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Bertrand's father here. I'm humbled to see his page show up on HN. HN was one of the sites that first picked up Bertrand's story years ago and it played a big

Bertrand's father here. I'm humbled to see his page show up on HN. HN was one of the sites that first picked up Bertrand's story years ago and it played a big role is several of the events that followed, such as when he was confirmed to be the first and (then) only patient in the world with his ultra-rare genetic disorder. The subsequent explosion on social media led to the discovery of other patients; to an acceleration of the science; to the development of treatments; to my pivot from academic computer science to precision medicine; to working at The White House to launch President Obama's Precision Medicine Initiative. When Bertrand passed away unexpectedly in October, I've thought long and hard about how to ensure he leaves behind an active legacy. Toward that end, bringing more computer science and computer scientists into medicine is one of my goals, and as a first step toward that I published a lengthy (living) draft on his site that explains the step by step process that Bertrand taught me for doing precision medicine: http://bertrand.might.net/articles/algorithm-for-precision-medicine/ http://bertrand.might.net/articles/algorithm-for-precision-m...

keyanp 6y ago
My condolences to your family Matt. > Toward that end, bringing more computer science and computer scientists into medicine is one of my goals Besides donating to the appropriate organizations, do you have suggestions for if/how software engineers can contribute to this cause? Are there open source projects in need of contributors or notable organizations that one could work for? Perhaps even a way for technical folks with biology backgrounds to get in touch with and help non-technical families navigate all the jargon?
- nextos 6y ago
  My condolences too. > Besides donating to the appropriate organizations, do you have suggestions for if/how software engineers can contribute to this cause? There's a massive amount of stuff that CS people can do. For example, many protein features (signal peptides, GPI anchors, transmembrane domains, glycosylation sites, phosphorylation sites, E/R retention signals, etc.) can be modeled as formal languages or as probabilistic formal languages. Literally, that's what they are, amino acid codes. In order to help people with rare diseases, it is very important to identify which variant is knocking off one of those features. In most cases, that's the cause. For example, haemophilia (which is the archetypal rare disease) arises due to a mutation that abolishes a signal peptide in either Factor VIII or Factor IX. Furthermore, it has to be done as quickly and as automatically as possible. Otherwise, it doesn't scale. Most research funding agencies are sadly quite uninterested in rare diseases.
- mattmight 6y ago
  The Precision Medicine Institute that I now run produces mediKanren: https://github.com/webyrd/mediKanren https://github.com/webyrd/mediKanren It's an open source logical reasoning engine (read: 1960's AI) for drug repurposing that we deploy routinely to help patients. There is always a need for better relationalization of biological data sets that feed such tools too. For example, SemMedDB is really showing its age for NLP of the scientific literature and yet it is still astonishingly useful for helping patients even as is.
jwdunne 6y ago
Ahhh, I’m so, so sorry for your loss. I could never imagine the true pain of losing a child. But, as a father, it must be a hell that you would never wish upon even your worst enemy. My deepest condolences and regrets. I remember reading Bertrand’s story a few years ago. His struggle reached the UK, along with his many achievements and progress. Not many children of his age have such a global reach, especially for such a profound cause. R.I.P
caleb-allen 6y ago
Hey Matt! I've interacted with you on twitter before, but I wanted to thank you again for your work, it has impacted me greatly. One of the first mathematics papers I ever read was your paper on Gödel hashes. Coming from a patchwork self-taught software background it opened my eyes to just how much more there was to CS than "writing code". So, so much more. I still have a copy in my desk! I had dropped out of the U of U's CS program, and this was the first thing that really made me question my decision. I've also admired your work in with Bertrand and I'm hopeful at the legacy it will leave, and at the future of precision medicine. Thanks! Caleb
- mattmight 6y ago
  Thank you for the kind words -- and also for reminding me about the Godel hashing work!! That was one of the last things I did before the hard pivot into academic medicine.
flobosg 6y ago
I’m sorry to read of Bertrand’s passing. I’ve been following your writing for a while, including your son’s story, and I find nothing short of admirable the lengths that you and your family have gone to ensure that he was loved and cared for. I had a look at your draft and, as someone working in a related field, I’m really impressed by its exhaustiveness. Thank you for sharing your expertise.
- mattmight 6y ago
  Thank you for looking at the draft! Suggestions and corrections always welcome if you have any.
a_e_k 6y ago
Hi Matt, My wife and I were surprised and sorry when we heard Bertrand's passing last fall. It was a privilege getting to know your family first as neighbors and then as friends back in SLC. I was always humbled at seeing the effort that you and Christina put into moving heaven and earth out of your love for Bertrand. Not everyone can say they've made a lasting positive impact on the world, but you and your family certainly have. - Andrew
- mattmight 6y ago
  Thank you for the very kind words and friendship. I certainly hope Bertrand's legacy of science in the service of patients continues to grow with time.
Tomte 6y ago
I missed his passing, because I was taking an extended Twitter break. I've always felt a connection to your son, since I translated your article, even though we never met. I often think back to your Quora answer when I feel like a failure, and I try to remember that we can focus and we can re-direct our lives. All the best to you, your wife and your daughter.
- mattmight 6y ago
  Thank you :)

