#and missing my vertebrate evolution class

[sarcopterygiian]

i think we need a series of documentaries for people who ALREADY know a bunch about the topic. like i 100% love the ones like “our planet” that make science accessible and interesting, but they have to take 30 minutes to explain what evolution is. i want some that ARENT afraid to be jargony, that get into the real specifics. scientific papers are great but i think we deserve some fun cinematic netflix-david-attenborough-morgan-freeman documentaries please and thank you

[dinosaurnostalgia]

Random thoughts about dinosaurs being classified as birds and about the evolution of animals in general

When I was a kid dinosaurs being classified as birds was a theory, nowdays it seems like this is widely accepted in paleontology and zoology. Or at least, the most vocal dinosaur nerds make it seem like it is so. I'm not a scientist, so I know that my thoughts on the subject are of little value, but there are few questions that "dinosaurs are birds" raises in my mind.

If dinosaurs are birds, why are they not talked of as prehistoric birds then? Why do books and studies still refer to them as "dinosaurs" or "animals" rather than "prehistoric birds?" If they truly belong in the class Aves, why are they missing many of the characteristic traits of this class, such as lack of teeth? What classifies an animal belonging in a specific class even if it doesn't have all of its traits? What, specificly, makes an animal a bird?

To me it would make more sense to think of dinosaurs as a class of their own, not birds, not reptiles but a third secret thing; dinosaurs. It's very clear that birds evolved from dinosaurs but were they really birds themselves or a link in evolution toward the birth of the class of animals known as birds.

This made me think about the evolution of animal classes. With individual animals you can sometimes see a clear path of evolution, such as the evolution of horses with slight increase in size and lessening of toes in every step and in the end you have what we consider by modern standards a horse. But how does that work when we are talking about entire classes of animals? There has to have been some intermediary stages between fishes, amphibians, birds, reptiles, mammals and all the extinct vertebrate classes but where does one draw the line of one class having turned into a completely new one? When is a type of animal so distinct from its ancestors that it's consider not just a different species but a different class entirely?

If dinosaurs are birds, then what was the first bird (I know it's not Archaeopteryx, even though my childhood books talked about this animal as a missing link between dinosaurs and modern birds) and how did it differ from the animals it descended from? Why was it considered changed enough to be not just a different species but also a different class?

[encyclopika]

Animal Crossing Fish - Explained #7.5

Brought to you by a marine biologist who just has so much to say...

Fish I’ve Covered: Click Here So far, if you’ve missed some, I’ve covered the Barreleye, Sea Bass/Black Bass, Sturgeon, Football Fish, Goldfish, Sea Butterfly, and Coelacanth!

I say “7.5″ because I’m continuing coverage of the coelacanth, this time from the fossil section of the museum. It appears here as well because the “lobe-finned fish” are REALLY important to the evolution of tetrapoda, the group we as humans belong to, with 4 limbs (’tetra’ meaning ‘4′ and ‘poda’ meaning foot). Here’s what the fish section in AC:NH looks like (again, please ignore the Bunny Day get-up haha):

When we first visited the museum and went down to look at the fossils, I nerded SO HARD about the floor pattern. It’s a big phylogenetic tree! Yes, I’m a marine biologist BUT I also REALLY enjoyed my classes on Zoology and Evolution. Learning about how all animals are connected is fascinating to me, and of course, the fish are most interesting to me! 

Today we will cover the coelacanth’s placement here as sort of a starting point for a longer conversation about how fish evolved to live on land. There is a model of the coelacanth right by the exit up there.

Think of a fish randomly, and you’ll probably think of a ray-finned fish. These are fish that utilize fin rays to support and move their fins. There are no bones in their fins and all muscles controlling the fin are on the inside of the body. All the fish we have covered in this series until the Sea Butterfly were all “ray-finned fish”. Most fish in AC:NH are ray-finned fish, and that’s just how it is. Ray-finned fish are the most numerous of the vertebrates in terms of number of species at 33,000 species and counting. 

