Thursday, December 12, 2024

Fun with biology for weekend entertainment!

 We are often caught up in clips/news/forwards that are pushed by social as well as mainstream media that are mostly one or two minutes/pages long about things that are not going to matter much after a week or two To make sure our attention span is not monotonically getting atrophied, I nudge next gen youngsters in my circle to regularly read/listen/watch/focus on material related to ideas/research that span time & space, since that is what is going to have significant impact on societies in the longer term. I'd list the concepts behind mRNA vaccine or how High NA-EUV Lithography system works, as couple of such examples that took more than a decade to develop, with work spanning across a dozen countries/companies. 


To pull us back from the non-stop "Breaking News" cycle that mostly pumps out trivial stuff that is not going to matter next week, one approach suggests imagining a newspaper that gets published only once in 50 years. If you are the editor of that newspaper, what will you put out as the headlines (both good & bad) for the new issue going out next week?

Thinking along such slow lines, wanted to provide few good pointers I came across in the realm of biology.

Within the human body, we know blood flows all around, providing the needed nourishment for different body parts to function. Still there is a serious barrier at the brain that doesn't allow most things to get through. Here is an interesting article that nicely explains the blood-brain barrier.

Similarly, when a foreign body (e.g. a germ) enters our body, we know there is serious defense mechanism in place to fight it off. But when an expectant mother is carrying the baby, the fetus should normally be treated as a foreign body, as it has different blood type, DNA, etc. and so should be fought off by the mother's body. This doesn't happen. Why? It is because of the placenta, which is now understood to be a much more complicated organ than it was previously thought of. This Radiolab podcast does an excellent job of discussing this topic. A closely related article discusses discusses possibility of microbiome existing in human brain. 

On a somewhat related note, saw a nice video titled Post Human that talked about using our skin cells to create stem cells that can then be goaded to become egg & sperm cells, so that one can potentially have one's own baby without the need for another partner's sperm or egg. While this is one form of cloning, the documentary is not about cloning at all but about developments in biology (e.g. growing a baby outside the womb, developing a digital model that can be used to experiment drug or surgical procedures to see what will work for the real patient) in multiple areas that could be around the corner. https://youtu.be/88DPXE1thw4

If such things are possible, will it be possible to grow the human baby totally outside a woman's womb? That is the "What if?" question being explored in this Netflix movie, where in the near future, babies go through gestational development in a pod, provided by a private company. You can rent the pod, choose various options by paying for them, and use a crypto key to unlock the pod during the birthing process. While the concept is nicely explored, ending is just meh. https://youtu.be/rGMx_7oAeUM

Going back in time, Netflix also has a new movie titled Joy, that presents the development of IVF tech in the 1970's.

Robert Edwards & Patrick Steptoe, the pioneers that brought Louisa Brown (the first test tube baby) to this world, have written a book titled "A Matter of Life". It is one of the first non-fiction book I read in English, way back in the 1980's and so vividly remember, which is what this movie is about. Just like the way we are worried about the unknown repercussions of CRISPR based editing of human genome today, in the 1970s, there was massive opposition to IVF, since church, public and even the scientific community (including James Watson of DNA fame) were all worried that this is going against nature, that may produce Frankenstein monsters! 

Let me know how many of these pointers you were able to explore and what you found interesting or if you have pointers for me. 

Monday, December 9, 2024

Not so well disguised Book Reviews!

A while back I heard an interview of Nina Kraus on the radio discussing her book titled "Of Sound Mind - How our brain constructs a meaningful sonic world" that emphasized the importance of the sense of hearing, that we don't take as seriously as vision. The pun in the main title was amusing, making the book name stick to my mind. As I age, there has been some age based deterioration in my own hearing as shown in the chart below, and so I wanted to dig into this area a bit more to see if there is anything for me to do/practice to slow down or reverse the trend before I am forced to go for hearing aids, etc. in the future (very similar to what I was doing with CGM - Continuous Glucose Monitoring)

In a totally different context came across the old Pulitzer Prize winner "The Soul of a New Machine" (when straplines for book titles were not in vogue!) by Tracy Kidder that came out in 1981. Though I have heard of it, never picked it up, though it was considered a classic in computer science world. Decided to order a copy. Since I read these two books back-to-back, my usual triggers, comparing the authors' writing style, their background and how the material was presented were all swirling around in my mind. 

Just for fun, I first asked ChatGPT to write a book review in my style for the Soul of the machine book. I could do that by pointing it to my blogsite that has archives of my previous reviews so that it can learn. Here is the exact prompt I gave, and the review it wrote. This is to see how close its writeup is compared to how I felt. 

My prompt to ChatGPT: Write a book review for "The soul of a new machine" by Tracy Kidder in the style of Sundar Vedantham using book reviews posted at https://sundarvedantham.blogspot.com 

Here is what it came up with:

I was expecting it to write a review exactly like what I'd have written (i.e. if I copy/paste and send it out as my review, no one will know the difference). But it interpreted the prompt to mean that it should mimic someone else writing the review, referring to my style (hence the "as Vedantham would ask" lines). While it did manage to write prose that is similar to how I may write, actual takeaways were quite the opposite to what I felt reading the book! I have read couple of other books in the past, with major expectations that turned out to be duds for me. Along those lines, despite this one being a Pulitzer Prize winner, I didn't find it very engaging. Being a 4 decade old book, perhaps it hasn't aged well. It is written by the author Tracy Kidder who is a writer (i.e. not computer scientist). He was invited to hang around the design team of a computer company called Data General, as they were designing a new Mini-Computer (similar to DEC's PDP-11) called Eclipse. 

