A 'Modern Population Bottleneck?'

NPR has a story on the (almost) disappearance of modern humans here. It is not a hypothesis that I had heard of before. Robert Krulwich writes:

Once upon a time, says Sam [Kean], around 70,000 B.C., a volcano called Toba, on Sumatra, in Indonesia went off, blowing roughly 650 miles of vaporized rock into the air. It is the largest volcanic eruption we know of, dwarfing everything else...That eruption dropped roughly six centimeters of ash — the layer can still be seen on land — over all of South Asia, the Indian Ocean, the Arabian and South China Sea. According to the Volcanic Explosivity Index, the Toba eruption scored an "8", which translates to "mega-colossal" — that's two orders of magnitude greater than the largest volcanic eruption in historic times at Mount Tambora in Indonesia, which caused the 1816 "Year Without a Summer" in the northern hemisphere.

Although this is a provative hypothesis, it does not match modern genetic studies. Dennis Venema writes:

Studies based on SNP/LD approaches have now estimated ancestral population dynamics for various human groups over time in more detail than is possible with mutation-based estimates. African groups have a higher effective population size (~7,000) than do non-African groups (~3,000) over the last 200,000 years. This approach, though based on methods and assumptions independent of previous work, nonetheless continues to support the conclusion that humans, as a species, are descended from an ancestral population of at least several thousand individuals. More importantly, the scalability of this approach reveals that there was no significant change in human population size at the time modern humans appeared in the fossil record (~200,000 years ago), or at the time of significant cultural and religious development at ~50,000 years ago.

When the first mtDNA studies began to come out in the late 1980s and early 1990s, they all supported the recent African evolution of modern humans and they all came to the same general conclusion: that modern humans had originated in sub-Saharan Africa between 140 and 280 thousand years ago. The earliest fossil evidence we have for modernity in Africa are the Herto remains at 160,000, at the site of Bouri, in the Afar Triangle. These remains bear more than a passing similarity to the modern Skhul 4 and 9 remains from the Israeli site of Skhul (dated at around 100,000) and suggest a general northern migration of these populations.

The other problem is that this does not correspond to a die-out of Neandertals either. The Neandertals didn't go away until around 30,000 and interbred with the incoming moderns anyway. Indeed, it looks as if the incoming moderns simply swamped the Neandertal genome and assimilated them. It is hard to do this if you have a very small effective population size.

I have not read this book so he may have counters for all of these arguments but I would be really curious to know what they are.

Yet Another "Beside the Point" Post From the Discovery Institute

Michael Flannery pens yet another tiring post about the theology of Charles Darwin, as if, somehow, the religious persuasions of Darwin have any bearing on evolutionary theory.  He writes:

Darwin frequently claimed to be in a theological muddle. He often assumed this posture in letters to close friends and colleagues. But when it came to taking a stand on religion, the separation of the Atlantic Ocean seemed to have emboldened him. This is evident in his staunch support of American freethinker Francis Abbot (1836-1903), founder of the Free Religious Association and editor of its radical weekly voice, The Index. In the December 23, 1871, issue Darwin gave a rare and unequivocal glimpse of his religious beliefs. Responding to Abbot's radical manifesto Truths for the Times, he wrote that he admired Abbot's "truths" "from my inmost heart; and I agree to almost every word," adding, "The points on which I doubtfully differ are unimportant." So what exactly were those "truths" to which Darwin gave his complete -- even passionate -- approval?

It is fairly well known that Darwin rejected the idea of a personal savior due, in large part to the death of his beloved daughter Anna.  Darwin made no secret of this and no secret of the fact that he thought that intelligence and religious understanding had evolved.  Flannery continues:

Darwin's secular humanism and radical materialism was no late additions to his thinking either. In the spring of 1838, long before he had unveiled his theory to the world, Darwin asked in his private notebook, "Why is thought, being a secretion of brain, more wonderful than gravity a property of matter? It is our arrogance, it is our admiration of ourselves." Ironically, by dethroning god Darwin committed the greatest hubris of all: admiring only his theory and pacing his faith in man.

