Foundational Skills in Life Sciences

61. How I prepare for teaching how to read papers to professional students

Sun, 31 Aug 2025 22:00:00 -0400

What does it take to prepare a single lecture?

In this episode, I will talk about months-long process for crafting a lecture on how to read clinical papers.

I am passionate about teaching this foundational skill.

The preparation includes choosing a paper that is best fit for the interest of the student body. It also includes making presentation slides tailor-made for the specific paper.

I hope this episode is helpful for both fellow instructors and students.

This episode = mini-series: training-2.

(My email is active. But my website is under construction. Please wait for a while. Thank you for the patience!)

60. Postdoc training program (that I organized in my university)

Sun, 10 Aug 2025 21:00:00 -0400

I have set up a training program for the postdoctoral researchers (postdocs) in my home department. Today, I would like to talk about: how and why I have done it, what we do in the program and what (positive!) feedback that I received.

This episode might help you if you are a student looking for training opportunities or if you are a mentor who is already guiding your immediate trainees.

This episode = mini-series: training-1.

(My email is active. But my website is under construction. Please wait for a while. Thank you for the patience!)

59. Happy 2-year anniversary! (plus, how I am scripting episodes)

Wed, 30 Jul 2025 11:00:00 -0400

This podcast is now two years old. And it is the start of the third year! Thank you for listening and for your support!

I would like to give you my behind-the-scenes information, so that you will have some understanding about how I am preparing the scripts of the episodes for you.

This episode = podcast update 8.

This podcast is a product of my own thoughts, research, and voice. In other words, it is human-generated, not AI-generated.

(My email is active. But my website is under construction. Please wait for a while. Thank you for the patience!)

58. Paragraph 1 of Introduction, written by Nobel Laureates: meaning of each sentence therein

Sun, 13 Jul 2025 13:00:00 -0400

Let’s read the first paragraph of the Introduction section in a paper written by the Nobel Laureates. Specifically, we will read each sentence in the paragraph, and think about the meaning and the role of each sentence. One key point is that the structural components of the Abstract will help us understand the paragraphs and sentences of the Introduction.

We are reading the paper written by Dr. Katalin Karikó & Dr. Drew Weissman, that led to the Nobel Prize in Physiology or Medicine 2023. We call it the Milestone Article 1. Here are two sets of links related to the paper.

Milestone Article 1:

- “Suppression of RNA recognition by Toll-like receptors: the impact of nucleoside modification and the evolutionary origin of RNA” by Karikó, Buckstein, Ni & Weissman. Immunity, 23(2): 165-75, 2005.

- HTML: https://doi.org/10.1016/j.immuni.2005.06.008

- PDF: https://www.cell.com/immunity/pdf/S1074-7613(05)00211-6.pdf

- PubMed: https://pubmed.ncbi.nlm.nih.gov/16111635/

- See the pull-down menu “Article Info” near the top of the article webpage (Use the DOI above to reach it).

- Check the “User License” section which lists the “Elsevier user license”:

--- http://www.elsevier.com/open-access/userlicense/1.0/

--- https://www.elsevier.com/about/policies-and-standards/open-access-licenses/elsevier-user

This episode = mini-series: reading-38.

(My email is active. But my website is under construction. Please wait for a while. Thank you for the patience!)

57. How to read the main points of Introduction paragraphs

Sun, 06 Jul 2025 16:00:00 -0400

The Introduction section of a life-science paper tells the main story, sometimes even multiple related ones. But without helpful subheadings, understanding its core points can be challenging. Then, how do we effectively read Introduction paragraphs to understand the section?

We will talk about it today, and we will keep reading one of the best papers as our example.

Milestone Article 1:

- HTML: https://doi.org/10.1016/j.immuni.2005.06.008

- PDF: https://www.cell.com/immunity/pdf/S1074-7613(05)00211-6.pdf

- PubMed: https://pubmed.ncbi.nlm.nih.gov/16111635/

- See the pull-down menu “Article Info” near the top of the article webpage (Use the DOI above to reach it).

- Check the “User License” section which lists the “Elsevier user license”:

--- http://www.elsevier.com/open-access/userlicense/1.0/

--- https://www.elsevier.com/about/policies-and-standards/open-access-licenses/elsevier-user

This episode = mini-series: reading-37.

(My email is active. But my website is under construction. Please wait for a while. Thank you for the patience!)

56. How many paragraphs in Introduction?

Sun, 29 Jun 2025 19:00:00 -0400

In combination with the last episode, we will talk about an introduction to how to read the Introduction section. With these two episodes, we will be ready to analyze the content details, from the next episode.

Milestone Article 1:

- HTML: https://doi.org/10.1016/j.immuni.2005.06.008

- PDF: https://www.cell.com/immunity/pdf/S1074-7613(05)00211-6.pdf

- PubMed: https://pubmed.ncbi.nlm.nih.gov/16111635/

- See the pull-down menu “Article Info” near the top of the article webpage (Use the DOI above to reach it).

- Check the “User License” section which lists the “Elsevier user license”:

--- http://www.elsevier.com/open-access/userlicense/1.0/

--- https://www.elsevier.com/about/policies-and-standards/open-access-licenses/elsevier-user

This episode = mini-series: reading-36.

(My email is active. But my website is under construction. Please wait for a while. Thank you for the patience!)

55. Does the Introduction section have subheadings?

Tue, 24 Jun 2025 21:00:00 -0400

Sub-sections and subheadings will be helpful.

The Methods and the Results sections of life-science papers are divided into sub-sections. And the sub-sections will have subheadings, i.e., the titles that serve as signposts of the sub-sections.

How about the Introduction section? What would this finding mean to us, the readers?

We will talk about them by scanning the Introduction of a paper written by Dr. Katalin Karikó & Dr. Drew Weissman, that led to the Nobel Prize in Physiology or Medicine 2023. We call it the Milestone Article 1. Here are two sets of links related to the paper.

Milestone Article 1:

- HTML: https://doi.org/10.1016/j.immuni.2005.06.008

- PDF: https://www.cell.com/immunity/pdf/S1074-7613(05)00211-6.pdf

- PubMed: https://pubmed.ncbi.nlm.nih.gov/16111635/

- See the pull-down menu “Article Info” near the top of the article webpage (Use the DOI above to reach it).

