8 ms·

Scientists have located an algal virus that attacks human DNA

93 points by johnloeber 12y ago

deleted 12y ago
[deleted]
shkkmo 12y ago
That is absolutely terrifying. I don't want to know what applications the DOD comes up with once the vector is known...
- bdamm 12y ago
  Yeah, I will never again eat "Made in China" candy.
fchollet 12y ago
92 volunteers, 43.5% were infected -> exactly 40 volunteers were infected, and 52 weren't. Then they claim to have found that the infected sample performed "10% worse" on intelligence tests. Intellectual performance follows a gaussian distribution. If you take two random samples, one of 40 people, and one of 52 people, and you average the IQs in each sample, the probability that you will find a deviation 10% or greater one way to another is over 50%... in this particular case, to compute the probability of the null hypothesis precisely we would need the exact result distribution on the tests they used, but in any case, take these results with a pinch of salt.
- shkkmo 12y ago
  Very true. I wish the article had the statistics behind this claim: "The team carried out further tests, in which they injected uninfected and infected green algae into the mouths of mice and put them through a series of lab tests. The results revealed that infected animals took 10% longer to find their way out of mazes and spent 20% less time exploring new objects than uninfected mice." Which is the much stronger experimental manipulation.
  - rwhitman 12y ago
    There's a comment below with the full text of the study: https://news.ycombinator.com/item?id=8608989 https://news.ycombinator.com/item?id=8608989
  - anigbrowl 12y ago
    Furthermore 'ATCV-1 exposure in mice also resulted in the altered expression of genes within the hippocampus. These genes comprised pathways related to synaptic plasticity, learning, memory formation, and the immune response to viral exposure.' http://www.pnas.org/content/111/45/16106.abstract http://www.pnas.org/content/111/45/16106.abstract So it seems like they have opened up multiple avenues of scientific inquiry - this strikes me as a much stronger result than presented in the Newsweek article. Assuming for the sake of argument that their speculation is correct, it's a rather frightening thought that some ~40% of the population could be suffering a significant virally-induced cognitive impairment. Also, I wonder if elimination of this virus could result in an improvement in cognitive and immune function. The economic and public health implications of this research are potentially quite significant.
    - otakucode 12y ago
      That 40% likely applies fairly specifically geographically-speaking. There are other pathologies that degrade cognitive ability which are almost omni-present in developing nations. Hookworm, for instance, causes permanent IQ loss in children who are infected with it and it is nearly universal in Africa and many other places with inferior sanitation. The American US south had a big hookworm problem in the past, but intentional steps were taken to eliminate hookworm. The result was climbing average IQ scores across the south for nearly a century. Malaria also causes cognitive problems, not the least of which is causing missed school in children. Malaria, obviously, sees an awful lot of attention paid to it, but hookworm is not nearly as popular. If I could choose something to focus on, hookworm would probably come even before malaria in my mind. The negative cognitive effects of hookworm hamper everything that can be done to fight malaria and other things, preventing people from realizing how important hygeine and the like is.
- stillsut 12y ago
  I thought: E[IQ] = 100, SD[IQ] = 10 then SD (for n = 37) = (10 / sqrt(36)) =~ 2 So a 10 point deviation between groups is 5 sd's, p <.001 ?
  - tokenadult 12y ago
    The standard deviation of IQ scores is 15 by definition. (That is, raw scores on the item content of IQ test batteries are generally not reported at all, but rather what is reported for each test-taker is a standard score defined as performance at the norming population median level being an IQ of 100, and performance one standard deviation up from that being an IQ of 115, and so on. All mainstream individual IQ tests have been scored this way for just about all of my lifetime.) P.S. I would take four standard deviations up or down (the IQ range of 40 to 160) as the outer limit of validated IQ scores, and indeed few modern IQ test batteries purport to report scores outside this range. See https://en.wikipedia.org/wiki/IQ_classification https://en.wikipedia.org/wiki/IQ_classification and the published reference books cited there for more background. P.P.S. I should have mentioned when I first posted this comment that any IQ test has a standard error of measurement even if it is faultlessly administered and scored. Sometimes small-n studies like the study reported here have IQ score differences between two groups that are simply the result of the test errors showing a difference where no actual difference exists. IQ tests are often also very frequently administered incorrectly or scored incorrectly even if correctly administered, magnifying the size of the error band around the obtained score. For this study, I'm not sure if the human subjects tested were tested by test-givers who were "blind" to what group the test-takers were in, which could also be an issue.
    - innguest 12y ago
      > All mainstream individual IQ tests have been scored this way for just about all of my lifetime. Correct me if I'm wrong but I thought the Cattell tests were obviously scored in the Cattell scale (24 s.d.) and the Stanford-Binet tests in the Binet scale (16 s.d.). When I was into reading about psychometrics it seemed to me that the cut off percentile was a more straightforward way to talk about IQ than using either of those three scales (Wechsler, Binet, Cattell).
- leeber 12y ago
  Where in the world did you learn stats from? You would be correct if we were talking about a standard normal distribution with mean 0 and standard deviation 1. Very different. In the case of mean 100 and standard deviation ~15 or so, the probability of two samples being at least 10% different is very small like under 1%.
Gravityloss 12y ago
