Creationists–particularly those under the guise of intelligent design–love these. How could something as complex as the coagulation cascade simply appear, intact and whole, due to random chance? There are no intermediate steps where small refinements can be selected for! It’s all or nothing, baby! You know what that means….

Proof of GOD! Praise Jesus!

Really? Some new work, in the field of skeletal muscle differentiation, points to another way beyond the divine to generate a cascade.

If we’re going to figure out a way something could happen by evolution, it’s important to show each step has something can can be refined by selection for the most successful versions.

Let’s say the master regulator here (“Let’s make a birthday cake”) starts off as quite promiscuous, willing to turn on a whole set of tasks all at the same time–some things you’d want in cake, some things you wouldn’t.

The cake is going to be pretty bad. Things that do not belong in cake are going to end up in the finished product. Likewise, the order is all off. It would serve as a cake-like substance, but there’s much room for incremental improvement. For example, “apply ketchup” would be strongly selected against.

We also have something wrong here. The sub-regulators (“place candle” and others) also must be turning on a whole bunch of other smaller tasks. Why couldn’t they be turning each other on as well?

We get a cake again, and a little better better one at that. Now, over time these in-order connections between the sub-regulators will get selected for until they’re nearly as strong as the master regulator. (The out of order connections between the sub-tasks would be selected against; they’re in dashed green to indicate this.) If both the master regulator and the previous sub-regulator must be turned on in order to activate the next step, the result would be a pretty damn good cake. Therefore, natural selection will pick out those cascades with that trait.

The better ordered these steps, the better the cake turns out. So, the strength of the connections between steps, relative to that of the master regulator, will increase.

Eventually, the master regulator will only be able to turn on the first step. The result? A neat cascade:

This isn’t just speculation on my part. Scientists studying the differentiation of skeletal muscle cells have found direct evidence for this sort of evolutionary process. Pretty cool.

Darwin’s major accomplishment was to condense a lot of thought on the origins of life into two basic concepts: new traits arise randomly (mutation) and the most adaptive of these new traits would become dominant in the population (natural selection)–forming the first cohesive theory of evolution.

For proof, in these early days, we had Darwin’s observations on the Galapagos Islands and the fossil records showing the rise of new traits in the living population to match changes in or introductions to new environments.

Building off of Darwin’s ideas of natural selection and mutation generating new traits came Mendel, and his conception of genetics, a systematic way by which traits are passed from parents to children. Mendel’s genes passed unchanged from parent to child cause traits of living things. An individual has two copies of each gene, one from each parent. If you have a mixture of genes for a trait, one of these genes can dominate over the other, hiding the weaker recessive gene’s trait for the generation.

Watson, Crick, Wilkins and Franklin‘s discovery of the structure of DNA in the 1950′s gave genes a physical manifestation—understandable with fairly simple chemistry. The central dogma of biology followed shortly after, in which DNA encoding for genes is transcribed into messenger RNA and in turn proteins that cause the traits first observed by Darwin hundreds of years before.

Human understanding of life has come in these spurts, separated by decades of consolidation and grappling with new data or new ways of thinking about biology. We’re, right now, in midst of another spurt in our understanding of life.

Until about a decade ago, we only really knew DNA–the long ordered strands of the four basic letters of life–in patches and spurts, with little sense of the overall map of any living thing. With enormous effort and cost, we sequenced the human genome–the vast majority of all the DNA in a human cell. We discovered that a human being has about twenty-thousand pairs of Mendel’s genes.

In the past few years, sequencing DNA has become shockingly less expensive. What once cost four billion dollars can now be done for a few thousand. And the price is dropping dramatically every few years. As a result, we now have sequenced the genomes of many other organisms–fish, cows, dogs, mice, opossums, frogs, chickens, chimps to name just a few.

If we think about Darwin’s traits as tasks a living thing must accomplish–eating, carrying oxygen and so on–and Mendel’s genes as means of accomplishing these tasks–a beak, a histone protein to wrap DNA around, hemoglobin in red blood cells–by comparing the DNA sequences for given traits (a gene’s locus) in different organisms, we can see how evolution has adapted each organism to its environment and lifestyle.

Storing DNA should be little different for a fish, frog, mouse or human. The task is as ancient as eukaryotic life. Let’s look at the genetic locus coding for a protein responsible for this DNA-storing trait, comparing how close various other organism’s DNA is to human’s sequence.

