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Revert

Richard Keatinge has reverted my edit stating "Rv to last good version". I am not clear why. I deleted the comment on dark skin being doubtful, and he wrote on the talk page that he agreed with my comment on this. I also deleted another unreferenced comment. Neither change is vandalism, as the reference to the last good version implies. Dudley Miles (talk) 10:55, 29 July 2020 (UTC)

Agree with the removals by Dudley Miles: one source is a non-RS, the second is good but its inclusion is synthesis, the deleted para is unsourced. –Austronesier (talk) 11:41, 29 July 2020 (UTC)

Ah, sorry, absolutely no such implication intended, I apologize.

The "less certainly" comment was referenced to Walsh, S., Chaitanya, L., Breslin, K. et al. Hum Genet (2017) 136: 847. https://doi.org/10.1007/s00439-017-1808-5. Publisher Springer. Print ISSN 0340-6717 Online ISSN 1432-1203, which does indeed clearly support the comment, though not the suggestion that we have no information on Cheddar Man's skin color. The supplementary material of Brace et al similarly supports the comment.^[1] I feel that the comment should stay, probably with both references.

The comments "There was no genetic link with the other, less complete skeletons from Gough's Cave, which are 5,000 years older than Cheddar Man. For much of this intervening period, the last glaciation of Europe had made the area unsuitable for human life." would indeed benefit from referencing. The 5,000 years is a round number derived by simple subtraction between the date given by Bello et al for the earlier remains, 14,700 cal BP, and by the NHM date for Cheddar Man, 9,100 BP. It's probably allowable by OR policy, but we could just use the date for the other remains if that's preferred.

I'd suggest "There was no genetic link with the other, less complete skeletons from Gough's Cave, which are dated to about 14,700 cal BP, some 5,000 years older than Cheddar Man.^[2] For much of this intervening period, the last glaciation of Europe had made the area unsuitable for human life.^[3]^[4]"

References

[1]
Brace, Selina; Diekmann, Yoan; Booth, Thomas J.; Faltyskova, Zuzana; Rohland, Nadin; Mallick, Swapan; Ferry, Matthew; Michel, Megan; Oppenheimer, Jonas; Broomandkhoshbacht, Nasreen; Stewardson, Kristin; Walsh, Susan; Kayser, Manfred; Schulting, Rick; Craig, Oliver E.; Sheridan, Alison; Pearson, Mike Parker; Stringer, Chris; Reich, David; Thomas, Mark G.; Barnes, Ian, "Supplementary Material", Population Replacement in Early Neolithic Britain, bioRxiv 10.1101/267443, doi:10.1101/267443, Cheddar Man (UK, Mesolithic) Eye colour —There is 1 locus (LOC105374875 (formally known as SLC24A4) rs12896399) with low coverage (1x) hence a heterozygote is possible. Prediction includes a range that includes what the 1x coverage found (ancestral G allele) and the possibility of an A derived allele being present. LOC105374875 rs12896399 LOC105374875 rs12896399 (homozygote GG) (heterozygote GA) Blue eye 0.564 0.711 Int. eye 0.189 0.143 Brown eye 0.247 0.145 Prediction range: Blue eye 0.564 - 0.711 Int. eye 0.189 - 0.143 Brown eye 0.247 - 0.145 Final prediction: Intermediate (blue/green) eye colour Explanation: This individual has light or blue/green eye colour, it is not light blue, there are elements of brown/yellow in the eye to give a proposed perceived green colour. Better coverage at the low sequenced marker would clarify this but blue/hazel cannot be ruled out. It is certainly not a brown eyed or clear blue-eyed individual. Hair colour—There is 1 locus PIGU rs2378249 with low coverage (1x) hence a heterozygote is possible. Prediction is a range that includes what the 1x coverage found, ancestral A allele, but also includes the possibility of a heterozygote being present. PIGU rs2378249 PIGU rs2378249 (homozygote AA ) (heterozygote CA) Blond 0.014 0.013 Brown 0.719 0.759 Red 0.011 0.023 Black 0.257 0.205 Light 1 0.999 Dark 0 0.001 Prediction range: Brown 0.719 – 0.759 Black 0.257 – 0.205 Final Prediction: Dark Brown/Black hair colour Explanation: The probability value of black is >0.2 so it has an impact on prediction, and will darken the high brown probability. However there are light pigment alleles indicating a lighter shade phenotype. Better coverage at the low sequenced marker would help clarify this. This individual would be perceived as having dark brown hair. Black however cannot be ruled out. Skin pigmentation—There are 3 loci (BNC2 rs10756819, TYR rs1126809, MC1R rs3212355) missing, and the profile does contain 2 loci (LOC105374875 rs12896399 and PIGU rs2378249) with low coverage (n=1x) hence a heterozygote is possible at those sites. When factoring in possible genotype combinations, a prediction range may be generated. The range consists of assuming the two loci with low coverage are correct as homozygote for their sequenced allele (LOC105374875 rs12896399 G allele and PIGU rs2378249 A allele) and omitting the 3 missing loci from the prediction model as they have no coverage, to including these markers with their ancestral (BNC2 rs10756819-GG, TYR rs1126809-GG, MC1R rs3212355-CC) and also their derived allele counterparts. The following range for skin colour prediction is possible for this individual with these parameters: ancestral alleles used derived alleles used Very Pale 0 0 Pale 0 0 Intermediate 0.394 0.125 Dark 0 0 Dark-Black 0.606 0.875 Prediction range: Very Pale 0 Pale 0 Intermediate 0.394 - 0.125 Dark 0 - 0 Dark-Black 0.606 - 0.875 If we omit the three missing alleles, our tool produces 0.891 and 0.109 probabilities for the intermediate and dark-black category respectively, changing the prediction ranges to 0.891-0.125 and 0.109-0.875. However, note that this completely removes the locus from the prediction model, hence the prediction will not perform optimally (how the prediction model was made), therefore it is best to have some allele present to infer the most probable range for Cheddar Man and we therefore derive the ranges above from the extreme allele constellations only. Final prediction: Dark/Dark-to-black skin Explanation: The missing loci certainly impact on this prediction; however utilizing the input of all ancestral alleles is the preferred option over the use of the derived alleles at these loci – hence 0.394 for intermediate and 0.606 for Dark-black would be the most probable profile. That being said a broad range is present in both the intermediate and dark-black categories due to the missing loci. Also this effect, of skipping a skin colour prediction category with regards probability values, tends to be observed more often in admixed individuals. What is important to note is the input of the dark-black prediction is significant on the intermediate category and therefore it is acceptable to propose a dark complexion individual over an intermediate/light prediction even though the intermediate range is large. It is unlikely that this individual has the darkest possible pigmentation, however it cannot be ruled out. Better sequencing coverage would clarify to what degree this individual has a dark complexion. {{citation}}: horizontal tab character in |quote= at position 320 (help)
[2]
Bello, Silvia M.; et al. (February 2011). "Earliest Directly-Dated Human Skull-Cups". PLoS ONE. 6 (2): e17026. doi:10.1371/journal.pone.0017026. PMC 3040189. PMID 21359211. Retrieved 2011-02-17.{{cite journal}}: CS1 maint: article number as page number (link) CS1 maint: unflagged free DOI (link)
[3]
Severinghaus, Jeffrey P.; et al. (1998). "Timing of abrupt climate change at the end of the Younger Dryas interval from thermally fractionated gases in polar ice". Nature. 391 (6663): 141–146. Bibcode:1998Natur.391..141S. doi:10.1038/34346.
[4]
Atkinson, T. C.; et al. (1987). "Seasonal temperatures in Britain during the past 22,000 years, reconstructed using beetle remains". Nature. 325 (6105): 587–592. Bibcode:1987Natur.325..587A. doi:10.1038/325587a0.

