MedWorm Tags: evolution

Scientists Study The Shape Of The Nose And Its Relationship With Climate

Better Health — Sun, 28 Aug 2011 12:00:00 +0100

The basic function of the human nose is to warm and humidify the air before it reaches the lungs. Because of the wide variation of human habitats from the polar cold and dry air to the equatorial hot and humid weather, one would expect the nose to accommodate to these climate extremes accordingly through evolutionary pressures. In essence, logically one would expect the nose to change shape to enhance time that air is in contact with the warm and moist nasal interior in cold and dry climates compared to the opposite environmental extreme. German scientists evaluated this hypothesis through (more…) *This blog post was originally published at Fauquier ENT Blog* (Source: Better Health)

One Fungus, One Name

Fungal Genomes and Comparative Genomics — Tue, 09 Aug 2011 02:29:17 +0100

The naming of organisms is an important part of how we communicate. When a fungus is found, be it a mycelium from a rotting fruit, a mushroom from the forest, or something growing on a petri dish, we have used morphological and other phenotypic characteristics to group them together and identify if it is an already known species or a new one. However, some fungi have very different shapes and forms that occur during asexual and sexual (after mating with a partner) stages, some incredible elaborate and even (to some people) beautiful. Because these stages mean that fungi can look very different, and often these fungi are not amenable to life in the laboratory (e.g. we can’t get it to complete the lifecycle in an petri dish in the lab), it was the case that observed asexual (or anamorp...

Mass General sanctions Joseph Biederman, Thomas Spencer and Timothy Wilens:violating hospital ethics guidelines for non-disclosure of pharma income

soulful sepulcher — Fri, 01 Jul 2011 21:26:00 +0100

(Source: soulful sepulcher)

"Why Neuroscience Matters"

the Brain Science Podcast and Blog with Dr. Ginger Campbell — Sat, 25 Jun 2011 12:00:30 +0100

On May 11, 2011 Ginger Campbell, MD gave a talk entitled "Why Neuroscience Matters" at the London Skeptics in the Pub. Episode 42 of Books and Ideas is an edited version of that talk, including the lively Q and A with the audience. Listen to Episode 42 of Books and Ideas Free Episode Transcript (Download PDF) Subscribe to Books and Ideas Podcast: References Bayes, A., Grant, S., et al. "Characterization of the proteome, diseases and evolution of the human postsynaptic density." Nature Neuroscience 14, 19–21 (2011) (Published online 12/23/2010). Libet, B. "Do We Have Free Will?" Journal of Consciousness Studies, 6. No. 8-9, 1999, pp. 47-57. On Being Certain: Believing You Are Right Even When You're Not (2008) by Robert Burton; p 127. Philosophy in t...

Miss USA Contestants: America in Glamourcosm?

Cato-at-liberty — Tue, 21 Jun 2011 13:31:25 +0100

By Neal McCluskeyA rabid fan of both Cato’s Center for Educational Freedom and The Miss USA Pageant (some may know him as Jim Harper) just sent me a link to this YouTube video. In the vid, all the contestants in the just-completed, aforementioned pageant discuss whether the theory of evolution should be taught in schools. I didn’t tally their responses, but just listening to the contenders it seems their consensus answer represents America in microcosm: Most seem to have serious doubts about evolution, but support teaching it along with other viewpoints. It reflects both the overall split within the American public—40 to 50 percent of Americans are creationists, and roughly the same segment evolutionists—as well as the consensus view on teaching human origins: ...

Still time to sign up for EMBO Comparative Genomics meeting

Fungal Genomes and Comparative Genomics — Mon, 20 Jun 2011 20:18:12 +0100

[via Teun Boekhout] This year looks like another great lineup of speakers for the EMBO Comparative Genomics of Microorganisms: ‘Understanding the Complexity of Diversity’ 15-20 Oct 2011 Sant Feliu de Guixols, Spain. Andrew Allen J. Craig Venter Institute US Anders Blomberg Göteborg University SE Chris Bowler École Normale Supérieure FR Gertraud Burger University of Montreal CA Bernard Dujon Institut Pasteur FR Toni Gabaldón CRG, Barcelona ES Ursula Goodenough Washington University US Michael Gray Dalhousie University CA Joseph Heitman Duke University US Christiane Hertz-Fowler University of Liverpool UK Regine Kahmann Max Planck Institute DE Patrick Keeling University of British Columbia CA Nicole King UC, Berkeley US Edda Klipp Humboldt Univers...

We Each Have About 60 Unique Genetic Mutations

FuturePundit — Mon, 13 Jun 2011 23:00:00 +0100

You are a mutant. Don't deny it. Accept your role in the mutant horde. Each one of us receives approximately 60 new mutations in our genome from our parents. This striking value is reported in the first-ever direct measure of new mutations coming from mother and father in whole human genomes published today. For the first time, researchers have been able to answer the questions: how many new mutations does a child have and did most of them come from mum or dad? The researchers measured directly the numbers of mutations in two families, using whole genome sequences from the 1000 Genomes Project. The results also reveal that human genomes, like all genomes, are changed by the forces of mutation:... (Source: FuturePundit)

TWiM 8: Live in NOLA

virology blog — Fri, 03 Jun 2011 14:21:49 +0100

Hosts: Vincent Racaniello, Michael Schmidt, Stan Maloy, Andreas Baümler, Nicole Dubilier, and Paul Rainey. Vincent, Michael, and Stanley recorded episode #8 of the podcast This Week in Microbiology live at the 2011 ASM General Meeting in New Orleans, with guests Andreas Baümler, Nicole Dubilier, and Paul Rainey. They spoke about how pathogens benefit from disease, symbioses between chemosynthetic bacteria and marine invertebrates, and repetitive sequences in bacteria. Click the arrow above to play, or right click to download TWiM #8 (60 MB, .mp3, 87 minutes). Subscribe to TWiM (free) on iTunes, Zune Marketplace, via RSS feed, by email or listen on your mobile device with the Microbeworld app. Links for this episode: Salmonella invasion from the gut lumen into tissues (PLoS Pathogens)...

The Rap Guide to Evolution

Dr Shock MD PhD — Wed, 25 May 2011 05:57:16 +0100

is a hip-hop exploration of modern biology, created by Canadian rap artist Baba Brinkman. The project owes its origins to the geneticist Dr. Mark Pallen, who specially requested “a rap version of the Origin of Species” for Charles Darwin’s 200th birthday in 2009. Baba went on to perform the show to critical acclaim at the Edinburgh Fringe Festival and off-Broadway in New York. The music videos and teaching resources on this site were developed with the support of the Wellcome Trust, in partnership with London’s SPL Productions. Find out more, more videos on this site. Thanks Scope No related posts. (Source: Dr Shock MD PhD)

The Natural Evolution Of Science: As Knowledge Grows, Treatments Change

Better Health — Tue, 26 Apr 2011 13:00:00 +0100

I read with interest a blog post by Robert Krulwich of NPR fame on why there is so much public resistance to accept changes in truth with new scientific discoveries (some of which was new to even me)… 1) Triceratops with their beautifully placed 3 horns is actually the teenage dinosaur version of the adult Torosaurus (who had ugly asymmetric horns). Now… a decision had to be made regarding which name to stick with. Ultimately, “Triceratops” won out, perhaps because of the “Save the Triceratops” Facebook page??? 2) The same unfortunately is not true for the Brontosaurus. It was clear that Apatosaurus is the same dinosaur and as such, the “Brontosaurus” name is no more much to the dismay of many lay public… (more…) *This b...

Discovering the Ocean’s Microscopic World

blog.hippokranet.eu — Sun, 24 Apr 2011 14:06:04 +0100

Watch this AMNH Bio Bulletin and NYT Slideshow to learn more about the Census of Marine Life. (Source: blog.hippokranet.eu)

Evolution of human ‘super-brain’ tied to development of bipedalism, tool-making

Biosingularity — Fri, 22 Apr 2011 15:02:06 +0100

Scientists seeking to understand the origin of the human mind may want to look to honeybees — not ancestral apes — for at least some of the answers, according to a University of Colorado Boulder archaeologist. CU-Boulder Research Associate John Hoffecker said there is abundant fossil and archaeological evidence for the evolution of the human [...] (Source: Biosingularity)

Five feisty science books on David’s desk

Sciencebase Science Blog — Sat, 16 Apr 2011 16:00:33 +0100

Five super science books landed on my desk during the last week or two, everything from a Haynes manual for the Space Shuttle to hacking life and from astrobiology to the discovery of Lucy by way of the fact of evolution. The Fact of Evolution – Opponents of evolution are wont to say it's "just" a theory, as if that somehow implies it's a fiction or not proven. Scientists often dislike talking in plain or making absolute, definitive statements. But, science writers and some scientists really don't mind telling it like it is. Forget the wishy-washy word "theory" with its non-scientific baggage, this is the Fact of Evolution. The onus is on opponents to prove otherwise by coming up with evidence for their own "theory". Biopunk: DIY Scientis...

Tips To Start Journaling

World of Psychology — Mon, 04 Apr 2011 16:39:01 +0100

Journaling — the act of writing things down somewhere (where doesn’t really matter) — has many benefits. Here’s an important one: “It’s not in the rereading that one finds solace but in the writing itself. It’s like crying—you don’t know why, but you feel so much better afterward. Everything pours, streams, flows, out of you aimlessly,” writes Samara O’Shea in her beautifully written book Note to Self: On Keeping A Journal And Other Dangerous Pursuits. Here’s another: Journaling is a profound — and simple — way to get to know yourself better. To figure out what makes you tick. What makes you happy. What makes you defensive. What makes you giggle or grateful or grieve. What makes you who you are. Quite simply, it’s a grea...

A fix of five fresh science stories

Sciencebase Science Blog — Sat, 26 Mar 2011 18:00:04 +0100

Incognito – If the conscious mind – the part you consider you – is just the tip of the iceberg, what is the rest doing? In this sparkling and provocative new book, renowned neuroscientist David Eagleman navigates the depths of the subconscious brain to illuminate surprising mysteries. (9781847679383): David Eagleman Biopunk: DIY Scientists Hack the Software of Life – The most revolutionary discoveries in science and technology often emerge from out-of-the-way places, forged by brilliant outsiders with few resources besides boundless energy and great ideas. That describes the "biohacking" movement now in its early, heady days. In the next few years, companies will start selling libraries of genetic LEGOs that amateur scientists will use to build ...

Why Everyone’s a Hypocrite

Channel N — Tue, 22 Mar 2011 21:24:02 +0100

Are We All Hypocrites? The author of the new book Why Everyone (Else) Is a Hypocrite: Evolution and the Modular Mind gives an accessible talk on his area of expertise, evolutionary psychology and hypocrisy. (Source: Channel N)

Evolution of intelligence at Cogn-IQ blog

Intelligent Insights on Intelligence Theories and Tests (aka IQ's Corner) — Sat, 26 Feb 2011 16:57:00 +0100

Bob Williams has authored an interesting article on the evolution of human intelligence over on the Cogn-IQ blog.- iPost using BlogPress from my Kevin McGrew's iPadintelligence IQ tests IQ testing IQ scores CHC intelligence theory CHC theory Cattell-Horn-Carroll human cognitive abilities psychology school psychology individual differences cognitive psychology neuropsychology psychology special education educational psychology psychometrics psychological assessment psychological measurement IQs Corner neuroscience evolution Generated by: Tag Generator (Source: Intelligent Insights on Intelligence Theories and Tests (aka IQ's Corner))

I Said Believe!

Cato-at-liberty — Mon, 31 Jan 2011 19:43:39 +0100

By Neal McCluskeySince its beginning, one of the primary drivers behind public schooling — government schooling — has been a desire to compel belief, whether in “American” values, God, the primacy of science, or myriad other things that some people have thought it essential for all people to accept. The result has been constant conflict that, rather than uniting diverse people — a companion goal of public schooling — has divided them. And not only have crusades to force belief created ongoing conflicts, there’s generally been little evidence they’ve actually changed the targeted beliefs. So we’ve gotten all the downside of trying to force alterations to hearts and minds without actually changing them. Case in point, t...

