Wednesday, May 13, 2015

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.


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.

Tuesday, May 12, 2015

Geology in Pop Culture - Disney's California Adventure

Not much in the way of "Geological wonders" in California Adventure in Disneyland, however there is one cool spot in Cars Land. The backdrop of the Radiator Springs Racers ride is the awesome looking panorama, evoking a southern Utah feel to it. They even provide a National Park Service type brochure explaining all of the features.

The Ornament Valley Brochure is below. I tried to do a panorama shot on it but it is really hard to do that on an iPhone for a static picture so I also took an overall picture. They have fantastic references to actual geologic features like "Pipe's Peak", "Mount Ever Rust", "Lincoln Continental Divide", and "Mount Hood".

I also had to take a picture of this sign that I ran by during my Half Marathon that went through part of the park.

Monday, May 04, 2015

Dinos in Pop Culture - Jurassic World Dino Gummies

Would you like a prehistoric snack? 
Well now you can munch on some dinosaurs with Jurassic World fruit flavored snacks.

Truth be told, I am actually quite fond of fruit snacks and these taste like any others that you are going to find in the grocery aisle.

You can match the shapes up with what they had and the shapes were pretty cool. It was hard to get a picture showing the detail of the fruit snacks, but it's there if you look. The yellow one was the hardest to notice any detail on, even in person. 

Wednesday, April 08, 2015

Dinos/Geology in Pop Culture - SLC FanX 2015

Continuing on of my coverage of the Dinosaurs and Geology in Pop Culture of the Salt Lake City comic conventions (Comic Con and FanX), we have the 2015 entry of FanX, which was held January 29th-31st, 2015. A bit of dinosaurs this time around.

As with Salt Lake Comic Con a few years ago we have a company with the animatronic dinosaur suit walking around, however it appears to be a different company and a different type of suit this year around. This year it is from I felt the previous suit was a bit more realistic, however this one is not bad.

A picture of the dinosaur suit.

View from above, later while he was walking around. The person in the suit could have tried to match the coloring with his clothes a bit better though. The previous dinosaur suit the person was wear spandex the same color and pattern as the suit.

There was also a Jurassic Park panel, where some filmmakers discussed the world of Jurassic Park and the upcoming Lost World. During the panel, they had a clever bit where the dinosaur invaded and interacted with the panel.


Also new to the Salt Lake Comic scene is this nice Jurassic Park replica jeep. This couple from near my house in Utah runs a Facebook page called Jurassic Jeep 01

 They came with a nice Alan Grant costume and pet Velociraptor.

 Some fossil replicas including a real fossil of an Apatosaurus vertebrae.

And of course, what Jurassic Park crew isn't complete without Ellie Sattler.


And last, but not least. The Lego Club builders of Utah presented a nice little Lego model of our famous rock arch from Arches National Park.

Saturday, March 28, 2015

Drunk on Geology - Lithology Beer (Kickstarter Campaign)

The next up on the Drunk on Geology series is the Lithology Beer by the Lithology Brewing Company from Long Island, New York. 

This beer is unique in my Drunk on Geology series because it is not an established brewery. Yet. This is from an old friend of mine who is currently searching for the funds through a Kickstarter Campaign to help establish their award winning brew into an official brewing company.
How often do you say to yourself, "I just wish there were more geological beers available"?

Well now you can help an up and coming, award winning, brew become a geological beer that you, yourself can take home and enjoy surrounded by your rocks and minerals. All you need to do is click on the Kickstarter link below to help support a geologically based brew.

Here is why they went with Lithology from their website.
​​Lithology, a geological term, is the study of the physical characteristics of rock and sediment. Besides forming the land we walk on, rock and sediment are earth’s natural water filters, and since water is the basis of life (as well as beer) the connection seemed a perfect fit. The Lithology Brewing name pays homage to the sediments and rocks that filter our unique and delicious New York water. Think about it: What’s the key ingredient to making a true New York pizza? A genuine New York bagel? It’s the water! You can’t get exceptional New York food and beverages if you don’t recognize the water. And if all of that is too much to remember, you can always just say that Lithology Brewing rocks!
Logo for the brewery.
Calling the bear "Lithology" on Long Island is an apt name, with it's wide variety of rock types and soils that are able to be found on the island. The geological formation of Long Island was the result of the end limit of a glacier pausing for a long period of time in that area twice. These glacial pauses formed two parallel features called moraines, otherwise known as piles of unsorted debris that the glacier dumps at it's end, sort of like a giant bulldozer. The southern terminal moraine is the Ronkonkoma Moraine, formed about 55,000 years ago. The northern terminal moraine is the Harbor Hill Moraine, formed about 18,000 years ago. The presence of these moraines, which are composed of till (otherwise known as unsorted glacial debris), resulted in a wide variety of geologically diverse soils and beaches across long island from very rocky shores on the northern shore, to nice sandy beaches on the southern shore and a wide variety of soil types from almost 100% clay to 100% sand. The till is also composed of all of the rocks found towards the north of Long Island into Canada, making these moraines a treasure trove of rocks and minerals not often found condensed in one locality.
Long Island Moraines
And you know what else is a key ingredient in Geology, Beer.

A variety of beer that they offer of course is the Rock Hammer!

The proposed Keg Collar for their beer. 

So, what are you waiting for? Go click on the Kickstarter link above and support some Geology Brew.

Thursday, March 05, 2015

Drunk on Geology - Mönchhop Mosel Slate Riesling

The next up on the Drunk on Geology series is the Mosel Slat Riesling wine from the nchhof winery from the Mosel region of Germany.

