June 2012 Archives

#dimensionsZA - Blyde River Canyon

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That's a view of Blyde River Canyon from where we (Jane, Caroline, Christopher, Mark, and I) sampled a population of Protea laetans on Thursday. In all we sampled seven species of Protea we have not sampled before and one species of Pelargonium. Tomorrow we head south to Barberton, where we expect to pick up several more. We're looking for Pelargonium as hard as we can, but none of us are as good at finding them as Cindi, Kerri, and Carl, so I'm sure we're missing some - perhaps many.

I'm sorry that there haven't been any tweets, but if you saw my last one, you'll know that Verizon screwed me up again. My iPhone isn't working, so I can only get to the Internet when I can find a connection like the free one tonight at the restaurant where we're having dinner. I should be able to get it fixed, but maybe not until I get to Cape Town on the 10th of July. Once I get it fixed, expect a tweet at least once a day. Until then, the few of you who care will have to be satisfied with a blog post once every two or three days.

Location:Louis Trichardt Ave,Graskop,South Africa

#dimensionsZA -- Dimensions 2012

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Protea_obtusifolia-De_Hoop.jpg

Protea obtusifolia in the De Hoop Nature Reserve,Western Cape,
South Africa
Photograph by Kent Holsinger
Click on the image for a high-resolution image in a new window.

#dimensionsZA is the hashtag I'll be using for posts I make to Twitter while I'm in South Africa for fieldwork on our Dimensions of Biodiversity project. My plane leaves Bradley this afternoon, and after stops in Philadelphia and Amsterdam, I'll arrive in Johannesburg Monday night (Monday afternoon East Coast time). One post-doc will be traveling with me, and we'll meet another post-doc, her husband, and her brother when we arrive. We'll spend a couple of weeks in Mpalunga and Kwa-Zulu Natal collecting both Protea and Pelargonium before moving to Capetown for work in the experimental gardens, participation in the annual Fynbos Forum (in Cape St. Elizabeth this year), and work in the Kogelberg and De Hoop.1 I'll try to make a few blog posts while I'm there, but Internet access is liable to be a bit spotty, and even when it's not, I'll be spending nearly all of my computer time updating spreadsheets with data.

So if you want to see what the Protea team is up to while I'm in the field, you can either follow me on Twitter (@keholsinger) or follow the #dimensionsZA hashtag.

Our work isn't organized the same way as it was last year. Last year we had a community team based in Baviaanskloof, and the Protea and Pelargonium teams traveled and worked together the whole time we were in the field. This year the ecology team is sampling community diversity at several different sites in the western Cape, the Protea team is collecting both Protea and Pelargonium in Mpalunga and Kwa-Zulu Natal as well as collecting detailed trait data on some species we've studied before in the Kogelberg and De Hoop.

There will be two different Pelargonium teams. One will collect detailed trait data similar to what we'll be collecting in the Kogelberg and De Hoop. Late in July, we'll overlap with them for a few days in Kogelberg. The other team will be traveling through parts of the Western Cape and Northern Cape collecting species of Pelargonium that they weren't able to collect last year. Another Pelargonium team will return in late October and early November to collect taxa in the Eastern Cape, and one of the post-docs will stay in South Africa until then collecting additional data from the populations targeted for detailed trait measurements this July and August.2

BeeSmart

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This is National Pollinator Week, an annual event managed by the Pollinator Partnership.1

Five years ago the U.S. Senate's unanimous approval and designation of the final week in June as "National Pollinator Week" marked a necessary step toward addressing the urgent issue of declining pollinator populations. Pollinator Week has now grown to be an international celebration of the valuable ecosystem services provided by bees, birds, butterflies, bats and beetles. The growing concern for pollinators is a sign of progress, but it is vital that we continue to maximize our collective effort. The U.S. Secretary of Agriculture signs the proclamation every year.
For more information about Pollinator Week, visit the Pollinator week web page (http://pollinator.org/pollinator_week_2012.htm). There you'll find links to resources and activities.

