De-Extincting Lost Molecules

(!)

De-extinction is not just for Mammoths!

One of the interesting discoveries of the twenty first century has been how much genetic material we (i.e., Homo sapiens) have that came from our extinct Neanderthal and Devonian cousins. 

We don’t know exactly what happened to these groups, but it is now obvious that they were very close relations.  As in, family.  Literally, blood relations.

This is an interesting question because many of the genes we have identified that seem to have come from our Neanderthal relatives are quite valuable for our health.  When we interbred, the children inherited stuff from both lines, and some of those genes were good for them and their descendants.

When Neanderthals and Devonians died out, most of their genes died with them.  Genes that we could have inherited, but, didn’t.

This fall researchers at the University of Pennsylvania report an interesting study that “de-extincts” molecules from these ancient genomes [2].   “Molecular de-extinction”.

The basic idea is to search for peptides encoded in ancient DNA, looking for molecules that have anti-microbial properties.

The methodology is a bit round about.  They build a machine learning model (naturally!) that analyzes DNA to predict what peptide will be produced.

No, I don’t understand the chemistry, or exactly what the ML is doing.

The results are zillions of peptides, which they tested and found a handful of interesting prospects, i.e., that helped mice fight infections.

One reason why this is interesting is that the DNA of living or once living organisms is likely to preserve the blueprints “useful” compounds more than random stuff.  Most of the compounds probably have little to do with fighting microbes, but it’s a good place to look for them.

This round about approach is a bit “goofy” [1].   But, looking for candidate compounds is basically searching through a near infinite number of possibilities.  So any method that brings in even a few hits can be a win.

The researchers report that this method scores “hits” that are not found by conventional search methods, suggesting that this is adding to the overall search.

This strategy actually makes sense, in that the ancient DNA isn’t part of our current genome, but was part of a living genome.   I.e., Neanderthals and Devonians “discovered” and retained these genes, so, there is stuff encoded there that was good for them.  We don’t have those genes, but they are probably compatible.

In short, this is a good place to look for stuff that might be good for us.

Interesting.

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1. Katie Hunt, Scientists are bringing molecules back from the dead in quest to fight superbugs, in CNN News, December 15, 2023. https://www.cnn.com/2023/12/15/health/superbugs-antibiotics-neanderthal-woolly-mammoth-scn
2. Jacqueline R. M. A. Maasch, Marcelo D. T. Torres, Marcelo C. R. Melo, and Cesar de la Fuente-Nunez, Molecular de-extinction of ancient antimicrobial peptides enabled by machine learning. Cell Host & Microbe, 31 (8):1260-1274.e6, 2023/08/09/ 2023. https://doi.org/10.1016/j.chom.2023.07.001

PS.  Another great name for a band:

“De-extinction”

Southern Ocean During Last Glaciation

Speaking of heat flows….

One of the big scientific questions of the early twenty first century is, where will all the heat go?  We are heating up the Earth’s atmosphere at unprecedented rates, but the planet Earth is not a brick.  It is a complicated ball covered with a blanket of water and air, both of which heat and cool, and slosh around.  The Earth is also inhabited by a lot of living things, all of which move heat around. 

The same is true for key chemicals that strongly affect heating and cooling.  Carbon is taken up and emitted by living things, and moves around the atmosphere and oceans.  Increases in CO2 in the atmosphere are moving into the oceans, changing the chemistry, and affecting aquatic life.  But CO2 also sinks to the bottom of ocean, eventually, and may turn to mud and rock. 

It’s very complicated, and the timing of these events will determine just what and how fast our own lives are affected.  For example, oceans have been absorbing CO2 and heat from the atmosphere for decades, which has slowed the effects of CO2 induced warming.  If this changes, we may well see effects in our weather and lives, possibly very rapidly.

These kinds of changes have happened in the past.  In the last glacial period, 60,000 plus years ago, oceans rose and fell, the atmosphere warmed and cooled, and ocean currents switched on and off.  It was a period of unstable climate, and we have pretty good geological records for a lot of it. This makes it a really good model for our own future.

This fall, researchers at Sao Paulo report a study of fossil records of the last 70,000 years form the South Atlantic [2]. The cores contain foraminifera, plankton that are “thermocline-dwelling”, i.e., live in water at specific temperatures.  These remains give a record of the water temperature at various depths, and the sediments can also yield indications of the chemical composition.  Of particular interest here is the amount of C13 isotope, which indicates whether the Carbon came from the air or from deep water.

The researchers were focused on periods of warming that occurred in between cold periods, which are associated with the abrupt weakening of the Atlantic meridional overturning circulation (AMOC).  This change results in less heat moving north, so the North Atlantic gets colder and the Southern Ocean around Antarctica gets warmer.  The warming results in upwelling of ancient Carbon from deep in the Southern Ocean, i.e., a large increase in CO2 in the atmosphere. 

Assuming these results hold up, the implication of this scenario are clear.  When the AMOC weakens, this can cause a release of Carbon that has been stored at the bottom of the ocean for millennial.  Releasing this Carbon into the atmosphere would probably spur even more warming.

