Category Archives: Evolution

Current Biological Diversity

Current Biological Diversity The latest re-post of my BIO101 lecture notes (this one originally from June 05, 2006). I know I will have to rewrite everything about the Three Domain Hypothesis, but you also tell me if I got other stuff wrong or if this can be in some way improved for the classroom use.

Continue reading

“What God Created on the Fourth Day?” is not an SAT question, sorry!

Most of our anti-Creationist battles are over efforts to infuse Christian religion into K-12 education. One common battlefield is the courtroom where our side has (so far, until/unless the benches get filled with more clones of Priscilla Owen) won. But another place where we can stop them is the college admission office.
Sara Robinson of the Orcinus blog (which everybody should read daily) revisits, in more detail than I ever saw on any science blogs at the time this first started, the legal battle between the University of California and the Calvary Chapel Christian School over what constitutes permissible educational standards:

The battle started back in late 2005, when UC reviewed Calvary’s courses and decided that several of them — including “Special Providence: Christianity and the American Republic and “Christianity’s Influence on America,” both history courses; “Christianity and Morality in American Literature,” an English course; and a biology class — did not meet their curriculum standards, and would not be counted toward the admission requirements when Calvary students apply to UC.

Sara goes on to say later on something that I expect our resident science philosophers, historians and ethicists to chime in on:

When it comes to the history and English courses, they’re absolutely right. We all look at language and history through the filters of culture. The subjects lend themselves to multiple interpretations, depending on your perspective. Understanding this, and being exposed to the full range of perspectives in these fields — including religious ones — is an essential part of secondary and undergraduate education.
But nobody, save the Christian schools, teaches science or math that way. There is no African-American or Latino or feminist or Jewish or Russian science (Hitler and Stalin notwithstanding). There’s just a method, and a group of techniques, and the skill-building and knowledge base required to use them well. Scientists do their best — with varying degrees of success — to uncover their cultural biases and move beyond them. The greatest ones regard bias as a dangerous source of error: it can blind you, and lead you to draw the wrong conclusions from the observed facts. For that reason, any textbook that starts off by telling you to believe a 2,000-year-old religious scripture over your own lying eyes is not teaching science. It’s putting students on the path to a Christian version of Lysenkoism.

But the whole essay was prompted by Sara’s initial sense of despair she felt before discovering this case:

I’ve been saying for a long while now that the power to end the Intelligent Design fiasco, firmly and finally and with but a single word, rests in the manicured hands of the chancellors of America’s top universities. The message is short and simple: “Teach what you like, it’s all fine with us. But if you put ID in your science courses, we will not accept those courses as adequate for admission to our campus.”
Making this kind of public statement would be one small step for a university chancellor; and one giant leap for American science education. Somebody, somewhere, needs to set a firm standard. If our universities — which bear responsibility for training our professional scientists, and maintain the labs and faculties responsible for much of our best research — won’t stand up and draw that line, then we really are well and truly lost.

Well said. Feel free to add comments either here or over on Orcinus .
Technorati Tag: teaching-carnival

Evolution, Interactions, and Biological Networks

Here is a new paper that just came out on PLoS-Biology. What do you think?

Nobody here but us chickens…

I have just realized that I keep mentioning David Sloan Wilson a lot (see the list of links below), always in a positive light as I think he is one of the pioneers of modern evolutionary theory (as soon as those drunk on Williams 1966 and Dawkins’ opus retire or die) but have never really written a good post on group selection. I’ll have to do this one day soon – that may be my contribution to the Basic Concepts collection.
Anyway, Wlison just gave a talk in which he presented my favourite example of the test of group selection – in chickens:

Two experiments using chickens show another aspect of evolution regarding selection. In the first experiment, groups of chickens in cages were evaluated for egg-laying. The best egg-layer within each cage was chosen and put together with the other prolific egg-layers. The second experiment took the best caged groups of egg-layers. The result of the second experiment after a few generations was healthy, sociable, egg-laying chickens. The result of the first experiment after a few generations was fighting and anti-social chickens that maimed and killed each other.
“You pick the best,” Wilson joked, “and in six generations you get sociopaths.”

Those two papers actually came out in Poultry Science, not Evolution, thus they are not as well known by the evolutionary community as they should be. What Wilson did not mention in his talk is that the group-selection experiments resulted, over just a few generations, in a greater egg-production than ever achived in a couple of thousand years of selective breeding of chicken. It also resulted in a complete loss of need for de-beaking of chickens, which is a nasty procedure in poultry industry.
Perhaps these chicken don’t peck each other to death because they all adopted the identical religious beliefs LOL!
You can see my earlier mentions of Wilson here (really this), here, here here, here, here, here, here, and here.
Update: Mike has more.

Origin of Biological Diversity

Origin of Biological DiversityContinuing with the Thursday series of the BIO101 lecture notes. Check for errors of fact. Suggest improvements (June 01, 2006):

Continue reading

Rate vs. Speed of Evolution

Science Daily should know better. The title is OK:
Annual Plants May Cope With Global Warming Better Than Long-living Species
But look at the first sentence:

Countering Charles Darwin’s view that evolution occurs gradually, UC Irvine scientists have discovered that plants with short life cycles can evolutionally adapt in just a few years to climate change.

Excuse me, but there is nothing there countering Darwin, or countering gradual evolution!
They are mixing two senses of the word “slowly”. Under the same strength of selective pressure, all organisms will evolve at the same rate. That does not mean they will evolve over the same time period. Rate is calculated in relation to the number of generations, not in absolute times.
So, humans, tomatoes and bacteria evolve at the same rate (roughly). But, in, let’s say 30 years, humans will only have one switch of generations, tomatoes will have thirty, and bacteria will have 10,000 generations. If evolving at the same rate, bacteria will evolve much faster in terms of absolute time than tomatoes which, in turn, will evolve faster than humans in terms of absolute time.
While this distinction is relevant to the problem of a fast-changing climate, organisms differ not in how gradually they can evolve – that is roughly equal – but how many generations they can squeeze into the same absolute time period. So, annuals and perennials evolve at the same rate, but annuals evolve faster.

How the Giraffe Got Its Neck?

The Icons of Evolution finally tested! Who won? Lamarck or Darwin?
Under the fold:

Continue reading

From Genes To Species: A Primer on Evolution

From Genes To Species: A Primer on EvolutionThe eighth part of my lecture notes series. As always, please pitch in and make my lectures better by pointing out the factual errors or making suggestions for improvement (originally posted on May 17, 2006):

Continue reading

Why do we have sex?

Part 1
Part 2
Part 3

Cephalopods don’t need a mirror test – they are mirrors themselves .

PZ probably already knows about this, but I found this discovery of super-reflective skin cells in squid, cuttlefish and octopus quite amazing!

Hanlon’s team discovered that the bottom layer of octopus skin, made up of cells called leucophores, is composed of a translucent, colourless, reflecting protein. “Protein reflectors are very odd in the animal kingdom,” says Hanlon, who is a zoologist. What’s even more odd is just how reflective these proteins are — they reflect all wavelengths of light that hit at any angle. “This is beautiful broadband reflection,” Hanlon told the Materials Research Society at their meeting in Boston last month. The result is a material that looks startlingly white in white light, and blue in the bluish light found beneath the waves. “These cells also match the intensity of the prevalent light,” says Hanlon’s research associate Lydia Mathger. All this helps the creatures to blend into their surroundings.

Hat-tip: Matt Dowling

Mammoth Behavior and Bear Taxonomy

Did mammoths scratch themselves against rocks?

Parkman believes, and he has a growing body of evidence to prove that mammoths and other large Ice Age creatures once used these very rocks near Duncan’s Landing, along the Sonoma Coast State Beach, to scratch their backs. He claims the giant mammals rubbed so much that large swaths of rock have been buffered smooth.

Bears scratch against the trees, but which species is which? Lumpers vs. Splitters.