You'll also learn that there's a pollinator app -- BeeSmart, and it's available for both iPhone and Android.

With the Bee Smart™ Pollinator Gardener's easy user interface, browse through a database of nearly 1,000 native plants. Filter your plants by what pollinators you want to attract, light and soil requirements, bloom color, and plant type. This is an excellent plant reference to attract bees, butterflies, hummingbirds, beetles, bats, and other pollinators to the garden, farm, school and every landscape.
If you're a gardener and you have an iPhone or Android device, consider downloading the app and trying it out.


UConn Today

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A month and a half ago, CLAS Today had a nice piece about me. When I booted up my browser today,1 I saw that UConn Today has republished the piece under a different title. The CLAS Today piece was titled, “Diversity describes Kent Holsinger”. The UConn Today piece is titled, “Distinguished Professor Kent Holsinger Uses Statistics to Analyze Genetic Data”. The UConn Today title is more informative, but I like the CLAS Today title better.

The impact of Open Access

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kohom.jpg

Distribution of journal publications in different fields. (from Nature). Click on the image to see a larger version.

@NatureNews: Richard Van Noordern writes in Nature News about the Finch report. It recommends actions to promote greater access to the results of publicly funded research. The figure to the left is taken from the Nature News article, and you'll find links to some of the reactions to the report below. I haven't had a chance to read the report, and I've only glanced at a few of the reactions. I hope to find time to post my own thoughts before I leave for South Africa on Sunday.1 For now I just wanted to point out one thing that leapt out at me in the description of this figure.

Notice that parenthetical comment at the top of the figure describing where the data come from -- "as indexed by Web of Science". You'd probably get a similar result if you used Scopus as the source of your data, but I have to wonder whether the proportion of open access titles is larger or smaller among the universe of journals not indexed in Web of Science. Could this survey understate the extent to which open access journals are used. I presume that if you were to count papers posted on arXiv as published, for example, the open access wedge in physics would get a lot larger.


Principles for constructing better statistical graphics

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Rafe Donahue teaches in the Department of Biostatistics at Vanderbilt. In 2008, 2010, and 2011 he offered a course in statistical graphics at the Joint Statistical Meetings. He's also offered a follow-up version of the course as part of the American Statistical Association's LearnStat program. His course notes are available on-line as a PDF (http://biostat.mc.vanderbilt.edu/wiki/pub/Main/RafeDonahue/fscipdpfcbg_currentversion.pdf). I haven't had a chance to study them carefully yet, but it looks as if they have some good ideas, and Andrew Gelman thinks "it looks pretty good". That's a pretty good indication that it's worth taking a look at.

Monday pen

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I last wrote about pens more than a year ago when I wrote about a 2011 limited edition from Graf von Faber Castell. They've done it again. That's their 2012 Pen of the Year to the left.

It features 24K gold leaf applied over oak embedded in resin and trimmed with 24K gold-plated fillings. Just as with last year's pen, I'll have to admire this one from a distance. It lists for $4695.

Here's some of what the current Fahrney's catalog has to say about it:

Scarcely any other wood expresses such an enigmatic beauty as ancient wetland oak. The sought-after and extremely rare pieces of wood have been buried for as many as 8,000 years in German bogs and marshes. A sensitive and masterly touch is demanded if the gold leaf is to mold perfectly to the grain of the oak.

The gold leaves are applied by hand using a fine squirrel-hair brush in a technique that dates back to the Egyptians. Such extraordinary craft demands particular artistry and skill and is mastered today by only a select few. Layer upon layer of 24K gold leaf is applied to the pen barrel in an intricate and detailed process and embedded in resin. This reveals a unique pattern of reflections that only the purest gold can produce.

Each individually numbered Graf Von Faber-Castell 2012 Pen of the Year pen holds an 18K gold, bi-color nib and is accented with 24K gold-plated fittings. The masterpiece is crowned by a chessboard-faceted citrine gemstone set in the cap. A certificate, signed personally by the gilder, attests to the authenticity of the 24K leaf gilding and the 1,700 year old German oak.

