Health & Biotechnology

Automated Medical Discovery: the RX Project

A computer, tirelessly combing through patient records, looking for new medical knowledge. That was my Stanford PhD thesis project four decades ago — an early example of data mining and machine learning under AI control.

RX garnered many awards and contracts and was presented worldwide by myself and my co-PI and thesis advisor, Stanford CSD Professor, Gio Wiederhold (deceased, December 2022.)

Imagine how hard it was to do in the late 1970s in the era of mag tape (hand-carried by me), crawling CPUs, and "vast megabytes of memory."

Nobody else (was foolish enough to try or) tried to do this in the seventies. Now, in the current era of big data, everybody's trying to do it. (If you think your work tops the RX Project, please let me know.)

Carmat: Artificial Heart

Carmat Heart

French biotech Carmat has developed a total artificial heart — a stunning breakthrough. Although a heart transplant is preferable (if you're one of the few to get a suitable donor heart,) Carmat's device could become the second best option for terminal heart patients — and there are millions. The Carmat heart features biologic membranes throughout, pulsatile blood flow, and electronic autoregulation. (In this review I also cite competing American biotech makers of left- and bi-ventricular assist devices.

Carmat has already been implanted in over twenty patients in Europe initially as part of its PIVOTAL Trial and since 2021 under a newly granted CE Mark. The first implant in the United States took place in July 2021 at Duke University. That patient, a 39 year old man, has done well and has been discharged. Two other patients were recently implanted at the University of Louisville/ Jewish Hospital.

The Carmat heart and its competitors are principally offered as a bridge to transplant within six months.

Here is former Vice President Dick Cheney "arrestingly" chatting after his battery-powered LVAD was implanted but before his 2012 heart transplant.

Origin of Covid-19: Leak from Chinese Lab?


In early April, 2020 I saw an explosive video documentary on the origin of SARS-CoV-2, the virus that causes Covid-19. That video, by Epoch Times reporter Joshua Philipp, has been seen four million times on YouTube.

But, is the documentary fiction or nonfiction? I had to find out.

The definitive evidence that SARS-CoV-2 was NOT cooked up in a biowarfare lab in Wuhan is contained in a 17 March 2020 Nature Medicine paper by five expert virologists. The paper is tough sledding for non-biologists, but I attempt to explain it.

My verdict (concurring with several other science writers) is that while SARS-CoV-2 is unlikely to've been deliberately synthesized, the possiblity that this bat-related virus might've accidentally leaked from a Chinese virology lab cannot be completely dismissed.

Optimal Nutrition: Are Fats Killers or Saviors?

USDA Food Pyramid, traditional, lots of carbs

Health, wealth, wisdom, work, love and freedom.
Those are the keys to the kingdom of happiness.

But, health always comes first. As the saying goes — without it, you've got nothing. Now, here are the keys to good health — nutrition, sleep, exercise, freedom from pain and stress, and freedom from infections and toxins. (Toxic relationships are also potent poisons. Stanford Biz school's Prof. Bob Sutton calls this the "No A**hole Rule!" )

Nutrition is a difficult piece to get right, but it's well worth the effort.

You're a community of thirty seven trillion cells each in equilibrium with what you eat. So, what's the optimal recipe?

Let's say you eat 2400 calories a day, and let's say 400 calories are protein. How many of the remaining 2000 calories should come from carbs and (hence) how many should come from fats.

This issue has vexed medical researchers for decades. Here, I examine this in detail and show you some of the best free articles and videos on nutrition.

Epoch Times Live Panel with Virologists

Joshua Philipp

On 18 April 2020 The Epoch Times hosted a video panel which fielded audience questions directed to Joshua Philipp, narrator of the megahit documentary above; Sean Lin, PhD, former head of the virology lab at the US Army's Walter Reed Hospital; and Joe Wang, PhD, a vaccine expert.