Today on PLoS – Biology

Interspecific Communicative and Coordinated Hunting between Groupers and Giant Moray Eels in the Red Sea:

The article offers a description and accompanying videos, such as the one showing a grouper and eel swimming side by side as if they are good friends on a stroll. It also offers quantification, which is truly hard to achieve in the field, of the tendencies involved in this mutually beneficial arrangement. The investigators were able to demonstrate that the two predators seek each other’s company, spending more time together than expected by chance. They also found that groupers actively recruit moray eels through a curious head shake made close to the moray eel’s head to which the eel responds by leaving its crevice and joining the grouper. Groupers showed such recruitment more often when hungry.
Given that cooperative hunting increases capture success for each of the two predators, and that they don’t share with each other but swallow the prey whole, their behavior seems a form of “by-product mutualism,” defined as a form of cooperation in which both parties achieve rewards without sacrificing anything for the other. They are both out for their own gain, which they attain more easily together than alone.

Divergent Selection on Opsins Drives Incipient Speciation in Lake Victoria Cichlids:

Though Lake Victoria cichlids appear millions of years younger than their counterparts in nearby Lake Malawi, both groups display an enormous range of physical and behavioral traits. This staggering diversity in such young species provides compelling evidence for adaptive radiation, which occurs when divergent selection operates on ecological traits that favor different gene variants, or alleles, in different environments. When divergent selection on an ecological trait also affects mate choice–promoting reproductive isolation of diverging populations–ecological diversity and speciation may proceed in tandem and quickly generate numerous new species.
Despite substantial theoretical and some experimental support for such “by-product speciation,” few studies have shown that selection has “fixed” alleles (that is, driven its frequency in a population to 100%) with different effects on an adaptive trait in closely related populations. But now, Yohey Terai, Norihiro Okada, and their colleagues have bridged that gap by demonstrating divergent selection on a visual system gene that influences both ecological adaptation and mate choice in cichlids.

Books: Michael Pollan – The Omnivore’s Dilemma

Amanda just reviewed Michael Pollan’s book The Omnivore’s Dilemma and also recently wrote a post on the same topic while under the influence of the book. I agree with her 100%, so go and read both posts.
I have read the book a couple of months ago and never found time to write a review of my own. I also remember that I finished the book on a Thursday afternoon – an important piece of information as it is on Thursday afternoons that there is a Farmers’ Market here in Southern Village, barely a block from me. The first thing I did when I closed the book was to walk up to the Farmers’ Market, buy some locally grown food and talk to the farmers about all the issues raised in the book and, lo and behold, they all agree with Pollan on everything I asked them about.
They were also a little taken aback that I tried to talk to them. But, I grew up in the Balkans. A big part of going to the Farmer’s Market is to chat with the farmers, banter, joke, complain about the government, haggle over prices, and make sure a kilo of cheese is reserved for you for next week – it is a very friendly and talkative affair. Great fun! Here, there is much more of a class divide. The farmers set the prices. The elegantly dressed city-slickers pick and pay. And all of that is done pretty silently, with a minimal exchange of words. No eye-contact. Nobody is haggling! At the Farmers’ Market nobody is haggling!?*@#%$^&! Travesty and Heresy!
In his book, Michael Pollan initially set out to make three – industrial, organic and personal – types of meals, but once he learned more, he realized he had to do four: industrial, industrial-organic, local-sustainable, and personal.
So, although the book officially has three parts, it really has four. Each of the four parts also reads differently and has a different style and tone:
The first part (industrial) is full of facts, stats, governmental documents, etc. – it reads like Molly Ivins’ Bushwacked or Chris Mooney’s Republican War On Science, although I heard he played loose with some stuff, i.e., cited as true some studies that are very contentious within the scientific community.
While I am a biologist, focusing on animals made me “plant blind” and I learned more about biology of corn from this book than I ever knew before.
The key event, according to Pollan, is the change, during Nixon administration, in the way farmers are paid for corn – everything else flows from that single event: the monoculture, the oil, the feedlots, the fertilizers and pesticides, environmental destruction, obesity and McDonalds.
The second part (industrial organic) is a little bit less of an onslaught of information and he gets a little looser and slower, a bit more personal. He looks at the way organic food production changed since the 1960s hippy farms to today’s giant organic producers who are, more and more, playing by the rules of Big Agra.
While the food they produce is still better than the Industrial and the practices are still more energy and environmentally friendly than Industrial, it only looks good because it is compared to the Big Industrial which is totally atrocious. This part of the book resulted in a big back-and-forth debate between Pollan and John Mackey, the CEO of Whole Foods, resulting in some changes in the way Whole Foods operates. You can find the relevant links on Pollan’s website.
The third part (local-sustainable) is totally fascinating – it is a mix of a travellogue and analysis – he keeps jumping back and forth between his dialogues with his host – Joel Salatin of the Polyface Farms – and the data. This is really the most riveting part of the book and the key element of it. This is also a part of the book that covers most new ground, not stuff found in Fast Food Nation or other well-known books. It also exposes, even better than the first part, the perniciousness of the way our agricultural system is set up, the way Big Agribusiness controls legislation and regulation, and eliminates small farmers from the competition.
Joel Salatin is a Virginia farmer who has perfected amazing agricultural practices on his farm – practically nothing has to be bought by the farm and nothing gets thrown away. Everything has its use and re-use. Everything makes sense when patiently explained to the reader. I actually bought Salatin’s book Holy Cows and Hog Heaven and read it immediately after Pollan’s.
Interestingly, although the guy is a conservative, libertarian, Christian Creationist, I agree with him on almost everything. His distrust of the Government is perhaps a little bit over the top for my taste, but his Creationism is fascinating because his whole philosophy and his whole methodology of the way he runs the farm reveals a deep understanding of evolution and ecology. His farming practice is BASED on evolutionary thinking. He is, for all practical purposes, an evolutionary biologist. Yet, he says he does not believe in evolution. How is that possible? Because he has no idea what he word “evolution” means. He probably has some “chimp is your uncle” cartoon notion of evolution, while at the same time not giving his own evolutionary ideas any name at all. Someone should tell him.
The fourth part (personal) of the Pollan’s book is in a completely different mood, very introspective, sometimes even mystical. One important thing that sets this part apart is that the type of food production described in it is the only one of the four that cannot in any way be affected by legislation, politics or activism – unless one completely bans hunting, gathering, catching, picking, stealing from neighbors, planting stuff in your garden, or collecting yeast from the air!
The best part of this portion of the book is his look at animal rights and his dialogue with Peter Singer. He, being such a typical city-slicker and “Birckenstock liberal” (Come on – slaughtering a chicken, and later a pig, made him sick? Has he never watched or participated in any kind of animal slaughter in his long life yet? Never spent some time on a farm? Dissected an animal in a biology class? What a woefully unnatural and alienated existence!), started out very sympathetic to the idea, but, over a dozen pages or so, dissects the underlying logic and discovers its fatal flows and exposes it in a brilliant paragraph – the best one in the book. You’ll find it and recognize it immediately once you read it – and you will read it because Omnivore’s Dilemma is one of the most important books written in the last few years, and should be a battle cry for many political activists and a source of ideas for many candidates for political office.
In the meantime, go read Amanda’s review.

Evolution

This file was too large to upload.
(hat-tip)

Where do people find information about evolution?

I am sure glad that others have started parsing the numbers of the new report on ‘The Internet as a Resource for News and Information about Science’.
Duane Smith takes a close look at a couple of tables in the report and concludes that, while relatively few people say they get their information on evolution directly from the Bible and Church, many do so indirectly, by beeing steeped in their comunities’ beliefs transmitted by family, friends and neighbors (as well as local and church-run media). Interesting take (and I agree with him on this). What have you found so far?

Creatures of Accident

You know that I think that Wallace Arthur is one of the sharpest writers on evolution today and that his Biased Embryos and Evolution is one of the best books I’ve read recently on the topic. I just saw that he has a new book out, Creatures of Accident. Has anyone read it yet? Is it good? Just in case, I placed it on my amazon wish list, so, if you think it is worth my while, I can get it once I get hold of some cash.

