The known unknowns of biology: welcome to the unknome

'Genome' is now a pretty standard word in our social vocabulary. We have to put up with overloaded metaphors like "blueprint" and reverent talk like "language of god" but it does seem to me that the word is reasonably well understood by laypeople—not as jargony as "gene expression" or as inscrutable as "chromatin." The word was born in 1920 when someone blended 'gene' with 'chromosome'. (The -some in 'chromosome' is from a root that means 'body' as in 'somatic' or 'psychosomatic'.)

So, a genome is a "body" of genetic material, and specifically the whole body of genetic material in an organism (or a cell or a species). For decades now, science has been regularly adding more -omes. The proteome is the full body of proteins. The transcriptome the full body of transcripts. It gets a bit weirder: the phenome is the full body of phenotypes. There's even the spliceome, the full body of splice variants. Many of those are pretty jargony; the point is that -ome is a suffix that's being used a lot like -gate is used in political news (to indicate a kind of scandal, as in Watergate or Gamergate). Among the -omes (let's call it the omeome, ha ha!), the best by far is the unknome: the set of all genes of unknown function.

How big is the unknome? In other words, how many of the 20,000 or so genes in the human genome are unknown (in function)? Is there a gradient of unknown-ness? A new paper in PLOS Biology by Rocha and colleagues introduces us to the unknome and then adds some good stuff, which is the least the authors can do after telling us how little we know about human gene function.

Harmful genes, and sneaky, too: Genetic hitchhiking in the human genome

Genetic hitchhiking is thought to be an inevitable result of strong positive selection in a population. The basic idea is that if a particular gene is strongly selected for (as opposed to selected against), then the chunk of the genome that carries that gene will become very common in the population. The result is a local loss of genetic diversity: all (or nearly all) of the individuals in the population will have that same chunk of genetic information, whereas before the selection process acted, there might have been a lot of variation in that chunk throughout the population. And this means that areas of the human genome that are less variable between people are suspected sites of recent positive selection. Within that chunk, there are potentially many genes and genetic elements that became more common in the population by virtue of their placement near the gene that was actually selected for. Those other genes are the hitchhikers. And it's likely that some hitchhikers are bad news – they're harmful mutations that would normally become rare or extinct in the population, but instead have become common by hitchhiking.

In the last few years, large amounts of genetic information have become available that have enabled biologists to look for evidence of such phenomena in the human genome. Specifically, two major projects have collected genetic data for the purpose of analyzing genetic variation among humans. One project, the International HapMap Project, mapped and quantified sites in the human genome that are known to vary among humans by a single genetic letter. These sites are called single nucleotide polymorphisms, or SNPs (pronounced "snips"). The project has mapped millions of these sites in a group of 270 humans representing various lineages. Another project that has made the news recently is the 1000 Genomes Project, which also seeks to provide a picture of human genetic variation using more people (more than 1000 at present) and slightly different technology. Efforts like these have taken analysis of the human genome to a new level. No longer do we merely wonder what "the" human genome is like – we can begin to learn about how genetic differences give rise to biological differences such as susceptibility to particular diseases.

Genetic hitchhiking in English

The next post will discuss recent evidence for genetic hitchhiking in humans. So, what do we mean when we say that genes can hitchhike? To make sense of this phenomenon, we first need to review chromosomes and sexual reproduction.

Most people know that sexual reproduction creates offspring that are genetically distinct from both of the their parents. That's true, but the genetic scrambling that occurs is more significant than is sometimes reported. Let's start by looking at chromosomes.

Like every other animal (or plant or pretty much any other organism), your genetic endowment is carried in chunks of DNA called chromosomes. You have 23 of these chunks, which are rather like volumes in a set of encyclopedias. More completely, you have 23 pairs of these volumes; one set was contributed by your mother and the other by your father. Each of your parents had a complete set, also consisting of a set from Mom and a set from Dad. When your mother made the egg that became the zygote that became you, she provided you with one copy of each volume in the set, and she chose those copies randomly. For example, she may have chosen her dad's copy of chromosome 1, but her mom's copy of chromosome 2. Just by virtue of this random picking process, she made an egg with a shuffled version of her own genetic cards. Dad did the same when he made his sperm, and so your genetic complement is an amalgamation of your parents' genomes which were amalgamations of your grandparents' genomes, and so on.

Alu need to know about parasitic DNA: Alu elements and blindness

Age-related macular degeneration (AMD) is a leading cause of blindness in humans, and the leading cause of visual impairment during advanced age. The condition comes in two basic forms, the most severe of which is untreatable. Called geographic atrophy (GA), this condition involves the steady destruction of the retinal pigment epithelium, a layer of tissue in the eye that is essential for the health and maintenance of the photoreceptors in the retina. Loss of the pigment epithelium means certain death for the photoreceptors, and that means visual impairment and then blindness for the affected person.

A major publication in Nature last month (Kaneko et al., "DICER1 deficit induces Alu RNA toxicity in age-related macular degeneration," Nature 17 March 2011) now points to one likely cause of AMD, and in the process provides a chilling example of what can happen when the parasitic Alu elements in our genomes (see the previous post for an introduction) are left unrestrained.

Alu need to know about parasitic DNA: Introduction to Alu elements

Defenders of intelligent design theory often dwell on the topic of "junk DNA," which has been molded into a masterpiece of folk science. The ID approach to "junk DNA" involves a fictional story about "Darwinism" discouraging its study, and a contorted and simplistic picture of a "debate" about whether "junk DNA" has "function." The fictional story is ubiquitous despite being repeatedly debunked. But the picture of an ongoing "debate" about "function" is harder to sort out. Like most propaganda, that picture contains enough truth to sound plausible. (Browse my "Junk DNA" posts, and work by Ryan Gregory and Larry Moran, for more information on errors and folk science associated with these topics.)

