Tuesday, September 24, 2019

Denisovans More Closely Related to Modern Humans than Neandertals

Science Daily has a post relating recent research on the genetic studies involving the Denisovan material from Siberia.  The research, done by CNRS in France has this to report:
Now a team of scientists from the Institut Jacques Monod (CNRS / Université de Paris) has measured and photographed another fragment found in Denisova Cave. Genomic analysis reveals it is the missing piece of the same phalanx whose proximal fragment enabled initial sequencing of the Denisovan genome.

Together with colleagues from the PACEA laboratory (CNRS / University of Bordeaux / French Ministry of Culture) and the University of Toronto (Canada), the scientists compared the new fragment to the phalanges of Neanderthals and anatomically modern humans. Their analysis indicates it is very close to the latter, and less like the former..
This research suggests that there was considerable population mixing and genetic variability in this population, given the news that came out last year detailing the finding of a child skeleton that was, as nearly as the researchers could tell, the offspring of a Neandertal and a modern human.This just continues to solidify the idea that these groups interbred routinely throughout the late Pleistocene. 

Wednesday, August 21, 2019

More Information About the Denisovans

Discover Magazine has an article on new finds at Denisova and their context in early modern human evolution.  Bridget Alex writes:
Nestled in foothills of Russia’s Altai Mountains, Denisova Cave has been a research mecca since 2010, when fossil DNA from the site revealed a previously unknown human lineage, now called the Denisovans. Scientists have been working hard to reconstruct the cave’s history, through ongoing excavations as well as new analyses of materials recovered years ago.

First, what everyone wants to know: Yes, they found more human remains. In addition to the four Denisovan specimens (one pinky finger, two adult molars and a baby tooth), the cave has yielded 12 fossils from ancient humans, including teeth, toes, fingers and unclassifiable fragments.

Based on their genomes, proteins and physical appearance, the collection contains four Denisovans, three Neanderthals and one hybrid cross between the two human types. Excavators have also found four more fossils that belong to the Homo genus, but haven’t yet been assigned to a particular human species. Additional DNA sequences, recovered directly from the dirt, suggest the presence of even more individuals.
As reported last year, Denisova 11 has been determined to be the offspring between a Neandertal mother and Denisovan father. As with other finds in Asia, we are finding that there appears to have been considerable population mixing over the course of at least 100 thousand years. Although the article indicates that the Neandertals were “sandwiched” in between two modern human occupations, that is difficult to square with any hybridization model. I suspect that the habitation patterns were more complex.

Wednesday, August 07, 2019

Space X Launch Fails After Rocket Bounces Off Firmament

I think I worried my family last night by laughing so hard at this story that they thought I was going to herniate.  Those of you who follow the news know that Babylon Bee is in a tussle with Snopes about whether or not their stories constitute “fake news.”  Anyone with two grey cells to rub together knows the difference, including Snopes, but they are trying to get the Bee de-platformed because quite a few of the Bee's stories point out the idiocy of some of their favorite political positions.

Anyway, the Bee is not above poking fun at just about anything in the Christian world and I missed this story when it came out.
A SpaceX launch ended in tragedy Thursday as the rocket intended to carry a cellular satellite into orbit around the earth bounced off the firmament described in the opening chapters of Genesis, sources confirmed.

The rocket accelerated higher and higher above the flat earth and toward the sun and moon a mere 3,000 miles away before suddenly bouncing off the glass-like dome containing the earth.

“We totally didn’t see this coming,” a SpaceX launch expert told reporters moments after the crash. “Where we seem to have gone wrong is in using NASA’s fake globe model rather than employing flat-earth models drawn by conspiracy theorists operating off ultra-literalist readings of the King James Bible.”

“We won’t make that mistake again, I tell you what,” he added.
They manage to skewer the literal reading of Genesis and the biblical evidence for a flat earth in one post.  Many Christian writers, including Phil Senter and John Walton, have written about the language describing the firmament and have argued (persuasively, in my opinion) that it can only be read as a hard dome because that is how the ANE people saw it. 

Humor at its best.

