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Bert Hubert 🇺🇦 Profile picture
Bert Hubert 🇺🇦
@bert_hu_bert
Formerly PowerDNS. DNA, Code, 🇪🇺. Galileo/GNSS: @GalileoSats, DNA: @DNAntonie, Nederlands: @bert_hubert. Mastodon: @bert_hubert@fosstodon.org
2 subscribers
Jul 10, 2022 • 8 tweets • 4 min read
This is huge news, but easy to miss. We don't all have the same DNA, but many genes exist in different versions. For example, we have a blood type because there are 3 different ABO genes around. Yet up to now the "downloadable human genome" was static, w/a single blood type! 1/ The currently downloadable human genome also appears in significant part to come from @JCVenter, who has done awesome things, but his DNA can't represent us all. Enter the pan-genome - a file format that can encode multiple variations for each point. 2/ berthub.eu/articles/posts…
Jun 21, 2022 • 18 tweets • 8 min read
A fun decryption story! In 1914, The Netherlands sent a peace mission to Albania (I did not know this either). The mission commander, Major Lodewijk Thomson, was killed in battle under circumstances that are still unclear. And we'd love to know! en.wikipedia.org/wiki/Lodewijk_… Recently (2009), an encrypted Albanian telegram from that time was found in Dutch military archives. Could this perhaps shed some light on the situation? Intriguingly, no one had ever been able to decrypt the message.
Nov 5, 2021 • 9 tweets • 4 min read
Wonderful news below on Pfizer's PAXLOVID pill! Here a brief thread what this impressive new medicine does. 1/ The SARS-COV-2 genome has several genes (or ORFs).
Note in green the famous S spike protein. This is what all the vaccines contain or make in your cells. The green proteins are all "structural", so they end up as part of a new virus particle.
Source: chemistryworld.com/the-coronaviru… 2/
Oct 1, 2021 • 16 tweets • 6 min read
Brief thread on how Molnupiravir works. This is the promising COVID-19 antiviral that appears to prevent 50% of hospitalizations/deaths, and maybe 100% of deaths, when given very early to high risk COVID-19 patients. merck.com/news/merck-and… In general, many many things will stop a virus or a disease, as explained in this @xkcd comic. But that is not what we are looking for. We want something that stops a virus dead, but keeps us alive. Image
May 24, 2021 • 10 tweets • 5 min read
If you are into reverse engineering, the EU Galileo navigation satellites are currently transmitting a new signal that enables centimeter level accurate positioning. But! They haven't yet released a description of this format, but the data is there & unencrypted. 1/2 Let me know if you want a dump of many hours of data. The data likely includes a distance vector that describes a correction to a satellite's position, plus a velocity vector, plus a time offset correcting the atomic clock, plus administrative details ('issue of data number') 2/2
May 10, 2021 • 7 tweets • 4 min read
I love the EU (honestly!), but I also love the Internet. Through the NIS 2 Directive, the EU is attempting to regulate each and every root server operator (RSO), even those outside of the EU. Doing so will have bad consequences. 1/6
berthub.eu/articles/posts… There are 12 RSOs. There are over 1300 active root servers. None of these RSOs are 'providers of essential services' individually. Up to 11 of them could fail, and nobody would notice. In 40 years, "the root" has never gone down. 2/6
Mar 24, 2021 • 4 tweets • 2 min read
BREAKING! Stanford scientists have analysed the Moderna and BioNTech vaccines to determine the mRNA code in there. This is the first time we are seeing the Moderna sequence. Get it here while it is still online: github.com/NAalytics/Asse… To see what this means, do head over to this page: berthub.eu/articles/posts…
Jan 30, 2021 • 12 tweets • 4 min read
Recently I learned something about DNA that blew my mind, and in this thread, I'll attempt to blow your mind as well. Behold: Chargaff's 2nd Parity Rule for DNA N-Grams.
If you are into cryptography or reverse engineering, you should love this.
Thread: Image DNA consists of four different 'bases', A, C, G and T. These bases have specific meaning within our biology. Specifically, within the 'coding part' of a gene, a triplet of bases encodes for an amino acid Image
Dec 31, 2020 • 6 tweets • 4 min read
New leader in the BioNTech vaccine RNA optimization challenge: @pkuhar! With some pretty Python code that can server as a great starting point for other entries: github.com/unrelatedlabs/…. Context: berthub.eu/articles/posts… New leader @naomicodes, 76% , using DNA Chisel from edinburgh-genome-foundry.github.io/DnaChisel/ - well done!
