8 ms·

Why the African genome project is so useful

64 points by jkuria 5y ago

neonate 5y ago
https://archive.is/7boW0 https://archive.is/7boW0
loufe 5y ago
I had no idea such a project was ever undertaken elsewhere in the world. In any case, I wish some examples of lessons or facts learned during similar studies elsewhere were presented. It sounds fascinating!
withthewind 5y ago
Opening statement is doing a disservice. Most parts of the world racism is defined on language/cultural maps, not literally black and white skin. For example the Rwandan genocide, is based on ethnic clashes where all people there have the same literal skin color. But they are part of different ethnicities. Then you have the bosnian genocide, same skin color and even language. But culturally they were different enough for some other humans to target.
- tootallgavin 5y ago
  Weird how science still claims race exists, even as they show a dark skinned scientist When can we be post-race?
  - AlotOfReading 5y ago
    Science absolutely does not claim biological human races exist. Almost all of the major anthropological societies have a statement somewhere like this: https://physanth.org/about/position-statements/aapa-statement-race-and-racism-2019/ https://physanth.org/about/position-statements/aapa-statemen... Or this: https://www.americananthro.org/ConnectWithAAA/Content.aspx?ItemNumber=2583 https://www.americananthro.org/ConnectWithAAA/Content.aspx?I... Those statements also explain why being post-race is more difficult than it should be.
    - axguscbklp 5y ago
      I think that statements like this are usually written more for political than for scientific reasons. Yes, "races do not exist" is true in the sense that 19th century classifications made by racist Europeans do not do a good job of mapping the reality of human genetic diversity. However, race does exist in the sense that, for example, two randomly selected people from China are likely to be closer to each other genetically than either is to a randomly selected person from England - and not only that, but it is also likely that the average person or, for that matter, computer algorithm will do a fairly good job of guessing people's genetic distance based on their visual appearance, at least for relatively large genetic distances. I feel that too often, politically motivated people pick up on such academic statements and use them to justify implying that the very concept of racial difference is inherently empty or wrong and perhaps should even be tabooed. It is a bit of a motte and bailey technique: you first say, "Look at these statements - see, science rejects the very concept of race - any discussion of racial difference is thus unscientific and in any case what are you, some sort of bigot?" And if anyone pushes you more closely on the matter you can just retreat to the actually justifiable position, "Oh well of course I did not mean that there are no identifiable patterns in human genetic diversity, that would be absurd, I just meant that old European racial classifications are inaccurate."
      - dale_glass 5y ago
        The problem is that scientific "race" doesn't quite work that way. To be scientific about it, you have to be willing to conclude things like that a diverse looking group of people are actually all the same race because they happen to share common genetics, or that what looks like an all white group is really 5 distinct genetic groups that just happen to look similar. To really find what scientifically accurate genetic group a given person falls into you'd have to be scientific about it, and look at the genetics or at the very least their detailed ancestry. Simply looking at them doesn't cut it. Science is all about precision and eliminating biases. At that point, what is even the point? You know enough about them to treat them as an individual regardless of what they happen to look like.
      - deleted 5y ago
        [deleted]
  - gjhh244 5y ago
    Probably not any time soon. The current trend among the woke crowd seems to be emphasizing importance of race, rather than trying to get past it. Worst racists of today are ones who divide people to privileged and underprivileged simply based on their skin colour, when the reality is way more complicated.
    - fogihujy 5y ago
      It's funny how the rest of the World is suddenly expected to adhere to U.S. cultural boundaries even though they simply don't apply. All of a sudden I've somehow changed ethnicity to "White". Simultaneously, people of African, Middle-Eastern and Indian origin -- some of the most ethnically diverse areas on the entire planet -- are just considered "Black" and thought of as a single group. It's outright ridiculous.
      - desktopninja 5y ago
        "Racism" is a fancy word for "Tribalism".
    - zingar 5y ago
      I like that you recognise that reality is complicated. However your comment underestimates racism. It may not have happened in front of your eyes, but in this world there are people who will for example: - be willing to verbally _or physically_ assault a person because of their skin colour (yes, to the point of serious injury or death) - deliberately undermine a good candidate's chances of getting a job or promotion _because of their skin colour_ - deliberately undermine a good tenant's chances of finding a place to live close to work or a good school Most people (including myself) are shocked to learn of situations like this once presented with evidence of it. I'm honestly talking about something as straightforward and undeniably racist as: a landlord asking a real estate startup to screen out any black tenants. There's also a huge range of experiences where the above happen across lines of race but more accidentally. Racist outcomes without racist intentions. All the kids who can afford to live near the good schools are white, all the informal mentorship happens to people who are similar in background to the founder, etc. The reason "emphasising importance of race" happens is because there's no chance of avoiding or preventing these situations if we pretend/hope that they don't happen. I might have misinterpreted you, but "trying to get past it" feels like pretend/hope rather than a willingness to fix things.
- chewz 5y ago
  > Most parts of the world racism is defined on language/cultural maps, not literally black and white skin. Also social class - protecting skin from sun had been a display that you are of non-working class rather then different genetic pool...
- enriquto 5y ago
  > Opening statement is doing a disservice. Most parts of the world racism is defined But this was written by a journalist. You have to translate Journalistese into English as you read it. For example "in most parts of the world" means "here where I live". In a similar way, "everybody" means "a cousin of mine", and so on. Once you get used to their language, newspapers start to make more sense. A bit less interesting, but definitely more informative.
