Can anyone vouch for the validity of nebula's privacy respecting testing? I've told people around me that I'd get it done as soon as I could trust they wouldn't sell me data. AFAIK I'm just German and Irish, but I've been mistaken as Turkish, Hispanic, and Chinese at different points in my life (by members of these ethnicities). I also have heterochromia, and worry that it might be related to inbreeding.
No but I can attest to my friend using Dante labs. Nebula and Dante as well as all others outsource the lab tests and buy"bulk vouchers". The privacy isn't an issue, Dante has been known to hire really bad labs that lose or mislabel data and latness is a problem. If you choose one for privacy, they'd be the best since they are the worst.
The data isn't stored by the labs (not Dante, the testing lab) and, and these mishaps happening is further evidence it isn't. You don't need to have Dante keep your data after transfer and the information gleaned isn't that powerful or useful. Full genomes of people, a DNA dox is available from many people and you can download all several gigs of their data. Good luck doing something with it, it's like LLMs but more random, larger files, and hard to find definite information even from GWAS.
Turns out I am a lucky guy (that has found quite a lot in anonymous genome data set). I am a bioinformatician and have worked with population sequencing data set like gnomAD. There is a huge inherent value in genomes without metadata and we (the research group I am working in) are using them every day. There is a large world beyond GWAS.
I am definitely more on the privacy verse side, and do not personally know a single person working in genomics that got their genome sequenced. However, there are so many people now which did. So I do not think it can be a huge concern as too many would be affected if it was a big issue at some point (and technically, so one does really just need a little more that a hair from you to be able to get the same info). In addition to that, I think there is a lot more benefit in those data than concern.
However, this data is ultimately valuable. Insofar it makes sense to me that who ever has such data will have incentives to use it for their own benefit, whatever that may be. Its not so much 'I have nothing to hide', but rather 'I do not want you to use my picture without my consent'.
I spoke to razib Khan a bit and he was the only sample from bengal for a while, to be used. He was also the first that sequenced his kids DNA in the womb.
I knew someone who worked at Grail, the problem with government is they're too conservative with the data usage. Nothing as useful can be gleaned do people choose to dump their data into private databases to get caught up on research.
If you want to sequence your genome entirely privately, the only real option is via https://store.nanoporetech.com/eu/minion.html (i.e buy a small sequencer and do it at home). Be warned that this will be expensive (more than the listed price here, e.g you also need a pipette etc.) and very much trial and error but ultimately it can be done at home.
I'm not certain my social reputation can handle asking friends and neighbors if they'll float me $150 to privately sequence their DNA in my basement but as long as I don't break out any skull calipers it might be fine.
I don’t know how nebula is these days, but I had the worst time with them. I sent my kit I and six months later they had nothing and they kept telling me it was coming, It was coming until they said there was something wrong with it and I would have to do it again.
I asked for money back and they delayed and delayed and delayed until I said I was going to sue them when they finally gave me my money back.
It takes exceptionally determined individuals and considerable effort to build and setup software and systems that deviate from mainstream "best-practices", for example to keep your data actually safe (in every sense of the word) long-term. These companies probably have their hands full solving their domain problems and running a business. Security is not mentioned as a main selling point on their respective websites.
Without a higher public awareness of data security, severe punishment for any breaches and failures to keep data safe, and a software ecosystem that prioritizes security much higher I feel you are right expecting the worst.
If you’re as sick as I was these concerns of privacy become minuscule because I probably would’ve been dead right now if I did not get my genetics 15 years ago.
I got my genetics from 23 and me and I’m well aware that they are using my genetic code for drug research. As far as someone getting my DNA you can pretty much get it for me anytime you want by following me around and taking a swab from a cup or whatever.
At least they genetics at 23 and me are anonymized. And I would think people can figure more out about you if they have your Gmail address then your genetics.
Any EU based companies? As a EEA citizen any US based company is off the table for me.
Also, any companies that just send you the raw genetic data and maybe a summary report and doesn't want to provide you with a life-time "service"? That doesn't force a data breach liability on you and your family for the rest of your life? That would be great.
This is the first time I'm hearing that inonophore term.
I get the concept of hydrophilic membranes in the cell.