There is some evidence that the AMOC is weakening.  If this continues, it could trigger major changes in the South Atlantic and Southern Ocean that cause a spike in CO2 [1]. 

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1. José Tadeu Arantes, Analysis of carbon cycle during last glacial period can help monitor climate crisis, in Agência FAPESP – News, November 29, 2023. https://agencia.fapesp.br/analysis-of-carbon-cycle-during-last-glacial-period-can-help-monitor-climate-crisis/50324
2. Tainã M. L. Pinho, Cristiano M. Chiessi, Marília C. Campos, Rodrigo C. Portilho-Ramos, Gema Martínez-Méndez, Igor M. Venancio, Rodrigo A. Nascimento, Stefano Crivellari, Ana L. S. Albuquerque, Helge W. Arz, Ralf Tiedemann, André Bahr, and Stefan Mulitza, Thermodynamic air-sea equilibration controls carbon isotopic composition of the South Atlantic thermocline during the last glacial period. Global and Planetary Change, 229:104223, 2023/10/01/ 2023. https://www.sciencedirect.com/science/article/pii/S0921818123001960

PS. A couple of ideas for band names

Thermocline-dwelling
Overturning circulation

How Old Are the White Sands Footprints?

One of the oldest questions in Paleontology is when humans came to the Americas.  We know that humans originated in Africa, and spread out to Europe and Asia, and then, at some point, to the Americas, Australia, and everywhere.  Humans were definitely in the Americas at the end of the last ice age, some 10,000 years ago–or later.  But how did they get here, and when did they come?

As always, the evidence is sparse and ambiguous, and prone to over interpretation.  With minimal evidence and uncertain dating, interpretations are heavily influenced by assumptions.  When I was in school, the generally accepted hypothesis was that humans came to the Americas at the end of the last glacier, rapidly—extremely rapidly—diffusing through ice free areas, and down into Central and South America.

This timeline make contemporary indigenous cultures 10,000 years or less old, and raises many questions about how to account for the diversity of Native Americans, and just how this rapid migration happened.

(Indigenous scholars have long disputed this theory, believing that their cultures are far older than that.)

In recent decades, a number of archaeological finds have shown dates much older that this conventional theory.  A date of 15,000 years ago in Patagonia implies that humans must have been up North much earlier than that.  Other evidence suggests humans present in Texas 20,000 years ago—which the ice was still at its maximum.

In the last few years, fossil trackways of human footprints have been excavated at White Sands, New Mexico.  These are dramatic evidence that people were here when the now petrified clay was soft!

The investigators Carbon dated pollen found in the footprints, and calculated that they were 23,000 years old!  If so, then humans were not only in North America, they were way into North America.  And, if they were here at that time, they certainly could not have walked through Alaska, because it was a mile deep in ice.

Archeological dates are always iffy, and a single find must be taken skeptically.  Even a handful of dates must be viewed with caution, and correlated with other evidence.

This fall, researchers have published additional dating of this site, using other measures [3]. Each data point is at least somewhat uncertain, but taken together they show a consistent date for the footprints, 23,000- 21,000 years ago.

Which is … wow!

There seems to be growing evidence that at least a few humans were wandering the Americas during the last ice maximum.  We know pretty much nothing else about them.  Where did they live?  How did they live?  Where did they come from?

This also suggests that the well documented post-glacial diffusion, and the ascendance of the Clovis tool makers needs to be rethought.  If there was an immigration across the Bering land bridge and down the coast, it would likely have encountered inhabitants who had been there for 10,000 years already!  Was this an invasion?  A replacement?  An integration?

I’ll note that there is also growing evidence that people were moving north as the ice melted, i.e., there people already in America, moving north into Alaska at the time that Asians were moving south from the land bridge.  It is quite possible that people from America crossed west into Asia starting at this time.

And evidence suggests that there were people in South America at this time, vastly extending the time that people have been living in the Amazon basin and the steppes to the south. 

In short, humans seem to have been in the Americas long before the glaciers retreated.  They seem to have been everywhere. The continent was not empty and waiting for immigrants from the old world, like the theory went when I was young.

Cool.

And, by the way, the cool thing about trackways is that they may lead somewhere…like a camp, with lots of interesting remains to examine. In the future, it may be possible to follow the trail and see what else in waiting in the mud!

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1. Alice Fordham, Fossil footprints in New Mexico suggest humans have been here longer than we thought, in NPR News -Science, October 7, 2023. https://www.npr.org/2023/10/07/1204031535/fossil-footprints-in-new-mexico-suggest-humans-have-been-here-longer-than-we-tho
2. Bente Philippsen, Dating the arrival of humans in the Americas. Science, 382 (6666):36-37, 2023/10/06 2023. https://doi.org/10.1126/science.adk3075
3. Jeffrey S. Pigati, Kathleen B. Springer, Jeffrey S. Honke, David Wahl, Marie R. Champagne, Susan R. H. Zimmerman, Harrison J. Gray, Vincent L. Santucci, Daniel Odess, David Bustos, and Matthew R. Bennett, Independent age estimates resolve the controversy of ancient human footprints at White Sands. Science, 382 (6666):73-75, 2023/10/06 2023. https://doi.org/10.1126/science.adh5007
4. Carl Zimmer, Ancient Footprints Push Back Date of Human Arrival in the Americas, in New York Times. 2023: New York. https://www.nytimes.com/2021/09/23/science/ancient-footprints-ice-age.html

A Pleistocene Human Die-off?

