itok=yQw_eG_q" width="100" height="100" alt="User Image" typeof="foaf:Image" class="img-responsive" /> </a> </div> </article> </footer> </article> <article data-comment-user-id="0" id="comment-830264" class="js-comment comment-wrapper clearfix"> <mark class="hidden" data-comment-timestamp="1452270484"></mark> <div class="well"> <strong></strong> <div class="field field--name-comment-body field--type-text-long field--label-hidden field--item"><p>Chris, re</p> <blockquote><p>See Noevo: Can you do anything else besides sneer at the articles?</p></blockquote> <p>sn has claimed in numerous places that he had an elite ivy league education and so can understand things about science others can't. Like "evolution predicts an animal of one species will give birth to one of another species" and since that hasn't been seen, evolution is a myth.</p> <p>So, back in the real word - he can't do anything except sneer.</p> </div> <drupal-render-placeholder callback="comment.lazy_builders:renderLinks" arguments="0=830264&amp;1=default&amp;2=en&amp;3=" token="1kBYfAiRmstNhaBzVYj-S1dkVuCos9VXORtCdo5VoFo"></drupal-render-placeholder> </div> <footer> <em>By <span lang="" typeof="schema:Person" property="schema:name" datatype="">dean (not verified)</span> on 08 Jan 2016 <a href="https://www.scienceblogs.com/taxonomy/term/17/feed#comment-830264">#permalink</a></em> <article typeof="schema:Person" about="/user/0"> <div class="field field--name-user-picture field--type-image field--label-hidden field--item"> <a href="/user/0" hreflang="und"><img src="/files/styles/thumbnail/public/default_images/icon-user.png?itok=yQw_eG_q" width="100" height="100" alt="User Image" typeof="foaf:Image" class="img-responsive" /> </a> </div> </article> </footer> </article> <article data-comment-user-id="0" id="comment-830265" class="js-comment comment-wrapper clearfix"> <mark class="hidden" data-comment-timestamp="1452301887"></mark> <div class="well"> <strong></strong> <div class="field field--name-comment-body field--type-text-long field--label-hidden field--item"><p>Thanks for an entertaining and informative piece on the convergent evolution of limbs. It has been a while since I last visited your blog and I am glad to see you still at it. And lucky you! You have your own creationist trolls too.</p> </div> <drupal-render-placeholder callback="comment.lazy_builders:renderLinks" arguments="0=830265&amp;1=default&amp;2=en&amp;3=" token="DwYN8WVFTS-xseqqVsC133riLFRz3Z8MHai7XggJYA4"></drupal-render-placeholder> </div> <footer> <em>By <span lang="" typeof="schema:Person" property="schema:name" datatype="" content="David Ehecatl Carroll">David Ehecatl … (not verified)</span> on 08 Jan 2016 <a href="https://www.scienceblogs.com/taxonomy/term/17/feed#comment-830265">#permalink</a></em> <article typeof="schema:Person" about="/user/0"> <div class="field field--name-user-picture field--type-image field--label-hidden field--item"> <a href="/user/0" hreflang="und"><img src="/files/styles/thumbnail/public/default_images/icon-user.png?itok=yQw_eG_q" width="100" height="100" alt="User Image" typeof="foaf:Image" class="img-responsive" /> </a> </div> </article> </footer> </article> </section> <ul class="links inline list-inline"><li class="comment-forbidden"><a href="/user/login?destination=/pharyngula/2016/01/06/a-tale-of-three-arms%23comment-form">Log in</a> to post comments</li></ul> Wed, 06 Jan 2016 16:50:00 +0000 pharyngula 14213 at https://www.scienceblogs.com Evo devo in the real world https://www.scienceblogs.com/pharyngula/2015/12/29/evo-devo-in-the-real-world <span>Evo devo in the real world</span> <div class="field field--name-body field--type-text-with-summary field--label-hidden field--item"><p class="lead">I disagree with Razib Khan on a lot of things, but he's <a href="http://www.unz.com/gnxp/epigenetics-does-not-a-revolution-make/">exactly right on recent fads in biology</a>.</p> <blockquote><p>Periodically I get frankly stupid comments that seem to imply that the incredible swell of results coming out of molecuar genetics and genomics are revolutionizing our understanding of evolutionary and population genetics. Over the past generation it’s been alternative splicing, then gene regulation and evo-devo, and now epigenetics is all the rage. The results are interesting, fascinating, and warrant deeper inquiry (I happen to see graduate school admission applications for genetics, and I can tell you that conservatively one out of three applicants mention an interest in epigenetics; the hype is grounded in reality, as epigenetics may be a pretty big deal in human health that we can effect).</p> </blockquote> <p>All those phenomena he mentioned are real and often very interesting, but they're not changing deep concepts in evolutionary biology. You're most often going to hear that they're revolutionary from people who don't understand evolution very well.</p> <p>He's got a good assessment of evo devo, too.</p> <blockquote><p>There are some Christians who assert that their religion is the natural completion of Judaism and Greek philosophy.