Richard Keatinge (talk) 12:08, 29 July 2020 (UTC)

Walsh does not mention Cheddar Man. It should not be cited as that is WP:SYNTH. The supplementary information does not support the statement that the skin colour is less certainly known. It discusses the possiblity of an intermediate colour but says "Final prediction: Dark/Dark-to-black skin". I do not see any reason in these sources to say that the colour is less certainly known.

You're right about Walsh. We have however had references, which I feel we should acknowledge, to people saying that we really can't tell what the skin colour was,(https://www.newscientist.com/article/2161867-ancient-dark-skinned-briton-cheddar-man-find-may-not-be-true/) and Brace does seem a little less certain about the skin colour than about eye colour:

"Final prediction: Dark/Dark-to-black skin

Explanation: The missing loci certainly impact on this prediction; however utilizing the input of all ancestral alleles is the preferred option over the use of the derived alleles at these loci – hence 0.394 for intermediate and 0.606 for Dark-black would be the most probable profile. That being said a broad range is present in both the intermediate and dark-black categories due to the missing loci. Also this effect, of skipping a skin colour prediction category with regards probability values, tends to be observed more often in admixed individuals. What is important to note is the input of the dark-black prediction is significant on the intermediate category and therefore it is acceptable to propose a dark complexion individual over an intermediate/light prediction even though the intermediate range is large. It is unlikely that this individual has the darkest possible pigmentation, however it cannot be ruled out. Better sequencing coverage would clarify to what degree this individual has a dark complexion."

As always I would bow to consensus, but I still feel that the previous formulation was quite a good one. Richard Keatinge (talk) 18:41, 29 July 2020 (UTC)

On your second point, it is obviously unlikely that there was a genetic link with skeletons before the Younger Dryas (not the Late Glacial Interstadial, which your link pipes to). But do either of your sources specifically say there was no link? If not, it is synth. Dudley Miles (talk) 13:36, 29 July 2020 (UTC)

Younger Dryas, indeed, thanks.

Hmm, digging through the article history the point about no connection with the Magdalenian remains seems to have come from a 2018 press release, First modern Britons had 'dark to black' skin, Cheddar Man DNA analysis reveals. Hannah Devlin Science correspondent Wed 7 Feb 2018 The previous analyses - of mitochondrial DNA - had been announced with the hokey "discovery" that Cheddar Man was an ancestor of a local family. It was probably worth making the point explicit at that time. I'd probably keep it in now, but shan't argue further if anyone wants to take it out. Richard Keatinge (talk) 18:41, 29 July 2020 (UTC)

You cite the New Scientist article. It is not a reliable source, as I pointed out in the 'Brace 2018 vs Other stances' section above. Your comment: "Brace does seem a little less certain about the skin colour" is not a basis for querying the findings. We should not say there is doubt unless a reliable source specifically says so, and I am not aware of one that does. As to no connection with pre-Younger Dryas specimens it is very likely, but we need a reliable source. Presumably it is a question of tracking down the source cited by the Guardian report you link to. Dudley Miles (talk) 19:52, 29 July 2020 (UTC)

Quite clearly, Dudley Miles is being Ignorant to the findings & facts available. One who wishes a prediction to be fact is one who knows no facts.

The New Scientist article which he states is "unreliable" make a statement a follows: (One of the geneticists who performed the research) says the conclusion is less certain, and (according to others) we are not even close to knowing the skin colour of any ancient human.

First of all, you cannot get a better or more reliable source than one of the very core Scientists who extracted & examined the DNA of the very remains in question, simply if any one of the examining scientist could be wrong, they they all could be and would this scientist not be questioned for integrity?

Others: Genealogists from all over the world have agreed the Out of Africa theory is a belief based on the fact we today have no hard evidence that Humanity migrated out of Africa, and we have no evidence that links all Asians and Europeans to Africa, if we did the theory would be called The Out Of Africa fact. Scientists globally know DNA testing cannot successfully prove skin colour, hence why its stated as a prediction.