There is, in fact, some scientific disagreement about functions of various elements in genomes, but it's not the crude standoff that ID apologists depict, and it has very little to do with "Darwinism." The debate, if we must call it that, is about at least two matters: 1) the extent to which certain genomic elements contribute to normal function or development of organisms; and 2) the means by which we might determine this. The debate is not about whether non-coding DNA can have function, or even about whether some segments of non-coding DNA do have function. That debate was invented by anti-evolution propagandists.

Introns. Let's think about this, people. Part IV.

So why is it that I and many other biologists hypothesize that introns are mostly non-functional?

(I'll assume that you've read the previous posts, and that you understand what it is that I mean when I challenge claims that introns are functional elements in an information-rich genome. And to avoid confusion, I'll speak only for myself, although I surmise that a tiny minority of biologists would agree with creationist characterizations of the human genome.)

Here are the basic data that lead me to conclude that intron sequences are mostly dispensable for biological function. I've provided links to key references, and we can go into more detail in further posts or in the comments.

Introns. Let's think about this, people. Part III.

What does it mean to claim that an intron has a function?

The question is obviously important, at least as long as there are disputes about whether introns have "functions" and whether science ignored them for decades.

Now, I can't help the ID people with their propensity for repeating falsehoods about the history of "junk DNA" and the role of "Darwinism" in its characterization. But I do think we can move a little closer together on this intron thing. So, first a discussion of the types of functions that are associated with introns then some comments on my specific dispute with Richard Sternberg.

Introns. Let's think about this, people. Part II.

Before we explore what introns are and how they work, let me correct the misuse of my words by one of the ID attack kittens. Months ago, referring to Steve Meyer's claim that introns "are now known to play many important functional roles in the cell," I sought to put intron "function" into context as follows:

The human genome contains at least 190,000 introns (though it's been recently estimated to contain almost 210,000). Together those introns comprise almost 1/4 of the human genome. One fourth. That's 768 million base pairs. And biologists have identified "important functional roles" for a handful of them. How many? Oh, probably a dozen, but let's be really generous. Let's say that a hundred introns in the human genome are known to have "important functional roles." Oh fine, let's make it a thousand. Well, guys, that leaves at least 189,000 introns without function, and gosh, they're snipped out of the transcripts and discarded before the darn things even leave the nucleus.

One critic has interpreted me as claiming that I know that 189,000 introns have no function. That's not my point, and I think most people know that.

In rage deaf as the sea, hasty as fire.

No one should take advice from this character, I'll grant you. But even King Richard II could see the obvious:

Then call them to our presence: face to face,
And frowning brow to brow, ourselves will hear
The accuser and the accused freely speak:
High-stomach’d are they both, and full of ire,
In rage deaf as the sea, hasty as fire.

--The Tragedy of King Richard the Second, Act I, Scene I, The Oxford Shakespeare

So Richard Sternberg, that aggrieved martyr of the Smithsonian Institution, butchered at the hands of Evil Darwinists and now among his people in Seattle, has posted a nasty rebuttal to a three-month-old post of mine on Signature in the Cell. I had resolved to ignore the minions of that awful place, but I'll grace Richard with a response since he's found a mistake that I do need to correct.

Behe and probability: one more try

Almost two years ago, I reviewed Michael Behe's latest book, The Edge of Evolution, here on the blog. I was unimpressed, to say the least, and remain of the opinion that Behe should not be considered a serious scientific thinker given his failure in that ludicrous book.

Since then, my posts have been referenced occasionally in the blogosphere, typically by people trying to explain Behe's surprisingly crude mishandling of probability in the context of genetics. One particular point has been singled out as a mistake on my part, and some ID defenders want that mistake to rescue Behe's argument. Let me describe the so-called mistake, then explain why I'm right.

Introns and design

Mike Gene has posted an interesting series on introns that's worthy of a few comments. His thesis is that "introns facilitated the evolution of multicellular life."

A. The idea is interesting and rational but not novel. Research on introns and evolution is active and lively, and one prominent scientist in the field, Eugene Koonin, has proposed that introns drove many aspects of the evolution of eukaryotes (i.e., non-bacteria).

Signature in the Cell: beginning the review

So Stephen Meyer of the Discovery Institute, a founder of the ID movement, wrote a book called Signature in the Cell: DNA and the Evidence for Intelligent Design. It came out last summer, and I ignored it. I ignored it because it didn't seem interesting or important or new, and there's always something interesting and important and new to read. (I recently finished The Road. Wow.) It didn't matter to me that the ID people said it was "groundbreaking" or "seminal" or "a blueprint for twenty-first-century biological science" since they said things like that about Behe's last book. And that is a terrible book, one that reflects very poorly on its author. It seemed reasonable to assume that the ID movement wasn't going to generate any serious new arguments, and that if they did it would be obvious. Signature in the Cell gave no indication that it contained anything new.

Carnival of Evolution 14

Welcome to Quintessence of Dust and to the 14th Edition of the monthly Carnival of Evolution. Thanks for stopping by, and for supporting scientific carnivalia, members of a taxon that seems to be flirting with extinction.

One good reason to visit a carnival: brain stimulation. Brain Stimulant offers some thoughts and speculations on Free Will and the Brain, touching briefly on themes of selection and adaptation, and he doesn't charge as much as the clinic would.

Another good reason: you can bump into real scientists, the kind who actually work on evolution. Ryan Gregory has a day job as an expert on genome evolution, but somehow finds the time to blog at Genomicron. Recent entries there include fascinating pictures of ongoing field work. For this month's carnival, be sure to read two reviews of the ideas of Stephen Jay Gould, focusing on controversial papers by Gould published in 1980 and 1982. You may find that you have been misinformed about Gould's positions, and you'll surely learn more about evolution.

Michael White at Adaptive Complexity is another blogging scientist, and he writes very clearly about parasitic DNA in Selfish Gene Confusion.

