A new PBS series, Earth: A new wild, will highlight China’s breeding of giant pandas with the intention of introducing them into the wild. One goal of the series is to demonstrate that humans and nature are interdependent, according to its producer, M. Sanjayan. The 5-part series will begin on February 4. You may see a 1.5-min clip from the show at the link above. You may also see photographs of newborn panda triplets here.
There is no truth to the rumor that our colleague Professor Steve Steve sired any of the baby pandas.
Acknowledgment. Thanks to Debbie Bloom Garelick for the initial link.
Ark Park attendance is estimated to be no more than 640,000 visitors in its best year, down from 1.24 million, according to a report by Tom Loftus in The (Kentucky) Courier-Journal. That is not as bad as it appears – or as good as it appears, depending how you look at it – considering that the project has been scaled back from $172.5 million with many additional attractions to $73 million without.
The Kentucky Secular Society obtained a redacted copy of a report by Hunden Strategic Partners, of Chicago, through the Kentucky Open Records Act and distributed a press release to a handful of reporters. According to the press release, Hunden examined two scenarios: a “mainstream approach” and a religiously based approach “that may represent a specific viewpoint more associated with the Creation Museum.” The religiously based approach would net an attendance of 325,000 in the first year, a maximum of 425,000 in the third year, and then a decline to 275,000 by the tenth year. Ken Ham of Answers in Genesis had said in October that “the full-size Noah’s Ark, when it opens in 2016, is estimated to attract up to 2 million visitors a year,” but this estimate was probably based on the earlier proposal. Hunden also estimates a “fiscal impact” of $4.9 million, kind of a paltry return on a total tax-incentive package of $18.25 million.
Hunden also points to a steady decline in previous attendance at the Creation “Museum,” including a projected steep decline in 2014, but the precise figures have been redacted. I cannot tell from the wording whether to credit the report or the Kentucky Secular Society, but the press release claims that the attendance dropped precipitously after the debate between Ken Ham and Bill Nye in February.
Ed Hensley of the Kentucky Secular Society notes in the KSS press release,
The Hunden Report adds more evidence that the Commonwealth of Kentucky made the correct decision in rejecting the Ark Encounter application for tax incentives. Ken Ham, Ark Encounter, and Answers in Genesis are currently threatening to sue the Commonwealth for the right to have tax-supported religious discrimination in employment. We should consider the contrasting claims of the Hunden report while evaluating their threats.
I am sure we all read it in the papers several weeks ago: Two-thirds of all cancers are caused by bad luck. The New York Times said so. Science magazine, which published the original article said so too.
Only problem, the original article did not say that, and to her credit, Jennifer Couzin-Frankel, the Science reporter who “said so too,” corrected the record in a sort of meditation on the difficulty of getting difficult scientific concepts correct while working on deadline.
In fact, the authors did not say that “[r]andom mutations may account for two-thirds of the risk of getting many types of cancer, leaving the usual suspects—heredity and environmental factors—to account for only one-third, …” as the Times put it. What they said was more subtle, that two-thirds of the difference in cancer rates between different tissues could be explained by random bad luck. That is, “[s]ome tissues are overtaken by cancer more readily than others, and mutations accumulating in stem cells explained two-thirds of that variability,” in Couzin-Frankel’s words.
It is good to know that Science is self-correcting.
What do flamingoes and pigeons have in common? You might say very little—after all, flamingoes are long–legged, vibrantly–colored water–dwellers and the pigeons we often see inhabiting our cities appear to be completely the opposite. But according to a study published last month in Science magazine, flamingoes and pigeons are more closely related than previously thought.
The groundbreaking new study used phylogenomics to compare the genes of 48 bird species. It is the first study of its kind to use whole genomes to construct the tree of birds, thousands of genes altogether. Prior studies attempting to resolve some of the more controversial bird relationships only examined 10–20 genes, meaning that the researchers in the new study had much more data to analyze and could be more confident in their results.
