Monday, March 27, 2017

Paper 35 - R. Kiat

Paper 35: Raup and Sepkoski , 1982 – by Rebecca K.

Raup, D. M., & Sepkoski, J. J. (1982). Mass extinctions in the marine fossil record. Science, 215(4539), 1501-1503.
Commentary by Jessica Theodor

David M. Raup
-        Professor of Paleontology at the University of Chicago (before retiring)
-        PhD from the Harvard University
-        Passed away in 2015

David M. Raup - Excerpts from the New York Times:

“He used to say he went into paleontology because it was a field with a lot of data that no one was analyzing,” his wife said in an interview.

As an author and theorist, Dr. Raup raised questions about extinction patterns and biodiversity.
Dr. Raup challenged the conventional view that changes in diversity within major groups of creatures were continuous and protracted, and advanced the theory that such changes can be effected by random events.

And he questioned the accepted notion that biodiversity — that is, the number of extant species — has vastly increased over the past 500 million years, pointing out, among other things, that because newer fossils embedded in newer rock are easier to find than older fossils in older rock, it is possible that we simply have not uncovered the evidence of many older species whose existence would undermine the theory. His conclusion, that the data of the fossil record does not allow the unambiguous presumption that biodiversity has increased, has profound implications.

Dr. Raup’s most famous contribution to the field may have been the revelation in 1983, after a six-year study of marine organisms he conducted with J. John Sepkoski Jr., that over the last 250 million years, extinctions of species spiked at regular intervals of about 26 million years.

J.John Sepkoski Jr
-        Professor of Paleontology at the University of Chicago
-        PhD from the Harvard University
-        Passed away in 1999

J.John Sepkoski Jr - Excerpts from the New York Times:

''No one had ever done it before,'' said Dr. Stephen Jay Gould, a paleontologist at Harvard University who was Dr. Sepkoski's graduate school adviser. ''He compiled a completely consistent data set on all groups, terrestrial, marine, single-celled, multicelled, animals and plants, everything.''

Dr. Sepkoski's most important finding, researchers say, was the discovery of what appears to have been three distinct faunas, each dominating hundreds of millions of years in the fossil record, patterns never before documented or even proposed by others.

''Jack was the first one to recognize those,'' said Dr. Douglas Erwin, a paleobiologist at the National Museum of Natural History at the Smithsonian Institution. The effort, Dr. Erwin added, prompted considerable follow-up research by others.

''In the 80's, when I was in graduate school,'' he said, ''his work influenced what most people did, what most people were thinking about.''

Paper Summary:

            In this paper, Raup and Sepkoski provide us statistical evidence for what is now commonly known as the Big Five mass extinctions. By compiling a large, global dataset from the marine fossil record, Raup and Sepkoski demonstrated the extinction rate (per million years) through time for marine invertebrates and vertebrates that were divided based on families (Fig. 1). There were four distinct extinction events that stood out as statistically significant and well above the baseline extinction rates; these five extinctions occurred in the late Ordovician, Permian, Triassic and Cretaceous. There is also the late Devonian which although appeared noticeable, was not statistically significant - the authors later argue that this is likely due to either sampling error (smearing of extinctions as they are distributed over two stages) or an extinction event that was dragged on over a longer period of time. Fig. 1 also shows that background extinction rates has decreased over recent geological time.

Another figure in the paper, Fig. 2, demonstrates the number of families of marine invertebrates and vertebrates over time. The magnitude of the abrupt drops in the diversity curve during the five extinctions is important to consider as it shows how much percentage of marine diversity was loss during these events (note: although not significant in Fig 1., Fig. 2 shows a substantial drop in diversity during the late Devonian extinction). From Fig. 2 it can also be seen that overall marine diversity has increased in recent years.

Although these extinctions had been recognized before this, it wasn’t solidly established throughout the literature, nor had been statistically proven, especially with such a comprehensive dataset – which is definitely a hallmark of the paper with using a mass quantitative approach to paleontology. The paper also demonstrated the magnitude of these extinction events, as well as the how quickly they occurred as extinctions events repeated in geologic time.

Notes & Questions:
1)    Was ‘shelly’ a references to invertebrates with exoskeletons?
2)    Would we be able to go through the methods in class? For example, I’m not sure I follow what is meant by lower resolution series-level data when they talk about making modifications.

*I came across an article by one of the authors, Sepkoski, called “Extinctions of Life”. I found it to be a useful general guide to understanding paleontology (background and methods) better in light of this paper, specifically: https://fas.org/sgp/othergov/doe/lanl/pubs/00285846.pdf

*Another more ‘recent’ paper which discusses marine diversity with microbial carbonates in particular if anyone might be interested: http://www.robertriding.com/pdf/riding2006mc.pdf

(Riding, R. (2006). Microbial carbonate abundance compared with fluctuations in metazoan diversity over geological time. Sedimentary Geology, 185(3), 229-238.)

Wednesday, March 15, 2017

Jetz et al. 2004 by T. Hawkins

The Scaling of Animal Space Use
By Walter Jetz, Chris Carbone, Jenny Fulford, and James Brown
Blog by Tanner Hawkins

Energetics and metabolism have a lot of explanatory power in ecology at the individual and population level. It explains body and population size very neatly, from an empirical and theoretical standpoint. However, it’s not entirely sure whether energetics can explain other population traits, or if interspecific interaction muddle these effects. The impetus behind Jetz et al. writing this paper is if home range can be well described as a function of metabolic rate.