David Basanta is a biologist who runs a cool blog called Cancerevo: Evolution and cancer, which is subtitled "Studying cancer as an evolutionary disease." Check it out, and don't miss his recent piece on Stem cells and ecosystems.

Zen Faulkes is a biologist who blogs at Neurodojo. That's cool enough, but the subtitle of that blog is "Train your brain." Hey, this could be a theme for the whole carnival! He recently wrote about a walking bat in New Zealand. Bat evolution...we can't get enough of that. I've written about it myself.

Brains and their origins come up in an extensive discussion of early animal evolution at AK's Rambling Thoughts. The post is The Earliest Eumetazoan Progression.

At The Loom, the peerless Carl Zimmer discusses AIDS in chimps and the relevance of the story to conceptions of scientific progress. AIDS and The Virtues of Slow-Cooked Science is engrossing and important. And John Wilkins discusses some new fossil apes in an excellent recent post at Evolving Thoughts.

John Lynch reviews a new book on Alfred Russell Wallace. Caveat lector. Brian at Laelaps takes us on a historical tour of the work of Florentino Ameghino. Are those elephants or not? Brian's discussion is typically excellent.

At The Spittoon, AnneH discusses new findings concerning both the past and the future of the mammalian Y chromosome.

Hoxful Monsters is a future host of this carnival; Nagraj recently reviewed some recent work on pattern formation in the development of spiders. Wonderful evo-devo stuff.

Someone at Wired wrote some swill about the "10 Worst Evolutionary Designs" which annoyed a few smart bloggers. At Deep-Sea News, Dr. M sets the record straight. The title is self-explanatory: Worst Evolutionary Designs? No! Brilliant Solutions to the Complexity of Nature and Constraints.

Larry Moran at Sandwalk is attending a conference entitled Perspectives on the Tree of Life. He's posted reviews of days one and two so far.

And that's our carnival. Thanks for reading, and on the way out I hope you'll look at my nearly-complete series on Notch and deep homology.

Next month's edition will appear at Southern Fried Science. To submit posts, use the submission form found at the Carnival of Evolution site. And if you like the carnival, help us promote it with a link, and/or consider hosting. More info at the carnival site.

Mendel's Garden, 28th Edition

Hello and welcome to the 28th edition of the genetics blog carnival known as Mendel's Garden, where we celebrate blogging on topics related to anything touching on what Mendel discovered (or thought he discovered).

While reading these interesting and informative pieces, please think about work that should be featured in a future edition and/or blogs (like yours) that would serve well as future hosts.

So do tomato seeds get you excited? No? Oh. Well, they should, if you're at all interested in evolutionary genetics. Michael White at Adaptive Complexity explores some new findings in which evolutionary changes in seed size in tomatoes are explained to a large extent by variation in a single gene, pinpointed through the use of standard genetic crosses. He summarizes the work as "a clear case of natural genetic variation controlling the size of seeds, variation for evolution (or plant breeders) to work on when larger or smaller seed sizes are needed to adapt to a new environment." Not peas, but close. Mendel would be proud.

"Mendel would be proud" happens to be the title of a post by Michael at Ricochet Science, pointing to a new educational site which he hopes will help students and laypersons learn genetics.

Ouroboros describes experiments on an interesting DNA repair enzyme called Ercc1. One might think that deletion of the gene encoding this protein (it controls nucleotide excision repair) would be a Bad Thing, but in fact mice that have been so altered are strikingly cancer-resistant. And there's more, but you'll have to check out the excellent Ouroboros blog (focused on aging and related biology) yourself.

At the Spittoon, Erin introduces her post entitled "Miss Con-GENE-iality" with this teaser: "If Facebook is starting to take over your life, maybe your genes are partly to blame." The subject is heritability of various aspects of social connectedness, and instead of whining "I could quit Facebook anytime I want" just go read about these new genetic analyses of our social behavior.

On a more serious note, Razib at Gene Expression explores the genetics that might underlie the interesting case of Sandra Laing, a woman born to apparently white parents but who appeared to be "of a different race." And in South Africa. For more on the genetics of human appearance, see the Eye on DNA interview with Dr. Tzung-Fu Hsieh, developer of a test for the red hair gene.

Oh, and before you give your credit card number to a personal genomics outfit, spend some time at Genetic Future – Daniel notes when a company is charging too much, and comments on some recent remarks by Francis Collins on the future of "consumer genetics."

Organic transgenic food might sound like an oxymoron, but Anastasia at Genetic Maize explains why it's not and introduces the new word for such methods: orgenic.

Jonathan Eisen at The Tree of Life is recruiting people to help with analysis of metagenomic data. Go there to learn more. I forgot to inquire about salary and benefits.

Back to evolutionary genetics: Todd at Evolutionary Novelties reports on an extraordinary example of evolutionary convergence, involving proteins called opsins which are best known for their roles in vision.

Need more evolution (with genetics)? Go read about pink iguanas at Nothing's Shocking. This should get you thinking about speciation, and that means it's time to read about "speciation genes" at Evolving Thoughts. John's not crazy about the term. What a grouch.

And here's a new twist on the whole "species boundary" concept: Ed at Not Exactly Rocket Science writes about a single gene in glowing bacteria that accounts for the ability of the same bacterial species to colonize (in a mutualistic relationship) two completely different organisms (pinecone fish with glowing "headlights" and squid with a luminous "cloaking device"). Now that's cool.

Let's give the Digital Cuttlefish the last word, at least because the blogosphere recently treated us to intensely disturbing images of cuttlefish meeting violent ends. At that little piece of blogospheric heaven, the Digital Cuttlefish reports on the cuttlefish genome project. It's not what you think – it's better.

Thanks for reading, and look for the next edition of Mendel's Garden the first Sunday in March at Biofortified.

