I raced with him on his boat. During a gybe once, he was swept overboard and the mainsheet wrapped around his torso. He was dragged through the water, but somehow held onto the rail until I was able to pull him back aboard by the loop on his foullies.
He was an interesting guy. He had been a medic during the Vietnam War, and his old boat, Sorcerer II, became a platform for his Global Ocean Sampling Expedition from 2003 to 2010, which discovered millions of new marine microbial genes.
He collected a lot of friends, and definitely a few enemies, and, in his own strange and remarkable way, seemed to have lived a complete human experience here on Earth.
I'd MUCH rather consider the completeness of my experience based on what I was able to experience, rather than how long I'd lived for.
Sorry for the tangent, but this is a pet peeve of mine. From my perspective, it seems like our modern quest for safety in all things has the effect of wrapping the whole world, and ourselves, in bubble wrap. The goal seems to be to extend that number as far as possible, without regard to how the life that we experience during that period is diminished by all the safeguards.
It bothers me that we've made it a mantra, telling each other "have a safe trip", or "be safe", and so on. I can't remember anyone saying "have the richest experience you can manage".
This is just a tragic way to view the world, on so may levels: 79 is a great run for anybody. And more importantly, Craig Venter did more in 79 years than most people could do in two or three lifetimes. Lastly, of course, life is literally the longest thing you will ever experience, regardless of how long it lasts.
I learned a lot about Craig Venter after reading My Life Decoded in college. Truly an amazing person.
Average life expectancy for males in the US is 76.5 years. During the pandemic it dipped below 74. So he was definitely already on the lucky side of the distribution. He also famously once said: "If you want immortality, do something meaningful with your life."
A complete human experience is to have relatively little time, no point in doing anything if you have 500 years to do it IMO.
Edit: Maybe there wouldn't be nilihism, but I don't think you could get more fulfilled with the extra time. I feel like an insect that lives 24 hours and a shark that lives several hundred have an equal feeling of accomplishment.
You seem to be implying that at after a certain number of years (e.g. 79) you wake up one day and say "I'm fulfilled and have nothing left I'd like to achieve".
As someone who occasionally works with terminal patients, I've never seen that in practice. In reality most people desperately wish that they could carry on living, and have plenty of unfinished business that they'd like to see through. The only exception I've seen is when someone is in so much pain that they just want to end the suffering.
If we turn your argument on its head, a person who dies at 20 is just as fulfilled as a person who dies at 79. So why should anyone bother trying to live a long and healthy life?
More likely that he would live most of those years with compounding mental and physical health issues, quality of life degrading to the point where most would wish for death instead.
This is a common misconception. Namely, that increasing lifespan just means extending the part where your health degrades continuously. That's actually a very unrealistic outcome for life extension technology. In general, the things that cause your health to degrade as you age are interlinked with the things that cause you to die. If you find a way to increase lifespan, chances are you've also found a way to increase healthspan. In fact, all of the best methods we currently have to live longer do exactly that (e.g. exercise, eat healthily, avoid smoking, etc.).
I recognize and appreciate that you likely believe your contribution is one of optimism, but respectfully, I feel ill reading things like this.
Ever heard of Chesterton's fence? I don't believe we are more clever than our mother, the computational machinery of the universe. If we remove death, there will be great consequence.
Heck, it's arguable that the slow decline and death spiral we're in on this planet (empathatically NOT just human well-being metrics here), that this is already due to pushing death back, and systematically allowing power/opportunity to accumulate ever more deeply at scale of the selfish individual...
I know it's cliche, but if he knew he (any of us) knew we might live to 790, would we live life so fully?
I kind of think that's what is behind some people versus others—those that have an intrinsic, constant sense of the brevity of life are the ones that try to experience life to the fullest.
There is absolutely zero proof that more years would mean more accomplishments. Bad assumptions are bad assumptions even in fantasy land. No-brainer indeed.
When I was a kid, I saw an interview with him on 60 minutes. He talked about how he had dropped out of college after letting go of his dreams of being an olympic swimmer. He then served as a medic in Vietnam, and tried to commit suicide by jumping off a navy ship (but of course survived on account of being a near olympic class athlete. With a full head of hair).
Later I saw him in real life give a talk at Cornell University with his old friend geneticist Andy Clark on the human genome. Dude was larger than life, tall, and bald.
A few years later, I moved to San Diego, and got into surfing. Was reading a surfing website, and boom, Craig Venter pops up in an ad for luxury watches! Sailing in the ocean and rocking a Jaeger-LeCoultre watch that was probably worth more than my grad stipend at the time..
A few years after that and I interviewed at one of his companies, Synthetic Genomics. The bioinformatics team had their heads spinning from the number of pivots the company had been doing. They had gone from biofuel production to working on genetically engineering pigs to produce kidneys that could be donated to humans. Lo and behold, within a few years, someone got the idea to actually work.