Feels crazy to target these gates with supplements without more concrete science or theory.
I do take Green Tea extract but it adds to my daily caffeine load (30-40mg) with my morning coffee.
-----
I supplement using Micro Zinc from Nootropics Depot.
"
MicroZinc is a zinc supplement encased in large hollow spheres known as phospholipid micelles.
...
The sucrester protects the sucrosome from breaking down and aids in the absorption and bioavailability of zinc
"
I might've been bought into marketing here but the more I learn about the importance of our minerals, most of which I think I get from my food, the more I try to invest into higher quality mineral supplement sources.
I don't take more than 20-40mg a day. This did not help me from getting my butt kicked by my first common cold in 3 years recently. I did an all nighter which led to me being sick.
Sleep is so damn important in maintaining the immune system, I'd bet it figures into the immune systems of our ancestors in distinct ways.
Omega 3 (EPA/DHa) is way way more crucial to zinc transport, specifically with the transporter they’re talking about in the article. This would make sense since most of these people were probably eating a very high seafood diet like my ancestors did (Sami).
That’s a pretty strong statement in the headline, given how fluffy the article is. “X caused Y” rapidly softens into “Z might cause Y, and Z is possibly from X.”
I can't find the article now (it was on SlateStarCodex), but Scott Alexander wrote a great article where he broke down all of the genes that have a tendency to break either toward a genetic advantage (like high intelligence) or a genetic disadvantage (like cerbral palsy) and how it's always a dice-roll of the genetic expression whether it ends up helping or harming you.
This is a really important finding. I think it's not obvious to most modern humans that the majority of Human life has been spent in relatively cold temperatures [1]
This really only applies to northern Europeans. We are the only cold adapted peoples because of the ice age.
But it’s a really really huge finding for more natural cures to both mood disorders and immune disorders. If zinc deficiency was tested more regularly in the population, with schizophrenia and bipolar disorder, we would probably find a lot of people would be helped by taking zinc and possibly some other supplements.
Yes, we all came in the same people. But there will be many people who inhabit Europe now who came from southern Europe and the caucuses. These people came from a later migration from Africa then the cold adapted people who came earlier. There were two migrations out of Africa, and this will determine if a person has called adapted or not.
Are you sure it only applies to northern Europeans? The linked article states the genetic variant is found all over the planet, although it's less frequent in Africa.
>This really only applies to northern Europeans. We are the only cold adapted peoples because of the ice age.
Incorrect. Northeast Asians had to deal with arguably harsher cold climates than northern Europeans. Some examples of research on this subject (just the first couple I found through search):
Not to mention, this article on the zinc metabolism gene variant explicitly states:
>Although the variant was established in Asia as a result of interbreeding between Denisovans and sapiens, it also spread to European and native American populations.
Those east Asians are carrying the same cold adapted genes from the same people the Northern Europeans got them from. The Denisovans and Neanderthal have a common ancestor.
The ice age you’re talking about and what I’m talking about are different. The age I’m talking about is the one that caused that split. And it happened 400,000 years ago.
“ Given the essential role of the mitochondria in skeletal muscle thermogenesis, we propose that the derived G allele, which we have shown provides better protection to the mitochondria, may have been positively selected to facilitate adaptation to cold while providing higher susceptibility to neuropsychiatric traits. This is a plausible scenario for a case of archaic adaptive introgression, as Denisovans and Neanderthals were probably already well adapted to the local environmental conditions modern humans encountered when expanding across Eurasia.”
I admit to my over generalization Only because it can get too complicated explaining it all on HN.
The Western centric view of world history strikes again. The article is talking about Denisovans and last I checked, Denisova Cave wasn’t in Northern Europe.
Yeah, I’m sorry I was over generalizing and I was being Eurocentric for a reason. But the Denisovans and the Neanderthals both came from the same ancestor during the Ice Age I’m talking about which was 400,000 years ago.
These people were split because of the ice age. And that’s what caused the same cold adapted genes.
