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Aphid's Color Comes From a Fungus Gene

kdawson posted more than 4 years ago | from the long-jump dept.

Biotech 132

Iron Nose writes with an account from Byte Size Biology of horizontal gene transfer from a fungus to an insect. The author suspects that we will see lots more of this as we sequence more genomes. "The pea aphid is known for having two different colors, green and red, but until now it was not clear how the aphids got their color. Aphids feed on sap, and sap does not contain carotenoids, a common pigment synthesized by plants, fungi, and microbes, but not by animals. Carotenoids in the diet gives many animals, from insects to flamingos, their exterior color after they ingest it, but aphids do not seem to eat carotenoid-containing food. Nancy Moran and Tyler Jarvik from the University of Arizona looked at the recently sequenced genome of the pea aphid. They were surprised to find genes for synthesizing carotenoids; this is the first time carotenoid synthesizing genes have been found in animals. When the researchers looked for the most similar genes to the aphid carotenoid synthesizing genes, they found that they came from fungi, which means they somehow jumped between fungi and aphids, in a process known as horizontal gene transfer."

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132 comments

1 yeyaye (-1)

Anonymous Coward | more than 4 years ago | (#32070280)

first!!!!

QA?? No APPLE News Today?? (-1, Offtopic)

Anonymous Coward | more than 4 years ago | (#32070774)

Damn, where's my apple fix !! I gotz to have my apple !!

Aphids? Give me a frickin' brake on that !!

The "tanning" gene ! (1)

Taco Cowboy (5327) | more than 4 years ago | (#32071526)

Since the caratenoid gene can make things as red as cooked lobsters, why don't scientists find a way to transfer that gene into those tanning-philes?

One treatment and you got free tanning for life !

Re:The "tanning" gene ! (2, Funny)

arisvega (1414195) | more than 4 years ago | (#32073458)

Imagine of all those green people posing as magenta people.

wiki (1, Informative)

hh4m (1549861) | more than 4 years ago | (#32070282)

Re:wiki (0, Redundant)

mrmeval (662166) | more than 4 years ago | (#32070334)

They state with authority the gene came from a fungi but they have not shown where they have observed this happening. The fact that the genes are identical does not mean they're of the same origin.

Re:wiki (1)

Thanshin (1188877) | more than 4 years ago | (#32070350)

The fact that the genes are identical does not mean they're of the same origin.

I've got little knowledge on the topic but I'd guess it's a matter of numbers.

The larger the identical combination, the more probable is their common origin.

Re:wiki (0)

Anonymous Coward | more than 4 years ago | (#32071310)

Yes. And here's how. [wikipedia.org]

Re:wiki (3, Informative)

masterwit (1800118) | more than 4 years ago | (#32070370)

Carotenoids are colored compounds produced by plants, fungi, and microorganisms and are required in the diet of most animals for oxidation control or light detection. Pea aphids display a red-green color polymorphism, which influences their susceptibility to natural enemies, and the carotenoid torulene occurs only in red individuals. Unexpectedly, we found that the aphid genome itself encodes multiple enzymes for carotenoid biosynthesis. Phylogenetic analyses show that these aphid genes are derived from fungal genes, which have been integrated into the genome and duplicated. Red individuals have a 30-kilobase region, encoding a single carotenoid desaturase that is absent from green individuals. A mutation causing an amino acid replacement in this desaturase results in loss of torulene and of red body color. Thus, aphids are animals that make their own carotenoids.

That's the abstract from the in-text link, whatever a Phylogenetic analyses is...my guess:

Phase 1: Found genes......Phase 2: ???......Phase 3: Science! (good point mrmeval)

Re:wiki (2, Informative)

Anonymous Coward | more than 4 years ago | (#32071578)

Well, they can't publish their entire paper in the abstract - the details cost you money, unfortunately. However, it's likely that the method they followed involved statistical comparisons of the nucleotide sequence for similarity. Initially, this seems to be pseudo-scientific, but there are a number of factors to consider: Eukaryotes(animals and fungi + others) make several modifications to the "raw" sequence before translation machinery can code protein from an mRNA template(exons, for example: http://en.wikipedia.org/wiki/Exon). Now, if the coding (post-splice) sequence bears sufficient similarity, you can with fair confidence say that the genes probably have a recent common origin (on the scale of geological time.)
Phylogenetic analysis is basically doing this for a wide array of organisms, essentially looking for the most similar gene in terms of 1:1 exon similarity, then using that data to state with high confidence that this gene in aphids is more related to that gene in fungi than any other potential candidate for the source of this gene.

Re:wiki (2, Informative)

Anonymous Coward | more than 4 years ago | (#32070416)

...they have not shown where they have observed this happening.

It's like paternity tests: you can't exactly get in a time machine and go observe it happening but when you calculate the probabilities based on reasonable assumptions they can come out pretty high.

Re:wiki (4, Informative)

morty_vikka (1112597) | more than 4 years ago | (#32070444)

The fact that the genes are identical does not mean they're of the same origin.

Actually, if the genes are identical in terms of nucleotide sequence then it is absolutely irrefutable that they are of the same origin. Even genes that are evolutionarily conserved vary in sequence between members of the same genus, let alone organisms from completely different kingdoms of life.

Re:wiki (0)

Anonymous Coward | more than 4 years ago | (#32070486)

Or it's evidence some mold got into the tissue sample that was being stored for sequencing :)

Re:wiki (1)

Stooshie (993666) | more than 4 years ago | (#32070828)

What? and inserted itself into the genes in a place where it could naturally be processed? Also, in every sample! Puh-lease!

Re:wiki (0)

Anonymous Coward | more than 4 years ago | (#32071352)

Humans accrue roughly 40 new single-point mutations every time they reproduce. And we've got really stable genomes. If two organisms actually have the same sequence for the same gene in nucleotide sequence and not just amino acid sequence (there's a big difference, remember, and actually homology analyses are only conducted using the latter), then they're probably near relatives, not just of the same species.

Re:wiki (1)

smellsofbikes (890263) | more than 4 years ago | (#32073464)

The fact that the genes are identical does not mean they're of the same origin.

Actually, if the genes are identical in terms of nucleotide sequence then it is absolutely irrefutable that they are of the same origin.

