adam-and-eve-cast-out-of-paradise-after-eating-from-the-tree-of-knowledge-in-the-garden-of-eden.pngI would like to introduce everyone to James Downard, and his website Troubles in Paradise (TIP). TIP is available at or

James Downard is an activist with decades of experience tracking the creationists, stretching back to encounters with Stephen Meyer in Washington state in the early 1990s. In 2010, he did a guest post for PT, “An Ill Wind in Tortuca”, available at:[…]wind-in.html

Troubles in Paradise is a massive review of the creationism/ID movement, its people, and its arguments, along with a similarly massive review of relevant scientific evidence and literature. TIP primarily covers the movement up to about 2004, which of course was just about the peak of the ID movement, leading up to the 2005 Kitzmiller v. Dover case.

I think it is extremely valuable to the pro-science community to have such a historical review available: the ID movement actively tries to conceal what it was saying pre-Kitzmiller, and of course the “intelligent design” label itself was an attempt to disguise connections to creation science. (And, “creation science,” particularly the whitewashed version put forward for the Edwards v. Aguillard case, was its own attempt at obscuring connections to religious fundamentalism.) (On this, see especially: Matzke, N. (2009), “But Isn’t It Creationism? The beginnings of ‘intelligent design’ and Of Pandas and People in the midst of the Arkansas and Louisiana litigation.” In: But Is It Science?: The Philosophical Question in the Creation/Evolution Controversy, Updated Edition, eds. Pennock & Ruse, Prometheus Books, 377-413; google Scholar)

Today in 2015, it is not uncommon for commentators new to the creationism/ID debate to start producing writings almost totally ignorant of the history of the issue. Hopefully Downard’s effort will help correct this problem, and will serve as a resource that science fans can link to and cite.

Troubles in Paradise is really several books’ worth of work, so if you’ve ever gone to the bookstore and bought a science book, please think about making a similar donation so that Downard can continue his efforts.

Below, I post Downard’s short description of the project, which includes a Q & A email interview I conducted with him, and links to his GoFundMe page, Please reblog, retweet, and spread the word! PS: James Downard’s Twitter is: @RJDownardNick Matzke


Short description of Troubles in Paradise, by James Downard:

Welcome to TIP, a new open access resource for defenders of sound science who get really unsettled by the claims of antievolutionists (be they Young Earth Creationists or the newer brand of Intelligent Design) but may not have all the best science information ready to drop on their claims.

The TIP files (all in pdf format) cover all aspects of antievolutionism (from paleontology and biology to the social and political ramifications of antievolutionism as they play out in schoolrooms and school boards or in state legislatures, Congress, or even candidates for President.

The Old TIP files form the base of the project, drawing on over 5500 sources, and step by step I am updating that material with a much larger set of newer data (over 36,000 sources and counting, including over 14,000 technical science sources aimed at claims popping up in over 6000 antievolutionist works) to keep TIP constantly current. The new modules also have an index to help locating all specific topics and people covered.

There are more pdfs & offsite web links in Other Stuff, including the 3ME illustrated guide to the Cambrian Explosion, and the origin of birds and mammals, the perfect heavy brick to lob at antievolutionists who make the mistake of claiming “there’s no evidence for macroevolution.” 3ME not only shows how wrong that is, it also pulls back the curtain to see just how antievolutionists manage to evade all that evidence (not a pretty picture, but has to be done).

Check out all the material here on TIP, all open access to download and share freely with anyone you think needs evens stronger evidence to counter the claims of antievolutionists.

Q & A with James Downard:

Q: Why did you decide to call your project “Troubles in Paradise” (TIP)?

Physics trumps biology

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Or, perhaps more precisely, Did dark matter kill the dinosaurs?, which is the way that an article in ScienceNOW put it.

Readers of PT doubtless know that there have been a half-dozen or so mass extinctions in the history of the earth, and they appear with a periodicity on the order of 30 million years. You can see an early graph here. The vertical arrows are separated by approximately 30 million years. Not every vertical arrow points to a mass extinction, so it might be better to say that the first harmonic of the data set is 30 million years; that is, if the periodicity is real, it sometimes skips a beat.

What is interesting is that some of the extinctions appear to have been caused by collisions with an asteroid, whereas others may be the result of long periods of extreme volcanism – yet all the extinctions occur with the same period of 30 million years.

… And I will tell you the outcome. I cannot find the origin of that quotation, and I am pretty sure it is not original, but I thought of it when I read this article in Science. In a nutshell, Willie Soon, a part-time employee of the Smithsonian Institution, has published a number of articles linking changes in Arctic air temperature with changes in the sun’s output. His conclusion is at variance with the well established theory that anthropogenic carbon dioxide has caused those changes. The science historian Naomi Oreskes told the New York Times that “Willie Soon is playing a role in a certain kind of political theater” designed to give the impression that there is debate about global warming.