The coelacanth is different, though! Its fins are not only muscular, but they have bones! And not just any bones - these are analogous to the bones in our hands! They are part of a tiny group of fish called the “lobe-finned fish”. Take a look at the this nifty chart I found (I don’t take credit for it):

Other animals you may be familiar within the lobe-finned fish group are lungfish. These animals are considered the beginning of the transition from water to land for vertebrates, or animals with backbones (or bones at all...no other group of animal has bones). This transition is so important that AC:NH has included 2 fossils of lobe-finned fish for you to find: Eusthenopteron and Acanthostega. 

Lobe fins are thought to have arisen in freshwater fish; the sturdy fins aiding the fish through mud, reeds, and other shallow habitat close to land. As the fins became sturdier, the fish could venture further and further from deep water until they could support themselves on dry land. There were more adaptations that needed to happen for the transition to be permanent, but I’ll leave it there!  

And there you have it. Fascinating stuff, no?

[a-travels]

taken: 4 jun, 2017 Shree Chamundeshwari Temple, Mysore, India

three lefts make a right

Just to get it out of the way, no I don’t think the monkey is sucking his thumb. I’d like to think it held it there specifically to pose and look all pensive for the shot. I’m definitely good enough to get a wild monkey to pose for me. Finally, a purpose for my monkey-like sensibilities.

I’d like to think of myself as a perfectionist. I don’t think that’s necessarily a bad thing, and it’s certainly not my response to the classic, “Tell me a weakness about yourself” interview question, though I do think sometimes it actually is. But I’ve found it is often a great strength of mine, and I think is a strength when harnessed in the right way. I mean not even just for myself, but I think there is incredible value in catching small details, seeing things that someone else might miss. Sure, sometimes it can be irritating to others, seeming like you’re nitpicking, pointing out the smaller details that an ordinary person may not notice. I’ve always been taught to go the extra mile in whatever I do and I think that eye for detail really has helped in that pursuit in many regards, though to my mother’s chagrin, I may sometimes go “too far”. 

Whether it’s extra time or extra effort or a little less sleep, to me I can’t rest till I know I’ve done everything to my level of standards and quality. If it’s a powerpoint, I will sometimes belabor for hours making sure the fonts, spacing, colors, formatting, animations, figures, everything is right. Even if I may hate the assignment, even if I hate myself for spotting every small detail that needs to be made just right. Hell, I had a 2-minute presentation to make for my CT Scans of vertebrates class in senior year of undergrad and I spent 2 hours on a figure that was perhaps useful for 20 seconds of dialogue? Credit where it’s due, I was still very proud of it, comparing the different sizes of saber-tooth lions, cross-referencing the sizes of the animals, making my own scale, being able to relatively scale them by holding a ruler up to the computer screen. I made it minimalist and chose the colors, I added shadows because I’m insane, and for what? It’s not like that figure alone was the determinant between an A- and an A. The rest of my presentation was solid and I probably would have done well anyway. But yet I did it anyway. I can’t probably explain to you why, but at the time, I knew I wanted a graphic showing the sizes of the different saber-tooth lions (since my project was a CT scan of a saber-tooth lion skull) and that there were no good ones available, and the one that was available was small, low quality and grainy. In terms of thinking it through, I probably didn’t. I thought my presentation’s quality would be worse and I spent the time to fix it and make it better. (Also I think I’ve beaten this image to death so you might as well see it if you're curious, just click here)

I think it speaks to my larger desire/need to do things “right” and do them “right” the first time especially. Honestly, at this point, I’m sure you see all my posts and think I’m a psychopath worrying about bothering others, being right, being genuine enough (tbh I’m probably a bit insane). Point being, my detail-oriented mindset speaks to the larger need to want to do something “right” or be “right”. In my head, I know that pursuit of perfection and “rightness” is just a fool’s errand⸺no one can be right all the time. Ha, well you better believe I know I’m not right. I know this in my head, I know I can’t be “right”, I know I’m often not, and yet I still feel this nagging compulsion to try for it anyway. Mind you this doesn’t extend to everything; I don’t think this ever extended to my grades, I never shot for or wanted to be a valedictorian or something, or wanted to be the best martial artist or swimmer. It was specific things, here and there, and I can’t really describe what made something different or want me to be “right”. It probably is one reason why I keep thinking about self-correcting messages, if I said the “right” thing or not, from two posts back.

