Writing in Biology

Screencasts for making multipanel scientific figures using Inkscape

Creating Figures: Part 1. Compositing
Creating Figures: Part 2. Labels and Arrows
Creating Figures: Part 3. Document Properties and Exporting

Hints

• Think ahead of time. What is your figure going to look like? Should you crop imagery ahead of time? Do you need to adjust image or exposure? (Note: Some journals don't allow digital manipulation of imagery). Do this in a bitmap editing program (e.g. GIMP or Photoshop).
• Do all your work in a folder. Put your image files in there. Save your SVG file in there. Save early and often.

Workflow

1. Import all your images: Either Link or Embed. Note things can be “above” or “below” others. Click or drag over to select. Hold the “shift” key to select multiple objects.
2. Composite your images to make your design: Lock proportions to avoid stretching. Turn “snapping” on or off. Set height and width directly to resize. Use Align and Distribute (switch to "relative to first selected").
3. Construct one label: Make a square box, make both stroke and fill the same (black or white). Put a text field in and add a letter. Use sans font. Use align and distribute to center letter.
4. Duplicate label to make more: Select both, duplicate object, move. Repeat as necessary.
5. Finish each label: Replace each letter as necessary. Use Align and Distribute to center. Select both and group. Use align and distribute to put labels at corners of each panel.
6. Create arrows: Use the Line Tool to draw a straight line segment (click, click-click). Then use Fill and Stroke tool to set the line width and add arrow head to start (or end).
7. Set the Page Size: Open Document Properties. Resize Page to Drawing. Set background to not be transparent (increase alpha channel to 255).
8. Export Finished Figure: Export PAGE. Set width to 1200pixels. Save with name “Lastname-Original.png” The resultant PNG file is your finished figure.

Note: Do not share your finished figure or include in your METHODS manuscript until your methods have been followed!

When reviewing the website “Save the Pacific Northwest Tree Octopus,” it is hard not to notice how much effort had been put into the design of the website. The website has a similar layout to most other conservation websites, including an FAQ, links for more information, and describing ways a person can help. However, upon further examination, it becomes quite obvious that the website is purely for humor. For example, on the tab that is supposed to include images of the creature, there are pictures of plastic toy octopuses in trees, and poorly photoshopped pictures of hawks carrying an octopus. The most interesting page on the website is the links page. On this page, there are three sets of additional websites: cephalopod websites, other animals of interest, and conservation websites. On the cephalopod websites, there is only information on the aquatic cephalopods and no mention of the tree octopus. Next, all of the other “animals of interest” that are listed are also satirical animals, like the “mountain walrus” and “prairie crayfish”. Finally, all of the conservation links are well known and reputable animal conservation websites, however upon research of those sites, the pacific northwest tree octopus is never mentioned. Ultimately, this website is a joke, and it can be noticed rather quickly if it is analyzed with any effort. The website is well made, but there is no semblance of truth to the information that it is stating, because its references do not support it at all.

-        Example 2: Chocolate. In this example, a box of chocolates was initially given to two brothers, but the older brother had eaten them all for himself, acting unjustly. In this modified example however, the chocolates were only given to the older brother. If the older brother refuses to share, Thomson argues, he is being greedy but just. (60-61)

-        Example 3: Henry Fonda. In the initial Henry Fonda example. A man with a cool hand can save the authors life, but he is across the country and must fly to her to save her life. However, in this new example, Fonda need only walk across the room and touch the author to save her life. Here he is making little sacrifice to help in comparison to the initial example. (61)

-        Thomson argues that even when the task is easy, it does not make refusing to do so unjust, She states “Nobody is morally requires to make large sacrifices of health, of all other interests and concerns, of all other duties and commitment, for nine years, or even nine months, in order to keep another person alive.” (61-62)

In my plant physiology class we are discussing the properties of water and how exactly the hydrogen bond properties allow water to interact the world around us and its truly fascinating. Waters hydrogen bonds are easily broken, but they are also very easily remade, meaning it requires alot of energy and heat in order to permenatley excite the molecules and raise the temperature of the water. This phenomenom of raising a substances temperature is called specific heat and in the realm of organic molecules waters​ specific heat is extremely. Another fascinating property of water cohesion, whihc is its ability to stick to itself via the hydrogen bond network. But its binding partners arent limited to other water molecules. It also has a property of cohesion, which is the ability to bind to other organic molecueles using the same hydrogen bond network. Lastly water is a superb solvent, this is mostly attributed to its polarity and charged complex, the polarity of water means its able to interact and dissolve other polar compounds, which is extremely useful in a lab setting. Overall I've found this weeks in class discussion fascinating, I never knew that water was such a unique compound. 

Summary of Thomson, “A Defense of Abortion”

In this article, Thomson defends abortion using several metaphors. In section 5 until the end, Thomson discusses the previous metaphors further by evaluating them as easy or difficult situation, good Samaritan and minimally decent Samaritan scenarios, and discusses when there is a requirement to help.

1. Easy vs. Difficult, Long-term vs. Short-term

Thomson discusses cases in which it would be morally indecent to detach a person from your body at the cost of their life.

-        Example 1: Violinist. Thomson refers to the violinist example where you wake up to find yourself attached to a famous violinist against your will. Being attached from your kidney to the violinist’s heart is keeping the violinist alive. In the initial example, you must remain attached to the violinist for 9 years so that the violinist may live. In this modified scenario, the violinist needs you only for an hour, and being attached to the violinist wouldn’t affect your health. Thomson suggests that in this scenario, it is unjust to disconnect yourself even though you did not consent because you make little sacrifice to keep another alive. (60)

Brachypodium distachyon is worthwhile to study because it is related to many of the grass species which we use for food, feed, and biomass; being closely related to rice, corn and wheat (Yang, et al., 2010). B. distachyon is a monocot, and because many monocot species are used for bioethanol production, it has become a model organism for advancing our understanding of species used to produce biofuels (Man Bo, et al., 2016). The plant is also excellent for laboratory use because of its quick regeneration time, small size, and compact genome (Yang, et al., 2010). B. distachyon is also well studied, and as a result its full genome had been sequenced and is an available resource for those studying it.

