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Scientists say they can read nearly the whole genome of an IVF-created embryo

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Re: Scientists say they can read nearly the whole genome of an IVF-created embryo

#61

Post by TOMDM »

topynate wrote: post #45
areoform wrote: post #43

Earlier quoted context omitted.

The error rate for sequencing is significant and can easily lead to incorrect assumptions + decisions, > The average error rate determined was 0.24 ± 0.06% per base and the percentage of mutated sequences was found to be 6.4 ± 1.24%. https://www.nature.com/articles/s41598-018-29325-6

Won't matter for highly polygenic traits. For monogenetic disorders like Tay-Sachs, it will provide another line of defence along with conventional pre-implantation screening and pre-natal screening.

I think what people are worried about is that parents may neglect to take measures they otherwise would based on overconfidence in genetic screening.

Re: Scientists say they can read nearly the whole genome of an IVF-created embryo

#62

Post by unsupp0rted »

legalcorrection wrote: post #40
ajconway wrote: post #39

Earlier quoted context omitted.

The world is massively unfair as it is. Would anyone even notice already "privileged" societies becoming a little bit more privileged? Who knows, maybe our IQ 120 overlords will be kind to make the tech available for everyone else.

A 120 average IQ population would run circles around a 100 average IQ population, even starting from a much lower position. Of course, there's still the question of whether society is organized such that people of exceptional talent rise to power, and whether they have the incentive to do great things. My main concern isn't the tech being inaccessible to poorer people or countries. International intellectual property…

The average IQ in Singapore is 105 and next door in Malaysia is 88.

Singapore does run circles around Malaysia on most measures.

The hard part is attributing any of this to average IQ, or determining if average IQ has been measured accurately enough.

Re: Scientists say they can read nearly the whole genome of an IVF-created embryo

#63

Post by dekhn »

015UUZn8aEvW wrote: post #15

Embryo selection based on genome sequencing is already being done: https://astralcodexten.substack.com/p/welcome-polygenically-...

Your example is "genetic" testing- it only samples a limited number of locations in the genome. This method is more like whole genome sequencing.

Re: Scientists say they can read nearly the whole genome of an IVF-created embryo

#64

Post by llebttam »

programmertote wrote: post #60

Coincidentally, I have a friend who is in the second cycle of this IVF procedure to select an embryo that does not carry the genes associated with polycystic kidney disease (PKD). When I heard it last week for the first time, I thought it is already an established procedure. Here, I'm learning that it is a relatively cutting-edge approach and I am now looking forward to asking my friend more about this next time we m…

Commercial products in the space have been around for several years but can only screen for a small number of genetic diseases at a time. For example, Natera's Spectrum screens for chromosomal abnormalities (eg Down Syndrome) plus one custom genetic problem for a single condition of greatest concern. https://www.natera.com/womens-health/spectrum-preimplantatio...

Some polygenic screening services that look at a much larger number of conditions are just reaching market now (eg Orchid Health), though our ability to map genes correlated with polygenic traits to phenotype results is still in its early stages. https://www.orchidhealth.com/

Re: Scientists say they can read nearly the whole genome of an IVF-created embryo

#65

Post by ch4s3 »

legalcorrection wrote: post #10

Thinking about the social and political implications of this in the long run. Any society or segment of any society that isn't producing average 120 IQ babies with superior sensory perception, physical strength, dexterity, and so forth, is going to turn itself into a permanent human underclass. Eugenics is here to stay this time.

We don't have a very good understanding of the genetics of many of these traits. Intelligence is especially thorny, involves numerous genes, and is probably only about half hereditable which is actually reasonably high.

We're likely to get a bunch of tall people, until everyone remembers they die younger due to cardiovascular strain. We'll probably wipe out most single gene hereditable diseases, which will be great. We're also somewhat likely to see fads around eye color in "designer" babies. We may also get people selecting for a single gene that make for great endurance athletes.

Anything much beyond that is science fiction in the near future. The knock on effects of tinkering with more than a handful of well understood genes is going to be really dangerous.

Quick Edit* There are around 1000 genes that have some bearing on intelligence. The 22 most impactful together account for 5% of variation.

Re: Scientists say they can read nearly the whole genome of an IVF-created embryo

#66

Post by dekhn »

exdsq wrote: post #6
jkingsman wrote: post #4

Earlier quoted context omitted.