Friday, August 02, 2019

Lutheran Church Tackles Creation Days

Christian Post has an article on the recent Lutheran Synod resolution involving the “creation days.” Michael Gryboski writes:
The Lutheran Church—Missouri Synod passed a resolution at their convention affirming the belief that God created the Earth “in six natural days.”

At the 67th Regular Convention of The Lutheran Church—Missouri Synod on Tuesday, the theologically conservative denomination adopted Resolution 5-09A, titled “To Confess the Biblical Six-Day Creation.”

“We confess that the duration of those natural days is proclaimed in God’s Word: ‘there was evening and there was morning, the first day,’” resolved the resolution.

The resolution also declared that the creation of Adam as the first human being was a “historical event” and rejected the claims of the theory of evolution.
As noted in the article, there is some debate about what the word “natural” means in this context.
Another delegate expressed concern over the alleged “lack of clarity” on the definition of the word “natural” as used in the resolution.

Supporters responded that the term “natural” was defined by the Bible’s own words, describing the days as having an evening and a morning.
This has always struck me as a peculiar defense given how the scriptures actually reads:
14 And God said, “Let there be lights in the vault of the sky to separate the day from the night, and let them serve as signs to mark sacred times, and days and years, 15 and let them be lights in the vault of the sky to give light on the earth.” And it was so. 16 God made two great lights—the greater light to govern the day and the lesser light to govern the night. He also made the stars. 17 God set them in the vault of the sky to give light on the earth, 18 to govern the day and the night, and to separate light from darkness. And God saw that it was good. 19 And there was evening, and there was morning—the fourth day. (Genesis 1:14-19, NIV)
Every translation reads pretty much the same way.  That happens on the fourth day. Without the sun and moon, you cannot have “evening and morning.”  There is no reasonable context for it.  To argue this implies that the entire universe revolves around a 24-hour earth day.  We know this is not so.

It is notable that the vote was 662 in favor and 309 against, so there is quite a bit of dissent about the resolution.  The rider involving evolution, while not taking center stage, is a slap in the face to those congregants who accept it.  The rising science of coalescence theory is hard to square with the idea of Adam and Eve being the first humans.   As Dennis Venema and Scot McKnight put it in their book Adam and the Genome,
As our methodology becomes more sophisticated and more data are examined, we will likely further refine our estimates in the future. That said, we can be confident that finding evidence that we were created independently of other animals or that we descend from only two people just isn’t going to happen. Some ideas in science are so well supported that it is highly unlikely new evidence will substantially modify them, and these are among them: The sun is at the center of our solar system, humans evolved, and we evolved as a population.
I always find it somewhat interesting that these large denominations fight tooth-and-nail over social issues that are somewhat fluid in society, such as homosexuality and female ordination, and yet, for issues in which there is actually hard, scientific evidence, retreat to a very flat, conservative interpretation of scripture.

Interestingly, the new T-shirt being issued by the Evangelical Lutheran Church of America celebrates both science and LGBT rights.  That is not true for the science part.

Sunday, July 28, 2019

New Poll From Gallup on Human Origins

Gallup has released a new poll on what people think about human evolution.  Here is their takeaway blurb:
Forty percent of U.S. adults ascribe to a strictly creationist view of human origins, believing that God created them in their present form within roughly the past 10,000 years. However, more Americans continue to think that humans evolved over millions of years -- either with God's guidance (33%) or, increasingly, without God's involvement at all (22%).
Beyond this are details in the numbers.The poll was conducted from June 3-16 and contained a random sample of 1015 adults.  Some of this is not new and has changed little since the last poll.  There is a high correlation between those with a college education and those who accept human evolution.  The correlation is also high between those who have no religious affiliation and those who accept human evolution.

Other interesting tidbits from the attached PDF:
  • Acceptance of God-guided human evolution does not seem to change with political party affiliation, gender or ethnic background
  •  Acceptance of God-guided human evolution rises only slightly with age
  • The idea that God created humans in their present form drops substantially from 55% (Republican) to 34% (independent and Democrat) as well as ideology (54% Republican, 29% democrat)
There are more observations buried in the data. Have a look.