From the study:
Given the essential role of the mitochondria in skeletal muscle thermogenesis, we propose that the derived G allele, which we have shown provides better protection to the mitochondria, may have been positively selected to facilitate adaptation to cold while providing higher susceptibility to neuropsychiatric traits. This is a plausible scenario for a case of archaic adaptive introgression, as Denisovans and Neanderthals were probably already well adapted to the local environmental conditions modern humans encountered when expanding across Eurasia.
I posted this because I have both an immune deficiency and a serious mood disorder and I carry the polymorphisms they talk about in this article. I was blown away when I found this because I knew it was true that zinc cured both of my issues for the most part.
I finally got my doctors to give me a zinc test and I was deficient even though I was eating oysters, nearly daily and taking zinc supplements. So I have this transport problem with zinc and slc30a9, but also I have several genes that seem to need zinc more than other people. (PNP for one)
I’ve compared my genetics with a group of 12 other peoples genetics who are friends of mine so I know how much of an oddball I am.
I am bragging here, because I found this out by myself. My haplotype is a very ancient haplotype, which originates around 50,000 years ago, and this links me with the Denisovans as well.
I found it was not only the zinc, but omega-3 from seafood was even more crucial. Also, lowering my omega 6. Omega 3 three increases the transport of zinc through these zinc transporters.
When I was first found deficient , I took 200 mg of zinc sulfate which has 50 mg of elemental zinc for quite a few weeks, and there was no change. It wasn’t until I changed my fatty acid intake that my levels got up to .81.
Also, I found that Zand zinc lozenges, which contain, zinc, methionine, will raise my zinc faster than a lot of tablet supplements. It may be that I get more absorption in my mouth, then in my gut.
But before doing this, you should get both your zinc and copper tested. Zinc will inhibit copper absorption and can end up in a deficiency after a while.
I still eat a lot of muscles since they’re very well balanced in zinc and copper.
Interesting, thanks for the info. It's good that you found a simple dietary intervention that improved your life so significantly. I eat a lot of fish, mostly herring and almost every day, so I wonder if my omega 3 is high or could be higher and if so, what the effects might be.
Maybe I misunderstood something, but the article seems to highlight how the genetic variant of SLC30A9 is protective against lack of zinc and cold, while it predisposes to some mental health issues. So individuals with the variant are less likely to be zinc deficient.
It reads to me like they don't know the specific effects on zinc requirements or deficits for a subject with this variant.
Just vague statements that it "affects zinc transport" and "causes a new zinc balance within the cell".
Maybe this variant increases survival rates with an otherwise zinc deficient diet, by essentially allocating more zinc to basic survival needs and less zinc to fluff like mental wellbeing?
It’s also possible that they were eating a lot more high zinc foods in cold climates (think organ meats and seafood like mussels). Getting too much zinc is as bad as getting too little so genetic adaptation would favor slower intestinal zinc transport and higher mitochondrial, zinc export which is what the SLC30A9 gene does.
So now, those of us who carry this variant and are eating a lower zinc diet get way too deficient to easily.
> Maybe this variant increases survival rates with an otherwise zinc deficient diet, by essentially allocating more zinc to basic survival needs and less zinc to fluff like mental wellbeing?
That's interesting idea, it sounds plausible but I'm not an expert in this area. I'd like to add that in the article paper they talk about "hard selective sweeps" for this gene variant, which implies that the variant had especially strong influence on survival. AFAIK these selective sweeps often bring on some secondary traits which are a "side product" (spandrel) of the primary trait.
There was an observation about natural selection I heard a few months ago which is pretty obvious once you see it it: adaptations only matter during the period that you're fertile.
Mutations that increased long-term mental illness didn't matter if nobody lived past 30. Mutations that increased attractiveness but caused issues down the road would be selected for by definition.
In this case people with this gene would be actually available as mates, as opposed to the others who presumably tended to freeze to death.
The people they talk about didn’t have mental illnesses in the past, we have them in the present, because our genes do not match our environment.
These called adaptive traits were beneficial in a cold environment, not so beneficial in a warmer environment. And then you have all the dietary changes, etc.
Also, the average lifespan being short was not the same as nobody living past 30.
Childhood mortality was INSANE even into the 19th century, but if you made it to 20 you still had pretty good odds of making into your 50s, 60s, or even 70s.
Adaptations are better if they help some offspring survive and reproduce during some window of time.
