Tuesday, June 2, 2015

Diet of large herbivores in Africa

Tyler Kartzinel's (and coauthors') new paper is out on diets of African herbivores.

This has the potential to be a classic. Or at least the start of a number of classic studies.

The authors examine the diets of 7 large mammalian herbivores at Mpala in Africa. Taken over a 2 month period, it's essentially a snapshot of the diets of the animals. The authors'  main goal was to better understanding dietary niches in order to better understand the maintenance of herbivore diversity.

The authors do a great job of just quantifying the diets of the herbivores. This has never been done with so many animals in one place. Even just determining the proportion of grasses and legumes for the herbivores is interesting. Seeing how much mallow buffalo (generally considered a grazer) upends their dietary strategy.

The authors also then look essentially species by species at dietary overlap (see above). It's a fine-grained approach to understanding who eats what plants.

One of the authors' main conclusions is probably the most important for rethinking large herbivores: "dietary similarity was sometimes greater across grazing and browsing guilds than within them."

Yes, grazers and browsers can be identified, but it is much more complex than that. 

As more samples are taken over time and more sites compared, the broader web of interactions among plants and their herbivores are likely to be better understood. 

For example, how consistent are these diets over time?

Are their times of year when niche overlap (and maybe competition) is greatest?

How flexible are the diets of these animals?

Only time will tell....

Kartzinel, T. R., P. A. Chen, T. C. Coverdale, D. L. Erickson, W. J. Kress, M. L. Kuzmina, D. I. Rubenstein, W. Wang, and R. M. Pringle. 2015. DNA metabarcoding illuminates dietary niche partitioning by African large herbivores. Proceedings of the National Academy of Sciences:201503283.

Tuesday, March 17, 2015

One more thought on Galileo's Middle Finger

One more thought on the book...

When I think of the role of science in broader society, one of the dominant ideas is that political ideology trumps knowledge. There is research to show that, if I remember correctly, for understanding climate change, the more educated the individuals, the more views diverge between political affiliations. In the US, the greatest divide in opinions on climate change is between the most, not the least, educated Democrats and Republicans.

The corollary from this research is that scientific knowledge does not matter.

The idea that knowledge doesn't matter is corrosive. And it plays into the doubts of scientists that have been steadily and progressively witnessed increased attacks and financial pressures.

Dreger's book offers an alternative: evidence does matter.

And not theoretically. She provides example after example of where evidence came to effect change.

Her most concentrated thoughts on this are found in the epilogue.

"When I run into such academics--people who will ignore and, if necessary, outright reject any fact that might challenge their ideology, who declare scientific methodologies 'just another way of knowing'--I feel this crazy desire to institute a purge. It smells like fungal rot in the hoof of a plow horse we can't afford to lose. Call me ideological for wanting us all to share a belief in the importance of seeking reliable, verifiable knowledge, but surely that is supposed to be the common value of the learned...These must be people who have never had to fear enough to desperately need truth, the longing for truth, the gift of truth. Surely, the 'scholar' who thinks truth is for children at Christmastime is the person who has never had to fear the knock of the secret police at her door."

Knowledge is not the answer to all problems. And truth can be illusory as competing hypotheses can be stubborn to separate. Yet, there must be a counterpoint to the idea that evidence carries not weight.

Dreger offers that counterpoint. 

Monday, March 16, 2015

Book Review: Galileo's Middle Finger

There aren't too many books that would have blurbs on its cover from both Dan Savage and E. O. Wilson. This is probably the only one. And I've never read a book like it.

Dreger is a science historian. The book has really little to do with Galileo**. It is mostly a memoir of her battles as a historian and activist over scientific issues.

