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Oldest Human DNA Yet Found Raises New Mysteries (nytimes.com)
143 points by Irene on Dec 4, 2013 | hide | past | favorite | 56 comments



It's so mind boggling to think that the "Homo Erectus" existed as far back as 1.8 million years ago, yet most of our recent (and known history) happened in the last 5000 years, and we see that as a huge evolution.

What the heck happened between 1 million years ago and now? The human race changed a lot and matured very much, but it's so incredible that such a big evolution only happened in the last few thousand years and the rest has taken hundreds of thousands of years.


In the Chauvet Cave there are cave paintings that are 32,000 year old[1]. But what's even more interesting, is that some of these paintings are only 27,000 year old. Meaning, that these people knew about the place for almost 5000 years. Can you imagine that kind of continuity?

The documentary Cave of Forgotten Dreams[2] presents the cave in a breathtaking detail, definitely worth a watch.

[1] http://en.wikipedia.org/wiki/Chauvet_Cave#Dating

[2] http://www.youtube.com/watch?v=kULwsoCEd3g


[T]hese people knew about the place for almost 5000 years. Can you imagine that kind of continuity?

They must have been members of what David Deutsch calls a "static society". These are societies which actively try to keep things the same, and stamp out any innovation or differences. Things change there so slowly that the change is not noticeable within a single generation. In a 2011 interview with Ken Rose (https://groups.google.com/d/msg/beginning-of-infinity/dr64n4...), Deutsch said that "progress, from the point of view of the human species as a whole, is very recent and very rare. Through most of human history, people would live their entire lives without ever encountering an innovation, whereas now, we take it for granted that iPhone updates come more often than is comfortable."

For more, see his superb book The Beginning of Infinity (2010).


Isn't it that they were just close to the zero on the exponent curve (kurzweil accelerating returns). Constraints very high with little knowledge and little meta-knowledge (just knowing something exists and is possible) giving a very slow pace


And carbon dating showed that some paintings were finished many hundreds of years after they began.


Agriculture. It's a several orders of magnitude improvement in the population density an area can support, which makes population centres possible, which makes specialisation viable, which makes everything else possible. If someone had developed agriculture 100,000 years ago, we'd currently be about 90,000 years more advanced than we are now.

Agriculture appears to have been developed independently in the Middle East, China and Americas about 10,000 years ago, but I and some others believe there was more dissemination of ideas, mainly via individual travellers or small groups of travellers, than conventional historians take into account.


One problem with the conventional history is that it's very much oriented around agriculture on plains, using irrigation, with buildings made of stone or clay. This kind of agricultural culture is good for archaeologists because it leaves intact traces that are easy to dig for. But it's not the only kind of agriculture.

There have also been agricultural civilizations that grew rain-fed crops on forest sites and built houses of wood. Like the Maya, or ancient southeast Asian civilizations.

Luckily those peoples did help us out by building stone temples, but I would assume that probably several more civilizations have practiced slash-and-burn jungle agriculture and just not happened to have built monumental temples.

Supporting my hypothesis, one early layer of Jericho seems to reflect a forestal mode of production - something about acorn horticulture[0].

So, I think if we are to find the hidden backstory behind the sudden simultaneous 10,000 YE agricultural revolutions, the place to look would be in the trees. But what do I know.

[0] http://en.wikipedia.org/wiki/Natufian_culture#Settlements "Settlements occur in the woodland belt where oak and Pistacia species dominated...The superstructure was probably made of brushwood. No traces of mudbrick have been found."


This seems to beg the question of what caused agriculture to appear. Although given that it did appear, your explanation seems like a plausible explanation of how it spread and led to the rapid progress we have seen since.

A boring answer to this question is that it was simple incremental changes driven by random mutations and natural selection (eg. evolution). For example, we might have started to occasional plant the seeds of plants as we found them, which could become us regularly doing so. Then we might have started moving the seeds to more central locations, and eventually arrive at agriculture as we know it today. These adaptations may have started before homo-sapiens. If it happened long enough before (so that there is another species with a common ancestor that did this), we could check this by looking for agricultural tendencies in species related to us (If anyone is aware of research on this hypothesis, please post).

