Why Evolution is True is a blog written by Jerry Coyne, centered on evolution and biology but also dealing with diverse topics like politics, culture, and cats.
Sadly, there are a fair amount of comments that arrive here, and are held in moderation, without either a name or an email address. They are innocuous comments that would be posted if they bore a name and an email address (the latter is never shown on the site). As I said before, I’ve started trashing these comments because we can never identify a specific commenter so long as he/she uses “anonymous”. If this site is to work, we have to have a person associated with each name, real or not, and you must stick with your name unless for some reason that’s impossible.
When you make a comment, PLEASE fill in your name and email address (they don’t have to be the right ones, though I’d appreciate a correct email address since I sometimes contact readers), and make sure it’s in there when you submit the comment. Otherwise your comment won’t show up.
Yes, I know WordPress is being wonky these days and I’m trying to do something about it. But until we can identify the issue and fix it, please fill in your name and email.
Thanks to the many WEIT readers who have tried their hand (or eyes) at reading the German handwriting on the side of a deer’s jaw, we have arrived at what I believe is a correct reading. Special thanks to Aldo Matteucci, who immediately recognized the second word as “hirsch” (meaning deer), Michael Fisher who edited the images for easy comparison, and to Heidrun Wenisch, who made what I believe to be the correct reading of the first word. Michael Sternberg brought Heidrun’s reading to my attention, and suggested the key empirical test– what exactly did the deer’s antlers look like? They look like this:
Schadhirsch it is, sir
Heidrun wrote, “The 2 words of the first line are Schad Hirsch. The word Schadhirsch is hunters’ jargon only and is used when speaking of an older male red deer.” Michael Sternberg then asked me, “How do the associated antlers look that you mentioned in the article? Branched at several points like you’d expect given the age, or just a single spike (“Spieß”) with possibly short buds, thus “defective”, as the hunter’s jargon term translates?” As you can see, it’s definitely “Spieß”. Michael elaborated, “A 2-year old Hirsch with such antlers would be said Spießer, but if the higher age is correct for this specimen (as derived from the degree of tooth grinding as you mentioned), then Schadhirsch applies and explicitly calls out that the age is higher than a first glance at the antlers would indicate.”
Looking carefully at the writing, this reading is not, to my mind, ruled out by any features of the letters, and fits the specimen perfectly. Problem solved! Thanks again to all who took the time to study and comment on the photos.
Please remember this site if you have some good wildlife photos, and send them in. Thanks.
In honor of International Beetle Day (yes, I made that up), we have some photos of beetles by Tony Eales from Australia. His captions are indented.
Still getting through the Borneo insects, order by order. This time some of the Coleoptera.
We were thrilled to find a large Three-horned Rhinoceros Beetle (Chalcosoma moellenkampi) that came in to the lights at the field centre. It’s always surprising how strong these beetles are as anyone who has held one can attest.
It often seems like most beetles are leaf beetles in the family Chrysomelidae. There are estimates that there is some 50,000 species of which about 37,000 are known. Two I photographed were from the sub-family Galerucinae. The blue one shone like a jewel in the forest.
On one night walk we found this incredible Firefly larvae family Lampyridae. One of the most alien looking things I’ve ever seen.
We were also shown a site where Violin Beetles are regularly found. These large unusual beetles were one of the highlights of the trip.
There were also scarab beetles family Scarabaeidae and many tiny beetles that came to the lights at the kitchen which I have no idea even the family.
The date was selected because more than a century earlier (February 24, 1821), the “Plan de Iguala” or “Plan de las tres garantías” was proclaimed by Agustin de Iturbide and General Vicente Guerrero. This plan was based in three principles: “Religion, Independence and Unity”, which were represented on the flag’s colors. On this same date, Jose Magdaleno Ocampo tailored the first three color flag for what would soon be an independent Mexico. This flag, commonly known as the “Pendon Trigarante”, had the colors: white, green and red in that order, arranged diagonally with three eight-point gold stars, one on the center of each color banner.