Flamingoes and pigeons are more closely related than you might think, according to a new study. Images: Wikipedia
Scientists have been revising our understanding of the tree of birds using phylogenetics over the past decade. In 2006, when the cost to sequence a single genome was $10 million, Ericson et. al. published one of the earliest phylogenetic bird papers, using 5 genes from 87 species for their analysis. Hackett et. al. conducted another phylogenetic study of birds in 2008, when sequencing a genome had fallen to $1 million, this time using 19 genes from 169 species for comparison. While these studies were able to divide modern birds into their larger classifications, some of the deeper relationships remained unresolved and the researchers were still unable to establish with certainty the timing of the bird “big bang”—the rapid and successive divergence of birds into many species. Scientists agree that this divergence occurred around the time of the mass extinction of non-avian dinosaurs about 65 million years ago, but they debate whether birds diversified before or after the mass extinction.
Jarvis et. al. (2014) found that the bird big bang happened immediately after the extinction, taking a relatively short 10–15 million years. Using thousands of genes, they could draw this and other conclusions with more certainty. But with so much data, the researchers could not use standard phylogenetic analysis tools; they needed to develop new ones.
First of all, the team developed a custom algorithm for filtering out gene sequences that were unaligned or incorrectly aligned. Once the data from the aligned genes were gathered, the researchers used a new and more efficient program (implementing a maximum likelihood model) to construct the phylogenetic relationships from the raw data. Finally, the researchers used a method called data binning to reduce errors that arise from the mathematical assumption that species divergence occurred instantaneously (when it more likely occurred gradually). Using these new methods and the added information from so many genes, the researchers were able to confirm and reject with more conviction some of the branches proposed by the previous studies, like the flamingo-pigeon relationship.
The red-billed tropicbird is a member of the Tropicbird family, which is excluded from Pelecaniformes in the new phylogenetic tree of birds. Image: Wikipedia
Along with this relationship and resolving the timing of the bird divergence, the researchers discovered several other important findings about birds. From some of the traits of the bird tree, they could conclude that the common ancestor of land birds was an apex predator, or a predator at the top of the food chain with no predators of its own. Also, the new tree of birds contradicts previous trees by excluding eagles and New World vultures from Falconiformes, the group containing falcons, kestrels, and other birds of prey. Similarly, the group Pelecaniformes excluded tropicbirds, a family of seabirds. Finally, the study revealed some characteristics about the way songbirds gained their vocal abilities with a gene that is similar to the one giving humans the ability to learn speech. This finding has gained a lot of recognition because of its potential application to the study of human speech.
As we’ve talked about in previous posts, using a complete set of genomic data can give us a more accurate phylogenetic tree and more confidence in results like the ones we just mentioned, as long as the analytical methods are appropriate for big data sets. Because the researchers in this new study improved their methods to reduce the error and noise that can be found in big data sets, their tree is probably the most accurate tree of birds produced so far. But all mathematical models of natural phenomena are at least somewhat incorrect, so it is likely that researchers will make further improvements to the methods and the tree.
Regardless, the field of phylogenetics is changing to realize the full potential of genome sequencing. As the tools to analyze these data improve, we’ll continue to gain new insights into species relationships and evolution with greater confidence than ever before. Who knows what other surprising relationships we’ll discover?
See the complete tree of birds here.
This series is supported by NSF Grant #DBI-1356548 to RA Cartwright.
The subtitle of this book by frequent PT commenter Carl Drews is “Crossing the Red Sea with faith and science.” Mr. Drews achieved a modicum of fame a few years ago for his master’s thesis, in which he speculated that Moses and his followers had crossed the Sea of Reeds during a wind setdown, that is, an event where the wind blows so hard on a body of water that the water level on the windward side drops, sometimes to 0. It is in some sense the opposite of a storm surge.
Judging by the book, it was a splendid master’s thesis indeed! Mr. Drews carefully evaluated possible locations, chose one, and modeled it, showing that the wind setdown could plausibly have occurred for a plausible wind velocity. See here for Mr. Drews’s own brief description of his work. Sorry, Cecil B. DeMille, no walls of water!
