Author: James Vornov

I'm an MD, PhD Neurologist who left a successful academic career on the Faculty of The Johns Hopkins Medical School to develop new treatments in Biotech and Pharma. I became fascinated with how people actually make decisions based on the science of decision theory and emerging understanding of how the brain works to make decisions. My passion now is this deep explanation of what has been the realm of philosophy, psychology and self help but is now understood as brain function. By understanding our brains, I believe we can become happier, more successful people.

Notes for Wednesday, October 13, 2021

Some overlap in Scott Young’s reading list with some of my most important reads. My ODB book features James and Lakoff pretty prominently as writers who shaped my approach here. In fact, the book that Scott mentions, Metaphors We Live By by Lakoff was the first of his I read and made the first connection for me between the neural maps of the brain and the semantic versions that seem abstract but are always rooted in the physical world. Our world of words and ideas are metaphors for concrete reality since that reality is all our brain was ever built to deal with. We’ve added this semantic layer of meaning on top, much like an augmented reality. I see a bit of shiny metal but think and associate spoon. And soup. And ice cream. It was Where Mathematics Comes From: How the Embodied Mind Brings Mathematics into Being which Lakoff wrote with Nunez that really cemented for me this idea that our ideas are all based in metaphors drawn from the physical world.

I’ve stopped bothering with dropping Amazon affiliate links when I discuss books. I’ve never seen enough monetary return to go through the trouble of looking up the link at Amazon. Although it is a nice affordance for a reader who’s thinking about buying the book.

One of my new habits has been to download Kindle samples of interesting books and read the first couple of chapters. Often enough to get the idea with minimal commitment.

Speaking of Amazon, I really think they are hurting themselves with this emphasis on sponsored ads at the top of and throughout organic searches. I know a few people who don’t always realize that many or most of the results are not actually what they searched for. And often are overpriced copies or imitations of the object being sought. Twitter too is polluting my timeline with more and more sponsored, page filling ads. It used to be the occasional click bait. Now its straight ads and topic suggestions. Instagram still seems like a nice place to visit.

An endorsement goes out to Pen Tips from Groningen in the Netherlands. These are conical, silicon tips that fit on the end of the hard plastic of the Apple Pencil. I loved the idea of the Pencil with the iPad, but hate the slippery, bouncy feel of plastic on glass. And I can’t degrade the iPad screen with one of the matte protectors that is said to be a – feel. These Pen Tips provide enough cushion and friction to make using the Pencil practical for me. It’s not the tactile spring of a fountain pen on good paper, but then I would expect these digital tools to every really feel like that.

I actually spent a week or so in Groningen many years ago conducting a clinical trial. The highlight was a day trip to Schiermonnikoog National Park, one of the barrier islands in the North Sea. It’s is a quick ferry ride from the mainland and then one can only bicycle to get around the island. The images were shot with my first DSLR, the Olympus E1.

Another endorsement goes to Apple Fitness. I’ve wound down my summer cycling activity with 3 big rides over the last month and am now it what they like to call “Transition”, being off the bike and doing some cross training. So finally I’ve tried Apples workouts, so far sticking to Pilates, Strength Training and Treadmill. Actually I did try one Yoga workout. These workouts are not dumbed down and by no means easy. They let you set your own intensity, say by picking your own dumbbell weights. They are fast an efficient, going from exercise to exercise without rest over 10 to 30 minutes. You get instruction- verbal and visual plus get to work out at home in a very short period of time. I will be incorporating some of this year round.

While I’m writing here, I make slow halting progress on the book manuscript. I’ve made an editing run through the first three chapters, but its harder to do in short chunks compared to getting out that first full draft. I’m hopeful that winter will bring some time to work on it, but my work life has been busy with taking care of family and cycling being the two big priorities.