The UK is not the world, we have human remains dating back hundreds of thousands of years which have never been determined as black or white! Why is this? We could prove all European remains had dark to black skin if we could do as such.

The cheddar man was not the first Briton, we know this as a fact and older remains than the cheddar man which have been found show no indication if they were 100% white or black. It is a prediction that he (may) have had dark to black skin, there is no factual basis to believe the cheddar man had dark to black skin.

New Scientist obtains its sources on an international stage where the supplying information comes directly from scientists, institutions and those of high standing within the community to provide information mainly in the form of interview which is considered globally as a reliable source of factual information retaining the title as the Worlds most popular magazine/ source in science & tech.

So unless Dudley Miles can provide evidence the worlds most popular & successful source is unreliable, I ask readers to dismiss this claim. You cannot get a more reliable source than a Scientist who was on the main examining team. 2A00:23C8:8580:1C00:C425:2DFE:927B:3FFF (talk) 12:26, 1 September 2020 (UTC)Sreader.

Wikipedia should be based on reliable sources, that is books by experts and peer reviewed articles, not a journalist's version of what someone said. The findings may well be disputed by reliable sources, but I am not aware of any. If anyone knows of such a source, please supply a link and we can discuss it. Dudley Miles (talk) 13:41, 1 September 2020 (UTC)

The New Scientist is a reliable source for the information that researcher A or research team B currently does research about topic C. The only reliable source for research results are peer-reviewed publications. –Austronesier (talk) 13:55, 1 September 2020 (UTC)

Again I have removed inappropriate expatiation on the basis of the New Scientist article. Per discussion above, this article is not an appropriate place to discuss the uncertainty of assigning phenotypes from DNA analysis. We already use the word "probably" and refer it to the New Scientist article, which is an entirely adequate presentation. Richard Keatinge (talk) 13:41, 26 March 2021 (UTC)

The New Scientist article is from 2018. I wonder what happened to this research in the last three years? Genetics is highly "publish-or-perish", so either there must be a better source in the meanwhile (at least a pre-print), or their results were not as conclusive as expected. –Austronesier (talk) 13:50, 26 March 2021 (UTC)

Similar to the below Richard Keatinge seems to object to a New Scientist article that references the actual person who did the DNA study. Professor Walsh states "It is his most probable profile, based on current research." Elsewhere it is reported that "Walsh believes that the tests can't prove Cheddar Man's skin colour and that his DNA may have degraded over the past 10,000 years.

https://www.dailymail.co.uk/sciencetech/article-5453665/Was-Cheddar-man-white-all.html

The facts support that it is possible that Cheddar Man had dark skin. The research comes up with that as the 'most probable' profile, but the authors question the accuracy. This is obviously an interesting debate, but as a debate it needs the whole story. How they came to the 'probability' and how accurate that probability is. The New Scientist article is therefore important to understand the whole story and should not be removed from the references. — Preceding unsigned comment added by 82.13.226.29 (talk) 13:57, 26 March 2021 (UTC)

The predictions are the most accurate available, and we present them with appropriate words of caution. An author pointed out in 2018 that predictions of phenotype from ancient DNA are not the same as measuring those actual phenotypes. This is not a controversial statement, it's just a fact. Further discussion of this point might (given suitable sources, which have not been presented here) be appropriate on another page. But not here. Richard Keatinge (talk) 11:06, 27 March 2021 (UTC)

It seems questionable that the single word "probably" is much of a word of caution. In my mind it means much more likely than not, not just a 51/49% difference. It doesn't mean that in the next few years the whole thing may be proved to be entirely bollocks. Or that the researchers chose to fill in gaps in ways that influence the final results. It should be stated clearly that this is just the state of the science today. I suggest more significant emphasis be placed on any legitimate debate. Dynasteria (talk) 08:52, 16 May 2021 (UTC)

Supposed descendants of Cheddar Man

Rbezar has recently added information about Adrian Targett and Craig Dent, who were stated in the Independent and the Guardian respectively to be ‘descendants’ of Cheddar Man. But in fact it is clear from the articles that the link is via the mitochondrial DNA, which is not passed on by men, so that there is no evidence that Mr Targett and Mr Dent are directly descended from Cheddar Man. The BBC article says that the mitochondrial type is shared by approximately 10% of modern Europeans. So this does not seem to me to be worthy of remark, and I am deleting the reference to the supposed ‘descendants’ from the article. Sweet6970 (talk) 11:05, 29 January 2021 (UTC)

Agree. Both individuals are not "descendants" of the Cheddar Man, but have shared maternal ancestors with him; the Guardian article explicitly says so. –Austronesier (talk) 13:07, 29 January 2021 (UTC)

Agreed. This is a meaningless factoid—Cheddar Man lived so long ago that he is guaranteed to be either the ancestor of nobody or of practically everybody—and yet more evidence that newspapers aren't reliable sources for articles on archaeology (see above). – Joe (talk) 13:37, 29 January 2021 (UTC)

It is doubly or even triply meaningless as the haplogroup which they matched - U5a, has been shown to be wrong, probably as a result of older PCR testing used by Brian Sykes' team, than the more modern methods that the Natural History Museum used. This is explained in a talk by Dr. Tom Booth of the Natural History Museum who was on the team who studied Cheddar Man's remains here

https://www.youtube.com/watch?v=h5hZBvD7sbU&t=508s

some comments on the skin pigmentation, he points out that it is mainly the fact these hunter gatherer populations lack the modern variants which point to lighter skin pigmentations which makes them assume they may have had darker skin, but he says, since the mesolithic population was totally or near totally replaced by neolithic farmers in Britain, it is 50-50 that he may have had lighter skin with a variant which no longer exists in modern populations.

https://www.youtube.com/watch?v=h5hZBvD7sbU&t=1038s

Plutonto (talk) 09:31, 22 May 2021 (UTC)