It's indicative that they're the same, but not absolutely irrefutable. Any given sequence of DNA will be 25% identical to any other sequence, just because there are only four bases, while on the other end of the spectrum, even the DNA coding for something highly conserved, like cytochrome C, that exists in just about every eukaryote on the planet, isn't 100% identical across all eukaryotes.

As such, if you have a gene that's only a couple dozen bases long, it's fairly likely that if you find exactly the same sequence in another genome, they're either related or there's been horizontal gene transfer -- but only fairly likely, because a sequence of 30 bases could easily show up twice just by chance. But really massively long DNA sequences, even if they show very slight differences within them, are extremely likely to indicate ancestral relationships. For instance, while the general function of eyes has evolved 30 or 40 different times (or more, according to Ernest Mayr) the genes coding for the proteins that detect light, enabling vision, generally called opsins [wikipedia.org] have probably only evolved twice, one for bacteria and once for all eukaryotes. But even then, the two gene groups are amazingly similar for having different ancestries.

My point being: extremely strong indicator, yes. But nothing in science is absolutely irrefutable, and gene similarity is significantly less irrefutable than many scientific theories, because gene content is constantly changing.

Re:wiki (0)

Anonymous Coward | more than 4 years ago | (#32070708)

They state with authority the gene came from a fungi but they have not shown where they have observed this happening. The fact that the genes are identical does not mean they're of the same origin.

Can I use the same argument when denying partenity of my future children?

Horizontal gene transfer?? (5, Funny)

Anonymous Coward | more than 4 years ago | (#32070288)

Well fuck me sideways.

Re:Horizontal gene transfer?? (1)

pieisgood (841871) | more than 4 years ago | (#32070514)

*slow clap*

I commend your creativity.

Re:Horizontal gene transfer?? (1)

SETIGuy (33768) | more than 4 years ago | (#32073076)

It's too bad scores are limited to 5.

fungi (0)

Anonymous Coward | more than 4 years ago | (#32070310)

fungi grow out of insects all the time.

Re:fungi (1)

masterwit (1800118) | more than 4 years ago | (#32070336)

fungi grow out of insects all the time.

Read the article, this is not about fungi growing on insects as it is about gene transfer.

An article published today in Science shows the first case of animals synthesizing carotenoids.

Indeed, when they looked for the most similar genes to the aphid carotenoid synthesizing genes they found that they came from fungi, which means they somehow jumped between fungi and aphids, in a process known as horizontal gene transfer. Horizontal gene transfer is not unheard-of in animals, and is actually quite common in plants (yeah, fungi are not plants, I know that), but this is the first time someone has shown a jump from fungi to animals, and that the trait that this gene conveys — color — became embedded and functional in the genome.

:)

Re:fungi (-1)

Anonymous Coward | more than 4 years ago | (#32070364)

through what mechanism, I ask you..

Re:fungi (1)

MichaelSmith (789609) | more than 4 years ago | (#32070516)

through what mechanism, I ask you..

DNA strands move between organisms all the time.

Re:fungi (0, Redundant)

Cassius Corodes (1084513) | more than 4 years ago | (#32071116)

To completely blow your mind - did you know we have virus DNA in our DNA? Some of which has even been adapted for our internal use.

I knew it! (5, Informative)

masterwit (1800118) | more than 4 years ago | (#32070320)

As an aside, many of our pseudogenes and other contents of “junk DNA” are thought to have been acquired by horizontal gene transfer.

The guy behind the genetically mutated guido, look at his hand. (I'm sorry you cannot un-see that)

On a more serious note, my roommate, a biology/pre-med major, found this article very interesting and said thanks.

Apparently horizontal gene transfer (or at least inserting useless bits of DNA) is not very hard to do in a lab environment and is very common in bacteria, viruses, and other single celled organisms. Here is another link I found from 08 that talks about bacteria (E.coli) if anyone wants a read http://genomebiology.com/2008/9/1/R4 [genomebiology.com] (full text). Whatever I'm no expert in this field, but I like this type of stuff.

Movies (2, Funny)

Thanshin (1188877) | more than 4 years ago | (#32070340)

I wonder how soon I'll see this used in a movie.

My bet is: Man becomes werewolf after eating many wolves.

Re:Movies (0)

Anonymous Coward | more than 4 years ago | (#32070418)

Awesome! I'm gonna be a dorito!

This news also brings up a disturbing image of why some people are such assholes.....

Captcha:abutters (That's weird.)

Re:Movies (2, Funny)

Thanshin (1188877) | more than 4 years ago | (#32070442)

Awesome! I'm gonna be a dorito!

Nonono. You didn't get it.

You only get some genes, so you'll just be crispier. Or have a better taste.

Careful in your next visit to the zoo.

Re:Movies (4, Funny)

celibate for life (1639541) | more than 4 years ago | (#32070476)

Or have a better taste.

You have never eaten Doritos, obviously.

Re:Movies (2, Insightful)

Thanshin (1188877) | more than 4 years ago | (#32070488)

Or have a better taste.

You have never eaten Doritos, obviously.

Or I don't share your fondness for human flesh.

Re:Movies (1)

camperdave (969942) | more than 4 years ago | (#32073100)

... or turn orange.

Re:Movies (1)

ZeroExistenZ (721849) | more than 4 years ago | (#32070652)

I wonder how soon I'll see this used in a movie.

District 9 [imdb.com] : African leader wants to eat a human mutating into an alien to gain his mutant-properties.
The way this works isn't explained, yet it's implied it's a voodoo-belief.

Re:Movies (1)

foniksonik (573572) | more than 4 years ago | (#32070972)

No that's classic cannabalism. Eat your enemies to gain their power. See the movie Ravenous or wikipedia cannabalism.

Re:Movies (1)

Clueless Nick (883532) | more than 4 years ago | (#32071246)

Is this the very first instance of the noun wikipedia being used as a verb, or is it the very first time I have seen it?

By the way, and movies aside, read The Ancestor's Tale by Richard Dawkins. It has a brilliant explanation of the various evolutionary genetic processes.

Re:Movies (1)

Idiomatick (976696) | more than 4 years ago | (#32073086)

I've seen 'wiki it' a few times before.... And does Ancestor's tale go into detail about horizontal gene transfer methods? Or just touch on them?