Notes for Tuesday, October 12, 2021

The 2022 Hobonichi orders opened last month and for the first time in a few years I didn’t immediately place an order. The Hobonichi has been my daily morning diary for organizing the coming day and I can’t see moving away from it. I just realized that shipping was was equal to the price of of the book itself and it would be better to patronize one of the US shops selling it. So far, only the English version is available and I really prefer the Japanese layout even though the quotes that decorate the bottom of the page are meaningless to me. I’m hoping that Jet Pens or someone else has it soon, but ordering from Japan remains an option.

I logged into Dave Winer’s Drummer Blogging tool and I’m envious of the environment. It’s the equivalent of my casual photography approach. It’s outline based and focused purely on daily posts. I’m reminded of the Bullet Journal approach of simple lines that are todo’s, recording of events, thoughts or lists. I don’t think I want to leave my WordPress setup here, but will take the inspiration to see if I can start casual blogging like my casual photography.

The blogging workflow today is capturing links and thoughts in Drafts using Markdown which will get tidied and uploaded with MarsEdit or the WordPress app if the Markdown works. It’s a little variation from the usual flow aimed at creating a collection of notes that can be quickly edited and posted. Not quite Drummer’s direct writing to the web with paragraph by paragraph permanent links and generation of an RSS feed. This is a bit more like the newsletter approach that so many are using as a substitute or supplement to blogging.

John Scalzi, like me, appreciates how WordPress enables website ownership without technical hassle. While I’d love a blog that lived as an OPML outline like my old Bloxsom site lived in text files, I’ve come to appreciate that these blogs are transient entities. After all, this is ODB 3.0 as the old EditThisPage site hosting was abandoned and the text file system was too simple for the modern web world.

I’m looking at the surviving Link Blogs for inspiration, realizing only now that on a phone, any one of these paragraphs is a screen or two or three of text. And that’s where we read now.

Yes, I did buy a Mac Mini. As a small consumption device for reading and serving streaming music.

COVID-19: Science working in real time.

My real job is Drug Development, so I design and run clinical trials for a living. The mRNA vaccines are a triumph of molecular biology that owe their origins to the Human Genome Project and people like Francis Collins and Craig Venter. People forget or have never learned this history. I was there and have experienced the revolution in medicine we’re currently living through. But a discussion of the vaccine development is for another time.

Today I heard this report on NPR which was a bit different from my understanding regarding spreading of infection by vaccinated individuals. Breakthrough COVID may not be as threatening as scientists thought : NPR. Just like those recently infected may have virus mRNA detectable by nasal swab but be no longer capable of infecting others, vaccination may do this as well, maybe even better. Directly contradicts this from NPR just a few months ago. CDC: Data Shows Vaccinated People Can Spread The Delta Variant : Coronavirus Updates : NPR. Or maybe the truth is that COVID vaccines cut the risk of transmitting Delta — but not for long

This is science. This is where I live day to day. Conflicted evidence and uncertainty. Really tough on the public health authorities asked to provide policy and guidance to the public, to businesses and to government. It’s true we tend to be conservative under conditions of uncertainty like this. But there’s no question that any risk of vaccination is clearly outweighed by the benefit to oneself and to others in your community. And where there’s spread, masking and social distancing are the only tools we have to flatten the curve of exponential spread of infection. Those facts are clear.

We’re learning huge amounts about viral pandemics from these events. Learning about viral mutation through the course of a pandemic. Learning about how this new vaccine technology works in the real world- the right dose, the right schedule and how to monitor for adverse events when a complete new medical treatment is rolled out to hundreds of millions of people in the course of 6 months. Just amazing science and medicine.

Believe me, we’ll not only get through this and the pandemic will end over the next year or so. But our understanding of the events is only just starting. And that’s how science has always worked.

Notes for Monday, October 11, 2021

As my contribution to the rebirth of blogging, here’s a few quick thoughts in no particular order:

A note of thanks to Dave Rogers for his appreciation of my intermittent efforts here. Dave’s writing is always both personal and insightful and example of what a public personal journal can aspire to be. I also think of Dave as a model of my ideal reader, curious and educated, but no expert in the many esoteric areas I write about here.