Chin

While the much publicized reconstruction shows a man with a fairly prominent but rather narrow chin, the skeletal remains seem to indicate a more jutting and rounded jaw or chin. Is this an optical illusion? My own bad interpretation? Dynasteria (talk) 09:13, 10 May 2021 (UTC) Oddly enough, the model makers themselves have chins which look more like what I have in mind. Adrie and Alfons Kennis: https://phys.org/news/2018-02-dna-modern-briton-dark-skin.html Dynasteria (talk) 09:21, 10 May 2021 (UTC)

The chin question is about morphology and that issue is not represented in the article. It should be. On a larger scale, my question is about the validity of interpreting Cheddar Man's other characteristics such as skin color. The Kennis brothers are not scientists, as far as I can tell, and certainly are not world class geneticists. Yet the world at large is touting their artistic interpretation of Cheddar Man. Should WP weigh in here? The image created by the Kennis brothers is everywhere and now is the definitive version of Cheddar Man in most people's minds. The same is true for numerous other interpretative efforts on other ancient remains (e.g.Ötzi). Another issue to consider is that the blue/green eye color is apparently not disputed in Cheddar Man yet in modern populations light eye color and light skin color are demonstrably linked. If the chin, which is an obvious detail, can be misinterpreted then how much more so can hidden characteristics (i.e. skin color) be gotten wrong? If Wikipedia is unwilling or unable to present both sides of an issue (light or dark skin) then perhaps WP shouldn't bring it up at all. Dynasteria (talk) 07:43, 12 May 2021 (UTC)

If you can present reliable sources discussing his chin, we can include the matter here. On the issue of his skin colour, we give a neutral point of view based on reliable sources, and without the image you mention which is copyright. Feel free to develop a consensus here for any changes you may wish to suggest. Richard Keatinge (talk) 09:39, 12 May 2021 (UTC)

To start with, according to the following article the original research was done for a TV documentary. (https://www.newscientist.com/article/mg23731673-200-does-cheddar-man-show-there-is-such-a-thing-as-bad-publicity/) Which may explain why the list of research participants is so long. It also may explain why the rush to judgment was so great and perhaps why there has been little discussion of its validity since. I'm not a scientist and I don't have access to academic journals, but I shall soldier on and keep pecking away at what evidence I can find. The primary concern to me and I hope others is that the conclusions may not be very rigorous. Dynasteria (talk) 20:26, 12 May 2021 (UTC)

The following article, among others, indicates the team, including Selina Brace, endorses the Kennis representation. She says it's "really, really cool". https://www.nhm.ac.uk/discover/news/2018/january/documentary-to-reveal-surprising-face-of-cheddar-man.html Brace is on the far left in the photo. Of course, forensic DNA expert Susan Walsh of Purdue University says that predicting Cheddar Man's skin color is difficult and by no means a settled issue. My point, again, is that if they can get the chin wrong, how wrong can the skin color be? Dynasteria (talk) 08:25, 13 May 2021 (UTC)

The comments of Susan Walsh are according to a journalist. So far as I can discover, the only comment she has made in a reliable source is as a co-author of the article estimating the skin colour as dark/dark to black. If she does express doubts in a reliable source, we should of course include them in the article. Dudley Miles (talk) 09:04, 13 May 2021 (UTC)

(ec) Just curious: by what parameters did they "get the chin wrong"? Putting aside for the moment that this statement needs a reliable source; if it's OR: have you had the opportunity to make a 3D comparison of the skull and the artistic reconstruction? Or at least a visual comparison from all angles?

If you want to soldier on, you should provide reliable sources on par with the sources which present hard quantified data about the genetic markers that allow to make an estimate about the skin color of the specimen. Using a vague impression to devalidate laboratory results is not just apples and pears, but it's apple sauce and Poire Williams. –Austronesier (talk) 09:21, 13 May 2021 (UTC)

Responding to both comments above. Not sure what the problem is with using a legitimate English expression ("soldier on"). I'm not really using anything to invalidate anything. I'm merely pointing out how easy it may be to get things wrong and how quickly misinterpretations can spread when there's enough popular will behind it, not to mention TV and lots of publicity and probably money. Sorry. To be fair, I should have said: "If in fact it is the case that, as I intuit, they got the chin wrong, then I question how wrong the skin color might be given the complexity of the DNA analysis and the relative newness of the science and techniques coupled with the ancient status of Cheddar Man's DNA." That would have been a more accurate statement of my concern. And, yeah, I agree that journalists aren't the best source for questions of science. However, one notices that WP uses massive amounts of journalism as authoritative sources for politics, etc. Thanks to both of you for responding. Dynasteria (talk) 12:12, 13 May 2021 (UTC)

Footnote 2

Is the title of the article quoted incorrectly in footnote 2?

"Population Replacement in Early Neolithic Britain", Nature Ecology & Evolution, 3: 765–771

When you follow the link you get:

"Ancient genomes indicate population replacement in Early Neolithic Britain"

Or is it acceptable to use only part of a title? Note also the different use of upper case letters. Perhaps one reason this makes a difference is that the article is actually available to readers without library access here:

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6520225/pdf/emss-82120.pdf

Which is more difficult to find without the correct title but would make the footnote a lot more meaningful to WP readers. Perhaps the footnote link could go there instead. Dynasteria (talk) 08:32, 16 May 2021 (UTC)

I think you should just correct according to your judgment. Dudley Miles (talk) 10:05, 16 May 2021 (UTC)

The displayed title was the older title of the bioRxiv preprint.

Fixed. –Austronesier (talk) 12:49, 16 May 2021 (UTC)

If you read the manual, the HIrisPlex-S system is not reliable. I've also had a phone call with the professor supervising the research to let him know of the error (though I don't think he was doing all of the work). He was entirely reasonable and acknowledges the scope for error in the tool. The way people are arguing about how scientists are almost infallible and things like that doesn't really seem appropriate to me.