I Like M&Ms

I am still sleepy from all that tryptophan in turkey meat and the Evolution wine, so I don’t think I have the energy to write a big post now – I’ll leave much of my thoughts on the matter for a post-weekend post reviewing Dawkins’ The God Delusion.
But I have to chime in briefly by sending you to the relevant links and copying some of the comments I wrote on those comment threads. Brace yourself for a lot of reading as there are several posts and many comments on each of the posts. Sorry, the links are not neccessarly in order, but you’ll get the gist of the argument anyway.
Ed Brayton starts out here and responds to criticisms here.
Larry Moran fires the first salvo here and responds here.
Pat Hayes pitches in here and here.
John Lynch has three posts on the topic: here, here and here.
Buridan clears up some definitions here.
John Pieret takes his side here and here.
John Wilkins just in with this.
PZ Myers (and a gazillion commenters) responds to the whole brouhaha here.
[Update: Josh Rosenau and Mike Dunford have some thoughts on the issue as well.]
[Update 2: Ed Brayton, John Pieret and John Lynch have added further responses.]
[Update 3: Razib, John and Ed have more…and now Josh again! And a good one from Tyler again. And now also Daniel Rhoads. And also Paul Decelles.]
Whoa! What an internecine war! By now, you know that “M&M” stands for Myers&Moran and my title of this post tells you where I stand.
First, let me copy a little quote from my review of Ken Miller’s talk:

“A few years ago, I was of the mind that something like theistic evolution is a good idea to spread the message that evolution is not evil. I thought that people like Ken Miller are great messengers to soften up the people (step 1) and prepare them for eventual compIete abandonment of the Creator (step 2). And even those who never get to Step 2 are less dangerous than straight-out creationists.
I certainly have no problems with anyone personally believing whatever they want. But I am more and more moving to the opinion that this is not a good strategy. It is just providing the apologia for the believers who have a problem with being perceived as medieval, and allowing them to, then, provide apologia for their more extreme brethren. They – the moderates and the fundies – flock together when the going gets tough and it really counts – the political battles between 15th and 21st centuries.
The moderates are no friends of reason when it counts the most, outside of comfortable chats on panels on campuses. Evolution battle is not a battle of science, it is a battle of mindsets and worldviews: medieval vs. modern. Giving a helping hand to those who give their helping hand to the medieval bigots and authoritarians is not a good strategy. They need to be made uncomfortable – Dawkins-style – and forced to choose and come clear with which side they are on. Otherwise, they’ll play nice with us when it does not matter, and stick their fingers in their ears and sing “la-la-la” when real action is required.”

People who focus narrowly on preventing IDC form entering schools do not see the big picture, i.e., that Creationism Is Just One Symptom Of Conservative Pathology (go read that post now!). Thus, people like Dawkins, Myers (or me) are fighting against the bad politics of the church.
While Lennonnesque Imaginings of a world without religion are cute fantasies, we are a little bit more realistic. We know that religion is here to stay no matter what we do and we know that even organized religion can be and has been harnessed for change for good (as in Civil Rights movement). So, we want to fight against the political (added clarification: conservative) aggressiveness of churches in all spheres – creationism being just one of the prongs of their multi-prong strategy to roll back Enlightement.
While evolutionary biologists and philosophers of science are best suited to counteract creationism (and reproductive and developmental biologists to counteract abstinence-only education, opposition to abortion, stem-cell research and cloning, and psychologists and others should use their knowledge to counteract other prongs of their strategy), we need to all be aware that there is a big picture and that we need to work on it all together.
Part of the battle is to force the mealy-mouthed “moderates” to choose sides. ‘Mealy-mouthed’ moderates are, for instance, “liberal Christians” who believe in evolution and are generally on right side of issues but do not raise any voices against their fundie brethren and, when push comes to shove, side with them (as they are all Christians) against us. [added: this group also includes closet atheists/agnostics too afraid to speak up]
Different targets will respond to different tactics. Dawkins/Harris/Dennett tactic WILL work as one part of the strategy, targeting particular groups, and moreover changing the environment in which the debate is fought (a little bit of niche-construction). Ken Miller and those folks have their roles and can move over other types of people to choose sides.
The M&M approach is only going to push the true fundies away and they are already as far away as can be. The moderates – those who are culturally religious but on the right side on most scientific, moral and social issues – are unlikely to be pushed away by M&M rhetoric, and may even get a validation from it and get pushed in the opposite direction.
Dawkins, Harris and Dennett are changing the landscape of the discourse, forming an environment in which it is possible to talk about atheism and religion on a level field. Without them, we’d be forced to hide our atheism even more than before and allow the fundies to define us as amoral.
In other words, focusing only on preventing creationism from entering schools is missing the forest for the trees. We have managed to win a bunch of court cases, the latest one in Dover. But we have not won in the court of public opinion. And, if the entire religious plan succeeds, the courts of the future will be filled with clones of Priscilla Owen and all our victories against Creationism (and the Pledge of Allegiance, prayer in school, ten commandments in courthouses…) will be reversed.
Thus, in order to win the war, we have to engage the enemy at all fronts, not just the one where we feel like it. Let’s look at some previous success stories.
Women did not gain equality by being quiet and not rocking the boat. African-Amercans did not gain equality by being quiet and not rocking the boat. Gays did not gain equality by being quiet and not rocking the boat.
What those three groups did, and are still doing, is changing the discourse by being darn loud! A hundred years ago, a woman was a man’s property – not any more, and it is deemed extremely vile to suggest so in this day and age. Fifty years ago, stating that Blacks and Whites should be separated because Blacks are stupid and dangerous was a mainstream position – try saying that today and see what happens to you! Ten years ago, saying you are gay invited getting beaten up. See what just a decade of loud agitation has done – some kind of movement towards the right direction (gay marriage of civil unions) in several US states, Canada, Spain, UK, South Africa, now even Israel!
The first, loud pioneers set the stage for the debate and move the goalposts. They often endanger themselves initially, but their example prompts many others to come out of the closet. There are always those who are too afraid to speak out, to rock the boat. They try to talk the enemy out of destroying them instead of exposing the enemy for the brute it is. Being moderate, playing nice, and appeasing the fundies hellbent on destroying you is not a working strategy. Building a large, loud, uncompromising and powerful movement is. Ridiculing the enemy in the public sphere and changing the discourse – what is mainstream and what is not – gradually wins our wars against the anti-Enlightement forces.
If you go to feminist, Black and LGTB blogs, you’ll see that it is easy for them to make fun of latest rantings by white, rich males, like Brooks, Tierney and Derbyshire. But they have particular ire against people of their own who either side with the enemy or allow to be manipulated by the enemy – the antifeminist women, the Blacks who push (as Republican officials, usually) the anti-Black agenda, the Mehlmans and other gays in the GOP who actively work on anti-gay legislation. Why is it suprising that such a thing would not happen in the, much newer and younger, atheist movement?
The silent reverence for religion is something quite American. You need to read this to understand where I come from. In Yugoslavia, in 1941 everyone was officially religious, in 1951 some people were religious but were too afraid to say so because they feared persecution, in 1961, some people were still religious (although getting older), they went to church on Sunday but did not tout their religiosity in fear of ridicule. By the time I was aware of my surroundings in the 1970s and 1980s, only very few people were religious, those were very old and mostly in the countryside and nobody my age believed in God:

“The resurgence of religion in the area in the 1990s is fascinating to me. I do not believe that most of those people are really religious i.e., believe in God. It is purely a political instrument, as well as a way to use easily recognizable signals to differentiate between ethnic groups that are otherwise indistinguishable. Thus Serbs started sporting Orthodox paraphernalia, Croats Catholic stuff, and Bosnians Islamic symbols.”

