This is a wonderful video: it’s Richard Dawkins interviewing Craig Venter and getting a tour of his amazing sequencing facility. It also reveals how much the technology is changing.
I’ve been busy — I’m teaching genetics this term, and usually the first two thirds of the course is trivial to prepare for — we’re covering Mendelian genetics, and the early stuff is material the students have seen before and are at least generally familiar with the concepts, and all I have to do is cover them a little deeper and with a stronger quantitative component. That’s relatively easy.
The last part of the course, though, is where we start moving into uncharted waters for them, and every year I have to rethink how I’m going to cover the non-Mendelian concepts, and sometimes my ideas work well, and sometimes they don’t. If I teach it for another 20 years, I’ll eventually reach the point where every lecture has been honed into a comprehensible ideal. At least that’s my dream.
Anyway, one of the subjects we’re covering in the next lecture or two is imprinting, and I know from past experience that this can cause mental meltdowns in my students. This makes no sense if you’re used to thinking in Punnett squares! So I’ve been reworking this little corner of the class, and as long as I’m putting together a ground-up tutorial on the subject, I thought I might as well put it on the web. So here you are, a basic introduction to imprinting.
Genome sequencing is getting cheaper and faster, and more and more people are having it done. A new addition to the ranks is Steve Pinker, who contemplates the details of his personal genome in an interesting essay. It’s got to be fascinating, in a terribly self-centered way — I’d love to have a copy of mine someday. It’s an opportunity to see a manifestation of one’s own lineage, your biological history all laid out for you. There’s the ability to compare with others, and see hints of statistical correlations and associations with specific traits and even, unpleasantly, diseases. Pinker also makes the point that you are not determined by your genome — the man famously has a wild head of hair, and as it turns out, he’s also carrying a bit of sequence that seems to predispose carriers to baldness.
At the same time, there is nothing like perusing your genetic data to drive home its limitations as a source of insight into yourself. What should I make of the nonsensical news that I am “probably light-skinned” but have a “twofold risk of baldness”? These diagnoses, of course, are simply peeled off the data in a study: 40 percent of men with the C version of the rs2180439 SNP are bald, compared with 80 percent of men with the T version, and I have the T. But something strange happens when you take a number representing the proportion of people in a sample and apply it to a single individual. The first use of the number is perfectly respectable as an input into a policy that will optimize the costs and benefits of treating a large similar group in a particular way. But the second use of the number is just plain weird. Anyone who knows me can confirm that I’m not 80 percent bald, or even 80 percent likely to be bald; I’m 100 percent likely not to be bald. The most charitable interpretation of the number when applied to me is, “If you knew nothing else about me, your subjective confidence that I am bald, on a scale of 0 to 10, should be 8.” But that is a statement about your mental state, not my physical one. If you learned more clues about me (like seeing photographs of my father and grandfathers), that number would change, while not a hair on my head would be different. Some mathematicians say that “the probability of a single event” is a meaningless concept.
Another thing I should think having a copy of your genome should drive home is how much of it is incomprehensible; we simply don’t know what most of it does, and even in the example mentioned above, we don’t have a causal relationship between one variant of the rs2180439 SNP and head hair, only a rough correlation. That’s the promise of the future, that we can now get copies of this book of our genome…we just have to get to work learning how to read it.
I’ve got my eye on the progress in genome sequencing. When the price hits $1000 (which isn’t at all unlikely to occur in my lifetime), I know I’m going to have it done, just because it’s a book I’ve been waiting most of my life to read.
The Institute for Creation Research has a charming little magazine called “Acts & Facts” that prints examples of their “research” — which usually means misreading some scientific paper and distorting it to make a fallacious case for a literal interpretation of the bible. Here’s a classic example: Chimps and People Show ‘Architectural’ Genetic Design, by Brian Thomas, M.S. (Note: this is not the peer-reviewed research paper implied by the logo to the left — that comes later.) The paper is a weird gloss on recent work on CNVs, or copy number variants. Mr Thomas makes a standard creationist inference that I have to hold up for public ridicule.
This is a very simple, lucid video of Spencer Wells talking about his work on the Genographic Project, the effort to accumulate lots of individual genetic data to map out where we all came from.
I’ve also submitted a test tube full of cheek epithelial cells to this project, and Lynn Fellman is going to be doing a DNA portrait of me. I had my Y chromosome analyzed just because my paternal ancestry was a bit murky and messy and potentially more surprising, and my mother’s family was many generations of stay-at-home Scandinavian peasantry, so I knew what to expect there. Dad turned out to be not such a great surprise, either. I have the single nucleotide polymorphism M343, which puts me in the R1b haplogroup, which is just the most common Y haplogroup in western Europe. I share a Y chromosome with a great many other fellows from England, France, the Netherlands, etc., which is where the anecdotal family history suggested we were from (family legend has it that the first American Myers in my line was a 17th or 18th century immigrant from the Netherlands). Here’s a map of where the older members of my lineage have been from: Africa (of course!) by way of a long detour through central Asia.
Hello, many-times-great-grandpa! That’s quite the long walk your family has taken. Howdy, great big extended family! We’ll have to get together sometime and keep in touch.