Our ancestors have been around for quite a while now, a couple of million years or so, depending on how you define things.  Most of that time, there weren’t very many of us, and, like any species, we were never all that far from extinction.  This much we know, on general principles.  Details are extremely hazy, though, and evidence is sparse.

Theories, however, are relatively abundant.

This summer, researchers in Shanghai and their colleagues report a new study of the human genome using a statistical analysis of mutations [2].  If I understand correctly, the idea of this method is to model how pieces of the genome slide around over time.  DNA sequences “coalesce” as short sequences disappear, scrunching together nearby sequences.  Statistically modelling this process attempts to reconstruct the history of present sequences.  This history is used to estimate the nearest possible ancestor for two genomes, and, in this case, to estimate how many genomes were extant, i.e., how big was the population.

The results of the study imply that there was a period in the late Pleistocene, 900,000 years ago, when there were less than 2,000 humans in the world—for 100,000 years or so.  As the inevitable headlines scream, “Humanity’s Ancestors Nearly Died Out” [3].

The period identified by the new statistics has a sparse fossil record, with only a number of remains more or less securely dated to that time [1].   (Considering how sparse the fossil record for human ancestors is in total, a “sparse period” must be really, really sparse.)

The researchers speculate that the population decline corresponds to, and presumably was caused by, a global cooling period.  At that time, more or less, there was a general cooling, with increase glaciation and, presumably, dryer conditions. 

This study is certainly a “provocative” ([3])!  And it definitely calls attention to how close to extinction humans may well have been at one or more periods in the past.  And, of course, it points to the possible existential threat of climate change, now as well as then.

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OK.  Maybe.

I tend to be very skeptical of all theorizing about human ancestry, because there is so little evidence and the evidence that exists is limited and ambiguous. 

I also tend to be very, very skeptical of inferences about family trees based on statistical models.  In addition to the sparsity of the data, the analysis rests on a ton of assumptions about genetics and evolution. 

I’m not an expert, but I can see that this method seems to assume populations migrate, change, and mix in pretty simple ways.  We know that real populations generally have very complicated behaviors, so the model is probably overly simple.

So, overall, I’m super skeptical of this study.  Even if the data is reliable, the interpretation is a big stretch.

Sure, something like this could have happened.  But did it really happen this way? 

One big problem is that the basic results are literally inexplicable.  We don’t know why the world wide population would drop so far, so fast, stay at that level for thousands of years (just barely hanging on), and then recover. 

A world wide population less than 2,000 for 100,000 years, without going extinct?  This seems very unlikely, and hard to explain.

Second, a purported world wide catastrophe should be evident in the fossil record.  But there is no specific sign of it, other than the sparsity of the record. 

Third, the geographic distribution makes little sense if this were a global climate catastrophe [1].  The bottleneck seems to be different in different parts of the world, which is difficult to attribute to climate cooling.

And if it wasn’t caused by climate change, then what would cause it?  There are plenty of possibilities, but no real strong candidate. 

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Overall, this study will need to be reinforced by other evidence, and by additional studies using the new technique.  With so few data points, there are many models that could fit, so it will be interesting to try to do comparative studies (i.e, alternative evolutionary scenarios), and also to try to correlate climate and fossil records with versions of a genetic model.

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1. Nick Ashton and Chris Stringer, Did our ancestors nearly die out? Science, 381 (6661):947-948, 2023/09/01 2023. https://doi.org/10.1126/science.adj9484
2. Wangjie Hu, Ziqian Hao, Pengyuan Du, Fabio Di Vincenzo, Giorgio Manzi, Jialong Cui, Yun-Xin Fu, Yi-Hsuan Pan, and Haipeng Li, Genomic inference of a severe human bottleneck during the Early to Middle Pleistocene transition. Science, 381 (6661):979-984, 2023/09/01 2023. https://doi.org/10.1126/science.abq7487
3. Carl Zimmer, Humanity’s Ancestors Nearly Died Out, Genetic Study Suggests, in New York Times. 2023: New York. https://www.nytimes.com/2023/08/31/science/human-survival-bottleneck.html

Prehistoric Fires Related to Mass Extinction

I saw a headline, “Ancient Fires Drove Large Mammals Extinct” and I wondered what the link was supposed to be [1].

I’ve been reading archaeology for quite a while now, and even in my own lifetime I’ve watched the fads come and go.  Read the interpretations of Troy or Pompei over the years.  Read the stories about extinctions of Neanderthals or the North American megafauna.

So much of the “big picture” theorizing is a projection of current anxieties and preoccupations.  Ancient disasters are attributed to war or revolution or economic depression.  Sometimes catastrophe is blamed on ecological collapse, with or without human rapacity and overconsumption involved. I’m sure that there will be a spate of stories about ancient pandemics.

By now, I tend to be pretty skeptical about such pontificating, especially popularized versions.  There is very little evidence to stand on, and a lot of psychological projection.  And the popular renditions may well fly a lot farther than the evidence suggests. 

