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California City Considers Restarting Desalination Plant To Fight Drought

GAATTC Positive feedback loop (420 comments)

Consumption -> energy use -> global warming -> worse droughts -> desalinization -> energy use ->->-> This is a very poor long term solution

about 3 months ago
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Minerva CEO Details His High-Tech Plan To Disrupt Universities

GAATTC Re:No lab courses - no meaningful science educatio (106 comments)

Just to clarify. Lab experiences = building recombinant DNA constructs, making transgenic organisms, using $500k microscopes, taking advantage of staffed greenhouses and animal facilities. No amount of online simulation can come anywhere close to replicating time spent in a real research lab.

about 3 months ago
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Minerva CEO Details His High-Tech Plan To Disrupt Universities

GAATTC No lab courses - no meaningful science education (106 comments)

I teach Biology at a small prestigious liberal arts college. My students do their real learning in the laboratories associated with each course and in their independent research projects. Their research projects often run for more than a year and include full time summer research experiences - it is an apprenticeship. This is where they learn to be Biologists and where they get the value out of the college. No amount of book learning or seminar participation can prepare them for the challenges of actually doing science. Growing living organisms, troubleshooting experimental protocols, interpreting data, and having to write and talk about their results (which are rarely 'clean') gives them the skills to make discoveries which will drive technology forward.

about 3 months ago
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Single-Celled Organism Converted Into Electronic Oscillator For Bio-Computing

GAATTC One step closer to Moldies (34 comments)

"a human corporation called ISDN retaliates against the boppers by infecting them with a genetically modified organism called chipmold. The artificial disease succeeds in killing off the boppers, but when it infects the boppers' outer coating, a kind of smart plastic known as flickercladding, it creates a new race of intelligent symbiotes known as moldies " - from Rucy Rucker's Ware Tetrology series (http://en.wikipedia.org/wiki/Ware_Tetralogy). Notably, this set of three books was released free by the author (http://www.rudyrucker.com/wares/).

about 4 months ago
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Drive With Google Glass: Get a Ticket

GAATTC Wearing Glass was the third violation on ticket! (638 comments)

Note she was cited for speeding and a second violation. Wearing Glass was the third violation on the image of the ticket she posts. Speeding while distracted by a web enabled heads up display - how bad would she have felt if she'd killed someone.....

about 9 months ago
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Lessons From the Healthcare.gov Fiasco

GAATTC Complexity - Obamacare vs Obama Campaign (501 comments)

When Obama was re-elected there was a whole string of articles in the press (and associated Slashdot discussions) of how good the technical team who built his campaign infrastructure was. I keep thinking that it is a shame that he did/could not hire the same people to make the health care marketplace work well. It's nearly as if the same contractors who produced ORCA for Mitt Romney got hired to bring about this fiasco. So educate me - is the health care marketplace system much more complicated than the election system? And if not was there a compelling reason to go with large contractors vs. the smart guys from the election team with a demonstrated track record?

about 10 months ago
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Giant Snails Invade Florida

GAATTC And yet people worry about GMO crops (245 comments)

It always amazes me that people worry so much about moving one or two genes around in plants in a thought out and carefully controlled manner yet they hardly worry about the introduction of whole functional genomes (i.e. invasive species) into ecosystems. Given the clear and deleterious impacts of introduced species (as opposed to those for GMOs which are debatable at best) you would think there would be large organizations of anti-introduced genome activists.

about a year ago
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How to Become an IT Expert Companies Seek Out and Pay Well (Video)

GAATTC Re:Consultant ~= prostitute with none of the benef (207 comments)

Trust me - benefits cost a lot more than $300 a month. The benefits that I pay for my $35k entry level employee add up to about $14k per year on top of the salary - and about half of that scales linearly with salary. Benefits include retirement (10% of salary), health insurance (>$300 a month even for an individual if you're providing decent insurance), contributions to social security and medicare, disability insurance, life insurance, unemployment insurance, and a couple of others that I am sure I'm forgetting right now. While you're obviously correct that you can buy 'benefit packages', the value of the benefits at a company that treats it's workers (even the entry level ones) well is significant. No doubt you can include these costs in consulting fees, but $300 a month it is not.

about a year and a half ago
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Ask Slashdot: What Do You Like To Read?

GAATTC Anything by Haruki Murakami (647 comments)

I'm currently reading 1Q84 and, like all the rest of his books, it is fantastic.

more than 2 years ago
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Genome Researchers Have Too Much Data

GAATTC Re:Wrong problem (239 comments)

Completely true - I did not mean to make light of the storage issues that come along with big genomic data sets. The point was more that storage issues are easier to address (you can for the most part throw $$ at these issues until you get to really big data sets) than the challenges of analyzing the data which cannot necessarily be solved with brute force approaches.

about 2 years ago
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Genome Researchers Have Too Much Data

GAATTC Re:Wrong problem (239 comments)

We're trying to do a good job with the annotation which includes manually curating the gene families we are interested in, characterize splicing isoforms, and we're looking for genes/gene families that may be expanded or unique and provide us with insights into the evolution of the unique morphological structures we study in our critter.

about 2 years ago
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Genome Researchers Have Too Much Data

GAATTC Re:Wrong problem (239 comments)

Nope - the bottleneck is largely analysis. While the volume of the data is sometimes annoying in terms of not being able to attach whole data files to emails (19GB for a single 100bp flow cell lane from a HiSeq2000) it is not an intellectually hard problem to solve and it really doesn't contribute significantly to the cost of doing these experiments (compared to people's salaries). The intellectually hard problem has nothing to do with data storage. As the article states "The result is that the ability to determine DNA sequences is starting to outrun the ability of researchers to store, transmit and especially to analyze the data.". We just finished up generating and annotating a de novo transcriptome (sequences of all of the expressed genes in an organism without a reference genome). Sequencing took 5 days and cost ~$1600. Analysis is going on 4 months and has taken at least one man year at this point and there is still plenty of analysis to go.

