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CPU's Heat Output to Amplify DNA Could Make Drastically Cheaper Tests

timothy posted about two weeks ago | from the only-waste-heat-is-wasted dept.

Biotech 27

MTorrice (2611475) writes "Researchers have harnessed that heat from a computer CPU to run the polymerase chain reaction (PCR) to amplify DNA in a blood sample. The team developed software that cycles the temperature of the CPU to drive PCR's three distinct steps.The method allowed them to detect miniscule amounts of DNA from a pathogenic parasite that causes Chagas disease. They hope their technique will lead to low-cost diagnostic tests in developing countries." (Always good to put waste heat to a practical purpose.)

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You completely missed the point of the article (2, Insightful)

Anonymous Coward | about two weeks ago | (#47817867)

The big deal is they could do this with the existing machine, and they didn't need to make modifications.

Waste heat has nothing to do with it.

Re:You completely missed the point of the article (1)

EvilSS (557649) | about two weeks ago | (#47817923)

The big deal is they could do this with the existing machine, and they didn't need to make modifications.

Waste heat has nothing to do with it.

Thank you. I was trying to figure out what the heck I was missing in the summary that would make this a big deal.

Re:You completely missed the point of the article (3, Informative)

thesupraman (179040) | about two weeks ago | (#47820953)

No, it is a stupid article. Someone has come up with an over-complex solution to a non existent problem.

The use of the CPU to create temperature is a overly complex and difficult approach, compared to using a simple regulated heater which would be much simpler, more reliable, more repeatable, and cost less.
Really, they are using a whole computer just to generate the heat, and a separate computer (cellphone) to run the reaction. stupid and overly complex.
If there is a demand for a usb controlled accurate heat generator it would be trivial to build one with a usb microcontroller, its pwm output, and a heating resistor.
it would cost less, be more accurate, smaller, waste less power, more reliable, cheaper. I doubt it would be difficult to find a suitable device already from some
similar application.

Temperature regulation is absolutely NOT a contributing factor to high cost of such tests.

Hell, a power supply, some switches, and some resistors would do it if you didnt want automatic control.

Re:You completely missed the point of the article (1)

Doubting Sapien (2448658) | about two weeks ago | (#47821211)

Mod parent up. I've read only the abstract of the article, but even still, the proposed system as described is a terribly expensive way to do PCR for another reason. Typical PCR reaction runs usually thermocycle around 20-30 times. That is 20 to 30 times you will need to change the temperature of your heat sink from a high denaturing temp to a low annealing temp to facilitate DNA replication. One of the first things I was taught in heat transfer as an electrical engineer is that the overwhelming factor involved in electronics failure is material fatigue due to thermo expansion/contraction. If you try to turn the CPU of a commodity PC into a thermocycling heat sink, you are going kill that machine really fast. Better to put in the investment for a proper thermocycler and related equipment designed to do the job correctly and reliably. Molecular biology is cheap enough these days that you don't need to do these crazy ostentatious hacks.

Re:You completely missed the point of the article (1)

MattskEE (925706) | about two weeks ago | (#47821913)

Indeed. Using a CPU as a heater is just silly, it would be like frying an egg on the engine block of your Ferrari: technically possible but there are better and cheaper ways to get the same thing done. It wouldn't be that hard to hack together a decent computer controlled heater and sample holder/heat exchanger from a few hundred to a thousand bucks in parts (depending on how much labor you want to put into it).

Instead they have this fiddly system where they have to load samples onto the heatsink of a running computer with the motherboard out in the open, and they must be careful not to drop anything onto the motherboard which could damage it, there are ESD damage concerns, and liquid damage concerns. The temperature control cannot be that good, given the vertical temperature gradient along the heatsink base to top.

It's also disingenuous (but common) for them to merely compare the raw part cost of a DIY system to a pro system. The Pro system is much more capable and robust, support is available, and it includes the labor cost of designing and assembling it. Too many DIY projects claim a "cost" which treats labor as a free commodity.

Re:You completely missed the point of the article (1)

pepty (1976012) | about two weeks ago | (#47822471)

1. You're right, temperature control is pretty tangential to the costs, but you absolutely do need automated control. 2. The cell phone acts as an imager for the results, it doesn't control the reaction.

