Coffee Bean Gene Mapped

brian6string writes "According to this article at ABC News Online (Australia), scientists in (where else?) Brazil say they have created the first complete map of the genetic structure of the coffee plant and Brazil's Agriculture Minister says the country will now work to develop a 'super coffee.'"

Comments

obvious mod

[Froze]

Make it produce 20 times the caffiene of a normal bean. Then it can compete with brazils other export the coca plant.

Re:obvious mod

[macdaddy357]

Already the inferior bitter tasting species, robusta, has twice as much caffeine as Arabica, the good tasting stuff. Already, a pot of purely robusta will give you the shakes. 20 times more caffeine might be lethal.

Re:obvious mod

[Froze]

and a cocaine overdose isn't lethal? Me thinks that you missed the point of comparing coffee to cocain as a tongue in cheek bit of humor.

Re:obvious mod

[Marxist Hacker 42]

Yes- but what a way to go- bet you could do an entire lifetime's work in the hour or so before your heart explodes.

Re:obvious mod

[dacarr]

If you drink five cups of it, yeah, it is.

I think the LD50 of caffeine is right around 8-10 grams, and since one cup of joe on average contains 100 mg caffeine, the LD50 of coffee is roughly 80 cups of coffee. But, your body will burn off caffeine faster than you can drink all that coffee normally, so the only way to get that much caffeine from coffee directly is to pump it straight into your stomach - and even then, you're more likely to get internal injuries and diarrhea than a fatal case of coffee shakes from that.

Re:obvious mod

[Anonymous Coward]

Then it can compete with brazils other export the coca plant. erm... that would be Colombia.

Re:obvious mod

[payslee]

True, you can die from caffeine, and it has happened. Probably seven years ago, when I lived in Boston, there was a widely publicized case of an MIT student who OD'd on NoDoze, after taking some unbelievable amount on a dare. Most of the talk was that MIT students should know better, and it interested me as anecdotal proof that intelligence and common sense do not necessarily equate.

Re:obvious mod

[timpaton]

So what you're saying is that American coffee being weak as piss is for safety. If it was as strong as normal coffee, you might not survive your third super-sized (8 gallon) cup of the morning...

Re:obvious mod

[dacarr]

Actually, it's as weak as it is not for safety, but for some other weird reason.

Not sure when it happened, but in the middle of the 20th century the seeming fad with coffee was to brew it in such a way that you could see through it. Perhaps it was around the depression as to save money, I don't know. That carried into an ettiquette thing, and nowadays people are accustomed to drinking coffee that, to misquote Monty Python, is like making love in a canoe. Fucking close to water.

Now of all the bile I have for Starbucks Coffee, I have to give them credit for one thing - bringing back strong coffee. Naturally, that part didn't pick up completely - many people find Starbucks to make their coffee too strong. Instead, the "gourmet coffee" thing picked up on that - many people put the word "gourmet" on their labels, so now you have McDonalds selling their exclusive blend. But, nothing has changed, naturally. So you have your coffee houses and your home drinkers that drink coffee strong enough to burn a hole in your plumbing, and you have everywhere else that just brews the same stuff - but had felt the need to expand (7-11) or rebrand (McD's) to compete with the likes of Starbucks.

Now excuse me while I drink a cup of coffee I couldn't see through if you blasted it with arc lights powerful enough to blind.

Just what Sun needs

[HMA2000]

More competition for Java

Addictive

[hubs99]

As if StarBucks wasnt addictive enough.

Sorry about this...

[JasonMaggini]

I for one welcome our new ultra-caffeinated overlords.

Sorry.

Starbucks rejoice!

[tod_miller]

I would say something like, bring on the high caffeinated programmer brand of Java, but instead:

By enabling intergenetic breeding, the genes from a cocoa plant can be placed direclty into coffee beans, alongside genes from a cow.

Add sugar cane, and you can see the possibilities ;-) Hi Starbucks, how you doin'?

Then you could have different coffee plant varieties:

Mocha
White Mocha
2 sugars, no milk variety

Now if they could make one that does a decent frappe...

Re:Starbucks rejoice!

