"De novo" means "starting from scratch", that is: you type the desired sequence into a computer, and the synthesize it.
The "de novo" part is important, because it distinguishes this from the already well solved problem of duplicating DNA from an existing DNA template, which is what all our cells do daily, and which can already be done very efficiently in vitro with polymerase chain reaction.
Many startup companies are attempting to create more efficient de novo synthesis methods:
Notably, the dream of most of those companies is to have a machine that sits on a lab bench, which synthesises whatever you want.
TODO current de novo synthesis costs/time to delivery after ordering a custom sequence.
The initial main applications are likely going to be:but the real pipe dream is building and bootstraping entire artificial chromosomes
- polymerase chain reaction primers (determine which region will be amplified
- creating a custom sequence to be inserted in a plasmid, i.e. artificial gene synthesis
News coverage:
- 2023-03 twitter.com/sethbannon/status/1633848116154880001
AnsaBio created the world's longest DNA oligo produced using de novo synthesis! 1,005 bases! 99.9% stepwise yield
- 2020-10-05 www.nature.com/articles/s41587-020-0695-9 "Enzymatic DNA synthesis enters new phase"
A software that implements some database system, e.g. PostgreSQL or MySQL are two (widely extended) SQL implementations.
Marc Verdiell is a human electrical engineer best known for being the creator and host of the CuriousMarc YouTube channel.
Marc made $58.4m from the sale of LightLogic, an optoelectronics company he founded, to Intel in 2001:
- www.courthousenews.com/inventor-barred-from-proceeds-of-intel-buyout/. His full name is actualy Jean-Marc Verdiell. ppubs.uspto.gov/dirsearch-public/print/downloadPdf/20160274316 also suggests he may have a seldom used middle name "André", though that would be unusual in French custom
- mergr.com/intel-acquires-lightlogic
2.5.0 manual prebuilt download install on Ubuntu 20.04 just worked. Launch directly from unzip without install. Play with examples under
install/Examples
Their docs are a reasonable way to learn Csound: cabbageaudio.com/docs/introduction/
Generate public private key, test encrypt and test decrypt:
# Create your pubkey.
gpg --gen-key
gpg --armor --output pubkey.gpg --export <myemail>
# Encrypt using someone's pubkey.
gpg --import pubkey2.gpg
echo 'hello world' > hello.txt
gpg --output hello.txt.gpg --encrypt --recipient <other-email> hello.txt
# Double check it is not plaintext in the encrypted message.
grep hello hello.txt.gpg
# Decrypt.
gpg --output hello.decrypt.txt --decrypt --recipient <myemail> hello.txt.gpg
diff -u hello.decrypt.txt hello.txt
Sponsor Ciro Santilli's work on OurBigBook.com by Ciro Santilli 35 Updated 2025-01-10 +Created 1970-01-01
Ciro Santilli is actively looking for donations and contracts so he can continue to work full time on OurBigBook.com sustainably, and develop free hardcore university-level STEM education for all ages!
At 100k USD, I quit my job to work full time on it for one year. During this year I will use my contacts with STEM students of a world leading university near where I live and solve as many of their problem sheets as possible, mostly by referring to OurBigBook.com articles I'll be writing. The goal is to get as much STEM knowledge as possible into the world, and highlight how flawed presencial and sequential Higher Education is, while positioning OurBigBook.com as an alternative way to organize humanity's knowledge. Quite grand.
Status: ~144k / 200k USD reached. 1st year locked in and started 1st June 2024 to 31st May 2025[ref], 2nd year stretch goal open. A second year greatly improve chances of success: year one I solve a bunch of courses, year two I come guns blazing with the content and expand further. Donation breakdown:More details: Section "Accounting method"
- 2024-03-18: $126,352 (!!!): anonymous 1000 Monero donation to self-custody wallet. Further comments: 1000 Monero donation.
- 2024-03-13: $1,375: anonymous 10 Monero donation to self-custody wallet
- 2023-11-20: $14.563: anonymous 100 Monero donation to Binance wallet
- 2023-09: $810: anonymous 0.032 Bitcoin donation to Coinbase wallet
- subscriptions up to 2024-01: $143,795
At 1M USD I retire and work on open STEM education forever.
Note to potential anonymous crypto donors: anonymous donations incur a regulatory risk. I cash out most of such donations and announce it very clearly to the government and banks. For example, at one point Barclays even froze my UK account. But things seem manageable for now. On one hand, such donations serve as a fun test of the financial system. But on the other, if all banks reject my money or if the government decides to take it, I will write off the anonymous donation at zero.
How to give:And if you have a different preferred payment mechanism not listed above, please contact Ciro, and he will set it up.