If you’re interested in finding out what clump of humanity you belong to, it’s easy: you can order a $100 kit, swab out a few cheek cells (just like they do on CSI or Law & Order!), mail it back, and a few weeks later, they send you your results. It’s not very detailed — they only analyze a small number of markers — but it’s enough to get a rough picture of where your branch of the family tree lies. And for a bit more, Lynn can turn it into something lovely for your wall.
By the way, Lynn and I will be talking about the science and art of human genetics in a Cafe Scientifique session in Minneapolis in February.
Epigenetics is the study of heritable traits that are not dependent on the primary sequence of DNA. That’s a short, simple definition, and it’s also largely unsatisfactory. For one, the inclusion of the word “heritable” excludes some significant players — the differentiation of neurons requires major epigenetic shaping, but these cells have undergone a terminal division and will never divide again — but at the same time, the heritability of traits that aren’t defined by the primary sequence is probably the first thing that comes to mind in any discussion of epigenetics. Another problem is the vague, open-endedness of the definition: it basically includes everything. Gene regulation, physiological adaptation, disease responses…they all fall into the catch-all of epigenetics.
RPM of Evolgen disagrees with my definition of synteny! This is terribly distressing. Especially since, strictly speaking, he is precisely correct. The word has evolved in its usage from the pure form that RPM is describing to a more colloquial, pragmatic, somewhat sloppier sense as used by people looking at comparative genomics rather than classical Drosophila genetics.
If you read contemporary evo-devo papers, my definition is more useful in comprehending what they’re saying. If you want to read Drosophila genetics papers, you better know what RPM is talking about, or god help you (and there is no god).
This is an amphioxus, a cephalochordate or lancelet. It’s been stained to increase contrast; in life, they are pale, almost transparent.
It looks rather fish-like, or rather, much like a larval fish, with it’s repeated blocks of muscle arranged along a stream-lined form, and a notochord, or elastic rod that forms a central axis for efficient lateral motion of the tail…and it has a true tail that extends beyond the anus. Look closely at the front end, though: this is no vertebrate.
It’s not much of a head. The notochord extends all the way to the front of the animal (in us vertebrates, it only reaches up as far as the base of the hindbrain); there’s no obvious brain, only the continuation of the spinal cord; there isn’t even a face, just an open hole fringed with tentacles. This animal collects small microorganisms in coastal waters, gulping them down and passing them back to the gill slits, which aren’t actually part of gills, but are components of a branchial net that allows water to filter through while trapping food particles. It’s a good living — they lounge about in large numbers on tropical beaches, sucking down liquids and any passing food, much like American tourists.
These animals have fascinated biologists for well over a century. They seem so primitive, with a mixture of features that are clearly similar to those of modern vertebrates, yet at the same time lacking significant elements. Could they be relics of the ancestral chordate condition? A new paper is out that discusses in detail the structure of the amphioxus genome, which reveals unifying elements that tell us much about the last common ancestor of all chordates.
Let’s play the most boring card game in the universe!
Here are the rules. We start with a fully sorted deck of 52 cards, and we deal out four hands. We don’t deal in the ordinary way, either: we give the top 13 cards to the first player, then the next 13 to the second, and so forth. (We could also do the usual deal, but it makes the illustration and logic a little more difficult to see. We’ll keep it simple for now.)
This is what the table will look like.
| Hand 1 | A |
K |
Q |
J |
10 |
9 |
8 |
7 |
6 |
5 |
4 |
3 |
2 |
| Hand 2 | A |
K |
Q |
J |
10 |
9 |
8 |
7 |
6 |
5 |
4 |
3 |
2 |
| Hand 3 | A |
K |
Q |
J |
10 |
9 |
8 |
7 |
6 |
5 |
4 |
3 |
2 |
| Hand 4 | A |
K |
Q |
J |
10 |
9 |
8 |
7 |
6 |
5 |
4 |
3 |
2 |
Next, we play the game, whatever it is. It really doesn’t matter, since we know exactly what hand everyone has, right? So don’t worry about the rules for that. What’s important is that next the dealer carefully picks up each hand in reverse order and stacks them, restoring the original arrangement of the deck.
Finals week is upon me, and I should be working on piles of paper work right now, but I need a break … and I have to vent some frustration with the popular press coverage of an important scientific event this week, the publication of a draft of the platypus genome. Over and over again, the newspaper lead is that the platypus is “weird” or “odd” or worse, they imply that the animal is a chimera — “the egg-laying critter is a genetic potpourri — part bird, part reptile and part lactating mammal”. No, no, no, a thousand times no; this is the wrong message. The platypus is not part bird, as birds are an independent and (directly) unrelated lineage; you can say it is part reptile, but that is because it is a member of a great reptilian clade that includes prototherians, marsupials, birds, lizards and snakes, dinosaurs, and us eutherian mammals. We can say with equal justification that we are part reptile, too. What’s interesting about the platypus is that it belongs to a lineage that separated from ours approximately 166 million years ago, deep in the Mesozoic, and it has independently lost different elements of our last common ancestor, and by comparing bits, we can get a clearer picture of what the Jurassic mammals were like, and what we contemporary mammals have gained and lost genetically over the course of evolution.
We can see that the journalistic convention of emphasizing the platypus as an odd duck of a composite creature is missing the whole point if we just look at the title of the paper: “Genome analysis of the platypus reveals unique signatures of evolution.” This is work that is describing the evidence for evolution in a comparative analysis of the genomes of multiple organisms, with emphasis on the newly revealed data from the platypus.