- Check the “User License” section which lists the “Elsevier user license”:

--- http://www.elsevier.com/open-access/userlicense/1.0/

--- https://www.elsevier.com/about/policies-and-standards/open-access-licenses/elsevier-user

This episode = mini-series: reading-35.

(My email is active. But my website is under construction. Please wait for a while. Thank you for the patience!)

54. Can you explain the role of Introduction in one sentence?

Sat, 14 Jun 2025 16:00:00 -0400

The single-sentence rule for understanding research paper Introductions. Have you thought about what the Introduction section of a life-science paper really does?

In this episode, we will address that question and discuss a simple rule. We will share a single sentence that encapsulates the entire role of the Introduction. It will make it easy to grasp the authors' intention and the paper’s core logic.

Hint: it is related to the key trio in the Abstract: the "Background-Known-Unknown" trio from Episode #53.

This episode = mini-series: reading-34.

(My email is active. But my website is under construction. Please wait for a while. Thank you for the patience!)

53. Minimum features of well-written abstracts

Sat, 07 Jun 2025 20:00:00 -0400

In today’s episode, we will learn which structural components will be minimally essential for an abstract, and which will be additionally necessary for a well-written abstract. These are the abstracts of primary research papers in life sciences, both in clinical- and basic-science fields.

There are very many variations in the structures of published abstracts. Why do we want to discuss the above topic?

This is because understanding the essential components of abstracts will help us anticipate key information and understand the content more effectively!

This episode = mini-series: reading-33.

(My email is active. But my website is under construction. Please wait for a while. Thank you for the patience!)

52. Example of a well-written abstract (other than the one by Nobel Laureates)

Tue, 06 May 2025 14:00:00 -0400

Let’s talk about an excellent abstract that I read this week. It was so well written, and I was so excited to read it that I wanted to talk about it with you today. The beauty of it is that the first 3 structural components guide us through the authors’ intention and question very clearly. But there was also a little twist to the structure: we will talk about it, too.

The abstract that we talked about today was from the following paper:

“A meta-analysis of technology use and cognitive aging”
Benge & Scullin, Nature Human Behaviour, 2025
“Online ahead of print” (thus, no volume number or page numbers) as of the date of this episode upload.
PubMed link: https://pubmed.ncbi.nlm.nih.gov/40229575/
Journal link: https://doi.org/10.1038/s41562-025-02159-9

We can read its abstract on either of the above websites.

Unfortunately, the other parts of the paper are subscription-based. So, they are accessible, if you or your institutions have a subscription to the journal.

This episode = mini-series: reading-32.

(My email is active. But my website is under construction. Please wait for a while. Thank you for the patience!)

51. Have you read an abstract that was not written well?

Sun, 20 Apr 2025 19:00:00 -0400

My students selected a paper to read in a journal club. The abstract (and the rest of the paper) was not written well. The abstract gave us two precious lessons.

Lesson 1: Good structural organization will help the readers understand the content.
Lesson 2: Abstracts of peer-reviewed papers can be disorganized.

I hope you learn them in this episode, too!

This episode = mini-series: reading-31.

(My email is active. But my website is under construction. Please wait for a while. Thank you for the patience!)

50. Happy 50th episode!

Fri, 04 Apr 2025 00:00:00 -0400

We have reached 50 episodes! Thank you for listening.

Today, we will briefly talk about how I have kept sustainable podcasting so far. The most important thing may be that I have set my goal simple and single: It is to create high-quality content for you. That’s it.

Here are links to two sources of podcast statistics that I mentioned in the episode.

(My email is active. But my website is under construction. Please wait for a while. Thank you for the patience!)

49. Another well-crafted logic loop in Abstract by Nobel Laureates (mini-series: reading-30)

Thu, 27 Mar 2025 22:00:00 -0400

We will talk about the second of the two, well-crafted loops of logic, in the Abstract of a paper written by the Nobel Prize Laureates.

Not all abstracts have this second loop. But when it is present, it gives a better overview of the impact of the presented work. We can find one of the best examples in our Abstract.

We are reading the paper written by the Laureates, Dr. Katalin Karikó & Dr. Drew Weissman, that led to the Nobel Prize in Physiology or Medicine 2023. We call it the Milestone Article 1. Here are two sets of links related to the paper.

Milestone Article 1:

“Suppression of RNA recognition by Toll-like receptors: the impact of nucleoside modification and the evolutionary origin of RNA” by Karikó, Buckstein, Ni & Weissman. Immunity, 23(2): 165-75, 2005.
DOI: https://doi.org/10.1016/j.immuni.2005.06.008
PDF: https://www.cell.com/immunity/pdf/S1074-7613(05)00211-6.pdf
PubMed: https://pubmed.ncbi.nlm.nih.gov/16111635/

See the pull-down menu “Article Info” near the top of the article webpage (Use the DOI above to reach it).
Check the “User License” section which lists the “Elsevier user license”:
--- http://www.elsevier.com/open-access/userlicense/1.0/
--- https://www.elsevier.com/about/policies-and-standards/open-access-licenses/elsevier-user

For finding our Milestone Articles 1, 2 and 3 (i.e., three papers written by the Laureates that led to the Nobel Prize), visit the following website that shows the “Press Release” of the Nobel Prize in Physiology or Medicine 2023. Look for "Key publications" section.

https://www.nobelprize.org/prizes/medicine/2023/press-release/

We discussed how to find Milestone Articles 1~3 as above, in Episode #10. Here is the link to the episode:

https://synaptologica.buzzsprout.com/2219599/episodes/14122755

(My email is active. But my website is under construction. Please wait for a while. Thank you for the patience!)

48. Well-crafted logic loop in Abstract by Nobel Laureates (mini-series: reading-29)

Thu, 20 Mar 2025 10:00:00 -0400

I can visualize two well-crafted loops of logic, in the Abstract of a paper written by the Nobel Prize Laureates. Can you?

We will talk about one of them in today’s episode. Such a loop, together with a linear progression, highlights the authors’ clear and logical thought process.