- wesleywt 5y ago
  The target audience for the article are white Europeans living in the USA or Europe, where racism is often targeted at black Africans or African heritage.
wolfretcrap 5y ago
Too bad no such projects in India despite having such a huge genetic diversity in the subcontinent
- igitur 5y ago
  In general, genetic differentiation in populations of India is low (0.26-1.7%), but overall genetic differentiation in 18 mixed populations of India is higher (2.23%), similar to the largest single study on 16 tribal groups from central India (2.18%). https://pubmed.ncbi.nlm.nih.gov/8908794/ https://pubmed.ncbi.nlm.nih.gov/8908794/
- deleted 5y ago
  [deleted]
- SideburnsOfDoom 5y ago
  "The genetic diversity in Africa is greater than in any other region in the world" https://blogs.bcm.edu/2018/07/19/genetic-diversity-in-africa-is-greater-than-in-any-other-region-in-the-world/ https://blogs.bcm.edu/2018/07/19/genetic-diversity-in-africa... "Africans have world's greatest genetic variation" https://www.nbcnews.com/id/wbna30502963 https://www.nbcnews.com/id/wbna30502963 This is not surprising, it supports the "out of Africa" model of human origins.
- wesleywt 5y ago
  Cultural diversity is not the same as genetic diversity.
- bongoman37 5y ago
  Genetic diversity is actually not that high in India. There have been genetic sequencing projects in Indian groups (look up Dr. Thangaraj's publications from CCMB), and Indian caste groups have low diversity due to strict endogamy.
aswegs8 5y ago
If you make a connection between genes and disease, it is often a complex/weak link. Most of the on/off genes have already been discovered, by now we have gotten down to the more complex ones based on interactions, etc. Having worked with genetic data a lot I know that the reason for the wealth of European genetic data therefore lies in the limited generalizability based on more diverse datasets. If you try to generalize from a worldwide genetic dataset, you will probably fail. Your inferences from this diverse dataset to individual genomes will be abysmal. Predictions are already difficult to make from a country-specific dataset to an inhabitant of such country. I don't know why people always want to see race everywhere. For scientific reasons, it has been way more convenient to sequence more people of European origin. In my opinion, that has nothing to do with racism. It is a matter of what data has better availability and is more valuable right now (not even in terms of application - simply in terms of being able to detect complex underlying patterns). Now that the cost of sequencing is getting lower and lower and availability increases everywhere, it is great to see more diverse genomes sequenced. This will help us understand more of the genome - still, this is no magic bullet by a long shot. The problems stated above get bigger with dissimilarity. Many discoveries made in African genomes can probably not be generalized unto the remaining world. Current methods are just not sufficient to dig deep into the genome and its mechanics. At this point, we would probably need to sequence the whole of earths population a few times to be able to make consistently accurate and significant predictions across many complex traits and diseases.
- AlotOfReading 5y ago
  > For scientific reasons, it has been way more convenient to sequence more people of European origin. I'm personally interested in human origins, so from my perspective yet another "convenience" dataset from Europe is nearly useless. There's a lot more reasons to build this than just the search for medical magic bullets.
- nextaccountic 5y ago
  There is more genetic variability within Africa than the whole rest of world combined https://www.geneticsandsociety.org/article/study-africans-more-genetically-diverse-rest-world https://www.geneticsandsociety.org/article/study-africans-mo... That's a scientific reason to sequence the genes of African people more.
concordDance 5y ago
If the author's think genetic mapping will cure racism they're very naive. It's still a great project though.
cortexio 5y ago
nice ad... seriously, why share something that others cant read unless they pay????
avipars 5y ago
Here is the outline version - https://outline.com/xtux5S https://outline.com/xtux5S
TX0098812 5y ago
First word of the article: RACISM. I'm sure there are more things related to black/African people that can be discussed than racism. There is more than one subject out there.
- api 5y ago
  It’s a popular journalistic piece. They almost always open with something to relate the article to something familiar or contemporary.
ttt0 5y ago
I'm not quite sure if I understand what they're trying to do. Are they trying to say that it isn't just skin color? That's the entire point of "racism", that it's not just visible characteristics. By the way, why there is no author?
- Zababa 5y ago
  > That's the entire point of "racism", that it's not just visible characteristics. The way I learned it is that racism is believing that races exists AND that there is a (one dimensional) hierarchy between these races. Europeans are better at lactose tolerance than Africans and Asians. That's a fact. In no way that makes them have more worth as humans being or put them "above" the others. Believing that would be racism.
  - ttt0 5y ago
    There certainly are individuals who believe that, just like there are some Black individuals (Black nationalists/Israelites) who believe the exact opposite - that Whites are "inferior" and Blacks are "superior". But at core this really isn't what nationalist/separatist movements are about. It's that races are distinct both genetically and culturally - not inherently better or worse, just different - and incompatible with each other. Furthermore, if you look at the current and historic nationalist movements, the motivation is rarely (if ever) "we're superior, they're subhumans, why won't we just kill them", but perceived oppression from the other side.
    - desktopninja 5y ago
      Tribalism! :)
- elb2020 5y ago
  > By the way, why there is no author? Because it's the Economist, they never run a byline on any of their published content, normally.
ultrablack 5y ago
I wonder how mich racism there is internally among the people of Africa.
- developer93 5y ago
  Anecdotally among my Nigerian friends, quite a lot. Almost as if we're all similar..
  - desktopninja 5y ago
    Not even anecdotally. Different color, same vicious sentiment. Mind you this is not a majority way of thinking. A small minority get a high enough profile to perpetuate conflict.