about 2 years ago
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With Troop Drawdown, IT Looks To Hire More Vets

GAATTC Military technical skills translate very well n=1 (212 comments)

In our Biology department we have a high end confocal microscope. This is a very expensive, sophisticated and complicated microscope with complex optical, mechanical, and control systems. The technician who services it and keeps it running was a sonar technician in a submarine for many years before he got a job working on microscopes. He is very good - logical, careful, and responsible. Obviously this is a small sample size but if his training in the navy has anything to do with his performance in his current job then this is a nice example of military training actually translating well into a civilian technology position.

more than 2 years ago
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US Funding Five Game-Changing Energy Projects

GAATTC Drop in the bucket (529 comments)

$130 million dollars for 8 projects - this is truly a drop in the bucket (if it is even that much). Consider the fact that the government essentially insures nuclear plants against disasters Price Andersen act. With a disaster (3 in the past 30 years) bound to happen again in this country, and given a possible cost of a nuclear disaster in the trillion dollar range if it occurs close to a major city, $130 million dollars is peanuts. Consider the direct tax subsidies for oil exploration and extraction - in the billions of dollars per year (oil subsidies). The sad fact is that the only reason that this kind of funding is news is that our energy policy is so incredibly beholden to entrenched interests that it is a miracle that there is any funding for alternative energy sources.

more than 3 years ago
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MIT Researchers Harness Viruses To Split Water

GAATTC Is this basic, applied or vaporware research? (347 comments)

Press release stories like this should get a special Slashdot category - something like scientific vaporware. While this is potentially an important discovery, none of the information needed to determine if this could ever be an energetically or economically viable way of producing hydrogen is provided. I split water into hydrogen and oxygen every day when I run gels in my lab. The energy you could potentially get from the hydrogen that this electrolysis produces is smaller than the amount of energy it takes to run the gel. Basic research is cool and all (so cool it's what I do for a living), but without more data I would guess that this discovery is very much on the basic end of the basic-->applied research spectrum. Discoveries like this are made all the time - only a tiny fraction end up being useful in real life.

more than 4 years ago
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Help Me Get My Math Back?

GAATTC Re:If you can't handle calculus, science isnt for (467 comments)

If you read my original post you will see that I stated that "I cannot remember ever having to (directly) use calculus in the last 20 years for any of my research". The word 'directly' was used very purposefully. I do realize that the math that underlies some of the statistical and analytical tools that I use includes calculus. However, I have not had to directly deal with solving problems involving integration or derivatives for a long long time.
For example, for some of our PCR based genotyping assays, the data we produce is a melting curve (amount of double stranded DNA measured as fluorescence vs temperature). See Melting curve analysis for a reasonable explanation. To make the data easy to visualize we plot the derivative of the fluorescence vs temperature - this gives us nice peaks centered around the melting temperatures of the PCR products. To get the curves I click a button built into the real time PCR machine software - I never do the math myself. This is not to say that I could not do it (although it would take me a lot longer now than when I was in a math class and practiced this kind of thing on a regular basis).

Just trying not to be preposterous....

more than 4 years ago
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Help Me Get My Math Back?

GAATTC Re:If you can't handle calculus, science isnt for (467 comments)

As a scientist I learned a long time ago not to make general and unsubstantiated claims like "No matter what kind of scientist you plan to be, your knowledge of calculus will be essential." As a practicing molecular geneticist and cell biologist I use statistics quite often. I cannot remember ever having to (directly) use calculus in the last 20 years for any of my research. I really enjoyed all of the calculus (and linear and set theory and ...) that I took a long time a ago. When I look back at it what I really got out of all my math classes (and O-Chem too for that matter) was the the knowledge that I could learn anything I really set my mind to - if I have to.

more than 4 years ago
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Clemson Staffer Outlines College Rankings Manipulation

GAATTC Alternatives to US News ranking (163 comments)

One alternative is to bow out http://web.reed.edu/apply/news_and_articles/college_rankings.html of the rankings game and take a principled stand as Reed College has done. One way of thinking about attending a fine school like this is that you "want to go to a school that isn't interested in selling out its education." Perhaps not surprisingly, US News didn't actually remove Reed from the rankings, they just ranked Reed (lower) with an incomplete data set. The other alternative could be called 'open source' ranking. The University and College Accountibility Network http://www.ucan-network.org/ ranks colleges in a common format, has useful information, and best of all, you don't have to buy a copy of US News to get the rankings!

more than 5 years ago

Submissions

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Plant temperature perception imaged using open source microscopy software

GAATTC GAATTC writes  |  about 10 months ago

GAATTC (870216) writes "How plants sense temperature is not well understood. An automated microscopy system controlled by Micro-Manager open source microscope automation software has been used to capture the dynamics of plant high temperature gene expression responses. A surprising finding is that waves of gene expression sweep down the roots as they grow after exposure to high temperatures."
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Open source laser pointer whole building graffiti

GAATTC GAATTC writes  |  about 7 years ago

GAATTC (870216) writes "A 60mW laser pointer, camera, laptop, and a 5000 lumen projector are tied together with some open source code to produce the best whole building interactive graffiti ever. A bicycle mounted system consiting of a camera connected to a laptop tracks a laser pointer signal on the side of buildings. A connected projector projects what is drawn in real time with a variety of effects, like the tools available in Photoshop. What a great way to get your political message across without running the risk of getting arrested for property damage."

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