In light of this there would seem to be only three choices for theistic evolutionists. First, simply accept the incompatibility -- learn to live with the contradictory idea that a God of purpose and intentionality has created and sustained a universe of (in John Herschel's famous phrase) "higgledy-piggledy." After all, God can do what He wills.

His other two options are humanism and nihilism.

This is nonsense. Albert Einstein contributed more to the study of relativity and quantum physics than anybody before or since. Yet we know that, despite his belief in a higher power, he also rejected a personal God. Should all physicists adopt his theological perspectives as well? Of course not. His theological views are divorced from his studies in physics, just like our study of evolutionary biology have no bearing on our theological views, unless it is to show us the grandeur and inventiveness of God's creation. Some who accept evolution are Christians, some are deists, and some are atheists, just as there are some of each that practice physics.

He closes with this gem:

But then why trust the theory that emanated from Darwin's mind any more than those of a monkey's? Whether it's his theory of evolution or his ideas about god that emanate from it, the monkey is still on Darwin's back.

Aside from being insulting, I wonder if Mr. Flannery is aware that the idea of natural selection was co-authored by Alfred Russel Wallace. Would he also fit Wallace into his thinking?  Furthermore, I wonder if he is aware of the 150 years of evolutionary research that have not only corroborated Darwin's and Wallace's theoretical constructs but extended them to include population mathematics, genetics, biogeography and a whole host of disciplines.  Probably not.  Like David Klinghoffer and David Berlinski, also from the Discovery Institute, he seems trapped in the late 1800s. 

Off Topic: Perilous

I just picked up a (signed) copy of Glass Hammer's new CD Perilous.  After two listens through, I think it is as good as their last two, If and Cor Cordium but it is very different, having shorter song construction.  Good mystical Christian prog rock. 

A Plea From Dennis Venema

Dennis Venema, who has written many good posts for BioLogos has written an article for the Colossian Forum titled “What I Would Like To Hear A Young-Earth Creationist Say.”  Rather than wax scientifically, he focuses, instead, on the things that we should have in common:

...the most important thing I would like to hear a YEC say to someone of my views isn’t a scientific statement at all – it’s a statement of unity in Christ. It’s the simple “brother” or “sister” that says – “we’re both part of the same family.” Even if we disagree on the mechanism of creation, affirming our unity in Christ needs to be the starting point for the conversation.

For those of us who are Evolutionary creationists/theistic evolutionists, he writes about a hypothetical conversation which, for some of us, is a constant fear:

“So, what do you do for work?”
 
“I’m a biologist. I teach up at the local Christian university.”

“Oh, really? You must really love the work that (insert the individual’s favorite anti-evolution ministry) does. It’s so good to have Christians like you who fight against evolution.” 

“Well, actually…”

 I have many friends in church to which I dare not bring up the evolution/creation debate.  I remember when one of of my friends from Bible Study was looking at my poster of the Tower of Time, a small version of the one by John Gurche that hung in the Smithsonian for years.  She remarked "How can you believe any of this?"  Implicit in her comment that was the poster represented an anti-God, anti-biblical  view of the world.  How do you bring someone like my friend, who had little to no scientific background, up to speed on the evidence.  Even if you could, would it matter?

Venema suggests (and I agree) that this issue should always be of secondary importance to the call of Christ and the unity that we should feel and express with each other:

So, to my YEC brothers and sisters, I would make this request. Without minimizing the importance of the exegetical issues that the creation/evolution controversy raises, let’s first and foremost sit at the Lord’s table and break bread together, recognizing each other as brothers and sisters in Christ and members of the same body. Those of us who see things from an EC perspective may need to repent of belittling our YEC brothers and sisters as scientifically ignorant or theologically naive. Those of a YEC perspective may need to repent of condemning their EC brothers and sisters as “compromisers” or theologically liberal.

