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What's the state of the art for solving the following problem. You imagine a set of features that you want a life-form to have. Just to take an arbitrary example, say you want your life-form to have a) a strong sense of smell, b) the ability to fly and c) a comfortable couch shaped saddle on its back. What's the sequence of steps you need to take so that you can create this life-form in the lab?

I realize that we are probably far away from solving this very general problem. But perhaps there are some smaller subproblems that we do know how to solve.

For example, as far as I gather, you can probably make any living being fluorescent green in color by inserting into its genome the gene responsible for expressing the Green Fluorescent Protein. So may be if we limit the set of features one is allowed to choose from, the above problem can be solved. So my first question of the set of questions is:

1) What features can be easily inserted into almost any organism easily?

Next, I imagine that to design and create an artificial life-form will consist of three steps:

  1. Figure out which proteins will give rise to those feaures,
  2. Design a genome that will express those proteins in the right quantities and
  3. Implant that genome into a cell and actually let the being grow.

2) Is the above sequence of steps correct, or am I missing something?

3) What is the state of the art for each of these steps?

Finally, in light of the recent spur in the open source biology groups and DIYbio enthusiasts, I feel that there might be some very simple but really cool things related to my question that you can already do in your garage. For example, may be there is some very simple single-cell life-form that's so well understood that you can add or subtract tons of features from it with a budget of a few hundred dollars. So my final question is:

4) What is the cheapest experiment you can perform at your own home without access to a biology lab which involves changing the genome of a living organism in a way that's functionally visible? (An arbitrary example: Can you create an apple that's blue in color with a budget of $500? By create, I mean you should be able to hold the blue apple in your hand.)

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    $\begingroup$ You may want to try splitting this into multiple questions (along the delineations you've already set up). It will keep the answers better organized. $\endgroup$ – jonsca Jun 22 '12 at 4:49
  • $\begingroup$ This would seem to be far too localised: the situation will inevitably change every year. And you've asked several questions in one, which is very strongly discouraged. $\endgroup$ – EnergyNumbers Jun 23 '12 at 10:38
  • $\begingroup$ @EnergyNumbers: I doubt that the situation of creating your transgenic life form in your garage with $500 will change anytime soon... $\endgroup$ – nico Jun 23 '12 at 16:06
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    $\begingroup$ @nico: Can't all E.coli be induced competent under heat shock? Just need calcium chloride additionally. Also I thought you can buy the pGLO plasmid pre-prepared. $\endgroup$ – Armatus Jun 24 '12 at 10:08
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    $\begingroup$ To put GFP into E.coli you would also need an autoclave or some other way to sterilize your medium and IPTG for induction in most cases. Naturally found E. coli would probably not be suitable, not even speaking on the difficulty of isolating them specifically (and the dangers if you accidentally isolate one of the dangerous strains). You probably would need to get some E. coli K12 and the plasmid from a friendly academic lab to be able to do this on a budget. $\endgroup$ – Mad Scientist Jun 24 '12 at 10:26
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The problem is of course very complex so take my answers as simplifications.

Most transgenesis so far has been done on unicellular beings (bacteria, yeast), which we can change as much as we want fairly "easily", plants, insects and some mammals. Notably, for the latter case, mice are the species which has been used the most for transgenesis, as they are cheap (compared to, say, using pigs), do not take lots of space, have big litters and a quick reproductive cycle (~20 days). Aside from mice we've seen GFP rats, pigs, dogs, cats, sheep and probably there is more, but I will mostly restrict my answers to mice (as far as I know there are big technical difficulties in applying transgenics procedures to something bigger than a mouse, but to be honest I could not explain you the details on this as I have never done it).

What features can be easily inserted into almost any organism easily?

Well, essentially, it is easy to give rise to monogenic traits (i.e. traits that depend on a single gene). Generally speaking, when you want to have more traits, or need more than 1 gene to have the trait you create single transgenics and then breed them together.

So, if your phenotype depends on the presence of gene A and B you will generate a (mouse) line expressing A, one expressing B, you breed them together and, if you are lucky, a part of the pups will be expressing both.

Next, I imagine that to design and create an artificial life-form will consist of three steps: 1. Figure out which proteins will give rise to those feaures, 2. Design a genome that will express those proteins in the right quantities and 3. Implant that genome into a cell and actually let the being grow.
Is the above sequence of steps correct, or am I missing something?

No, that is not how it is done!

There has been, to my knowledge, only one (very impressive) attempt to do that, a project led by Craig Venter at Celera Genomics. The project resulted in the creation of the first synthetic life form, named Mycoplasma laboratorium (see also the original paper on Science). Doing this for a multicellular being is, presently, science-fiction.

What normally you would do is to insert or remove just the piece of DNA you need in the genome.