* There are others who rather argue that Christianity was a radical revolution against all that came before. Historically the latter has been a minority view. The Marcionites failed, and the Jewish origins of Christianity were sewn into the fabric of its foundational scripture in the form of the Old Testament. And despite periodic revolts, the reality is that intellectual Christianity speaks with a Greek philosophical voice. Ultimately this debate is of purely academic interest for me. But it exhibits a similarity with academic arguments and debates. In <a rel="nofollow" href="http://www.amazon.com/gp/product/0393327795/ref=as_li_tl?ie=UTF8&amp;camp=1789&amp;creative=390957&amp;creativeASIN=0393327795&amp;linkCode=as2&amp;tag=pharyngula0e-20&amp;linkId=LDGII5X45QMGWTJO"><i>Endless Forms Most Beautiful: The New Science of Evo Devo</i></a><img src="http://ir-na.amazon-adsystem.com/e/ir?t=pharyngula0e-20&amp;l=as2&amp;o=1&amp;a=0393327795" width="1" height="1" border="0" alt="" style="border:none !important; margin:0px !important;" /><br /> Sean B. Carroll takes a traditionalist approach which suggests that novel results from the new field of evolutionary developmental biology firmly supports and extends the Neo-Darwinian Synthesis. Carroll’s book is under 400 pages. It is elegantly written and economical of prose, and it proposes an evolution in our thinking about the nature of the variation which serves as the raw material for natural selection. Contrast that with the late Stephen Jay Gould’s <a rel="nofollow" href="http://www.amazon.com/gp/product/B00IVHCTOY/ref=as_li_tl?ie=UTF8&amp;camp=1789&amp;creative=390957&amp;creativeASIN=B00IVHCTOY&amp;linkCode=as2&amp;tag=pharyngula0e-20&amp;linkId=TB227ASIOUPF2CRI"><i>The Structure of Evolutionary Theory</i></a><img src="http://ir-na.amazon-adsystem.com/e/ir?t=pharyngula0e-20&amp;l=as2&amp;o=1&amp;a=B00IVHCTOY" width="1" height="1" border="0" alt="" style="border:none !important; margin:0px !important;" />, which came in at nearly 1,500 pages. Published in the early 2000s, much of it was written earlier. There are only two references to epigenetics within it. If Gould had not died in 2002 he would probably have come out with a new revised edition by now, and I’m rather confident that epigenetics would loom very large indeed. Though Sean B. Carroll is a very eminent scientist, he remains a bit player on the public intellectual scene. That’s because he does not promise revolution, he comes bearing a twist on the orthodoxy. In contrast, Gould’s prolix prose was rich with the promise of paradigms shattered and lost, and grand visions of heretics risen up to prophetic status, as the statues of the grand old men of the Neo-Darwinian orthodoxy were torn down to make way for the new idols (this old <a href="http://www.pkarchive.org/theory/evolute.html">Paul Krugman slap at Gould</a> is pretty on point about why he was so popular in the 1990s). Reality is more prosaic than intellectual revolts plotted in used bookstores!</p> </blockquote> <p>I agree, <em>except</em> that I don't think Krugman's comments on Gould were that much on point. He dismisses punctuated equilibrium as wrong; it's not. The problem with it is what Khan is saying here, that Gould took what should have been a good idea <em>within</em> the field of population genetics and puffed it up as revolutionary.</p> <p>As for Carroll…yes, the big push in his evo devo book was for more recognition of the importance of regulation in evolution, which I think fits quite well within mainstream genetics. Some people seemed to bristle at the idea that cis regulatory elements could possibly be as important as coding genes, but they're just cranky and wrong. <a href="http://freethoughtblogs.com/pharyngula/2012/02/21/the-problem-with-evo-devo/">I've also argued that evo devo is not revolutionary</a>.</p> <p>At least evo devo never was seized upon by creationists, like punctuated equilibrium (<q>it's hopeful monsters all over again!</q> <q>They just invented PE to leap over gaps in the fossil record!</q>), nor was it rapturously embraced by New Age cranks, like epigenetics (<q>You can change your evolution just by thinking about it!</q>). I think that's because most of evo devo's proponents were fairly sober about presenting it as a facet of evolutionary theory, not a replacement for it.</p> <p>Wait! I wrote that last paragraph and then realized that yes, there have been cranks touting evo devo. How could I have forgotten <a href="http://rationalwiki.org/wiki/Altenberg_16_controversy">Susan Mazur and her Altenburg freak-out</a>? And then I remembered <a href="http://www.integralworld.net/visser61.html">Rupert Sheldrake and his morphogenetic fields</a>. Nope, sorry, evo devo has suffered with its share of weirdos, too.</p> </div> <span><a title="View user profile." href="/pharyngula" lang="" about="/pharyngula" typeof="schema:Person" property="schema:name" datatype="">pharyngula</a></span> <span>Tue, 12/29/2015 - 15:41</span> <div class="field field--name-field-blog-tags field--type-entity-reference field--label-inline"> <div class="field--label">Tags</div> <div class="field--items"> <div class="field--item"><a href="/tag/development" hreflang="en">development</a></div> <div class="field--item"><a href="/tag/evolution" hreflang="en">evolution</a></div> </div> </div> <section> <article data-comment-user-id="0" id="comment-830236" class="js-comment comment-wrapper clearfix"> <mark class="hidden" data-comment-timestamp="1451426987"></mark> <div class="well"> <strong></strong> <div class="field field--name-comment-body field--type-text-long field--label-hidden field--item"><p>PZ, Reading this article reminds me of why I do not like<br /> journalists. The only thing they are good at is throwing<br /> a lot of words around without saying anything.<br /> Congratulations to you on that accomplishment.