Data General was a badass computer company in the 70's. It was known for aggressive sales techniques, bold advertisements (look up "They Say IBM’s Entry Into Minicomputers Will Legitimize The Market. The Bastards Say, Welcome." advertisement that never actually went out) and so forth. While the DG's efforts & style were unique and heroic compared to IBM type companies at that time, to me Kidder kept sounding like a total outsider (perhaps because I am an insider) who was trying to sound like an insider, explaining geeky technical details of computer design in not so easy to understand prose for common audience. Author who is not a techie trying to sound like he is very tightly integrated as part of the tech team, describing how he was in the lab, went fishing with the tech leads, ate dinner with them, describing everything in first person singular (I did this, I asked him, my wife said) sounded odd. Reminded me of Carly Fiorina, when she became CEO of HP, putting up her picture next to Hewlett & Packard in their corporate office. It made HP engineers giggle since they didn't see her as an equivalent techie that deserved to have her portrait next to the founders, both of whom had passed away! Kidder certainly didn't go that far. But more of an observer style reporting in third person might have come across better. Perhaps it is just me. If you have read it and consider it a classic, educate me as to what I am missing and what impressed you so much.  

OTOH, Kraus is a Prof. at Northwestern University, running a lab called Brainvolts for decades, guided about 30 PhD students and has written just this one book that captures her lifelong work spanning decades. While this profile matches that of some very good books I have read in the past, I found Kraus' prose unnecessarily technical for a mass audience book. Here is an example, "Their hearing threshold did not change, but the way the auditory cortex responded to sound changed, reflecting a disorganized tonotopic pitch-processing mechanism". Takes a while to get used to her discussing the differences between afferent (moving upstream from ear towards brain) and efferent (moving downstream) in such language elaborately. I often complain that books usually contain walls and walls of text but instead should sprinkle around many more figures & pictures to help illustrate the discussion. While I was delighted to see Kraus using a lot of pictures, I found many pictures that didn't add much value. They felt so unnecessary, perhaps only helping to increase page count nudging it towards the 300-page mark, which is typical for books of this kind (this one is only 267 pages long). In addition, there were several pictures reused with permission from somewhere else. Probably the originals were color pictures that were meant to be seen in larger format. Rendered in B&W, small format portrayal in this book, things written inside those images by hand were hard to read and so again were annoying. 

But once we get past those annoyances, this book nicely covers the importance of good auditory capacity we should strive to retain for our mental health. Kraus writes in first person, talking often about her family, children, husband, mother, and students. In this case, since it is all her research, it does sound appropriate, at least to my ears. She covers the subject from multiple angles, the ear-brain functionality that enables us to hear & comprehend sound, bird songs, poverty are just few angles she takes up. Often when you dig into any specific areas of research, you unearth very interesting facts and nuances that are not intuitive. Kraus does a lot of research by measuring midbrain electrical signals that can be measured from our scalp (FFR - Frequency Following Response), that she uses as a point of departure to study the effects of sound on autism, aging, and so on. Here are some such findings Kraus talks about:

- Both musicians and athletes are better at hearing & understanding speech under noisy conditions. But the brains of the musicians amplify the signal (i.e. speech) to understand what is being said better, while athletes suppress the noise to reach the same level of understanding. 

- Plants are able to "hear" or are sensitive to sound. Her team demonstrates it using a pot that has two diverging legs at the bottom. Since plants grow their roots towards the area where water is found, without really providing water, but by creating the sound of water, they are able to observe the root growing towards that leg of the pot!

- Marine lives thrive near coral reefs that have a lot of activity reflected by the level of sound. By playing marine sounds through speakers near dead coral, we are able to attract more fish and other marine beings to settle down in that area, helping the area revive!

- Being a practicing bilingual and performing music of any kind are two areas that really help. 

- I have attached a 7 min long radio interview she gave. Near minute 6:30 see how by measuring the electric signals on the scalp as our brain listens to a piece of audio (few seconds of music, in this case) we can even recreate the audio back. 

I went for an audiology exam recently. The plot below shows my left/right (blue/red respectively) hearing thresholds. This is typical age-related hearing deterioration at different frequencies. 


I did do well on speech audiometry, word recognition tympanometry, and other such tests. Bur from previous test results completed couple of years ago, I can see a 5db drop in most frequencies. Kraus points out how if we see bleary road signs, we won't blame the highway department for installing fuzzy signs but get our eyes checked but when we don't hear well, we blame the noise around us and don't rush to get our ears tested! As we lose hearing slowly, as almost all of us will as we age, conversations become difficult. We slowly become apprehensive and hesitant about annoying others by asking them to repeat what they said. We then start to avoid interactions and tend to become more and more isolated leading to depression. We may also see this behavior in our own family elders. Simple fixes are getting tested by an audiologist to track any deterioration over time, learning a new language, playing music, avoiding excessive noise that can damage our ears, getting the right kind of hearing aids, and so on. I am planning to put these ideas into practice in my life. Do check out the Brainvolts lab website that has interesting short videos, papers, tests. If you won't pick up this book, you can search for her name online and listen to interviews/talks.