**The short introduction on Galileo is still an important read. Dreger uses it to anchor the importance of evidence-based evaluation. Galileo once got into a discussion of whether ancient Babylonians could cook an egg by twirling it around in a sling. His uniformitarian response? "If we do not achieve an effect which others formerly achieved, it must be that in our operations we lack something which was the cause of this effect succeeding, and if we lack but one single thing, then this alone can be the cause. Now we do not lack eggs, of slings, or sturdy fellows to whirl them; and still they do not cook, but rather they cool down faster if hot. And since nothing is lacking to us except being Babylonians, then being Babylonians is the cause of the eggs hardening…"

Dreger has been a pivotal player in a number of battles over the science of sex and related social justice. Hermaphrodism, genital mutilation of intersex babies, defining transgender, hormonal therapy for embryos...she was in the thick of it. Add to that debates over sociobiology, attacks on scientists for research on rape, and homosexuality in animals. She was involved.

All within 10 years by my count.

These stories are not easy reads. These are stories of the role in science in influencing what often become life and death decisions. And the attacks on the scientists (and her) attempting to collect evidence on the issues are ferocious. She chronicles it well.

What stands out about her craft is her intensity for fact-checking. Her thesis is the importance of evidence. She articulates this better than almost any modern writer. In her writing, she assembles evidence to ensure there are no loose threads, yet not to the detriment of the narrative. If Sagan had once said that "Extraordinary claims require extraordinary evidence", Dreger methodically accumulates evidence to often show that a person's extraordinary claim does not have the extraordinary evidence required. She's thorough and it shows.

Somehow, the book ends on a hopeful note. Evidence comes to light. Positions are changed. Careers are restored. The importance of academia is reaffirmed.

Tuesday, March 3, 2015

Reviewing literature on bison and nutrition

I'm going through the old literature on bison...not that there is much new literature.

One thing I still haven't found is whether bison gain weight better with low-quality forage than cattle.

The feeding trials on these are often suspect because bison don't like to be penned up. So, part of the problem is the wrong types of studies have been run. Another problem is that they don't push the nutritional envelope hard enough, e.g. feeding the animals 5-6% protein.

The question that evolves parallels the C-S debate in plants. Are cattle better at putting on weight than bison at all nutritional levels while bison just are better at tolerating stresses? Or do bison actually grow better on low-quality diets?

We know bison are better adapted to cold. They are thermoneutral down to -40°C. Cattle (like Hereford) are thermoneutral down to about -5°C.

We also know bison drop their metabolic rate by half in the winter.

They just don't need to eat much. They also seem to have better digestive efficiency than cattle. What they consume gets digested to a greater degree than what cattle consume.

But the definitive study that shows a nutritional niche still hasn't been found.

It's a bit frustrating this work hasn't been done and isn't slated to be done any time soon.

When we don't have the basics, it's hard to get at the more complicated questions...

some notes for me...

Schaeffer et al. 1978.
--longer retention time than cattle.
--greater digestive efficiency (food is digested to a greater degree).
--greater nitrogen absorption from food.

Keith 1981
--when fed a diet higher in N, there are greater concentrations of urea in their blood, saliva, and urine

Rutley and Hudson 2000
--during the winter, bison take in about half the energy they do in the summer.
--food remains in the digestive system for twice as long in the winter as summer (46 vs. 24 h).
--when it’s snowy, bison intake rate drops a lot. 

Christopherson et al. 1978.
--stuck bison, yak, Scottish Highland, and Hereford calves in a freezer (20°C, 0°C, and -30°C).
--The metabolic rate of bison at -30°C was the lowest as other animals increased their metabolic rate when exposed to extreme cold. 
--Authors estimate that bison are thermoneutral below -40°C. In contrast, Hereford were good down to just -3°C in March.

Hawley et al. 1981.
--bison digest their food better than cattle (Hereford).
--during the summer, dry matter intake was 1.6% of body mass.

Galbraith et al. 1998
--bison switch on metabolically by April
--the digest their food more efficiently than deer or wapiti
--they also produce more methane

Koch et al. 1995.
--bison don’t gain weight at a higher rate than cattle on a low-protein diet
--bison don’t like to be penned in feeding trials like these, which may reduce weight gain.

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.


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...