I've been struggling with finding a good workflow for taking notes on the journal articles which I read. I collate articles using Zotero, yet its in-built notetaking features (and comment scraping from PDFs) is quite poor. So, my alternative so far has been to write up notes by hand, but this is pretty cumbersome and makes it take some time to refer to my notes. My approach is clearly not effective!

How do you take notes on the papers which you read? Do you prefer to use written notes, or do you type your notes? In any case, what is your preferred means of storing and categorising your notes? And are there particular software which you use, if you opt for typed notes? (At present, I use an A5 notebook. Yet, this is not alphabetised or organised by topic, which compounds my struggles.)

Hi Tilders! I am new here, but my experience with the community thus far has encouraged me to post an AMA. I've specifically decided to post this AMA in ~talk rather than ~science for more exposure, and because I am hoping to field questions ranging from scientifically well-read to less-read, technical to curious, why care to who cares, and everything in between.

I won't be posting "verifying proof", because like many of you, I love my anonymity here. However, I will include peer-reviewed citations to question answers when I feel it necessary. I will do my best to share free-access articles, but this won't always be possible. If I link an article of interest to you that is paid-access, message me; maybe, I may be able to get a copy to you. Also, please be patient for my replies. Even though it is summer where I am, I am still busy in the lab and thoughtful responses take time.

Here is a brief background on the Rice Blast fungus to help get the conversation started:

Rice is an important staple food consumed by nearly half of the global population Khush. 2005. From 10 - 30% of the annual rice harvest is lost to disease caused by Magnaporthe oryzae, which is enough rice to feed greater than 60 million people Skamnioti and Gurr. 2009. To cause infection, a three-celled asexual spore called a conidium attaches to the rice plant's leaves, stems, and even roots. Once attached, a germ tube emerges from one of the three cells and grows along the surface of the plant. Hydrophobic molecules on the plant surface, called hydrophobins, induce a developmental change in the growing germ tube. The growing germ tube tip begins to form a dome-shaped structure called the appressorium. This specialized structure swells and generates up to 80 Mpa of pressure, enough to penetrate kevlar. A penetration peg penetrates the plant cell tissue, and bulbous invasive hyphae colonize the plant cell tissue. The fungus keeps the invaded plant cell alive, while it consumes its nutrients, with the plant cell dying only when the invading growth moves to an adjacent cell Cruz-Mireles et al. 2021. Schematic.

The Rice Blast research community focuses on all stages of its development. My work is focused on nuclear division during different developmental stages, and I am specifically working on understanding which and how motor proteins are involved in nuclear division in this fungus. Understanding the nuclear dynamics and the involved machinery will hopefully open avenues for controlling the plant infection and reducing the global crop loss.

I hope you all find Rice Blast interesting, and I hope I will be able to answer many interesting questions!

Openly published research makes science advance at a wonderful rate. In my experience scientists and researchers support open research in a nearly dogmatic fashion. Personally I am generally for it. However here is my concern.

I believe that humanity is in a terrible race. One of the competitors is the advancement of science, which of course can sometimes be used in a dangerous ways. The other competitor is our society moving towards murder and war becoming obsolete. The science is obvious and needs no examples. Societies move towards the sanctity of life is shown here.

"Violence has been in decline over long stretches of time", says Harvard professor Steven Pinker, "and we may be living in the most peaceful time in our species' existence."

Now to get to my point. In the past scientific advancement has created some really scary things. Atomic weapons, bio and chemical warefare, etc. However, those weapons took a lot of people and capital to produce, and had relatively un-scalable effects. Now with open research on advancements like CRISPR, we are nearing a time where in the near future a smart high school biology student with a few thousand dollars and an internet connection will be able to create self-replicating custom viruses that could kill millions. The asymmetric threat has never been greater.

Do you agree with my assessment and concerns?

If so, do you believe that there should be limits on publication of research in certain areas?

Edit: I should have said CRISPR and gene drives. Here is a TED talk on how gene drives can change and entire species, forever.