11 May 2018

How to read a scientific paper 4.1

This artist’s impression shows how the Milky Way galaxy would look seen from almost edge on and from a very different perspective than we get from the Earth. The central bulge shows up as a peanut shaped glowing ball of stars and the spiral arms and their associated dust clouds form a narrow band.

This post is a continuation of the last step in reading the papers, reading the whole paper. I chose an article about Discovery of Gamma-Ray Emission from the X shaped Bulge of the Milky Way. You can find a full article for free at arxiv.org. And if you feeling posh, you can also buy the version that was published in Nature.
Here is a ‘triage’ average grad student uses when reading scientific papers, and I follow that ‘triage’ here. Links will lead you to the posts that covered previous steps. 

1. Read an abstract.
2. Look at the images and read captions
3. Read conclusion/summary
4 Read the paper in details. part one, 

Read the paper in details - continuation

We’re on the fourth paragraph now. Here we can find a continuation of the method description. If you read carefully you’ll see that they really described the procedure step by step. As someone who has Ph.D. in a slightly different area, I still can get what they did, and even guess how they did it from what they said because I too had to analyze the spectra for the energy signatures.
I noticed before among my students that there is a slight confusion when someone says to analyze the spectra. So just in case…
This analysis does not mean that we’re staring at the pictures of the rainbow details. No. We are using graphs to describe light and stare at the tiny details on those lines. Yeah, scientists love graphs. Below you can see how spectral graph looks compared with the part of the spectra.

Screen Shot 2018-05-09 at 08.45.28
Screenshot from the French academia page that offers an excellent tool for observing the solar spectra. http://bass2000.obspm.fr/solar_spect.php

But I have to admit, at this point, I really have no clue how did authors exactly performed the analysis, or what is bin-by-bin analysis technique, but that number 18 next to the technique name shows me that there is an earlier paper in which the technique is described in sufficient details. So if I wish to repeat their analysis, I would have to read that paper too, and all other papers that are cited in that one, until I reach the knowledge level that I already have.
In a way, when I get a paper to review before it is published, that’s what I’m doing.
So, back to the paragraph. Here we also get an explanation about the green crosses in Figure 1. Telling us, that after the authors tested the technique on the known source, they discovered additional ones that matched the ‘description’.
I would also draw your attention to the last sentence of this paragraph. Scientists there are adding a warning, saying in essence, yeah, you know guys, we’re not 100% sure. And this is a hallmark of a good scientist. We are suspicious ba…ds, so suspicious that sometimes we do not trust ourselves.
Allow me to go on a tangent here. The fact that scientists doubt even themselves helps the overall science to rise above the biases. In the scientific community, this suspicion is cultivated starting with grad students. I remember how shocking was for me to realize that during the conference or any representation of the scientific results, we all have to be extra careful about what words we use. Suddenly, the ease of communication I had before, where it was more important what a person wanted to say than how they said it was gone.
I still struggle with this concept. And I still make mistakes, as you can tell from reading my blog. As a non-native English speaker, I had to devote extra time to learn about nuances of word meanings. Like the difference between meanings of rather and quite. I’m still grateful to two Australian colleagues, Mark, and Robert, who helped me when I had to write my thesis. And I still remember Robert’s explanation about nuances in meaning differences.
But this particular concept is important. The whole scientific method is established to fight against tendencies of the human ego to exert its own opinion. That ego can be so strong, that humans keep on insisting they are right despite the evidence. And since scientists are humans you can find such people in science too. I met a few of them. I even was part of the crowd who destroyed the pet theory of one of such scientists.

Fifth paragraph

This paragraph is short. It just repeats that their method is better and gives some numbers that describe why is it better. This time they do not repeat that details are in an appendix. There is no need, that information was already conveyed in previous paragraphs. Scientific papers tend to be short and succinct. Very rarely information is repeated. So if the info is repeated in a scientific paper, you can bet it is really important.

Sixth paragraph

This paragraph is now leading us into a discussion of the results. The authors mention that observed energy might be caused by unresolved stars and not the dark matter. In this paragraph, scientists are citing several earlier research papers that support their line of thoughts. Each argument is followed by the number in brackets, marking the previous work.
Each time a new result is uncovered, it has not only to bring new stuff but also successfully explain all previously observed facts. An example: often people say that Einstein made the ‘revolution’ in science. This does not mean the same as it means in politics, where old order is removed by the new one. Nope. Quite opposite. Revolution in science means a new insight that severely tests our prejudice about the world, but does not remove the old proven explanations. Einstein did that. He brought forth incredible new insight into gravitation. But you see, his explanation of gravitation did not nullify previous Newton’s one. Quite contrary, Newton’s law of gravity became a special case of Einstein’s theory. Of course, Einstein work did contribute to the removal of the old explanation, the one that invoked the existence of aether. He explained perfectly results of the Michelson-Morely experiment, while none of the existing aether theories could do so. So prejudice was removed, while new theory fitted perfectly with the observed experimental results, i.e. reality.
Similarly, every new scientific discovery brings a new building block of knowledge that ends up being stacked on top of the old ones. That’s why, every scientific paper includes discussion of the results, where authors are doing their best to connect their work with the existing body of knowledge and explain how their work is building upon that knowledge.

Seventh paragraph

Here we have continuing discussion of their results and effects of their model. Scientists describe what is the next step they took and how their model performed. This paragraph describes the motivation of removing the nuclear galaxy bulge and how their model successfully captures and removes the majority of the known sources, leaving the more exact residuals to analyze.

Eight paragraph

Here we have now extended discussion about how to fit the model and why this particular method to fit is effective. There is only one citation in this paragraph, this means that the knowledge needed to understand the math here is mostly covered in math, physics, and astrophysics university courses. Depending on which majors you had as an undergrad, you might have seen all that math already.
It is the same with me, I can recognize math, I’ve seen it and learned about it. There is some very complex math behind this. But even I would have to go and search for the particularities of the models the authors are mentioning. The recognition of the math will just help me to narrow my search to the particular parts of the mathematics, instead desperately staring at the enormous body of the knowledge in the math. Fun fact: it would take approximately 20 human lives for you to learn all the math existing today.

Notification:I have to apologize to you in advance. I had to accept a part-time job in a local business. And since I'm still trying to start my own little research company, this means I will have to write the blog once every two weeks from now on. I hope the situation will change when I get one of my grand funded. But for now, that's the situation.
If you are interested, I can also make some posts about grant proposal writing, and all 'fun' stuff I'm bumping in during that process.


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