Thursday, October 19, 2017

Book Purchase: Adam's Quest

I hate it when books come out that escape my attention.  Such is the case with a book titled Adam's Quest, by Tim Stafford.  In it, Stafford has interviewed eleven scientists who have struggled with their understanding of how their faith fits in with their pursuit of science.  In a sense, this is like the book Four Views on the Historical Adam, in that it surveys Christians from different perspectives.  He has interviewed young earth creationists, supporters of intelligent design and evolutionary creationists.

As readers of this blog will note, I have been extremely critical of young earth creationists and intelligent design supporters, not so much for their beliefs (which I also find issue with, though) but for their ham-handed and often deceptive way in which they treat the scientific evidence for an ancient earth and evolution.  At least Todd Wood, one of the assembled scientists, has also had issue with this and, from what little I have read of Kurt Wise, he has as well.

Patheos has a short introduction to the book, which focuses on the first group, the young earth creationists, and some of their consternation at the way that science is examined.  There is a passage with a particularly damning quote from Kurt Wise about this:
After that, Wise lost interest in creationist apologetics, especially as he began to realize that many of the creationist evidences from his reading were wrong. “At first I thought it was ignorance.” As he learned more though, he became convinced that the mistakes in creationist literature were willful. … Wise concluded that for many creationists the end justifies the means. For them, “it doesn’t matter if what you say is true. It matters if it brings people to the right conclusion.” (p. 15-16)
This is, perhaps, why I find people like Ken Ham and his organization, Answers in Genesis so contemptible. They pretend to address the scientific concerns in an honest way but misinterpret evidence, arrive at faulty conclusions and smear hard-working scientists as a matter of course.  As i just told my oldest child, I am not going to come right out say they are lying, but it sure looks like it. 

Perhaps one of the scariest parts of the book and one of the principle reasons that I picked it up are in the sample that is available from Amazon, in which the author recounts his upbringing, which is almost word-for-word what I experienced growing up.  He then recounts every Christian parents' nightmare: the falling away from the faith of one of his children, in part because of the strains of learning correct science and being told that he could not be part of his circle of church friends if he continued to accept an old earth. 

Right now my children are in a home school group that is heavily young earth creation-based and I know that several of the parents of their friends would be horrified if they knew that I was an evolutionary creationist.  I simply don't advertise it. One of them thinks of Ken Ham as a hero of the faith.  How would it be of value for me to confront her with the notion that I think he is a charlatan and a heretic? 

As of yet, my oldest child does not seem to be tracking in any scientific direction so I doubt that this will have a huge impact on his life.  The same does not seem to be true with my second child, who is enamored with botany.  She will hit evolutionary biology head-on in college and I will have to prepare her for that and how to hold onto her faith throughout.  That will be, perhaps the greatest challenge that faces me. 

I look forward to reading this book with interest and would encourage downloading the sample.

Thursday, October 12, 2017

Uh Oh

Answers in Genesis is expanding into Canada, according the its leader, Ken Ham.  Patheos reports the following:
Answers in Genesis, the Creationist ministry run by Ken Ham, is evolving. Ham says that an Answers in Genesis–Canada is scheduled to open in 2018, with an online store launching earlier. It’ll be run by Calvin Smith, an Ontario native who has spoken about Creationism at churches across the nation since 2001.
From the Answers in Genesis website:
According to a recent study, a mere 15% of Canadians have any kind of creationist belief. The church there desperately needs AiG resources to be equipped to stand on the authority of the Word of God and boldly preach the gospel. We’re excited to be part of encouraging and equipping our Canadian brothers and sisters through speaking events, resources, conferences, and more.

AiG produces the world’s leading creation-apologetics resources including books, DVDs, curricula, the Answers Bible Curriculum (used in over 10,000 churches), and one of the top Vacation Bible School (VBS) programs used by over 5,000 churches last year.
For those of us who view Ken Ham's efforts in this direction with great apprehension, this is not good news. As Joel Edmund Anderson and Ted Davis note, Ken Ham preaches heresy and revisionist history. The more I read of the AiG site, the more I am convinced this is true.It is worth quoting Anderson again, here:
The heresy of Ham that is actively “subverting, destabilizing, and destroying” the core of the Christian faith is the claim that a modern, scientific interpretation of Genesis 1-11 as literal history is fundamental prerequisite for the trustworthiness of the Gospel of Christ. It is the claim that if the universe is not 6,000 years old, if there was no historical Adam and Eve, and if there was no worldwide flood 4,000 years ago, then that would make God a liar, that would mean there is no such thing as sin, and that would mean Christ died for nothing. Such a message is heresy, and that message has subverted, destabilized, and destroyed the Christian faith of many people, has destroyed careers, and unfortunately, has taken root within a significant portion of Evangelical Christianity.

