Monday, June 18, 2012

The importance of reporting negative results in science--

"I have approximate answers and possible beliefs in different degrees of certainty about different things, but I'm not absolutely sure of anything, and of many things I don't know anything about, but I don't have to know an answer. I don't feel frightened by not knowing things, by being lost in the mysterious universe without having any purpose which is the way it really is as far as I can tell, possibly. It doesn't frighten me."

-Richard Feynman

Since its inception, one of the cornerstones of science has been the rigorous examination and scrutiny of claims about reality. Increasingly, scientists have developed a wide variety of statistical tools used to quantitatively analyze hypotheses about the world. These include the use of so-called probability values (a.k.a. 'p-values'), which allow for the formal evaluation of certain statistical hypotheses (e.g. whether there is any evidence that measured bill lengths of birds come from two different sample populations). Scientists have established a threshold for these probability values of 5%. To somewhat oversimplify, this indicates that when using p-values, we are willing to accept that an observed difference will be a false positive 5% of the time, or 1 time in 20 events. However, one of the common critiques of the use of p-values is that those analyses that fall outside of the 5% threshold are often unreported, especially in congruence with the pressure to report positive results in an effort to publish a given paper in a more prestigious journal. This, I feel, severely handicaps our ability to perform good science and best examine the world on its own terms. In fact, it may be that the publication of negative results is just what is needed to spur a scientific field forward into new theoretical realms.

For example, suppose that a researcher is interested in understanding how a variety of abiotic factors affect the reproduction of fish in a group of stream systems. Knowing what past research has been done on these areas, the researcher measures a variety of variables including stream temperature, nutrient quality, water velocity, etc. After determining that he has a sufficient sample size given the variability the researcher has seen in the data to properly detect effects if they exist, he runs a series of analyses and finds no significant results on any of the measured variables. The researcher is then met with a choice: scrap the whole analysis, continue to use new and possibly inappropriate statistical techniques until he finds a positive result, or report the negative results found by the analyses. It is the last option that I feel too few researchers choose, and also one that is often remarkably undervalued, because it's when our previous understanding of the likely causal drivers in these sorts of systems doesn't bear fruit that we are able to more fully develop our thinking and come up with new ideas of what is driving the behavior of these systems. For instance, there may be a species of invasive predator whose feeding habits strongly negatively influences the reproduction of the fish due to heavy levels or predation or increased stress levels and their associated decrease in fecundity. If researchers do not report on these sorts of negative results, the ecological 'man behind the curtain' may never be seen otherwise.

Beyond other unfortunate effects inherent in the lack of reporting of negative results (e.g. biased meta-analyses, which are used to synthesize information across many published studies), I feel that the avoidance of publishing negative results is a ready recipe for scientific stasis, and that it would best suit science if it was stopped altogether. There are many social factors that make this difficult (e.g. the career pressure to publish in high impact journals, which is most readily done when a researcher has significant positive results to discuss), but I think that science as a whole would be supremely benefited in the long run if the trend was bucked.

Sunday, May 20, 2012

Field season imminent--

In two days, I will begin the trip to Yaak, Montana to begin training for my position as an assistant technician for the Cabinet-Yaak Grizzly Bear DNA Project, collecting grizzly bear (and other) hair from strategically placed snares throughout an extensive study area.

I will be paid for outdoors adventure and science. This pleases me.

Saturday, April 28, 2012

Non-comprehensive list of links on wildlife biology and ecology--

This list will be sporatically updated over time. Enjoy.


Blog articles on ecology and science as a career:


Blog posts from wildlife biologists in the field doing what wildlife biologists do:


Other posts related to wildlife biology and ecology:


Yale ecology lectures:

