Biotech: Tools of the trade

tools-biotech.com

So, you’ve got yourself a team of dedicated Biology grads, or you’ve taught yourself all the basics of Molecular/Synthetic Biology. It’s time to make a start-up  !

But wait, aren’t you forgetting something?

  • Knowledge workers Check.
  • Tons and tons of ideas Check.
  • a workspace/large-sized dorm room Check.
  • equipment che…wait, what ?

Yes, there’s a large difference between a Software startup and a Biotech startup… the equipment needed to test your humongous collection of semi-viable ideas !

For a software startup, the equipment needed are easy :

  1. Code monkey(s).
  2. Computer(s).

While a Biotech company, on the cheap, will at least need the following to test their ideas:

  1. PCR equipment 
    Many Biotech projects will be manipulating DNA — operons for metabolic pathways, genes for specific molecules… — and to do that you need to be able to manipulate the specific piece of Genome you’ve decided to test, modify, or study. To do that, a PCR is essential, and there are several to choose from. Going from “industrial/lab” strength to DIY/biohacker grade.
  2. Reagents, Culture media, etc…
    (this is highly dependable upon the idea/project, but since you’re doing Biotech, it’s very probable you at least have a few cell cultures to take care of).
  3. Basic Lab Equipment (test tubes, Erlenmeyers, etc…).
  4. Microscope(s).
    (This depends on whether you need to observe something in-vivo or not, or if your project requires it).

There are many probably other basics I’m missing, like safety & health equipment, etc…

So, how would a wannabe-bioentrepreneur get started ? How can you validate the ideas if you’re low on funds ?

There are several options, depending on how much you/your team can muster together, if you have jobs on the side, etc… :

  1. “Collaborate” with a local university.
    This works particularly well if you can get your hands on an interested professor or researcher, who might plea with the administration on your behalf to grant you access to their equipment.
  2. Work in a hackerspace.
    Hackerspaces adapted to this kind of work are slowly creeping up all around the world, they tend to be very well versed in open source and open hardware (OpenPCR, etc…) and can be a good place to validate the ideas in themselves (when validated, you’ll still need market research and probably funding at some point, if you plan on launching a product).
  3. Buy time for specific parts of your experiment on University or industrial equipment, using ScienceExchange, a marketplace for experiments !

So, that will be all for today,

Have fun !


I’m currently going through the Fizzle introduction courses, and the one I’m in — Finding your Subject — has led me to evaluate a dozen or so possible subjects with a Weighted Decision Matrix (fun little tool, I’ll probably use that again in the future !).

I’ve narrowed it down to one of these (or a combination…):

  • Biotechnology.
  • Crowdfunding.
  • Wearable Technology (+- App Development).

The final part of the course is to write 5 blog posts ( + a hypothetical product outline) on each of the ideas.

This is number 5/5 of the Biotechnology subject.

PS: The Fizzle Show is an excellent podcast, go listen !

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GMO produce VS produce made in GMO’s.

Hija, hope everyone is well.

Today we’ll examine the difference between eating a GMO and eating something produced by a GMO.

Most GMO’s nowadays are pesticide resistant, or produce their own pesticides. There’s a very important distinction !

No matter how optimistic, it has to be said that a GMO that is resistant to a pesticide like Round-Up will at some point accumulate more Round-Up than a plant that’s not resistant, simply because of the act of spraying… Of course, a lot of studies are still needed to determine if some pesticides are truly toxic in the doses we consume, if they accumulate, etc… (Though said studies are approaching the end…and it does NOT look good for Monsanto !)

But the GMO’s one has to REALLY be careful with remain the ones that produce their own pesticides, as this is, technically, what toxic plants do… The effect of the new metabolic process creating said pesticides might also produce byproducts that could be harmful, but studies and tests before the product can be cultured should weed the truly toxic GMO’s out.

But many people lump GMOs and GMO produced proteins together, and this is a BIG mistake !

A protein is, in it’s simplest form, a succession of small “beads”. So to recreate it fatefully, you can simply align identical “beads” and Presto ! You have an identical protein !

Therefore, it doesn’t really matter if it’s a GMO or a normal plant that “makes” the protein, as the end-product is the same (well, there have been a few corporations who’ve tried to jump the gun with imperfect proteins, but the laws have been updates, and it should thankfully be more rare nowadays !).

That’s pretty much what I wanted to say…

I’m really running low on creativity with these posts !


I’m currently going through the Fizzle introduction courses, and the one I’m in — Finding your Subject — has led me to evaluate a dozen or so possible subjects with a Weighted Decision Matrix (fun little tool, I’ll probably use that again in the future !).

