User:Inquisitio scientiae/sandbox

Week 14: FINAL ARTICLE
Respiration, for many amniotes, is achieved by the contraction and relaxation of specific muscle groups (i.e. intercostals, abdominal muscles, and/or a diaphragm) attached to an internal rib-cage that can expand or contract the body wall thus assisting airflow in and out of the lungs. The ribs of Chelonians, however, are fused with their carapace and external to their pelvic and pectoral girdles, a feature unique among turtles. This rigid shell is not capable of expansion and by rendering their rib-cage immobile Testudines have had to evolve special adaptations for respiration.

Turtle pulmonary ventilation occurs by using specific groups of abdominal muscles attached to their viscera and shell that pull the lungs ventrally during inspiration, where air is drawn in via a negative pressure gradient (Boyle's Law). In expiration, the contraction of the transversus abdominus is the driving force by propelling the viscera into the lungs and expelling air under positive pressure. Conversely, the relaxing and flattening of the oblique abdominis muscle pulls the transversus back down which, once again, draws air back into the lungs. Auxiliary muscles used for ventilatory processes are the pectoralis, which is used in conjunction with the transverse abdominis during inspiration, and the serratus, which moves with the abdominal oblique accompanying expiration.

The lungs of Testudines are multi-chambered and attached their entire length down the carapace. The number of chambers can vary between taxa, though most commonly they have three lateral chambers, three medial chambers, and one terminal chamber. As previously mentioned, the act of specific abdominal muscles pulling down the viscera (or pushing back up) is what allows for respiration in turtles. Specifically, it is the turtles large liver that pulls or pushes on the lungs. Ventral to the lungs, in the coelomic cavity, the liver of turtles is attached directly to the right lung, and their stomach is directly attached to the left lung by the ventral mesopneumonium, which is attached to their liver by the ventral mesentery. When the liver is pulled down, inspiration begins. Supporting the lungs is the post-pulmonary septum, which is found in all Testudines, and is thought to prevent the lungs from collapsing.

Week 12: Start going Live
Added a section in the main turtle article for respiration. Arranged the existing respiration information to that section and added information to the beginning.

"Respiration, for many amniotes, is achieved by the contraction and relaxation of specific muscle groups (i.e. intercostals, abdominal muscles, and/or a diaphragm) attached to an internal rib-cage that can expand or contract the body wall thus allowing air to flow in and out of the lungs. In Testudines, however, their shell and a lack of intercostal muscles prevent this type of costal ventilation from occuring.  "

Added comments to talk page.

Yelena and Jackie practicing going live, working out kinks in transferring citations, links, etc: (thanks Heather)

Yelena:

Turtles exhibit one of two methods of neck retraction by their assignment into the Cryptodira or Pleurodira suborder. The Pleurodira are characterized by retraction of the head in the vertical plane, which permits for primarily vertical movements and restricted lateral movements outside of the shell. These motions are largely due to the morphology and arrangement of cervical vertebrae. Of all recent turtles, the cervical column consists of nine joints and eight vertebrae.

(This section was added as it has multiple citations, which all appear to be functioning correctly. The actual portion going live, which features one citation, can be found below.)

These motions are largely due to the morphology and arrangement of cervical vertebrae. Of all recent turtles, the cervical column consists of nine joints and eight vertebrae.

Jackie:

The mechanism of neck retraction differs phylogenetically: the suborder Pleurodira retracts laterally to the side, anterior to shoulder girdles, while the suborder Cryptodira retracts straight back, between shoulder girdles.

Since these vertebrae are not fused and are rounded, the neck is more flexible, being able to bend in the backwards and sideways directions. The primary function and evolutionary implication of retracting the neck is thought to be for feeding rather than protection. Neck retraction is a neck extension adaptation so the turtle can reach out further to capture prey while swimming.

Week 11: Add an Illustration
Respiration, for many amniotes, is achieved by the contraction and relaxation of specific muscle groups (i.e. intercostals, abdominal muscles, and/or a diaphragm) attached to an internal rib-cage that can expand or contract the body wall thus allowing air to flow in and out of the lungs. In Testudines, however, their rigid shell and a lack of intercostal muscles prevent this type of costal ventilation from occuring. The ribs of chelonians are fused with their carapace and external to their pelvic and pectoral girdles, a feature unique among turtles. However, by rendering their rib-cage immobile Testudines have had to evolve special adaptations in overcoming their rigid shell to allow for respiratory processes.