The modern flag of Mexico, which depicts an eagle, a snake, and a cactus:
On this day in 1582, according to Wikipedia, Pope Gregory XIII proclaimed the Gregorian calendar, which began in October. The change was announced via a Papal Bull, which looks like this:
On February 24, 1803, in the famous case of Marbury v. Madison, the Supreme Court began the procedure of “judicial review”, meaning that courts could nullify legal statutes that were deemed unconstitutional. On this day in 1854, the first perforated stamp for public distribution was issued, the “Penny Red.” And here it is (some specimens are worth £ 500,000):
On this day in 1868, President Andrew Johnson became the first U.S. President to be impeached by the House of Representatives, but he was acquitted by the Senate. On this day in 1920, the Nazi Party was founded (I was surprised that it started so soon after WWI). It’s no longer in existence thanks to stalwarts like Dan Arel. On February 24, 1946, Juan Perón was elected to his first term as Argentina’s President. He was elected twice more before he was overthrown.
On February 24, 1980, completing its “Miracle on Ice”, the U.S. hockey team took gold in the Lake Placid Winter Olympics, defeating Finland 4-2. And here is that victory:
On this day in 1989, Ayatollah Ruhollah Khomeini issued a fatwa (complete with a $3 bounty on the author’s head) against Salman Rushdie for writing The Satanic Verses. Now the Ayatollah is dead and Rushdie is not. Finally, it was on this day 11 years ago that Fidel Castro resigned as President of Cuba, though he kept his position as head of the Communist Party for another 3 years.
Those born on this day include Joseph Banks (1743), Winslow Homer (1836), Honus Wagner (1874), Chester Nimitz (1885), Abe Vigoda (1921), and Judith Butler and Eddie Murray (both 1956).
In my view, Homer is an underrated painter. Here’s one of his paintings in Chicago’s Art Institute, “The Herring Net” (1885), description here.
And here’s Vigoda in the first Godfather movie, taken away to be killed for treason to the Family. It’s a poignant scene:
Notables who expired on February 24 include Henry Cavendish (1810), Malcolm Forbes (1990), Claude Shannon (2001), Don Knotts (2006), and Harold Ramis (2014).
Meanwhile in Dobrzyn, Hili is out exploring, but she’s wary:
Hili: What’s there?
A: Partially burned root.
Hili: It looks threatening.
In Polish:
Hili: Co tam jest?
Ja: Nadpalony korzeń.
Hili: Wygląda groźnie.
This tweet from the BBC tells a touching story of death, guilt, and redemption. It’s ineffably sweet, and you can read more about Foulds and his story here.
As you probably know from reading this site, ID creationist Michael Behe has a new book coming out this week: Darwin Devolves: The New Science About DNA That Challenges Evolution (note the unclear antecedent, which could be either “New Science” or “DNA”). Various scientists have weighed in, none of them positively, and there’s been considerable criticism by biologists Nathan Lents, Joshua Swamidass, and Rich Lenski, including a damning review in Science.
Lents continued his criticism on The Human Evolution Blog (see here, here and here) and Lenski, whom Behe attacked strongly in the book, promised a three-part rebuttal of Behe’s ideas on his own website, Telliamed Revisited, which is now being extended (see here and here for Lenski’s parts 1 and 2).
Yesterday Lenski put up part 3 (screenshot below), which is an expansion of earlier criticism by Lents on whether a gene likely involved in the adaptive evolution of polar bears—a gene concerned with fat metabolism—was really “broken” or “damaged”.
One of Behe’s major theses in the book is that evolution is self-limiting, as, he argues, nearly all adaptations are based on damaged genes, and when a gene is damaged or inactivated, it can accumulate more mutations that eventually render it functionless and unable to revive. Thus, he concludes, evolution by natural selection runs itself into the ground. God An Intelligent Designer then has to step in to make things right.
Behe is wrong. Indeed, although we have examples of adaptive evolution based on inactivated genes, we also have many that don’t involve “broken genes”, and as long as a reasonable number of mutations involve changes in gene function or regulation, or things like gene duplication, chimeric genes, and so on, Behe’s claim holds no water.
One of the genes that Behe claimed was inactivated during adaptive evolution of polar bears from ancestral brownish bears was ApoB, which regulates the amount of fat in the blood. Behe claimed in his book that the gene’s evolution in polar bears involved many “inactivating” mutations. Lents pointed out that there was no evidence for this; on the contrary, even the authors of the paper analyzing the sequence of that gene found evidence that some of those substitutions were not involved in breaking the gene, but improved its function.