Wednesday, October 11, 2017

Taboo on Incest May Go Back at Least 34K Years

ZME Science is reporting on a study done from the site of Sunghir, in Russia that preserves “complex social structures,” indicating that, even at 34,000 years ago, there were precautions against inbreeding. Why do we think this?
The Upper Paleolithic burial site contains the complete remains of an adult male, the symbolically incomplete remains of another male, as well as those of two younger individuals. All of these people lived at this site during the same time. Unusual for similar finds from this period, all the four males were buried together.

When a team of scientists at the Cambridge University and the University of Copenhagen analyzed the genomes of these individuals, they were surprised to find they were not closely related. At most, one of the adults was no more related to the boys than a great-great-grandfather.

The researchers speculate that artifacts found at this location, which includes pieces of jewelry, may have been used in ceremonies and rituals that celebrated the exchange of mates between groups. Perhaps such exchanges foreshadowed modern marriage ceremonies.

In addition to the evidence that modern humans formed close-knit communities more than 30,000 years ago, this evidence also indicates that they deliberately sought mates beyond their immediate family.
Humans changed from a promiscuity-based relational strategy to pair-bonding at some point in their evolutionary history, which resulted in more stability.  Read the whole thing. 

Tuesday, October 10, 2017

The Effect of Neandertal DNA on Modern Humans

After the 2013 sequencing of the Neandertal DNA, Janet Kelso, of the Max Planck Institute undertook a study to see what genes present in Neandertals still had an effect on modern humans.  The study employed the data from a genotyping project done by UK Biobank, which surveyed 500,000 people.  What did they find? 
Kelso and her team first narrowed the sample to include only the 112,338 individuals with white European ancestry (whose genomes contain Neanderthal DNA), and used these data to tease out which traits are influenced by Neanderthal genetic variants. The traits they identified included those that affect hair color, skin color, skin tanning and burning, sleeping patterns, mood, and tobacco use.

For example, being a self-described night owl and being prone to daytime napping were both traits positively influenced by Neanderthal variants, as were loneliness, low mood, and smoking. Genetic loci associated with having red hair were found to be devoid of Neanderthal variants, suggesting red-headed Neanderthals were either rare or non-existent. The new study also supports Capra and colleagues’ previous observations that Neanderthal variants are associated with sun-induced skin lesions, mood disorders, and smoking.

That traits such as skin color, sun-burning, and sleep patterns were identified by the analyses might be explained by the Neanderthals’ adaptations to life at more northern latitudes, suggests Capra. But for other traits, he notes, determining how the effects seen in present-day people might once have affected Neanderthals themselves “is one of our crucial challenges.” For example, he says, “of course, Neanderthals were not smoking.”
Maybe I am behind the times but I did not know there was a “trait” for tobacco use. I figured you either did that or you didn't. Like Robin Williams says in Dead Again: either be a smoker or don't be a smoker. Choose it and be it.

I suspect we will continue to find effects of the Neandertal genome, especially since our understanding of how much interbreeding there was continues to change.  It is also a testament to the stability of the human genome that, even after a separation of some several hundred thousand years, interbreeding was still possible.  

Friday, October 06, 2017

Creation Museum Having Positive Impact on Economy of Florence, KY is running a story about the impact that the Creation Museum is having on the economy of a nearby town, Florence, Kentucky.  Chris Mayhew writes:
Comfort Suites opened 84 rooms off Houston Road at 5905 Merchant St., Florence, in July. A busload of tourists from Alabama visiting the Creation Museum and Ark Encounter filled 24 Comfort Suites rooms for three days Sept. 27-29.

Tourism for Newport on the Levee, Downtown Cincinnati and the Creation Museum bring regular visitors, owner Ravi Narsinghani said.

Comfort Suites was Narsinghani's second hotel in Florence he owns with his brother. The brothers will open a third Florence hotel soon.

"We have an upscale extended stay coming," he said.
It is good that the local economies are getting a needed boost from this, even if it is for the wrong reasons.

Thursday, October 05, 2017

NCSE Post Reflecting on Kitzmiller, Twelve Years Later, by Eugenie Scott

NCSE has a guest post by Eugenie Scott, in which she remembers some of the points about Kitzmiller that might not have been public at the time.  It is part one of two.  In the run-up to the Kitzmiller trial, the plaintiffs did not know who the judge would be:
Well, the case was assigned to John E. Jones III, a fiftyish Republican who had been appointed by George W. Bush to the federal bench a few years before. “Intelligent design” proponents were delighted! In their blogs, they were quick to point out that Jones was a mover and shaker in Pennsylvania GOP politics, was a self-described conservative Republican, and was a church-going Lutheran, who certainly would be likely to find the ID policy constitutional.