Green economy

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Rio+20 opens on the 20th of June in Rio de Janeiro. News announcements are now emerging daily to highlight the challenges and accomplishments facing those who attend.

Envisaged as a summit involving head of state, it will mark the 20th anniversary of the 1992 United Nations Conference on Environment and Development (UNCED), in Rio de Janeiro, and the 10th anniversary of the 2002 World Summit on Sustainable Development (WSSD) in Johannesburg. (source)
The most interesting announcement I've seen so far is for a new report from the United Nations Environment Program, The Business Case for the Green Economy: Sustainable Return on Investment (PDF). Here are a few examples of case studies highlighted in the report (taken from the press release announcing it):

  • Unilever's Sustainable Living Plan, which aims to integrate sustainability into business models, has led to savings of over US $10 million dollars annually. At the same time, their "one rinse" washing formulas, which save an average of 30 litres per wash, are now used across 12.5 million households worldwide - a 60 per cent increase over 2010.
  • AVIVA, who launched its insurance product for Low-Carbon and Environmental Goods and Services in 2011, expects the sector to grow by an estimated UK £45 billion by 2015, supported by government decisions and financial incentives.
  • PUMA conducted the first Environmental Porfit and Loss Account in 2010, in collaboration with Pricewaterhousecooper and Trucost. The value of environmental impact was calculated at €145 million (seen as negative financial impact). Using the tool allows PUMA to reduce future financial loss while strengthening its operating margin by taking into account emerging risks. The company committed itself to having 50 per cent of its products made from sustainable materials by 2015.
  • IGeneral Motors saved more than US $30 million in 6 years through their resource productivity programme, they also reduced waste volume by 40 per cent.

  • In China, the Zhangzidao Fishery Group saw revenues grow by 40 per cent annually between 2005 and 2010 (compared to the industry's 13 per cent average) through offering an alternative to monoculture methods. The integrated Multi-Tropic Aquaculture approach employed by the company provided for a more balanced ecosystem, taking into account local conditions and environmental quality.
  • The Colombian Coffee Growers Federation ensures a sustainable income for more than 27,000 coffee growers with its Rainforest Alliance certified coffee, as part of the Nespresso AAA Sustainable QualityTM program

Silent Spring -- 50th anniversay

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English: Rachel Carson, author of Silent Sprin...

Image via Wikipedia

Fifty years ago today, the New Yorker began a three issue series entitled "Silent Spring" written by Rachel Carson. I don't think I need to introduce Rachel Carson or "Silent Spring" to anyone who reads this blog, but there's a very nice historical perspective on the history of "Silent Spring" at The Pop History Dig. If you're at all interested in Rachel Carson, you owe it to yourself to click through and read it.

Not endangered?

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WASHINGTON - As a result of unprecedented commitments to voluntary conservation agreements now in place in New Mexico and Texas that provide for the long-term conservation of the dunes sagebrush lizard, the U.S. Fish and Wildlife Service has determined that the species does not need to be listed under the Endangered Species Act.

...

State-led voluntary conservation efforts to protect existing shinnery oak dune habitat and greatly reduce the impact of oil and gas development across the species' range now cover over 650,000 acres in New Mexico and Texas, totaling 88 percent of the lizard's habitat. These measures also minimize the anticipated impacts of other threats, such as off-road vehicle traffic, wind and solar development, and increased predation caused by development.

...

After a careful analysis of the scientific data and the protections provided by the voluntary conservation efforts, Service biologists determined the lizard is no longer in danger of extinction, nor likely to become endangered in the foreseeable future.

The Service will closely monitor the conservation measures to ensure they are being implemented and effectively address identified threats. The Service can reevaluate whether the dunes sagebrush lizard requires Endangered Species Act protection. (from the press release, Department of the Interior, 13 June 2012)



A year ago, John Cornyn (R-TX) and Steve Pearce (R-NM) tried to stop listing of the dunes sagebrush lizard. In December, the U.S. Fish & Wildlife Service delayed its final decision for 6 months. I hope that the Service's decision reflects scientific evidence indicating that because of the conservation agreements reached, the lizard is no longer in danger of extinction.