Why I'm not a Behe fan: conclusion and a challenge

About 2 months ago, I finished a series on Michael Behe's latest book, The Edge of Evolution. I concluded that it was a terrible book, displaying significant errors of both fact and judgment. The book's main argument is a population genetics argument, and Behe seems to have little knowledge or understanding of that difficult subject. The book is a joke, and I believe it will someday be seen as one of the more disastrous mistakes made by the ID movement. But I think it's important to distinguish between Behe's errors (which reflect on his scientific credibility and on his decision-making habits) and his thesis. His book is full of mistakes, but that doesn't mean that his proposal is known to be false. So I'd like to make it clear what my verdict on his book actually is, then present an outline of one way to actually test Behe's hypothesis.

1. In The Edge of Evolution, Behe correctly identified a biological process – the generation of genetic variants that lead to evolutionary change – as a likely focus of deliberate design. Having concluded that common descent is true, he reasoned that the trajectory of change through the tree of life might be expected to show evidence of non-random direction. Design, as he and others in the ID movement conceive it, might be manifested in the pattern by which the tree of life came to be. (Some might go as far as to say that it must be manifested in such a way, but I don't think Behe suggests this.) My point is that there is nothing stupid, irrational, or unscientific about Behe's reasoning. So, Behe conceived a hypothesis, which I will restate as follows:

• Based on the consideration of life's complexity, specifically on the consideration of the integrated complexity that characterizes the molecular machinery of the cell, it is proposed that random mutation and subsequent selection cannot fully account for the evolutionary development of biological systems.
• Consequently, it is proposed that the process of mutation is non-random.

Again, I find nothing outrageous or stupid about the hypothesis, or even its rationale. Molecular machines are astoundingly complex and integrated, and I do think it's reasonable to wonder how such things can come about without the aid of a superintelligence. In other words, Behe's proposal is not inherently incoherent or otherwise easily dismissed. Might the machinery of life have emerged through non-random processes? Sure. EoE is a joke, but not because the proposal is a joke.

EoE is a joke because Behe seems not to have even attempted to establish the strength of the hypothesis. Very little of the book is devoted to this central concern, and those sections that take up the task are so laughably wrong that they have led me to question Behe's scientific integrity. (Sorry, no apologies: the errors are too basic, and the proposal too world-altering, to give someone who is vying for scientific immortality a pass on standards of scientific conduct.)

But this is important: Behe's failure to even attempt an honest defense of his proposal does not imply that the proposal has been falsified. It hasn't. It remains possible that the development of biological machines – especially in the early days of the tree of life – was characterized by a non-random, directed trajectory. (I happen to doubt this, but that's not relevant here.) Behe's book is a failure, but his hypothesis stands.

So here we are: an interesting and potentially revolutionary hypothesis has been advanced. It has a certain explanatory appeal, and it has unquestioned relevance for believers of many kinds. It is empirical and rational. And, I maintain, it is testable, at least in principle. And so I'm offering to collaborate on a real effort to test it.

2. Behe's proposal leads to certain types of testable predictions. He claims that the genetic changes that underlie certain levels of evolutionary change occurred non-randomly. In other words, he claims that there is a dramatic mismatch between rates of genetic mutation and rates of evolutionary change. His efforts in EoE were ridiculously inadequate. Here is an outline of an approach that could succeed.

• One major mistake that Behe made was to devote most of his attention to a "case study" in which significant genetic change did not occur. His case study was poorly suited to his purpose, but even if it had been better conceived it would be worthless. We can't learn about how evolution works by analyzing examples in which it didn't occur. (Well, of course it did occur in Behe's case study, but the changes that he claims are non-random are different by his own definition.)
• So, any approach to the detection of non-random influences on evolutionary change needs to focus on case studies that actually involve the relevant level of evolutionary change. Examples should be easy to find, by considering the tree of life and the branching levels at which one would hypothesize non-random change.
• The evolutionary lineage(s) selected for analysis should be fairly well-documented, so that the nature of the relevant common ancestors can be reasonably inferred. This probably means that much deeper lineages (such as eukaryotes or even multicellular eukaryotes) would not make good subjects of analysis. Since Behe is pretty sure that design characterizes differences at the level of class (and deeper), this concern is not a barrier to addressing his hypothesis, at least at those levels of divergence. The tetrapod lineage could serve well, but there are any number of evolutionary trajectories that could be considered.
• Within the selected lineage(s), one or more evolutionary changes would be selected for genetic analysis. Changes could be simple (such as the molecular evolution of a particular protein of interest) or more complex (such as the development of a particular attribute like teeth or feathers or lungs), and could even include the sum total of the genetic changes in a lineage, but must be amenable to genetic description. Most importantly, the evolutionary changes that are analyzed must be associated with the specific design postulate. The goal is to examine the genetic changes underlying an evolutionary transition that Behe would identify as designed.
• Once the genetic changes of interest have been identified, analysis can proceed the way Behe pretended to proceed in EoE: inferred mutational trajectories can be considered in the light of estimated mutation rates and estimated generation numbers. If non-random mutation is clearly necessary for the evolutionary changes in question, it should be apparent that even the simplest mutational paths leading to change are well beyond the explanation of random mutation.

My description makes the undertaking sound straightforward, and in principle it is, but of course such examination of even a relatively simple evolutionary change is a significant and demanding project. Inferring the genetic makeup of the common ancestor is a project all by itself, and constructing postulated mutational pathways is the kind of work that occupies many professional biologists full-time. (Consider the work of Joe Thornton and his group, considered among the best analyses of this kind.) Estimates of generation number will span huge ranges even after the most careful consideration of the variables.

But this is the work that any real scientist and scholar would know has to be done. Behe's hypothesis is completely untested, and only the kind of study that I have outlined can change that. I invite any scholar with interest in undertaking this project to contact me. I would be interested in joining a collaborative effort to test the non-random mutation hypothesis, and I have some significant resources that could be brought to bear on the problem. This is a serious offer, and I would encourage readers to forward it to anyone who might be interested in discussing the details.

Wait...did you say "eldritch?"