64 points by jkuria 5y ago

https://archive.is/7boW0 https://archive.is/7boW0

I had no idea such a project was ever undertaken elsewhere in the world. In any case, I wish some examples of lessons or facts learned during similar studies elsewhere were presented. It sounds fascinating!

withthewind 5y ago

Opening statement is doing a disservice. Most parts of the world racism is defined on language/cultural maps, not literally black and white skin. For example the Rwandan genocide, is based on ethnic clashes where all people there have the same literal skin color. But they are part of different ethnicities. Then you have the bosnian genocide, same skin color and even language. But culturally they were different enough for some other humans to target.

tootallgavin 5y ago
Weird how science still claims race exists, even as they show a dark skinned scientist When can we be post-race?
- AlotOfReading 5y ago
  Science absolutely does not claim biological human races exist. Almost all of the major anthropological societies have a statement somewhere like this: https://physanth.org/about/position-statements/aapa-statement-race-and-racism-2019/ https://physanth.org/about/position-statements/aapa-statemen... Or this: https://www.americananthro.org/ConnectWithAAA/Content.aspx?ItemNumber=2583 https://www.americananthro.org/ConnectWithAAA/Content.aspx?I... Those statements also explain why being post-race is more difficult than it should be.
  - axguscbklp 5y ago
    I think that statements like this are usually written more for political than for scientific reasons. Yes, "races do not exist" is true in the sense that 19th century classifications made by racist Europeans do not do a good job of mapping the reality of human genetic diversity. However, race does exist in the sense that, for example, two randomly selected people from China are likely to be closer to each other genetically than either is to a randomly selected person from England - and not only that, but it is also likely that the average person or, for that matter, computer algorithm will do a fairly good job of guessing people's genetic distance based on their visual appearance, at least for relatively large genetic distances. I feel that too often, politically motivated people pick up on such academic statements and use them to justify implying that the very concept of racial difference is inherently empty or wrong and perhaps should even be tabooed. It is a bit of a motte and bailey technique: you first say, "Look at these statements - see, science rejects the very concept of race - any discussion of racial difference is thus unscientific and in any case what are you, some sort of bigot?" And if anyone pushes you more closely on the matter you can just retreat to the actually justifiable position, "Oh well of course I did not mean that there are no identifiable patterns in human genetic diversity, that would be absurd, I just meant that old European racial classifications are inaccurate."
    - dale_glass 5y ago
      The problem is that scientific "race" doesn't quite work that way. To be scientific about it, you have to be willing to conclude things like that a diverse looking group of people are actually all the same race because they happen to share common genetics, or that what looks like an all white group is really 5 distinct genetic groups that just happen to look similar. To really find what scientifically accurate genetic group a given person falls into you'd have to be scientific about it, and look at the genetics or at the very least their detailed ancestry. Simply looking at them doesn't cut it. Science is all about precision and eliminating biases. At that point, what is even the point? You know enough about them to treat them as an individual regardless of what they happen to look like.
    - deleted 5y ago
      [deleted]
- gjhh244 5y ago
  Probably not any time soon. The current trend among the woke crowd seems to be emphasizing importance of race, rather than trying to get past it. Worst racists of today are ones who divide people to privileged and underprivileged simply based on their skin colour, when the reality is way more complicated.
