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How neanderthal are you? And what is your ideal diet like?

by (56596)
Updated about 13 hours ago
Created July 18, 2011 at 4:21 PM

Chris and I were having a conversation about how some people do really awesome on pretty low carb and some people feel sick. I started getting curious about whether this might have something to do with "neanderthal ancestry." If you have DNA data you can go to http://esquilax.stanford.edu/#explore and select the neanderthal exercise. It counts how many of your alleles are derived/"neanderthal." I have only 7 of these. Chris has 10. We both do better on diets with 100-150 grams carbs a day.

alt text

*yes, I know there are other carb metabolism genes out there

EDIT: 23andme now has a neanderthal meter in their labs sections

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1069 · July 20, 2011 at 8:26 PM

I tried the gedmatch tool and while it is very detailed it was still totally and completely wrong for me. I was homozygous for multiple melanin blocking and low melanin alleles. The color predicted was a very light blue - nothing like my dark brownish hazel eyes.

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3703 · July 20, 2011 at 3:11 PM

Thank you --great :)

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10497 · July 20, 2011 at 5:18 AM

Hey Grace --- have something interesting to send you wrt Neanderthals. Check your inbox.

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18671 · July 20, 2011 at 1:05 AM

Heh. Not on your, er, coffee!

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11986 · July 19, 2011 at 9:34 PM

Some East Africans have "neandertal" genes too (in quotes because some still reserve judgment as to the actual origin of these genes): http://dienekes.blogspot.com/2011/03/neandertal-genes-in-east-africa.html

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2977 · July 19, 2011 at 5:04 PM

@A - it is an appealing idea for sure. Like, among those 84 genes was a later mutation that later conferred better metabolism of carbs (probably not "carbs" directly but some tiny improvement in the chain of events from consumption to inflammation). It'd be an interesting study.

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2977 · July 19, 2011 at 4:52 PM

Darn - can I trade you my 'Fast Caffeine Metabolism' for your 'Extreme Longevity'? I'll toss in a 'Photic Sneeze' allele as a bonus..

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11986 · July 19, 2011 at 3:49 PM

Ooh, that's cool. I'll send you my list of Neandertal alleles if you'll send me yours. ;)

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18671 · July 19, 2011 at 3:35 PM

I also get a high chance of extreme longevity, now, which is comforting.

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18671 · July 19, 2011 at 3:33 PM

Rose, now that I've done this right, I'm second only to you so far, which is interesting.

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18671 · July 19, 2011 at 3:32 PM

Melissa, see my edit after loading my data properly.

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18671 · July 19, 2011 at 3:28 PM

Spot-on WyldKard! Thank you! See my edit above.

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56596 · July 19, 2011 at 2:48 PM

yeah it should be a .txt file

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1906 · July 19, 2011 at 12:20 PM

Ambimorph, it's possible you didn't load your data correctly. You have to unzip the raw data file after you download it. Check some of the other features of the site and see if you're getting expected data. The first time I tried, I used the zip download and also got 0s, but then realized the file wasn't loading properly after exploring some more. My understanding is that unless you're African, it's unlikely (but not impossible) for you to score a 0.

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56596 · July 19, 2011 at 2:27 AM

I'm about 1/2 Celtic. I think the Russian part is where I got some neanderthal genes ;)

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5838 · July 19, 2011 at 2:25 AM

I sent him a message, Melissa. Thank you for the help :)

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18671 · July 19, 2011 at 2:00 AM

Fascinating. Are you a Celt too, then, Melissa?

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56596 · July 19, 2011 at 1:58 AM

Honestly I was surprised how few I have, but I guess the evidence is that Celts are a later population migrating into the continent from Iberia...who knows where before...maybe n. africa

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56596 · July 19, 2011 at 1:57 AM

if you don't have any, it just means that your copies of these alleles are mostly ancient from the African ancestral pool.