Turtle pulmonary ventilation occurs by using specific groups of abdominal muscles attached to their viscera and shell to pull the lungs down and then push them back up. In expiration, the contraction of the transversus abdominus is the driving force by propelling the viscera into the lungs and pushing out air. Conversely, the relaxing and flattening of the oblique abdominis muscle pulls the transversus back down, thereby allowing air to flow back into the lungs due to the negative air pressure inside the lungs relative to the higher pressure in the coelomic cavity. Other muscles used in ventilation, though not the impetus, are the pectoralis, used in conjunction with the transverse abdominis during inspiration, and the serratus, which moves with the abdominal oblique allowing expiration to occur.

The lungs of Testudines are multi-chambered and attached their entire length down the carapace. The number of chambers can vary between taxa, though most commonly they have three lateral chambers, three medial chambers, and one terminal chamber. As previously mentioned, the act of specific abdominal muscles pulling down the viscera (or pushing back up) is what allows for respiration in turtles. Specifically, it is the turtles large liver that pulls or pushes on the lungs. Ventral to the lungs, in the coelomic cavity, the liver of turtles is attached directly to the right lung, and their stomach is directly attached to the left lung by the ventral mesopneumonium, which is then attached to their liver by the ventral mesentery. When the liver is pulled down, inspiration begins. Supporting the lungs is the post-pulmonary septum, which is found in all Testudines, and is thought to prevent the lungs from collapsing.

Week 10: Draft #2
Respiration, for many amniotes, is achieved by the contraction and relaxation of specific muscle groups (i.e. intercostals, abdominal muscles, and/or a diaphragm) attached to an internal rib-cage that can expand or contract the body wall thus allowing air to flow in and out of the lungs. In Testudines, however, their rigid shell and a lack of intercostal muscles prevent this type of costal ventilation from occuring. The ribs of chelonians are fused with their carapace, and external to their pelvic and pectoral girdles, a feature unique among turtles. However, by rendering their rib-cage immobile Testudines have had to evolve special adaptations in overcoming their rigid shell to allow for respiratory processes. However, the turtle has evolved unique adaptations to overcome their rigid shell and fused ribs by using specific groups of abdominal muscles attached to their viscera and shell to pull the lungs down and then push them back up. In expiration, the contraction of the transversus abdominus is the driving force by propelling the viscera into the lungs and pushing out air. Conversely, the relaxing and flattening of the oblique abdominis muscle pulls the transversus back down, thereby allowing air to flow back into the lungs due to the negative air pressure inside the lungs relative to the higher air pressure in the coelomic cavity. Other muscles used in ventilation, though not the impetus, are the pectoralis, used in conjunction with the transverse abdominis during inspiration, and the serratus, which moves with the abdominal oblique allowing expiration to occur.

The lungs of Testudines are attached their entire length down the carapace, and are multi-chambered, however, the number of chambers can vary between taxa though most commonly they have three lateral chambers, three medial chambers, and one terminal chamber. As previously mentioned, the act of specific abdominal muscles pulling down the viscera (or pushing back up) is what allows for respiration in turtles. Specifically, it is the turtles large liver that pulls or pushes on the lungs. Ventral to the lungs, in the coelomic cavity, the liver of turtles is attached directly to the right lung, and their stomach is directly attached to the left lung by the ventral mesopneumonium, which is then attached to their liver by the ventral mesentery. When the liver is pulled down, inspiration begins. Supporting the lungs is the post-pulmonary septum, which is found in all Testudines, and is thought to prevent the lungs from collapsing.

Week 9: Peer Review Response
Many comments pointed out that I had not actually drafted an article but discussed with my group what I was reviewing. This will definitely be rectified and a completed draft will be uploaded. One reviewer's comment suggested discussing the possible association of the turtles partial aquatic lifestyle in reference to respiration and its shell, and while the name "turtle" is commonly associated with an aquatic or partially aquatic reptile, this is a misnomer. Turtles, tortoises, and terrapins all belong to the order Testudines, which all have the bony shells with fused vertebrae and external girdles, and tortoises are terrestrial. That being said, if this information is not in the wiki turtle article, then I would be more than happy to add this information with the appropriate citations. After reading the peer reviews I will change or add context to the following:


 * adding the proper in-text citations
 * expanding on the complications of respiration in turtles vs. other vertebrates and how the turtles bodily functions have been affected and adapted
 * uploading pictures (after dissection) of:


 * 1) turtle lungs
 * 2) Muscles involved in respiration, if possible [ Inspiration : transverse abdominus, pectoralis. Expiration : abdominal oblique,serratus]
 * 3) Ventral surface of carapace with fused vertebrae and external girdles

Microbat vision/Teeth size
Neutral content: Yes

Reliable sources: Yes, and I agree with your own assessment about finding a couple more sources. This will strengthen your draft and make for a more balanced article. I would re-write your last sentence on microbat vision. It is plagiaristic, in my opinion. The drafted version is a little too similar to the authors leading sentence in their abstract: Also, the last sentence on microbat teeth should be re-written. It is also too similar to the original authors paper. Other than the issues addressed above, this is the beginning of a good start to your wiki contribution. I would suggest trying to find images comparing palate size and tooth size among microbats. That would be an interesting juxtaposition to see.
 * Drafted : “These cells are responsible for the microbat's ability to respond to light and plays a role in both non-image forming vision, such as circadian rhythms, sleep regulation, and pupil responses, as well as image forming vision”
 * Original author : “Intrinsically photosensitive retinal ganglion cells (ipRGCs) respond to light and play roles in non-image forming vision, such as circadian rhythms, pupil responses, and sleep regulation, or image forming vision…” (,abstract)
 * Original author : “With few exceptions, the microchiropteran insectivores, carnivores, and frugivores have relatively large teeth on small palates, and microchiropteran nectarivores and megachiropterans have relatively small teeth on large palates (Figure 9.1C). Megachiropteran nectarivores have relatively smaller teeth on the palate than megachiropteran frugivores. These relative proportions are maintained regardless of the size of the bat” (p.143)
 * Drafted : “Microbats and megabats display differences in their palate and teeth size depending on their type of diet. Microbats that have large teeth and small palates are insectivores, carnivores, and frugivores; however, microbats that feed on nectar have small teeth and large palates. Regardless of the size of the bat, the proportion of the teeth and palate size are maintained.”

Fluid Intake
Second sentence could be re-written for better flow. It just reads a little awkwardly. Other than that, you have a good source, but I would find a couple more to strengthen your article

Flying/Torpor
You have a really nice section done, but you could use more sources -- at least two more to strengthen your draft and keep it balanced.

Your second sentence is a little run-on. I would break it up for better flow of the article. Other than that, I did not notice any major grammatical or structural issues with your draft.

Venom
Very interesting topic! You have a lot of good information in your draft and only a few minor syntaxes and grammatical errors. Your sources seem sound and are reliable. Overall, I think this will be a good input for the wiki article. Getting a picture of the spine during dissection is a great idea.

“The venom of the stingray has been relatively unstudied at the current moment. '''[Past and present tense is used in the same sentence. A better version would be “At the current moment, the venom of the stingray is relatively unstudied” or alternatively, “The venom of the stingray has been relatively unstudied”.]''' This is because when the venom is released, it also contains mucus from the external layer of the stingray. Do to the mixture of mucus in [the] venom, researchers have struggled when aiming to test the chemical content of only the venom and not have the mucus get contaminate the sample. '''[Sentence reads a little confusing here. “Get contaminate the sample” seems to be missing a word – in the sample? Suggestion: “Testing the chemical content of the venom without contamination from the mucus has been a struggle for researchers”.]''' There has been one study that was successful in separating the mucus and the venom from each other. [You should cite that study here.] What we do know '''[“Current research indicates”, or something similar, should be used instead of “what we do know”. Although in some academic papers it may be appropriate to use first-person pronouns, I believe that it is unnecessary to use them here.]''' is that the venom is produced and stored in the secretory cells of the spine at the mid-distal region (da Silva Jr., N., et. al., 2015). Typically, other venomous creatures have been known to create and store their venom in a separate gland. '''[Interesting information in these last two sentences. I would suggest expanding on the venom storage of stingrays and other venomous creatures. Is stingray venom storage unique?]''' The toxins that have been confirmed to be within the venom are cystatins, peroxiredoxin, and galectin (Baumann, K., et. al., 2014). Galectin induces cell death in its victims and cystatins inhibits defense enzymes. In humans, these toxins lead to increased blood flow in the superficial capillaries and cell death (Dos Santos., et. al., 2017)."

Locomotion
This type of locomotion used by stingrays (and mantas) is called rajiform locomotion. You have a good description of the pectoral undulations that propel stingrays around. I would suggest expanding on this topic. How is the movement quicker or more accurate for benthic organisms? What are the specific muscles used in their undulations? All in all, good sources and well-done!