Milestone Article 1:

“Suppression of RNA recognition by Toll-like receptors: the impact of nucleoside modification and the evolutionary origin of RNA” by Karikó, Buckstein, Ni & Weissman. Immunity, 23(2): 165-75, 2005.
DOI: https://doi.org/10.1016/j.immuni.2005.06.008
PDF: https://www.cell.com/immunity/pdf/S1074-7613(05)00211-6.pdf
PubMed: https://pubmed.ncbi.nlm.nih.gov/16111635/

See the pull-down menu “Article Info” near the top of the article webpage (Use the DOI above to reach it).
Check the “User License” section which lists the “Elsevier user license”:
--- http://www.elsevier.com/open-access/userlicense/1.0/
--- https://www.elsevier.com/about/policies-and-standards/open-access-licenses/elsevier-user

(My email is active. But my website is under construction. Please wait for a while. Thank you for the patience!)

47. Why is the 2nd sentence important in an abstract? (mini-series: reading-28)

Thu, 13 Mar 2025 22:00:00 -0400

Let's analyze a single sentence in the Abstract of an impressive paper. It is the paper that led to the 2023 Nobel Prize in Physiology or Medicine. This is the paper that we call the milestone article 1 (Please see below for details).

We will analyze the second sentence. Why is this sentence important? We will discuss four of my approaches to see that this sentence is important, beautiful and helpful for readers outside the field.

It is fun to spend one episode for just a single sentence, and think deep about how it reveals the authors' logic.

Here are two sets of links related to the paper written by the Laureates, Dr. Katalin Karikó & Dr. Drew Weissman of the Nobel Prize in Physiology or Medicine 2023.

Milestone Article 1:

“Suppression of RNA recognition by Toll-like receptors: the impact of nucleoside modification and the evolutionary origin of RNA” by Karikó, Buckstein, Ni & Weissman. Immunity, 23(2): 165-75, 2005.
DOI: https://doi.org/10.1016/j.immuni.2005.06.008
PDF: https://www.cell.com/immunity/pdf/S1074-7613(05)00211-6.pdf
PubMed: https://pubmed.ncbi.nlm.nih.gov/16111635/

See the pull-down menu “Article Info” near the top of the article webpage (Use the DOI above to reach it).
Check the “User License” section which lists the “Elsevier user license”:
--- http://www.elsevier.com/open-access/userlicense/1.0/
--- https://www.elsevier.com/about/policies-and-standards/open-access-licenses/elsevier-user

(My email is active. But my website is under construction. Please wait for a while. Thank you for the patience!)

46. Let’s analyze the Abstract of a paper written by Nobel Laureates (mini-series: reading-27)

Wed, 05 Mar 2025 00:00:00 -0500

Today, we will analyze the Abstract of an impressive paper. It is the paper that led to the 2023 Nobel Prize in Physiology or Medicine. This is the paper that we call the milestone article 1.

We will have two essential pre-analysis sub-steps, and then we will analyze each sentence. During this analysis, we will read each sentence of the Abstract, examine the role of each sentence, and assign each sentence to a structural component, so that we will be able to understand the authors’ intention for each sentence.

Here are two sets of links mentioned in this episode. All are related to the Laureates, Dr. Katalin Karikó & Dr. Drew Weissman of the Nobel Prize in Physiology or Medicine 2023.

Milestone Article 1:

“Suppression of RNA recognition by Toll-like receptors: the impact of nucleoside modification and the evolutionary origin of RNA” by Karikó, Buckstein, Ni & Weissman. Immunity, 23(2): 165-75, 2005.
DOI: https://doi.org/10.1016/j.immuni.2005.06.008
PDF: https://www.cell.com/immunity/pdf/S1074-7613(05)00211-6.pdf
PubMed: https://pubmed.ncbi.nlm.nih.gov/16111635/

See the pull-down menu “Article Info” near the top of the article webpage (Use the DOI above to reach it).
Check the “User License” section which lists the “Elsevier user license”:
--- http://www.elsevier.com/open-access/userlicense/1.0/
--- https://www.elsevier.com/about/policies-and-standards/open-access-licenses/elsevier-user

(My email is active. But my website is under construction. Please wait for a while. Thank you for the patience!)

45. Let’s read the Abstract of a paper written by Nobel Laureates (mini-series: reading-26)

Thu, 13 Feb 2025 22:00:00 -0500

Today, we will take a significant step towards understanding the 2023 Nobel Prize in Physiology or Medicine. We will read the Abstract of the Laureates’ most important paper that led to the Nobel Prize. This is the paper that we call the milestone article 1.

We will have two essential pre-reading sub-steps, and then we will conduct the initial readings. These sub-steps will set the stage for a more in-depth exploration in the next episode.

Here are two sets of links mentioned in this episode. All are related to the Laureates, Dr. Katalin Karikó & Dr. Drew Weissman of the Nobel Prize in Physiology or Medicine 2023.

YouTube video of Nobel announcement (starting at ~2 minutes and 20 seconds)

Embedded in Nobel website: https://www.nobelprize.org/prizes/medicine/2023/prize-announcement/
Standalone with time stamp: https://www.youtube.com/watch?v=0JP-yDsLc3k&t=2m20s

Milestone Article 1: Immunity, 2005

(My email is active. But my website is under construction. Please wait for a while. Thank you for the patience!)

44. An evolving reader: my phases through reading textbooks (Q&A-5: textbooks, part 2)

Sun, 26 Jan 2025 20:00:00 -0500

How are you reading life-science textbooks?

My approach to reading textbooks has evolved significantly throughout my academic career, from student to researcher to instructor to course director. Today’s episode is part 2. We will discuss the last two phases of my experience.

I am now in the fourth phase. I fully appreciate how well the authors summarized a vast amount of knowledge in one field of life sciences, in coherent and consistent manners.

Please enjoy listening to my different phases of reading textbooks. It will be great if these episodes serve in stimulating your thoughts about how to read textbooks.

(My email is active. But my website is under construction. Please wait for a while. Thank you for the patience!)

43. An evolving reader: my phases through reading textbooks (Q&A-5: textbooks, part 1)

Thu, 09 Jan 2025 15:00:00 -0500

How are you reading life-science textbooks?

