How to destroy the world using Python and a synthetic virus
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00:00
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CAN busComputer virusProteinMixture modelMereologyCellular automatonCommunications protocolProduct (business)Data storage deviceTraffic reportingComputer virusMultiplication signInformationLatent heatVector spaceBitMechanism designChaos (cosmogony)Complex systemDependent and independent variablesPower (physics)Large eddy simulationComputer animation
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Transcript: English(auto-generated)
00:04
We are Elena and Marina, and we will talk to you about how to destroy the world using Python and synthetic pages. So it may be a little clickbait, but, well, it could be, it could seem a little clickbait, but I assure you that it is not.
00:23
So as I said, well, I am Elena, and I'm a specialist in pharmaceutical regulation and quality in the industry. And I am Marina, I am a biomedical engineer in present a Ph.D. in biophysics and bioengineering,
00:41
and we both are part of the Python Spain and PyCon Spain working groups. So we are going through all these sections. First, we will start with a little bit of, well, a little bit of concepts of introduction concepts regarding synthetic biology and viruses.
01:04
Then we will go through very little basic genetics. I promise it's a very quick genetics class, so please don't be afraid. Just the basics to understand perfectly the practical case, in which, well, a spoiler, we will create with the help of Python that synthetic virus to destroy the world
01:26
and humanity in general. To then have in mind some important considerations, the final conclusions, and the questions and answers around on your part. So we can start with the introduction.
01:43
As I said, we will have, we will use this tool, the synthetic biology tool, for creating and modifying this virus that we will see in a minute. And synthetic biology is the field of knowledge that is focused on the design and construction of new biological entities, or the modification of the existing ones
02:05
to achieve new functionalities. And this is a field that is applied to many areas. For example, medicine for drugs and vaccine design, in agriculture for transgenics and engineered plants or foods,
02:23
in industry for sustainably produced fuels, materials, and medicines, and for the environment side, we have also tools for bioremediation. So today we will focus on the medicine part for this virus creation,
02:40
well, modification, and in order to understand the virus part perfectly, well, we have to review very quickly what is a virus, which is an infectious agent that can replicate only within a host organism. Viruses are quite weird.
03:00
They are not considered like a living being, like 100% a living being, because they don't have the basic viral functions of a living being, like nutrition and the interaction with the social environment, like, for example, all of us have.
03:22
But they have the reproduction viral function. But, as I said, they need that host organism, that cell or that animal or that organism, to replicate. There are many types of viruses. We are not entering in that very large field.
03:44
The only thing for your interest, just for you to know, on the right part of the slide you can see two types of viruses, just for you to see that we have a genome, a genetic content, encapsulated in a capsid.
04:01
And also there are more complex viruses with that genome, that capsid, and also an envelope, just for protection. So, well, the part that we are interested in in this introduction, basic concepts, is the replication of the viruses.
04:21
As I said, the viruses need a host organism for the reproduction, the replication, and here you can see the scheme. It consists of the virus attaching to a human cell, well, an animal cell or any cell, in which it releases the genetic content.
04:43
This genetic content is replicated using the host, the cell mechanisms and resources. And then the new viruses with that replicated genetic content assemble and they are ready to be exported from the host cell
05:01
and will infect other organisms or cells or whatever. So this is all for the introduction. Now, as I said, very quick, I'm so sorry, but very quick, basic genetics class, okay? It is very simple and it is just for you to understand perfectly the practical case.
05:23
So, very basic concepts from the beginning, a gene which is a segment of DNA that determines a trait. For example, a gene, well, many genes that determines the color of our eyes, for example. What is the DNA? The DNA is nothing more than a double helix of bases.
05:43
The bases are just letters. All of our DNA is composed by four letters. This is a very, very large string of four letters. So in here you can see that four letters, the A, the T, the C and the G.
06:01
And something that you need to know is that these letters are complementary. If we have an A in a helix of the DNA in the other helix, the complementary one, we have a T. And if we have a C, we have a G in the other one and this way.
06:21
So, well, we have this DNA that is the one that composes the genes and these genes are the ones that said that our eyes are green, for example. But it is not so direct. From the DNA, we have like another molecule, a child molecule, which is the RNA
06:43
and this RNA is the one that gives place to the protein, which is the one that makes our eyes green, for example. This RNA is also important today in this talk. You need to know just that RNA is a single helix that is complementary to the parent DNA.