The short version is… not really. While phenomena such as population density generally agrees with the metabolic theory put forth by West et al. and Damuth’s description of population dynamics as a function of energy, they don’t explain home range as well. The key reason why is defensibility. As body and population size reach a certain point, the amount of resources needed to maintain it requires such a large amount of resources, that a population has to be mobile to get enough resources, and once a population becomes mobile, it makes having exclusive resources that much harder to defend from neighboring populations. This can be shown empirically, as the home range and metabolism become less correlated as body size increases.


While I understand that there’s a pragmatic reason why, it’s interesting that in these mechanism papers they test whether the final model is true, but never the intermediate steps. The authors may have gotten the end result correctly, but for the wrong reasons, and we may never know for sure. Is there an alternative mechanism that others have put forward to explain this data?

Monday, March 13, 2017

West et al. 1997 by K. Sullivan

West et al. 1997 Paper
A General Model for the Origin of Allometric Scaling Laws in Biology
Paper Authors:  Geoffrey B. West, James H. Brown,* Brian J. Enquist
Geoffrey B. West

·       Theoretical Physicist 
·       Distinguished Professor of the Santa Fe Institute
·       Bachelor of  Arts, Cambridge University, 1961
·       Ph.D., Stanford University, 1966

Research Interests:

Geoffrey West is a theoretical physicist whose primary interests have been in fundamental questions in physics, especially those concerning the elementary particles, their interactions and cosmological implications”.


James H. Brown                

·       Professor of Biology at the University of New Mexico
·       Bachelor of Arts, Zoology, 1963, Cornell University
·       Ph.D., Zoology, 1967, University of Michigan

Research Interests:

“Community ecology and biogeography, with special projects on granivory in desert ecosystems; biogeography of insular habitats; and structure of dynamics of geographic-scale assemblages of many species”.

Brian J. Enquist
·       Professor – Department of Ecology and Evolutionary Biology at the University of Arizona
·       External Professor at the Santa Fe Institute
·       Ph.D. Biology, 1998, University of New Mexico.
·       M.S. Biology, 1994. University of New Mexico,
·       B.A. Biology (With Distinction), 1991. The Colorado College

Research Interests:

“Macroecology, Global Ecology, Comparative Biology, Ecophysiology and Functional Ecology”.  “My collaborative lab group strives to develop a more integrative, quantitative, and predictive framework for biology, community ecology, and large-scale ecology. In particular, we aim to link biological measures across spatial and temporal scales in ecology and evolution”.


Main Points
Allometric scaling relations, including quarter (3/4)-power scaling, refers to the characteristic shared by all organism, and the way in which essential materials are transported through “space-filled fractal networks of branching tubes” that run throughout the body.  The model applies to systems with tree-like structures with terminating ends and include such distribution systems as, plant vascular systems, animal circulatory systems (this was the data they used), and bronchial tubes in animal lungs.   
The paper, which focuses on quarter-power scaling for metabolism and body size in mammals and how these physiological patterns tend to be even multiples of ¼, assumes surface area and volume of the cardiovascular system directly correlate with body size.  However, it isn’t entirely clear why quarter-power scaling is exhibited by nearly all kinds of animals.  This paper attempts to better understand this, by proposing a common mechanism underlying these laws:
“Living things are sustained by the transport of materials through
linear networks that branch to supply all parts of the organism”.

Based on this hypothesis, “a quantitative model that explains the origin and ubiquity of quarter-power scaling” to “predict the essential features of transport systems, such as mammalian blood vessels and bronchial trees, plant vascular systems, and insect tracheal tubes”.   It was developed based on three assumptions:

1.     A fractal-like branching pattern that is space-filling is required.

2.     “The final branch of the network is a size-invariant unit” (i.e. the size (radii, length, & other characteristics) of the minimal elements in the network are the same for all organisms).

3.     “The energy required to distribute resources is minimized” (i.e. fluid resistance is minimized due to the terminating structural nature of the network).

They sought to demonstrate how the quarter-power scaling of metabolic rate, along with other biological traits are the products of fractal-like resource distribution system such as the cardiovascular system in mammals.  By applying the assumption above, West managed to realistically and quantitatively show how the model accurately predicts scaling parameters and absolute values regarding serval traits of the cardiovascular system in mammals.

Questions

1.     Is the quarter-power scaling law supported by allomatric data for classes other than mammals, such as birds and/or reptiles?

2.     Do other types of scaling laws like the quarter-power scaling law exist?  If so, how might they relate to macroecology?

You may be interested in reading a critique published in 2004 by J. Kozlowski and M. Konarzewski entitled “Is West, Brown and Enquist’s model of allometric scaling mathematically correct and biologically relevant?”  In it, the authors criticize the model, deeming it ‘mathematically incorrect’ and ‘biologically unjustified’.  West et al, countered by publishing the paper “Yes, West, Brown and Enquist’s model of allometric scaling is both mathematically correct and biologically relevant”, in which they, again, justify their findings as being biologically and mathematically sound.