keyanp 6y ago

My condolences to your family Matt. > Toward that end, bringing more computer science and computer scientists into medicine is one of my goals Besides donating to the appropriate organizations, do you have suggestions for if/how software engineers can contribute to this cause? Are there open source projects in need of contributors or notable organizations that one could work for? Perhaps even a way for technical folks with biology backgrounds to get in touch with and help non-technical families navigate all the jargon?

nextos 6y ago
My condolences too. > Besides donating to the appropriate organizations, do you have suggestions for if/how software engineers can contribute to this cause? There's a massive amount of stuff that CS people can do. For example, many protein features (signal peptides, GPI anchors, transmembrane domains, glycosylation sites, phosphorylation sites, E/R retention signals, etc.) can be modeled as formal languages or as probabilistic formal languages. Literally, that's what they are, amino acid codes. In order to help people with rare diseases, it is very important to identify which variant is knocking off one of those features. In most cases, that's the cause. For example, haemophilia (which is the archetypal rare disease) arises due to a mutation that abolishes a signal peptide in either Factor VIII or Factor IX. Furthermore, it has to be done as quickly and as automatically as possible. Otherwise, it doesn't scale. Most research funding agencies are sadly quite uninterested in rare diseases.
mattmight 6y ago
The Precision Medicine Institute that I now run produces mediKanren: https://github.com/webyrd/mediKanren https://github.com/webyrd/mediKanren It's an open source logical reasoning engine (read: 1960's AI) for drug repurposing that we deploy routinely to help patients. There is always a need for better relationalization of biological data sets that feed such tools too. For example, SemMedDB is really showing its age for NLP of the scientific literature and yet it is still astonishingly useful for helping patients even as is.

jwdunne 6y ago

Ahhh, I’m so, so sorry for your loss. I could never imagine the true pain of losing a child. But, as a father, it must be a hell that you would never wish upon even your worst enemy. My deepest condolences and regrets. I remember reading Bertrand’s story a few years ago. His struggle reached the UK, along with his many achievements and progress. Not many children of his age have such a global reach, especially for such a profound cause. R.I.P

caleb-allen 6y ago

Hey Matt! I've interacted with you on twitter before, but I wanted to thank you again for your work, it has impacted me greatly. One of the first mathematics papers I ever read was your paper on Gödel hashes. Coming from a patchwork self-taught software background it opened my eyes to just how much more there was to CS than "writing code". So, so much more. I still have a copy in my desk! I had dropped out of the U of U's CS program, and this was the first thing that really made me question my decision. I've also admired your work in with Bertrand and I'm hopeful at the legacy it will leave, and at the future of precision medicine. Thanks! Caleb

mattmight 6y ago
Thank you for the kind words -- and also for reminding me about the Godel hashing work!! That was one of the last things I did before the hard pivot into academic medicine.

flobosg 6y ago

I’m sorry to read of Bertrand’s passing. I’ve been following your writing for a while, including your son’s story, and I find nothing short of admirable the lengths that you and your family have gone to ensure that he was loved and cared for. I had a look at your draft and, as someone working in a related field, I’m really impressed by its exhaustiveness. Thank you for sharing your expertise.

mattmight 6y ago
Thank you for looking at the draft! Suggestions and corrections always welcome if you have any.

a_e_k 6y ago

Hi Matt, My wife and I were surprised and sorry when we heard Bertrand's passing last fall. It was a privilege getting to know your family first as neighbors and then as friends back in SLC. I was always humbled at seeing the effort that you and Christina put into moving heaven and earth out of your love for Bertrand. Not everyone can say they've made a lasting positive impact on the world, but you and your family certainly have. - Andrew

mattmight 6y ago
Thank you for the very kind words and friendship. I certainly hope Bertrand's legacy of science in the service of patients continues to grow with time.

Tomte 6y ago

I missed his passing, because I was taking an extended Twitter break. I've always felt a connection to your son, since I translated your article, even though we never met. I often think back to your Quora answer when I feel like a failure, and I try to remember that we can focus and we can re-direct our lives. All the best to you, your wife and your daughter.

mattmight 6y ago
Thank you :)