What I taught yesterday: master genes and maps

On Wednesdays, I try to break away from the lecture format and prompt the students to talk about the science of development. We’re working our way through Sean Carroll’s Endless Forms Most Beautiful, and yesterday we talked about chapters 3 and 4.

Chapter 3 has an overview of basic molecular biology — transcription and translation, that sort of thing — and since these are junior and senior students who’ve already heard that a few times, we skipped right over it and they explained to me what master genes are, with specific examples of homeobox-containing genes like the Hox genes and Pax6. They caught on fast that what we call master genes are actually just transcription factors located high up in a regulatory hierarchy.

I think we also got across a less-than-naive idea of the evolution of Hox genes. There is a recognizable, conserved motif in each of these genes, but the proteins are far more than just their homeodomains, and can exhibit considerable variation — necessary functional variation, because the expression of different Hox genes are going to have distinct morphological consequences.

Chapter 4 has a general theme of maps and geography — what does it mean for a cell to be in a particular position and to have a particular fate? We also get into details. This is a very fly-centric chapter, and we get a picture of early development in the fly and the specific patterning and positional organization in the early embryo of that organism, with an introduction to many genes we’ll be hearing much more about during the course of the term. We also got enough information on vertebrate development that I could ask them to play the compare and contrast game: what’s different and what’s the same in fly and mouse development? I’m trying hard to be the Reese’s Peanut Butter Cup of development in this class: it’s so easy to say, “they’re the same!” and focus on common molecular mechanisms, or to say “they’re different!” and talk about the numerous quite radical innovations between them (especially in the fly, which is a weird, highly fine-tuned machine for rapid robust development). I’m trying to get across that both statements are absolutely true, and they really taste great together.

Friday is their first exam. Next Monday, class will be an overview of nematode development, to prime them for the lab exercises for the next two weeks which will be all about photomicrography of worm development and behavior, and also more details about early fly embryology to get them prepared for a couple of weeks of nothin’ but flies. I also warned them that next Wednesday we’ll be discussing chapter 5 in Carroll, just chapter 5, because I’ve found in the past that that’s usually the brain-clogger chapter, with all its talk of boolean logic and gates and circuits.

Ending bobcat trapping in California

I mentioned a bit ago that some yahoos have been trapping bobcats in my neighborhood. That trapping has attracted the attention of reporter Louis Sahagun, who cracked the lid off the topic this weekend with an article in the Los Angeles Times. Sahagun interviewed some of my neighbors as well as a couple of trappers, one of whom — Mercer Lawing of Barstow, California — came up with this little bon mot:

“We love those animals more than the people who are complaining about us trapping them do.”

That link above is to Mercer Lawing’s bobcat trap business page, which contains potentially disturbing photos. He took down his Facebook page yesterday after my followup piece at KCET linked to it. I’m sure that was just a coincidence.

I’d been meaning to write something at KCET on the issue for a couple weeks, and since Sahagun had done all the hard work and beaten me to it,  I followed his article with an analysis of the California Department of Fish and Wildlife’s epically crappy science on bobcats, and a call to ban bobcat trapping in California altogether.

My KCET piece is here. Short version:

The last time anyone came close to counting bobcat numbers in California was in the 1970s. Back then an estimated 72,000 cats lived in the state, and a scientific panel established by President Ford figured hunters and trappers could take one fifth of that population every year without damaging the species in California. The actual science was so tenuous that a judge stopped exports of California bobcat pelts in 1982, saying trade in pelts could resume only when the Fish and Wildlife Service came up with more authoritative numbers. That never happened, and the ban on bobcat pelt exports was lifted a few months later when changes in the federal Endangered Species Act made the case moot.

Bobcat

Also, an excuse to sneak a kitteh picture past PZ.

In the 30 years since, California bobcat trappers have had no limit on the number of cats they can kill. Five a day, ten, a thousand? It’s all the same to the California Department of Fish and Wildlife. Aside from the trapping season, which runs from November through January, the only limit on bobcat trapping is that DFW closes the season early if the haul reaches 14,400 cats — a fifth of the controversial population estimate in the 1970s, which has not been updated. As the price of spotted cat fur goes up, the haul of California bobcats does too, with DFW sitting on its hands as long as that magical “14,400 dead cats” number isn’t reached.