I’ve narrowed it down to one of these (or a combination…):

  • Biotechnology.
  • Crowdfunding.
  • Wearable Technology (+- App Development).

The final part of the course is to write 5 blog posts ( + a hypothetical product outline) on each of the ideas.

This is number 4/5 of the Biotechnology subject.

PS: The Fizzle Show is an excellent podcast, go listen !

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“Would you rent your body out as data storage?” and other post-human musings.

I recently finished a short Science-fiction story — “Cody” by Pat Cadigan — that I found in my November issue of Clarkesworld, a Sci-fi/fiction magazine.

They talked about a “courier” who transported heavily encrypted information in his blood. The story is superb, but I find the ethical dilemma it brings to light even more interesting:

When/If we arrive at a level of technology where we can engineer cells to do almost anything, What limits will we set?

Will we still consider the human body as sacred — using biotech only to heal, never to improve –, or will we consider the “body” as just a vessel for our mind, customizable at will ?

Fan Art of the novel "Snow crash". Found here

Fan Art of the novel “Snow crash”. Found here

There are a few Fiction genres (there’s a novel, Snow Crash — definitely on my Reading list now — that apparently has a superb cyberpunk aspect , like the picture above shows)that focus on the “limit” between man and machine/biotech, but how profound will this limit be ? Will it even exist?

If you lost your legs, would you go the extra mile to not just regain, but improve upon them?

Ok, that’s actually easy –> OF COURSE you would, it’s your legs.

The real question isn’t if you’re ready to accept a semi-artificial replacement that might just be better than the original, but whether you’d go the distance and CHOOSE to replace, for example, your perfectly functional eyes with these:

But this might, in a way, still be described as simply Augmented Humanity, AKA., we’re not adding anything NEW, just replacing old “components” with newer, more functional ones.

It’s when you enter REALLY deep into fiction that you begin so see the kind of modifications where you’re not just passively adding or removing, you’re literally changing the definition of what a human IS.

I’m talking about:

  • bionic wings for personal flight — integrated directly into your skeleton and neural stem, of course ! –.
  • Augmented respiratory systems (think adding the ability to breath underwater — a classic — or breath differently composed atmospheres, filtering out chemical and biological contaminants)
  • “Augmented” metabolisms (One idea I had a few years back : If some insects can digest wood because of their gut bacteria, why not engineer said gut bacteria to be able to live in the human gut ?)
  • more limbs ! (… a few tentacular “arms” ? Octopus are known for the flexibility of their limbs, we might be able to use that flexibility in manual work !) + Who hasn’t dreamt of being Shiva ;)
  • Symbiotic organisms for filtering harmful chemicals from your bloodstream, anyone ?

Personally, I’d jump at the chance to get an extra (fully functional) limb, or bionic eye, but I’m a future scientist… We’re not known for our mental balance !

Of course, It’d also scare the HELL out of people if I were to suddenly pat them on the head with an actual prehensile tentacle ;).


I’m currently going through the Fizzle introduction courses, and the one I’m in — Finding your Subject — has led me to evaluate a dozen or so possible subjects with a Weighted Decision Matrix (fun little tool, I’ll probably use that again in the future !).

I’ve narrowed it down to one of these (or a combination…):

  • Biotechnology.
  • Crowdfunding.
  • Wearable Technology (+- App Development).

The final part of the course is to write 5 blog posts ( + a hypothetical product outline) on each of the ideas.

This is number 3/5 of the Biotechnology subject.

PS: The Fizzle Show is an excellent podcast, go listen !

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Mushrooms. From “Food” to Biotechnological marvel

Ah, mushrooms, what wonders they are !

There are, of course, a lot of toxic shrooms in our world, but I believe the few eatable — delicious — mushrooms more than make up for the many killers in the culinary domain.

My personal favorite is Coprinus Comatus, because it grows on University grounds and is simply DELICIOUS… (Sadly, no specimens large enough for eating remain — I wonder why ;) –, though some of the smaller ones seem to be staying at the juvenile stage for an abnormal length of time… Strange… I’m pretty sure it’s been a week and it’s the same shrooms at the same stage of growth !).

Coprinus Comatus

For the mass public, Mushrooms remain a delicacy, and the most “tech” they get is when we farm them, as mushroom farming is especially complicated (involving, for the most dedicated, the creation of culture media, sterilization, several growth stages, and hot potatoe stew for dinner.. Yes’ I’m serious, just observe PDA Method N1 here).