For example, if I drop dead at 30 there's less of a chance that I can help protect/guide my offspring. If I live past 30 their chances of survival (and reproduction) increase.
Nope. Maybe if you are a housefly, but humans spend considerable amounts of time and effort raising their children (and grandchildren, nieces/nephews, cousins…).
65 comments
[ 3.1 ms ] story [ 133 ms ] threadhttps://www.illumina.com/techniques/sequencing/dna-sequencin...
https://nebula.org/whole-genome-sequencing-dna-test/
However, this data is ultimately valuable. Insofar it makes sense to me that who ever has such data will have incentives to use it for their own benefit, whatever that may be. Its not so much 'I have nothing to hide', but rather 'I do not want you to use my picture without my consent'.
I knew someone who worked at Grail, the problem with government is they're too conservative with the data usage. Nothing as useful can be gleaned do people choose to dump their data into private databases to get caught up on research.
I asked for money back and they delayed and delayed and delayed until I said I was going to sue them when they finally gave me my money back.
Without a higher public awareness of data security, severe punishment for any breaches and failures to keep data safe, and a software ecosystem that prioritizes security much higher I feel you are right expecting the worst.
I got my genetics from 23 and me and I’m well aware that they are using my genetic code for drug research. As far as someone getting my DNA you can pretty much get it for me anytime you want by following me around and taking a swab from a cup or whatever.
At least they genetics at 23 and me are anonymized. And I would think people can figure more out about you if they have your Gmail address then your genetics.
Also, any companies that just send you the raw genetic data and maybe a summary report and doesn't want to provide you with a life-time "service"? That doesn't force a data breach liability on you and your family for the rest of your life? That would be great.
I’ve seen green tea extract (EGCG) mentioned as a promising ionophore, but there are probably way more.
I get the concept of hydrophilic membranes in the cell.
Feels crazy to target these gates with supplements without more concrete science or theory.
I do take Green Tea extract but it adds to my daily caffeine load (30-40mg) with my morning coffee.
-----
I supplement using Micro Zinc from Nootropics Depot.
" MicroZinc is a zinc supplement encased in large hollow spheres known as phospholipid micelles. ... The sucrester protects the sucrosome from breaking down and aids in the absorption and bioavailability of zinc "
I might've been bought into marketing here but the more I learn about the importance of our minerals, most of which I think I get from my food, the more I try to invest into higher quality mineral supplement sources.
I don't take more than 20-40mg a day. This did not help me from getting my butt kicked by my first common cold in 3 years recently. I did an all nighter which led to me being sick.
Sleep is so damn important in maintaining the immune system, I'd bet it figures into the immune systems of our ancestors in distinct ways.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4145306/
This is a really important finding. I think it's not obvious to most modern humans that the majority of Human life has been spent in relatively cold temperatures [1]
[1]https://www.nature.com/articles/nature19798
Also, you just made me realize I never have actually given any thought to how much the last ice age affected climates beyond Europe.
But it’s a really really huge finding for more natural cures to both mood disorders and immune disorders. If zinc deficiency was tested more regularly in the population, with schizophrenia and bipolar disorder, we would probably find a lot of people would be helped by taking zinc and possibly some other supplements.
Incorrect. Northeast Asians had to deal with arguably harsher cold climates than northern Europeans. Some examples of research on this subject (just the first couple I found through search):
* Extreme climate, rather than population history, explains mid-facial morphology of Northern Asians (https://pubmed.ncbi.nlm.nih.gov/24374801/)
* Searching for Signatures of Cold Climate Adaptation in TRPM8 Gene in Populations of East Asian Ancestry (https://www.frontiersin.org/articles/10.3389/fgene.2019.0075...)
Not to mention, this article on the zinc metabolism gene variant explicitly states:
>Although the variant was established in Asia as a result of interbreeding between Denisovans and sapiens, it also spread to European and native American populations.
https://evolution.berkeley.edu/wp-content/uploads/2020/08/ev...
The ice age you’re talking about and what I’m talking about are different. The age I’m talking about is the one that caused that split. And it happened 400,000 years ago.
https://cdn.serc.carleton.edu/images/eslabs/cryosphere/timel...