07:02
There is. If in the original DNA we have a C, in the RNA we'll have a G. G is complementary, these letters that I have explained before. And also another specialty of RNA is that it has use instead of this.
07:20
Just that. You just need to know that this is a very large field of knowledge. If you are curious, you can get deep into that. Final basic concepts is what is a mutation, which is a letter or letters change with respect to the original DNA.
07:42
And with these basic concepts, finally, the end of the genetic class is the CRISPR-Cas. This is important. This is, again, a spoiler. The tool that we are going to use for editing that virus and for destroying the world, basically.
08:01
So, CRISPR-Cas is the cut and paste of DNA and RNA. It is the tool that is used for gene editing. And it is, well, CRISPR-Cas is consisted by a Cas, a happy protein, that is the one that cuts the DNA or the RNA.
08:22
And it is, Cas knows where to cut because it has in one hand a guide, which is RNA, this is important, and it knows what to paste in that side that it has cut because in the other hand, it has a mold, which is DNA.
08:42
Here, you can see, well, you will see an example of this, if this is our original DNA. In here, you can see an example of a guide, which is the complementary segment of that center area of the original DNA.
09:01
And for example, we can have this mold that if you look close, you can see that the second letter is different from the one of the original DNA. Well, with this guide, the Cas will cut in these two places. And if we take a look at the mold, we can see that the edited DNA
09:25
will have that second letter in the center of the original DNA sense. And, well, this is all the genetics that you need to know. I hope you are not like this guy right now and that you could understand the practical case with these concepts.
09:45
So, now onto the practical case. Now we have this powerful tool, but what can we use it for? And, of course, we can only use it for good things, but I don't know. Maybe you're not having the best day, or maybe your boss
10:02
hasn't given you the raise that they had been promising for the last year. I don't know. And you will decide to worship chaos. So, now we're going to explain how you can use this tool for not so good of a name. So, first of all, we need a virus, and, of course, we can create a virus from scratch,
10:24
but biology already offers us a lot of options. In this case, we will be using an adenovirus, which is a virus that are viruses that can be found all around the world. In this specific case, we will be using adenovirus serotype 41 that is known for causing acute gastroenteritis.
10:43
And in this map, you can see the places in which a significant amount of virus particles have been found in the water supply, so it can reach the population of those nations faster. So, well, before we start modifying this adenovirus serotype 41
11:06
with the mutations that Elena is going to explain in a minute, we will need that genetic sequences of this adenovirus serotype 41 and the genes that we want to edit or to add to this virus.
11:23
Just for your interest, here I present to you a genetic database, which is one of the most used databases in biology in general, in which you can download these genetic sequences.
11:40
For example, I show you here one of the adenovirus 41. This is the page of this virus, and if you click in Send To, you can download it in format FASTA. The FASTA files are text files, but they have a header, like a first line that is a header with the info of the gene,
12:03
but they are text files. And also, I show you here, well, we will work with Ebola genes. Again, you can search for this Ebola virus, and also you have the details of each gene that this would be of interest in the practical case, just in a moment.
12:23
And again, you can download these genes in brown, you can see the gene highlighted, and you can again save it in FASTA format for working with these genes. I'll show you the code. You can see this code, you have this code, this slides the files that we are going to use in the practical case
12:43
and all the info in this repository of my GitHub that you can see here. Just in case you want to revise or even try the code with genes of your interest at home or whatever. So I'm going to explain you the code just very quickly. It's very simple.
13:03
For the practical case, we are going to, as Elena said, modify an existing virus. So, well, this is the main of the code. It simply takes the FASTA file of the virus that you want to modify, in this case, the adenovirus serotype 41,
13:23
and it makes simple modifications. Just as I said, it removes the header of this specific header of the FASTA files and replaces all the jumps, of the line jumps, to have a string of that four letters that we saw before.
13:41
And this code will give to you the guide and mold that are necessary for the CRISPR experiment and also for your interest in the mutated sequence. In order to, well, and we have, if you take a look at the guide piece of code,
14:05
you see a DNA to RNA function that is very simple. It just changes the letters of the original DNA to the complementary letters that correspond to the RNA, always using, as I said in the introduction,
14:20
use instead of this. And, well, the main, well, the principal function, the function of interest in this case is this one. This is the function that is going to do all the magic, in which, again, we have to select the file of that gene
14:40
that we want to add to the adenovirus serotype 41 in this case. Again, it removes the header and does the string of things. And here, the code will ask us the position of the, where do we want to add the gene. Well, that's a simple comparison.