The final determination (PDF) doesn't make me rest easy. The first peer review comment pointed out that the narrow range and specific ecological requirements make the lizard particularly susceptible to extinction. The Service's response:

While having a small geographic range and specialized habitat may make a species more susceptible to threats, we have determined the dunes sagebrush lizard does not meet the definition of an endangered or threatened species because the previous threats have been alleviated. (emphasis added)
The question isn't whether the previous threats have been alleviated. I'm willing to believe the Service when they tell me they have been. The question is whether the species is in danger of extinction, because of its narrow geographical range and specialized requirements. I can't say whether it is or it isn't, because I don't know anything about the lizard, but I worry that the Service's decision depends on shifting the baseline, taking the status quo as OK when it may already represent a degraded condition in which the lizard is likely to go extinct.

iSpot Southern Africa

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06804692ee361aa5e9c4c5e023b9f284.jpgI was out of the office on Tuesday, so I missed the official launch of iSpot Southern Africa (http://www.ispot.org.za/).

"iSpot Launch Celebratory Observations" will commence at 15h00 and continue to 24h00. Any observations outside of this period will be untagged. All observations with the tag will be displayed at the launch, commencing at 17h30.

You are requested to please stop posting at 18h45. iSpot will be launched with a special observation, and you are welcome to refresh your webpage until it is posted at just before 19h00. Thereafter, it would be superb if you could agree to the identification (only if you recognize the species) and thereafter continue submitting observations. Further celebratory observations will be aired until the launch dinner is over at about 20h00.

The idea is to obtain a cross-section of celebratory observations and users as a permanent record of the event, and that can perhaps be revisited and perhaps repeated at special anniversaries.

Please join us in the launch of iSpot. (from the iSpot Southern Africa launch announcment)

If you'd like to see the celebratory observations, follow the link to http://www.ispot.org.za/taxonomy/term/7617. My favorite is the image here of Protea punctata by iSpot user outramspann.



 

Serial commas - again

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Brad DeLong (@delong) provides more evidence that the serial comma is essential:

serial-comma.png
Comments on the site indicate that the cover was Photoshopped.1


Science pulling in

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Cedar Riener (@criener) is onto something:
Science outreach needn't be just reaching out, but also pulling in. In
this age when new forms of communication facilitate dialogue rather than
broadcast, being a good innovative scientist should mean occasional
interaction with a wide variety of people in a wide variety of
disciplines. When people discourage science outreach, I think they hold a
mistaken caricature of what outreach is (as merely broadcasting,
instead of dialogue), but also, they perpetuate a needlessly limited and
conservative view of science, as progress in isolated niches rather
than a fundamentally multidisciplinary exercise.
Calling it "science outreach" is a disservice. "Science communication" is a little better, because communication involves a dialogue. But even communication doesn't capture what Cedar is suggesting. "Science interaction" would be closer.
As attractive as that vision is, though, I have to admit to a bit of skepticism. First, I know I'm peculiar, and I know I'm not particularly creative, but it's really hard for me to see how someone without a strong background in evolutionary biology, ecology, population genetics, statistics, or plant biology could give my colleagues me any new ideas for the Dimensions of Biodiversity project my colleagues and I are involved in. Any "interaction" about that project will likely be with other scientists -- with one interesting exception. We are putting photographs from our field work on iSpot southern Africa, a site where citizen scientists can share observations and post questions.1 I hope that we can use iSpot not only to share our work with others, but also to get ideas from them about places we should visit and species at which we should take a closer look.
But as for my blogging...
Well, if you've read many of the posts here, you'll realize that very few of them have anything to do with my science. Most of them are commentaries of one sort or another.2 It may be different for other science bloggers, Rosie Redfield for example, but I don't expect to get new research ideas or scientific advice from readers of this blog.3 I simply hope that a few non-scientist readers learn a little something about biodiversity, the environment, or academics that they find useful and interesting. And I hope that a few of them might share some of their thoughts with me and with other readers of this blog.