“The stingray uses Median Paired Fins (MPF) [as] opposed to pure undulations [maybe give an example of a fish that uses caudal fin propulsion, like a tuna] where the caudal fin is the source of locomotion. MPF provides quicker and more accurate movement needed for benthic organisms (Wang, Y., et al., 2015). The wave-like motion is performed by coordinated sequential movements between the pectoral and pelvic fins. The pectoral fins preform an undulation followed by a pelvic fin pull on the benthic floor (Macesic, L., et al., 2013).”

Anatomy
I think creating a section on anatomy is a good idea. Describing the anatomy of the stingray will lead to their spines, which would be a good segway for your teammate's venom contribution. Anatomy, of course, also into in to locomotion neatly. Your sources look good and I am interested to see your results in the dissection – I’ve never seen a stingray jaw and teeth before! You don’t have very many grammatical errors that I noticed in your draft, but I would suggest varying the lengths of your sentences to allow the reader to flow along. Right now, it almost reads like bullet points. Adding some transitions will improve that readability. That being said, you have great information and a strong start to your draft!

“Stingrays are composed of cartilaginous skeletons with portions that are [delete 'are'] strengthen through the process of calcification. [1] The cartilage allows the fish to stay afloat despite its lack a swim bladder. The vertebral column of the stingray is composed of the pre-caudal and caudal vertebrate [vertebrate {singular} or vertebrae {plural}], with the pre-caudal forming first. [2] Stingrays are counter shaded, meaning the dorsal side is darker than the ventral side allowing for the stingray to camouflage with it's [no apostrophe needed here] surroundings whether it is swimming around or at the bottom of the ocean. [3] The mouth of the stingrays are [is should be used here {subject verb disagreement}] located on the ventral side of the animal. The teeth are large, modified placid scales that have the appearance of flat plates [,] which aid in the crushing of hard[-]shelled prey.”

Spiracle
Picture plan seems interesting. I would suggest expanding and talking about the muscles involved in the control of the spiracle, to tie in with your proposed dissection pictures. The paragraph has only minor grammar or syntax errors. Some of the language seems a little informal to me, so I would suggest making it sound a little less so, but other than that – good job!

“The stingrays respiratory is rather complex, as they have two separate ways to take in water to utilize the oxygen. Most of the time stingrays will pull in water using their mouth, which then is sent through the gills for gas exchange. While efficient, they are unable to use their mouth when hunting as they bury themselves in the ocean floor waiting for prey to swim by. This is where their second system comes into play [this beginning seems a little informal], using a dorsal opening on the head called a spiracle, they can draw in [delete 'in'] water directly into their gills for gas exchange[4]. While [Delete ‘while’, start sentence with ‘This’.] this system is less efficient as the spiracle is unable to pull in the same amount of water as the mouth, [however] it is plenty for the stingray to survive on while awaiting its prey.”

Week 6: Narrow Focus on Turtle Draft #1
I want to look at the muscles that allow for respiration in the turtle. Turtles have a unique adaptation for respiration due to their full enclosed shells. They have ribs that are external to their pelvic and shoulder girdles, which is seemingly unique among vertebrates. Many vertebrates have muscles that connect to their ribs which pulls the rib cage out to expand and this allows air to enter the lungs. A turtles ribs is fused with their shell and thereby they do not have muscles attached to ribs because the ribs are immobile. Turtles evolved muscles that attach to the posterior limiting membrane and shoulder girdles which pulls the lungs down and pushes them back up. Viscera is attached to lungs ..... weight of viscera pulls or pushes lungs up with the movement of certain muscles used during respiration I could also touch upon which adaptation came first: turtle shell or a turtles unique respiratory adaptations
 * Inspiration
 * transverse abdominus
 * pectoralis
 * Expiration
 * abdominal oblique
 * serratus
 * Science believes that the muscle slings were a precursor to the turtle shell
 * Eunotosaurus africanus -- used muscle sling but did not have a solid shell.