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18671 · July 19, 2011 at 1:56 AM

English/Irish/Scottish.

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56596 · July 19, 2011 at 1:55 AM

what is your ethnicity?

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11986 · July 19, 2011 at 1:44 AM

Good to know. I don't see why it's not possible. There are what, 84 identified (possible) alleles? Sounds like you've got none of the "Neandertal" variants. Interesting discussion in the comments here, btw: http://spittoon.23andme.com/2010/05/06/new-evidence-suggests-interbreeding-between-humans-and-neanderthals/

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11986 · July 18, 2011 at 10:30 PM

I'd love to see some comparisons of PaleoHackers' entire datasets. It would be cool to be able to do something like the 23andWe research, and not impossible with current software, either. Razib Khan at the Gene Expression blog talks about this kind of grassroots analysis on genomic data all the time.

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13692 · July 18, 2011 at 10:05 PM

CaveRat -I agree that they are different and didn't mean to imply otherwise. I was more questioning if any basis for the "scams" like this and the blood type diets might possibly have some merit based on the underlying science. Like others posts in the past about "low carb right for the wrong reasons". Anyway I look forward to the development of this science!

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2977 · July 18, 2011 at 9:49 PM

We'd be a pretty good sample, even if not huge, for some enterprising enthusiast.

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2977 · July 18, 2011 at 9:40 PM

Aravind: Metabolic typing is different - and from what I understand a total scam. You send in a sample and they give you some meaningless diet recommendations. What we're talking about here is real genome sequencing.

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56596 · July 18, 2011 at 9:20 PM

he also has a contact form http://www.cholesterol-and-health.com/contact-cholesterol-and-health.html

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1069 · July 18, 2011 at 9:06 PM

I shouldn't be complaining because I got the test as part of a $100 promotion a year and a half ago - upgrading to the new chip costs $49 + $9/ month, or $299 for a subscription for "the lifetime of the platform," whether that means the lifetime of the new chip or the lifetime that marketing and sales thinks they can get away with before demanding more money remains to be seen... I get that it's a business model but it rubs me the wrong way when hidden costs and "upgrades" come up, and I really don't like subscriptions at all.

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5838 · July 18, 2011 at 9:02 PM

Alas, I don't have a FB. I could possibly be one of the few left who don't. Sorry, but I thank you for trying :)

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56596 · July 18, 2011 at 8:40 PM

yeah, maybe they don't have to do with anything, but interesting to collect some data

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56596 · July 18, 2011 at 7:39 PM

lol actually that thing is even more inaccurate for me :( It gives me gray blue eyes...I wish!!!

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56596 · July 18, 2011 at 7:34 PM

You will get more accurate eye color results from this tool: http://ww2.gedmatch.com:8007/autosomal/eye_color_pred1.php

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56596 · July 18, 2011 at 7:33 PM

Todd, try posting on his FB page https://www.facebook.com/pages/Chris-Masterjohn/108150349220602

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11986 · July 18, 2011 at 7:32 PM

Cool! Thanks so much, CR.

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2977 · July 18, 2011 at 7:16 PM

I also have the the blue eyes marker, but really have green - which for me is sort of blue with hazel mixed in. I guess I'm on the 'new chip' - did you have to pay the full amount for a new test?

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13692 · July 18, 2011 at 6:45 PM

I know the likes of Kurt Harris have written that metabolic typing is b*llsh*t. So does this perhaps suggest that there is a basis for it after all?

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2977 · July 18, 2011 at 6:33 PM

btw, Rose: the way it works is that you export your genome from 23andme as a text file. Then that file can be uploaded to other sites, or parsed with the promethease application - or whatever you like.

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2977 · July 18, 2011 at 6:25 PM

Melissa - that's correct and I DID have that (so I wasn't crazy :-) Actually I've got both alleles for rs526934(G,G): "G allele associated with lower serum Vitamin B12. 'The TCN1 rs526934 G variant may reduce transport of cobalamin, resulting in lower plasma vitamin B12 levels.'"