But as much as Mushrooms are a delicacy, our future may be intrinsically linked to them in other — not-so-comestible — ways:

What would you say to replacing plastic with Fungi, or mimicking Mycelium enzymes to create the perfect medicine delivery system (or the perfect bioweapon, depending if the circumstances get very bad…).

There’s also other — let’s just say “interesting” — applications, like Fungi Furniture (I signed up for New-Scientists competition to win one of the first designer ones in 2012-2013 — Sadly I didn’t win… –. By the way, they’re holding a giveaway of the most popular books right now, why not check it out? ) or Moss Graffiti (This one was shared by my mother on FB… one of the many times her web-surfing on strange sites turn up something fascinating !)

There remains, in my opinion, an immense realm of possibilities when it comes to Fungi, and it’s application to our everyday lives

  •  monitoring environmental conditions.
    Mushrooms are fickle when it comes to their growing conditions. maybe we can use that to our benefit — Note: Already done 
  •  Increasing agricultural yields
    Mycorrhizae, the symbiotic association between fungi and root-bearing plants…Aaand this association just happen to one of the decisive factors in plant evolution, as plants without mycorrhizae tend to develop poorly, be more susceptible to disease…   So, why not engineer the Mycorrhizae to be more effective, spread farther, give them aerial parts with chlorophylles (okay… now I’m digressing into Wonderland, I’ll stop !).
  •  Atmosphere scrubbing on space stations.
    Mycelium “roots” should, in the future, be able to catch contaminants (be it to use or dispose of) from the air, scrubbing harmful chemicals from the air. If this is combined with the famous “Bio-Scrubbers” AKA plants that are, at least in Sci-fi, used to scrub the air of Carbon Dioxide and release Oxygen, keeping the atmosphere in a space-station acceptable, it could be even more interesting !

Also, why not replace vacuum cleaner filters with mycelium ? Inherently degradable, and if the right kind is chosen could allow passage of air with a tight filtering of contaminants !

To sum up, there are a LOT of applications for Mycelium in the future, who knows? Maybe I’ll even be a part of it ! (still a bit indecisive on what I’ll focus my studies on, but Mycology is a definite option, though I may try for a Biotech Engineering school in Bordeaux after my L2 / L3 first…)


I’m currently going through the Fizzle introduction courses, and the one I’m in — Finding your Subject — has led me to evaluate a dozen or so possible subjects with a Weighted Decision Matrix (fun little tool, I’ll probably use that again in the future !).

I’ve narrowed it down to one of these (or a combination…):

  • Biotechnology.
  • Crowdfunding.
  • Wearable Technology (+- App Development).

The final part of the course is to write 5 blog posts ( + a hypothetical product outline) on each of the ideas.

This is number 2/5 of the Biotechnology subject.

PS: The Fizzle Show is an excellent podcast, go listen !

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Today’s Biotech Trends

Biotech is defined as the manipulation of Life, so it’s understandable that many are afraid of what will happen when we TRULY plunge into the depths of possibilities this field represents.

If you look at mass media, you get the impression that the only Biotech out there is to do with Agriculture (TB crops) or Medicine (Gene Therapies).

But the truth of the matter is that Biotech is a nascent, but rapidly expanding field !

If you look in the right places, that is !

When examining the top scientific publication sites (Cell, Biomedcentral, Nature, PLOS), we can find a lot of interesting ideas floating around, here’s the ones I can extract from just a rapid reading of the current articles:

  • Curing cancer (there is a LOT of research in this domain right now).
  • Better, more effective, manipulation techniques for RNA/DNA or proteins.
  • Controlling gene expression with our thoughts.
  • Cellular computers ( 01 is boring… why not ACGT instead ?).
  • Optimizing plants instead of modifying them (if the plant is hardy by nature, is there really a need to include new genes for weather resistance, or can you just improve the effects of the old ones?)

I’m currently going through the Fizzle introduction courses, and the one I’m in — Finding your Subject — has led me to evaluate a dozen or so possible subjects with a Weighted Decision Matrix (fun little tool, I’ll probably use that again in the future !).

I’ve narrowed it down to one of these (or a combination of):

  • Biotechnology.
  • Crowdfunding.
  • Wearable Technology App Development.

The final part of the course is to write 5 blog posts ( + a hypothetical product outline) on each of the final ideas.

This is number 1/5 of the Biotechnology subject.

PS: The Fizzle Show is an excellent podcast, go listen !

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Designer Insects.

Hello, today I’m going to be talking about something very interesting.

Some of you may be following this blog (hell, I expect my family is momentarily stalking me when I post something, just to see if I’ve gone nuts or not ) and know that I’m currently studying biology/ecology in a French university.

