Sunday, February 14, 2021

Genes For Tetrapod Evolution Appeared Earlier Than Thought

Science News is reporting on a study involving genes of modern fish that code for tetrapod limbs.  Elizabeth Pennisi writes:

In the trio of studies published last week in Cell, genes in living fish took the place of fossils as a way to peer back in time. One set of clues came from studies of mutagenized zebrafish, a favorite model for studying development. M. Brent Hawkins, then a Harvard University graduate student and now a postdoc, was shocked to discover zebrafish mutants with two bones resembling the forelimb bones of land animals in their front fins, complete with muscles, joints, and blood vessels. The finding is “quite spectacular,” says Marie-Andrée Akimenko, a developmental biologist at the University of Ottawa.

Further sequencing of lungfish showed something additionally startling:
The genome of the lungfish offers a glimpse of later adaptations along the path to terrestrial life. It includes additional pulmonary surfactant genes that the ray-finned fishes lack, as well as DNA for specifying five toes, connecting nerves to limb muscles, and for sensitizing the brain to react fast. All those genes were previously thought to be unique to tetrapods.
The authors conclude that, since modern teleost fish do not possess these genes, that they must have been present in the common ancestors of tetrapods and modern fish. The authors further note that all of these studies suggest that “...the origin of tetrapods was something that was waiting to happen.”

Tuesday, August 11, 2020

How Old is the Universe?

An astrophysicist at the University of Oregon suggests that the universe might not be 13.8 billion years old but maybe just 12.6—a drop of 8.7%. From the university website:

Dating the Big Bang, which gave birth to the universe, has relied on mathematics and computational modeling, using distance estimates to the oldest stars, the behavior of galaxies and the rate of the universe’s expansion. The idea is to compute how long it would take all objects to travel backward to the beginning. 
A key calculation is the Hubble constant, named after Edwin Hubble, the namesake of the Hubble Space Telescope, who first calculated the universe’s expansion rate in 1929. A more recent technique uses observations of leftover radiation from the Big Bang. It maps echoes in spacetime, known as the cosmic microwave background, and reflects conditions in the early universe as set by the Hubble constant. 
The science for such research, [University of Oregon physicist Jim] Schombert said, is ruled by mathematical patterns expressed in equations that often reach different conclusions. The universe’s age, under the differing scenarios, ranges from 12 billion to 14.5 billion years.

The new calculations use something called the baryonic Tully–Fisher relation (bTFR) rather than the Hubble Constant, which makes use of much more refined infrared measurements. The publication appears in The Astronomical Journal and is pretty dense to the non-astrophysicist.

That didn't stop Ken Ham from weighing in.  In an Answers in Genesis post, he writes: 

So which is it? 13.8 billion years or 12.6 billion years? That’s just a difference of a “mere” 1.2 billion years, after all, but why such conflicting results? Well, it’s because both have the wrong starting point—man’s ideas of naturalism and billions of years.

The correct starting point for our thinking isn’t billions of years. That’s a belief imposed on the observable evidence, such as the cosmic microwave background and light from distant galaxies. Because the models of these researchers have the wrong starting point (i.e., wrong assumptions), they’re drawing wrong interpretations and conclusions from the evidence.

But we can know the age of the earth and universe because Scripture gives us the information we need to determine how old earth and the universe are. Genesis chapter 1 tells us God created everything in six days (Exodus 20:11 reaffirms this), so we know earth and the universe are roughly the same age.

It is quite true that an 8.7% change is sizeable and, subject to further refinements, we will probably be able to narrow down the discrepancy in age. 

Do you know what the astronomers didn't find, though?  They didn't find a universe that is 6,000 years old (a decrease in age of 230,000,000%).   Ken Ham wants us to believe that, because our older estimates were 8.7% off, we have no idea how old the universe actually is.  This is similar to his arguments against radiometric dating, and they are just as faulty.  Even if we did not have the astrophysical estimates, we know, based on geological and radiometric evidence that the earth is vastly older than 6,000 years. 