Basically Venter and his accomplishments have been the background to my entire adult career in biology, genetics, bioinformatics and machine learning.
RIP Craig Venter! Sometimes to get great science to happen you need larger than life personalities!
Great stories. I asked him about the pig thing, after he pivoted from biofuels (I think they raised $150m from Exxon). If I recall he teamed up with another infamous founder Martin, now Martine, Rothblatt who created SeriusXM and United Therapeutics.
Somewhat ironically, he'd spent the last years of his life working on prolonging life [1], and was selling a $25,000 "proactive healthcare service" consultation to anyone who could afford it [2].
1: The company's website, humanlongevity dot com, seems to have been compromised, and as "captcha" will try to have you install a Trojan. So here's the Wikipedia page instead: https://en.wikipedia.org/wiki/Human_Longevity
Craig Venter was famously involved in the Human Genome Project. He announced the first draft of the human genome alongside President Clinton and Francis Collins.
"Involved" in the sense that he took the public data, added in a small amount of his own privately generated data and was trying to get the first assembly. The scientists in the Human Genome Project thought he was going to try to patent the whole thing so others would have to pay him. Back then, it was not clear what was and was not patentable.
So the involvement was in spurring the Human Genome Project to race to an assembly, a massive computational problem that hadn't been fully planned for by the public effort:
It was essentially a jigsaw puzzle, and Venters insight was that computational power was just as important to the project as biology. The Human Genome Project was essentially trying to sequence the human genome by finding large chunks of DNA and fitting them together like a jigsaw, finding which bits unambiguously matched up.
Venters idea was that you could do the same with small chunks of DNA, if you approached it as a computational problem and used computers to try/evaluate/reject the millions of ways the pieces could be fit together. So he recruited mathematicians, computer scientists etc and got them to work on the problem. He speeded the project up massively by making the biology bits simpler (smaller pieces of DNA) and shifting the effort to the computational problem.
So he made a big difference. And his insight that it was a computational problem is kindof obvious now but it wasn't obvious 25 years ago.
It was very obvious that it was a computational problem, all DNA analysis was highly computational then, as it is now. His guess was that ~500bp fragments would be enough to get a usable assembly.
But the Human Genome Project's approach of reconstructing larger chunks first was also feasible, and produced an assembly too, with a heroic four weeks effort of a former game programmer who even built cluster software at the same time.
He wasn't the only one who saw the problem computationally. Famously, the mathematician Michael Waterman sat on the other-side of the race for the human genome.
Involved in the sense that his method worked and the one the Human Genome Project insisted on didn't. In the end, they had to use his method to catch up enough that everybody could pretend they did it together and collaboratively -- even though Venter clearly got there first. Venter deserved a Nobel Prize for that and, quite frankly, the Human Genome Project guys deserved a firing.
Craig Venter had his genome sequenced in 2007. It was the first individual human genome that was sequenced and released publicly.
The human reference genome is ~70% from a man with African and European ancestry who lived somewhere around Buffalo, NY. Most of the rest is from ~20 other individuals in the same area. They were supposed to sequence the samples more evenly, but apparently there were some technical reasons that made them prioritize a single sample.
I worked on this back in the 90s and there multiple data sets being used. We had one that was Mennonite family with like 5 living generations and 100ish individuals.
It gets a little fuzzy when talking about Celera and the human genome project. The two efforts were very much competitors, but there was a lot of crossover (mainly from Celera pulling in the public data).
But, Venter claimed that he was the a good chunk of the genome that Celera sequenced, so I think it's fair to say he was one of the people included in the draft human genome (at least the Celera version of it).
> After leaving Celera in 2002, Venter announced that much of the genome that had been sequenced there was his own. [1]
I am not sure what is "the draft human genome" you are talking about. Two separate human genomes were published in 2001: the HGP genome and the celera genome. The HGP genome then didn't use Venter DNA. It evolved into the current human reference genome. The celera genome contained Venter DNA but it has been completely forgotten nowadays.
He was pretty shockingly an entrepreneur and inventor in all the best ways,’in a field dominated by very cautious scientists (who are great too, but who likely never would have gotten the genome sequenced within 10-20 years of when he did it). It was basically the Apollo Project in a field which was more like 1980s NASA in culture.
> in a field dominated by very cautious scientists (who are great too, but who likely never would have gotten the genome sequenced within 10-20 years of when he did it).
I did a bio undergrad and one of my professors was involved. She was adamant that the Human Genome Project finished ahead of Celera and that the HGP published reference data that Venter and team fundamentally relied upon to even have their shotgun approach work.
i worked for ham smith and my understanding through him is that both sides relied on data that the other produced.
here are technical details, both were more or less independent, the celera sequence did include data from the other side as useful reference points but the assembly would have happened without it.
https://pmc.ncbi.nlm.nih.gov/articles/PMC123615/
iiuc it was hamilton smith who insisted that shotgun sequencing would work. the nih side insisted on primer walking until celera started assembling the genome so rapidly that the nih had to get in on shotgun too
I belive you are mixing assembling the genome by combining sequences of individual, overlapping inserts of cosmids, fosmids, PACs and BACs (bacterial vectors with human DNA inserts of 40-150kbp) to whole genome shotgun.