Here I provide a detailed transcription of that one hour panel. Why did I bother? 1) Epoch Times gets a lot of flak for their one-sided attacks on the Chinese Communist Party. So, can their reporting be relied upon? My answer is — all news sources need to be carefully fact-checked (even my beloved Science and Nature.) 2) The content of this panel is so straightforwardly honest that it's important to set before the public. (Without the mood music in the popular documentary, it has received a mere 60,000 views. But to my mind it greatly enhances their credibility.)

Measuring Your Vitamins and Micronutrients:
SpectraCell and Vibrant America Labs

Foods that are rich in micronutrients

After two years on a very spartan diet, my health took a nosedive. With intolerable dizziness and burning in my feet, I was desperate for an answer.

I got a first clue after a lengthy workup. My vitamin B1 (thiamine) had dropped to a dangerously low level

After taking vitamin B1 supplements my health gradually began to improve, but I wondered "what else might I be low in?"

The answer was "a lot." My blood plasma and WBCs (specifically, lymphocytes) were low on over a dozen intermediary metabolites and other micronutrients. The only way to determine their levels is to measure them in a lab.

Here, I describe the extensive micronutrient panels that I got from two companies: SpectraCell and Vibrant America. If you can get a micronutrient panel cheaply through your health insurance, do that — it's a no-brainer. If you're paying cash, it may still be worth it.

My 1986 CV

Here's my CV from 1986 when I left Stanford to go back into clinical practice (for twenty years at Kaiser.) Reasons for leaving academic AI:
1) emergency medicine can be a thrill, 2) higher salary, 3) local family ties, 4) love of Silicon Valley, 5) impending AI Winter.

I retired from clinical medicine in 2007 and came back to Stanford (as an Affiliate of the Center for Mind, Brain, and Computation.) I've been a perennial student of cognitive neuroscience since my undergrad days at MIT in the sixties. I continued that interest as a neuroscience MD,PhD student at UCSF, also (after finishing my residency,) as a research associate/ principal investigator in AI at Stanford.

MD/ PhD students, perhaps, daunted by my career switches, occasionally ask me for career advice. Basically, a career choice is constrainted by 1) what you love, 2) your skills, 3) the market for your skills, and 4) where you and your family want to live.

Coronary Artery CT Scans

If famed newscaster Tim Russert had had a coronary CT Scan, he might still be alive.

Here, I argue in favor of getting scanned. (If you've got calcified arteries, they show up like Christmas tree lights.)

This is a story with a highly personal angle. (I've got coronary calcifications, and if you're a man my age you do, too.)

Ladies — your biology gives you a ten year reprieve. (But, here's what many of my women friends also do that contributes to their longevity: watch their weight, eat salads, relax, take care of themselves, and "tend and befriend.")

Calorie Restriction Slows Aging in Monkeys

calorie restricted monkey

This was a "stop-the-presses" story that broke in July, 2009. A 20 year study found that Rhesus monkeys fed a nutritious, low-calorie diet had far less heart disease, cancer, and diabetes than controls that ate 30% more. Monkeys on the diet out-survived the controls by 50% and had much less cerebral atrophy. Lose weight now — if you want to look more like the sleek fellow on your left.

Transcend: Live Forever

Transcend is a 2009 work by Ray Kurzweil and Terry Grossman.

I had avidly read their previous health book, Fantastic Voyage and benefited by its recommendations.

This is my review, as posted on Amazon. The book rated a B+.

(My review got over a thousand upvotes — pretty good — but not as good as Bruno Mars, doing Uptown Funk, at 2.9 billion!)

My personal favorite longevity recommention is dancing.
Here's Dick Van Dyke, now 90!

Dick's agent wanted him to write a "secrets of longevity" book, and Dick replied, "it would only be two words long - keep movin'!"

Transcend Drugs!

After finishing Ray's and Terry's book above, I wondered which (if any) of their recommended vitamins and supplements I should take. I researched them all.