The tool has a major usability issue with scrambles the input. The issue is because of the two DNA strands. People choose which side of it to use inconsistently so the letters switch for SNP alleles.

It caught me out when I ran my own DNA through it. It also caught out the scientists who ran the test on Cheddar Man. Even correcting for this, we don't get results from the tool that we can be sure about. When we correct for the errors we don't get a black result any more. We get something that might look more intermediate Indian or Chinese in terms of skin colour. Though we also get brown hair with some ambiguity as to how light or dark it is. We still get blue eyes, though with a few reasons to be uncertain about it.

Can someone please update the page to reflect this uncertainty and close this argument once and for all?

You can cite this:

https://www.quora.com/What-is-the-evidence-that-Cheddar-Man-was-not-black-Scientists-who-sequenced-his-DNA-said-he-had-no-genes-for-light-coloured-skin-He-had-genes-for-skin-colour-consistent-with-Subsaharan-populations-What-is-the/answer/John-Baker-1665 — Preceding unsigned comment added by 80.5.255.120 (talk) 05:01, 15 October 2021 (UTC)

Please take a look at our policy on original research and our guideline on reliable sources to find out why we cannot take action on your suggestion. This has nothing to do with a supposed belief in the infallibility of scientists. Generalrelative (talk) 05:13, 15 October 2021 (UTC)

You can look at that link. It links to their own data. It also links to the hirisplex tool and manual. You can take their data, read the manual and try the tool yourself. They put in the wrong value for the SNP on ASIP (which I keep mixing up for ASIP2 for some reason). That means this article is citing a source that can as a matter of fact be proven as wrong.

Check it yourself if you don't believe me:

https://hirisplex.erasmusmc.nl/

https://www.nhm.ac.uk/content/dam/nhmwww/our-science/our-work/origins-evolution-futures/cheddar-man-pigmentation-data.xlsx

https://hirisplex.erasmusmc.nl/pdf/hirisplex.erasmusmc.nl.pdf

https://walshlab.sitehost.iu.edu/hpsconvertsonline.R

https://walshlab.sitehost.iu.edu/pages/tools.html

Please pay excruciatingly close attention to rs6119471, including in the manual.

As you can see here it is crucial in differentiating between subsaharan-African pigmentation (or potentially South Asian, etc) and Eurasian pigmentation:

https://www.researchgate.net/publication/316918714_Global_skin_colour_prediction_from_DNA

Obviously, the sources you have quoted are not reliable because the definition of reliable is not a source that makes a mistake to the effect of a typographical error producing scrambled results. How did you make the determination that the source is reliable and how can I submit these findings then to a "reliable" source so that they can be used to update the article here?

You have a serious problem here because you're citing sources that obviously aren't reliable and have not been properly peer reviewed at all by anyone. The most basic reproduction of their work shows they made a data entry mistake.

This isn't reliable source tier work. This is an extremely basic low skilled labour activity. You have a larger problem if identifiable mistakes like this in your sources are impossible to patch upstream and you only accept upstream material. — Preceding unsigned comment added by 80.5.255.120 (talk) 20:15, 22 January 2022 (UTC)

If a so-called 'reliable source' says that Cheddar Man had dark skin, we say that Cheddar Man had dark skin. If then another so-called 'reliable source' says that Cheddar Man had intermediate skin, then we say that source A says Cheddar Man had dark skin, but source B says that Cheddar Man had intermediate skin. If these are the only so-called 'reliable sources', and both of those sources are wrong, then Wikipedia will also be wrong. Welcome to Wikipedia. Tewdar (talk) 21:01, 22 January 2022 (UTC)

How can I submit these findings then to a "reliable" source so that they can be used to update the article here? Here you go: https://www.nature.com/nature/for-authors/initial-submission. Best of luck. Tewdar (talk) 21:26, 22 January 2022 (UTC)

(edit conflict) Dear IP expert: how is a paper in Nature Ecology & Evolution not properly peer-reviewed? If you have different insights about the skin color of Cheddar Man, go ahead and write an article and succeed to have it published in a peer-reviewed (and non-predatory) journal. If it gets a reasonable number of citations in other peer-reviewed articles, we might consider it for mention here. This is how WP works, and it is good that WP works this way. Otherwise, WP would just be collection of arbitrary assertions made by people with unverifiable credentials (or no credentials at all). –Austronesier (talk) 21:31, 22 January 2022 (UTC)

It's extremely hard to keep my composure in this case. Nature Communications regularly releases things that are complete garbage and it's a shame because they also release a lot of good things. However, this didn't come from Nature. Have you checked the sources they cite to actually get to the root of this?

This work was done by/for NHM, a commercial entity for a commercial venture, to present a new exhibit, TV program and working in conjunction with the press as a promotional campaign. Originally the research was released on a blog for the university (UCL) and was not published via normal means. By the time there was any opportunity to peer review it, it was too late, there was already a TV documentary on it, interviews in the press, and other things being broadcast to the public.

The reason this really upsets me is not just because a bit of due diligence could have sniffed out there might be something wrong with the source. If someone opens up a new exhibit showing a skeleton of some kind of weird chimera of unlikely features like it turns out the person had wings, a tail, scales and a proboscis then you would call foul.

When you have results here with an unlikely and suspect array of features, use your head. This is the kind of thing I would expect to see in Pravda or something in the weird and whacky section along with people who live on nothing but sunshine. This is just another Piltdown. You only need to look at it. It's ridiculous. This is something that you should be suspicious about on face value and ask to check the results. I've given you all the links you need to do that. Check it then please do what you do, have a committee or something to sort out how things like this are slipping you by.

