[HN Gopher] Svante Paabo awarded Nobel Prize for studies of exti...
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Svante Paabo awarded Nobel Prize for studies of extinct human
ancestors
Author : shantanu_sharma
Score : 130 points
Date : 2022-10-03 09:47 UTC (13 hours ago)
(HTM) web link (www.quantamagazine.org)
(TXT) w3m dump (www.quantamagazine.org)
| User23 wrote:
| Is there enough extant Neanderthal DNA in some Homo Sapiens
| lineages to restore Homo Neanderthalensis by back crossing?
| Actually doing so would almost certainly be highly unethical, but
| I still wonder if it's possible.
| BurningFrog wrote:
| Probably not.
|
| But I think we have pretty complete Neanderthal DNA from
| fossils, so, with a few more decades of gene engineering, they
| could probably be created.
|
| Then I guess we'd have to ask them if their creation was
| ethical :)
| j7ake wrote:
| Love Paabos work, but spinning the work as giving "huge insights
| into human physiology" is a bit of a stretch. If the bar were
| insights in human physiology there would be a lot more people who
| have done more important work.
| soderfoo wrote:
| Forgive me, but can you expand a bit on this? I am completely
| uninformed in this area and like to have a holistic view when
| endeavoring to learn anything new.
| c7b wrote:
| wikipedia already updated, quite impressive always:
| https://en.wikipedia.org/w/index.php?title=Svante_P%C3%A4%C3...
| astrange wrote:
| I read Svante Paabo's autobiography, which is basically a story
| of him continually getting the scientific equivalent of promoted,
| and thought it was interesting that he refuses to give his
| discoveries Latin species names like "Homo denisova" on the basis
| that they're pretentious. So Denisovans still don't have one.
|
| Also, at one point he steals his labmate's wife, and then later
| hires them both for his own lab.
|
| It's a good book and his work is very significant - this is a
| well deserved prize.
| ygram wrote:
| It is illegal to own people in Sweden, so you can't steal them.
| astrange wrote:
| Do you know another verb for being the person someone is
| cheating on their spouse with?
| heavenlyblue wrote:
| The wife of his labmate got bored of her current partner
| and instead went for someone less boring?
| mongol wrote:
| That was interesting. I looked what Wikipedia says
|
| "Denisovans may represent a new species of Homo or archaic
| subspecies of Homo sapiens (modern humans), but they are known
| from too few fossils to erect a proper taxon. Proactively
| proposed species names for Denisovans are H. denisova[2] or H.
| altaiensis.[3]"
| arcanus wrote:
| Katalin Kariko was robbed, unless they are giving mRNA vaccines
| as chemistry.
| dosshell wrote:
| Why Katalin Kariko and not Robert Malone? [0]
|
| [0] https://en.wikipedia.org/wiki/Robert_W._Malone
| fsh wrote:
| From your link:
|
| The New York Times, in an article about Malone, reported:
| "While he was involved in some early research into the
| technology, his role in its creation was minimal at best, say
| half a dozen Covid experts and researchers, including three
| who worked closely with Dr. Malone."
| kken wrote:
| I know nothing about this, but this passage in the Wiki
| article that you linked points at some controversy:
|
| >While Malone promotes himself as an inventor of mRNA
| vaccines,[1][7] credit for the distinction is more often
| given to the lead authors on the major papers he contributed
| to (such as Felgner and Wolff), later advances by Katalin
| Kariko and Drew Weissman,[3][19] or Moderna co-founder
| Derrick Rossi.[13] Ultimately, mRNA vaccines were the
| decades-long result of the contributions of hundreds of
| researchers, including Malone.[3][20] The New York Times, in
| an article about Malone, reported: "While he was involved in
| some early research into the technology, his role in its
| creation was minimal at best, say half a dozen Covid experts
| and researchers, including three who worked closely with Dr.
| Malone."[7]
| dosshell wrote:
| Addon: I do not promote that Malone get Nobel price (just
| first google hit). What I meant to ask was what Karino did
| that is special related to all other work in this field.
| ISL wrote:
| The Nobel Committees sometimes take quite a while to get around
| to deserving researchers. It is not a rapid-response
| organization.
|
| The only exception I'm aware of in modern times is the high-Tc
| superconductor prize in Physics. Results announced in March,
| prize awarded in October -- it was so obviously important and
| trivially demonstrated as correct.
| dooglius wrote:
| LIGO is another example
| ISL wrote:
| GW150914 was detected in September of 2015 -- the
| associated prize wasn't awarded until 2017. That award
| followed the very important detection of GW170817 in August
| 2017, which featured the critical detection of an optical
| signature in parallel with the GW signal.