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2977 · July 18, 2011 at 6:20 PM

Shows what I'm a noob I am. It was B6 - which I'm interested in because it's mentioned a lot around thyroid issues. I used Promethease, which is a small application from SNPedia.com. The data is presented in pretty raw format, but gets you directly to research papers that mention the SNP: ---- rs4654748(C;T) References:41.45 ng/mL lower Vitamin B6 blood concentration...more...(hide) ---- rs2282679(A;C) References:2somewhat lower vitamin D levels...more...(hide) rs2282679, located in the group-specific component (vitamin D binding protein) GC gene on chromosome 4p12, ...

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56596 · July 18, 2011 at 6:18 PM

she might have found it via promethease http://www.snpedia.com/index.php/Rs526934

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11986 · July 18, 2011 at 6:09 PM

CaveRat, which markers look at serum levels of D and B12? I can't find anything on the 23andme site.

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5838 · July 18, 2011 at 6:04 PM

Melissa - What blog was he going to write that for? How could I e-mail him with that request? Thanks :)

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5838 · July 18, 2011 at 6:03 PM

Thank you CaveRat - I'll look into that.

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56596 · July 18, 2011 at 5:51 PM

I think Chris was going to write a post. You should email him and tell him to do that :P Basically it showed he was homozygous for two hemochrom genes and blood tests showed he was in the higher range, though not in the overload range. He's been donating blood now.

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2977 · July 18, 2011 at 5:36 PM

Todd - I used 23andme after reading Melissa's post on her blog. It's fantastic, and I think is more suited to the amateur than other services. I believe MIT has a review of the different services - maybe Google can find it. Note that this particular Neanderthal thing only accepts data from 23andme and Limuigenex

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4080 · July 18, 2011 at 5:25 PM

Melissa -how did the genetic test help to pinpoint Chris's diagnosis? Did it show a gene for that? I think I want to do this test! I need serious help and maybe that test could give me a leg up! I read your blog post about your results, has Chris made one about his? Link?

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20519 · July 18, 2011 at 4:55 PM

There was a special on PBS last year called Becoming Human that broke the "did we or didn't we" out. They still can't pinpoint the why/when/where of modern humans and neanderthals co-mingling, babies!, but it was interesting to find out that there are populations that have the neanderthal DNA and others that don't, and moremoremore. Seriously fascinating stuff.

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5838 · July 18, 2011 at 4:52 PM

Not sure if you remember some of my posts, but I've been trying to pin down a Hemochromatosis diagnosis for over a year now. Has Chris been able to successfully navigate it, through diet and phlebotamy? My hematologist refuses to think that's what it is. But my bloodwork says I have one of the genes, and my iron sat. has been well over 60% for the past year

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56596 · July 18, 2011 at 4:30 PM

http://celticcurse.org/

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56596 · July 18, 2011 at 4:30 PM

Chris and I have used it and we like it. Chris was diagnosed with hemochromatosis though it.

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5838 · July 18, 2011 at 4:29 PM

I've been hearing more about the "23andMe" site. I'm curious how many people have used it, and if so, did you find the information useful? Would you recommend it?

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15966 · July 18, 2011 at 4:28 PM

Interesting. From what I've read it does seem that there was mating between homo saps and Neanderthals. Also fr what I've read it seems that the Neanderthals had the heavier meat diet generally.

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9 Answers

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11986 · July 18, 2011 at 8:08 PM

What a great little gadget! I just ran mine and got a score of 20. I've been thriving on a "zero-carb" diet for the last two years, and have found that vegetables -- with the exception of some nuts (walnuts, macadamias) and dark leafy greens (e.g. kale, but not broccoli or other brassicas) -- cause joint pain and weight gain. And unlike many people, I never got "induction flu" when I went from the SAD to VLC eating, four years ago.