I’m troubled by our inability to fix pharmaceutical pricing in the US. Even though I know that money controls much of our governments policies, this is one of those popular, reasonable and necessary changes that can’t get done becuae of how our politics is controlled by influence rather than public good. And I’ve spent the last 30 years in Drug Development so I know how pricing, reimbursement and rebates obscure the real prices paid and passed to patients.

We’re getting more and more detail on how our expectations shape our perception even at the lowest level of sensory processing. The subjective impression that we’re looking at
“what is” is so powerful! In truth, that experience is a construction patched together from fragmentary input that creates a model of where and who we are in the world. All mechanims that can be revealed in experiments, but that we have no access to and can’t examine in any way.

Another illusion is that decisions are rational because we have subjective access to the process when we are aware of choosing. But the options we imagine are generated subjectively and limited to what we can imagine, the values of different outcome are pure subjective feelings about what we want and the chances of success are subjective guesses. Where’s the rationality in imagination, feelings and guesses?

First Draft of On Deciding Better Manuscript Complete

I surprised myself this morning by writing what seemed to be the final words in my first draft of the book I call “On Deciding . . . Better: The New Ecology of Mind and Brain”.

This version of the book started with an outline in Google Docs on May 19, 2020 and took about a year to turn into a very rough first draft. As I’ve talked about before, the process of creating what Scribe Writing calls a “vomit draft” got me unstuck from all of my previous attempts.

The manuscript as it stands is pretty close to how I outlined it, which may not surprising given that this is a project I’ve been mulling over for a long time. More than 20 years if you start counting when I starting this blog in late 1999. The central ideas in the book were mostly present in the earliest posts I made here, but I’ve made some progress and had wanted to create something coherent from all of the work.

I’ve struggled with the problem expressing the ideas contained in the book as short posts in a blog. It’s clear that a manuscript provides the space to build the  concepts that can guide a reader through this journey out of simple enlightenment rationality. So I tried to document the journey I’ve made from the rational theories of decision theory to the ways we really make decisions which are based in ecology and evolution.

The book is a bit over 60,000 words which they tel me is a 300 or so page published book. Now comes editing, which I’m guessing will both remove a good bit of text but identify some gaps that need some more material, so net-net this seems about right.

For the edit, I hope I can focus on coherency and finding those gaps so that I can have a manuscript I trust someone could read and understand the general flow and arguments I’m making. It’s only at that point I can imagine anyone else reading it. I’d like to get it into some final form eventually and move on to another long term project to explore this ever facinating area of what it means to be human. It will be fun to get back into an exploratory mode rather than the grind of 250 to 500 words a day, aimed at filling in an outline of what I’ve learned.

I’m not sure what I’ll do with the ODB book once its done. At this point I don’t have much interest in all of the book promotion activity that goes along with publishing these days and I doubt a major publisher would be interested in this niche of neuroscientific philosophy book on decision making. On the other hand, I would like it to reach as large an audience as possible, so I guess that means releasing it on some platform or other and doing some promotion.

So on to editing!

A Very Good Day

Some advice to myself to mark the day.

Make some time to create today and everyday. Be sure you use whatever means of self expression is at hand, whether words, images or sounds. Don’t be concerned about how many likes it gets on Instagram or even whether you yourself like it.

Trust that you know enough to start, then use that feeling to do something that tells everyone else what’s inside you. The value is in making yourself bigger than the chatter and imagination in your head. You’ll be impressed with what you can do.

Someone’s personal junkyard. Nikon D850 24-120mm f/4G ED VR

Why You Need to Publish Your Notebook

Note taking seems to be having one of its many turns as an internet topic. The world of analog journalling is flourishing, propelled by (mostly) Japanese stationary brands like Midori with its Traveler’s Notebook and the Hobonichi Techo, but some stalwart European and British brands like Rhodia and even Filofax. On the digital side there’s a new crop of back linking network note taking apps that join the still relevant categories of GTD task managers, plain text approaches, Wikis and Hypertext (like my favorite, Eastgate’s Tinderbox), and integrated note systems from Evernote to Ulysses to Markdown editors to the latest like Craft. And then there’s the handwriting on iPad apps like Notability and Good Notes. I almost forgot the emerging ePaper device category, which has tempted me a few times ((But I know that fountain pen and paper just works for me better than stylus on iPad and probably one of these cool, single purpose devices)).