I thought the book went downhill from here. Mr. Drews, though he denies it, is virtually a biblical literalist. To be sure, he is far more sophisticated than, say, Ken Ham or even Hugh Ross. He knows that the parts of the Bible that so bemuse Mr. Ham are poetry and not to be taken seriously. But he states flatly that he believes in the miracles that Jesus of Nazareth purportedly performed and thinks that they were a suspension of natural law. And he believes firmly that the Exodus happened as described in the Bible, so he looks for evidence how it happened, rather than whether it happened. A wind setdown is certainly plausible but has little more hard evidence to support it than the idea that the plagues were caused by the eruption of the Thera volcano.
Anyone who relies on the Supreme Court to guarantee that creationism will not be taught in public school or that the Ark Park’s threatened lawsuit will necessarily fail might want to read an article by Erwin Chemerinsky in the January 1 issue of The Washington Spectator. In that article, which I take to be a longish abstract of his book, Chemerinsky argues that the Court has generally not lived up to its “lofty expectations” and indeed has more often “upheld discrimination and even egregious violations of basic liberties.” The Chemerinsky article does not appear on the Spectator website, so I will abstract it very briefly below the fold.
Update, January 5, 2015. The article is now available here, so you may read it for yourself and not take my word for what Chemerinsky says.
Michael Behe is very thrilled that a PNAS paper published this year “confirms a key inference I made in 2007 in The Edge of Evolution.” The Discovery Institute is also thrilled, enough so to reprint Behe’s July 14, 2014 op-ed on ENV as this year’s #4 in the top-story countdown.
Says Behe, regarding what he describes as “the need for multiple, specific changes in a particular malarial protein (called PfCRT) for the development of resistance to chloroquine” :
… thanks to Summers et al. 2014…One of their conclusions is that a minimum of two specific mutations are indeed required for the protein to be able to transport chloroquine. … The need for multiple mutations neatly accounts for why the development of spontaneous resistance to chloroquine is an event of extremely low probability – approximately one in a hundred billion billion (1 in 1020) malarial cell replications – as the distinguished Oxford University malariologist Nicholas White deduced years ago. The bottom line is that the need for an organism to acquire multiple mutations in some situations before a relevant selectable function appears is now an established experimental fact.
No where does either Discovery Institute piece make any mention of Brown biologist Ken Miller’s epic takedown of Behe’s new claims of vindication. More below the fold.
Photograph by Jim Kocher.
Photography contest, Honorable Mention.
Painted Wall – Black Canyon of the Gunnison River, Montrose, Colorado, May, 1999; Kodachrome 64. Proterozoic schists intruded by pegmatite dikes (~1.25 Ga). Vertical relief is ~2,200 ft.
According to a blurb in Science yesterday, researchers have discovered a fossilized fish whose eyes show traces of pigment and also fossilized rods and cones. The existence of the cones suggests that color vision developed at least 300 Ma ago. You may read the full article, which appears in Nature Communications, by following the link from the Science article; you can read it only on screen – a pdf will cost you $32.
P.S. Yes, I learned about Nature‘s sharing policy by tracing the link from Science. If you follow the link to the Nature article itself, you get only the abstract.
I would not exactly call it a Christmas present, but today I happened to learn of a press release circulated by the Nature Publishing Group on December 2 of this year. The press release was not exactly a model of clarity, but if I understand it correctly, subscribers to any of a number of the publishing group’s journals can legitimately make articles available to individual colleagues who are not subscribers. In addition, readers of “100 media outlets and blogs … will be able to provide their own readers with a link to a full text, read-only view of the original scientific paper.”
Recognizing that “researchers are already sharing content, often in hidden corners of the Internet or using clumsy, time-consuming practices,” Nature has decided to “present a new way to conveniently share and disseminate this knowledge using technology from one of our innovative and disruptive divisions – Digital Science – to provide a real solution to the global problem of how to efficiently and legitimately share scientific research for the benefit of all.”
I consider this development very welcome indeed.
That is, are male members of the species Homo sapiens idiots? No, but according to a recent article, they are more likely to be idiots than women are.