These are extremely ancient cold adaptive genes.
From the study:
“ Given the essential role of the mitochondria in skeletal muscle thermogenesis, we propose that the derived G allele, which we have shown provides better protection to the mitochondria, may have been positively selected to facilitate adaptation to cold while providing higher susceptibility to neuropsychiatric traits. This is a plausible scenario for a case of archaic adaptive introgression, as Denisovans and Neanderthals were probably already well adapted to the local environmental conditions modern humans encountered when expanding across Eurasia.”
I admit to my over generalization Only because it can get too complicated explaining it all on HN.
These people were split because of the ice age. And that’s what caused the same cold adapted genes.
From the study:
Given the essential role of the mitochondria in skeletal muscle thermogenesis, we propose that the derived G allele, which we have shown provides better protection to the mitochondria, may have been positively selected to facilitate adaptation to cold while providing higher susceptibility to neuropsychiatric traits. This is a plausible scenario for a case of archaic adaptive introgression, as Denisovans and Neanderthals were probably already well adapted to the local environmental conditions modern humans encountered when expanding across Eurasia.
I finally got my doctors to give me a zinc test and I was deficient even though I was eating oysters, nearly daily and taking zinc supplements. So I have this transport problem with zinc and slc30a9, but also I have several genes that seem to need zinc more than other people. (PNP for one)
I’ve compared my genetics with a group of 12 other peoples genetics who are friends of mine so I know how much of an oddball I am.
I am bragging here, because I found this out by myself. My haplotype is a very ancient haplotype, which originates around 50,000 years ago, and this links me with the Denisovans as well.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4145306/
When I was first found deficient , I took 200 mg of zinc sulfate which has 50 mg of elemental zinc for quite a few weeks, and there was no change. It wasn’t until I changed my fatty acid intake that my levels got up to .81.
Also, I found that Zand zinc lozenges, which contain, zinc, methionine, will raise my zinc faster than a lot of tablet supplements. It may be that I get more absorption in my mouth, then in my gut.
But before doing this, you should get both your zinc and copper tested. Zinc will inhibit copper absorption and can end up in a deficiency after a while.
I still eat a lot of muscles since they’re very well balanced in zinc and copper.
Most people don’t realize that we make our own endogenous cannabinoids and they’re made from omega-3. No need for the weed!
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4145306/
I had an order in with nebula genomics, but it fell through.
I guess I should use the raw data explorer and enter SLC30A9, but what should I expect to see if I have this issue?
Just vague statements that it "affects zinc transport" and "causes a new zinc balance within the cell".
Maybe this variant increases survival rates with an otherwise zinc deficient diet, by essentially allocating more zinc to basic survival needs and less zinc to fluff like mental wellbeing?
So now, those of us who carry this variant and are eating a lower zinc diet get way too deficient to easily.
That's interesting idea, it sounds plausible but I'm not an expert in this area. I'd like to add that in the article paper they talk about "hard selective sweeps" for this gene variant, which implies that the variant had especially strong influence on survival. AFAIK these selective sweeps often bring on some secondary traits which are a "side product" (spandrel) of the primary trait.
I have decent consumption and decent sun and yet wind up deficient every couple of years
https://medlineplus.gov/genetics/gene/cyp2r1/#:~:text=The%20....
Mutations that increased long-term mental illness didn't matter if nobody lived past 30. Mutations that increased attractiveness but caused issues down the road would be selected for by definition.
In this case people with this gene would be actually available as mates, as opposed to the others who presumably tended to freeze to death.
The people they talk about didn’t have mental illnesses in the past, we have them in the present, because our genes do not match our environment.
These called adaptive traits were beneficial in a cold environment, not so beneficial in a warmer environment. And then you have all the dietary changes, etc.
Childhood mortality was INSANE even into the 19th century, but if you made it to 20 you still had pretty good odds of making into your 50s, 60s, or even 70s.
What do you mean by this? There was less on average, or that mental illness didn't exist at all?
Adaptations are better if they help some offspring survive and reproduce during some window of time.
For example, if I drop dead at 30 there's less of a chance that I can help protect/guide my offspring. If I live past 30 their chances of survival (and reproduction) increase.