I ask myself, “With all this note taking, where’s the shared content being shared?”

Lots of notes, lots of systems, lots of discussion. Not so much content coming back out of these notes outside of work product like academic publications, corporate reports and the commercial content universe of the internet which has replaced magazines and newspapers, but tends toward the slick and superficial.

I miss the individual voices of the early internet and it seems that all of this note taking should provide some path for sharing what we’re all learning outside of commercial sites.

An Appeal To Contribute

I often see mention of how Google/YouTube has turned the web into a closed system by controlling search and advertising. For a long time, its been noticeable how many searches return no real results on the first or event the second page. I get advertising, shopping and howto Youtube videos.

If I see real content it’s often a link to Reddit, a company support forum or, sometimes a post on Medium. In fact, I’ve subscribed to Medium because so often search results take me there. Since most of the web writing going on is on commercial sites selling courses or subscription content, even when I get sent to a content page, it’s often a teaser for some course or software. I rarely get linked to one of the sites I follow through RSS feeds via NetNewsWire. In fact, I’ll often add a word or two to the search to make sure that I get an answer from Thom Hogan on photography plus others who may have commented on his opinion.

Curiously, huge amounts of the internet are generally completely cut out of these searches- Twitter, Instagram, Facebook. And email subscription newsletters. And Substack. We’re in a world of walled gardens and click farms.

Sadly, this isn’t entirely the fault of the Machine Learning algorithms that now rule the world and decide how to rank the results on a Google search page. There’s definitely less for the search engines to point to and less interchange between web sites that leads to links an interest.

Where’s the useful content then?

Now I’ll admit my own guilt here. I lost the drive to create useful content here when that early blogging community dissipated. I do learn things I ought to be sharing. There’s a steady stream of traffic here, so I could contribute more. I read, take notes, come to conclusions. My notebooks are full, my blog is empty.

An example? Is it worth the cost to buy a 16GB M1 Mac or should I get the quickly available 8GB memory model? Once I found a few examples of limitations, it seemed clear that for my use, processing big RAW files in Photoshop with Nik filters, a 16GB upgrade was going to be worth it. And it is. I don’t have a suite of test results, but I did see how fast the Apple Silicon Photoshop beta processed gaussian filters to create the now infamous Orton Effect ((If you haven’t heard, the Orton effect is that glowy landscape look, taking over from the overdone HDR workflow (which is not at all natural looking!) as getting likes on Flickr. Previously, I participated in the oversaturated landscape movement, to my everlasting shame.))

Another one? Should I switch to editing this website with the WordPress Gutenberg editor or keep my existing MarsEdit staging workflow? It looks like it makes sense to do only early drafts in MarsEdit to take advantage of creating links and pulling in media from Photos, but then publishing is best out of the new WordPress interface. And it looks like there’s no reason to move off of WordPress to any other system.

Workflows. How to use tools. Hacks, tricks and lessons learned in the course of exploration and implementing. All interesting reads and worth sharing.

If I needed any evidence of the value of sharing useful lessons, I need look no further than the content that is seen here. By far, the most viewed page is How Bill Gates Takes Notes, which is a short piece about the tale of his using the Cornell note taking system during meetings. I wrote that page because I found it interesting and there was no where left on the web where it was ell documented. I also have some photography pages and note taking workflow pages that get a hit or two day. Mostly from Google based on questions asked about how to do something or what something is, bypassing all the shopping and YouTube content.

3 Keys To Writing More

During the pandemic I seem to have figured out a few things. Like how to actually write a book manuscript. The method is simple really, just hard to sustain. But know that most everyone has a book or two in them already.