|
| mRNA is definitely in a similar regime today. A promising
| technology led to vaccines in trials by autumn 2020, and
| oodles of shots-in-arms by autumn 2021. In 2022, the mRNA
| technology is on very solid footing for having saved
| millions of lives. The Committees definitely could award
| one or more mRNA prizes this year, but they may have other
| prizes they need to award before a worthy recipient passes
| away.
| shusaku wrote:
| Nice! One of those areas of science which I think really capture
| the public imagination.
| GameOfFrowns wrote:
| diego_moita wrote:
| If anyone wants to understand the huge impact paleogenomics is
| having on writing human history a very good book is "Who We Are
| and How We Got Here" by David Reich.
|
| It describes the seminal work of Dr. Paabos and many others. The
| main focus are the 3 big migrations of hominids to Europe (early
| nomadic settlers, farmers from Anatolia and the corded
| culture/horse riders from South-Central Asia).
|
| The book also discusses the inter-breeding of Neanderthals and
| Sapiens, Denisovarian and Sapiens, the migrations and
| castes/class system that shaped the ethnic diversity on the
| Indian subcontinent and the surprising genetic evidence of
| colonization of South America by Pacific islanders.
|
| It is mind blowing stuff...
| Gumbercules wrote:
| xorcist wrote:
| Here, have a UTF8 code point for the next comment: a
|
| You're welcome!
| Rebelgecko wrote:
| I recently started reading that book have been constructing a
| drinking game based on it. I'd definitely recommend the book so
| far, but wouldn't necessarily recommend this drinking game:
|
| * Every time a new process is described as being a factor of x
| times faster/cheaper/better than its predecessor, take log(x)
| sips of your drink
|
| * Take a sip of your drink for every unique 3-Population Test
| or a 4-Population test that is described (where uniqueness is
| defined as the set of populations going into the test).
|
| * Take a shot every time the difference between Population X's
| DNA and East Asian DNA is used as a unit of measure. Take an
| additional shot for the quantity if it's more than one, e.g.
| "The difference between Denisovan and European Hunter Gatherer
| DNA is twice as large as the difference between Denisovan and
| modern East Asian DNA." would result in two shots.
|
| * Take a shot every time certain events are described as
| happening in sequence, but the years also have overlapping
| error bars
| treis wrote:
| >"Who We Are and How We Got Here" by David Reich
|
| IMHO, I'd take the conclusions offered here with a grain of
| salt. It's applying statistical methods to very improbable
| events (ancient bones surviving with DNA) to determine other
| very improbable events (evolutionary DNA change). The
| conclusions at least somewhat rest on the assumption that those
| two things have relatively consistent probabilities. That could
| be true but it's probably not and if it's not it's somewhat
| unclear how that would bias the results that the book draws its
| conclusions from.
| diego_moita wrote:
| > other very improbable events (evolutionary DNA change)
|
| Sorry, I don't understand this part.
|
| Are you suggesting that evolution is a "very improbable
| event"?
|
| Among serious scientists evolution is already settled and
| beyond dispute.
|
| I don't see any basis for an argument if you're suggesting
| that.
|
| Denying evolution belongs to religion, not science.
| dekhn wrote:
| No, they are referring to the fact that the events that
| lead to permanent changes in the genome are extremely rare-
| the vast majority of mutations are not fixed.
| 11101010001100 wrote:
| > statistical methods to very improbable events
|
| What is the alternative?
| treis wrote:
| If I had one I'd be clearing a space on my shelf for my
| Nobel Prize
|
| Seriously though, I don't think there's any way to know for
| sure. Like imagine if it were dice rolls. You can look at
| the results and draw conclusions to see if it's a weighted
| dice. But what if my table biased rolls or if some results
| were lost? It's probably reasonable to conclude that they
| weren't but no way that I can see to be sure.
| enviclash wrote:
| Random walks.
| bhickey wrote:
| I'm surprised that the prize wasn't awarded jointly with Reich.
| dkural wrote:
| The Nobel Prize tends to favor initial breakthroughs.
| Svante's lab sequenced the very first complete Neandertal
| genome, showing it was possible to reconstruct genomes from
| ancient DNA, with high-throughput sequencers, and developing
| the necessary lab protocols and software to put it all
| together (with his lab). Svante was senior author on the
| Denisova paper as well. So, I am not surprised. There was no
| major advance needed for Reich to do his work further
| elucidating the origin and dispersion of various hominin
| species and ancient human populations.
| dekhn wrote:
| Paabo told me (when he visited to give a talk at my
| institution) that the first few years of Neandertal
| sequencing, he was just sequencing his own genome
| accidentally, since he didn't have truly stringent lab
| technique. He was out ahead of everybody else for at least
| 2-3 years at the time, and could demonstrate to people
| trying to replicate his results that they were just using
| contaminated samples. Sequencing is absurdly sensitive- it
| can pick up a real signal from just a few individual
| molecules.