If this is real and a cure can be developed, think about the huge free boost it gives to humanity in total since it might affect such a large amount of people. On the other hand, I'm skeptical. With such drastic effects, wouldn't the evolutionary pressure for the immune system to deal with it have been tremendous?
- GFK_of_xmaspast 12y ago
  You could have said the same thing about hookworm, and yet: material reality.
- TeMPOraL 12y ago
  Since it apparently doesn't affect sexual performance much, would it? Also it might be the case that the infection vector is something relatively new to us, something not present in the ancestral environment, like the tap water idea of ChuckMcM - https://news.ycombinator.com/item?id=8608780 https://news.ycombinator.com/item?id=8608780.
  - AnimalMuppet 12y ago
    If it lowers intelligence and/or increases response time, it could affect survival. It's not enough to be able to reproduce, you have to live long enough to do it. So, yes, it would be subject to selection pressure.
    - pm90 12y ago
      Subject to pressure yes, annhilated by it, no. Does natural selection really affect human population anymore? Genuinely curious, because what I see is that the the people with tons of kids aren't usually the most intelligent one (anecdotal evidence, of course)
- jobu 12y ago
  This virus may also give us more clues at which parts of our DNA affect intelligence - something that has difficult to pin down: http://www.nature.com/news/smart-genes-prove-elusive-1.15858 http://www.nature.com/news/smart-genes-prove-elusive-1.15858
tokenadult 12y ago
This is a preliminary research study and may not be replicated. Things I would want to know, after a replication study is published, is what the effect size is across more than one animal model (both mice and rats should be tried, and different strains of inbred mice with known differences in cognitive performance on mouse cognitive tasks should definitely be tried). I would also want a broader survey of human patients from more different parts of the world to see how many human beings show the same clinical sign the authors report here. And I'd want some of the human surveys to include very young participants, to see if rates of purported infection increase as human beings age. Right now, if I were to bet on this, my bet is that this result doesn't even replicate. (That's a reasonably good bet, as only about 50 percent of all scientific first findings, even those that have been published in a peer-reviewed journal, ever do replicate.)
ChuckMcM 12y ago
One of the interesting things about tap water is that it periodically suffers from algae 'blooms' (which is addressed by chlorine but the remnants of the algae persist. I've asked Dr Yolken for a copy of the paper and if they have checked that vector. Once again I find myself thinking I should get a DNA sequencer so that I could analyze my own tap water more quickly. [1] Original paper -- http://www.pnas.org/content/111/45/16106.abstract http://www.pnas.org/content/111/45/16106.abstract
- Blahah 12y ago
  When the Oxford Nanopore MinION comes out of the early access trials, you will actually be able to do this for a cost of somewhere around $1000.
  - ChuckMcM 12y ago
    I am totally going to buy one of those when it becomes available.
  - kolev 12y ago
    Illumina already sells a $1,000-genome machine. By the way, what's happened with the ambitious SV-based Halcyon Molecular, which was supposed to deliver a $100-genome sequencer? P.S. Halcyon has shut down 2 years ago [1]. [1] https://gigaom.com/2012/08/19/halcyon-molecular-quietly-shuts-down/ https://gigaom.com/2012/08/19/halcyon-molecular-quietly-shut...
    - razzmataz 12y ago
      Actually, Illumina's $1000-genome machine is 10 machines, and the way you get the $1000 genome cost is by running around 18000 samples thru in a year.... And when the bioinformatics folks talk about a '$1000 genome', they actually mean the cost of reagents.
      - kolev 12y ago
        This is what I meant [1]. It seems that only a few Australian companies do this for external parties for about $1,500/genome. I'm tired of waiting for the price to get down and to be offered publicly - is it possible to do personal sequencing somewhere in the US below $2,000? Is there another way? I don't mind donating my genome if there are ways to get this cheaper (or free) and do more if necessary. [1] http://systems.illumina.com/systems/hiseq-x-sequencing-system.html http://systems.illumina.com/systems/hiseq-x-sequencing-syste...
panzagl 12y ago
Do you want zombies? Cause this is how you get zombies.
twic 12y ago
So they tested a bunch of people, and found that those of them who regularly eat algae are a little less intelligent. Well, yeah.
- DanBC 12y ago
  The Japanese regularly eat algae. Are they less intelligent?
  - jacquesm 12y ago
    Sweetwater algae vs saltwater algae is quite a difference.
- vegedor 12y ago
  >ATCV-1 exposure in mice also resulted in the altered expression of genes within the hippocampus. These genes comprised pathways related to synaptic plasticity, learning, memory formation, and the immune response to viral exposure.
KerrickStaley 12y ago
The researchers at this lab do lots of other interesting work: http://stanleylab.org/staff/ http://stanleylab.org/staff/ (Or at least things that have been hot on HN lately, e.g. Toxoplasmosis)
inglondon 12y ago
I posted this a few days ago here: https://news.ycombinator.com/item?id=8583393 https://news.ycombinator.com/item?id=8583393
oldspiceman 12y ago
Reminds me of that cat virus linked to schizophrenia. http://en.wikipedia.org/wiki/Toxoplasma_gondii http://en.wikipedia.org/wiki/Toxoplasma_gondii
- xico 12y ago
  Knowing that most of the Western Europe people are infected by toxoplasma, it is hardly a ‘cat’ virus (well, maybe in the US were the contamination is low due to the low diversity and extreme cooking of the food).
- jarin 12y ago
  It's not a virus, it's a protozoan.
blackbagboys 12y ago
I suppose it would be a gross overreaction to rush out and try to get to tested for this virus?
- gwern 12y ago
  Yes. I'm not sure how you would either, unless you have access to a genetics/microbiology lab and the expertise to cluster and interpret the data.
tomrod 12y ago
> Researchers found no connection between slower brain function and variables such as differences in sex, education level, income, race, and even cigarette smoking. They have 92 observations. I don't think they have enough data to control for these sufficiently.

