Scientists have located an algal virus that attacks human DNA | Hacker News Reader

Scientists have located an algal virus that attacks human DNA

newsweek.com

93 pointsjohnloeber47 comments

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

Fulltext: https://pdf.yt/d/dr3uP9XOtT1BPimU / https://dl.dropboxusercontent.com/u/5317066/2014-yolken.pdf / http://libgen.org/scimag7/10.1073/pnas.1418895111.pdf

Thanks for this!

Nowhere, so far that I have read, have the scientists used the word "stupidity" as has the originally linked Newsweek article.

It was completely unnecessary for Newsweek to dumb down the research this way. Firstly cognitive impairment is not the same as general understanding of "stupidity" - a pejorative. Many things account for what we would usually term stupid behaviour. Personality, stress, hormonal balance are good examples. Then again, cognitive impairment includes a myriad of brain function impairments including memory loss ... forgetting something is hardly considered "stupid".

The research is important, but the careless use of words by Newsweek doesn't do justice.

Cognitive impairment is formally saying stupidity. Do they need to spell it out?

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.

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-shut...

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.

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-syste...

I am totally going to buy one of those when it becomes available.

If you know what you're looking for, you just need a couple of enzymes and one of these OpenPCRs [1].

[1]http://openpcr.org/

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.

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%.

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.

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

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.

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.

There's a comment below with the full text of the study: https://news.ycombinator.com/item?id=8608989

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 ?

Guys, we're programmers here not statisticians:

def test():

... n1 = numpy.average(numpy.random.normal(100,15,52))

... n2 = numpy.average(numpy.random.normal(100,15,40))

... return abs(n1-n2) / ((n1+n2)/2.0)

...

>>> vals = [test() for i in xrange(0,1000)]

>>> numOver10 = len([v for v in vals if v > .1])

>>> numOver10

Crucial in your code is the standard deviation of 15. Where is that coming from?

Ah, I see. Standard IQ normalizations.

http://en.wikipedia.org/wiki/Intelligence_quotient

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

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.

> 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).

The current Stanford-Binet test (and the next one, which is in preparation) use the typical 15 points per standard deviation scoring. The Cattell test is not a "mainstream" IQ test and correlates rather poorly with expected variables that ought to correlate well with IQ like academic achievement. Standard scores by the current definition are readily converted to percentile ranks by look-up tables, by the definition of standard deviation assuming a roughly normal distribution. As above, it's important to note that there is error in any IQ test. I've now had a chance to read the underlying papers related to this thread (which go back at least to 2008), and the IQ tests used in this study are even less mainstream than I feared. "A total of 240 individuals were evaluated with the Repeatable Battery for the Assessment of Neuropsychological Status (RBANS) and the Wisconsin Card Sorting Test (WCST)."

doi:10.1016/j.bbi.2008.04.156

That is true, but we can't translate 10% longer time taken on performing some task into 10% less effective IQ.

No, but there aren't really any good parameters for IQ, and time taken is a damn good, reliable, objective measure.

Yes, but without knowing standard deviations and mean time taken for both groups we can't do math and claim any likelihood of observed result occurring in a random distribution.

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.)

> 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.

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?

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.

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.

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)

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

You could have said the same thing about hookworm, and yet: material reality.

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

It's not a virus, it's a protozoan.

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).

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

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.

The researchers at this lab do lots of other interesting work: http://stanleylab.org/staff/

(Or at least things that have been hot on HN lately, e.g. Toxoplasmosis)

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

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

>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.

The Japanese regularly eat algae. Are they less intelligent?

Sweetwater algae vs saltwater algae is quite a difference.

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

Yeah, I will never again eat "Made in China" candy.

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