Ciro Santilli @cirosantilli 34

DNA detection means determining if a specific DNA sequence is present in a sample.

This can be used to detect if a given species of microorganism is present in a sample, and is therefore a widely used diagnostics technique to see if someone is infected with a virus.

You could of course do full DNA Sequencing to see everything that is there, but since it is as a more generic procedure, sequencing is more expensive and slow.

The alternative is to use a DNA amplification technique.

Can be seen as a cheap form of DNA sequencing that only test for a few hits. Some major applications:

What big companies have been created in Europe after World War II, that have not been bought or utterly defeated by American or Japanese companies?Because of all these failures, much fanfare was made as Spotify reached a $50B market capitalization in 2020. An art company, so cute!

As of 2023, the LVMH was the most valuable company in Europe by market capitalization^[ref]. Luxury goods. An area of industry that borders between the useless and the evil.

Europe has basically become an outsourcing hub for the United States. The fact that its starts are all sold if they become large enough just means that R&D is also outsourced.

ASML, and perhaps more maeaningfully its parent/predecessor ASM International from 1964 is perhaps the biggest exception.

The key problem is that there are so many small countries in Europe, that any startup has to deal with too many incompatible legislation and cannot easily sell to the hole of Europe and scale. So then a larger company from a more uniform country comes and eats it up!

Talent mobility is another issue:

So why can't Europe unify its laws?

Because the countries are still essentially walled off by languages. Europe is the perfect example of why having more than one natural language is bad for the world.

There isn't true mobility of people between countries.

You just can't go study or work in any other country (except for the UK, when it was still in the EU) without putting a huge effort into learning its language first.

Without this, there isn't enough mixing to truly make cultures more uniform, and therefore allow the laws to be more uniform.

Europe can't even unify basic things like:

Equally so, it can't force little fiscal paradises who effectively benefit from being in Europe like Ireland, Luxembourg, Monaco, Switzerland ("not European", but should that be allowed?) and Cyprus (the EU can't even maintain its territorial integrity, let alone fiscal) to not offer ridiculously low taxes and incentives which make them entry points for foreign companies to rape Europe.

For this reason, Europe will only continue to go downhill with the years, and the United Kingdom will continue to try and endosymbiose into a state of the United States (although at times it seems that it would rather endosymbiose with China instead).

Historically, this disunion is partly due to the European balance of power, whereby countries would form alliances with old enemies to prevent another country from taking over. Also linked are failed military unification attempts by Napoleon and Hitler, though we are likely better off without the latter succeeding!!! Though those also partly failed due to wider balance of power issues involving the United Kingdom, the Soviet Union and USA, not only due to internal balance. Of course, none of that matters anymore after World War II, where other more unified Europe-sized potencies rose, first the USA and the Soviet Union, and then China, and now European disunion is nothing but a burden.

Evidence such as those makes it clear that the European Union is a failure.

One thing must be said in favour of Europe's mess however: it favours international collaboration in huge projects as a more neutral middle ground. This can be seen more clearly in the ITER and the fiasco that was the Superconducting Super Collider that was cancelled a couple of billion dollars in partly because it failed to attract any foreign investment, compared to the Large Hadron Collider which went on to find the Higgs boson as mentioned at www.scientificamerican.com/article/the-supercollider-that-never-was/.

In the case of indel mutations (see limits of gel electrophoresis for minimal size difference issues), it is possible to determine the allele with gel electrophoresis. You can just read out the alleles right in the gel. It is a thing of beauty.

As of 2020, this method appears to be much cheaper than DNA sequencing approaches.

See also: github.com/cirosantilli/awesome-whole-cell-simulation

As of 2019, the silicon industry is ending, and molecular biology technology is one of the most promising and growing field of engineering.

Such advances could one day lead to both biological super-AGI and immortality.

Ciro Santilli is especially excited about DNA-related technologies, because DNA is the centerpiece of biology, and it is programmable.

First, during the 2000's, the cost of DNA sequencing fell to about 1000 USD per genome in the end of the 2010's: Figure 2. "Cost per genome vs Moore's law from 2000 to 2019", largely due to "Illumina's" technology.

The medical consequences of this revolution are still trickling down towards medical applications of 2019, inevitably, but somewhat slowly due to tight privacy control of medical records.