Saturday, August 08, 2020

Another Mystery Ancestor Joins The Group

Science Daily has a story on genetic work done by researchers at Cornell University and Cold Spring Harbor Laboratory that suggests that there is, as yet, another unnamed ancestor to the modern human line. They write:

In the new paper, the researchers developed an algorithm for analyzing genomes that can identify segments of DNA that came from other species, even if that gene flow occurred thousands of years ago and came from an unknown source. They used the algorithm to look at genomes from two Neanderthals, a Denisovan and two African humans. The researchers found evidence that 3 percent of the Neanderthal genome came from ancient humans, and estimate that the interbreeding occurred between 200,000 and 300,000 years ago. Furthermore, 1 percent of the Denisovan genome likely came from an unknown and more distant relative, possibly Homo erectus, and about 15% of these "super-archaic" regions may have been passed down to modern humans who are alive today.
The paper is available in PLoS Genetics, which means that it is free to the public.  The above-description makes it sound like bootstrapping on stilts.  Here is a paragraph from the paper, itself, that describes the process:
In this paper, we describe a powerful and highly general new method, called ARGweaver-D, that samples ancestral recombination graphs (ARGs) [18–20] conditional on a generic demographic model, including population divergence times, size changes, and migration events. After introducing ARGweaver-D, we present simulation studies showing it can successfully detect Nea→Hum introgression, even when using a limited number of genomes, and that it also has power for older migration events, including Hum→Nea, Sup→Den, and Sup→Afr events. Finally, we apply this method to modern-day Africans and ancient hominins, and characterize both new and previously reported cases of introgression between humans and archaic hominins.
Okay, it still sounds like bootstrapping on stilts.  I am not sure how you can do a simulation to detect older migration events when that is what you are looking for in the first place.  What exactly is an ancestral recombination graph, you ask?  From a previous paper on this subject:
It is possible to capture these complex relationships using a representation called the ancestral recombination graph (ARG), which provides a complete description of coalescence and recombination events in the history of the sample. However, previous methods for ARG inference have not been adequately fast and accurate for practical use with large-scale genomic sequence data. In this article, we introduce a new algorithm for ARG inference that has vastly improved scaling properties. Our algorithm is implemented in a computer program called ARGweaver, which is fast enough to be applied to sequences megabases in length. With the aid of a large computer cluster, ARGweaver can be used to sample full ARGs for entire mammalian genome sequences.

The best data we have suggests that Neandertals and African archaics split some 600 ky ago when a group of Homo ergaster migrated out of Africa and took up residence in western Europe, leading to branching events that eventually included H. antecessor and the Neandertals.  This is supported by this research, which found about 7% introgression into the Neandertal genome of archaic H. sapiens.  The surprise was that 1% of the Denisovan genome likely came from an, as yet, undiscovered hominin.  

Increasingly, there is evidence that considerable interbreeding occurred throughout the middle to late Pleistocene, continuing through the interbreeding that occurred in China and Europe.  As I wrote about the 105-130 ky old Chinese Xuchang skulls:

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.”
This likely represents only a small part of the vast scope of population mixing. I will be curious to see where the ARG research leads.

Friday, August 07, 2020

Glenn Morton Has Died

 Glenn Morton, one of the first people to go public with his recantation of young earth creationism has died.  Todd Wood has the news:

I just got word that Glenn Morton passed away on August 5. You can see a brief obituary here. I never met Glenn, but I certainly knew of him. Back in the 1980s, Glenn was an active young-age creationist researcher, looking at questions in by geology. As he continued "digging," he had an increasingly difficult time figuring out how to explain his findings in the context of the Flood geology of the day. So he left, and eventually became a fairly regular critic of young-age creationism.
I remember reading one of Glenn's posts that was cross-linked on the old newsgroup Talk Origins.  The classic post by Morton, which appeared on Old Earth Ministries, detailed his tortuous, painful break from young earth creationism:
In order to get closer to the data and know it better, with the hope of finding a solution, I changed subdivisions of my work in 1980. I left seismic processing and went into seismic interpretation where I would have to deal with more geologic data. My horror at what I was seeing only increased. There was a major problem; the data I was seeing at work, was not agreeing with what I had been taught as a Christian. Doubts about what I was writing and teaching began to grow. Unfortunately, my fellow young earth creationists were not willing to listen to the problems. No one could give me a model which allowed me to unite into one cloth what I believed on Sunday and what I was forced to believe by the data Monday through Friday. I was living the life of a double-minded man--believing two things. By 1986, the growing doubts about the ability of the widely accepted creationist viewpoints to explain the geologic data led to a nearly 10 year withdrawal from publication. My last young-earth paper was entitled Geologic Challenges to a Young-earth, which I presented as the first paper in the First International Conference on Creationism. It was not well received. Young-earth creationists don't like being told they are wrong. The reaction to the pictures, seismic data, the logic disgusted me. They were more interested in what I sounded like than in the data!
I never corresponded with Glenn but now wish I had. He will be missed.

Thursday, June 04, 2020

An Honest Evolution Debate?