For IVF embryos, it's the small amount of genetic material which makes accurate sequencing difficult. For standard human whole genome sequencing (WGS), the fastest times are down to five hours[1] (although that is exceptional), for which the imaging was massively parallelized and it seems that the choke point was computational for that particular case (sequencing like this basically multiples the DNA, shreds all the…

Thanks for your response! So is it true to say every genome could be sequenced, assuming time and money isn’t an issue?

if you're asking whether we could sequence 7 billion people, yes, it would be absolutely possible. Obtaining samples would be harder than the sequencing. If you really took this seriously there would be only 3 sequencing sites in the world and they would be located close to the largest datacenters. Each sequence is about 100G data (the raw data file that's shipped around) so if you really wanted to keep all of that it's 700 exabytes, but since you're sequencing everybody, you can instead create a tree structure of deltas from references with additional nodes representing major haplotypes and other structure. This would be more like ~1M-1G/person, so 7 petabytes to 7 exabytes, well within the storage limits of a modern datacenter cluster. To go along with that storage, you'd also need ~1M fast CPUs and ~250K fast GPUs, plenty of RAM, and a really good privacy and security story.

All of that could be formatted for large-scale analytics and the problem treated much like machine learning/data science problems in ads and other similar areas.

If you're really serious, this is just a bulk buy for one of the data center providers and they would be happy to make a fixed profit margin contract to do this for you. I helped set up all the infrastructure to enable google to do this ~10 years ago (I got a patent on compressing DNA for storage) and now they're at the point of hosting this sort of service (terra bio). I could do everything I described above for $25B but there is absolutely no medical reason to do anything of this scale.

Re: Scientists say they can read nearly the whole genome of an IVF-created embryo

#67

Post by dekhn »

legalcorrection wrote: post #10

Thinking about the social and political implications of this in the long run. Any society or segment of any society that isn't producing average 120 IQ babies with superior sensory perception, physical strength, dexterity, and so forth, is going to turn itself into a permanent human underclass. Eugenics is here to stay this time.

This is sort of naive. Even the chinese have backed off from their plans on doing this, both before and after the Jiankyu debacle. https://singularityhub.com/2013/03/19/chinas-bgi-to-sequence... https://www.technologyreview.com/2015/08/20/166465/is-it-pos...

By the way, I spent about 20 years of my life pursuing this goal, and I've concluded that most cultures aren't that keen on superintelligent babies right now.

Re: Scientists say they can read nearly the whole genome of an IVF-created embryo

#68

Post by whatshisface »

mywittyname wrote: post #55
whatshisface wrote: post #18

Earlier quoted context omitted.

> now nobody would have genetic diseases. Nobody with parents who can afford IVF would have genetic diseases. Nobody would rise from an ignoble birth to greatness ever again... or at least not in countries without universal healthcare.

Those kids would still potentially breed the normal way. If a rich kid knocks up a bunch of poor ones, those children will have similar genetic advantages. And rich people fall from grace all the time. It's difficult for families to hold onto their wealth over successive generations. One of the keys to maintaining wealth is to keep it from being diluted, which means that some kids are going to get cut off.

>If a rich kid knocks up a bunch of poor ones, those children will have similar genetic advantages.

This doesn't set off your dystopia alarm?

Re: Scientists say they can read nearly the whole genome of an IVF-created embryo

#69

Post by whatshisface »

bpodgursky wrote: post #58
taylorius wrote: post #54

Earlier quoted context omitted.

>>an insufferable hell beyond comprehension >That would be, like... a typical office full of programmers Well, quite... ;-)

Spend a week in a workplace with an average IQ of 80 and get back to me about which feels worse.

All of our culture deals with interactions between average people. People with significantly greater or less intelligence than average do not have a bank of ancient answers to ancient questions to draw on. One simple example of that would be norms against debt and lending - if you are very clever they don't apply to you, but that doesn't mean you don't need any norms. In fact someone who borrows and lends needs more guidelines and more complex guidelines if they're going to navigate business risks successfully.

Re: Scientists say they can read nearly the whole genome of an IVF-created embryo

#70

Post by [deleted] »

mywittyname wrote: post #52
whatshisface wrote: post #31

Earlier quoted context omitted.

> A society of 120 IQ adults would probably be an insufferable hell beyond comprehension, considering the track record of intellectual movements and the proclivity of smart individuals, probably like yourself, to vastly overestimate the merits of rationality and concepts that can be limited to the mind of one human. The world is full of societies of 120 IQ individuals. That would be, like... a typical office full of…

>A society of 120 IQ adults would probably be an insufferable hell beyond comprehension > That would be, like... a typical office full of programmers. Is this an argument in support of the OP? Anyway, much like with global warming, the issue isn't so much the averages, but the impact on the extremes. Now the world suddenly has 10x as many 140 people or 100x as many 160s, etc. This cuts both ways too. A smart person i…

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