I must say, our lawyers, who pay attention to judges more than we science types do, were a little apprehensive. What was this guy going to do? He’d only been a federal judge for a couple of years, so there wasn’t much of a record to go on.

His being a person of faith wasn’t an automatic concern. It’s so easy to misconstrue the creationism/evolution controversy falsely as “science versus religion,” when really it is one particular religious perspective versus everyone else’s. People are sometimes surprised to learn that our best allies in support of teaching evolution are other Christians: Catholics and mainstream Protestants— such as Disciples of Christ [with which Transylvania University is affiliated]—don’t want children taught Monday through Friday in science class that God specially created the universe in its present form 6,000 years ago, and then have to straighten them out on Sunday—because their theology is that God created through evolution.
One of the things that came out of the trial was how much the defense lied about what their true motives were. Although her post does not mention these events, it is an interesting account.

Wednesday, October 04, 2017

Why Is Homo floresiensis Still Such a Mystery?

Cosmos Magazine has an article by Debbie Argue, biological anthropologist from Australian National University, about Homo floresiensis and why it has been a struggle to accurately and adequately place this hominin within the framework of human evolution.

 Here was the initial assessment:
Peter Brown and colleagues originally proposed two competing hypotheses about the origins of H. floresiensis. One is that the species is an early hominin similar to the earliest identified in the Homo genus. The fossils for these species are known only from Africa and are between one and two million years old. This implies that the ancestors of H. floresiensis could have got to Flores Island in the vicinity of a million years ago and survived there until at least 60,000 years ago.

Their alternative hypothesis was that H. floresiensis is a dwarfed descendant of Homo erectus, which is the only known non-sapiens hominin to once have existed in Indonesia. Its remains have been found on the island of Java. According to this view, the dwarfing of H. erectus was an evolutionary response to being isolated on an island with a limited food supply. Just as the Asian elephant evolved into the dwarfed Flores stegodon after becoming marooned on the island, H. erectus could have met a similar fate.
It was also proposed that this hominin might have expressed microcephaly.  This idea failed to explain other aspects of the skeleton, however, such as its diminutive height (around 3 feet), long arms and feet and primitive skull features. Here is an image of H. floresiensis compared to a modern human, who had been running around the landscape for at least 100k years while H. floresiensis was extant.

This all saw at least some resolution with the discovery and description of some remains  on another areas of the island Flores that were very similar to the H. floresiensis remains but dated to some 600 thousand years earlier than the remains in Liang Bu.  This lent more credence to the idea that H. floresiensis was, in fact, an offshoot of Homo erectus.

So, Argue, along with Colin Groves, Bill Jungers and Mike Lee, performed statistical tests (this story does not say which kind, a peculiar omission) on a number of different hominin species, comparing them to H. floresiensis.  What did they find?
We therefore hypothesise that H. floresiensis shared a common ancestor with H. habilis. We do not know who that ancestor was or when it lived, but it would have to be older than the oldest H. habilis specimen known, so older than 1.75 million years. The implication is that the H. floresiensis ancestor evolved before that time in Africa, dispersed from that continent, and arrived on Flores earlier than 700,000 years ago, judging by the age of the jaw and teeth found at Soa Basin. This represents a hitherto unknown movement of very early hominins out of Africa.
Presently, the earliest evidence for hominins outside of Africa come from Europe, the Near East and Asia, and date to between 1.5 and 1.8 million years ago. Argue's hypothesis would suggest that H. floresiensis appearance in east Asia represents a separate migration out of African sometime either before or after the wave that saw Homo erectus show up in Trinil and Sangiran, in Indonesia.

Questions still abound as to why this species never saw the evolutionary trajectory that other hominins went through in terms of cranial expansion, increase in height and changes in brachial and crural indices. On the other hand, if evolution proceeds through what we have termed systematics, then advanced traits will show up in related species and if the ancestors of H. floresiensis were cut off, they would just go on their merry way.  We know that such a pattern holds for H. naledi, in South Africa, which coexisted with archaic Homo sapiens, in some way, shape or form. 

