
Salk scientists find genetic signatures of biological aging - melling
https://www.sandiegouniontribune.com/business/biotech/sd-me-salk-genetic-signs-aging-detected-20181224-story.html
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th0br0
For those geowalled: [https://outline.com/dp7dyU](https://outline.com/dp7dyU)

This is the actual study:
[https://genomebiology.biomedcentral.com/articles/10.1186/s13...](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-018-1599-6)

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oneplane
It's not just the geowalling that is annoying, but the fact that they would
rather not comply for everyone's good.

It's like they decided that not knowing what data they process and where it's
going and what is being done with it is good for everyone.

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rladd
Or maybe the majority of their advertising is local, so it makes sense to
block non-local people if supporting them is an added expense and produces no
additional revenue.

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oneplane
Then why only start geoblocking after gdpr came into effect?

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perl4ever
The illogical thinking implied in the article upsets me.

They are taking a model, confirming that it performs as expected on some
examples, and then assuming that discrepancies on other examples will mean
something. But once you obtain those measurements, maybe they just mean the
model never worked. It's machine learning magic - you don't have a theory for
why the model should be correct, so how can you learn anything from using it?

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sharno
Out of some little experience doing some machine learning genetic research
that's a lot similar to this study, I feel like the effect of such studies is
merely directing us towards finding out the functionality of some parts of DNA
that we don't know about.

But the study is having a low number of samples for a machine learning
algorithm to yield perfectly accurate results, so I'd say any study with
machine learning algorithms without a big enough sample, the results should be
always taken with a bit of skepticism. There's no real substitute for good old
biology research to know the exact functionality of genes, proteins ... etc

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louprado
Perhaps skin samples from different parts of the body would yield different
age predictions. The actual study makes no mention which seems like a
significant omission if someone were to try to reproduce this experiment.

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apathy
Unless they’re dense they used the inside of the upper arm to avoid sun
damage.

The bigger issue is that Steve Horvath calibrated and has successfully
marketed a DNA methylation based “epigenetic clock” accurate to within a
couple of years, from blood, with hundreds of not thousands of citations and
successful replications since 2013. DNA is more stable than RNA, and blood is
easier to come by than fibroblasts (skin punches), so this seems like a
nonstarter to me.

Horvath’s clock works in arbitrary other tissues; we’ve applied it to
pediatric and adult tumors, adjacent normal, and blood samples at diagnosis,
remission, and relapse, and it works quite well (unlike the knockoffs that
followed). I don’t see the point of a less reliable, less proven clock on less
stable molecules (RNA), when I can use a handful of targeted amplicons to run
Horvath’s for $30/sample on blood DNA (even dried blood) or other tissues.

Ref:
[https://genomebiology.biomedcentral.com/articles/10.1186/gb-...](https://genomebiology.biomedcentral.com/articles/10.1186/gb-2013-14-10-r115)

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Gatsky
It is a mystery to me how these press releases end up on HN. Why this press
release about a mildly interesting paper, with no methodological novelty, of
likely no significance? There are any number of more important, more
interesting abd more novel papers coming out every week.

The RNASeq analysis they did isn’t even that up to scratch, they use an
outdated unit (FPKM) which isn’t consistent across different samples, and
don’t seem to check for batch effects or carry out any normalisation.