Water is one of the most important parts of the success of life on earth. The fact that water is polar gives it properties that a lot of other liquids don't have. One of these properties is cohesion, it is the ability of water molecules to hydrogen bond to each other. It allows water to stick together and be tugged through plant xylem via negative pressure. The cohesion in water gives it a tensile strength that rivals other substances that are much more solid. In addition to cohesion, water molecules are also good at adhesion. Adhesion is the property of water that allows it to bond to other polar surfaces. Adhesion is the reason that water can "walk" up a thin capillary tube. The ability to move up a tube also has to do with the surface tension of the water. As water climbs up the walls of the glass tube, the surface area of the water increases. The force of surface tension wants to decrease the surface area of the water, so it tugs the water up in order to maintain a more stable surface area. All of these forces play a role in moving water up a tube, however they are all stopped eventually by gravity.

During the methods part of Rosenzweig's research, several experimental factors had to be considered. In order to avoid bias, the examiners were not told which rat’s brain belonged to which of the three environments. After the treatment period, the brains were measured, weighed and analyzed to determine cell growth and levels of neurotransmitter activity. A neurotransmitter called acetylcholinesterase was the focus of the chemical examination. This neurotransmitter is responsible for faster and more efficient transmission of neural impulses. The cerebral cortex of the brain is responsible for experiences, movement, learning and sensory input. It was found to be heavier and thicker in rats raised in the enriched environment compared to the rats raised in the impoverished environment. The rats that inhabited the enriched environment also had increased acetylcholinesterase activity, had larger neurons and a higher RNA to DNA ratio. No differences were found between the number of neurons. Rosenzweig assumed that these differences implied higher levels of chemical activity had taken place. These results were seen again when they performed the same experiment several more times. The cortex increased in weight in response to the type of experience in each environment type, but the sub-cortex (the rest of the brain) changed very little. This measurement of the cortex to the sub-cortex was the most accurate measurement because overall brain weight varies with the overall weight of each animal (there is no correlation). They also found that enriched synapses were much larger in the rats that came from the enriched environment. These experimental results all supported the hypothesis which stated that animals raised in highly stimulating environments would demonstrate differences in brain growth and chemistry when compared to animals reared in plain/dull circumstances.

Continuing my notes from draft #3 of this week –
Discussion: There were many critics of his research. One of the biggest reasons as to why there was so much criticism was due to the fact that such type of experiment and also his theory have never been performed nor wondered about. What was the role of nature in a humans development? Is it correct to assume that all the results of this experiment applied to humans as well? These were the big questions. The researchers answered honestly saying that, no, we cannot assume that this applies to humans as well but we can assume that these results can be used for further research (as technology develops) which is the most important aspect of our results. This was a very broad criticism but there were more specific questions posed. Critics said that the differences in the brains of enriched v. impoverished environments could be due to stress and handling, since the rats from the enriched environment were handled 2 times a day and the impoverished rats weren’t handled at all. Rosenzweig tested this by setting up an experiment where he put rats in the same type of environment (but two separate cages) and handled one set of rats 2 times a day and the other set zero times a day and he found that there were no differences in brain size, weight and cortex to sub-cortex ratios. Even in later studies of the main experiment, they handled all the rats the same and they found no differences. Some critics also said that stress could have caused the differences they saw and not the enriched environment experience. But other evidence from separate research saw no differences either.

Rosenzweig’s research
Theory: The experiences that a human faces during early development has an effect on the development of the brain
Hypothesis: Animals raised in an enriched (highly stimulating) environment will demonstrate differences in brain growth and chemistry when compared to animals raised in a plain/dull environment
Why use rats? First of all, using humans would be ethically wrong for this experiment. Using rats (versus using another animal) is a better option for many reasons. Their brains are smooth therefore it can be measured and examined more easily after they are killed, they are small and inexpensive and last but not least, large litters allow researchers to also study the role of genetics which is especially useful in nature vs. nuture experiments such as this one.
Methods:
- 12 sets of rats, 3 male rats from the same litter, each of the 3 “brothers” placed in the 3 separate environments
- 3 different environments: the control = with the rest of their colony or in an enriched environment or in an impoverished environment
- treatment period was 4-10 weeks
To avoid bias, the examiners were not told which rat’s brain belonged to which of the 3 environments. After the treatment period, the brains were then measured, weighed and analyzed to determine cell growth and levels of neurotransmitter activity. A neurotransmitter called Acetylcholinesterase was the focus of the chemical aspect of the examination. This neurotransmitter is responsible for faster and more efficient transmission of neural impulses
Results: The cerebral cortex is the part of the brain that responds to experiences, responsible for movement, learning and sensory input, therefore it was the center of the study. It was found to be more heavy and thicker in the enriched environment compared to the other two environments. The brains that inhabited the enriched environment also had increased acetylcholinesterase activity, there were larger neurons (however, no differences between the number of neurons) and the RNA:DNA ratio was higher in the rats that came from the enriched environment. They assumed that this implies higher level of chemical activity had taken place. These results were repeated when they performed the same experiment several more times. The cortex increased in weight in response to experience, but the sub-cortex (the rest of the brain) changed very little. The measurement of the cortex compared to the sub-cortex was the most accurate measurement of all the other measurements because overall brain weight varies with the overall weight of each animal. They also found that enriched synapses were much larger in the rats that came from the enriched environment.