Don't know if it's my Neandertal alleles, but what an interesting idea. Thanks for posting this.

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11986 · July 19, 2011 at 3:49 PM

Ooh, that's cool. I'll send you my list of Neandertal alleles if you'll send me yours. ;)

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18671 · July 19, 2011 at 3:33 PM

Rose, now that I've done this right, I'm second only to you so far, which is interesting.

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2977 · July 18, 2011 at 5:28 PM

This is SO cool!

UPDATE: I got a '12' (had to switch to Google Chrome to get it to work). Personally I do quite well with VLC, though have been considering introducing some 'starchy tubers' as an experiment. I'd like to test my wife, see if her 'O negative' blood type makes her more 'primal.'

I've had my genome tested recently (at 23andme.com) and it's a huge and fascinating wealth of data, and includes some tidbits useful to "Paleo" types. For instance, I have a marker for low serum levels of vitamins D and B12 - though having the marker doesn't mean I actually have that symptom (always something to keep in mind when looking at genetic data). I'm also a "fast caffeine metabolizer" - which explains why I can drink coffee at night and sleep like a baby. Reduced risks for certain diseases (e.g., Alzheimer's, Norovirus) and increased risk for others (e.g., Cardiovascular Disease) - all great stuff if kept in perspective.

There is a lot to learn, but I'm discovering that there are different sites - like this one - that will 'slice' the info in different ways or compare against different databases.

There are sites that review scanners. My sense is that 23andme is more consumer-oriented, with nice graphical summary pages of certain syndromes - for instance it displays my cardiovascular risk as a chart mapping the various genes and their cumulative impact. Other sites might be more technical but harder for the non-expert to interpret. The price seemed cheap to me: $99 for the test and $9/month for a year of updates.

I'll update this post with my Neanderthal 'rating' when it completes.

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11986 · July 18, 2011 at 7:32 PM

Cool! Thanks so much, CR.

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2977 · July 18, 2011 at 6:33 PM

btw, Rose: the way it works is that you export your genome from 23andme as a text file. Then that file can be uploaded to other sites, or parsed with the promethease application - or whatever you like.

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2977 · July 18, 2011 at 6:25 PM

Melissa - that's correct and I DID have that (so I wasn't crazy :-) Actually I've got both alleles for rs526934(G,G): "G allele associated with lower serum Vitamin B12. 'The TCN1 rs526934 G variant may reduce transport of cobalamin, resulting in lower plasma vitamin B12 levels.'"

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2977 · July 18, 2011 at 6:20 PM

Shows what I'm a noob I am. It was B6 - which I'm interested in because it's mentioned a lot around thyroid issues. I used Promethease, which is a small application from SNPedia.com. The data is presented in pretty raw format, but gets you directly to research papers that mention the SNP: ---- rs4654748(C;T) References:41.45 ng/mL lower Vitamin B6 blood concentration...more...(hide) ---- rs2282679(A;C) References:2somewhat lower vitamin D levels...more...(hide) rs2282679, located in the group-specific component (vitamin D binding protein) GC gene on chromosome 4p12, ...

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56596 · July 18, 2011 at 6:18 PM

she might have found it via promethease http://www.snpedia.com/index.php/Rs526934

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11986 · July 18, 2011 at 6:09 PM

CaveRat, which markers look at serum levels of D and B12? I can't find anything on the 23andme site.

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1906 · July 18, 2011 at 8:26 PM

From recollection, I scored a 7 also. I didn't get "induction flu" when I started paleo, though tend to feel a lot hungrier if I don't eat tubers or other starchy foods every few days. Other than the hunger feeling, I feel fine on VLC otherwise.

I'm not convinced these neanderthal alleles have anything to do with this, though.

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11986 · July 18, 2011 at 10:30 PM

I'd love to see some comparisons of PaleoHackers' entire datasets. It would be cool to be able to do something like the 23andWe research, and not impossible with current software, either. Razib Khan at the Gene Expression blog talks about this kind of grassroots analysis on genomic data all the time.

