Wednesday, November 26, 2014

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.

Tuesday, November 25, 2014

Geology Through Literature - A Connecticut Yankee in King Arthur's Court

The next story up in the Geology Though Literature thread is A Connecticut Yankee in King Arthur's Court by Mark Twain.

This story is essentially a time travel story so there are several aspects of "historical geology" in play for the book. The first part involves the occurrence of a solar eclipse.
"I knew that the only total eclipse of the sun in the first half of the sixth century occurred on the 21st of June, A.D. 528, O.S., and began at 3 minutes after 12 noon. I also knew that no total eclipse of the sun was due in what me was the present year --i.e., 1879." Chapter 2
As the story progresses it turns out that the narrator had the incorrect day and actually the eclipse occurred on the 20th. However that small change of a day does not really effect our interpretation in a scientific aspect.

The benefit of determining when solar eclipses have happened in the past is that eclipses have a pattern to them. They occur in cycles due to the repetitive motions of the sun, moon, and Earth. And it is possible to calculate out when exactly eclipses have occurred or will likely to occur. Luckily NASA has already done this for us.  The link goes to a document which catalogs all of the eclipses that have occurred from 2000 BC estimated up through 3000 AD. Unfortunately, Twain did not have access to such a document, or even the knowledge of when eclipses occurred. Since there are no written records from the sixth century listing all of the solar eclipses we have to assume that what is in the list is mostly accurate. There is a possibility that the dates and the times may be off, but there is a strong certainty that they are not off by much. According to the list, there were 4 eclipses during the year 528 (Feb 6th, Mar 6th, Aug 1st, Aug 30th). And even then, only two of those were visible in the northern hemisphere (Feb 6th and Aug 30th). So even with problems linking up the calendars (prior to 1582 a different calendar was used, the Julian calendar), it is unlikely that there was any total eclipse during 528 AD and not even a partial one in May, June, or July (the months surrounding the incident in the book).

The narrator also mentions that there was a total eclipse in 1879. There were 2 eclipses in 1879 (Jan 22nd and Jul 19th). Both of these are listed as Annular Solar Eclipses, which means that the moon is too far from the Earth to completely cover the sun (as pictured above) and produces what is known as a "ring of fire". So, even though this is not a total solar eclipse, it is rather noticeable, and could be thought of in a similar sense since the moon is entirely in front of the sun. This essentially negates both of the assumptions in the book based on the eclipses. So based on this, I would not be using A Connecticut Yankee in King Arthur's Court for my eclipse estimations.

The second entry has to do with the formation of geology as a science in general.
 "He said the most of Sir Dinadan's jokes were rotten and the rest were petrified. I said "petrified" was good; as I believed, myself, that the only right way to classify the majestic ages of some of those jokes was by geologic periods. But that neat idea hit the boy in a blank place, for geology hadn't been invented yet. He failed to catch on. However, I made a note of the remark, and calculated to educate the commonwealth up to it if I pulled through. It is no use to throw a good thing away merely because the market isn't ripe yet." Chapter 4
Geology in and of itself is an ancient study. It is known from the period of Aristotle, where he made comments on the geological rates of features. One of his pupils, Theophrastus, who was born in 371 BC also wrote up a book called On Stones where:
"...he goes on to classify them based on their reaction to heat, on their hardnesses, and on their power of attraction. He describes a great variety of stones according to their use and origins. He writes on coal and it's use as a source of heat by metal-workers, he writes on the minerals used on the fabrication of glass, of different pigments, of plaster. He traces the origins of pumice-stones to volcanos, of pearls to shell-fish, and speaks about fossilized remains of organic life. Theophrastus was also the first known person to have made reference to pyroelectricity, the capacity, by certain materials, to produce voltage when heated or cooled. From his text as well as from a later text by Pliny the Elder (Naturalis Historia from 77AD) the science of mineralogy emerged, arguably the founding science for geology."
Theophrastus could be considered as one of the founders of geology. However, modern geology does have a significantly different approach to it. The introduction of modern geology took a long road from these origins though. There are a couple of people who are credited with having founded modern geology. One of them being Nicholas Steno (1638-1686), who is credited with the main laws of stratigraphy: The law of superposition (the stuff on the bottom is older than the stuff on top), the principle of original horizontality (rocks are laid down horizontally), and principle of lateral continuity (rock units stretch over large areas of land). Later works by James Hutton (1726-1797) , such as his published ideas on uniformitarianism (everything happening now has happened in the past) are also credited with ushering us into the modern age of geological thought. Hutton is often considered to be the Father of Modern Geology although Steno surely also has a significant place at the top.