Behe replied, calling Lents an “incompetent reviewer” (without even giving his name!) and presenting some data that, he said, showed that the ApoB substitutions were “possibly damaging” or “probably damaging.
That was a mistake, for, as Lents showed, Behe was duplicitous in his reply, having omitted from his table all the mutations that the authors’ algorithm said were “benign”. Lents is charitable about this, but I can see no explanation except that Behe left out data inimical to his hypothesis. And that seems misleading and deceptive. As I said, Lents is kinder to Behe than I would have been:
In Behe’s defense, he doesn’t explicitly say that he’s presenting the whole Table. So he isn’t lying exactly. Instead, he says that he is presenting “the relevant information” from the Table. I find this deeply misleading. This whole discussion is about the nature of adaptive mutations in the evolution of species and Behe’s arguments is that most of them are damaging. By presenting only the mutations that are predicted to fit that argument, he is intentionally leaving out evidence that is contrary to his position.
After all, what is the purpose of showing the chart at all? To show that some mutations that drove polar bear evolution are damaging? He didn’t need a chart to make that point and no one would argue with that. I suspect that if the unaltered Table S7 gave the impression that the overwhelming number of adaptive mutations were damaging, Behe would have shown the whole thing.
In reality, Table S7 does not give that impression at all, and so he slices it up with surgical precision so that he can present “the relevant information,” that is, the information that appears to support his position. And, at least when it comes to APOB, even the selectively edited information probably doesn’t support his position either, regardless of what the predictive algorithm says, as I (and the study’s authors!) explain above.
The evolution of polar bears is the opening story of Behe’s book, the example he uses to describe his concept of “devolution.” But if you actually consult the data itself, it tells a very different story than Behe does.
Lenski’s new post (click on screenshot), goes into the polar bear gene in detail, and also explains how scientists determine whether a mutation in a gene is advantageous, benign, or damaging—not an easy matter when all you have is its DNA sequence.
Lenski points out that the algorithm used by the real scientists who did the ApoB study is unable to detect adaptive changesthat improve the function of the protein: it is limited to detecting “benign”, “possibly damaging” or “probably damaging” mutations. Not only did Behe leave out the “benign” mutations, but didn’t bother to mention that the algorithm can’t show changed or improved function for any mutations. And I call that duplicitous. Here’s Lenski’s take; the emphases are his.
The program simply cannot detect or suggest that a protein might have some improved activity or altered function.
The authors of the paper recognized these limiting assumptions and their implications for the evolution of polar bears. In fact, they specifically interpreted the APOB mutations as follows (p. 789): “… we find nine fixed missense mutations in the polar bear … Five of the nine cluster within the N-terminal βα1 domain of the APOB gene, although the region comprises only 22% of the protein … This domain encodes the surface region and contains the majority of functional domains for lipid transport. We suggest that the shift to a diet consisting predominantly of fatty acids in polar bears induced adaptive changes in APOB, which enabled the species to cope with high fatty acid intake by contributing to the effective clearance of cholesterol from the blood.” In a news piece about this research, one of the paper’s authors, Rasmus Nielsen, said: “The APOB variant in polar bears must be to do with the transport and storage of cholesterol … Perhaps it makes the process more efficient.” In other words, these mutations may not have damaged the protein at all, but quite possibly improved one of its activities, namely the clearance of cholesterol from the blood of a species that subsists on an extremely high-fat diet.
It appears Behe either overlooked or ignored the authors’ interpretation. Determining whether those authors or Behe are right would require in-depth studies of the biochemical properties of the protein variants, their activities in the polar bear circulatory stream, and their consequences for survival and reproductive success on the bear’s natural diet. That’s a tall order, and we’re unlikely to see such studies because of the technical and logistical challenges. The point is that many proteins, including ApoB, are complex entities that have multiple biochemical activities (ApoB binds multiple lipids), the level and importance of which may depend on both intrinsic (different tissues) and environmental (dietary) contexts. In this example, Behe seems to have been too eager and even determined to describe mutations as damaging a gene, even when the evidence suggests an alternative explanation.