You see the quotes around every “right” I write? That’s because “right”, as you know is often subjective. It means different things for different people. The “right” flavor for someone in a dish may be for less spice than in mine, or more spice, or more salt. I think that makes things all the more challenging because navigating the realm of options and finding my “right” is half of my battle. It’s almost definitely why I think I’m so indecisive. I was literally deciding where to go to college until 10 minutes before the deadline. And that’s the heart of the problem: in my pursuit for being “right”, I tend to delay.

That combination of a detail-mindset with constant drive to work hard is a potent combo, one because always working and fixing details is probably exhausting (I get exhausted from my own way of being), but also because I think that mix can result in the drive to work but to the level of quality and detail that I like to work towards. And then there’s me, the detail-mind but perhaps less driven. I don’t know if it’s a lack of drive, but the best way I can describe it is a kind of lethargy. “Wait.” “It’s not right yet.” “I can’t do it now, it won’t be right.” I often find myself pushing things off and waiting to do something. Like just yesterday, I put off writing a paper all Thanksgiving break thinking of all the details I needed, comparing it to the details other sample papers had and would end up going down rabbit holes, till I realized last night I never actually started writing the damn paper. Maybe not a decision per se, but the same holds true with decisions. Though, when I do make a decision, I own it, I stick with it, and I do not tend to regret it. And I think that’s the upside to working towards a “right” choice, that if the due diligence is there, then you can rest easy with the choices you make. Where it goes astray is when you don’t have the luxury of time with an action or a choice, which is almost in every scenario.

For some time recently and even now, I’ve been wracking my brain over doing something. And I apologize if I sound cryptic, but I told myself to wait till the moment was “right” to do this “thing”. My own doubt around doing this continues to bounce around my head and I don’t know if I’ll ever know if there’s the moment to go for it and do what I want to. But for now, I just sit like this monkey, waiting, for the moment when I think it is “right”, or for that time when I wisen up and realize that there never will be such a perfect, “right” moment like I seek.

Life doesn’t work in such an idealistic way where you get to be “right” or do “right” all the time. Life is not always “right”, and yet I strive for it, as I know others do (I think. I hope?). Life gets its color from being a bit messy and wrong. If everything was “right”, there wouldn’t be evolution, there would be spontaneous creation (which I guess is the basis of creationism⸺the idea that we are “perfect” and were made that way and not actually a series of millions of years of failed random chemical and biological experiments). I know it’s ok to be wrong, not perfect. I know I’m far, far, far from a perfect human being (I can’t say definitively if I’d make it to The Good Place), but that doesn’t mean I don’t want to work towards being one. Just because you can’t be “right” doesn’t mean you shouldn’t try, right? I don’t want to necessarily stop being detail-oriented, but I think I need to be able to discern when I need it and when I don’t.

tl;dr - wait, am I right?

[enddaysengine]

Non-Fiction Resources for Chronicles of Darkness by Gameline

June 6th Update: It seems that Tumblr has a limit to how many links you can put in one post. As a result, I’ve moved the resources for Dark Eras, as well as the links organized by topic, to a separate post that you can find at this link. 

*************

Much like I did for Eberron, I’m putting together some links to non-fiction materials you could use for Chronicles of Darkness. Since CofD is set in a dark mirror of our world, there are a lot of materials that could go in this post, but I will try to be selective. While I am keeping Chronicles in mind while I do this, you could use these links for any other RPG that is set on historical Earth (I’m looking at you, Call of Cthulhu!) Some links may show up more than once if they fit in multiple categories.

This post is very much a work in progress and probably will never be complete because of the broad availability of applicable materials. If you know of a resource that you don’t see on my list, please feel free to reblog/reply/DM me to say what the resource is and why it should be included on the list. I’ll do my best to add it in.

General Websites

Crash Course: It’s free, it’s on Youtube, and it’s in a ten-minute episodic format. 

Coursera: Coursera is a website where university level classes are available for free. You can also get certifications from Coursera for a fee so you can build your resume while planning your next chronicle. 