At that time I had access to the Natural Standard — an encyclopedic reference written by a group of university clinicians. Here, I posted my findings.

My general rule is — get your nutrition from food. Skip the supplements!

I do take a few of those recommended in the book (eg, vitamin D.)

Does Drug X Really Work?

Want a one-word answer? "No!"

(The snake oil merchants are always ahead of the scientists.)

This was a long overdue essay on evaluating medical evidence.

Every new vitamin or supplement is greeted by unbridled enthusiasm.

I spent a decade studying biostatistics. The default hypothesis is that drug X does not work. This essay shows you what it takes to show it does.
(It takes years of effort!)

Synthetic Coronary Artery Bypass Grafts

Atherosclerotic coronary artery disease is the major killer in the United States.

If the artery was a plugged kitchen drain pipe, you'd simply buy a replacement. So, why aren't replacement (synthetic) coronaries available?

This is a brief overview of one company's struggle to develop a synthetic graft. (2012 Note: That company, known as Cardiotech in 2009, discontinued this development.)

There's been plenty of R & D since then — that's a reminder to me to update this.

The Inner Life of a Cell

This beautiful animation was done for Harvard by BioVisions.

Their director, David Bolinksy (TED Talk) tells the whole story here.

And, this version labels the molecules and subcellular organelles.

All three videos somehow managed to omit the key topic of the animation — the biochemistry of atherogenesis. Atherosclerosis is the major killer in the developed world.

And here, biology animator Drew Berry shows us the incredible "nanotech" involved during cell division, when DNA replicates and is pulled apart by microtubules.

Meanwhile, kinesin (a motor transport protein) walking along a microtubule towing a vesicle manages to be simultaneously funny and instructive.

And, here's a brand new one (2016.) This supercomputer model/ animation of DNA wrapped around histones (from the Riken Institute, Japan) is must-viewing. Watch this now — and memorize it!

In each of your ten trillion+ cells, two meters of DNA is stuffed into a ten micron diameter nucleus. The DNA is tightly wrapped around histone proteins like thread wrapped around hundreds of spools. Thousands of segments of that DNA must be unspooled and transcribed by RNA in real-time.

Super-Resolution Fluorescence Microscopy

Among the hundreds of molecular biology and neurobiology talks I attend every year, none attract larger crowds than those presenting new tools for high resolution light microscopy. The 2014 Nobel for Chemistry was awarded to Stefan Hell, Eric Betzig, and William Moerner, each of whom contributed separately to these stunning advances.

In February, 2017, HHMI Prof. Eric Betzig presented his work on lattice light-sheet microscopy to an SRO crowd at Stanford's annual lecture honoring Linus Pauling. Some of Betzig's stunning videos are shown above. And here Prof. Betzig tells us how his twenty year collaboration with Herald Hess led to the elaboration of photoactivated localization microscopy (PALM.)

Diabetes Research Connection: DRC

The DRC is a brand new approach to funding research to prevent and cure Type 1 (insulin-dependent) Diabetes (T1DM.) Founded by entrepreneur David Winkler and inspired by Kickstarter, one hundred percent of donations goes to funding distinguished young investigators with new approaches to T1DM. During 2017 the DRC launched seventeen projects (at about fifty thousand dollars each.) And, one successful project (Replacement Beta-Cells from an Unexpected Source) has already precipitated an addition million dollar grant (from the Keck Foundation.)

Separately, in other T1DM news, in April, 2018, Eli Lilly announced a huge collaboration with beta-cell start-up Sigilon Therapeutics. Sigilon is a new, beta-cell encapsulation device maker that was spun off from work at Harvard from the lab of Douglas Melton and from MIT from the labs of Robert Langer and Daniel Anderson.

Whole Genome for a Hundred Dollars

One of the show-stoppers of the 2010 Foresight Nanotech Conference was the above video showing Pacific Biosciences' SMRT tech, which sequences DNA bases in real-time (msecs) as DNA polymerase incorporates each base.