1. The nature of evolution: selection, inheritance, and history

2. Basic transmission genetics

3. Adaptive evolution: natural selection

4. Neutral evolution: genetic drift

5. How selection changes the genetic composition of populations

6. The origin and maintenance of genetic variation

7. The importance of development in evolution

8. The expression of variation: reaction norms

9. The evolution of sex

10. Genomic conflict

11. Life history evolution

12. Sex allocation

13. Sexual selection

14. Species and speciation

15. Phylogeny and systematics

16. Comparative methods: trees, maps, and traits

17. Key events in evolution

18. Major events in the geological theatre

19. The fossil record and life's history

20. Coevolution

21. Evolutionary medicine

22. The impact of evolutionary thought on the social sciences

23. The logic of science

24. Climate and the distribution of life on Earth

25. Interactions with the physical environment

26. Population growth: density effects

27. Interspecific competition

28. Ecological communities

29. Island biogeography and invasive species

30. Energy and matter in ecosystems

31. Why so many species? The factors affecting biodiversity

32. Economic decisions for the foraging individual

33. Evolutionary game theory: fighting and contests

34. Mating systems and parental care

35. Alternative breeding strategies

36. Selfishness and altruism


Other talks on wildlife biology and/or conservation:

E.O. Wilson on saving life on Earth

Corneille Ewango is a hero of the Congo forest

Alan Rabinowitz: Saving big cats

John Kasaona: how poachers became caretakers


Wildlife documentaries:

In search of the jaguar:

Lost land of the tiger:

Wednesday, April 18, 2012

Unusual deaths amongst the Felidae--

Few organisms are as often associated with grace, grandeur, and grit as those belonging to the Felidae. And, so much as they can be said to hold those traits in life, so too may they may hold them in death. However, being wild animals that are frequently exposed to a wide variety of often unpredictable conditions, they may be met with a demise that is somewhat unbecoming of their notoriously feral reputation. 

Two such instances were reported by Frank Nicholls in the Journal of the Bombay Natural History Society in the early 1950s.

Imagine, if you will, that you are in the jungles of India. The temperature is sweltering, and the humidity is complimentarily oppressive. You yawn and stretch, taking a break from the seemingly never-ending trail that you have been following, and see a woman walking towards a stone well. Pleased to have some degree of human company, you saunter towards her, but you quickly pause when you hear the sharp snap of a twig.  Looking for the source of the unexpected sound, your eyes are drawn to a nearby cluster of vegetation, and are met with the face of the most iconic organism in all of India. 

The tiger lunges forward with such speed and ferocity that you are rendered speechless. It seems to close the gap between the woman and itself in an instant, and leaps into the air towards her. By some great stroke of luck, the woman bends down to retrieve some much-needed water from the well. And, to the tiger's misfortune (and your own astonishment), you see the tiger plunge into the well and out of sight.


The next day, while wandering a nearby labor camp, you hear a great commotion, as though though a lion were caught in a blender mid-roar. You run towards the unnerving cacophony, and see a leopard lying on its side, with a pile of blood pooled immediately in front of him. 

As you lower yourself for a closer look, you gasp in astonishment. Inside the leopard's mouth, as still as the leopard itself, you see the back half of a domestic cat. As well as you can surmise, the leopard had attempted to predate upon the fierce creature, and had been killed by it while it was struggling for survival inside its gaping maw. 

Tuesday, February 21, 2012

The Felidae: an introduction

Hello, and welcome to Felidae, a blog exclusively devoted to disseminating information on the research, ecology, and conservation of the world's felid species.


Whence the Felidae?

The Felidae comprises a group of extant and extinct carnivorans whose origins, according to genetic data (and corroborated by fossil data), can be found at the end of the Eocene epoch, ~ 32 million years ago. The end of the Eocene and the beginning of the Oligocene epoch was characterized by rapid environmental change, with a marked contraction of tropical forests and the initial development of modern grasslands. With rapid environmental change comes increased opportunities for speciation, and it is probable that the Felidae owes its existence to said environmental alterations.

From this initial branching, two distinct groups emerged ~ 13-14 million years ago in Europe and in Asia: the Machairodontinae (colloquially "saber-toothed cats") and the Felinae (colloquially "conical-toothed cats"), a clade that includes all living felid species. Machairodontines were most notably characterized by a variety of cranial adaptations that facilitated an increased gape size of the mouth, likely related to their often remarkably long and flat canines. Representatives included the iconic Smilodon, Homotherium, Dinofelis, and Megantereon. Though the function of said hypertrophied canines is still debated, it may be noteworthy that the extant clouded leopard (Neofelis nebulosa and Neofelis diardii) has several convergent cranial characteristics, and has been recorded killing relatively large-sized deer and pigs with a deep bite to the nape.