Rap Guide to Evolution

Dr Shock MD PhD — Sat, 08 Jan 2011 06:30:55 +0100

The Rap Guide to Evolution is Baba Brinkman’s comedy rap science show and full-length album, winner of the Scotsman Fringe First Award for outstanding new writing at the 2009 Edinburgh Fringe. The Rap Guide uses hip-hop music and culture to communicate concepts from modern evolutionary theory. A grant from the Wellcome Trust has provided the initial funding to make 12 rap music videos based on the album tracks, making sense of artificial selection, sexual selection, unity of common descent, the evolution of aggression and altruism, and much more. No related posts. (Source: Dr Shock MD PhD)

Hollywood Boost for Evolutionary Medicine?

Life in the Fast Lane — Wed, 29 Dec 2010 06:10:04 +0100

The LITFL team hopes a new movie about the life of Charles Darwin will help raise the profile of evolutionary medicine. (Source: Life in the Fast Lane)

Presents for the holidays – Plant pathogen genomes

Fungal Genomes and Comparative Genomics — Thu, 23 Dec 2010 16:11:50 +0100

Though a bit cliche, I think the metaphor of “presents under the tree” of some new plant pathogen genomes summarized in 4 recent publications is still too good to resist. There are 4 papers in this week’s Science that will certainly make a collection of plant pathogen biologists very happy. There are also treats for the general purpose genome biologists with descriptions of next generation/2nd generation sequencing technologies, assembly methods, and comparative genomics. Much more inside these papers than I am summarizing so I urge you to take look if you have access to these pay-for-view articles or contact the authors for reprints to get a copy. These include the genome of biotrophic oomycete and Arabidopsis pathogen Hyaloperonospora arabidopsidis (Baxter et al). Wh...

Science sightings from sciencebase

Sciencebase Science Blog — Thu, 18 Nov 2010 10:00:05 +0100

My latest science news updates First stem cell trial in stroke patient, how did the media do – In its regular assessment and critique of reporting on medical happenings, NHS Choices looked at the recent early test of stem cell therapy for a stroke victim and reports (amazingly) that "In general, the media coverage has been accurate." Sex and CERN and Rock ‘n Roll – Forget mini Big Bangs, benchtop black holes and the God particle, scientists at CERN are releasing an album called Resonance Music from their LHC Atlas Experiment. You'll have to ask them if the first bit of my title is relevant or not. Brain size and a trip to Disneyland – Could the enormous relative size and complexity of the human brain be explained by that trip to Disneyland your paren...

TWiV 107: Warning – this virus contains email

virology blog — Mon, 15 Nov 2010 02:46:32 +0100

Hosts: Vincent Racaniello, Dickson Despommier, Alan Dove, and Rich Condit On episode #107 of the podcast This Week in Virology, Vincent, Dickson, Alan, and Rich answer listener questions about poliovirus, social media, dengue, influenza, evolution, gel filtration, and much more. Download TWiV #107 (68 MB .mp3, 94 minutes) Subscribe to TWiV (free) in iTunes , at the Zune Marketplace, by the RSS feed, or by email, or listen on your mobile device with Stitcher Radio. Links for this episode: tre recombinase: paper one and two Universal influenza vaccines Mitochondrial and chlorophast phage-type RNA polymerase in plants Protein Data Bank Letters read on TWiV 107 Weekly Science Picks Rich – Protein Synthesis: An epic on the cellular level Dickson – The Patchwork Mouse by Joseph R....

Immune Cells Help Reshape Brain

FuturePundit — Tue, 02 Nov 2010 00:00:00 +0100

Microglia cells helps form connections between neurons. Immune cells known as microglia, long thought to be activated in the brain only when fighting infection or injury, are constantly active and likely play a central role in one of the most basic, central phenomena in the brain the creation and elimination of synapses. The findings, publishing next week in the online, open access journal PLoS Biology, catapult the humble microglia cell from its well-recognized duty of protecting the brain to direct involvement in creating the cellular networks at the core of brain behavior. Its apparent role as an architect of synapses junctions between brain cells called neurons comes as a surprise to researchers long accustomed to thinking of... (Source: FuturePundit)

National Standards to Help Crush Annoying Dissenters

Cato-at-liberty — Mon, 25 Oct 2010 16:58:17 +0100

By Neal McCluskeyOne of the most regrettable outcomes of government schooling is constant, wrenching conflict as diverse people are forced to fight over the uniform school system they all have to support. Sadly — and in complete opposition to the foundational American value of individual liberty — one of the few ways these conflicts can be resolved is by crushing groups with insufficient political power, keeping them from getting the education they want for their children. Unfortunately, making it easier to do exactly that seems to have motivated at least some people in Kansas to support their state’s adoption of federally backed “Common Core” standards. Under the guise of removing politics from public schooling – meaning, crippling the ability of th...

How Will Humans Evolve?

FuturePundit — Sat, 09 Oct 2010 23:00:00 +0100

Alex Tabarrok and Tyler Cowen have been arguing with each other about how humans evolve. Tyler sees better looking people who are less creative and less driven. Let us assume that scientific progress continues. My view is that parents don't so much like "difference," unless it is very directly in their favor. Using technology, parents will select for children who are taller, smarter in the way that parents value, better looking, and perhaps also more loyal to their families. The people in the wealthy parts of the world will look more like models and movie stars, but they will be quite recognizable. These children may also be less creative and some of them will be less driven. It's a bit... (Source: FuturePundit)

Popular Misconceptions About Evolution

Life in the Fast Lane — Sun, 26 Sep 2010 00:00:50 +0100

Ask the average lay person what they take the word evolution to mean, and few will reply “the change in the genetic frequency of a population over time”. The lack of understanding can be further evidenced by US figures where only 45% of people hold true the statement “human beings, as we know them, developed from earlier species of animals”. More worrying was a study conducted by the Jewish Theological Seminary and HCD Research in Flemington, New Jersey where 34% of doctors reportedly believed that the Intelligent Design was a superior explanation. (Source: Life in the Fast Lane)

Joseph Biederman and friends defend their agenda: "Pediatric Mental Health Care Dysfunction Disorder?" Letter to NEJM

soulful sepulcher — Fri, 17 Sep 2010 15:13:00 +0100

(Source: soulful sepulcher)

A complete summary (probably TMI) about my time at the human #microbiome meeting #HMP2010

The Tree of Life — Mon, 06 Sep 2010 00:23:41 +0100

Well, I am writing this on my flight heading back from St. Louis after going to the "Human Microbiome Research Conference" I have already posted some summaries of the meetings Day 1 and Day 2 and will soon do one about Day 3. And you can find out more about the meeting from multiple other sources such as here, here, here and here. But what I thought I would do here is give some of the story behind the meeting - why I went and what it was like behind the scenes, at least for me. Note - I know this is very long - but hopefully it will give people a feel both for some of the science, some of the behind the scenes, and some of (my) history relating to this meeting. Some prelude to the meeting I headed out to the meeting from Davis on the afternoon on the Mon...

A new kind of monograph – online

Fungal Genomes and Comparative Genomics — Sat, 04 Sep 2010 17:26:24 +0100

A critical part of understanding and documenting the diversity is formal descriptions of species and their relatives. This can be a laborious task and is usually captured in the form of a monograph of a species where a group of species are described in careful detail along with the phylogenetic relationships of them. This has served as the basis for documentation of the the natural history and morphological descriptions of species. The information is typically presented in the form of a book that goes to a library or your shelf which can be pulled down and poured over when trying to determine traits for a group of organisms. Books are great but sharing images and the Ryan Kepler, a PhD student at Oregon State, is writing a monograph about the ever so cool Cordyceps fungi which have ...

Quick blog post: interesting piece on the evolution of ecology by Simon Levin

The Tree of Life — Tue, 10 Aug 2010 16:45:37 +0100

There is a very interesting piece in the Chronicle of Higher Education by Simon Levin on the "Evolution of Ecology." See The Evolution of Ecology - The Chronicle Review - The Chronicle of Higher EducationIn it Simon, who I consider both a friend and colleague and who has been an inspiration to me for much of my work, discusses the history of the concept and the field of ecology. He repeats a key phrase he has used elsewhere:Ecology, the unifying science in integrating knowledge of life on our planet, has become the essential science in learning how to preserve it.I like this phrase and plan to use it a bit here and there, with attribution of course.Levin also discusses how Darwin's Voyage of the Beagle helped launch the field of ecology because it defined a new and synthetic way of looking...

Lack of neutrality in bacteria and where pseudogenes go when they die

The Tree of Life — Tue, 10 Aug 2010 06:51:58 +0100

Pseudogenes, which are in essence regions of the genome that used to be genes but no longer able to produce a functional unit, have long been considered to be models of the genetic equivalent of Switzerland's neutrality. With this assumption of neutrality in hand, researchers have used studies of pseudogenes to better understand what happens to DNA when it is not visible to any form of natural selection. That is, pseudogenes have been thought to be neither harmful (as in, they are not under negative selection) or helpful (i.e., they are not under positive selection).And from this assumption we have supposedly learned about mutation rates and patterns (because if they are neutral then the changes in pseudogenes should be reflective of mutational processes, not selection) as well as all sort...

Evolution and Liberty

Cato-at-liberty — Tue, 13 Jul 2010 16:10:48 +0100

By Jason KuznickiPolitical scientist Larry Arnhart heads this month’s Cato Unbound. He argues that libertarians need to integrate biological evolution into their thinking about human cultures and even politics. More provocatively, he claims that the “a Darwinian science of human evolution supports classical liberalism.” This is the case, he argues, even though market competition differ[s] radically from biological competition. Biological competition is a zero-sum game where the survival of one organism is at the expense of others competing for the same scarce resources. But market competition is a positive-sum game where all the participants can gain from voluntary exchanges with one another. In a liberal society of free markets based on voluntary exchanges, success dep...

Dilution

Medicine and Man — Mon, 12 Jul 2010 18:43:28 +0100

(http://xkcd.com/765/) addthis_url = 'http%3A%2F%2Fmedicineandman.com%2Fblog%2F2010%2F07%2F12%2Fdilution%2F'; addthis_title = 'Dilution'; addthis_pub = ''; (Source: Medicine and Man)

Evolution diet for pets. Why not for people? Oh wait, of course that has been thought of before

The Tree of Life — Tue, 06 Jul 2010 12:40:00 +0100

Yup, that is right. There are evolution based diets for pets. Do you think people will use them if they don't believe in evolution? Do pets believe in evolution? Is an evolution based diet better than other diets? Actually, for the last question, it seems plausible that evolution informed diets could be of some use, but still seems funny to see it in pet food. Why isn't there an evolution diet for people yet? Oh wait, there is. And there is all sorts of stuff out there about evolution and diet includingThe Evolution Diet Evolution, Diet and Health The New Evolution Diet | Hunter-Gatherer Just goes to show you, with google you can find that just about everything you can think of already exists. -------- This is from the "Tree of Life Blog" of Jonathan Ei...

Summary of #iEVOBIO Day 2, #phylogenetics #informatics #opensource #biodiversity #evolution

The Tree of Life — Tue, 06 Jul 2010 00:15:44 +0100

This is a continuation of notes on iEVOBIO meeting. Much of this comes from twitter. Additional comments will be posted over the next few days. See notes on Day 1 here. Note - thanks to the people who answered my query on twitter about how to remove spurious html code from pages - I wrote this post a few days ago but somehow the copying and pasting I did from twitter broke blogger with some weird html. I ended up using Zubrag which was suggested by brendanwlocke. Day 2. Beginning. Since I was leaving that PM I could not borrow a hotel bike and bike over again. So I walked from the hotel, along the river 2 or so miles, after getting coffee. I got to the meeting a bit late and thus missed much of the opening Keynote, which was a bummer since it seem...