Re:Movies (1)

rcuhljr (1132713) | more than 4 years ago | (#32073292)

First time you've seen it, you've heard of googling something I hope?

Betsey Dexter Dyer on color (4, Interesting)

CuteSteveJobs (1343851) | more than 4 years ago | (#32070356)

According to this hottie (see link) black and brown are natural colors produced by pigments; usually red, oranges and yellows are the carotenoids which animals get from foods, and blues and greens (in birds) come from microstructure rather than actual color. (Obviously a green caterpillar gets the color from the diet. A bit different for animals, since I've never seen a green cow.)

http://www.learnoutloud.com/Catalog/Science/Biology/Basics-of-Genetics/31316 [learnoutloud.com]

She also says that horizontal gene transfer is very common, and that 90% of our DNA is viral. The viruses we hear about are the ones that make us sick. The ones that have no ill effects we don't notice so much; these are also called viruses or jumping genes.

http://wheatoncollege.edu/quarterly/q2003fall/bacteria.html [wheatoncollege.edu]

Re:Betsey Dexter Dyer on color (4, Interesting)

MichaelSmith (789609) | more than 4 years ago | (#32070482)

90% of our DNA is viral. The viruses we hear about are the ones that make us sick. The ones that have no ill effects we don't notice so much; these are also called viruses or jumping genes

This is why I wonder about sexual behaviour which doesn't lead to reproduction. Could our genes have found ways to propagate themselves without reproduction?

Re:Betsey Dexter Dyer on color (1)

WindBourne (631190) | more than 4 years ago | (#32071088)

It is only a matter of time before our genes make their way back to other species due to virus. Likely it will be short lived species that is in constant contact with us and mosquito's. I would suggest that Canine evolution is still on-going with dogs getting brighter and brighter possibly due to our genes being slowly transferred to them

Re:Betsey Dexter Dyer on color (1)

Xtravar (725372) | more than 4 years ago | (#32072448)

I would suggest that Canine evolution is still on-going with dogs getting brighter and brighter possibly due to our genes being slowly transferred to them

lol really? Domesticated dogs smarter than wolves?

Re:Betsey Dexter Dyer on color (1)

TheLink (130905) | more than 4 years ago | (#32074586)

Re:Betsey Dexter Dyer on color (1)

mutube (981006) | more than 4 years ago | (#32072544)

In order for genetic material to persist it has to get into the germline cells - that is, sperm or egg - of the host. It's highly unlikely that 'just being around' humans would allow this to happen at all. Bacteria/fungal transfer is possible because, as an infecting pathogen, it can presumably get to where it is in close association with these germline cells - including, and probably limited to, the sexual orifices. So no, I seriously doubt dogs are getting smarter because they're picking up our genes.

Saying that, if you have found some other way of getting your DNA into your dogs semen, I wish you the best of luck. I suspect you'll need it.

Re:Betsey Dexter Dyer on color (1)

WindBourne (631190) | more than 4 years ago | (#32073790)

So, you do not think that virus work their way back into germ cells? Hmmm. What exactly do you think feeds those? Do not think that blood is involved? Something new? And by what mechanism are virus blocked from entering germ cells?

Now, if you have solutions for those (a different form of circulation other than bood and lymphatic that isolates the germ cells; and a means of blocking all virus from germ cells), then please share with the world, since you will win an INSTANT nobel prize.

BTW, back in 77-81, I was used to taking hits by my profs. Back then, I was arguing that DNA/RNA HAD to do work (like a protein). Why? Because Life assumes the lowest level of energy possible. It will excise an extra RNA/DNA that is not needed. Carrying that around is VERY expensive. Yet, it does carry it around. Interestingly, Tom Czech got a nobel prize for paying attention. This is the exact same thing.

Re:Betsey Dexter Dyer on color (1)

mutube (981006) | more than 4 years ago | (#32074192)

To be honest I missed the part in your post about the viral vector - I thought you were suggesting some direct gene transfer human-dog which was bizarre.

It still seems a stretch to suggest that horizontal transfer from human to virus, then virus to dog could occur on anywhere the level required to produce an observable effect on canine intelligence. The vast majority of viruses are species-locked or species-limited and even if the virus can infect a host, the virus is further limited in which cells in the body it is capable to infect - not just by access (blood supply - there is actually a testis-blood barrier, similar to the brain to prevent autoimmunity, but I'll admit to being unsure of it's role in preventing infection) but by receptor specificity. The only canine viral zoonose I know if is rabies (please feel free to correct me), and I can't find any evidence of that infecting germline cells - it's neurotropic. Bacteria and parasites are probably a better bet, but not by much.

Apologies for missing the point of your OP, but I still have a hard time buying it.

Re:Betsey Dexter Dyer on color (1)

osgeek (239988) | more than 4 years ago | (#32072004)

According to this hottie (see link)

Yes, that static-like sound you hear is the cacophony of Slashdotters furiously mashing mouse buttons all over the planet.

Re:Betsey Dexter Dyer on color (1)

Judinous (1093945) | more than 4 years ago | (#32073628)

I'm not sure that I buy that 90% number. The percentage of our DNA that is composed of endogenous retroviral material [wikipedia.org] is around 5-8% [nih.gov] . ERVs are horizontal gene transfers that occur in germ-line [wikipedia.org] cells, such as sperm, ova, and all of the cells in their ancestry back to the original zygote for that individual. Genetic changes to these cells (and only these cells) will be passed down to future generations.

Now, it's true that ERVs are not the only type of viral DNA that an individual may have in their cells. Any infection of a somatic (non-germ-line) cell by the appropriate type of virus since the individual's conception will lead to chimeric DNA in some part of the body. For example, well over 90% of American adults have had some form of herpes [wikipedia.org] infection during their lives, such as chicken pox or herpes simplex. This becomes a permanent addition to the DNA in the infected portions of the body, but it is NOT passed down to offspring.