| bjelkeman-again wrote:
| Does this mean that inexpensive DNA tests you can buy
| online are likely to contain contaminated samples? As the
| person taking the sample at home hardly has stringent lab
| tech available?
| dekhn wrote:
| No, tests like that work with an abundance of DNA and so
| contamination is less likely. A DNA test typically works
| with saliva or blood which contains a ton of DNA> That
| DNA can then be amplified, which amplifies both the
| signal and the noise, but the noise is very low and can
| be trivially ignored after the fact.
|
| With paleogenomics, you're collecting a tiny amount of
| DNA, mostly degraded, from ancient samples, and so the
| "noise" (contamination DNA) ends up being close to or
| more than the signal you get from the sample.
|
| Details here:
| https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3926038/
| jhbadger wrote:
| The issue with paleo DNA is that the target is much lower
| in concentration than potential contaminants from the lab
| worker. etc. This wouldn't be the case in DNA tests where
| the concentration of the sample would be comparatively
| high.
| jhbadger wrote:
| That was a common problem in Paabo's early work. He also
| "sequenced an Egyptian mummy" that turned out to be
| himself as well.
| hajimuz wrote:
| Seriously? Nobody was verifying that end to end?
| searine wrote:
| As it turns out, paleogenomics takes next level
| cleanliness, far more than anyone expected, particularly
| when you're trying to sequence something so close to
| human DNA.
| dekhn wrote:
| Sometimes verifying the little details can get in the way
| of publication velocity. It's a risk many advanced
| scientists take because the chance of getting caught
| (publishing something that is later shown to be obviously
| false using careful control experiments) is low, and the
| risk to your career of being second to publish.
| dkural wrote:
| This reminds me of another story - BGI was sequencing the
| chicken genome, and for a while, a lot of people who did
| other sequencing projects kept receiving chicken DNA in
| their sequencing data files (as contamination).
| carbocation wrote:
| My feelings exactly. (That aside - delighted that Paabo and
| his field are getting this recognition.)
| birriel wrote:
| I've recently begun reading Harari's Sapiens. Does Dr. Paabo's
| research throw any light unto the interbreeding/replacement
| debate regarding extinct humans?
| diego_moita wrote:
| Yes, it does.
|
| The most interesting aspect it brings are numbers. It allows to
| measure how much of our DNA comes from which group of humans
| (Neanderthals, Denisovarians, etc). It also shows that the
| migratory currents had a lot of details that we barely got to
| understand.
|
| To understand Dr. Paabo's (and others) work, I suggested above
| "Who We Are and How We Got Here" by David Reich.
|
| Read it. It is easy reading. If you liked Sapiens I guarantee
| you will like that book too.
| birriel wrote:
| Thank you for the info, much appreciated!
| Tomte wrote:
| Leipzig... he's a colleague of McElreath (of Statistical
| Rethinking).
| dang wrote:
| Related:
|
| https://www.nobelprize.org/prizes/medicine/2022/press-releas...
|
| (via https://news.ycombinator.com/item?id=33065326, but we merged
| that thread hither)
| mhneu wrote:
| This is important work, and this award choice is a good one.
| amatic wrote:
| Congrats Svante Paabo! I saw his lecture in person a year or two
| ago, it's really fascinating how the new genetic analysis tools
| revolutionized the study of human evolution and migration.
| ArtWomb wrote:
| I had the similar pleasure of attending a Svante Paabo lecture
| at Princeton. A bit after the Cell paper was published. The
| entire team seemed like scientists genuinely chagrined at the
| attention. Of course it should surprise no one that Neanderthal
| / Homo Sapiens "gene flow" would spark imaginations ;)
|
| It's the Year 2022, and it appears we've evolved
| technologically to the point that Nobel calibre bioinformatics
| can be done on consumer laptops. It should be enough to
| literally calculate a personal Neanderthal / Denisovian
| admixture ratio on your own, provided you have access to your
| own sequence. With prices dropping on an Illumina machines,
| gene sequencers could be as ubiquitous as the PC shortly.
| Which, it's quite easy to see, results in the private sector
| human gene hacking industry, where humans in competitive play
| seek to "amp" their hominid characteristics for performance
| advantage ;)
|
| https://github.com/PrincetonUniversity/IBDmix
| amatic wrote:
| I thought he was Finnish, judging by the last name, but
| according to Wikipedia, "Paabo was born in Stockholm and grew
| up with his mother, Estonian chemist Karin Paabo."
|
| Also interesting, "His father was biochemist Sune Bergstrom,
| who shared the Nobel Prize in Physiology or Medicine with Bengt
| I. Samuelsson and John R. Vane in 1982"
| BurningFrog wrote:
| Karin Paabo is a WW2 Estonian child refugee.
