About

Welcome to my new blog! Well, I already have a blog, but it's more of a personal/general one. I felt that some of what I wanted to post would be far too detailed or technical for that blog... Hence this new one ☺

You might be curious about the name, Julian's Polymath Explorations.

Polymath (also an adjective): a person of varied learning in several fields of study.

Anyone who knows me, knows that the above word "describes me to a T"... Ever since 4th grade!

My formal training – mostly from undergraduate & graduate school at UC Berkeley – spans Math, Computer Science, Molecular/Cell Biology, Chemistry and Physics. But my interests range far and wide.

One of my main research areas is in Theoretical Neuroscience / Neuro Computing, which straddles biology, math and computer science - a sweet spot where several of my interests overlap!

I'm also very interested in Knowledge Representation, and am quite active in Brain Annex, which is being formed as a non-profit organization offering tools for Knowledge and Media Management, soon to be released as open source.

A more recent area of active research for me has been Interactomics/Computational systems biology, which I introduce in this blog entry, in particular in the context of Biomedical Longevity research; I'm quite interested in quantitative modeling of Eukaryote organelles and whole-cell Prokaryotes.

A Big Love of mine has always been Physics, especially its foundations - and the Big Questions about Cosmology, the fabric of spacetime and the nature of existence and of consciousness.

Other interests of mine include Quantum Computing, and the control of chaotic systems.

I currently work at the pharmaceutical company GSK, after a tenure as the CTO of a biomedical company in the Longevity field.

Well, topics big and small will percolate into this new blog, and I hope you will enjoy some of the entries… Thoughtful comments always appreciated!

I may be reached on LinkedIn.

This blog is dedicated to the memory of professor Jacob T. Schwartz, my mentor at New York University, where I started college. Definitely a polymath himself, he was a Great Man of immense intellect and remarkable generosity.
Among other things, he gifted to the world SETL, the computer language - far ahead of its times - that later inspired Python. Blog entry about him.

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Discussing Neuroscience with ChatGPT

UPDATED Apr. 2023 - I'm excited by ChatGPT 's possibilities in terms of facilitating advanced learning . For example, I got enlightening answers to questions that I had confronted when I first studied neuroscience. The examples below are taken from a very recent session I had with ChatGPT (mid Jan. 2023.) Source: https://neurosciencestuff.tumblr.com In case you're not familiar with ChatGPT, it's a very sophisticated "chatbot" - though, if you call it that way, it'll correct you! 'I am not a "chatbot", I am a language model, a sophisticated type of AI algorithm trained on vast amounts of text data to generate human-like text'. For a high-level explanation of how ChatGPT actually works - which also gives immense insight into its weaknesses, there's an excellent late Jan. 2023 talk by Stephen Wolfram, the brilliant author of the Mathematica software and of Wolfram Alpha , a product that could be combined with ChatGPT to imp...

Graph Databases (Neo4j) - a revolution in modeling the real world!

UPDATED Oct. 2023 - I was "married" to Relational Databases for many years... and it was a good "relationship" full of love and productivity - but SOMETHING WAS MISSING! Let me backtrack. In college, I got a hint of the "pre-relational database" days... Mercifully, that was largely before my time, but - primarily through a class - I got a taste of what the world was like before relational databases. It's an understatement to say: YUCK! Gratitude for the power and convenience of Relational Databases and SQL - and relief at having narrowly averted life before it! - made me an instant mega-fan of that technology. And for many years I held various jobs that, directly or indirectly, made use of MySQL and other relational databases - whether as a Database Administrator, Full-Stack Developer, Data Scientist, CTO or various other roles. UPDATE: This article is now part 1 of a growing, ongoing series on Graph Databases and Neo4j But ther...

Using Schema in Graph Databases such as Neo4j

UPDATED Feb. 2024 - Graph databases have an easygoing laissez-faire attitude: "express yourself (almost) however you want"... By contrast, relational databases come across with an attitude like a micro-manager: "my way or the highway"... Is there a way to take the best of both worlds and distance oneself from their respective excesses, as best suited for one's needs? A way to marry the flexibility of Graph Databases and the discipline of Relational Databases? This article is part 5 of a growing, ongoing series on Graph Databases and Neo4j Let's Get Concrete Consider a simple scenario with scientific data such as the Sample, Experiment, Study, Run Result , where Samples are used in Experiments, and where Experiments are part of Studies and produce Run Results. That’s all very easy and intuitive to represent and store in a Labeled Graph Database such as Neo4j . For example, a rough draft might go like this: The “labels” (b...

What are Graph Databases - and Why Should I Care?? : "Graph Databases for Poets"

This is a very gentle introduction to the subject. The subtitle is inspired by university courses such as "Physics for Poets"! (if you're technically inclined, there's an alternate article for you.) It has been said that "The language of physics (or of God) is math". On a similar note, it could be said that: The language of the biological world - or of any subject or endeavor involving complexity - is networks ('meshes') What is a network? Think of it as the familiar 'friends of friends' diagram from social media. Everywhere one turns in biology, there's a network – at the cellular level, tissue level, organ level, ecosystem level. The weather and other earth systems are networks. Human societal organization is a network. Electrical circuits, the Internet, our own brains... Networks are everywhere! What can we do with networks, to better understand the world around us, or to create something that we need? Broadly ...