Dr. Soon (according to the Times) is neither an astrophysicist nor a climatologist. He has nevertheless received funding from a utility company with considerable holdings in coal and is alleged not to have disclosed that funding in a number of scientific publications that require such disclosure. Professor Oreskes opines that any papers that have failed to disclose corporate funding, when required, should be withdrawn (and, incidentally, warns that universities need to look closely at this problem).

Dr. Soon has further received funding from a group called Donor’s Trust, which according to Science funnels anonymous donations to groups “championed by political conservatives.” Further, Greenpeace has asked the IRS to investigate whether Dr. Soon has been supported by a foundation funded by Charles Koch, possibly in violation of rules that prohibit non-profits from trying to influence legislation.

The Times reports that Dr. Soon has received a “warm welcome” from such luminaries as Sen. James Inhofe, who believes or pretends to believe that climate change is a widespread hoax.

The Smithsonian Institution, for its part, has sicced its Inspector General on Dr. Soon; the IG will investigate whether Dr. Soon has violated the conflict-of-interest policies of the journals in which he published.

Q&A in the WASP nest

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By Steven Mahone.

What would happen if a dyed-in-the-wool secularist was given the opportunity to speak with students from one of the most religiously conservative school districts in the country? Well, I had the privilege of finding out first hand.

The Classical Academy (TCA) is an affluent, public charter high school in north Colorado Springs, so imagine my surprise at receiving an invitation to represent the secular and scientific viewpoint for a week-long seminar titled “Worldviews: The Scientific, Religious, and Cultural Underpinnings of Our Society”. The school is situated two miles from Focus on the Family (an evangelical stronghold for 19th century Christian “values”) and New Life Church, a 10,000-member mega-church that was once pastored by Ted Haggard. (You might recall that Haggard had a parking lot “altercation” with Richard Dawkins when Dawkins attempted to interview him for a BBC special. You can’t help but appreciate the irony when six months after he admonished Dawkins for living a lie behind the veil of science, Haggard was caught with methamphetamines and a male prostitute.) Also sharing the same zip code with the school are the corporate headquarters for Compassion International, The Association of Christian Schools International, and Cook Ministries. I bring this up only to set the stage for my mindset before I ever arrived at the school’s parking lot.

Pygoscelis papua

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Photograph by Dan Phelps.


Pygoscelis papua – gentoo penguin, Danco Island, Antarctica.

Imagine that you want to analyze the 3.2 billion bases of the human genome. If you recruited every undergraduate student at ASU, all 70,000 of us, to type those data into a spreadsheet, it would still take about 13 hours. So you develop a computer program that analyzes the data for you. But then you find out that your huge data set amplified small errors in your algorithm and gave you the wrong answer. This is the issue facing evolutionary biologists using genomic data, a practice that is becoming standard to construct reliable phylogenies (see our previous posts about the new bird and insect phylogenies). Our lab, working under Dr. Reed Cartwright, has developed a novel method to quickly analyze genomic data and produce an accurate phylogeny that improves upon previous techniques.

The giant panda genome was assembled using de novo techniques in 2010, but better methods of phylogeny construction are in development. Image: Wikipedia

Historically, scientists have compensated for potential inaccuracies in genomic-size data in two ways: by using better statistical tools to analyze the data after they have been acquired or by acquiring fewer, more informative data.

In the first method, you start with sequenced genomes in the form of short fragments (about 100 base pairs) and develop computational algorithms to compare those sequences to a reference genome for reassembly, like Liu et al. did in their 2003 analysis of primate genomes. The reference genome is one that we know with a high level of confidence; for example, the human genome is reliably known and often used as a reference. If, however, a reference is unavailable or unreliable, you could use a computer program to assemble the sequences with a process known as de novo assembly, which Li et al. used to construct the giant panda genome in 2010. These programs, called assemblers, use graphical techniques (for example, De Brujin graphs) to remove errors in phylogenetic trees and resolve repeated data that are harder to determine in short sequences than longer ones. Algorithms like this can greatly improve the accuracy of conclusions made from genomic data, but de novo assembly without a reference genome requires high quality annotation of the sequences and, once the genome is reconstructed, time-consuming alignments of similar sequences to produce a phylogenetic tree.

