The interface between living tissues and silicon is the hardest part of making anything implantable. Almost all current "biocompatible" materials are actually simply non-toxic, so they are quietly covered with a mucus membrane and don't cause inflammation. This problem severely limits the number and spatial resolution of connections that can be established between implants and neurons in vivo, so thinking about large scale integration between the two is a long way off. For such integration, one would need electrode materials (coatings) that stimulate neurons to make connections with the inorganic component, as opposed to the current methods that jam in an electrode by brute force and just rely on surrounding neurons' ability to learn what the periodic voltage pulses from this object may actually mean. Again, there is a difference between producing a coating that does not kill a neuron, which is forced to live on a chip (as done in these cell-chip fusion experiments), and a coating that will meaningfully interface with neurons in a living organism.
Being able to grow living neurons on chips is however useful for studying how neurons function (on silicon chips, anyway - another known major caveat of in vitro studies). In this case, the high spatial resolution of the electrodes on the chip can help to study processes (like signal propagation) within a single neuron and in (hopefully increasingly larger) networks of neurons.
Since apparently not everyone can sign up right now, I put together Creating a GooglePage sampler with a few screenshots of the interface (WYSIWYG and HTML Editor) and some of the standard page layout templates. I figure that these servers can't be slashdotted, right?
The interface is actually quite easy and straightforward, although I have not found a template that I am completely happy with yet. A problem that I find a bit ironic is that I can't use the spellcheck option from the Google Toolbar in the WYSIWYG editor window, because it simply creates a mess. But this feature is not unique to googlepages - I have the same problem with the rich-text view of the wordpress.com blog editor as well.
I know that it's a little late in the day, but since I didn't see anybody mention the costs involved - the short answer is thousands of dollars.
The cost of (buying) DNA varies dramatically depending on the length and the purity of a sample, largely because DNA samples of different length are produced by different methods. The cost purification can also add up to more than that of the production. This is one of the reasons why the Nature article specifically mentions common assumptions about the requirements for DNA components that can be used in this type of programmed self-assembly - essentially he has demonstrated that this can be done a lot cheaper than people have assumed.
The short "staples" in this case are synthetic single-stranded DNA (also called oligonucleotides or oligos). These can be ordered on-line, and the price is typically described as 1$/base. Each oligo is synthesized by adding one base at a time and each time there is about 1% chance of an error - the exact number will depend on the process, but one vendor (IDT) explains that for a 27-mer about 30% of the sample will contain mistakes. Purifying the sample to keep only the correct 70% of the oligos can make it 2-3 times more expensive, hence the article specifically mentions that the proposed method works with cheap unpurified staples. But still, a hundred of different staples each about 30 bases long will be about 3000$.
Even from the short description above, it is clear that the same method can not be used to produce the template that is 1000's of bases long, so they use a natural sequence that can be multiplied by cloning - a relatively cheap process, although with extraction and purification the costs add up - 80% of the total cost according to TA.
Adding up the above estimates, my educated guess is that the total cost of materials in this work adds up to about 10k $ quite easily - custom synthesized and purified DNA is still more expensive than gold on a per gram basis, but then again, so are most nanomaterials. The saving grace is that in some cases you need very little of them to improve or make a product, but until we find a way to make custom-designed nanomaterials on an industrial scale, none of this stuff will be affordable for projects outside of research labs.
Thank you for the thoughtful answer - reading the posts today I'm glad that I've chosen this thread over the one where the debate has shifted to who is a bigger moron! I don't think that it is profitable to continue the debate on the merits of the post - perhaps the discussion is more important than the post itself, which is certainly not the first such case on Slashdot.
I looked at the suggested links, but I didn't quite see what I was looking for. I am interested in DNA structure, mostly that of oligos (less than 50 bases long) for surface-based applications. So actually a couple of the options on the GD site appear to suit my needs more than the full-blown genomics/proteomics resources that are indeed easy to find. The information that I need (Tm's, hairpins, construction of orthogonal oligo sets, maybe choosing a couple of restriction enzymes) is rather basic, but at the same time, most tools give different answers (e.g., for Tm's), and none are actually valid for the conditions (high-salt buffers) that I need to use.
It's basically the problem of being at the interface between two disciplines. The interface is considered as trivial by both of the parent fields, while neither of the two parent methodologies strictly apply. So yes, I have asked quite a few people, but so far have not found anything that fits my needs. But if you or others care to make any additional suggestions (either here or to biohack [at] nanowiz.mailshell.com), they will be appreciated!
I am not sure why simply because it is about one of many available tools, the post is out of place on Slashdot. I am not a member of a huge biochem or medical lab, but I am trying to learn and use biochemistry, so I can use every bit of help. My situation is also not unique - many researchers with background in "hard sciences" are now working with DNA in nanobiotechnology and biosensor projects. So user-friendly software that automates basic, routine calculations, and thus helps non-experts to avoid costly errors, is very welcome. Having many choices of such programs is great - just as it is great to have countless free and open-source replacements for Notepad. Since you apparently are quite familiar with other software for DNA design and analysis, perhaps you could share links to a few that you find particularly useful?