</p> </div> <drupal-render-placeholder callback="comment.lazy_builders:renderLinks" arguments="0=830236&amp;1=default&amp;2=en&amp;3=" token="6_Toc7LiTH4uQdWRRxGylwXa5SAtyDnvaIPCAbc2gck"></drupal-render-placeholder> </div> <footer> <em>By <span lang="" typeof="schema:Person" property="schema:name" datatype="">Jerry Standley (not verified)</span> on 29 Dec 2015 <a href="https://www.scienceblogs.com/taxonomy/term/17/feed#comment-830236">#permalink</a></em> <article typeof="schema:Person" about="/user/0"> <div class="field field--name-user-picture field--type-image field--label-hidden field--item"> <a href="/user/0" hreflang="und"><img src="/files/styles/thumbnail/public/default_images/icon-user.png?itok=yQw_eG_q" width="100" height="100" alt="User Image" typeof="foaf:Image" class="img-responsive" /> </a> </div> </article> </footer> </article> <article data-comment-user-id="0" id="comment-830237" class="js-comment comment-wrapper clearfix"> <mark class="hidden" data-comment-timestamp="1451440077"></mark> <div class="well"> <strong></strong> <div class="field field--name-comment-body field--type-text-long field--label-hidden field--item"><p>There’s little, if any, “real world” about evolutionary developmental biology.</p> <p>It’s about as “real world” as unicorn biology.</p> <p>The only difference is that, with the former, a lot more people actually get paid to write about it. Creative writing more appropriate for an English Lit Department, with zero impact on actual science, medicine, or technology.</p> </div> <drupal-render-placeholder callback="comment.lazy_builders:renderLinks" arguments="0=830237&amp;1=default&amp;2=en&amp;3=" token="0MN4LaMhmBdJJ2JkBRXHOmANJOJUMrlaXPMRRtfnePU"></drupal-render-placeholder> </div> <footer> <em>By <span lang="" typeof="schema:Person" property="schema:name" datatype="">See Noevo (not verified)</span> on 29 Dec 2015 <a href="https://www.scienceblogs.com/taxonomy/term/17/feed#comment-830237">#permalink</a></em> <article typeof="schema:Person" about="/user/0"> <div class="field field--name-user-picture field--type-image field--label-hidden field--item"> <a href="/user/0" hreflang="und"><img src="/files/styles/thumbnail/public/default_images/icon-user.png?itok=yQw_eG_q" width="100" height="100" alt="User Image" typeof="foaf:Image" class="img-responsive" /> </a> </div> </article> </footer> </article> <article data-comment-user-id="0" id="comment-830238" class="js-comment comment-wrapper clearfix"> <mark class="hidden" data-comment-timestamp="1451482411"></mark> <div class="well"> <strong></strong> <div class="field field--name-comment-body field--type-text-long field--label-hidden field--item"><p>"Revolutionary" is like "humorous" - overwhelmingly dependent on the cognitive rules of the person making the judgment. This is why an explained joke cannot be very funny and why, for example, I cannot judge a new, super-conducting epigenetometer as revolutionary. </p> <p>In the cases of both humor and revolution, at least one assumed rule of our cognitive framework must be violated in some way, typically in object categorization. </p> <p>Where we lack such rules, we cannot experience the humor, nor appreciate the surprise factor that triggers SME's in a particular field to broadly agree that X is revolutionary.</p> </div> <drupal-render-placeholder callback="comment.lazy_builders:renderLinks" arguments="0=830238&amp;1=default&amp;2=en&amp;3=" token="6r8wKkrYRLMNf-GL39VOiLyYwGKIxisZCa9jZtmz-_g"></drupal-render-placeholder> </div> <footer> <em>By <span lang="" typeof="schema:Person" property="schema:name" datatype="">Buck Field (not verified)</span> on 30 Dec 2015 <a href="https://www.scienceblogs.com/taxonomy/term/17/feed#comment-830238">#permalink</a></em> <article typeof="schema:Person" about="/user/0"> <div class="field field--name-user-picture field--type-image field--label-hidden field--item"> <a href="/user/0" hreflang="und"><img src="/files/styles/thumbnail/public/default_images/icon-user.png?itok=yQw_eG_q" width="100" height="100" alt="User Image" typeof="foaf:Image" class="img-responsive" /> </a> </div> </article> </footer> </article> <article data-comment-user-id="0" id="comment-830239" class="js-comment comment-wrapper clearfix"> <mark class="hidden" data-comment-timestamp="1451490725"></mark> <div class="well"> <strong></strong> <div class="field field--name-comment-body field--type-text-long field--label-hidden field--item"><blockquote><p>There’s little, if any, “real world” about evolutionary developmental biology.</p></blockquote> <p>Thousands of scientists around the world, and hundreds of thousands of research articles, show that you are wrong.</p> <p>But, since you've never opened a science book, choosing to play the typical lying creationist, your latest blatantly false post is no surprise.</p> </div> <drupal-render-placeholder callback="comment.lazy_builders:renderLinks" arguments="0=830239&amp;1=default&amp;2=en&amp;3=" token="h1hVcDEocy1v2hhwBK2RuiNyD7LvTzKDMrgN9Pbd9WY"></drupal-render-placeholder> </div> <footer> <em>By <span lang="" typeof="schema:Person" property="schema:name" datatype="">dean (not verified)</span> on 30 Dec 2015 <a href="https://www.scienceblogs.com/taxonomy/term/17/feed#comment-830239">#permalink</a></em> <article typeof="schema:Person" about="/user/0"> <div class="field field--name-user-picture field--type-image field--label-hidden field--item"> <a href="/user/0" hreflang="und"><img src="/files/styles/thumbnail/public/default_images/icon-user.png?itok=yQw_eG_q" width="100" height="100" alt="User Image" typeof="foaf:Image" class="img-responsive" /> </a> </div> </article> </footer> </article> </section> <ul class="links inline list-inline"><li class="comment-forbidden"><a href="/user/login?destination=/pharyngula/2015/12/29/evo-devo-in-the-real-world%23comment-form">Log in</a> to post comments</li></ul> Tue, 29 Dec 2015 20:41:59 +0000 pharyngula 14208 at https://www.scienceblogs.com An honest appraisal of evo devo https://www.scienceblogs.com/pharyngula/2015/12/28/an-honest-appraisal-of-evo-devo <span>An honest appraisal of evo devo</span> <div class="field field--name-body field--type-text-with-summary field--label-hidden field--item"><p class="lead">In a review of a new book edited by Alan Love, <i>The evolution of “evo-devo”</i>, Adam Wilkins makes a few telling criticisms of the sub-field I enjoy.