It looks like Nebula Genomics has a 12-hour sale (as of this posting). This means you can get medical-grade 30x sequencing for $299. I do not recommend 100x because that gives you little bang-for-the-buck.
Nebula has had issues with timeliness in the past, so don’t purchase it expecting a rapid turnaround. But this seems like a good opportunity to get whole genome sequencing.
The main reason to do this download the raw data and put it in a lockbox somewhere. You have it for the rest of your life then.
Recently The New Yorker had a long feature on the German social experiment from the 1970’s to early 2000’s which placed homeless boys in foster care with pedophiles. The whole thing seems totally incomprehensible today. But, I always explain to adults who don’t remember the sexual environment of the 1970’s that pedophilia was a much more open question on the radical fringes then than today. I point out that Allen Ginsberg and Harry Hay were both pro-NAMBLA. Ginsberg is still a cultural figure, but Hay was a huge mover and shaker in the gay liberation movement of the 20th century. The basic radical theory is that children had sexual rights and feelings which were being repressed.
But this is an intellectual matter. What was happening “on the ground”? I decided to look back into the archives of The New York Times, and I stumbled upon the fact that in the late 1970’s New Jersey had reduced the age of consent to 13, before moving it back to 16 in 1979. The reasons for this are complicated and have to do with the implicit criminalization of sex between teens and Romeo and Juliet laws, but the way the legislation was written it seems it was legal for adults to have sex with 13-year-old teens in New Jersey for a time in the late 1970s.
Leaders of the New Jersey Assembly, responding to widespread fears about a new criminal code that lowers the age of sexual consent to 13 years, said today they expected the Assembly to pass a stopgap measure tomorrow to restore 16 as the age of consent. The legislators hope to allay fears that the state is endorsing sexual activity by teen‐agers.
The reduced age of consent had been included in the criminal code, which takes effect Sept. 1, at the urging of the National Organization for Women. An official of the organization, Roberta Kaufman, said it had lobbied for making the age of consent 13 not to encourage sex among young teen‐agers, but to keep teen‐agers under 16 from becoming entangled in the law if they did engage in sex.
Reading the archives from that period a lot of things were on the table. Apparently, New Jersey was looking to legalize incest between adults over the age of 16 and necrophilia.
Perhaps the current radical cultural moment will pass too, and we’ll forget all about it?
We note that our estimated TMRCA to Neanderthal within Neanderthal-introgressed segments in all non-African populations is recent, ~74 ka ago, and implies therefore that little genetic drift separates admixed humans from sequenced Neanderthals in these segments. This recent TMRCA suggests that the majority of Neanderthal ancestry in modern humans originated from Neanderthal gene flow into the ancestors of all non-Africans before populations diversified. It also suggests that at least one of the Neanderthal genomes used here is closely related to the Neanderthal(s) involved in this admixture event. The slightly elevated Neanderthal ancestry that others have described in Central and East Asian populations also appears to have originated in this first pulse, as Central and East Asian Neanderthal haplotypes are mostly shared with other, geographically distant populations. This observation favors the hypothesis that the increased Neanderthal ancestry in these populations relative to others is due to weaker selection against alleles that may be mildly deleterious (32), made possible because of smaller historical population sizes in this part of Eurasia, rather than to additional admixture events (22). Our evidence of many small-scale, population-specific admixture events, however, together with a simulation study that found a single-pulse admixture model followed by drift unable to explain the discrepancies in admixture proportions in European and Asian genomes (49), hints at a complex history of admixture throughout Eurasia not fully captured by either of these two hypotheses.
I don’t think that it’s weaker selection in East Asians. I think it’s complex demography.
The apportionment of human genetic diversity within and between populations has been measured to understand human relatedness and demographic history. Likewise, the distribution of archaic ancestry in modern populations can be leveraged to better understand the interaction between our species and its archaic relatives, and the impact of natural selection on archaic segments of the human genome. Resolving these interactions can be difficult, as archaic variants in modern populations have also been shaped by genetic drift, bottlenecks, and gene flow. Here, we investigate the apportionment of archaic variation in Eurasian populations. We find that archaic genome coverage at the individual- and population-level present unique patterns in modern human population: South Asians have an elevated count of population-unique archaic SNPs, and Europeans and East Asians have a higher degree of archaic SNP sharing, indicating that population demography and archaic admixture events had distinct effects in these populations. We confirm previous observations that East Asians have more Neanderthal ancestry than Europeans at an individual level, but surprisingly Europeans have more Neandertal ancestry at a population level. In comparing these results to our simulated models, we conclude that these patterns likely reflect a complex series of interactions between modern humans and archaic populations.