It's exciting to live in the era of evolutionary genomics, when new genomes are being published approximately once a week, and the light of genomic analysis is being trained on more and more branches of the tree of life. This week sees the unveiling of the genome of Amphioxus, a primitive vertebrate that has long been known to be a key piece of the puzzle of animal evolution, and the results are sharpening our hypotheses about the genesis of major animal groups.

First a little about the results published in this week's Nature. Amphioxus is the fancy name for lancelets, which are small and simple sea-going creatures that represent a very interesting branch on the tree of life: they constitute a group called the cephalochordates, which is one of the three living groups of chordates. (Remember "kingdom, phylum, class, order, family, genus, species"? Humans are vertebrates, and vertebrates are a subdivision of the chordates.) Vertebrates and tunicates (sea squirts) are the other two groups. Because the lancelets are similar in structure to vertebrates, more so than are the tunicates, they were long thought to be more closely related to vertebrates, and so it was postulated that tunicates were more "basal" on the evolutionary tree. But two years ago, new analyses strongly suggested that it is the lancelets that are the most basal group. And so the lancelets became even more interesting: understanding their genomic structure would surely provide clues to the nature of the original chordate genome.

The examination of the lancelet genome (well, it's the genome of one lancelet of one species) provides substantial new insight into vertebrate evolution. For some solid overviews, check out Nobel Intent at Ars Technica, and the press release from UC Berkeley. Here are just a few tidbits that got my attention:

• The findings strongly support the hypothesis that the vertebrate gene set was diversified through two ancient whole-genome duplications. This phenomenon and its role in the generation of new gene functions have been discussed here before.
• The lancelet genome contains roughly the same number of genes as the human genome.
• Comparison of the various chordate genomes reveals that there are very few chordate-specific genes. Specifically, the authors described 239 "chordate gene novelties" out of 22,000 genes in the lancelet. The nature and function of these genes is intensely interesting, and indeed the authors devote a separate report to issues related to this. But think about it: only 1% of the genes in chordates (vertebrates and all their relatives) are "novel" among genes from all other organisms.
• So if the toolbox isn't all that different between lancelets and lions, despite divergence at least 550 million years ago, then what is different? Anything? As John Timmer notes on Nobel Intent, the authors could find relatively few examples of regulatory DNA sequences that are conserved between lancelets and vertebrates, pointing to the likelihood that changes in regulation of a (mostly) common genetic toolkit is a major factor in evolution of form. (Okay, so that was just a plug for evo-devo. It's my blog.)

But one more thing. Why the bizarre title for this blog entry? Well, Henry Gee at Nature wrote a very nice News & Views summary of the genome report, and here are a few not-so-randomly-selected excerpts:

The age of genomics has rescued the amphioxus from chthonic obscurity, as new data — now including Putnam and colleagues’ paper and three companion reports in Genome Research — have reinvigorated the study of the origin of the vertebrates.

Is there a typo in there?

The 520-megabase genome of B. floridae would, therefore, be nothing much more than a curiosity without the comparative context offered by the increasing number of completed or draft animal genomes from humans to sea anemones... Such studies reveal the amphioxus genome to be, in fact, of preternatural importance.

Uh...

But with Putnam and colleagues’ publication on page 1064 of the draft genome sequence of Branchiostoma floridae, one of the 25 or so recognized species of amphioxus, this eldritch organism is set to re-enter public life.

Eldritch? Eldritch?? What the heck?!

'Preternatural' I can handle, barely, but 'eldritch' and 'chthonic'... Yes, there's a story here, and it's very funny. Enjoy, and have fun in your next Scrabble game.

Finches, bah! What about Darwin's tomatoes?

Charles Darwin collected all sorts of cool stuff (like a vampire bat, caught while feeding on his horse) on his journey aboard the Beagle, and it has to be said that he understood little of it until after he got back. The finches that bear his name were identified as such by someone else, and his own bird collections from the Galapagos were nearly worthless due to the fact that he hadn't bothered to label specimens as to their place of origin. It was only upon their correct identification as different species of finch that Darwin realized that the birds represented what we now call an adaptive radiation.

Darwin collected a lot of plant material, too, and much of it was completely new to science. J.D. Hooker was a botanist and contemporary of Darwin, and in 1851 he wrote a little paper, "An Enumeration of the Plants of the Galapagos Archipelago; with Descriptions of those which are new" describing his studies of Darwin's collection. It was more than 100 pages long.

One unique feature of the collection was a pair of species of tomato plant. Like all other species in the archipelago, the Galapagean tomatoes resemble South American species, but are subtly different. More interestingly, the two Galapagean species are highly similar to each other (and reproductively compatible), but occupy separate habitats and exhibit some odd variations, including a striking divergence in leaf shape.

Image from Figure 1 of Kimura et al., cited below. On the left is S. cheesmaniae; on the right is S. galapagense.

How might such a variation arise in evolution? A nice study published in Current Biology two weeks ago provides the interesting answer, and addresses an important question raised by evo-devo theorists. The article is "Natural Variation in Leaf Morphology Results from Mutation of a Novel KNOX Gene," by Seisuke Kimura and colleagues at UC Davis.

Look again at the picture: the leaves pictured on the left are "normal" tomato leaves, as one might see in a Michigan garden or on the South American plants thought to be the ancestors of the Galapagean species. The leaves on the right are significantly more complex. (For lovers of botanical detail, the "normal" leaves are unipinnately compound, while the S. galapagense leaves are three- or four-pinnately compound. For the botanically challenged like me, the leaves on the right are more snowflake-like.)

This trait has long been known to be under the control of a single gene, but the nature of that gene and its effects were unknown before the experiments of Kimura et al. They did some pretty intense genetic mapping, and zeroed in on a rather small piece of the genome. Specifically, they ended up examining a region 1749 base pairs in length. Inside that region, they found exactly one change that could account for the leaf variation: a deletion of a single base pair. One DNA letter, removed from the genome, makes all that difference.