Dan Carlin’s Hardcore History: Dan loves historical “What if?” moments, and with good reason. If you want to hear the most badass historical stories, examine how drugs, alcohol, and human stupidity impacted history, or get a sense of what it was like to live through the most brutal historical eras, this is the place for you.

edX: Another excellent site with free courses that you can upgrade for a certificate. A good place to look for courses in the humanities and religion. 

Great Course/Great Courses Plus: GC and GC+ are not free services, but they have such an extraordinarily high production value that you can understand why. History, science, culinary theory, economics, anything you can think of is covered in the Great Courses catalogue. Great Courses Plus is their streaming service, which at $15/month for an annual subscription is a killer deal.

Google Books/Google Scholar: My first goto for research of any kind, and the first place I advise my students to begin their research. Seriously, I’ve written papers, then had them published just using these two. Use them. 

JSTOR: If you have operated in any kind of academic circle for the last two and a half decades, you know JSTOR. Full access is tough to come by unless you are currently enrolled in a university, but you can still sign up for free to get access to journals on topics you just can’t find anywhere else (like the Mutapa Empire). Sign up with multiple users if you have to. It works. Trust me. 

Open Yale Courses: University classes, taped lectures, and course materials, all from one of the best educational institution in the world. Take advantage of them. 

The Vault: Declassified FBI documents. A lot more of them involve the paranormal than you may expect. An excellent source of inspiration both for things that actually happened or that people think happened. 

Writing with Colour: The best place to go to check yourself for unintentionally problematic depictions of POC in your games. Also a great read if you are looking for details and cultural beats for NPCs you don’t share a background with. They are awesome and you’d be surprised how many chronicle ideas you can get just by binging their archive. 

******************

Mortal Chronicles

Foundations of Eastern Civilization

Maya to Aztec - Ancient Mesoamerica Revealed: Awesome resource if you are planning to run a Skinchangers game using the Aztec Dark Era. 

Medical School for Everyone - Pediatric Grand Rounds: A good place to look for ideas for Innocents 

Understanding Japan - A Cultural History

Beast the Primordial

General

Ancient Marine Reptiles: Yeah, I know, Beast is supposed to be about dragons and monsters, but I guarantee you that plenty of ancient reptiles are also stalking the Primordial Dream. Plus, aquatic reptiles are awesome and don’t get enough face time with the public, so you might want to think about your next Beast being one. 

Dino 101: The ultimate course about Dinosaurs. Very beastly. 

Early Vertebrate Evolution: What’s so scary about ancient fish, you ask? Only razor jaws and bone for skin. 

Secrets to Sleep Science

Theropod Dinosaurs and the Origins of Birds: At five lessons long, this course is pretty short, and the content matter is fascinating (says the biology teacher).

Dark Eras

African-American History: From Emancipation to the Present

The Civil War and Reconstruction Eras

History of the United States 2nd Edition

Signature Settings

Foundations of Eastern Civilization

History of the United States 2nd Edition

Mountains 101: If you are going to visit Kathmandu, you better be thinking about how mountains will impact your Chronicle!

Understanding Japan - A Cultural History

Changeling the Lost

General

Secrets to Sleep Science

Successful Negotiation - Essential Strategies and Skills: A very, very Changeling course. 

Dark Eras

Atlas Historique de Paris: I can’t read French, but I am assured by people who do that this is an excellent resource. 

Foundations of Eastern Civilization

Underground Atlas of Paris

Signature Settings

Foundations of Eastern Civilization

History of the United States 2nd Edition

Understanding Japan - A Cultural History

Demon the Descent 

General

Bitcoin and Cryptocurrency Technologies

Crash Course Computer Science 

Crash Course Games

Digital Signal Processing

Internet History, Technology, and Security

Inventions That Changed the World

Robotics - Ariel Robotics

Successful Negotiation - Essential Strategies and Skills: Also a very, very Demon course. 