The reason that your 90% figure doesn't pass the sniff test is because it would mean that more than 80% of the DNA in an individual's body would be acquired AFTER birth. If this were true, then wouldn't we expect to see huge, obvious differences between individuals throughout the entire genome? This is definitely not what we see when we sequence DNA. After all, which diseases an individual contracts, when they contract them, and in what order is essentially never the same. Hell, the difference between a human and a chimpanzee's genome is only about 4% [nationalgeographic.com] . The difference between individual humans is far smaller than that, so it seems likely that only a small (probably 1%) percentage of an individuals genome is made up of viral material obtained since birth. This passes the sniff test as well; you'd expect the genetic insertions that have accumulated over millions upon millions of years in germ-line cells to far outweigh the horizontal gene transfers that happen within a single individual's lifetime.

Re:Betsey Dexter Dyer on color (1)

TheLink (130905) | more than 4 years ago | (#32075002)

> For example, well over 90% of American adults have had some form of herpes infection during their lives, such as chicken pox or herpes simplex.
> This becomes a permanent addition to the DNA in the infected portions of the body, but it is NOT passed down to offspring.

In most cases no. But in other cases see this: http://www.redorbit.com/news/science/1833268/herpes_virus_can_integrate_its_dna_into_human_chromosomes/index.html [redorbit.com]

Quote: "The USF team also confirmed preliminary results by other investigators that, a long time ago, the virus inserted its DNA into the DNA of human sperm and egg cells. As a result, some people (about 1 percent of people in the U.S.) are born with the virus's DNA in every cell in their body. Indeed, HHV-6 is the first functional virus of any type reported to be passed through the human germ line."

As for other sorts of DNA transfer, I wouldn't say "never", after all an aphid can somehow get a fungus gene...

> Hell, the difference between a human and a chimpanzee's genome is only about 4%. The difference between individual humans is far smaller than that,

A bit offtopic, but since this keeps coming up, I find it strange that scientists can say that sort of stuff and also say there are no racial differences in humans.

If http://www.healthfinder.gov/news/newsstory.aspx?docid=638412

Plenty of other examples.

Even the ability to digest milk, and process alcohol differs significantly. And the ability to run 100 metres really fast ;).

To me it's silly to not think there's a human significant[2] difference between a 7 foot tall "West African" human breed and a Mbenga pygmy human breed. Maybe dogs can even smell the difference between those two breeds.

[1] This "big difference" is of course relative, to some alien creature made of "dark matter and dark energy", all the stuff on the Earth could look pretty much the same to them - and rather strange (we're the abnormal ones since most of the universe is apparently made of something else ;) ).

[2] Significant for human stuff, at a human level.

Re:Betsey Dexter Dyer on color (1)

TheLink (130905) | more than 4 years ago | (#32075048)

(Sorry reposting with corrections - lost a chunk due to forgetting how slashdot processes "plain old text")

> For example, well over 90% of American adults have had some form of herpes infection during their lives, such as chicken pox or herpes simplex.
> This becomes a permanent addition to the DNA in the infected portions of the body, but it is NOT passed down to offspring.

In most cases no. But in other cases see this: http://www.redorbit.com/news/science/1833268/herpes_virus_can_integrate_its_dna_into_human_chromosomes/index.html [redorbit.com]

Quote: "The USF team also confirmed preliminary results by other investigators that, a long time ago, the virus inserted its DNA into the DNA of human sperm and egg cells. As a result, some people (about 1 percent of people in the U.S.) are born with the virus's DNA in every cell in their body. Indeed, HHV-6 is the first functional virus of any type reported to be passed through the human germ line."

As for other sorts of DNA transfer, I wouldn't say "never", after all an aphid can somehow get a fungus gene...

> Hell, the difference between a human and a chimpanzee's genome is only about 4%. The difference between individual humans is far smaller than that,

A bit offtopic, but since this keeps coming up, I find it strange that scientists can say that sort of stuff and also say there are no racial differences in humans.

If 4% can make such a big[1] difference between chimpanzees and humans, it seems foolishness to say that humans are all the same (and also DNA fingerprint humans ;) ). Yes, race is very imprecise term, but there are certainly breeds of humans. They're not as clearly distinct as say dog breeds, but there are differences.

Lots of diseases affect different breeds of humans differently: http://www.healthfinder.gov/news/newsstory.aspx?docid=638412 [healthfinder.gov]

Plenty of other examples. Even the ability to digest milk, and process alcohol differs significantly. And the ability to run 100 metres really fast ;).

So to me it's silly to not think there's a human significant[2] difference between a 7 foot tall "West African" human breed and a Mbenga pygmy human breed. Maybe dogs can even smell the difference between those two breeds.

[1] This "big difference" is of course relative, to some alien creature made of "dark matter and dark energy", all the stuff on the Earth could look pretty much the same to them - and rather strange (we're the abnormal ones since most of the universe is apparently made of something else ;) ).

[2] Significant for human stuff, at a human level.

Correlation fallacy, much? (0, Redundant)

Rogerborg (306625) | more than 4 years ago | (#32070358)

From the source paper:

Phylogenetic analyses show that these aphid genes are derived from fungal genes, which have been integrated into the genome and duplicated.

Until you observe the process happening, all you've got is correlation. Even if it is gene transfer, how do you know the transfer wasn't the other direction? I call XKCD on that [xkcd.com] .

Re:Correlation fallacy, much? (0, Troll)

Clueless Nick (883532) | more than 4 years ago | (#32070392)

By looking at other aphids.

Re:Correlation fallacy, much? (1)

Clueless Nick (883532) | more than 4 years ago | (#32071494)

I know this is bad etiquette, but 'looking at other aphids' means genome sequencing of other aphid species, which can clarify if the same gene / allele appears in other species' genome.

It would be a very very rare chance by which a highly similar gene / allele mutates and evolves independently in a fungus as well as an aphid.

Re:Correlation fallacy, much? (5, Informative)

brusk (135896) | more than 4 years ago | (#32070454)

Most knowledge about evolutionary biology is based on evidence like this, and there are lots of ways to be pretty confident about such conclusions, even if there's no way to 100% rule out chance. If this gene and/or others like it are widespread in fungi, that's a hint that it developed in fungi--and under some conditions you might be able to show that the gene evolved in fungi before aphids even existed. Conversely, if no other aphids or related species have anything like this gene, it's a good bet that it came from outside. If the gene evolved suddenly in one lineage of aphids and transferred to a fungus, you would expect only a limited range of fungi, and only those that evolved after aphids did, to have the gene.