Alternatively, you could acquire fewer data in the first place. You would need to determine which markers in a genome are informative and necessary to draw certain conclusions and then only obtain those data. By reducing the size of the data set and eliminating unnecessary information, we improve the accuracy without having to implement sophisticated analytical techniques. McCormack et al. used this principle in 2012 to determine the tree of placental mammals from certain markers. However, the major drawback of this method is that markers appropriate for a particular project or species most likely cannot be reused for other projects. The ability to recycle genomic data reduces the cost and time of phylogenomic studies.

Our lab is working on a program that constructs phylogenetic trees more quickly and easily than either of these methods. The program, called SISRS, combines genome assembly with identification of homologous genes to rapidly reconstruct phylogenies without the need of a reference genome or annotation. In the next post, we’ll go into detail about how SISRS works and what makes it a better way to analyze genomic data.

This series is supported by NSF Grant #DBI-1356548 to RA Cartwright.

Four pandas in a captive breeding population have died of canine distemper, one is “stable,” and four are “sick,” according to an article in today’s Science magazine. The pandas have been quarantined, and close contact with tourists, who may carry the disease, has been eliminated. The authorities have also repaired fences to keep dogs out. There is, fortunately, no indication that the disease has spread to a wild breeding population, which is apparently on the far side of a mountain range. The article notes that there is a vaccine to protect against canine distemper, but it is “unclear” whether the breeding center has used the vaccine.

The article goes on to describe the practice of introducing adults bred in captivity into the wild. The government maintains reserves for the pandas and has established corridors that, according to the article, cover 85 % of the pandas’ natural habitat. The article also describes a controversy over the breeding program, in particular, over the practice of taking cubs in the wild from their mothers prematurely, so that the mothers can breed more often, without regard to the needs of individual pandas.

Finally, researchers are awaiting the results of a survey which will ascertain the quality of the protected habitat and help scientists decide how many pandas they may introduce.

Chelepteryx collesi

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Photograph by Jim Foley.


Chelepteryx collesi – white-stemmed gum moth, Canberra, Australia. Mr. Foley writes, “The caterpillar is about 12 cm long! Yet another member of the Australian fauna you don’t want to mess with. … We seem to have more venomous stuff than most places: lots of snakes, stonefish, spiders, jellyfish, blue-ringed octopus, etc., not to mention the crocodiles and sharks.”

A somewhat outraged (but entirely justified) article by Timothy Egan in the Times reminded me of an interview I heard the other day on Fresh Air.

First, the Egan article: Mr. Egan is properly outraged at the New York Attorney General’s finding that dietary “supplements” sold by major retailers often contain none of the “active ingredient.” Sorry, the scare quotes are mine, not Mr. Egan’s, but I think they are entirely apt. Indeed, the fact that the “supplements” contains no active ingredient and people write testimonials to their efficacy hints that even dietary supplements that actually contain the active ingredient may be no more than placebos. Nobody knows, in part, because the dietary supplement industry in the US is virtually unregulated (see also the Times editorial here).

Which brings me to Fresh Air. Terry Gross interviewed Johns Hopkins neuroscientist David Linden, the author of a recent book on the science of touch. Fascinating interview, but then, at the 29-min mark, Ms. Gross asked Professor Linden about the placebo effect. He paused and then answered,

The general thing I take from this is that, in the end, the substrate is biology. When things work, whether they are drugs or the placebo effect or acupuncture or meditation or psychotherapy, they work because they are changing the functions of brain circuitry, and my feeling is that, if it works, it works, and it should be used. There is no reason to abandon something that works just because we don’t understand all the biological steps in the way it works. In truth, many of the most popular drugs in the armamentarium for neuropsychiatric disorders – we don’t understand how they work anyway. We don’t understand how antidepressants work. We don’t understand how lithium works for bipolar disorder. So if the placebo effect works, then let’s use it.

I cannot disagree that, if the placebo effect works, then we should use it. But how? Is it OK to lie to a patient and claim that some worthless herb is in fact a medication or that sticking needles here and there has some specific therapeutic effect? Or is there potentially a better way to harness the placebo effect and really make it work? Professor Linden may have been taken aback by the question, but I thought his response was a bit facile; I will be especially curious to read comments on how others, especially medical professionals, answer these questions.

The tenth annual Evolution Weekend, February 13-15, is almost upon us. To check out what’s going on in your neighborhood, click here. This year’s theme is Science and Religion in Dialogue: Past, Present, and Future. The Evolution Weekend website notes,

Evolution Weekend is an opportunity for serious discussion and reflection on the relationship between religion and science. An ongoing goal has been to elevate the quality of the discussion on this critical topic, and to show that religion and science are not adversaries. Rather, they look at the natural world from quite different perspectives and ask, and answer, different questions.