- one time donations:
- cryptocurrency: note that Ciro is not a regular crypto user, so you might want to make a smaller test donation and confirm that it worked by contacting Ciro before going for colossal amounts (one can dream):
- Monero address: 4A1KK4uyLQX7EBgN7uFgUeGt6PPksi91e87xobNq7bT2j4V6LqZHKnkGJTUuCC7TjDNnKpxDd8b9DeNBpSxim8wpSczQvzf. Secret view key: 7ccaf885ff5540b0ff18927e6ac5da30130afb1eaee09ad95d3c4536a6337e0f. This is a self-custody wallet on a "clean" dedicated Monero laptop connected the Internet. I check for incoming transactions from my dirty main laptop via a view-only wallet each weekend. The cash out method used is latest simplest thing that wasn't yet blocked in my country on a given week, the last time that was centralized swappers[ref]. The fact that the cash out method changes weekly confirms that Monero privacy hadn't yet been broken by countries and that Monero is still one of the most useful cryptocurrencies: Section "Are cryptocurrencies useful?". For transparency, I announce all non-trivial transactions on social media, and the full list of transactions can be seen by anyone with the secret view key provided. I previously had different addresses, so pre-existing donations on older addresses will not be visible there.
- Bitcoin address: 3KRk7f2JgekF6x7QBqPHdZ3pPDuMdY3eWR. This is a Coinbase wallet, off-chain transactions with no transaction fees accepted from other Coinbase users. This method has been tested, I have been able to receive funds from this address in 2023. Fees: non-fixed trading fees[ref] + 0% withdrawal fee on top of any Bitcoin network for on-chain transactions[ref]
- Ethereum address: 0x44cF8C9C015F46d3b2Df730b6492823FD7A91044. Test transaction recommended.
- Solana address: DjdaGawoVFdqxJEqpBGsSWuR4G4MVFNiNkAEu89HuKcE. Test transaction recommended.
- TransferWise tag: wise.com/pay/me/cirod3. It shows as "Ciro Duran Santilli" and that's correct. No fees apparently? Love it!
- PayPal: paypal.me/cirosantilli. Note that dots in Gmail address are ignored, and it is perfectly normal if the email you see has some extra dots in it. Fees: 2.9% + 0.30 GBP[ref].
- cryptocurrency: note that Ciro is not a regular crypto user, so you might want to make a smaller test donation and confirm that it worked by contacting Ciro before going for colossal amounts (one can dream):
- monthly subscriptions of 1$/month or more on either:Symbolic 1 dollar/month donation are extremely welcome to signal your interest! This way if a certain critical mass of sponsors is ever reached (~100?), Ciro can start to more actively asking slightly higher amounts to really try to achieve full time self sufficiency.
- GitHub Sponsors: github.com/sponsors/cirosantilli. Fees: 0% for individuals, up to 6% for organizations[ref]
- Patreon: www.patreon.com/cirosantilli. Fees: 8% pro plan + 1% PayPal withdrawal capped at 20 USD[ref]. We are waiting to reach the cap to withdraw!
- larger grants/contracts from filthy rich individuals or organizations: contact Ciro as mentioned at: Section "How to contact Ciro Santilli" to discuss.Ciro is interested in contracts/voluntary work that would be compatible/synergic with the OurBigBook.com project. Some possibilities include:
- interacting directly with classes of university students to help them learn the class subject, while at the same time spreading the university knowledge outside of the university walls
- one-to-one mentoring of individuals of any age that are looking to make an impact in the world, and not just pass their exams
- fixing specific bugs in related projects Ciro has experience in. These could be either via one-off contracts, or on platforms such as:
Ciro's current ambitions require him to remain in developed countries, because Ciro wants to document advanced science and technology by liaising with top universities, and there is not nearly as much high technology in poor countries. Remaining in developed countries is also a required due to family reasons.
If you would like public acknowledgement for your support, Ciro will very gladly give it, just let Ciro know how you'd prefer it. Due to Ciro Santilli's campaign for freedom of speech in China, many supporters have chosen to be anonymous, and that is totally fine, not everyone is interested in politics, or has a situation where going public is acceptable, so we don't have a standard setup yet, let's build it together. A acknowledgement section at the bottom of this page would be a minimum, but I for larger donations we could add a your advertisement in a locations such as:
- near the top of of the accounts controlled by Ciro Santilli, e.g. one of Ciro Santilli's Twitter accounts, github.com/cirosantilli or stackoverflow.com/users/895245
- near the top of cirosantilli.com
100k USD/year is a semi arbitrary amount that sounds nice. My last day job total compensation as of 2024 was about 150k USD/year.
Ciro Santilli is very happy to meet people with related interests, he really loves his like-minded online friends. Even if you don't have something a specific goal in mind for the contact, please just say hi.