There are different approaches to do that: for instance, you can start from embryonic stem cells, from fertilized oocytes or from spermatozoa.

This is the general process for making a transgenic mouse:

Making a transgenic mouse
Source: https://web.archive.org/web/20161212170103/http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/T/TransgenicAnimals.html

Now, depending on how you inject your gene you can distinguish between transgenics and knock-in mice. In a transgenic mouse you insert the gene somewhere in the genome and, although there are method to understand where it ended up you generally do not know. Knock-in animals, instead, target a specific region of the genome. This is usually used in order to change an existing gene, to improve its function or to remove its function (knock-out animals). This process, called gene targeting relies on the biological process called homologous recombination.

So, why don't we just synthesize a new genome each time? Aside from Venter's dream, the process would:

  1. have incredibly high cost
  2. be extremely complicated technically
  3. be extremely long (mostly for reason 2)
  4. suffer from the problem that there is so much we do not know about genome regulation in a bacteria, let alone in a mouse! You have to think that the genome is not just a series of genes one after another: there is a big part of regulatory regions that define things like the 3D form of the genome, which determines when and how much genes are accessible for transcription, when and where they are activated and so on. Also, more and more attention is now drawn to something called epigenetics marks, modifications of the DNA, or its associated proteins that can also modulate its transcription.

What is the cheapest experiment you can perform at your own home without access to a biology lab which involves changing the genome of a living organism in a way that's functionally visible? (An arbitrary example: Can you create an apple that's blue in color with a budget of $500? By create, I mean you should be able to hold the blue apple in your hand.)

Quick answer: no you cannot.

  1. Health authorities will be not very happy if you start to produce transgenic organisms in your garage
  2. The sole cost of the reagents which you will need to create the transgene will be >$500. You would then need various machines (e.g. a thermocycler, probably a spectrophotometer, a hood, etc etc.).
  3. I personally don't have a clue how one creates a transgenic plant, but I suspect it is not much easier than an animal. And definitely you don't want a mouse colony in your garage, do you?

An easy experiment you can do is extracting (fairly unpurified) DNA with stuff you have at home. More than that it gets really complicated.

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  • $\begingroup$ In principle a very good answer, but I think there are some points where science can actually do a bit more than you describe - I'll try to write up an additional answer with these points later :) $\endgroup$ – Nicolai Jun 28 '18 at 13:20
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This answer is mostly meant to be an addition to nico's answer, which while correct and on the point, does not completely cover what we can do nowadays.

1) What features can be easily inserted into almost any organism easily?

The short version of nico's answer here is 'any monogenic trait', which is basically the GFP example.
I would however say that - with additional, sometimes years of work of course - synthetic biology is at a point, where we can make a single cell perform pretty much any non too complicated task (ballpark something you can describe in one simple sentence): the creation of regulatory networks that react to a certain extra-cellular signal is totally possible, as is the generation of multiple proteins (genes) as output. (These two video's might give an idea, I couldn't find a good source right now that isn't overly specific.)

However, this is still very far away from things like sense of smell, flying or making certain body parts, all of which require the coordinated interplay of many different cells.

2) Next, I imagine that to design and create an artificial life-form will consist of three steps:

  1. Figure out which proteins will give rise to those feaures
  2. Design a genome that will express those proteins in the right quantities and
  3. Implant that genome into a cell and actually let the being grow.

nico mostly focused on the problem with the second and third point: we don't make genomes - we change them. For adding or changing single genes this has only recently become relatively easy (this is what CRISPR is for), and even adding multiple things in one big block is doable. But at some point you need to start doing this iteratively, which comes with its own set of further complications.

However even with the first point there can be a problem: what if there is no single one protein that makes the function you want? Often you'll need multiple proteins interacting or you need to start combining multiple functions into one protein (which opens the box of protein design - I'm just not gonna go into that though)

4) What is the cheapest experiment you can perform at your own home without access to a biology lab which involves changing the genome of a living organism in a way that's functionally visible? (An arbitrary example: Can you create an apple that's blue in color with a budget of $500? By create, I mean you should be able to hold the blue apple in your hand.)

This may actually be the only point, where I think nico's answer is not really spot on.
He's right that there are considerable safety, legal and equipment barriers, but still 'open bio science' is a thing: from (mostly local) open wetlab spaces to 3D-printable laboratory equipment there is a lot of possibility out there. That being said, its is very illegal in most countries to make GMOs (which the blue apple would likely be) without the corresponding licenses etc.

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  • $\begingroup$ Very good points Nicolai, and I definitely agree with you! Indeed it's incredible how fast things have changed since I wrote my original answer... thank you for improving on it! $\endgroup$ – nico Jun 29 '18 at 8:03

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