James Haught once wrote a column, now appearing in the Good Men Project on how science is an honest endeavor.  He writes:

To me, the whole issue hinges on honesty. Let me explain: Science, from a Latin word meaning knowledge, is simply a search for trustworthy facts. It is human intelligence at work. The process is honest, because every researcher’s claim is challenged by other researchers. They test and retest by many methods, until a new idea fails or holds firm. (A researcher who falsifies data is a loathsome criminal in the eyes of fellow scientists.)

While some individual scientists are pig-headed, an entire field cannot be. Science goes where the evidence leads. Science is honest enough to admit mistakes. When new evidence shatters a previous assertion, the old belief is dropped or modified. No such setbacks have hit the theory of evolution.

After 140 years of research, virtually the entire scientific world now agrees that evolution is a fundamental aspect of nature.
As you might guess, there are quite a few people who would disagree with this perspective.  It is, nonetheless, true.  

Wednesday, June 03, 2020

Libby Anne: Ken Ham is Playing at Science

She's not wrong.  Libby Anne, a writer for Patheos has latched onto something that has been an issue with Ken Ham for quite some time: he is scientifically ignorant.  One of Ham's persistent arguments is that we can't know historical science (or predictive science) because, as he puts it, “Were You There”? A moment's thought about this perspective reveals it to be facile.  Libby Anne agrees:
Ham argues that some science uses observation and experimentation (what he calls “experimental or observational science”) while other science (what he calls “origins or historical science”) does not. Throughout his publications, he insists that young earth creationists do real science, but even as he does so, he uses terms scientists simply don’t use. Ham uses the term “observational evidence” here because he wants to contrast what he argues is “real” science with what he claims is a separate, less reliably category of scientific research: “origins science” or “historical science.”
Ham's insistence that we cannot know past events because we “weren't there” ignores the vast amount of detective work that goes on every day to reconstruct past events in criminology, biology, genetics and may other fields.  He is the only one who believes this.

Tuesday, June 02, 2020

Homo erectus 200,000 Years Older Than We Thought

UPI has a story about a discovery in South Africa of a Homo erectus infant that is 200 ky older than the oldest known specimen currently in existence.  From the original Science article
Fossil hominins from South Africa are enriching the story of early human evolution and dispersal. Herries et al. describe the geological context and dating of the hominin-bearing infilled cave, or palaeocave, at a site called Drimolen in South Africa (see the Perspective by Antón). They focus on the age and context of a recently discovered Homo erectus sensu lato fossil and a Paranthropus robustus fossil, which they dated to ∼2.04 million to 1.95 million years ago. This makes Drimolen one of the best-dated sites in South Africa and establishes these fossils as the oldest definitive specimens of their respective species ever discovered. The age confirms that species of Australopithecus, Paranthropus, and early Homo overlapped in the karst of South Africa ∼2 million years ago
The goofy thing about this is that, in East Africa,  early Homo was still running around and out-competing the robust australopithecines (Paranthropus).  The fossil was uncovered and described over a five year period at the site of Drimolen, which is part of the UNESCO World Heritage Site in South Africa that contains the important fossil sites of Swartkrans and Sterkfontein. 

From the UPI story:
“One of the questions that interests us is what role changing habitats, resources, and the unique biological adaptations of early Homo erectus may have played in the eventual extinction of Australopithecus sediba in South Africa,” said study co-author Justin Adams, researcher at Monash University's Biomedicine Discovery Institute.
“Similar trends are also seen in other mammal species at this time. For example, there are more than one species of false sabre tooth cat, Dinofelis, at the site -- one of which became extinct after two million years,” Adams said. “Our data reinforces the fact that South Africa represented a truly unique mixture of evolutionary lineages -- a blended community of ancient and modern mammal species that was transitioning as climates and ecosystems changed.”
Just a few short years ago, it was thought that Australopithecus sediba might be ancestral to early Homo based on the characteristics of its hands, pelvis and the proximity of stone tools to the Rising Star Cave.  This was an idea championed by Lee Berger, but it now seems likely that it was another, earlier form that gave rise to Homo erectus

Here is the photo of DNH134, taken by Jesse Martin, Reanud Joannes-Boyau, and Andy I. R. Herries

Monday, June 01, 2020

Oldest Evidence of Siberian Crossing of Native Americans

UPI has a story about evidence from around Lake Baikal that links populations of Siberia to the earliest groups who came over from Siberia to the New World.  Brooks Hays writes:
New genomic analysis of ancient remains in Siberia -- detailed this week in the journal Cell -- have offered scientists fresh insights into the movements of human populations across Eurasia and into the Americas at the end of the Stone Age.