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2977 · July 18, 2011 at 9:49 PM

We'd be a pretty good sample, even if not huge, for some enterprising enthusiast.

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56596 · July 18, 2011 at 8:40 PM

yeah, maybe they don't have to do with anything, but interesting to collect some data

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18671 · July 19, 2011 at 1:35 AM

It looks like I have a count of 0. Is that even possible? All the counts on the far right of the table are 0, and the meter reads 0.

Anyway, I'm a ZC'er out of necessity, so that doesn't fit the proposed pattern.

Edit next day: Thanks to WyldKard, I realized I hadn't loaded my data properly. Now I score 16, which does fit the proposed pattern. Neat!

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18671 · July 20, 2011 at 1:05 AM

Heh. Not on your, er, coffee!

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2977 · July 19, 2011 at 4:52 PM

Darn - can I trade you my 'Fast Caffeine Metabolism' for your 'Extreme Longevity'? I'll toss in a 'Photic Sneeze' allele as a bonus..

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18671 · July 19, 2011 at 3:35 PM

I also get a high chance of extreme longevity, now, which is comforting.

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18671 · July 19, 2011 at 3:28 PM

Spot-on WyldKard! Thank you! See my edit above.

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56596 · July 19, 2011 at 2:48 PM

yeah it should be a .txt file

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1906 · July 19, 2011 at 12:20 PM

Ambimorph, it's possible you didn't load your data correctly. You have to unzip the raw data file after you download it. Check some of the other features of the site and see if you're getting expected data. The first time I tried, I used the zip download and also got 0s, but then realized the file wasn't loading properly after exploring some more. My understanding is that unless you're African, it's unlikely (but not impossible) for you to score a 0.

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56596 · July 19, 2011 at 2:27 AM

I'm about 1/2 Celtic. I think the Russian part is where I got some neanderthal genes ;)

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18671 · July 19, 2011 at 2:00 AM

Fascinating. Are you a Celt too, then, Melissa?

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56596 · July 19, 2011 at 1:58 AM

Honestly I was surprised how few I have, but I guess the evidence is that Celts are a later population migrating into the continent from Iberia...who knows where before...maybe n. africa

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56596 · July 19, 2011 at 1:57 AM

if you don't have any, it just means that your copies of these alleles are mostly ancient from the African ancestral pool.

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18671 · July 19, 2011 at 1:56 AM

English/Irish/Scottish.

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56596 · July 19, 2011 at 1:55 AM

what is your ethnicity?

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11986 · July 19, 2011 at 1:44 AM

Good to know. I don't see why it's not possible. There are what, 84 identified (possible) alleles? Sounds like you've got none of the "Neandertal" variants. Interesting discussion in the comments here, btw: http://spittoon.23andme.com/2010/05/06/new-evidence-suggests-interbreeding-between-humans-and-neanderthals/

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1069 · July 18, 2011 at 7:08 PM

I have a neandertal score of 9. I tried doing VLC but found that I had terrible insomnia and felt shitty most of the time. I do well following something similar to the Perfect Health Diet with around 100 g of carb, with white rice and fermented dairy, but no alcohol, ever.

I was actually a little disappointed when I got my 23andMe results... I am homozygous for the markers they have for blue eyes over brown, and blue eyes over green, but in reality I have hazel eyes that tend towards brown most of the time... I feel that the true utility of the service will come about in at least a few years, but those of us "early adopters" are being told we need to get the new chip and sign up for the subscription. Ugh. Wasn't my initial investment enough?

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1069 · July 20, 2011 at 8:26 PM

I tried the gedmatch tool and while it is very detailed it was still totally and completely wrong for me. I was homozygous for multiple melanin blocking and low melanin alleles. The color predicted was a very light blue - nothing like my dark brownish hazel eyes.