A more interesting hypothesis is that agriculture was the result of an abiotic change. Instead of gradually developing agricultural tendencies, we 'immediately' became agricultural following some other event, such as a change in climate. This seems to be consistent with my understanding of climate history, which puts us in a relatively short window of nice climate.


10,000 years ago is the end of the last ice age, before which climates were shifted, sea levels were lower, and most of the land humans tend to like to live on (near sea level) are now deeply submerged.

We think agriculture and city-building started around that time, but it's possible we just haven't found older evidence because it was destroyed when the ice age ended and sea levels rose.

It seems incredibly arrogant to me to think that our ancestors, who were virtually identical to us much of those million+ years, required at-minimum hundreds of thousands of years to figure out what seeds are and how to make them grow. These are people who knew how to live off the land and were far more familiar with plants and animals than most of us could dream of being. These people invented astronomy, art, religion, clothes, tools, fire. They'd notice that plants produced seeds, that seeds wound up on the ground, and that new plants grew where the seeds fell.


I don't buy the atlantis "they're all under the sea" theory at all. We are expected to believe that they only built cities by the coast and none at all along rivers or round lakes? None of these civilizations spread to areas where the sea level has not risen so much? Far too contrived for my tastes.

Il flip your arrogance accusation around. These people developed agriculture and even cities tens of thousands of years ago, yet none of them managed to put together a sustainable survivable civilization? None of them managed to go from basic agriculture to even slightly more advanced agriculture that would have launched them on the track to specialization, even given hundreds of thousands of years in which to try? Why not? What was wrong with them?

To a hunter-gatherer, which is a nomadic lifestyle, cultivation in a fixed area for long enough to both sow and later reap a crop is not at all obvious.


I'm not completely convinced that they were genetically identical to ourselves, we used to evolve quite fast, and faster still after we developed agriculture.

Anyway, if you look at tribes native to the America, about all of them knew about agriculture (it's in their culture), but not all established an agricultural society. What we are calling "developing agriculture" probably is a much more complex phenomenon, with several different (near) contemporary developments, and probably none of them was learning that plants grow from seeds.

* Ok recent humans certainly were similar, and agriculture could probably have appeared a few thousand years earlier, I'm not sure we can extend that to hundreds of thousands, or maybe even tens of thousands.


Climate change is the working hypothesis at the moment. Specifically, general drought/desertification that drove the people at the origins of agricultural technology to a few great river valleys (notably the Nile and the Indus).


http://www.sciencedaily.com/releases/2003/01/030120100451.ht...

"Fungus-growing ants practice agriculture and have been doing so for the past 50 million years according to research published in the Jan. 17 issue of Science. These ants not only grow fungus gardens underground for food but also have adapted to handling parasitic "weeds" that infect their crops."


Nice, but fungus is not a plant strictly speaking "[..] These organisms are classified as a kingdom, Fungi, which is separate from plants, animals, protists and bacteria. [..]" [1]

Which leads to an off-topic question: Is mushroom cultivation considered as agriculture?

[1]: http://en.wikipedia.org/wiki/Fungus


I also believe in this explanation, but it would be better if we had hard evidence of certain types of human population thriving and other ones disappearing based on the presence or lack of agriculture.


> the "Homo Erectus" existed as far back as 1.8 million years ago, yet most of our recent (and known history) happened in the last 5000 years, and we see that as a huge evolution.

an exponential process (of life complexity in this case) looks the same at any scale. The Earth has existed for 4B years, life is ~3B years, life as a cell with nucleus ~2B (yea, 1B years to develop nucleus :)

http://www.caveofthemounds.com/geotimeline.htm


Yet, do you have any explanation for why that process looks like an exponential? It does not fit the "rate of change is proportional to raw size" template that normally creates exponents in nature.


>It does not fit the "rate of change is proportional to raw size"

i kind of see it here. The evolution speed depends on the speed of generating of changes and on the speed of selection of the generated changes.

Wrt. the speed of generating of changes. The more complex a system (i.e. types and number of actors/components and relationships between them) - the more diverse set of small gradual changes/variations to components/relationships/behaviors can happen while the system will still be functioning. In particular it is applicable to biological systems, ie. single cells, colonies, multicell organisms and various groups/societies of it. For example, in general, 2 different species of cells can produce more diverse set of natural variations than 1 species even if the total number of cells is the same in both cases. An example at different scale - one science - philosophy of Ancient Greeks has become a multitude of sciences through the same process of branching/specialization and the speed of this process is proportional to the number of branching/specializing sciences. Following the same principle - there is no way US tax code (or the law in general :) will become simpler anytime in the future :)


Many changes/advancements drastically increase opportunities for further changes/advancements.