Saturday, July 27, 2019

Chris Stringer: Meet the Relatives

Chris Stringer has a post in the Financial Times titled Meet the Relatives.  It is sort of a whirlwind tour through the evolution of the genus Homo.    He writes:
The discoveries of Homo floresiensis, Homo luzonensis, Denisovans and Homo naledi in the past 15 years remind us that the fossil record of humans is still very patchy — stone tools are scattered across much of Africa as a witness to widespread human occupation, yet fossil evidence has been recovered from less than 10 per cent of that continent’s area.

The percentage coverage for Asia is hardly any better: there is, for example, currently only one significant human fossil from the whole of the Indian subcontinent. The discoveries of the past few years underline just how much evolutionary history remains unknown, with other extinct lineages no doubt still to be revealed.

Many of the new finds challenge how we classify fossils in relation to Homo sapiens today. I continue to call the Neanderthals a different species from us, based on their distinctive skeletons and skulls; others feel that the recent evidence of interbreeding and increasing evidence of sophisticated behaviour mean that we should merge them, and the Denisovans, into our species.
I think that the discovery of the Xuchang hominins indicates that there has been considerable population mixing for several hundred thousand years.  As I wrote at the time:
These two Chinese skulls stand at the crossroads of these population movements. While showing clear Neandertal characteristics, they also express modern traits, possibly reflecting mixing with the late, modern human arrivals represented by the recent modern human finds at Daoxian. Yet they also express a clear link to ancient East Asian populations. The implications of these skulls are stark: there has been widespread population mixing and regional continuity in Europe and Asia for at least 400 thousand years. Not only did the Neandertals feel enough cultural kinship to mate and have children with these East Asian people, the early modern humans coming out of Africa did, as well. As Chris Davis of China Daily News put it: “One big happy family.”
Whether this represents such behavior at the peripheries of different species or that of one polytypic species is, as yet, unclear.  It is very clear that our understanding of how these populations interacted is rudimentary, at best. 

Friday, July 26, 2019

Earliest Art Made By Humans?

Artnet News has a post on a discovery in Henan Province, China that purports to be the oldest indications of consciously-created art.  From Sarah Gascone:
Abstract patterns carved on bone fragments discovered in China could be the oldest art ever made, dating back to between 105,000 and 125,000 years ago.

The marks on two bones were found at a site in Henan Province thought to be populated by Denisovans, an extinct species or subspecies of ancient humans, according to a new study in the Cambridge University Press journal Antiquity. The markings on the weathered rib bones contain traces of ochre on one specimen, the earliest evidence of pigment’s use for decorative purposes.

The newly discovered artworks pre-date even the 73,000-year-old markings—thought by some to be abstract drawings—found last year on a rock excavated from a South African cave, and previously thought to be the earliest-known example of human artistic activity.
Here is an image of the markings:

Photo Credit: Francesco d’Errico and Luc Doyon.

There seems to be a persistent thought that people of this age simply could not make art of this kind. I think it more stems from the fact that this kind of representation rarely survives in the fossil record. We know that as far back as 300k, there was division of labor and that there was quite a bit of population mixing this far back.  There is also a record of Neandertal cave paintings at 65k.  It is nice to find this kind of artistic expression but it ought not to surprise us. 

Tuesday, July 09, 2019

DNA Proteins Revealing Information About Human Evolution

Since the advent of population genetics and modern techniques to examine DNA, research has focused on, first, Mitochondrial DNA and then nuclear DNA.  Now we have another weapon in our arsenal.  Matthew Warren of Nature News relates new research done on palaeoproteomics.  This is the study of proteins found in fossilized human ancestors.  How is this possible, you ask?
Some time in the past 160,000 years or so, the remains of an ancient human ended up in a cave high on the Tibetan Plateau in China. Perhaps the individual died there, or parts were taken there by its kin or an animal scavenger. In just a few years, the flesh disappeared and the bones started to deteriorate. Then millennia dripped by. Glaciers retreated and then returned and retreated again, and all that was left behind was a bit of jawbone with some teeth. The bone gradually became coated in a mineral crust, and the DNA from this ancient ancestor was lost to time and weather. But some signal from the past persisted.