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1069 · July 18, 2011 at 9:06 PM

I shouldn't be complaining because I got the test as part of a $100 promotion a year and a half ago - upgrading to the new chip costs $49 + $9/ month, or $299 for a subscription for "the lifetime of the platform," whether that means the lifetime of the new chip or the lifetime that marketing and sales thinks they can get away with before demanding more money remains to be seen... I get that it's a business model but it rubs me the wrong way when hidden costs and "upgrades" come up, and I really don't like subscriptions at all.

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56596 · July 18, 2011 at 7:39 PM

lol actually that thing is even more inaccurate for me :( It gives me gray blue eyes...I wish!!!

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56596 · July 18, 2011 at 7:34 PM

You will get more accurate eye color results from this tool: http://ww2.gedmatch.com:8007/autosomal/eye_color_pred1.php

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2977 · July 18, 2011 at 7:16 PM

I also have the the blue eyes marker, but really have green - which for me is sort of blue with hazel mixed in. I guess I'm on the 'new chip' - did you have to pay the full amount for a new test?

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1436 · July 19, 2011 at 4:20 PM

I'm a 10 also. FWIW, Eating VLC made me feel crappy, but then again I'm pretty active (lifting, cycling), and tend to eat about 100-150g of carbs per day.

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1688 · December 18, 2011 at 3:23 PM

Just tried the tool - I'm a 7 and VLC doesn't do a whole lot for me. It makes little difference on weight loss and I feel pretty weak if I don't eat at least around 70 or 80 mg of carbs a day.

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3703 · July 20, 2011 at 4:09 AM

That is REALLY COOL :) Thank you for posting!!

Just recently something was published so I wonder if the Stanford group has the new updated findings? http://www.wired.com/wiredscience/2011/07/neanderthal-human-mating/

WIRED SCIENCE: The ancestors of the Neanderthals are believed to have left Africa between 400,000 to 800,000 years ago. However, by 30,000 years BC, they had disappeared. The ancestors of modern man left Africa between 80,000 and 50,000 years BC, suggesting that there was a definite crossover between the two.

Discovery News adds: “The team believes most, if not all, of the interbreeding took place in the Middle East, while modern humans were migrating out of Africa and spreading to other regions.”

This finding comes nearly ten years after Labuda and team identified a piece of DNA in the human X chromosome (called haplotype) that seemed different. A release detailing the findings explains: “When the genome of Neanderthals was sequenced in 2010, they quickly compared to 6,000 chromosomes from across the world with the haplotype of the Neanderthal. The sequence of the Neanderthal man was found in people of all continents, including Australia, but with the exception of sub-Saharan Africa.”

Have you heard of a specific dopamine receptor subtype DRD4 7R also related to Neanderthal genes? http://www.huffingtonpost.com/garret-loporto/surprising-way-your-neand_b_568455.html

(that guy cracks me up -- love that video...)

I'm not too surprised about Chris' hemachromatosis -- one of my uncle's has it and is a business/entrepeneurial HUNTER and brilliant. I think it goes along with other parts that make us uniquely neanderthal -- out of the box thinking, adhd-like restlessness and gluten sensitivity.

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3703 · July 20, 2011 at 3:11 PM

Thank you --great :)

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10497 · July 20, 2011 at 5:18 AM

Hey Grace --- have something interesting to send you wrt Neanderthals. Check your inbox.

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884 · July 19, 2011 at 9:06 PM

Apparently, if you're not of African descent, you're probably pretty neanderthal.

Non-Africans Are Part Neanderthal, Genetic Research Shows http://www.sciencedaily.com/releases/2011/07/110718085329.htm

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11986 · July 19, 2011 at 9:34 PM

Some East Africans have "neandertal" genes too (in quotes because some still reserve judgment as to the actual origin of these genes): http://dienekes.blogspot.com/2011/03/neandertal-genes-in-east-africa.html

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