[tod_miller]

intergenetic breeding? I might patent that... :-)

Re:Starbucks rejoice!

[jafuser]

By enabling intergenetic breeding, the genes from a cocoa plant can be placed direclty into coffee beans, alongside genes from a cow.

Even better, how about doing research for gene therapy so that my body makes it's own caffiene =)

Re:Starbucks rejoice!

[phillymacmike]

I'm sorry, but the idea of a cow's teat, full of frappacino, growing out of my chest, doesn't seem like that good an idea....

Hmmm... I just rtfa

[Froze]

They are going to use the mapped gene literally as a map. Since Brazil has banned GMO's the genome will be used as a guide for determining which cross pollinations etc. will be most effective.

So if you modify the genes by natural methods its not GM, but if you use artificial means to accomplish the exact same result, it is GM. God! I love the un-inteeligent masses that find this acceptable.

Re:Hmmm... I just rtfa

[wind]

So if you modify the genes by natural methods its not GM, but if you use artificial means to accomplish the exact same result, it is GM. God! I love the un-inteeligent masses that find this acceptable.

Clarification question: Find GM acceptable or find this supposed confounding acceptable?

Anyway, call me Dr. Stupid, but I think there is a substantive difference between having the means to be really selective about your breeding and splicing genetic code out of one species to put into another.

It seems to me that we are where we are today because clever, patient people "genetically modified" their animals and crops through careful breeding. I don't see how what Brazil is proposing is different. I'm pleased that they'd using this method instead of going in with the high tech equivalent of knives and tweezers to play switcheroo and put genes together in combinations that nature hasn't pre-tested for us.

Re:Hmmm... I just rtfa

[Froze]

Note carefully what I said..."exact same result"

I am not advocating gene splicing from other organisms etc. All I find odd is that if you apply cross breeding and get gene sequence 'gattaca' it is OK, but if you use tweezers and knives and get gene sequence 'gattaca' it is evil.

Re:Hmmm... I just rtfa

[kent_eh]

So if you modify the genes by natural methods its not GM, but if you use artificial means to accomplish the exact same result

That's not the complaint that I hear in most anti-GM arguements.
The problem is with creating splices/hybrids that cannot be created through "natural" methods of crossbreeding.

Re:Hmmm... I just rtfa

[Anonymous Coward]

All I find odd is that if you apply cross breeding and get gene sequence 'gattaca' it is OK, but if you use tweezers and knives and get gene sequence 'gattaca' it is evil.

Many people think one is more dangerous than the other. For me good and evil doesn't come into play at that point. You need people for good and evil.

For example sneaking GM corn into the American food supply without the majority of Americans knowing is evil. Creating the GM corn isn't.

Re:Hmmm... I just rtfa

[belg4mit]

You must count yourself among them masses then. There are huge differences between your average GMO and what they have proposed
1) you typically need a vector to add the new genes.
2) are *adding new genes* vs. selecting for existing ones
2b) these new genes often come from completely unrelated creatures and the result is not possible with traditional breednig and nybridization techniques, these are the so called frankenfoods.

Re:Hmmm... I just rtfa

[Tackhead]

> The problem is with creating splices/hybrids that cannot be created through "natural" methods of crossbreeding.

Are you trying to say that the coffee bean and, say, the duck-billed platypus, have no natural common genetic ancestor?

Because if you are, you're either a Creationist or a believer in Panspermia. Nothing wrong with either faith, except that it tells me you sure as fuck don't know much about where genes come from.

Given enough random mutations and enough time, you can create anything.

Not Just Brazil

[martyb]

Brazil is not the only place performing these analyses... check out what they are doing in Hawaii

Super Coffee!

[Anonymous Coward]

(Formerly known as meth)

Better watch the IP issues

[dpilot]

They MUST be infringing on SCO IP, somewhere, somewow!

Columbia in pursuit of perfection too.

[saden1]

Not to be outdone, the Columbian Ministry of Agriculture announced a new project to map the genetic make up of the Coca Plant. The ministry wasn't specific but has indicated that it plans to create super “something.”