The only thing surprising about this conclusion is that it is so unsurprising. For years now, whenever my daughter or I see a bicyclist dash madly across 4 lanes of traffic, we announce to each other, “Another male trying to improve the gene pool.” We are uncertain who said it first, but my daughter somewhat sheepishly thinks it was she. Which, of course, makes me think that we brought her up right.
The study that drew the unsurprising conclusion looked at the recipients of the Darwin Awards over the past 20 years. To qualify for a Darwin Award, you have to remove yourself from the gene pool, generally by killing yourself, but I suppose that castration would do about as well.
After the usual mutterings about selection bias and noting that the study was retrospective (double-blind would have been kind of tricky), the authors conclude that ~90 % of Darwin Award winners were male. They propose a Male Idiot Theory, which to my mind is at least as good as Molière’s diagnosis, she is mute because she has lost her speech.
NPR reported on the article here. Some of the comments are interesting, and some suggest a sociobiological explanation, which I will leave to your imagination – suffice it to say that among our early ancestors, only the men had to take the risk of hunting elephants. Or whatever.
The authors of the original article assure us that they plan an observational study and even now are scheduling holiday parties, both with and without alcohol.
(Reprinted from Recursivity.)
As each year draws to a close, we can expect being treated to the annual ritual of self-congratulation by intelligent design advocates. Why, they have accomplished so much in the last year! The movement is simply overflowing with ideas! And honest, god-fearing people! And real scientists! And publishing successes! Not at all like those dogmatic, liberal, communistic, intolerant, censoring, Nazi-like evolutionists!
2014 is no different. Here we have the DI's official clown, David Klinghoffer, comparing himself to Leon Wieseltier (in part because, he says, their surnames sound similar -- I kid you not) and the Discovery Institute to The New Republic.
Actually, there are two big similarities I can think of: when TNR tried to come up with a list of 100 "thinkers" whose achievements were most in line with things that TNR cares about, science didn't even merit its own category. But theology did! And TNR's Wieseltier wrote a review of Nagel's book that demonstrated he didn't have the vaguest understanding of why Mind and Cosmos was nearly universally panned. Wieseltier even adopted intelligent design tropes like "Darwinist mob", "Darwinist dittoheads", "bargain-basement atheism", "mob of materialists", "free-thinking inquisitors", "Sacred Congregation for the Doctrine of the Secular Faith", and "scientistic tyranny". Don't let the door hit you on your way out, Leon.
Klinghoffer claims "In the evolution controversy, it's supporters of intelligent design who stand for ideas (disagree with us or not) and idealism." Well, that's something that we can actually check. Since ID is so brimming with ideas, let's look at ID's flagship journal, Bio-Complexity, and see how many papers were published this year. ID supporters are always complaining about how their groundbreaking word is censored by evil Darwinists. If true (it's not), then in Bio-Complexity they have no grounds for complaints: nearly all of the 32 people listed on the "Editorial Team" are well-known creationists and hence automatically friendly to any submission.
How many papers did Bio-Complexity manage to publish this year? A grand total of four! Why, that's 1/8th of a paper per member of the editorial team. By any measure, this is simply astounding productivity. They can be proud of how much they have added to the world's knowledge!
Looking a little deeper, we see that of these four, only one is labeled as a "research article". Two are "critical reviews" and one is a "critical focus". And of these four stellar contributions, one has 2 out of the 3 authors on the editorial team, two are written by members of the editorial team, leaving only one contribution having no one on the editorial team. And that one is written by Winston Ewert, who is a "senior researcher" at Robert J. Marks II's "evolutionary informatics lab". In other words, with all the ideas that ID supporters are brimming with, they couldn't manage to publish a single article by anyone not on the editorial team or directly associated with the editors.
What happened to the claim that ID creationists stand for ideas? One research article a year is not that impressive. Where are all those ideas Klinghoffer was raving about? Why can't their own flagship journal manage to publish any of them?
As 2015 draws near, don't expect that we will get any answers to these questions. Heck, not even the illustrious Robert J. Marks II can manage to respond to a simple question about information theory.