The inserts of the above bacterial vectors were sequenced using shotgun, but the gaps in the sequence were closed with custom primers.
I remember being in 5th grade and hearing about the Human Genome Project. It was presented as a radical undertaking. 30 years later, look how far we've come. Just the other day I was reading about the UK Biobank leaks (https://news.ycombinator.com/item?id=47875843), and it was mentioned that some large number of complete human genomes were leaking out. And I thought wow, back in the day people thought Craig Venter was out there.
Sad news. I met Craig very briefly at a conference probably a decade back. I pretty much was a self-study in genetics at the time... so let's just say I wasn't in Craig's league. Despite this he was very engaged and took the time for a very thoughtful chat.
A world-class (and possibly universe-class) egotist who published the first diploid human genome sequence. It was his own DNA. He did not stop at broadcasting his achievement to a human audience: "Since my own genome was sequenced, my software has been broadcast into space in the form of electromagnetic waves, carrying my genetic information far beyond Earth."
I met Craig about a year ago or so at a synthetic biology conference. Even though his institute was the one which created the first synthetic cell, he pretty much just talked about how disappointing it was that we couldn't engineer the ribosome more. Was a funny memory :) guess you always want more once you do something great.
At the time they announced the full genome sequence I was an intern in molecular biology. We had a thermocycler in the lab and I had to book my slot on a paper agenda. I remember this portrait of him in front of multiple racks each plenty of thermocyclers. He taught me something about scale and he proved that sometimes it's worth looking at what you have and ask what if I could 200x this. In software this might seem obvious with GPU arrays etc.. but when you are trained in a wet lab and the instrument paper agenda, I wonder if we could have more breakthroughs in life sciences if we could use some bruteforce now and then. RIP
I'm a statistician. My wife does basic (biological) science. Almost every time she asks my advice on an experiment I want to tell her to 10x the sample size. But the academic community has certain ideas about how big sample sizes should be, and trying to use radically larger samples runs into all sorts of barriers ranging from ethics concerns (for animal experiments) to funding.
At the end of the day there's only so much you can learn from a sample size of 12. I'm not sure it's more ethical to have a bunch of wasted experiments with 12 mice each where you don't learn anything than to use 100 mice and actually have statistical power to identify something other than the hugest effect sizes.
Lack of appropriate funding leads to cutting corners to the point that some results may not be worth the price of the paper to describe them. I had a passing experience with epigenetics. Even experiments with basically free of ethics issues cell lines could be screwed up by using single end, too short sequencing reads. Combined with too low coverage, less than perfect controls it gives the input data I which the state of the art peak callers will just throw the towel. So the "trick" is to use some way more forgiving peak caller and get a rather crappy results.
Using the outdated human genome assembly (hg19), and old genome mapping programs just puts an extra cherry on the cake...
I just read your comment and also just discovered that I have aphantasia.
Edit: Doing more reading. Weird. I don't have problems with autobiographical memory or facial recognition. I'm totally dogshit at remembering peoples _names_ though but I'll recognize faces of people I've barely met for decades.
RIP. He was an amazing human. I worked for a time at JCVI when it was in Rockville, shortly after he had left Celera Genomics. He led a team that did something which was considered intractably difficult-- sequencing whole genomes. Then he did it again with global ocean sampling and synthetic genomics and other things. That is not to say that "he did it single-handedly", Venter was a hybrid of scientific and organizational talent that was able to make this stuff happen by coordinating stuff that's super hard to coordinate.
I read his autobiography. Besides the genome work, which undoutedly was of historical importance, one thing that impressed me the most, was how he slept on the surgery table in the opersting room after cleaning blood from it in Vietnam. Somehow it was safer than in the barracks. I was like wow, this guy definitely knew how to think outside the box!
He seems like a complicated character, but like the article says “Quod licit Jovis, non licit bovis” (“What is permitted Jove is not permitted a cow.”).
Woah - I just drove by the JCV institute in La Jolla yesterday and felt thinking that the organization was really monumental to synthetic biology. Rest in peace
This is (specifically) unfortunate - let me explain why.
Some comments are critical of Craig; this may be understandable as he always liked having media focus on either his personality or on what he is/was doing.
Craig was, in my opinion, mostly a business person first, scientist second, but I think he was also genuinely fascinated and interested in science. Others already brought the example of the human genome project (HGP: https://en.wikipedia.org/wiki/Human_Genome_Project, although I remember it as HUGO - strange how Wikipedia uses another name for this. I can't say for certain whether my memory fails me, or Wikipedia seems to "forget". Anyway.).