Check out the whole KCET piece for more detail on that, plus a natural history story about how bobcats might be Joshua trees’ best ally in a warming world.

As someone who likes to eat venison, I’m no anti-hunt person per se. But essentially unregulated trapping of top-level carnivores is altogether different. And doing so with no scientific justification is even worse.

The Center for Biological Diversity, which has also been tracking the issue, has set up an action alert page where Californians can send a preformatted but editable letter to the appropriate California legislator urging them to ban bobcat trapping in the state. I hope you’ll consider signing it and sharing it around your circles, should you have friends in California.

And a few bobcat enthusiasts in my neighborhood have set up a site called Project Bobcat, where they’ll be posting updates and background information. Check it out.

 

 

Need more paleontological women

The latest issue of Priscum, the newsletter of the Paleontological Society (pdf), has an interesting focus: where are the women in paleontology? They have a problem, in that only 23% of their membership are women, and I hate to say it, but the stereotype of a paleontologist is Roy Chapman Andrews — most people don’t imagine a woman when they hear the word paleontologist (unjustly, I know!)

On the other hand, 37% of the paleontology presentations at the GSA were by women. They’re there, but they aren’t getting far up the ladder of success. They’re not achieving high status positions within the society at the same rate as men, and then there’s this skewed distribution:

genderdisparity

So women are over-represented in the student category, but under-represented in the professional category. The optimistic way to look at that is that there is an opportunity for change, and maybe that wave of current students will move on up and change the distribution ten years from now. More pessimistically, it suggests that there could be barriers that preferentially block the advancement of women in the field; if the distribution doesn’t change in the next decade, that says that there were more frustrated women who left the discipline than men.

So why would women experience greater barriers to advancement? It isn’t about evil men keeping the women down, and I wish we could clear away the resentment some men express when they hear that there are greater obstacles to women’s progress — too often I hear angry responses to accusations of academic sexism taken personally, as if it were a statement of personal criminality. It’s a product of the system, and men and women mostly contribute to it by neglect and an unwillingness to change the status quo.

What I most often see is statements of fact that I don’t disagree with, such as that women on average have lower publication rates than men, but the problem is that these advocates of blaming the inherent properties of women for their failure don’t think it through. Why do women have lower publication rates? Are there structural/cultural/professional properties that conflict and cause problems that men don’t see? And most importantly, if there are, what can we do to correct those institutional biases? Just saying that “women publish less” begs the question.

This article had a very helpful diagram illustrating the contributing factors, taken from a paper discussing a similar problems among evolutionary biologists.

womeninscicycle

Right there in the center is issue of lower publication rates in women, but it looks deeper at consequences and causes. Follow the arrows. I’ve seen similar charts before — it looks a heck of a lot like an extinction vortex, a self-perpetuating cycle of defeat.

Another article in the same newsletter describes the distribution of the leadership of the Paleontological Society. It shows steady improvement in the proportion of women in the society leadership, but still, most of the executive positions have been held by women less than 10% of the time. The more recently the position was created, the higher the proportion of women. I also noticed one outlier: 67% of the Education and Outreach Coordinators (a very new position) have been women. That’s another stereotype, too, that women are better suited to teaching. Look at the diagram above: going into teaching is also one of the factors that hurts research productivity, and as long as research is more highly valued than teaching, and teaching is considered ‘women’s work’, it’s going to skew representation of the sexes.

They have a proposal to correct the imbalance. Notice that it doesn’t involve simply declaring that they have equality of opportunity (which they don’t!) and doing nothing. Correcting these kinds of biases requires active intervention.

Societies are strengthened by incorporating diversity (of gender, of ethnicity, of abilities, of ideas, and of disciplines). As a society, we need to be aware of equity issues and take intentional steps to counteract imbalances. The recommendations below relate to increasing ALL types of diversity. So far, we have data on gender equity, but there are many other types of diversity we should work to improve. This set of recommendations applies to all of them.