Uh wut? (0)

Anonymous Coward | about two weeks ago | (#47817909)

Has this summary been round-tripped through Google translate, or is it just a jumble of random words?

Cooking Instructions... (0)

Anonymous Coward | about two weeks ago | (#47817935)

$ctrPCR = 3;
do {
        print "Cooking...Iterations left: " . $count ";
        $count--;
} until ($ctrPCR == 0);
print "DING...Please wait 1 minute as product will be hot to the touch.\n";

Actual Link And Better Details (0)

Anonymous Coward | about two weeks ago | (#47817967)

If you don't want to be redirected, go here: http://cen.acs.org/articles/92/web/2014/09/Computers-Heat-Sink-Used-Slash.html Shortened URLs should be banned on Slashdot. Who types in URLs from a website? Just click it or copy+paste.

In addition to the computer and cell phone, the equipment and reagent costs for this new method are $41.50, far less than standard PCR equipment that costs about $19,000. The team hopes their low-cost method will allow diseases such as Chagas to be better monitored and treated in the field.

The takeaway is that PCR equipment sounds far more expensive than it needs to be. Not being a medical professional, I really hope they are more than just adjustable heaters. These guys are putting tiny test tupes into the fins of a CPU heatsink and giving it busy work to change the temperature. A cell phone app is used as the controller.

Clickable version of the link [acs.org]

Re:Actual Link And Better Details (2)

UnderCoverPenguin (1001627) | about two weeks ago | (#47818359)

The takeaway is that PCR equipment sounds far more expensive than it needs to be.

A lot of equipment is more expensive than it could be. Doing more than a cosmetic redesign opens up a vendor to liability issues. Until either the lawyers are comfortable that the cost savings of a new design sufficiently outweigh the potential cost of law suits or they see competitor stealing too much of their business, they won't be willing to take the risk. Right now, these third world countries don't look like good enough markets to bother with.

Re:Actual Link And Better Details (1)

Anonymous Coward | about two weeks ago | (#47819049)

Cost of heater: $50
Cost of computer programmer: $3000
Cost of clinical trial of 50,000 patient samples: $5 million dollars
Break-even cost assuming they sell 280 of these devices: $18,928.75

Re:Actual Link And Better Details (1)

Jason Goatcher (3498937) | about two weeks ago | (#47820699)

I wonder if they might be willing to do useful work, like distributed computing stuff. Haven't crunched in forever, but my old team Free-DC would probably love for them to join and add a bit of oomph to our team.

Why?? (1)

gurps_npc (621217) | about two weeks ago | (#47818087)

The basics of dna replication are well known. We know they need to cycle heat.

They should have been using a standard heater, using the CPU's chip seems like a kludge.

It might work, but it seems unlikely to be the better than a purpose built device. At most it saves a bit of cash and energy, at the expense of accuracy and complex programming.

Re:Why?? (1)

wonkey_monkey (2592601) | about two weeks ago | (#47818721)

They hope their technique will lead to low-cost diagnostic tests in developing countries.

Re:Why?? (0)

Anonymous Coward | about two weeks ago | (#47819419)

Low cost PCR machine already exist. Not to mention that the per sample larger share of the cost is not in the equipment but in the enzyme master mix and the primers. If you wanted dirt cheap equipment, three water baths would be hard to beat.

Reminds me of (2)

UnderCoverPenguin (1001627) | about two weeks ago | (#47818095)

This reminds me of a CPU fan that is powered by the heat using a tiny Sterling Engine. Maybe not the kind of "practical use" of the waste heat the editor had in mind, but still an interesting idea.

not waste heat, they purposefully cycle the CPU (0)

Anonymous Coward | about two weeks ago | (#47818119)

The process they invented requires a heat cycling of the materials to work and knowing that computers are readily found almost everywhere, they wrote a small app which causes a computer CPU to generate heat cycles as needed. So it's really not waste heat since the purpose of the application is to generate this heat.

Seems like overkill (2)

Rich0 (548339) | about two weeks ago | (#47818121)

Do you really want to stick a whole PC in a lab, expose it to chemicals, and put its CPU through repeated heat/cool cycles just to save on a thermocycler?