The article ends on a very peculiar note, in which she suggests the remote possibility that H. floresiensis is still alive out there, somewhere:
Could the Hobbit still exist in the wild mountain forests of Flores? When H. floresiensis was announced, the media picked up on the local folklore that small human-like creatures roam the forests. Descriptions of sightings are well recorded and quite detailed. The similarity to H. floresiensis is intriguing. But most researchers would say ‘show me the bones!’
This reminds one of the stories involving the Yeti/Sasquatch/Abominable Snowman, which likely derive from the finding of the bones of the Miocene ape Gigantopithecus, which was close to ten feet tall, when standing.  Is H. floresiensis still out there?  Probably not, but I am sure that the cryptozoologists haven't given up hope. 

Tuesday, October 03, 2017

Genetic Model Identifies Paranthropus boisei as Vector For Transmission of Herpes Virus

CNN (usual caveats) reports on a study that identifies Paranthropus boisei as the likely transmission vector of genital HSV-1.  From the story:
Herpes has been around a long time, to say the least.
Ancient chimpanzees genetically passed oral herpes (herpes simplex 1, or HSV-1) to the earliest humans millions of years ago when our lineage split. And we almost missed out on catching that other scourge, genital herpes (HSV-2) -- almost. Unlike HSV-1, HSV-2 didn't make the leap to early humans on its own.
Unfortunately for modern humans, millions of years ago, an early human ancestor was in the right place at the right time to catch HSV-2. And it might not have happened if it weren't for that meddling hominin species Paranthropus boisei, according to a new study in the journal Virus Evolution.
Why Paranthropus boisei, you ask? After all, P. boisei was not even on the main line of human evolution, coexisting with all manner of early Homo species at the same time, who likely out-competed them into extinction.  From the article, which is highly technical:
Paranthropus boisei would have been well placed to act as an intermediate host for HSV2. It most likely contracted the infection through hunting or more likely scavenging infected ancestral-chimpanzee meat. Processing (with or without tools) and consumption of raw meat would act as a simple path for ChHV1 to have crossed into P.boisei via open cuts or sores. Tropical refugia during hot dry periods may have driven chimpanzees into higher concentrations in certain areas, driving them into contact and competition with P.boisei and H.habilis as the margins of tropical forest blended into more open savannah-like habitats (Julier et al. 2017). Violent confrontation or hunting/scavenging and butchery practices would have provided a viable path of transmission for HSV2. Homo habilis remains have been recovered from the same layers as stone tools and bones carrying evidence of butchery, supporting a possible transmission–through-hunting/scavenging hypothesis for the initial anc-chimp to H.habilis transmission (Clarke 2012). Paranthropus aethiopicus, P. boisei, and P. robustus are associated with the Oldowan stone tool complex (De Heinzelin et al. 1999), and P.boisei explicitly with butchery (Domínguez-Rodrigo et al. 2013) lending support to the hypothesis that bushmeat hunting/scavenging and butchery may have led to the initial transmission of HSV2 to the hominins.
The entire exercise is very mathematical and relies on somewhat limited evidence of P. boisei behavior. It is, nonetheless, intriguing since it posits considerable interaction between the various hominin groups. 

Here is a mugshot of one of the perpetrators, the Zinj skull from Olduvai Gorge, found in 1959. 

Saturday, September 30, 2017

Did Humans Become a Distinct Species 350, 000 Years Ago?

The hits just keep on coming.  On the heels of the discovery in Morocco, at Jebel Irhoud, of a skull with some modern characteristics dated to 315 thousand years ago, we now have a genetic study that proposes that our species emerged between 350 and 260 thousand years ago.  How did a genetic study reveal this?  Science News reports:
The trick was retrieving a complete version of the ancient boy’s DNA from his skeleton to compare with DNA from people today and from Stone Age Neandertals and Denisovans. Previously documented migrations of West African farmers to East Africa around 2,000 years ago, and then to southern Africa around 1,500 years ago, reshaped Africans’ genetics — and obscured ancient ancestry patterns — more than has been known, the researchers report online September 28 in Science.
The ancient boy’s DNA was not affected by those migrations. As a result, it provides the best benchmark so far for gauging when Homo sapiens originated in Africa, evolutionary geneticist Carina Schlebusch of Uppsala University in Sweden and her colleagues conclude.
In line with the new genetically derived age estimate for human origins, another team has proposed that approximately 300,000-year-old fossils found in northwestern Africa belonged to H. sapiens (SN: 7/8/17, p. 6). Some researchers suspect a skull from South Africa’s Florisbad site, dated to around 260,000 years ago, qualifies as H. sapiens. But investigators often place our species’ origins close to 200,000 years ago (SN: 2/26/05, p. 141). There is broad consensus that several fossils from that time represent H. sapiens.
What is important to understand is that we have the fossils from Herto and Omo that date to between 150 and 200 thousand but that does not mean that is the earliest time that our species may have actually showed up. The Jebel Irhoud material is only partly modern—in the face mostly—and we do not know how the genetics for this population would look. It is possible that, as some investigators are saying, the Jebel Irhoud material represents the earliest fossil representation of our clade and that over the next 100 thousand years, the modern form fully evolved.   

