Personal Thoughts - Search for primary source of information

I have been wanting to write a post lately describing the search for the primary information in the literature. What I mean by this, is searching for where an idea originated. Frequently people will just cite the source where they read the information, not caring if that idea was cited from some previous source. The problem though lies in the fact that that information came from somewhere else, and your citation does not adequately represent the source of the information. But there is another problem. Perhaps they changed the purpose of that information a little, and the people they are citing changed it a little, and so on back to the source. It is like a game a telephone, where the original source of the information has very little in common with the final source.

Take for instance my search for the "Grey-weighted distance transform" which I used in my paper: Lehane and Ekdale, 2014, Analytical tools for quantifying the morphology of invertebrate trace fossils. The grey-weighted distance transform is a technique that I used in order to help determine Network Tortuosity of a trace fossil by calculating the tortuosity for each path through the trace.

Figure 6 from Lehane and Ekdale (2014) showing the calculation of the Network Tortuosity. 

When I was looking for a technique to do this, I stumbled upon Wu et al.'s (2006) paper on doing this type of network tortuosity measurements on fracture patterns. In the paper they state:

"The path length was determined using the ‘gray-weighted distance transform’ (Verbeek and Verwer, 1990). This algorithm calculates the path that results in the shortest traveling time when going from a set of predefined starting points to any other point in the image."

 So clearly this appears to be a computer program set to calculate the length of the shortest paths across a surface. So I went to the article they cited, Verbeek and Verwer (1990). In that paper they state:

"Already in 1968 Rutovitz (1968) introduced the grey-weighted distance transform in which the  distance of a point to a set of reference points (the sources) is calculated as the lowest path sum of grey values (i.e. the lowest of the sums over all possible paths from that point to the sources)."

A couple of things are noticeable here. 1. Wu et al. (2006), changed the spelling of the "grey" to "gray" to match the language designations of where they were publishing, even though it was an already established title to an algorithm . 2. Even though the original idea for the process came from Rutovitz (1968), there is no citing of his paper anywhere in the Wu et al. (2006) paper.

And that is where part of my issue lies. This is not a slight against Wu et al. (they were a tremendous help to me on my dissertation) mainly because this is not an isolated incident. Should researchers be expected to find the primary source of  information or is the information cited far along in the game of telephone more relevant than the original source? Or should all of the links in the chain be cited?

To continue in our search backwards we go to Rutovitz (1968) who states under his section "Grey-weighted distance transform":

"Let S be a subset of the integer coordinate plane. The result of the pure distance transform of the characteristic function of S is a function d defined on S such that at each point (i,j) ϵ S, d(i,j) is the minimal path distance from (i,j) to S. Suppose though that we have a function g defined on S, and that we think of the values of g as heights of a surface above the (i,j)-plane. We want to set up a modified distance function on S, such that points accessible from outside of S via low-lying paths have lower values than points accessible only by higher paths of the same length. Of course, optimal relative weightings for the values of the function g in relation to the lengths of paths in the raster must be found."

So, how much relevance does this have, from a time before computers to the modern application, where the computers used would have been even beyond comprehension at the time the original algorithm was conceived.  The basic theory is generally similar, but the use and changes that it has undergone through the decades has changed it. Is the original even relevant anymore?

Personally, I feel all such applications should be cited. From the original source, up through the modern example, because they all had a hand in crafting what it had became so that I was able to use it in my research.

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Lehane, J.R. and Ekdale, A.A. 2014. Analytical tools for quantifying the morphology of invertebrate trace fossils: Journal of Paleontology, v. 88, p. 747-759

Rutovitz, D. 1968. Data structures for operations on digital images, p. 105–133. In G. C. Cheng, R. S. Ledley, D. K. Pollock, and A. Rosenfeld (eds.), Pictorial Pattern Recognition. Thompson, Washington DC.

Verbeek, P. W. and B. J. H. Verwer. 1990. Shading from shape, the eikonal equation solved by grey-weighted distance transform. Pattern Recognition Letters, 11:681–690.

Wu, Y. S., L. J. Van Vliet, H. W. Frijlink, and K. Van der Voort Maarschalk. 2006. The determination of relative path length as a measure for tortuosity in compacts using image analysis. European Journal of Pharmaceutical Sciences, 28:433–440.

My Dissertation Highlights and a link to Download it

My dissertation has finally been posted online for all the world to see. Click on the title below if you with to download it:

Applications of quantitative methods and chaos theory in ichnology for analysis of invertebrate behavior and evolution

Since it finally has been published I wanted to share some highlights of it.

Individual published chapters:

Chapter 2: Fractal analysis of graphoglyptid trace fossils

Chapter 3: Pitfalls, traps, and webs in ichnology: Traces and trace fossils of an understudied behavioral strategy

Chapter 4: Analytical tools for quantifying the morphology of invertebrate trace fossils

Dissertation Abstract
Trace fossils are the result of animal behaviors, such as burrowing and feeding, recorded in the rock record. Previous research has been mainly on the systematic description of trace fossils and their paleoenvironmental implications, not how animal behaviors have evolved. This study analyzes behavioral evolution using the quantification of a group of trace fossils, termed graphoglyptids. Graphoglyptids are deep marine trace fossils, typically found preserved as casts on the bottom of turbidite beds. The analytical techniques performed on the graphoglyptids include calculating fractal dimension, branching angles, and tortuosity, among other analyses, for each individual trace fossil and were performed on over 400 trace fossils, ranging from the Cambrian to the modern.