People also stated how the scientists back then got scared by Craig, aka "he will finish before we do, we are too slow", or "he will patent the ESTs and sell it, we must hurry up" (https://en.wikipedia.org/wiki/Expressed_sequence_tag). This was in the 1990s primarily, late 1990s. Now - I leave everyone to their thoughts here, but in my opinion, Craig kind of was like a destabilizer in a positive manner, in that he got scientists to focus more. Kind of like a shocker system in a defibrillator. A defibrillator isn't extremely enjoyable, but the use case is to try to get a halted heart to pulse again (in the ideal outcome). In some ways I think Craig kind of was like that for the larger scientific community. He became famous during the human genome research, even if media attention was also driven here, and lateron in synthetic biology (first synthetic cell) and some more. One can easily say that everything would have been done or discovered without Craig, that's fine, but in many ways he kind of also acted as an accelerator here. Today research-to-product is really quite rapid; in the 1990s my memory kind of says that we all were slower back then. And while those changes may all have come without Craig too, I think he kind of pushed others towards more effective speed too - perhaps not always positive, but in some cases I think Craig was acting as an accelerator. Which I think is not a net-negative per se. (Also, as for patenting information such as DNA - I am of course, as any logical person, absolutely against that, but the problem here is not Craig, the problem is that the USA has a completely broken patent system. For instance you can patent something but then forbid others from using it AND you yourself also don't use it. I fail to see how this benefits anyone, other than market control and market competition. That should be different. Many more things too, but this is not about the patent situation; it is about critisizing Craig for patents. Numerous others benefit from the patent situation, so why are these not critisized too?)
The way I describe it is that his actions (even before the human genome) clearly showed that the individual-driven, "artisinal" sequencing was far less productive.
When I started in computational biology (1994) the E.Coli genome was not even done, and there was one lab doing the work, very slowly. You'd FTP to some server every week or so and download a few more kilobytes. It really felt like slow science (https://en.wikipedia.org/wiki/Slow_science). Venter helped convince people (Lander was another) that sequencing was an industrial process that could be accelerated significantly.
* I can't say for certain whether my memory fails me, or Wikipedia seems to "forget". *
Sure it does. Some 'editor' decides the article violates some arcane 'rule', or doesn't like the content for some reason, or doesn't like you for some reason, and poof.
I raced with him on his boat. During a gybe once, he was swept overboard and the mainsheet wrapped around his torso. He was dragged through the water, but somehow held onto the rail until I was able to pull him back aboard by the loop on his foullies.
He was an interesting guy. He had been a medic during the Vietnam War, and his old boat, Sorcerer II, became a platform for his Global Ocean Sampling Expedition from 2003 to 2010, which discovered millions of new marine microbial genes.
He collected a lot of friends, and definitely a few enemies, and, in his own strange and remarkable way, seemed to have lived a complete human experience here on Earth.
Only 79… far from a complete human experience. It’s incredibly sad how little time we get here, especially the best of us.
I'd MUCH rather consider the completeness of my experience based on what I was able to experience, rather than how long I'd lived for.
Sorry for the tangent, but this is a pet peeve of mine. From my perspective, it seems like our modern quest for safety in all things has the effect of wrapping the whole world, and ourselves, in bubble wrap. The goal seems to be to extend that number as far as possible, without regard to how the life that we experience during that period is diminished by all the safeguards.
It bothers me that we've made it a mantra, telling each other "have a safe trip", or "be safe", and so on. I can't remember anyone saying "have the richest experience you can manage".
The longer your lifespan, the more chances you have to waste chunks of it in a rut of zero experience, but have time to work your way out of it.
At just 60 ~ 90 years, a rut of a single decade can take up > 15% of your lifespan.
This is just a tragic way to view the world, on so may levels: 79 is a great run for anybody. And more importantly, Craig Venter did more in 79 years than most people could do in two or three lifetimes. Lastly, of course, life is literally the longest thing you will ever experience, regardless of how long it lasts.
I learned a lot about Craig Venter after reading My Life Decoded in college. Truly an amazing person.
>79 is a great run for anybody
Average life expectancy for males in the US is 76.5 years. During the pandemic it dipped below 74. So he was definitely already on the lucky side of the distribution. He also famously once said: "If you want immortality, do something meaningful with your life."
> Only 79… far from a complete human experience
It seems you’re judging his life solely on the age when he died rather than all the things he did.
I think he’s really just trying to spur your imagination into imagining if someone like that had lived longer.
Anyway, this conversation has been had repeatedly. Many people seem to be unable to imagine that positive benefit of much longer lives.
Suppose that’s why “Science advances one funeral at a time.”
Imagine what a guy like that could do with 79 more years... or 10x of that.