Actually, I just finished the first “exam” of the year !! (I’m so happy, even though we were tested on just about 3-4 weeks of introductory content).

To my surprise -and delight- The University’s library has got a few magazine subscriptions going, notably to Nature, Science, and, my favorite, NewScientist (I’ve been reading all 5 recent issues out since I began here), and one particular issue of this last magazine has sparked the need for me to share, specifically, the “special” issue of the 21 September (yeah…they’re sadly not THAT up to date, preferring, I think, to get this weeks magazine next week.).

 

So, let’s begin:

Imagine walking down a road on a sunny day in Spain, minding your own business, enjoying the mild mid-day sun near your favorite, shade-giving, olive trees, when you notice something odd, the familiar buzzing of olive fruit flies, which have been driving the local olive farmers mad, decimating nearly a quarter of their crop, isn’t as accentuated as it used to be.

You encounter a group of Scientists, quietly taking notes in the silence, observing that, though subdued, the flies are still present, and, to your shock, releasing MORE of them !!

Demanding to know what they are doing to your local farmer’s crop, you are surprised when the farmer, himself, walks up to you and says:

“Don’t you worry, these here flies work for us !”.

 

 

So, seeing as you probably thought I’d get straight to the point, you might be wondering why I just hit you on the head with a narrative, well, I thought I’d experiment and see if a little storyline helped people remember, understand, or just pay attention to, what I write (You’re free to comment on what effect this had on you, especially if you’ve read some of my other posts in the past.).

 

On to the point then, recently,  there’s been a retake on the idea of Genetically Modified Organisms (GMO’s).

First, there is now a proposal to release GM olive fruit flies “into the wild” (we’re talking a first-step test-release under a bunch of trees covered by a “anti-GM-escapee” mesh so as to study the effect the climate, temperature, environment, etc… has on them, not a full-scale release.).

Now, these flies –maybe a way of the scientific community to prove they’ve learned their lesson– do NOT have pesticide-generating cells, or some other stupid invention reusing old technology.

No, these little buggers are engineered so that the Female offspring sired by the Male GM flies, will effectively die out before even ending their larval stage, which means that, as the generations pass, there will only remain a few female non-GM flies, all the surviving offspring of the GM Males being, well, Male.

This, as many people might have realized upon reading it, is effectively programmed regional genocide, and might appear as a VERY bad move, especially from an ethical view-point.

Now, I shall remind you that, on an ethical level, nearly ALL pesticides currently employed on farms, including the ones employed –though ineffectively– on the olive flies, also tend to kill nearly all other insect and arachnoid species.

Also, their death, caused by pesticides, are, in many cases, slow ones, whereas the GM flies tend to live long enough to live part of their natural lives for the males, and part of their “glorious olive-feasting” larval stage for the females.

 

So, to the ethics in the audience, I pose the following anthropocentric question (based upon not just this case but future cases):

Would you use an ineffective, hard-to-control and highly toxic method, or rather a ‘relatively’ (we have yet to see the test results after all) safe, non-toxic, species-specific method to safeguard crops?

 

Also, as if this wasn’t enough, here’s a little shocker,

They’re already doing similar stuff, and have been for a while :

  • Seven years ago, several millions of GM boll-worms were released in the US, to test a technique of tackling a cotton pest, with no problems arising at the moment (seven years is PLENTY of time to check the basic technique).
  • In Brazil, GM mosquitoes are already a-buzzing, wiping out their dengue-carrying brethren locally, this time more aggressively by preventing any offspring from reaching breeding age.

The company responsible for the GM mosquitoes, and the planned GM flies, is Oxitec, a biotechnology company from England, and Alphey, the co-founder of Oxitec,  is saying the release is more about getting the technology off the ground that proving that it works, since that much is obvious already.

 

 

Source of this article:

  1. NewScientist Issue 2935, released the 21 September 2013, page 5 and 11.
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Art and Forts

Today, I’ll just give you some links so that you may reconsider (or discover) a game I’m addicted to, Dwarf Fortress.

Here’s the links to some content that, even thought not directly linked to the game, is linked to the stories that people have been able to live out in the game, and what they’ve made to represent those stories

The !!ART!! of Dwarf Fortress (also known as Slaves to Armok II: [random gory title here for your reading torture]) :

oilfurnace

Bronzemurder, another one by Tim Denee

Timblr link to some DF related stuff

DFwiki’s list of Dwarf fortress webcomics, only tried a few of these myself.

 

And here’s a peek at the l33t glory of Dwarf Fortress in pure ASCII with no graph packs:

 

http://sebsauvage.net/rhaa/images/201107/rha_20110726_df_screenshot.png

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