(click for a larger version)

Each row represents the equivalent gene in another species (zebrafish, xenopus frogs, chickens, opossums, mice, dogs and macaque respectively.) The higher the blue, the closer the DNA sequence matches that of humans; given that our common ancestor with these organisms were millions, hundreds of millions for the majority, of years ago, this is a very high degree of sequence conservation. The task hasn’t changed (the goals of the trait) so the gene hasn’t changed much either.

Now let’s look at the gene responsible for the trait of carrying oxygen in our blood, the beta-chain of hemoglobin. For a fish or a frog, the demands of the task of capturing and carrying oxygen are dramatically different than those for a purely land-dwelling animal; we’d expect the DNA sequence for the equivalent gene in these animals to be quite different from human’s.

Indeed, that’s the case:

Today, on Darwin’s 200th birthday, I encourage you to browse around, comparing human genes to those of our distant and close relatives in the animal kingdom. (Check out Opsin 1, for color vision, or the NMDA neurotransmitter receptor for some other fun genes.) You are living in a golden age of biology, in which our understanding of life is jumping by leaps and bounds every year. Within your lifetime already, we’ve gained astonishing abilities to peer into the nature, structure and function of life. Despite the centuries of advancement, Darwin’s (and Mendel’s) carefully crafted ideas of evolution and genetics have not only endured, but provided an invaluable map to understanding this vast new collection of data. Be proud.

No one really argues about the validity of natural selection. Only the most hardened of young Earth creationists contest that organisms with more adaptive traits will preferentially survive and reproduce. The Intelligent Design crowd tends to wave this off as a trivial truth. Of course, they say, better traits are selected for. They instead claim you need a designer to provide these traits. How could something as complicated as a metabolic pathway simply arise from chance? Where’s the proof that such beneficial traits can simply arise, with no guiding hand?

Zachary Blount, Christina Borland, and Richard Lensk, from Michigan State University, set out to test this tricky question in evolution.

E. Coli, a gut bacteria commonly used in the lab, cannot eat citrate. While other organisms can, it takes a whole complicated set of interacting genes that E. Coli lack. Could E. Coli, by random chance, mutate such a family of genes? How long, how many and how many generations of bacteria would it take?

In 1988, cultures of E. Coli were started in media with little sugar, but much citrate. Any bacteria that could eat citrate would have a huge selective advantage. After 31,500 generations, one colony finally gained the ability to eat citrate. Going back to the freezer, and looking at the earlier colonies frozen back, it became clear that the pieces started to come together in parts at around 20,000 generations.

What an amazing finding! Just by being in a selective environment, that rewarded bacteria that could learn to do a complex new task, the part could form by a series mutations and eventually be selected for. Exactly as evolution would predict–an elegant demonstration of both halves of evolution, natural selection and the arising of complex traits by random mutation. It’s a stinging slap in the face of the Intelligent Design creationists, whose entire loudly touted faith-system is based on the impossibility of this event.

(Salim Virji)

Who doesn’t love the platypus? This is a creature bizarre enough to make marsupials feel better about themselves. The platypus, lactates (mammal!) and lays eggs (reptile!), grows fur (mammal!) and venom (reptile!).

This might be the single most interesting creature, from an evolutionary point of view, on the planet. About 315 million years ago, Amniotes–a primitive vertebrate with four legs, pretty much resembling a blurry picture of every animal that comes to mind–split into two groups. The Sauropsids eventually became all reptile-like creatures, including Dinosaurs, snakes, lizards and birds. The Synapsids became, well, us and all other mammals. Almost 170 million years ago, the Platypus split off from the rest of the Synapsids and hung out on a little evolutionary twig of its very own.

This is all a bit like reading the Silmarillion or Numbers, so I’m moving on to the big, exciting, point for evolutionary biologists. 170 million years ago, we and the Platypus shared a common ancestor. If you want to reconstruct how we evolutionarily came to have external testicles, nipples, separate opening for pee and poop–all things we have but the Platypus doesn’t–we could compare how a Platypus is put together, its genome, to our own. Our common ancestor probably lacked all these things. Likewise, the Platypus has been busy since departing our common ancestor, figuring out how do things we can’t–like make poison or see the world using only electricity. How’d that happen?

Well, we now have a draft of the Platypus genome. This’ll be fun.

Right off, the male Platypus has five X and five Y chromosomes. Huh? By comparison, every other male mammal has one X and one Y. One of the more pleasant observations is how similar we are to them. Over 80% of the genes in the Platypus strongly resemble those in humans or mice.