The Western pundits, steeped in their own culture, quite erroneously labeled the Balkan conflict a “religious war”. It was more a war between the fans of Red Star, Dinamo and Zeljeznicar soccer clubs. And while the decade of wars and economic sanctions, coupled with migrations of the best-educated abroad and the country-folks into cities, made public religiosity by Right-wing extremists OK, the country is still predominantly atheist and secular. See this if you don’t believe.
Here in the USA, we cannot institute a top-down government-sponsored ridicule of religion. The system works differently here. Big societal changes, including changes in how we think about issues, are brought about by large, loud movements. But if atheists form such a movement – and this looks like a great time for a backlash against the fundamentalist overreaching – the discourse will change. Nobody in the next generation will fall for the idiotic notion that atheists are immoral. And, just like the communist government in the old Yugoslavia realized, there is no need for any kind of legislation banning religion and religious activities – public ridicule does the job marvelously on itself.
In this post (another must-read) I wrote:

Thus, we need to see the battle over evolution not as a separate battle, but as a part of a bigger war between Enlightement and Anti-Enlightement. One cannot be won without the other. And while some battles in this war can be and should be fought at the level of national politics, the battle over education, including the battle over evolution, requires us to get at their kids. For that, we need to go local. Winning cases in court works only for the short term – they will come again and again and, with conservative activist judges being appointed left and right, they will start winning soon. Getting elected to school-boards, teaching in schools, teaching the teachers, pushing for non-test-based educational systems, pushing for tests of critical thinking (including evolutionary thinking) in schools as well as for home-schooled children, …those are the ways to fight them long term, thus the only way to win this battle. Winning this battle – the battle over childrearing and education – will be the key for winning the whole war long term. Without new recruits from the new generations of children, the forces of Anti-Enlightement will dwindle in numbers, lose power, and finally die out. As a liberal, I am an optimist, a believer in progress, and cannot see how, in the long term they can win and we can lose. But in the meantime we need to fight to prevent them from incurring too much damage while they still have the power. Explaining evolution over and over again is not the way to do it.

But the project I describe here can only be succesful if the social and political environment allows it. And to change the discourse, to start getting taken seriously, and to change what is mainstream and what is not we need more M&Ms. If reason prevails and fundamentalism looses, then nobody will ever overturn our legal victories against Creationists. If we keep winning anti-IDC cases but ignore the environment in which it all happens, we will soon start loosing in courts as well. It’s fine if Ken Millers of the world want to help out in IDC cases and to move some minds on their lecture circuits, but in the long run, they’ll have to decide are they on the side of reason or on the side of their religion which also includes the most politically active fundies.
Dawkins is correct:

I tell Dawkins what he already knows: He is making life harder for his friends. He barely shrugs. “Well, it’s a cogent point, and I have to face that. My answer is that the big war is not between evolution and creationism, but between naturalism and supernaturalism. The sensible” – and here he pauses to indicate that sensible should be in quotes – “the ‘sensible’ religious people are really on the side of the fundamentalists, because they believe in supernaturalism. That puts me on the other side.”

Shermer on Evolution

Michael Shermer has an interview in the latest American Scientist on Creationism and his new book Why Darwin Matters.

Ken Miller talk

Last night I went back to my old campus to attend the Dr. Robert Rabb Lecture by Ken Miller. The Stewart Theater was packed. I saw a lof of old friends, but, as it was crowded, only got to spend some time talking to a couple of them.
Oh, there were bloggers there, too, of course. I first met up with Reed and Professor Steve Steve. Steve Steve is omnipresent (today in Raleigh, NC, yesterday in Vancouver, before that in Australia), omniscient and omnipotent (knew how and then fixed the computer and projector for the speaker) and benevolent (endless patience getting his picture taken with everyone – will post once available). Mr R was also there with his wife, but had to leave during the break between the lecture and the panel discussion, so we met for only a few seconds.
Rev.BigDumbChimp is Dr.Rabb’s grandson. He drove up from South Carolina for the occasion. Reed and I were worried how we were going to find him in the crowd. I suggested we get up to the microphone and ask for Big Dumb Chimp and hope he’d raise his hand and yell “It’s me”. I do not recall now why we decided not to pursue this strategy. Anyway, he walked in with the rest of the Rabb family and we immediatelly recognized each other (having a picture on one’s blog is sometimes a good idea) and got to chat a little bit. Hopefully, he’ll come to the Science Blogging Conference in January so we can have more time to talk.
Ken Miller is a very polished and energetic speaker. I had to remind myself that I was an unusually well-informed person in the audience of academics there – I actually knew the details of the Dover trial and have read big chunks of Judge Jones’ decision, I have recognized the authors of all quotes before he revealed them (including the quote from the Pope), and I new all the examples of evolutionary findings he used (whale evolution, Tiktaalik, immune system evolution, bacterial flagellum evolution). But I read science blogs all the time, including the Panda’s Thumb. Scientists do not – they read scientific papers all the time and are not as well informed about the creationist shenannigans, so much was probably new to them last night. In any case, it was fun, and getting a little bit of internal information from the courtroom proceedings was great.
But then, in the last part of the talk, he started on his apologetics for theistic evolution, slamming Dawkins for being “pessimistic” and totally misunderstanding the Darwin quote (the last paragraph in the Origin):
“There is grandeur in this view of life, with its several powers, having been originally breathed into a few forms or into one; and that, whilst this planet has gone cycling on according to the fixed law of gravity, from so simple a beginning endless forms most beautiful and most wonderful have been, and are being, evolved.”
This does not mean there is a God making the world wondrous, it means that there is no need for the God hypothesis to see the grandeour. Actually, the God hypothesis impoverishes one’s sense and prevents one from being able to see the full scope of the grandeur of the Universe.
The panel afterwards was worse, with six “liberal” clergy-members on it: Miller is Catholic, there was a Baptist, a Presbyterian, a guy leading the Campus Crusade for Christ, a Moslem and a Reform Rabbi (the only one I knew from before – Rabbi Lucy Dinner of Temple Beth Or, the only woman on the panel). There was no representative of atheism on the panel, so these six people were free to preach “love”, and the power of prayer, and the Non-overlapping Magisteria without being challenged. I was sitting there watching them and thinking – hey, of all the hundreds of smart people in the auditorium, they picked the six with emotional problems to tell us all how to think?! OK, they were not the worse – there was also a local Creationist (YEC) group there, too scared to ask questions in public so they tried their hand afterwards, with Ken Miller enjoying himself visibly while rebuffing all their claims.
A few years ago, I was of the mind that something like theistic evolution is a good idea to spread the message that evolution is not evil. I thought that people like Ken Miller are great messengers to soften up the people (step 1) and prepare them for eventual compIete abandonment of the Creator (step 2). And even those who never get to Step 2 are less dangerous than straight-out creationists.
I certainly have no problems with anyone personally believing whatever they want. But I am more and more moving to the opinion that this is not a good strategy. It is just providing the apologia for the believers who have a problem with being perceived as medieval, and allowing them to, then, provide apologia for their more extreme brethren. They – the moderates and the fundies – flock together when the going gets tough and it really counts – the political battles between 15th and 21st centuries.
The moderates are no friends of reason when it counts the most, outside of comfortable chats on panels on campuses. Evolution battle is not a battle of science, it is a battle of mindsets and worldviews: medieval vs. modern. Giving a helping hand to those who give their helping hand to the medieval bigots and authoritarians is not a good strategy. They need to be made uncomfortable – Dawkins-style – and forced to choose and come clear with which side they are on. Otherwise, they’ll play nice with us when it does not matter, and stick their fingers in their ears and sing “la-la-la” when real action is required.
Note: the links to bloggers are now links to their own commentaries on the talk.