Deep in the hominin’s teeth, proteins lingered, degraded but still identifiable. When scientists analysed them earlier this year, they detected collagen, a structural support protein found in bone and other tissues. And in its chemical signature was a single amino-acid variant that isn’t present in the collagen of modern humans or Neanderthals — instead, it flagged the jawbone as belonging to a member of the mysterious hominin group called Denisovans. The discovery of a Denisovan in China was a major landmark. It was the first individual found outside Denisova Cave in Siberia, where all other remains of its kind had previously been identified. And the site’s location on the Tibetan Plateau — more than 3,000 metres above sea level — suggested that Denisovans had been able to live in very cold, low-oxygen environments.
As the author notes, this kind of research has opened many other doors that, up until now, have been shut to researchers. The realization that proteins have much longer staying power than DNA could radically reshape our understanding of human evolution:
Previously, scientists had recovered proteins from 1.8-million-year-old animal teeth and a 3.8-million-year-old eggshell. Now, they hope that palaeoproteomics could be used to provide insights about other ancient hominin fossils that have lost all traces of DNA — from Homo erectus, which roamed parts of the world from about 1.9 million to 140,000 years ago, to Homo floresiensis, the diminutive ‘hobbit’ species that lived in Indonesia as recently as 60,000 years ago. By looking at variations in these proteins, scientists hope to answer long-standing questions about the evolution of ancient human groups, such as which lineages were direct ancestors of Homo sapiens.
Whether that level of resolution will ever be possible remains to be seen, especially given that the modus operandi of modern palaeontology is focused on clade relationships. It will be interesting to see.

Monday, July 08, 2019

Patterns in the Fossil Record

Science Daily has a post on research about patterns in the fossil record that comes out of the Santa Fe Institute.  They write:
Throughout life's history on earth, biological diversity has gone through ebbs and flows -- periods of rapid evolution and of dramatic extinctions. We know this, at least in part, through the fossil record of marine invertebrates left behind since the Cambrian period. Remarkably, extreme events of diversification and extinction happen more frequently than a typical, Gaussian, distribution would predict. Instead of the typical bell-shaped curve, the fossil record shows a fat-tailed distribution, with extreme, outlier, events occurring with higher-than-expected probability.

While scientists have long known about this unusual pattern in the fossil record, they have struggled to explain it. 
Now, at last, there is something of an answer.
“Within a lineage of closely related organisms, there should be a conserved evolutionary dynamic. Between different lineages, that dynamic can change,” says [Andy] Rominger. “That is, within clades, related organisms tend to find an effective adaptive strategy and never stray too far. But between these clade-specific fitness peaks are valleys of metaphorically uninhabited space. It turns out, just invoking that simple idea, with some very simple mathematics, described the patterns in the fossil record very well.”
Sometimes, it just pays to rethink something from a different angle. This may open up doors to understanding other patterns in the fossil record.

Sunday, June 30, 2019

Neandertals Occupying Open-Air Site in Israel

There is evidence of Neandertal occupation at an open-air site in northern Israel called Ein Qashish.  From the researchers:
Whereas many open-air settlements are thought to be short-lived and chosen for specialized tasks, 'Ein Qashish appears to be the site of repeated occupations each of which hosted a range of general activities, indicating a stable and consistent settlement system. The authors suggest that within a complex settlement system, open-air sites may have been more important for prehistoric humans than previously thought.
The vast majority of Neandertal sites in France and the Levant are cave sites so this represents a sharp contrast in societal behavioral patterns.  The site appears to have been repeatedly occupied by Neandertals from around 70 to possibly 54 thousand years ago, representing potentially an 18 thousand year span, although the span is probably 70-60 kya.  Although the hominin remains at the site are fragmentary,  a designation of Neandertal was made based on the morphology of a third molar and a complete femur. 

This is more evidence that Neandertal society and life-styles were much more complex and advanced than most researchers have allowed.

Here is a link to the open-access PLoS ONE paper, Persistent Neanderthal occupation of the open-air site of ‘Ein Qashish, Israel.