The human genome can vote and will soon be able to legally drink
First, a warm welcome to all the new readers of this newsletter. Thanks for signing up. I post a mix of original content and links to cool science every week. This week I have one topic I want to talk about.
The human genome at twenty
Twenty years ago, with the release of the draft of the human genome, the largest and most expensive project in biology came to an end. Or did it?
In 2003, a finished version of the sequence of all the letters in the human genome was published. That wasn’t the end either. Just a few weeks ago, twenty years later some of the remaining gaps of the most inaccessible bits and long repeats of DNA were sequenced. That’s over 3 billion chemical letters.
I finally wrote a piece on the human genome at twenty. You can read my column here.
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I had followed the Human Genome project with much interest through the Nineties and I arrived in the U.S. as a Ph.D. student with two suitcases shortly after the two papers with the draft sequence were published in Nature and Science.
On Saturday, we found out that genome editing, can be used to cure human diseases by injecting the CRISPR-Cas9 system into the bloodstream.
The news made some headlines, but I cannot stress how important it is both as a result, and also as a milestone for the future. Genome editing has finally come of age.
I have made no secret of the fact that I think CRISPR is the best thing since sliced bread. It won its discoverers the Nobel Prize in Chemistry last year (though arguably, some others could’ve also received the nod too).
I worked with one of the geniuses responsible for the CRISPR-Cas9 system, Jennifer Doudna, in a professional capacity for a few years (just before and around the time of the CRISPR discovery). And I certainly will have more to say about it in the future.
But if you do read a book on CRISPR, I highly recommend Kevin Davies’ riveting Editing Humanity: The CRISPR Revolution and the New Era of Genome Editing. I look up to Kevin both as an author and a former colleague (and I was fortunate enough to get Kevin to write an endorsement for my book on COVID-19).
If you are short on time or just want a quick explainer, then this video is very good.
CRISPR is the latest revolution in genomics, but sequencing has improved significantly in the last two decades too.
Sequencing has gotten cheaper, a lot cheaper. Think, one million times cheaper.
And as I mention in my book on COVID-19, this is a critical aspect of the current pandemic that we tend to overlook. It took years to get the sequence of HIV, months to get the sequence of SARS, and only a few days to get the sequence of SARS-CoV-2. Quick sequencing has allowed us to track the rise of variants too.
The next generation sequencing market is worth over $10 billion and expected to triple in ten years.
In the healthcare realm fast sequencing is already helping in cancer treatments, precision medicine for people when common drugs don’t work, and in detecting rare diseases in infants.
Nature heralded the promise in rare diseases:
Children born with disorders not readily explained by standard tests can sometimes be diagnosed through genome sequencing and analysis.
On the 10th anniversary of the -omics revolution I wrote in an editorial:
Technological advances over the past decade now allow genomes to be sequenced at breathtaking speed for a fraction of the cost required even a few years ago.
This is certainly not the first or the last time I will write about the human genome either. I’ve written about cancer genomics, precision medicine, and translational science, and will continue to do so.
The halcyon days of the Nineties when bioinformatics was the Next Big Thing alongside the internet were different.
The scientific and social worlds were very different twenty years ago when the draft genome was released. The news media greeted the release of the genome with much fanfare and grandstanding mentioning that it was only a matter of time before most diseases would be conquered. Twenty years later, that still hasn’t happened, of course, because biology is hard and our ability to generate data in the field is often much easier than making sense of it.
We were optimistic about liberal democracies, the power of the internet, globalization, and the innate goodness of people. This was before 9/11 and the War on Terror and before we all started to live in Alternate Realities. This was before the Tech Bubble burst and the Great Recession when markets only went up regardless of true valuation.
2.0 became 3.0 became whatever-the-social-media-mess-is-that-we-have-now. Desktops became laptops became smartphones as cool things to brag about. Programs became apps. Appetizers became apps. Pirating music from Napster became streaming video on multiple devices.
We don’t hear much of Craig Venter anymore and he has been replaced in the smart and rich supervillain pantheon by Elon Musk. We also don’t hear much of Sabeer Bhatia, eligible desi bachelor and cofounder of Hotmail (which got devoured by Microsoft). He seems to have gone the way of Y2K. Bill Gates, on the other hand, has had surprising staying power in headlines through the years.
Bioinformatics has also become mainstream and as argued in a perspective in PLoS Biology entitled “Is bioinformatics dead?” has been supplanted by data science- the so-called fourth paradigm of science.
Make no mistake. There is a tremendous amount of data from fitness trackers to phones to sequencing machines- but keeping track of it, making sense of it, and acting on it remains a challenge.
What else I’ve read this week:
China has been declared malaria-free by the WHO.
Teeth evolved 400 million years ago. Birds lost them 100 million years ago. Frogs keep losing teeth- they have lost them more than 20 times!
“The Australian lungfish has the largest animal genome ever sequenced. The fish has a whopping 43 billion base pairs, around 14 times longer than the human genome.”
Alcohol-related diseases increased as some people drank more during the COVID-19 pandemic.
“There are more individual viral particles inhabiting the oceans alone at any given time than the estimated number of stars in the known Universe — and researchers are rapidly identifying legions of new species. “