Dinosauroids

dinosauroid%20r%26s.jpgI took a class with Dale Russell a few years ago. It was one of the most memorable classes ever, mainly because of Dale’s overwhelming enthusiasm for the subjects of dinosaurs and evolution (as well as the coolest field-trip to the vaults of Carnegie Museum, getting to touch and hold and discuss fossils never seen by general public).
But I was always uneasy with Dale’s overly-anthropomorphic depiction of ‘alternative’ evolution, i.e., what if dinosaurs did not go extinct. First of all, there is no reason to believe that anything as intelligent as us would ever have evolved. But even if it did, and even if it evolved out of dinosaurian ancestors, there is no reason why it would ever look similar to us in morphology. Now Darren Naish explains why and provides (in the comments) some examples of fish and birds (parrots, of course) with large brain:body ratios comparable to ours.

Elephants pass the mirror test

Humans do it, great apes do it, dolphins do it, now elephants (also here) have also been shown to do it – recognize themselves in the mirror, i.e., realize that the image in the mirror is the image of themselves and not a strange animal. That’s a biggie in the world of cognitive science and the study of evolution of consciousness:

When the mirror was unveiled in their yard, they immediately walked over and began poking and prodding and inspecting and playing. They used their trunks to inspect it and then themselves. Two got on their hind legs to look on top of the mirror. One got on the ground to inspect the bottom of it. They opened their mouths, exploring an area of their body they were familiar with but had never seen. They even brought their food over to eat in front of the mirror.
“All three of the elephants demonstrated this self-directed behavior,” said Joshua Plotnik, a co-author of the study and a graduate student at Emory. And like children inspecting their own bodies, the elephants put their eyes right up to the mirror, seemingly to figure out what it was and how it worked, he said. Then they investigated parts of their bodies they had never seen. They grabbed one of their ears and pulled it towards the mirror for inspection. “These are behaviors that they don’t normally do,” he added.
The scientists used a non-toxic paint to mark a small spot on one side of each animal’s forehead, which would be visible when it looked in the mirror. They also marked an identical spot on the other side of the forehead, but invisible paint was used to test whether the animals were seeing rather than feeling the mark.
Happy was the only one of the three who noticed the spot and used her trunk to examine it — over and over again. She did not go after the invisible spot on the other side of her forehead.

Scary Stories of Drug Resistance

A brief history of antibiotics and the resistance to them, resistant TB and resistance to Triclosan (antibacterial soap).

Morlocks and Eloi, oy vey!

Razib and commenters are commenting on this article which appears to be 19th century SF-fantasy repackaged as “serious science” about the future evolution of the human species. Actually, the article is so silly, Razib does not even want to waste time on it and points out only one of the obvious fallacies of the argument, the one about skin color. On the other hand, Lindsay does a thorough and delightful fisking that you may enjoy!
I don’t even know in which ‘channel’ to put this post. I guess it is “biology” but only nominally… as we do not have a “nonsense and having fun with it” channel here on scienceblogs.
Update: John Wilkins adds his 2 cents – and you should listen to him, speciation is his area of expertise.
Update 2: John Hawks and PZ Myers also chime in.
Update 3: Mouse Trap and Darren Naish have their own takes on the story.

Evolution Project And A Truly Fair And Balanced Fox

Evolution Project And A Truly Fair And Balanced FoxMeandering Musings on evolutionary psychology and many other things (from February 15, 2005)…

Continue reading

(Non) Adaptive Function of Sleep

(Non) Adaptive Function of SleepFrom November 01, 2005, a review of a review…

Continue reading

Perhaps on another planet, it really is like that….

In the light of this years’ Nobel Prizes in Physiology and Chemistry (all RNA all the time), it would be interesting to think how would transcription, translation, gene regulation and replication work if DNA has evolved to be like this!?

New study on evolution of vision

For easy-to-understand quick look at the evolution of vision I have to refer you to these two posts by PZ Myers, this post of mine, and these two posts by Carl Zimmer.
Now, armed with all that knowledge, you will curely appreciate the importance of this new study:
Compound Eyes, Evolutionary Ties:

Biologists at the University of California, San Diego have discovered that the presence of a key protein in the compound eyes of the fruit fly (which glow at center due to a fluorescent protein) allows the formation of distinct light gathering units in each of its 800 unit eyes, an evolutionary change to an “open system” that enabled insects to make significant improvements in visual acuity and angular sensitivity. In contrast, beetles (shown surrounding the fruit fly), bees and many mosquito species have the light-gathering units fused together into a “closed system.”
In a paper published in this week’s early online edition of the journal Nature, the scientists report that one of three proteins needed to form these light gathering units is present in the visual system of fruit flies, house flies and other insects with open eye systems, but conspicuously absent in beetles, bees and other species with closed systems. The researchers showed that the loss of this protein, called “spacemaker,” can convert the eyes of fruitflies–which normally have open eye systems–into a closed one. In contrast, the introduction of spacemaker into eyes with a closed system transformed them into an open one.
Charles Darwin was so enamored by the intricate complexity of the eye that he wondered how it could have evolved. “These results help illustrate the beauty and power of evolution and show how ‘little steps’–like the presence of a single structural protein–can so spectacularly account for major changes in form and function,” said Charles Zuker, a professor of biology and neurosciences at UCSD and a Howard Hughes Medical Institute investigator, who headed the research team.

It’s Getting Warm

In these days of global warming it is important to realize how important temperature is in regulation of a variety of biological processes. Here is today’s sampler of examples:
Why Do Cold Animals Make Bigger Babies?:

Reproduction involves a critical decision: Should an organism invest energy in a few large offspring or many small ones? In a new study from the American Naturalist, biologists used a new statistical approach that can test multiple theories at the same time, an approach they hope will shed light on many evolutionary problems. They used data from many populations of Eastern Fence Lizards (Sceloporus undulatus), which revealed that the lizards in colder environments produce larger offspring than lizards in warmer environments.

Chilly Bugs’ Unique Gene Regulation Gives Them Survival Advantage At Bottom Of The World:

The larvae of Antarctic midges never stop producing special proteins that minimize environmental stress, allowing them to withstand a range of intense environmental conditions in one of the world’s harshest environments. Scientists found that adult midges (Belgica antarctica) lose their ability to continually express these protective heat-shock proteins.

New Study Explains Why Hotter Is Better For Insects:

Organisms have been able to adapt to environments ranging from cold polar oceans to hot thermal vents. However, University of Washington researchers have discovered a limit to the powerful forces of natural selection, at least when it comes to the adaptation of insects to cold temperatures.

Easy On The Eyes

Beauty And The Brain:

Experiments led by Piotr Winkielman, of the University of California, San Diego, and published in the current issue of Psychological Science, suggest that judgments of attractiveness depend on mental processing ease, or being “easy on the mind.”
“What you like is a function of what your mind has been trained on,” Winkielman said. “A stimulus becomes attractive if it falls into the average of what you’ve seen and is therefore simple for your brain to process. In our experiments, we show that we can make an arbitrary pattern likeable just by preparing the mind to recognize it quickly.”

Read the whole thing and comment.

Teaching Evolution Successfully

Teaching Evolution SuccessfullyFirst posted on December 12, 2005 on Science And Politics, then re-posted on January 16, 2006 on The Magic School Bus and most definitely worth reposting again here…

Continue reading

You’re ugly, but I like your kids anyway

Mother Birds Give A Nutritional Leg Up To Chicks With Unattractive Fathers:

Mother birds deposit variable amounts of antioxidants into egg yolks, and it has long been theorized that females invest more in offspring sired by better quality males. However, a study from the November/December 2006 issue of Physiological and Biochemical Zoology shows that even ugly birds get their day. Providing new insight into the strategic basis behind resource allocation in eggs, the researchers found that female house finches deposit significantly more antioxidants, which protect the embryo during the developmental process, into eggs sired by less attractive fathers.

It’s moved from sex steroids to antioxidants, I see. Can someone please send me this paper so I can comment more fully?