Intentional nominations. Think about the excellent female colleagues you have. Now nominate at least one of them for a leadership position (we have several open this year!) or a society award. All Society positions are open nominations, so please share your ideas!

Mentoring. Establish professional relationships with young women in paleontology (students and early career professionals). Spend some extra time at poster sessions meeting some of our student members. Encourage women to submit abstracts for oral presentations. Established women, share your career stories and experiences.

New initiatives. PS Council is dedicated to increasing equity for all types of diversity in our membership. Please share any ideas you may have for initiatives with [the author] or other council members—now and in the future.

This just in: Fox News ‘experts’ are lying shitsacks

You might have seen this already: Media Matters caught it and it’s making the rounds, including at my green energy joint at KCET. Fox News talking head Shibani Joshi says the reason Germany’s leading the U.S. in solar power installations by a factor of about 20 is that Germany has more sun than we do in the U.S. It’s toward the end of the clip:

Money quotes: Gretchen Carlson asked “What was Germany doing correct? Are they just a smaller country, and that made it more feasible?” Joshi: “They’re a smaller country, and they’ve got lots of sun. Right? They’ve got a lot more sun than we do.”

Here’s the inconvenient truth (as they say), courtesy the National Renewable Energy Laboratory:

NREL-Insolation-map-2-8-13

It’s almost like they just don’t care they’re lying.

A quick desert bobcat-related note

A few days back my neighbor Teddy Quinn asked me if I’d be willing to provide a minute or so of audio on the whole “bobcat trapping in Joshua Tree” issue I mentioned this week. Said audio would be aired on his new project, Radio Free Joshua Tree, a community podcast.

He asked me for a minute and I gave him five, but he played the whole thing anyway. It’s at minute 17 of hour 2 of his variety show for February 3, the whole thing of which you should check out. My neighborhood is replete with good musicians, and Teddy is kind of a local impresario curating their work and boosting their careers.

But if you don’t have time for that, or if you hate music, I’ve posted just my audio at Coyote Crossing as well.

I was reminded, doing this, of how easy and fun audio work is. I’ve decided I want to do more. Probably mostly ruminations on life in the desert, that kind of thing. If you want to be kept in the loop, my Twitter account is probably where I’ll announce new recordings more reliably. Follow me there to be part of the in-crowd.

SICB opposes “drill baby drill”

It’s always gratifying to see a scientific organization step up and use their collective expertise to make a clear statement on a political and economic issue. The Society for Integrative and Comparative Biology (SICB) has published an open letter to President Obama rejecting the Keystone XL pipeline. The pipeline is a ghastly stopgap that hinders the promotion of better, cleaner alternative energy sources by encouraging ever more desperate and destructive efforts to harvest marginal energy sources…efforts to keep us on our petroleum addiction until the last drop of oil is wrung out of the earth, at any cost.

How about taking the billions that would be squandered building a big ugly pipe and instead invest it in research and conservation?

6 February 2013

From the Presidents of the Society for Integrative and Comparative Biology

An open letter to President Barack Obama,

Members of the Society for Integrative and Comparative Biology are biologists from throughout the U.S. with the broadest possible perspectives—from microbes to whales, from molecules to ecosystems. The undersigned current and past presidents of the Society have watched with increasing dismay the deterioration of the life support system of our planet, threatening all life as we know it. It has long been known that one product of burning fossil fuel, carbon dioxide, is a powerful greenhouse gas, and more recently that this gas has been associated with drastic climate variations in Earth’s past. Consequently, it is no surprise that prodigious worldwide burning of fossil fuel is creating large-scale climate change with increasing disruption of life on the planet. While many in the western developed nations still enjoy relative prosperity – despite the horrific storms experienced in the U.S. in recent years – it is in poor nations around the world that the impacts of climate change are currently most destructive. Pacific Island nations are disappearing beneath the tides as sea level rises. Desertification is destroying agriculture in northern Africa and massive floods have devastated Pakistan, Bangladesh and Thailand in the last two years.