Re:Columbia in pursuit of perfection too.

[jhoffoss]

It's spelled Colombia.

Re:Columbia in pursuit of perfection too.

[dbIII]

new project to map the genetic make up of the Coca Plant

They will get 1% done, announce the results to be incredibly fantastic and not listen to anyone else about it.

Hmmm

[Otter]

Bloomberg has a story that's less cutesy but more interesting. Some excerpts:

``This a jump of at least two decades in the race to unlock the coffee genome,'' Brazilian Agriculture Minister Roberto Rodrigues said in a statement on his ministry's Web site.

A two-year government project studied 200,000 sequences of coffee DNA and identified 35,000 genes, which in combination give the drink its flavor and aroma, the statement said.

The DNA database will be open to Brazilian companies in about five or six years, and foreign competitors will be able to access patented information on payment of royalties, Clayton Campanhola, the head of Brazilian agricultural research agency Embrapa, was cited by Reuters as telling journalists in Brasilia.

Rodrigues told reporters that Brazil would produce a ``super coffee'' through cross-pollination of coffee plants and not through genetic modification, according to the British Broadcasting Corp.

Brazil has banned the planting and sale of genetically modified crops.

This makes minimal sense to me, although it does explain why the other stories don't mention a publication. They spend two years, it's a jump of two decades, they're done but Brazilian companies can't see the data for five or six years and foreign companies will have to offer royalties? Pardon my cynicism, but what exactly do they have right now? Some shotgun coverage? ESTs?

Meanwhile, this is a few months work for any of the major genome centers. If there's really any commercial value to this, I can't imagine the coffee industry wouldn't just sponsor a publically-available ccommercial genome, like every other major agricultural crop has or will have. No one is going to wait five years and then give Brazil royalties.

Re:Hmmm

[ianbean]

They're probably ESTs. I think the coffee genome is 500-750Mb (depending on the species), so 200,000 shotgun reads are only going to give you 20% of the genome at best. No way you'd identify 35k genes from that.

You're right - it's hard to see the value of this. WashU does that many sequencing reads in a day - it would probably cost about $1M.

Normally I'm happy to see scientists get recognition for their hard work, but if the data isn't public then, really, why should anyone care?

Anyone here ever actually HAD brazilian coffee?

[Toxygen]

That stuff is strong enough as it is. My boss is from Brazil and the coffee he has from there is powerful stuff. North America doesn't just have the worse beer it seems. They drink it in an expresso sized cup and it's got enough caffeine to keep you going for hours. It's so strong that when I drink it (and I drink a lot of coffee) I need to add the coffee to my sugar!

For a country that puts out the illusion that they're all laid back beach patrollers, they sure do like getting juiced up!

Re:Anyone here ever actually HAD brazilian coffee?

[Sogol]

Most of the coffee in the USA comes from Columbia, and is grown not known for its quality.

Re:Anyone here ever actually HAD brazilian coffee?

[renehollan]

South American coffee, in general, is lousy, though Columbian is probably the worst. Most (if not all) of it is Robusta, which, while higher in caffiene content than Arrabica beans, lacks in the tastefullness department. The thing to do is to increase the caffiene content of Arrabica beans, not Robusta beans.

Of course, if an Arrabica espresso isn't enough of a jolt for you, just make it a doppio (a double).

Personally, I prefer African coffees, and have a fondness for Kenya AA beans as far as run of the mill coffee goes, though many find them too strong (tastewise).

Re:Anyone here ever actually HAD brazilian coffee?

[BerntB]

North America doesn't just have the worse beer it seems.

Well, not being an American -- but isn't both of these changing?

Arguably with all the microbreweries the US should have at least as good beer as the average in Europe (except for e.g. the British islands and Belgium).

Then we have the Starbucks revolution. It's a first step, but soon they will have coffee culture, too!

US is on the way to become a civilized place. :-)

Re:Anyone here ever actually HAD brazilian coffee?

[Vellmont]

Well, not being an American -- but isn't both of these changing?

Arguably with all the microbreweries the US should have at least as good beer as the average in Europe (except for e.g. the British islands and Belgium).