Re:Correlation fallacy, much? (0)

Anonymous Coward | more than 4 years ago | (#32070854)

But maybe it's all God's fault?

Re:Correlation fallacy, much? (5, Informative)

Anonymous Coward | more than 4 years ago | (#32070464)

The transfer definitely did not go in the other direction, as the genes for the carotenoids would have had to travel back up the phylogenetic tree and down its other branches to all the other organisms containing carotenoids. The argument that the aphids evolved genes to express carotenoids in parallel to the part of the phylogenetic tree containing them does not fit into the current model for evolution, as a gene only evolves once, and any other organism containing that gene is descended from the organism that originally mutated to express that gene (this uses statistics and probabilities too!).

Anyway, in almost every science nothing is solidly proven, there are merely theories. Everyone objecting to the validity of this article has been doing too much statistics and not enough biology. You can rest assured the article went under much more intense scrutiny than comparison to a webcomic to get published in Science (no matter how awesome that webcomic is).

Re:Correlation fallacy, much? (0)

Anonymous Coward | more than 4 years ago | (#32070474)

http://xkcd.com/386/

Re:Correlation fallacy, much? (0)

Anonymous Coward | more than 4 years ago | (#32070540)

there is an error in DNA replication once in every ~10,000 times, factor in the 30,000 base pairs that need to be changed to the right base (1/4), and that they need to not be selected against (interrupting a vital gene, intermediate evolutionary forms becoming detrimental, etc.), be associated with the right promoters (shine-delgarno sequences), i would guess off the top of my head that the odds of aphids evolving the gene for carotenoids is 1 in 10^100,000,000 at least.

Re:Correlation fallacy, much? (0, Offtopic)

Hurricane78 (562437) | more than 4 years ago | (#32070586)

I had to be reminded yesterday, that we can never ever directly observe causation anyway. All that we can observe, is correlation with as much other variables removed as possible. This is because physics at least demands the spacetime volumes to be different for two different (fermion-based) objects. (Pauli exclusion principle [wikipedia.org] )

So observation alone still is not worth much more. Example: When I observe rain, I also observe that less people are outside. But that does not mean that people cause sunshine. :))

By the way: Have you also read the mousover text on that xkcd comic?

Re:Correlation fallacy, much? (1)

Paltin (983254) | more than 4 years ago | (#32071050)

So, correlation does not imply causation.

But, that's not what is happening here. The systems of genetic transfer and mutation are very well understood. There are extremely robust models that explain this exact process and how to detect that have withstood the test of time.

For an example, here's one from wikipedia:

B causes A (reverse causation)

The more firemen fighting a fire, the bigger the fire is going to be. Therefore firemen cause fire.

The above example is simple and easy to understand. The strong correlation between the number of firemen at a scene and the size of the fire that is present does not imply that the firemen cause the fire. Firemen are sent according to the severity of the fire and if there is a large fire, a greater number of firemen are sent; therefore it is rather that fire causes firemen to arrive at the scene.

In that example, the absurdity is that we know that larger fires are responded to by firemen, and more come when there is a fire. You're arguing that unless we actually saw the fire growing THIS time, we can only say there is correlation. That's stupid. We have a model of fire growth and fireman response then has been developed through empirical observation. We have a model of evolutionary change and of horizontal gene transfer that has been tested and validated through many, many studies. You need to present an alternative that is more likely in order to explain this away, not just wave your hands, close your eyes, and go "Nyah nyah nyah!"

Re:Correlation fallacy, much? (1)

telomerewhythere (1493937) | more than 4 years ago | (#32071520)

Fahrenheit 451 was wrong? Say it ain't so.

More proof you Darwinist fools have it all wrong! (1, Funny)

Anonymous Coward | more than 4 years ago | (#32070434)

Find something your precious "evolution" can't explain and suddenly it's "horizontal evolution"? Can't you see the facts as clear as day? This is the Intelligent Designer porting features from one creature to another!

Re:More proof you Darwinist fools have it all wron (1)

MichaelSmith (789609) | more than 4 years ago | (#32070498)

Well he's doing a shit job. Probably using ClearCase.

Re:More proof you Darwinist fools have it all wron (0)

Anonymous Coward | more than 4 years ago | (#32071044)

U know, there are probably idiots around the USA, and likely on this site, that buy into that garbage.

Re:More proof you Darwinist fools have it all wron (0)

Anonymous Coward | more than 4 years ago | (#32072208)

Like Echolocation?
the mosquito bit a bat, then bit a dolphin!!! ftw!!!

Re:More proof you Darwinist fools have it all wron (0)

Anonymous Coward | more than 4 years ago | (#32072428)

He can't be all that intelligent, considering fungi aren't creatures. ...Or are they?

Kinda like mother nature doing dna tie dyes (3, Funny)

Bob_Who (926234) | more than 4 years ago | (#32070504)

Deadhead Aphids always like their fungus for the visual effect.

Just wait until... (3, Insightful)

Errol backfiring (1280012) | more than 4 years ago | (#32070530)

Individuals are sued by Monsanto for being polluted by their patented genes.

Re:Just wait until... (0)

Anonymous Coward | more than 4 years ago | (#32071230)

Individuals are sued by Monsanto for being polluted by their patented genes.

FDA hearing, 2234:"Monsanto wishes to add mammalian submissiveness genes to corn. Granted. Nothing worse than unruly vegetables."

A long-standing theory is, that this is normal. (-1, Flamebait)

Hurricane78 (562437) | more than 4 years ago | (#32070610)

And that it happens for Humans too. For example, that what we eat changes us, and that this is the reason some people look more like the animals their predecessors are.

I’d say (non-judgemental!) that some Germans or Polish people look a bit more like pigs and cows, while Arabic mountain-dwellers have a bit of similarity to goats. Which also are the animals they eat most. (Again: This is not meant as an insult, and I don’t associate good or bad to looks anyway. So if you felt offended [which I don’t think you are], that would be because of what you’d think of me. Which would not be very nice. :)

Re:A long-standing theory is, that this is normal. (-1, Offtopic)

wrencherd (865833) | more than 4 years ago | (#32070824)

. . .this is the reason some people look more like the animals their predecessors are.

And some think a lot like their animal ancestors too, eh. ;)

I think you meant to type, "ate" rather than "are", no?