At the very least you have a problem accepting things posted on university blogs as sources or things like the NHM. That needs to be reevaluated. You also have a problem when what might usually be more reliable sources make the same mistake of accepting publications from sources that have the appearance of being legitimate but are not. Perhaps the first time around it's hard to catch but once something like this has been detected then sources should be reclassified.

I'm sorry but I don't want to spend ages messing around with LaTeX either to submit to a journal. Can you please present me with a journal source that accepts common English in standard formatting rather than esoteric conventions?

To give you instruction on how to find the error: Copy the xlsx results to the hirisplex tool normally matching up the letters. You should get a result for black. Now you'll notice you will have matched two C alleles for the ASIP SNP. Look this up online: https://www.ncbi.nlm.nih.gov/snp/rs6119471?horizontal_tab=true

Now please see this in the manual:

"*if you are using sequencing data, than you may need to flip strand orientation in your result before inputting into this prediction model. The only SNP that may cause confusion and therefore must be converted (from NCBI’s forward orientation) is rs6119471. All other G/C, A/T SNPs are in the correct orientation for input or are opposite alleles i.e. SNP G/A, input requests C/T."

If you like, test this with other European genetic samples. You'll see that flipping rs6119471 often significantly darkens them. The confusion here is that the alleles are usually G or C and these are complementary so if you get the read direction the wrong way around then you end up using the wrong allele. When you correct for this you get an intermediate skin result (though you also get a result that confuses the tool somewhat). On top of this the spectrum from very light to very dark isn't strictly speaking uniform and those words alone are misleading unless you're pointing to their definition as provided by the tool which you can find in the manual.

The R script which is intended for sequenced data like Cheddar Man's shows this:

"online$rs6119471_C<-gsub('CC', '0', online$rs6119471_C)"

It's counter intuitive but for that SNP in this case if you have a C rather than matching it you're meant to treat it as a non match. Thus, a data entry error is determining the end result in this case. This says if you have two Cs then even though it's asking for C put 0 Cs. The other SNPs usually work the other way around.

— Preceding unsigned comment added by 80.5.255.120 (talk) 12:28, 24 January 2022 (UTC)

https://www.nature.com/srep/author-instructions/submission-guidelines#texlatex-files Our preferred format for text is Microsoft Word, with the style tags removed. While we await publication of your article, do you have any published reliable source (not Quora, mind you) that gives a different prediction specifically for Cheddar Man's phenotype? Because I'll add it to the article within an hour. Tewdar (talk) 13:30, 24 January 2022 (UTC)

I'll have a go though it's a lot of work, it won't be quick when I haven't touched that kind of formatting for years. Note something I missed is that even with rs6119471 being ambiguous is a huge problem when it's pivotal in cases like this for discerning African or Eurasian phenotypes. Sort of makes it useless, a coin toss if it's right or wrong. — Preceding unsigned comment added by 80.5.255.120 (talk) 13:32, 24 January 2022 (UTC)

What "kind of formatting"? MS Word? If we have a source, published by Nature Ecology & Evolution, about Cheddar Man's phenotype, we pretty much have to include it here. If then no other published article refutes the claim, we cannot just paste up the results of random hobbyists on random blogs doing amateur fun with HIrisPlex. Do you see the position we're in here? Tewdar (talk) 13:47, 24 January 2022 (UTC)

To publish a paper there's usually a whole load of conventions and additional requirements. It's not accessible or inclusive. Most people treat it like an elite club for the rich where you won't get in without an unaffordable suit or something. It's not really about science. For someone with Asperger's Syndrome that can spend weeks correcting a single pixel out of place and who cares not for ritual things like this are very difficult. However I'll make an attempt and see how that goes. — Preceding unsigned comment added by 80.5.255.120 (talk) 15:18, 24 January 2022 (UTC)

Walsh, Susan (2017). "Global skin colour prediction from DNA"

Clarified skin color

‘All British Mesolithic individuals’

In popular culture - query

(Unqualified) individuals, Brexit supporters...

Here's what the source says, verbatim: The ongoing response to this man’s skin colour can be sampled by searching online for the term ‘Cheddar Man debunked’. This reveals multiple voices disputing claims made by the research team, and revisionism and scepticism of expertise that conforms to the ‘post-truth’ environment of the Brexit hypothesis. Attempts were made to pre-empt such interpretations, with team member Tom Booth informing The Guardian that “[Our research] really shows that these imaginary racial categories that we have are really very modern constructions […] that really are not applicable to the past at all” (Devlin 2018). Booth also responded to political interpretations of the story in broadcast interviews and on Twitter. By pushing back against inappropriate interpretations of research, archaeologists can subvert the Brexit hypothesis—although this had limited success in the case of Cheddar Man.

Now, it's pretty clear (to me at least) that the article is not talking about claims that are being disputed by research scientists in peer-reviewed journals here. Although this extract does not actually call these people unqualified, it does use language ("revisionism, scepticism of expertise, post-truth, inappropriate interpretations") that I do not think is captured by just 'individuals'. Anyone got any better suggestions? Tewdar 13:46, 15 January 2023 (UTC)

This says nothing about ‘Brexit supporters’. And that the source refers to a supposed ‘‘post-truth’ environment of the Brexit hypothesis’ indicates that this is more of an opinion piece than serious reporting. I am leaning towards deleting this last para of the section altogether. Sweet6970 (talk) 14:46, 15 January 2023 (UTC)

here's the link to the Antiquity article from CUP. There is more context to this which I didn't add for copyvio reasons. It is certainly not an opinion piece. Tewdar 15:03, 15 January 2023 (UTC)

I also do not want to use the term 'Brexit supporters'. Tewdar 15:07, 15 January 2023 (UTC)

And here is a discussion of post-truth politics and misinformation in the context of Brexit and the Vote Leave campaign. Tewdar 15:15, 15 January 2023 (UTC)

Hmm… let’s not get into a discussion about Brexit, “truth”, and sociology….. How about changing ‘individuals’ to ‘members of the public’? Sweet6970 (talk) 16:30, 15 January 2023 (UTC)