Sunda clouded leopard displaying the wide gape and elongate teeth.
Image courtesy of Flickr user 'timogan', registered under a creative commons license.

However, the exact function of their unusual dentition may never be known, as the last of the Machairodontinae went extinct during the Quaternary extinction event, leading to a single living clade of felids.

Through genetic data, modern Felinae has been divided into 8 distinct lineages. The first of these lineages, the Panthera lineage, diverged ~ 10.8 million years ago, and includes both species of the primitive-most extant felid, the clouded leopard (Neofelis nebulosa and Neofelis diardii, native to south-eastern mainland Asia and Sumatra/Borneo respectively), the lion (Panthera leo), the jaguar (Panthera onca), the leopard (Panthera pardus), the tiger (Panthera tigris), and the snow leopard (Panthera uncia). 

Sunda clouded leopard.
Image courtesy of Flickr user 'canorus', registered under a creative commons license.

The second lineage to diverge (circa 9.4 million years ago), the bay cat lineage, is restricted to southern Asia and consists of three species of the Pardofelis genus. These include the little-studied and elusive bay cat (Pardofelis badia), the marbled cat (Pardofelis marmorata), and the Asiatic golden cat (Pardofelis temminckii). 

Bay cat.
Image courtesy of Jim Sanderson, registered under a creative commons license.

The Caracal lineage, diverging ~ 8.5 million years ago, consists of the caracal (Caracal caracal), the African golden cat (Profelis aurata), and the serval (Leptailurus serval).

Image courtesy of Flickr user 'orkomedix', registered under a creative commons license.

The fourth lineage to diverge, the Ocelot lineage, consists of seven species of small-bodied New World felids, including the ocelot (Leoparadus pardalis), the margay (Leopardus wiedii), the Geoffroy's cat (Leopardus geoffroyi), the oncilla (Leopardus tigrinus), the guiƱa (a.ka. 'kodkod', Leopardus guigna), the colocolo (a.k.a. 'pampas cat', Leopardus colocolo), and the Andean cat (Leopardus jacobita).

Image courtesy of Flickr user 'siwild', registered under a creative commons license.

The fifth Felinae lineage, the Lynx lineage (diverging ~ 7.2 million years ago) contains four species of a single genus, of which two are native to North America and two are native to Europe and Asia. These include the Eurasian lynx (Lynx lynx), the critically endangered Iberian lynx (Lynx pardinus), the bobcat (Lynx rufus), and the Canada lynx (Lynx canadensis). 

Eurasian lynx.
Image courtesy of Flickr user 'dogrando', registered under a creative commons license.

The Puma lineage, diverging ~ 6.7 million years ago, consists of the puma (Puma concolor), the small-bodied jaguarundi (Puma yagouaroundi), and the cheetah (Acinonyx jubatus). 

Image courtesy of Flickr user 'Lil Rose', registered under a creative commons license.

The Leopard cat lineage diverged at ~ 6.2 million years ago and consists of five species of Old World felids, including the Leopard cat (Prionailurus bengalensis), the Pallas's cat (Otocolobus manul), the flat-headed cat (Prionailurus planiceps), the rusty-spotted cat (Prionailurus rubiginosus), and the fishing cat (Prionailurus viverrinu). 

Leopard cat.
Image courtesy of Flickr user 'siwild', registered under a creative commons license.

Similarly, the domestic cat lineage diverged ~ 6.2 million years ago, and comprises the wildcat (Felis silvestris), the Chinese mountain cat (Felis bieti),  the black-footed cat (Felis nigripes), the sand cat (Felis margarita), and the jungle cat (Felis chaus).  

Scottish wild cat.
Image courtesy of Flickr user 'Fred Dawson', registered under a creative commons license.

The Felidae contains some of the most elusive and imperiled carnivore species alive today. Knowledge of their ecology is crucial to their conservation, and it is my hope that the things you learn from this blog will help spur your interests in these remarkable animals. Furthermore, I will be documenting my own journeys in the field of felid conservation biology, and hope that you find them to your enjoyment as well.

Until next time!