So, what does this new study really show us?

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The new study investigated the dates for a collection of fossils from the La Brea tar pits [2].  The dates give some relatively precise estimates for when the post-glacial fauna died out, in a relatively short time after 11,000 years ago. 

This precise dating of extinctions is related to climate records which show a 300 year warm, dry spell in the region at that time.  Unsurprisingly, this deep drought was also a time of increased wild fires. 

And, perhaps significantly, this was also the time when humans spread through the area.

Overall, these data are consistent with what we already know:  in this area there was a “state change” from forest to chaparral, i.e., things got dry and firey.  Many species of large animals died out during this period.  And, yes, humans arrived in large numbers during this period.

This is not news.

The news is that this study has good enough data to play around with regression statistics to look for evidence of causation.  Their modeling shows unsurprising relationships between drying conditions and extinctions, and drying conditions and fires, and fires and extinctions.  The analysis also finds that human presence caused increased fires.

None of these relationships are particularly surprising.  With all of this happening at the same time, the question is whether this rapid “state change” was triggered by one or more of these stimuli, and if there was something that pushed the climate over a tipping point. 

And specifically, was human activity the trigger?

The researchers conclude that the regression study is consistent with a key role for humans. I.e., human hunting and burning change the vegetation and populations, and created feedback loops, accelerating the dessication and fire damage, leading to rapid extinction of the largest species.

“Anthropogenic hunting and burning could have precipitated a state shift toward today’s chaparral ecosystem”.

([2], p. 7)

Note the exact words here: “could have”. 

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Let’s be clear:  we didn’t need a regression study to know that human activities could have contributed to the sudden climate change and extinctions.  The important thing about this study is that these regressions could potentially have found little or no evidence of human causation.  So, what is important that the hypothesis remains very possible.

Just how much are today’s events similar to 11,000 years ago?  That’s tricky to know, but it’s obvious why people are worrying about it.

The news story makes clear that the role of humans is very much on the mind of Californian paleontologists, living in the middle of a rapidly drying and igniting California today [1]. 

It is interesting to see that one of the researchers comments, “we caused this, we have the power to stop it.” (Dr. Emily Lindsey quoted in [1])

Well, maybe. 

This study doesn’t actually show that human activity—or inactivity—could have prevented the state change, nor what exactly humans could have done in the past or now that would prevent or reverse such a state change and sudden extinctions. 

We don’t really know how to stop it, and nothing in this study addresses the question.

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For the record, I personally believe that human hunting probably was a major factor in the extinction of the large fauna, because we see the same pattern all over the planet (people arrive, large animals die out).

The relationship of humans and fire is not as clear.  We know that fires happen all the time, especially during dry spells.  We also are pretty sure that humans have used fire to deliberately shape ecologies, as well as contributing to accidental fires. 

How much of the “state change” in California was (or is) due to drying climate, and how much to humans is hard to say. 

The bottom line is that this study is consistent with a suspicion that human activity contributed to rapid changes in post-glacial ecologies.  We also have abundant evidence that human activity is driving massive, rapid ecological changes today.  How similar are these two eras?  I’m not sure.  Are there lessons to be drawn from the past for today?  I’m not sure. 

But, do we really need to know that our ancestors killed off the Sabretooth cats 11,000 years ago; to know that we need to try to not kill off ourselves in the next century? 

Not really, no.

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1. Katrina Miller, Ancient Fires Drove Large Mammals Extinct, Study Suggests, in New York times. 2023: New York. https://www.nytimes.com/2023/08/17/science/climate-paleontology-mammals.html
2. F. Robin O’Keefe, Regan E. Dunn, Elic M. Weitzel, Michael R. Waters, Lisa N. Martinez, Wendy J. Binder, John R. Southon, Joshua E. Cohen, Julie A. Meachen, Larisa R. G. DeSantis, Matthew E. Kirby, Elena Ghezzo, Joan B. Coltrain, Benjamin T. Fuller, Aisling B. Farrell, Gary T. Takeuchi, Glen MacDonald, Edward B. Davis, and Emily L. Lindsey, Pre–Younger Dryas megafaunal extirpation at Rancho La Brea linked to fire-driven state shift. Science, 381 (6659):eabo3594,  https://doi.org/10.1126/science.abo3594

Dino v Mammal

Everybody knows that mammals lived in the shadows of the great non-avian dinosaurs before Chicxulub.  Mammals were small, creeping, nocturnal, egg stealers. 

But, of course, there were lots of mammals and lots of dinosaurs and lots of time.  So, who knows all the ways these animals interacted?

This summer researchers from Hainan and Canada report an astonishing fossil from the Yixian Formation, which appears to be a fight to the death between a mammal and a dinosaur [2]. Whoa!  

“The entombed individuals represent the small ceratopsian dinosaur Psittacosaurus lujiatunensis entangled with the even smaller gobiconodontid mammal Repenomamus robustus”

([2], p. 3)

The two skeletons are nearly complete, and they are coiled around each other.  Not only that, but they are biting each other! In fact, the researchers hypothesize that the mammal is attacking the dinosaur! Chomp!   