I confess that belittling is easy to do and that is where the problem lies. It is too easy to do that and not to see the unity in Christ. We enjoy arguments and we enjoy disagreements. It gets the blood flowing and the dander up. But at some point, we have to see beyond that. Are the Christians that espouse the YEC viewpoint going to heaven? Yup. Are those of us that are EC going to heaven. I certainly believe so.

Having said all of this, we do have a responsibility to honestly treat the evidence that we encounter and to learn about God's creation from it. That does not change. To point out the variances from this is a worthy cause, but we should never believe that those who espouse those positions are not saved by grace, because, when the dust settles, we are all in need of that. 

Going on Vacation

I am going on vacation with the family for the week so probably will not be able to post anything.  Keep checking NCSE, BioLogos and Panda's Thumb as well as others that may come to mind.

Wouldn't You Like To Be A Pepper Too?

Another brouhaha has erupted, this time over a Dr. Pepper commercial on Facebook that features someone becoming more human after encountering Dr. Pepper.  Here is the ad.

Here is what Time Magazine had to say:

This is, of course, still the Internet — so plenty of comments in question are loaded with snark from people who mainly appear to be provoking for the sake of provocation. Several commenters, however, expressed disapproval of Dr. Pepper — believing, apparently, that the ad showed support for the scientific theory of evolution — and vowing to boycott the product. “I ain’t no freaking chimp. No more Dr Pepper for my household. God Bless y’all,” one user wrote. Another chimed in with, “I have lost all respect for Dr Pepper and if Dr Pepper wants business from thousands of people they will need to apologize.”

Yahoo had this observation:

One person wrote, "I love Dr Pepper but hate this photo. Forget evolution." Another person wrote, "Well, there goes my support for this company." It's unclear how many of the entries were sarcastic, but the post now has more than 3,000 comments, with most of them debating evolution. Among those supporting evolution were people encouraging everyone to calm down. One person wrote, "It's just a joke. People gotta lighten up and just live life."

Ya Think?????

Is It My Imagination...

...or is the ID community slowly abandoning the fossil record as being unfruitful in promoting their arguments?

Another Republican Congressman Beclowns Himself

The Associated Press is reporting on a speech given by Georgia congressman Paul Broun, who is quoted as saying:

“God's word is true,” Broun said, according to a video posted on the church's website. “I've come to understand that. All that stuff I was taught about evolution and embryology and Big Bang theory, all that is lies straight from the pit of hell. And it's lies to try to keep me and all the folks who are taught that from understanding that they need a savior.”

Evidently, he was also quoted as believing that the earth is around 9 000 years old and was made in six days.

The truly scary thing about this is that he has a post on the House Committee on Science, Space and Technology. How does someone this scientifically stupid get on a committee like that?? Once again, this calls for some kind of rudimentary test of basic science knowledge and understanding to weed people out before they are appointed to these kinds of committees. In any sort of formal discourse, he will be next to useless because he doesn't accept the basic tenets of so many different scientific theories.

It is yet another example of a Republican congressman demonstrating for all to see that his education in science has completely failed him.

It is also an example of the narrow mindedness of modern fundamentalist evangelical Christianity, a movement that seeks to divorce itself from any deep historical roots or modern academic understandings of the world in which it finds itself.  I am reminded of what Bruce Waltke said about this movement:

“If the data is overwhelmingly in favor of evolution, to deny that reality will make us a cult ... some odd group that is not really interacting with the world. And rightly so, because we are not using our gifts and trusting God's Providence that brought us to this point of our awareness,...”

Amen.

Hominin Meat Eating As Early As 1.5 Mya

Science Daily has a story detailing evidence that early hominins (and by this I mean probably Homo habilis or Homo ergaster) eat meat.  Although it is almost in the form of negative evidence. They write:

The two-inch skull fragment was found at the famed Olduvai Gorge in northern Tanzania, a site that for decades has yielded numerous clues into the evolution of modern humans and is sometimes called `the cradle of mankind.'