Technological advancement tends to follow that pattern, and I imagine many evolutionary changes do, too.


I've heard it suggested that language made the big difference. We bummed around for 998 million years, not able to improve our lot much - but somehow, 2 million years ago we developed language, and after that we were able to rapidly improve (and even co-evolve with our improvements - I've heard that the invention of the baby sling allowed our brains to grow larger than without it).


Interesting technologies form ~1 million years ago (Homo erectus):

* stone hand-axe: http://en.wikipedia.org/wiki/Acheulean

* fire: http://en.wikipedia.org/wiki/Control_of_fire_by_early_humans


I believe the prevailing hypothesis is that there was a tiny mutation in a human brain ~50,000 years ago that causes spoken language to be possible, but there are other ideas. It's a fascinating area of research:

http://en.wikipedia.org/wiki/Behavioral_modernity


I've seen the idea batted around that the hybridization of neanderthals and cromagnons set off something of an explosion in evolutionary terms. Art and technology only started getting anywhere in the areas where they had contact some 50,000 years ago. Modern humans are apparently something like 4% neanderthal.


Nothing of interest, really. Just grunts and horrible screams. And lots of f*cking, of course, to compensate for the massive losses due to disease, wild animals, and famine cycles (which, thankfully, modern age shields us from--well, not the f-ing, I mean the rest.)

Sadly, I must once more indicate that this post is sarcastic, for the humor-challenged ones.


It is possible for people to understand that you are joking, yet not like it and consider it conversational noise.


Conversational noise? Does one consider things one does not like to be "conversational noise?" Oh well. One learns, someday, to welcome dissent.


There's a difference between "I do not like this, but it adds to the conversation" and "I do not like this, and it adds nothing to the conversation." The point of the moderation system here is to reduce noise and promote signal. One-liners and drive-by sarcasm do not add much to the conversation.


They have more on this on the Nature podcast. I also highly recommend listening to the Nature podcast. It's free, and they usually interview authors of these articles, and it's presented in an elevated fashion that you won't get by reading the NYTimes.

http://www.nature.com/nature/podcast/


That NYT author, Carl Zimmer, is also pretty solid. He's doing a twitter Q&A now if you want to ask him Qs: https://twitter.com/carlzimmer/status/408327412250734592


Yeah this article is actually quite good, better than most science articles I've read from most major media outlets. I wasn't meaning to belittle this specific article, but I thought I'd point an actual interview with author Svante Pääbo.

Also, again, I think the Nature podcast is by far the best podcast for general science, so if "[people] fucking love science", I'd recommend listening to it weekly over liking a facebook page, especially as they cover their weekly publication on a slightly more accessible level. Also, Science (the periodical) has a pretty okay podcast too.


The age of this DNA reinforces just how much of what we value today about "what makes us human" (creativity, intelligence, language, etc.) has lots to do with the knowledge accumulated via our culture, and relatively little to do with genetic differences.

Whenever someone talks about how smart we are genetically, ask yourself if this is the kind of smart we were 10,000+ years ago.


> Whenever someone talks about how smart we are genetically, ask yourself if this is the kind of smart we were 10,000+ years ago.

You want a more shocking thought?

Imagine how much knowledge spanning the 400,000 years since this specimen is forever lost to us because it was limited to oral tradition.

These people didn't had a wealth knowledge available one click-away to build upon, but I see no reason to believe they dramatically less intellectually capable than us because of genetics. They certainly possessed a lot of empirical knowledge about the things around them, necessary for survival.

Considering how some tribes knew for eons about the uses of medicinal herbs which are today used on our modern drugs, it's fascinating to think about what we might be missing. If even relatively recent knowledge (300 BC) gets lost [1], imagine how much science will "rediscover" things our descendants might have already known.

[1] http://en.wikipedia.org/wiki/Damascus_steel


There's a relevant book from 1715, which I discovered while researching the existence of "ever-burning lamps": The History of Many Memorable Things Lost Which Were In Use Among the Ancients - https://openlibrary.org/books/OL6961227M/The_history_of_many...