  - fogihujy 5y ago
    It's funny how the rest of the World is suddenly expected to adhere to U.S. cultural boundaries even though they simply don't apply. All of a sudden I've somehow changed ethnicity to "White". Simultaneously, people of African, Middle-Eastern and Indian origin -- some of the most ethnically diverse areas on the entire planet -- are just considered "Black" and thought of as a single group. It's outright ridiculous.
    - desktopninja 5y ago
      "Racism" is a fancy word for "Tribalism".
  - zingar 5y ago
    I like that you recognise that reality is complicated. However your comment underestimates racism. It may not have happened in front of your eyes, but in this world there are people who will for example: - be willing to verbally _or physically_ assault a person because of their skin colour (yes, to the point of serious injury or death) - deliberately undermine a good candidate's chances of getting a job or promotion _because of their skin colour_ - deliberately undermine a good tenant's chances of finding a place to live close to work or a good school Most people (including myself) are shocked to learn of situations like this once presented with evidence of it. I'm honestly talking about something as straightforward and undeniably racist as: a landlord asking a real estate startup to screen out any black tenants. There's also a huge range of experiences where the above happen across lines of race but more accidentally. Racist outcomes without racist intentions. All the kids who can afford to live near the good schools are white, all the informal mentorship happens to people who are similar in background to the founder, etc. The reason "emphasising importance of race" happens is because there's no chance of avoiding or preventing these situations if we pretend/hope that they don't happen. I might have misinterpreted you, but "trying to get past it" feels like pretend/hope rather than a willingness to fix things.
chewz 5y ago
> Most parts of the world racism is defined on language/cultural maps, not literally black and white skin. Also social class - protecting skin from sun had been a display that you are of non-working class rather then different genetic pool...
enriquto 5y ago
> Opening statement is doing a disservice. Most parts of the world racism is defined But this was written by a journalist. You have to translate Journalistese into English as you read it. For example "in most parts of the world" means "here where I live". In a similar way, "everybody" means "a cousin of mine", and so on. Once you get used to their language, newspapers start to make more sense. A bit less interesting, but definitely more informative.
wesleywt 5y ago
The target audience for the article are white Europeans living in the USA or Europe, where racism is often targeted at black Africans or African heritage.

wolfretcrap 5y ago

Too bad no such projects in India despite having such a huge genetic diversity in the subcontinent

igitur 5y ago
In general, genetic differentiation in populations of India is low (0.26-1.7%), but overall genetic differentiation in 18 mixed populations of India is higher (2.23%), similar to the largest single study on 16 tribal groups from central India (2.18%). https://pubmed.ncbi.nlm.nih.gov/8908794/ https://pubmed.ncbi.nlm.nih.gov/8908794/
deleted 5y ago
[deleted]
SideburnsOfDoom 5y ago
"The genetic diversity in Africa is greater than in any other region in the world" https://blogs.bcm.edu/2018/07/19/genetic-diversity-in-africa-is-greater-than-in-any-other-region-in-the-world/ https://blogs.bcm.edu/2018/07/19/genetic-diversity-in-africa... "Africans have world's greatest genetic variation" https://www.nbcnews.com/id/wbna30502963 https://www.nbcnews.com/id/wbna30502963 This is not surprising, it supports the "out of Africa" model of human origins.
wesleywt 5y ago
Cultural diversity is not the same as genetic diversity.
bongoman37 5y ago
Genetic diversity is actually not that high in India. There have been genetic sequencing projects in Indian groups (look up Dr. Thangaraj's publications from CCMB), and Indian caste groups have low diversity due to strict endogamy.

