A biblical experiment.

The Telegraph reports an interesting list of the most disturbing passages from the Bible, as compiled in a light-hearted project entitled “Chapter and Worse” at the Christian site Ship of Fools.

Here’s the list, in case you’re curious:

No. 1: St Paul’s advice about whether women are allowed to teach men in church:

“I do not permit a woman to teach or to have authority over a man; she must be silent.” (1 Timothy 2:12)

No. 2: In this verse, Samuel, one of the early leaders of Israel, orders genocide against a neighbouring people:

“This is what the Lord Almighty says… ‘Now go and strike Amalek and devote to destruction all that they have. Do not spare them, but kill both man and woman, child and infant, ox and sheep, camel and donkey.’” (1 Samuel 15:3)

No. 3: A command of Moses:

“Do not allow a sorceress to live.” (Exodus 22:18)

No. 4: The ending of Psalm 137, a psalm which was made into a disco calypso hit by Boney M, is often omitted from readings in church:

“Happy is he who repays you for what you have done to us – he who seizes your infants and dashes them against the rocks.” (Psalm 137:9)

No. 5: Another blood-curdling tale from the Book of Judges, where an Israelite man is trapped in a house by a hostile crowd, and sends out his concubine to placate them:

“So the man took his concubine and sent her outside to them, and they raped her and abused her throughout the night, and at dawn they let her go. At daybreak the woman went back to the house where her master was staying, fell down at the door and lay there until daylight. When her master got up in the morning and opened the door of the house and stepped out to continue on his way, there lay his concubine, fallen in the doorway of the house, with her hands on the threshold. He said to her, ‘Get up; let’s go.’ But there was no answer. Then the man put her on his donkey and set out for home.” (Judges 19:25-28)

No. 6: St Paul condemns homosexuality in the opening chapter of the Book of Romans:

“In the same way also the men, giving up natural intercourse with women, were consumed with passion for one another. Men committed shameless acts with men and received in their own persons the due penalty for their error.” (Romans 1:27)

No. 7: In this story from the Book of Judges, an Israelite leader, Jephthah, makes a rash vow to God, which has to be carried out:

“And Jephthah made a vow to the Lord, and said, ‘If you will give the Ammonites into my hand, then whoever comes out of the doors of my house to meet me, when I return victorious from the Ammonites, shall be the Lord’s, to be offered up by me as a burnt-offering.’ Then Jephthah came to his home at Mizpah; and there was his daughter coming out to meet him with timbrels and with dancing. She was his only child; he had no son or daughter except her. When he saw her, he tore his clothes, and said, ‘Alas, my daughter! You have brought me very low; you have become the cause of great trouble to me. For I have opened my mouth to the Lord, and I cannot take back my vow.’” (Judges 11:30-1, 34-5)

No. 8: The Lord is speaking to Abraham in this story where God commands him to sacrifice his son:

‘Take your son, your only son Isaac, whom you love, and go to the land of Moriah, and offer him there as a burnt-offering on one of the mountains that I shall show you.’ (Genesis 22:2)

No. 9: “Wives, submit to your husbands as to the Lord.” (Ephesians 5:22)

No. 10: “Slaves, submit yourselves to your masters with all respect, not only to the good and gentle but also to the cruel.” (1 Peter 2:18)

There’s lots of stuff like this, of course, and often these are ignored in favour of passages more compatible with one’s existing views (or, more disturbingly, these may be invoked for the same reason). The point is that it is difficult to know which parts of the Bible to take as literal rules about how to live, which are metaphors, and which are, at best, outdated notions that society has rightly long rejected. But what would happen if you tried to actually live the Bible literally today?

As it happens, this little experiment has been tried by best-selling author and editor of Esquire magazine, A.J. Jacobs. He describes his trials and tribulations (and new insights) during a year of following every rule in the Bible that he can in his book The Year of Living Biblically. (Obviously some parts, like the stoning of adulterers, had to be handled in a diplomatic way).

I happened to grab the book at an airport bookstore as I thought it might be interesting — and indeed it was. It’s not nearly as irreverent as one might expect — in fact, he makes a significant effort to understand those who live by (some) Biblical rules all the time, and to derive what lessons he can from his experience.

Recommended, regardless of where you stand on religion.

Breaking news: evidence for evolution found!