Dark Eras

Living in the French Revolution and the Age of Napoleon

Maya to Aztec - Ancient Mesoamerica Revealed

Ottoman Empire

Signature Settings

Cultural Competence - Aboriginal Sydney

A History of Hitler’s Empire

History of the United States 2nd Edition

Hollywood: History, Industry, Art

Ottoman Empire

World War II - A Military and Social History

Geist the Sin-Eater

General

Death: Seriously, that’s all the course is called. It’s Yale, its good, the name is just to the point. 

Soul Beliefs 1 - Historical Foundations

Soul Beliefs 2 - Belief Systems

Soul Beliefs 3 - How Does It All End?

Dark Eras

Foundations of Eastern Civilization

The Great War

History of the United States 2nd Edition

Indigenous Canada

Signature Settings

The Early Middle Ages (284-1000)

History of the United States 2nd Edition

World War II - A Military and Social History

Hunter the Vigil

General

Introduction to Forensics

Aegis Kai Doru

Archaeology - An Introduction to the World’s Greatest Sites

Introduction to Ancient Greek History

Ahl al-Jabal (Source)

Ismaili Gnosis: Okay, breaking alphabetical order here, but this one is special. If you have a passing familiarity with Islam, you may have had the initial thought that the write-up of Ahl al-Jabal doesn’t look like anything you’ve seen before. That’s because Ahl al-Jabal are Nizari Ismaili Shiites and trust me when I say it is extremely accurate (minus the vampire hunting). Ismaili Gnosis is an excellent source for current events, history, and particularly metaphysics as it applies to Ismailis. 

Assassin Legends: The Assassin State of the Crusades is legendary, but what most people know about them is just that: legend. If you are using the Ahl al-Jabal, either in historical or modern chronicles, let Farhad Daftary bust the myths about the Nizari State for you. This link only gives you a preview on Google Books, so some pages will be missing, but it is still worth a read. 

Ama-San (Source) 

Oceanography- Exploring Earth’s Final Wilderness

Understanding Japan - A Cultural History 

Ascending Ones

History of Ancient Egypt

Ashwood Abbey

Wine Tasting - Sensory Techniques for Wine Analysis: Are you really part of the Abbey if you aren’t a wine connoisseur? 

Ave Minerva (Source)

The History of Rome Podcast 

Azusa Miko (Source)

Understanding Japan - A Cultural History 

Barrett Commission (Source)

Crash Course US Government & Politics 

The Bear Lodge (Source) 

Mountains 101

Bijin (Source)

Understanding Japan - A Cultural History 

The Cainite Heresy (Source)

Gnosticism - From Nag Hammadi to the Gospel of Judas

Lost Christianities 

Cheiron Group

Critical Business Skills for Success

Economic History of the World Since 1400

Division Six (Source)

Crash Course US Government & Politics: Division Six may not actually be a part of the US Government, but they sure think they are, so understanding how they think they fit in isn’t a bad idea. 

The Faithful of Shulpae (Source)

The Ancient Near East - History, Society, and Economy

Habibti Ma  (Source)

The United States and the Middle East - 1914 to 9/11

Hototogisu (Source)

Understanding Japan - A Cultural History 

The Hunt Club (Source)

Forensic History

Illuminated Brotherhood (Source)

Addiction and the Brain

The Addictive Brain

Drugs and the Brain

Keepers of the Source (Source)

Understanding the Mysteries of Human Behaviour

Keepers of the Weave (Source)

Indigenous Canada 

Knights of Saint Adrian (Source)

Why Evil Exists

Knights of Saint George (Source)

The History of Christianity

Les Mysteres (Source)

Crash Course Mythology 

Cultural Literacy for Religion

Great Mythologies of the World

Les Voyageurs (Source)

Indigenous Canada 

The Long Night

The Apocolypse - Controversies and Meanings in Western History

The History of Christianity

Lost Christianities 

The Loyalists of Thule

A History of Hitler’s Empire

World War II - A Military and Social History

The Lucifuge

Why Evil Exists

Maiden’s Blood Sisterhood (Source)

How to Become a Superstar Student

The Modern Political Tradition

Malleus Maleficarum

The History of Christianity

Lost Christianities 

Why Evil Exists

The Merrick Institute (Source)