To contact Ciro publicly about any general subject that is not covered in a more specific GitHub repository, including saying hi or suggestions about his website either:
- create a GitHub issue at: github.com/cirosantilli/cirosantilli.github.io/issues/new or Giscus thread
- at mention Ciro's main Twitter account
For comments about China, first read:
and then create a GitHub issue at: github.com/cirosantilli/china-dictatorship/issues/new
Publicly viewable contact is preferred if possible to more effectively share Ciro's wisdom with the world.
But if you feel more comfortable with private contact, no problem, either:
- email:
cirosantilli
with provider ProtonMail which has domain nameproton.me
. All lowercase and removing the placeholder characters<
and>
. Note that Ciro also controls the Gmail address with that same username, and keep in mind that dots are ignored in Gmail addresses. But ProtonMail preferred because why should we give our private minds to the CIA by default? Push notifications disabled. - Signal: username
cirosantilli.89
signal.me/#eu/BuJjV0enXYTOnFFc1FZV5LFcWodL1a2Oy9VZ5uyQU7xrYxqw+npIcaHBqghWudrI. 89 is a reference to Ciro Santilli's birth year 1989. Push notifications enabled, but treat like email unless we are actively chatting back and forth.
For other less good methods that will also work, use direct messages of the following profiles from under Section "Accounts controlled by Ciro Santilli":
- LinkedIn: www.linkedin.com/in/cirosantilli
- Reddit: www.reddit.com/user/cirosantilli
- Facebook: www.facebook.com/cirosantilli
- Telegram: telegram.me/cirosantilli. Note that end-to-end encryption is present on secret chats only, which don't have device sync. Ridiculous.
If you are a privacy freak or are going to tell Ciro state secrets Ciro has this GNU Privacy Guard public key: pubkey.gpg.
Disqus comments were removed from his website in 2019-05-04, a manual dump is available here, removal rationale at: why Ciro Santilli removed Disqus comments from his website in 2019-05-04.
Ciro Santilli's Open Source Enlightenment by Ciro Santilli 35 Updated 2025-01-10 +Created 1970-01-01
Firstly, in 2012, while he was at École Polytechnique, Ciro Santilli was introduced to LaTeX (thank God for French mathematical obsession), and his mind was blown:he though. Why isn't everyone doing that!
Ha, so I can write my own books, and so can anyone, for free?
One particular event stood out: Ciro made a small change to his teacher's course material, who blessed be him (dude's a legend, Ciro just noticed he has some Chinese publications with another French dude, e.g. www.amazon.co.uk/高效算法-应试与提高必修128例-克里斯托弗-Christoph-Durr/dp/B078SJQPVK "High-efficiency algorithm competitions 128 examples", did he write it the Chinese himself?? Must be of course to complement the notoriously low French professor salaries), made it available, and then Ciro gave him back the .tex file. Ciro was just a bit worried about how the teacher would be able to tell what he had changed in the file to validate the change. The teacher just said of course, "no problem, I'll just use
diff
". Ciro had never heard of diff. Let alone Git of course, though yes, this was a bit early in Git's history version control systems had been around since forever of course. This was 2011 or 2012, about 4 or 5 years into a superior education curricula with various courses involving computers, some requiring quite a lot of "fill these empty functions" style programming. Education is a joke. Anyways, this was a prelude to exactly what Ciro wanted to do in OurBigBook.com. This might have been the one actually: webia.lip6.fr/~durrc/Iut/Notes580.pdfNot long afterwards, Ciro started playing with Linux. Until then, Ciro had had some contacts with the mysterious operating system at university, and was a bit puzzled what the point of it was! He clearly remembers:University should be forced to use only open source software and hardware in undergrad teaching courses by law BTW.
- at the University of São Paulo that they had some "UNIX" computers in some classes, and at the library
- at École Polytechnique, he took a course about mathematical analysis and there was a "lab" where students were supposed to use FreeFem, great initiative BTW. And Ciro distinctly remembers being paried with a nice Chilian colleague, and the guy was alreay super at ease with the shell: "cd", "ls", etc. WTF was all that!
Then came an Ubuntu live disk on his own machine, and finally a measly 40GB dual book partition in a Microsoft Windows machine on a laptop. At first, it took a lot of time to learn all the crazy new terminal stuff! Yes, at this point, Ubuntu was already usable enough without the terminal, an accomplishment actually. But as a programmer, Ciro felt obliged to learn. Many hours were spent reading man pages at the library. But it all just felt so right, and sometimes powerful... true wizardry.
And ten years later, Ciro was seriously considering buying a computer without Windows pre-installed. He had not used Windows a single tie on a personal machine even once in those ten years!
Finally, to finish things off Ciro found two websites that changed his life forever, and made be believe that there was an alternative: Stack Overflow and GitHub.
The brutal openness of it all. The raw high quality content. Ugliness and uselessness too no doubt. But definitely spark in a sea of darkness.
Random fun mentions:
z
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