93 points by johnloeber 12y ago

deleted 12y ago

[deleted]

shkkmo 12y ago

That is absolutely terrifying. I don't want to know what applications the DOD comes up with once the vector is known...

bdamm 12y ago
Yeah, I will never again eat "Made in China" candy.

fchollet 12y ago

92 volunteers, 43.5% were infected -> exactly 40 volunteers were infected, and 52 weren't. Then they claim to have found that the infected sample performed "10% worse" on intelligence tests. Intellectual performance follows a gaussian distribution. If you take two random samples, one of 40 people, and one of 52 people, and you average the IQs in each sample, the probability that you will find a deviation 10% or greater one way to another is over 50%... in this particular case, to compute the probability of the null hypothesis precisely we would need the exact result distribution on the tests they used, but in any case, take these results with a pinch of salt.

shkkmo 12y ago
Very true. I wish the article had the statistics behind this claim: "The team carried out further tests, in which they injected uninfected and infected green algae into the mouths of mice and put them through a series of lab tests. The results revealed that infected animals took 10% longer to find their way out of mazes and spent 20% less time exploring new objects than uninfected mice." Which is the much stronger experimental manipulation.
- rwhitman 12y ago
  There's a comment below with the full text of the study: https://news.ycombinator.com/item?id=8608989 https://news.ycombinator.com/item?id=8608989
- anigbrowl 12y ago
  Furthermore 'ATCV-1 exposure in mice also resulted in the altered expression of genes within the hippocampus. These genes comprised pathways related to synaptic plasticity, learning, memory formation, and the immune response to viral exposure.' http://www.pnas.org/content/111/45/16106.abstract http://www.pnas.org/content/111/45/16106.abstract So it seems like they have opened up multiple avenues of scientific inquiry - this strikes me as a much stronger result than presented in the Newsweek article. Assuming for the sake of argument that their speculation is correct, it's a rather frightening thought that some ~40% of the population could be suffering a significant virally-induced cognitive impairment. Also, I wonder if elimination of this virus could result in an improvement in cognitive and immune function. The economic and public health implications of this research are potentially quite significant.
  - otakucode 12y ago
    That 40% likely applies fairly specifically geographically-speaking. There are other pathologies that degrade cognitive ability which are almost omni-present in developing nations. Hookworm, for instance, causes permanent IQ loss in children who are infected with it and it is nearly universal in Africa and many other places with inferior sanitation. The American US south had a big hookworm problem in the past, but intentional steps were taken to eliminate hookworm. The result was climbing average IQ scores across the south for nearly a century. Malaria also causes cognitive problems, not the least of which is causing missed school in children. Malaria, obviously, sees an awful lot of attention paid to it, but hookworm is not nearly as popular. If I could choose something to focus on, hookworm would probably come even before malaria in my mind. The negative cognitive effects of hookworm hamper everything that can be done to fight malaria and other things, preventing people from realizing how important hygeine and the like is.
stillsut 12y ago
I thought: E[IQ] = 100, SD[IQ] = 10 then SD (for n = 37) = (10 / sqrt(36)) =~ 2 So a 10 point deviation between groups is 5 sd's, p <.001 ?
- tokenadult 12y ago