I believe it does refer to Damascus steel, as well as many other lost Classical through Dark Ages inventions. It digresses into talking about bygone social customs in places, but many of the descriptions are excellent and illustrative.


Fascinating, albeit hard for me to read due to the language. Thank you very much for the link.


You're welcome! It did take me some hours to get through most of it. The content is unique enough to make it worthwhile. I was especially intrigued not only by the excellent breakdown of "ever-burning lamps", which are a more or less real thing, but by a mention of ancient Greek water organs, a musical instrument which involved water inside some sort of tubes.


The way I think about it is that there is a tipping point in intelligence where a species can build on its own discoveries at a much accelerated rate, similar to the concept of a singularity in AI. As 10,000 years is not that long from an evolutionary perspective, we are about the dumbest that a species could possibly be in order to reach that singularity point, otherwise we would have done it earlier.

Of course, this ignores factors such as non intelligence based adaptations (such as thumbs), antibiotic factors (climate). It also ignores the facts that intelligence is composed of many components, and our singularity might have happened after an improvement is some metric that does not contribute much to overall intelligence. For example, the ability to speak does not make an individual animal more intelligent, but it does facilitate the accumulation of intelligence through generations.


What makes you think we've advanced in a straight line? We're surrounded by the ruins of lost civilizations, who often built things we would find very challenging to reproduce even with our modern machinery, if we could reproduce it at all. It seems much more likely that human civilization has advanced and been knocked back multiple times in multiple places, and we're currently at a high point.

We're probably the first ones to figure out how to use coal and oil to generate power and do far more work than can be achieved with animal and slave labor. I suspect that's the key to how high our high point is. But I also suspect that there are other sciences where we're not as advanced as our predecessors, and maybe even some we haven't discovered yet.


Why do we need a tipping point?

Proposal:

1) Human progress arises from the development and improved use of tools/technology (and I'm including concepts like "if", as well as skills, as kinds of technology)

2) Our tool use abilities interact multiplicatively/geometrically. E.g., [what I can do with a hammer and a shovel] is not the sum of the [things I can do with hammers] and [the things I can do with shovels]

3) Our tool-use-abilities started meagre

4) Tool use is not uniquely human, but humans are better at it

5) Accidents of history and human development have allowed for the accumulation of tools (agriculture, e.g.)

... this "explanation" (or what have you) yields exponential growth curves that, I propose, would look very similar to those of humans. If there was a "tipping point" perhaps it was (5) -- the introduction of some substrate upon which cultural knowledge could grow.


I think language works as a tipping point in that sequence. For technology to interact as you say, it has to spread easily.


Why do we take as the default hypothesis that language is, as you seem to be implying, a monolithic "thing"?

A more plausible hypothesis seems to me to be that language itself is constituted by a suite of cultural tools/skills. A language with a very limited vocabulary (especially one restricted to largely unhelpful words, e.g. "Justin Bieber", or "toe wart") is much weaker than one that has benefited from decades of cultural and generational digestion and iteration (i.e., a language that includes concepts like "however", or "on the condition that", or "art", or "gravity").


As another comment says, the author of this New York Times article, Carl Zimmer, is a very solid science writer who knows a lot about evolution. I have occasion to discuss human population genetics with psychologists who study behavior genetics, and when population genetics issues come up in those discussions, some of the new discoveries are surprising even to them. It's hard for reporters, us, and even the working researchers to keep up with the new findings in human population genetics. I'll share a finding here that surprised some researchers I discussed it with this week.

The first human genome to be sequenced was that of Craig Venter, who would be called a "white" man in the United States. The second human genome to be sequenced was that of James Watson, who is also regarded as "white" in either the United States or Britain. One of the first dozen or so human genomes to be sequenced was that of Korean scientist Seong-Jin Kim,[1] and his genome, even though "Asian," is more similar to Venter's than Venter's is to Watson's, and more similar to Watson's than Watson's is to Venter's.[2] Even though lineages are traceable in broad outlines by looking at human genes, there are quite a few human beings who resemble someone in someone else's group more than they resemble people in their own group. "The fact that, given enough genetic data, individuals can be correctly assigned to their populations of origin is compatible with the observation that most human genetic variation is found within populations, not between them. It is also compatible with our finding that, even when the most distinct populations are considered and hundreds of loci are used, individuals are frequently more similar to members of other populations than to members of their own population. Thus, caution should be used when using geographic or genetic ancestry to make inferences about individual phenotypes."[3]