My approach to reading textbooks has evolved significantly throughout my academic career, from student to researcher to instructor to course director. Today’s episode is part 1. We will discuss the first two phases of my experience.

My overall goal of the two-part episodes is to highlight the unique roles that textbooks play, different from those of primary research papers. Knowing these different purposes will help us read textbooks more effectively.

(My email is active. But my website is under construction. Please wait for a while. Thank you for the patience!)

42. Happy Holidays!

Fri, 27 Dec 2024 12:00:00 -0500

Happy Holidays to you, and I wish you the very best in 2025!

41. Exclude or include seemingly irrelevant experiences in your academic CV? (Q&A-4: CV)

Wed, 27 Nov 2024 19:00:00 -0500

“Should I exclude irrelevant experiences from my academic CV?”

This is a question that students often ask. In this episode, I would like to give you my thoughts about this question.

In general, there is a way of creating a comprehensive CV: it will show that you have unique experiences, and you are a careful and a thoughtful writer. The key would be for you to be proud of what you did in the past. I hope that this discussion will be useful for you.

(My email is active. But my website is under construction. Please wait for a while. Thank you for the patience!)

40. Short or long CV for applying for a research position? (Q&A-3: CV)

Fri, 01 Nov 2024 00:00:00 -0400

“Should my CV be short or long, when I apply for a research assistant position in a college/university lab?”

This is a question that students often ask. In this episode, I would like to give you my thoughts about this question.

The content in a CV depends on the person’s career stage. But I have one common viewpoint for CVs at all stages. I would like to view the descriptions in the CV, during and after the undergraduate education, as the defining statements of the person. My thoughts about today’s question will be related to this viewpoint.

At the same time, I agree that different professors and different students may have opinions different from mine. Let’s discuss them and share diverse perspectives, so that our thoughts will become deeper.

(My email is active. But my website is under construction. Please wait for a while. Thank you for the patience!)

39. Eight key components define the Abstract structure (mini-series: reading-25)

Thu, 24 Oct 2024 23:00:00 -0400

How do top-tier scientific journals, like Nature, make sure their abstracts are clear and impactful?

In today’s episode, we will identify the eight key components that make those abstracts effective, by naming the components in our own words, and clarifying their roles and order.

Our system was inspired by the Nature document for the Abstract guidelines that we discussed in the Episode #38.

Here is the URL that brings you directly to the Nature document:

https://www.nature.com/documents/nature-summary-paragraph.pdf

(My email is active. But my website is under construction. Please wait for a while. Thank you for the patience!)

38. The journal, Nature, dissects the Abstract structure (mini-series: reading-24)

Tue, 15 Oct 2024 06:00:00 -0400

What is the best way to learn how to read the Abstract of a scientific paper?

In my view, the best way is to learn how the Abstract is structured in any paper.

Today, we will learn it, by reading a very short document. It is a one-page document that describes the Abstract guidelines, provided by the journal, Nature.
Here is the URL that brings you directly to the Nature document:

https://www.nature.com/documents/nature-summary-paragraph.pdf

Here is the URL of the webpage for the Instructions for Authors by Nature. The above document can be found as the hyperlink to the note, “annotated example” in the “Articles” section:

https://www.nature.com/nature/for-authors/formatting-guide

Here are the links to the Milestone Article 1 (Immunity, 2005) by the Laureates, Dr. Katalin Karikó & Dr. Drew Weissman of the Nobel Prize in Physiology or Medicine 2023.

DOI: https://doi.org/10.1016/j.immuni.2005.06.008
PDF: https://www.cell.com/immunity/pdf/S1074-7613(05)00211-6.pdf
PubMed: https://pubmed.ncbi.nlm.nih.gov/16111635/

(My email is active. But my website is under construction. Please wait for a while. Thank you for the patience!)

37. Announcement of The Nobel Prize in Chemistry 2024, relevant to life scientists!

Wed, 09 Oct 2024 21:00:00 -0400

The 2024 Nobel Prize was announced! Two days ago, it was in Physiology or Medicine. Yesterday, it was in Physics. Today, it was in Chemistry.

The Nobel Prize in Chemistry was awarded to Dr. David Baker “for computational protein design”, and to Dr. Demis Hassabis and Dr. John Jumper, “for protein structure prediction.”

Their work is directly related to life sciences.

Let’s learn about the work by watching a YouTube video. It is the archived video of the announcement of The Nobel Prize.

I am sure you enjoy listening to podcasts. I am also happy to report to you that Dr. David Baker launched “The Baker Lab Podcast” just two weeks before this recording!

Here is the URL of the YouTube video:

https://www.youtube.com/watch?v=bPjB9NRu8Jc

Here is the URL of the same video, but with a timestamp at the start of slide presentation:

https://www.youtube.com/watch?v=bPjB9NRu8Jc&t=4m40s

Here is the URL of the same video, but embedded on the Nobel Prize website:

https://www.nobelprize.org/prizes/chemistry/2024/prize-announcement/

Here is the URL of a new podcast, “The Baker Lab Podcast” hosted by Dr. David Baker:

https://www.bakerlab.org/podcast/

Enjoy the video and the podcast!

(My email is active. But my website is under construction. Please wait for a while. Thank you for the patience!)

36. Announcement of The Nobel Prize in Physics 2024, relevant to life scientists!

Tue, 08 Oct 2024 23:00:00 -0400

The 2024 Nobel Prize was announced! Yesterday, it was in Physiology or Medicine. Today it was in Physics.

It was awarded to Dr. John Hopfield, and Dr. Geoffrey Hinton, “for foundational discoveries and inventions that enable machine learning with artificial neural networks.”

It is somewhat (indirectly) related to my field, neuroscience!

Let’s learn about the work by watching a YouTube video. It is the archived video of the announcement of The Nobel Prize.

Here is the URL of the YouTube video:

https://www.youtube.com/watch?v=SBGG4WNweEc

Here is the URL of the same video, but embedded on the Nobel Prize website:

https://www.nobelprize.org/prizes/physics/2024/prize-announcement/

Enjoy the video!

(My email is active. But my website is under construction. Please wait for a while. Thank you for the patience!)