The natural interpretation is that these animals were fighting and were caught in a sudden volcanic event which rapidly buried them, preserving them together.

This fossil is amazing!  But is it too good to be real?

This kind of Hollywood find is often a fake, assembled into a cool story from separate fossils.   There have been fakes as long as fossils have been studied, and the researchers were properly skeptical.  One of the neat things about the paper is the careful analysis of the authenticity.

The rock matrix does seem to be from the specified location, and both skeletons are embedded in the stone together.  The team exposed one of the teeth still in the matrix, and found it was, indeed, embedded in the rib of the antagonist.

As Dr. Jordan Mallon put it, if it’s a fake, it’s “the best I’ve ever seen.” (quoted in [1])

Wow!

Now I would expect a version of this scene to show up in the next Jurassic Park sequel, “Jurassic Park: The Rechompment.  Did you call me an “egg stealer”?”

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1. Kate Golembiewski, This Fossil Is a Freeze-Frame of a Mammal Fighting a Dinosaur, in New York Times. 2023: New York. https://www.nytimes.com/2023/07/18/science/dinosaur-fossil-fighting-mammal.html
2. Gang Han, Jordan C. Mallon, Aaron J. Lussier, Xiao-Chun Wu, Robert Mitchell, and Ling-Ji Li, An extraordinary fossil captures the struggle for existence during the Mesozoic. Scientific Reports, 13 (1):11221, 2023/07/18 2023. https://doi.org/10.1038/s41598-023-37545-8

Stone Flakes Made by Monkeys

Speaking of stuff I learned in school long ago….

When I was an Anthropology major (a zillioin years ago), we spent uncounted hours learning about stone tools and what the different styles of stone mean.  How were they made?  Who made what?  What came first, what influenced what? 

Underlying this immense, and highly speculative, literature is the assumption that only humans make stone tools.  Indeed, for some, the creation and use of tools is the signature difference between humans and animals.  “Homo habilis” and all that. 

Since stone tools are long lasting, we know quite a bit about the history of stone blades and hammers.  The distribution of worked stone is interpreted as representing the presence and activity of different groups of humans.  Becasue they must have been made by humans.

For example, H. neanderthal left behind a characteristic style of stone artifacts, quite easy to distinguish from their H. sapiens neighbors’ stones.  (Even a relative dunce like myself can recognize a “Mousterian hand axe”.) These differences in their tools might reflect different life styles, different mental abilities, or simple artistic choice–no one knows.

Deeper in time, flaked stones and stone flakes could be just natural rocks or simple tools made by our ancestors.  Stone artifacts that can be identified as made by homonids can tell us where these ancients lived and what they did.  But it isn’t easy to be sure what is deliberately made, and what is just a rock.  Oceans of ink have been expended arguing about how to interpret ambiguous ancient stones.

This winter, an international team of researchers throw another curveball into this picture:  they report that a population of long-tailed macaques routinely use rocks to crack nuts [2].  This behavior sometimes accidentally cracks a flake off their hammerstone, leaving behind a characteristic flake, and a flaked stone. 

This isn’t intentional stone working, though the flakes look exactly like intentional stonework.  In fact, the distribution of these stones throughout the landscapce looks pretty much the same as putative pre-historic ‘lithic assemblages’ which have been interpreted as left by early human ancestors.

“In the absence of behavioral observations, the assemblage produced by monkeys would likely be identified as anthropogenic in origin and interpreted as evidence of intentional tool production.”

([2], p. 1)

Oops!

The presence of chipped stone is a whole lot more ambiguous than a lot of theories posit.  They may be natural breakage, they might be accidental byproducts, or they may be deliberate products.  And they might be made by humans or by other species (possibly even birds).  So they must be interpreted very carefully, and unfortunately probably cannot be used for precise dating of very old sites.

The observations of macaques also show that these “nonflaking percussive activities” ([2], p. 5) (which would be a great name for a band!) might be a precursor to deliberate stone working.  It makes sense to see stone tool making as an extension of existing stone hammering techniques that our ancestors shared with many other primates [1].

This hypothesis makes sense. People created the first stone tools by repurposing something people already knew how to do is clever, but incrementally clever.  Notably, learning to make stone tools involves a) “deliberate errors”, i.e., intentionally breaking a tool, and b) doing something clever with the mistake.  That sounds pretty human to me!

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1. Nell Greenfieldboyce, Stone flakes made by modern monkeys trigger big questions about early humans, in NPR News – Shots – Health News, March 10, 2023. https://www.npr.org/sections/health-shots/2023/03/10/1161652099/monkey-stone-flakes-early-humans-tools
2. Tomos Proffitt, Jonathan S. Reeves, David R. Braun, Suchinda Malaivijitnond, and Lydia V. Luncz, Wild macaques challenge the origin of intentional tool production. Science Advances, 9 (10):eade8159,  https://doi.org/10.1126/sciadv.ade8159

PS. “nonflaking percussive activities” would be a great name for a band!

Call Me “Mister Penguin”

After the Chicxulub catastrophe wiped out huge swaths of life on Earth, including most of the non-avian dinosaurs, life came back.  It took a while, and it was mostly new.  But it came back.