  The standard deviation of IQ scores is 15 by definition. (That is, raw scores on the item content of IQ test batteries are generally not reported at all, but rather what is reported for each test-taker is a standard score defined as performance at the norming population median level being an IQ of 100, and performance one standard deviation up from that being an IQ of 115, and so on. All mainstream individual IQ tests have been scored this way for just about all of my lifetime.) P.S. I would take four standard deviations up or down (the IQ range of 40 to 160) as the outer limit of validated IQ scores, and indeed few modern IQ test batteries purport to report scores outside this range. See https://en.wikipedia.org/wiki/IQ_classification https://en.wikipedia.org/wiki/IQ_classification and the published reference books cited there for more background. P.P.S. I should have mentioned when I first posted this comment that any IQ test has a standard error of measurement even if it is faultlessly administered and scored. Sometimes small-n studies like the study reported here have IQ score differences between two groups that are simply the result of the test errors showing a difference where no actual difference exists. IQ tests are often also very frequently administered incorrectly or scored incorrectly even if correctly administered, magnifying the size of the error band around the obtained score. For this study, I'm not sure if the human subjects tested were tested by test-givers who were "blind" to what group the test-takers were in, which could also be an issue.
  - innguest 12y ago
    > All mainstream individual IQ tests have been scored this way for just about all of my lifetime. Correct me if I'm wrong but I thought the Cattell tests were obviously scored in the Cattell scale (24 s.d.) and the Stanford-Binet tests in the Binet scale (16 s.d.). When I was into reading about psychometrics it seemed to me that the cut off percentile was a more straightforward way to talk about IQ than using either of those three scales (Wechsler, Binet, Cattell).
leeber 12y ago
Where in the world did you learn stats from? You would be correct if we were talking about a standard normal distribution with mean 0 and standard deviation 1. Very different. In the case of mean 100 and standard deviation ~15 or so, the probability of two samples being at least 10% different is very small like under 1%.

Gravityloss 12y ago

If this is real and a cure can be developed, think about the huge free boost it gives to humanity in total since it might affect such a large amount of people. On the other hand, I'm skeptical. With such drastic effects, wouldn't the evolutionary pressure for the immune system to deal with it have been tremendous?

GFK_of_xmaspast 12y ago
You could have said the same thing about hookworm, and yet: material reality.
TeMPOraL 12y ago
Since it apparently doesn't affect sexual performance much, would it? Also it might be the case that the infection vector is something relatively new to us, something not present in the ancestral environment, like the tap water idea of ChuckMcM - https://news.ycombinator.com/item?id=8608780 https://news.ycombinator.com/item?id=8608780.
- AnimalMuppet 12y ago
  If it lowers intelligence and/or increases response time, it could affect survival. It's not enough to be able to reproduce, you have to live long enough to do it. So, yes, it would be subject to selection pressure.
  - pm90 12y ago
    Subject to pressure yes, annhilated by it, no. Does natural selection really affect human population anymore? Genuinely curious, because what I see is that the the people with tons of kids aren't usually the most intelligent one (anecdotal evidence, of course)
jobu 12y ago
This virus may also give us more clues at which parts of our DNA affect intelligence - something that has difficult to pin down: http://www.nature.com/news/smart-genes-prove-elusive-1.15858 http://www.nature.com/news/smart-genes-prove-elusive-1.15858

tokenadult 12y ago

This is a preliminary research study and may not be replicated. Things I would want to know, after a replication study is published, is what the effect size is across more than one animal model (both mice and rats should be tried, and different strains of inbred mice with known differences in cognitive performance on mouse cognitive tasks should definitely be tried). I would also want a broader survey of human patients from more different parts of the world to see how many human beings show the same clinical sign the authors report here. And I'd want some of the human surveys to include very young participants, to see if rates of purported infection increase as human beings age. Right now, if I were to bet on this, my bet is that this result doesn't even replicate. (That's a reasonably good bet, as only about 50 percent of all scientific first findings, even those that have been published in a peer-reviewed journal, ever do replicate.)