Q&A With Lee Berger on Human Evolution

The Sunday Times has an interview with Lee Berger about human evolution, in advance of his new book, co-written with John Hawks, Almost Human: The Astonishing Tale of Homo naledi and the Discovery That Changed Our Human Story. As was reported earlier, the original fossils were undated but appeared to be reflective of an early stage in the development of Homo. This idea was shattered when new dates were derived.  As I wrote at the time:
Homo naledi, however, was missing a date—until recently. Nearly everyone in the scientific community thought that the date of the Homo naledi fossils, when calculated, would fall within the same general time period as other primitive early Homo remains. We were wrong. The radiometric dates—recorded using several methods carried out at different laboratories—yielded almost identical ages of between 236 and 300 thousand years before the present (BP). This was an order of magnitude younger than we expected. To say we were surprised would be an understatement.
Interestingly, the interviewer asks no important questions about Homo naledi or the Dinaledi Star cave, itself.  Amid all of the sturm und drang of his tortuous relationships with Ron Clarke and Philip Tobias (✟ 2012), there is one interesting question about human evolution in general:
Throughout the final chapters of the book you often mention how much there still is to learn about Homo naledi and that it’s very likely that there are more early hominim species which are yet to be discovered. The skeletal material you recently came across in the Lesedi Chamber shares similarities with Homo naledi and adds to this statement. What can/does this new discovery tell us about human evolution in Africa?

I think the clear picture that has come from both the discovery of Australopithecus sediba and Homo naledi is that the story of human evolution is not a simple, linear, straightforward one but that ours is a complex history. Naledi and sediba show us that there is more to be found – it’s clear that we don’t really know their ancestral history and the few fossils of other species found across Africa don’t help us much with interpreting where they fit in our family tree – and that’s exciting. We currently are back in the Dinaledi and Lesedi Chambers and making new discoveries – particularly exciting is we seem to have strong evidence that Homo naledi did indeed come down the narrow chute the way our “underground astronauts” come – and that is wonderful and hard to explain – but it’s exciting!
This has been a contentious issue: whether or not the fossil remains were “placed” there or were brought in by scavengers. What is also not clear is if the book was published before the new dates became available, or not.  I will have to buy the book to find that out.  While the rest of the interview is a tad unsubstantive, it is interesting.

Friday, September 29, 2017

Five Peculiar Fossils

Colin Barras of The New Scientist has a very short, very peculiar article on five hominin fossils that have been used to define new species and addresses the validity of each in very cursory fashion.  The strength of the article is in the links that it provides.  About Sahelanthropos, he writes this:
Features at the skull’s rear suggest it sat atop a vertical spine like that of a human, hinting that S. tchadensis walked upright. To make sure, other fossils will be needed – particularly from the legs. Unconfirmed reports suggest that a thigh bone was found with the skull, but this has not yet been discussed in a scientific paper. With so little evidence to go on, some are sceptical that S. tchadensis can really yet be defined as a hominin rather than some other form of ape – yet.
These are the least of its problems, as it is likely a surface find. Aside from this, when Wolpoff and colleagues examined the cranial base, here is what they found:
The prominence of the nuchal muscles, so important in head balance and loading, and shoulder movements, is enhanced by the significant development of the tuberculum linearum. The point is not that the TM 266 cranial rear and posterior portion of the cranial base was unlike hominids because the region looks like apes, but that TM 266 had a posture that is not upright because the region reflects nuchal functions similar to those of apes.

The foramen magnum - orbit plane angle does not directly address posture or locomotion in these hominoid primates (contra Zollikofer et al., 2005). Without a key postcranial element such as a pelvis or femur, none of these data provide compelling evidence for upright posture or obligate bipedal locomotion, and the various details of the nuchal plane argue against it. This functional implication has a phylogenetic consequence—by itself it is sufficient to disprove the phylogenetic hypothesis that TM 266 was a hominid.
This isn't skepticism. This is the door slamming shut.  It can be a surface find and still be a Miocene ape. In my recent piece for BioLogos, it did not occur to me to include this fossil since there are so many problems with it.  At this point, in Africa, the earliest reasonable evidence we have for hominins is Orrorin tugenensis

Read the whole (short) thing.