An unpaleontological lament for lost molecules and shattered cells and the cruelty of time

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Sometimes, I really hate fossils. I hate them with the passion of a spurned lover, one who is consumed with desire but knows that he will never, ever be satisfied. They drive me mad.

Right now we’re at a point in our technology where we can take a small sample from a living organism and break it down into amazing detail — we can extract every gene, throw them into a computer, and compare them with every other gene that has been similarly sampled. We can look for the scars of evolution, we can analyze and figure out where on the tree of life this cell resides, we can even figure out what local populatons it lived in, who its ancestors bred with, and to a certain extent, what various alleles contributed to its form and physiology. We don’t know everything, but every time someone works out some new detail in a related species, it goes into the databases and presto, the information cascades through every other relative. I’d call it magic, but that would insult the science with cheap understatement.

We can’t do that with most fossils (with some recent exceptions). The cells are gone. Their contents are obliterated — DNA fragmented, dissolved, corrupted, lost. And the farther back in time we go, the less information we have, but the more interesting the problems become.

All organisms are built of cells — they’re like the Lego building blocks of biology, with specific features that snap them together. With Legos, of course, you can build all kinds of different forms: stick them together and build a Lego Triceratops or a Lego T. rex. Different on the outside, different in arrangement, different in pattern, but all fundamentally built of the same kinds of blocks. I can get into the coolness of digging up a Triceratops or a T. rex, but these are all variations on a theme of phylum Chordata, superclass Tetrapoda, and they’re all using the same building blocks, and all the really interesting stuff, the details in the genome that make one morphology different than another, have all been bled out on the sands of time and gnawed by all-devouring bacteria and reduced to at best a non-specific smear of carbon. That makes me frustrated.

Even worse, most familiar fossils are big bony animals — they’re all pretty much the same, deep down. If they’re built of Legos, there are whole other clades of multicellular organisms that are the equivalent of meccano, lincoln logs, Capsela, and tinkertoys. How were they put together? And how did they evolve these different patterns of connections? To know that, we have to go way back into deep time, and look at the unicellular organisms, the cells that first pioneered patterns of interactions and laid down the possible rules of development that enabled big clumsy multicellular to accumulate the bulk that made them more likely to be fossilized. Those pioneers are practically nonexistent in the fossil record.

What prompts my lament for lost cells is this recent amazing discovery: a collection of fossilized multicellular organisms unearthed in Gabon that are 2.1 billion years old. Keep in mind that in comparison, the Cambrian explosion, the event that was the root of familiar animal diversity, was a mere half billion years ago, so these are genuinely ancient. They’re also beautiful.

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(Click for larger image)

Samples show a disparity of forms based on: external size and shape characteristics; peripheral radial microfabric (missing in view d); patterns of topographic thickness distribution; general inner structural organization, including occurrence of folds (seen in views b and c) and of a nodular pyrite concretion in the central part of the fossil (absent in views a and b). a, Original specimen. b, Volume rendering in semi-transparency. c, Transverse (axial) two-dimensional section. d, Longitudinal section running close to the estimated central part of the specimen. Scale bars, 5 mm. Specimens from top to bottom: G-FB2-f-mst1.1, G-FB2-f-mst2.1, G-FB2-f-mst3.1, G-FB2-f-mst4.1.

These small, flat, furrowed sheets lived at a kind of temporal boundary, a few hundred million years after a rise in atmospheric oxygen called the Great Oxygenation Event — a crisis in the history of life on earth which occured when the production of oxygen by photosynthetic organisms could no longer be buffered by reacting chemically with minerals, and began to build up in the atmosphere. This was catastrophic for most of the organisms living at that time, which were anaerobic and found oxygen to be a caustic poison. It was an advantage to a subset that adapted to use oxygen as a fuel in chemical reactions, though, so there was also the beginnings of new forms which exploited this newly oxygenated atmosphere. That’s where these mysterious blobs come in; they were found in formations that had a chemical signature indicating the presence of free oxygen.

These were almost certainly colonial organisms that took advantage of the higher concentration of oxygen to build denser mats on top of the sea floor. They probably weren’t true multi-cellular organisms; they were a step up from a colony of bacteria that you might see growing on a petri dish, but with additional molecular features that permitted greater coordination and the development of more elaborate spatial patterning.

We also know that these had to have been very different from organisms that exist now. Those are not animals, they are not plants, they are not fungi — they are something primeval and radically different, organisms that most likely do not have any living descendants. Those are real aliens in the photo above. There is no category in your experience which you can put them into.

It’s what we don’t know that inflames my curiousity. One of the other things that was going on during the Great Oxygenation Event was the steady loss of dissolved iron in the seas — it was all being oxidized, rusted out, and precipitating out, forming geological structures like the banded iron formations. It was also facilitating the preservation of these organisms by pyritizing them — all their soft gooey bits, the whole of creature, were being replaced by fool’s gold, iron pyrite. There are no cells left here. We don’t even know for sure that these are eukaryotic cells; they probably are, indicated by the presence of a sterane chemical signature in the rocks that is characteristic of eukaryotes, but there isn’t even enough fine detail to tell whether there was a nucleus in these cells. It just breaks my heart.