35. Announcement of The Nobel Prize in Physiology or Medicine 2024

Mon, 07 Oct 2024 17:00:00 -0400

The 2024 Nobel Prize was announced! This year’s Nobel Prize in Physiology or Medicine was awarded to Dr. Victor Ambros, and Dr. Gary Ruvkun, “for the discovery of microRNA and its role in post-transcriptional gene regulation.”

Let’s learn about the work by watching a YouTube video. It is the archived video of the announcement of The Nobel Prize.

Here is the URL of the YouTube video:

https://www.youtube.com/watch?v=Ln5rCmDqua0

Here is the URL of the same video, but embedded on the Nobel Prize website:

https://www.nobelprize.org/prizes/medicine/2024/prize-announcement/

Enjoy the video!

(My email is active. But my website is under construction. Please wait for a while. Thank you for the patience!)

34. Lessons learned from Nobel Laureates' work, about positive and negative controls (mini-series: reading-23)

Mon, 16 Sep 2024 23:00:00 -0400

We will complete the analysis of positive and negative controls in the milestone article of the Nobel Laureates of 2023. The article shows us one of the best examples of how to use positive and negative controls in life-science experiments. This episode will be Part 2 of a 2-part summary of control experiments. This will also conclude Step 11 of reading the article, which is to examine the key graph of the article. We can learn a lot from the Nobel Laureates!

Here are the links to the Milestone Article 1 (Immunity, 2005) by the Laureates, Dr. Katalin Karikó & Dr. Drew Weissman of the Nobel Prize in Physiology or Medicine 2023.

DOI: https://doi.org/10.1016/j.immuni.2005.06.008
PDF: https://www.cell.com/immunity/pdf/S1074-7613(05)00211-6.pdf
PubMed: https://pubmed.ncbi.nlm.nih.gov/16111635/

Here are the links to the YouTube video of Nobel announcement.

Embedded on Nobel website: https://www.nobelprize.org/prizes/medicine/2023/prize-announcement/
Standalone with time stamp: https://www.youtube.com/watch?v=0JP-yDsLc3k&t=2m20s

(My email is active. But my website is under construction. Please wait for a while. Thank you for the patience!)

33. How to do a good oral presentation? Hidden, but important tip (Q&A-2: presentation)

Mon, 09 Sep 2024 16:00:00 -0400

Question of today: What is a practical tip for effective oral presentations? There are many important things to do, for delivering oral presentations successfully. But I will be happy to give you my number one tip and the reasons why. And this tip is not discussed often in scientific communities. I hope you will find it useful!

Disclaimer: What I'm going to tell you is my personal opinion. It is possible that it does not apply to you in your own specific situation, in your program, in your own institution, and in your country. And each professor could have a different opinion. So, please listen to my comment, not as definitive advice, but just as a reference. I hope my comment will still serve you as a starting point for your thought.

(My email is active. But my website is under construction. Please wait for a while. Thank you for the patience!)

32. Is it important to include positive and negative controls in each experiment? Lesson from Nobel Laureates' work (mini-series: reading-22)

Thu, 29 Aug 2024 12:00:00 -0400

We will examine the positive and negative controls in the milestone article of the Nobel Laureates. The article shows us one of the best examples of how to use positive and negative controls in life-science experiments. We will compare a total of eight figure panels. And we will learn important lessons from them, for designing experiments and for reading figures. This episode will be Part 1 of a summary of control experiments.

Here are the links to the Milestone Article 1 (Immunity, 2005) by the Laureates, Dr. Katalin Karikó & Dr. Drew Weissman of the Nobel Prize in Physiology or Medicine 2023.

DOI: https://doi.org/10.1016/j.immuni.2005.06.008
PDF: https://www.cell.com/immunity/pdf/S1074-7613(05)00211-6.pdf
PubMed: https://pubmed.ncbi.nlm.nih.gov/16111635/

(My email is active. But my website is under construction. Please wait for a while. Thank you for the patience!)

31. Is it OK to say, “I don’t know” in response to technical questions? (Q&A-1: interview)

Wed, 21 Aug 2024 01:00:00 -0400

The first Q&A session! Question of today: Is it OK to say, “I don’t know” in response to technical questions in an interview when you apply for a life-science research position in a laboratory? I will give you my answer and the reasons why.

Disclaimer: What I'm going to tell you is my personal opinion. It is possible that it does not apply to you in your own specific situation, in your program, in your own institution, and in your country. And each professor could have a different opinion. So, please listen to my comment, not as definitive advice, but just as a reference. I hope my comment will still serve you as a starting point for your thought.

(My email is active. But my website is under construction. Please wait for a while. Thank you for the patience!)

30. Positive controls in another experiment by Nobel Laureates (mini-series: reading-21)

Sat, 17 Aug 2024 00:00:00 -0400

We will keep analyzing the specific positive controls that the Nobel Laureates used in their milestone article 1 that led to the Nobel Prize. We will examine the four positive controls in the third figure of this paper, and in other figures as well. Those positive controls did not necessarily show positive responses in multiple figures. We will observe that positive controls can show variable behaviors in a paper. We will also discuss how a modified definition of positive controls will be helpful for understanding them.

Here are the links to the Milestone Article 1 (Immunity, 2005) by the Laureates, Dr. Katalin Karikó & Dr. Drew Weissman of the Nobel Prize in Physiology or Medicine 2023.

DOI: https://doi.org/10.1016/j.immuni.2005.06.008
PDF: https://www.cell.com/immunity/pdf/S1074-7613(05)00211-6.pdf
PubMed: https://pubmed.ncbi.nlm.nih.gov/16111635/

(My email is active. But my website is under construction. Please wait for a while. Thank you for the patience!)

29. Positive controls in experiments by Nobel Laureates (mini-series: reading-20)

Tue, 06 Aug 2024 22:00:00 -0400

Let’s analyze the specific positive controls that the Nobel Laureates used in their milestone article 1 that led to the Nobel Prize. We will look at the first two figures and four positive controls therein. As always, we are impressed by the meticulous design of the experiments by the Laureates.