Last year, I mentioned I was renewing my effort to do some longer form writing on what I’ve learned over the last 20 years. It’s turned out to be a busy year for my work in drug development even with travel curtailed by the COVID-19 pandemic. I’ve found myself working from home for most of the year, but with a pretty packed day of calls and need to get out work product. How was I going to push the writing project forward.

Fortunately, about this time last year I found Tucker Max’s website ((Check out the web site Scribe Writing. Download the free ebook. Follow the directions. In a few months, you’ll have a first draft of a manuscript.)). His company provides services to authors like you and me who have books in them but perhaps no real ambition for a career in writing. Books can boost careers, publicize businesses and influence public discourse. I don’t have any these motives really. I’m just interested in sharing what I’ve learned from what I think is a unique perspective as a neuroscientist working in business environments.

Tucker provides a lot of free content on the site besides selling courses and services to writers. I extracted three key insights :

  1. Use the tools at hand to get words into the computer. Word, Google Docs, Notes- anything. I know I have way too many tools. So I picked Ulysses because it’s plain text, semistructured and syncs across Mac and iOS.
  2. Writers write. A book of 100 to 200 pages is 20 to 40 thousand words. Write 250 words a day, every day for at least 30 minutes a day. 60 minutes a day is reasonable and 120 is optimal. Since my schedule is different every day given project meetings, fitness schedule and work product due dates, I simply decided that my first 30 minutes free at my desk would be dedicated to getting at least 250 words out. Sometimes I’ve gotten 500 or more if I had an hour, but I just put fingers on keyboard and got the ideas down.
  3. The first draft is a marathon to get the words out. A lousy first draft. A vomit draft. At 250 words a day, 100 days of work equals a short book. What I have is nothing I’d want to share with anyone, but I think that after the first editing round I could serialize the chapters on the website here. Ulysses telsls me I’ve gotten 30,348 words down and I’m about halfway through the outline. So half of a 200 page book done.

I found that Tucker will actually answer questions, just as he promises on his website. One of my biggest obstacles was how much material I already had at hand. 20 years of blog posting and at least 2 previous attempts at turning the material into a book. I wanted to edit it into a book to save the time writing.

So I asked Tucker how to deal with the mass of material I’ve collected over all this time. Several manuscripts in volume really. He suggested I use it as reference, but start with a fresh outline and start writing anew.

Starting over turned out to be exactly the right approach. His assertion that people like me have a book in our heads already is absolutely right. And I’ve done this many times before as it turns out. I’ve often written research papers, review articles and book chapters by referring to. references, but then doing the careful citation and fact checking during editing once the ideas and flow were down on the page. The principle is that that the author has the book inside already, it just needs to get out of their head and into that linear computer file called a book manuscript.

As I’ve been writing, I’ve gotten a clearer idea where this is all going, so I spend some other time diving into some of the newest insights into brain mechanisms for decision making as well as my guidepost books on self improvement and making better decisions.

I hope to share the effort at some point, but given that I have no ambition to an author, the whole exercise has been a personal project to clarify some of the ideas I’ve had over the years about the relationhsip between decision making, brain function and the philosophy of ethics.

New Virtual Journal Club- Conant and Ashby (1970)

I’ve taken my notes on one of the important papers I’ve been reading and created a page here that I’ve called a “virtual journal club”. Many times in my career I’ve had the pleasure of working with a group that shared what they were learning on a weekly or monthly basis. Since I’m reading and taking notes, I might as well share what I’m reading here.

I anticipate a benefit for me will be the deeper understanding I’ll gain from the discipline of needing to read closely enough to summarize papers. ((This has been entered internet lore as The Feynman Technique based on comments he made about how he tackled difficult questions. ))

The paper Every Good Regulator of a System Must Be a Model of That System by Conant and Ashby is a formal attempt to prove that to control a system, a regulator has to contain a model of the system. If true, then the brain embodies a model of the body in the real world. It becomes the basis of the approach of Friston and his Free Energy Principle which I think is fundamental to how the brain actually makes decisions on a moment to moment basis. I think one of the Friston papers would be a logical next step to create some background that is hard to create in blog posts.