Now this may seem an arcane discussion about protein function, but if you’ve gathered anything from this post, Lenski’s post, and Lents’s posts, it should be that Behe has not been intellectually honest in treating the data in a key example used to make his case that natural selection nearly always relies on broken genes. But what do you expect from a creationist who’s deeply religious and who’s counting on the data to make the case for God?
I’m told that Behe really believes the kind of palaver he uses to make the case for “irreducible complexity” and Intelligent Design. But really, how can you leave out data and distort the conclusions of others, without being conscious of what you’re doing? One might almost conclude that Behe is lying for God.
Lenski isn’t done with taking Behe to the woodshed yet: as he says, “I initially planned to write three posts, but it will now be more than that, as I delve deeper into several issues.” Behe’s tuchas is going to be smarting after this!
For the spring semester, my colleague Dave Rogers and I are teaching a seminar class entitled “Human Phylogeography.” Phylogeography is the study of the history of the genetic variation, and of genetic lineages, within a species (or closely related group of species), and in the seminar we are looking at the phylogeography of human populations. DNA sequencing now allows a fine scale mapping of the distribution of genetic variation within and among populations, and, remarkably, the ability to sequence ancient DNA from fossil remains (including Neanderthals). The seminar is based primarily on a close reading of David Reich’s (2018) Who We Are and How We Got Here (published by OUP in the UK).
Although rarely under that rubric, human phylogeography has been a frequent topic of discussion here at WEIT, by Jerry, Matthew, and myself, including our several discussions of Neanderthals (or Neandertals) and Denisovans. So it may be of interest for WEIT readers to follow along. Below the fold I’ve placed the course syllabus, which includes the readings, and links to many newspaper articles of interest, and online postings, including many here at WEIT, and also from John Hawks Weblog, a site we’ve recommended on a number of occasions when discussing human evolution. (The newspaper links appear as images; just click to go to the story.) We just finished our third meeting, and I’ve been quite impressed by the students’ discussion and writing. We’re fortunate to have some students from anthropology or with some anthro background.
Please read along with us, or browse what seems interesting below. If you have questions or comments, post them here, and I’ll be looking in.
Reader Alexander called my attention to this item in the Science Focus section of the BBC. (Note that it’s in the science section, not the “religion” section!) It’s a 33-minute podcast interview with John Lennox, whose Wikipedia page says this (my emphasis, and yes, that’s THE Templeton Foundation, which now has a damn Oxford College named after it):
John Carson Lennox (born 1943) is a Northern Irish mathematician specialising in group theory, a philosopher of science and a Christian apologist. He is Emeritus Professor of Mathematics at the University of Oxford and an Emeritus Fellow in Mathematics and Philosophy of Science at Green Templeton College, Oxford University. He is also an Associate Fellow of the Saïd Business School.
. . . Lennox has been part of numerous public debates defending the Christian faith, including debates with Christopher Hitchens, Michael Shermer, Richard Dawkins, Lawrence Krauss, Peter Atkins, Victor Stenger, Michael Tooley, Stephen Law, and Peter Singer.
Green Templeton College resulted from a merger in 2008 between Green College and Templeton College, and here are the facts (my emphasis):
The college was founded in 1965 as the Oxford Centre for Management Studies. The College was based at Egrove Park in Kennington, south of Oxford. Its buildings were opened in 1969, and were awarded listed status in 1999.
It was renamed Templeton College in 1983 as a result of a donation from Sir John Templeton, in honour of his parents, Harvey Maxwell and Vella Handly Templeton. The intention was to raise professional standards in British management. The endowment was one of the largest endowments ever made to a British educational establishment. Initially a “society of entitlement” in the University, Templeton College began admitting graduate students in 1984 and became a full graduate college of the University by Royal Charter in 1995.
The podcast interview with Lennox is below (click on the link), though you may not get through much of it before your digestive system goes awry.
The podcast notes:
With science providing more and more insights into the workings of the Universe, many people have turned their backs on religion entirely. Why invoke a God to explain the world, the argument goes, when science does a perfectly good job? Professor John Lennox, however, begs to differ.
Emeritus Professor of Mathematics at the University of Oxford, Lennox is both a scientist and a Christian. In his new book, Can Science Explain Everything? (£7.99, The Good Book Company), Lennox argues that the worldviews of religion and science are not incompatible. In fact, he goes one step further, arguing that science actually points towards the existence of God.