But there's more. That change isn't in the coding region of a gene, meaning that the mutation doesn't affect the structure of any protein. Like the genetic variation that Cretekos et al. studied in their analysis of bat wing development, this is an example of a change in a regulatory region of the DNA, the kind of change that evo-devo theorists have predicted to be fairly common in the evolution of new forms.

The authors showed that the teeny little one-letter change results in a huge increase in the amount of a protein called TKD1. And they did a compelling experiment similar to the one that Cretekos and colleagues did with the bat and the mouse: they took that piece of regulatory DNA (with the one-letter change) and stuck it into a tomato plant, and showed that it could induce a complex-leaf trait all by itself. No change in protein structures, just a one-letter change in a regulatory DNA region. Isn't that cool?

Kimura et al. went on to show that TKD1 reduces the formation of a complex between two other proteins, and their data suggest that the levels of TKD1 constitute a dimmer switch-like (rheostat) control on that complex, which ultimately controls the development of leaf shape.

Now, here's why this result is interesting in the context of evo-devo. A structural mutation in a protein that controls development can result in dramatic changes in form, for sure. But such a mutation will likely alter all of the processes controlled by that protein, resulting in widespread developmental reorganization. (Think "hopeful monster" here.) Evo-devo thinkers assert that regulatory changes are better suited (in general) for the induction of evolutionary changes in form, because such changes can affect isolated developmental processes without affecting the overall development of the organism. In this case, the excess TDK1 protein is able to inhibit the action of a particular complex in particular areas at particular times, without interfering in the functions of those other proteins elsewhere and at other times. Here are the concluding sentences of the paper:

Mutations affecting the expression levels of transcription factors can modify the function of a major developmental regulatory complex in some organs without interfering with its other essential roles in morphogenesis. Such dosage-sensitive interactions may be broadly responsible for evolutionary change and provide a relatively simple mechanism for the generation of natural variation.

I hope you agree that studies like this one and the bat-wing story are inherently interesting. But I hope you also see how sadly foolish it is to disparage evolutionary science as mere mythology, or to pretend to invalidate a century of evolutionary genetic analysis with a few bogus calculations. Scientists are weird enough to think tomato plant leaves on the Galapagos are worth subjecting to detailed genetic analysis, and maybe that means we're a bit on the obsessive side. But come on: we're not stupid.

Article(s) discussed in this post:

KIMURA, S., KOENIG, D., KANG, J., YOONG, F., SINHA, N. (2008). Natural Variation in Leaf Morphology Results from Mutation of a Novel KNOX Gene. Current Biology, 18(9), 672-677. DOI: 10.1016/j.cub.2008.04.008

How the bat got its wing

Nothing can be more hopeless than to attempt to explain this similarity of pattern in members of the same class, by utility or by the doctrine of final causes. The hopelessness of the attempt has been expressly admitted by Owen in his most interesting work on the 'Nature of Limbs.' On the ordinary view of the independent creation of each being, we can only say that so it is;—that it has so pleased the Creator to construct each animal and plant.

The explanation is manifest on the theory of the natural selection of successive slight modifications,—each modification being profitable in some way to the modified form, but often affecting by correlation of growth other parts of the organisation. In changes of this nature, there will be little or no tendency to modify the original pattern, or to transpose parts. The bones of a limb might be shortened and widened to any extent, and become gradually enveloped in thick membrane, so as to serve as a fin; or a webbed foot might have all its bones, or certain bones, lengthened to any extent, and the membrane connecting them increased to any extent, so as to serve as a wing: yet in all this great amount of modification there will be no tendency to alter the framework of bones or the relative connexion of the several parts.

– from On the Origin of Species, 1st Edition (1859), Charles Darwin

The wing of a bat is an amazing thing. It's not just a wing; it's clearly a modified mammalian limb. A bat looks like a lot like a rodent with really long, webbed fingers on elongated arms.

Image from Animal Diversity Web at the University of Michigan.

Recent genetic analyses have yielded a fairly solid outline of the evolutionary history of bats, which have left a somewhat poor fossil record in which the earliest fossil bats look pretty much like modern bats. It seems that bats arose relatively quickly during evolution, acquiring their distinctive feature – powered flight – in a few million years. No transitional forms have yet been found, which is a shame, because this particular evolutionary transition is the kind that is otherwise reasonably approachable for the detailed study of how changes in form come about.

The fossils can't yet show us how paws gave rise to wings, but that doesn't mean we can't test specific hypotheses regarding the paths that evolution could have taken. In fact, developmental biologists have enormous resources that can be brought to bear on the question, by virtue of decades of research on the development and genetics of the wingless terrestrial bat better known as the mouse. A few months ago, an interesting new report described one kind of genetic change that can lead to bat-like bodies, and the findings put some new wind in the sails of evo-devo.

Two of the more remarkable aspects of bat wing structure are the forelimbs and the forelimb digits, what humans would call the arms and the fingers. Both are dramatically elongated in the adult animal, despite getting off to a very typical start during early development. Check it out: in the picture below, bat and mouse limbs are compared with the image scaled so that body lengths are comparable.

Image from Figure 1 of Cretekos et al., cited below.

Developmental biologists have some pretty good ideas about how this might arise physiologically: certain growth factors (called bone morphogenetic proteins, or BMPs) are known to control limb growth, and some BMPs seem to be turned up in developing bat fingers. But the genetic mechanisms underlying these processes are unknown.

Enter Chris Cretekos and colleagues, then working in a group in Houston headed by Richard Behringer. They set out to examine the genetic underpinnings of the elongation of the forelimbs (arms) of bats, using the formidable tools of mouse developmental genetics. And, clearly, they also sought to directly test one of the central hypotheses of evo-devo: that changes in regulatory DNA sequences (as opposed to changes within the genes themselves) are a potent source of variation in evolution. Consider the beginning of their abstract:

Natural selection acts on variation within populations, resulting in modified organ morphology, physiology, and ultimately the formation of new species. Although variation in orthologous proteins can contribute to these modifications, differences in DNA sequences regulating gene expression may be a primary source of variation.