Well, you said that using a phrase like ‘post-truth’ environment of the Brexit hypothesis’ was characteristic of an opinion piece - I merely pointed out that this is, erm, probably not quite accurate. 😁 Members of the public is fine with me. Tewdar 16:40, 15 January 2023 (UTC)

Thanks for making the change to the article. But what does 'bah' mean? Sweet6970 (talk) 16:47, 15 January 2023 (UTC)

In this context, it pretty much translates as, "I want to write that these criticisms are coming from people who wouldn't know the difference between a SNP and the SNP, but the source isn't quite explicit enough in saying this and I'm too busy to find another source right now." 😁 Tewdar 17:01, 15 January 2023 (UTC)

I agree that unqualified and Brexit supporters - my suggestion - are both unsatisfactory, but I think that individuals and members of the public are too vague. How about "Cheddar Man's dark skin colour and the expertise of the authors of the study have been disputed on social media." Dudley Miles (talk) 16:57, 15 January 2023 (UTC)

I already added a reference to social media, so for now, I think it's not too bad. I just want to make it clear that these criticisms are coming from random bloggers and tweeters, not scientific articles. I'll try and find something better, but it's probably alright for the time being in my opinion. Tewdar 17:04, 15 January 2023 (UTC)

I do not think "members of the public" is OK. It is so vague that it conveys nothing useful to the reader. It does not convey people with an agenda, which is what the source is saying, and we have to convey what our sources say. Dudley Miles (talk) 17:58, 15 January 2023 (UTC)

It conveys that they are not commenting as subject experts. The quotation above includes: multiple voices disputing claims made by the research team, which does not sound to me as if all these ‘multiple’ voices have the same agenda. I don’t think the source justifies anything more definite than ‘members of the public’. Sweet6970 (talk) 18:20, 15 January 2023 (UTC)

There are problems with any description. That is why I suggested a wording, "Cheddar Man's dark skin colour and the expertise of the authors of the study have been disputed on social media.", which gets round the issue. Dudley Miles (talk) 18:28, 15 January 2023 (UTC)

Your wording sounds fine. Tewdar 18:32, 15 January 2023 (UTC)

If the suggested wording is to replace the last sentence of the section, I would be happy with that. Sweet6970 (talk) 20:36, 15 January 2023 (UTC)

Sounds good. The preceding sentences in the paragraph already provide sufficient information about the background and nature of the discourse. –Austronesier (talk) 20:52, 15 January 2023 (UTC)

Done. Dudley Miles (talk) 21:07, 15 January 2023 (UTC)

Skin Colour - Wiki Edits - Falsehood

The falsehood of this article is deliberately aimed to protect the theory's that the study predicts accurately that he had brown to dark skin.

The actual report states light to white skin cannot be ruled out.

Those who worked on the study states we do not know his colour, yet the wiki admins are arguing he most likely has brown to dark skin, based on what?.

I see the wiki theory, the chatter about DNA, but no proof?

Nothing on this article proves he had brown to dark skin.

New Scientist along with other actual scientists including those who conducted the study have retracted their statements he was brown to dark skinned, evidence showing it was unlikely.

I remember this article including the sources stating he may have not been brown to dark skinned, now removed & page locked.

The realistic fact is that wiki is bias, bias admins on many wiki pages who are willing to lock pages, block sources if comments do not fit certain agendas, we can see it on many wiki pages.

This page has no right to imply those who argue his colour are anti migrant, i am dark skinned and a son of migrants in the UK, yet I do not dismiss the facts so easily.

I also know white people existed in western Europe 10.000+ years ago, there are many study that show it.

Could he have been light skinned, or white - yes

Do official sources, including the actual study argue he may not have been brown, or dark - yes.

So such sources should be permitted in the page freely.

Finally, the DNA testing could not go back 10.000 years as a facr, they also used living DNA of dark, ethnic sources to conclude, therefore as stated the results could have been inaccurate as a fact. 2A02:C7F:C7A:4A00:4907:F625:E78B:CCF7 (talk) 20:18, 13 May 2024 (UTC)

So the article currently says that Cheddar Man had a most likely phenotype of blue-green eyes, dark brown or black hair, and dark or dark-to-black skin. What would you like it to say? That Cheddar Man might have been pale skinned, despite the study concluding the most likely phenotype was dark skin? We already go further here on caveating that prediction than any other ancient individual's predicted phenotype. Tewdar 20:46, 17 December 2025 (UTC)

Inconsistent statements in Ancestry Section

Lightening of the European Ancestors

HIrisPlex-s results "debunked"

2018 predictions of Cheddar Man's pigmentation were developed before dark skin alleles were discovered (in fact the discovery occurred several months before publication of the 2018 study, but the 2018 study had already been ongoing for years; authors were either ignorant of the new information or neglected to incorporate it). The use of HIrisPlex-s a: did not involve any understanding of the alleles which impart dark skin to human populations (e.g. MFSD12), and b: used a very restrictive sample base for its pigmentation predictions. Numerous researchers have pointed out that it predicts substantial quantities of e.g. Uyghurs, Oroqens, Southern Chinese and Native Americans as having the same "dark to very dark skin" that Cheddar Man is predicted to have had, suggesting that the software is biased towards predicting "dark to very dark skin". A 2019 study in Brazil (https://archive.ph/GEJFL) found that the software had a 19.16% accuracy rate. The paper calls it a "failure in predicting intermediate phenotypes." Having a poor sample basis and no understanding of dark skin alleles would probably yield such results.

HIrisPlex's own manual (https://hirisplex.erasmusmc.nl/pdf/hirisplex.erasmusmc.nl.pdf) states (page 2) that a particular SNP (rs6119471) has to be reversed in order to get an appropriate prediction. This was not done in the case of Cheddar Man (https://genoplot.com/discussions/topic/29897/cheddar-man-near-totally-debunked-the-blue-eyed-black-skinned-ancient-briton). When Cheddar Man's genes are put through the software appropriately, we apparently get "intermediate skin tone, intermediate eyes, reddish hair".