One of the new developments in this early recovery was the emergence of penguins:  birds that can’t fly through air, but fly underwater.  These animals seem to have originated in what is now New Zealand, where descendants still live. 

And with all the big animals extinct, there was room at the top.  So these successful birds got big.   Very big.

Restoration of Kumimanu biceae. (The new fossil, K. fordycei, is even bigger!)
(Credit: Nobu Tamura CC BY-SA 4.0, via Wikimedia Commons)

This winter researchers from New Zealand and elsewhere report yet another ancient ancestral penguin, Kumimanu (constructed from Maori words for “monster” and “bird”) [1].  From the recovered fragments, it’s hard to estimate the size of the living animal precisely, but it was definitely larger than contemporary Emperor penguins, and larger than other fossil penguins.  Big enough to look you in the eye and knock you down.  We’re talking something like a black bear.

The big guy (or gal) lived among other, smaller penguins.  The researchers speculate that the larger body size would not only protect from predators, but would retain body heat which would allow hunting in deeper, colder waters.  With no dinosaurs or whales around, this would be a niche.

These large penguins lived about 60 million years ago, i.e., right after the dinosaurs died out.  The larger penguins died out at the same time as whales and other marine mammals spread through the oceans.  This is probably not a coincidence.  These big, walrus-y penguins were probably out-walrused by mammals.

“The lack of spatiotemporal overlap between the largest known fossil penguins and similar-sized marine mammals is consistent with this hypothesis.”

([1]. p.18)

Cool.

The researchers speculate that these penguins are just about as big as a penguin can get [2].  (Incautious conclusions like this are just begging for even larger fossils to come to light! : – ))  Overall, it looks like penguins scaled up very quickly evolution-wise, spawning groups with very large size relatively early.  This might have been possible because of the relatively empty ecology after Chicxulub had many opportunities. 

Then, mammals evolved to inhabit similar niches, and quickly displaced penguins that directly competed.  Smaller penguins, which had been living beside large penguins continued to live beside similar sized mammals.

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1. Daniel T. Ksepka, Daniel J. Field, Tracy A. Heath, Walker Pett, Daniel B. Thomas, Simone Giovanardi, and Alan J. D. Tennyson, Largest-known fossil penguin provides insight into the early evolution of sphenisciform body size and flipper anatomy. Journal of Paleontology:1-20,  2023. https://www.cambridge.org/core/article/largestknown-fossil-penguin-provides-insight-into-the-early-evolution-of-sphenisciform-body-size-and-flipper-anatomy/8D4A78B2CA0A716134F8E60169A633FD
2. Jack Tamisiea, The Biggest Penguin That Ever Existed Was a ‘Monster Bird’, in New York Times. 2023: New York. https://www.nytimes.com/2023/02/08/science/giant-penguin-fossil.html

Neanderthals Hunted Elephants

By now, most of us realize that Neanderthals were capable of doing anything H. sap. can do.  But the archaeological record is, as always, sparse and ambiguous.  There are many things that Neanderthals did that left no trace, so we can only surmise. (Including, most of all, what kind of language they used.)

This winter, researchers in Germany and Netherlands report an analysis of a large deposit fossilized elephant bones from 125,000 years ago [1].  The presence of so many remains at a single site is evidence of something.  But what?

The site was definitely inhabited by Homo neanderthalis, and here as elsewhere, many of the bones show signs of humans butchering as well as scavenging by other carnivores.  It is likely that Neanderthals harvested meat from these bodies.  But did they hunt and kill them, too?  Or did they scavenge bodies they found?

This collection is especially important because there are enough specimens to perceive patterns.  And the most important pattern is that single, mature males are over represented.  The researchers argue that these animals may well have lived solitary lives as contemporary elephants do, and so could be hunted by relatively small groups with well-known techniques (e.g., pits or traps and stabbing spears).  Thus, the collection is consistent with human hunters picking off lone male elephants.

If so, then this site is a location where neanderthal people hunted and then butchered 6-10 ton animals.  The dating is uncertain, but the collection seems to show a kill every 5 years or so.  So—this behavior was not an accident.  This was a strategy and it was carried at least a few generations.

The researchers call attention to the implications of these observations.

Butchering such a large animal takes hundreds of person hours, several days at least, depending on the number of people participating.  And it produces thousands of meals worth of meat, enough to feed a small group for months, or a large group for a week or more.  This was not a small deal, this was a huge win—assuming that the meat could be harvested and used before it spoiled.

The researchers suggest two scenarios. 

One is that the kill was done and processed by a local group, 25 or so individuals.  (This is a common size for neanderthal groups.)  The butchering would take a week, and would produce months worth of food.  Exploiting the full animals would require the ability to preserve the meat through smoking, salting, or other means.  They would also likely remain in the same area for a relatively long time, as long as the meat held out. (No one knows what preservation techniques the neanderthal people knew and used.)

A second scenario would be that multiple small groups gathered together to process the kill.  This would include groups from a wide area coming together, amounting to several hundred altogether.  A larger group could process the animal in a day or so, and would have enough to eat for a week.  Such a gathering would, of course, be an opportunity for many kinds of exchange, including genetic.