– From C.J. Cretekos et al., "Regulatory divergence modifies limb length between mammals, Genes & Development 22:141-151, 15 Jan. 2008

Besides their expertise in mouse genetics, the authors brought two major assets to their study: 1) they had already carefully mapped the development of the short-tailed fruit bat (Carollia perspicillata, "our model Chiropteran"); and 2) they knew a lot about the genetic control of limb length in other mammals. In particular, they knew that the protein Prx1 is known to influence limb elongation, by controlling the expression of other genes. So they hypothesized that changes in the activity or level of Prx1 might underlie the difference in limb length between bats and mice, and they were well-equipped to do the experiments.

First, the authors examined the Prx1 gene in the two species, and found that the overall structure of the gene is very similar in both mice and bats, and that the actual coding sequences of the two genes are almost completely identical. (Aligning the coding sequences showed that more than 99% of the amino acids are the same in both species.) In other words, the part of the Prx1 gene that codes for protein is almost certainly not a source of variation between mice and bats. This could mean that Prx1 doesn't have anything to do with the difference between forelimb length in these two species, or it could mean the the difference is generated, at least in part, by variation in the regulation of the gene. Cretekos et al. postulated that altered Prx1 regulation might be involved, and designed a cool experiment to address this possibility.

They already knew that the Prx1 gene in mice contains known regulatory elements in particular locations within the gene. (Such elements are often located in the DNA sequences that precede the coding region.) When they looked at the bat gene, they found similar elements in the same location, but these elements showed some intriguing variation: when the two regions were aligned, they shared only 67% identity, meaning that a third of the DNA bases were different in mouse and bat. They did some nifty cell biology to show that this region did function as a regulator of the expression of Prx1, then did something that biologists could only dream about before the genomic era: they altered the mouse genome by replacing the mouse regulatory region with the corresponding region from the bat genome. In other words, they gave a mouse a piece of a bat's genome, without actually changing the coding sequence of any gene.

The result was dramatic, although it won't sound that way at first. The mice with the bat DNA displayed forelimbs that were 6% longer than normal. Why is this a dramatic result? Well, first of all, think about a 6% change in a major structural attribute. If adult males in a certain country average 5'10" in height, a 6% increase would mean an increase of more than 4 inches. But more importantly, the Prx1 gene is known to account for about 12% of forelimb length – mice that lack the gene altogether show a 12% reduction in forelimb length. That 6% change reflects a huge change in Prx1 activity, a change that was completely due to alterations in regulatory DNA sequences without any change in coding sequence.

If that's not impressive enough, the authors went on to examine the importance of this regulatory region in mice, by deleting it altogether. The result was very surprising, but very interesting: limb length in mice was completely unaffected by the loss of this chunk of regulatory DNA. (The region we're discussing is 1000 bases in length.) This means that the Prx1 gene of both bats and mice contains a regulatory region that is completely dispensable for normal development but that can be altered to generate significant changes in limb length, which points to significant evolutionary potential in genetic regions that seem unimportant. Here's how the authors say it:

Maintenance of redundant enhancers for essential developmental control genes would allow changes in expression pattern to arise from mutations that alter regulatory activity while preserving the required gene function.

So, why is this significant? Here are two aspects of the story that are worth highlighting.

1. The results provide strong (and rare) experimental support for the ideas of the evo-devo school. The currently-heated debate over the merits of evo-devo is focused on the central evo-devo claim that morphological evolution (i.e., evolutionary changes in form) is driven to a large extent by changes in the regulation of gene expression, and less so by changes in the structures of the proteins that are encoded. To simplify, evo-devo postulates that significant evolutionary change – like that discussed here – is more likely a result of the varied use of a protein toolkit than a result of modification of the toolkit itself. Cretekos et al. have presented a case in point, and one that is considered outstanding in that it documents a morphological gain; many previous examples showed only losses.

2. The results provide a sharp picture of what Darwin's vision of "successive slight modifications" means in terms of developmental biology. In this case, the modifications (of a redundant regulatory region) can yield significant anatomical remodeling without altering protein structure at all.

The article was a notable advance for evo-devo and for evolutionary science, but soon there will surely be many others like it. Desperate or ignorant creationists will always find a way to avoid facing the explanatory power of common descent, but scientists are just plugging away, and for every blog post by a creationist ignoramus, there are 30 unheralded publications in the biological literature that advance our understanding of common descent and the mechanisms that generate biological novelty. And they're fun to read.

Article(s) discussed in this post: Cretekos, C.J. et al. (2008) Regulatory divergence modifies limb length between mammals. Genes & Development 22:141-151.

Weekly sampler 17

It'll be a breakout week after a slow month on the blog. To the Edge of Evolution – and beyond!

1. Ian Musgrave over at Panda's Thumb provides a nice summary of the evolution of clotting systems and some new genomic data that could be used, by ID proponents like Michael Behe, to bolster their claims regarding the "irreducible complexity" of the clotting system. I've been saying it since the beginning here at QoD: genomic data has already made it nearly impossible to respectably doubt common descent, and it gets much worse every day.

2. Massimo Pigliucci gibbers on the Problem of Evil and Francisco Ayala. Not that I'm buying Ayala's theodicy either...

3. Dale Purves is an eminent neuroscientist whose work I've followed for two decades. In the last several years, he's expanded from developmental neurobiology into cognitive neuroscience. His lab's web page is loaded with good stuff, which is probably why it was recently honored by The Scientist. The resources page includes a bunch of interesting illusions and the full text of two of his out-of-print books.

Ebola virus, electron micrograph. Image from PHIL, ID# 1835.