Summary of #iEVOBIO Day 1 #evolution #phylogenetics #informatics #opensource

The Tree of Life — Mon, 05 Jul 2010 17:48:15 +0100

Well, just getting around to writing up some thoughts on the iEVOBIO meeting I went to earlier this week. It was really quite excellent so here are some thoughts/notes. Today I am writing about the background and Day 1. Most of this is simply a catalog of what happened along with some twitter details ... In a few days I will write up a post on what I think it meant .... The background: how I heard about iEVOBIO (skip to below if you just want to know about what happened in the meeting) The first I heard about regarding the meeting was Dec 7, 2009, in a Direct Message on Twitter from @rdmpage. That would be Rod Page, who I had never met, but followed remotely via twitter, his blog, his software and his papers. He wrote Hi Jonathan, hope you got my ema...

Women Like Masculine Men (Thank You, Science)

Breastfeeding 1-2-3 — Tue, 29 Jun 2010 18:24:48 +0100

photo: Thinkstock You’re with your girlfriends at a restaurant, and the waiter takes your order. “Whoa!” your friend says, “He was totally checking you out!” He was? You didn’t notice the waiter looking at you. This could be because his face wasn’t masculine enough. New research shows that the more exaggerated sex-specific features a person has, the faster you notice him or her looking at you. Scientists think this might be an evolutionary technique, since feminine women and masculine men were shown to make the healthiest mate in previous studies. We think it might just be because hunky guys catch our eye. Which is sort of what the research is saying, so… Bring on the lumberjacks, construction workers, and firemen. How do you think the proces...

A mushroom on the cover

Fungal Genomes and Comparative Genomics — Tue, 29 Jun 2010 17:35:11 +0100

I’ll indulge a bit here to happily to point to the cover of this week’s PNAS with an image of Coprinopsis cinerea mushrooms fruiting referring to our article on the genome sequence of this important model fungus. You should also enjoy the commentary article from John Taylor and Chris Ellison that provides a summary of some of the high points in the paper. Stajich, J., Wilke, S., Ahren, D., Au, C., Birren, B., Borodovsky, M., Burns, C., Canback, B., Casselton, L., Cheng, C., Deng, J., Dietrich, F., Fargo, D., Farman, M., Gathman, A., Goldberg, J., Guigo, R., Hoegger, P., Hooker, J., Huggins, A., James, T., Kamada, T., Kilaru, S., Kodira, C., Kues, U., Kupfer, D., Kwan, H., Lomsadze, A., Li, W., Lilly, W., Ma, L., Mackey, A., Manning, G., Martin, F., Muraguchi, H., Natvig, D.,...

Where can I get orthologs?

Fungal Genomes and Comparative Genomics — Thu, 24 Jun 2010 01:13:09 +0100

There are several databases that include orthology prediction for fungi. These all have pros and cons. Some are more comprehensive and have many more species. Some are curated orthologies and paralogy which should be pretty stable. Some are automated and groupings and ortholog group IDs change at each iteration. A phylogenetic approach from a Saccharomyces perspective is at PhylomeDB. Fungal Orthogroups is based on Synergy algorithm from I. Wapinski formerly of the Regev group at the Broad Institutue. Yeast gene order browser (YGOB) for Saccharomyces spp and CGOB for Candida spp. OrthoMCL database based on whole genomes, not a ton of fungi but useful starting set. Ensembl Genomes provides ortholog prediction as part of the Compara pipeline though there is a limited phylogenetic diversity ...

Salmonella evolution

Microbiology Blog: The weblog for microbiologists. — Tue, 15 Jun 2010 23:00:00 +0100

Evolutionary trends associated with niche specialization as modeled by whole genome analysis of egg-contaminating Salmonella enterica serovar Enteritidisfrom Jean Guard, Devendra Shah, Cesar A. Morales and Doug Call writing in Salmonella: From Genome to FunctionThe mosaic nature of the Salmonella enterica genome facilitates its access to multiple environments. Many large scale genomic events have been described that contribute to the combinatorial complexity of the pathogenic Salmonellae. However, the impact of small scale genetic change occurring at the level of single nucleotide polymorphism (SNP) on the emergence of niche specialization is just now becoming appreciated. A recent review describes concepts behind the evolution that culminated in the remarkable ability of Salmonella enteri...

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Microbiology Blog: The weblog for microbiologists. — Tue, 15 Jun 2010 23:00:00 +0100

Twisted tree of life award #5: Nicholas Wade & use of higher, lower, ladders, etc

The Tree of Life — Sat, 12 Jun 2010 22:52:04 +0100

Nicholas Wade has a new article in the New York Times critiquing some aspects of the human genome project (A Decade Later, Gene Map Yields Few New Cures - NYTimes.com) Whether one agrees with his critiques or not, I hope that everyone can recognizes that one section on evolution is, well, awful. Wade writes First was the discovery that the number of human genes is astonishingly small compared with those of lower animals like the laboratory roundworm and fruit fly. The barely visible roundworm needs 20,000 genes that make proteins, the working parts of cells, whereas humans, apparently so much higher on the evolutionary scale, seem to have only 21,000 protein-coding genes.While Mr. Wade may want to believe he and humans in general are somehow "higher" on some evolutionary ladder than other ...

Neurotic Women In Poor Countries Make More Babies

FuturePundit — Tue, 08 Jun 2010 23:00:00 +0100

Neuroticism and extraversion are being selected for in countries with the highest birth rates. The study, which was published yesterday (7 June 2010) in the Proceedings of the National Academy of Sciences, found that women with higher levels of neuroticism and more extravert men, are likely to give birth to a larger number of children in societies with traditionally high birth rates. I'd really like to know which personality traits are being selected for in Western industrial societies. Natural selection has not stopped. But in industrial societies selective pressures change. Since more educated people have fewer kids intelligence is being selected against. But what other cognitive traits are selected for or against? Women with higher neuroticism were also less able... (Source: FuturePundi...

Ancestors and Offspring - evolution and synthetic biology (video)

A Blog Around The Clock — Sun, 30 May 2010 03:05:20 +0100

A fascinating discussion with John Hawks and my Scibling Christina Agapakis about synthetic biology and other related topics - worth your time: Read the comments on this post... (Source: A Blog Around The Clock)

Has Technology Hindered Evolution

Dr Shock MD PhD — Sat, 22 May 2010 06:47:28 +0100

Short example of the evolutionary advantage of good eye sight Related posts:Evolution of Life in 60 Seconds The Technology Profile Inventory for Nerds, Geeks, Medbloggers? Health Information Technology A Safety Net for Physicians (Source: Dr Shock MD PhD)

The evolutionary psychology of war

neurodudes — Sun, 16 May 2010 20:29:44 +0100

Nothing too shocking here for students of evolutionary psychology but it’s always interesting to see real world examples of how our shared behavior. There is a new book by Sebastian Junger called War, in which he recounts how men do not fight for larger ideological goals (eg. “a safer Iraq”, “finding Bin Laden”) but instead they can overcome fears because “they’re more concerned about their brothers than what happens to themselves individually”. Here’s Junger on Good Morning America: After the jump some more from Junger and a nice talk from Robert Sapolsky about similar behaviors in chimps. Another example from soldiers in Afghanistan is the “blood-in, blood-out” ritual for increasing group cohesiveness and testing individ...

The Evolution Of The Pill And Its Effect On Sex

Better Health — Thu, 13 May 2010 20:00:03 +0100

What role has the birth control pill played in human sexuality? Dr. Jon LaPook looks at the evolution of sex as the pill turns 50 and discusses the effect of the pill on female sexuality with sex therapist and educator Miriam Baker. Watch CBS News Videos Online Does The Pill Lower Sex Drive? The pill that ushered in the sexual revolution may have also thrown cold water on women’s libido. Fifty years ago, on May 9th, 1960, the FDA announced the approval of oral contraception. The birth control pill has allowed women to control their reproductive cycle, delay childbearing, and develop careers. But it also may have the potential to disrupt sexuality by blocking normal hormonal surges that occur in a woman’s cycle. Here’s how. (more…) (Source: Better Health)

Tibetans Genetically Adapted To High Altitude

FuturePundit — Wed, 12 May 2010 23:00:00 +0100

Tibetans carry several genetic variants that adapt them better to high altitude living. SALT LAKE CITYResearchers have long wondered why the people of the Tibetan Highlands can live at elevations that cause some humans to become life-threateningly ill and a new study answers that mystery, in part, by showing that through thousands of years of natural selection, those hardy inhabitants of south-central Asia evolved 10 unique oxygen-processing genes that help them live in higher climes. In a study published May 13 in Science Express, researchers from the University of Utah School of Medicine and Qinghai University Medical School in the People's Republic of China report that thousands of years ago, Tibetan highlanders began to genetically adapt to prevent polycythemia... (Source: FutureP...

Virology lecture #22: Evolution

virology blog — Mon, 10 May 2010 16:47:38 +0100

Download: .wmv (393 MB) | .mp4 (102 MB) Visit the virology W3310 home page for a complete list of course resources. (Source: virology blog)

Holy lateral transfer batman; amazing story on fungal to aphid transfer from Nancy Moran

The Tree of Life — Mon, 03 May 2010 19:33:26 +0100

As many know, I generally do not write a lot about papers in non open access journal because I like readers to be able to access all the papers which I write about. But this is one of the exceptions to my normal rule. An amazing paper was published a few days ago in Science by Nancy Moran and Tyler Jarvik. Lateral Transfer of Genes from Fungi Underlies Carotenoid Production in Aphids -- Moran and Jarvik 328 (5978): 624 -- ScienceI first found out about this from Ed Yong's blog post here (just a note - his Not Exactly Rocket Science is such a frigging incredible blog). He really does the whole story on this so I am just posting a bit here.Anyway Moran and Jarkiv paper focuses on genes in the aphid genome that encode enzymes for carotenoid synthesis. These enzymes are involved in red and/or ...

A plant virus that switched to vertebrates

virology blog — Tue, 27 Apr 2010 03:05:54 +0100

Viruses can be transmitted to completely new host species that they have not previously infected. Usually host defenses stop the infection before any replication and adaptation can take place. On rare occasions, a novel population of viruses arises in the new host. These interspecies infections can sometimes be deduced by sequence analyses, providing a glimpse of the amazing and unpredictable paths of virus evolution. One example is a plant virus that switched hosts and infected vertebrates. Circoviruses infect vertebrates and have small, circular, single-stranded DNA genomes. Nanoviruses have the same genome structure, but infect plants. The genes encoding one of the viral proteins – called the Rep protein – appear to be hybrids, and share significant sequence similarity. They...

Was There a Libertarian Golden Age?

Cato-at-liberty — Thu, 22 Apr 2010 20:05:32 +0100

By David BoazRecently I wrote an article arguing that there never was a golden age of liberty and that in particular libertarians should not hail 19th-century America as a small-government paradise, at least not without grappling with the massive problem of slavery. Jacob Hornberger, author of an article that I criticized, responded in Reason, and I then responded here. Meanwhile, an interesting discussion took place on a email list of libertarian scholars, and I’m pleased to have gotten the permission of several participants to include some of that discussion here: Aeon J. Skoble: The ideals of freedom which led to the tangible improvements [Boaz] mentions – I’m concerned that those ideals are eroding/have eroded. Example: say you have a robust theory of rights, but your soci...

Admixture between humans and the Others

Gene Expression — Wed, 21 Apr 2010 04:32:06 +0100

Mr. Carl Zimmer points me to a new article in Nature, Neanderthals may have interbred with humans. The details within the article are more tantalizing, it seems to me, than the headline would imply. The topline is this, researchers presented the following at the recent meeting of the American Association of Physical Anthropologists: * An analysis of 614 highly variant loci, microsatellites, in ~2,000 people from diverse populations imply some variants which seem to be derived from human lineages outside of the mainline which led to the anatomically modern humans who left Africa 50-100,000 years before the present to settle the world. I assume there were “long branches” on the phylogenies of some loci, indicating that some of the alleles were “separated” from others ...