The "dark skinned Cheddar Man" meme constitutes misinformation. There are no grounds whatsoever for asserting that Cheddar Man had anything other than European skin, eye, and hair tones. Wikipedia is, of course, eternally a fortress of specific kinds of misinformation, so I don't expect people to remove it quickly or happily. But over time it will become increasingly clear that without MFSD12 etc., no European has ever been "African black" as per Cheddar Man's 2019 reconstruction. At best we're looking at sincere error; at worst we're looking at intentional disinformation. 80.189.58.169 (talk) 19:44, 12 August 2025 (UTC)

The article is based on reliable sources. You cite what is apparently a personal opinion is a discussion on a site which I do not have access to. This is not a reliable source. Dudley Miles (talk) 08:25, 13 August 2025 (UTC)

There are no grounds whatsoever for asserting that Cheddar Man had anything other than European skin, eye, and hair tones. - other than the peer-reviewed research article. What have you got, apart from SYNTH, OR, and discussion fora? Tewdar 12:52, 13 August 2025 (UTC)

"Peer review" - of course, Brazilians using the software to try to predict the pigmentations of living human beings, failing to come up with accurate results with any degree of security, is not part of the "peer review" process. The paper had already been "reviewed," though against what I know not (there are to my knowledge no predecessors for HIrisPlex-s and the like). There is no systematic "re-reviewing" of papers whose methodological errors are discovered in future papers, hence, in part, our "replication crisis," and my general condemnation of Wikipedia's information standards.

Shall we not at the very least include a reference and link to the Brazilian paper which found a 19.16% accuracy rating across skin, hair, and eye pigmentation predictions for this software - not SYNTH since the conclusion of the Brazilian paper includes specifically that the software used in the 2018 Cheddar Man study performs poorly in the majority of use cases - or shall we allow the general public to imagine that there has been no academic kickback against the use of this software, despite the fact that there has been? Considering the Brazilian paper's publication date was 2019, HIrisPlex-s would've been in roughly the same state it was as in 2017-18 during the Cheddar Man study: the findings presumably cast some light on that study. If, indeed, as the paper claims, "intermediate" pigmentations are not isolated properly by the software, there is a significant chance that Cheddar Man's prediction is wrong.

As it stands this Wikipedia entry links to a New Scientist article suggesting that the "dark to very dark" prediction may be wrong, and shouldn't be touted as fact. This link is provided as a reference for the statement "... he most likely had... dark to dark-black skin." Is there any better sign of the disingenuity of this part of the entry? The "dark Cheddar Man" theory is presented on the basis of a single paper (do successors count as separate?); I have provided a second paper which challenges the possible accuracy of the first. If Cheddar Man's prediction couldn't be made with greater than 20% accuracy, it shouldn't be presented as if it were the case; it should simply be presented as a result, albeit one which has been called into question not only by subsequent research, but by people on the original team.

For further reference, here's another Brazilian paper (https://pubmed.ncbi.nlm.nih.gov/32385594/) which puts my initial point across in the abstract: "MFSD12... and TYRP1... were not investigated as part of the HIrisPlex-S selection process, and therefore not included in the HIrisPlex-S model. Our results indicate that these SNPs account for a substantial part of the skin colour variation in individuals of admixed ancestry. Hence, we suggest that these SNPs are considered when developing future skin colour prediction models."

Here's a much more favourable paper pertaining to modern Spanish populations (https://www.researchgate.net/publication/385055036_Exploring_Eye_Hair_and_Skin_Pigmentation_in_a_Spanish_Population_Insights_from_Hirisplex-S_Predictions) whose conclusion still maintains that there were "difficulties... in skin pigmentation prediction, with significant misclassification observed, particularly among individuals with dark and pale skin" (interestingly this is the inverse of what the 2019 Brazilian paper found - that intermediate skin was the most poorly predicted - showing how population variance can affect not only the accuracy of the software but the ways in which it is inaccurate).

Since the "peers" would appear to disagree with one another as to the usefulness/usability of this software, I rather imagine Wikipedia is behooved to acknowledge the discrepancies. It is clearly not the case that academics in general accept the use of HIrisPlex-s for anything other than predicting modern European populations' pigmentations (and even for the latter there arise significant "difficulties" as per the Navarro-Lopez paper). Since Cheddar Man was not a modern European, one would require a paper proving that HIrisPlex-s could appropriately predict prehistoric, unadmixed populations' pigmentations - sadly such a paper is impossible, since we don't have time machines and cannot witness firsthand the pigmentations of prehistoric, unadmixed populations. All we can say, I suppose, is "verifiably, Western Hunter-Gatherers did not have genetic markers for dark skin; verifiably they had some markers which are associated with light skinned populations today" (e.g. IRF4 - plenty of light-skinned people lack SLC24A5 and SLC45A2; there's a range of skin-lightening genes). 80.189.58.169 (talk) 18:34, 13 August 2025 (UTC)

All we need is a peer-reviewed article literally stating that Brace et al. is wrong, and literally Cheddar Man's most likely phenotype is something else. As far as I am aware such an article does not exist. Tewdar 18:41, 13 August 2025 (UTC)

The article disclaimer: While the relevant genetic markers on the Cheddar Man genome have low sequencing coverage, limiting the accuracy of the predictions, they suggest (based on their associations in modern populations whose phenotypes are known) that he most likely had... - that's more than good enough. Tewdar 18:51, 13 August 2025 (UTC)

Cheddar Man looks more like an Aboriginal Australian than a sub-Saharan African. 2A0A:EF40:13E7:A201:10C7:CA9A:3703:91FF (talk) 17:53, 9 September 2025 (UTC)