Saturday, January 17, 2015

The smell of rain (on dirt).


I guess I had always realized that a light rain brings out that "it-just-rained" smell more than heavy rains, but never thought about why.

I really need to be more curious.

https://newsoffice.mit.edu/2015/rainfall-can-release-aerosols-0114


Friday, December 19, 2014

Authorship: the trillion dollar question.

Every year, over a trillion dollars is spent on scientific research and development. 

Publication of that research is a requirement for most of that money. 

And authorship is the construct that assigns credit and responsibility to that publication.

Despite the centrality of authorship to the scientific process, the institution of authorship is rickety. 

It's like a car held together with tape and wire with knitted seat belts. 

"As long as you don't go over any bumps, you should be fine..." 

Authorship issues are rare, but a lot is at stake for a person to be considered an author or not. 

Not including a person as a coauthor when it is deserved deprives an individual of credit. Including a person that does not deserve or desire coauthorship dilutes the credit given to others and potentially creates liability for an individual on research with which they might not agree.

Almost every principle associated with coauthorship is tenuous. 

Let me elaborate on one: determining the list of authors.

There are three main bodies to examine here. The Committee on Publication Ethics. The International Committee of Medical Journal Editors. The Council of Science Editors. 

Here is how the CSE approaches the issue.

The Council of Science Editors states that there is general consensus on some points regarding the principles of authorship. One of these is that 

"Identification of authors and other contributors is the responsibility of the people who did the work (the researchers) not the people who publish the work (editors, publishers). Researchers should determine which individuals have contributed sufficiently to the work to warrant identification as an author."

To this point, there is no recommendation that at the point of initial submission, all authors sign a form that states that everyone agrees that each author listed deserves to be an author. 

Yet, let's say that during the review process, one author requests to be removed from the list of coauthors. Maybe they don't agree with a statement that has been inserted, or they have decided that their contribution was not substantial enough to warrant coauthorship. Alternatively, during the revision process a new author might be added due a contribution that arises as a manuscript is modified.

How should a journal deal with that?

CSE recommends that: 

"Any changes the authors wish to make to the author byline after the initial submission of a manuscript should be made in writing and the document should be signed by all authors, including those being added or removed."

This statement is a solution looking for a problem. 

And it's a solution that has the potential to create more problems than it solves.

First, it seems to directly contradict the consensus principle that the journals should not determine who is a coauthor. 

Second, it imposes inconsistent requirements. If there is no need for a statement that all coauthors agree that all other coauthors should be a coauthor initially when a manuscript is submitted, why during the review process?

Third, it forces a particular model of agreement on authors for determining coauthorship. All coauthors must agree, including any coauthor that has been removed. Before, it could be the lead author that determines whether a contribution was significant. Now, it's consensus.

If everything works perfectly, this imposes a slight burden on the authors. If the authorship list is long, the burden is somewhat greater and can delay publication somewhat substantially. 

But what if it doesn't work perfectly?

Here's a scenario to consider. Let's say a new statement is added to a paper during revision. One  coauthor disagrees with the statement. It might even be a statement that is independent of their previous contribution. All other coauthors agree with the statement and deem it necessary. If this happened before submission, the coauthors could agree to recognize that author's contribution in the acknowledgments. 

With the CSE requirements, by not signing a form for the journal, that coauthor now has the power to effectively block the publication of the manuscript in that journal. 

If the journal can override the requirement of all coauthors signing it, then why have it at all?

Here's another scenario. Let's say that a coauthor desires to be removed from the list of authors. Another coauthor thinks that they should remain. Again, this could effectively scuttle publication. 

Has this ever happened?

No idea, but that is immaterial. That it could happen is all that matters.

And we shouldn't have systems in place that only function when they aren't tested.

ICJME and COPE really do not provide much more clarity on the issue. 