Here are the links to the Milestone Article 1 (Immunity, 2005) by the Laureates, Dr. Katalin Karikó & Dr. Drew Weissman of the Nobel Prize in Physiology or Medicine 2023.

(My email is active. But my website is under construction. Please wait for a while. Thank you for the patience!)

28. Defining positive controls in life-science experiments (mini-series: reading-19)

Tue, 30 Jul 2024 20:00:00 -0400

In this episode, we shift our focus from negative controls to their counterparts: positive controls. We will begin by defining what we mean by positive controls. Then we will refine that definition to encourage practical and cautious thinking.

Here are the links to the Milestone Article 1 (Immunity, 2005) by the Laureates, Dr. Katalin Karikó & Dr. Drew Weissman of the Nobel Prize in Physiology or Medicine 2023.

(My email is active. But my website is under construction. Please wait for a while. Thank you for the patience!)

27. One-year anniversary: I started podcasting to help you (podcast update 5)

Tue, 23 Jul 2024 18:00:00 -0400

One-year anniversary of this podcast channel! Thank you for listening. Why did I start podcasting? The motivation or the trigger was the students’ feedback to my teaching and training: they loved it. My goal is to help you learn and polish your skills in life sciences. In this episode, I will talk about a little story of how I started podcasting.

(My email is active. But my website is under construction. Please wait for a while. Thank you for the patience!)

26. Lessons learned from a failed experiment. Part 2 (mini-series: reading-18)

Tue, 16 Jul 2024 18:00:00 -0400

This episode continues from the last one. This will mark the end of our story about the life-science experiment that did not work at first, but worked well after extensive troubleshooting. We will talk about the remaining three lessons we can learn from the story. They will be about thoughtful approaches, and about probably the most important mindset in life sciences (What will it be?).

This is Part 18 of the reading mini-series "Let’s read a paper written by Nobel Prize Laureates, 2023."

(My email is active: ideas@synaptologica.com. But my website is under construction. Please wait for a while. Thank you for the patience!)

25. Lessons learned from a failed experiment. Part 1 (mini-series: reading-17)

Wed, 10 Jul 2024 00:00:00 -0400

In the last episode, we finished discussing details of the life-science experiments in our story. We observed that negative controls can be powerful tools for troubleshooting and ensuring data quality. The story gave us invaluable learning experience. What lessons can we learn? We will talk about three lessons related to negative controls today. They will help us design good research and evaluate results well.

This is Part 17 of the reading mini-series "Let’s read a paper written by Nobel Prize Laureates, 2023."

(My email is active: ideas@synaptologica.com. But my website is under construction. Please wait for a while. Thank you for the patience!)

24. Negative controls put the pieces together in troubleshooting experiments (mini-series: reading-16)

Tue, 02 Jul 2024 21:00:00 -0400

We will see how the experimenters implemented a good, troubleshooting idea into a protocol that appeared to be challenging at first. We are continuing to discuss the troubleshooting of a real, life-science experiment in our story. Sophisticated thought processes made the experiment possible in the end. This episode celebrates the power of well-designed experiments. We'll see how meticulous planning and a systematic approach to troubleshooting can overcome seemingly insurmountable obstacles.

This is Part 16 of the reading mini-series "Let’s read a paper written by Nobel Prize Laureates, 2023."

(My email is active: ideas@synaptologica.com. But my website is under construction. Please wait for a while. Thank you for the patience!)

23. Refining a troubleshooting idea: the power of identifying unknowns (mini-series: reading-15)

Tue, 25 Jun 2024 14:00:00 -0400

We will discuss the fourth and final idea, for troubleshooting a real, life-science experiment in our story. This idea was based on the previous three ideas. Then the experimenters took an impressive step. They identified key unknowns about the experiment, and refined and updated their idea. The updated idea laid the foundation for designing the crucial, fourth and final troubleshooting experiment that we will discuss in the next episode.

This is Part 15 of the reading mini-series "Let’s read a paper written by Nobel Prize Laureates, 2023."

(My email is active: ideas@synaptologica.com. But my website is under construction. Please wait for a while. Thank you for the patience!)

22. Negative controls unveil a hidden culprit in a problematic experiment (mini-series: reading-14)

Tue, 18 Jun 2024 06:00:00 -0400

We continue our deep exploration into negative controls and their importance in troubleshooting life-science experiments. We follow a real-life story of an experiment that yielded unexpected results. Through the third troubleshooting experiment utilizing negative controls, the experimenters finally uncovered the culprit. We discuss how negative controls helped identify the problem and pave the way for further investigation.

This is Part 14 of the reading mini-series "Let’s read a paper written by Nobel Prize Laureates, 2023."

(My email is active. But my website is under construction. Please wait for a while. Thank you for the patience!)

21. An exciting new way to stay connected (email newsletter; podcast update 4)

Tue, 11 Jun 2024 12:00:00 -0400

We will be happy to announce the launch of a new way to stay connected with the show - a FREE email newsletter! Sign up to get updates on upcoming episodes, behind-the-scenes insights, and more. Please join the community by sending an email to: ideas@synaptologica.com.

(My email is active. But my website is under construction. Please wait for a while. Thank you for the patience!)

20. Detective work of troubleshooting a puzzling experiment: negative control as a guide (mini-series: reading-13)

Mon, 06 May 2024 13:00:00 -0400

We will experience the fascinating world of scientific troubleshooting. In this episode, we will revisit a life-science experiment where researchers aimed to see if a specific chemical compound could enhance a particular function in cultured cells. Their plan seemed straightforward - a pilot experiment with a positive control (active compound) and a negative control (inactive compound). They wanted to confirm everything worked as expected. But the results were strange! Both the positive and negative controls showed unexpectedly high cell function, leaving the researchers scratching their heads. Join us as we explore the initial troubleshooting steps. Help us by showing your idea: where in the protocol the problem could be hiding. Stay tuned for the next episode where we continue this exciting discussion.

This is Part 13 of the reading mini-series "Let’s read a paper written by Nobel Prize Laureates, 2023."

(My email is active. But my website is under construction. Please wait for a while. Thank you for the patience!)