Very much so. There's micro-breweries all over the place now, and many restaraunts have their own brewery on-site. 20 years ago it was all bud, miller, and old milwaukee. Today you can at least go into a bar and expect to get a palatable beer, and have a decent chance of getting a quite good beer.

sadly a super coffee

[xutopia]

means a coffee that will get you even more addicted, will grow for a quarter of the cost, produce more beans per square-foot and require less sunshine and water.

Oh yeah, it won't taste as good but that's alright cause most people won't care after their first sip.

Just not my cup of tea.

Re:sadly a super coffee

[Wireless Joe]

I just tried this new super coffee, and it's like a koala crapped a rainbow in my brain! They should call it Stimutacs.

Sinners! Heathens! Heretics!

[Anonymous Coward]

However, it hopes to use the data to raise production of gourmet, organic and new caffeine-free beans within two years.

Caffeine-free coffee! How dare they!?

Re:Sinners! Heathens! Heretics!

[raider_red]

It's not necessarily bad, just utterly pointless.

thinkgeek.com

[Damingo]

So the map of a coffee bean. thinkgeek have already got a caffine molecule on a T-Shirt so how long till they have a genitic map of a coffee bean on a T-Shirt. You saw it here first guys, so i recon that if they do then all /.ers should get a free T! Damingo

Sequencing

[IBX]

a soccer player genome will be next

Service Pot 2?

[Rie Beam]

My only concern - will we have to patch our coffee pots?

Imagine Juan Valdez

[Man in Spandex]

He must be one pissed mofo to have scientists work on beans.
and I quote from beavis & butthead

"It is in these hills that Juan Valdez and his trusty goat gather coffee beans every morning."

Cross-breeding

[ALeavitt]

I'm betting that they add a ton of caffeine, then splice it with genes from tobacco, coca, and poppies, and make the most addictive substance known to man.

Wont this also create another problem?

[Thrymm]

Super cocaine, wouldnt this have an effect on it? Street prices would skyrocket for the product as im sure prison terms.

Re:Wont this also create another problem?

[dacarr]

Nah, you'd just have an extremely low LD50.

Disingenuous Lying

[Red Rocket]

So if you modify the genes by natural methods its not GM, but if you use artificial means to accomplish the exact same result, it is GM. God! I love the un-inteeligent masses that find this acceptable.

This is just blatant "un-inteeligent" propaganda. In order to get the "exact same result" researchers would have to first use selective breeding to get the traits they want, then take the original plant and splice the exact same altered sequences into that plant's DNA. It would simply be looking at how nature would change the genes and duplicating the process. That would be a pointless exercise in reverse engineering rather than genetic engineering and nobody would waste time doing that.

Natural methods create "fact-checked" documents while GM methods create self-replicating potential time bombs. Your understanding of the issue is very shallow.

And I love the way Slashdotty modders love to mod up industry propaganda as "insightful." It happens every time.

Re:Disingenuous Lying

[Sgt York]

Natural methods create "fact-checked" documents while GM methods create self-replicating potential time bombs. Your understanding of the issue is very shallow.

Perhaps my understanding is simply shallow as well, but what do you mean by "fact-checked documents"? I honestly don't understand what you mean by that.

And how is the result of selective breeding not "self-replicating"? For that matter, what is the argument behind saying that a selectively bred organism is not a "potential time bomb"? You could easily accidentally create an unusually hardy organism through breeding selection that, if released, could wreack havoc.

I understand that you didn't overtly make the negative claims about selective breeding, but the implication is there.

Re:Disingenuous Lying

[Red Rocket]

...what do you mean by "fact-checked documents"?

I mean that the DNA (the "document") has been combined in an eons-old method that has been vetted by natural selection to generate combinations that are tuned to live in harmony with their environment. Humans have a poor understanding of the functions and effects of their unnatural DNA tinkering. Breeding keeps natural laws intact for the most part. DNA splicing bypasses the checks and opens us up for disaster.

And how is the result of selective breeding not "self-replicating"?

I never said they weren't. They're just more trustworthy for replication than GMOs.