It’s a beautiful tease. We can see that life was exploring the edges of multicellularity over 2 billion years ago, but…the molecular sinews that stitched them together are all gone. The signals and receptors that enabled communication between them are all gone. The genes that drove their growth are all gone. There is nothing left but a blurry crystal-ruptured outline of what once was.

I have to shake an angry fist at you, fossils. I won’t go all Mel Gibson in incoherent rage at you because I like you too much, but still…you taunt me. I want your cells. Nothing less will do.


El Albani A, Bengtson S, Canfield DE, Bekker A, Macchiarelli R, Mazurier A, Hammarlund EU, Boulvais P, Dupuy JJ, Fontaine C, Fürsich FT, Gauthier-Lafaye F, Janvier P, Javaux E, Ossa FO, Pierson-Wickmann AC, Riboulleau A, Sardini P, Vachard D, Whitehouse M, Meunier A. (2010) Large colonial organisms with coordinated growth in oxygenated environments 2.1 Gyr ago. Nature 466(7302):100-4.


Chris Nedin, who should know, does not think these fossils represent multicellular organisms at all — they are fossilized, folded microbial mats. Which is fine by me — 2 billion year old microbial mats are also exceedingly cool, and I still want their cells.

You do know that if you want to know more about anything pre-Cambrian, you should be reading Ediacaran, right?

I ♥ this letter

I wish Samuel Clemens were still alive, so I could piss him off and he’d write something like this back to me. It would be such an honor.

Nov. 20. 1905

J. H. Todd
1212 Webster St.
San Francisco, Cal.

Dear Sir,

Your letter is an insoluble puzzle to me. The handwriting is good and exhibits considerable character, and there are even traces of intelligence in what you say, yet the letter and the accompanying advertisements profess to be the work of the same hand. The person who wrote the advertisements is without doubt the most ignorant person now alive on the planet; also without doubt he is an idiot, an idiot of the 33rd degree, and scion of an ancestral procession of idiots stretching back to the Missing Link. It puzzles me to make out how the same hand could have constructed your letter and your advertisements. Puzzles fret me, puzzles annoy me, puzzles exasperate me; and always, for a moment, they arouse in me an unkind state of mind toward the person who has puzzled me. A few moments from now my resentment will have faded and passed and I shall probably even be praying for you; but while there is yet time I hasten to wish that you may take a dose of your own poison by mistake, and enter swiftly into the damnation which you and all other patent medicine assassins have so remorselessly earned and do so richly deserve.

Adieu, adieu, adieu!

Mark Twain

Mark Twain would have been an awesome blogger.

CellCraft, a subversive little game

A lot of people have been writing to me about this free webgame, CellCraft. In it, you control a cell and build up all these complex organelles in order to gather resources and fight off viruses; it’s cute, it does throw in a lot of useful jargon, but the few minutes I spent trying it were also a bit odd — there was something off about it all.

Where do you get these organelles? A species of intelligent platypus just poofs them into existence for you when you need them. What is the goal? The cells have a lot of room in their genomes, so the platypuses are going to put platypus DNA in there, so they can launch them off to planet E4R1H to colonize it with more platypuses. Uh-oh. These are Intelligent Design creationist superstitions: that organelles didn’t evolve, but were created for a purpose; that ancient cells were ‘front-loaded’ with the information to produced more complex species; and that there must be a purpose to all that excess DNA other than that it is junk.

Suspicions confirmed. Look in the credits.

Also thanks to Dr. Jed Macosko at Wake Forest University and Dr. David Dewitt at Liberty University for providing lots of support and biological guidance.

Those two are notorious creationists and advocates for intelligent design creationism. Yep. It’s a creationist game. It was intelligently designed, and it’s not bad as a game, but as a tool for teaching anyone about biology, it sucks. It is not an educational game, it is a miseducational game. I hope no one is planning on using it in their classroom. (Dang. Too late. I see in their forums that some teachers are enthusiastic about it — they shouldn’t be).

No, it doesn’t

Rachel Roberts says, “I don’t know how, but homeopathy really does work“. Oh, I thought, let’s give it a try and hear why. But then I was five paragraphs in and getting nothing but this inane anecdote about how when she was 21, and she was at this party, see, and this lady said she used to have some ailment of an unspecified nature and then she took two sugar pills and zip-zap-alakazam, a couple of days later, she was cured!!! Of what, I don’t know. Could have been a cold. Coulda been terminal pancreatic cancer. Coulda been the Zombie Plague, and the lady could have been green and dead with her left arm gnawed off and moaning for “braaaains”, and now she’s serving tea at the Ladies Club and singing every Sunday in the church choir. We don’t know. But whatever it was, it convinced Rachel Roberts to throw away her scholarship to a graduate program in neuroscience and go to homeopathy school.

The Zombie Plague theory acquires a little more credibility. That dinner party encounter seems to have sucked her brains out.