Development of Spots on Buterfly Wings

A really cool new study:
DailyScience: How Butterflies Got Their Spots: A ‘Supergene’ Controls Wing Pattern Diversity:

To explore the genetic backgrounds of each of these species, the authors crossed different races of each species and genotyped the offspring in order to identify genes responsible for the color patterns. Thus, they were able to map the color pattern controlling loci in each species: N, Yb, and Sb for H. melpomene; Cr for H. erato; and P for H. numata. Using molecular markers within the pattern encoding genic regions, the authors then found that the loci controlling color pattern variation for each species lie within the same genomic equivalent locations.
This “supergene” region therefore seems to be responsible for producing wing pattern diversity in Heliconius butterflies. Such a locus plays what researchers call a “jack-of-all-trades flexibility” rather than a constraining role. Under natural selection, this region presumably functions as a “developmental switching mechanism” by responding to a wide range of mimetic pressures to produce radially divergent, locally adapted wing patterns.

PLoS-Biology Synopsis: Jack-of-All-Trades “Supergene” Controls Butterfly Wing Pattern Diversity:

Using molecular markers developed in the region of the pattern genes, they found that the three loci controlling color pattern variation for each species inhabit the same genomic location. Indeed, the elements controlling white and yellow pattern variation in H. melpomene (N, Yb, and Sb) and H. erato (Cr) are tightly linked to genetic markers that occupy the same position in both species. Similarly, the locus P, which controls whole-wing variation in H. numata, is also linked to the same series of markers.
These results, Joron et al. conclude, suggest that a single conserved locus is responsible for producing wing pattern diversity in Heliconius butterflies. Rather than a constraining role, this locus provides what the researchers call a “jack-of-all-trades flexibility.” It presumably functions as a “developmental switching mechanism” for natural selection, they explain, by responding to a wide range of mimetic pressures to produce radically divergent, locally adapted wing patterns. Now researchers can begin to identify and determine the modus operandi of the genes at the center of what has been called a “developmental hotspot” to better understand how they drive the adaptive evolution of mimetic color pattern shifts.

The PDF of the paper is here.

Lions’ manes

I saw this ScienceDaily report earlier today and thought: “What’s new?” I recall a study with similar conclusions from just a couple of months ago, and even that was not that new – I used the example in teaching about 5-6 years ago (then dropped the example as the literature got more and more contentious).
But a few minutes ago, Afarensis posted about this and cleared it up for me – the previous study was from zoos and this one is from the wild. Also, the new study incorporates ontogenetic data – the effects of age.
So, the size and color of the lion’s mane is not driven by sexual selection, but by thermoregulatory needs and it seems it takes some of the lions quite a lot of time to grow a big mane:

According to the overall findings of the study, wild lions generally develop manes in accordance with local climate regimes. In Equatorial east Africa, climate is determined by elevation. Thus lions with the most profuse manes occur at the upper limit of their altitudinal range, while similar aged males in the lowest and warmest environments like Tsavo typically carry only modest or scanty manes.
However, the authors also found, paradoxically, that the majority of lions in regions like the greater Tsavo ecosystem (which is famed for its “maneless” lions), did appear to acquire respectable manes, eventually, contrary to most recent popular and scientific accounts of the lions from that region.
“We knew about the climate/elevation correlation since we were the first to publish those preliminary results in GEO 2001, but this new development really threw us for a loop,” says Tom Gnoske, of the Field Museum’s Zoology Department and senior author of the paper. “However once we analyzed all of the statistical data we found a very strong correlation linking increased age and continued mane development, a significant variable ignored by all previous authors.”
Statistical data from this study demonstrates that the onset of mane development in lions living below an altitude of 800 meters on or near the equator is delayed, and that the “rate” or speed at which a mane develops in lions from those regions is slower on average than that of the more familiar lions living in the cooler, higher altitudes of the greater Serengeti ecosystem and elevated plains extending northward, such as the Athi/Kapiti Plains and beyond. According to the researchers, in environments like Tsavo that have especially high minimum temperatures throughout the year, lions in their reproductive prime–from the approximate ages of five thru seven years old–usually possess only very marginally developed manes, while most of the more thoroughly maned lions in those same territories were already well past their breeding prime.
Furthermore, the researchers found compelling evidence indicating that manes of lions from all populations continue to develop long after a lion has achieved sexual maturity, such that the best-maned lions in any region are typically of an older age class. “Usually lions are well past their breeding prime when they carry the most extensive and often darkest manes of their lives,” explains Kerbis Peterhans Adjunct curator of Mammals at The Field Museum, Professor at Roosevelt University, and co-author of the study.

Read the rest

But HOW do they do it?

Bird Moms Manipulate Birth Order To Protect Sons:

—————-snip——————-
Since 2002, Badyaev, Oh and their colleagues have been intensively documenting the lives of a population of house finches (Carpodacus mexicanus) on the UA campus.
Throughout the year, the researchers capture birds several times a week to band and measure them and to take DNA and hormone samples. During the breeding season, the researchers locate the nests, keep track of activity in the nest, follow nestling growth and development, and take DNA samples from the chicks.
The researchers have also been counting the numbers of mites on the birds and documented a seasonal pattern. When breeding starts in February, the mites are absent. As winter turns to spring, mites start showing up on the adult females, in their nests and on their nestlings. The exact timing depends on the year.
Mites can kill nestlings.
“When it is safer inside the nest than outside, then there’s no need for young to leave the nest until growth is complete, but when mortality risk of staying in the nest is great, chicks need to complete their growth fast and get out as soon as they can,” Badyaev said. “What should a mother do in the face of shifting mortality risk?”
“To leave the nests sooner and still survive outside of nests, the kids need to grow faster,” Badyaev said. “But the mechanisms which regulate nestling growth in relation to changing mortality were not known.”
So the researchers looked to see how finch moms changed their child-rearing strategy so as to always do best by their kids.
The birds lay one egg per day. To successfully raise baby finches in the presence of mites, the mothers altered the order in which male and female eggs were laid.
When mites were absent, the chances of any particular egg being male or female were even. But once mites came into the picture, the mothers laid female eggs first and male eggs last.
Males that grew during mite season did more of their development in the egg before hatching. Their mothers accelerated their sons’ growth, both in the egg and after they hatched.
“Mothers essentially hid their sons in the eggs,” Badyaev said.
It’s remarkable that the fledglings have such similar morphology with or without mites, he said. “Mothers did that by modifying the order of laying of male and female eggs and the pattern of their growth.”

This is cool ecology and evolution. But where is the physiology, i.e., the mechanism of birth-order of sexes?

Revenge of the Zombifying Wasp

Revenge of the Zombifying WaspOne of the coolest parasites ever (from February 04, 2006):

Continue reading

Cooperative Hithhiking

Baby bugs team up for sex scam

The moment they’re born, beetles of one species join forces for a curious drill.

The larvae hatch out of their eggs and together, as a group, climb to the tip of the plant. There, they secrete a sex pheromone that attracts a male of a bee who tries to couplate with the ball of larvae. They jump on him. He flies away carrying the little buggers.
When he finds a female to mate with, the larvae jump ship and go away hithhiking on her. When she goes back to her nest they disembark, eat the nectar she collected and her eggs before their final metamorphosis.
Arthropods are known to hitch rides on other animals, including larger arthropods, but this is the first documented case of a group hithchiking together.

ERVs in sheep, though essential, do not make them smart

Remember this post from a couple of weeks ago? It was quite popular on tagging sites like Digg, Reddit and Stumbleupon. It was about endogenous retroviruses and their role in the evolution of placenta (which made the evolution of other mammalian traits possible).
Now, there is a new study in sheep, on this same topic, and it looks very good at first glance:
Researchers Discover That Sheep Need Retroviruses For Reproduction:

A team of scientists from Texas A&M University and The University of Glasgow Veterinary School in Scotland has discovered that naturally occurring endogenous retroviruses are required for pregnancy in sheep.
In particular, a class of endogenous retroviruses, known as endogenous retroviruses related to Jaagsiekte sheep retrovirus or enJSRVs, are critical during the early phase of pregnancy when the placenta begins to develop.
—————snip—————-
The idea that endogenous retroviruses are important for reproduction in mammals has been around for about 30 years, Spencer said. Studies in cultured cells have shown that a protein of a human endogenous retrovirus might have a role in development of the human placenta.
The team blocked expression of the envelope of the enJSRVs using morpholino antisense oligonucleotides, which inhibit translation of specific messenger RNA. When production of the envelope protein was blocked in the early placenta, the growth of the placenta was reduced and a certain cell type, termed giant binucleate cells, did not develop.
The result was that embryos could not implant and the sheep miscarried, Spencer said.