For that matter, what is the argument behind saying that a selectively bred organism is not a "potential time bomb"? You could easily accidentally create an unusually hardy organism through breeding selection that, if released, could wreack havoc.

It's not impossible, but I would consider it less dangerous because, if breeding created a more hardy competitor, don't you think nature would have created it by now over the 4.5 billion years it's been at work? Also, "unusually hardy" is a far cry from flat-out destructive. We can't fully predict how an organism will behave when we start splicing genes together. Nature has already done the vetting of the unhealthy combinations.

Re:Disingenuous Lying

[Sgt York]

generate combinations that are tuned to live in harmony with their environment

That s not really right. On an individual scale, natural selection does not seek harmony with the environment. Natural selection seeks nothing, and tunes to nothing except the amplification of oneself. Organisms do not seek to live in harmony with the environment, they seek to exploit it the best they can. The environment (i.e., the other organisms around it) counter this by trying to exploit each other in the same manner. This is natural selection. Selective breeding accelerates this process drastically.

Where a gene may provide a benefit that will increase its frequency over a period of several thousand years under the influence of natural selection, selective breeding can do it in a century or less. Selective breeding is far from a natural process. Selective breeding acts on one species, and accelerates the selection in that species for a given trait or set if traits. The surrounding species (the environment) do not experience the same increase in rate.Remember; I am not comparing GM to natural selection, but to selective breeding.

if breeding created a more hardy competitor, don't you think nature would have created it by now over the 4.5 billion years it's been at work?

This should be fairly obvious, but it has resulted in a hardier competitor. Many, many times. That's evolution. And simply stating that something is "flat out destructive" does not make it so. I'm not saying that GM is de facto safe, just that it's not by default unsafe, either. In fact, the resarch that has been done points to "safe".

Also, I can't think of a single mechanism other than improved hardiness that would cause an organism to be destructive. Otherwise, it wouldn't be able to compete with indigenous species and would be wiped out.

Re:Disingenuous Lying

[Red Rocket]

On an individual scale, natural selection does not seek harmony with the environment.Natural selection seeks nothing, and tunes to nothing except the amplification of oneself. Organisms do not seek to live in harmony with the environment, they seek to exploit it the best they can.

This is demonstrably untrue. While effective exploitation of resources is imperative, unrestrained exploitation of resources will lead to a quick extinction due to loss of livelihood. Many species will reduce their fertility, for example, during times of reduced availability of resources. Organisms, while seeking to thrive, must also harmonize with their environment.

The environment (i.e., the other organisms around it)...

Why do you restrict your definition of "environment" to living organisms? There are many other features including water, weather, sunlight, topography, and minerals.

...counter this by trying to exploit each other in the same manner. This is natural selection. Selective breeding accelerates this process drastically.

No it doesn't. Selective breeding alters organisms to meet the needs of people. These species would most likely go extinct in a rapid manner if not for human husbandry.
You're caviling.

This should be fairly obvious, but it has resulted in a hardier competitor. Many, many times. That's evolution.

That was my point, duh. We're already living with the more hardy competitors so that's pretty good proof that selective breeding (natural or man-made) is unlikely to create the problems you alluded to.

And simply stating that something is "flat out destructive" does not make it so.

What, exactly, did I claim was flat out destructive? I pointed that out as a distinct possibility because we really don't know what we're doing yet. Remember, these organisms are self-replicating. That's a huge power and one we would be foolish to treat lightly as you advocate.

I'm not saying that GM is de facto safe, just that it's not by default unsafe, either. In fact, the resarch that has been done points to "safe".

That's like saying, "I've pointed this gun at my head and pulled the trigger three times and nothing happened to me. That's a good indication that this is safe." As I said, our knowledge is incomplete. Best to keep these organisms tightly in biohazard containment until we're lots more knowledgeable.

Also, I can't think of a single mechanism other than improved hardiness that would cause an organism to be destructive. Otherwise, it wouldn't be able to compete with indigenous species and would be wiped out.