The fragment belonged to a 2-year-old child and showed signs of porotic hyperostosis associated with anemia. According to the study, the condition was likely caused by a diet suddenly lacking in meat.

"The presence of anemia-induced porotic hyperostosis…indicates indirectly that by at least the early Pleistocene meat had become so essential to proper hominin functioning that its paucity or lack led to deleterious pathological conditions," the study said.

This is common in dietarily compromised populations today.The general consensus is that hominins' brains expanded when they began incorporating meat into their diet, although it has been commonly thought that that did not occur until Homo erectus, for which there is direct evidence of hunting. 

A Creationist Parable: “It's a Duck”

This came from one of my email contacts and it is a great parable for the YEC point of view.

In Case You Happen To Live in Texas...

The Texas Freedom Network has released a voter's guide to the up-coming State Board of Education elections.  The astonishing thing about the first statement: "Science classes should NOT present creationism and/or "intelligent design" alongside evolution as credible scientific theories" is that, of nineteen candidates, only ONE agreed with that statement. This is a far cry from the Don McLeroy-dominated board of even a few years ago and, assuming some on the list are not prevaricating, a welcome change.

The Fossil Record According to Creationism

Popular Science usually has some outlandish articles and truly goofy science news.  They ran this howler yesterday.  It is the Geological Time Scale According to Creationists as an infographic.

My favorite part is the comment that King Henry VIII was the last king of the Devonian period.  A tad irreverent in places but very funny, nonetheless. 

Fossil Data and Genetic Data More Concurrent Than Thought

It is now coming out that the “clocks” that are used to calculate mutation rates are badly calibrated. Ewen Callaway of Nature writes:

Geneticists have previously estimated mutation rates by comparing the human genome with the sequences of other primates. On the basis of species-divergence dates gleaned—ironically—from fossil evidence, they concluded that in human DNA, each letter mutates once every billion years. “It’s a suspiciously round number,” says Linda Vigilant, a molecular anthropologist at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany. The suspicion turned out to be justified.

Now it seems that the clock is off by half. This means that a bunch of divergence dates can be recalculated. One is particular is mentioned:

Take the 400,000–600,000-year-old Sima de Los Huesos site in Atapuerca, Spain, which yielded bones attributed to Homo heidelbergensis, the direct ancestors of Neanderthals. Genetic studies have suggested that earlier ancestors of Neanderthals split from the branch leading to modern humans much more recently, just 270,000–435,000 years ago. A slowed molecular clock pushes this back to a more comfortable 600,000 years ago.

It isn't a magic bullet, there are still some kinks to be worked out but it has remarkable potential for getting a handle on when the Denisova genome might have arisen.It might also give us a believable figure for the LCA of apes and humans since the current, 5 million year date is plainly not so.

Very Busy...

I am working on my next BioLogos post and trying to not fall behind in teaching my class, which, because of the new online format, is eating my lunch. I will try to get something up in a bit.

One of My Favorite Quotes

My wife and I have been invited to a bible study tonight and, to hear of it, the topic might be the creation/evolution debate. I think it is time to remember a favorite quote of mine by a giant in the evangelical world: Billy Graham. He once upon a time wrote:

“I don't think that there's any conflict at all between science today and the scriptures. I think that we have misinterpreted the Scriptures many times and we've tried to make the Scriptures say things they weren't meant to say, I think that we have made a mistake by thinking the Bible is a scientific book. The Bible is not a book of science. The Bible is a book of Redemption, and of course I accept the Creation story. I believe that God did create the universe. I believe that God created man, and whether it came by an evolutionary process and at a certain point He took this person or being and made him a living soul or not, does not change the fact that God did create man. ... whichever way God did it makes no difference as to what man is and man's relationship to God.”

Billy Graham: Personal Thoughts of a Public Man, 1997. p. 72-74

Amen.