One of Doug Futuyma’s great quotes is this one:

“…no biologist today would think of publishing a paper on ‘new evidence for evolution’… it simply hasn’t been an issue in scientific circles for more than a century.”
– Futuyma, 1998 Evolution Biology, 3rd edition

Press officers are a different story. Here’s one from the University of California, Riverside:

Molecular decay of enamel-specific gene in toothless mammals supports theory of evolution

Biologists at the University of California, Riverside report new evidence for evolutionary change recorded in both the fossil record and the genomes (or genetic blueprints) of living organisms, providing fresh support for Charles Darwin’s theory of evolution. Read more

It’s a cool study, linking fossil and genomic data. But it’s not cool because it provides “fresh support for Charles Darwin’s theory of evolution”. This is about the historical path and genetic mechanisms of evolution — the fact has been well established for 150 years.

Here’s the actual abstract and author summary:

Abstract
Vestigial structures occur at both the anatomical and molecular levels, but studies documenting the co-occurrence of morphological degeneration in the fossil record and molecular decay in the genome are rare. Here, we use morphology, the fossil record, and phylogenetics to predict the occurrence of “molecular fossils” of the enamelin (ENAM) gene in four different orders of placental mammals (Tubulidentata, Pholidota, Cetacea, Xenarthra) with toothless and/or enamelless taxa. Our results support the “molecular fossil” hypothesis and demonstrate the occurrence of frameshift mutations and/or stop codons in all toothless and enamelless taxa. We then use a novel method based on selection intensity estimates for codons (ω) to calculate the timing of iterated enamel loss in the fossil record of aardvarks and pangolins, and further show that the molecular evolutionary history of ENAM predicts the occurrence of enamel in basal representatives of Xenarthra (sloths, anteaters, armadillos) even though frameshift mutations are ubiquitous in ENAM sequences of living xenarthrans. The molecular decay of ENAM parallels the morphological degeneration of enamel in the fossil record of placental mammals and provides manifest evidence for the predictive power of Darwin’s theory.

Author summary
Enamel is the hardest substance in the vertebrate body. One of the key proteins involved in enamel formation is enamelin. Most placental mammals have teeth that are capped with enamel, but there are also lineages without teeth (anteaters, pangolins, baleen whales) or with enamelless teeth (armadillos, sloths, aardvarks, pygmy and dwarf sperm whales). All toothless and enamelless mammals are descended from ancestral forms that possessed teeth with enamel. Given this ancestry, we predicted that mammalian species without teeth or with teeth that lack enamel would have copies of the gene that codes for the enamelin protein, but that the enamelin gene in these species would contain mutations that render it a nonfunctional pseudogene. To test this hypothesis, we sequenced most of the protein-coding region of the enamelin gene in all groups of placental mammals that lack teeth or have enamelless teeth. In every case, we discovered mutations in the enamelin gene that disrupt the proper reading frame that codes for the enamelin protein. Our results link evolutionary change at the molecular level to morphological change in the fossil record and also provide evidence for the enormous predictive power of Charles Darwin’s theory of descent with modification.

I can see why the reporter got somewhat confused. But note what they say, as there is a subtle but important distinction: this provides evidence for the predictive power of evolutionary theory. This is news, because it is sometimes argued that evolutionary research is purely descriptive. Examples like this and the discovery of Tiktaalik in the type and age of rocks where an intermediate fossil was predicted to occur show just how strong modern evolutionary ideas are.

As evidence for the fact of evolution, though… *yawn* … just put it on the pile with all the rest.

Reference

Meredith, R.W., Gatesy, J., Murphy, W.J., Ryder, O.A., and Springer, M.S. 2009. Molecular Decay of the Tooth Gene Enamelin (ENAM) Mirrors the Loss of Enamel in the Fossil Record of Placental Mammals. PLoS Genetics 5(9): e1000634.

_____________
UPDATE:

For descriptions of the study, see Ed Yong and Carl Zimmer (both among my top science writers list).

Here’s another one! Evolution still scientifically stable
(it also has a wicked typo: “they therefore stand as proof that Darwin’s theory of evolution breaks down at the molecular level,” Professor Lithgow said.”)

Evolutionary music.

I have added several items to Evolver Zone in the “music” category. Check them out. (The Rap Guide to Evolution, in particular, is outstanding and very highly recommended).

Bonus:

“I am a paleontologist” by They Might Be Giants, from their album Here Comes Science.

Health care in the USA — some data.