</p> <blockquote><p>Evo-devo has come a long way since 1981 though the Dahlem Conference laid some of the important groundwork for what followed and was, indeed, widely appreciated as having done so. Yet, troublingly, the field remains, for many evolutionary biologists, something of a side-show, a “boutique” subject within evolutionary biology as a whole. Several of us, in the 1990s, warned that this might happen. This is in contrast to some of the early expectations, which involved positing a coming central role for this discipline within evolutionary biology as a whole. A few of the contributors evidently feel that it has achieved such a position but I think that a broad survey within biology would reveal that not to be the case. If it failed to develop its full potential, why? Opinions will vary but my own hunch is that <b>one factor is that the field has largely avoided incorporating much of the rich material that developmental genetics offers for understanding developmental and morphological change</b>. The one general concession to such genetics, noted in passing in one of the chapters, is the insistence that most developmental change in evolution involves alterations in cis-regulatory elements for regulatory genes. There is, of course, good evidence for this but it is not the whole story and ignores both other mechanisms and the possible dynamics of the incorporation of such change in populations. That last thought, however, introduces what is, in my view, the second weakness of the field: <b>evo-devo remains largely a zone devoid of population thinking</b>. The great strength of classical evolutionary biology was that it focused on the nature of transformation of populations over time – both genetically and phenotypically – and provided a crude general mechanism for understanding such transformations. Its corresponding failing was that it largely ignored the details of the source materials for such change. Evo-devo's main strength and weakness are just the reverse. These reciprocal differences in emphasis amount to perceptual and intellectual differences about what is important in considering evolutionary change. Such differences in attitude continue to create a divide between evo-devo and classical evolutionary biology. This volume does not address this issue at all and I think that is a regrettable omission.</p> </blockquote> <p>I've highlighted the two key points, although I think they're both rooted in the same problem. 1) I think there is a superficial focus on developmental genetics, but what we're missing is the experimental perspective. 2) True enough that there is a lack of population studies (I can think of the stickleback work on recent evolution of small populations as a counter-example), but there the problem is that if you're focusing on the great grand questions of evolution, like <a href="http://freethoughtblogs.com/pharyngula/2015/12/28/building-a-chordate-the-notochord/">where the notochord came from</a>, you're simply not going to find much variation within extant groups. All fish have notochords. All zebrafish populations have notochords. You're just not going to have any material to work with if you try to study how the expression of notochords vary in a population that is over half a billion years removed from an ancestral population that <em>did</em> have interesting differences in a nascent structure.</p> <p>The key problem is that the field has long been interested in morphological and molecular differences at the phylum and class level. What we need to do is ask <em>better questions</em> that are appropriate on a smaller scale, and are more amenable to experiment and genetic analysis. Narrow the scope, more work on differences in fruit fly wings and in the circuitry of tissue specification in closely related species of echinoderms, for instance.</p> <p>Of course, the appeal of evo-devo is often in those gigantic huge intractable questions that involve comparing fruit flies and echinoderms. Evo-devo without the grandiosity is harder to market.</p> <hr /> <p class="ref">Wilkins AS (2015) The evolution of “evo-devo”. BioEssays 37(12):1258–1260.</p> </div> <span><a title="View user profile." href="/pharyngula" lang="" about="/pharyngula" typeof="schema:Person" property="schema:name" datatype="">pharyngula</a></span> <span>Mon, 12/28/2015 - 16:01</span> <div class="field field--name-field-blog-tags field--type-entity-reference field--label-inline"> <div class="field--label">Tags</div> <div class="field--items"> <div class="field--item"><a href="/tag/development" hreflang="en">development</a></div> <div class="field--item"><a href="/tag/evolution" hreflang="en">evolution</a></div> </div> </div> <section> <article data-comment-user-id="0" id="comment-830234" class="js-comment comment-wrapper clearfix"> <mark class="hidden" data-comment-timestamp="1451344255"></mark> <div class="well"> <strong></strong> <div class="field field--name-comment-body field--type-text-long field--label-hidden field--item"><p>“I’ve highlighted the two key points, although I think they’re both rooted in the same problem. 