Either scenario seems possible, and both are interesting.  Either way, this site indicated sophisticated expertise in not only regular hunting and gathering, but also in specialized hunting and handling of large targets.   As Britt M. Starkovich commented, “Neanderthals knew what they were doing. [2]”

Neanderthals knew what they were doing. They knew which kinds of individuals to hunt, where to find them, and how to execute the attack. Critically, they knew what to expect with a massive butchery effort and an even larger meat return. 

([2] p. 2)

If these folks returned again and again to the same area to do the same things, this was a deliberate strategy, continued for many generations. They definitely knew what they were doing. I’m certainly not surprised.

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1. Sabine Gaudzinski-Windheuser, Lutz Kindler, Katharine MacDonald, and Wil Roebroeks, Hunting and processing of straight-tusked elephants 125.000 years ago: Implications for Neanderthal behavior. Science Advances, 9 (5):eadd8186,  https://doi.org/10.1126/sciadv.add8186
2. Britt M. Starkovich, Perception versus reality: Implications of elephant hunting by Neanderthals. Science Advances, 9 (5):eadg6072,  https://doi.org/10.1126/sciadv.adg6072

Preserving Source Code for 1,000 Years?

I’ve been reading science fiction since I learned to read, so I am very, very familiar with post-apocalyptic life in all its many forms.  We’ve been imagining the “last people on Earth” for more than a century now, and I have to say that my own conclusion is “avoid this situation if at all possible.”  Rebuilding everything from scratch would be very hard work, and not likely to succeed.

There have always been people who want to act out these fantasies right now, at least partially, for a little while.  The basic back-to-the-land, dropping off the grid, simple life turns out to have a lot of permutations.  Many people are motivated by religious or ideological ideas, expecting and hoping for the unsatisfactory present to collapse, leading to a new age of moral renewal.

Others are driven by extreme self-interest, looking for personal immortality even in the face of the expected collapse of the unsatisfactory present.  Silicon Valley billionaires are particularly interested in life extension, pouring GDP levels of money into technologies that are intended to keep them alive for many current lifetimes, possibly “forever”.  (Unsurprisingly, they are able to find people who will take their money as long as they are willing to spend it, possibly “forever”.)

And then there are technologists who have a bug in their ear about how transient our current technology actually is.  Many of the great technical achievements of our civilization are invisible, and are already disappearing if not gone.

For instance, my own master’s project in the 80’s describes software written for an operating system that doesn’t exist anymore, in a language that doesn’t exist any more, running on computers that don’t exist, made by a company that doesn’t exist any more.  (The paper itself was supposed to be preserved on microfilm and maybe paper, but looking for it right now I can’t find any trace.  It probably still exists, but it’s certainly not readily accessible. Not that you or anyone needs to see it.)

A more important example is the US National Archives, which is required by law to preserve “historically significant” materials,.This certainly should include many aspects of the space program, such as the software from the Apollo moon landings.  Software that was written for an operating system that doesn’t exist any more, etc., etc.

Most of us don’t worry too much about this.  I mean, I’m just as happy that the world can’t see my youthful follies.  I don’t take myself  or my own work all that seriously.

But, some people are concerned that this short-term mentality is harmful.  Indeed, not thinking that our actions will matter in a thousand or more years is a good way to, say, fill the atmosphere with CO2 and melt all the ice.  Or carelessly wipe out all living things that, oops, make human life possible.

And, of course, some people are just romantically attached to the notion of creating something that will last a thousand or ten thousand years.  Aside from the archivists’ reflexive desire to preserve a record of our civilization, there is a certain super villain-ish desire to have future beings know your works.  (See Ryan North, Chapter 9.)

Can you say, “hubris”?

This fall I read about an interesting effort along these lines, The GitHub Arctic Code Vault.  Conceptually, this is an effort to preserve a snapshot of the GitHub open source software to be readable in 1,000 years [2]. Physically, this is a steel vault containing images (on tape?) of QR codes that record source code from Github.  The vault is located near the Borgen Seed Bank, geographically and psychologically.

A lot of thought has gone into the design.  The outside is decorated to make it attractive, i.e., to encourage you to believe that it is valuable and to look inside [1].  (This is the inverse of the principle that radioactive waste stores should be repulsive—highly visible but not at all inviting.)

So what’s in it?  It contains a snapshot of every github project active on 02/02/2020.  This is millions of projects, from huge, important things like linux, to tiny, little used dinks.  Github projects generally include source code, documentation, test data, and metadata about who did what.

This snapshot was apparently encoded in QR codes which are stored on long lasting tapes.  The QR codes can be decoded by eye if necessary, and are relatively robust to minor damage like scratches or stains.  I.e., you can reconstruct what’s on a QR code even if it’s a bit crumpled.

“On 02/02/2020 GitHub captured a snapshot of every active public repository.”

(From The Archive Project)

There is also documentation explaining how to read QR codes and what Github is.  Apparently, there is also a small library of “how to” books. And a copy of wikipedia!  And, interestingly, an almost completely random collection of fiction

Phew!  Can you say, “hubris”?