Using Neo4j with Python : the Open-Source Library "NeoAccess"

So, you want to build a python app or Jupyter notebook to utilize Neo4j, but aren't too keen on coding a lot of string manipulation to programmatic create ad-hoc Cypher queries? You're in the right place: the NeoAccess library can do take care of all that, sparing you from lengthy, error-prone development that requires substantial graph-database and software-development expertise! This article is part 4 of a growing, ongoing series on Graph Databases and Neo4j "NeoAccess" is the bottom layer of the technology stack provided by the BrainAnnex open-source project . All layers are very modular, and the NeoAccess library may also be used by itself , entirely separately from the rest of the technology stack. (A diagram of the full stack is shown later in this article.) NeoAccess interacts with the Neo4j Python driver , which is provided by the Neo4j company, to access the database from Python; the API to access that driver is very p...

Anti-Aging Research: Science, not Hype

Last updated May 2023 Q: "How is aging a disease?" A: It's a dynamic system that veers away from its homeostasis (normal equilibrium point): hence a form of slow-progressing illness. Labeling it as 'natural' is a surrender to our traditional state of ignorance and powerlessness, which fortunately is beginning to be changed! Aging is "normal" only from the point of view of the "selfish gene", for whom the body is a disposable carrier. Individuals organisms - for whom self-preservation has a different meaning than for genes - have received scant help from evolution... with rare exceptions such as the T. dohrnii jellyfish (which I discuss here )... but now the time has finally arrived for our rational design to remedy some of the cellular flaws that evolution never bothered to correct! The above is my standard answer to an oft-asked question. The science of aging is by all evidence very misunderstood by the general public. Hype,...

Interactomics + Super (or Quantum) Computers + Machine Learning : the Future of Medicine?

[Updated Mar. 2022] Interactomics today bears a certain resemblance to genomics in the 1990s... Big gaps in knowledge, but an explosively-growing field of great promise. If you're unfamiliar with the terms, genomics is about deciphering the gene sequence of an organism, while interactomics is about describing all the relevant bio-molecules and their web of interactions. A Detective Story Think of a good police-detective story; typically there is a multitude of characters, and an impossible-to-remember number of relationships: A hates B, who loves C, who had a crush on D, who always steers clear of E, who was best friends with A until D arrived... Yes, just like those detective stories, things get very complex with our biological story! Examples of webs of interactions, familiar to many who took intro biology, are the Krebs cycle for metabolism or the Calvin cycle to fix carbon into sugars in plant photosynthesis. Now, imagine vastly expanding those cyc...

Visualization of Graph Databases Using Cytoscape.js

(UPDATED APR. 2024) I have ample evidence from multiple sources that there are strong unmet needs in the area of visualization of graph databases. And whenever there's a vacuum, vendors circle like vultures - with incomplete, non-customizable, and at times ridiculously expensive, closed-box proprietary solutions. Fortunately, coming to the rescue is the awesome open-source cytoscape.js library , an offshoot of the "Cytoscape" project of the Institute for Systems Biology , a project with a long history that goes back to 2002. One can do amazing custom solutions, relatively easily, when one combines this Cytoscape library with: 1) a front-end framework such as Vue.js 2) backend libraries (for example in python) to prepare and serve the data For example, a while back I created a visualizer for networks of chemical reactions, for another open-source project I lead ( life123.science ) This visualizer will look and feel generally ...

Life123 : Quantitative Dynamical Modeling of Biological Systems

(UPDATED 8/2022) - Are we ready to embark on a next-generation detailed quantitative modeling of complex biological systems , including whole-cell simulations? An anticipated up-jump in computing power may be imminent from Photonics computers (which I discuss here ), and GPU's are rapidly gaining power as well... Are we in ready state to put existing - and upcoming - power to good use? This is a manifest, and a call to action What's Life123? It's about detailed quantitative modeling of biological systems in 1-D, 2-D and full 3-D, as well as a multi-faceted software platform for doing so. What's (pseudo-)1D? For now, let's say it's like the inside of a long, thin tube - with no interactions with the tube. Likewise, (pseudo-)2D can be thought of as a Petri dish, with no interactions with the lid or the bottom. Website : https://life123.science A purposeful decision to also utilize 1D and 2D But why? Yes, it's in part about "walk before you run...

Photonic Computer - a "supercharged GPU" with very low energy consumption

Yes, we all wish for Quantum Computers... but in the meantime we need something here and now! Could Photonic Computers fit that role? Just about everyone has heard of fiber optics – using light for data transmission – but did you know that light can also be used for computing? There's a new commercial product expected for early next year (2022) . I contacted the CEO, Nicholas Harris, of a 4-y.o. startup, Lightmatter , interviewed in April 2021 here . Photonic computers, at least in their first commercial appearance, are essentially accelerator cards for Linear Algebra - and so of special interest for Machine Learning and some types of simulations. Their claims are remarkable: 10X faster than some of the best GPUs using 90% less energy can be used with existing software stacks, such as TensorFlow commercially available early next year (2022) a lot of future growth, as additional wavelengths of light get used in parallel My own inte...

Julian's Polymath Explorations

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