1) I think there is a superficial focus on developmental genetics, but what we’re MISSING is the EXPERIMENTAL perspective…<br /> What we need to do is ask better questions that are appropriate on a smaller scale, and are more amenable to EXPERIMENT and genetic analysis. Narrow the scope, more work on differences in fruit fly wings…”</p> <p>I’ll highlight three points:</p> <p>1)Yes, you’re MISSING EXPERIMENTAL perspective to support evolutionary theory,<br /> 2)You’re also missing OBSERVATIONAL perspective (i.e. SEEING evo IN ACTION),<br /> 3)You need a lot more than “differences in fruit fly wings”. You need how a fruit fly becomes, say, a fruit bat.</p> <p>You're 0-for-3.<br /> …………….<br /> Ethan Siegel recently titled a blog “Why String Theory Is Not A Scientific Theory.”<br /> Given the above, I propose Evolution Theory Is Not A Scientific Theory.</p> </div> <drupal-render-placeholder callback="comment.lazy_builders:renderLinks" arguments="0=830234&amp;1=default&amp;2=en&amp;3=" token="eosAv1ODI_s42Js2wE6L-wcXcTg5QIK1aRgMWuAUFNE"></drupal-render-placeholder> </div> <footer> <em>By <span lang="" typeof="schema:Person" property="schema:name" datatype="">See Noevo (not verified)</span> on 28 Dec 2015 <a href="https://www.scienceblogs.com/taxonomy/term/17/feed#comment-830234">#permalink</a></em> <article typeof="schema:Person" about="/user/0"> <div class="field field--name-user-picture field--type-image field--label-hidden field--item"> <a href="/user/0" hreflang="und"><img src="/files/styles/thumbnail/public/default_images/icon-user.png?itok=yQw_eG_q" width="100" height="100" alt="User Image" typeof="foaf:Image" class="img-responsive" /> </a> </div> </article> </footer> </article> <article data-comment-user-id="0" id="comment-830235" class="js-comment comment-wrapper clearfix"> <mark class="hidden" data-comment-timestamp="1451356030"></mark> <div class="well"> <strong></strong> <div class="field field--name-comment-body field--type-text-long field--label-hidden field--item"><p>sn, your three points are uniformly false - but since you intentionally refuse to educate yourself and choose to blatantly lie, this is no surprise. </p> <p>"How a fruit fly becomes a fruit bat"? Really - that level of stupidity would be astounding coming from anyone but you (it's par for the course for you.)</p> </div> <drupal-render-placeholder callback="comment.lazy_builders:renderLinks" arguments="0=830235&amp;1=default&amp;2=en&amp;3=" token="uy_Q1yzuexSOWiUf3ZW9xFlaBSsmu_uUuobcnVq2BR0"></drupal-render-placeholder> </div> <footer> <em>By <span lang="" typeof="schema:Person" property="schema:name" datatype="">dean (not verified)</span> on 28 Dec 2015 <a href="https://www.scienceblogs.com/taxonomy/term/17/feed#comment-830235">#permalink</a></em> <article typeof="schema:Person" about="/user/0"> <div class="field field--name-user-picture field--type-image field--label-hidden field--item"> <a href="/user/0" hreflang="und"><img src="/files/styles/thumbnail/public/default_images/icon-user.png?itok=yQw_eG_q" width="100" height="100" alt="User Image" typeof="foaf:Image" class="img-responsive" /> </a> </div> </article> </footer> </article> </section> <ul class="links inline list-inline"><li class="comment-forbidden"><a href="/user/login?destination=/pharyngula/2015/12/28/an-honest-appraisal-of-evo-devo%23comment-form">Log in</a> to post comments</li></ul> Mon, 28 Dec 2015 21:01:11 +0000 pharyngula 14207 at https://www.scienceblogs.com Building a chordate: the notochord https://www.scienceblogs.com/pharyngula/2015/12/28/building-a-chordate-the-notochord <span>Building a chordate: the notochord</span> <div class="field field--name-body field--type-text-with-summary field--label-hidden field--item"><p><a href="http://scienceblogs.com/pharyngula/files/2015/12/pmn.jpg"><img src="http://scienceblogs.com/pharyngula/files/2015/12/pmn-96x150.jpg" alt="pmn" width="96" height="150" class="alignright size-thumbnail wp-image-17350" /></a><br /> </p><p class="lead">I know this is a horrible photo -- I just snapped a picture of the journal hardcopy, which I own, instead of grabbing a PDF from the web, because it's from 1985 and I'd have to pay to get a copy of my own paper -- but this is what I was doing in grad school. I started as somebody who was interested in neurons and the nervous system, so what you're seeing is a transverse section of the spinal cord of a zebrafish, with a couple of motoneurons labeled black with a tracer enzyme. I spent most of my time teasing apart how those cells grew and made connections.</p> <p>But all the while there was this one prominent feature of the animal that kept trying to distract me. See that big clear white space below the spinal cord? That's the notochord. It's huge, a long transparent cylinder built like a stack of glass coins, running from the neighborhood of the hindbrain all the way back to the tip of the tail. The image from Stemple () below is much clearer, since the notochord has been painted pink.</p> <p><a href="http://scienceblogs.com/pharyngula/files/2015/12/pinknoto.jpg"><img src="http://scienceblogs.com/pharyngula/files/2015/12/pinknoto-500x186.jpg" alt="pinknoto" width="500" height="186" class="aligncenter size-large wp-image-17351" /></a></p> <p>Its superficial function is obvious: it's a springy rod that the muscles of the fish's body act upon for swimming and escape behaviors. While I was just doing neural circuitry work, that was sufficient -- it's part of the motor apparatus. Neurons make muscles twitch which flexes the notochord and generates the back and forth motion that propels the animal through the water. Case solved.