It's my impression that quite a few Polish and German people are Jewish, which would preclude them from eating pork.

Yet I don't remember ever seeing any Poles or Germans who look like whitefish (though I have met quite a few people, across all nationalities and religions, whom I would classify as "lox").

Nature's own GMO (2, Insightful)

mspohr (589790) | more than 4 years ago | (#32070914)

This is an example of why I don't worry about man-made genetically modified organisms. It you have studied biology, you realize that nature is constantly shuffling DNA from one organism to another across species, genera, phyla and here across kingdoms.

Nature is constantly performing billions of genetic engineering experiments, most of which don't work out. Sometimes there is a small evolutionary advantage. I don't worry about the "frankenfoods" taking over the world. Nature is constantly performing these experiments and the result is the the current highly optimized system we call "life on earth". Anything man creates just goes into the universal gene pool and has to compete with an already highly evolved system.

Re:Nature's own GMO (4, Insightful)

biryokumaru (822262) | more than 4 years ago | (#32071096)

To play devil's advocate here, a tiger represents millions of years of predatory evolution, yet we can still hunt it to extinction. Just because nature's been doing this a lot longer then we have doesn't mean its aims are the same as ours.

When you're talking about evolution on the scale of millions of years, there's a selective pressure not to kill everything else around you. GE crops have no such incentive, and could quite possibly be extremely hard on the soil. Planting crops without regard to the needs of the soil is what led to the dust bowl.

Of course, it's more than likely anything we create will be able to perform its intended function fairly well, but be utterly unable to cope with any other situation and quickly die out. I don't imagine we'd create anything highly adaptable, that's nature's thing.

Re:Nature's own GMO (1)

mspohr (589790) | more than 4 years ago | (#32071190)

Large animals are relatively easy to hunt to extinction. (The disappearance of woolly mammoths and saber tooth tigers, among others, corresponds clearly with the "rise" of humans). However, genes are nearly impossible to get rid of... the genes of extinct animals live on in their relatives.

I would argue that "selective pressure" is a competition designed to get rid of "less fit" genes, not to encourage them. However, as in the case of large animals, even "unfit" genes have a way of hanging around forever as a small reservoir of "inactive" or "junk" DNA that lies in wait for external conditions to favor its return... kind of like a government in exile.

Re:Nature's own GMO (2, Informative)

osgeek (239988) | more than 4 years ago | (#32072476)

I don't imagine we'd create anything highly adaptable, that's nature's thing.

Genetic tinkerers don't create anything in the "from scratch" sense. They copy complex and fully-formed genes from one life form to another.

It's like using a well-debugged library in a new application.

Re:Nature's own GMO (1)

snowgirl (978879) | more than 4 years ago | (#32073060)

To play devil's advocate here, a tiger represents millions of years of predatory evolution, yet we can still hunt it to extinction. Just because nature's been doing this a lot longer then we have doesn't mean its aims are the same as ours.

When you're talking about evolution on the scale of millions of years, there's a selective pressure not to kill everything else around you. GE crops have no such incentive, and could quite possibly be extremely hard on the soil. Planting crops without regard to the needs of the soil is what led to the dust bowl.

Of course, it's more than likely anything we create will be able to perform its intended function fairly well, but be utterly unable to cope with any other situation and quickly die out. I don't imagine we'd create anything highly adaptable, that's nature's thing.

Like Corn/Maize... which can't propagate without human intervention. If we disappeared, the first generation of corn would overseed the soil, and each kernel would compete against all the others to grow, and result in each one starving out.

We don't need GMO to make plants that are "utterly unable to cope with any other situation".

Re:Nature's own GMO (1)

biryokumaru (822262) | more than 4 years ago | (#32073414)

Like Corn/Maize... which can't propagate without human intervention.

I've always felt that artificial selection should be considered genetic engineering. I don't know why it isn't.

Re:Nature's own GMO (0)

Anonymous Coward | more than 4 years ago | (#32073742)

Because people, in general, are not very well educated?

Re:Nature's own GMO (1)

Urkki (668283) | more than 4 years ago | (#32074522)

Like Corn/Maize... which can't propagate without human intervention.

I've always felt that artificial selection should be considered genetic engineering. I don't know why it isn't.

Because genetic engineering means manipulating the genes directly. Artificial selection doesn't do that, it let's the "normal" natural processes to do al the actual gene manipulation. I guess the borderline case is analyzing the DNA and performing artificial selection based on genotype. On the "traditional" side of that is artifical selection based on phenotype, and on the genetic engineering side is manipulating the genome directly (as opposed to let any DNA altering things happen in the "natural" way).

Or to put it the other way, "genetic engineering" means engineering based on genes. If you're not dealing with genes directly (be it just sequencing or actively altering), you're not doing genetic engineering.

If artificial selection is like an illiterate selecting books from a pile somebody else carried out of the library (of the Congress) based on how nice they look, genetic engineering is like actually going into the library and opening and reading books it before selecting, and making footnotes, and actually replaceing pieces of text and (eventually) writing entire new chapters, even writing new books (even farther into the future).

So if you want to call plain old artificial selection "genetic engineering", then "genetic engineering" needs a new name.

Re:Nature's own GMO (1)

snowgirl (978879) | more than 4 years ago | (#32074686)

Civil engineers on occasion still dig trenches. (in German, I'd say "let a trench be dug," and it sounds fine, but in English it sounds like I'm being a pompous bitch.)

Just because it's not the "high brow" version, or bleeding edge version, doesn't mean it doesn't qualify.

Artificial selection is simply a tool of genetic engineering. And considering the differences between Maize and its closest cousin Teosintes; round-up ready crops are insignificantly different.

Re:Nature's own GMO (1)

ChromeAeonium (1026952) | more than 4 years ago | (#32074594)

It isn't because there is a technical difference (randomly mixing thousands genes via controlled pollination vs. inserting one gene precisely) even if the end product is similar, indeed, I don't see how any GMO trait could not be achieved with sufficient time and breeding (although we might be talking on an evolutionary timescale here), but let's call a spade a spade, the reason so many people act like there's such a huge difference is mostly because genetic engineering is new and creepy and they don't understand it, and a dash of scientific illiteracy doesn't help either. Breeding is something kindly old folks do in tune with nature in the bright warm orchard, genetic engineering is something arrogant crazy haired wild eyed mad scientists cook up in some creepy lab. But at the end of the day, they both result in plants that have had their genetic make-up altered to suit humans.