TWiV #78: Darwin gets weird

virology blog — Sun, 18 Apr 2010 16:56:38 +0100

Hosts: Vincent Racaniello, Alan Dove, Dickson Despommier, and Rich Condit Vincent, Alan, Dickson, and Rich talk about treating arthritis with a tanapox virus protein, Darwinian evolution of prions in cell culture, and the connection between cold weather fronts and outbreaks of avian H5N1 influenza in Europe. This episode is sponsored by Data Robotics Inc. Use the promotion code TWIVPOD to receive $75-$500 off a Drobo. Win a free Drobo S! Contest rules here. Download TWiV #78 (53 MB .mp3, 73 minutes) Subscribe to TWiV (free) in iTunes , at the Zune Marketplace, by the RSS feed, or by email. Links for this episode: Treating arthritis with a tanapox virus protein that antagonizes TNF (press release and research article) Darwinian evolution of prions in cell culture (abstract) Simple diagram ...

When diversity is good for disease

Gene Expression — Thu, 15 Apr 2010 15:01:08 +0100

In this study they established the existence of this group rather clearly, but is it due to the peculiarities of Madagascar’s population mixture and history? True, Brazil also has an admixed population whose Duffy allele frequencies are interchangeable with that of Madagascar, but Brazil has been settled for only the past ~300 years or so, with much of the population being of more recent origin (Brazil had the highest slave attrition rate on the American mainland, which explains the African nature of Afro-Brazilian culture. Many of the slaves were from Africa, or first generation, at emancipation). A lower bound for Madagascar is ~1,000 years, and the coexistence of Barito and African populations is likely closer to ~2,000 years. So the existence of P. vivax lines which can penetrate...

When a trait isn’t a trait isn’t a trait

Gene Expression — Mon, 12 Apr 2010 13:15:19 +0100

One of the great things about evolutionary theory is that it is a formal abstraction of specific concrete aspects of reality and dynamics. It allows us to squeeze inferential juice from incomplete prior knowledge of the state of nature. In other words, you can make predictions and models instead of having to observe every last detail of the natural world. But abstractions, models and formalisms often leave out extraneous details. Sometimes those details turn out not to be so extraneous. Charles Darwin’s original theory of evolution had no coherent or plausible mechanism of inheritance. R. A. Fisher and others imported the empirical reality of Mendelism into the logic of evolutionary theory, to produce the framework of 20th century population genetics. Though accepting the genetic inh...

Michael McCullough on the Situation of Revenge and Forgiveness

The Situationist — Tue, 06 Apr 2010 15:57:36 +0100

From TempletonFoundation: Why is revenge such a pervasive and destructive problem? Why is forgiveness so difficult? In “Beyond Revenge,” Michael E. McCullough argues that the key to creating a more forgiving world is to understand both the evolutionary forces that gave rise to these intimately human instincts and the social forces that activate them in our minds today. Drawing on the latest breakthroughs in the social and biological sciences, McCullough offers practical and often surprising advice for how individuals, social groups, and even nations might move beyond our deep penchant for revenge. * * * * * * * * * * * * * * * To read a sample of related Situationist posts, see “The Situation of Punishment (and Forgiveness),” “The Situation of Revenge,” �...

Most important paper ever in microbiology? Woese & Fox, 1977, discovery of archaea

The Tree of Life — Tue, 06 Apr 2010 15:09:02 +0100

Well, today in my "Microbial phylogenomics" class at UC Davis we are discussing what I think might be the most important paper (well, actually, series of papers) in the history of microbiology. The papers are the ones where Carl Woese, George Fox and colleagues outline the evidence for the existence of a "hidden" third major branch in the tree of life - what is now known as the archaea. The evidence for this third branch was first laid out in a series of papers in 1977 including:An ancient divergence among the bacteria. Balch WE, Magrum LJ, Fox GE, Wolfe RS, Woese CR.J Mol Evol. 1977 Aug 5;9(4):305-11. Classification of methanogenic bacteria by 16S ribosomal RNA characterization. Fox GE, Magrum LJ, Balch WE, Wolfe RS, Woese CR. Proc Natl Acad Sci U S A. 1977 Oct;74(10):4537-454...

grace at all times

soulful sepulcher — Tue, 06 Apr 2010 00:02:00 +0100

(Source: soulful sepulcher)

The many lives of an inverted genomic region

Gene Expression — Mon, 05 Apr 2010 10:49:25 +0100

About five years ago Kari Stefansson published an interesting paper, A common inversion under selection in Europeans. The basic thrust of the results was that a particular genomic region in Europeans exhibited a pattern of variation whereby there was one variant which was inverted in relation to the modal type. They labelled them “H2″ and “H1″ respectively. The region in question is spans ~900 kilobases on chromosome 17 and has within it the MAPT gene which is implicated in several neurological diseases. Stefansson et al. argued that H2 and H1 were long coexistent lineages, prevented from recombining due to the molecular genetic constraints of the chromosomal inversion, and each preserved within several human populations by balancing selection dynamics. That is, n...

Increased rate of encephalization

Gene Expression — Mon, 05 Apr 2010 06:16:28 +0100

A week ago I pointed to a controversy about the rate of growth of human cranial capacities over the past few million years. I asserted that the rate of growth was gradual, with no major discontinuity. Over at Genetic Inference Luke Jostins’ has done a more formal analysis. He finds: The model shows a definite speed-up of brain size increase recently, and fits the data significantly better than a simple trend line (F(1,90) = 15.8, p < 10^-5). I estimate that the speed-up occured 252kya, and can say with 95% confidence that it lies between 203 and 377 kya. This result is pretty robust to exactly what model we use; I also tried using a model where brain size grew exponentially with time, and this gave a similar break-point: 250kya, with a 95% interval of 167-402 kya (see this graph). Re...

When sickliness is manliness

Gene Expression — Wed, 31 Mar 2010 10:25:11 +0100

Below I note that sex matters when it comes to evolution, specifically in the case of how sexual reproduction forces the bits of the genome to be passed back and forth across sexes. In fact, the origin of sex is arguably the most important evolutionary question after the origin of species, and it remains one of the most active areas of research in evolutionary genetics. More specifically the existence of males, who do not bear offspring themselves but seem to be transient gene carriers is a major conundrum. But that’s not the main issue in this post. Let’s take the existence of males as a given. How do sex differences play out in evolutionary terms shaping other phenotypes? Consider Bateman’s principle: Bateman’s principle is the theory that females almost always in...

The ways of the forefathers & foremothers

Gene Expression — Wed, 31 Mar 2010 02:17:23 +0100

Fascinating post by Bayes, Phylogenetics, cultural evolution and horizontal transmission: For some time now, evolutionary biologists have used phylogenetics. It is a well-established, powerful set of tools that allow us to test evolutionary hypotheses. More recently, however, these methods are being imported to analyse linguistic and cultural phenomena. For instance, the use of phylogenetics has led to observations that languages evolve in punctuational bursts, explored the role of population movements, and investigated the descent of Acheulean handaxes. I’ve followed the developments in linguistics with particular interest; after all, tracing the ephemeral nature of language is a daunting task. The first obvious road block is that prior to the invention of writing, the uptake of which i...

The sexual straightjacket

Gene Expression — Wed, 31 Mar 2010 01:21:03 +0100

Earlier I pointed to the possibility of biophysical constraints and parameters in terms of inheritance shaping the local trajectory of evolution. Today Olivia Judson has a nice post [link fixed] on how the existence of two sexes in many species results in a strange metastable tug-of-war in terms of phenotypic evolution: In sum, the traits that make a “good” male are often different from those that make a “good” female. (Note: I’m only talking about “good” in evolutionary terms. That means a trait that improves your chance of having surviving offspring.) Since many of these traits have a genetic underpinning, male and female genes are thus being sculpted by different forces. But — and this is the source of the tension I mentioned — males and females are formed from the sam...

Thomas Malthus was right. Mostly

Gene Expression — Mon, 29 Mar 2010 23:38:08 +0100

John Hawks has an excellent post rebutting some misinformation and confusion on the part of Colin Blakemore, an Oxford neurobiologist. Blakemore asserts that: * There was a sharp spike in cranial capacity ~200,000 years ago, on the order of 30% * And, that the large brain was not deleterious despite its large caloric footprint (25% of our calories service the brain) because the “environment of early humans was so clement and rich in resources” Hawks refutes the first by simply reposting the chart the above (x axis = years before present, y axis = cranial capacity). It’s rather straightforward, I don’t know the paleoanthropology with any great depth, but the gradual rise in hominin cranial capacity has always been a “mystery” waiting to be solved (see Gro...

Looking to open access (preferably w/ CC licenses) review papers covering introduction to phylogenetic trees and methods

The Tree of Life — Sun, 28 Mar 2010 18:39:14 +0100

I am teaching a class this spring and as part of the class am having one lecture on "Phylogenetic trees and methods." I would like to link to (and be able to mix and match material from) some review paper on this topic. So I am searching for something that is Open Access and preferably with a broad Creative Commons license. Anyone know of anything good? -------- This is from the "Tree of Life Blog" of Jonathan Eisen, an evolutionary biologist and Open Access advocate at the University of California, Davis. For short updates, follow me on Twitter. -------- (Source: The Tree of Life)

The Mysterious Other

Gene Expression — Sun, 28 Mar 2010 07:41:48 +0100

Last week Nature published a paper which may have found a new ‘branch’ of the hominin evolutionary bush which may have been coexistent which modern humans and Neandertals. I recommend The Atavism, Carl and John Hawks on this story. Interesting times. (Source: Gene Expression)

Others in Siberia

Gene Expression — Wed, 24 Mar 2010 20:04:16 +0100

The complete mitochondrial DNA genome of an unknown hominin from southern Siberia: With the exception of Neanderthals, from which DNA sequences of numerous individuals have now been determined…the number and genetic relationships of other hominin lineages are largely unknown. Here we report a complete mitochondrial (mt) DNA sequence retrieved from a bone excavated in 2008 in Denisova Cave in the Altai Mountains in southern Siberia. It represents a hitherto unknown type of hominin mtDNA that shares a common ancestor with anatomically modern human and Neanderthal mtDNAs about 1.0 million years ago. This indicates that it derives from a hominin migration out of Africa distinct from that of the ancestors of Neanderthals and of modern humans. The stratigraphy of the cave where the bone wa...

Does gene function predict molecular evolutionary rate?

Fungal Genomes and Comparative Genomics — Tue, 23 Mar 2010 18:07:31 +0100

Gene sequences evolve at different rates due to different constraints, either due to chromosome position, functional constraint, and status as a single-copy or multi-copy gene. In a recent paper, Allen Rodrigo (the new NESCent director by the, way, congrats!) the authors hypothesize that correlation in branch lengths of gene trees suggest they operate in the same pathway or have a similar function. To do this they took alignments of orthologous genes from 10 bacterial species which were seeded with E. coli as the target species. The alignments were used to build trees with MrBayes and only those which recovered the known species topology were retained. The ortholog groups were assigned GO terms via similarities. They then looked at the branch lengths of gene trees and found a correla...

