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.

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.

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.
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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.
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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.

Photograph by Alice Levine.

Equus quagga burchellii – Burchell’s zebra, Namibia.

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.
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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.
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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.