</p> <p>Except…you can't think of the notochord all by itself. Fish don't flex vertically, they undulate laterally, and that implies auxiliary structures have to be present in order to constrain vertical movement. In particular, on top of the notochord is a specific part of the spinal cord, the floorplate, and beneath the notochord is another fibrous tissue, the hypochord. Together, these help constrain the movement of the animal for swimming.</p> <p><a href="http://scienceblogs.com/pharyngula/files/2015/12/floorhypo.jpg"><img src="http://scienceblogs.com/pharyngula/files/2015/12/floorhypo-500x361.jpg" alt="floorhypo" width="500" height="361" class="aligncenter size-large wp-image-17352" /></a></p> <p>I can't describe it any better than Stemple did, so I'm stealing this:</p> <blockquote><p>To understand notochord structure, it is helpful to consider the notochord as part of a mechanical system required for locomotion (Fig. 4). Zebrafish embryos, for example, are able to flip their tails within 1 day of fertilisation, and hatch and swim within 3 days. By analogy, the notochord is like a fire hose, possessing a strong but flexible sheath that can resist high hydrostatic pressures. Consider then a situation in which the fire hose is filled with water balloons, each pushing against the other and against the sheath. In such an arrangement, the fire hose would be elongated and stiff, but able to bend in any direction. Finally, with cables running along the top and bottom of the inflated fire hose, the cables would resist any upward or downward bending of the hose, and any force acting on the fire hose would deflect it laterally. For the zebrafish embryo, the equivalent of the fire hose is the peri-notochordal basement membrane and the water balloons are the vacuolated notochord cells. Running along the top of the notochord is the floor plate and along the bottom is the hypochord. Consistent with this structural role, both the floor plate and the hypochord express a variety of cartilage proteins, such as type II collagen. In addition, mutations in genes such as oep and cyclops, which lead to substantial loss of floor plate, also produce embryos with a profound downward curvature. Thus, although not yet directly established, it is possible that the floor plate and hypochord act as cables on the respective dorsal and ventral sides of the notochord.</p> </blockquote> <p>But wait! There's so much more. The notochord isn't just a mechanical structure, it's also a source of inductive signals that tell the spinal cord to form neurons. The first growth cones -- the motile tip of a growing neuron -- emerge where the spinal cord meets the notochord, and they creep along the surface of the notochord before charging off into the muscles. If I wanted to know how the nervous system builds that circuitry I was studying, I should look further into interactions with that long rod.</p> <p>Also, I was beginning to appreciate the importance of the notochord to <em>everything</em>. In gastrulation, it's those first cells that tuck in and migrate into the interior of the animal that are going to form axial mesoderm, which will eventually form the notochord. Oh, what a devious structure: it got me thinking about things other than the nervous system that develop, as well as appreciating how development is an integrative process that can't actually be thoroughly understood by examining organs in isolation.</p> <p>The floorplate is induced by the notochord -- that is, chemical signals from the notochord instruct cells of the nervous system to differentiate into the floorplate. The notochord also instructs mesoderm to make the horizontal septum, the seam between dorsal and ventral blocks of muscle that runs the length of the animal. And then floorplate in turn signals to other cells in the spinal cord to differentiate into motoneurons, and interactions at the horizontal septum trigger formation of fast and slow muscles in the periphery. Basically, every thing I was studying was a product of negotiations in development between the notochord and nerves or muscle.</p> <p>So I have to blame the notochord for my drift from neuroscientist to developmental biologist.</p> <p>There was further wickedness. Notochords are kind of unique to chordates (with qualifications I'll discuss below). All chordates have them, and they're absolutely central to normal development of the organism, but -- shock, horror -- cephalopods don't, and they develop just fine without one. This is actually the subject that first drew me into evolutionary biology, and as a nice side effect, also made me interested in cephalopods and other invertebrates. </p> <p>Because, damn, the deep phylogeny of the notochord is a wicked mess. For a good, brief introduction to the evolutionary history of the notochord, I recommend a recent review by Annona <i>et al.</i>. Basically, in the early 19th century, Cuvier's view that animals could be divided into four grand <i>embranchements</i>, groups that represented distinct body plans, prevailed. The world had the radiates (cnidarians and echinoderms), the articulates (arthropods<br /> and annelids), the molluscs, and the vertebrates, and each had unique features that meant one could not possibly have evolved into another. The vertebrates, for instance, had the notochord, which had no homolog in any other animal, therefore imagining some transitional form between vertebrates and any other of the embranchements was pure folly.