So what's going in these studies of early hominid DNA is that we necessarily have tiny sample sizes, and we actually have no idea how much genetic variation there was in the population we call Neanderthal, how much in the population we call Denisovan, and so on. We will want to sequence as much ancient DNA as we can, and meanwhile sequence more modern human DNA from more people from more places around the world. But we won't be able to trace back the ancestry relationships unerringly, no matter what we do.

[1] http://genome.cshlp.org/content/early/2009/05/26/gr.092197.1...

[2] http://www2.webmatic.it/workO/s/113/pr-1611-file_it-Barbujan...

[3] http://www.genetics.org/content/176/1/351.full


Ok, I have to ask this, and I apologize in advance for it being out of topic.

How on earth are you well informed on so many topics spanning different fields of science and literature? Your comments are amazingly well informed, and I would like to know how you do it.


[Blush] Thanks for your kind question. Let me first of all say that there is a lot that is discussed here on HN that I know nothing about, and in threads on those topics, I am in lurk mode, learning from the rest of you. So thanks.

On some topics, I have a different perspective just because I am older than most people here, so I remember history that other participants have to read about. Genetics research to be a responsible popular author about that research is part of my work, so this topic was work-related. I got lucky over the weekend, because I had just looked up the human population research articles to get ready for some contentious editing on Wikipedia, and thus all of the sources were at hand. Some of the other topics I comment about are also work-related, or related to my former work or my higher education degrees (neither of which were in computer science).


Dr. Peter Venkman: Ray, pretend for a moment that I don't know anything about metallurgy, engineering, or physics, and just tell me what the hell is going on.

Dr Ray Stantz: You never studied.

(I think the answer is simple: he has an interest in all those things, so he follows them).


qubitsam, let me introduce you to my favorite commenter on HN: tokenadult :)


He knows how to sound informed, which is the important part. Large walls of text, big words, selective citation of valid sounding papers.


He's probably also disciplined enough not to sound off on topics that he doesn't know anything about.

I was consulting (software) at a client site and one of the employees at the client remarked that I seemed to know everything about everything. I just replied that it was a trick - I only talk about the things I'm informed on, and when a question came up on a topic I didn't know anything about, I just redirected the conversation back to my expertise. I had a hammer and worked hard to make everything a nail. :)


So... when you're not a consultant with a need to impress people, you instead redirect the conversation to subjects other people know, which interests you? :-)


There was actually a pretty good article about the Denisova human in one of the recent National Geographics. One of the researchers mentioned in the article made a similar point, that for him the most likely indication of the Desnisova find is that we currently are separating into sub-species where there aren't any and that what we are finding are differences between individuals and not new sub-species. I wonder when/if that will be the established view and some of these species will be consolidated.


If the raw number of DNA differences don't scale with genealogically and morphological 'similarity' - does that imply that the number of genes that get expressed in ways visible to us (facial shape, hair, etc) are really few in number?

Either that, or the analysis you described was plain incorrect, or we are looking at DNA 'wrong' - seeing patterns in noise and noise in patterns.


How is it that your interpretation of this evidence is so different to not only Zimmer's summary, but also all of the people quoted in the article? I think you would be more convincing if you addressed why these people interpreted the results so differently to you, than simply claiming that Zimmer has overlooked something.


You're reading into my statement above something I didn't say.


OK, but you are still claiming that the correct interpretation of this evidence is very different to everyone in the article. Given that the facts you describe are very well known and basic, I doubt the people are unaware of them. They may, for example be using a measure of genetic difference that works better for distinguishing between groups.


http://imgur.com/a/Ow9ab

It's funny how when you look at the faces you can probably see the genetic distance. Watson was a kinda weird looking dude.


fun fact: Denisovan sounds a bit like Dennis, doesn't it? Surely a coincidence... The remains were found in the Denisova Cave, which was named after a hermit who live there, Denis http://en.wikipedia.org/wiki/Denisova_Cave#History


Simpler explanation/story (Pun intended) == Battlestar Galactica




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