ChuckMcM 12y ago

One of the interesting things about tap water is that it periodically suffers from algae 'blooms' (which is addressed by chlorine but the remnants of the algae persist. I've asked Dr Yolken for a copy of the paper and if they have checked that vector. Once again I find myself thinking I should get a DNA sequencer so that I could analyze my own tap water more quickly. [1] Original paper -- http://www.pnas.org/content/111/45/16106.abstract http://www.pnas.org/content/111/45/16106.abstract

Blahah 12y ago
When the Oxford Nanopore MinION comes out of the early access trials, you will actually be able to do this for a cost of somewhere around $1000.
- ChuckMcM 12y ago
  I am totally going to buy one of those when it becomes available.
- kolev 12y ago
  Illumina already sells a $1,000-genome machine. By the way, what's happened with the ambitious SV-based Halcyon Molecular, which was supposed to deliver a $100-genome sequencer? P.S. Halcyon has shut down 2 years ago [1]. [1] https://gigaom.com/2012/08/19/halcyon-molecular-quietly-shuts-down/ https://gigaom.com/2012/08/19/halcyon-molecular-quietly-shut...
  - razzmataz 12y ago
    Actually, Illumina's $1000-genome machine is 10 machines, and the way you get the $1000 genome cost is by running around 18000 samples thru in a year.... And when the bioinformatics folks talk about a '$1000 genome', they actually mean the cost of reagents.
    - kolev 12y ago
      This is what I meant [1]. It seems that only a few Australian companies do this for external parties for about $1,500/genome. I'm tired of waiting for the price to get down and to be offered publicly - is it possible to do personal sequencing somewhere in the US below $2,000? Is there another way? I don't mind donating my genome if there are ways to get this cheaper (or free) and do more if necessary. [1] http://systems.illumina.com/systems/hiseq-x-sequencing-system.html http://systems.illumina.com/systems/hiseq-x-sequencing-syste...

panzagl 12y ago

Do you want zombies? Cause this is how you get zombies.

twic 12y ago

So they tested a bunch of people, and found that those of them who regularly eat algae are a little less intelligent. Well, yeah.

DanBC 12y ago
The Japanese regularly eat algae. Are they less intelligent?
- jacquesm 12y ago
  Sweetwater algae vs saltwater algae is quite a difference.
vegedor 12y ago
>ATCV-1 exposure in mice also resulted in the altered expression of genes within the hippocampus. These genes comprised pathways related to synaptic plasticity, learning, memory formation, and the immune response to viral exposure.

KerrickStaley 12y ago

The researchers at this lab do lots of other interesting work: http://stanleylab.org/staff/ http://stanleylab.org/staff/ (Or at least things that have been hot on HN lately, e.g. Toxoplasmosis)

inglondon 12y ago

I posted this a few days ago here: https://news.ycombinator.com/item?id=8583393 https://news.ycombinator.com/item?id=8583393

oldspiceman 12y ago

Reminds me of that cat virus linked to schizophrenia. http://en.wikipedia.org/wiki/Toxoplasma_gondii http://en.wikipedia.org/wiki/Toxoplasma_gondii

xico 12y ago
Knowing that most of the Western Europe people are infected by toxoplasma, it is hardly a ‘cat’ virus (well, maybe in the US were the contamination is low due to the low diversity and extreme cooking of the food).
jarin 12y ago
It's not a virus, it's a protozoan.

blackbagboys 12y ago

I suppose it would be a gross overreaction to rush out and try to get to tested for this virus?

gwern 12y ago
Yes. I'm not sure how you would either, unless you have access to a genetics/microbiology lab and the expertise to cluster and interpret the data.

tomrod 12y ago

> Researchers found no connection between slower brain function and variables such as differences in sex, education level, income, race, and even cigarette smoking. They have 92 observations. I don't think they have enough data to control for these sufficiently.