“Previous studies observed the genetic differences between individuals from different time periods, but didn't investigate the differences by dating the admixture events,” lead study author He Yu, postdoctoral researcher at the Max Planck Institute for the Science of Human History in Germany, told UPI in an email. “Our study reports a 14,000-year-old individual, which actually fills in a large blank of ancient genomes in this region, between 23,000 and approximately 8,000 years ago.”
By using the DNA of a tooth from the 14 ky old individual, Yu and his team have established links to the earliest Native Americans.
“The deep connection observed in this study is sharing of the same admixed ancestry between Upper Paleolithic Siberian and First Americans," Yu said. "We are not suggesting interbreeding between Native American and Siberian, or any back flow of Native American ancestry into Siberia. But we are suggesting that, the First American ancestry was formed in Siberia and also existed there, in a large range of time and space, so we can detect it in ancient Siberian individuals.”
There have always been conflicting theories about how and when the migrations to the New World occurred and there has always been evidence for movements from the Lena River, in Siberia and the northern Amur river in northern China.

Interestingly, they also found genetic evidence of the plague in some of the Bronze age populations from the area, which they hypothesized came from Europe, indicating that there was considerable movement between these populations.

Tuesday, March 17, 2020

BioLogos: Approaching Adam

BioLogos has a post on how to approach the teaching of the historical Adam aimed specifically at parents as they talk to their kids. Christy Hemphill writes:
If your kids are hearing a young earth creationist perspective at church or a Christian school, they may find those ideas very appealing and convincing for a time. Depending on your situation and personality, you may have to be careful not to put your kids in the middle of your own power struggles or debates with other adults in your lives. Kids need space and time to build their worldviews and figure stuff out for themselves. If you consistently model openness to questions and how to seek out reliable information to answer them, that will pay off. But at the end of the day, it will be your honesty and unconditional acceptance that will make you trustworthy to your kids, not the strength of your answers and arguments.

The other issue she discusses is something that rears its ugly head in my household regularly:
Most parents in the American context have to decide how to handle Santa Claus in their family. If you are one of the families that introduces the idea of Santa Claus to your children as make believe from the beginning, you probably still don’t want your kids to make themselves a persona non grata by ensuring every other kid in preschool is clued in. The analogy breaks down, of course, especially if you believe that Adam and Eve are historical figures, but most parents don’t want their kids to alienate others or be ostracized in some way for having different insights into Genesis than their peer group. What do you do when all your kids’ cousins, or friends from Sunday School, or classmates at the homeschool co-op are being taught something very different about Adam and Eve and the origins of humans?
I have been open with my kids about the fact that I am an evolutionary creationist and accept not just an old universe but evolution as it pertains to all life, including humans. We have not had a really good conversation about Adam and Eve because my thoughts are not concrete on this issue. While it is possible they were real people, it is clear from the account in Genesis that the entire episode is stylized, geographically truncated (what was happening on the rest of the planet at that time?) and reads like myth.  John Walton argues that the story is presenting theological truths at the expense of literal facts and that it mirrors other accounts of creation at that time period.

Dennis Venema presents some strong genetic evidence that the human population could never have been below the effective size of 10,000 and was likely much larger.  The other issue is the source for the original Mitochondrial Eve and Male Y chromosome.  As he puts it:
Current estimates place mitochondrial Eve just after the dawn of Homo sapiens as recorded in the fossil record, at about 180 KYA. This places her within our species. Until recently, Y-chromosome Adam was dated later, at about 50 KYA, the time of significant human migration out of Africa. Recently, however, a rare Y-chromosome variant has been found in modern humans that pushes back the last common ancestor of all human Y-chromosome DNA to approximately 210 KYA – which, interestingly enough, is right at the cusp of our own species as recorded in the fossil record. Since our species arose as a continuous population that gradually diverged from other hominins, there is no reason to expect that all of our DNA variation will come back to a common ancestor (or coalesce, to use the technical term) within our species. Indeed, some of our regular chromosomal variation does not coalesce within our species or even as far back as our common ancestral population with chimpanzees.
The problems for the literal Adam begin to mount very quickly and it becomes hard to make sure that you don't kill a child's faith with these nagging bits of evidence.

This is a thorny topic because it cuts to the beginning of the Bible and how we understand the notion of original sin.  As far as the historical Adam and Eve being the first people, the science since is unclear.

Monday, March 16, 2020