Medical School for Everyone - Pediatric Grand Rounds 

Secrets to Sleep Science

Network Zero

Internet History, Technology, and Security

Night Watch (Source)

Why Evil Exists

Null Mysteriis

Animal Behaviour

Introduction to Forensics

Mountains 101 

Otodo (Source)

Understanding Japan - A Cultural History 

Why Evil Exists

The Promethean Brotherhood  (Source)

Decoding the Secrets of Egyptian Hieroglyphs

Greek 101

Latin 101

Miracles of Human Language - An Introduction to Linguistics 

The Story of Human Language

Protectors of the Light (Source)

Indigenous Canada 

The Reckoning (Source)

Heroes and Legends - The Most Influential Characters in Literature

The Scarlet Watch (Source)

History of the United States 2nd Edition

Task Force VALKYRIE

Crash Course US Government & Politics 

History of the United States 2nd Edition

World War II - A Military and Social History

Talbot Group (Source)

Psychological First Aid

The Union

Cities Are Back in Town - Urban Sociology

Utopia Now (Source)

Great Works of Utopian and Dystopian Literature

Vanguard Serial Crimes Unit (Source) 

Introduction to Forensics

The Vault: The FBI’s online archive of popular declassified documents. Lots of weird stuff, and the perfect source of inspiration for VSCU.

Yuri’s Group (Source)

De-Mystifying Mindfullness

Healing with the Arts

How Music Can Change Your Life

Dark Eras

Foundations of Eastern Civilization

History of Ancient Egypt

History of the United States 2nd Edition

Indigenous Canada

Understanding Japan - A Cultural History

Signature Settings

History of the United States 2nd Edition

Mage the Awakening

General

Addiction and the Brain: Mage 2e’s theme is “Addicted to Mysteries.” Understanding that addiction is a good place to start. 

The Addictive Brain

Ancient Philosophy - Aristotle & His Successors

Ancient Philosophy - Plato & His Predecessors: If there is one course on philosophy you take for Mage, it should probably be this one. At four lessons, this is a pretty quick one to complete. 

Gnosticism - From Nag Hammadi to the Gospel of Judas

Magic in the Middle Ages

Dark Eras

Great Zimbabwe in Historical Archaeology

History of Ancient Egypt

Introduction to Ancient Greek History

Politics and Long-Distance Trade in the Mwene Mutapa Empire

World War II - A Military and Social History

Signature Settings

Foundations of Eastern Civilization

History of the United States 2nd Edition

Hollywood: History, Industry, Art

Understanding Japan - A Cultural History

Mummy the Curse

General

Archaeology - An Introduction to the World’s Greatest Sites: Let’s go find some Relics!

History of Ancient Egypt

Introduction Ancient Egypt and Its Civilisation

Soul Beliefs 1 - Historical Foundations

Soul Beliefs 2 - Belief Systems

Soul Beliefs 3 - How Does It All End?

Dark Eras

The Early Middle Ages (284-1000)

Foundations of Eastern Civilization

The Great War

Great Zimbabwe in Historical Archaeology

Ottoman Empire

Politics and Long-Distance Trade in the Mwene Mutapa Empire

Signature Settings

The American Revolution

History of the United States 2nd Edition

Promethean the Created

General

Introduction to the Biology of Cancer

Understanding Cancer Metastasis

Dark Eras

African-American History: From Emancipation to the Present

Epidemics in Western Society since 1600

Signature Settings

Antarctica: From Geology to Human History

Foundations of Eastern Civilization

History of the United States 2nd Edition

National Geographic Polar Explorations: Follow the steps of Doctor Frankenstein. 

World War II - A Military and Social History

Understanding Japan - A Cultural History

Werewolf the Forsaken

General

Animal Behaviour

Dark Eras

African-American History: From Emancipation to the Present

The Ancient Near East - History, Society, and Economy

Cybele: The Great Mother of the Augustan Order

The Great War

Hardcore History - Punic Nightmares

The Early Middle Ages (284-1000)

History of the United States 2nd Edition

Signature Settings

The Civil War and Reconstruction Eras

Foundations of Eastern Civilization

History of the United States 2nd Edition

Mountains 101: An awesome course in general, but especially useful for Werewolf’s signature setting, the Colorado Rockies. 