The remaining fifth is where all the fun actions occurs! Like what? The genes for chemical receptors, that make the nose work, are totally different. Genes for making eggs? Different from just about anything. The eggs are tiny and the baby Platypus hatches much earlier than is typical in egg-laying creatures. The baby then licks milk off the belly of the mother–remember, no nipples! If you wanted a snapshot of the evolution of mammals, that don’t lay eggs and nurse their young, this is pretty much it.

Ok, enough of my wonderment. Read the paper, if you can! If you can’t, bitch to your representative about the publication of publicly funded research in private, subscription only journals.

(cartoon via xkcd)

Ideas are tested by experiment. That’s all there is to science. This is the only bar an idea must be taller than to take the ride of science as a legitimate hypothesis.

An untestable, unknowable, incomprehensible supernatural force is required for the existence of living things–the central idea behind Intelligent Design, creation science, creationism, or whatever you want to call it–is inherently unscientific. If the idea is untestable, it cannot be scientific and has no place in a science curriculum–save it for the philosophy courses, or evenings after eating too many enhanced baked goods.

This latest assault by the anti-science, pro-creationist crowd–to whine that their ideas aren’t given a fair shake in the scientific community due to some overarching conspiracy–is a three year old having a temper-tantrum upon being told he is too short to go on a roller coaster. This idea of a supernatural being, at its very core, refuses to be tested. It might be true, it might be false, but it’s certainly never going to be scientific.

I’ve gone down this rabbit hole and attempted even a gentle analysis of Intelligent Design’s ideas. “What must this designer be able to do?” “By what mechanisms could the designer do these things?” “Can we disrupt or enhance these mechanisms by any human technique?” “How was the designer designed?”

Good luck trying to get any sort of coherent answer, or even speculation, along these lines in the ID movement. Mostly it’s a bunch of whimpering about this or that in evolution theory—primarily moldy old discredited critiques from the 19th Century, buffed up for the 21st. The ID crowd wraps a handful of difficult to explain observations in living things in the wrapper of “some magical being, beyond human conception or understanding, must exist because you cannot fully explain this random observation with current technology and theory.” Here’s another shocker for you: such a critique isn’t particularly scientific.

Think of how human scientific knowledge expands: Via new technologies allowing new ways of observing, new observations from existing or new technology or new ways of interpreting existing observations. The observations underlying evolutionary theory are essentially uncontested. Most of the central observations require no technology beyond your eyes, ears and some careful recordkeeping; modern molecular biology yields new observations that are perfectly in sync with those made by Darwin and others nearly two centuries ago or earlier. Darwin’s jump was borne less of new observations, but rather new ways of thinking about the existing available information.

These are the trickiest ideas to test, and thus make scientific. One manner is to say, “if this interpretation is correct, it would predict the following…” For example, if the interpretative theory of evolution is correct, we would predict the rise of drug resistance bacteria, and the spread of drug resistance genes, shortly after the introduction of antibiotics. The predictions one can make, if assuming evolution is true, fit observed reality far better than if one instead assumes that a supernatural being is behind all life–because we can understand more of the steps completely when we aren’t saying “something magic happens.”

Accepting, scientifically, an interpretive hypothesis does not require perfect evidence, for all outstanding questions to be settled. Rather, all that one should require is that the interpretation best fits the observations of reality that we can presently make, that the predictions of the interpretive idea closely what we observe when we look. Science is the art of taking many imperfect observations together to craft a reasonable interpretation–not demanding perfect information without holes. This is testing by experiment, not demanding immaculate evidence but working with the best you can do. Requiring, or claiming, inerrant proof is the realm of religious belief, not scientific.

Who cares, you might be saying at this point. Why not let the ID crowd have their say? Because of how profoundly unscientific it is to demand perfect information before making a decision. Teaching students irrefutable evidence is required before accepting an unpleasant idea, is one of the worst lessons one can teach in a science classroom. The entire idea of what is a good experiment, what are acceptable results from an experiment, is deeply distorted by ID-like thinking.

An example:

Additives used to soften plastics, called phthalates, are currently banned in Europe but still legal in the United States. Both European and American regulators have access to the same scientific observations–that many phthalates disrupt endocrine function, particularly male sex hormones, and can readily enter the body from plastics doped with the chemcials–yet come to very different interpretations. The Europeans considered all the (imperfect and incomplete) evidence and decided the preponderance was in favor of banning the additives. The Americans continue to demand better, more complete (perhaps even impossibly perfect) evidence before acting. The net result: American children and patients (via IV tubes) continue to receive large doses phthalates, despite the majority of evidence pointing to some danger to health.

It’s crummy, unscientific, decision-making–and essentially the same illogic as Intelligent Design’s critique of evolution.