It's not that outlandish: sharks, turtles, etc get far more years than we do.
It's shocking all billionaires aren't devoting all their resources to solving this cosmic crime against humanity.
A complete human experience is to have relatively little time, no point in doing anything if you have 500 years to do it IMO.
Edit: Maybe there wouldn't be nilihism, but I don't think you could get more fulfilled with the extra time. I feel like an insect that lives 24 hours and a shark that lives several hundred have an equal feeling of accomplishment.
You seem to be implying that at after a certain number of years (e.g. 79) you wake up one day and say "I'm fulfilled and have nothing left I'd like to achieve".
As someone who occasionally works with terminal patients, I've never seen that in practice. In reality most people desperately wish that they could carry on living, and have plenty of unfinished business that they'd like to see through. The only exception I've seen is when someone is in so much pain that they just want to end the suffering.
If we turn your argument on its head, a person who dies at 20 is just as fulfilled as a person who dies at 79. So why should anyone bother trying to live a long and healthy life?
500 years is as arbitrary a number as 79 is.
A Craig Venter that lives (a healthy life) to 158 is quite likely to accomplish at least 1 more great thing than one who lives to 79.
More likely that he would live most of those years with compounding mental and physical health issues, quality of life degrading to the point where most would wish for death instead.
This is a common misconception. Namely, that increasing lifespan just means extending the part where your health degrades continuously. That's actually a very unrealistic outcome for life extension technology. In general, the things that cause your health to degrade as you age are interlinked with the things that cause you to die. If you find a way to increase lifespan, chances are you've also found a way to increase healthspan. In fact, all of the best methods we currently have to live longer do exactly that (e.g. exercise, eat healthily, avoid smoking, etc.).
What an un-hacker ethos: the idea is to continuously fix problems so that, if anything, quality of life improves from year to year.
"un-hacker ethos". I'll put that on the shelf next to "it's only an engineering problem" and "assume a spherical cow".
I recognize and appreciate that you likely believe your contribution is one of optimism, but respectfully, I feel ill reading things like this.
Ever heard of Chesterton's fence? I don't believe we are more clever than our mother, the computational machinery of the universe. If we remove death, there will be great consequence.
Heck, it's arguable that the slow decline and death spiral we're in on this planet (empathatically NOT just human well-being metrics here), that this is already due to pushing death back, and systematically allowing power/opportunity to accumulate ever more deeply at scale of the selfish individual...
Why didn't anybody warn Alexander Fleming about Chesterton's fence?
I know it's cliche, but if he knew he (any of us) knew we might live to 790, would we live life so fully?
I kind of think that's what is behind some people versus others—those that have an intrinsic, constant sense of the brevity of life are the ones that try to experience life to the fullest.
Yes. A lot of people would live life so fully if they knew they had 790 years: in fact more so.
Right now the most ambitious projects people start barely scratch a decade or two.
They might be less willing to get on a sail boat where they could be swept off and nearly drown.
Thiel might be, but Thiel is also someone who gets infinitely mocked
With that having been said a lot of the health industry is fraud
Looking at his life. This is as complete human experience as we can hope to get.
What is sad is having a world view where the value of a human life is duration, not accomplishment.
If you value accomplishment, then adding more years to accomplish more things is a no-brainer
There is absolutely zero proof that more years would mean more accomplishments. Bad assumptions are bad assumptions even in fantasy land. No-brainer indeed.
When I was a kid, I saw an interview with him on 60 minutes. He talked about how he had dropped out of college after letting go of his dreams of being an olympic swimmer. He then served as a medic in Vietnam, and tried to commit suicide by jumping off a navy ship (but of course survived on account of being a near olympic class athlete. With a full head of hair).
Later I saw him in real life give a talk at Cornell University with his old friend geneticist Andy Clark on the human genome. Dude was larger than life, tall, and bald.
A few years later, I moved to San Diego, and got into surfing. Was reading a surfing website, and boom, Craig Venter pops up in an ad for luxury watches! Sailing in the ocean and rocking a Jaeger-LeCoultre watch that was probably worth more than my grad stipend at the time..
A few years after that and I interviewed at one of his companies, Synthetic Genomics. The bioinformatics team had their heads spinning from the number of pivots the company had been doing. They had gone from biofuel production to working on genetically engineering pigs to produce kidneys that could be donated to humans. Lo and behold, within a few years, someone got the idea to actually work.
Basically Venter and his accomplishments have been the background to my entire adult career in biology, genetics, bioinformatics and machine learning.
RIP Craig Venter! Sometimes to get great science to happen you need larger than life personalities!
Great stories. I asked him about the pig thing, after he pivoted from biofuels (I think they raised $150m from Exxon). If I recall he teamed up with another infamous founder Martin, now Martine, Rothblatt who created SeriusXM and United Therapeutics.