They mention costs like $19k to obtain one otherwise. I'm sure they sell for that much just as I'm sure you can go spend $2000 on a linux license, but all a thermocycler needs to do is heat samples and cool them. Clearly the CPU isn't going to be a high-performance cycler - you could probably build a little cycler that just uses radiative cooling and some resistive heating for $50. I see peltier heat sinks selling for $40 these days, so I'm sure for $100 you could build a thermocycler on the cheap.

An ideal thermocycler just needs to heat samples to about 95C for a few seconds, cool them down to about room temperature for a few seconds, and then hold them at something around body temperature for a minute or two, The time spent ramping temperature up/down is basically dead time, and you have to repeat this 20-30 times, so if your cycler can change temperature in seconds instead of minutes you can save a LOT of time per test. Peltier effect tends to be the way things are done, or at least it was back when I was using these in the labs.

It looks like openpcr.org has a unit for $600. I'm sure it could be improved on, but I imagine that as you get cheaper, you lose precision, and that does matter. I can't imagine that a CPU can maintain a temperature +/- 0.5C without quite a bit of effort.

Re:Seems like overkill (0)

Anonymous Coward | about two weeks ago | (#47818513)

A precision heater could probably be constructed from the e-waste sent to the area. Calibration, like always, is not optional.

Re:Seems like overkill (0)

Anonymous Coward | about two weeks ago | (#47822917)

The CPU or its packaging has a built-in temperature sensor, and one can always be added on USB or RS-232. Software can control clock and voltage, or at worst these can be set precisely in the BIOS setup. At an example, let's run an old Athlon 64 fanless in semi-hot summer weather, in an open case with no air flow except for a slow and quiet 80mm PSU fan. It will eventually reach 105C, trip on that limit and shut down, but you can set lower CPU frequency and vcore, halving the maximum power output. Now the temp reached after some heating with a program like "cpuburnK7" will be a safe and stable one such as 90C. That's what I got of it. The goal was just to get the machine working reliably (to store and play music) even though it was missing a fan. Seems easy though winds or changes in ambient temperatures would act as factors to mess it up.

Re:Seems like overkill (1)

Rich0 (548339) | about two weeks ago | (#47825165)

Sure, the CPU has a temperature sensor, but how precise is it? And how much power does that CPU consume to do the job, vs a dedicated machine? And how long will the test take - I can't see a CPU dropping from 90C to 45C in nearly the same time as a thermocycler that uses peltier cooling backed by variable speed fans.

The CPU temperature sensor is also in the CPU core, not at whatever point in the heatsink the sample is placed at. This would probably make a difference as well.

If it really saved $19k it might be worth it, but the current DIY thermocycler I referenced is $600. I bet that could be improved on if you wanted to make compromises, and I imagine you could still make it better/cheaper than doing it with a CPU.

useless publicity stunt (1)

Anonymous Coward | about two weeks ago | (#47818125)

A PCR reaction needs 3 temperatures - a denaturing temp (usually 95C), an annealing temp (usually around 55C), and an elongation temp (usually around 75). The reaction is cycled between the temperatures to cause a 2^n increase in copy number in the reaction where n is one cycle through the temperatures.

A low-tech heating solution could be obtained for less than $50, would not require any special modifications of reaction conditions (the article states that they used DMSO to lower the denaturing temperature), and would not require you to open up a computer case in a low-tech environment.

Useless publicity stunt.

Re:useless publicity stunt (0)

Anonymous Coward | about two weeks ago | (#47822953)

Throw away or reuse the computer's door (a largeish, more or less thin rectangular slice of metal) and then opening up the case is no longer a concern.

Obligatory XKCD (2)

gerf (532474) | about two weeks ago | (#47818145)

Obviously they use the spacebar to toggle the heat on and off. https://xkcd.com/1172/ [xkcd.com]

Re:Obligatory XKCD (0)

Anonymous Coward | about two weeks ago | (#47818379)

No, they just press the start button on a Windows PC. They tried using Linux but couldn't get the CPU above 50c at 100%.

Re:Obligatory XKCD (1)

lazy genes (741633) | about two weeks ago | (#47822483)

They are trying to find an excuse to mine bitcoins in the lab. They will probably end up with a new altcoin called CPUCOIN.

Yeah, no (0)

Anonymous Coward | about two weeks ago | (#47823347)

PCR Thermal cyclers, especially ones without fancy accessories, are very cheap.

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