</p> <p>Well, that wasn't going to stand. Even in Cuvier's day, Etienne Geoffroy St. Hilaire was speculating about ways arthropods and vertebrates could transform into one another. Then one breach was discovered in Cuvier's scheme: tunicates, which Cuvier had placed in the molluscan embranchement, were discovered to have a notochord in their larval stages, which required a taxonomic scramble to put them in the same phylum with vertebrates, as chordates. During the nineteenth and early twentieth century, there was an almost incomprehensible dash to discover the homolog of the notochord in all kinds of invertebrates. Members of every other embranchement were at some point proposed as the ancestor to the vertebrates: obscure structures, like the stomochord of enterepneusts, were proposed as the precursor to the notochord on the basis of appearance or position in relation to other tissues. Looking back on it, it's almost embarassing how hard scientists struggled to fit weak data and limited character knowledge to an evolutionary model. Just for completeness' sake, here are some diagrams of the various schemes people contrived to generate a vertebrate from an invertebrate.</p> <div style="width: 510px;display:block;margin:0 auto;"><a href="http://scienceblogs.com/pharyngula/files/2015/12/notoevomodels.jpg"><img src="http://scienceblogs.com/pharyngula/files/2015/12/notoevomodels-500x299.jpg" alt="Notochords in phylogeny: invertebrate chordates, annelids, and nemerteans. a Midsagittal section of early neurula of amphioxus with blastopore (bp) and notochord rudiment (nr, horizontal hatching). b Cross section at level indicated by dotted line in a; notochord rudiment (nr) and somites indicated, respectively, by horizontal and diagonal hatching. c Cross section of later neurula of amphioxus showing notochord (no) and dorsal nerve cord (nc); somites indicated by diagonal hatching. d, e Early and late larvae, respectively, of an ascidian tunicate. Cross sections through the tail showing nerve cord (nc); muscles (diagonally hatched) and notochord (no); asterisk indicates endodermal strand (discovered by Seeliger). f, g Inverted annelid scenario (after Semper); following inversion (f looped arrow), fibers (fi) associated with the nerve cord (nc) are precursors of the notochord (no) in g. h, i Variant annelid theory (after Ehlers); annelid after inversion (h, looped arrow), the position of the siphon (si) corresponds to the vertebrate notochord (no) in i. j–n Nemertean scenario (after Hubrecht); gastrula (j) has a first invagination (arrowhead) for gut and a second invagination (arrow) for the proboscis, while mesenchyme cells (mc) ingress into the blastocoel. Subsequently k, a through gut forms from mouth (m) to anus (a), and mesenchyme cells condense around the proboscis (pr). l Schizocoely produces a proboscis coelom (prc) and a proboscis sheath (prs). The arrow in m indicates the proboscis (pr) pulling out of the proboscis coelom (prc), leaving behind a few mesenchyme cells. In n, the mesenchyme cells in the proboscis coelom have extensively proliferated to form the notochord (no); the remains of the proboscis have become the anterior pituitary (ap), while the dorsal nerve cord (nc) has formed by the dorsal migration and fusion of the lateral nerve cords. " width="500" height="299" class="size-large wp-image-17353" /></a> Notochords in phylogeny: invertebrate chordates, annelids, and nemerteans. a Midsagittal section of early neurula of amphioxus with blastopore (bp) and notochord rudiment (nr, horizontal hatching). b Cross section at level indicated by dotted line in a; notochord rudiment (nr) and somites indicated, respectively, by horizontal and diagonal hatching. c Cross section of later neurula of amphioxus showing notochord (no) and dorsal nerve cord (nc); somites indicated by diagonal hatching. d, e Early and late larvae, respectively, of an ascidian tunicate. Cross sections through the tail showing nerve cord (nc); muscles (diagonally hatched) and notochord (no); asterisk indicates endodermal strand (discovered by Seeliger). f, g Inverted annelid scenario (after Semper); following inversion (f looped arrow), fibers (fi) associated with the nerve cord (nc) are precursors of the notochord (no) in g. h, i Variant annelid theory (after Ehlers); annelid after inversion (h, looped arrow), the position of the siphon (si) corresponds to the vertebrate notochord (no) in i. j–n Nemertean scenario (after Hubrecht); gastrula (j) has a first invagination (arrowhead) for gut and a second invagination (arrow) for the proboscis, while mesenchyme cells (mc) ingress into the blastocoel. Subsequently k, a through gut forms from mouth (m) to anus (a), and mesenchyme cells condense around the proboscis (pr). l Schizocoely produces a proboscis coelom (prc) and a proboscis sheath (prs). The arrow in m indicates the proboscis (pr) pulling out of the proboscis coelom (prc), leaving behind a few mesenchyme cells. In n, the mesenchyme cells in the proboscis coelom have extensively proliferated to form the notochord (no); the remains of the proboscis have become the anterior pituitary (ap), while the dorsal nerve cord (nc) has formed by the dorsal migration and fusion of the lateral nerve cords. </div> <p>Don't think about it too hard. You'll go mad.</p> <p>The definitive answer is not going to be determined by embryological morphology. The notochord is a structure that is strongly tied into the development of many tissues, so what we need to look at is gene regulatory networks -- are there homologous patterns of gene activity in any of the hypothesized invertebrate homologs? And the answer so far is…no. In particular, one of the defining genes expressed in the vertebrate notochord is a transcription factor called <i>Brachyury</i>, also known as T in mice. None of the putative homologs express <i>Brachyury</i>, which suggests that any other regulatory genes are going to be irrelevant, as far as notochord fate goes.