In this episode of the Science Focus Podcast, he speaks to BBC Focus staff writer James Lloyd.
Listen to as much of this podcast as you can stand, and then, perhaps, to the much shorter video below.
Just a few comments. First, note that Lloyd, the interviewer, does ask hard (and good) questions. Lennox wiggles and weasels but ultimately shows his hand. His schtick is to conflate science and religion by taking two familiar paths: changing the definition of “faith” so that scientists are said to have faith, and arguing that science and rationality also point to the existence of God. (That, of course, is the mission of the Templeton Foundation.)
As for the first bit, he notes that science deals with unrepeatable events, like cosmology, and so to investigate them—or to do any science—requires “faith in the rational intelligibility of the universe”. As he says, “In science there’s a mixture of faith and there’s a mixture of investigation and observation and all the rest of it.” In other words, he’s equating science with his Christianity, which, he says, also requires a mixture of faith and empirical evidence.
This is of course bogus. We don’t have faith in the rational intelligibility of the universe: we try to find out if the universe is intelligible, and if it obeys rules. It does, because we can make predictions based on the ubiquity of those rules. An intelligible universe, then, is not an article of faith but a conclusion based on observation of repeated patterns and fulfilled predictions. It’s like having “faith” that the sun will rise tomorrow. And that is very different from religious faith. (See here for more of my take on this issue.)
As far as “science” supporting Christianity, Lennox argues that the grounding principle of Christianity—the existence of a divine Jesus who was resurrected—is strongly supported by history. Here are some of my notes and transcribed quotes:
“Christianity is a rational faith, but when it comes to the historical side, then we use the kind of abductive inference we use in historical science.”
Ancient historians produce “very powerful evidence”; they are “very sure of . . . most of the basic facts of Jesus’s life and so on.”
And, says Lennox, Christianity also makes sense: The God and Christ explanations make sense of what we discover because an explosion of science occurred under Galileo, Kepler and Newton, “all of whom were religious”.
That’s also bogus. There were also Jews, Hindus, Muslims and atheists who made profound scientific discoveries, not to mention the “pagan” Greeks. The faith of someone who makes a discovery is not evidenced by the nature of that discovery. Kepler’s laws no more buttress Christianity than does the structure of DNA (determined by two atheists) show that there is no God. What science does show is that we make discoveries by assuming there is no God, and that adding the assumption of a God has never pushed science forward one iota—except to the limited extent that some religionists may be inspired to do science by their religious faith. But of course that doesn’t show there is a God. These days, of course, most accomplished scientists are atheists, and we don’t need God to make further progress.
Lennox also sees, beyond the copious “historical evidence for Jesus” (is he aware that it’s limited to what’s in the Bible?), further evidence for God and Jesus based on his “experience.” He regards this “experiential evidence” as quasi-scientific. For instance, Lennox asserts that “Christ’s claims can be inductively tested”. Jesus said, argues Lennox, that He would return, and “if we trusted Him as Saviour and Lord then we would experience forgiveness, peace and inner harmony and power to deal with life.” And, says Lennox, he’s seen that happen over and over again in people who have accepted Jesus. Ergo, PROOF! (Of course, you can cite examples of people who have said they gained inner harmony and forgiveness from accepting the tenets of Islam, Hinduism, or Judaism, or even atheism, but somehow Lennox forgets that.)
Finally, Lennox claims that miracles do occur, and that there are at least three times God intervened in nature beyond reviving Jesus: the Big Bang (he doesn’t think it could happen naturalistically), the origin of life, and the evolution of humans. He seems to accept the rest of evolutionary biology, but argues, like a true Intelligent Design proponent, that the origin of life and the evolution of humans either couldn’t happen naturalistically and thus involved the hand of God. This kind of human exceptionalism is a trademark of the ID/creationist Discovery Institute.
Why did the BBC put this on? And if they did, why don’t they have ME on to argue that science and religion are incompatible? I’m here, Mr. Lloyd!
Altogether, for a smart professor, Lennox makes some remarkably weak and almost humorously stupid arguments. But this is how religion distorts the rationality of wish-thinkers. Lennox is a serious wish thinker. You can get a precis of his ideas in this three-minute video:
As for Lennox’s debates against atheists, here are three videos. I haven’t watched any of them, but will look in.