The narrator's comment also plays into the concept of the age of the Earth. The boy in the quote was not used to thinking of the Earth as an old place. To people before 1600, the bible was seen as a literal truth where everyone thought that the Earth was 6,000 years old. In the narrator's own time (1879 as mentioned before), Lord Kelvin had just estimated the Earth to be about 98 millions years old. Even though this is far younger than we now understand the Earth to be (4.55 billion years old), the narrator still understood his Earth to be much older than that of the boy in his presence. This lends weight to his "majestic ages" comment, where millions of years denotes the ages quite a bit better than thousands of years.

This paragraph involves two aspects of Historical Geology. The first part is that even though geological concepts were thought of prior to the "inventing of geology" in the 16 to 17 hundreds, it is possible to say that geology had not been "invented" yet. And it is without modern geology that the true age of the Earth was unknown with the only source for that information having been the Bible, which would have placed that age approximately 6,000 years before. The Earth being a very old place was the basis of the joke which the narrator tells to the boy, and without that long age, the joke would likely have fell on deaf ears.

Wednesday, November 19, 2014

A Plate Tectonics Pioneer - Frank Bursley Taylor

To start off, I was going to say recently but it has apparently been almost a year now, but "recently" I came across this blog post by GSA entitled "On the Shoulders of Giants: A 125th Anniversary Retrospective" which talked about several of the older GSA members and geologists. There was one story which caught my attention:
 "In 1908, Taylor presented an oral paper at the GSA meeting wherein he proposed Continental Drift as a mechanism for the origin of mountain belts. His 1910 paper in the GSA Bulletin is spooky to read these days. He talked about the mid-Atlantic Ridge being a place where “plates” were moving apart. He talked about the Himalayas being the place where the Asian continent was being thrust out onto the Indian crust. He talked about the Aleutians being thrust out onto the Pacific Ocean floor. Taylor’s oral presentation was four years before Alfred Wegner’s oral presentation, and his publication was five years before Wegner’s. But, Taylor’s affliction was that he was publishing in an American scientific journal, and Wegner published in German.  Back then, if anything was important, it was published in German. So, most of the geological community is unaware of Taylor’s amazing analysis."
And it linked to a GSA Today article from July, 2005 which briefly mentioned the original Taylor paper. Well I wanted to go back and actually see what was stated in the paper 5 years before Wegner published his theories. Even though the paper is often painful to read, due to what we now know about plate tectonics, it is interesting in parts to see how much he got right. Here are some excerpts from the paper:

Taylor, F.B. 1910. Bearing of the Tertiary mountain belt on the origin of the Earth's plan. Bulletin of the Geological Society of America. v. 21. pp. 179-226

General crustal movement
"It is admitted by all that the mountains of the great Tertiary belt, like the older ranges of fold-mountains, were produced chiefly by compressive forces acting in a horizontal direction, and that the total amount of compression involved is equivalent to many miles of horizontal movement of the of the Earth's crust. What was the nature of those movements? In what direction did the crust move in producing the Tertiary mountains of Asia-from the ocean toward the land or from the land toward the ocean? This is a crucial point."
The Himalayas
" seems apparent that it was the obstructing action of the Indian peninsula which produced the great Himalaya re-entrant. It was the tremendous resistance offered by this fragment of the ancient Gondwana-land which held back the advancing folds to the line of the Himalaya. The effect seen in horizontal plan is as though India had held back an advancing curtain in a very pronounced way, as indeed it did, for the curtain was the crustal sheet of Asia."
He also refers to "moving crustal sheets" and "plates" are also brought up.
"It would be expected, for example, that the folds would be most closely pressed together at the most northerly point of the resisting obstacle, where the obstructing effect would be greatest, and that the folds would bend or lap around on either side of the obstructing mass so as to inclose it within a re-entrant angle of the general front. It would be expected also that the vertical component of movement expressed by positive elevation of mountain ranges and plateaus would be greatest against that same point."
Taylor seems to think that all movement was from the poles to the equator. This is what produced the bulging outward effect of the Earth at the equator.