Turtle
Please see User:Petrikyv/sandbox for collaborations
 * 1) Numerical Study of the Mechanical Response of Turtle Shell
 * 2) Ventilation and gas exchange in two turtles: Podocnemis unifilis and Phrynops geoffroanus (Testudines: Pleurodira)
 * 3) The anatomy of the respiratory system in Platysternon megacephalum Gray, 1831 (Testudines: Cryptodira) and related species, and its phylogenetic implications
 * 4) Breathing and locomotion: Comparative anatomy, morphology and function
 * 5) The metabolic cost of breathing in red-eared sliders: An attempt to resolve an old controversy
 * 1) Breathing and locomotion: Comparative anatomy, morphology and function
 * 2) The metabolic cost of breathing in red-eared sliders: An attempt to resolve an old controversy
 * 1) The metabolic cost of breathing in red-eared sliders: An attempt to resolve an old controversy
 * 1) The metabolic cost of breathing in red-eared sliders: An attempt to resolve an old controversy

Things that were noticed when looking over the Turtle wiki page:

 * 1) Lead section needs summation to reflect the overall wiki page.
 * 2) Of the 365 known species of turtle, how many are endangered? – Author went from very specific to very vague. Search and see if this information is available.
 * 3) 2nd paragraph needs work. It doesn’t flow smoothly and topics kind of jump around. Talks about metabolic rate and leatherback sea turtles. Is it only leatherback sea turtles? Clarify and possibly make a separate paragraph discussing the unique features (if that's the case) of leatherbacks vs. other chelodians.
 * 4) Neck retraction section could be expanded and broken into two paragraphs discussing the anatomical differences (and/or similarities) between the pleurodira and cryptodira necks.
 * 5) Skin and molting section needs references.
 * 6) The limb and senses sections have zero citations.
 * 7) We should create a section specifically on respiration – cloacal and “normal”.
 * 8) Citations needed when discussing temperature-dependent sex determination in turtles. Also, this should be expanded. TSD is not as simple as cold temp makes boys and warm temps make girls.

Endostyle

 * 1) The deuterostome context of chordate origins
 * 2) The draft genome of ciona intestinalis: insights into chordate and vertebrate origins
 * 3) Endostyle-like features of the dorsal epibranchial ridge of an enteropneust and the hypothesis of dorsal-ventral axis inversion in chordates
 * 4) Key characters uniting hemichordates and chordates: homologies or homoplasies?
 * 5) Palaeontology: on being vetulicolian
 * 6) Primitive deuterstomes from the Chengjiang Lagerstatte (Lower Cambrian, China)
 * 7) A possible Early Cambrian chordate

Things I could do to enhance the endostyle wiki article...:

 * First fossil evidence we have; when does it first appear?
 * what species/order? where was it found?
 * How is it homologous to thyroid?
 * Talk more about ammocoete to lamprey endostyle to thyroid metamorphosis
 * What are the genes/proteins/etc. associated with the endostyle and thyroid that makes them homologous?
 * Discuss the endostyle with regards to different groups (e.g. urochordates, cephalochordates, ammocoetes...Is there any differences in the endostyle or is everything the same?)

Week 4: Group Dissections

 * 1) Bat - Non-echolocating and echolocating bats have been found to have the same size cochlea during early development (relative to the size of their skulls) which may suggest that, at some point, Chiropterans had a common ancestor who echolocated and somewhere along the evolutionary chain some bats lost this trait.
 * 2) * Megabat
 * 3) * Egyptian fruit bat
 * 4) * Yangochiroptera
 * 5) Turtle - Turtles have a unique body plan and I am curious to learn more about what adaptations they have that may have attributed to their survival over the last few million years.
 * 6) * Ectotherm
 * 7) * Pleurodira
 * 8) * Carapace
 * 9) Rattlesnake - Honestly, I just think the fangs of solenglyphous snakes and their kinetic jaws are cool.
 * 10) * Venomous snake
 * 11) * Constriction
 * 12) * Viperidae

Week 3: Add to an Article
Endostyle ***New edit***
 * Fix spelling for ammocoetes on endostyle page.
 * Look at grammar
 * Work on editing re-organizing sentence structure
 * The mucus produced by the endostyle adheres to food particles suspended in the water and this mixture is then passed through the pharynx of the organism and into the esophagus through the sweeping movement of the cilia.

Week 2: Article Evaluation
There really is not much written on the endostyle. This article briefly touches upon its homologous relationship to the thyroid gland and I believe it could be improved by expanding on how the endostyle functions in the different types of chordates and if (or when) it metamorphoses in adults [compare and contrast]. I would also improve some of the language in the article. Particularly referring to "lower" chordates. This sounds biased and could be interpreted by others as being "less than" rather than an ancestral. In addition, some of the style of the writing is static and could be rewritten for better flow.

I did not notice any instances of plagiarism on the page, however, in the talk section it was mentioned that there was some plagiarism in the past, but it looks like the author took steps to rectify the situation.

The citations seem to work, and there are many links to other Wikipedia articles that are relevant to the endostyle.