The evolution of morals

Gene Expression — Mon, 22 Mar 2010 04:09:01 +0100

I have a short piece up at Comment is Free at The Guardian, The origins of morality do not matter. Its flavor is a bit different from my typical blog posts because the format enforces more brevity, so I decided to try and leverage some analogies. I conclude: … Our moral consensus is a river whose course shifts across the plain, constrained by the hills thrust upward by biology. Only history knows where the river will flow next, though evolution can hint at the range of possibilities. On a note related to this piece, I will be posting a review of The Price of Altruism: George Price and the Search for the Origins of Kindness in a few months. (Source: Gene Expression)

Phyloseminar.Org 3/29 Streaming talk by Jens Lagergren on Gene Family evolution

The Tree of Life — Sat, 20 Mar 2010 07:36:57 +0100

Just got his email from the organizer of Phyloseminar.Org: On March 29th, phyloseminar.org will present Jens Lagergren speakingon "Probabilistic analysis of gene families with respect with geneduplication, gene loss, and lateral gene transfer." Abstract below. NOTE: the seminar will begin at 10h PST, which is three hours earlierthan the previous seminars. This is 13h Eastern Standard Time, 19h Central European Time, and 6hin Christchurch and Auckland! Here's the abstract: Incongruences between gene trees and corresponding species trees arecommon. Gene duplication, gene loss, and lateral gene transfer arethree types of evolutionary events that can cause such incongruences.I will first describe a probabilistic process that contains standardmodels of nucleotide substitutions (i.e.,...

Evolutionary history reversible

Gene Expression — Thu, 18 Mar 2010 06:13:08 +0100

At least in this case, Troglomorphism, trichobothriotaxy and typhlochactid phylogeny (Scorpiones, Chactoidea): more evidence that troglobitism is not an evolutionary dead-end: The scorpion family Typhlochactidae Mitchell, 1971 is endemic to eastern Mexico and exclusively troglomorphic. Six of the nine species in the family are hypogean (troglobitic), morphologically specialized for life in the cave environment, whereas three are endogean (humicolous) and comparably less specialized. The family therefore provides a model for testing the hypotheses that ecological specialists (stenotopes) evolve from generalist ancestors (eurytopes) and that specialization (in this case to the cavernicolous habitat) is an irreversible, evolutionary dead-end that ultimately leads to extinction. Due to their c...

New Textbooks, Y’all!

Donna Trussell — Tue, 16 Mar 2010 23:04:46 +0100

New cartoon by Trussell & Trussell on AOL’s Politics Daily. New Textbooks, Y’all! Filed under: Politics Daily Tagged: chaos theory, creationism, education, evolution, political cartoon, texas, textbook (Source: Donna Trussell)

Creation, Evolution, and Christians

Baggas' Blog — Fri, 12 Mar 2010 03:41:12 +0100

Tim Keller is a pastor of a big church in NYC who has written some excellent books. In this article attempting to reconcile religion and science he posits a third way between fundamentalist creationists and militant atheists for which evolution becomes a world-view rather than just science. He provides some useful answers to some key questions often faced by those who want to be faithful to God and the Bible yet not blindly reject the vast body of scientific evidence supporting evolutionary biology. Well worth reading. (Source: Baggas' Blog)

Very bad title, "highly evolved"

Gene Expression — Fri, 05 Mar 2010 02:14:55 +0100

National Geographic has a coverage of the Kanzawa paper. The title: Liberals, Atheists Are More Highly Evolved? I get what's going on with terms like "highly evolved," but I think it's really problematic when media which serves as an interface with the public in regards to evolutionary ideas uses this sort of terminology, as it reinforces misleading perceptions. For whatever reason people default to a great chain of being model in relation to evolution, and to really communicate the science as opposed to intuition you need to break people of these tendencies. This is why I have qualms with phrases such as "oldest known lineage of human modern humans". If you have a deep interest in phylogenetics you intuitively grasp what's trying to be communicated, but for the public it just spreads the ...

The Evolutionary Time Bomb

ShrinkWrapped — Thu, 04 Mar 2010 18:02:04 +0100

In December of 2008, I wrote about Race, Ethnicity, and the Genetic Time Bomb and the great danger inherent in our burgeoning knowledge of genetics: The accumulation and interpretation of information derived from our increased ability to parse the genetic code contains within it a potential time bomb of epic proportions. The damage that the nuclear bomb of genetic knowledge threatens to produce is incalculable, potentially made far worse by our inability to think about, let alone talk about, the data. It remains early in the science of genetics. Decoding the human genome is a recent advance; as with all forms of information science, the cost of decoding the human genome has been rapidly decreasing (following its own Moore's Law of exponential progress) and early in...

Quantitative genetics strikes back! (?)

Gene Expression — Sun, 28 Feb 2010 03:26:30 +0100

The Genetics of Human Adaptation: Hard Sweeps, Soft Sweeps, and Polygenic Adaptation: There has long been interest in understanding the genetic basis of human adaptation. To what extent are phenotypic differences among human populations driven by natural selection? With the recent arrival of large genome-wide data sets on human variation, there is now unprecedented opportunity for progress on this type of question. Several lines of evidence argue for an important role of positive selection in shaping human variation and differences among populations. These include studies of comparative morphology and physiology, as well as population genetic studies of candidate loci and genome-wide data. However, the data also suggest that it is unusual for strong selection to drive new mutations rapidly...

Ian Tattersall on Darwin and Human Evolution

Living the Scientific Life (Scientist, Interrupted) — Fri, 19 Feb 2010 17:59:20 +0100

tags: Center for Inquiry, CFI, NYC Skeptics, Free Inquiry and Secular Humanism, Darwin Day 2010, Ian Tattersall, Massimo Pigliucci, public education, outreach, New York City, NYC, education, streaming video On the day after the anniversary of Charles Darwin's birthday, prominent paleoanthropologist Ian Tattersall gave a public lecture about Darwin and his impact on what we know about human evolution. Tattersall, curator in the anthropology department at the American Museum of Natural History, then sat down for a conversation with Massimo Pigliucci, Chair of the Philosophy Department at City University of New York (CUNY) at Lehman College. This event was sponsored by the Center for Inquiry in New York City, New York City Skeptics, and the student group Free Inquiry and Secular Huma...

Science of Love: Romance and Patterns of Attraction

Channel N — Sun, 14 Feb 2010 14:00:57 +0100

Lust, Romance & Attachment: The Science of Love and Whom We Choose As part of the Girls Night Out series at the New York Academy of Sciences (NYAS), neuroanthropologist Fisher talks about romantic love, misconceptions about love, its effects on the brain, and why we choose one mate over another. She discusses her early research as well as recent work with Chemistry.com. Slides are not visible, but still a fascinating lecture with 27 minutes of Q&A. A Valentine’s fave here at Channel N, see also this Stonybrook lecture, another 2006 lecture, an interview, and a New York Times interview. (Source: Channel N)

Pediatric Bipolar Disorder & DSM-5 : "Temper Dysregulation Disorder"

soulful sepulcher — Wed, 10 Feb 2010 16:38:00 +0100

(Source: soulful sepulcher)

Origins and evolution of pathogens

Fungal Genomes and Comparative Genomics — Mon, 08 Feb 2010 12:30:01 +0100

An article in PLoS Pathogens by Morris et al describe a hypothesis about the evolution and origins of plant pathogens applying the parallel theories to the emergence of medically relevant pathogens. The authors highlight the importance of understanding the evolution of organisms in the context of emerging pathogens like Puccinia Ug99 for our ability to design strategies to protect human health and food supplies. Both bacterial and fungal pathogens of plants are discussed but I (perhaps unsurprisingly) focus on the fungi here. The authors suggest that theories on the emergence of diseases proposed in medical epidemiology apply to plant pathogens as well. Some of these ideas are quite provocative on the evolution of intracellular pathogens and how environmental microbes become pathogen...

Charles Darwin was a genius (I think)

Gene Expression — Mon, 08 Feb 2010 10:15:19 +0100

After watching Creation last week I decided to take the plunge and read Origin of Species. As I've mentioned before I did read Origin early in my teen years, but in hindsight with minimal comprehension. Since then I've occasionally started to read Origin, or perused an extract, but I've never made it from front to back as a sentient adult. At this point I'm 3/4 of the way through, and I need to get something off my chest: I now believe that Charles Darwin was a very smart man, a genius. I had heard other people to refer to Darwin in such a fashion, but reading his original works has brought home to me much more viscerally his incredible power of insight. One of the reasons I hadn't reread Origin of Species was that I assumed that because it was the modern root of evolutionary biology what...

Carnival of Evolution #20! is out and it's got some good stuff ...

The Tree of Life — Thu, 04 Feb 2010 03:05:30 +0100

Just a quick post here to suggest people check out the Carnival of Evolution (#20) being hosted at Skeptic Wonder (see Skeptic Wonder: Carnival of Evolution #20!). It's has some juicy evolution posts discussed and (perhaps) best of all has a "phylogenetic" tree based on the postings. I recommend everyone check it out ... -------- This is from the "Tree of Life Blog" of Jonathan Eisen, an evolutionary biologist and Open Access advocate at the University of California, Davis. For short updates, follow me on Twitter. -------- (Source: The Tree of Life)

Story behind the science: #PLoS Genetics "Evolutionary mirages" paper

The Tree of Life — Wed, 03 Feb 2010 15:53:35 +0100

Conclusions: Lynch has eloquently argued that biologists are often too quick to assume that organismal and genomic complexity must arise from selection for complex structures and too slow to adopt non-adaptive hypotheses. Our results lend additional support to this view, and extend it to show that indirect and non-adaptive forces can not only produce structure, but also create an illusion that this structure is being conserved. We do not doubt that many aspects of transcriptional regulation constrain the location of transcription factor binding sites within enhancers. Indeed a large body of experimental evidence supports this notion, and we remain committed to identifying and characterizing these constraints. But if this process is to be fueled by comparative sequence analysis, as we belie...

The evolutionary underpinnings of metastasis: a non geneticist view

Cancerevo: Evolution and cancer — Wed, 03 Feb 2010 04:16:14 +0100

Metastasis, the spread of a tumour from a primary site to secondary ones, is the reason cancers become life threatening. Metastasis requires tumour cells to acquire a number of capabilities, mainly the capacity to get into the bloodstream (or any other system that would allow the cells to reach other parts of the organism like the lymphatic system, or the bones), the capacity to get out of it and finally the capacity to grow and prosper in the new location. Interestingly, not all these capabilities are beneficial from the evolutionary view point. A tumour cell in a primary site that gets in a blood vessel is unlikely to be able to contribute to the metastatic potential of the primary tumour. Metastasis is also an extremely wasteful process in which only a tiny minority of cells in the bloo...

Evolution of Plastids

Microbiology Blog: The weblog for microbiologists. — Tue, 02 Feb 2010 14:40:00 +0100

Photosynthesis is one of the most successful energy production strategies on the planet and has been co-opted numerous times throughout evolutionary history via the uptake and retention of photosynthetic cells by non-photosynthetic eukaryotic heterotrophs. Whereas the result of this process is clear, what is not settled is the mode and tempo of plastid movement among eukaryotes, particularly plastids of red algal derivation. Recent changes in our understanding of the relationships between eukaryotic supergroups have only served to complicate the picture further. Of particular interest is the evolution of plastids, the relationships among photosynthetic eukaryotes, the process of endosymbiogenesis and the variation in ways plastids have been modified to suit the light harvesting needs of th...

The Evolution of Empathy

SharpBrains — Tue, 02 Feb 2010 14:28:30 +0100

(Editor’s Note: we are pleased to bring you this article thanks to our collaboration with Greater Good Magazine). The Evolution of Empathy Empathy’s not a uniquely human trait, explains primatologist Frans de Waal. Apes and other animals feel it as well, suggesting that empathy is truly an essential part of who we are. Once upon a time, the United States had a president known for a peculiar facial display. In an act of controlled emotion, he would bite his lower lip and tell his audience, “I feel your pain.” Whether the display was sincere is not the issue here; how we are affected by another’s predicament is. Empathy is second nature to us, so much so that anyone devoid of it strikes us as dangerous or mentally ill. At the movies, we can’t help but get insi...