Nature: “Science wins over creationism in South Korea”

Nature News is reporting that the South Korean government has gone on the offensive, urging textbook makers to ignore requests to remove information on evolution from high school textbooks. Soo Bin Park writes:

The move follows a campaign earlier this year by the Society for Textbook Revise (STR), which argued that details about the evolution of the horse and of the avian ancestor Archaeopteryx should be removed from the books (see ‘South Korea surrenders to creationist demands’).

The STR, an offshoot of the Korea Association for Creation Research, says that students should learn “various” theories about the development of life on Earth. It argued that the textbooks used flawed examples of evolution that are under debate by evolutionary scientists.

A victory for the home team, hopefully.

Discovery Institute Science and Faith Conference

The Discovery Institute is running a conference titled Science and Faith: Friends or Foes? on October 12-13 at Covenant Seminary in St. Louis. A quick look at the speakers reveals that the conference is heavy on the ID side, with Paul Nelson, Ann Gauger, Jay Richards and John West featured prominently. Attend at your own risk.

More on Modern Human Origins

Scientific American is running a story on more news from the Max Planck Institute. Now, the entire genome of the hominins represented by the material from Denisova Cave has been sequenced. Here is what we find:

Unfortunately, the Denisovan genome doesn't provide many more clues about what this hominin looked like than a pinky bone does. The researchers will only conclude that Denisovans likely had dark skin. They also note that there are alleles "consistent" with those known to call for brown hair and brown eyes. Other than that, they cannot say.

Yet the new genetic analysis does support the hypothesis that Neandertals and Denisovans were more closely related to one another than either was to modern humans. The analysis suggests that the modern human line diverged from what would become the Denisovan line as long as 700,000 years ago—but possibly as recently as 170,000 years ago.

Given the amount of genetic similarity in the three groups, it makes more sense that the number is closer to 170,000, especially since there is evidence of hybridization between the three groups. What also seems to be true is the Denisova group shows some level of founder effect in the sense that the genetic variability is more restricted than that found in modern humans. Who the population split off from is anybody's guess right now.

Bill Nye on Evolution

Here is a YouTube clip by Bill Nye on the denial of evolution.



It is short and doesn't include a whole lot of information but it is heartfelt and some of the warnings are certainly good.

ABC News covered this here. The best quote is:

“And I say to the grownups, if you want to deny evolution and live in your world, in your world that's completely inconsistent with everything we observe in the universe, that's fine, but don't make your kids do it because we need them. We need scientifically literate voters and taxpayers for the future. We need people that can - we need engineers that can build stuff, solve problems.”

The parents don't get this information in a vacuum. It is groups like the ICR and AiG that should be held accountable for the distortions of science. They are the ones that are doing so much harm.

Baton Rouge Advocate on Louisiana and the Loch Ness Monster

In an editorial dated August 19, the editors of the Baton Rouge Advocate address the controversy surrounding the Louisiana voucher program and the Loch Ness Monster. They write:

The state has no intention, apparently, of launching any serious investigation of the Loch Ness monster in school curriculums. Instead, it will pay and pay, for years, and — if students do poorly on science tests at some future date — the state Department of Education might raise the question of why mythology is part of a school’s curriculum.

“In the event that there is basic academic incompetence, the state (education) department can intervene,” White says. “The most effective way of testing all of this is to literally see what do the students know and what do they achieve, and we’re doing that through the state test.”

A more-effective way would be for the department to open its eyes to this kind of educational malpractice before children’s futures are endangered.

The problem, of course, is by the time you get academic incompetence, how do you go about re-educationg these kids? By then the damage is done. Then what you have is kids that go to college (if they go to a mainstream college) who get their faith rocked by the scientific “real world.”

Then supposing you do find academic incompetence because of the curricula. How do you go about getting rid of the bad curricula without lawsuits, court cases, injunctions, and other delay tactics?

“Darwin just made it up.” Great googlymoogly!

Hat Tip to Glenn Branch.