For example, ICJME states that 

"It is the collective responsibility of the authors, not the journal to which the work is submitted, to determine that all people named as authors meet all four criteria; it is not the role of journal editors to determine who qualifies or does not qualify for authorship or to arbitrate authorship conflicts." 

This is consistent with CSE. 

What does ICJME recommend if there is a change in authorship?

"If authors request removal or addition of an author after manuscript submission or publication, journal editors should seek an explanation and signed statement of agreement for the requested change from all listed authors and from the author to be removed or added."

Same as CSE.

Why should the journal require this if it is not the responsibility of the journal to determine who qualifies as a coauthor?

Yes, one can think of nefarious situations where a higher power should step in and deliver justice. But, if something is outside the jurisdiction of a journal, it is outside the jurisdiction of a journal.

If disputes arise, what does ICJME recommend? 

"If agreement cannot be reached about who qualifies for authorship, the institution(s) where the work was performed, not the journal editor, should be asked to investigate."

Considering most work is done across institutions, which one should investigate? What if the work was not done at any institution? And if the institutions disagree? 

Let me turn anabolic for a minute. 

How should these issues be dealt with?

Here is the simplest solution. We need to redefine the responsibilities of the lead author. If we state that it is the lead author's responsibility, using generally accepted principles, to determine coauthorship, then all of these inconsistencies do not need to exist.

This adds liabilities and responsibilities to being the lead author, but they are pretty minor. And it codifies generally recognizable principles of how papers are constructed. 

What happens if something goes wrong under this construct? If an author is included in a paper against their will, that author can petition the journal to have their name removed. If an author is not included when they feel they should be, then they can petition the lead author's institution to investigate. Or the funding agency. If coauthors disagree on statements or inclusion of authorship, tie goes to the lead author.

It might seem imperial, but it's clean. 

I don't think these issues arise too often. And hopefully, we will not get to the point where we need scientific courts to resolve these issues. 

Still, that doesn't mean that our policies should not be as clear and consistent as possible.


Tuesday, November 4, 2014

Quick video on bison shrinking with warming


I had some requests to post a quick video summarizing why bison are likely to shrink with warming...


Sunday, October 26, 2014

Alpine herbivore shrinking


A long term record of alpine chamois weights from the Alps shows that body mass has been declining since 1979.

Using mass of over 10,000 carcasses from hunters, the authors show that the weights of juvenile chamois have been declining over the past few decades. Although some of the decline is due to increasing population density (stricter hunting laws), it appears that high temperatures also have been directly causing declines in mass.

The authors propose greater thermoregulatory demands as contributing to the declines, but the authors were unable to determine whether forage quality had declined.

Mason et al. Frontiers in Zoology 2014, 11:69
http://www.frontiersinzoology.com/content/11/1/69

Saturday, October 25, 2014

Ben Bradlee passes away


Ben Bradlee, editor of the Washington Post for many years, passed away at age of 93.

Bradlee was the editor who published the Pentagon Papers. For those who don't know the story of the Pentagon Papers, it's an important history lesson.

Washington Post published an essay of his from 1997 where he discusses the role of the press and lies from public officials:

Where lies the truth? That’s the question that pulled us into this business, as it propelled Diogenes through the streets of Athens looking for an honest man.

If it wasn't for investigative journalists and editors like Bradlee, the world would be a different place.

Thursday, October 16, 2014

Evolution of monarch butterflies


A quick note on a new paper in Nature on the evolution of monarch butterflies. 

The authors (Zhan et al.) examine genomes of 101 genomes from the Danaus genus. 

First, basic ignorance. I had no idea there were so many populations of monarchs around the world. That was nice to know.

Second, the ability of genomic research to identify the specific genes that were the basis of selection is really astounding. As someone who measures a lot of plant traits, to dive into the genomes of so many populations and species to identify traits that define species is pretty special. 

With the genomic work, they really are identifying traits that we didn't know exist at the organismal level. 