1OK. I confess. If you search for "kholsinger" on iSpot, you'll find only one observation that I've contributed. Jane made the rest of the contributions from 2011.
2And I get very little feedback. Comments come along very rarely.
3Though I'd be delighted if I did.



1OK. I confess. If you search for "kholsinger" on iSpot, you'll find only one observation that I've contributed. Jane made the rest of the contributions from 2011.
2And I get very little feedback. Comments come along very rarely.
3Though I'd be delighted if I did.

Password compromised

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This is old news now, but 6.5 million LinkedIn users (including me) had our passwords compromised. You may not worry too much about someone hacking your LinkedIn profile, though who knows what kind of embarrassing things they might post. But if you happen to use the same password on LinkedIn and on some other site with more sensitive information -- your bank, a credit card company, Amazon.com -- you could find a lot of unusual financial activity in your account if you don't change your passwords soon.

LastPass.com has a tool that will allow you to determine whether you are one of the lucky 6.5 million whose account was compromised. I was. The URL of the LastPass tool is https://lastpass.com/linkedin/. That link is active, and you can click on it. If you do, make sure that you check the URL in your browser bar to ensure that it matches. I learned about the LastPass.com tool via C|Net: What the password leaks mean to you (FAQ).


Phishing -- Be careful

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Many, perhaps most, computer security breaches occur not because software is out of date or because hackers have discovered some obscure backdoor in the most recent version but because the person sitting at the keyboard fall victim to some clever social engineering.

You get an e-mail from your IT department that tells you their doing maintenance on the e-mail server and they need you to logon to the system to re-verify your credentials. You click on the handy link, see your familiar logon screen, and enter your credentials. Only later do you realize that the site to which you gave your credentials wasn't run by your IT department at all. Someone, quite possibly a criminal, now has your credential, and you have to hope you can get them changed before the criminal has a chance to use them.

Sound farfetched? Think you'd never fall for such a scam? Meet Brad DeLong, professor of economics at UC Berkeley and deputy assistant secretary of the U.S. Treasury during the Clinton administration. The scenario I described is roughly what happened to him, as he describes in a blog post entitled "Phishers 1, DeLong 0."

You have been warned!


Today in DC

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Video launch poster promo.jpg
If you're in DC and you read this in time to get to the National Museum of Natural History by 2:00pm today, you can see the first of six videos sponsored by the United Nations Environment Programme on World Oceans Day. If you aren't in DC or you can't make it to the NMNH in time, here's a video from www.rona.unep.org/toomey describing the project.

You can also head over to http://www.rona.unep.org/toomey/ for links to the 6 videos. Enjoy!

Why science outreach is hard

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@scicurious sums it up pretty well. It's not our day job. Her day job (as a post-doc) includes this list of things:

1. Research on my project
2. Research on my PI's project
3. My own grants
4. My PI's grants
5. Publishing findings
6. Wrangling undergrads
7. Wrangling grad students
8. Collaborative projects
9. Writing more grants
10. Analyzing data
11. Getting more data
12. Etc

A typical PI/professor could cross off 2 & 4, but only because those would be subsumed in a bigger 8. And to that a typical PI/professor would add:

  1. Prepare and deliver lectures
  2. Serve on committees
  3. Review papers
  4. Review grant proposals
  5. Make presentations at professional meetings and invited seminars
As she says, "something's got to give." Some of what will give is that universities will come to value outreach more as more and more of us spend time on things like blogging, but those changes will be slow and incremental. There are only so many hours in my day, and the paucity of posts in the last few days is all the evidence you need that even finding time to make one post a day is a challenge. Doing more? It ain't going to happen.

Fortunately, @scicurious has a good suggestion -- hire scientists whose job is public outreach. Maybe you put them on the faculty, as the University of Birmingham did earlier this year, or maybe you hire them in public relations departments. Either way, by hiring scientist whose job is public outreach, you make sure it gets done, and you're more likely to get it done well.