15:02
We are not developers, so this, of course, could be done in many different ways. But, well, if that's a quick comparison, if it is an integer, a positive integer or not. And then, well, it defines the guide in DNA that later we will change to RNA. It takes the mutation position that we have entered to this script,
15:25
a plus or minus 25 bases, just to not take one letter, because if we take one letter, we will cut in so many places of the DNA, of course. Then the mutated virus sequence is just the sequence of the original virus
15:43
up to the mutation position, the added gene, and the rest of the original virus. And the mold is that plus or minus 25 bases of the guide, of where the cast has cut, plus this add gene sequence that we want to add.
16:05
And, well, that is all the code. It is very simple, but it's in order to help us to build this guide mold and all the sequences that we need for the CRISPR, for CRISPR in the virus. That's it. So now we want to spread this virus even more.
16:27
So adenoviruses per se are in, we cannot do that with the original virus, so we can modify the virus we have, adding then a specific characteristic. For example, we can add a little membrane.
16:42
It's like the envelope of the virus to make it resistant for adverse weather conditions so it can be spread into other nations. This will help to spread the virus to, for example, environments with higher IV radiation or a string cold.
17:03
And for this we can use, we can add genes, BP24, GP, and BP40 from Ebola virus, and now we can see how we can do it. So as an example, well, this is all the same. We are, in every gene, we want to add it in some position.
17:22
I'll show you as an example with Python, adding the BP24 gene from this Ebola virus. We want to add it in the position, well, this position, very last position, just because this is a promoter position. Well, biology things that are not quite important right now,
17:41
but it is a strategical position, that's it. So, well, you can see here, these are, well, the segments of these FASTA files that I have said before. In the upper part of the slide, you can see a fragment of the original adenovirus 41,
18:01
and below you can see that the whole BP24 gene from this Ebola virus that we want to add in that position. So with the help of this script of Python, we have in return the guide in RNA, of course.
18:20
You can see in the fragment of the original adenovirus 41 in blue, the segment, the plus minus 25 bases that we select according to this position that we entered for the mutation, and the guide is the same but in RNA and complementary to this segment.
18:40
So with this guide, Cas will cut this segment of the original adenovirus. Then, well, this is a messy slide, I'm so sorry, but I wanted to have like the whole BP44 gene. You can see that the mold is just that guide segments highlighted in blue, and in the middle,
19:05
the whole BP44 gene that we want to add in that position. So with this mold, Cas will paste this whole sequence in the virus. With this, we will have in our adenovirus this whole gene,
19:21
this new gene that in the beginning it was not there. With Python, we have these sequences automatically. This is something that in clinic is actually done in many cases manually. So when we have this, we only need to synthesize in our laboratory
19:41
these sequences and perform our CRISPR-Cas experiment in which we will inject in the virus these sequences with the Cas, and we will edit the genome of the DNA. And also, the Python script gives also the mutated adenovirus
20:01
in which, again, you can see, well, I highlighted the blue segments of the guide for you to see it. And in the middle, we have this whole BP44 gene from the Ebola virus. So with this example, it's the same for other genes, and we can add more abilities to be in other places of the world.
20:23
For example, the ability to infect with vectors like mosquitoes. And this will be interesting for us with heat and humidity. And you can see then highlighted in pink in the map. And we can use genes NS1, NS4B, and NS5 from the dengue virus.
20:42
And last but not least, we need to add virulence from Ebola virus, and we kill all humanity once and for all. So, okay, now that you have learned all this, there's some things that we have to have in mind. And it's important to know that maybe like in a zombie movie,
21:06
you always think that you will be the hero that will see for humanity, but the most probably scenario is that two weeks into the apocalypse, you will be part of the crew of zombies, and it will not be funny, and you will cry. But now, in a more serious matter, why this is,
21:22
it's not only that this is really dangerous, but not even possible, because there's a lack of knowledge still in biology. Research in biology is happening right now, because we don't really know how the mechanisms or how genes interact with each other, or how some genes become certain proteins.
21:44
Related to that, biology is really unpredictable. Cells are a complex system that are not compartmentalized, so it's a mixture of molecules, and everything can interact with each other, and maybe some molecules interact with other molecules.