Understanding Japan - A Cultural History

War for the Greater Middle East

Vampire the Requiem

General

Clans

Animal Behaviour

History of Ancient Egypt

Introduction Ancient Egypt and Its Civilisation

Carthian Movement

Circle of the Crone

Magic in the Middle Ages

Invictus

Lancea et Sanctum

Magic in the Middle Ages

Ordo Dracul

Ottoman Empire

Dark Eras

African-American History: From Emancipation to the Present

The Civil War and Reconstruction Eras

The Early Middle Ages (284-1000)

Epidemics in Western Society since 1600

The Great War

Living in the French Revolution and the Age of Napoleon

Ottoman Empire

Digital Tour of Tutor London

Signature Settings

Foundations of Eastern Civilization

History of the United States 2nd Edition

Introduction to Ancient Greek History

Understanding Japan - A Cultural History

[blastdnasquencing-blog]

DNA Sequencing is a BLAST!

Introduction/Initial Hypothesis

           This lab introduces the value of DNA sequence analytics to group organisms based on phylogenetics rather than morphological features or arbitrary taxonomy. Since DNA serves as a physical heritable factor that can be traced and sequenced, biologists use it as the most effective tool to classify organisms. As father of modern binomial nomenclature, Carl Linnaeus (1707-1778) set the foundation of classifying organisms based on common similarities and thus established a hierarchy to place any living creature depending on their outward appearance. However, only after Charles Darwin (1809-1882) introduced his theory of evolution in On the Origin of Species did biologists seek to classify species based on their lineage of inheritance, spurring the field of phylogeny. Phenotypic traits originally seemed to be shared between evolutionarily linked species were sometimes instead seen to possess analogous structures, which arose from twin adaptations to combat similar environments. The emergence of DNA analysis, especially nucleotide sequencing also gave biologists a concrete method to determine similar descent. Suddenly the age of Linnaean classification crumbled as previously thought monophyletic taxons (groups with all descendants sharing common ancestry) instead became paraphyletic (missing a descendant) or polyphyletic (containing species with no evolutionary descent). In addition, the discovery of parallel gene transfer in some bacteria has led some to question vertical evolutionary charts in favor of circular ones.

           In this particular laboratory activity, I was given a picture of a fossil specimen collected near Lioning Province in China. Based on its morphological features shown in the amber, I was able to make some initial references that would contribute to my hypothesis. For instance, I could spot some very thin sprouting along the backbone of the animal (easily classifying it as a vertebrate, or part of the Chordata phylum) and assumed it was a group of feathers, thus placing this animal perhaps in the Aves category (birds). In addition, I could not discern any temple openings in its skull, thus classifying it as an Anapsid and part of the Reptilia class. Finally, I could make out that this organism did not have any opposable thumbs, disqualifying it as part of the Primate order in Mammalia and noticed that it was a tetrapod. Thus, I tentatively placed it in the Aves class. By comparing four different gene sequencing found in this sample with the BLAST site database, this experimentation would either corroborate or question my hypothesis. My proposed class the organisms would sit within is circled in red on the following cladogram:

Methods/Materials

           I utilized my computer and the four ASN files given by the lab handout (the gene sequencing) as well as the Basic Local Alignment Search Tool (BLAST website) in order to obtain DNA sequencing evidence. I entered all four ASN files into the “Saved Strategies” page and both observed the alignment distributions of the top 100 subject sequences and the “Distance tree of results” page, which gave a prediction of where the targeted organism would fall within. Using all eight pages, I formulated a qualitative analysis of the data.

Data

           In order to group the data systematically, I first listed the two most similar species based on their DNA sequencing score, which combined the Identification percentage (the proportion of nucleotides that were identical between the two species, the target and the compared species) and the Query cover (the percentage of the identical nucleotides aligned correctly). As independent identifiers, a low Query cover but a high Identification score could indicate a good nucleotide match but with one containing more introns or having insertions and deletions rather than substitutions between the identical groups of nucleotides.

           I listed the most similar species with their most identical protein scores with the convention of the numbers in the parentheses being (Query cover, Identification percent).