Dec 31, 2020 • 6 tweets • 3 min read
Reverse engineers! Cryptographers! I have a fun challenge & contest for you. The BioNTech SARS-CoV-2 vaccine contains copy-pasted RNA from the actual virus. The vaccine RNA encodes for (almost) the unmodified virus S protein. But, the RNA has been optimized somehow. But how? 1/ You can change RNA quite a lot without changing the protein that comes out. It is known that replacing RNA letters to G and C to the RNA enhances vaccine efficiency. And lo, the designers of the vaccine have done just that - GC content went from ~36% to ~57%: 2/
Dec 24, 2020 • 4 tweets • 2 min read
Preparing a blog post on the BioNTech/Pfizer vaccine & compared the live SARS-CoV-2 spike protein to the one in the mRNA vaccine. And indeed as described, it only differs by two amino-acids. The two Proline substitutions that make the vaccine work (KV -> PP, with the !!): 1/3 If the vaccine would have contained the unmodified Spike protein, this would have "looked" different from the real one. The real one is mounted in the virus body, which gives it a certain shape. With these two changes, the vaccine protein "looks normal" to our immune system. 2/3
Dec 24, 2020 • 4 tweets • 1 min read
"S glycoprotein signal peptide (extended leader sequence), which guides translocation of the nascent polypeptide chain into the endoplasmic reticulum" - part of the BioNTech/Pfizer vaccine. I don't ever want to hear anyone question fundamental science again. 1/2 The level of control and understanding we now have over our biology came from literally millions of person-years spent working on things that at the time were obscure and "useless". And now? We can leverage all this into a 95% efficient vaccine _at the first try_. 2/2
Dec 23, 2020 • 7 tweets • 3 min read
Shout out to @BioNTech_Group who found time to answer this small time blogger's question! @hildabast I have it in writing now, a 30 microgram dose of BNR162b2 actually contains 30 micrograms of mRNA. And in addition, there are the lipids, salts, sucrose and water. This means that by my calculations, every shot of this vaccine contains around 2000 billion mRNA strands that encode the stabilised spike protein. At 0,53*10^-21 grams per RNA nucleotide, this represents ~25 petabyte of mRNA per injection. #cantwait
Jul 15, 2020 • 11 tweets • 4 min read
So the fine writeup of SIGRed (CVE-2020-1350) includes a brief discussion of a neat technique to make a Microsoft browser perform DNS lookups to arbitrary nameservers, which can then also be infected. /cc @EyalItkin & @omriher 1/9 research.checkpoint.com/2020/resolving… Normally, you can't really do DNS lookups using the DNS protocol from browsers. Sure, the browser will resolve names for you, but it chooses how to do that. You can't direct the query anywhere, or do non-standard lookups. This is pretty good. 2/9
Apr 7, 2020 • 16 tweets • 4 min read
Governments are pondering if apps can help them perform contact tracing for COVID-19 infected people. The "why" of this is explained very well here: 1/16
Some countries just track the location of everyone all the time and perform matching on a government server. This is a privacy nightmare. 2/16
www1.cbn.com/cbnnews/israel…
Jan 20, 2020 • 4 tweets • 2 min read
The discussion on if Huawei should power 5G networks misses the point. Most European service providers have long lost control over their networks. Banning Huawei will do nothing to change that. Instead, providers should focus on regaining technical skills
berthub.eu/articles/posts… It is remarkable how the current debate would make one think that picking a specific vendor for 5G would suddenly change things. Instead, most service providers have already outsourced their operations to companies far away. /cc @shashj @cryptoron
Jul 19, 2019 • 5 tweets • 2 min read
Fellow geeks - if after all the Galileo outage stuff you feel the need to go down the wire and receive every GPS/Galileo/GLONASS/Baidu/whatever health message, I can recommend the "NAVILOCK 62524 GPS". It has a stonking chipset (u-blox 8) which delivers the goods. 1/5 There is a huge PDF with full details on how to get the chipset to emit what you need, find it here: u-blox.com/sites/default/… 2/5
Mar 27, 2019 • 4 tweets • 2 min read
Mozilla confirms it will default Firefox DNS to @Cloudflare DNS based on an "Ok, got it" style notification, but will include a button to not accept that. Some further details & nuance can be found in this statement:mailarchive.ietf.org/arch/msg/doh/p… Note that if Mozilla likes your ISP and it also offers DoH, Firefox may offer the user the option of continuing to use that ISP DNS. But you have to be on the Mozilla "approved list":
Jan 22, 2019 • 9 tweets • 2 min read
I suggest ignoring this thread on EDNS Flag Day. Reading it will leave you misinformed. DNS has two kinds of servers: Authoritative and Caching/Resolving servers. Back in 1999, an extension to DNS was defined called EDNS. It was then also defined how any kind of server that receives a question with EDNS on it should respond. In 1999! 2/
Dec 14, 2018 • 7 tweets • 3 min read
Cloudflare has huge legal liabilities because it (re)hosts content for "denied entities" ("terrorists"). This is usually enough to kill a US company dead & it is somewhat odd US DoJ has not yet acted on this. It already has big implications for the internet at large though. 1/5 Since Cloudflare is obviously in potential hot water with the US government, something that is especially bad if you are heading for an IPO, they will have vital interest in anything that makes this issue go away. So, what does Cloudflare have on offer to fix their problem? 2/5