Some hypotheses about a possible connection between malaria and jet-lag

Blogging on Peer-Reviewed Research

Some hypotheses about a possible connection between malaria and jet-lagHypotheses leading to more hypotheses (from March 19, 2006 – the Malaria Day):

Continue reading

More on cannibalism in mantises

If you are interested in the pros and cons of cannibalism in praying mantises, you should check out the latest Carl’s post and article on the topic.

Monkey see, monkey do

Chimpanzees Can Transmit Cultural Behavior To Multiple ‘Generations’:

Transferring knowledge through a chain of generations is a behavior not exclusive to humans, according to new findings by researchers at the Yerkes National Primate Research Center of Emory University and the University of St. Andrews, Scotland. For the first time, researchers have shown chimpanzees exhibit generational learning behavior similar to that in humans. Unlike previous findings that indicated chimpanzees simply conform to the social norms of the group, this study shows behavior and traditions can be passed along a chain of individual chimpanzees. These findings, based upon behavioral data gathered at the Yerkes Field Station in Lawrenceville, Ga., will publish online in the August 28 early edition of the Proceedings of the National Academy of Sciences.
—————————-snip———————————-
“The chimpanzees in this study continued using only the technique they observed rather than an alternative method,” said Horner. “This finding is particularly remarkable considering the chimpanzees in the control group were able to discover both methods through individual exploration. Clearly, observing one exclusive technique from a previous chimpanzee was sufficient for transmission of behavior along multiple cultural generations.”

How animals lose legs

What’s with manatees in the news lately? First intelligence, and now this:
Manatee Bones Lead To New Insight On Evolution:

“Most research professors spend their days writing grants, teaching and managing graduate students, so when Stanford’s David Kingsley, PhD, ventured from his office to his lab, pulled out a scale and started weighing 114 pairs of manatee pelvic bones, it was a sign that something was afoot.
The results of Kingsley’s efforts make his departure from the routine worthwhile. He found that in almost every case, the left pelvic bone outweighed the right. Although seemingly trivial in difference–the average left pelvic bone is a mere 10 percent larger than its right-side partner–that difference carries big weight in evolutionary significance. It suggests that mutations in the same gene may be responsible for the evolution of leglessness in animals as distantly related as 1,000-pound manatees in Florida and fish smaller than an index finger living in lakes and streams around the world.”

You have to read the whole thing to get the details, but the work suggests that the same genetic mutation is responsible for evolution of leglessness in a vast array of vertebrates – from fish, through snakes, to mammals. A surprisingly general occurence if correct. Or is it really surprising in light of everything we learned from evo-devo over the past couple of decades?

Happy that the Common Ancestor is Common

As we age, our sleep gets less well consolidated: we take more naps during the day and wake up more oftenduring the night. This happens to other mammals as their age. Now we know that it also happens in Drosophila:

“As humans age, so I’m told, they tend not to sleep as well. There are all sorts of reasons — aches and pains, worries about work and lifelong accumulations of sins that pretty much rule out the sweet sleep of innocence.
But what about fruit flies? Not as a cause of insomnia. What about the problems fruit flies have sleeping?
Yes, Drosophila melanogaster also suffer sleep disruption when they get older. And a report on the troubled sleep of drosophila is being published online this week in The Proceedings of the National Academy of Sciences.
This is the kind of science that makes you wonder.
For instance, are the male flies getting up to go to the bathroom threetimes a night? Are the female flies complaining about hot flashes? Of course not. Fruit flies don’t have bathrooms.
Or you might wonder what troubles are keeping the flies up. They don’t have to worry about family values, illegal immigration or debt. They don’t have families or money.
And given the ubiquity of fruit and of scientific research, I’m guessing drosophila, bless their little genomes, must benefit from something close to full employment.”

But that is just the impetus for James Gorman to wonder why so many people deny evolution and why don’t other, like he does, enjoy the wonder of being related to every living organism on this planet:

“What I wonder is why people waste time worrying about whether we evolved from animals. But they do. A disconcerting number of North Americans doubt the fact of evolution. The U.S. seems almost evenly divided on the matter, says a recent report in Science.
Some of the worriers concentrate on apelike ancestors, showing a lack of vision.
There are stranger connections to agonize over, like drosophila and beyond. We share sleep problems with fruit flies. We have a huge amount of DNA in common with yeast.
Those are our distant cousins we consume in leavened bread, our fellow multi-celled organisms undergoing dreadful experiments in the drosophila lab. For instance, scientists have heated up the ambient temperature in fruit flies’ environment to see what happens. At 64 degrees Fahrenheit they live twice as long as at 84 degrees. Live hot, die young.
What does that mean for us?
We really do share a lot with drosophila. Fruit flies have sleep-wake cycles that become fragmented as they age, suffering a “loss of sleep consolidation, namely increased daytime sleep and increased night-time wakefulness in the elderly,” as Kyunghee Koh at the Howard Hughes Medical Institute and three colleagues describe it.
Sound familiar?Some of the same genes related to circadian rhythms occur in humans and in flies. Mutations in some of these shared clock genes can cause sleep disorders in people.
We also share genes related to learning and alcohol sensitivity. But even these commonalities are not worth worrying about. The genes are just details. We have the same basic cell machinery — DNA, for example — with everything living.
The bacteria in my gut accounts for more genes than I have in my chromosomes. We not only have a lot in common with microbes, in a way that is only beginning to be understood, we are microbes.
This is fine with me. I’m delighted to be related to flies, yeast, frogs, chimps and blue-green algae.
I find the serenity of algae restful and the ambition of yeast admirable.
Frogs are great jumpers. Chimps have hands at the end of their feet, sort of.
And fruit flies, well, I never met a fruit fly that I was ashamed to share genes with, and I certainly can’t say that about human beings.”

Wonderfully put. I just had to go over what is appropriate and save all those words here and not let them dissappear into the Black Hole of newspaper archives. Thank you, Mr Gorman.

Did A Virus Make You Smart?

Did A Virus Make You Smart?Not really a review of Greg Bear’s “Darwin’s Radio” and “Darwin’s Children” but musing (practically SF itself) on the topic of these books (from April 20, 2005):

Continue reading

Books: “Coming To Life” by Christiane Nusslein-Volhard

Several ScienceBloggers are reviewing Coming To Life today (see reviews by Janet, Shelley, RPM, Nick and PZ Edit: Razib has also posted his take), each one of us from a different perspective and looking from a different angle, so go read them to get the full scoop.
PZ Myers reviewed the book a few weeks ago. Someting that struck me was that PZ said that the book :

“….assumes nothing more than that the reader is intelligent and curious. Seriously, you don’t need a biology degree to read it!”

…while a reviewer, Edward F. Strasser (a math PhD whose hobby is reviewing books from this angle – how readable they are for laypeople) on Amazon.com states the opposite:

“I don’t think that a person who has never seen this material before is ready for this book, but I think that many people who need it for review will be OK.”