19. Negative controls are important: a story (mini-series: reading-12)

Tue, 16 Apr 2024 00:00:00 -0400

There are many reasons why life-science experiments do not work well. Today, I will tell you a real story about an experiment. It is an experiment that did not go well. We will explore the problem that researchers encountered. In the following episodes), we will discuss how they identified the problem, and how they solved the problem. The story will help us understand the importance of negative controls, especially how to design them for the experiments, and how to use them for trouble-shooting problematic experiments.

This is Part 12 of the reading mini-series "Let’s read a paper written by Nobel Prize Laureates, 2023."

(My email is active. But my website is under construction. Please wait for a while. Thank you for the patience!)

18. In-depth analysis of negative controls: using Nobel Laureates’ as example (mini-series: reading-11)

Sun, 31 Mar 2024 16:00:00 -0400

Today's focus: negative controls. In life-science experiments, negative controls play critical roles. In my view, they are more important than the positive controls! They form such a rich topic that we will spend at least a few episodes on discussing them. Today, we introduce basic aspects: 1) what the negative controls do in life-science experiments, 2) our practical definition by modifying the typical and ideal one, 3) how the negative control was used in our milestone graph (Fig. 3D of milestone article 1 by the Laureates of the Nobel Prize in Physiology or Medicine 2023), and 4) two critical assumptions for negative controls to work properly.

This is Part 11 of the reading mini-series "Let’s read a paper written by Nobel Prize Laureates, 2023."

(My email is active. But my website is under construction. Please wait for a while. Thank you for the patience!)

17. Links to 3 milestone articles & YouTube video presentation: Nobel Prize for Physiology or Medicine 2023 (mini-series: reading-10)

Sat, 09 Mar 2024 22:00:00 -0500

I will list four sets of links mentioned in this episode. All are related to the Laureates, Dr. Katalin Karikó & Dr. Drew Weissman of the Nobel Prize in Physiology or Medicine 2023.

Milestone Article 1: Immunity, 2005
- DOI: https://doi.org/10.1016/j.immuni.2005.06.008
- PDF: https://www.cell.com/immunity/pdf/S1074-7613(05)00211-6.pdf
- PubMed: https://pubmed.ncbi.nlm.nih.gov/16111635/

Milestone Article 2: Molecular Therapy, 2008
- DOI: https://doi.org/10.1038/mt.2008.200
- PDF: https://www.cell.com/action/showPdf?pii=S1525-0016%2816%2932681-8
- PubMed: https://pubmed.ncbi.nlm.nih.gov/18797453/

Milestone Article 3: Nucleic Acids Research, 2010
- DOI: https://doi.org/10.1093/nar/gkq347
- PDF: https://academic.oup.com/nar/article-pdf/38/17/5884/16767310/gkq347.pdf
- PubMed: https://pubmed.ncbi.nlm.nih.gov/20457754/

YouTube video of Nobel announcement
- Embedded in Nobel website: https://www.nobelprize.org/prizes/medicine/2023/prize-announcement/
- Standalone with time stamp: https://www.youtube.com/watch?v=0JP-yDsLc3k&t=2m20s

Enjoy and let's learn from them!

This is Part 10 of the reading mini-series "Let’s read a paper written by Nobel Prize Laureates, 2023."

(My email is active. But my website is under construction. Please wait for a while. Thank you for the patience!)

16. Graph axis labels by Nobel Laureates: the secret method of scientific communication (mini-series: reading-9)

Thu, 07 Mar 2024 17:00:00 -0500

Today's focus: the power of text elements in figures. We explore how category axis labels in bar graphs, when meticulously organized, reveal key experimental conditions at a glance. For a prime example, take Fig. 2B from our milestone article 1 by the Laureates of the Nobel Prize in Physiology or Medicine 2023. Here, the labels use two key strategies: 1) precise keywords accurately represent each condition, and 2) a three-layered structure visually communicates relationships between conditions. The next time you encounter a graph, take a moment to appreciate the labels and how they efficiently convey information.

This is Part 9 of the reading mini-series "Let’s read a paper written by Nobel Prize Laureates, 2023."

(My email is active. But my website is under construction. Please wait for a while. Thank you for the patience!)

15. Let's read a bar graph made by Nobel Laureates (mini-series: reading-8)

Wed, 14 Feb 2024 22:00:00 -0500

Dive deep into Step 11 of reading the milestone article written by Nobel Laureates. We will examine the most important bar graph. We will read the labels and the legend, and combine our knowledge with the Nobel Committee video. We will use the information flexibly to understand the story the graph tells.

This is Part 8 of the reading mini-series "Let’s read a paper written by Nobel Prize Laureates, 2023."

(My email is active. But my website is under construction. Please wait for a while. Thank you for the patience!)

14. Let’s read a paper written by Nobel Prize Laureates, 2023: Part 7 (mini-series: reading-7)

Mon, 29 Jan 2024 11:00:00 -0500

Visual elements in scientific papers often convey information faster than words. In Part 7 of reading mini-series, we will discuss previewing the paper content by scanning the figures and tables. This step will help us gain a quick overview of Nobel Prize-winning research.

(My email is active. But my website is under construction. Please wait for a while. Thank you for the patience!)

13. Let’s read a paper written by Nobel Prize Laureates, 2023: Part 6 (mini-series: reading-6)

Mon, 15 Jan 2024 17:00:00 -0500

In Part 6 of reading mini-series, we will discuss key steps before diving into a paper. We will verify the paper's identity and map its structure. These simple actions will give us a bird's-eye view of the paper and set us up for a deeper, rewarding reading experience.

(My email is active. But my website is under construction. Please wait for a while. Thank you for the patience!)

12. Let’s read a paper written by Nobel Prize Laureates, 2023: Part 5 (mini-series: reading-5)

Fri, 05 Jan 2024 21:00:00 -0500

Welcome to Part 5 of our mini-series on reading. Today, we will discuss a crucial step before diving into a paper. This powerful step will shift your focus from passively absorbing the written content to actively engaging with the authors' intent. By understanding what they are doing with each sentence and paragraph, you will gain a clearer overview of the paper's meaning. So, what is this important step?

(My email is active. But my website is under construction. Please wait for a while. Thank you for the patience!)