UConn has a Vice Provost for Engagement. I'll be sending him a link to this blog post and encouraging him to help the University do a better job of sharing the work that UConn scientists do. Wish me luck!

Selected works

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I now have a page on bepress.com. It's an easy way to find articles that I've deposited in DigitalCommons@UConn. I haven't signed the Open Access petition at whitehouse.gov,1 but I do try to make the text of all of my papers available through DigitalCommons@UConn.

My SelectedWorks of Kent E. Holsinger page makes many of my recent papers freely available. Enjoy.

Top 10 new species

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2012top10_compositer2_final.jpg
Every year the International Institute for Species Exploration at Arizona State University highlights 10 species first described in the preceding calendar year to illustrate the wonder and diversity of life on earth.

On this year's top 10 new species list are a sneezing monkey, a beautiful but venomous jellyfish, an underworld worm and a fungus named for a popular TV cartoon character. The top 10 new species also include a night-blooming orchid, an ancient walking cactus creature and a tiny wasp. Rounding out this year's list are a vibrant poppy, a giant millipede and a blue tarantula.

"The top 10 is intended to bring attention to the biodiversity crisis and the unsung species explorers and museums who continue a 250-year tradition of discovering and describing the millions of kinds of plants, animals and microbes with whom we share this planet," said Quentin Wheeler, an entomologist who directs the International Institute for Species Exploration at ASU. (source)

The composite image at the left shows each of the top 10 species for 2011. There's also a photo gallery on-line that provides a little more information about each of them. There are also YouTube videos of the sneezing monkey and the Bonaire banded box jelly. Click through to watch them.

Citizen science and citizen policy

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Via scicheer (@scicheer)

Expert & Citizen Assessment of Science & Technology (ECAST) network cordially invites you to the USA launch of the World Wide Views on Biodiversity project:
A distributed, agile, collaborative, and non-partisan 21st century approach that integrates citizen participation, deliberation, expertise, and assessment into government policy making, management, research, development, informal education, and dissemination at the national and international levels

11AM - 2PM, Tuesday, June 5, 2012 (Lunch Provided)
Koshland Science Museum,
525 E Street, NW, Washington, DC 20001
RSVP: http://tinyurl.com/wwvlaunch

...

On Saturday September 15th, 2012, groups of one hundred ordinary citizens in Washington, Boston, Denver and Phoenix will join similar groups across the globe to learn about biodiversity issues, discuss important policy choices, make up their minds, and express their views. The citizen meetings will start at dawn in the Pacific and continue until dusk in the Americas. All meetings will have the same agenda and use the same approach in order to make results comparable and useful for policymakers who will gather the following month in India to discuss future measures for preserving biological diversity. (source)

A national mammal

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English: Bison bison. Original caption: "...

(Photo credit: Wikipedia)

On May 24th, Senators Mike Enzi (R-Wyoming) and Tim Johnson (D-South Dakota) introduced S.3248, A bill to designate the North American bison as the national mammal of the United States. As the New York Times editorial board puts it:

It is hard to think of a better or more deserving creature for that distinction.

The bison is already a part of America's official iconography. It appears on the obverse of the buffalo nickel, a much-loved coin minted from 1913 to 1938. And, in hindsight, we can see the tragic parallel between the eagle and the bison. The founding fathers could not have known that the eagle would nearly become extinct, partly because of the spread of DDT. Nor could anyone who saw the immense North American herds of bison imagine that they would nearly be hunted out by the 1880s, which was a disaster for the species, for the ecosystem that bison shaped and for American Indians, who depended on bison. At one time, they numbered fewer than 1,000 animals.
Nine other senators (from Colorado, North Dakota, Nebraska, South Dakota, Kansas, New Mexico, and Rhode Island) joined as co-sponsors. I hope this bill makes it through the Senate and the House this summer. I like the idea of having a national mammal, and what could be more fitting than a bison?


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