Obviously, any effort to create this kind of time capsule must face long odds that it will survive at all, and if it survives, someone will notice it, and if noticed, will be interpreted in any meaningful way.  Archaeology is full of lost artifacts, ignored artifacts, and artifacts that are not understood or comically misunderstood.

It’s not nice to root against them.

But I can’t help wondering if I even want them to “succeed”. 

Of course, there are plenty of technical quibbles.  QR codes may be ubiquitous today, but they weren’t around even 50 years ago, and probably won’t be in another fifty.  And if you don’t use digital computers—because quantum computing—what does a “QR encoding” of data even mean?

I have to wonder about the art work that is supposed to be alluring. Artistic taste is notoriously fickle, so it’s got to be a crap shoot trying to appeal to a completely unknown audience in a completely unknown context.

But anyway.

I’ll also note that survival for 1,000 years generally doesn’t hinge on putting stuff in a single, very pretty box.  That’s a formula for getting it looted.  If you want something to last 1,000 years you want there to be many, many copies; stored in many, many media; with lot’s of cross references so people know that it exists and what to look for.  (See, for example, the account of the rediscovery of Lucretius.)

For that matter, the entire idea we call “source code” has changed rapidly over the last 70 years, and surely will change in the near future.  When I was a lad, “source code” was something that mostly came in big, heavy boxes of punched cards.  Twenty years ago it came on portable disks.  These days it comes from github.  Who knows what it will look like inf the future?

Worse, the actually ideas expressed in what we call “source code” has evolved dramatically.  When I was a lad, we were moving tiny bits of data around tiny little computers. (OK, the computers were physically huge, but they were logically tiny).  And we had to code everything.  Now we can move around preposterous amounts of stuff with a few lines, and we generally use components to sub-contract out lots of detail.  Plus, our source code resides thousands of kilometers away from the computers where it runs. (And, by the way, we might well not even know where it executes.) Who knows what we’ll do in the quantum future.

The point is, even if I had the source code from 1972, it would be gibberish to me because it did something totally different than code I write today to accomplish the same thing. Stuff works different.

In short, there is good reason to wonder if future historians will be able to even understand what this archive is about.

qua githubAnd then there is the whole thing about github.  Yes, github is extremely popular.  This is a huge sample of software.  But is it a representative sample?  Of the millions of projects included, all but a few are basically trivial.

And, of course, most software is not open source, let along stored in github.  The entire idea of “open source” is controversial, contested, and ever changing.  This is a sample, of software, but what does it represent?

And then there is the “cultural” context.  The archive includes a bunch of “how to” books which you have to wonder about.  Telling people 1,000 years from now how computers worked a few years ago seems like a pretty pointless thing.  If they have computing, it will work differently than our stuff.  If they don’t, then they probably won’t understand, and arguably don’t need to understand our stuff.

And no, the details of say, Python or Ruby, are not timeless gems for the ages. Most of the details are messy and, frankly, it is embarrassing to think they might be examined by future archeologists.

And then there is the “cultural context”.  Wikipedia is awesome, but it isn’t everything.  And it’s pretty clear that you couldn’t reconstruct our civilization from Wikipedia.  It’s an interesting question what you actually would understand, if you just had Wikipedia (even setting aside technical details of language and encoding).

There is also an eclectic collection of other materials, including a tiny handful of fiction.  It’s a weird collection, for sure.  It like like a 16-year old’s summer reading list.  In the UK. In 1999.

This list is supposed to convey “the history and culture of our time”. Hmm.

Why is “I, Claudius” in this list?  Even more disturbing, why is “1984” here?  Just what would you think about “our time” from “Crime and Punishment”, “The Complete Works of William Shakespeare”, and Homer’s poems translated to English?

There are no git repositories of source code in any of these works.  It’s going to take a lot of head scratching to figure out what these have to do with the stuff in this vault. (Because they have nothing to do with it.)

The point is, to accomplish this 1,000 year mission, there are huge, huge semantic gulfs to overcome.  Even if the material is technically accessible, I have to wonder what, if anything, future accessors might actually understand. 

And here’s a real puzzler for future readers.  Github is really, really ethnocentric.  It is dominated by the English language, it is part of a sub-culture that shares an array of conceptual ideas about technology, society, and human life. 

For example, even if you know a bit about the early twenty first century, you don’t necessarily know anything about, say, how “Linux” got its name.  So it’s going to be a hell of a job trying to grok these QR codes, that’s for sure.

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Overall, the odds of success are low.  And it’s not even clear what this might accomplish if it does “succeed”. 

Personally, I consider it a waste of time and resources.  (The seed banks are not a wasted effort, though they are just as much a long shot.)

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1. Jon Evans, “If you don’t make it beautiful, it’s for sure doomed”: putting the Vault in GitHub’s Arctic Code Vault, in Github Blog, September 20, 2022. https://github.blog/2022-09-20-if-you-dont-make-it-beautiful-its-for-sure-doomed-putting-the-vault-in-githubs-arctic-code-vault/
2. Liam Tung, Open-source software that lasts a thousand years? GitHub adds to its frozen Arctic Code Vault, in ZDNet, September 21, 2022. https://www.zdnet.com/article/open-source-software-that-lasts-a-thousand-years-github-adds-to-its-frozen-arctic-code-vault/