It is too late to avoid substantial disruption, but further damage can be reduced if we act immediately to keep remaining fossil fuel deposits in the ground, out of the air and sea. A most immediate decision is yours: whether or not to approve the Keystone XL pipeline. More important than the fact that the pipeline itself will endanger aquifers and life along its length, the pipe will deliver the dirtiest, most CO2-producing petroleum source known to the refineries of the Gulf Coast. Additionally, the Athabasca tar-sands mine is destroying vast regions of northern Alberta that have been home and hunting and fishing grounds for First Nations peoples for thousands of years.

Even before fossil fuels are burned, releasing climate-altering greenhouse gases, the extraction phase itself produces environmental disasters, including toxins in water supplies due to hydraulic fracturing for natural gas, degradation of watersheds by mountain-top coal mining, and the loss of marine life from offshore drilling. Permits for all of these activities lie in the hands of agencies of your administration.

Alternative sources of energy are at hand. We do have the individual and collective intelligence and technology to see the urgently needed transition through to better times. What we require is sufficient political will on a global scale to meet the challenge. The U.S., for the last three federal administrations, has been a major impediment to ratification of international climate treaties. Clearly, the future demands that we – through your administration – reverse this pattern and join with leaders of other nations to ratify agreements that will quickly and drastically reduce greenhouse gas emissions.

Mr. President: you are arguably the most powerful person in the wealthiest and most powerful nation on the globe. To be clear: change will come, one way or another. Your task is no less than to steer the course of history away from its current devastating trajectory toward a sustainable existence for humankind.

Signed by:
Billie Swalla, University of Washington* President, 2013-2014
Peter Wainwright, University of California, Davis*
President-elect, 2013-2014
Ken Sebens, University of Washington* Past President, 2010-2012
Rich Satterlie, University of North Carolina, Wilmington*
Past President, 2009-2010
John Pearse, University of California, Santa Cruz*
Past President, 2007-2008
Sally Woodin, University of South Carolina* Past President, 2005-2006
Marvalee Wake, University of California, Berkeley*
Past President, 2001-2002
Alan Kohn, University of Washington* Past President, 1997-1998
Mike Hadfield, University of Hawaii* Past President, 1995-1996
David Wake, University of California, Berkeley*
Past President, 1992
* Affiliations for identification only and do not represent endorsement by the organization”.
Lynn Riddiford, University of Washington* Past President, 1991
Albert Bennett, University of California, Irvine*
Past President, 1990
Stephen Wainwright, Duke University* Past President, 1988
William Dawson, University of Michigan* Past President, 1986
Patricia Morse, University of Washington* Past President, 1985
Edwin L. Cooper, University of California, Los Angeles*
Past President, 1983
F. John Vernberg, University of South Carolina*
Past President, 1982
Mary E. Rice
Past President, 1979

Approved by the Executive Committee of the Society for Integrative and Comparative Biology, 5 February 2013, as was the Society’s Resolution on Climate Change and Ocean Acidification, which was approved on 1 March 2012: http://www.sicb.org/resources/resolutions.php3#climate

Finally! My own personal time machine!

I’ve been playing with it for a while. It turns out that when you go back to Cretaceous Morris, you need to be able to swim really well, but Cambrian Morris is high and dry on a fairly small landmass (whoa, but oxygen is way down and carbon dioxide way up). You can have your own time machine, too — it’s the EarthViewer app for iPad, and it’s free from HHMI Here’s what it has:

• Data and continental reconstructions dating back billions of years

• Climate and carbon dioxide data for the last 100 years

• The ability to manipulate the globe and zoom to any location

• Track the location of modern cities back over 500 million years

• In depth features on major geological and biological events in Earth history

• Clickable details on geologic eons, eras, and periods

• Automated play modes

• An extensive reference list

• Suggestions for classroom use

• Tutorial videos

Did I mention that it’s free? This HHMI thing is pretty danged sweet.