Somewhat ironically, he'd spent the last years of his life working on prolonging life [1], and was selling a $25,000 "proactive healthcare service" consultation to anyone who could afford it [2].
1: The company's website, humanlongevity dot com, seems to have been compromised, and as "captcha" will try to have you install a Trojan. So here's the Wikipedia page instead: https://en.wikipedia.org/wiki/Human_Longevity
2: https://fortune.com/2017/02/21/craig-venter-human-longevity/
It appears he had cancer and something about the treatment caused his death.
Craig Venter was famously involved in the Human Genome Project. He announced the first draft of the human genome alongside President Clinton and Francis Collins.
"Involved" in the sense that he took the public data, added in a small amount of his own privately generated data and was trying to get the first assembly. The scientists in the Human Genome Project thought he was going to try to patent the whole thing so others would have to pay him. Back then, it was not clear what was and was not patentable.
So the involvement was in spurring the Human Genome Project to race to an assembly, a massive computational problem that hadn't been fully planned for by the public effort:
https://archive.is/2022.02.14-091753/https://www.nytimes.com...
It was essentially a jigsaw puzzle, and Venters insight was that computational power was just as important to the project as biology. The Human Genome Project was essentially trying to sequence the human genome by finding large chunks of DNA and fitting them together like a jigsaw, finding which bits unambiguously matched up.
Venters idea was that you could do the same with small chunks of DNA, if you approached it as a computational problem and used computers to try/evaluate/reject the millions of ways the pieces could be fit together. So he recruited mathematicians, computer scientists etc and got them to work on the problem. He speeded the project up massively by making the biology bits simpler (smaller pieces of DNA) and shifting the effort to the computational problem.
So he made a big difference. And his insight that it was a computational problem is kindof obvious now but it wasn't obvious 25 years ago.
https://en.wikipedia.org/wiki/Shotgun_sequencing
How Perl Saved the Human Genome Project: https://bioperl.org/articles/How_Perl_saved_human_genome.htm...
It was very obvious that it was a computational problem, all DNA analysis was highly computational then, as it is now. His guess was that ~500bp fragments would be enough to get a usable assembly.
But the Human Genome Project's approach of reconstructing larger chunks first was also feasible, and produced an assembly too, with a heroic four weeks effort of a former game programmer who even built cluster software at the same time.
He wasn't the only one who saw the problem computationally. Famously, the mathematician Michael Waterman sat on the other-side of the race for the human genome.
He was known informally as the Venterpillar.
Involved in the sense that his method worked and the one the Human Genome Project insisted on didn't. In the end, they had to use his method to catch up enough that everybody could pretend they did it together and collaboratively -- even though Venter clearly got there first. Venter deserved a Nobel Prize for that and, quite frankly, the Human Genome Project guys deserved a firing.
i believe he also was the human genome project, he arranged to have one of the samples be him
Craig Venter had his genome sequenced in 2007. It was the first individual human genome that was sequenced and released publicly.
The human reference genome is ~70% from a man with African and European ancestry who lived somewhere around Buffalo, NY. Most of the rest is from ~20 other individuals in the same area. They were supposed to sequence the samples more evenly, but apparently there were some technical reasons that made them prioritize a single sample.
I worked on this back in the 90s and there multiple data sets being used. We had one that was Mennonite family with like 5 living generations and 100ish individuals.
"RP11" is that man from Buffalo who comprises 74% of the human reference genome [1].
[1] https://undark.org/2024/07/09/informed-consent-human-genome-...
The majority of the genomic sequencing done by Celera for their initial released draft genome was on Venter's sample.
You are confused by the human genome project vs the celera genome project. No, the human genome project didn't include his sample.
It gets a little fuzzy when talking about Celera and the human genome project. The two efforts were very much competitors, but there was a lot of crossover (mainly from Celera pulling in the public data).
But, Venter claimed that he was the a good chunk of the genome that Celera sequenced, so I think it's fair to say he was one of the people included in the draft human genome (at least the Celera version of it).
> After leaving Celera in 2002, Venter announced that much of the genome that had been sequenced there was his own. [1]
[1] https://www.technologyreview.com/2007/09/04/223919/craig-ven...
I am not sure what is "the draft human genome" you are talking about. Two separate human genomes were published in 2001: the HGP genome and the celera genome. The HGP genome then didn't use Venter DNA. It evolved into the current human reference genome. The celera genome contained Venter DNA but it has been completely forgotten nowadays.
Yes. For folks looking for more:
* Celera genome, first published 2004: https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_000002115.1...
* Human reference genome, first published 2001 and most recently updated in 2022: https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_000001405.4...
Yes, his was the first complete genome ever sequenced (by a private entity).