Darwin wuz wrong, part n

Gene Expression — Fri, 29 Jan 2010 08:44:00 +0100

A review of a new book, What Darwin Got Wrong. Co-authored by Jerry Fodor, who has been continuing his war against natural selection. I've already read Darwinian Fairytales: Selfish Genes, Errors of Heredity, and Other Fables of Evolution (at the suggestion of a reader who found the arguments within incredibly persuasive, convincing me to simply ignore anything that reader ever asserted after finishing the book), so I think I have my quota of philosopher-declaring-evolution-the-naked-emperor under my belt. Meanwhile, there are real scholars grappling with the issues which emerged in the wake of the Neo-Darwinian Synthesis and its discontents, and pushing science forward.Yes, Darwin was wrong about many things. But how many scientists will still have such an impact 150 into the future? He's...

The Evolutionary Situation of Behavior

The Situationist — Thu, 28 Jan 2010 05:00:54 +0100

Thomas Brennan and Andrew Lo recently published their interesting paper, titled “The Origin of Behavior,” on SSRN. Here’s the abstract. * * * We propose a single evolutionary explanation for the origin of several behaviors that have been observed in organisms ranging from ants to human subjects, including risk-sensitive foraging, risk aversion, loss aversion, probability matching, randomization, and diversification. Given an initial population of individuals, each assigned a purely arbitrary behavior with respect to a binary choice problem, and assuming that offspring behave identically to their parents, only those behaviors linked to reproductive success will survive, and less reproductively successful behaviors will disappear at exponential rates. This framework gen...

The last Iberian Neandertal

Gene Expression — Wed, 27 Jan 2010 06:00:07 +0100

Conclusions/Significance These findings have implications for the understanding of the emergence of anatomical modernity in the Old World as a whole, support explanations of the archaic features of the Lagar Velho child's anatomy that invoke evolutionarily significant Neandertal/modern admixture at the time of contact, and counter suggestions that Neandertals could have survived in southwest Iberia until as late as the Last Glacial Maximum. The paper is pretty long, and probably as opaque to most readers who are as unfamiliar as I with the nuts & bolts of physical anthropology, so ScienceDaily is worth reading: These findings have important implications for the understanding of the archaic features found in the anatomy of a 30,000 year old child unearthed at Lagar Velho, Portugal. With th...

the beginning of the misdiagnosis discussion : it was not childhood bipolar in 1999 and it still isn't, a decade long journey part one: a ramble

soulful sepulcher — Sun, 24 Jan 2010 16:41:00 +0100

(Source: soulful sepulcher)

Neurospora 2010 and upcoming fungal conferences

Fungal Genomes and Comparative Genomics — Fri, 22 Jan 2010 19:03:23 +0100

Don’t forget to register for Neurospora 2010 held at the beautiful Asilomar Conference center in Pacific Grove, CA held April 8-11, 2010. Get your filamentous fungi fix here! Also save the date for some other important upcoming conferences you may consider attending American Society of Microbiology, Candida and Dimorphic Fungi Meeting, March 22-26, Miami, FL, USA Joint Genome Institute, 2010 User Meeting, March 24-26, Walnut Creek, CA, USA New and emerging fungal diseases of animals and plants, April 17-21, Roscoff Biological Station (near Brest), Brittany, FRANCE American Society of Microbiology, 110th Annual Meeting, May 23-27, San Diego, CA, USA Cellular and Molecular Fungal Biology Gordon Conference, June 13-18, Holderness, NH, USA Mycological Society of America meeting, June 2...

Confronting Intelligent Design arguments directly in the scientific literature

The Tree of Life — Wed, 20 Jan 2010 14:57:54 +0100

A representative from Wiley publishing sent me a link to an interesting new paper. Entitled "Using Protistan Examples to Dispel the Myths of Intelligent Design" by Mark Farmer, from the University of Georgia and Andrea Habura, from the University at Albany, New York. It is from the Journal of Eukaryotic Microbiology and is based upon a presentation they gave at a workshop at a conference. Basically, the article is a detailed discussion of how examples relating to microbial eukaryotes (I hate the term protist ...) that are used by Intelligent Design advocates are, well, BS. And the article discusses the evidence that refutes the ID arguments. One thing they discuss is the issue of the Cambrian Explosion. ID supporters, such as Stephen Meyer have made many arguments abou...

Y Chromosome Still Evolving

FuturePundit — Wed, 13 Jan 2010 00:00:00 +0100

Some have theorized that the Y chromosome is in decline, that the chromosome that makes men into men is losing out in the rush of evolution. But no. I'm sure many guys will be happy to know that the Y chromosome is evolving under heavy evolutionary pressure. CAMBRIDGE, Mass. (January 13, 2010) Contrary to a widely held scientific theory that the mammalian Y chromosome is slowly decaying or stagnating, new evidence suggests that in fact the Y is actually evolving quite rapidly through continuous, wholesale renovation. By conducting the first comprehensive interspecies comparison of Y chromosomes, Whitehead Institute researchers have found considerable differences in the genetic sequences of the human and chimpanzee Ysan indication that these chromosomes have evolved... (Source: FutureP...

The Funniest Thing I have Read Today

My M.D. Journey! — Thu, 07 Jan 2010 22:24:00 +0100

While reading through comments on a topic I found in a group on Facebook, I came across this:"People fortunately became educated enough to refute the theory of evolution which was constantly imposed on ordinary masses. Gravity is felt that's why it is believed where as evolution is not even felt. Evolution is a great deception of Satan which is not a new theory propsed by Master Mason - Darwin rather it belongs to Ancient Egyptians and other Pagan dogmas.-Majid Khan"Thought I'd share it with you.Thanks for reading :) ... http://prep4md.blogspot.com/ (Source: My M.D. Journey!)

Story behind the science: #PLoS Biology paper on cichlid vision evolution

The Tree of Life — Tue, 05 Jan 2010 22:24:39 +0100

This study was a long time in the making. We started studying the visual system of cichlids in the 1990’s. We learned quickly that there was a lot of variation in opsin expression within the Lake Malawi species. However, we had only examined a few species. In 2005, Tom Cronin and Justin Marshall (world experts on aquatic visual systems) agree to come to Lake Malawi with us and help examine a greater number of species. Justin brought his underwater spectrometer and characterized the light environment. Tom and I measured fish colors (that paper is under review) and I extracted retina for quantifying gene expression. Because Lake Malawi and Lake Victoria both contain large cichlid radiations and had such different light environments, Ole Seehausen and I s...

Primitive man had "Neandertal teeth"

Gene Expression — Tue, 05 Jan 2010 22:09:18 +0100

Dental maturational sequence and dental tissue proportions in the early Upper Paleolithic child from Abrigo do Lagar Velho, Portugal: Neandertals differ from recent and terminal Pleistocene human populations in their patterns of dental development, endostructural (internal structure) organization, and relative tissue proportions. Although significant changes in craniofacial and postcranial morphology have been found between the Middle Paleolithic and earlier Upper Paleolithic modern humans of western Eurasia and the terminal Pleistocene and Holocene inhabitants of the same region, most studies of dental maturation and structural morphology have compared Neandertals only to later Holocene humans. To assess whether earlier modern humans contrasted with later modern populations and possibly a...

You may think you're African-American, but...

Discovering Biology in a Digital World — Mon, 04 Jan 2010 17:13:32 +0100

An NSF post on Twitter this morning described an interesting study from the University of Pennsylanvia and Cornell University, that found that some people who call themselves "African Americans" may only be 1% West African, according to their DNA. The University of Pennsylvania press release contains other interesting findings as well. 365 individuals were studied and 300,000 genetic markers were examined. Some of the findings were: If you're African American, the genes most likely to have an African origin are those on your X chromosome. The article didn't mention it, but I would guess that also be true of your mitochondrial genes since X chromosomes and mitochondria are inherited from your mother. The median amount of European DNA in African Americans was 18.5 percent. The re...

Stitching different web tools to organize a project

Public Rambling — Sun, 03 Jan 2010 18:12:00 +0100

A little over a year ago I mentioned a project I was working on about prediction and evolution of E3 ligase targets (aka P1). As I said back then, I am free to risk as much as I want in sharing ongoing results and Nir London just asked me how the project is going via the comments of that blog post so I decided to give a bit of an update. Essentially, the project quickly deviated from course since I realized that predicting E3 specificity and experimentally determining ubiquitylation sites in fungal species (without having to resort to strain manipulation) were not going to be an easy tasks. So, since the goal was to use these data to study the co-evolution of phosphorylation switches (phosphorylation regulating ubiquitylation) it makes little sense to restrain the analysis speci...

PRDM9 and the evolution of recombination hotspots

Gene Expression — Sat, 02 Jan 2010 19:48:00 +0100

This week in Science, three papers report that the product of the gene PRDM9 is an important determinant of where recombination occurs in the genome during meiosis. Though this may sound like something of an esoteric discovery, it's actually pretty remarkable, and brings together a number of lines of research in evolutionary genetics. How so?A bit of background.A few somewhat related facts:1. A major goal in the study of speciation is the identification of the genes that underlie reproductive barriers between species. In 2008, the first such gene in mammals was found--in a cross between two subspecies of mouse where the male offspring are sterile (note that this follows Haldane's rule), a introduction of the "right" version of a single gene was sufficient to restore fertility. This gene? P...

The year of Darwin in Cancerevo reviewed

Cancerevo: Evolution and cancer — Fri, 01 Jan 2010 21:55:26 +0100

The year of Darwin is over and I decided to go over some posts in this blog that I felt were particularly Darwinian (not a small feat as the main topic of this blog is evolution in the context of cancer). The posts highlight (or at least that would be my hope) the importance of understanding that tumours evolve, that evolutionary dynamics make cancer a very difficult disease to treat, that ignoring these dynamics is one of the reasons for the limited success in the fight against cancer and that evolutionary enlightened (as a colleague at Moffitt likes to refer to them) treatments are our best hope for a cure. Some of these topics were treated in my post about the paper Darwinian medicine: a case of cancer in February. A darwinian enlightened therapy should then exploit the limitations of e...

Barcoding, taxonomy and citizen CSI

The Tree of Life — Fri, 01 Jan 2010 17:32:47 +0100

I just love the continued coverage of the story of the students from Trinity School in New York (a high school) who do investigative DNA barcoding projects. (There is a good new story about this on the LA Times blogs at:Think that sheep's mik cheese comes from a sheep? DNA doesn't lie | Booster Shots | Los Angeles Times) In the most recent example, two students, Brenda Tan and Matt Cost, did some home barcoding in collaboration with people from the AMNH and Rockefeller University. Among their findings: "an invasive species of insect in a box of grapefruit from Texas" "what could be a new species or subspecies of New York cockroach" multiple mislabelled food products including (quoted from the press release, I note) An expensive specialty “sheep’s milk” cheese made in fact from co...

Predictions for 2010

Cato-at-liberty — Thu, 31 Dec 2009 20:55:42 +0100

By David BoazI was just listening to the December CatoAudio interview with Tom Palmer and Ian Vasquez about the fall of the Soviet empire 20 years ago, and Tom mentioned that even as late as October 7, 1989, when the East German government held a gala celebration of its 40th year in power, no one anticipated that within a month the Wall would open and communism would come to an abrupt end in eastern Europe. And then I looked at the predictions of various scholars and pundits at Politico’s Arena one year ago today and noticed how wrong most of them were — Terry McAuliffe would be elected governor of Virginia, Rod Blagojevich would still be governor in April, Iran would test a nuclear weapon, several Republican members of Congress would switch to the Democratic Party (!), Justice...

What Darwin Never Knew (online)

Gene Expression — Thu, 31 Dec 2009 10:31:11 +0100

If you missed it, you can still watch it online. Read the comments on this post... (Source: Gene Expression)

More coverage of the GEBA "Phylogeny Driven Genomic Encyclopedia"

The Tree of Life — Tue, 29 Dec 2009 09:43:20 +0100

Just a quick note here to post some links to additional stories about my new paper on "A phylogeny driven genomic encyclopedia of bacteria and archaea" which was published last week in Nature. Carl Zimmer has an article today in the New York Times "Scientists Start a Genomic Catalog of Earth’s Abundant Microbes" about the paper and the project. In the article he interviews me and Hans-Peter Klenk, who was a co-author and led the culturing part of the project. A few things to note about this: It is rare to have archaea mentioned in the New York Times. There is a tree that goes along with the article which is a modified version of the tree we had in our paper. I think theirs is very nice. Kudos to their artist There is a quote by Norm Pace generally supportive of ...