Religious people from many diverse faith traditions and locations around the world understand that evolution is quite simply sound science; and for them, it does not in any way threaten, demean, or diminish their faith in God. In fact, for many, the wonders of science often enhance and deepen their awe and gratitude towards God.

While I do not entirely agree with the sentiment expressed in the first paragraph, it is better than some of the alternatives.

Finally, NCSE reminds us that the anniversary of Darwin’s birth is February 12, and House Resolution 67 would recognize

Charles Darwin as a worthy symbol on which to focus and around which to build a global celebration of science and humanity intended to promote a common bond among all of Earth’s peoples.

Rep. Jim Himes introduced the bill on February 2, and, according to a press release from the American Humanist Association, it is the latest in a series of such resolutions, the previous four having been introduced by Rep. Rush Holt and Rep. Pete Stark. Although the PR is not explicit, I think we may infer that none has so far passed the House.

Wave 3, which appears to be Channel 3 in Louisville, Kentucky, reported yesterday that the Ark Park indeed plans to sue the state over tax incentives that were denied last month. Wave 3 reports,

Lawyers say this encounter is about to make an appearance in court and it’s all over tax incentives. The lawyer for the Ark Encounter says it will sue the state in federal court to try to regain the rebates it believes the state should give it for building the biblical attraction.

The link is approximately a transcript of the Wave 3 television broadcast, but the broadcast itself is worth watching – the television reporters got a tour of the construction site, and it looks like they are actually building the model Ark. A nice slideshow, Constructing the Ark Park, is also linked to the Wave 3 Web page.

The lawyer for the Ark Park, Mike Johnson, made an interesting statement:

They had to move over a million cubic tons, I think it was, of dirt.

If that is true, then the ton must be a unit of length, or else they are building the model in a 9-dimensional space. Maybe that is how Noah snuck so many creatures onto the Ark: he dropped them off into some of the extra dimensions. Works as well as any explanation promulgated by AIG. I hope that Mr. Johnson is as good a lawyer as he is an engineer.

At Jerry Coyne’s bl*g Why Evolution Is True he has a new post calling attention to a web site on The Third Way of Evolution. It was apparently put up last year by James Shapiro, Denis Noble, and Raju Pookottil. It presents statements by 43 people expressing their view that a new Way of Evolution is needed. It has apparently been up for over 8 months, but only recently was mentioned by Denyse O’Leary at Uncommon Descent.

None of these people are, as far as I can tell, creationists. Many are working, or retired scientists or engineers. Jerry gives telling analyses of the views of some of the more prominent critics among them, citing his own past demolitions of their views. An interesting point is that all of these people are said to have agreed to being listed on the TWOE website.

A unified statement by 43 people, mostly scientists of some reputation, laying out a new evolutionary synthesis, should attract a lot of attention. However, the Third Way site does not do that. The difficulty is that each of these people seems to march to a different drummer, and in a different direction. They go off over the horizon in different directions, each convinced that theirs is the promising new direction. The common theme is that “The Modern Synthesis is dead, and I have a replacement for it!” But there is no agreement on what the replacement should be.

It is fun reading. Let’s have a thread there. Calling these folks creationists is not helpful; overwhelmingly they simply aren’t creationists. (The Second Way is, Shapiro et al. point out, creationism. To me it is a bit strange to hear creationism cited as a Way of Evolution, when what it actually says is “no way”.)

A very useful activity would be to characterize the views of some of the 43. Are they:

  • Lamarckians?
  • Mutational teleologists?
  • Saltationists?
  • (etc.)

Let’s discuss. I will, as usual, try to vigorously pa-troll the comments and send off-topic comments to the Bathroom Wall. Interventions by our usual creationist trolls and replies to those will go to the BW.

What comes to mind when you think about insects? For a lot of people, the word sends a shiver up their spine as they imagine the tiny, creeping legs, buzzing wings, stinging tails, and biting fangs. But what those people may not know is that insects comprise one of the most important classes of animal; there are more species of insect than any other animal group, and they can claim being the first animals to achieve many things, including flight and social societies.

Insect evolution is historically poorly understood, and the lack of a well-resolved and supported tree of insects has left researchers with many questions about their evolutionary relationships. For example, how are grasshoppers, crickets, cockroaches, and termites related? Which species are the closest living relatives to Holometabola, the group containing beetles, moths, butterflies, wasps, bees, and ants? What is the timeline of insect evolution? Answering these questions could help us understand how different insect traits evolved, which could reveal insights into the mechanism of evolution itself.