Ciro Santilli predicts that when the 100 dollar mark is reached, every person of the First world will have their genome sequenced, and then medical applications will be closer at hand than ever.

But even 100 dollars is not enough. Sequencing power is like computing power: humankind can never have enough. Sequencing is not a one per person thing. For example, as of 2019 tumors are already being sequenced to help understand and treat them, and scientists/doctors will sequence as many tumor cells as budget allows.

Then, in the 2010's, CRISPR/Cas9 gene editing started opening up the way to actually modifying the genome that we could now see through sequencing.

What's next?

Ciro believes that the next step in the revolution could be could be: de novo DNA synthesis.

This technology could be the key to the one of the ultimate dream of biologists: cheap programmable biology with push-button organism bootstrap!

Just imagine this: at the comfort of your own garage, you take some model organism of interest, maybe start humble with Escherichia coli. Then you modify its DNA to your liking, and upload it to a 3D printer sized machine on your workbench, which automatically synthesizes the DNA, and injects into a bootstrapped cell.

You then make experiments to check if the modified cell achieves your desired new properties, e.g. production of some protein, and if not reiterate, just like a software engineer.

Of course, even if we were able to do the bootstrap, the debugging process then becomes key, as visibility is the key limitation of biology, maybe we need other cheap technologies to come in at that point.

This a place point we see the beauty of evolution the brightest: evolution does not require observability. But it also implies that if your changes to the organism make it less fit, then your mutation will also likely be lost. This has to be one of the considerations done when designing your organism.

Other cool topic include:

It's weird, cells feel a lot like embedded systems: small, complex, hard to observe, and profound.

Ciro is sad that by the time he dies, humanity won't have understood the human brain, maybe not even a measly Escherichia coli... Heck, even key molecular biology events are not yet fully understood, see e.g. transcription regulation.

One of the most exciting aspects of molecular biology technologies is their relatively low entry cost, compared for example to other areas such as fusion energy and quantum computing.

For those that know biology and just want to do the thing, see: Section "Protocols used".

The PuntSeq team uses an Oxford Nanopore MinION DNA sequencer made by Oxford Nanopore Technologies to sequence the 16S region of bacterial DNA, which is about 1500 nucleotides long.

This kind of "decode everything from the sample to see what species are present approach" is called "metagenomics".

This is how the MinION looks like: Figure 1. "Oxford Nanopore MinION top".

The 16S region codes for one of the RNA pieces that makes the bacterial ribosome.

Before sequencing the DNA, we will do a PCR with primers that fit just before and just after the 16S DNA, in well conserved regions expected to be present in all bacteria.

The PCR replicates only the DNA region between our two selected primers a gazillion times so that only those regions will actually get picked up by the sequencing step in practice.

Eukaryotes also have an analogous ribosome part, the 18S region, but the PCR primers are selected for targets around the 16S region which are only present in prokaryotes.

This way, we amplify only the 16S region of bacteria, excluding other parts of bacterial genome, and excluding eukaryotes entirely.

Despite coding such a fundamental piece of RNA, there is still surprisingly variability in the 16S region across different bacteria, and it is those differences will allow us to identify which bacteria are present in the river.

The variability exists because certain base pairs are not fundamental for the function of the 16S region. This variability happens mostly on RNA loops as opposed to stems, i.e. parts of the RNA that don't base pair with other RNA in the RNA secondary structure as shown at: Code 1. "RNA stem-loop structure".

                A-U
               /   \
A-U-C-G-A-U-C-G     C
| | | | | | | |     |
U-A-G-C-U-A-G-C     G
               \   /
                U-A
|             ||    |
+-------------++----+
    stem        loop

This is how the 16S RNA secondary structure looks like in its full glory: Figure 5. "16S RNA secondary structure".

Since loops don't base pair, they are less crucial in the determination of the secondary structure of the RNA.

The variability is such that it is possible to identify individual species apart if full sequences are known with certainty.

With the experimental limitations of experiment however, we would only be able to obtain family or genus level breakdowns.

Sequence alignment is trying to match a DNA or amino acid sequence, even though the sequences might not be exactly the same, otherwise it would be a straight up string-search algorithm.

This is fundamental in bioinformatics for two reasons:

These can be used to break cells apart from tissue, and also break up larger DNA or RNA molecules into smallers ones, suitable for sequencing.