DNA replication lifehack [en]

I’ve recently posted about these talks on “DNA: The Code of Life” that I found. I really enjoyed them, even though most of the contents were not fundamentally new to me. However, I want to highlight one specific topic that I did learn, and that kinda blew my mind…

I had not even been aware of this particular DNA replication problem, let alone the solution. One part of that replication process is adding nucleosides to match the single-stranded-DNA template and forming phosphodiester bonds in the backbone of the daughter strand. That’s the job of DNA polymerase. It turns out that these highly conserved enzymes only work in one direction: they always traverse the DNA template from ‘3 end to ‘5 end. (In other words, they move along the growing daughter strand in 5’ to ‘3 direction and add nucleosides at the 3’ end.)

That’s pretty straight-forward for one of the daughter strands, called the leading strand. There, the DNA polymerase sits right behind the replication fork and traverses the DNA template in its ‘3 to ‘5 direction. The leading strand “grows” in the same direction, so no problem here.

However, the other daughter strand, called the lagging strand, is anti-parallel to that. It “grows” in ‘5 to 3’ direction of the template strand. But DNA polymerase does not work in that direction! Instead, it has to work backwards on the lagging strand, assembling the daughter strand segment by segment. There’s an intricate machinery of other enzymes that coordinate that, which includes forming temporary loops of DNA. Here’s an illustration of what it looks like:

My description and illustration are not very intuitive. It becomes more clear when watching the video from this original source:

What’s truly weird is that there are no fundamental chemical or physical reasons that would prevent the existence of a polymerase enzyme that works in the other direction. It just seems that a polymerase that traverses the DNA template from ‘3 end to ‘5 end evolved first, alongside the “hack” described above. Since then, different variations of DNA polymerases have evolved in various branches of the tree of life. But they are all variations on the same theme, whereas it would require a major re-haul for a polymerase to work the other way round. I think this is similar to the homochirality observed elsewhere in biology.

There are many more molecular biology videos at that WEHI place. I’ve seem similar ones elsewhere, but I’m surprised how old these are. Looks pretty neat for 2003. It seems that some of that has been used in a Björk video a while back.

Biting my style [en]

So I’m working at a huge software company and in my department we have this nice tradition of lunch-talks. The company buys pizza and we all eat it, while one hungry person gives ~1h talk. (Well, that was before the pandemic, now everything is remote and we have to fend for ourselves.)

Most of the topics are work related, e.g. about new technology, cool open-source projects, and latest developments in our own software. But there is also a lot of other stuff: hobby IT projects, soft skills, charity, you name it…

I’ve given lunch-talks myself in the past, mostly on security topics (e.g. XSS and other injection vulnerabilities). I’ve also had this idea floating around for years, that I’d like to give a lunch-talk about analogies between biology and computer science. But I’m not a great presenter and it takes me a lot of preparation work to compensate for that. So I’ve just been too lazy to implement this idea. Well, it turns out that someone has beaten me to it. And he did a brilliant job at it. And not just one talk, but two, but more about that later…

Or biting his style?

Let me first explain, how I found out about it in the first place. I was searching for information on RNA vaccines, and somehow I stumbled upon this article about Reverse Engineering the source code of the BioNTech/Pfizer SARS-CoV-2 Vaccine.

That’s a very cool article by itself, but it also pointed me to this other one, by the same author: DNA seen through the eyes of a coder. Turns out that page has been around since the early 2000s and it’s been constantly updated and improved.

Not only that, but the author (Bert Hubert) has also put most of the contents into two talks:

There’s also an dedicated article summarizing both talks, with videos embedded, slides for download, and heaps of links.

These talks touch on almost every topic that I had envisioned for my own lunch-talk. They cover DNA and RNA basics, chromosomes, proteins, ribosomes, the genetic code, the central dogma, genes and other types of DNA, promotion, repression, regulation, splicing, HOX genes, CRISPR-Cas9, etc. And they point out really interesting analogies to computing phenomena.

The talks also cover other biology topics, like evolution, the tree of life, RNA-world, LUCA, the three domains, viruses, horizontal gene transfer, epigenetics, endosymbiosis, and more. All of that is enriched with great examples and numbers, both from bio-technology (sequencing, editing) and from life itself. This includes comparisons of genome sizes, reproduction rates, the bacterial flagellum and how it is regulated in search for food, and the good old comparison between human and octopus eyes.

I’ll try to share some thoughts about specific contents of these talks. In the meantime, let me end with a random quote of the presenter:

Are we anthropomorphising nature, which it really hates?