The authors of House Bill 597, the anti-common core science distorting bill introduced in the Ohio legislature, is dead for now. According to the Cleveland Plain Dealer (via NCSE), the bill won’t be debated or voted on this term. However, according to the bill’s author, Republican State Representative Andy Thompson, the issue will be revived in the next term of the Legislature. I’ll note that the Bill’s co-author, Republican Speaker Pro Tem Max Huffman, will be term-limited out of the Legislature and thus won’t be around to shepherd it.
As I argued previously on the Thumb, the Bill also enshrines a distorted representation of science education, focusing students on memorizing facts rather than learning the processes of science (see here and here and here). I’ll be interested to see if that same distortion appears when the issue is revived, if it is in fact revived.
This is the fourth in a series of articles for the general public focused on understanding how species are related and how genomic data is used in research. Today, we talk about some common fallacies in phylogenomics.
Where do humans fit on the evolutionary tree of life? This is an important topic in evolutionary biology. A lot of people believe humans are the most important and highly-evolved organisms, but in reality, all modern species are equally evolved. Our natural tendency to assume that humans are evolutionarily superior has led to a few misconceptions about phylogenetic trees.
To understand the first misconception, let’s look at a phylogenetic tree of plants (from “The Amborella Genome and the Evolution of Flowering Plants”). Eudicots and monocots are two classes of flowering plants, or angiosperms, and the plants in black are non-flowering plants. The term “basal” refers to the base of a phylogenetic tree, and a basal group is a species that branches closer to that base. The authors chose to label the angiosperms that are not eudicots or monocots as “basal angiosperms.” But this label is arbitrary; all the angiosperms are equidistant from the common ancestor and thus equally evolved. We sometimes tend to give more weight to branches that contain the species of interest and call other branches basal, almost assigning them a lesser importance. In this case, the species of interest is plants that consist of many foods that humans eat; a species is often deemed more important as it relates to humans. But modern species are equally evolved from a root common ancestor regardless of when their branch diverged from the common ancestor. To avoid confusion, it might be best to eliminate the “basal” term altogether.
This type of thinking also leads us to place humans at the end of phylogenetic trees. However, this placement is arbitrary and trees can be drawn in many equivalent ways. For example, compare a tree of primates with the branches rotated. The tree on the left, with humans at the top of the tree, is one you might see more often. But both of these trees are actually identical, and the relationships between species that can be inferred from the tree on the right is the same as the relationships in the tree on the left. Species at the tip of a tree are equidistant from the root common ancestor, so they can be considered evolutionarily equivalent.
Similarly, a common misconception is that humans evolved directly from monkeys. Monkeys, though, are modern species just like we are and have been evolving and changing over time. The common ancestor we share with monkeys may have looked much different than monkeys do now. This assumption that modern species represent an ancestral state of human evolution is what T. Ryan Gregory calls the platypus fallacy. Gregory uses the example that we can’t examine the traits of platypuses and think that humans at one point in their evolution possessed these same traits. We can no more infer the traits of human ancestor species from platypuses than platypuses can infer the traits of their ancestors from us.
Human-centered thinking is very prevalent in our society, affecting our laws, religions, and customs. While it probably influences all of us on a personal level, it can lead to false conclusions and misconceptions in science, like thinking that humans are the most highly evolved species. But all modern species are evolutionarily equivalent because they have been evolving for the same amount of time. Eliminating this fallacy will enable us to better understand the evolutionary process.
For more information on basal groups, check out: “Which side of the tree is more basal?, Krell, Frank et al. Systematic Entomology (2004).
This series is supported by NSF Grant #DBI-1356548 to RA Cartwright.
Update, 12/11/2014, 12:30-ish MST: A Lexington Herald-Leader editorial has a [f]ew questions for Answers in Genesis, not least,
Why does God need so much taxpayer help?
Really, has God been so lame spreading the good news that AIG must “counter the myths floating around about the Bible-upholding Ark Encounter,” on a digital video board in New York’s Times Square?
Does God need to be defended with the demagogic language AIG and its founder Ken Ham use in the holy war against “intolerant liberal friends,” “secularists,” “Bible-scoffers,” and, the most telling, “agitators outside the state?”