Story behind the story for new #PLoSOne paper on Bayesian phylogenetics

The Tree of Life — Tue, 22 Dec 2009 16:06:24 +0100

There is an interesting new paper in PLoS One" Long-Branch Attraction Bias and Inconsistency in Bayesian Phylogenetics" by Brian Kolaczkowski and Joseph Thornton. The work focuses on methods for inferring phylogenetic history and in particular two types of statistical approaches: Likelihood and Bayesian. These methods are related to each other in that both attempt to use statistical models of evolution and then test different possible phylogenetic trees related taxa by how well certain data sets about those taxa map into the different possible trees. What they did in this new paper was test, with some simulations, and with some mathematical analyses. And somewhat surprisingly, they find that Bayesian methods, which have become more popular recently, appear to be more...

Wired for justice?

Gene Expression — Fri, 18 Dec 2009 02:52:47 +0100

Since my last post was rather pessimistic, I thought I'd point to something a little more cheerful, Social Scientists Build Case for 'Survival of the Kindest': Researchers at the University of California, Berkeley, are challenging long-held beliefs that human beings are wired to be selfish. In a wide range of studies, social scientists are amassing a growing body of evidence to show we are evolving to become more compassionate and collaborative in our quest to survive and thrive. In contrast to "every man for himself" interpretations of Charles Darwin's theory of evolution by natural selection, Dacher Keltner, a UC Berkeley psychologist and author of "Born to be Good: The Science of a Meaningful Life," and his fellow social scientists are building the case that humans are successful as a ...

Shellfish & the human bottleneck

Gene Expression — Thu, 17 Dec 2009 02:02:00 +0100

How shellfish saved the human race:Turns out, somewhere between 130,000 to 190,000 years ago, the human species was reduced to less than 1000 breeding individuals--just a few thousand people in total. Ancient, naturally driven climate change pushed our species to the brink, said Curtis Marean, Ph.D., a professor with the Institute of Human Origins and the School of Human Evolution and Social Change at Arizona State University.What saved us? According to Marean, the answer may be "shellfish"."They're a great source of protein," he said. "And shellfish are immune to colder ocean temperatures. In fact, when the water gets colder, those populations go up."Marean used climate models to pinpoint locations in Africa where human hunter-gatherers could have hunkered down during a long glacial perio...

Nice Darwin Art at #UCDavis Evolution/Ecology Dept.

The Tree of Life — Sun, 13 Dec 2009 00:16:01 +0100

For more on this see The Face of Darwin where K. Garvey explains the history of the mural in more detail. -------- This is from the "Tree of Life Blog" of Jonathan Eisen, an evolutionary biologist and Open Access advocate at the University of California, Davis. For short updates, follow me on Twitter. -------- (Source: The Tree of Life)

The Situation of Kindness

The Situationist — Wed, 09 Dec 2009 04:01:24 +0100

Yamin Anwar wrote an interesting press release about recent and ongoing research at University of California, Berkeley suggesting that the kindest, and not just the fittest, survive. Here are some excerpts. * * * Researchers at the University of California, Berkeley, are challenging long-held beliefs that human beings are wired to be selfish. In a wide range of studies, social scientists are amassing a growing body of evidence to show we are evolving to become more compassionate and collaborative in our quest to survive and thrive. In contrast to “every man for himself” interpretations of Charles Darwin’s theory of evolution by natural selection, Dacher Keltner, a UC Berkeley psychologist and author of “Born to be Good: The Science of a Meaningful Life,” a...

The downside of beauty

Gene Expression — Tue, 08 Dec 2009 10:30:24 +0100

Well, I don't quite know about that, but that's the sort of take-away from a new paper in PLoS Biology which looks at the downsides of female attractiveness. A Cost of Sexual Attractiveness to High-Fitness Females: Adaptive mate choice by females is an important component of sexual selection in many species. The evolutionary consequences of male mate preferences, however, have received relatively little study, especially in the context of sexual conflict, where males often harm their mates. Here, we describe a new and counterintuitive cost of sexual selection in species with both male mate preference and sexual conflict via antagonistic male persistence: male mate choice for high-fecundity females leads to a diminished rate of adaptive evolution by reducing the advantage to females of expr...

Amazing post-doc fellowship opportunity: Center for population biology at #UCDavis

The Tree of Life — Mon, 07 Dec 2009 19:17:25 +0100

No bias here --- but this really is an incredible post doc opportunity in population biology here at U. C. Davis. See below: EFFECTIVE: December 7, 2009 DEADLINE: January 20, 2010 POSTDOCTORAL FELLOW IN POPULATION BIOLOGY--The Center for Population Biology at UC Davis invites applications for a Postdoctoral Fellowship in Population Biology, broadly defined to include ecology, phylogenetics, comparative biology, population genetics, and evolution. We particularly encourage applications from candidates that have recently completed, or will soon complete, their PhD. The position is for TWO YEARS, subject to review after one year, and can begin as early as 1 July 2010. It has an annual salary of $38,000 plus benefits, and $6,000 per annum in research support. The Fello...

Those humanitarian founders!

Gene Expression — Sat, 05 Dec 2009 20:23:54 +0100

Darwin's idea has cost lives: Truths that America's founding fathers had held to be self-evident - that all men were created equal and endowed with certain inalienable rights - were now scorned as gross sentimentalities that had been overtaken by Darwinian science. Within a decade the self-styled "scientific racialists" had begun to classify other groups as genetically inferior. Immigrants from Spain and Italy were held to be a threat to the quality of the American gene pool and spurious scientific evidence was adduced to "prove" that Jewish immigrants were near-imbeciles whose admission in large numbers might lead to a lowering of the average level of intelligence of the American people. In fact, this cohort of Jewish immigrants would go on to supply more Nobel Prize winners than any othe...

BioLogos

Baggas' Blog — Wed, 02 Dec 2009 02:30:54 +0100

Discovered an interesting new blog site today on the topic of science and religion – Science and the Sacred from the BioLogos Foundation. It features a number of well-respected authors in this field and the general gist is to attempt to reconcile the findings of science (particularly biological) with the disciplines of theology and biblical studies to construct a more integrated worldview on issues of creation and science. Too often this discussion is polarized and driven by extremists like the militant atheist Richard Dawkins on one side and fundamentalist whackos like Ken Ham on the other side. Belief in God and belief in science don’t need to be mutually exclusive. This is a site I will be following with interest… (Source: Baggas' Blog)

Humans are naughty & nice by nature

Gene Expression — Tue, 01 Dec 2009 19:03:25 +0100

We May Be Born With an Urge to Help: What is the essence of human nature? Flawed, say many theologians. Vicious and addicted to warfare, wrote Hobbes. Selfish and in need of considerable improvement, think many parents. But biologists are beginning to form a generally sunnier view of humankind. Their conclusions are derived in part from testing very young children, and partly from comparing human children with those of chimpanzees, hoping that the differences will point to what is distinctively human. The somewhat surprising answer at which some biologists have arrived is that babies are innately sociable and helpful to others. Of course every animal must to some extent be selfish to survive. But the biologists also see in humans a natural willingness to help. When infants 18 months old...

Climate & the Out of Africa migration(s)

Gene Expression — Mon, 30 Nov 2009 18:07:02 +0100

Wet phases in the Sahara/Sahel region and human migration patterns in North Africa: The carbon isotopic composition of individual plant leaf waxes (a proxy for C3 vs. C4 vegetation) in a marine sediment core collected from beneath the plume of Sahara-derived dust in northwest Africa reveals three periods during the past 192,000 years when the central Sahara/Sahel contained C3 plants (likely trees), indicating substantially wetter conditions than at present. Our data suggest that variability in the strength of Atlantic meridional overturning circulation (AMOC) is a main control on vegetation distribution in central North Africa, and we note expansions of C3 vegetation during the African Humid Period (early Holocene) and within Marine Isotope Stage (MIS) 3 (≈50-45 ka) and MIS 5 (≈120-110...

Abortion Does Not Change Brain Evolutionary Pressures?

FuturePundit — Mon, 30 Nov 2009 00:00:00 +0100

Ron Guhname (not his real name), The Inductivist, used data from the General Social Survey to look at the question of whether the legalization of abortion in America caused a change in selective pressures for intelligence. Using the GSS Wordsum test as a rough measure of intelligence Ron finds that abortion did not appear to change the selective pressures for higher or lower intelligence. The selective pressures for lower intelligence continued unchanged. The first year of the General Social Survey was 1972. I looked at white women ages 50 and over for all surveys conducted in the 70s. The mean number of kids for dull women (Wordsum 0-4) was 3.02. It was 2.22 for smart women (Wordsum 8-10). That's a... (Source: FuturePundit)

Why whales get no bigger

Gene Expression — Wed, 25 Nov 2009 01:33:00 +0100

Carl Zimmer reports that it might be a function of physics. Bigger whales have proportionality bigger mouths, but at some point the biological engineering runs up against constraints:s they report today in the Proceedings of the Royal Society, Goldbogen and his colleagues found that big fin whales are not just scaled-up versions of little fin whales. Instead, as their bodies get bigger, their mouths get much bigger. Small fin whales can swallow up about 90% of their own body weight. Very big ones can gulp 160%. In other words, big fin whales need more and more energy to handle the bigger slugs of water they gulp. As their body increases in size, the energy their bodies demand rises faster than the extra energy they can get from their food....If the scientists are right, they may have disco...

My favorite evolution stuff 2. Charles Darwin Tobacco Card

The Tree of Life — Tue, 24 Nov 2009 17:11:49 +0100

In honor of Charlie D. I am posting one of my favorite Darwin items. I got this from Ebay years ago. It is a Darwin card - about 3 x 5 cm. From Ogden's Cigarettes, much like baseball cards. Also see my previous "Favorite Darwin thing" - a post card from 1900 or so. -------- This is from the "Tree of Life Blog" of Jonathan Eisen, an evolutionary biologist and Open Access advocate at the University of California, Davis. For short updates, follow me on Twitter. -------- (Source: The Tree of Life)

The Faith Instinct: How Religion Evolved & Why It Endures

Gene Expression — Thu, 19 Nov 2009 10:03:26 +0100

During the first few years of ScienceBlogs there was a lot of talk about religion. Yes, there's talk about religion now, but it's toned down in the wake of the ebbing of the publicity around The God Delusion. Naturally in the wake of the New Atheism a raft of conventional apologetics have been published, The Dawkins' Delusion being a typical example. More recently more nuanced books which wend the middle ground between militant atheism and conventional apologetics have taken center strage. Karen Armstrong's The Case for God approaches this from a philo-theistic angle, while Robert Wright's The Evolution of God is predicated on materialist presuppositions. Nicholas Wade's The Faith Instinct: How Religion Evolved and Why It Endures is of the same genre as Robert Wright's The Evolution of Go...

Ancient DNA & the moa

Gene Expression — Thu, 19 Nov 2009 03:54:02 +0100

The evolutionary history of the extinct ratite moa and New Zealand Neogene paleogeography: ...We synthesize mitochondrial phylogenetic information from 263 subfossil moa specimens from across NZ with morphological, ecological, and new geological data to create the first comprehensive phylogeny, taxonomy, and evolutionary timeframe for all of the species of an extinct order. We also present an important new geological/paleogeographical model of late Cenozoic NZ, which suggests that terrestrial biota on the North and South Island landmasses were isolated for most of the past 20-30 Ma. The data reveal that the patterns of genetic diversity within and between different moa clades reflect a complex history following a major marine transgression in the Oligocene, affected by marine barriers, tec...