These techniques were used to determine various behavioral activities of the trace makers, including feeding and behavioral evolution. Graphoglyptids have been previously identified as representing mining, grazing, farming, and/or trapping. By comparing graphoglyptids to known mining burrows and grazing trails, using fractal analysis, it was possible to rule out mining and grazing behaviors for graphoglyptids. To determine between farming and trapping, a review of all known trapping burrows was required. The hypothesis that graphoglyptids were trappers was based entirely on the hypothesized feeding behaviors of the worm Paraonis. Close examination of Paraonis burrows indicated that the burrows are not traps. This means that, since Paraonis does not trap prey, graphoglyptids should not be considered traps either. Therefore, graphoglyptids likely represent farming behavior. This study also shows that previous interpretations of graphoglyptid behavioral evolution was far too simple. The results of the morphological analyses indicate that major changes to the behavioral evolution occurred during the Late Cretaceous and the Early Eocene. Previous hypotheses about Late Cretaceous evolutionary influences were validated. However there were additional influences like the Paleocene-Eocene Thermal Maximum that were not overly emphasized before. Finally, of the many theories about the driving force of evolution, chaos theory has often been overlooked. Chaos theory is a powerful tool, such that, by knowing the similarities between chaos theory and evolutionary theory, it may be possible to map out how environmental changes could shift the evolution of a species.

Oldest Reference
I tried to see how old a reference I could get in there. 1844 was the best I could do. I have a friend who managed to cite the Bible. I'm a bit jealous.

Emmons, E. 1844. The Taconic System: Based on Observations in New-York, Massachusetts, Maine, Vermont, and Rhode-Island. Carroll and Cook, Albany, NY.

Newest Reference
This entry was published about 2 weeks before my dissertation went final final. I was able to squeeze it in during formatting edits.

Ekdale, A. A., and J. M. de Gibert. 2014. Late Miocene deep-sea trace fossil associations in the Vera Basin, Almería, Southeastern Spain. Spanish Journal of Paleontology 29(1):95-104.

Call Outs
In addition to the references I also make mentions of:

Return of the Jedi
The Lost World by Michael Crichton
Mr. Potato Head

Stats and Numbers
There are 433 numbered pages with a total of 446 pages.
6 Primary chapters.
     - 3 currently published chapters.
     - 2 publishable chapters currently in review.
12 Appendices
107 Figures
13 Tables
291 References


My entire PhD took 1,806 days to complete


Right as I was starting to do my analyses, I had saved a backup of my data around once or twice a week. I figured I could actually track the size of my data as it was growing through the analyses. I used a lot of GIS files, and anyone who knows anything about GIS files knows that for every file you create, you are actually creating 7 or 8 files. So the number of files escalated really fast. A lot of the jumps in file size were actually due to me starting a new analysis. In the end, I ended up worth over 34,000 files and 35 GB of data.

Not sure how useful this is, but I found it interesting to watch it grow.

The Star Wars Intro to My Dissertation Defense

As some people may know I have been very busy working on my PhD Dissertation, causing me to rather neglect this blog. I did, however, pass my dissertation defense last Friday (November 22nd), so hopefully I will have a little more free time. The title of my defense was Behavioral evolutionary studies of graphoglyptid trace fossils through the geologic record.

When I give a presentation I like to have a little fun with it. So there were several little jokes and me-isms scattered throughout my defense. The most notable though would be my introductory slide (after the title slide) which played the following clip. I am attaching it here for those of my friends and colleagues who couldn't make it to my defense.



I hope you enjoy it.

A Question and Perhaps a Puzzle

I have a question for the geo- and paleo-minded folks out there:

How deep can a benthic diatom burrow?

Now the reason I ask this question is that the worm Paraonis makes spiral burrows (pictured above) that have been identified as "traps" for diatoms (Minter et al, 2006). This means that the diatoms must be able to burrow to at least the depth that the sprials are produced but I have read that diatoms have only been identified as burrowing up to 3 mm (which is a big deal for such a small creature) (Hay et al, 1993) but Paraonis burrows have been identified up to 10 cm down (Risk and Tunnicliffe, 1978). Quite a contrast.

This means that either they are wrong (this is not a diatom trap), they are eating other things (which they don't think so), or diatoms are burrowing deeper than I can find literature on.

So I was wondering if anyone has any knowledge of diatom burrowing depths. If you do please comment or send me an email.



Hay, S.I., Maitland, T.C., & Paterson, D.M., 1993, The speed of diatom migration through natural and artificial substrata: Diatom Research, v. 8, p. 371-384.

Minter, N.J., Buatois, L.A., Lucas, S.G., Braddy, S.J., & Smith, J.A., 2006, Spiral-shaped graphoglyptids from an Early Permian intertidal flat: Geology, v. 34, p. 1057-1060.

Risk, M.J., & Tunnicliffe, V.J., 1978, Intertidal spiral burrows; Paraonis fulgens and Spiophanes wigleyi in the Minas Basin, Bay of Fundy: JOURNAL OF SEDIMENTARY RESEARCH, v. 48, p. 1287-1292.