Greenland Rift Zones
"Baffin Land, therefore, appears to have been pulled away from Greenland in the same direction as Grant Land, and, what is more significant, it appears to have moved the same distance."
"The relation of the coast of Labrador to the west coast of the south part of Greenland is truly remarkable"
"...although now 560 miles apart in the direction of the rift along the northwest side of Greenland, are almost exactly parallel and the geological age and structure of the rocks, so far as known, are the same."
"We seem to have here a great irregular rift line along which North America has been torn away from Greenland." 
Mid-Ocean Ridge
"It is apparently a sort of horst ridge-a residual ridge along a line of parting or rifting - the earth-crust having moved away from it on both sides."
 "The great westward bulge of Africa north of the equator appears to fit very closely into the westward bend of the mid-Atlantic ridge, suggesting that Africa has drifted eastward from that position."
"It is probably much nearer the truth to suppose that the mid-Atlantic ridge has remained unmoved, while the two continents on opposite sides of it have crept away in nearly parallel and opposite directions." 
African Weight Gain
"There appear to be conflicting evidences on this point, but the great rift valleys of the lake region in Africa suggest moderate uplift. These valleys are roughly meridional and suggest a slight girth-expansion of the Earth.

Not sure how the Earth gains girth... maybe too much Turkey. (ba dum dum :-D)

Wednesday, November 12, 2014

My Failures in Science - Measuring the Earth Part 2

In response to my failure to measure the Earth before (See post here for background and details) I again attempted to measure the Earth using the length of the shadows during the the days before and after the summer solstice. To recap here is the background:

~2200 years ago, a man named Eratosthenes made a pretty good estimation of the size of the Earth using the length of shadows during the summer solstice at two different locations.

To repeat this experiment there are some requirements:

1. I needed a measuring stick that was perpendicular to a board to measure the length of the shadow.

2. I needed two locations north and south of each other that fell along the same longitude, so that I could calculate a direct polar circumference.

3. I needed to find out when "noon" was, since daylight noon (the highest point of the sun) is not the same time as clock noon.


1. To fix some of the problems that stemmed from the last experiment I created a larger and better measuring stick.

Here is my handy assistant making calculations and measurements.

I used comments on my previous post to improve on this on. I increased the size of the vertical stick, chose a metal rod since it was not warped and not likely to become warped without noticing, and on the bottom I placed screw feet so I could adjust the levelness of the board. 

High Noon time was set for 1:29 pm on both the day before and after the summer solstice. 

From the previous post I am going to take 2 readings from two locations that are approximately along the same line of longitude. (C and B on the diagram below). From these I will calculate the difference in the angle and therefore can calculate the size of the Earth.

This time I went for a bit further and ended up at a distance of 66,758.87 m apart from each measurement. I had hoped this would help with the accuracy of the results. 

I had double checked and my math previously was correct, where:

Circumference = Arc Length * Difference in the angles/360

For this experiment:
Arc length = 66,758.87 m
Difference in the angles = 1.4149 degress

  C = 66,758.87 * 1.4149/ 360
  C = 16,985.79 km

Still I am majorly off. Only by 57% this time. A 3% improvement. Good?


Next year I will perform the experiment again. This time with a larger measuring device and more distant measuring localities.

Friday, November 07, 2014

Geology In Pop Culture - License Plate Geology #1

I have been on the look out for geological based license plates recently and I captured this one the other day. A but blurry (from the phone) but you can still see that it says "Karste" quite clearly.

I am not sure the rules of posting the images of license plate but I don't think there is really anything wrong with it, especially since we see them on the road everyday. And I figured that if I don't post any of the other information of the car owner, make, model, etc. along with the license plate I should be all set. Well I cropped out the the rest of the car just to be safe.

noun, Geology.
1. an area of limestone terrane characterized by sinks, ravines, and underground streams. (

Wednesday, November 05, 2014

Geological Pop-Cultural References

I came across this interesting article the other day: 

Pop Culture Mentions Of Global Warming Have Plummeted Since 2007

which leads people to a program where users are able to put in a set of words and see how many times they have been mentioned in movies (and in various other mediums) in the past 100 years (or so). This got me thinking about how references to geology and paleontology have varied through time. 

The following graphs are made with a 2 year rolling average of the points, that way the mentions didn't show up as individual points, and general trends could be easier to discern. They also show the percent of the words for each particular year since just producing straight number of words would show an increase just because more TV and movies are produced now than they used to be.

Here is a link to the Movies version: There are other links accessible from the website which can give you scientific article searches and the such. A future post will do these same searches in different mediums to compare the results. Unfortunately I can't seem to save the images any larger. If you do the search you are able to see the specific references in each year. Very fun game.

Dinosaurs and Fossils
 *date to be aware of: Jurassic Park came out in 1993.

Evolution and Creation
  *date to be aware of: Cosmos came out in 1980.

Paleontology and Paleontologist

Geology and Geologist

Plate Tectonics

Rock and Stone
 *Pretty sure this mostly refers to the "rock" in rock and roll and drug use under "stone", but interesting none the less. 

Volcano and Earthquake