The method is pretty neat. Read this closely. Here are some takeaways:
– European Neanderthal ancestry is lower than East Asian, but more diverse
– South Asians clearly have different Denisovan ancestry than East Asians
– Population structure matters…South Asian rare allele frequency is due to admixture between divergence groups
Basically, Neanderthal and Denisovan admixture is more complex than our simple stylized models.
About seven years ago I got my hands on some white South African individuals from the Family Tree DNA database. It was immediately clear that a subset of them had clear and consistent non-European ancestry. More precisely, this ancestry was a mix of African and Asian. In contrast, some of the other white South Africans were Ashkenazi Jews, and others seemed to be English with no African ancestry.
1) Likely Khoi ancestry related to the ǂKhomani
2) Sub-Saharan African ancestry, but closer West Africans and even East Africans than neighboring Bantu
3) Indian ancestry
4) East Asian ancestry
The East Asian ancestry is almost certainly from what is today Indonesia. The ubiquity of Indian slaves in the 17th century should make #3 unsurprising. And the Khoi people were indigenous to the Cape when the Dutch arrived.
The second component is harder to parse. But, it seems that the arrival of a few external slave ships was critical. The non-European admixture into the Afrikaners dates to the earliest period of settlement, not to later centuries when there was much more ubiquitous contact with Bantu-speaking populations. By then the whites were endogamous. Or, the mixed offspring were being assimilated into the Coloured community, rather than into the whites.
Curiously, the European ancestry of the Afrikaners was not subject to a strong bottleneck. Perhaps this is due to the heterogeneity of its source? Dutch, French Huguenots, and Germans, all played a role.*
* Not an apples-to-apples comparison, but it is clear that self-identified non-Hispanic whites of European heritage have a much lower proportion of non-European ancestry than Afrikaners.
Is it my imagination, or is Charles Murray’s new book, Facing Reality: Two Truths about Race in America getting more traction than his previous book? Probably due to the engagement with the “heterodox academy” types.
I wrote about the crime spike for my Substack in late April, and a lot of people told me that I was pretty bold for having done so. Of course, by mid-May our propaganda media did a heel-turn and decided to start talking about the issue in unison. I can’t express how disgusted I am with American media in 2021. They’re no better than they were during the Iraq War II period. Just new masters.
Unless you’ve been asleep, you know there are new hominins discovered galore. I posted a long (free) Substack on it and my perspective. Please share and retweet, etc.
This is apropos of nothing… but I have a lot of friends in academia who think they are “based” and dissent from the regnant orthodoxy. For almost 20 years I’ve been taking fire and absorbing hits because I’ll say what I think (to the point of being physically attacked at scientific conferences). A lot of you appreciate it. But in general, you’re cowards and keep your head down.
Sit down and wonder what you’ll tell your kids in the future about the courage you showed, and how you measured up to the values you claim to hold dear. And ask yourself if perhaps the collapse of the world you valued will have had something to do with your craven behavior. You know the answer. Don’t pretend you’re something you aren’t. My kids are starting to be old enough to know who I am. I’m not ashamed. Would you be? If not, perhaps you should be.
All known archaic groups with ancient DNA evidence interbred. Repeatedly. Seemingly every time they came into contact. Three distinct groups of Denisovans, all known from their ancient interbreeding with modern people. So. Much. Interbreeding. pic.twitter.com/AkZkSjacUF
Chimamanda Ngozi Adichie has posted a reflection on her experience with ‘cancel culture’ and young people whom she helped who then turned on her immediately when the mob demanded it. This part is important:
There are many social-media-savvy people who are choking on sanctimony and lacking in compassion, who can fluidly pontificate on Twitter about kindness but are unable to actually show kindness. People whose social media lives are case studies in emotional aridity. People for whom friendship, and its expectations of loyalty and compassion and support, no longer matter. People who claim to love literature – the messy stories of our humanity – but are also monomaniacally obsessed with whatever is the prevailing ideological orthodoxy. People who demand that you denounce your friends for flimsy reasons in order to remain a member of the chosen puritan class.
I refuse to turn on people and denounce them on demand from the mob. You all know what I’m talking about. Some of my friends have been called on to denounce me, and some have. They are weak. Most people are weak. This period is useful because it will help us separate the true friends from those whose friendship is conditional on the winds of favor.
More generally, social media makes preening performance public and scalable in a way that it never was. The behavior described by Adichie is as old as humanity itself. The main difference is today it is produced and distributed on an industrial scale. As Ray Kurzweil likes to say, information technology is exponential…
Thank you to everyone here who subscribed to my Substack. For those of you who subscribe to the paid content, I am hoping you can tell I’m putting a lot of effort into the writing!