Gene 1: Gallus gallus (100%/99%) and Coturnix japonica (100%/97%)

Gene 2: Drosophilia melanogaster (92%/99%) and Drosophilia yakuba (95%/97%)

Gene 3: Taeniopygia guttate (95%/100%) and Corvus brachyrhynchos (95%/99%)

Gene 4: Alligator sinesis (100%/99%) and Alligator mississippiensis (91%/83%)

           In addition, the following are the predicted phylogenetic tree containing the most immediate evolutionary ancestors of the target organism. Using these trees, I was able to quickly discern which class or family or organisms the compared species were originated.

Analysis/Conclusions

           Overall, I believe that my hypothesis that the target organism fell underneath the Aves class was adequately supported. Thus, my conclusive cladogram would be the same as my hypothesis:

           There are several reasons for my reasoning. First of all, looking at the data, the closest relative species based on both nucleotide similarity and alignment happened to be included in groups chickens (aves), fruit flies (arthopoda), finches (aves), and alligators/crocodiles (reptilia), it seems fair to group the target organism in aves as two of the four closely related species belonged to that group. Why not arthropoda? Looking at the morphological data, the organism possessed a backbone (thus it is part of the Chordata phylum) and as a basal group, the arthropods are farther than aves than reptilia. It is interesting to note that the Query cover for the arthropod species are the lowest (92% and 95%) of all the other species even though the Identification score is high, alluding that perhaps while the nucleotide bases might have been preserved through evolution, many insertions and deletions between them could have caused wildly different protein to be synthesized.

           In addition, the Aves class is less inclusive than the Reptilia group, and especially to be noted is that birds may be thought as a subset of reptiles because they are reptiles’ evolutionary descendants. Although the Reptilia class could be an alternate supported hypothesis, I would put a higher precedent on the Gallus gallus because it has a higher Query cover with a near perfect Identification percent, meaning that of the 99% nucleotides that are identical, they are all aligned the same as well.

           Finally through interesting research outside this laboratory, I found a species of dinosaur named Sinosauropteryx that bears close resemblance to this laboratory’s fossil specimen, and even may be the same species. It was the first dinosaur recorded that possessed feathers, and may have been the bridge species between reptiles and birds.

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What is TRANSITIONAL FOSSIL? What does TRANSITIONAL FOSSIL mean? TRANSITIONAL FOSSIL meaning - TRANSITIONAL FOSSIL definition - TRANSITIONAL FOSSIL explanation. Source: Wikipedia.org article, adapted under http://ift.tt/yjiNZw license. A transitional fossil is any fossilized remains of a life form that exhibits traits common to both an ancestral group and its derived descendant group. This is especially important where the descendant group is sharply differentiated by gross anatomy and mode of living from the ancestral group. These fossils serve as a reminder that taxonomic divisions are human constructs that have been imposed in hindsight on a continuum of variation. Because of the incompleteness of the fossil record, there is usually no way to know exactly how close a transitional fossil is to the point of divergence. Therefore, it cannot be assumed that transitional fossils are direct ancestors of more recent groups, though they are frequently used as models for such ancestors. In 1859, when Charles Darwin's On the Origin of Species was first published, the fossil record was poorly known. Darwin described the perceived lack of transitional fossils as, "...the most obvious and gravest objection which can be urged against my theory," but explained it by relating it to the extreme imperfection of the geological record. He noted the limited collections available at that time, but described the available information as showing patterns that followed from his theory of descent with modification through natural selection. Indeed, Archaeopteryx was discovered just two years later, in 1861, and represents a classic transitional form between dinosaurs and birds. Many more transitional fossils have been discovered since then, and there is now abundant evidence of how all classes of vertebrates are related, much of it in the form of transitional fossils. Specific examples include humans and other primates, tetrapods and fish, and birds and dinosaurs. The term "missing link" has been used extensively in popular writings on human evolution to refer to a perceived gap in the hominid evolutionary record. It is most commonly used to refer to any new transitional fossil finds. Scientists, however, do not use the term, as it refers to a pre-evolutionary view of nature.