Silverfish (left) evolved to lose their wings and other appendages independently from other insects like jumping bristletails (right), and they make up their own branch on the new phylogenetic tree of insects. Images: Wikipedia

Scientists with the international 1KITE project set out to answer these questions and more by using phylogenomics to compare 1478 genes among 103 species of insect. First, they sequenced the DNA to find genes that were present in all the species, most of which coded for proteins involved in translation, protein transport, neurogenesis, and other basic cellular functions. Similar to the study of birds that we talked about last time, Misof et al. used improved methods of analysis to reduce errors from such a large dataset. Before analyzing the data, the researchers accounted for possible sources of bias by removing confounding factors; for example, they removed any data that violated the assumption that evolution is a time-reversible process. They then discarded any sequences that were misaligned and generated their tree with maximum likelihood models as well as a partitioning scheme to improve the accuracy of the assumed model of evolution. Using data from two sources, nucleotides and amino acid sequences, the researchers generated two matching phylogenetic trees.

The new phylogenetic tree was able to answer many questions about insects with a higher statistical confidence than previous studies:

  • Earwigs, ground lice, stoneflies, crickets, gladiators, ice crawlers, webspinners, stick and leaf insects, praying mantids, and termites comprise a branch on the tree (a monophyly) called Polyneoptera, a hypothesis proposed in previous studies.
  • The study proposed the new conclusion that lice are the closest living relatives to beetles, moths, butterflies, wasps, bees, and ants.
  • Insects originated around 479 million years ago, a finding that contradicts previous estimates of about 400 million years ago.
  • Insects inhabited land at about the same time as plants (around 450 million years ago) and developed flight after they had established colonies, corroborating a 2013 study.
  • Remipedia, a class of blind crustaceans found in caves, is the closest living species to insects, confirming prior studies.
  • Silverfish comprise their own branch on the tree, as other recent studies have proposed, implying that they evolved to lose their head endoskeleton, leg-like structures called styli, and the sacs on their legs (coxal vesicles) in parallel to but separately from winged insects.

While many of the conclusions drawn by the new study are not completely new findings, the history of insect evolution is controversial and relationships previously proposed lacked certainty. The ability of the 1KITE researchers to confirm and deny these relationships with such high confidence shows the power of genomic analysis. But as with the recent bird phylogeny paper, the methods of analysis had to change to accommodate a larger dataset; specifically, confounding factors that could lead to biased conclusions were a larger concern than for previous studies. Jarvis et al. chose with their bird analysis to modify their programs to create a better phylogenetic tree, while Misof et al. removed data with these confounding factors during analysis. It remains to be seen which genomic data analyses produce the best results, but what we do know is that genome sequencing will play a major role in future phylogenetic studies of all species.

This series is supported by NSF Grant #DBI-1356548 to RA Cartwright.

Maroon Bells

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Maroon Bells, Aspen, Colorado.

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.

See here for an article on the threatened lawsuit and here for an article on the Ark Park’s hiring practices.
Acknowledgment: Thanks again to Alert Reader for forwarding the press release.

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.

Equus quagga burchellii

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Photograph by Alice Levine.


Equus quagga burchellii – Burchell’s zebra, Namibia.

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  • phhht: It’s Stomach Turning. Alabama says: But that is not the case. The Windsor Court did not make a judgment that a married couple has more dignity than an unmarried read more
  • stevaroni: Ummm er.…Should Be “But here’s a similar sentiment from Alabama’s Supreme Court, from their Tuesday night order forbidding Alabama officials to stop from marrying same-sex couples.” read more
  • stevaroni: Ya gotta love his logic, though… Yeah! Set us straight, Floyd. Imagine the gall of people who want to have rights based on that pesky second-rate Constitution rather than read more
  • Scott F: Hi James, I don’t want the throw a wet blanket on your parade. What you are doing is important, and should be done. But I hope you can keep read more
  • stevaroni: Yes, and I can demonstrate that I can ignite dried leaves with an electrical spark, thereby establishing that “intelligent lightning sources” are required to start forest fires, and thereby read more
  • stevaroni: Um, no. There are things that are easily described as digital codes in DNA, because it’s a decent allegory* There are things that are easily described as molecular machines read more
  • Just Bob: Damn, and I was about to warm up a slice of pizza for a bedtime snack. Give a guy an appetite spoiler alert next time. read more
  • phhht: I wanted to quote his blog post here to show how, even as he tries to deny it, hatred just squirts out of Flawd like pus from a gangrenous read more
  • phhht: I dislike directing traffic to Flawd’s blog. I expected that anyone who wished to find the source could do so on his own. read more
  • Dave Luckett: phhht, it might be as well to state that FL didn’t write that on PT. It’s on his own baloneous screed, called “Genesis Station”, which has something to do with read more



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