She does throw out a little flurry of studies that have shown the efficacy of homeopathy, but I’m unconvinced. I’ve looked into a few of those papers in the past — the homeopathic dilutions of thyroxine inhibiting metamorphosis sounded interesting — and found nothing but confusing protocols, extremely weak effects, and poor experimental design, not to mention the complete absence of a mechanism and that their results contradict good studies on the effects of concentration of thyroxine on frog metamorphosis (we have very good data on how increasing the concentration of thyroxine speeds up metamorphosis, with charts and tables and everything.) It’s funny how when advocates do some sloppy research, they get an effect…and when critics start controlling for bias and errors, the effects disappear. Almost as if they weren’t really there.

Skip Rachel Roberts. Read Ben Goldacre instead.

Creationists are geniuses

Really, they are. A while back, the Institute for Creation Research moved to Texas, where they expected a friendly welcome, and instead they got spanked: their request to be allowed to hand out degrees was turned down by the Texas Higher Education Coordinating Board. This made the ICR angry, and they made a wacky lawsuit. A genuinely deranged brief. Their minds work in very twisty weird ways.

They’ve gone down in flames — they are not authorized to give out degrees. But those creationist brains that scuttle sideways and inside out are not daunted by this mere legal restriction! Their website now proudly proclaims that they offer a Master of Christian Education (M.C.Ed.) degree. How can they do that?

11. Is ICR’s School of Biblical Apologetics program accredited?

Due to the nature of ICR’s School of Biblical Apologetics—a predominantly religious education school—it is exempt from licensing by the Texas Higher Education Coordinating Board. Likewise, ICR’s School of Biblical Apologetics is legally exempt from being required to be accredited by any secular or ecumenical or other type of accrediting association.

That’s freakin’ brilliant. Are they offering accredited degrees? NO. The THECB refused to license them. But instead of saying that, they cleverly dodge the question. Imagine some poor gullible teacher suckered into getting a Masters in “Christian Education”, and then going back to her school administrators and waving her diploma around to justify getting a promotion.

“Is that an accredited degree from a licensed university?”

“They are exempt from licensing.”

“So it’s not licensed…is it accredited?”

“They are legally exempt from being required to be accredited.”

“So it’s not accredited.”

“WHERE’S MAH RAISE?”

The Vatican has been beaming cancer rays into children!

That’s the latest news, anyway: radio masts operated by the Vatican have been implicated in an increased incidence of cancers nearby.

It is such a juicily evil story — it would just fit the Pope’s Bond villain image so well — but, and I really, really hate to defend the Vatican, I don’t buy it. Sorry. I know it’s my mission to smack the Catholic church around, but this is a case where I just find it highly unlikely.

I have not read the report; all I’ve seen so far is the accusation, the small numbers (19 deaths in 23 years) and the excessive charges — 6 people are being investigated on criminal charges of manslaughter. Something’s just not right here.

These stories crop up regularly. People claim power lines or cell phones cause cancer, but none of the data really support it — there is no plausible mechanism where these very weak fields could be causing cancer, and at best the epidemiological studies show there can be only a very small effect…or more likely, no effect at all.

Maybe there are some new and persuasive data and statistics in this new Italian study, but even if they actually have a believable measure of an effect, it’s not going to justify criminal charges. It’s also peculiar to focus on just the Catholic church; are there no other shortwave radio antennas in Italy?

Apparently there are: the Italian navy has radio masts in the same area, but to make the report even weirder, only Catholic antennas and not naval antennas cause cancer. I’d like to know how they determined that, and what makes Catholicism carcinogenic.

Chickens, eggs, this is no way to report on science

Bleh. MSNBC is running a terrible article that claims they have “proof” that chickens came before eggs. It’s just an awful mess, and one of the scientists is at least partly responsible.

The scientists found that a protein found only in a chicken’s ovaries is necessary for the formation of the egg, according to the paper Wednesday. The egg can therefore only exist if it has been created inside a chicken.

“It had long been suspected that the egg came first but now we have the scientific proof that shows that in fact the chicken came first,” said Dr. Colin Freeman, from Sheffield University’s Department of Engineering Materials, according to the Mail.

No. What they found was a specific molecule called ovocleidin which is a member of a family of C-type lectin-like proteins. These things are all over the place; they’re cell adhesion molecules, some are involved in cell signaling, some function in modulating the immune system and blood clotting pathways. They’re even found in snake venoms. They’re found in everything from C. elegans to mammals. Their key property is that they bind calcium.

In birds, these proteins have been coopted to regulate egg shell formation. They bind calcium and can seed the crystallization of calcium carbonate, and also control the rate of crystal formation. Chickens have ovocleidin, but geese have an ortholog, ansocalcin, and ostriches have struthiocleidin. There seems to be a lot of lability in what particular calcium-binding protein is used in shell formation, and it’s probably the case that most of the sequence is free to mutate without affecting the nucleating function.

You simply can’t make the conclusion the reporter was making here. The species ancestral to Gallus gallus laid eggs, the last common ancestor of all birds laid eggs, the reptiles that preceded the birds laid eggs…the appearance of egg laying was not coincident with the evolution of ovocleidin. The first chicken that acquired the protein we call ovocleidin now by mutation of a prior protein also hatched from an egg.

What were the people involved in this story thinking?