People act as if there is a rift between genetic engineering and breeding techniques. There's not, they're just different tools for different situations, and each have their uses. You wouldn't try to saw a board with a level or pound in a nail with a wrench, yet these anti-GE people expect all plant advances to come through breeding, and that's just not going to happen. Why should it, that's just silly. We need both. Theoretically GE can replace breeding entirely one day but that day will not come for a long time, so in the mean time, we need both types of genetic manipulation. I think everything commercially grown should be genetically modified, plenty of benefits and no known negatives, but thanks to all the baloney floating around the net about GMOs, that seems like an extremist, radically pro-science position any more.

I can't imagine the reaction we'd be getting today of things like breeding and grafting were invented today. I'm reminded of a story about people who went to Africa to teach people in Cameroon about grafting and breeding and they were met with skepticism over the 'white man's magic,' but they soon came to realize the benefits. If they had access to people propagating misinformation and spreading FUD I wonder if their situation would have become similar to the one the developed world now faces with GMOs.

Personally, my two biggest horticultural interests are improving agricultural biodiversity by improving underutilized fruit crops, like pawpaw, goumi, jaboticaba, zabala, dragon fruit, ect., through breeding (because we presently really can't use genetic engineering to manipulate flavor; there are too many genes involved there and it is too complex for us right now) and improving other traits like hardiness or virus/pest resistance through genetic engineering, and I think it is a darned shame so many asshole groups have used misinformation and scare tactics to get the public so scared over something we should be embracing with open arms.

Re:Nature's own GMO (2, Interesting)

ChromeAeonium (1026952) | more than 4 years ago | (#32071542)

AMEN. As one planning on going into this area, I think about genetic engineering a lot, and that was the first thing that came to my mind too. I love how the anti-GE guys out there rail against the 'dangers' of foreign DNA being inserted into plants yet are blissfully unaware that species get foreign DNA all the time. Humans are 3-8% viral DNA depending on who you ask, and we're more genetically similar to chimps than two unrelated types of corn are to each other. My worry is that, in typical crank fashion, they'll take something like this and say 'See, we were right, inserted genes can jump to other plants, nya, nya, nya!' and totally miss the fact that it could happen with anything, especially in plants. But this won't stop them from parading their ignorance any more than facts stopped anti-vacationists or any other denialist group. They're right, and damn it, any science that proves them wrong, no matter how overwhelming, is clearly part of a plot by Monsanto to make them sick (cause killing your customers is a great business model), and therefore it to be dismissed or misused. A few million years of accumulated random mutations and horizontal gene transfer and a little human selection is fine and dandy, but add one gene in a controlled setting in a precise manner, and suddenly you've gone too far and no amount of testing well catch any problems all because scientists are either arrogant ebil B-movie villains or unethical, bribed off conspirators. Riiiiight.

Re:Nature's own GMO (1)

V for Vendetta (1204898) | more than 4 years ago | (#32072096)

I love how the anti-GE guys out there rail against the 'dangers' of foreign DNA being inserted into plants yet are blissfully unaware that species get foreign DNA all the time.

Yes. Perhaps with the little insicnificant difference that nature tests its "genetic engineering" thouroughly a couple of million years before releasing it to the public ...

Re:Nature's own GMO (1)

ChromeAeonium (1026952) | more than 4 years ago | (#32073006)

You must be joking. Tell that to to people who are allergic to peanuts, or have celiac's and can't eat wheat, or had a drug interaction with a grapefruit, or died from eating a starfruit. Don't anthropomorphize nature. It doesn't care of how things turn out, it doesn't care if you have an anaphylactic reaction to kiwis or whatever, it just is. It just goes, and while it does so fantastically, it doesn't care what effects any given mutation will have. Giving it any traits beyond that is just magical thinking.

Re:Nature's own GMO-- NOT! (1)

Will.Woodhull (1038600) | more than 4 years ago | (#32072924)

This is an example of why I don't worry about man-made genetically modified organisms. It you have studied biology, you realize that nature is constantly shuffling DNA from one organism to another across species, genera, phyla and here across kingdoms.

And the above statement is precisely why I have begun to worry about genetically modified organisms.

The whole concept of safety in GMO is defined in terms of species and genus, and that these abstract categories humans use to think about biology are somehow intrinsic in reality. That genes can migrate so easily across these categories shows this is not the case. Species, genus, phylum, and kingdom turn out to be convenient fictions, like centrifugal force. These fictions are an inadequate framework for working with GMO concepts in a safe manner.

We need a much better understanding of really basic biological principals to replace the rigid classification hierarchy with a way of thinking about the flows of information, materials, and energy that are an ecosystem. Until we have that more realistic framework and can use it to guide research and applications, I find the concept of using GMO in the field rather disturbing. At a very basic level, scientists and engineers involved in GMO research and applications don't know what the f*ck they are doing.

That disturbs me.

Re:Nature's own GMO-- NOT! (1)

ChromeAeonium (1026952) | more than 4 years ago | (#32073426)

The whole concept of safety in GMO is defined in terms of species and genus

Safety is assessed based on if it can be shown to cause health effects, even if it produces a new chemical that could cause those effects. The evidence to indicate that the vast majority of GMOs possess these health concerns is hugely underwhelming. I don't know where you get that taxonomy plays into it.

We need a much better understanding of really basic biological principals to replace the rigid classification hierarchy with a way of thinking about the flows of information, materials, and energy that are an ecosystem. Until we have that more realistic framework and can use it to guide research and applications, I find the concept of using GMO in the field rather disturbing. At a very basic level, scientists and engineers involved in GMO research and applications don't know what the f*ck they are doing.

And when will that be? What amount of knowledge will be sufficient to safely work with individual genes instead of mixing thousands of genes like we've been doing with selective breeding? Think about it, where else have we heard this appeal to ignorance with claims that the experts don't know what they're doing and moving the goalpost every time more info comes in? Oh yeah, the guys who brought back measles said the same thing about vaccinations. Same argument, same tactics, different topic, and it makes about as much sense. The science is there, and while GMOs certainty have the potential for doing bad things, the evidence to indicate that they are/will become dangerous is scant indeed.