Here I won’t comment directly on the health care “debate” in the USA, not even as a citizen of a country that already has universal health care (i.e., any developed nation other than the USA). Instead, I will just post this clip from New Scientist, which talks about some of the actual data on health care costs and effectiveness.

Here are the links mentioned in the video:

HT: Evolving Thoughts

Mendeley (and other free software).

Some time ago, I posted about my search for a new reference management program for Windows that would be the rough equivalent of Papers for Mac (which is the rough equivalent of iTunes for PDFs).

I played around with Zotero, but I prefer something standalone rather than embedded within a browser. You may like it, though, so feel free to check it out.

Instead, I have decided to make the switch to Mendeley, a desktop application with an optional online sync function. It is still in beta, but is coming along nicely and soon should be able to do all the things I want. Specifically, allowing PDFs to be linked with records and read within the program, searching within PDFs, creating “playlists” rather than separate files for each paper I am working on, and automatic organization and renaming of PDFs in a single folder.

The program is not quite there yet, but I am now very optimistic. For now, the automatic metadata extraction is pretty much useless when you import a PDF, but then again I currently have to enter everything manually anyway with my existing program. In this case, you can have the PDF open in the same screen as the record update window. This alone is much easier than flipping back and forth or printing every reference.

[UPDATE: The metadata extraction works a lot better if you set up a Mendeley account and mostly use newer reprints, and even better if you then do a “search by title” once the file is imported).

Another issue is that it is dreadfully slow when loading if you have a lot of PDFs. Apparently this only happens when you first input a bunch of new papers, but we’ll see. I have thousands of papers that will need to be entered, so if it can’t handle it, then it’s not going to work. Also, it has a tendency to crash when inputting a lot of papers.

In short, the program looks like it will be great once the bugs are worked out and some other missing features are incorporated.

This raises a larger point, which is that free, community-driven projects are getting to be my preferred kind of software. This is because the programmers are usually very responsive to user feedback, and in many cases users themselves can create add-ons for specific functions that make the software even more useful. Here are some additional examples:

Firefox — A great browser, with an unbelievable collection of user-provided plugins.

Google Earth — Simply awesome.

iGoogle and Google Reader — Also awesome. (Google Desktop looks good too, but I haven’t used it).

IrfanView — A nice image viewing program.

Mesquite — Phylogenetic analysis software (there are many others, but I am partial to this one).

OpenGoo — A free lab management program that lets students and advisors keep track of projects, share files, and set schedules.

OpenOffice.org — A free office suite with counterparts to Word, Excel, and PowerPoint.

R — My statistician colleagues swear by this open source stats program, but I haven’t really tried to figure it out yet.

Skype — Free online video chat and inexpensive long-distance to land lines. Extremely useful for keeping in touch with friends and family.

Thunderbird — If you don’t have Outlook, try this free email software.

WinTidy — Simple little application that restores your icon positions on the Windows XP desktop if they get moved around (e.g., following a crash).

WordPress — Not just for blogs. Entire websites can be created using it (e.g., Evolver Zone), and there are lots of user-created themes and add-ons available.

Xobni — A plugin for Outlook that indexes email and makes searches vastly easier.

Zone Alarm — A free firewall program.

If you have other suggestions, leave a comment and I may add them to this list.

Self-quoting.

I usually have a rule that it is best to read one’s own work only when it is unavoidable (because one often finds things that could have been done better, etc.). However, I have been working on finishing up my most recent paper for Evolution: Education and Outreach, and I have had to go back through a few of my previous articles in the process. In a few places, I noted a particularly decent line that I thought I would probably quote sometime if it had been written by someone else. It then occurred to me that one can, in blog format at least, quote oneself and not feel too vain about it. So, here are the ones I liked.

From Evolution as fact, theory, and path:

“That evolution is a theory in the proper scientific sense means that there is both a fact of evolution to be explained, and a well-supported mechanistic framework to account for it. To claim that evolution is “just a theory” is to reveal both a profound ignorance of modern biological knowledge and a deep misunderstanding of the basic nature of science.”

“Evolutionary biology has as its purview the entire history and diversity of life, encompassing an unbroken chain of ancestry and descent involving innumerable organisms and spanning billions of years. In light of the tremendous scope and complexity of its subject matter, it should come as no surprise that details regarding the path and mechanisms of evolution are often subject to heated debate. The fact of evolution, however, remains unsinged.”