4. The CDC (Centers for Disease Control & Prevention) has a free online image library called PHIL (Public Health Image Library). Now you know where to go to get your pictures of Ebola Virus for when you make your own Get Well Soon cards. Don't miss this little disclaimer:

WARNING: This library includes subject matter that might be unsuitable for children. Viewing discretion is advised.

Yikes!

5. Get to Gordon Glover's Beyond the Firmament blog for a superb series on "Science and Education" focused on questions surrounding natural science (mostly origins) and Christian education. He's covering folk science right now, in his excellent style. And you don't even have to pay.

6. Last week saw the unveiling of the platypus genome, and it included lots of interesting surprises. The media coverage has been typically spotty (with regard to accuracy); to get well-grounded, start with the brief piece at the New York Times then check out Ryan Gregory's thoughts (at his new blogging home) and perhaps the usual clarity dispensed by the cuddly PZ Myers.

Weekly sampler 15

Last quiz on genome size, with animals chosen at random. The first quiz post explains what this is all about, the second one has additional commentary, and the answers to both previous quizzes are in previous Weekly samplers.

Which organism has the larger genome?
	This one?	Or this one?
1
2
3
4

Here's some help for you. These are the C-values (amount of DNA per cell) for those animals, in ascending order:

0.23 -- 1.50 -- 2.24 -- 2.72 -- 2.91 -- 3.00 -- 3.29 -- 5.87

And here's a hint: the biggest number does not go with the biggest animal. Good luck!

1. We're living in the postgenomic era, and comparative genomics has already made it impossible to be an intellectually fulfilled anti-evolutionist. I've written before about genome sequencing and the imminence of large-scale and inexpensive sequencing. Well, the first super-fast (4 months vs. more than a decade for the Human Genome Project), super-cheap ($1.5 million vs. billions for the HGP) human genome sequence is now official. It's Jim Watson's genome. Blecch. Someone should use BLAST to search his coding sequences for this amino acid sequence:
Alanine - Serine - Serine - Histidine - Glutamine - Leucine - Glutamic acid
Don't get it? Think about this guy's conduct, then check out the amino acid code.

2. If you think I'm never nice to Reasons To Believe, check out the discussion this week at the ASA listserv. The topic: RTB's statement in which they distance themselves from Expelled.

3. Speaking of Expelled, which I will do infrequently, here's a good reason to avoid the movie and its cynical attempt to enlist and co-opt evangelical Christendom: its indefensible linkage of "Darwinism" with Nazism. If that's not bad enough, check out John Lynch's examination of the diabolical credentials of one "expert" interviewed in the film.

If you're a Christian who thinks that the Nazis are a useful polemical tool against evolution, then maybe you should read about some of Hitler's best-known influences. In my view, if you can read Luther's words and still think there's any moral high ground surrounding the Holocaust that can be claimed by Christendom, then you're crazy. The Holocaust is an unspeakably abhorrent stain on the Church, if you ask me, and it's not Darwinists (whoever they are) who have hard questions to answer. I, for one, believe that Christians should be overwhelmingly humbled by the occurrence of the Holocaust, and not because of the Problem of Evil.

Christopher Heard has several recent posts on Expelled that are worth checking out. Just promise me you won't give any money to these chowderheads.

I say: skip Expelled. Send the money to Compassion International. Or give it to a library or school. Say no to the minions of the Discovery Institute who have given up the pretense of "scientific" explorations of "design" and have lustily embraced full frontal culture war. [spits]

3. [Deep breath] So, were you alive in the 1980's? Remember Bloom County? It's my favorite comic strip of all time (apologies to Calvin & Hobbes). The strip often tracked current events; during the 1981 Arkansas creationism trial, Bloom County presented the famous "penguin evolution" trial in which "scientific penguinism" was being advocated by certain characters. Some classic excerpts from that brilliant series are illicitly available in the blogosphere; don't miss the one (second from the bottom) in which the scientific expert states, "Penguin evolution is a fib." You can find some similarly scintillating examples on Berkeley Breathed's site. My favorites: the first and the next to last.

4. Kevin Corcoran writes this about a recent piece by Stanley Fish on deconstruction:

John Searle said it first, but it applies here: it’s stuff like this that gives bullshit a bad name.

Now that's funny.

5. The online repository of Darwin's works at the University of Cambridge announced this week that they were making available a gigantic collection of Darwin's private papers, including "the first draft of his theory of evolution" and notes from the Beagle voyage. One little tidbit: apparently they sold tickets to lectures at the University of Edinburgh. Hmmmm. [rubs chin]
Via my brilliant brother, who works at HP and helps his wife run her cool small business.

6. There was a lot of cyberspace snickering when Answers Research Journal started up, and some of the articles there are pretty lame (the metaphysical piece would, I think, do poorly in a 200-level philosophy course at Calvin). But have a look at the new article on peer review; the authors are worth listening to, and their discussion of peer review from a Christian perspective is worth considering. I'm not crazy about the occasional proof-texting, and the authors frequently address the YEC community specifically. But here's the type of clear-headed wisdom you'll find in their paper:

By striving for excellence, we also love our neighbors. In our modern, western culture, many people view scientific pronouncements as authoritative. Christians who are also scientists therefore have an even higher duty to speak with excellence than the average Christian, simply because of the perceived authority that they possess. Errors made by Christians speaking in the name of science, no matter how well intentioned, can become “common wisdom” and thereby very difficult to correct. Even greater responsibility lies upon the scholar who professes ideas to the general public rather than just scholarly colleagues. In doing so, the scholar becomes a teacher, with all the attendant responsibilities (e.g., Matthew 5:19, 18:6; James 3:1). We therefore love our neighbors by striving to present the excellence of God in our written work and avoid the dangerous alternative of leading them into error.

I probably don't need to explain why that passage rang true. You might notice, by the way, the links take you to the New King James Version. What is it with the conservative/fundamentalist fondness for 400-year-old prose bearing the name of an English monarch?