</p> <p>That's why I told you not to think too hard about that complicated diagram above. A lot of old models are being rendered obsolete by new molecular data.</p> <p>That leaves us with an extremely interesting idea, that the notochord actually was a completely novel innovation in chordate evolution. Some peculiar population of Precambrian worms acquired a mutation that, for instance, coupled <i>Brachyury</i> expression to a band of early endomesoderm, which in turn caused vacuolation of the roof of the archenteron, pushing out a subpopulation of cells to form a tail, and it was good, and they thrived with this new springy tail.</p> <p>You might have some reservations about that, if you're concerned about where these genes came from. The thing is, <i>Brachyury</i> is really old, and is found in all of Cuvier's embranchements. Its initial role seems to have been in defining the location of the blastopore, which led to further roles in specifying the body axis, and then, in vertebrates, was drafted into specific jobs regulating mesoderm.</p> <div style="width: 510px;display:block;margin:0 auto;"><a href="http://scienceblogs.com/pharyngula/files/2015/12/brachyuryEvo.jpg"><img src="http://scienceblogs.com/pharyngula/files/2015/12/brachyuryEvo-500x355.jpg" alt="Scenario of the role of Brachyury during key events in animal evolution: emergence of the first body axis, the second body axis and the third germ layer, the mesoderm. Arrows intend to indicate that molecules implicated in these transitions were present before in a different context and that these transitions were brought about by inventing and recruiting developmental control genes to specific body regions or functions. These events might have occurred independently for the three major steps or, more likely, they may have been linked to and facilitate each other. Drawings represent gastrulae or post-gastrula larvae of different organisms. Brachyury expression is indicated in blue, presumptive mesoderm that overlaps with Brachyury expression regions in red hatched lines. Orientation is indicated by foregut (Fg) and hindgut (Hg). Other abbreviations: VCM, visceral cauddal mesoderm; AM, axial mesoderm. " width="500" height="355" class="size-large wp-image-17354" /></a> Scenario of the role of Brachyury during key events in animal evolution: emergence of the first body axis, the second body axis and the third germ layer, the mesoderm. Arrows intend to indicate that molecules implicated in these transitions were present before in a different context and that these transitions were brought about by inventing and recruiting developmental control genes to specific body regions or functions. These events might have occurred independently for the three major steps or, more likely, they may have been linked to and facilitate each other. Drawings represent gastrulae or post-gastrula larvae of different organisms. Brachyury expression is indicated in blue, presumptive mesoderm that overlaps with Brachyury expression regions in red hatched lines. Orientation is indicated by foregut (Fg) and hindgut (Hg). Other abbreviations: VCM, visceral cauddal mesoderm; AM, axial mesoderm. </div> <p>So what was involved was not crafting a whole new assortment of functions, but wiring an existing gene into a network, where it then generated novel tissues. This is exactly why it's not at all surprising that such different organisms as annelid worms, arthropods, and vertebrates share so many similar genes, yet have such different morphologies: what matters is how the building blocks of the genome interact with one another, so we can get different forms by changing switches.</p> <hr /> <p class="ref">Annona G, Holland ND, D'Aniello S (2015) Evolution of the notochord. Evodevo 6:30.</p> <p class="ref">Stemple DL (2005) Structure and function of the notochord: an essential organ for chordate development. Development 132(11):2503-12.</p> <p class="ref">Technau U (2001) Brachyury, the blastopore and the evolution of the mesoderm. Bioessays 23(9):788-94.</p> </div> <span><a title="View user profile." href="/pharyngula" lang="" about="/pharyngula" typeof="schema:Person" property="schema:name" datatype="">pharyngula</a></span> <span>Mon, 12/28/2015 - 08:11</span> <div class="field field--name-field-blog-tags field--type-entity-reference field--label-inline"> <div class="field--label">Tags</div> <div class="field--items"> <div class="field--item"><a href="/tag/development" hreflang="en">development</a></div> <div class="field--item"><a href="/tag/evolution" hreflang="en">evolution</a></div> <div class="field--item"><a href="/tag/neurobiology" hreflang="en">neurobiology</a></div> </div> </div> <div class="field field--name-field-blog-categories field--type-entity-reference field--label-inline"> <div class="field--label">Categories</div> <div class="field--items"> <div class="field--item"><a href="/channel/brain-and-behavior" hreflang="en">Brain and Behavior</a></div> </div> </div> <section> </section> <ul class="links inline list-inline"><li class="comment-forbidden"><a href="/user/login?destination=/pharyngula/2015/12/28/building-a-chordate-the-notochord%23comment-form">Log in</a> to post comments</li></ul> Mon, 28 Dec 2015 13:11:07 +0000 pharyngula 14206 at https://www.scienceblogs.com