From The evolution of complex organs:

“As a career, science would hold very little appeal if all it entailed were the confirmation of existing knowledge or the memorization of long lists of well established facts. Science thrives on what is not yet known: the more vexing a problem, the more inspiring it is to investigate.”

“…the evolution of complex organs does not involve re-design from scratch at each stage; whether by direct adaptation or shifts in function, the process builds upon and modifies what is already present. “

“By definition, natural selection is the non-random differential success of individuals on the basis of heritable variation and therefore the cumulative outcome of this process – adaptation – is the opposite of random chance.”

“Because organs are built by tinkering rather than design, their features are impacted by historical contingency and inevitably reflect holdovers of past states. The net result is that all complex organs represent a mixture of optimizations and imperfections, both of which are accounted for by their evolutionary history.”

“Following in the tradition of Paley (1802) from two centuries ago, it is sometimes asserted that if a natural explanation is unavailable to account for an observation, then the only alternative is to assume a supernatural one. Such an assumption misses the obvious third option, and the one that drives scientific inquiry: that there is a natural explanation that is not yet known.”

From Artificial selection and domestication: modern lessons from Darwin’s enduring analogy:

“No reliable observation has yet been made to refute the notion that livestock, pets, and crops evolved from wild predecessors. On the contrary, the details of when, where, and how this occurred are becoming increasingly clear. Where there is disagreement, it relates not to the fact of evolutionary descent but to specific points about the mechanisms, locations, or timing of change. All of these considerations apply in the study of evolution by natural selection as well.”

From Understanding natural selection: essential concepts and common misconceptions:

“The occurrence of any particular beneficial mutation may be very improbable, but natural selection is very effective at causing these individually unlikely improvements to accumulate. Natural selection is an improbability concentrator.”

“The process of adaptation by natural selection is not forward-looking, and it cannot produce features on the grounds that they might become beneficial sometime in the future. In fact, adaptations are always to the conditions experienced by generations in the past.”

“Intuitive interpretations of the world, though sufficient for navigating daily life, are usually fundamentally at odds with scientific principles. If common sense were more than superficially accurate, scientific explanations would be less counterintuitive, but they also would be largely unnecessary.”

“…it is abundantly clear that teaching and learning natural selection must include efforts to identify, confront, and supplant misconceptions. Most of these derive from deeply held conceptual biases that may have been present since childhood. Natural selection, like most complex scientific theories, runs counter to common experience and therefore competes – usually unsuccessfully – with intuitive ideas about inheritance, variation, function, intentionality, and probability. The tendency, both outside and within academic settings, to use inaccurate language to describe evolutionary phenomena probably serves to reinforce these problems.”

“Natural selection is a central component of modern evolutionary theory, which in turn is the unifying theme of all biology. Without a grasp of this process and its consequences, it is simply impossible to understand, even in basic terms, how and why life has become so marvelously diverse.”

_________

Some more (I will use this page as the main collection):

From Darwin’s two-for-one deal (Globe and Mail):

“There are two major reasons that scientists accept common descent as fact. The first is that it is supported by, and accounts for, a multitude of independent observations, including data from genetics, developmental biology, the fossil record, comparative anatomy, and the geographical distribution of species. The second is that not a single observation or inference made over the past 150 years has provided convincing evidence that modern species are not descended from common ancestors. The notion of common descent has even withstood the rise of entirely new scientific disciplines, including molecular genetics and, most recently, comparisons of entire genomes.”

“Evolution is not “just a theory,” any more than germs, atoms, or gravity are “just a theory”. The common ancestry shared by all life is the unifying principle of biology, making sense of an otherwise bewildering array of diversity and complexity. Our understanding of how this has occurred is, itself, constantly evolving.”

The evolution of eyes.

Those of you who have been following this blog will know about the special issue of Evolution: Education and Outreach on the evolution of eyes that I edited last year (see below). There is now another excellent collection of papers on this subject in Philosophical Transactions of the Royal Society B, edited by eye experts Trevor D. Lamb, Detlev Arendt, and Shaun P. Collin.