| nodding_smiling wrote:
| It's even more remarkable that Paabo never really had much of
| a relationship with his father but still managed to follow
| him in getting a Nobel Prize. Something to fuel nature-
| nurture debates...
| enviclash wrote:
| Are you underestimating the choices of his mother and her
| capacity for creating an unprecedented intellectual
| atmosphere?
| strikelaserclaw wrote:
| so this guy had nature and nurture on his side, nice!
| enviclash wrote:
| That is the clear and smart way of phrasing it, I did not
| have enough clarity to make the point, thanks!
| asguy wrote:
| Please try not to be tedious. If you want to stir the
| pot, bring up the fact his mother selected a Nobel prize
| winner to have kids with, so clearly had bias, or
| something more creative.
| enviclash wrote:
| Your statement leaves little doubt to my unsettling
| question, thanks for the clarity!
| asguy wrote:
| Or, I just pointed out that you went into the
| conversation with a boring assumption. It's transparent.
| enviclash wrote:
| Yes yes, we know the problem.
| rurban wrote:
| No COVID-19 vaccination breakthrough awarded?
| whizzter wrote:
| The ones most likely to receive the prize isn't that old yet,
| also since the DDT scandal they do prefer to wait a bit to
| hedge on delivering prize before side-effects are known (Often
| one wishes the ones awarding the peace prize had kept that in
| mind).
| folli wrote:
| TIL
|
| > Muller was awarded the Nobel Prize in Physiology or
| Medicine in 1948 "for his discovery of the high efficiency of
| DDT as a contact poison against several arthropods".
| benrapscallion wrote:
| Atrocious that David Reich and Nick Patterson were not
| recognized, although this is typical of the Nobel committee.
| nodding_smiling wrote:
| I hadn't considered that Reich and Patterson might have
| deserved recognition. I think a case could possibly be made for
| that, especially if the prize-winning work had been defined
| more broadly as ancient DNA research in general rather than
| sequencing archaic hominins and identifying introgression into
| modern humans more specifically. Reich and Patterson were after
| all heavily involved in the analysis identifying gene flow from
| Neanderthals into modern non-Africans. But Reich's and
| Patterson's (very successful and important) careers have
| focused on more recent, within-sapiens population history, and
| I think their role in archaic hominin work was less
| "irreplaceable" than Paabo's. There are plenty of very
| important archaic hominin papers from Paabo and collaborators
| which did not involve Reich and Patterson at all: the earliest
| Neanderthal mtDNA and autosomal sequences, Denisovan mtDNA
| (which came out before the autosomal paper), much of the
| biochemically focused work on gene expression differences
| between species and so on, Sima de los Huesos... Reich and
| Patterson also came into the picture quite a bit after Paabo
| initiated the whole ancient DNA field - I think about 10 years
| later. So, even though I would have for personal reasons
| preferred that Reich and Patterson be recognised too, I think
| Paabo's contributions in the more narrowly defined field of
| archaic hominin research are very clearly much more
| comprehensive and vital than theirs.
| bhickey wrote:
| My greatest contribution to scientific progress came in 2010
| when I was having lunch with Nick. He described an admixture
| problem to me, summarizing: "I've got observed populations and
| I want to build a tree where I pick points for unobserved
| populations such that it minimizes the edge length of the tree.
| I can't seem to come up with a good algorithm for it."
|
| "Nick, that's the Steiner Tree problem! It's NP-complete!" He
| probably would've wasted a few more days going down that rabbit
| hole.
|
| Edit: Nick has some great Cold War spy games stories that I've
| only heard him tell in broad strokes.
| qclibre22 wrote:
| Any hope of solving it using quantum computing?
| jjtheblunt wrote:
| NP-complete isn't necessarily bad, depending on the size of
| inputs, right?
| dekhn wrote:
| Most problems in this space have reasonable-time
| approximations that get you close to the right answer for
| far less computational complexity. Even without ever
| having looked at Steiner trees before, I guess that there
| were reasonable approximations, and confirmed that was
| true without looking too hard. Letting Patterson know
| about the problem mapping ("your problem is an instance
| of <X>") is typically enough for a person of his calibre
| to research approximate solutions good enough for him to
| run some experiments.
|
| (many people say the protein folding problem is NP-
| complete, but the community generally believes you can
| predict the folding pathways of all proteins without
| explicitly running such calculations).
| bhickey wrote:
| Looks like there's a quantum speedup:
| https://arxiv.org/abs/1904.03581 IIRC there's no epsilon
| approximation.
| dekhn wrote:
| I thought the latter name sounded familiar and then I realized
| I met with him at the Broad Insitute and he told an off color
| joke about getting DNA from mosquito's testicles. Interesting
| guy who worked on UK crypto before genomics.
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