So, when I started reading the book I decided to try to empty my mind of all the knowledge I have and to read it like a complete lay-person. I wanted to see who is right – PZ or Strasser – and try to determine who is the real audience for the book.
First, I have to tell you that I absolutely LOVED the book. And that may be its biggest problem. The book will be appreciated the best by people like me – biologists with expertise in another field who want to brush up on their evo-devo (and just devo) and have an easy reference on the bookshelf. The book does absolutely great for people like that.
But, will it do the same for others? Developmental biologists do not have a need for it because they already know everything in it and 100 times more. But how about complete laymen, people with minimal formal science education but a keen interest in science, people who read popular science magazines, watch Discovery channel and read ScienceBlogs?
I’d say Yes, but very cautiously. In a way, the book is deceptive. Its small size and pretty cover art suggest a breezy read. But it is not. It is a textbook disguised as a non-fiction bestseller. The tone is a matter-of-fact, unexcited monotone. Trying to speed though it will be a disaster. Why?
A textbook on developmental biology would be an expensive, 1000-page, lushly illustrated avalanche of nitty-gritty details. Making the book small by eliminating a lot of that detail means that what remains is highly concentrated. Every sentence matters. Every sentence is a summary of a thousand papers.
There is no “filler” material, e.g., anecdotes and personal stories or interesting examples of, for instance, exceptions to the the rules in a strange species, or philosophical musings, kind of stuff that will let your focus wane every now and then without serious consequences to understanding. Only occasionally she slides in a little bit of history which is always a welcome change of pace on top of being very informative and placing the material in a historical context.
You need to slow down and read every sentence with concentration. Perhaps stop and think what it means every now and then. Sometimes you wish she has NOT omitted some of the details which may serve as a useful illustration of a big principle she is describing in that sentence or paragraph.
Several times I caught her using a technical word without explaining (or at least defining) it first. If you did not have Intro Bio recently, or are not generally well informed on basic genetics and molecular biology, that would throw you off, and make you rush to the back of the book to check the Glossary – something that breaks the flow of reading any book.
So, the book is great for people who have some biology background (at any level) but not much knowledge of developmental biology – people like sophomore biology majors. But how do you get them to slow down and read the book carefully? Well, use it as a textbook! For an Introduction to Development course. I am serious! It’s that good.
The instructor could spend time in class explaining the principles described in the book – a process which slows down the reading of the book. Then, each instructor is free to add as much or as little detail in lectures as the level of the course requires, plus cool examples, flashy images and videos, etc, and add a couple of more readings, e.g., scientific papers and reviews.
Heck, it could be used even for a General Biology class for science majors (e.g., a summer speed class). Genetics, development and evolution are the core of biology, so adding a couple of lectures (with additional notes or a similar book) on physiology, behavior and ecology at the end (and those can be built upon the edifice of genetics, development and evolution covered before), would work just fine in some contexts, eliminating the need for students (like mine, the adults) to buy huge expensive textbooks that only intimidate them with the wealth of detail. It would give the instructor more freedom to design a course well.
Why do I think that this book is better as a potential textbook than the usual texts? Apart from size, price, friendliness and giving the instructor greater freedom, I really like the way the material is explained.
From the very first sentence, and reinforced throughout the book, the message is that the cell is the smallest unit of life. Not genes. Cells. While most textbooks fall into the philosophically untenable habit-of-mind that “genes use cells to make more genes” or “cells are places where genes perform the work of life”, Nusslein-Volhard constantly explains stuff within the proper way of thinking – “genes are tools that cells use to change, to do their job within the organism, and to make more cells”. The shift is subtle. She rarely states it this directly and openly, but if you are reading the book specifically looking for it (as I did), you notice that the word-choice and the way of explainig things is always within this mode of thought. She also, whenever that is appropriate, never forgets to mention important influences of the internal and/or external environment on cells and tfe developing organisms.
The book also makes a gradual progression over levels. After basic introductions to evolution, heredity and molecular biology, she starts with the cell and how it uses genes to change its own and neighboring cells’ properties. As the chapters move on, there is less and less talk of genes and more and more talk of cells, tissues organs and whole organisms, ending with the return to evolution in an excellent chapter on Body Plans.
Understanding that most of the readers will be anthropocentric, she then devotes a chapter to the development and reproduction in those lousy lab animal models – humans.
The final chapter on controversial aspects of developmental biology and its practice – covering stuff like cloning, stem-cell research etc., is as calm and even-tempered (almost dry) as the rest of the book. More importantly, the conclusions given there are derived directly from the science described in the rest of the book, with no Culture-Wars code-words that can trigger automatical resentment on the part of readers that are involved in Culture Wars on one side or the other. Again, it provides the neccessary background that can be useful for a class discussion. And its dry, science-y tone is exactly what is needed for such a discussion.
So, if you are a biologist and you want to refresh and update your knowledge of development really fast and easy – get this book, it is better than any other in this respect.
If you are not a biologist, but have a keen interest and some background, get the book but do not expect to breeze through it in two hours. Do not be deceived by the small size and pretty illustrations Dr.Volhart drew herself. Give yourself a week to read this book, then read it slowly and with full concentration. Read that way, it is worth its weight in gold.
And if you are more interested in the “evo” side of evo-devo and a more future-oriented book (Coming To Life summarizes current knowledge with no speculations about the future), read “Biased Embryos and Evolution” (see my review) – the two books nicely complement each other.
My question to Dr.Nusslein-Volhard: Is it possible to turn Developmental Systems Theory into a useful experimental program and, if so, will that provide discoveries and insights that are lacking within the current paradigm?

Why All Lard Is White

Why Piglets Shudder To Keep Warm:

Brown fat helps newborn mammals maintain their body temperature by burning fat, which converts into heat. The protein UCP1 (Uncoupling Protein 1) has a key role in this energy conversion, which takes place in the cell mitochondria.
No brown fat or UCP1 protein has been found in domesticated pigs, however. In their study, Berg and colleagues show that the UCP1 gene was shut down about 20 million years ago in an ancestor of the wild boar. They identified four different mutations, each of which would be sufficient to knock out the function of the protein.
This ancestor of pigs thereby lost the ability to use brown fat to maintain body temperature after birth. A reasonable explanation for this is that brown fat was not essential during a period in the evolution of pigs, in which they lived in a warm climate, says Leif Andersson, who directs the research team.
The ancestor of the domesticated pig, the wild boar, is the only pig that lives in cold climates. All other species inhabit tropical or subtropical climates. The wild boar has compensated for the loss of brown fat by a series of adaptations for survival in a cold climate. It is the only hoofed animal that builds a den when it is time to give birth see, and its young shudder to maintain their body temperature. In modern pig production, heat lamps are used to help the newborn piglets retain their body temperature.
The findings show that an important biological function can be lost if it is not vital to life during a period in the evolutionary history of a species; and that if the living conditions once again change, compensatory mechanisms can be developed. The findings we present are fully consistent with the theory of evolution. An important trait can be lost if it is not absolutely necessary to life during the development of a species, says Leif Andersson.

Books: “The Cultural Origins of Human Cognition” by Michael Tomasello, part II

CogBlog - Tomasello: Chapter 2 The review of the second chapter was written on September 06, 2005:

Continue reading

Books: “The Cultural Origins of Human Cognition” by Michael Tomasello, part I

CogBlog - Tomasello: Chapter 1 The Cultural Origins of Human Cognition by Michael Tomasello was the first book (and still the only one so far) we were reading in the newly minted CogBlogGroup, a group of bloggers reading stuff about cognitive science. You can download the whole book in PDF or the first chapter only in html. This was the first of two parts (I never finished the book nor rerview!), originally posted on August 20, 2005:

Continue reading

Evolution and Design class

Allen McNeill’s Cornell course on Evolution and Design is now over and the student papers have been posted online.
Dan comments on some of them.

Another case of Evo-Psych abuse…

Have you heard about the stupid German study that uses evo-psych Just-So-Stories about, supposedly, women losing interest in sex shortly after marriage?
I wanted to dissect it when it first came out but Real Life and time-constraints prevented me. In the meantime, Dr.Petra, Shakespeare’s Sister, Amanda and Echidne ably debunked and destroyed the study and the media reporting on it, so I don’t have to do anything but link to them.

Bring back the mammoth, or, not so fast!

Archy is on top of the story, as usual when the story is about people trying to resurrect mammoths!