London Calling 2026 Preview

My series on Craig Venter is on a small pause since I didn't get it out before I arrived here in London for Oxford Nanopore's annual shindig at Old Billingsgate.  On the plus side (well, I hope my readers find it a plus), I've sketched out an additional piece - I realized that our world of fast whole genome sequencing powered by long read technologies such as Oxford Nanopore may make it challenging for many to remember the genomics world of the 1990s and how there were great differences in opinion on how to go about sequencing genomes.  But back to London Calling - this is an interesting moment in the history of the company and it shows in the program. So without more ado, here are some key topics and questions on my mind.

Personal Reflections on Craig Venter: Expressed Sequence Tags

Venter's big Expressed Sequence Tag - soon known as ESTs -  paper came out in June during my final summer as an intern; I photocopied it at my internship. I looked it up, and it had only a bit over 600 sequences - a small beginning to what would become an industry-wide exercise.  That was a momentous time for me, as only the past December had I pivoted from thinking I would get a degree in experimental plant molecular biology to focusing on computational genomics. Venter was not the first person to feed an RNA library into a DNA sequencing workflow without prior screening; I believe Gregor Sutcliffe holds that milestone.  But Venter did it on a much larger scale and with much more flash.  He pitched it as a way to skim the cream of the human genome when the official Human Genome Project was just getting going.  And as would characterize much of his career, it is the response of others in the community that was as much his contribution as his own work.

Personal Reflections on Craig Venter: Preface

Craig Venter's sudden passing has triggered many writings about his life and work.  I'm overdue on my own personal reflections, and am breaking them into three thematic pieces. While I only met him a few times and never one-on-one, his career had an enormous impact on mine. So I am going to write a series of posts this week reviewing, in a very personal way, Venter's enormous impact on genomics and synthetic biology. I'm sure I won't do it proper justice, and I won't be surprised if my memory plays tricks on me - please do point out any egregious errors of fact and feel free to contest my opinions if you feel they are unfounded.

If My Agent Can't See Your Catalog, Will It Exist Much Longer?

Another edition of my dabbling with AI.  Somewhat like what I reported before - a customer asked if Ginkgo Cloud Lab's Echo-MS option could configure an assay to replicate the analytical results in a published paper, so I'm using Claude to do the heavy lifting.  Plus part of what I described earlier showed some issues on review.  But the big thing I'm keying into this morning is Claude is having difficulty with accessing a major chemical catalog I pointed it at - and I wonder how long that situation will be tenable.  Maybe not for a big company, but how many small companies will have an existential crisis when it turns out AI co-scientists and full agentic scientists have been silently passing them by?

Crossing the Vibicon

Vibe coding - solving problems by extended conversation with a machine learning program rather than writing the code yourself - is all the rage.  But I hadn't really been partaking, finding one excuse after another.  I don't have time.  It's a lazy approach to the craft I've honed.  Abandonment of my skills.   But I've also taken to referring to myself as a "lapsed computational biologist", as I was never doing any coding - or looking at biological data.  I'm business development now, which is a bit of a euphemism for salesperson.  Still, a bit of a pang - and all of my colleagues were vibing away.  And then an old friend/colleague said they fed my recent column on LinkedIn to an AI and it generated code to replicate my little parser  - and this colleague has never programmed!  He sent me the code, which I've skimmed but not tested - looks about right.  And so confession time - I have drunk from the well of vibe coding and do not plan to stop drinking from it anytime soon

An artistic depiction of Julius Caesar's transgression, pulled from Wikimedia

Invivoscribe PrepQuant: Streamlining Clinical DNA Extraction

The liquid biopsy space continues to grow and heat up - just this week Roche's Foundation Medicine unit announced the acquisition of Minimal Residual Disease (MRD) test developer Saga Diagnostics for just over a half billion dollars.  Numerous MRD and Multi-Cancer Early Detection (MCED) companies continue to spring up, with even more analyte types - first it was cell-free DNA, but now cell-free RNA and exosomes have entered the picture and probably a bunch more.  Extracting DNA from biofluids - mostly plasma, but sometimes urine or something else - is a critical step with many available methods - and many of those are labor intensive or incompletely automated.  As testing volumes scale, there will be a need to reduce the hands-on effort both to keep costs down and consistency up.  Just before AACR, Invivoscribe unveiled a new instrument for cell-free DNA purification and quantification which intends to reduce hands on time significantly over existing methods.

AGBT Agriculture 2026: A Few Paragraphs on Graphs

AGBT Agriculture was a really nice meeting - lovely venue in the Arizona desert, a meeting size that you felt you could (but weren't compelled to) introduce yourself to everyone, good food, great scientific content, and everyone super-friendly.  I came for the workshops on Sunday, and there were two on graph genomes / pangenomes.  Which was a theme throughout the meeting - not every talk or paper mentioned these topics, but a huge fraction did.  The agriculture world - both plant and animal (hmmm, no mushroom talks that I can recall) - is completely sold on the utility of graph genomes.  Ideally really large ones not only capturing the complete genomic diversity of a species, but also layering in information from related species so that the graph can service questions of when particular genomic features arose in evolution.