Salk scientists find genetic signatures of biological aging | Hacker News Reader

Salk scientists find genetic signatures of biological aging

sandiegouniontribune.com

110 pointsmelling13 comments

For those geowalled: https://outline.com/dp7dyU

This is the actual study: https://genomebiology.biomedcentral.com/articles/10.1186/s13...

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.

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.

Then why only start geoblocking after gdpr came into effect?

"comply for everyone's good"

Nope. Some of us dont appreciate the EU thinking it can regulate what events one can remember.

It's annoying enough getting these dumb EU cookie popups.

and this is the GitHub repo with the notebook: https://github.com/jasongfleischer/Predicting-age-from-the-t...

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?

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

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.

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-...

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.

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