aswegs8 5y ago

If you make a connection between genes and disease, it is often a complex/weak link. Most of the on/off genes have already been discovered, by now we have gotten down to the more complex ones based on interactions, etc. Having worked with genetic data a lot I know that the reason for the wealth of European genetic data therefore lies in the limited generalizability based on more diverse datasets. If you try to generalize from a worldwide genetic dataset, you will probably fail. Your inferences from this diverse dataset to individual genomes will be abysmal. Predictions are already difficult to make from a country-specific dataset to an inhabitant of such country. I don't know why people always want to see race everywhere. For scientific reasons, it has been way more convenient to sequence more people of European origin. In my opinion, that has nothing to do with racism. It is a matter of what data has better availability and is more valuable right now (not even in terms of application - simply in terms of being able to detect complex underlying patterns). Now that the cost of sequencing is getting lower and lower and availability increases everywhere, it is great to see more diverse genomes sequenced. This will help us understand more of the genome - still, this is no magic bullet by a long shot. The problems stated above get bigger with dissimilarity. Many discoveries made in African genomes can probably not be generalized unto the remaining world. Current methods are just not sufficient to dig deep into the genome and its mechanics. At this point, we would probably need to sequence the whole of earths population a few times to be able to make consistently accurate and significant predictions across many complex traits and diseases.

AlotOfReading 5y ago
> For scientific reasons, it has been way more convenient to sequence more people of European origin. I'm personally interested in human origins, so from my perspective yet another "convenience" dataset from Europe is nearly useless. There's a lot more reasons to build this than just the search for medical magic bullets.
nextaccountic 5y ago
There is more genetic variability within Africa than the whole rest of world combined https://www.geneticsandsociety.org/article/study-africans-more-genetically-diverse-rest-world https://www.geneticsandsociety.org/article/study-africans-mo... That's a scientific reason to sequence the genes of African people more.

concordDance 5y ago

If the author's think genetic mapping will cure racism they're very naive. It's still a great project though.

cortexio 5y ago

nice ad... seriously, why share something that others cant read unless they pay????

avipars 5y ago

Here is the outline version - https://outline.com/xtux5S https://outline.com/xtux5S

TX0098812 5y ago

First word of the article: RACISM. I'm sure there are more things related to black/African people that can be discussed than racism. There is more than one subject out there.

api 5y ago
It’s a popular journalistic piece. They almost always open with something to relate the article to something familiar or contemporary.

ttt0 5y ago

I'm not quite sure if I understand what they're trying to do. Are they trying to say that it isn't just skin color? That's the entire point of "racism", that it's not just visible characteristics. By the way, why there is no author?

Zababa 5y ago
> That's the entire point of "racism", that it's not just visible characteristics. The way I learned it is that racism is believing that races exists AND that there is a (one dimensional) hierarchy between these races. Europeans are better at lactose tolerance than Africans and Asians. That's a fact. In no way that makes them have more worth as humans being or put them "above" the others. Believing that would be racism.
- ttt0 5y ago
  There certainly are individuals who believe that, just like there are some Black individuals (Black nationalists/Israelites) who believe the exact opposite - that Whites are "inferior" and Blacks are "superior". But at core this really isn't what nationalist/separatist movements are about. It's that races are distinct both genetically and culturally - not inherently better or worse, just different - and incompatible with each other. Furthermore, if you look at the current and historic nationalist movements, the motivation is rarely (if ever) "we're superior, they're subhumans, why won't we just kill them", but perceived oppression from the other side.
  - desktopninja 5y ago
    Tribalism! :)
elb2020 5y ago
> By the way, why there is no author? Because it's the Economist, they never run a byline on any of their published content, normally.

ultrablack 5y ago

I wonder how mich racism there is internally among the people of Africa.

developer93 5y ago
Anecdotally among my Nigerian friends, quite a lot. Almost as if we're all similar..
- desktopninja 5y ago
  Not even anecdotally. Different color, same vicious sentiment. Mind you this is not a majority way of thinking. A small minority get a high enough profile to perpetuate conflict.