Re:Nature's own GMO-- NOT! (1)

ChromeAeonium (1026952) | more than 4 years ago | (#32073522)

Ack, forgot a part: Safety assessment for environmental damage- again, nothing hugely great to indicate that there's much worry there, although I have heard reports of cross pollination in wild populations of corn (by which I assume they mean corn relatives). Not sure just how prevalent it is or how accurate those reports were, but either way, the issue here isn't so much what harm they cause to the environment as the net harm. Farming is very bad for the environment, especially with our large population, so it isn't if GMOs cause harm, but if their use is a net reduction in damage, which it appears to be.

Re:Nature's own GMO (1)

Urkki (668283) | more than 4 years ago | (#32073852)

This is an example of why I don't worry about man-made genetically modified organisms. It you have studied biology, you realize that nature is constantly shuffling DNA from one organism to another across species, genera, phyla and here across kingdoms.

Nature is constantly performing billions of genetic engineering experiments, most of which don't work out. Sometimes there is a small evolutionary advantage. I don't worry about the "frankenfoods" taking over the world. Nature is constantly performing these experiments and the result is the the current highly optimized system we call "life on earth". Anything man creates just goes into the universal gene pool and has to compete with an already highly evolved system.

Yes, but if this "natural experimentation" hits something extraordinary, it may be a disaster for the current ecosystem. It doesn't happen much in nature, in fact it's very rare on human time-scales. But when we start to do it, it suddenly happens much more frequently, and therefore also changes that may ravage ecosystems happen much more frequently. Also, in nature, every change is "out there", even if they actually do nothing. Humans purposefully design changes that do something, and only "working" changes are released into the nature. So humans are much more, let's say, efficient than nature at messing with ecosystem gene pools.

It's pretty much the same argument as this: Since animals shit in the nature, it's ok for humans dump their sewage into the nature as well, just like has happened throughout the history. Clearly a wrong conclusion, if you're worried about well-being of people.

The reason is simple (1)

WindBourne (631190) | more than 4 years ago | (#32070964)

There are a LOT more virus running around and we have very little appreciation for what they (and the lowly mosquito) do. Basically, as biologists continue to explore and some more get a bit of logic, they will realize that the vast majority of virus are asymptomatic (at least in a short term). Oddly, it will take time for ppl to accept the fact that virus do the majority of gene transfer (iow, it is not from mutation). Several interesting implications for this is that bio-diversity is conferred by bird/mosquito's/virus vectors moving from one SPECIES to another.Most will be in the same area, though some will travel. So, what this means is that as we wipe species, we will lose OUR evolution. In addition, as we grow larger and larger in density, then it is only a matter of time before we see another species acquire intelligence. We will credit it to Darwinian evolution, when in fact, it will be simply that virus carrying OUR genes, took enough snippets to enable it.

IOW, Virus is the 3'rd major form of genetics (sex/mutation) that does more introducing new genes into a species than another other form.

Wow (1)

Niubi (1578987) | more than 4 years ago | (#32070982)

interesting news like this is why I love slashdot almost as much as dubli!

mo3 up (-1, Troll)

Anonymous Coward | more than 4 years ago | (#32071064)

meh, wotz up doc? (1)

MrKaos (858439) | more than 4 years ago | (#32071162)

Carotenoids in the diet gives many animals, from insects to flamingos, their exterior color after they ingest it

Doesn't explain why WW2 night fighter pilots didn't turn orange.

Re:meh, wotz up doc? (1)

telomerewhythere (1493937) | more than 4 years ago | (#32072612)

http://healthmad.com/health/carrot-addicts-may-turn-orange/ [healthmad.com]

On a related but different thought: I thought I could find it, but I remember a story where scientists modified beta carotene and it produced modified eyesight in some animals or humans. Can anyone help? I'd love to read that again, or was I just dreaming?

Exhibit A (1)

srussia (884021) | more than 4 years ago | (#32071290)

Carrot Top!

spon6e (-1, Troll)

Anonymous Coward | more than 4 years ago | (#32071436)

Gov't Money (0, Flamebait)

windcask (1795642) | more than 4 years ago | (#32071632)

Your tax dollars at work: Finding out why nearly-microscopic bugs are colored.

It adds a whole new meaning to .... (0)

Anonymous Coward | more than 4 years ago | (#32071992)

This adds a whole new meaning to the phrase: "You are what you eat" ....

Myrmecos talks about this... (1)

antdude (79039) | more than 4 years ago | (#32073412)

... in his Science Blog [scienceblogs.com] .

Another challenge to dogma (1)

dorpus (636554) | more than 4 years ago | (#32074366)

Not so long ago, transposons (jumping genes) were thought to happen only in "lower" animals, not in humans. We now know that transposons are common in humans. They also said the same of copy number variations, or of DNA letters different from A/C/G/T.

The current dogma of genetics says that DNA homology between species is caused solely by evolutionary relationships. How long before we realize that this isn't true either?

I'm not an evolution denialist, but I do think the current scientific understanding of evolution has a religious zeal.

Re:Another challenge to dogma (1)

CorporateSuit (1319461) | more than 4 years ago | (#32074840)

I'm not an evolution denialist, but I do think the current scientific understanding of evolution has a religious zeal.

The fact that this type of finding actually refutes most current hypotheses of evolution, yet people are attempting to use evolution to explain it, and the article is tagged "evolution", I would say that you made a bit of an understatement.

Re:Another challenge to dogma (1)

Shipud (685171) | more than 4 years ago | (#32074994)

Actually, it does not refute anything. HGT has been known to exist for a long time in all of life's kingdoms, and has no impact on the Theory of Evolution. It is yet another genetic variety generating mechanism, on top of sex. The authors provide a very plausible mechanism to explain how the gene got fixed in the population. BTW, if you don't believe in evolution, how can you on the one hand accept their inference of HGT which is based on evolutionary considerations (sequence similarity and homology), but on the other hand claim that the conclusion from that inference is that evolution is wrong. that's like saying that You calculate the area of a circle using Pi=3.14, and then claim that Pi=3.5. Doesn't make sense.
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