— Bert Hubert, 2017

It’s been a while [en]

My last post here has been over 4 years ago. I’ve really neglected this blog. Let’s see, if I can change that…

Part of the problem was the rotten technology underneath. Even apart from WordPress. It was running on some weird virtual server at a local hosting provider. Weird, because it was neither full virtualization nor light-weight containerization. It felt like it combined the worst of both worlds.

It certainly wasn’t fun to work with it, so I didn’t. The server was down for several months in a row at multiple times. I never installed a TLS certificate that would be accepted by mainstream browsers. I had no backups whatsoever. And everything was set up manually.

During the past few weeks, I have changed most of that. By now, the technology is in good enough shape that I feel comfortable blogging again. I hope to share more about that shortly. And I guess there will be more cooking recipes, too.

Thai Pumpkin Soup [en]

2 Onions
2 tbsp Olive Oil
2 tbsp Green Curry Paste
4 cups Vegetable Stock
2 Carrots
1 kg Pumpkin (peeled and seeded)
2 Kumara (a.k.a. sweet potato)
400 ml Coconut Cream
1 tbsp Soy Sauce
Coriander Leaves


  1. Chop and sauté onions using olive oil.
  2. Add curry paste, boil and stir for 2-3 minutes.
  3. Add vegetable stock and keep cooking.
  4. Add sliced carrots, then diced pumpkin and kumara.
  5. Cover and boil for 10 to 12 minutes.
  6. Sieve vegetables, purée them, and re-add to soup.
  7. Add coconut cream and soy sauce, bring to boil again.

Serve hot, garnished with coriander leaves.


Step 6 – sieve the vegetables – is kinda controversial. My original notes on this recipe didn’t anything about re-adding them. That would make this a rather clear soup. I prefer adding them back in, which makes the soup nice and thick. Usually I don’t bother sieving the veggies out, and just treat the whole soup with a hand blender.


Not sure how Thai this recipe actually is. I got it from a co-worker (forgot her name) in Tauranga, New Zealand. That’s why I like to stick to the word Kumara for sweet potato. I think it’s of Maori origin, but it’s in common use all over the place.

The weather in Tunisia [en]

So I’ve spent waiting for wind on the island of Djerba, Tunisia, for almost one week to no avail. (With one exception yesterday, that is, when I finally got the opportunity to go kite-surfing. For about 30 mins.)

All forecasts for today looked equally bleak: around 5 knots in the early morning, afterwards nothing for most part of the day. So I went to the spot early trying to  seek out the last remains of wind.

Then, this happens:

Wind and Weather on Djerba TodayThe wind was already at 18 knots when I arrived, so I hurried into the water. Pretty soon I was overpowered with my 14 m² kite – unexpectedly the wind went stronger, not weaker.

Around noon, it was a full-blown storm. This also meant nearby lightning, so I had to get off the water after roughly 2 hours. It took quite some time for the thunderstorm to clear, and I was eager to go for another round. However, before we realized the storm was over, all the wind was gone. Never seen it fall from the mid twenties to almost zero so rapidly.

Weird day. Great spot nevertheless. I may be back some time…

Postcard from Sri Lanka [en]

Never was a big fan of paper postcards, let alone Facebook postings. Hence, I’m going to dump random travel impressions here instead. Alongside some generic pics. And shout-outs to all my friends! Here goes…

Firstly, getting around can get exciting in itself in Sri Lanka. The way of right always belongs to the vehicle with the most inertia. Which makes the ubiquitous buses preferable, as compared to puny tuktuks. However, the latter can be more tasty…



Some may skip road traffic altogether and prefer the railway. While being surprisingly sluggish, it does offer very scenic views, especially in the central highlands. Cup of tea then?


These highlands are also home to one of Sri Lanka’s most prominent sights, Sri Pada. This mountain peak is popular amongst both foreign tourists (due to the impressive landscape) and locals (due to mythological connotations).

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Of course, nature in 2015-12-11_EllaRawanaFalls_002other parts of Sri Lanka has it’s own charm. Traveling at the end of a Monsoon season ensures that waterfalls, reservoirs, and otherwise dry bush lands are flooded with water. The water buffaloes seem to like it that way – as do all the bats in the trees.

There’s also some cultural goods to be seen throughout the country. Personally I don’t seem overly receptive to that. So don’t ask me about the difference between a Stupa and a Dagoba!


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Last but not least, Sri Lanka holds a plethora of beaches. Some invite to fishing, others to surfing, yet others just to chill…

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