For example, the authors identify selection on a collagen gene that affects flight muscle function. 

That's not easy to identify empirically. 

In all, I'll admit I'm jealous of what the authors could put together on the monarchs and related species. Biogeography, evolution, and function all wrapped up into one paper redefining our understanding of monarch butterflies.

I'm royally jealous. 

Friday, October 10, 2014

How large a bison herd?

The idea of the buffalo commons provoked many people to think in the late 80's and early 90's. With the commons, a large herd of bison--maybe millions--would roam the open expanses of the West.

Today, bison reintroductions continue, but most of the herds are small. Maybe a few hundred. By comparison, the largest public herd--Yellowstone--is roughly at 4000 animals.

So, realistically, how much larger could we get? How big a herd is possible?

There are a few constraints on figuring out how large a bison herd is realistic.

If you don't cull the bison, then you have to rely on predation. Unfortunately, wolves just are not a significant check on bison population. Yellowstone National Park, which has the most active wolf packs interacting with bison, still relies on culling animals when they leave the park to hit their target population size, which is actually about 1000 animals less than what are out there. Wolves don't keep them in check.

If predation isn't a check, then the upper limit becomes food and/or disease. This is an effective regulator, but that means periodic mass starvation and/or disease epidemics. 

I'm not sure people in North America have the stomach for that yet. 

Even Oostvaardersplassen hasn't quite made it to that level of hands off.

In reality, periodic culling is going to be necessary to manage a large bison herd.

If so, how big a herd is realistic?

Assuming that land area is not a limitation, a couple key numbers here to work off of.

First, is the intrinsic growth rate of a bison herd. This is going to vary, but a 25% growth rate is reasonable for most herds.**

**This is going to vary with sex ratios and other factors, but it's a good start.

Second, is how many animals a work crew could process. Bison have to be rounded up, worked individually, and then sorted. Some of those animals go back to the herd. Some are sorted off to go to market.

In general, a single crew can work about a bison a minute. 400 bison in a day is a good estimate of how many bison can be worked in a day. That translates to 2000 bison in a week. If you dedicate a month to working animals, then that would be approximately 8000 bison.

With a growth rate of 25% and 8000 bison that you can work in a month, that means a winter herd size of 6400 and culling off of 1600 animals.

So, if you dedicate one work crew and corral system for one month to processing animals, then your maximum herd size is 8000.

8000 animals in a corral at one time, is not a small corral. And it would take a lot of hay to keep them fed while they are being processed.

What if we relax the assumption that some animals are returned?

What if just the first 8000 get shipped off?

This would mean calves, yearlings, males, females. Whoever is caught in the "net" goes.

If you remove the assumption that 75% of the animals are returned to the herd, then roughly that would let you have a herd size of about 32,000 animals. This would roughly be stable if every year 8000 animals are shipped off and growth rate is 25%.

Assume natural mortality regardless of how ugly: no limit on herd size.
Assume you don't have to round up animals, but could just shoot them in place: no limit as long as you feel comfortable shooting thousands of animals.
Assume have to round up with one crew for a month, but don't sort the animals: 32,000.
Assume have to round up with on crew for a month, but do sort the animals: 8,000.

Can you add corrals, or sort longer than one month? Yes, but there is no precedent for this.

What about field harvests? With field harvests, animals are often shot in the field and processed in trailers on-site. Yet, the typical rate for a crew is 8 animals per day. Over a 6 month period, that's still just a 1000 animals per day. Harvesting bison sustainably this way would never permit a herd size of more than a few thousand at best.

So what are the likely prospects for a bison megaherd?

Assuming you can get the land, it's going to be hard to have more than 8000 animals in a herd.

So, how big an area is that? Depending where you are in the world, it might be about 100,000 - 200,000 ha (40-80k ha). Put in perspective, that's a square about 10-20 miles on a side.

That's really nothing. Maybe $20-$100 million to buy the land for that (depending on a lot).