The evolution of phototransduction and eyes

edited by Trevor D. Lamb, Detlev Arendt, and Shaun P. Collin
Philosophical Transactions of the Royal Society B, vol. 364, issue 1531, Oct. 19, 2009

The evolution of phototransduction and eyes
Trevor D. Lamb, Detlev Arendt, and Shaun P. Collin

Evolution of phototaxis
Gáspár Jékely

The ‘division of labour’ model of eye evolution

Detlev Arendt, Harald Hausen, and Günter Purschke

Eye evolution: common use and independent recruitment of genetic components
Pavel Vopalensky and Zbynek Kozmik

The evolution of eyes and visually guided behaviour

Dan-Eric Nilsson

The evolution of irradiance detection: melanopsin and the non-visual opsins
Stuart N. Peirson, Stephanie Halford, and Russell G. Foster

Evolution of vertebrate rod and cone phototransduction genes

Dan Larhammar, Karin Nordström, and Tomas A. Larsson

Evolution of opsins and phototransduction
Yoshinori Shichida and Take Matsuyama

Evolution and the origin of the visual retinoid cycle in vertebrates
Takehiro G. Kusakabe, Noriko Takimoto, Minghao Jin, and Motoyuki Tsuda

Evolution of vertebrate retinal photoreception

Trevor D. Lamb

The evolution of early vertebrate photoreceptors

Shaun P. Collin, Wayne L. Davies, Nathan S. Hart, and David M. Hunt

Evolution and spectral tuning of visual pigments in birds and mammals
David M. Hunt, Livia S. Carvalho, Jill A. Cowing, and Wayne L. Davies

Evolution of colour vision in mammals

Gerald H. Jacobs

The evolution of eyes
edited by T. Ryan Gregory
Evolution: Education and Outreach, vol. 1, issue 4, Oct. 2008

Editorial

351. Editorial by Gregory Eldredge and Niles Eldredge (PDF)

352-354. Introduction by T. Ryan Gregory (PDF)

355-357. Casting an Eye on Complexity by Niles Eldredge (PDF)

Original science / evolution reviews

358-389. The Evolution of Complex Organs by T. Ryan Gregory (PDF)
(Blog: Genomicron)

390-402. Opening the “Black Box”: The Genetic and Biochemical Basis of Eye Evolution by Todd H. Oakley and M. Sabrina Pankey (PDF)
(Blog: Evolutionary Novelties)

403-414. A Genetic Perspective on Eye Evolution: Gene Sharing, Convergence and Parallelism by Joram Piatigorsky (PDF)

415-426. The Origin of the Vertebrate Eye by Trevor D. Lamb, Edward N. Pugh, Jr., and Shaun P. Collin (PDF)

427-438. Early Evolution of the Vertebrate Eye—Fossil Evidence by Gavin C. Young (PDF)

439-447. Charting Evolution’s Trajectory: Using Molluscan Eye Diversity to Understand Parallel and Convergent Evolution by Jeanne M. Serb and Douglas J. Eernisse (PDF)

448-462. Evolution of Insect Eyes: Tales of Ancient Heritage, Deconstruction, Reconstruction, Remodeling, and Recycling by Elke Buschbeck and Markus Friedrich (PDF)

463-475. Exceptional Variation on a Common Theme: The Evolution of Crustacean Compound Eyes by Thomas W. Cronin and Megan L. Porter (PDF)

476-486. The Causes and Consequences of Color Vision by Ellen J. Gerl and Molly R. Morris (PDF)

487-492. The Evolution of Extraordinary Eyes: The Cases of Flatfishes and Stalk-eyed Flies by Carl Zimmer (PDF)
(Blog: The Loom)

493-497. Suboptimal Optics: Vision Problems as Scars of Evolutionary History by Steven Novella (PDF)
(Blog: NeuroLogica)

Curriculum articles

498-504. Bringing Homologies Into Focus by Anastasia Thanukos (PDF)
(Website: Understanding Evolution)

505-508. Misconceptions About the Evolution of Complexity by Andrew J. Petto and Louise S. Mead (PDF)
(Website: NCSE)

509-516. Losing Sight of Regressive Evolution by Monika Espinasa and Luis Espinasa (PDF)

Book reviews

548-551. Jay Hosler, An Evolutionary Novelty: Optical Allusions by Todd H. Oakley (PDF)

Good science writers.

I believe that it is important to give both credit and criticism where they are due. Unfortunately, I don’t seem to do these in equal measure when it comes to science reporting. So, as a small corrective, here is a list of science writers whose work I have praised in the past:

Everyone likes to get a pat on the back now and then, and I know several of them read the blog.