The editorial concludes,
Perhaps Answers in Genesis should give up thanking God that intolerant liberals “can’t sink this ship,” and ask the deity instead whether it can be built without more government handouts.
I noted in a comment to another article that, according to reporter Joe Sonka, writing in Insider Louisville, The Lost Ark: Kentucky will not grant tax incentives to Ark Encounter,
Kentucky’s Tourism Arts & Heritage Cabinet Secretary Bob Stewart informed representatives of the proposed Ark Encounter tourist attraction today that their project will not be eligible for up to $18 million in tax incentives from the state, due to their refusal to pledge not to discriminate in hiring based on religion.
and further that
Stewart cited AiG CEO Ken Ham’s Nov. 19 fundraising letter that accused the Beshear administration of religious persecution and reaffirmed their desire to discriminate in hiring based on religion. He also cited other statements throughout the year from AiG officials claiming the purpose of the park is to evangelize and indoctrinate its visitors.
Mr. Stewart wished Ark Encounter well but noted,
“Certainly, Ark Encounter has every right to change the nature of the project from a tourism attraction to a ministry,” wrote Stewart. “However, state tourism tax incentives cannot be used to fund religious indoctrination or otherwise be used to advance religion. The use of state incentives in this way violates the Separation of Church and State provisions of the Constitution and is therefore impermissible.”
Mr. Sonka appends to his article two letters: The first is from Bob Stewart, the secretary of the state’s Tourism Cabinet, to James Parsons, an attorney for the Ark Park, and outlines the state’s reason for denying the tax incentives. The second is from Mr. Parsons to Mr. Stewart; it looks as though they may have crossed in the mail. Mr. Parsons observes that Ark Encounter is (now) wholly owned by Answers in Genesis and argues that it should therefore be treated as a religious nonprofit. He continues with a lot of material that only a lawyer could love and concludes,
For all these reasons, if you insist on the newly imposed condition in your Letter [sic], it will amount to unconstitutional viewpoint discrimination[,] and my client will have no choice but to seek redress in federal court. [Boldface in original document.]
Viewpoint discrimination generally refers to limiting speech in a public or semi-public space; I would like to hear from a lawyer as to whether that concept can reasonably be extended to a case such as this or whether Mr. Parsons is just whistling past the graveyard.
Thanks again to my Indefatigable Informant for the tip.
The Hebrew Bible says that God made humans from dust,* but maybe it was a slurry of clay and water. That is a tentative conclusion you might draw from an experiment that used a (very) high-powered laser beam to zap a suspension of clay in an aqueous solution of formamide, a very simple organic compound. The result has been reported in the press, but there is a somewhat more-precise article in Science magazine. (You may find the abstract of the original article here and the supporting information here. I did not get access to the full article.)
In a nutshell, a team at the J. Heyrovský Institute of Physical Chemistry in Prague used a laser that can produce up to 1 kJ in a 300 ps pulse,** irradiated the suspension, and produced adenine, cytosine, guanine, and uracil, which are the bases of the RNA molecule. And apparently not a drop of thymine, one of the bases of DNA. The experiment is supposed to simulate the bombardment of the early Earth by comets and presumably supports the hypothesis that an RNA world came first.
* Actually, Job, Isaiah, Psalms, and I imagine elsewhere say clay, as in, “We are the clay, and you are our potter.” (Don’t get excited; I consider the fact to have no significance whatsoever.)
** I am a laser physicist and wrote my thesis on laser-produced plasmas, so you must forgive me for somewhat stressing the laser, which to this day gives me a certain amount of pulse envy.
I am a physicist, with a specialty in optics, so I was especially interested in The Mind’s Eye, by Oliver Sacks (not to mention the less well known The Island of the Colorblind). The Mind’s Eye is a fascinating book about the visual system, many of the things that can go wrong with it, and what we learn from them. It is also the book in which Dr. Sacks reveals that he suffers from prosopagnosia, or face blindness; is not a surgeon because he cannot visualize; and functions only with great difficulty now that he has monocular vision as a result of a retinal cancer. I have great difficulty recognizing faces, but nothing approaching prosopagnosia, and it is a marvel to me that he could cover it up for the better part of 80 years.