This reminds me of the interesting fact that
> Linnaeus is designated as the type specimen for the human species, Homo sapiens.
https://en.wikipedia.org/wiki/Carl_Linnaeus
He was pretty shockingly an entrepreneur and inventor in all the best ways,’in a field dominated by very cautious scientists (who are great too, but who likely never would have gotten the genome sequenced within 10-20 years of when he did it). It was basically the Apollo Project in a field which was more like 1980s NASA in culture.
> in a field dominated by very cautious scientists (who are great too, but who likely never would have gotten the genome sequenced within 10-20 years of when he did it).
I did a bio undergrad and one of my professors was involved. She was adamant that the Human Genome Project finished ahead of Celera and that the HGP published reference data that Venter and team fundamentally relied upon to even have their shotgun approach work.
i worked for ham smith and my understanding through him is that both sides relied on data that the other produced.
here are technical details, both were more or less independent, the celera sequence did include data from the other side as useful reference points but the assembly would have happened without it. https://pmc.ncbi.nlm.nih.gov/articles/PMC123615/
iiuc it was hamilton smith who insisted that shotgun sequencing would work. the nih side insisted on primer walking until celera started assembling the genome so rapidly that the nih had to get in on shotgun too
I belive you are mixing assembling the genome by combining sequences of individual, overlapping inserts of cosmids, fosmids, PACs and BACs (bacterial vectors with human DNA inserts of 40-150kbp) to whole genome shotgun. The inserts of the above bacterial vectors were sequenced using shotgun, but the gaps in the sequence were closed with custom primers.
No, at initial release, the human genome from the NIH side was done by bac-to-bac, not by shotgun.
RIP Craig Venter.
I remember being in 5th grade and hearing about the Human Genome Project. It was presented as a radical undertaking. 30 years later, look how far we've come. Just the other day I was reading about the UK Biobank leaks (https://news.ycombinator.com/item?id=47875843), and it was mentioned that some large number of complete human genomes were leaking out. And I thought wow, back in the day people thought Craig Venter was out there.
Thank you Craig Venter!
Sad news. I met Craig very briefly at a conference probably a decade back. I pretty much was a self-study in genetics at the time... so let's just say I wasn't in Craig's league. Despite this he was very engaged and took the time for a very thoughtful chat.
A world-class (and possibly universe-class) egotist who published the first diploid human genome sequence. It was his own DNA. He did not stop at broadcasting his achievement to a human audience: "Since my own genome was sequenced, my software has been broadcast into space in the form of electromagnetic waves, carrying my genetic information far beyond Earth."
I can't think of a better manifestation of the biological male imperitive.
Interesting comment from him:
"
SPIEGEL: So you don't consider Collins to be a true scientist?
Venter: Let's just say he's a government administrator.
"
https://www.science.org/content/blog-post/craig-venter-venti...
I met Craig about a year ago or so at a synthetic biology conference. Even though his institute was the one which created the first synthetic cell, he pretty much just talked about how disappointing it was that we couldn't engineer the ribosome more. Was a funny memory :) guess you always want more once you do something great.
At the time they announced the full genome sequence I was an intern in molecular biology. We had a thermocycler in the lab and I had to book my slot on a paper agenda. I remember this portrait of him in front of multiple racks each plenty of thermocyclers. He taught me something about scale and he proved that sometimes it's worth looking at what you have and ask what if I could 200x this. In software this might seem obvious with GPU arrays etc.. but when you are trained in a wet lab and the instrument paper agenda, I wonder if we could have more breakthroughs in life sciences if we could use some bruteforce now and then. RIP
I'm a statistician. My wife does basic (biological) science. Almost every time she asks my advice on an experiment I want to tell her to 10x the sample size. But the academic community has certain ideas about how big sample sizes should be, and trying to use radically larger samples runs into all sorts of barriers ranging from ethics concerns (for animal experiments) to funding.
At the end of the day there's only so much you can learn from a sample size of 12. I'm not sure it's more ethical to have a bunch of wasted experiments with 12 mice each where you don't learn anything than to use 100 mice and actually have statistical power to identify something other than the hugest effect sizes.
Lack of appropriate funding leads to cutting corners to the point that some results may not be worth the price of the paper to describe them. I had a passing experience with epigenetics. Even experiments with basically free of ethics issues cell lines could be screwed up by using single end, too short sequencing reads. Combined with too low coverage, less than perfect controls it gives the input data I which the state of the art peak callers will just throw the towel. So the "trick" is to use some way more forgiving peak caller and get a rather crappy results. Using the outdated human genome assembly (hg19), and old genome mapping programs just puts an extra cherry on the cake...
I'm in lab automation, we've come a long way from paper schedules (although those still get plenty of use :) )
RIP. I absolutely loved the book A Life Decoded: My Genome: My Life by J. Craig Venter.
I went to a talk of his once and discovered that I also have aphantasia. Seemed like a genuinely nice guy the little I interacted with him. RIP
I just read your comment and also just discovered that I have aphantasia.