Just because you have an impaired imagination it's no reason to advocate hazardous behavior.
How about a bacteria that multiplies rapidly and converts mass quantities of oxygen to methane faster than plants can replenish it? How about one that consumes hemoglobin? I could go on and on but truth is stranger than fiction and the reality is more daunting to me than anything I can imagine.

All of this avoids the big lie that you and the biotech industry want the public to believe -- that gene splicing is functionally equivalent to selective breeding. It is not. It never was and it never will be.

Re:Disingenuous Lying

[Sgt York]

1. I think you are confusing exploitation with overuse. These are distinct.

2. I do not restrict to other otganisms. It is just that these are the most readily affected.

3. Selection is any process by which the frequency of an allele is changed. Natural selection is just what it sounds like. Selective breeding is a process used by man to select for certain genes. Learn the terms if you plan to use them

4. This just illustrates a severe misunderstanding, on your part, of basic biology and the mechanisms of selection, natural and otherwise. You discuss what you obviously do not understand.

5. I think you misunderstand my thrust. Which is this: as for results, GM is the same as selective breeding. The difference is the timescale. The difference in timescale is the same as thed ifference between natural selection and selective breeding.

6. Have you read the reoptrts? Have you seen the experiemts? Do you knw what the observed effects are? Your analogy is flawed. Many people have put guns to their heads, pulled the trigger, and died. No one has planted a GM crop and had the dire consequences predicted, and these are studies done for nearly a decade.

This is almost laughable. How does one convert elemental oxygen into methane? Transmutation? I think you have CO2 confused with methane. Learn a little before you go off like that. There are thousands of organisms that digest hemoglobin. Like humans, for instance. And every bacterium that exists. I have an impaired imagination? Well, then, you come up with a single real scenario.

All of this avoids the big lie: that opponents of GM know anything at all about the technology they demonize. You have demonstrated a complete ignorance of basic biology, genetics, chemistry, and molecular biology. Learn these topics, then we can discuss it.

Re:Disingenuous Lying

[Red Rocket]

All right, then. Carry on, Icarus. Try not to get too near the sun.

Re:Disingenuous Lying

[Sgt York]

Point by point refutation of the arguments, and I get an ad hominem in return. Thank you for the intellectual stimulation up to this last post.

It's the size

[Red Rocket]

...so how long till they have a genitic map of a coffee bean on a T-Shirt.

Only available in size XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX-Large.

Re:It's the size

[Damingo]

good job that they are an american company then!

Natural Bud Breeding

[Anonymous Coward]

Marijuana is the perfect example of how cross pollination can result in incredible plants without artificial genetic engineering. If one can go from 2-4% THC and now hit upwards of 20% (the record is 33% found in Oregon) without mapping the cannabis gene pool then what happens when it is mapped? Super hemp plants for fiber, super seedy for food, and super stony for, err, recreational uses.

And with perfect control of the plants chemical production you can have absolutely certainty of stony plants, energy, munchy, physical, trippy and every other variety. All natural and organic of course, just bred really, really well.

Re:Natural Bud Breeding

[Halcyonandon]

Maybe they could genetically modify it so that hemp didn't produce the most god-awfully uncomfortable material on the planet!

It's been done

[squidfrog]

Some advertising folks have already gotten in trouble for making the comparison...

How long before...

[xtal]

Coffee today is 20 times more potent than the coffee you drank in college...

To rank coffee by country of procedence =Bad Idea

[Garabito]

In the country I live in (Costa Rica) there are many varieties of coffee; which are grown in many parts of the country, with diferent climates and altitudes.

Coffee from low and warm lands tends to be of lesser quality. The best coffee grown here (I think) is from "La Zona de Los Santos", which is a high land.

This is in a small country like Costa Rica. Bigger producers like Brazil should have more varieties; so there is no such a thing as the brazilian coffee or the columbian coffee.

Patented information ?

[Garabito]

From the ABC article:

"It may also be opened to foreign companies, on payment of royalties for patented information."

Can genome information be patented? I know GMOs have been patented, but I didn't know about this. I rather think that this information should be treated as trade secrets, or with NDAs.

Could someone confirm this? Is genome information pantentable, or are we just being victims of clueless journalism?