Celebrate Darwin's 200th birthday

A Blog Around The Clock — Wed, 18 Nov 2009 17:57:23 +0100

NESCent and SCONC: What: November SCONC-fest When: Thursday November 19th , 6-8pm Where: National Evolutionary Synthesis Center in Durham Please join us to commemorate Charles Darwin's 200th birthday and the 150th anniversary of "The Origin of Species." Learn about the wild world of Ice Age carnivores, brainy birds, and other creatures Darwin missed. Our tour guides will be four postdocs on the frontiers of biology. We'll begin at 6pm at the National Evolutionary Synthesis Center in Durham. Parking is free. National Evolutionary Synthesis Center (NESCent) 2024 W. Main Street, Suite A200 Durham, NC 27705 Map: http://bit.ly/rGmKM Travel Directions: The National Evolutionary Synthesis Center is near the corner of 9th St. and W. Main St. in Durham, on the 2nd floor of the Erwin Mill B...

FOXP2 in Nature

Gene Expression — Wed, 11 Nov 2009 22:08:00 +0100

Human-specific transcriptional regulation of CNS development genes by FOXP2:...It has been proposed that the amino acid composition in the human variant of FOXP2 has undergone accelerated evolution, and this two-amino-acid change occurred around the time of language emergence in humans...However, this remains controversial, and whether the acquisition of these amino acids in human FOXP2 has any functional consequence in human neurons remains untested. Here we demonstrate that these two human-specific amino acids alter FOXP2 function by conferring differential transcriptional regulation in vitro. We extend these observations in vivo to human and chimpanzee brain, and use network analysis to identify novel relationships among the differentially expressed genes. These data provide experimenta...

Levels of selection & the full Price Equation

Gene Expression — Wed, 11 Nov 2009 21:34:31 +0100

In the post below on the Price Equation I stayed true to George Price's original notation in his 1970 paper where he introduced his formalism. But here is a more conventional form, the "Full Price Equation," which introduces a second element on the right-side. Δz = Cov(w, z) / w + E(wΔz) / w One can specifically reformulate this verbally for a biological context: Change in trait = Change due to selection on individuals + Change due to individual transmission The first element on the right-side is explicable as selection upon a heritable trait. w is the conventional letter used for "fitness," so w is population mean fitness, and serves to normalize the relation. "z" is the trait. The term "individual" can mean any set of entities. The straightforward plain interpretation may...

The intersection of public policy, economics, & evolution

A Blog Around The Clock — Tue, 10 Nov 2009 23:22:49 +0100

Next Monday at NESCent: When: Monday November 16, 2009, 10-11:30am Where: NESCent, 2024 W. Main St., Durham, NC 27705, Erwin Mill Bldg, Suite A103 Directions: http://www.nescent.org/about/directions.php What do public policy and economics have to do with evolutionary theory? A lot, say participants in an upcoming meeting at the National Evolutionary Synthesis Center (NESCent) in Durham, NC. Nearly 30 scholars, policymakers, and entrepreneurs from both the academic and the business worlds will gather at the NESCent headquarters November 13-16, 2009. The purpose of the meeting is to discuss how evolutionary theory can contribute new insights to regulatory problems such as financial reform, environmental regulation, and the regulation of between-group conflict. Leading experts in the fi...

The Price Equation

Gene Expression — Tue, 10 Nov 2009 14:18:39 +0100

In the comments below I referred to the "Price Equation." Here is what William D. Hamilton had to say about George Price's formalism in Narrow Roads of Gene Land: A manuscript did eventually come from him but what I found set out was not any sort of new derivation or correction of my 'kin selection' but rather a strange new formalism that was applicable to every kind of natural selection. Central to Price's approach was a covariance formula the like of which I had never seen...Price had not like the rest of us looked up the work of the pioneers when he first became interested in selection; instead he had worked out everything for himself. In doing so he had found himself on a new road and amid startling landscapes.... In Selection and Covariance, a short letter to Nature in which he intro...

Microbial Systematics

Microbiology Blog: The weblog for microbiologists. — Tue, 03 Nov 2009 12:00:00 +0100

The higher taxonomic groups within prokaryotes are presently distinguished mainly on the basis of their branching in phylogenetic trees. In most cases, no molecular, biochemical or physiological characteristics are known that are uniquely shared by species from these groups. Analyses of genome sequences are leading to discovery of novel molecular characteristics that are specific for different groups of bacteria and archaea and provide more precise means for identifying and circumscribing these groups of microbes in clear molecular terms and for understanding their evolution (Xu, 2010).References:Xu, J. (2010) Microbial Population Genetics. Caister Academic Press, Norfolk, UK.Full range of books on microbiology at Microbiology Books (Source: Microbiology Blog: The weblog for microbiologist...

Microbial population genetics

Microbiology Blog: The weblog for microbiologists. — Tue, 03 Nov 2009 11:54:00 +0100

is a rapidly advancing field of investigation with relevance to many areas of science. The subject encompasses theoretical issues such as the origins and evolution of species, sex and recombination. Population genetics lays the foundations for tracking the origin and evolution of antibiotic resistance and deadly infectious pathogens and is also an essential tool in the utilization of beneficial microbes.References:Xu, J. (2010) Microbial Population Genetics. Caister Academic Press, Norfolk, UK.Full range of books on microbiology at Microbiology Books (Source: Microbiology Blog: The weblog for microbiologists.)

Materialism leads to inequality

Gene Expression — Sat, 31 Oct 2009 20:13:24 +0100

Intergenerational Wealth Transmission and the Dynamics of Inequality in Small-Scale Societies: Small-scale human societies range from foraging bands with a strong egalitarian ethos to more economically stratified agrarian and pastoral societies. We explain this variation in inequality using a dynamic model in which a population's long-run steady-state level of inequality depends on the extent to which its most important forms of wealth are transmitted within families across generations. We estimate the degree of intergenerational transmission of three different types of wealth (material, embodied, and relational), as well as the extent of wealth inequality in 21 historical and contemporary populations. We show that intergenerational transmission of wealth and wealth inequality are substant...

Remember the lizard men

Gene Expression — Thu, 29 Oct 2009 22:22:35 +0100

Carl Zimmer points me an article about a former anthropologist who has some weird ideas about the origin of man: Since his resignation from the university in 1990, however, Horn has changed his tune. Once a staunch Darwinist and tenured CSU anthropology professor, Horn has devoted the last 19 years of his life to the study of alternative theories of human origin. After receiving a doctorate in anthropology from Yale University and while teaching at CSU, Horn focused his energies on the study of the evolution of non-human primates, his wife Lynette Horn said. He now advocates the theory that modern man is not the result of a natural process of evolution, but that evolution was artificially aided by reptilian extraterrestrials. The reptilians bred mankind as servants and continue to rule t...

Alberta has no rats!

Gene Expression — Thu, 29 Oct 2009 07:11:59 +0100

There's something cool about Canada, I just found out that Alberta is the only large region of permanently inhabited human territory which lacks brown rats. One thing you have to remember is that the brown rat only began spreading within the last 1,000 years (in the process displacing the black rat), and it seems to have arrived in the British Isles only within the last two to three centuries. North America did not have the rat until Europeans arrived, and it didn't show up in Alberta until 1950. At that point the government attempted an eradication program. Apparently this can work because there aren't ecologically congenial corridors for the rats to constantly reappear through migration. Read the comments on this post... (Source: Gene Expression)

Svante Paabo didn't say what I suggested he said. Perhaps

Gene Expression — Wed, 28 Oct 2009 09:31:03 +0100

Dr. Thomas Mailund has posted a YouTube interview of Svante Paabo. Looks like the previous post was off-base, though I'm not really totally sure. Read the comments on this post... (Source: Gene Expression)

"What Darwin Said"

Gene Expression — Tue, 27 Oct 2009 22:58:48 +0100

My co-blogger at Gene Expression Classic, David, has completed a very interesting series today. 1: The Pattern of Evolution 2: Mechanisms of Evolution 3: Heredity 4: Speciation 5: Gradualism (A) 6: Gradualism (B) 7: Levels of Selection Read the comments on this post... (Source: Gene Expression)

Svante Paabo believes modern humans & Neandertals interbred

Gene Expression — Mon, 26 Oct 2009 21:20:00 +0100

Neanderthals 'had sex' with modern man:Professor Svante Paabo, director of genetics at the renowned Max Planck Institute for Evolutionary Anthropology in Leipzig, will shortly publish his analysis of the entire Neanderthal genome, using DNA retrieved from fossils. He aims to compare it with the genomes of modern humans and chimpanzees to work out the ancestry of all three species....Paabo recently told a conference at the Cold Spring Harbor Laboratory near New York that he was now sure the two species had had sex - but a question remained about how "productive" it had been."What I'm really interested in is, did we have children back then and did those children contribute to our variation today?" he said. "I'm sure that they had sex, but did it give offspring that contributed to us? We will...

Celebrate Darwin's 200th birthday

A Blog Around The Clock — Mon, 26 Oct 2009 13:57:23 +0100

Henry Markram on TED – video online

neurodudes — Thu, 22 Oct 2009 17:20:25 +0100

We had read that Dr. Henry Markram of the Blue Brain project had given a talk at TED (technology, entertainment, design), but the video wasn’t released until this month. This talk is geared towards a general audience, rather than getting into the specific details of the Blue Brain project, as he has before. It is engaging and includes many suggestions towards the future of neuroscience and AI. Watch it online at the TED website. (Source: neurodudes)

The arcs of evolutionary genetics always cross back

Gene Expression — Thu, 22 Oct 2009 12:13:07 +0100

If you have more than a marginal interest in evolutionary biology you will no doubt have stumbled upon the conundrum of sex & sexes. Matt Ridley's most prominent work, The Red Queen: Sex and the Evolution of Human Nature, covered both the theoretical framework and applied implications of the subject. Ridley leaned heavily upon William D. Hamilton's scientific work, which extended upon Leigh Van Valen's concept of the book's titular Red Queen. The complex interplay between pathogens & multicelluar organisms across the eons is a topic of such breadth and depth that a substantial proportion of the territory in evolutionary biology is still devoted to it, and how sex may relate this dance. Hamilton spent the second half of his career focusing on just this question, outlined in Narrow Roads of ...

The arc of evolutionary genetics may be irreversible

Gene Expression — Wed, 21 Oct 2009 14:33:34 +0100

One of the banes of modern life is the stack of papers in one's "to-read" list. I guess that goes to show how cushy modern life is, as what sort of complaint is that? In any case, I began to consider this after reading Joe Thornton's magisterial response to Michael Behe's giddy excitement over his most recent paper, An epistatic ratchet constrains the direction of glucocorticoid receptor evolution. Thornton dispatches Behe's muddled misconceptions with economy and precision, but after reading the paper, as opposed to cogent summaries such as Carl Zimmer's in The New York Times I'm even more at a loss as to how Behe arrived at the conclusions he did as to the paper's significance (please read the paper, available on Thornton's lab website, and then try and make sense of what Behe is asserti...

Being Michael Behe

Gene Expression — Wed, 21 Oct 2009 06:25:00 +0100

Reading Joe Thornton's response to Michael Behe, I'm struck by the de ja vu that the exchange induces. I remember reading Darwin's Black Box when it came out, and being confused as to why this was such an awesome challenge to evolution, and following the debates in its wake. Behe seems to think he's pwning everyone, when his arguments from outside of his charmed circle seem a bit flimsy and amateurish.But let's assume that Behe doesn't have any screws loose. There have to be presuppositions which allow for his arguments to seem rock-solid and irrefutable in his own cognitive universe. I know that some readers of this weblog have ID sympathies. Normally I just delete those sorts of comments because I'm an intolerant evolutionist/intolerant of idiocy (your selection of the two options obviou...