Edit: Doing more reading. Weird. I don't have problems with autobiographical memory or facial recognition. I'm totally dogshit at remembering peoples _names_ though but I'll recognize faces of people I've barely met for decades.
Sad news, I’ve worked at HumanLongevity and got to interact with Craig several times. He was a legend and truly will be missed.
RIP. He was an amazing human. I worked for a time at JCVI when it was in Rockville, shortly after he had left Celera Genomics. He led a team that did something which was considered intractably difficult-- sequencing whole genomes. Then he did it again with global ocean sampling and synthetic genomics and other things. That is not to say that "he did it single-handedly", Venter was a hybrid of scientific and organizational talent that was able to make this stuff happen by coordinating stuff that's super hard to coordinate.
Great scientist, but Celera was the worst financial investment I ever made.
I read his autobiography. Besides the genome work, which undoutedly was of historical importance, one thing that impressed me the most, was how he slept on the surgery table in the opersting room after cleaning blood from it in Vietnam. Somehow it was safer than in the barracks. I was like wow, this guy definitely knew how to think outside the box!
Sad news. This video https://www.youtube.com/watch?v=3E25jgPgmzk was interesting back in the day
Oh no! I did an internship at his lab when I went to UCSD. RIP.
Just read this review of his autobiography: https://www.atlassociety.org/post/what-shall-we-do-with-a-bu...
He seems like a complicated character, but like the article says “Quod licit Jovis, non licit bovis” (“What is permitted Jove is not permitted a cow.”).
That's unexpected. He was only 80, and as I understand it still working.
My his memory be a blessing.
Woah - I just drove by the JCV institute in La Jolla yesterday and felt thinking that the organization was really monumental to synthetic biology. Rest in peace
This is (specifically) unfortunate - let me explain why.
Some comments are critical of Craig; this may be understandable as he always liked having media focus on either his personality or on what he is/was doing.
Craig was, in my opinion, mostly a business person first, scientist second, but I think he was also genuinely fascinated and interested in science. Others already brought the example of the human genome project (HGP: https://en.wikipedia.org/wiki/Human_Genome_Project, although I remember it as HUGO - strange how Wikipedia uses another name for this. I can't say for certain whether my memory fails me, or Wikipedia seems to "forget". Anyway.).
People also stated how the scientists back then got scared by Craig, aka "he will finish before we do, we are too slow", or "he will patent the ESTs and sell it, we must hurry up" (https://en.wikipedia.org/wiki/Expressed_sequence_tag). This was in the 1990s primarily, late 1990s. Now - I leave everyone to their thoughts here, but in my opinion, Craig kind of was like a destabilizer in a positive manner, in that he got scientists to focus more. Kind of like a shocker system in a defibrillator. A defibrillator isn't extremely enjoyable, but the use case is to try to get a halted heart to pulse again (in the ideal outcome). In some ways I think Craig kind of was like that for the larger scientific community. He became famous during the human genome research, even if media attention was also driven here, and lateron in synthetic biology (first synthetic cell) and some more. One can easily say that everything would have been done or discovered without Craig, that's fine, but in many ways he kind of also acted as an accelerator here. Today research-to-product is really quite rapid; in the 1990s my memory kind of says that we all were slower back then. And while those changes may all have come without Craig too, I think he kind of pushed others towards more effective speed too - perhaps not always positive, but in some cases I think Craig was acting as an accelerator. Which I think is not a net-negative per se. (Also, as for patenting information such as DNA - I am of course, as any logical person, absolutely against that, but the problem here is not Craig, the problem is that the USA has a completely broken patent system. For instance you can patent something but then forbid others from using it AND you yourself also don't use it. I fail to see how this benefits anyone, other than market control and market competition. That should be different. Many more things too, but this is not about the patent situation; it is about critisizing Craig for patents. Numerous others benefit from the patent situation, so why are these not critisized too?)
The way I describe it is that his actions (even before the human genome) clearly showed that the individual-driven, "artisinal" sequencing was far less productive.
When I started in computational biology (1994) the E.Coli genome was not even done, and there was one lab doing the work, very slowly. You'd FTP to some server every week or so and download a few more kilobytes. It really felt like slow science (https://en.wikipedia.org/wiki/Slow_science). Venter helped convince people (Lander was another) that sequencing was an industrial process that could be accelerated significantly.
* I can't say for certain whether my memory fails me, or Wikipedia seems to "forget". *
Sure it does. Some 'editor' decides the article violates some arcane 'rule', or doesn't like the content for some reason, or doesn't like you for some reason, and poof.
I attended a lecture of his once. One of the topics was emailing biological viruses. Svante Pääbo was there too.
A giant in biology. This is a real loss.
The bad boy of science!
One of the few people who could give a TED Talk that wasn't complete BS. It actually had substance and some thought-provoking ideas.
You can definitely say that ego was the fountainhead of progress for him!