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The interface between living tissues and silicon is the hardest part of making anything implantable. Almost all current "biocompatible" materials are actually simply non-toxic, so they are quietly covered with a mucus membrane and don't cause inflammation. This problem severely limits the number and spatial resolution of connections that can be established between implants and neurons in vivo, so thinking about large scale integration between the two is a long way off. For such integration, one would need electrode materials (coatings) that stimulate neurons to make connections with the inorganic component, as opposed to the current methods that jam in an electrode by brute force and just rely on surrounding neurons' ability to learn what the periodic voltage pulses from this object may actually mean. Again, there is a difference between producing a coating that does not kill a neuron, which is forced to live on a chip (as done in these cell-chip fusion experiments), and a coating that will meaningfully interface with neurons in a living organism.
Being able to grow living neurons on chips is however useful for studying how neurons function (on silicon chips, anyway - another known major caveat of in vitro studies). In this case, the high spatial resolution of the electrodes on the chip can help to study processes (like signal propagation) within a single neuron and in (hopefully increasingly larger) networks of neurons.
Since apparently not everyone can sign up right now, I put together Creating a GooglePage sampler with a few screenshots of the interface (WYSIWYG and HTML Editor) and some of the standard page layout templates. I figure that these servers can't be slashdotted, right?
The interface is actually quite easy and straightforward, although I have not found a template that I am completely happy with yet. A problem that I find a bit ironic is that I can't use the spellcheck option from the Google Toolbar in the WYSIWYG editor window, because it simply creates a mess. But this feature is not unique to googlepages - I have the same problem with the rich-text view of the wordpress.com blog editor as well.
I know that it's a little late in the day, but since I didn't see anybody mention the costs involved - the short answer is thousands of dollars.
The cost of (buying) DNA varies dramatically depending on the length and the purity of a sample, largely because DNA samples of different length are produced by different methods. The cost purification can also add up to more than that of the production. This is one of the reasons why the Nature article specifically mentions common assumptions about the requirements for DNA components that can be used in this type of programmed self-assembly - essentially he has demonstrated that this can be done a lot cheaper than people have assumed.
The short "staples" in this case are synthetic single-stranded DNA (also called oligonucleotides or oligos). These can be ordered on-line, and the price is typically described as 1$/base. Each oligo is synthesized by adding one base at a time and each time there is about 1% chance of an error - the exact number will depend on the process, but one vendor (IDT) explains that for a 27-mer about 30% of the sample will contain mistakes. Purifying the sample to keep only the correct 70% of the oligos can make it 2-3 times more expensive, hence the article specifically mentions that the proposed method works with cheap unpurified staples. But still, a hundred of different staples each about 30 bases long will be about 3000$.
Even from the short description above, it is clear that the same method can not be used to produce the template that is 1000's of bases long, so they use a natural sequence that can be multiplied by cloning - a relatively cheap process, although with extraction and purification the costs add up - 80% of the total cost according to TA.
Adding up the above estimates, my educated guess is that the total cost of materials in this work adds up to about 10k $ quite easily - custom synthesized and purified DNA is still more expensive than gold on a per gram basis, but then again, so are most nanomaterials. The saving grace is that in some cases you need very little of them to improve or make a product, but until we find a way to make custom-designed nanomaterials on an industrial scale, none of this stuff will be affordable for projects outside of research labs.
Thank you for the thoughtful answer - reading the posts today I'm glad that I've chosen this thread over the one where the debate has shifted to who is a bigger moron! I don't think that it is profitable to continue the debate on the merits of the post - perhaps the discussion is more important than the post itself, which is certainly not the first such case on Slashdot.
I looked at the suggested links, but I didn't quite see what I was looking for. I am interested in DNA structure, mostly that of oligos (less than 50 bases long) for surface-based applications. So actually a couple of the options on the GD site appear to suit my needs more than the full-blown genomics/proteomics resources that are indeed easy to find. The information that I need (Tm's, hairpins, construction of orthogonal oligo sets, maybe choosing a couple of restriction enzymes) is rather basic, but at the same time, most tools give different answers (e.g., for Tm's), and none are actually valid for the conditions (high-salt buffers) that I need to use.
It's basically the problem of being at the interface between two disciplines. The interface is considered as trivial by both of the parent fields, while neither of the two parent methodologies strictly apply. So yes, I have asked quite a few people, but so far have not found anything that fits my needs. But if you or others care to make any additional suggestions (either here or to biohack [at] nanowiz.mailshell.com), they will be appreciated!
I am not sure why simply because it is about one of many available tools, the post is out of place on Slashdot. I am not a member of a huge biochem or medical lab, but I am trying to learn and use biochemistry, so I can use every bit of help. My situation is also not unique - many researchers with background in "hard sciences" are now working with DNA in nanobiotechnology and biosensor projects. So user-friendly software that automates basic, routine calculations, and thus helps non-experts to avoid costly errors, is very welcome. Having many choices of such programs is great - just as it is great to have countless free and open-source replacements for Notepad. Since you apparently are quite familiar with other software for DNA design and analysis, perhaps you could share links to a few that you find particularly useful?