The Mosel Slates are comprised of two main slate deposits, Ürziger Würzgarten and Erdener Treppchen

The Ürziger Würzgarten (pictured below) means "The Spice Gardens of Ürzig". These rocks are a very iron-rich Devonian slate mixed with volcanic rocks in the soil. Oxidation of the iron gives the rocks their characteristic red color. 

The Erdener Treppchen means "The Little Staircase of Erden" and consists of a red iron-rich slate as well. The little staircase is because of the steep nature of the valley, stairs needed to be cut into the hillside in order for it to be cultivated.

These slates are part of the Rhenohercynian within the Rhine Mountains of western Germany. The slates formed from a shallow marine shelf environment. These are low grade slates with many of them still containing fossils. Although the principle slates of the region have the distinctive red hue, there are the well known blue slates of the region from which the picture on the bottle was obtained.  

The back of the bottle states:

"The Mönchhof estate was founded in 1177, and today is managed by Robert Eymael. This Mosel Slate Spätlese was selected from the famous Erden Treppchen vineyard. The vineyard consists primarily of grey-blue slate which produces elegant wines with a crisp and refreshing acid structure."

Thursday, February 26, 2015

Dinos in Pop Culture - Camp Makela T-Shirt

So I recently permanently retired one of my favorite t-shirts. It was from the Museum of the Rockies Paleontology Field Camp program to Camp Makela. My favorite thing about the t-shirt was the "I dig dinosaurs" on the back, which I never noticed for the longest time. I just assumed it was the same as the front.

I met quite a few good friends through the program when I did it in 96' and 97', many of whom I am still friends with today, and I am sad to see the shirt finally die. The program seems to now be defunct, but there is more paleontology field programs than ever for those amateurs (like myself at the time) to go out and learn the tools of the trade.

Tuesday, February 17, 2015

Random Geology Picture - Temperature-Elevation Correlation

Here are some older pictures I had taken. They are panoramas of the Oquirrh Mountains (pronounced Oaker) looking east. I had taken the pictures to illustrate changes in the temperature gradient as you moved up in the atmosphere. While it was raining down in the valley, you can pick out the freezing point in the atmosphere by just looking at where the snow started. Also you can see by this snow line, that the mountains are sloped to the left (the north). 

Thursday, February 05, 2015

Random Geology Picture - Partial Lunar Eclipse

Going through some of my old photos, here are some shots of the partial lunar eclipse that occurred last year on April 15th (Thanks Katie for the date verification). 

Thursday, January 29, 2015

Drunk on Geology - Inversion IPA

The next up in the Drunk on Geology series is Inversion IPA  produced by Deschutes Brewery from Bend, Oregon.

An inversion is a naturally occurring phenomena when the temperature goes from normal (warmer near the Earth's surface and cooling upwards) to inverted (colder near the Earth's surface and warming upwards). This frequently happens in areas where a warm front is able to ride on top of a cold front. When the colder air is trapped in place for some reason, this condition can persist for a lengthy amount of time. In Salt Lake City, where I live, this condition occurs because Salt Lake is in a "bowl" surrounded by mountains. The cold air if frequently trapped in the valley when there are no storms to move it out. This causes the inversion, which wouldn't be a problem, except all of the pollution from cars and factories are contained in the valley as well, making the air often very unhealthy to breathe. The picture below is a view of today's inversion. There are mountains and a city usually in that shot.

Salt Lake City on a nice day of inversion.

A nice beer to calm all paranoia about what the inversion is doing to my lungs.

 A nice picture showing what an inversion looks like from above is pictured on the box.

I have been waiting for a "nice" inversion day to post this Drunk on Geology post. The worst days often occur during December and January, however this winter had been a rather mild inversion year.

I just wish they had included some words on what the meaning of an inversion was on the box or the bottles.  

Friday, January 16, 2015

Random Picture - Natural History Museum of Utah at night

Going through my old photos and here is one I wanted to post.

The museum was lit up for a special event, so when I left I was able to see the mammoth from outside the main entrance. I had been wanting to capture this shot for a while (I have a horrible time trying to not move while taking pictures on my iPhone) so I brought my camera specifically for this shot.

Thursday, January 15, 2015

Geology of the National Parks in Pictures - The Pony Express Trail

The next up on my tour of the National Parks in pictures:

Last year my family and I headed out to find some geodes in the Utah desert. Along the way we traveled along the Pony Express Trail. Although this trail spreads on through many states, here is a small portion of it, near Dugway, UT. 

 View looking east, as we passed through Dugway Pass.

This post marked the location of the Pony Express, which ran from 1860-1861.

Recreation of the Simpsons Springs site. It is clear when you enter the building though that many animals now use this as a shelter from the heat of the day.

Panorama of Simpsons Springs.

Tuesday, January 13, 2015

Dinos in Pop Culture - A "Real" Dinosaur Train

Last year my wife had purchased me tickets to the "Dinosaur Train" put on by the Heber Valley Railroad, here in Utah. It was a cute event where they had a variety of dinosaur related activities, and where you could talk to volunteers from the nearby museums. 

 One of the activities was digging in the sand for dinosaurs.

 It is hard to see but here is my daughter pulling out a Pachycephalosaurus.

 The train that was not in use with a giant inflatable dinosaur on the front. I want one.

 The actual train. It had a variety of dinosaur related decor inside.

 One of the main dinosaurs. Unfortunately he never actually went on the train with us, where there were other dinosaurs with us for the trip.

Pulling away as the sad dino wanders off by himself.

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.