22:01
You didn't expect that. Also, mutations happen, and it can happen inside of the genes that can make your virus not work. And the last part, this is not legal at all. We have the Geneva Protocol in the United Nations
22:20
that are overlooking not only the manufacturing and production and storage of bioweapons and toxic molecules, but also give annual reports of the current situation all around the world. And there are like 170 countries right now
22:41
that contribute to this information and overlook that we don't kill everyone. So now you may be thinking that you've wasted time, because this has no use at all. But it has uses in clinic, like gene correction, if you have a disease that is caused by a specific mutation.
23:01
You can change that. You can also create, modify cells to be used as treatment for cancer in the specific cells, or you can use adenoviruses also to treat cancer, not giving them these mutations, but in certain genes that can target cancer cells.
23:21
And also you can control the spread of vectors that spread diseases, modifying the insects. And now a bit of a similar self-promo, if you're more interested in the clinic use of this, of CRISPR, you can look at the talk
23:42
that we did in the PyConnes of 2023, that it's in Spanish but has English subtitles. So the final conclusions really quickly is that synthetic biology can be used as a powerful tool, and one of those tools is gene editing using CRISPR-Cast
24:00
that can be done using Python. This has a lot of uses. This is one of Dines and Les en Queos because we can create a living being on demand, but we always have to have in mind that we have a responsibility and also legally you only can use this power
24:21
to do good in the world. So thank you very much. Very cool talk. So don't do this at home, I guess.
24:41
There's a microphone in the front and already somebody there, so please ask your question. Thank you for an excellent talk. It was a very fun example. What I would like to point out is that actually, and I think everyone should do it at home, but in a real world scenario actually you won't be able to CRISPR-Cast inside the virus for a very simple reason
25:03
because virus lacks protein machinery and the CRISPR-Cast is relying on the protein machinery of partially mammalian, partially bacterial cell to edit. So what you would actually do for IAV production, at least what we do in the lab, is you will synthesize this piece.
25:21
You can put it in a little circular vector and you have two flunking segments that would allow your virus to be happy inside the host and this is how you would basically put this mutation in. And the CRISPR-Cast is an excellent tool, but it's mostly for more complex mammalian genomes.
25:43
But it is a cool example to show. Thank you for explaining that. This is only a silly example and the least thing we do is that you try to become bioterrorists with that. I'm not joking when I say that anything of this,
26:01
it's not that it is forbidden to do, but you wouldn't have a result that could kill anyone because you wouldn't have a virus. Okay, so it's for the safety. That's very smart. Thank you so much. Yes, go ahead. Ask your question.
26:21
My question is when this will be possible, we could do the same thing to reverse the virus, right? Two. The people are dead. You're doing this silly example because it's silly and it's nice and it's clickbaity, as you said.
26:41
But in the other side of the conversation is we should and could and will do this to reverse something like the Ebola virus, which is very deadly as we all know. Yes, and this is something that it was tested for the COVID, for the SARS-CoV-2 pandemic.
27:01
Yes, of course, this is used for reversing that virulence and that infectious potential of the viruses. The CRISPR-Cas was a tool that was used, for example, with the COVID pandemic. And as Elena explained, there are many clinical uses of this.
27:21
So this is used in reality. We have a very silly, well, clickbait example just for giving it the attention that we think that it is worth. But yeah, of course, this could be used and it is used.
27:40
It is actually used in the clinic and for viruses as you said. Hi, thank you very much for the talk. Incredibly polished slides. Yeah, really, really good. Probably a very basic question. It looked like the segments that you replaced with the genes
28:01
was what you were putting in was longer than what you were taking out. Is that correct or is that just me reading those slides? Do you mean the guide, the mold, or what segment? Sorry. So if you had like the slides, these ones, it looks like the top fragment is shorter than the following two fragments.
28:25
Does changing the length of the gene, the total thing? So you mean when we are introducing the new gene, that if it is a problem that it is like longer? No, it's no problem. Just you have to have like in the CRISPR cast system the mold.
28:42
And well, it is most commonly used for just single letters or specific mutations. But well, in theory, I think it is possible. So yeah, we are not geneticians, but I think it is possible. Okay, thank you very much. Just very quickly, same little promo again.
29:05
We are looking to see you at PyCon Spain in October. We have tickets available, so you can come to PyCon Spain. We are very nice people. Yes, everybody go to PyCon Spain.