11. 2023 Wrap-up (podcast update-3)

Fri, 29 Dec 2023 15:00:00 -0500

Thank you for listening. I started podcasting earlier in 2023. The total number of episode downloads reached 250 on the day of this recording. Please keep listening to the episodes to come!

10. Let’s read a paper written by Nobel Prize Laureates, 2023: Part 4 (mini-series: reading-4)

Sun, 10 Dec 2023 19:00:00 -0500

This episode is Part 4 of a multi-episode mini-series on reading. When we want to read a paper written by the Nobel Laureates, you might wonder which one to choose. We will discuss how to select the right paper from among the many that the Laureates have written. How do we do it? There's a simple way.

(My email is active. But my website is under construction. Please wait for a while. Thank you for the patience!)

9. Let’s read a paper written by Nobel Prize Laureates, 2023: Part 3 (mini-series: reading-3)

Mon, 04 Dec 2023 12:00:00 -0500

This episode is Part 3 of a multi-episode mini-series on reading. The biggest hurdle when we read a paper written by the Nobel Laureates is usually our lack of knowledge necessary to understand even the basics of the paper. We will talk about how to obtain the minimal amount of the most accurate background information. It is to watch a YouTube video. But it should not be any video related to the Laureates’ work. There is only one video that I would like to recommend watching. What would it be?

(My email is active. But my website is under construction. Please wait for a while. Thank you for the patience!)

8. Let’s read a paper written by Nobel Prize Laureates, 2023: Part 2 (mini-series: reading-2)

Mon, 20 Nov 2023 23:00:00 -0500

Let's enjoy the Nobel Prize announcement. How do we enjoy it? We will read one paper written by the Nobel Laureates, and dive deep. This episode is Part 2 of a multi-episode mini-series on reading. We will talk about: 1) how the Nobel Prize laureates are selected, 2) what a milestone article is, 3) why we would want to read the milestone article by the Nobel Laureates, and 4) who will benefit from this reading activity.

(My email is active. But my website is under construction. Please wait for a while. Thank you for the patience!)

7. Let’s read a paper written by Nobel Prize Laureates, 2023: Part 1 (mini-series: reading-1)

Sun, 12 Nov 2023 10:00:00 -0500

Let's enjoy the Nobel Prize announcement. How do we enjoy it? We will read one paper written by the Nobel Laureates, and dive deep. This episode is Part 1 of a multi-episode mini-series on reading. We will talk about two goals of reading the paper.

(My email is active. But my website is under construction. Please wait for a while. Thank you for the patience!)

6. Thank you for 100 downloads of episodes (podcast update-2)

Mon, 18 Sep 2023 13:00:00 -0400

I would like to report to you: the total number of my episode downloads reached 100! It took me 2 months. Thank you for listening. Please keep listening to the episodes to come!

5. Happy Birthday, Google! (mini-series: online information search-3)

Sun, 17 Sep 2023 20:00:00 -0400

Google celebrates the 25th birthday in September, 2023, when this episode is recorded. Google CEO, Mr. Pichai, reflects on the paths that Google chose to take in the past, and on the paths that Google is going to take from now. Similarly, we would like to reflect on 1) how the online information search looked like before Google, 2) how it has changed after Google, and 3) how generative AI could change our activities from now (There is no answer yet!).

(My email is active. But my website is under construction. Please wait for a while. Thank you for the patience!)

4. "Thank you for listening" in three languages (podcast update-1)

Fri, 25 Aug 2023 00:00:00 -0400

In this episode, I would like to thank you for listening. I will report to you the number of downloads for the first three episodes so far. It is a tiny but mighty audience! I will also report to you the three countries where my listeners are located. Then I would like to express my gratitude by thanking you in three languages of those countries. Well, English is one of them. What would be the two other languages? You will know by listening :-)

Please visit my webpage for more information about this episode (https://synaptologica.com/4).

Please send me an email, if you have questions, comments, requests, etc. (ideas@synaptologica.com).

Happy Learning Skills!

(My email is active. But my website is under construction. Please wait for a while. Thank you for the patience!)

3. ChatGPT is here. Do we still need Google search? (Part 2) (mini-series: online information search-2)

Wed, 02 Aug 2023 21:00:00 -0400

In this episode (Part 2) and the one before (Part 1), we are discussing how to search for life-science information online. What method would give us the reliable online information? Now, ChatGPT has arrived and it is becoming very popular. Shall we rely on ChatGPT and other tools of generative artificial intelligence? That’s what we will talk about.

Please visit my webpage for more information about this episode (https://synaptologica.com/3).

Please send me an email, if you have questions, comments, requests, etc. (ideas@synaptologica.com).

Happy Learning Skills!

(My email is active. But my website is under construction. Please wait for a while. Thank you for the patience!)

2. ChatGPT is here. Do we still need Google search? (Part 1) (mini-series: online information search-1)

Wed, 02 Aug 2023 21:00:00 -0400

This is the first episode of a mini-series. We rely very much on online information every day. How can we choose reliable websites for the correct information?

As an introduction to the mini-series, we will introduce two common search methods: the traditional Google Search and the new ChatGPT. To help us understand that we need high-quality information sources to think deep, we will virtually experience one practical situation where a beginning, life-science student is trained. Based on this experience, let’s think about which of the two methods will be helpful. This will be Part 1 of the introduction.

Please visit my webpage for more information about this episode (https://synaptologica.com/2).

Please send me an email, if you have questions, comments, requests, etc. (ideas@synaptologica.com).

Happy Learning Skills!

(My email is active. But my website is under construction. Please wait for a while. Thank you for the patience!)

1. Introduction to the Podcast

Sat, 15 Jul 2023 13:00:00 -0400

Welcome to the "Foundational Skills in Life Sciences" podcast.
I am your host, Dr. Synaptologica.

In this episode, I will introduce you to this series, by answering three key questions:
#1. What foundational skills are we going to discuss?
#2. What are life sciences?
#3. Who will be my target audience?

I hope you enjoy starting listening to my podcast.

Please visit my webpage for more information about this episode (https://synaptologica.com/1).

Please send me an email, if you have questions, comments, requests, etc. (ideas@synaptologica.com).

Happy Learning Skills!